COMPOSITIONS AND METHODS FOR THE TREATMENT OF HEMOGLOBINOPATHIES

Abstract
The present invention is directed to genome editing systems, reagents and methods for the treatment of hemoglobinopathies.
Description
BACKGROUND

CRISPRs (Clustered Regularly Interspaced Short Palindromic Repeats) evolved in bacteria as an adaptive immune system to defend against viral attack. Upon exposure to a virus, short segments of viral DNA are integrated into the CRISPR locus of the bacterial genome. RNA is transcribed from a portion of the CRISPR locus that includes the viral sequence. That RNA, which contains sequence complimentary to the viral genome, mediates targeting of a Cas9 protein to the sequence in the viral genome. The Cas9 protein cleaves and thereby silences the viral target.


Recently, the CRISPR/Cas system has been adapted for genome editing in eukaryotic cells. The introduction of site-specific single (SSBs) or double strand breaks (DSBs) allows for target sequence alteration through, for example, non-homologous end joining (NHEJ) or homology-directed repair (HDR).


SUMMARY OF THE INVENTION

Without being bound by theory, the invention is based in part on the discovery that CRISPR systems, e.g., Cas9 CRISPR systems, e.g., as described herein, can be used to modify cells (e.g., hematopoietic stem and progenitor cells (HSPCs)) to increase fetal hemoglobin (HbF) expression and/or decrease expression of beta globin (e.g., a beta globin gene having a disease-causing mutation), and that such cells may be used to treat hemoglobinopathies, e.g., sickle cell disease and beta thalassemia.


Thus, in an aspect, the invention provides CRISPR systems (e.g., Cas CRISPR systems, e.g., Cas9 CRISPR systems, e.g., S. pyogenes Cas9 CRISPR systems) comprising one or more, e.g., one, gRNA molecule as described herein. Any of the gRNA molecules described herein may be used in such systems, and in the methods and cells described herein.


In an aspect, the invention provides a gRNA molecule that includes a tracr and crRNA, wherein the crRNA includes a targeting domain that is complementary with a target sequence of the BCL11A gene, a BCL11a enhancer, or a HFPH region.


In another aspect, the invention provides a gRNA molecule that includes a targeting domain that is complementary with a target sequence of the BCL11A gene, e.g., is complementary with a target sequence within a BCL11a coding region (e.g., within a BCL11a exon, e.g., within BCL11a exon 2). In embodiments, the gRNA comprises a targeting domain that includes, e.g., consists of, any one of SEQ ID NO: 1 to SEQ ID NO: 85 or SEQ ID NO: 400 to SEQ ID NO: 1231.


In another aspect, the invention provides a gRNA molecule that includes a targeting domain that is complementary with a target sequence of a BCL11A enhancer.


In embodiments, the gRNA comprises a targeting domain that includes, e.g., consists of, any one of SEQ ID NO: 1232 to SEQ ID NO: 1499.


In embodiments, the gRNA to a target sequence of a BCL11a enhancer is to a target sequence within the +58 region of the BCL11a enhancer, and the targeting domain includes, e.g., consists of, any one of SEQ ID NO: 182 to SEQ ID NO: 277 or SEQ ID NO: 334 to SEQ ID NO: 341. In embodiments, the targeting domain includes, e.g., consists of, any one of SEQ ID NO: 341, SEQ ID NO: 246, SEQ ID NO: 248, SEQ ID NO: 247, SEQ ID NO: 245, SEQ ID NO: 249, SEQ ID NO: 244, SEQ ID NO: 199, SEQ ID NO: 251, SEQ ID NO: 250, SEQ ID NO: 334, SEQ ID NO: 185, SEQ ID NO: 186, SEQ ID NO: 336, or SEQ ID NO: 337. In embodiments, the targeting domain includes, e.g., consists of, SEQ ID NO: 248. In embodiments, the targeting domain includes, e.g., consists of, SEQ ID NO: 247. In embodiments, the targeting domain includes, e.g., consists of, SEQ ID NO: 245. In embodiments, the targeting domain includes, e.g., consists of, SEQ ID NO: 336. In embodiments, the targeting domain includes, e.g., consists of, SEQ ID NO: 337. In embodiments, the targeting domain includes, e.g., consists of, SEQ ID NO: 338. In embodiments, the targeting domain includes, e.g., consists of, SEQ ID NO: 335. In embodiments, the targeting domain includes, e.g., consists of, SEQ ID NO: 252. In an embodiment, the gRNA is a dgRNA that includes a crRNA that includes, e.g., consists of, e.g., from 5′ to 3′, SEQ ID NO: 248-SEQ ID NO: 6607, and a tracr that includes, e.g., consists of, e.g., from 5′ to 3′, SEQ ID NO: 6660. In an embodiment, the gRNA is a dgRNA that includes a crRNA that includes, e.g., consists of, e.g., from 5′ to 3′, SEQ ID NO: 247-SEQ ID NO: 6607, and a tracr that includes, e.g., consists of, e.g., from 5′ to 3′, SEQ ID NO: 6660. In an embodiment, the gRNA molecule is a sgRNA molecule and includes, e.g., consists of, e.g., from 5′ to 3′, SEQ ID NO: 338-SEQ ID NO: 6604-UUUU. In an embodiment, the gRNA molecule is a sgRNA molecule and includes, e.g., consists of, e.g., from 5′ to 3′, SEQ ID NO: 335-SEQ ID NO: 6604-UUUU. In an embodiment, the gRNA molecule is a sgRNA molecule and includes, e.g., consists of, e.g., from 5′ to 3′, SEQ ID NO: 336-SEQ ID NO: 6604-UUUU. In an embodiment, the gRNA molecule is a sgRNA molecule and includes, e.g., consists of, e.g., from 5′ to 3′, SEQ ID NO: 245-SEQ ID NO: 6604-UUUU. In an embodiment, the gRNA molecule is a sgRNA molecule and includes, e.g., consists of, e.g., from 5′ to 3′, SEQ ID NO: 337-SEQ ID NO: 6604-UUUU. In an embodiment, the gRNA molecule is a sgRNA molecule and includes, e.g., consists of, e.g., from 5′ to 3′, SEQ ID NO: 252-SEQ ID NO: 6604-UUUU.


In embodiments, the gRNA to a target sequence of a BCL11a enhancer is to a target sequence within the +62 region of the BCL11a enhancer, and the targeting domain includes, e.g., consists of, any one of SEQ ID NO: 278 to SEQ ID NO: 333. In embodiments, the targeting domain includes, e.g., consists of, any one of SEQ ID NO: 318, SEQ ID NO: 312, SEQ ID NO: 313, SEQ ID NO: 294, SEQ ID NO: 310, SEQ ID NO: 319, SEQ ID NO: 298, SEQ ID NO: 322, SEQ ID NO: 311, SEQ ID NO: 315, SEQ ID NO: 290, SEQ ID NO: 317, SEQ ID NO: 309, SEQ ID NO: 289, or SEQ ID NO: 281. In embodiments, the targeting domain includes, e.g., consists of, SEQ ID NO: 318.


In embodiments, the gRNA to a target sequence of a BCL11a enhancer is to a target sequence within the +55 region of the BCL11a enhancer, and the targeting domain includes, e.g., consists of, any one of SEQ ID NO: 1596 to SEQ ID NO: 1691. In embodiments, the targeting domain includes, e.g., consists of, any one of SEQ ID NO: 1683, SEQ ID NO: 1638, SEQ ID NO: 1647, SEQ ID NO: 1609, SEQ ID NO: 1621, SEQ ID NO: 1617, SEQ ID NO: 1654, SEQ ID NO: 1631, SEQ ID NO: 1620, SEQ ID NO: 1637, SEQ ID NO: 1612, SEQ ID NO: 1656, SEQ ID NO: 1619, SEQ ID NO: 1675, SEQ ID NO: 1645, SEQ ID NO: 1598, SEQ ID NO: 1599, SEQ ID NO: 1663, SEQ ID NO: 1677, or SEQ ID NO: 1626.


In another aspect, the invention provides a gRNA molecule that includes a targeting domain that is complementary with a target sequence of a hereditary persistence of fetal hemoglobin (HPFH) region. In an embodiment, the HPFH region is the French HPFH region. In embodiments, the targeting domain includes, e.g., consists of, any one of SEQ ID NO: 86 to SEQ ID NO: 181 or SEQ ID NO: 1500 to SEQ ID NO: 1595. In embodiments, the targeting domain includes, e.g., consists of, any one of SEQ ID NO: 100, SEQ ID NO: 165, SEQ ID NO: 113, SEQ ID NO: 99, SEQ ID NO: 112, SEQ ID NO: 98, SEQ ID NO: 1580, SEQ ID NO: 106, SEQ ID NO: 1503, SEQ ID NO: 1589, SEQ ID NO: 160, SEQ ID NO: 1537, SEQ ID NO: 159, SEQ ID NO: 101, SEQ ID NO: 162, SEQ ID NO: 104, SEQ ID NO: 138, SEQ ID NO: 1536, SEQ ID NO: 1539, SEQ ID NO: 1585. In embodiments, the targeting domain includes, e.g., consists of, SEQ ID NO: 100. In embodiments, the targeting domain includes, e.g., consists of, SEQ ID NO: 165. In embodiments, the targeting domain includes, e.g., consists of, SEQ ID NO: 113.


In any of the aforementioned embodiments, the gRNA molecule may further have regions and/or properties described herein. In an aspect, the gRNA molecule (e.g., of any of the aforementioned aspects or embodiments) includes a targeting domain that includes, e.g., consists of, 17, 18, 19, 20, 21, 22, 23, or 24 consecutive nucleic acids of any one of the recited targeting domain sequences. In embodiments, the 17, 18, 19, 20, 21, 22, 23, or 24 consecutive nucleic acids of any one of the recited targeting domain sequences are the 17, 18, 19, 20, 21, 22, 23, or 24 consecutive nucleic acids disposed at the 3′ end of the recited targeting domain sequence. In embodiments, the 17, 18, 19, 20, 21, 22, 23, or 24 consecutive nucleic acids of any one of the recited targeting domain sequences are the 17, 18, 19, 20, 21, 22, 23, or 24 consecutive nucleic acids disposed at the 5′ end of the recited targeting domain sequence. In embodiments, the 17, 18, 19, 20, 21, 22, 23, or 24 consecutive nucleic acids of any one of the recited targeting domain sequences do not include either the 5′ or 3′ nucleic acid of the recited targeting domain sequence. In any of the aforementioned aspects or embodiments, the targeting domain may consist of the recited targeting domain sequence.


In embodiments of the gRNA molecule, including in any of the aforementioned aspects and embodiments, the targeting domain includes 17, 18, 19, 20, 21 (if present in the reference sequence), 22 (if present in the reference sequence), 23 (if present in the reference sequence), 24 (if present in the reference sequence), or 25 (if present in the reference sequence) consecutive nucleic acids of any one of the recited targeting domain sequences. In other embodiments of the gRNA molecule, including in any of the aforementioned aspects and embodiments, the targeting domain consists of 17, 18, 19, 20, 21 (if present in the reference sequence), 22 (if present in the reference sequence), 23 (if present in the reference sequence), or 24 (if present in the reference sequence), or 25 (if present in the reference sequence) consecutive nucleic acids of any one of the recited targeting domain sequences. In embodiments of the gRNA molecule, including in any of the aforementioned aspects and embodiments, the 17, 18, 19, 20, 21 (if present in the reference sequence), 22 (if present in the reference sequence), 23 (if present in the reference sequence), or 24 (if present in the reference sequence), or 25 (if present in the reference sequence) consecutive nucleic acids of any one of the recited targeting domain sequences are the 17, 18, 19, 20, 21 (if present in the reference sequence), 22 (if present in the reference sequence), 23 (if present in the reference sequence), or 24 (if present in the reference sequence), or 25 (if present in the reference sequence) consecutive nucleic acids disposed at the 3′ end of the recited targeting domain sequence. In other embodiments of the gRNA molecule, including in any of the aforementioned aspects and embodiments, the 17, 18, 19, 20, 21 (if present in the reference sequence), 22 (if present in the reference sequence), 23 (if present in the reference sequence), or 24 (if present in the reference sequence), or 25 (if present in the reference sequence) consecutive nucleic acids of any one of the recited targeting domain sequences are the 17, 18, 19, 20, 21 (if present in the reference sequence), 22 (if present in the reference sequence), 23 (if present in the reference sequence), or 24 (if present in the reference sequence), or 25 (if present in the reference sequence) consecutive nucleic acids disposed at the 5′ end of the recited targeting domain sequence. In other embodiments of the gRNA molecule, including in any of the aforementioned aspects and embodiments, the 17, 18, 19, 20, 21 (if present in the reference sequence), 22 (if present in the reference sequence), 23 (if present in the reference sequence), or 24 (if present in the reference sequence), or 25 (if present in the reference sequence) consecutive nucleic acids of any one of the recited targeting domain sequences do not include either the 5′ or 3′ nucleic acid of the recited targeting domain sequence.


In an aspect, including in any of the aforementioned aspects or embodiments, the gRNA molecule includes a portion of the crRNA and a portion of the tracr that hybridize to form a flagpole, that includes SEQ ID NO: 6584 or 6585. In embodiments, the flagpole further includes a first flagpole extension, located 3′ to the crRNA portion of the flagpole, wherein said first flagpole extension includes SEQ ID NO: 6586. In embodiments, the flagpole further includes a second flagpole extension located 3′ to the crRNA portion of the flagpole and, if present, the first flagpole extension, wherein said second flagpole extension includes SEQ ID NO: 6587.


In an aspect, including in any of the aforementioned aspects or embodiments, the invention provides a gRNA molecule that includes a tracr that includes, e.g., consists of, SEQ ID NO: 6660 or SEQ ID NO: 6661. In embodiments, the crRNA portion of the flagpole includes SEQ ID NO: 6607 or SEQ ID NO: 6608.


In an aspect, including in any of the aforementioned aspects or embodiments, the invention provides a gRNA molecule that includes a tracr that includes SEQ ID NO: 6589 or 6590, and optionally, if a first flagpole extension is present, a first tracr extension, disposed 5′ to SEQ ID NO: 6589 or 6590, said first tracr extension including SEQ ID NO: 6591.


In an aspect, including in any of the aforementioned aspects or embodiments, the invention provides a gRNA molecule wherein the targeting domain and the tracr are disposed on separate nucleic acid molecules (e.g., a dgRNA molecule).


In an aspect, including in any of the aforementioned aspects or embodiments, the invention provides a gRNA molecule wherein the targeting domain and the tracr are disposed on a single nucleic acid molecule (e.g., a sgRNA molecule), and wherein the tracr is disposed 3′ to the targeting domain. In embodiments, the sgRNA molecule includes a loop, disposed 3′ to the targeting domain and 5′ to the tracr, e.g., a loop including, e.g., consisting of, SEQ ID NO: 6588.


In an aspect, including in any of the aforementioned aspects or embodiments, the invention provides a gRNA molecule including, from 5′ to 3′, [targeting domain]-:


(a) SEQ ID NO: 6601;
(b) SEQ ID NO: 6602;
(c) SEQ ID NO: 6603;
(d) SEQ ID NO: 6604; or

(e) any of (a) to (d), above, further including, at the 3′ end, 1, 2, 3, 4, 5, 6 or 7 uracil (U) nucleotides, e.g., 4 uracil nucleotides. In embodiments, there are no intervening nucleotides between the targeting domain and the sequence of any of (a)-(e).


In another aspect, the invention provides CRISPR systems, e.g., Cas CRISPR systems, e.g., Cas9 CRISPR systems, e.g., S. pyogenes Cas9 CRISPR systems, the include one or more, e.g., one, gRNA molecule of any of the aforementioned aspects and embodiments. In an aspect, the invention provides a composition including a first gRNA molecule of any of the aforementioned aspects and embodiments, further including a Cas9 molecule. In embodiments, the Cas9 molecule is an active or inactive s. pyogenes Cas9. In embodiments, the first gRNA molecule and Cas9 molecule are present in a ribonuclear protein complex (RNP).


In another aspect, the invention provides compositions that include more than one gRNA, e.g., more than one gRNA molecule as described herein, e.g., more than one gRNA molecule of any of the aforementioned gRNA molecule aspects or embodiments. Thus, in a further aspect, the invention provides a composition of any of the aforementioned composition aspects and embodiments, further including a second gRNA molecule; a second gRNA molecule and a third gRNA molecule; or a second gRNA molecule, a third gRNA molecule, and a fourth gRNA molecule, wherein the second gRNA molecule, the third gRNA molecule (if present), and the fourth gRNA molecule (if present) are a gRNA molecule as described herein, e.g., a gRNA molecule of any of the aforementioned gRNA molecule aspects or embodiments. In an embodiment, each gRNA molecule of the composition is complementary to a different target sequence. In an embodiment, each gRNA molecule is complementary to target sequences within the same gene or region. In an aspect, the first gRNA molecule, the second gRNA molecule, the third gRNA molecule (if present), and the fourth gRNA molecule (if present) are complementary to target sequences not more than 20000 nucleotides, not more than 10000 nucleotides, not more than 6000, not more than 5000 nucleotides, not more than 4000, not more than 1000 nucleotides, not more than 500 nucleotides, not more than 400 nucleotides, not more than 300 nucleotides, not more than 200 nucleotides, not more than 100 nucleotides, not more than 90 nucleotides, not more than 80 nucleotides, not more than 70 nucleotides, not more than 60 nucleotides, not more than 50 nucleotides, not more than 40 nucleotides, not more than 30 nucleotides, not more than 20 nucleotides or not more than 10 nucleotides apart. In another aspect, each gRNA molecule of the composition is complementary to target sequence within a different gene or region.


Specific and preferred combinations of more than one gRNA molecule of the invention are described herein. In an aspect, the composition includes a first gRNA molecule and a second gRNA molecule, wherein the first gRNA molecule and second gRNA molecule are complementary to different target sequences, and are:


(a) independently selected from the gRNA molecules described herein (e.g., above) to the BCL11a gene;


(b) independently selected from the gRNA molecules described herein (e.g., above) to the +58 BCL11a enhancer;


(c) independently selected from the gRNA molecules described herein (e.g., above) to the +62 BCL11a enhancer;


(d) independently selected from the gRNA molecules described herein (e.g., above) to the +55 BCL11a enhancer; or


(e) independently selected from the gRNA molecules described herein (e.g., above) to a HPFH region.


In an aspect, the composition includes a first gRNA molecule and a second gRNA molecule, wherein the first gRNA molecule and second gRNA molecule are complementary to different target sequences, and:


(a) the first gRNA molecule is selected from the gRNA molecules described herein (e.g., above) to the BCL11a gene, and the second gRNA molecule is selected from the gRNA molecules described herein (e.g., above) to the +58 BCL11a enhancer;


(b) the first gRNA molecule is selected from the gRNA molecules described herein (e.g., above) to the BCL11a gene, and the second gRNA molecule is selected from the gRNA molecules described herein (e.g., above) to the +62 BCL11a enhancer;


(c) the first gRNA molecule is selected from the gRNA molecules described herein (e.g., above) to the BCL11a gene, and the second gRNA molecule is selected from the gRNA molecules described herein (e.g., above) to the +55 BCL11a enhancer;


(d) the first gRNA molecule is selected from the gRNA molecules described herein (e.g., above) to the BCL11a gene, and the second gRNA molecule is selected from the gRNA molecules described herein (e.g., above) to a HPFH region;


(e) the first gRNA molecule is selected from the gRNA molecules described herein (e.g., above) to the +58 BCL11a enhancer, and the second gRNA molecule is selected from the gRNA molecules described herein (e.g., above) to the +62 BCL11a enhancer;


(f) the first gRNA molecule is selected from the gRNA molecules described herein (e.g., above) to the +58 BCL11a enhancer, and the second gRNA molecule is selected from the gRNA molecules described herein (e.g., above) to the +55 BCL11a enhancer;


(g) the first gRNA molecule is selected from the gRNA molecules described herein (e.g., above) to the +58 BCL11a enhancer, and the second gRNA molecule is selected from the gRNA molecules described herein (e.g., above) to a HPFH region;


(h) the first gRNA molecule is selected from the gRNA molecules described herein (e.g., above) to the +62 BCL11a enhancer, and the second gRNA molecule is selected from the gRNA molecules described herein (e.g., above) to the +55 BCL11a enhancer;


(i) the first gRNA molecule is selected from the gRNA molecules described herein (e.g., above) to the +62 BCL11a enhancer, and the second gRNA molecule is selected from the gRNA molecules described herein (e.g., above) to a HPFH region;


(j) the first gRNA molecule is selected from the gRNA molecules described herein (e.g., above) to the +55 BCL11a enhancer, and the second gRNA molecule is selected from the gRNA molecules described herein (e.g., above) to a HPFH region;


In another aspect, the composition that includes a first gRNA molecule and a second gRNA molecule, includes:


(a) a first gRNA molecule that is selected from the gRNA molecules described herein (e.g., above) to a HPFH region, and a second gRNA molecule includes a targeting domain that is complementary to a target sequence of the beta globin gene; or


(b) a first gRNA molecule that is selected from the gRNA molecules described herein (e.g., above) to a BCL11a enhancer, e.g., a +58 BCL11a enhancer, a +55 BCL11a enhancer or a +62 BCL11a enhancer, and a second gRNA molecule includes a targeting domain that is complementary to a target sequence of the beta globin gene.


In any of the aforementioned composition aspects and embodiments, the composition may consist of, with respect to the gRNA components of the composition, a first gRNA molecule and a second gRNA molecule.


In any of the aforementioned composition aspects and embodiments, the compositions may be formulated in a medium suitable for electroporation.


In another aspect, the invention provides nucleic acids encoding the gRNA molecule(s) and/or Cas molecules of the CRISPR systems. Without being bound by theory, it is believed that delivering such nucleic acids to cells will lead to the expression of the CRISPR system within the cell. In an aspect, the invention provides a nucleic acid sequence that encodes one or more gRNA molecules of any of the previous gRNA aspects and embodiments. In embodiments, the nucleic acid includes a promoter operably linked to the sequence that encodes the one or more gRNA molecules. In embodiments, the promoter is a promoter recognized by an RNA polymerase II or RNA polymerase III. In embodiments, the promoter is a U6 promoter or an HI promoter.


In further aspects, the nucleic acid further comprises sequence encoding a Cas9 molecule. In embodiments, the nucleic acid includes a promoter operably linked to the sequence that encodes a Cas9 molecule. In embodiments, the promoter is an EF-1 promoter, a CMV IE gene promoter, an EF-1α promoter, an ubiquitin C promoter, or a phosphoglycerate kinase (PGK) promoter.


In an aspect the invention provides a vector that includes the nucleic acid of any of the previous nucleic acid aspects and embodiments. In embodiments, the vector is selected from the group consisting of a lentiviral vector, an adenoviral vector, an adeno-associated viral (AAV) vector, a herpes simplex virus (HSV) vector, a plasmid, a minicircle, a nanoplasmid, and an RNA vector.


In another aspect, the invention provides a composition including one or more gRNA molecules, e.g., as described herein, e.g., in any of the previous gRNA molecule aspects and embodiments, and nucleic acid encoding a Cas9 molecule.


In another aspect, the invention provides a composition including nucleic acid encoding one or more gRNA molecules (e.g., as described herein, e.g., of any of the previous gRNA molecule aspects and embodiments), and a Cas9 molecule.


In another aspect, the invention provides a composition, e.g., a composition of any of the aforementioned composition aspects and embodiments, further including a template nucleic acid. In another aspect, the invention provides a composition, e.g., a composition of any of the aforementioned composition aspects and embodiments, further including nucleic acid sequence encoding a template nucleic acid. In embodiments, the template nucleic acid includes a nucleotide that corresponds to a nucleotide of a target sequence of the gRNA molecule. In embodiments, the template nucleic acid includes nucleic acid encoding human beta globin, e.g., human beta globin including one or more of the mutations G16D, E22A and T87Q. In embodiments, the template nucleic acid includes nucleic acid encoding human gamma globin.


In another aspect, the invention provides cells that include (or at any time included) a gRNA molecule, CRISPR system, composition or nucleic acid (e.g., as described herein, e.g., as in any of the aforementioned aspects and embodiments). In such aspects, the invention provides cells that have been modified by such inclusion.


Thus, in an aspect, the invention provides a method of altering e.g., altering the structure, e.g., sequence, of a target sequence within nucleic acid of a cell, including contacting said cell with:


1) one or more gRNA molecules of any of the aforementioned gRNA molecule aspects and embodiments, and a Cas9 molecule (e.g., as described herein);


2) one or more gRNA molecules of any of the aforementioned gRNA molecule aspects and embodiments, and nucleic acid encoding a Cas9 molecule (e.g., as described herein);


3) nucleic acid encoding one or more gRNA molecules of any of the aforementioned gRNA molecule aspects and embodiments, and a Cas9 molecule (e.g., as described herein);


4) nucleic acid encoding one or more gRNA molecules of the aforementioned gRNA molecule aspects and embodiments, and nucleic acid encoding a Cas9 molecule (e.g., as described herein); or


5) any of 1) to 4), above, and a template nucleic acid (e.g., as described herein);


6) any of 1) to 4) above, and nucleic acid including sequence encoding a template nucleic acid (e.g., as described herein);


7) a composition as described herein (e.g., of any of the aforementioned composition aspects and embodiments); or


8) the vector of any of the aforementioned vector aspects and embodiments.


In embodiments, the gRNA molecule or nucleic acid encoding the gRNA molecule, and the Cas9 molecule or nucleic acid encoding the Cas9 molecule, are formulated in a single composition. In other embodiments, the gRNA molecule or nucleic acid encoding the gRNA molecule, and the Cas9 molecule or nucleic acid encoding the Cas9 molecule, are formulated in more than one composition. In embodiments, the more than one composition are delivered simultaneously or sequentially.


In embodiments, the cell is an animal cell. In embodiments, the cell the cell is a mammalian, primate, or human cell. In embodiments, the cell is a hempatopoietic stem or progenitor cell (HSPC) (e.g., a population of HSPCs). In embodiments, the cell is a CD34+ cell. In embodiments, the cell is a CD34+/CD38−/CD90+/CD45RA− cell. In embodiments, the cell is a CD34+/CD90+/CD49f+ cell. In embodiments, the cell is a CD34+/CD38−/CD90+/CD45RA−/CD49f+ cell. In embodiments, the method includes a population of cells that has been enriched for HSPCs, e.g., for CD34+ cells.


In embodiments, the cell (e.g. population of cells) has been isolated from bone marrow. In embodiments, the cell (e.g. population of cells) has been isolated from mobilized peripheral blood. In embodiments, the cell (e.g. population of cells) has been isolated from umbilical cord blood.


In embodiments, the cell (e.g. population of cells) is autologous with respect to a patient to be administered said cell (e.g. population of cells). In embodiments, the cell (e.g. population of cells) is allogeneic with respect to a patient to be administered said cell (e.g. population of cells).


In embodiments, of the methods described herein, the altering results in an increase of fetal hemoglobin expression in the cell. In embodiments, of the methods described herein, the altering results in a reduction of fetal hemoglobin expression in the cell.


In another aspect, the invention provides a cell, altered by the method of any of the aforementioned method aspects and embodiments. In another aspect, the invention provides a cell, including a first gRNA molecule (e.g., as described herein), or a composition (e.g., as described herein), or a nucleic acid encoding the first gRNA molecule (e.g., as described herein), of any of the previous aspects and embodiments. In embodiments, the cell is an animal cell. In embodiments, the cell the cell is a mammalian, primate, or human cell. In embodiments, the cell is a hematopoietic stem or progenitor cell (HSPC) (e.g., a population of HSPCs). In embodiments, the cell is a CD34+ cell. In embodiments, the cell is a CD34+/CD38−/CD90+/CD45RA− cell. In embodiments, the cell is a CD34+/CD90+/CD49f+ cell. In embodiments, the method includes a population of cells that has been enriched for HSPCs, e.g., for CD34+ cells.


In embodiments, the cell (e.g. population of cells) has been isolated from bone marrow. In embodiments, the cell (e.g. population of cells) has been isolated from mobilized peripheral blood. In embodiments, the cell (e.g. population of cells) has been isolated from umbilical cord blood.


In embodiments, the cell (e.g. population of cells) is autologous with respect to a patient to be administered said cell (e.g. population of cells). In embodiments, the cell (e.g. population of cells) is allogeneic with respect to a patient to be administered said cell (e.g. population of cells).


In embodiments, the cell includes, has included, or will include a second gRNA molecule, e.g., as described herein, e.g., of any of the previous gRNA molecule aspects and embodiments, or a nucleic acid encoding the second gRNA molecule, wherein the first gRNA molecule and second gRNA molecule include nonidentical targeting domains.


In embodiments, expression of fetal hemoglobin is increased in the cell, e.g., relative to a cell of the same cell type that has not been modified to include a gRNA molecule (e.g., as described herein). In embodiments, expression of beta globin is decreased in the cell, e.g., relative to a cell of the same cell type that has not been modified to include a gRNA molecule (e.g., as described herein). In embodiments, expression of fetal hemoglobin is increased and expression of beta globin is decreased in the cell, e.g., relative to a cell of the same cell type that has not been modified to include a gRNA molecule (e.g., as described herein).


In an aspect, the cells of the invention (or methods comprising a cell) have been contacted with a stem cell expander, e.g., as described herein, e.g., compound 1, compound 2, compound 3 or compound 4. In an aspect, the cells of the invention (or methods comprising a cell) have been contacted with a stem cell expander, e.g., as described herein, e.g., compound 1, compound 2, compound 3, compound 4 or a combination thereof (e.g., compound 1 and compound 4). In an embodiment, the stem cell expander is compound 4. In an embodiment, the stem cell expander is a combination of compound 1 and compound 4. In embodiments, the contacting is ex vivo.


In another aspect, the invention provides methods of treatment, e.g., methods of treatment of hemoglobinopathies. In an aspect, the invention provides a method of treating a hemoglobinopathy, that includes administering to a patient a cell (e.g., a population of cells) of any of the previous cell or method aspects and embodiments.


In another aspect, the invention provides a method of increasing fetal hemoglobin expression in a mammal, including administering to a patient a cell of any of the previous cell or method aspects and embodiments. In an embodiment, the hemoglobinopathy is beta-thalassemia or sickle cell disease.


In another aspect, the invention provides a guide RNA molecule, e.g., as described herein, for use as a medicament, e.g., for use in the treatment of a disease. In embodiments, the disease is a hemoglobinopathy, e.g., beta-thalassemia or sickle cell disease.


In another aspect, the invention provides a gRNA molecule, e.g., as described herein, e.g., as described in any of the aforementioned gRNA molecule aspects and embodiments, wherein when a CRISPR system including the gRNA is introduced into a cell (e.g., a CD34+ cell, e.g., an HSC), at least about 15% of the indels produced include (a) a frameshift mutation; or (b) a large deletion, relative to unmodified target DNA, as measured by NGS. In embodiments, at least about 25% of the indels produced include (a) a frameshift mutation; or (b) a large deletion, relative to unmodified target DNA, as measured by NGS. In embodiments, at least about 40%, at least about 50%, at least about 60%, at least about 70% at least about 80%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% of the indels produced include (a) a frameshift mutation; or (b) a large deletion, relative to unmodified target DNA, as measured by NGS.


In another aspect, the invention provides methods for the ex vivo expansion and modification of HSPCs (e.g., CD34+ cells). In an aspect, the invention provides a method of modifying cells (e.g., a population of cells) including:


(a) providing a population of cells;


(b) expanding said cells ex vivo in the presence of a stem cell expander; and


(c) introducing into said cells a first gRNA molecule (e.g., as described herein, e.g., of any of the aforementioned gRNA molecule aspects and embodiments), a nucleic acid molecule encoding the first gRNA molecule, or a composition (e.g., as described herein, e.g., of any of the aforementioned composition aspects and embodiments);


such that hemoglobin, e.g., fetal hemoglobin, expression is increased in said cells relative to the same cell type which have not been subjected to step (c).


In embodiments, the cells are introduced into a subject in need thereof, e.g., a subject that has a hemoglobinopathy, e.g., sickle cell disease or beta thalassemia.


In embodiments, the cells are or comprise CD34+ cells. In embodiments, the cells are or comprise HSPCs. In embodiments, the cells are isolated from bone marrow, mobilized peripheral blood or umbilical cord blood. In a preferred embodiment, the cells are isolated from bone marrow. In other embodiments, the cells are isolated from mobilized peripheral blood. In aspects, the moblized peripheral blood is isolated from a subject who has been administered a G-CSF. In aspects, the moblized peripheral blood is isolated from a subject who has been administered a moblization agent other than G-CSF, for example, Plerixafor® (AMD3100). In embodiments, the cells are an enriched population of cells.


In embodiments, the stem cell expander is compound 1, compound 2, compound 3, or compound 4, e.g., compound 4. In embodiments, the stem cell expander is compound 1, compound 2, compound 3, compound 4, or a combination thereof (e.g., a combination of compound 1 and compound 4). In embodiments, the cells are contacted with compound 4 at a concentration of from about 1 to about 200 micromolar (uM). In an embodiment, the concentration of compound 4 is about 75 micromolar (uM). In embodiments, the expanding said cells ex vivo in the presence of a stem cell expander occurs for a period of about 1-10 days, e.g., about 1-5 days, e.g., about 2-5 days, e.g., about 4 days.


In embodiments, the cells are autologous to a patient intended to be administered said cells. In embodiments, the cells are allogeneic to a patient intended to be administered said cells.


In embodiments, the expanding of step (b) is further in the presence of thrombopoietin (Tpo), Flt3 ligand (Flt-3L), human stem cell factor (SCF) and human interleukin-6 (IL-6). In embodiments, the thrombopoietin (Tpo), Flt3 ligand (Flt-3L), human stem cell factor (SCF) and human interleukin-6 (IL-6) are each at a concentration of about 50 ng/mL. In embodiments, the thrombopoietin (Tpo), Flt3 ligand (Flt-3L), human stem cell factor (SCF) and human interleukin-6 (IL-6) are each at a concentration of 50 ng/mL.


Additional aspects and embodiments are described below.


In an aspect, the invention provides a gRNA molecule that includes a tracr and crRNA, wherein the crRNA includes a targeting domain that is complementary with a target sequence of a BCL11A gene (e.g., a human BCL11a gene), a BCL11a enhancer (e.g., a human BCL11a enhancer), or a HFPH region (e.g., a human HPFH region).


In embodiments, the target sequence is of the BCL11A gene, and the targeting domain includes, e.g., consists of, any one of SEQ ID NO: 1 to SEQ ID NO: 85 or SEQ ID NO: 400 to SEQ ID NO: 1231. These embodiments are referred to herein as gRNA molecule embodiment 2.


In other embodiments, the target sequence is of a BCL11a enhancer, and the targeting domain includes, e.g., consists of, any one of SEQ ID NO: 1232 to SEQ ID NO: 1499. These embodiments are referred to herein as gRNA molecule embodiment 3. In preferred embodiments, the target sequence is of a BCL enhancer, and the targeting domain includes, e.g., consists of, any one of SEQ ID NO: 182 to SEQ ID NO: 277 or SEQ ID NO: 334 to SEQ ID NO: 341. These embodiments are referred to herein as gRNA molecule embodiment 4. In more preferred embodiments, the targeting domain includes, e.g., consists of, any one of SEQ ID NO: 341, SEQ ID NO: 246, SEQ ID NO: 248, SEQ ID NO: 247, SEQ ID NO: 245, SEQ ID NO: 249, SEQ ID NO: 244, SEQ ID NO: 199, SEQ ID NO: 251, SEQ ID NO: 250, SEQ ID NO: 334, SEQ ID NO: 185, SEQ ID NO: 186, SEQ ID NO: 336, or SEQ ID NO: 337. These embodiments are referred to herein as gRNA molecule embodiment 5. In still more preferred embodiments, the targeting domain includes, e.g., consists of, any one of SEQ ID NO: 247, SEQ ID NO: 248, SEQ ID NO: 335, SEQ ID NO: 336, SEQ ID NO: 337, or SEQ ID NO: 338 (referred to herein as gRNA molecule embodiment 6), for example, includes, e.g., consists of, any one of SEQ ID NO: 248 or SEQ ID NO: 338 (referred to herein as gRNA molecule embodiment 7). In embodiments, the targeting domain includes, e.g., consists of, SEQ ID NO: 248 (referred to herein as gRNA molecule embodiment 8). In embodiments, the targeting domain includes, e.g., consists of, SEQ ID NO: 338 (referred to herein as gRNA molecule embodiment 9).


In other embodiments, the target sequence is of a BCL11a enhancer, and the targeting domain includes, e.g., consists of, any one of SEQ ID NO: 278 to SEQ ID NO: 333 (referred to herein as gRNA molecule embodiment 10). In preferred embodiments, the targeting domain includes, e.g., consists of, any one of SEQ ID NO: 318, SEQ ID NO: 312, SEQ ID NO: 313, SEQ ID NO: 294, SEQ ID NO: 310, SEQ ID NO: 319, SEQ ID NO: 298, SEQ ID NO: 322, SEQ ID NO: 311, SEQ ID NO: 315, SEQ ID NO: 290, SEQ ID NO: 317, SEQ ID NO: 309, SEQ ID NO: 289, or SEQ ID NO: 281 (referred to herein as gRNA molecule embodiment 11). In one preferred embodiment, the targeting domain includes, e.g., consists of, SEQ ID NO: 318 (referred to herein as gRNA molecule embodiment 12).


In other embodiments, the target sequence is of a BCL11a enhancer, and the targeting domain includes, e.g., consists of, any one of SEQ ID NO: 1596 to SEQ ID NO: 1691 (referred to herein as gRNA molecule embodiment 13). In preferred embodiments, the targeting domain includes, e.g., consists of, any one of SEQ ID NO: 1683, SEQ ID NO: 1638, SEQ ID NO: 1647, SEQ ID NO: 1609, SEQ ID NO: 1621, SEQ ID NO: 1617, SEQ ID NO: 1654, SEQ ID NO: 1631, SEQ ID NO: 1620, SEQ ID NO: 1637, SEQ ID NO: 1612, SEQ ID NO: 1656, SEQ ID NO: 1619, SEQ ID NO: 1675, SEQ ID NO: 1645, SEQ ID NO: 1598, SEQ ID NO: 1599, SEQ ID NO: 1663, SEQ ID NO: 1677, or SEQ ID NO: 1626 (referred to herein as gRNA molecule embodiment 14).


In other embodiments, the target sequence is of a HFPH region (e.g., a French HPFH region), and the targeting domain includes, e.g., consists of, any one of SEQ ID NO: 86 to SEQ ID NO: 181, SEQ ID NO: 1500 to SEQ ID NO: 1595, or SEQ ID NO: 1692 to SEQ ID NO: 1761 (referred to herein as gRNA molecule embodiment 15). In preferred embodiments, the targeting domain includes, e.g., consists of, any one of SEQ ID NO: 100, SEQ ID NO: 165, SEQ ID NO: 113, SEQ ID NO: 99, SEQ ID NO: 112, SEQ ID NO: 98, SEQ ID NO: 1580, SEQ ID NO: 106, SEQ ID NO: 1503, SEQ ID NO: 1589, SEQ ID NO: 160, SEQ ID NO: 1537, SEQ ID NO: 159, SEQ ID NO: 101, SEQ ID NO: 162, SEQ ID NO: 104, SEQ ID NO: 138, SEQ ID NO: 1536, SEQ ID NO: 1539, SEQ ID NO: 1585 (referred to herein as gRNA molecule embodiment 16). In still more preferred embodiments, the targeting domain includes, e.g., consists of, any one of SEQ ID NO: 98, SEQ ID NO: 100, SEQ ID NO: 1505, SEQ ID NO: 1589, SEQ ID NO: 1700, or SEQ ID NO: 1750 (referred to herein as gRNA molecule embodiment 17). In other preferred embodiments, the targeting domain includes, e.g., consists of, any one of SEQ ID NO: 100, SEQ ID NO: 165, or SEQ ID NO: 113 (referred to herein as gRNA molecule embodiment 18).


In embodiments, the gRNA molecule includes a targeting domain that includes, e.g., consists of, 17, 18, 19, 20, 21, 22, 23, or 24, preferably 20, consecutive nucleic acids of any targeting domain sequence described herein, for example a targeting domain sequence of Table 1 or Table 2. In embodiments, the 17, 18, 19, 20, 21, 22, 23, or 24, preferably 20, consecutive nucleic acids of any one of targeting domain sequences described herein, for example a targeting domain sequence of Table 1 or Table 2, are the 17, 18, 19, 20, 21, 22, 23, or 24, preferably 20, consecutive nucleic acids disposed at the 3′ end of the recited targeting domain sequence. In other embodiments, the 17, 18, 19, 20, 21, 22, 23, or 24, preferably 20, consecutive nucleic acids of any one of the targeting domain sequences described herein, for example a targeting domain sequence of Table 1 or Table 2, are the 17, 18, 19, 20, 21, 22, 23, or 24, preferably 20, consecutive nucleic acids disposed at the 5′ end of the recited targeting domain sequence. In other embodiments, the 17, 18, 19, 20, 21, 22, 23, or 24, preferably 20, consecutive nucleic acids of any one of the targeting domain sequences described herein, for example a targeting domain sequence of Table 1 or Table 2, do not include either the 5′ or 3′ nucleic acid of the recited targeting domain sequence.


In embodiments, the gRNA molecule includes a targeting domain that includes, e.g., consists of, 17, 18, 19, or 20, preferably 20, consecutive nucleic acids of any targeting domain sequence described herein, for example a targeting domain sequence of Table 5, Table 6, Table 7, Table 8 or Table 9. In embodiments, the 17, 18, 19, or 20, preferably 20, consecutive nucleic acids of any one of targeting domain sequences described herein, for example a targeting domain sequence of Table 5, Table 6, Table 7, Table 8 or Table 9, are the 17, 18, 19, or 20, preferably 20, consecutive nucleic acids disposed at the 3′ end of the recited targeting domain sequence. In other embodiments, the 17, 18, 19, or 20, preferably 20, consecutive nucleic acids of any one of the targeting domain sequences described herein, for example a targeting domain sequence of Table 5, Table 6, Table 7, Table 8 or Table 9, are the 17, 18, 19, or 20, preferably 20, consecutive nucleic acids disposed at the 5′ end of the recited targeting domain sequence. In other embodiments, the 17, 18, 19, or 20, preferably 20, consecutive nucleic acids of any one of the targeting domain sequences described herein, for example a targeting domain sequence of Table 5, Table 6, Table 7, Table 8 or Table 9, do not include either the 5′ or 3′ nucleic acid of the recited targeting domain sequence.


The following aspects describe features of the gRNA molecule that may be combined with any of the aforementioned aspects and embodiments. In embodiments, the gRNA molecule, including the gRNA molecule of any of the aforementioned aspects and embodiments, include a portion of the crRNA and a portion of the tracr that hybridize to form a flagpole that includes SEQ ID NO: 6584 or 6585. In embodiments, the flagpole further includes a first flagpole extension, located 3′ to the crRNA portion of the flagpole, wherein said first flagpole extension includes SEQ ID NO: 6586. In embodiments, the flagpole further includes (in addition to or in alternative to the first flagpole extension) a second flagpole extension located 3′ to the crRNA portion of the flagpole and, if present, the first flagpole extension, wherein said second flagpole extension includes SEQ ID NO: 6587.


In embodiments, including in any of the aforementioned aspects and embodiments, the tracr includes SEQ ID NO: 6660 or SEQ ID NO: 6661. In embodiments, the tracr includes SEQ ID NO: 7812, optionally further including, at the 3′ end, an additional 1, 2, 3, 4, 5, 6, or 7 uracil (U) nucleotides. In embodiments, the crRNA includes, from 5′ to 3′, [targeting domain]-: a) SEQ ID NO: 6584; b) SEQ ID NO: 6585; c) SEQ ID NO: 6605; d) SEQ ID NO: 6606; e) SEQ ID NO: 6607; f) SEQ ID NO: 6608; or g) SEQ ID NO: 7806.


In embodiments, including in any of the aforementioned aspects and embodiments, the tracr includes, from 5′ to 3′: a) SEQ ID NO: 6589; b) SEQ ID NO: 6590; c) SEQ ID NO: 6609; d) SEQ ID NO: 6610; e) SEQ ID NO: 6660; f) SEQ ID NO: 6661; g) SEQ ID NO: 7812; h) SEQ ID NO: 7807; i) SEQ ID NO: 7808; j) SEQ ID NO: 7809; k) any of a) to j), above, further including, at the 3′ end, at least 1, 2, 3, 4, 5, 6 or 7 uracil (U) nucleotides, e.g., 1, 2, 3, 4, 5, 6, or 7 uracil (U) nucleotides; 1) any of a) to k), above, further including, at the 3′ end, at least 1, 2, 3, 4, 5, 6 or 7 adenine (A) nucleotides, e.g., 1, 2, 3, 4, 5, 6, or 7 adenine (A) nucleotides; or m) any of a) to l), above, further including, at the 5′ end (e.g., at the 5′ terminus), at least 1, 2, 3, 4, 5, 6 or 7 adenine (A) nucleotides, e.g., 1, 2, 3, 4, 5, 6, or 7 adenine (A) nucleotides.


In embodiments, the targeting domain and the tracr are disposed on separate nucleic acids molecules. In embodiments of such gRNA molecules, the nucleic acid molecule including the targeting domain includes SEQ ID NO: 6607, optionally disposed immediately 3′ to the targeting domain, and the nucleic acid molecule including the tracr includes, e.g., consists of, SEQ ID NO: 6660.


In embodiments, the crRNA portion of the flagpole includes SEQ ID NO: 6607 or SEQ ID NO: 6608.


In embodiments, the tracr includes SEQ ID NO: 6589 or 6590, and optionally, if a first flagpole extension is present, a first tracr extension, disposed 5′ to SEQ ID NO: 6589 or 6590, said first tracr extension including SEQ ID NO: 6591.


In embodiments, including in embodiments of any of the aforementioned aspects and embodiments, the targeting domain and the tracr are disposed on separate nucleic acid molecules. In other embodiments, including in embodiments of any of the aforementioned aspects and embodiments, the targeting domain and the tracr are disposed on a single nucleic acid molecule, for example, the tracr is disposed 3′ to the targeting domain.


In embodiments, when the targeting domain and the tracr are disposed on a single nucleic acid molecule, the gRNA molecule further includes a loop, disposed 3′ to the targeting domain and 5′ to the tracr. In embodiments, the loop includes, e.g., consists of, SEQ ID NO: 6588.


In embodiments, when the targeting domain and the tracr are disposed on a single nucleic acid molecule, the gRNA molecule includes, from 5′ to 3′, [targeting domain]-: (a) SEQ ID NO: 6601; (b) SEQ ID NO: 6602; (c) SEQ ID NO: 6603; (d) SEQ ID NO: 6604; (e) SEQ ID NO: 7811; or (f) any of (a) to (e), above, further including, at the 3′ end, 1, 2, 3, 4, 5, 6 or 7 uracil (U) nucleotides. In embodiments, the gRNA molecule includes, e.g., consists of, said targeting domain and SEQ ID NO: 7811, optionally disposed immediately 3′ to said targeting domain.


In embodiments, including in any of the aforementioned aspects and embodiments, each of the nucleic acid residues of the gRNA molecule is an unmodified A, U, G or C nucleic acid residue and unmodified phosphate bonds between each residue of the nucleic acid molecule(s). In other embodiments, including in any of the aforementioned aspects and embodiments, one, or optionally more than one, of the nucleic acid molecules that make up the gRNA molecule includes: a) one or more, e.g., three, phosphorothioate modifications at the 3′ end of said nucleic acid molecule or molecules; b) one or more, e.g., three, phosphorothioate modifications at the 5′ end of said nucleic acid molecule or molecules; c) one or more, e.g., three, 2′-O-methyl modifications at the 3′ end of said nucleic acid molecule or molecules; d) one or more, e.g., three, 2′-O-methyl modifications at the 5′ end of said nucleic acid molecule or molecules; e) a 2′ O-methyl modification at each of the 4th-to-terminal, 3rd-to-terminal, and 2nd-to-terminal 3′ residues of said nucleic acid molecule or molecules; f) a 2′ O-methyl modification at each of the 4th-to-terminal, 3rd-to-terminal, and 2nd-to-terminal 5′ residues of said nucleic acid molecule or molecules; or f) any combination thereof.


In preferred embodiments, the invention provides a gRNA molecule (e.g., that is a sgRNA molecule) including, e.g., consisting of, the sequence: (a) SEQ ID NO: 342; (b) SEQ ID NO: 343; or (c) SEQ ID NO: 1762 (referred to in this summary of invention as gRNA molecule embodiment 41).


In other preferred embodiments, the invention provides gRNA molecule (e.g., that is a dual gRNA molecule) including, e.g., consisting of: (a) a crRNA including, e.g., consisting of, SEQ ID NO: 344, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; (b) a crRNA including, e.g., consisting of, SEQ ID NO: 344, and a tracr including, e.g., consisting of, SEQ ID NO: 346; (c) a crRNA including, e.g., consisting of, SEQ ID NO: 345, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; or (d) a crRNA including, e.g., consisting of, SEQ ID NO: 345, and a tracr including, e.g., consisting of, SEQ ID NO: 346 (referred to in this summary of invention as gRNA molecule embodiment 42).


In other preferred embodiments, the invention provides a gRNA molecule (e.g., that is a sgRNA molecule) including, e.g., consisting of, the sequence: (a) SEQ ID NO: 347; (b) SEQ ID NO: 348; or (c) SEQ ID NO: 1763 (referred to in this summary of invention as gRNA molecule embodiment 43).


In other preferred embodiments, the invention provides gRNA molecule (e.g., that is a dual gRNA molecule) including, e.g., consisting of: (a) a crRNA including, e.g., consisting of, SEQ ID NO: 349, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; (b) a crRNA including, e.g., consisting of, SEQ ID NO: 349, and a tracr including, e.g., consisting of, SEQ ID NO: 346; (c) a crRNA including, e.g., consisting of, SEQ ID NO: 350, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; or (d) a crRNA including, e.g., consisting of, SEQ ID NO: 350, and a tracr including, e.g., consisting of, SEQ ID NO: 346 (referred to in this summary of invention as gRNA molecule embodiment 44).


In other preferred embodiments, the invention provides a gRNA molecule (e.g., that is a sgRNA molecule) including, e.g., consisting of, the sequence: (a) SEQ ID NO: 351; (b) SEQ ID NO: 352; or (c) SEQ ID NO: 1764 (referred to in this summary of invention as gRNA molecule embodiment 45).


In other preferred embodiments, the invention provides gRNA molecule (e.g., that is a dual gRNA molecule) including, e.g., consisting of: (a) a crRNA including, e.g., consisting of, SEQ ID NO: 353, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; (b) a crRNA including, e.g., consisting of, SEQ ID NO: 353, and a tracr including, e.g., consisting of, SEQ ID NO: 346; (c) a crRNA including, e.g., consisting of, SEQ ID NO: 354, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; or (d) a crRNA including, e.g., consisting of, SEQ ID NO: 354, and a tracr including, e.g., consisting of, SEQ ID NO: 346 (referred to in this summary of invention as gRNA molecule embodiment 46).


In other preferred embodiments, the invention provides a gRNA molecule (e.g., that is a sgRNA molecule) including, e.g., consisting of, the sequence: (a) SEQ ID NO: 355; (b) SEQ ID NO: 356; or (c) SEQ ID NO: 1765 (referred to in this summary of invention as gRNA molecule embodiment 47).


In other preferred embodiments, the invention provides gRNA molecule (e.g., that is a dual gRNA molecule) including, e.g., consisting of: (a) a crRNA including, e.g., consisting of, SEQ ID NO: 357, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; (b) a crRNA including, e.g., consisting of, SEQ ID NO: 357, and a tracr including, e.g., consisting of, SEQ ID NO: 346; (c) a crRNA including, e.g., consisting of, SEQ ID NO: 358, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; or (d) a crRNA including, e.g., consisting of, SEQ ID NO: 358, and a tracr including, e.g., consisting of, SEQ ID NO: 346 (referred to in this summary of invention as gRNA molecule embodiment 48).


In other preferred embodiments, the invention provides a gRNA molecule (e.g., that is a sgRNA molecule) including, e.g., consisting of, the sequence: (a) SEQ ID NO: 359; (b) SEQ ID NO: 360; or (c) SEQ ID NO: 1766 (referred to in this summary of invention as gRNA molecule embodiment 49).


In other preferred embodiments, the invention provides gRNA molecule (e.g., that is a dual gRNA molecule) including, e.g., consisting of: (a) a crRNA including, e.g., consisting of, SEQ ID NO: 361, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; (b) a crRNA including, e.g., consisting of, SEQ ID NO: 361, and a tracr including, e.g., consisting of, SEQ ID NO: 346; (c) a crRNA including, e.g., consisting of, SEQ ID NO: 362, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; or (d) a crRNA including, e.g., consisting of, SEQ ID NO: 362, and a tracr including, e.g., consisting of, SEQ ID NO: 346 (referred to in this summary of invention as gRNA molecule embodiment 50).


In other preferred embodiments, the invention provides a gRNA molecule (e.g., that is a sgRNA molecule) including, e.g., consisting of, the sequence: (a) SEQ ID NO: 363; (b) SEQ ID NO: 364; or (c) SEQ ID NO: 1767 (referred to in this summary of invention as gRNA molecule embodiment 51).


In other preferred embodiments, the invention provides gRNA molecule (e.g., that is a dual gRNA molecule) including, e.g., consisting of: (a) a crRNA including, e.g., consisting of, SEQ ID NO: 365, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; (b) a crRNA including, e.g., consisting of, SEQ ID NO: 365, and a tracr including, e.g., consisting of, SEQ ID NO: 346; (c) a crRNA including, e.g., consisting of, SEQ ID NO: 366, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; or (d) a crRNA including, e.g., consisting of, SEQ ID NO: 366, and a tracr including, e.g., consisting of, SEQ ID NO: 346 (referred to in this summary of invention as gRNA molecule embodiment 52).


In other preferred embodiments, the invention provides a gRNA molecule (e.g., that is a sgRNA molecule) including, e.g., consisting of, the sequence: (a) SEQ ID NO: 367; (b) SEQ ID NO: 368; or (c) SEQ ID NO: 1768 (referred to in this summary of invention as gRNA molecule embodiment 53).


In other preferred embodiments, the invention provides gRNA molecule (e.g., that is a dual gRNA molecule) including, e.g., consisting of: (a) a crRNA including, e.g., consisting of, SEQ ID NO: 369, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; (b) a crRNA including, e.g., consisting of, SEQ ID NO: 369, and a tracr including, e.g., consisting of, SEQ ID NO: 346; (c) a crRNA including, e.g., consisting of, SEQ ID NO: 370, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; or (d) a crRNA including, e.g., consisting of, SEQ ID NO: 370, and a tracr including, e.g., consisting of, SEQ ID NO: 346 (referred to in this summary of invention as gRNA molecule embodiment 54).


In other preferred embodiments, the invention provides a gRNA molecule (e.g., that is a sgRNA molecule) including, e.g., consisting of, the sequence: (a) SEQ ID NO: 371; (b) SEQ ID NO: 372; or (c) SEQ ID NO: 1769 (referred to in this summary of invention as gRNA molecule embodiment 55).


In other preferred embodiments, the invention provides gRNA molecule (e.g., that is a dual gRNA molecule) including, e.g., consisting of: (a) a crRNA including, e.g., consisting of, SEQ ID NO: 373, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; (b) a crRNA including, e.g., consisting of, SEQ ID NO: 373, and a tracr including, e.g., consisting of, SEQ ID NO: 346; (c) a crRNA including, e.g., consisting of, SEQ ID NO: 374, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; or (d) a crRNA including, e.g., consisting of, SEQ ID NO: 374, and a tracr including, e.g., consisting of, SEQ ID NO: 346 (referred to in this summary of invention as gRNA molecule embodiment 56).


In other preferred embodiments, the invention provides a gRNA molecule (e.g., that is a sgRNA molecule) including, e.g., consisting of, the sequence: (a) SEQ ID NO: 375; (b) SEQ ID NO: 376; or (c) SEQ ID NO: 1770 (referred to in this summary of invention as gRNA molecule embodiment 57).


In other preferred embodiments, the invention provides gRNA molecule (e.g., that is a dual gRNA molecule) including, e.g., consisting of: (a) a crRNA including, e.g., consisting of, SEQ ID NO: 377, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; (b) a crRNA including, e.g., consisting of, SEQ ID NO: 377, and a tracr including, e.g., consisting of, SEQ ID NO: 346; (c) a crRNA including, e.g., consisting of, SEQ ID NO: 378, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; or (d) a crRNA including, e.g., consisting of, SEQ ID NO: 378, and a tracr including, e.g., consisting of, SEQ ID NO: 346 (referred to in this summary of invention as gRNA molecule embodiment 58).


In other preferred embodiments, the invention provides a gRNA molecule (e.g., that is a sgRNA molecule) including, e.g., consisting of, the sequence: (a) SEQ ID NO: 379; (b) SEQ ID NO: 380; or (c) SEQ ID NO: 1771 (referred to in this summary of invention as gRNA molecule embodiment 59).


In other preferred embodiments, the invention provides gRNA molecule (e.g., that is a dual gRNA molecule) including, e.g., consisting of: (a) a crRNA including, e.g., consisting of, SEQ ID NO: 381, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; (b) a crRNA including, e.g., consisting of, SEQ ID NO: 381, and a tracr including, e.g., consisting of, SEQ ID NO: 346; (c) a crRNA including, e.g., consisting of, SEQ ID NO: 382, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; or (d) a crRNA including, e.g., consisting of, SEQ ID NO: 382, and a tracr including, e.g., consisting of, SEQ ID NO: 346 (referred to in this summary of invention as gRNA molecule embodiment 60).


In other preferred embodiments, the invention provides a gRNA molecule (e.g., that is a sgRNA molecule) including, e.g., consisting of, the sequence: (a) SEQ ID NO: 383; (b) SEQ ID NO: 384; or (c) SEQ ID NO: 1772 (referred to in this summary of invention as gRNA molecule embodiment 61).


In other preferred embodiments, the invention provides gRNA molecule (e.g., that is a dual gRNA molecule) including, e.g., consisting of: (a) a crRNA including, e.g., consisting of, SEQ ID NO: 385, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; (b) a crRNA including, e.g., consisting of, SEQ ID NO: 385, and a tracr including, e.g., consisting of, SEQ ID NO: 346; (c) a crRNA including, e.g., consisting of, SEQ ID NO: 386, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; or (d) a crRNA including, e.g., consisting of, SEQ ID NO: 386, and a tracr including, e.g., consisting of, SEQ ID NO: 346 (referred to in this summary of invention as gRNA molecule embodiment 62).


In other preferred embodiments, the invention provides a gRNA molecule (e.g., that is a sgRNA molecule) including, e.g., consisting of, the sequence: (a) SEQ ID NO: 387; (b) SEQ ID NO: 388; or (c) SEQ ID NO: 1773 (referred to in this summary of invention as gRNA molecule embodiment 63).


In other preferred embodiments, the invention provides gRNA molecule (e.g., that is a dual gRNA molecule) including, e.g., consisting of: (a) a crRNA including, e.g., consisting of, SEQ ID NO: 389, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; (b) a crRNA including, e.g., consisting of, SEQ ID NO: 389, and a tracr including, e.g., consisting of, SEQ ID NO: 346; (c) a crRNA including, e.g., consisting of, SEQ ID NO: 390, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; or (d) a crRNA including, e.g., consisting of, SEQ ID NO: 390, and a tracr including, e.g., consisting of, SEQ ID NO: 346 (referred to in this summary of invention as gRNA molecule embodiment 64).


In other preferred embodiments, the invention provides a gRNA molecule (e.g., that is a sgRNA molecule) including, e.g., consisting of, the sequence: (a) SEQ ID NO: 391; (b) SEQ ID NO: 392; or (c) SEQ ID NO: 1774 (referred to in this summary of invention as gRNA molecule embodiment 65).


In other preferred embodiments, the invention provides gRNA molecule (e.g., that is a dual gRNA molecule) including, e.g., consisting of: (a) a crRNA including, e.g., consisting of, SEQ ID NO: 393, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; (b) a crRNA including, e.g., consisting of, SEQ ID NO: 393, and a tracr including, e.g., consisting of, SEQ ID NO: 346; (c) a crRNA including, e.g., consisting of, SEQ ID NO: 394, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; or (d) a crRNA including, e.g., consisting of, SEQ ID NO: 394, and a tracr including, e.g., consisting of, SEQ ID NO: 346 (referred to in this summary of invention as gRNA molecule embodiment 66).


In other preferred embodiments, the invention provides a gRNA molecule (e.g., that is a sgRNA molecule) including, e.g., consisting of, the sequence: (a) SEQ ID NO: 395; (b) SEQ ID NO: 396; or (c) SEQ ID NO: 1775 (referred to in this summary of invention as gRNA molecule embodiment 67).


In other preferred embodiments, the invention provides gRNA molecule (e.g., that is a dual gRNA molecule) including, e.g., consisting of: (a) a crRNA including, e.g., consisting of, SEQ ID NO: 397, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; (b) a crRNA including, e.g., consisting of, SEQ ID NO: 397, and a tracr including, e.g., consisting of, SEQ ID NO: 346; (c) a crRNA including, e.g., consisting of, SEQ ID NO: 398, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; or (d) a crRNA including, e.g., consisting of, SEQ ID NO: 398, and a tracr including, e.g., consisting of, SEQ ID NO: 346 (referred to in this summary of invention as gRNA molecule embodiment 68).


In embodiments, including in any of the aforementioned aspects and embodiments, the invention provides a gRNA molecule, wherein when a CRISPR system (e.g., an RNP as described herein) including the gRNA molecule is introduced into a cell, an indel is formed at or near the target sequence complementary to the targeting domain of the gRNA molecule. In embodiments, including in embodiments comprising a targeting domain complementary to a target sequence of a +58 Enhancer region, the indel does not include a nucleotide of a GATA-1 and/or TAL-1 binding site. In embodiments, the indel does not interfere with the binding of GATA-1 and/or TAL-1 to their binding sites. In embodiments, including in any of the aforementioned aspects and embodiments, the invention provides a gRNA molecule, wherein when a CRISPR system (e.g., an RNP as described herein) including the gRNA molecule is introduced into a population of cells, an indel is formed at or near the target sequence complementary to the targeting domain of the gRNA molecule in at least about 40%, e.g., at least about 50%, e.g., at least about 60%, e.g., at least about 70%, e.g., at least about 80%, e.g., at least about 90%, e.g., at least about 95%, e.g., at least about 96%, e.g., at least about 97%, e.g., at least about 98%, e.g., at least about 99%, of the cells of the population. In embodiments, including in any of the aforementioned aspects and embodiments, the invention provides a gRNA molecule, wherein when a CRISPR system (e.g., an RNP as described herein) including the gRNA molecule is introduced into a population of cells, an indel that does not include a nucleotide of a GATA-1 and/or TAL-1 binding site is formed at or near the target sequence complementary to the targeting domain of the gRNA molecule in at least about 20%, e.g., at least about 30%, e.g., at least about 35%, e.g., at least about 40%, e.g., at least about 45%, e.g., at least about 50%, e.g., at least about 55%, e.g., at least about 60%, e.g., at least about 65%, e.g., at least about 70%, e.g., at least about 75%, e.g., at least about 80%, e.g., at least about 85%, e.g., at least about 90%, e.g., at least about 95%, e.g., at least about 99%, of the cells of the population. In embodiments, including in any of the aforementioned aspects and embodiments, the indel is an indel listed in any of FIG. 25, Table 15, Table 26, Table 27 or Table 37. In embodiments, in at least about 30%, e.g., least about 40%, e.g., at least about 50%, e.g., at least about 60%, e.g., at least about 70%, e.g., at least about 80%, e.g., at least about 90%, e.g., at least about 95%, e.g., at least about 96%, e.g., at least about 97%, e.g., at least about 98%, e.g., at least about 99%, of the cells of the population, the indel is an indel listed in any of FIG. 25, Table 15, Table 26, Table 27 or Table 37. In embodiments, the three most frequently detected indels in said population of cells include the indels associated with any gRNA molecule listed in any of FIG. 25, Table 15, Table 26, Table 27 or Table 37. In embodiments, the indel (or pattern of top indels) is as measured by next generation sequencing (NGS), e.g., as described in the art. In embodiments, including in any of the aforementioned aspects and embodiments, the invention provides a gRNA molecule, wherein when a CRISPR system (e.g., an RNP as described herein) including the gRNA molecule is introduced into a cell, no off-target indels are formed in said cell, e.g., as detectible by next generation sequencing and/or a nucleotide insertional assay, e.g., assayed in an HPCS cell, e.g., a CD34+ cell. In embodiments, including in any of the aforementioned aspects and embodiments, the invention provides a gRNA molecule, wherein when a CRISPR system (e.g., an RNP as described herein) including the gRNA molecule is introduced into a population of cells, no off-target indel is detected in more than about 5%, e.g., more than about 1%, e.g., more than about 0.1%, e.g., more than about 0.01%, of the cells of the population of cells, e.g., as detectible by next generation sequencing and/or a nucleotide insertional assay, e.g., assayed in a population of HPSC cells, e.g., a population of CD34+ cells.


In embodiments, including in any of the aforementioned aspects and embodiments, the invention provides a gRNA molecule, wherein when a CRISPR system (e.g., an RNP as described herein) including the gRNA molecule is introduced into a cell, expression of fetal hemoglobin is increased in said cell or its progeny, e.g., its erythroid progeny, e.g., its red blood cell progeny. In embodiments, expression of fetal hemoglobin is increased in said cell or its progeny, e.g., its erythroid progeny, e.g., its red blood cell progeny, by at least about 20%, e.g., at least about 30%, e.g., at least about 40%, e.g., at least about 50%, e.g., at least about 60%, e.g., at least about 70%, e.g., at least about 80%, e.g., at least about 90%, e.g., at least about 95%, e.g., at least about 96%, e.g., at least about 97%, e.g., at least about 98%, e.g., at least about 99%. In embodiments, said cell or its progeny, e.g., its erythroid progeny, e.g., its red blood cell progeny, produces at least about 6 picograms (e.g., at least about 7 picograms, at least about 8 picograms, at least about 9 picograms, at least about 10 picograms, or from about 8 to about 9 picograms, or from about 9 to about 10 picograms) fetal hemoglobin per cell. In embodiments, including in any of the aforementioned aspects and embodiments, the invention provides a gRNA molecule, wherein when a CRISPR system (e.g., an RNP as described herein) including the gRNA molecule is introduced into a cell, levels of fetal hemoglobin (e.g., gamma globin) mRNA are increased in said cell or its progeny, e.g., its erythroid progeny, e.g., its red blood cell progeny. In embodiments, including in any of the aforementioned aspects and embodiments, the invention provides a gRNA molecule, wherein when a CRISPR system (e.g., an RNP as described herein) including the gRNA molecule is introduced into a cell, expression of BCL11a mRNA is decreased in said cell or its progeny, e.g., its erythroid progeny, e.g., its red blood cell progeny. In embodiments, including in any of the aforementioned aspects and embodiments, the invention provides a gRNA molecule, wherein when a CRISPR system (e.g., an RNP as described herein) including the gRNA molecule is introduced into a cell, levels of BCL11a mRNA are decreased in said cell or its progeny, e.g., its erythroid progeny, e.g., its red blood cell progeny.


In any of the aforementioned aspects and embodiments that mention a cell, the cell is (or population of cells includes) a mammalian, primate, or human cell, e.g., is a human cell or population of human cells. In embodiments, the cell is (or population of cells includes) an HSPC, for example, is CD34+, for example, is CD34+CD90+. In embodiments, the cell (or population of cells) is autologous with respect to a patient to be administered said cell. In other embodiments, the cell (or population of cells) is allogeneic with respect to a patient to be administered said cell.


In another aspect, the invention provides a composition including: 1) one or more gRNA molecules (including a first gRNA molecule) described herein, for example, one or more gRNA molecules of any of the previous aspects and embodiments, and a Cas9 molecule, for example, as described herein; 2) one or more gRNA molecules (including a first gRNA molecule) described herein, for example, one or more gRNA molecules of any of the previous aspects and embodiments, and nucleic acid encoding a Cas9 molecule (described herein); 3) nucleic acid encoding one or more gRNA molecules (including a first gRNA molecule) described herein, for example, one or more gRNA molecules of any of the previous aspects and embodiments, and a Cas9 molecule (described herein); 4) nucleic acid encoding one or more gRNA molecules (including a first gRNA molecule) described herein, for example, one or more gRNA molecules of any of the previous aspects and embodiments, and nucleic acid encoding a Cas9 molecule (described herein); or 5) any of 1) to 4), above, and a template nucleic acid; or 6) any of 1) to 4) above, and nucleic acid including sequence encoding a template nucleic acid.


In preferred embodiments, the invention provides a composition including a first gRNA molecule (e.g., described herein, e.g., a first gRNA molecule of any of the previous gRNA molecule aspects and embodiments), further including a Cas9 molecule (described herein).


In embodiments, the Cas9 molecule is an active or inactive s. pyogenes Cas9. In embodiments, the Cas9 molecule includes SEQ ID NO: 6611. In embodiments, the Cas9 molecule includes, e.g., consists of: (a) SEQ ID NO: 7821; (b) SEQ ID NO: 7822; (c) SEQ ID NO: 7823; (d) SEQ ID NO: 7824; (e) SEQ ID NO: 7825; (f) SEQ ID NO: 7826; (g) SEQ ID NO: 7827; (h) SEQ ID NO: 7828; (i) SEQ ID NO: 7829; (j) SEQ ID NO: 7830; or (k) SEQ ID NO: 7831.


In preferred embodiments, the first gRNA molecule and Cas9 molecule are present in a ribonuclear protein complex (RNP).


In embodiments, the invention provides a composition, e.g., a composition of any of the previous aspects and embodiments, further including a second gRNA molecule; a second gRNA molecule and a third gRNA molecule; or a second gRNA molecule, optionally, a third gRNA molecule, and, optionally, a fourth gRNA molecule, wherein the second gRNA molecule, the optional third gRNA molecule, and the optional fourth gRNA molecule are a gRNA molecule of a gRNA molecule described herein, e.g., a gRNA molecule of any of the previous gRNA molecule aspects and embodiments, and wherein each gRNA molecule of the composition is complementary to a different target sequence.


In embodiments, two or more of the first gRNA molecule, the second gRNA molecule, the optional third gRNA molecule, and the optional fourth gRNA molecule are complementary to target sequences within the same gene or region. In embodiments, the first gRNA molecule, the second gRNA molecule, the optional third gRNA molecule, and the optional fourth gRNA molecule are complementary to target sequences not more than 20000 nucleotides, not more than 10000 nucleotides, not more than 6000, not more than 5000 nucleotides, not more than 4000, not more than 1000 nucleotides, not more than 500 nucleotides, not more than 400 nucleotides, not more than 300 nucleotides, not more than 200 nucleotides, not more than 100 nucleotides, not more than 90 nucleotides, not more than 80 nucleotides, not more than 70 nucleotides, not more than 60 nucleotides, not more than 50 nucleotides, not more than 40 nucleotides, not more than 30 nucleotides, not more than 20 nucleotides or not more than 10 nucleotides apart.


In other embodiments, two or more of the first gRNA molecule, the second gRNA molecule, the optional third gRNA molecule, and the optional fourth gRNA molecule are complementary to target sequence within different genes or regions.


In embodiments, including in any of the aforementioned composition aspects and embodiments, the invention provides a composition including a first gRNA molecule and a second gRNA molecule, wherein the first gRNA molecule and second gRNA molecule are:


(a) independently selected from the gRNA molecules of gRNA molecule embodiment 4, and are complementary to different target sequences;


(b) independently selected from the gRNA molecules of gRNA molecule embodiment 5, and are complementary to different target sequences;


c) independently selected from the gRNA molecules of gRNA molecule embodiment 6, and are complementary to different target sequences; or


(d) independently selected from the gRNA molecules of gRNA molecule embodiment 7, and are complementary to different target sequences; or


(e) independently selected from the gRNA molecules of any of gRNA molecule embodiments 41-56, and are complementary to different target sequences.


In embodiments, including in any of the aforementioned composition aspects and embodiments, the invention provides a composition including a first gRNA molecule and a second gRNA molecule, wherein the first gRNA molecule and second gRNA molecule are:


(a) independently selected from the gRNA molecules of gRNA molecule embodiment 10, and are complementary to different target sequences; or


(b) independently selected from the gRNA molecules of gRNA molecule embodiment 11, and are complementary to different target sequences.


In embodiments, including in any of the aforementioned composition aspects and embodiments, the invention provides a composition, including a first gRNA molecule and a second gRNA molecule, wherein the first gRNA molecule and second gRNA molecule are:


(a) independently selected from the gRNA molecules of gRNA molecule embodiment 13, and are complementary to different target sequences; or


(b) independently selected from the gRNA molecules of gRNA molecule embodiment 14, and are complementary to different target sequences.


In embodiments, including in any of the aforementioned composition aspects and embodiments, the invention provides a composition, including a first gRNA molecule and a second gRNA molecule, wherein the first gRNA molecule and second gRNA molecule are:


(a) independently selected from the gRNA molecules of gRNA molecule embodiment 16, and are complementary to different target sequences;


(b) independently selected from the gRNA molecules of gRNA molecule embodiment 17, and are complementary to different target sequences;


(c) independently selected from the gRNA molecules of gRNA molecule embodiment 18, and are complementary to different target sequences; or


(d) independently selected from the gRNA molecules of any of gRNA molecule embodiments 57-68, and are complementary to different target sequences.


In embodiments, including in any of the aforementioned composition aspects and embodiments, the invention provides a composition, including a first gRNA molecule and a second gRNA molecule, wherein:


(1) the first gRNA molecule is: (a) selected from the gRNA molecules of gRNA molecule embodiment 4, (b) selected from the gRNA molecules of gRNA molecule embodiment 5, (c) selected from the gRNA molecules of gRNA molecule embodiment 6, (d) selected from the gRNA molecules of gRNA molecule embodiment 7, or (e) selected from the gRNA molecules of any of gRNA molecule embodiments 41-56; and


(2) the second gRNA molecule is: (a) selected from the gRNA molecules of gRNA molecule embodiment 10, or (b) selected from the gRNA molecules of gRNA molecule embodiment 11.


In embodiments, including in any of the aforementioned composition aspects and embodiments, the invention provides a composition, including a first gRNA molecule and a second gRNA molecule, wherein:


(1) the first gRNA molecule is: (a) selected from the gRNA molecules of gRNA molecule embodiment 4, (b) selected from the gRNA molecules of gRNA molecule embodiment 5, (c) selected from the gRNA molecules of gRNA molecule embodiment 6, (d) selected from the gRNA molecules of gRNA molecule embodiment 7, or (e) selected from the gRNA molecules of any of gRNA molecule embodiments 41-56; and


(2) the second gRNA molecule is: (a) selected from the gRNA molecules of gRNA molecule embodiment 13, (b) selected from the gRNA molecules of gRNA molecule embodiment 14.


In embodiments, including in any of the aforementioned composition aspects and embodiments, the invention provides a composition, including a first gRNA molecule and a second gRNA molecule, wherein:


(1) the first gRNA molecule is: (a) selected from the gRNA molecules of gRNA molecule embodiment 4, (b) selected from the gRNA molecules of gRNA molecule embodiment 5, (c) selected from the gRNA molecules of gRNA molecule embodiment 6, (d) selected from the gRNA molecules of gRNA molecule embodiment 7, or (e) selected from the gRNA molecules of any of gRNA molecule embodiments 41-56; and


(2) the second gRNA molecule is: (a) selected from the gRNA molecules of gRNA molecule embodiment 16, (b) selected from the gRNA molecules of gRNA molecule embodiment 17, (c) selected from the gRNA molecules of gRNA molecule embodiment 18, or (d) selected from the gRNA molecules of any of gRNA molecule embodiments 57-68.


In embodiments, including in any of the aforementioned composition aspects and embodiments, the invention provides a composition, including a first gRNA molecule and a second gRNA molecule, wherein:


(1) the first gRNA molecule is: (a) selected from the gRNA molecules of gRNA molecule embodiment 10, or (b) selected from the gRNA molecules of gRNA molecule embodiment 11; and


(2) the second gRNA molecule is: (a) selected from the gRNA molecules of gRNA molecule embodiment 13, (b) selected from the gRNA molecules of gRNA molecule embodiment 14.


In embodiments, including in any of the aforementioned composition aspects and embodiments, the invention provides a composition, including a first gRNA molecule and a second gRNA molecule, wherein:


(1) the first gRNA molecule is: (a) selected from the gRNA molecules of gRNA molecule embodiment 10, or (b) selected from the gRNA molecules of gRNA molecule embodiment 11; and


(2) the second gRNA molecule is: (a) selected from the gRNA molecules of gRNA molecule embodiment 16, (b) selected from the gRNA molecules of gRNA molecule embodiment 17, (c) selected from the gRNA molecules of gRNA molecule embodiment 18, or (d) selected from the gRNA molecules of any of gRNA molecule embodiments 57-68.


In embodiments, including in any of the aforementioned composition aspects and embodiments, the invention provides a composition, including a first gRNA molecule and a second gRNA molecule, wherein:


(1) the first gRNA molecule is: (a) selected from the gRNA molecules of gRNA molecule embodiment 13, (b) selected from the gRNA molecules of gRNA molecule embodiment 14; and


(2) the second gRNA molecule is: (a) selected from the gRNA molecules of gRNA molecule embodiment 16, (b) selected from the gRNA molecules of gRNA molecule embodiment 17, (c) selected from the gRNA molecules of gRNA molecule embodiment 18, or (d) selected from the gRNA molecules of any of gRNA molecule embodiments 57-68.


In embodiments, including in any of the aforementioned composition aspects and embodiments, the invention provides a composition, including a first gRNA molecule and a second gRNA molecule, wherein:


(1) the first gRNA molecule is: (a) selected from the gRNA molecules of gRNA molecule embodiment 16, (b) selected from the gRNA molecules of gRNA molecule embodiment 17, (c) selected from the gRNA molecules of gRNA molecule embodiment 18, or (d) selected from the gRNA molecules of any of gRNA molecule embodiments 57-68; and (2) the second gRNA molecule includes a targeting domain that is complementary to a target sequence of the beta globin gene; or


(1) the first gRNA molecule is: (a) selected from the gRNA molecules of gRNA molecule embodiment 4, (b) selected from the gRNA molecules of gRNA molecule embodiment 5, (c) selected from the gRNA molecules of gRNA molecule embodiment 6, (d) selected from the gRNA molecules of gRNA molecule embodiment 7, (e) selected from the gRNA molecules of any of gRNA molecule embodiments 41-56, (f) selected from the gRNA molecules of gRNA molecule embodiment 10, (g) selected from the gRNA molecules of gRNA molecule embodiment 11, (h) selected from the gRNA molecules of gRNA molecule embodiment 13, or (i) selected from the gRNA molecules of gRNA molecule embodiment 14; and (2) the second gRNA molecule includes a targeting domain that is complementary to a target sequence of the beta globin gene.


In embodiments, including in any of the aforementioned composition aspects and embodiments, the invention provides a composition, wherein the first gRNA molecule and the second gRNA molecule are independently selected from the gRNA molecules of any of gRNA molecule embodiments 41-68.


In embodiments of the composition, with respect to the gRNA molecule components of the composition, the composition consists of a first gRNA molecule and a second gRNA molecule.


In embodiments of the composition, each of said gRNA molecules is in a ribonuclear protein complex (RNP) with a Cas9 molecule described herein.


In embodiments, including in any of the aforementioned composition aspects and embodiments, the invention provides a composition, further including a template nucleic acid, wherein the template nucleic acid includes a nucleotide that corresponds to a nucleotide at or near the target sequence of the first gRNA molecule. In embodiments, the template nucleic acid includes nucleic acid encoding: (a) human beta globin, e.g., human beta globin including one or more of the mutations G 16D, E22A and T87Q, or fragment thereof; or (b) human gamma globin, or fragment thereof.


In embodiments, including in any of the aforementioned composition aspects and embodiments, the composition is formulated in a medium suitable for electroporation, for example, suitable for electroporation into HSPC cells. In embodiments of the composition which include one or more gRNA molecules, each of said gRNA molecules is in a RNP with a Cas9 molecule described herein, and wherein each of said RNP is at a concentration of less than about 10 uM, e.g., less than about 3 uM, e.g., less than about 1 uM, e.g., less than about 0.5 uM, e.g., less than about 0.3 uM, e.g., less than about 0.1 uM.


In another aspect, the invention provides a nucleic acid sequence that encodes one or more gRNA molecules described herein, for example, a gRNA molecule of any of the previous aspects and embodiments. In embodiments, the nucleic acid includes a promoter operably linked to the sequence that encodes the one or more gRNA molecules, for example, a promoter recognized by an RNA polymerase II or RNA polymerase III, for example, a U6 promoter or an HI promoter. In embodiments, the nucleic acid further encodes a Cas9 molecule, for example, described herein, for example, a Cas9 molecule that includes (e.g., consists of) any of SEQ ID NO: 6611, SEQ ID NO: 7821, SEQ ID NO: 7822, SEQ ID NO: 7823, SEQ ID NO: 7824, SEQ ID NO: 7825, SEQ ID NO: 7826, SEQ ID NO: 7827, SEQ ID NO: 7828, SEQ ID NO: 7829, SEQ ID NO: 7830, or SEQ ID NO: 7831. In embodiments, the nucleic acid includes a promoter operably linked to the sequence that encodes a Cas9 molecule, for example, an EF-1 promoter, a CMV IE gene promoter, an EF-1α promoter, an ubiquitin C promoter, or a phosphoglycerate kinase (PGK) promoter.


In another aspect, the invention provides a vector including the nucleic acid of any of the previous nucleic acid aspects and embodiments. In embodiments, the vector is selected from the group consisting of a lentiviral vector, an adenoviral vector, an adeno-associated viral (AAV) vector, a herpes simplex virus (HSV) vector, a plasmid, a minicircle, a nanoplasmid, and an RNA vector.


In another aspect, the invention provides a method of altering a cell (e.g., a population of cells), (e.g., altering the structure (e.g., sequence) of nucleic acid) at or near a target sequence within said cell, including contacting (e.g., introducing into) said cell (e.g., population of cells) with: 1) one or more gRNA molecules of any of the previous gRNA molecule aspects and embodiments and a Cas9 molecule (e.g., described herein); 2) one or more gRNA molecules of any of the previous gRNA molecule aspects and embodiments and nucleic acid encoding a Cas9 molecule (e.g., described herein); 3) nucleic acid encoding one or more gRNA molecules of any of the previous gRNA molecule aspects and embodiments and a Cas9 molecule (e.g., described herein); 4) nucleic acid encoding one or more gRNA molecules of any of the previous gRNA molecule aspects and embodiments and nucleic acid encoding a Cas9 molecule (e.g., described herein); 5) any of 1) to 4), above, and a template nucleic acid; 6) any of 1) to 4) above, and nucleic acid including sequence encoding a template nucleic acid; 7) the composition of any of the previous composition aspects and embodiments; or 8) the vector of any of the previous vector aspects and embodiments. In embodiments, the gRNA molecule or nucleic acid encoding the gRNA molecule, and the Cas9 molecule or nucleic acid encoding the Cas9 molecule, are formulated in a single composition. In other embodiments, the gRNA molecule or nucleic acid encoding the gRNA molecule, and the Cas9 molecule or nucleic acid encoding the Cas9 molecule, are formulated in more than one composition. In embodiments that include more than one composition, the more than one composition are delivered simultaneously or sequentially. In embodiments, the cell is an animal cell, for example, a mammalian, primate, or human cell. In embodiments, the cell, is a hematopoietic stem or progenitor cell (HSPC) (e.g., a population of HSPCs), for example, the cell is a CD34+ cell, for example, the cell is a CD34+CD90+ cell. In embodiments, the cell is disposed in a composition including a population of cells that has been enriched for CD34+ cells. In embodiments, the cell (e.g. population of cells) has been isolated from bone marrow, mobilized peripheral blood, or umbilical cord blood. In embodiments, the cell is autologous with respect to a patient to be administered said cell. In other embodiments, the cell is allogeneic with respect to a patient to be administered said cell. In embodiments, the method results in an indel at or near a genomic DNA sequence complementary to the targeting domain of the one or more gRNA molecules, for example, an indel shown on FIG. 25, Table 15, Table 26, Table 27 or Table 37, for example an indel associated with the targeting domain of the gRNA molecule as shown in FIG. 25, Table 15, Table 26, Table 27 or Table 37. In embodiments, the indel is an insertion or deletion of less than about 40 nucleotides, e.g., less than 30 nucleotides, e.g., less than 20 nucleotides, e.g., less than 10 nucleotides, for example, is a single nucleotide deletion. In embodiments, the method results in a population of cells wherein at least about 50%, e.g., at least about 60%, e.g., at least about 70%, e.g., at least about 80%, e.g., at least about 90% (e.g., at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99%) of the cells of the population have been altered, e.g., include an indel. In embodiments, the method (e.g., the method performed on a population of cells, e.g., described herein) results in a cell (e.g., population of cells) that is capable of differentiating into a differentiated cell of an erythroid lineage (e.g., a red blood cell), and wherein said differentiated cell exhibits an increased level of fetal hemoglobin, e.g., relative to an unaltered cell (e.g., population of cells). In embodiments, the method results in a population of cells that is capable of differentiating into a population of differentiated cells, e.g., a population of cells of an erythroid lineage (e.g., a population of red blood cells), and wherein said population of differentiated cells has an increased fraction of F cells (e.g., at least about 15%, at least about 20%, at least about 25%, at least about 30%, or at least about 40% higher) e.g., relative to a population of unaltered cells. In embodiments, the method results in a cell that is capable of differentiating into a differentiated cell, e.g., a cell of an erythroid lineage (e.g., a red blood cell), and wherein said differentiated cell produces at least about 6 picograms (e.g., at least about 7 picograms, at least about 8 picograms, at least about 9 picograms, at least about 10 picograms, or from about 8 to about 9 picograms, or from about 9 to about 10 picograms) fetal hemoglobin per cell. In embodiments, the method is performed ex vivo. In other embodiments, the method is performed in vivo.


In another aspect, the invention provides a cell, altered by the method of altering a cell of any of the previous method aspects and embodiments.


In another aspect, the invention provides a cell, obtainable the method of altering a cell of any of the previous method aspects and embodiments.


In another aspect, the invention provides a cell, including a first gRNA molecule, e.g., described herein, e.g., of any of the previous gRNA molecule aspects and embodiments, or a composition, e.g., described herein, e.g., of any of the previous composition aspects and embodiments, a nucleic acid, e.g., described herein, e.g., of any of the previous nucleic acid aspects and embodiments, or a vector, e.g., described herein, e.g., of any of the previous vector aspects and embodiments. In embodiments, the cell further includes a Cas9 molecule, e.g., described herein, for example, a Cas9 molecule that includes, e.g., consists of, any of SEQ ID NO: 6611, SEQ ID NO: 7821, SEQ ID NO: 7822, SEQ ID NO: 7823, SEQ ID NO: 7824, SEQ ID NO: 7825, SEQ ID NO: 7826, SEQ ID NO: 7827, SEQ ID NO: 7828, SEQ ID NO: 7829, SEQ ID NO: 7830, or SEQ ID NO: 7831. In embodiments, the cell includes, has included, or will include a second gRNA molecule, e.g., described herein, e.g., of any of the previous gRNA molecule aspects and embodiments, or a nucleic acid encoding a second gRNA molecule, e.g., described herein, e.g., of any of the previous gRNA molecule aspects and embodiments, wherein the first gRNA molecule and second gRNA molecule include nonidentical targeting domains. In embodiments, expression of fetal hemoglobin is increased in said cell or its progeny (e.g., its erythroid progeny, e.g., its red blood cell progeny) relative to a cell or its progeny of the same cell type that has not been modified to include a gRNA molecule. In embodiments, the cell is capable of differentiating into a differentiated cell, e.g., a cell of an erythroid lineage (e.g., a red blood cell), and wherein said differentiated cell exhibits an increased level of fetal hemoglobin, e.g., relative to a cell of the same type that has not been modified to include a gRNA molecule. In embodiments, the differentiated cell (e.g., cell of an erythroid lineage, e.g., red blood cell) produces at least about 6 picograms (e.g., at least about 7 picograms, at least about 8 picograms, at least about 9 picograms, at least about 10 picograms, or from about 8 to about 9 picograms, or from about 9 to about 10 picograms) fetal hemoglobin, e.g., relative to a cell of the same type that has not been modified to include a gRNA molecule. In embodiments, the cell has been contacted, e.g., contacted ex vivo, with a stem cell expander, e.g., described herein, e.g., a stem cell expander that is compound 1, compound 2, compound 3, compound 4, or a combination thereof (e.g., compound 1 and compound 4), for example, a stem cell expander that is compound 4. In embodiments, including in any of the aforementioned aspects and embodiments, the cell includes an indel at or near a genomic DNA sequence complementary to the targeting domain of the gRNA molecule (as described herein, e.g., a gRNA molecule of any of the aforementioned aspects and embodiments) introduced therein, for example, an indel shown on FIG. 25, Table 15, Table 26, Table 27 or Table 37, for example an indel shown on FIG. 25, Table 15, Table 26, Table 27 or Table 37 that is associated with the gRNA molecule (as described herein, e.g., a gRNA molecule of any of the aforementioned aspects and embodiments) introduced therein. In embodiments, the indel is an insertion or deletion of less than about 40 nucleotides, e.g., less than 30 nucleotides, e.g., less than 20 nucleotides, e.g., less than 10 nucleotides, for example, the indel is a single nucleotide deletion. In embodiments, including in any of the aforementioned cell aspects and embodiments, the cell is an animal cell, for example, the cell is a mammalian, a primate, or a human cell. In embodiments, including in any of the aforementioned cell aspects and embodiments, the cell is a hematopoietic stem or progenitor cell (HSPC) (e.g., a population of HSPCs), for example, the cell is a CD34+ cell, for example, the cell is a CD34+CD90+ cell. In embodiments, including in any of the aforementioned cell aspects and embodiments, the cell (e.g. population of cells) has been isolated from bone marrow, mobilized peripheral blood, or umbilical cord blood. In embodiments, including in any of the aforementioned cell aspects and embodiments, the cell is autologous with respect to a patient to be administered said cell. In embodiments, the cell is allogeneic with respect to a patient to be administered said cell.


In another aspect, the invention provides a population of cells including the cell of any of the previous cell aspects and embodiments. In embodiments, at least about 50%, e.g., at least about 60%, e.g., at least about 70%, e.g., at least about 80%, e.g., at least about 90% (e.g., at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99%) of the cells of the population are a cell according to any of the previous cell aspects and embodiments. In embodiments, the population of cells is capable of differentiating into a population of differentiated cells, e.g., a population of cells of an erythroid lineage (e.g., a population of red blood cells), and wherein said population of differentiated cells has an increased fraction of F cells (e.g., at least about 15%, at least about 20%, at least about 25%, at least about 30%, or at least about 40% higher) e.g., relative to a population of unmodified cells of the same type. In embodiments, the F cells of the population of differentiated cells produce an average of at least about 6 picograms (e.g., at least about 7 picograms, at least about 8 picograms, at least about 9 picograms, at least about 10 picograms, or from about 8 to about 9 picograms, or from about 9 to about 10 picograms) fetal hemoglobin per cell. In embodiments, the population includes: 1) at least 1e6 CD34+ cells/kg body weight of the patient to whom the cells are to be administered; 2) at least 2e6 CD34+ cells/kg body weight of the patient to whom the cells are to be administered; 3) at least 3e6 CD34+ cells/kg body weight of the patient to whom the cells are to be administered; 4) at least 4e6 CD34+ cells/kg body weight of the patient to whom the cells are to be administered; or 5) from 2e6 to 10e6 CD34+ cells/kg body weight of the patient to whom the cells are to be administered. In embodiments, at least about 40%, e.g., at least about 50%, (e.g., at least about 60%, at least about 70%, at least about 80%, or at least about 90%) of the cells of the population are CD34+ cells. In embodiments, at least about 10%, e.g., at least about 15%, e.g., at least about 20%, e.g., at least about 30% of the cells of the population are CD34+CD90+ cells. In embodiments, the population of cells is derived from bone marrow, peripheral blood (e.g., mobilized peripheral blood), umbilical cord blood, or induced pluripotent stem cells (iPSCs). In a preferred embodiment, the population of cells is derived from bone marrow. In embodiments, the population of cells includes, e.g., consists of, mammalian cells, e.g., human cells. In embodiments, the population of cells is autologous relative to a patient to which it is to be administered. In other embodiments, the population of cells is allogeneic relative to a patient to which it is to be administered.


In another aspect, the invention provides a composition including a cell of any of the previous cell aspects and embodiments, or the population of cells of any of previous population of cell aspects and embodiments. In embodiments, the composition includes a pharmaceutically acceptable medium, e.g., a pharmaceutically acceptable medium suitable for cryopreservation.


In another aspect, the invention provides a method of treating a hemoglobinopathy, including administering to a patient a cell of any of the previous cell aspects and embodiments, a population of cells of any of previous population of cell aspects and embodiments, or a composition of any of the previous composition aspects and embodiments. In embodiments, the hemoglobinopathy is a thalassemia, for example, beta-thalassemia, or sickle cell disease.


In another aspect, the invention provides a method of increasing fetal hemoglobin expression in a mammal, including administering to a patient a cell of any of the previous cell aspects and embodiments, a population of cells of any of previous population of cell aspects and embodiments, or a composition of any of the previous composition aspects and embodiments.


In another aspect, the invention provides a method of preparing a cell (e.g., a population of cells) including: (a) providing a cell (e.g., a population of cells) (e.g., a HSPC (e.g., a population of HSPCs)); (b) culturing said cell (e.g., said population of cells) ex vivo in a cell culture medium including a stem cell expander; and (c) introducing into said cell a first gRNA molecule (e.g., described herein, for example, a gRNA molecule of any of the previous gRNA molecule aspects and embodiments), a nucleic acid molecule encoding a first gRNA molecule (e.g., described herein, for example, a gRNA molecule of any of the previous gRNA molecule aspects and embodiments), a composition (e.g., described herein, for example, a composition of any of the previous composition aspects and embodiments), a nucleic acid (e.g., described herein, for example, a nucleic acid of any of the previous nucleic acid aspects and embodiments), or a vector (e.g., described herein, for example, a vector of any of the previous vector aspects and embodiments). In embodiments of said method, after said introducing of step (c), said cell (e.g., population of cells) is capable of differentiating into a differentiated cell (e.g., population of differentiated cells), e.g., a cell of an erythroid lineage (e.g., population of cells of an erythroid lineage), e.g., a red blood cell (e.g., a population of red blood cells), and wherein said differentiated cell (e.g., population of differentiated cells) produces increased fetal hemoglobin, e.g., relative to the same cells which have not been subjected to step (c). In embodiments, including in any of the aforementioned method aspects and embodiments, the stem cell expander is compound 1, compound 2, compound 3, compound 4 or a combination thereof (e.g., compound 1 and compound 4), for example, is compound 4. In embodiments, including in any of the aforementioned method aspects and embodiments, the cell culture medium includes thrombopoietin (Tpo), Flt3 ligand (Flt-3L), and human stem cell factor (SCF). In embodiments, including in any of the aforementioned method aspects and embodiments, the cell culture medium further includes human interleukin-6 (IL-6). In embodiments, including in any of the aforementioned method aspects and embodiments, the cell culture medium includes thrombopoietin (Tpo), Flt3 ligand (Flt-3L), and human stem cell factor (SCF) each at a concentration ranging from about 10 ng/mL to about 1000 ng/mL, for example, each at a concentration of about 50 ng/mL, e.g., at a concentration of 50 ng/mL. In embodiments, including in any of the aforementioned method aspects and embodiments, the cell culture medium includes human interleukin-6 (IL-6) at a concentration ranging from about 10 ng/mL to about 1000 ng/mL, for example, at a concentration of about 50 ng/mL, e.g., at a concentration of 50 ng/mL. In embodiments, including in any of the aforementioned method aspects and embodiments, the cell culture medium includes a stem cell expander at a concentration ranging from about 1 nM to about 1 mM, for example, at a concentration ranging from about 1 uM to about 100 uM, for example, at a concentration ranging from about 50 uM to about 75 uM, for example, at a concentration of about 50 uM, e.g., at a concentration of 50 uM, or at a concentration of about 75 uM, e.g., at a concentration of 75 uM. In embodiments, including in any of the aforementioned method aspects and embodiments, the culturing of step (b) includes a period of culturing before the introducing of step (c), for example, the period of culturing before the introducing of step (c) is at least 12 hours, e.g., is for a period of about 1 day to about 3 days, e.g., is for a period of about 1 day to about 2 days, e.g., is for a period of about 2 days. In embodiments, including in any of the aforementioned method aspects and embodiments, the culturing of step (b) includes a period of culturing after the introducing of step (c), for example, the period of culturing after the introducing of step (c) is at least 12 hours, e.g., is for a period of about 1 day to about 10 days, e.g., is for a period of about 1 day to about 5 days, e.g., is for a period of about 2 days to about 4 days, e.g., is for a period of about 2 days or is for a period of about 3 days or is for a period of about 4 days. In embodiments, including in any of the aforementioned method aspects and embodiments, the population of cells is expanded at least 4-fold, e.g., at least 5-fold, e.g., at least 10-fold, e.g., relative to cells which are not cultured according to step (b). In embodiments, including in any of the aforementioned method aspects and embodiments, the introducing of step (c) includes an electroporation, for example, an electroporation that includes 1 to 5 pulses, e.g., 1 pulse, and wherein each pulse is at a pulse voltage ranging from 700 volts to 2000 volts and has a pulse duration ranging from 10 ms to 100 ms. In embodiments, including in any of the aforementioned method aspects and embodiments, the electroporation includes, for example, consists of, 1 pulse. In embodiments, including in any of the aforementioned method aspects and embodiments, the pulse voltage ranges from 1500 to 1900 volts, e.g., is 1700 volts. In embodiments, including in any of the aforementioned method aspects and embodiments, the pulse duration ranges from 10 ms to 40 ms, e.g., is 20 ms. In embodiments, including in any of the aforementioned method aspects and embodiments, the cell (e.g., population of cells) provided in step (a) is a human cell (e.g., a population of human cells). In embodiments, including in any of the aforementioned method aspects and embodiments, the cell (e.g., population of cells) provided in step (a) is isolated from bone marrow, peripheral blood (e.g., mobilized peripheral blood), umbilical cord blood, or induced pluripotent stem cells (iPSCs), preferably bone marrow. In embodiments, including in any of the aforementioned method aspects and embodiments, the cell (e.g., population of cells) provided in step (a) is isolated from bone marrow, e.g., is isolated from bone marrow of a patient suffering from a hemoglobinopathy. In embodiments, including in any of the aforementioned method aspects and embodiments, the population of cells provided in step (a) is enriched for HSPCs, e.g., CD34+ cells. In embodiments, including in any of the aforementioned method aspects and embodiments, subsequent to the introducing of step (c), the cell (e.g., population of cells) is cryopreserved. In embodiments, including in any of the aforementioned method aspects and embodiments, subsequent to the introducing of step (c), the cell (e.g., population of cells) includes an indel at or near a genomic DNA sequence complementary to the targeting domain of the first gRNA molecule, for example, an indel shown on FIG. 25, Table 15, Table 26, Table 27 or Table 37, for example an indel shown in FIG. 25, Table 15, Table 26, Table 27 or Table 37 as associated with the first gRNA molecule. In embodiments, including in any of the aforementioned method aspects and embodiments, after the introducing of step (c), at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98% or at least about 99% of the cells of the population of cells include an indel at or near a genomic DNA sequence complementary to the targeting domain of the first gRNA molecule, for example, an indel shown on FIG. 25, Table 15, Table 26, Table 27 or Table 37, for example an indel shown in FIG. 25, Table 15, Table 26, Table 27 or Table 37 as associated with the first gRNA molecule.


In another aspect, the invention provides a cell (e.g., population of cells), obtainable by the method of preparing a cell of any of the previous aspects and embodiments. In another aspect, the invention provides a method of treating a hemoglobinopathy (for example a thalassemia (e.g., beta-thalassemia) or sickle cell disease), including administering to a human patient a composition including said cell (e.g., population of cells). In another aspect, the invention provides a method of increasing fetal hemoglobin expression in a human patient, including administering to said human patient a composition including said cell (e.g., population of cells). In embodiments, the human patient is administered a composition including at least about 1e6 cells (e.g., CD34+ cells, e.g., cells obtainable by a method of preparing a cell of any of the previous aspects and embodiments) per kg body weight of the human patient, e.g., at least about 1e6 CD34+ cells obtainable by a method of preparing a cell of any of the previous aspects and embodiments per kg body weight of the human patient. In embodiments, the human patient is administered a composition including at least about 2e6 cells (e.g., CD34+ cells, e.g., cells obtainable by a method of preparing a cell of any of the previous aspects and embodiments) per kg body weight of the human patient, e.g., at least about 2e6 CD34+ cells obtainable by a method of preparing a cell of any of the previous aspects and embodiments per kg body weight of the human patient. In embodiments, the human patient is administered a composition including from about 2e6 to about 10e6cells (e.g., CD34+ cells, e.g., cells obtainable by a method of preparing a cell of any of the previous aspects and embodiments) per kg body weight of the human patient, e.g., at least about 2e6 to about 10e6 CD34+ cells obtainable by a method of preparing a cell of any of the previous aspects and embodiments per kg body weight of the human patient.


In another aspect, the invention provides a gRNA molecule described herein, for example, a gRNA molecule of any of the previous gRNA molecule aspects and embodiments, a composition described herein, for example, a composition of any of the previous composition aspects and embodiments, a nucleic acid described herein, for example, a nucleic acid of any of the previous nucleic acid aspects and embodiments, a vector described herein, for example, a vector of any of the previous vector aspects and embodiments, a cell described herein, for example, a cell of any of the previous cell aspects and embodiments, or a population of cells described herein, for example, a population of cells of any of the previous population of cell aspects and embodiments, for use as a medicament.


In another aspect, the invention provides a gRNA molecule described herein, for example, a gRNA molecule of any of the previous gRNA molecule aspects and embodiments, a composition described herein, for example, a composition of any of the previous composition aspects and embodiments, a nucleic acid described herein, for example, a nucleic acid of any of the previous nucleic acid aspects and embodiments, a vector described herein, for example, a vector of any of the previous vector aspects and embodiments, a cell described herein, for example, a cell of any of the previous cell aspects and embodiments, or a population of cells described herein, for example, a population of cells of any of the previous population of cell aspects and embodiments, for use in the manufacture of a medicament.


In another aspect, the invention provides a gRNA molecule described herein, for example, a gRNA molecule of any of the previous gRNA molecule aspects and embodiments, a composition described herein, for example, a composition of any of the previous composition aspects and embodiments, a nucleic acid described herein, for example, a nucleic acid of any of the previous nucleic acid aspects and embodiments, a vector described herein, for example, a vector of any of the previous vector aspects and embodiments, a cell described herein, for example, a cell of any of the previous cell aspects and embodiments, or a population of cells described herein, for example, a population of cells of any of the previous population of cell aspects and embodiments, for use in the treatment of a disease.


In another aspect, the invention provides a gRNA molecule described herein, for example, a gRNA molecule of any of the previous gRNA molecule aspects and embodiments, a composition described herein, for example, a composition of any of the previous composition aspects and embodiments, a nucleic acid described herein, for example, a nucleic acid of any of the previous nucleic acid aspects and embodiments, a vector described herein, for example, a vector of any of the previous vector aspects and embodiments, a cell described herein, for example, a cell of any of the previous cell aspects and embodiments, or a population of cells described herein, for example, a population of cells of any of the previous population of cell aspects and embodiments, for use in the treatment of a disease, wherein the disease is a hemoglobinopathy, for example a thalassemia (e.g., beta-thalassemia) or sickle cell disease.





BRIEF DESCRIPTION OF THE DRAWINGS


FIG. 1: Cas9 editing of the Bcl11a +58 erythroid enhancer region. Fraction of editing detected by NGS in HEK-293 Cas9GFP 24 h post-delivery of crRNA targeting the +58 enhancer region and trRNA by lipofection. Each dot indicates a different crRNA, the trRNA was held constant. Genomic coordinates indicate location on Chromosome 2, e.g., in reference to hg38. (n=1)



FIG. 2: Cas9 editing of the Bcl11a +62 erythroid enhancer region. Fraction of editing detected by NGS in HEK-293 Cas9GFP 24 h post-delivery of crRNA targeting the +62 enhancer region and trRNA by lipofection. Each dot indicates a different crRNA, the trRNA was held constant. Genomic coordinates indicate location on Chromosome 2, e.g., in reference to hg38. (n=1)



FIG. 3. Gating strategy for selection of cells after introduction of the Cas9 editing system.



FIG. 4. Agarose gel electrophoresis of gene fragments from Cas9 editing system-treated CD34+ cells (shown are both CD34+CD90+ and CD34+CD90− cell populations, together with reference unsorted cells). The upper band represents uncleaved homoduplex DNA and the lower bands indicate cleavage products resulting from heteroduplex DNA. The far left lane is a DNA ladder. Band intensity was calculated by peak integration of unprocessed images by ImageJ software. % gene modification (indel) was calculated as follows: % gene modification=100×(1−(1−fraction cleaved)1/2), and is indicated below each corresponding lane of the gel.



FIG. 5. Erythroid enhancer region showing the sites of genomic DNA targeted by sgRNA molecules comprising targeting domains complimentary to the underlined nucleotides.



FIG. 6A/6B. NGS results for indel formation by sgEH1 (CR00276) (A) or sgEH2 (CR00275) (B) in CD34+ HSC cells. Insertions are in uppercase. Deletions are indicated by a dashed line. Regions of microhomology near the cutting site are highlighted in bold underline.



FIG. 6C/6D. NGS results for indel formation by sgEH8 (CR00273) (C) or sgEH9 (CR00277) (D) in CD34+ HSC cells. Insertions are in uppercase. Deletions are indicated by a dashed line. Regions of microhomology near the cutting site are highlighted in bold underline.



FIG. 7. NGS results and indel pattern formation across multiple donors for g7, g8 and g2. The sequences of the top 3 indels from two biological replicate experiments using g7 and g8 were identical, and the sequence of the top 3 indels using g2 were identical to those from a previous experiment.



FIG. 8. NGS results and indel pattern formation using a modified gRNA scaffold (BC). The sequences of the top 3 indels from these experiments are identical to those formed when using the standard gRNA scaffold.



FIG. 9. Comparison of indel pattern across different delivery methods. AVG % refers to the % of NGS reads exhibiting the indel indicated (Average of 2 experiments).



FIG. 10. Indel formation by co-introduction of g7 gRNA and g8 gRNA with either a non-extended flagpole region (“reg”) or with a first flagpole extension and first tracr extension (“BC”). PAM sequences for the two gRNAs are boxed.



FIG. 11: Top gRNA sequences directed to +58 enhancer region of BCL11a gene in CD34+ cells, as measured by NGS (n=3).



FIG. 12: Top gRNA sequences directed to +62 enhancer region of BCL11a gene in CD34+ cells, as measured by NGS (n=3).



FIG. 13: Predicted excision sizes when 2 gRNA molecules targeting the BCL11a +62 enhancer locus are introduced into HEK293_Cas9 cells, when either CR00187 (light grey bars) or CR00202 (dark grey bars) is held constant and co-inserted into the cells with a second gRNA molecule including the targeting domain of the gRNA indicated.



FIG. 14: Excision of genomic DNA within the +62 enhancer of BCL11a by addition of gRNA molecules including the targeting domain of CR00187 and the second gRNA molecule indicated in the graph. Stars (*) indicate excision observed at a frequency greater than 30%; Carats (̂) indicate excision observed at a lower frequency (<30%). Those predicted excision products resulting in a fragment less than 50 nt could not be distinguished.



FIG. 15: Excision of genomic DNA within the +62 enhancer of BCL11a by addition of gRNA molecules including the targeting domain of CR00202 and the second gRNA molecule indicated in the graph. Stars (*) indicate excision observed at a frequency greater than 30%; Carats (̂) indicate excision observed at lower frequency (<30%).



FIG. 16: % indel formation by 192 gRNA molecules targeted to the French HPFH region (Sankaran V G et al. A functional element necessary for fetal hemoglobin silencing. NEJM (2011) 365:807-814.)



FIG. 17. Experimental scheme of Cas9:gRNA ribonucleoprotein (Cas9-RNP) delivery to primary human CD34+ HSPC for genome editing, followed by genetic and phenotypic characterization.



FIG. 18. Cell viability following mock electroporation or electroporation of Cas9-RNP complexes into CD34+ HSPC. The HSPC were expanded in vitro for 48 hours after electroporation of RNP complexes and the cell viability monitored and percent viability determined. The names of gRNAs used to make RNP complexes are shown on x-axis and the corresponding cell viabilities on y-axis. The CRxxxx identifier indicates the targeting domain of the gRNA molecule.



FIG. 19. Mismatch detection using T7 endonuclease assay Human HSC were electroporated to deliver RNP complexes to introduce indels into +58 DHS region of BCL11A erythroid enhancer by NHEJ. PCR amplicons spanning the target region was subjected to the T7E1 assay and the resulting fragments analyzed by 2% agarose gel electrophoresis. Regions of +58 erythroid enhancer BCL11A were disrupted by both guide RNA formats (dual guide RNA—black; single guide RNA—gray (bottom graph and g7BCL11a-BC(1) and g7BCL11A-BC(2) from top graph)). The intensities of DNA bands were estimated by the ImageJ software (http://rsb.info.nih.gov/ij/) to determine the percent of edited alleles. Names of gRNAs used and corresponding gene editing efficiencies determined from mismatch detection assay are also shown in the table below the gel image.



FIG. 20: Percent allele editing by next generation sequencing. Labels are as described for FIGS. 18 and 19.



FIG. 21. Colony forming cell (CFC) unit assay showing colony number and types of colonies observed for five select gRNAs. The HSPCs genome edited at the +58 erythroid enhancer were plated in methylcellulose and clonal colonies classified and counted based on the number and types of mature cells using morphological and phenotypic criteria using STEMvision. The colonies were classified into colony forming unit-erythroid (CFU-E), burst forming unit-erythroid (BFU-E), colony-forming unit-granulocyte/macrophage (CFU-GM) and colony-forming unit-granulocyte/erythrocyte/macrophage/megakaryocyte (CFU-GEMM).



FIG. 22. Kinetics of cell division during erythroid differentiation. Total number of cells determined on day 0, 7, 14 and 21 during erythroid differentiation and the fold cell expansion calculated.



FIG. 23. BCL11A, gamma and beta-globin mRNA levels in genome edited and erythroid differentiated HSC. Relative mRNA expression of BCL11A, gamma- and beta-globin chains in unilineage erythroid cultures were quantified by real time PCR. Transcript levels were normalized against human GAPDH transcript levels.



FIG. 24A. Efficient editing of HSC obtained with dual gRNA/cas9 system for disruption of BCL11a enhancer (+58) resulted in high levels of induction of HbF. The HSC 48 hours after electroporation were subjected to in vitro erythroid differentiation and HbF expression was measured. The percent of HbF positive cells (F-cells) was monitored by FACS analysis at days 7, 14 and 21. Data shown in this figure was generated with dgRNA systems where the dgRNA included the indicated targeting domain.



FIG. 24B. Efficient editing of HSC obtained with sgRNA/cas9 system for disruption of BCL11a enhancer (+58) resulted in high levels of induction of HbF. The HSC 48 hours after electroporation were subjected to in vitro erythroid differentiation and HbF expression was measured. The percent of HbF positive cells (F-cells) was monitored by FACS analysis at days 7, 14 and 21. Data shown in this figure was generated with sgRNA systems where the sgRNA included the indicated targeting domain.



FIG. 25: Indel pattern produced in HSPCs by gRNAs including the indicated targeting domain.



FIG. 26A: Phenotyping of edited and unedited cultures in CD34+ cell expansion medium by cell surface marker staining. All gRNA molecules were tested in the dgRNA format. The Tmcr used was SEQ ID NO: 7808, and the crRNA had the following format and sequence with 2′O-Methyl (m) and Phosphorothioate Bond (*) modifications indicated: mN*mN*mN*rNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrGrUrUrUrUrArGrArGrCrUrArU*mG*m C*mU, where N's are the residues of the indicated targeting domain. Shown are representative dot plots showing the fluorescence of cells stained with each antibody panel or corresponding isotype controls as described in Materials and Methods. Cells shown were pre-gated on the viable cell population by forward and side scatter properties and DAPI (4′,6-Diamidino-2-Phenylindole) discrimination. The percentage of each cell population named at the top of the plot was determined by the gate indicated by the bold lined box.



FIG. 26B: Phenotyping of edited and unedited cultures in CD34+ cell expansion medium by cell surface marker staining. All gRNA molecules were tested in the dgRNA format. The Tmcr used was SEQ ID NO: 7808, and the crRNA had the following format and sequence with 2′O-Methyl (m) and Phosphorothioate Bond (*) modifications indicated: mN*mN*mN*rNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrGrUrUrUrUrArGrArGrCrUrArU*mG*m C*mU, where N's are the residues of the indicated targeting domain Shown is the percentage of each named cell population in edited and unedited cultures. Targeting domain of the edited cultures is as indicated.



FIG. 27. % F cells in erythrocytes differentiated from populations of CD34+ cells edited with RNPs comprising dgRNAs targeting two sites within the HPFH region. “g2” is the positive control (targeting domain to a coding region of BCL11a gene); “cntrl” is negative control (introduction of Cas9 only).



FIG. 28A. % Editing as determined by NGS in CD34+ HSPCs at day 2 following electroporation of RNP comprising the indicated dgRNA (unmod or modified as indicated). Controls include dgRNA comprising the targeting domain of CR00317 unmodified (CR00317-m), or electroporation in buffer only (No Cas9 or gRNA; “Mock”).



FIG. 28B. % Editing as determined by NGS in CD34+ HSPCs at day 2 following electroporation of RNP comprising the indicated dgRNA (unmod or modified as indicated). Controls include electroporation in buffer only (No Cas9 or gRNA; “Mock”).



FIG. 29. % Editing as determined by NGS in CD34+ HSPCs at day 2 following electroporation of RNP comprising the indicated sgRNA (unmod or modified as indicated. In each case the number corresponds to the CRxxxxxx identifier of the targeting domain, for example, Unmod sg312 refers to unmodified sgRNA comprising the targeting domain of CR00312). Controls include electroporation of Cas9 protein only (“Cas9”), electroporation with buffer only (“mock”), or with no electroporation (“WT”).



FIG. 30A. Normalized % Erythrocytes (% F cells in “Mock” subtracted) that are HbF+ after electroporation of CD34+ HSPCs with RNP comprising the indicated dgRNA (unmod or modified as indicated) and then induced to differentiate by culture in erythroid differentiation medium. Controls include electroporation of buffer only (“mock”).



FIG. 30B. Normalized % Erythrocytes (% F cells in “Mock” subtracted) that are HbF+ after electroporation of CD34+ HSPCs with RNP comprising the indicated dgRNA (unmod or modified as indicated) and then in induced to differentiate by culture in erythroid differentiation medium. Controls include electroporation of buffer only (“mock”).



FIG. 31. Normalized % Erythrocytes (% F cells in “Mock” subtracted) that are HbF+ after electroporation of CD34+ HSPCs with RNP comprising the indicated sgRNA (unmod or modified as indicated. In each case the number corresponds to the CRxxxxxx identifier of the targeting domain, for example, Unmod sg312 refers to unmodified sgRNA comprising the targeting domain of CR00312) and then in induced to differentiate by culture in erythroid differentiation medium. Controls include electroporation of Cas9 protein and tracr only (“Cas9+TracRNA only”), electroporation with buffer only (“Cells only+Pulse”), or with no electroporation (“Cells only no pulse”).



FIG. 32. Fold total cell expansion in culture at day 14 after erythroid differentiation after electroporation of RNP comprising the indicated sgRNA (in each case, the number corresponds to the CRxxxxxx identifier of the targeting domain, for example, Unmod sg312 refers to unmodified sgRNA comprising the targeting domain of CR00312) into CD34+ cells. Controls include electroporation of Cas9 protein and tracr only (“Cas9+TracRNA only”), electroporation with buffer only (“Cells only+Pulse”), or with no electroporation (“Cells only no pulse”).



FIG. 33. Assessment of potential off-target sites cleaved by Cas9 directed by dgRNA molecules targeting the BCL11a enhancer region. Triangles represent the on-target site while open circles represent a potential off-target site for each guide RNA tested.



FIG. 34. Editing efficiency at targeted B2M locus in CD34+ hematopoietic stem cells by different Cas9 variants, as evaluated by NGS and Flow cytometry. NLS=SV40 NLS; His6 or His8 refers to 6 or 8 histidine residues, respectively; TEV=tobacco etch virus cleavage site; Cas9=wild type S. pyogenes Cas9—mutations or variants are as indicated).



FIG. 35. Data show fold increase in cell number after a total of 10 days of culturing in expansion medium (3 days of culturing prior to electroporation and 7 days of culturing following electroporation). With all the guide RNAs tested, including both single and dual guide RNA formats, cell expansion ranged from 2-7 fold. CR00312 and CR001128, indicated by arrows, demonstrated a 3-6 fold increase after 10 days of cell expansion. Lables “Crxxxx” refer to dgRNA having the indicated targeting domain; “sgxxxx” refer to sgRNA having the targeting domain of the CRxxxxx identifier with the same number (e.g., sg312 has the targeting domain of CR00312); “Unmod” indicates no modification to theRNA(s); “O'MePS”, when used in relation to a dgRNA refers to a crRNA which has three 3′ and three 5′ 2′-OMe modifications and phosphorothioate bonds, paired with an unmodified tracr; “O'MePS”, when used in relation to a sgRNA refers to gRNA which has three 5′-terminal 2′-OMe modifications and phosphorothioate bonds, three 3′-terminal phosphorothioate bonds, and three 2′OMe modifications of the 4th-to-last, 3rd-to-last and 2nd-to-last 3′ nucleotides.



FIG. 36. Gating strategy to distinguish different HSPC subpopulations.



FIG. 37. Frequency of each hematopoietic subset after 48 hours ex vivo culture in the indicated medium (STF modified with IL6, Compound 4, or both IL6 and Compound 4), but before electroporation of a CRISPR system. STF=StemSpan SFEM.



FIG. 38. Frequency of each hematopoietic subset 7 days after electroporation introducing a CRISPR system targeting the +58 enhancer of BCL11a, cultured in the indicated medium (STF modified with IL6, Compound 4, or both IL6 and Compound 4). STF=StemSpan SFEM.



FIG. 39A. Cell viability upon gene editing using different RNP concentrations, with RNP containing dgRNAs targeting the +58 region.



FIG. 39B. Cell viability upon gene editing using different RNP concentrations, with RNP containing sgRNAs targeting the +58 region.



FIG. 40A. Gene editing efficiency measured by NGS upon gene editing using different RNP concentrations, with RNP containing dgRNAs targeting the +58 region.



FIG. 40B Gene editing efficiency measured by NGS upon gene editing using different RNP concentrations, with RNP containing sgRNAs targeting the +58 region.



FIG. 41A. Percentage of HbF induction measured by flow cytometry upon gene editing using different RNP concentrations, with RNP containing dgRNAs targeting the +58 region.



FIG. 41B Percentage of HbF induction measured by flow cytometry upon gene editing using different RNP concentrations, with RNP containing sgRNAs targeting the +58 region.



FIG. 42A. Gene editing efficiencies of RNPs with different Cas9 proteins. Gene editing was performed using different Cas9 variants (listed on the X-axis) coupled with either the unmodified version of sgRNA CR00312 and sgRNA CR001128, or a modified version of sgRNA CR00312 and sgRNA CR001128. Edited cells were subjected to NGS to determine % edit (Y-axis).



FIG. 42B. Induction of HbF+ cells upon gene editing using different Cas9 proteins. Gene editing was performed using different Cas9 variants (listed on the X-axis) coupled with either the unmodified version of sgRNA CR00312 and sgRNA CR001128, or a modified version of sgRNA CR00312 and sgRNA CR001128. Edited cells were differentiated into erythroid lineage and HbF production assessed by flow cytometry using an anti-HbF antibody conjugated with fluorophore.



FIG. 43. % Editing as determined by NGS in CD34+ HSPCs by electroporation of RNP comprising the indicated dgRNA or sgRNA (unmod or modified as indicated) (labels refer to the gRNA sequences as indicated in Table 36). Editing was determined at either 2 days (black bars) or 6 days (gray bars) post-electroporation. Less than 1.5% editing was detected at each site after control electroporation of Cas9 protein and Tracr only (“none”, data not shown). Mean+standard deviation of 2 electroporation replicates is shown.



FIG. 44. Percent of viable cells that are CD71+ after electroporation into CD34+ HSPCs of RNP comprising the indicated dgRNA or sgRNA (unmod or modified as indicated) (labels refer to the gRNA sequences as indicated in Table 36) and culture in erythroid differentiation conditions for 7 days. After electroporation, cells were maintained by Protocol 1 (black bars) or Protocol 2 (gray bars), as described in Example 4.7. Controls include electroporation of Cas9 protein and Tracr only (“none”). Mean+standard deviation of 2 electroporation replicates is shown.



FIG. 45. Percent of erythroid cells that are HbF+ after electroporation into CD34+ HSPCs of RNP comprising the indicated dgRNA or sgRNA (unmod or modified as indicated) (labels refer to the gRNA sequences as indicated in Table 36) and culture in erythroid differentiation conditions for 7 days. After electroporation, cells were maintained by Protocol 1 (black bars) or Protocol 2 (gray bars), as described in Example 4.7. Controls include electroporation of Cas9 protein and Tracr only (“none”). Mean+standard deviation of 2 electroporation replicates is shown.



FIG. 46. Percent of cells that are HbF+ after electroporation into CD34+ HSPCs of RNP comprising the indicated dgRNA or sgRNA (unmod or modified as indicated) (labels refer to the gRNA sequences as indicated in Table 36) and cultured in erythroid differentiation conditions for 14 days. After electroporation, cells were maintained by Protocol 1 (black bars) or Protocol 2 (gray bars), as described in Example 4.7. Controls include electroporation of Cas9 protein and Tracr only (“none”). Mean+standard deviation of 2 electroporation replicates is shown.



FIG. 47. Percent of cells that are HbF+ after electroporation into CD34+ HSPCs of RNP comprising the indicated dgRNA or sgRNA (unmod or modified as indicated) (labels refer to the gRNA sequences as indicated in Table 36) and cultured in erythroid differentiation conditions for 21 days. After electroporation, cells were maintained by Protocol 1 (black bars) or Protocol 2 (gray bars), as described in Example 4.7. Controls include electroporation of Cas9 protein and Tracr only (“none”). Mean+standard deviation of 2 electroporation replicates is shown.



FIG. 48. Fold total cell expansion in erythroid differentiation culture for 7 (black bars) or 21 days (black bars) after electroporation into CD34+ HSPCs of RNP comprising the indicated dgRNA or sgRNA (unmod or modified as indicated) (labels refer to the gRNA sequences as indicated in Table 36). After electroporation, cells were maintained by Protocol 2, as described in Example 4.7. Controls include electroporation of Cas9 protein and Tracr only (“none”). Mean+standard deviation of 2 electroporation replicates is shown.



FIG. 49. Assessment of potential off-target sites cleaved by Cas9 directed by dgRNA molecules targeting an HPFH region. Triangles represent the on-target site while open circles represent a potential off-target site for each guide RNA tested.





DEFINITIONS

The terms “CRISPR system,” “Cas system” or “CRISPR/Cas system” refer to a set of molecules comprising an RNA-guided nuclease or other effector molecule and a gRNA molecule that together are necessary and sufficient to direct and effect modification of nucleic acid at a target sequence by the RNA-guided nuclease or other effector molecule. In one embodiment, a CRISPR system comprises a gRNA and a Cas protein, e.g., a Cas9 protein. Such systems comprising a Cas9 or modified Cas9 molecule are referred to herein as “Cas9 systems” or “CRISPR/Cas9 systems.” In one example, the gRNA molecule and Cas molecule may be complexed, to form a ribonuclear protein (RNP) complex.


The terms “guide RNA,” “guide RNA molecule,” “gRNA molecule” or “gRNA” are used interchangeably, and refer to a set of nucleic acid molecules that promote the specific directing of a RNA-guided nuclease or other effector molecule (typically in complex with the gRNA molecule) to a target sequence. In some embodiments, said directing is accomplished through hybridization of a portion of the gRNA to DNA (e.g., through the gRNA targeting domain), and by binding of a portion of the gRNA molecule to the RNA-guided nuclease or other effector molecule (e.g., through at least the gRNA tracr). In embodiments, a gRNA molecule consists of a single contiguous polynucleotide molecule, referred to herein as a “single guide RNA” or “sgRNA” and the like. In other embodiments, a gRNA molecule consists of a plurality, usually two, polynucleotide molecules, which are themselves capable of association, usually through hybridization, referred to herein as a “dual guide RNA” or “dgRNA,” and the like. gRNA molecules are described in more detail below, but generally include a targeting domain and a tracr. In embodiments the targeting domain and tracr are disposed on a single polynucleotide. In other embodiments, the targeting domain and tracr are disposed on separate polynucleotides.


The term “targeting domain” as the term is used in connection with a gRNA, is the portion of the gRNA molecule that recognizes, e.g., is complementary to, a target sequence, e.g., a target sequence within the nucleic acid of a cell, e.g., within a gene.


The term “crRNA” as the term is used in connection with a gRNA molecule, is a portion of the gRNA molecule that comprises a targeting domain and a region that interacts with a tracr to form a flagpole region.


The term “target sequence” refers to a sequence of nucleic acids complimentary, for example fully complementary, to a gRNA targeting domain. In embodiments, the target sequence is disposed on genomic DNA. In an embodiment the target sequence is adjacent to (either on the same strand or on the complementary strand of DNA) a protospacer adjacent motif (PAM) sequence recognized by a protein having nuclease or other effector activity, e.g., a PAM sequence recognized by Cas9. In embodiments, the target sequence is a target sequence within a gene or locus that affects expression of a globin gene, e.g., that affects expression of beta globin or fetal hemoglobin (HbF). In embodiments, the target sequence is a target sequence within the globin locus. In embodiments, the target sequence is a target sequence within the BCL11a gene. In embodiments, the target sequence is a target sequence within the BCL11a enhancer region. In embodiments, the target sequence is a target sequence within a HPFH region.


The term “flagpole” as used herein in connection with a gRNA molecule, refers to the portion of the gRNA where the crRNA and the tracr bind to, or hybridize to, one another.


The term “tracr” as used herein in connection with a gRNA molecule, refers to the portion of the gRNA that binds to a nuclease or other effector molecule. In embodiments, the tracr comprises nucleic acid sequence that binds specifically to Cas9. In embodiments, the tracr comprises nucleic acid sequence that forms part of the flagpole.


The terms “Cas9” or “Cas9 molecule” refer to an enzyme from bacterial Type II CRISPR/Cas system responsible for DNA cleavage. Cas9 also includes wild-type protein as well as functional and non-functional mutants thereof. In embodiments, the Cas9 is a Cas9 of S. pyogenes.


The term “complementary” as used in connection with nucleic acid, refers to the pairing of bases, A with T or U, and G with C. The term complementary refers to nucleic acid molecules that are completely complementary, that is, form A to T or U pairs and G to C pairs across the entire reference sequence, as well as molecules that are at least 80%, 85%, 90%, 95%, 99% complementary.


“Template Nucleic Acid” as used in connection with homology-directed repair or homologous recombination, refers to nucleic acid to be inserted at the site of modification by the CRISPR system donor sequence for gene repair (insertion) at site of cutting.


An “indel,” as the term is used herein, refers to a nucleic acid comprising one or more insertions of nucleotides, one or more deletions of nucleotides, or a combination of insertions and delections of nucleotides, relative to a reference nucleic acid, that results after being exposed to a composition comprising a gRNA molecule, for example a CRISPR system. Indels can be determined by sequencing nucleic acid after being exposed to a composition comprising a gRNA molecule, for example, by NGS. With respect to the site of an indel, an indel is said to be “at or near” a reference site (e.g., a site complementary to a targeting domain of a gRNA molecule) if it comprises at least one insertion or deletion within about 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 nucleotide(s) of the reference site, or is overlapping with part or all of said reference site (e.g., comprises at least one insertion or deletion overlapping with, or within 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 nucleotides of a site complementary to the targeting domain of a gRNA molecule, e.g., a gRNA molecule described herein).


An “indel pattern,” as the term is used herein, refers to a set of indels that results after exposure to a composition comprising a gRNA molecule. In an embodiment, the indel pattern consists of the top three indels, by frequency of appearance. In an embodiment, the indel pattern consists of the top five indels, by frequency of appearance. In an embodiment, the indel pattern consists of the indels which are present at greater than about 5% frequency relative to all sequencing reads. In an embodiment, the indel pattern consists of the indels which are present at greater than about 10% frequency relative to to total number of indel sequencing reads (i.e., those reads that do not consist of the unmodified reference nucleic acid sequence). In an embodiment, the indel pattern includes of any 3 of the top five most frequently observed indels. The indel pattern may be determined, for example, by sequencing cells of a population of cells which were exposed to the gRNA molecule.


An “off-target indel,” as the term I used herein, refers to an indel at or near a site other than the target sequence of the targeting domain of the gRNA molecule. Such sites may comprise, for example, 1, 2, 3, 4, 5 or more mismatch nucleotides relative to the sequence of the targeting domain of the gRNA. In exemplary embodiments, such sites are detected using targeted sequencing of in silico predicted off-target sites, or by an insertional method known in the art.


The term “a” and “an” refers to one or to more than one (i.e., to at least one) of the grammatical object of the article. By way of example, “an element” means one element or more than one element.


The term “about” when referring to a measurable value such as an amount, a temporal duration, and the like, is meant to encompass variations of ±20% or in some instances ±10%, or in some instances ±5%, or in some instances ±1%, or in some instances ±0.1% from the specified value, as such variations are appropriate to perform the disclosed methods.


The term “antigen” or “Ag” refers to a molecule that provokes an immune response. This immune response may involve either antibody production, or the activation of specific immunologically-competent cells, or both. The skilled artisan will understand that any macromolecule, including virtually all proteins or peptides, can serve as an antigen. Furthermore, antigens can be derived from recombinant or genomic DNA. A skilled artisan will understand that any DNA, which comprises a nucleotide sequences or a partial nucleotide sequence encoding a protein that elicits an immune response therefore encodes an “antigen” as that term is used herein. Furthermore, one skilled in the art will understand that an antigen need not be encoded solely by a full length nucleotide sequence of a gene. It is readily apparent that the present invention includes, but is not limited to, the use of partial nucleotide sequences of more than one gene and that these nucleotide sequences are arranged in various combinations to encode polypeptides that elicit the desired immune response. Moreover, a skilled artisan will understand that an antigen need not be encoded by a “gene” at all. It is readily apparent that an antigen can be synthesized or can be derived from a biological sample, or might be macromolecule besides a polypeptide. Such a biological sample can include, but is not limited to a tissue sample, a cell or a fluid with other biological components.


The term “autologous” refers to any material derived from the same individual into whom it is later to be re-introduced.


The term “allogeneic” refers to any material derived from a different animal of the same species as the individual to whom the material is introduced. Two or more individuals are said to be allogeneic to one another when the genes at one or more loci are not identical. In some aspects, allogeneic material from individuals of the same species may be sufficiently unlike genetically to interact antigenically


The term “xenogeneic” refers to a graft derived from an animal of a different species.


“Derived from” as that term is used herein, indicates a relationship between a first and a second molecule. It generally refers to structural similarity between the first molecule and a second molecule and does not connotate or include a process or source limitation on a first molecule that is derived from a second molecule.


The term “encoding” refers to the inherent property of specific sequences of nucleotides in a polynucleotide, such as a gene, a cDNA, or an mRNA, to serve as templates for synthesis of other polymers and macromolecules in biological processes having either a defined sequence of nucleotides (e.g., rRNA, tRNA and mRNA) or a defined sequence of amino acids and the biological properties resulting therefrom. Thus, a gene, cDNA, or RNA, encodes a protein if transcription and translation of mRNA corresponding to that gene produces the protein in a cell or other biological system. Both the coding strand, the nucleotide sequence of which is identical to the mRNA sequence and is usually provided in sequence listings, and the non-coding strand, used as the template for transcription of a gene or cDNA, can be referred to as encoding the protein or other product of that gene or cDNA.


Unless otherwise specified, a “nucleotide sequence encoding an amino acid sequence” includes all nucleotide sequences that are degenerate versions of each other and that encode the same amino acid sequence. The phrase nucleotide sequence that encodes a protein or a RNA may also include introns to the extent that the nucleotide sequence encoding the protein may in some version contain an intron(s).


The term “effective amount” or “therapeutically effective amount” are used interchangeably herein, and refer to an amount of a compound, formulation, material, or composition, as described herein effective to achieve a particular biological result.


The term “endogenous” refers to any material from or produced inside an organism, cell, tissue or system.


The term “exogenous” refers to any material introduced from or produced outside an organism, cell, tissue or system.


The term “expression” refers to the transcription and/or translation of a particular nucleotide sequence driven by a promoter.


The term “transfer vector” refers to a composition of matter which comprises an isolated nucleic acid and which can be used to deliver the isolated nucleic acid to the interior of a cell. Numerous vectors are known in the art including, but not limited to, linear polynucleotides, polynucleotides associated with ionic or amphiphilic compounds, plasmids, and viruses. Thus, the term “transfer vector” includes an autonomously replicating plasmid or a virus. The term should also be construed to further include non-plasmid and non-viral compounds which facilitate transfer of nucleic acid into cells, such as, for example, a polylysine compound, liposome, and the like. Examples of viral transfer vectors include, but are not limited to, adenoviral vectors, adeno-associated virus vectors, retroviral vectors, lentiviral vectors, and the like.


The term “expression vector” refers to a vector comprising a recombinant polynucleotide comprising expression control sequences operatively linked to a nucleotide sequence to be expressed. An expression vector comprises sufficient cis-acting elements for expression; other elements for expression can be supplied by the host cell or in an in vitro expression system. Expression vectors include all those known in the art, including cosmids, plasmids (e.g., naked or contained in liposomes) and viruses (e.g., lentiviruses, retroviruses, adenoviruses, and adeno-associated viruses) that incorporate the recombinant polynucleotide.


The term “homologous” or “identity” refers to the subunit sequence identity between two polymeric molecules, e.g., between two nucleic acid molecules, such as, two DNA molecules or two RNA molecules, or between two polypeptide molecules. When a subunit position in both of the two molecules is occupied by the same monomeric subunit; e.g., if a position in each of two DNA molecules is occupied by adenine, then they are homologous or identical at that position. The homology between two sequences is a direct function of the number of matching or homologous positions; e.g., if half (e.g., five positions in a polymer ten subunits in length) of the positions in two sequences are homologous, the two sequences are 50% homologous; if 90% of the positions (e.g., 9 of 10), are matched or homologous, the two sequences are 90% homologous.


The term “isolated” means altered or removed from the natural state. For example, a nucleic acid or a peptide naturally present in a living animal is not “isolated,” but the same nucleic acid or peptide partially or completely separated from the coexisting materials of its natural state is “isolated.” An isolated nucleic acid or protein can exist in substantially purified form, or can exist in a non-native environment such as, for example, a host cell.


The term “operably linked” or “transcriptional control” refers to functional linkage between a regulatory sequence and a heterologous nucleic acid sequence resulting in expression of the latter. For example, a first nucleic acid sequence is operably linked with a second nucleic acid sequence when the first nucleic acid sequence is placed in a functional relationship with the second nucleic acid sequence. For instance, a promoter is operably linked to a coding sequence if the promoter affects the transcription or expression of the coding sequence. Operably linked DNA sequences can be contiguous with each other and, e.g., where necessary to join two protein coding regions, are in the same reading frame.


The term “parenteral” administration of an immunogenic composition includes, e.g., subcutaneous (s.c.), intravenous (i.v.), intramuscular (i.m.), or infrasternal injection, intratumoral, or infusion techniques.


The term “nucleic acid” or “polynucleotide” refers to deoxyribonucleic acids (DNA) or ribonucleic acids (RNA) and polymers thereof in either single- or double-stranded form. Unless specifically limited, the term encompasses nucleic acids containing known analogues of natural nucleotides that have similar binding properties as the reference nucleic acid and are metabolized in a manner similar to naturally occurring nucleotides. Unless otherwise indicated, a particular nucleic acid sequence also implicitly encompasses conservatively modified variants thereof (e.g., degenerate codon substitutions), alleles, orthologs, SNPs, and complementary sequences as well as the sequence explicitly indicated. Specifically, degenerate codon substitutions may be achieved by generating sequences in which the third position of one or more selected (or all) codons is substituted with mixed-base and/or deoxyinosine residues (Batzer et al., Nucleic Acid Res. 19:5081 (1991); Ohtsuka et al., J. Biol. Chem. 260:2605-2608 (1985); and Rossolini et al., Mol. Cell. Probes 8:91-98 (1994)).


The terms “peptide,” “polypeptide,” and “protein” are used interchangeably, and refer to a compound comprised of amino acid residues covalently linked by peptide bonds. A protein or peptide must contain at least two amino acids, and no limitation is placed on the maximum number of amino acids that can comprise a protein's or peptide's sequence. Polypeptides include any peptide or protein comprising two or more amino acids joined to each other by peptide bonds. As used herein, the term refers to both short chains, which also commonly are referred to in the art as peptides, oligopeptides and oligomers, for example, and to longer chains, which generally are referred to in the art as proteins, of which there are many types. “Polypeptides” include, for example, biologically active fragments, substantially homologous polypeptides, oligopeptides, homodimers, heterodimers, variants of polypeptides, modified polypeptides, derivatives, analogs, fusion proteins, among others. A polypeptide includes a natural peptide, a recombinant peptide, or a combination thereof.


The term “promoter” refers to a DNA sequence recognized by the synthetic machinery of the cell, or introduced synthetic machinery, required to initiate the specific transcription of a polynucleotide sequence.


The term “promoter/regulatory sequence” refers to a nucleic acid sequence which is required for expression of a gene product operably linked to the promoter/regulatory sequence. In some instances, this sequence may be the core promoter sequence and in other instances, this sequence may also include an enhancer sequence and other regulatory elements which are required for expression of the gene product. The promoter/regulatory sequence may, for example, be one which expresses the gene product in a tissue specific manner.


The term “constitutive” promoter refers to a nucleotide sequence which, when operably linked with a polynucleotide which encodes or specifies a gene product, causes the gene product to be produced in a cell under most or all physiological conditions of the cell.


The term “inducible” promoter refers to a nucleotide sequence which, when operably linked with a polynucleotide which encodes or specifies a gene product, causes the gene product to be produced in a cell substantially only when an inducer which corresponds to the promoter is present in the cell.


The term “tissue-specific” promoter refers to a nucleotide sequence which, when operably linked with a polynucleotide encodes or specified by a gene, causes the gene product to be produced in a cell substantially only if the cell is a cell of the tissue type corresponding to the promoter.


As used herein in connection with a messenger RNA (mRNA), a 5′ cap (also termed an RNA cap, an RNA 7-methylguanosine cap or an RNA m7G cap) is a modified guanine nucleotide that has been added to the “front” or 5′ end of a eukaryotic messenger RNA shortly after the start of transcription. The 5′ cap consists of a terminal group which is linked to the first transcribed nucleotide. Its presence is critical for recognition by the ribosome and protection from RNases. Cap addition is coupled to transcription, and occurs co-transcriptionally, such that each influences the other. Shortly after the start of transcription, the 5′ end of the mRNA being synthesized is bound by a cap-synthesizing complex associated with RNA polymerase. This enzymatic complex catalyzes the chemical reactions that are required for mRNA capping. Synthesis proceeds as a multi-step biochemical reaction. The capping moiety can be modified to modulate functionality of mRNA such as its stability or efficiency of translation.


As used herein, “in vitro transcribed RNA” refers to RNA, preferably mRNA, that has been synthesized in vitro. Generally, the in vitro transcribed RNA is generated from an in vitro transcription vector. The in vitro transcription vector comprises a template that is used to generate the in vitro transcribed RNA.


As used herein, a “poly(A)” is a series of adenosines attached by polyadenylation to the mRNA. In the preferred embodiment of a construct for transient expression, the polyA is between 50 and 5000 (SEQ ID NO: 6596), preferably greater than 64, more preferably greater than 100, most preferably greater than 300 or 400. poly(A) sequences can be modified chemically or enzymatically to modulate mRNA functionality such as localization, stability or efficiency of translation.


As used herein, “polyadenylation” refers to the covalent linkage of a polyadenylyl moiety, or its modified variant, to a messenger RNA molecule. In eukaryotic organisms, most messenger RNA (mRNA) molecules are polyadenylated at the 3′ end. The 3′ poly(A) tail is a long sequence of adenine nucleotides (often several hundred) added to the pre-mRNA through the action of an enzyme, polyadenylate polymerase. In higher eukaryotes, the poly(A) tail is added onto transcripts that contain a specific sequence, the polyadenylation signal. The poly(A) tail and the protein bound to it aid in protecting mRNA from degradation by exonucleases. Polyadenylation is also important for transcription termination, export of the mRNA from the nucleus, and translation. Polyadenylation occurs in the nucleus immediately after transcription of DNA into RNA, but additionally can also occur later in the cytoplasm. After transcription has been terminated, the mRNA chain is cleaved through the action of an endonuclease complex associated with RNA polymerase. The cleavage site is usually characterized by the presence of the base sequence AAUAAA near the cleavage site. After the mRNA has been cleaved, adenosine residues are added to the free 3′ end at the cleavage site.


As used herein, “transient” refers to expression of a non-integrated transgene for a period of hours, days or weeks, wherein the period of time of expression is less than the period of time for expression of the gene if integrated into the genome or contained within a stable plasmid replicon in the host cell.


As used herein, the terms “treat”, “treatment” and “treating” refer to the reduction or amelioration of the progression, severity and/or duration of a disorder, e.g., a hemoglobinopathy, or the amelioration of one or more symptoms (preferably, one or more discernible symptoms) of a disorder, e.g., a hemoglobinopathy, resulting from the administration of one or more therapies (e.g., one or more therapeutic agents such as a gRNA molecule, CRISPR system, or modified cell of the invention). In specific embodiments, the terms “treat”, “treatment” and “treating” refer to the amelioration of at least one measurable physical parameter of a hemoglobinopathy disorder, not discernible by the patient. In other embodiments the terms “treat”, “treatment” and “treating” refer to the inhibition of the progression of a disorder, either physically by, e.g., stabilization of a discernible symptom, physiologically by, e.g., stabilization of a physical parameter, or both. In other embodiments the terms “treat”, “treatment” and “treating” refer to the reduction or stabilization of a symptom of a hemoglobinopathy, e.g., sickle cell disease or beta-thalassemia.


The term “signal transduction pathway” refers to the biochemical relationship between a variety of signal transduction molecules that play a role in the transmission of a signal from one portion of a cell to another portion of a cell. The phrase “cell surface receptor” includes molecules and complexes of molecules capable of receiving a signal and transmitting signal across the membrane of a cell.


The term “subject” is intended to include living organisms in which an immune response can be elicited (e.g., mammals, human).


The term, a “substantially purified” cell refers to a cell that is essentially free of other cell types. A substantially purified cell also refers to a cell which has been separated from other cell types with which it is normally associated in its naturally occurring state. In some instances, a population of substantially purified cells refers to a homogenous population of cells. In other instances, this term refers simply to cell that have been separated from the cells with which they are naturally associated in their natural state. In some aspects, the cells are cultured in vitro. In other aspects, the cells are not cultured in vitro.


The term “therapeutic” as used herein means a treatment. A therapeutic effect is obtained by reduction, suppression, remission, or eradication of a disease state.


The term “prophylaxis” as used herein means the prevention of or protective treatment for a disease or disease state.


The term “transfected” or “transformed” or “transduced” refers to a process by which exogenous nucleic acid and/or protein is transferred or introduced into the host cell. A “transfected” or “transformed” or “transduced” cell is one which has been transfected, transformed or transduced with exogenous nucleic acid and/or protein. The cell includes the primary subject cell and its progeny.


The term “specifically binds,” refers to a molecule recognizing and binding with a binding partner (e.g., a protein or nucleic acid) present in a sample, but which molecule does not substantially recognize or bind other molecules in the sample.


The term “bioequivalent” refers to an amount of an agent other than the reference compound, required to produce an effect equivalent to the effect produced by the reference dose or reference amount of the reference compound.


“Refractory” as used herein refers to a disease, e.g., a hemoglobinopathy, that does not respond to a treatment. In embodiments, a refractory hemoglobinopathy can be resistant to a treatment before or at the beginning of the treatment. In other embodiments, the refractory hemoglobinopathy can become resistant during a treatment. A refractory hemoglobinopathy is also called a resistant hemoglobinopathy.


“Relapsed” as used herein refers to the return of a disease (e.g., hemoglobinopathy) or the signs and symptoms of a disease such as a hemoglobinopathy after a period of improvement, e.g., after prior treatment of a therapy, e.g., hemoglobinopathy therapy.


Ranges: throughout this disclosure, various aspects of the invention can be presented in a range format. It should be understood that the description in range format is merely for convenience and brevity and should not be construed as an inflexible limitation on the scope of the invention. Accordingly, the description of a range should be considered to have specifically disclosed all the possible subranges as well as individual numerical values within that range. For example, description of a range such as from 1 to 6 should be considered to have specifically disclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 5, from 2 to 4, from 2 to 6, from 3 to 6 etc., as well as individual numbers within that range, for example, 1, 2, 2.7, 3, 4, 5, 5.3, and 6. As another example, a range such as 95-99% identity, includes something with 95%, 96%, 97%, 98% or 99% identity, and includes subranges such as 96-99%, 96-98%, 96-97%, 97-99%, 97-98% and 98-99% identity. This applies regardless of the breadth of the range.


The term “BCL11a” refers to B-cell lymphoma/leukemia 11A, a RNA polymerase II core promoter proximal region sequence-specific DNA binding protein, and the gene encoding said protein, together with all introns and exons. This gene encodes a C2H2 type zinc-finger protein. BCL11A has been found to play a role in the suppression of fetal hemoglobin production. BCL11a is also known as B-Cell CLL/Lymphoma 11A (Zinc Finger Protein), CTIP1, EVI9, Ecotropic Viral Integration Site 9 Protein Homolog, COUP-TF-Interacting Protein 1, Zinc Finger Protein 856, KIAA1809, BCL-11A, ZNF856, EVI-9, and B-Cell CLL/Lymphoma 11A. The term encompasses all isoforms and splice variants of BLC11a. The human gene encoding BCL11a is mapped to chromosomal location 2p16.1 (by Ensembl). The human and murine amino acid and nucleic acid sequences can be found in a public database, such as GenBank, UniProt and Swiss-Prot., and the genomic sequence of human BCL11a can be found in GenBank at NC_000002.12. The BCL11a gene refers to this genomic location, including all introns and exons. There are multiple known isotypes of BCL11a.


The sequence of mRNA encoding isoform 1 of human BCL11a can be found at NM_022893.


The peptide sequence of isoform 1 of human BCL11a is:











        10         20         30         40



MSRRKQGKPQ HLSKREFSPE PLEAILTDDE PDHGPLGAPE







        50         60         70         80



GDHDLLTCGQ CQMNFPLGDI LIFIEHKRKQ CNGSLCLEKA







        90        100        110        120



VDKPPSPSPI EMKKASNPVE VGIQVTPEDD DCLSTSSRGI







       130        140        150        160



CPKQEHIADK LLHWRGLSSP RSAHGALIPT PGMSAEYAPQ







       170        180        190        200



GICKDEPSSY TCTTCKQPFT SAWFLLQHAQ NTHGLRIYLE







       210        220        230        240



SEHGSPLTPR VGIPSGLGAE CPSQPPLHGI HIADNNPFNL







       250        260        270        280



LRIPGSVSRE ASGLAEGRFP PTPPLFSPPP RHHLDPHRIE







       290        300        310        320



RLGAEEMALA THHPSAFDRV LRLNPMAMEP PAMDFSRRLR







       330        340        350        360



ELAGNTSSPP LSPGRPSPMQ RLLQPFQPGS KPPFLATPPL







       370        380        390        400



PPLQSAPPPS QPPVKSKSCE FCGKTFKFQS NLVVHRRSHT







       410        420        430        440



GEKPYKCNLC DHACTQASKL KRHMKTHMHK SSPMTVKSDD







       450        460        470        480



GLSTASSPEP GTSDLVGSAS SALKSVVAKF KSENDPNLIP







       490        500        510        520



ENGDEEEEED DEEEEEEEEE EEEELTESER VDYGFGLSLE







       530        540        550        560



AARHHENSSR GAVVGVGDES RALPDVMQGM VLSSMQHFSE







       570        580        590        600



AFHQVLGEKH KRGHLAEAEG HRDTCDEDSV AGESDRIDDG







       610        620        630        640



TVNGRGCSPG ESASGGLSKK LLLGSPSSLS PFSKRIKLEK







       650        660        670        680



EFDLPPAAMP NTENVYSQWL AGYAASRQLK DPFLSFGDSR







       690        700        710        720



QSPFASSSEH SSENGSLRFS TPPGELDGGI SGRSGTGSGG







       730        740        750        760



STPHISGPGP GRPSSKEGRR SDTCEYCGKV FKNCSNLTVH







       770        780        790        800



RRSHTGERPY KCELCNYACA QSSKLTRHMK THGQVGKDVY







       810        820        830



KCEICKMPFS VYSTLEKHMK KWHSDRVLNN DIKTE






SEQ ID NO: 21-1 (Identifier Q9H165-1; and NM_022893.3; and accession ADL14508.1).


The sequences of other BCL11a protein isoforms are provided at:


Isoform 2: Q9H165-2
Isoform 3: Q9H165-3
Isoform 4: Q9H165-4
Isoform 5: Q9H165-5
Isoform 6: Q9H165-6

As used herein, a human BCL11a protein also encompasses proteins that have over its full length at least about 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity with BCL11a isolorm 1-6, wherein such proteins still have at least one of the functions of BCL11a.


The term “globin locus” as used herein refers to the region of human chromosome 11 comprising genes for embryonic (ε), fetal (G(γ) and A(γ)), adult globin genes (γ and β), locus control regions and DNase I hypersensitivity sites.


The term “complementary” as used in connection with nucleic acid, refers to the pairing of bases, A with T or U, and G with C. The term complementary refers to nucleic acid molecules that are completely complementary, that is, form A to T or U pairs and G to C pairs across the entire reference sequence, as well as molecules that are at least 80%, 85%, 90%, 95%, 99% complementary.


The term “HPFH” refers to hereditary persistence of fetal hemoglobin, and is characterized in increased fetal hemoglobin in adult red blood cells. The term “HPFH region” refers to a genomic site which, when modified (e.g., mutated or deleted), causes increased HbF production in adult red blood cells, and includes HPFH sites identified in the literature (see e.g., the Online Mendelian Inheritance in Man: http://www.omim.org/entry/141749). In an exemplary embodiment, the HPFH region is a region within or encompassing the beta globin gene cluster on chromosome 11p15. In an exemplary embodiment, the HPFH region is within or emcompasses at least part of the delta globin gene. In an exemplary embodiment, the HPFH region is a region of the promoter of HBG1. In an exemplary embodiment, the HPFH region is a region of the promoter of HBG1. In an exemplary embodiment, the HPFH region is a region described in Sankaran V G et al. NEJM (2011) 365:807-814. In an exemplary embodiment, the HPFH region is the French breakpoint deletional HPFH as described in Sankaran V G et al. NEJM (2011) 365:807-814. In an exemplary embodiment, the HPFH region is the Algerian HPFH as described in Sankaran V G et al. NEJM (2011) 365:807-814. In an exemplary embodiment, the HPFH region is the Sri Lankan HPFH as described in Sankaran V G et al. NEJM (2011) 365:807-814. In an exemplary embodiment, the HPFH region is the HPFH-3 as described in Sankaran V G et al. NEJM (2011) 365:807-814. In an exemplary embodiment, the HPFH region is the HPFH-2 as described in Sankaran V G et al. NEJM (2011) 365:807-814. In an embodiment, the HPFH-1 region is the HPFH-3 as described in Sankaran V G et al. NEJM (2011) 365:807-814. In an exemplary embodiment, the HPFH region is the Sri Lankan (δβ)0-thalassemia HPFH as described in Sankaran V G et al. NEJM (2011) 365:807-814. In an exemplary embodiment, the HPFH region is the Sicilian (δβ)0-thalassemia HPFH as described in Sankaran V G et al. NEJM (2011) 365:807-814. In an exemplary embodiment, the HPFH region is the Macedonian (δβ)0-thalassemia HPFH as described in Sankaran V G et al. NEJM (2011) 365:807-814. In an exemplary embodiment, the HPFH region is the Kurdish β0-thalassemia HPFH as described in Sankaran V G et al. NEJM (2011) 365:807-814. In an exemplary embodiment, the HPFH region is the region located at Chr11:5213874-5214400 (hg18). In an exemplary embodiment, the HPFH region is the region located at Chr11:5215943-5215046 (hg18). In an exemplary embodiment, the HPFH region is the region located at Chr11:5234390-5238486 (hg38).


“BCL11a enhancer” as the term is used herein, refers to nucleic acid sequence which affects, e.g., enhances, expression or function of BCL11a. See e.g., Bauer et al., Science, vol. 342, 2013, pp. 253-257. The BCL11a enhancer may be, for example, operative only in certain cell types, for example, cells of the erythroid lineage. One example of a BCL11a enhancer is the nucleic acid sequence between exon 2 and exon 3 of the BCL11a gene gene (e.g., the nucleic acid at or corresponding to positions +55: Chr2:60497676-60498941; +58: Chr2:60494251-60495546; +62: Chr2:60490409-60491734 as recorded in hg38). In an embodiment, the BCL11a Enhancer is the +62 region of the nucleic acid sequence between exon 2 and exon 3 of the BCL11a gene. In an embodiment, the BCL11a Enhancer is the +58 region of the nucleic acid sequence between exon 2 and exon 3 of the BCL11a gene. In an embodiment, the BCL11a Enhancer is the +55 region of the nucleic acid sequence between exon 2 and exon 3 of the BCL11a gene.


The terms “hematopoietic stem and progenitor cell” or “HSPC” are used interchangeably, and refer to a population of cells comprising both hematopoietic stem cells (“HSCs”) and hematopoietic progenitor cells (“HPCs”). Such cells are characterized, for example, as CD34+. In exemplary embodiments, HSPCs are isolated from bone marrow. In other exemplary embodiments, HSPCs are isolated from peripheral blood. In other exemplary embodiments, HSPCs are isolated from umbilical cord blood.


“Stem cell expander” as used herein refers to a compound which causes cells, e.g., HSPCs, HSCs and/or HPCs to proliferate, e.g., increase in number, at a faster rate relative to the same cell types absent said agent. In one exemplary aspect, the stem cell expander is an inhibitor of the aryl hydrocarbon receptor pathway. Additional examples of stem cell expanders are provided below. In embodiments, the proliferation, e.g., increase in number, is accomplished ex vivo.


“Engraftment” or “engraft” refers to the incorporation of a cell or tissue, e.g., a population of HSPCs, into the body of a recipient, e.g., a mammal or human subject. In one example, engraftment includes the growth, expansion and/or differention of the engrafted cells in the recipient. In an example, engraftment of HSPCs includes the differentiation and growth of said HSPCs into erythroid cells within the body of the recipient.


The term “Hematopoietic progenitor cells” (HPCs) as used herein refers to primitive hematopoietic cells that have a limited capacity for self-renewal and the potential for multilineage differentiation (e.g., myeloid, lymphoid), mono-lineage differentiation (e.g., myeloid or lymphoid) or cell-type restricted differentiation (e.g., erythroid progenitor) depending on placement within the hematopoietic hierarchy (Doulatov et al., Cell Stem Cell 2012).


“Hematopoietic stem cells” (HSCs) as used herein refer to immature blood cells having the capacity to self-renew and to differentiate into more mature blood cells comprising granulocytes (e.g., promyelocytes, neutrophils, eosinophils, basophils), erythrocytes (e.g., reticulocytes, erythrocytes), thrombocytes (e.g., megakaryoblasts, platelet producing megakaryocytes, platelets), and monocytes (e.g., monocytes, macrophages). HSCs are interchangeably described as stem cells throughout the specification. It is known in the art that such cells may or may not include CD34+ cells. CD34+ cells are immature cells that express the CD34 cell surface marker. CD34+ cells are believed to include a subpopulation of cells with the stem cell properties defined above. It is well known in the art that HSCs are multipotent cells that can give rise to primitive progenitor cells (e.g., multipotent progenitor cells) and/or progenitor cells committed to specific hematopoietic lineages (e.g., lymphoid progenitor cells). The stem cells committed to specific hematopoietic lineages may be of T cell lineage, B cell lineage, dendritic cell lineage, Langerhans cell lineage and/or lymphoid tissue-specific macrophage cell lineage. In addition, HSCs also refer to long term HSC (LT-HSC) and short term HSC (ST-HSC). ST-HSCs are more active and more proliferative than LT-HSCs. However, LT-HSC have unlimited self renewal (i.e., they survive throughout adulthood), whereas ST-HSC have limited self renewal (i.e., they survive for only a limited period of time). Any of these HSCs can be used in any of the methods described herein. Optionally, ST-HSCs are useful because they are highly proliferative and thus, quickly increase the number of HSCs and their progeny. Hematopoietic stem cells are optionally obtained from blood products. A blood product includes a product obtained from the body or an organ of the body containing cells of hematopoietic origin. Such sources include un-fractionated bone marrow, umbilical cord, peripheral blood (e.g., mobilized peripheral blood, e.g., moblized with a mobilization agent such as G-CSF or Plerixafor® (AMD3100)), liver, thymus, lymph and spleen. All of the aforementioned crude or un-fractionated blood products can be enriched for cells having hematopoietic stem cell characteristics in ways known to those of skill in the art. In an embodiment, HSCs are characterized as CD34+/CD38−/CD90+/CD45RA−. In embodiments, the HSC s are characterized as CD34+/CD90+/CD49f+ cells.


“Expansion” or “Expand” in the context of cells refers to an increase in the number of a characteristic cell type, or cell types, from an initial cell population of cells, which may or may not be identical. The initial cells used for expansion may not be the same as the cells generated from expansion.


“Cell population” refers to eukaryotic mammalian, preferably human, cells isolated from biological sources, for example, blood product or tissues and derived from more than one cell.


“Enriched” when used in the context of cell population refers to a cell population selected based on the presence of one or more markers, for example, CD34+.


The term “CD34+ cells” refers to cells that express at their surface CD34 marker. CD34+ cells can be detected and counted using for example flow cytometry and fluorescently labeled anti-CD34 antibodies.


“Enriched in CD34+ cells” means that a cell population has been selected based on the presence of CD34 marker. Accordingly, the percentage of CD34+ cells in the cell population after selection method is higher than the percentage of CD34+ cells in the initial cell population before selecting step based on CD34 markers. For example, CD34+ cells may represent at least 50%, 60%, 70%, 80% or at least 90% of the cells in a cell population enriched in CD34+ cells.


The terms “F cell” and “F-cell” refer to cells, usually erythrocytes (e.g., red blood cells) which contain and/or produce (e.g., express) fetal hemoglobin. For example, an F-cell is a cell that contains or produces detectible levels of fetal hemoglobin. For example, an F-cell is a cell that contains or produces at least 5 picograms of fetal hemoglobin. In another example, an F-cell is a cell that contains or produces at least 6 picograms of fetal hemoglobin. In another example, an F-cell is a cell that contains or produces at least 7 picograms of fetal hemoglobin. In another example, an F-cell is a cell that contains or produces at least 8 picograms of fetal hemoglobin. In another example, an F-cell is a cell that contains or produces at least 9 picograms of fetal hemoglobin. In another example, an F-cell is a cell that contains or produces at least 10 picograms of fetal hemoglobin. Levels of fetal hemoglobin may be measured using an assay described herein or by other method known in the art, for example, flow cytometry using an anti-fetal hemoglobin detection reagent, high performance liquid chromatography, mass spectrometry, or enzyme-linked immunoabsorbent assay.


Unless otherwise stated, all genome or chromosome coordinates are are according to hg38.


DETAILED DESCRIPTION

The gRNA molecules, compositions and methods described herein relate to genome editing in eukaryotic cells using the CRISPR/Cas9 system. In particular, the gRNA molecules, compositions and methods described herein relate to regulation of globin levels and are useful, for example, in regulating expression and production of globin genes and protein. The gRNA molecules, compositions and methods can be useful in the treatment of hemoglobinopathies.


I. 2RNA Molecules

A gRNA molecule may have a number of domains, as described more fully below, however, a gRNA molecule typically comprises at least a crRNA domain (comprising a targeting domain) and a tracr. The gRNA molecules of the invention, used as a component of a CRISPR system, are useful for modifying (e.g., modifying the sequence) DNA at or near a target site. Such modifications include deletions and or insertions that result in, for example, reduced or eliminated expression of a functional product of the gene comprising the target site. These uses, and additional uses, are described more fully below.


In an embodiment, a unimolecular, or sgRNA comprises, preferably from 5′ to 3′: a crRNA (which contains a targeting domain complementary to a target sequence and a region that forms part of a flagpole (i.e., a crRNA flagpole region)); a loop; and a tracr (which contains a domain complementary to the crRNA flagpole region, and a domain which additionally binds a nuclease or other effector molecule, e.g., a Cas molecule, e.g., aCas9 molecule), and may take the following format (from 5′ to 3′):


[targeting domain]-[crRNA flagpole region]-[optional first flagpole extension]-[loop]-[optional first tracr extension]-[tracr flagpole region]-[tracr nuclease binding domain]


In embodiments, the tracr nuclease binding domain binds to a Cas protein, e.g., a Cas9 protein.


In an embodiment, a bimolecular, or dgRNA comprises two polynucleotides; the first, preferably from 5′ to 3′: a crRNA (which contains a targeting domain complementary to a target sequence and a region that forms part of a flagpole; and the second, preferrably from 5′ to 3′: a tracr (which contains a domain complementary to the crRNA flagpole region, and a domain which additionally binds a nuclease or other effector molecule, e.g., a Cas molecule, e.g., Cas9 molecule), and may take the following format (from 5′ to 3′):


Polynucleotide 1 (crRNA): [targeting domain]-[crRNA flagpole region]-[optional first flagpole extension]-[optional second flagpole extension]


Polynucleotide 2 (tracr): [optional first tracr extension]-[tracr flagpole region]-[tracr nuclease binding domain]


In embodiments, the tracr nuclease binding domain binds to a Cas protein, e.g., a Cas9 protein.


In some aspects, the targeting domain comprises or consists of a targeting domain sequence described herein, e.g., a targeting domain described in Table 1, 2, 3, 4, 5, or 6, or a targeting domain comprising or consisting of 17, 18, 19, 20, 21, 22, 23, 24, or 25 (preferably 20) consecutive nucleotides of a targeting domain sequence described in Table 1, 2, 3, 4, 5, or 6.


In some aspects, the flagpole, e.g., the crRNA flagpole region, comprises, from 5′ to 3′: GUUUUAGAGCUA (SEQ ID NO: 6584).


In some aspects, the flagpole, e.g., the crRNA flagpole region, comprises, from 5′ to 3′: GUUUAAGAGCUA (SEQ ID NO: 6585).


In some aspects the loop comprises, from 5′ to 3′: GAAA (SEQ ID NO: 6588).


In some aspects the tracr comprises, from 5′ to 3′: UAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGG UGC (SEQ ID NO: 6589) and is preferably used in a gRNA molecule comprising SEQ ID NO 6584.


In some aspects the tracr comprises, from 5′ to 3′: UAGCAAGUUUAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGG UGC (SEQ ID NO: 6590) and is preferably used in a gRNA molecule comprising SEQ ID NO 6585.


In some aspects, the gRNA may also comprise, at the 3′ end, additional U nucleic acids. For example the gRNA may comprise an additional 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 U nucleic acids at the 3′ end. In an embodiment, the gRNA comprises an additional 4 U nucleic acids at the 3′ end. In the case of dgRNA, one or more of the polynucleotides of the dgRNA (e.g., the polynucleotide comprising the targeting domain and the polynucleotide comprising the tracr) may comprise, at the 3′ end, additional U nucleic acids. For example, the case of dgRNA, one or more of the polynucleotides of the dgRNA (e.g., the polynucleotide comprising the targeting domain and the polynucleotide comprising the tracr) may comprise an additional 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 U nucleic acids at the 3′ end. In an embodiment, in the case of dgRNA, one or more of the polynucleotides of the dgRNA (e.g., the polynucleotide comprising the targeting domain and the polynucleotide comprising the tracr) comprises an additional 4 U nucleic acids at the 3′ end. In an embodiment of a dgRNA, only the polynucleotide comprising the tracr comprises the additional U nucleic acid(s), e.g., 4 U nucleic acids. In an embodiment of a dgRNA, only the polynucleotide comprising the targeting domain comprises the additional U nucleic acid(s). In an embodiment of a dgRNA, both the polynucleotide comprising the targeting domain and the polynucleotide comprising the tracr comprise the additional U nucleic acids, e.g., 4 U nucleic acids.


In some aspects, the gRNA may also comprise, at the 3′ end, additional A nucleic acids. For example the gRNA may comprise an additional 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 A nucleic acids at the 3′ end. In an embodiment, the gRNA comprises an additional 4 A nucleic acids at the 3′ end. In the case of dgRNA, one or more of the polynucleotides of the dgRNA (e.g., the polynucleotide comprising the targeting domain and the polynucleotide comprising the tracr) may comprise, at the 3′ end, additional A nucleic acids. For example, the case of dgRNA, one or more of the polynucleotides of the dgRNA (e.g., the polynucleotide comprising the targeting domain and the polynucleotide comprising the tracr) may comprise an additional 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 A nucleic acids at the 3′ end. In an embodiment, in the case of dgRNA, one or more of the polynucleotides of the dgRNA (e.g., the polynucleotide comprising the targeting domain and the polynucleotide comprising the tracr) comprises an additional 4 A nucleic acids at the 3′ end. In an embodiment of a dgRNA, only the polynucleotide comprising the tracr comprises the additional A nucleic acid(s), e.g., 4 A nucleic acids. In an embodiment of a dgRNA, only the polynucleotide comprising the targeting domain comprises the additional A nucleic acid(s). In an embodiment of a dgRNA, both the polynucleotide comprising the targeting domain and the polynucleotide comprising the tracr comprise the additional U nucleic acids, e.g., 4 A nucleic acids.


In embodiments, one or more of the polynucleotides of the gRNA molecule may comprise a cap at the 5′ end.


In an embodiment, a unimolecular, or sgRNA comprises, preferably from 5′ to 3′: a crRNA (which contains a targeting domain complementary to a target sequence; a crRNA flagpole region; first flagpole extension; a loop; a first tracr extension (which contains a domain complementary to at least a portion of the first flagpole extension); and a tracr (which contains a domain complementary to the crRNA flagpole region, and a domain which additionally binds a Cas9 molecule). In some aspects, the targeting domain comprises a targeting domain sequence described herein, e.g., a targeting domain described in Table 1, 2, 3, 4, 5, or 6, or a targeting domain comprising or consisting of 17, 18, 19, 20, 21, 22, 23, 24, or 25 (preferably 20) consecutive nucleotides of a targeting domain sequence described in Table 1, 2, 3, 4, 5, or 6, for example the 3′ 17, 18, 19, 20, 21, 22, 23, 24 or 25 (preferably 20) consecutive nucleotides of a targeting domain sequence described in Table 1, 2, 3, 4, 5, or 6.


In aspects comprising a first flagpole extension and/or a first tracr extension, the flagpole, loop and tracr sequences may be as described above. In general any first flagpole extension and first tracr extension may be employed, provided that they are complementary. In embodiments, the first flagpole extension and first tracr extension consist of 3, 4, 5, 6, 7, 8, 9, 10 or more complementary nucleotides.


In some aspects, the first flagpole extension comprises, from 5′ to 3′: UGCUG (SEQ ID NO: 6586). In some aspects, the first flagpole extension consists of SEQ ID NO: 6586.


In some aspects, the first tracr extension comprises, from 5′ to 3′: CAGCA (SEQ ID NO: 6591). In some aspects, the first tracr extension consists of SEQ ID NO: 6591.


In an embodiment, a dgRNA comprises two nucleic acid molecules. In some aspects, the dgRNA comprises a first nucleic acid which contains, preferably from 5′ to 3′: a targeting domain complementary to a target sequence; a crRNA flagpole region; optionally a first flagpole extension; and, optionally, a second flagpole extension; and a second nucleic acid (which may be referred to herein as a tracr), and comprises at least a domain which binds a Cas molecule, e.g., a Cas9 molecule) comprising preferably from 5′ to 3′: optionally a first tracr extension; and a tracr (which contains a domain complementary to the crRNA flagpole region, and a domain which additionally binds a Cas, e.g., Cas9, molecule). The second nucleic acid may additionally comprise, at the 3′ end (e.g., 3′ to the tracr) additional U nucleic acids. For example the tracr may comprise an additional 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 U nucleic acids at the 3′ end (e.g., 3′ to the tracr). The second nucleic acid may additionally or alternately comprise, at the 3′ end (e.g., 3′ to the tracr) additional A nucleic acids. For example the tracr may comprise an additional 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 A nucleic acids at the 3′ end (e.g., 3′ to the tracr). In some aspects, the targeting domain comprises a targeting domain sequence described herein, e.g., a targeting domain described in Table 1, 2, 3, 4, 5, or 6, or a targeting domain comprising or consisting of 17, 18, 19, 20, 21, 22, 23, 24, or 25 (preferably 20) consecutive nucleotides of a targeting domain sequence described in Table 1, 2, 3, 4, 5, or 6.


In aspects involving a dgRNA, the crRNA flagpole region, optional first flagpole extension, optional first tracr extension and tracr sequences may be as described above.


In some aspects, the optional second flagpole extension comprises, from 5′ to 3′: UUUUG (SEQ ID NO: 6587).


In embodiments, the 3′ 1, 2, 3, 4, or 5 nucleotides, the 5′ 1, 2, 3, 4, or 5 nucleotides, or both the 3′ and 5′ 1, 2, 3, 4, or 5 nucleotides of the gRNA molecule (and in the case of a dgRNA molecule, the polynucleotide comprising the targeting domain and/or the polynucleotide comprising the tracr) are modified nucleic acids, as described more fully in section XIII, below.


The domains are discussed briefly below:


1) The Targeting Domain:

Guidance on the selection of targeting domains can be found, e.g., in Fu Y el al. NAT BIOTECHNOL 2014 (doi: 10.1038/nbt.2808) and Sternberg S H el al. NATURE 2014 (doi: 10.1038/nature13011).


The targeting domain comprises a nucleotide sequence that is complementary, e.g., at least 80, 85, 90, 95, or 99% complementary, e.g., fully complementary, to the target sequence on the target nucleic acid. The targeting domain is part of an RNA molecule and will therefore comprise the base uracil (U), while any DNA encoding the gRNA molecule will comprise the base thymine (T). While not wishing to be bound by theory, it is believed that the complementarity of the targeting domain with the target sequence contributes to specificity of the interaction of the gRNA molecule/Cas9 molecule complex with a target nucleic acid. It is understood that in a targeting domain and target sequence pair, the uracil bases in the targeting domain will pair with the adenine bases in the target sequence.


In an embodiment, the targeting domain is 5 to 50, e.g., 10 to 40, e.g., 10 to 30, e.g., 15 to 30, e.g., 15 to 25 nucleotides in length. In an embodiment, the targeting domain is 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 or 25 nucleotides in length. In an embodiment, the targeting domain is 16 nucleotides in length. In an embodiment, the targeting domain is 17 nucleotides in length. In an embodiment, the targeting domain is 18 nucleotides in length. In an embodiment, the targeting domain is 19 nucleotides in length. In an embodiment, the targeting domain is 20 nucleotides in length. In an embodiment, the targeting domain is 21 nucleotides in length. In an embodiment, the targeting domain is 22 nucleotides in length. In an embodiment, the targeting domain is 23 nucleotides in length. In an embodiment, the targeting domain is 24 nucleotides in length. In an embodiment, the targeting domain is 25 nucleotides in length. In embodiments, the aforementioned 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 nucleotides comprise the 5′-16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 nucleotides from a targeting domain described in Table 1, 2, 3, 4, 5, or 6. In embodiments, the aforementioned 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 nucleotides comprise the 3′-16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 nucleotides from a targeting domain described in Table 1, 2, 3, 4, 5, or 6.


Without being bound by theory, it is believed that the 8, 9, 10, 11 or 12 nucleic acids of the targeting domain disposed at the 3′ end of the targeting domain is important for targeting the target sequence, and may thus be referred to as the “core” region of the targeting domain. In an embodiment, the core domain is fully complementary with the target sequence.


The strand of the target nucleic acid with which the targeting domain is complementary is referred to herein as the target sequence. In some aspects, the target sequence is disposed on a chromosome, e.g., is a target within a gene. In some aspects the target sequence is disposed within an exon of a gene. In some aspects the target sequence is disposed within an intron of a gene. In some aspects, the target sequence comprises, or is proximal (e.g., within 10, 20, 30, 40, 50, 100, 200, 300, 400, 500, or 1000 nucleic acids) to a binding site of a regulatory element, e.g., a promoter or transcription factor binding site, of a gene of interest. Some or all of the nucleotides of the domain can have a modification, e.g., modification found in Section XIII herein.


2) crRNA Flagpole Region:


The flagpole contains portions from both the crRNA and the tracr. The crRNA flagpole region is complementary with a portion of the tracr, and in an embodiment, has sufficient complementarity to a portion of the tracr to form a duplexed region under at least some physiological conditions, for example, normal physiological conditions. In an embodiment, the crRNA flagpole region is 5 to 30 nucleotides in length. In an embodiment, the crRNA flagpole region is 5 to 25 nucleotides in length. The crRNA flagpole region can share homology with, or be derived from, a naturally occurring portion of the repeat sequence from a bacterial CRISPR array. In an embodiment, it has at least 50% homology with a crRNA flagpole region disclosed herein, e.g., an S. pyogenes, or S. thermophilus, crRNA flagpole region.


In an embodiment, the flagpole, e.g., the crRNA flagpole region, comprises SEQ ID NO: 6584. In an embodiment, the flagpole, e.g., the crRNA flagpole region, comprises sequence having at least 50%, 60%, 70%, 80%, 85%, 90%, 95% or 99% homology with SEQ ID NO: 6584. In an embodiment, the flagpole, e.g., the crRNA flagpole region, comprises at least 5, 6, 7, 8, 9, 10, or 11 nucleotides of SEQ ID NO: 6584. In an embodiment, the flagpole, e.g., the crRNA flagpole region, comprises SEQ ID NO: 6585. In an embodiment, the flagpole comprises sequence having at least 50%, 60%, 70%, 80%, 85%, 90%, 95% or 99% homology with SEQ ID NO: 6585. In an embodiment, the flagpole, e.g., the crRNA flagpole region, comprises at least 5, 6, 7, 8, 9, 10, or 11 nucleotides of SEQ ID NO: 6585.


Some or all of the nucleotides of the domain can have a modification, e.g., modification described in Section XIII herein.


3) First Flagpole Extension

When a tracr comprising a first tracr extension is used, the crRNA may comprise a first flagpole extension. In general any first flagpole extension and first tracr extension may be employed, provided that they are complementary. In embodiments, the first flagpole extension and first tracr extension consist of 3, 4, 5, 6, 7, 8, 9, 10 or more complementary nucleotides.


The first flagpole extension may comprise nucleotides that are complementary, e.g., 80%, 85%, 90%, 95% or 99%, e.g., fully complementary, with nucleotides of the first tracr extension. In some aspects, the first flagpole extension nucleotides that hybridize with complementary nucleotides of the first tracr extension are contiguous. In some aspects, the first flagpole extension nucleotides that hybridize with complementary nucleotides of the first tracr extension are discontinuous, e.g., comprises two or more regions of hybridization separated by nucleotides that do not base pair with nucleotides of the first tracr extension. In some aspects, the first flagpole extension comprises at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more nucleotides. In some aspects, the first flagpole extension comprises, from 5′ to 3′: UGCUG (SEQ ID NO: 6586). In some aspects, the first flagpole extension consists of SEQ ID NO: 6586. In some aspects the first flagpole extension comprises nucleic acid that is at least 80%, 85%, 90%, 95% or 99% homology to SEQ ID NO: 6586.


Some or all of the nucleotides of the first tracr extension can have a modification, e.g., modification found in Section XIII herein.


3) The Loop

A loop serves to link the crRNA flagpole region (or optionally the first flagpole extension, when present) with the tracr (or optionally the first tracr extension, when present) of a sgRNA. The loop can link the crRNA flagpole region and tracr covalently or non-covalently. In an embodiment, the linkage is covalent. In an embodiment, the loop covalently couples the crRNA flagpole region and tracr. In an embodiment, the loop covalently couples the first flagpole extension and the first tracr extension. In an embodiment, the loop is, or comprises, a covalent bond interposed between the crRNA flagpole region and the domain of the tracr which hybridizes to the crRNA flagpole region. Typically, the loop comprises one or more, e.g., 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides.


In dgRNA molecules the two molecules can be associated by virtue of the hybridization between at least a portion of the crRNA (e.g., the crRNA flagpole region) and at least a portion of the tracr (e.g., the domain of the tracr which is complementary to the crRNA flagpole region).


A wide variety of loops are suitable for use in sgRNAs. Loops can consist of a covalent bond, or be as short as one or a few nucleotides, e.g., 1, 2, 3, 4, or 5 nucleotides in length. In an embodiment, a loop is 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 or more nucleotides in length. In an embodiment, a loop is 2 to 50, 2 to 40, 2 to 30, 2 to 20, 2 to 10, or 2 to 5 nucleotides in length. In an embodiment, a loop shares homology with, or is derived from, a naturally occurring sequence. In an embodiment, the loop has at least 50% homology with a loop disclosed herein. In an embodiment, the loop comprises SEQ ID NO: 6588.


Some or all of the nucleotides of the domain can have a modification, e.g., modification described in Section XIII herein.


4) The Second Flagpole Extension

In an embodiment, a dgRNA can comprise additional sequence, 3′ to the crRNA flagpole region or, when present, the first flagpole extension, referred to herein as the second flagpole extension. In an embodiment, the second flagpole extension is, 2-10, 2-9, 2-8, 2-7, 2-6, 2-5, or 2-4 nucleotides in length. In an embodiment, the second flagpole extension is 2, 3, 4, 5, 6, 7, 8, 9, or 10 or more nucleotides in length. In an embodiment, the second flagpole extension comprises SEQ ID NO: 6587.


5) The Tracr:

The tracr is the nucleic acid sequence required for nuclease, e.g., Cas9, binding. Without being bound by theory, it is believed that each Cas9 species is associated with a particular tracr sequence. Tracr sequences are utilized in both sgRNA and in dgRNA systems. In an embodiment, the tracr comprises sequence from, or derived from, an S. pyogenes tracr. In some aspects, the tracr has a portion that hybridizes to the flagpole portion of the crRNA, e.g., has sufficient complementarity to the crRNA flagpole region to form a duplexed region under at least some physiological conditions (sometimes referred to herein as the tracr flagpole region or a tracr domain complementary to the crRNA flagpole region). In embodiments, the domain of the tracr that hybridizes with the crRNA flagpole region comprises at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 nucleotides that hybridize with complementary nucleotides of the crRNA flagpole region. In some aspects, the tracr nucleotides that hybridize with complementary nucleotides of the crRNA flagpole region are contiguous. In some aspects, the tracr nucleotides that hybridize with complementary nucleotides of the crRNA flagpole region are discontinuous, e.g., comprises two or more regions of hybridization separated by nucleotides that do not base pair with nucleotides of the crRNA flagpole region. In some aspects, the portion of the tracr that hybridizes to the crRNA flagpole region comprises, from 5′ to 3′: UAGCAAGUUAAAA (SEQ ID NO: 6597). In some aspects, the portion of the tmcr that hybridizes to the crRNA flagpole regioncomprises, from 5′ to 3′: UAGCAAGUUUAAA (SEQ ID NO: 6598). In embodiments, the sequence that hybridizes with the crRNA flagpole region is disposed on the tracr 5′- to the sequence of the tracr that additionally binds a nuclease, e.g., a Cas molecule, e.g., a Cas9 molecule.


The tracr further comprises a domain that additionally binds to a nuclease, e.g., a Cas molecule, e.g., a Cas9 molecule. Without being bound by theory, it is believed that Cas9 from different species bind to different tracr sequences. In some aspects, the tracr comprises sequence that binds to a S. pyogenes Cas9 molecule. In some aspects, the tracr comprises sequence that binds to a Cas9 molecule disclosed herein. In some aspects, the domain that additionally binds a Cas9 molecule comprises, from 5′ to 3′: UAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGC (SEQ ID NO: 6599). In some aspects the domain that additionally binds a Cas9 molecule comprises, from 5′ to 3′: UAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUU (SEQ ID NO: 6600).


In some embodiments, the tracr comprises SEQ ID NO: 6589. In some embodiments, the tracr comprises SEQ ID NO: 6590.


Some or all of the nucleotides of the tracr can have a modification, e.g., modification found in Section XIII herein. In embodiments, the gRNA (e.g., the sgRNA or the tracr and/or crRNA of a dgRNA), e.g., any of the gRNA or gRNA components described above, comprises an inverted abasic residue at the 5′ end, the 3′ end or both the 5′ and 3′ end of the gRNA. In embodiments, the gRNA (e.g., the sgRNA or the tracr and/or crRNA of a dgRNA), e.g., any of the gRNA or gRNA components described above, comprises one or more phosphorothioate bonds between residues at the 5′ end of the polynucleotide, for example, a phosphrothioate bond between the first two 5′ residues, between each of the first three 5′ residues, between each of the first four 5′ residues, or between each of the first five 5′ residues. In embodiments, the gRNA or gRNA component may alternatively or additionally comprise one or more phosphorothioate bonds between residues at the 3′ end of the polynucleotide, for example, a phosphrothioate bond between the first two 3′ residues, between each of the first three 3′ residues, between each of the first four 3′ residues, or between each of the first five 3′ residues. In an embodiment, the gRNA (e.g., the sgRNA or the tracr and/or crRNA of a dgRNA), e.g., any of the gRNA or gRNA components described above, comprises a phosphorothioate bond between each of the first four 5′ residues (e.g., comprises, e.g., consists of, three phosphorothioate bonds at the 5′ end(s)), and a phosphorothioate bond between each of the first four 3′ residues (e.g., comprises, e.g., consists of, three phosphorothioate bonds at the 3′ end(s)). In an embodiment, any of the phosphorothioate modifications described above are combined with an inverted abasic residue at the 5′ end, the 3′ end, or both the 5′ and 3′ ends of the polynucleotide. In such embodiments, the inverted abasic nucleotide may be linked to the 5′ and/or 3′ nucleotide by a phosphate bond or a phosphorothioate bond. In embodiments, the gRNA (e.g., the sgRNA or the tracr and/or crRNA of a dgRNA), e.g., any of the gRNA or gRNA components described above, comprises one or more nucleotides that include a 2′ O-methyl modification. In embodiments, each of the first 1, 2, 3, or more of the 5′ residues comprise a 2′ O-methyl modification. In embodiments, each of the first 1, 2, 3, or more of the 3′ residues comprise a 2′ O-methyl modification. In embodiments, the 4th-to-terminal, 3rd-to-terminal, and 2nd-to-terminal 3′ residues comprise a 2′ O-methyl modification. In embodiments, each of the first 1, 2, 3 or more of the 5′ residues comprise a 2′ O-methyl modification, and each of the first 1, 2, 3 or more of the 3′ residues comprise a 2′ O-methyl modification. In an embodiment, each of the first 3 of the 5′ residues comprise a 2′ O-methyl modification, and each of the first 3 of the 3′ residues comprise a 2′ O-methyl modification. In embodiments, each of the first 3 of the 5′ residues comprise a 2′ O-methyl modification, and the 4th-to-terminal, 3rd-to-terminal, and 2nd-to-terminal 3′ residues comprise a 2′ O-methyl modification. In embodiments, any of the 2′ O-methyl modifications, e.g., as described above, may be combined with one or more phosphorothioate modifications, e.g., as described above, and/or one or more inverted abasic modifications, e.g., as described above. In an embodiment, the gRNA (e.g., the sgRNA or the tracr and/or crRNA of a dgRNA), e.g., any of the gRNA or gRNA components described above, comprises, e.g., consists of, a phosphorothioate bond between each of the first four 5′ residues (e.g., comprises, e.g., consists of three phosphorothioate bonds at the 5′ end of the polynucleotide(s)), a phosphorothioate bond between each of the first four 3′ residues (e.g., comprises, e.g., consists of three phosphorothioate bonds at the 5′ end of the polynucleotide(s)), a 2′ O-methyl modification at each of the first three 5′ residues, and a 2′ O-methyl modification at each of the first three 3′ residues. In an embodiment, the gRNA (e.g., the sgRNA or the tracr and/or crRNA of a dgRNA), e.g., any of the gRNA or gRNA components described above, comprises, e.g., consists of, a phosphorothioate bond between each of the first four 5′ residues (e.g., comprises, e.g., consists of three phosphorothioate bonds at the 5′ end of the polynucleotide(s)), a phosphorothioate bond between each of the first four 3′ residues (e.g., comprises, e.g., consists of three phosphorothioate bonds at the 5′ end of the polynucleotide(s)), a 2′ O-methyl modification at each of the first three 5′ residues, and a 2′ O-methyl modification at each of the 4th-to-terminal, 3rd-to-terminal, and 2nd-to-terminal 3′ residues.


In an embodiment, the gRNA (e.g., the sgRNA or the tracr and/or crRNA of a dgRNA), e.g., any of the gRNA or gRNA components described above, comprises, e.g., consists of, a phosphorothioate bond between each of the first four 5′ residues (e.g., comprises, e.g., consists of three phosphorothioate bonds at the 5′ end of the polynucleotide(s)), a phosphorothioate bond between each of the first four 3′ residues (e.g., comprises, e.g., consists of three phosphorothioate bonds at the 5′ end of the polynucleotide(s)), a 2′ O-methyl modification at each of the first three 5′ residues, a 2′ O-methyl modification at each of the first three 3′ residues, and an additional inverted abasic residue at each of the 5′ and 3′ ends.


In an embodiment, the gRNA (e.g., the sgRNA or the tracr and/or crRNA of a dgRNA), e.g., any of the gRNA or gRNA components described above, comprises, e.g., consists of, a phosphorothioate bond between each of the first four 5′ residues (e.g., comprises, e.g., consists of three phosphorothioate bonds at the 5′ end of the polynucleotide(s)), a phosphorothioate bond between each of the first four 3′ residues (e.g., comprises, e.g., consists of three phosphorothioate bonds at the 5′ end of the polynucleotide(s)), a 2′ O-methyl modification at each of the first three 5′ residues, and a 2′ O-methyl modification at each of the 4th-to-terminal, 3rd-to-terminal, and 2nd-to-terminal 3′ residues, and an additional inverted abasic residue at each of the 5′ and 3′ ends.


In an embodiment, the gRNA is a dgRNA and comprises, e.g., consists of:


crRNA:


mN*mN*mN*NNNNNNNNNNNNNNNNNGUUUUAGAGCUAU*mG*mC*mU, where m indicates a base with 2′O-Methyl modification, * indicates a phosphorothioate bond, and N's indicate the residues of the targeting domain, e.g., as described herein, (optionally with an inverted abasic residue at the 5′ and/or 3′ terminus); and


tracr:


AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACC GAGUCGGUGCUUUUUUU (SEQ ID NO: 6660) (optionally with an inverted abasic residue at the 5′ and/or 3′ terminus).


In an embodiment, the gRNA is a dgRNA and comprises, e.g., consists of:


crRNA:


mN*mN*mN*NNNNNNNNNNNNNNNNNGUUUUAGAGCUAU*mG*mC*mU, where m indicates a base with 2′O-Methyl modification, * indicates a phosphorothioate bond, and N's indicate the residues of the targeting domain, e.g., as described herein, (optionally with an inverted abasic residue at the 5′ and/or 3′ terminus); and


tracr:


mA*mA*mC*AGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUG GCACCGAGUCGGUGCUUUU*mU*mU*mU (SEQ ID NO: 346), where m indicates a base with 2′O-Methyl modification, * indicates a phosphorothioate bond, and N's indicate the residues of the targeting domain, e.g., as described herein, (optionally with an inverted abasic residue at the 5′ and/or 3′ terminus).


In an embodiment, the gRNA is a dgRNA and comprises, e.g., consists of:


crRNA:


mN*mN*mN*NNNNNNNNNNNNNNNNNGUUUUAGAGCUAUGCUGUU*mU*mU*mG, where m indicates a base with 2′O-Methyl modification, * indicates a phosphorothioate bond, and N's indicate the residues of the targeting domain, e.g., as described herein, (optionally with an inverted abasic residue at the 5′ and/or 3′ terminus); and


tracr:


AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACC GAGUCGGUGCUUUUUUU (SEQ ID NO: 6660) (optionally with an inverted abasic residue at the 5′ and/or 3′ terminus).


In an embodiment, the gRNA is a dgRNA and comprises, e.g., consists of:


crRNA:


mN*mN*mN*NNNNNNNNNNNNNNNNNGUUUUAGAGCUAUGCUGUU*mU*mU*mG, where m indicates a base with 2′O-Methyl modification, * indicates a phosphorothioate bond, and N's indicate the residues of the targeting domain, e.g., as described herein, (optionally with an inverted abasic residue at the 5′ and/or 3′ terminus); and


tracr:


mA*mA*mC*AGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUG GCACCGAGUCGGUGCUUUU*mU*mU*mU (SEQ ID NO: 346), where m indicates a base with 2′O-Methyl modification, and * indicates a phosphorothioate bond (optionally with an inverted abasic residue at the 5′ and/or 3′ terminus).


In an embodiment, the gRNA is a dgRNA and comprises, e.g., consists of:


crRNA:


NNNNNNNNNNNNNNNNNNNNGUUUUAGAGCUAUGCUGUUUUG, where N's indicate the residues of the targeting domain, e.g., as described herein, (optionally with an inverted abasic residue at the 5′ and/or 3′ terminus); and


tracr:


mA*mA*mC*AGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUG GCACCGAGUCGGUGCUUUU*mU*mU*mU (SEQ ID NO: 346), where m indicates a base with 20-Methyl modification, and * indicates a phosphorothioate bond (optionally with an inverted abasic residue at the 5′ and/or 3′ terminus).


In an embodiment, the gRNA is a sgRNA and comprises, e.g., consists of:


NNNNNNNNNNNNNNNNNNNNGUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUA GUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUU, where m indicates a base with 2′O-Methyl modification, * indicates a phosphorothioate bond, and N's indicate the residues of the targeting domain, e.g., as described herein, (optionally with an inverted abasic residue at the 5′ and/or 3′ terminus).


In an embodiment, the gRNA is a sgRNA and comprises, e.g., consists of:


mN*mN*mN*NNNNNNNNNNNNNNNNNGUUUUAGAGCUAGAAAUAGCAAGUUAAAAUA AGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCU*mU*mU*mU, where m indicates a base with 2′O-Methyl modification, * indicates a phosphorothioate bond, and N's indicate the residues of the targeting domain, e.g., as described herein, (optionally with an inverted abasic residue at the 5′ and/or 3′ terminus).


In an embodiment, the gRNA is a sgRNA and comprises, e.g., consists of:


mN*mN*mN*NNNNNNNNNNNNNNNNNGUUUUAGAGCUAGAAAUAGCAAGUUAAAAUA AGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCmU*mU*mU*U, where m indicates a base with 2′O-Methyl modification, * indicates a phosphorothioate bond, and N's indicate the residues of the targeting domain, e.g., as described herein, (optionally with an inverted abasic residue at the 5′ and/or 3′ terminus).


6) First Tracr Extension

Where the gRNA comprises a first flagpole extension, the tracr may comprise a first tracr extension. The first tracr extension may comprise nucleotides that are complementary, e.g., 80%, 85%, 90%, 95% or 99%, e.g., fully complementary, with nucleotides of the first flagpole extension. In some aspects, the first tracr extension nucleotides that hybridize with complementary nucleotides of the first flagpole extension are contiguous. In some aspects, the first tracr extension nucleotides that hybridize with complementary nucleotides of the first flagpole extension are discontinuous, e.g., comprises two or more regions of hybridization separated by nucleotides that do not base pair with nucleotides of the first flagpole extension. In some aspects, the first tracr extension comprises at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more nucleotides. In some aspects, the first tracr extension comprises SEQ ID NO: 6591. In some aspects the first tracr extension comprises nucleic acid that is at least 80%, 85%, 90%, 95% or 99% homology to SEQ ID NO: 6591.


Some or all of the nucleotides of the first tracr extension can have a modification, e.g., modification found in Section XIII herein.


In some embodiments, the sgRNA may comprise, from 5′ to 3′, disposed 3′ to the targeting domain:









a)







(SEQ ID NO: 6601)







GUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAAC





UUGAAAAAGUGGCACCGAGUCGGUGC;





b)







(SEQ ID NO: 6602)







GUUUAAGAGCUAGAAAUAGCAAGUUUAAAUAAGGCUAGUCCGUUAUCAAC





UUGAAAAAGUGGCACCGAGUCGGUGC;





c)







(SEQ ID NO: 6603)







GUUUUAGAGCUAUGCUGGAAACAGCAUAGCAAGUUAAAAUAAGGCUAGUC





CGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGC;





d)







(SEQ ID NO: 6604)







GUUUAAGAGCUAUGCUGGAAACAGCAUAGCAAGUUUAAAUAAGGCUAGUC





CGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGC;







e) any of a) to d), above, further comprising, at the 3′ end, at least 1, 2, 3, 4, 5, 6 or 7 uracil (U) nucleotides, e.g., 1, 2, 3, 4, 5, 6, or 7 uracil (U) nucleotides;


f) any of a) to d), above, further comprising, at the 3′ end, at least 1, 2, 3, 4, 5, 6 or 7 adenine (A) nucleotides, e.g., 1, 2, 3, 4, 5, 6, or 7 adenine (A) nucleotides; or


g) any of a) to f), above, further comprising, at the 5′ end (e.g., at the 5′ terminus, e.g., 5′ to the targeting domain), at least 1, 2, 3, 4, 5, 6 or 7 adenine (A) nucleotides, e.g., 1, 2, 3, 4, 5, 6, or 7 adenine (A) nucleotides. In embodiments, any of a) to g) above is disposed directly 3′ to the targeting domain.


In an embodiment, a sgRNA of the invention comprises, e.g., consists of, from 5′ to 3′: [targeting domain]-









(SEQ ID NO: 7811)







GUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAAC





UUGAAAAAGUGGCACCGAGUCGGUGCUUUU.






In an embodiment, a sgRNA of the invention comprises, e.g., consists of, from 5′ to 3′: [targeting domain]-









(SEQ ID NO: 7807)







GUUUAAGAGCUAUGCUGGAAACAGCAUAGCAAGUUUAAAUAAGGCUAGUC





CGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUU.






In some embodiments, the dgRNA may comprise:


A crRNA comprising, from 5′ to 3′, preferrably disposed directly 3′ to the targeting domain:











a)







(SEQ ID NO: 6584)









GUUUUAGAGCUA;







b)







(SEQ ID NO: 6585)









GUUUAAGAGCUA;







c)







(SEQ ID NO: 6605)









GUUUUAGAGCUAUGCUG;







d)







(SEQ ID NO: 6606)









GUUUAAGAGCUAUGCUG;







e)







(SEQ ID NO: 6607)









GUUUUAGAGCUAUGCUGUUUUG;







f)







(SEQ ID NO: 6608)









GUUUAAGAGCUAUGCUGUUUUG;



or







g)







(SEQ ID NO: 7806)









GUUUUAGAGCUAUGCU:







and a tracr comprising, from 5′ to 3′:









a)







(SEQ ID NO: 6589)







UAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACC





GAGUCGGUGC;





b)







(SEQ ID NO: 6590)







UAGCAAGUUUAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACC





GAGUCGGUGC;





c)







(SEQ ID NO: 6609)







CAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUG





GCACCGAGUCGGUGC;





d)







(SEQ ID NO: 6610)







CAGCAUAGCAAGUUUAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUG





GCACCGAGUCGGUGC;





e)







(SEQ ID NO: 6660)







AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG





UGGCACCGAGUCGGUGCUUUUUUU;





f)







(SEQ ID NO: 6661)







AACAGCAUAGCAAGUUUAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG





UGGCACCGAGUCGGUGCUUUUUUU;





g)







(SEQ ID NO: 7812)







AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG





UGGCACCGAGUCGGUGC





h)







(SEQ ID NO: 7807)







GUUUAAGAGCUAUGCUGGAAACAGCAUAGCAAGUUUAAAUAAGGCUAGUC





CGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUU;





i)







(SEQ ID NO: 7808)







AGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGG





CACCGAGUCGGUGCUUU;





j)







(SEQ ID NO: 7809)







GUUGGAACCAUUCAAAACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUU





AUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUU;







k) any of a) to j), above, further comprising, at the 3′ end, at least 1, 2, 3, 4, 5, 6 or 7 uracil (U) nucleotides, e.g., 1, 2, 3, 4, 5, 6, or 7 uracil (U) nucleotides;


l) any of a) to j), above, further comprising, at the 3′ end, at least 1, 2, 3, 4, 5, 6 or 7 adenine (A) nucleotides, e.g., 1, 2, 3, 4, 5, 6, or 7 adenine (A) nucleotides; or


m) any of a) to l), above, further comprising, at the 5′ end (e.g., at the 5′ terminus), at least 1, 2, 3, 4, 5, 6 or 7 adenine (A) nucleotides, e.g., 1, 2, 3, 4, 5, 6, or 7 adenine (A) nucleotides.


In an embodiment, the sequence of k), above comprises the 3′ sequence UUUUUU, e.g., if a U6 promoter is used for transcription. In an embodiment, the sequence of k), above, comprises the 3′ sequence UUUU, e.g., if an HI promoter is used for transcription. In an embodiment, sequence of k), above, comprises variable numbers of 3′ U's depending, e.g., on the termination signal of the pol-III promoter used. In an embodiment, the sequence of k), above, comprises variable 3′ sequence derived from the DNA template if a T7 promoter is used. In an embodiment, the sequence of k), above, comprises variable 3′ sequence derived from the DNA template, e.g., if in vitro transcription is used to generate the RNA molecule. In an embodiment, the sequence of k), above, comprises variable 3′ sequence derived from the DNA template, e.g, if a pol-II promoter is used to drive transcription.


In an embodiment, the crRNA comprises, e.g., consists of, a targeting domain and, disposed 3′ to the targeting domain (e.g., disposed directly 3′ to the targeting domain), a sequence comprising, e.g., consisting of, SEQ ID NO: 6607, and the tracr comprises, e.g., consists of









(SEQ ID NO: 6660)







AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG





UGGCACCGAGUCGGUGCUUUUUUU.






In an embodiment, the crRNA comprises, e.g., consists of, a targeting domain and, disposed 3′ to the targeting domain (e.g., disposed directly 3′ to the targeting domain), a sequence comprising, e.g., consisting of, SEQ ID NO: 6608, and the tracr comprises, e.g., consists of,









(SEQ ID NO: 6661)







AACAGCAUAGCAAGUUUAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG





UGGCACCGAGUCGGUGCUUUUUUU.






In an embodiment, the crRNA comprises, e.g., consists of, a targeting domain and, disposed 3′ to the targeting domain (e.g., disposed directly 3′ to the targeting domain), a sequence comprising, e.g., consisting of, GUUUUAGAGCUAUGCU (SEQ ID NO: 7806), and the tracr comprises, e.g., consists of,









(SEQ ID NO: 7807)







GUUUAAGAGCUAUGCUGGAAACAGCAUAGCAAGUUUAAAUAAGGCUAGUC





CGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUU.






In an embodiment, the crRNA comprises, e.g., consists of, a targeting domain and, disposed 3′ to the targeting domain (e.g., disposed directly 3′ to the targeting domain), a sequence comprising, e.g., consisting of, GUUUUAGAGCUAUGCU (SEQ ID NO: 7806), and the tracr comprises, e.g., consists of,









(SEQ ID NO: 7808)







AGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGG





CACCGAGUCGGUGCUUU.






In an embodiment, the crRNA comprises, e.g., consists of, a targeting domain and, disposed 3′ to the targeting domain (e.g., disposed directly 3′ to the targeting domain), a sequence comprising, e.g., consisting of, GUUUUAGAGCUAUGCUGUUUUG (SEQ ID NO: 6607), and the tracr comprises, e.g., consists of,









(SEQ ID NO: 7809)







GUUGGAACCAUUCAAAACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUU





AUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUU.






II. Targeting Domains Useful for Altering Expression of Globin Genes

Provided in the tables below are targeting domains for gRNA molecules for use in the various aspect of the present invention, for example, in altering expression of globin genes, for example, a fetal hemoglobin gene or a hemoglobin beta gene.









TABLE 1







gRNA targeting domains directed to BLC11a exon regions



















SEQ




Target

Targeting Site

ID


Id.
Target
Region
Strand
(hg38)
gRNA Targeting Domain
NO:
















53335_5_1
BCL11a
Exon 5
+
chr2: 60451170-60451195
CAGUCAUUAUUUAUUAUGA
400







AUAAGC





53335_5_2
BCL11a
Exon 5
+
chr2: 60451196-60451221
GGAAAUAAUUCACAUGCCA
401







AUUAUU





53335_5_3
BCL11a
Exon 5
+
chr2: 60451217-60451242
UAUUUGGCUAUCUUUUCAC
402







UAAGCU





53335_5_4
BCL11a
Exon 5
+
chr2: 60451233-60451258
CACUAAGCUAGGUAAUCUA
403







GCCAGA





53335_5_5
BCL11a
Exon 5
+
chr2: 60451236-60451261
UAAGCUAGGUAAUCUAGCC
404







AGAAGG





53335_5_6
BCL11a
Exon 5
+
chr2: 60451241-60451266
UAGGUAAUCUAGCCAGAAG
405







GUGGAU





53335_5_7
BCL11a
Exon 5
+
chr2: 60451245-60451270
UAAUCUAGCCAGAAGGUGG
406







AUAGGU





53335_5_8
BCL11a
Exon 5
+
chr2: 60451261-60451286
UGGAUAGGUAGGAUUUUCC
407







CCACUU





53335_5_9
BCL11a
Exon 5
+
chr2: 60451268-60451293
GUAGGAUUUUCCCCACUUA
408







GGUUCA





53335_5_10
BCL11a
Exon 5
+
chr2: 60451295-60451320
GCCUGUAUGUGAAUCUACA
409







GCACAC





53335_5_11
BCL11a
Exon 5
+
chr2: 60451359-60451384
UGCUAUGUUGUUUCUAAUU
410







CUCUUC





53335_5_12
BCL11a
Exon 5
+
chr2: 60451414-60451439
UGAGAAAAGUUCUGUGCAA
411







AUUAAC





53335_5_13
BCL11a
Exon 5
+
chr2: 60451415-60451440
GAGAAAAGUUCUGUGCAAA
412







UUAACU





53335_5_14
BCL11a
Exon 5
+
chr2: 60451462-60451487
CCUGUUUGUAGAUGUAACU
413







UAUUUG





53335_5_15
BCL11a
Exon 5
+
chr2: 60451477-60451502
AACUUAUUUGUGGCACUAA
414







UUUCUA





53335_5_16
BCL11a
Exon 5
+
chr2: 60451625-60451650
GUCUGCAUUAAGAUAUAUU
415







UCCUGA





53335_5_17
BCL11a
Exon 5
+
chr2: 60451630-60451655
CAUUAAGAUAUAUUUCCUG
416







AAGGUU





53335_5_18
BCL11a
Exon 5
+
chr2: 60451631-60451656
AUUAAGAUAUAUUUCCUGA
417







AGGUUU





53335_5_19
BCL11a
Exon 5
+
chr2: 60451687-60451712
ACUACUGACAUUUAUCACC
418







UUCUUU





53335_5_20
BCL11a
Exon 5
+
chr2: 60451754-60451779
UUAAAAGACAAAUUCAAAU
419







CCUGCA





53335_5_21
BCL11a
Exon 5
+
chr2: 60451786-60451811
CACCAAAAGCAUAUAUUUG
420







AAAAAC





53335_5_22
BCL11a
Exon 5
+
chr2: 60451792-60451817
AAGCAUAUAUUUGAAAAAC
421







AGGAUU





53335_5_23
BCL11a
Exon 5
+
chr2: 60451819-60451844
GCGUGCCAUAUUAUGCAUU
422







AUUUAA





53335_5_24
BCL11a
Exon 5
+
chr2: 60451847-60451872
UAUGCAAAUUAUAAGUCAG
423







ACAGUU





53335_5_25
BCL11a
Exon 5
+
chr2: 60451971-60451996
UUGAAAAUUUAUGCCAUCU
424







GAUAAG





53335_5_26
BCL11a
Exon 5
+
chr2: 60452037-60452062
AAAUCUGUUCCUCCUACCC
425







ACCCGA





53335_5_27
BCL11a
Exon 5
+
chr2: 60452038-60452063
AAUCUGUUCCUCCUACCCA
426







CCCGAU





53335_5_28
BCL11a
Exon 5
+
chr2: 60452048-60452073
UCCUACCCACCCGAUGGGU
427







GUCUGU





53335_5_29
BCL11a
Exon 5
+
chr2: 60452055-60452080
CACCCGAUGGGUGUCUGUA
428







GGAAAC





53335_5_30
BCL11a
Exon 5
+
chr2: 60452203-60452228
AGACAACAUAGAAUGUAUA
429







GAAACA





53335_5_31
BCL11a
Exon 5
+
chr2: 60452204-60452229
GACAACAUAGAAUGUAUAG
430







AAACAA





53335_5_32
BCL11a
Exon 5
+
chr2: 60452205-60452230
ACAACAUAGAAUGUAUAGA
431







AACAAG





53335_5_33
BCL11a
Exon 5
+
chr2: 60452209-60452234
CAUAGAAUGUAUAGAAACA
432







AGGGGU





53335_5_34
BCL11a
Exon 5
+
chr2: 60452210-60452235
AUAGAAUGUAUAGAAACAA
433







GGGGUU





53335_5_35
BCL11a
Exon 5
+
chr2: 60452211-60452236
UAGAAUGUAUAGAAACAAG
434







GGGUUG





53335_5_36
BCL11a
Exon 5
+
chr2: 60452237-60452262
GGACUCAUGCGCAUUUCCA
435







CAAUAC





53335_5_37
BCL11a
Exon 5
+
chr2: 60452245-60452270
GCGCAUUUCCACAAUACAG
436







GUAAUU





53335_5_38
BCL11a
Exon 5
+
chr2: 60452249-60452274
AUUUCCACAAUACAGGUAA
437







UUAGGU





53335_5_39
BCL11a
Exon 5
+
chr2: 60452253-60452278
CCACAAUACAGGUAAUUAG
438







GUUGGC





53335_5_40
BCL11a
Exon 5
+
chr2: 60452263-60452288
GGUAAUUAGGUUGGCUGGU
439







UUCAGA





53335_5_41
BCL11a
Exon 5
+
chr2: 60452264-60452289
GUAAUUAGGUUGGCUGGUU
440







UCAGAA





53335_5_42
BCL11a
Exon 5
+
chr2: 60452269-60452294
UAGGUUGGCUGGUUUCAGA
441







AGGGCC





53335_5_43
BCL11a
Exon 5
+
chr2: 60452270-60452295
AGGUUGGCUGGUUUCAGAA
442







GGGCCA





53335_5_44
BCL11a
Exon 5
+
chr2: 60452291-60452316
GCCAGGGCAUCACUCAUGA
443







CAGCGA





53335_5_45
BCL11a
Exon 5
+
chr2: 60452298-60452323
CAUCACUCAUGACAGCGAU
444







GGUCCA





53335_5_46
BCL11a
Exon 5
+
chr2: 60452299-60452324
AUCACUCAUGACAGCGAUG
445







GUCCAC





53335_5_47
BCL11a
Exon 5
+
chr2: 60452311-60452336
AGCGAUGGUCCACGGGCCC
446







UCUCUA





53335_5_48
BCL11a
Exon 5
+
chr2: 60452312-60452337
GCGAUGGUCCACGGGCCCU
447







CUCUAU





53335_5_49
BCL11a
Exon 5
+
chr2: 60452335-60452360
AUGGGACUGAUUCACUGUU
448







CCAAUG





53335_5_50
BCL11a
Exon 5
+
chr2: 60452336-60452361
UGGGACUGAUUCACUGUUC
449







CAAUGU





53335_5_51
BCL11a
Exon 5
+
chr2: 60452383-60452408
UUUUUAUUAAAAAAUAUAA
450







AUAAAA





53335_5_52
BCL11a
Exon 5
+
chr2: 60452392-60452417
AAAAAUAUAAAUAAAAUGG
451







CGCUGC





53335_5_53
BCL11a
Exon 5
+
chr2: 60452398-60452423
AUAAAUAAAAUGGCGCUGC
452







AGGCCU





53335_5_54
BCL11a
Exon 5
+
chr2: 60452402-60452427
AUAAAAUGGCGCUGCAGGC
453







CUAGGC





53335_5_55
BCL11a
Exon 5
+
chr2: 60452406-60452431
AAUGGCGCUGCAGGCCUAG
454







GCUGGA





53335_5_56
BCL11a
Exon 5
+
chr2: 60452416-60452441
CAGGCCUAGGCUGGAAGGA
455







CUCUGC





53335_5_57
BCL11a
Exon 5
+
chr2: 60452436-60452461
UCUGCAGGACUCUGUCUUC
456







GCACAA





53335_5_58
BCL11a
Exon 5
+
chr2: 60452444-60452469
ACUCUGUCUUCGCACAACG
457







GCUUCU





53335_5_59
BCL11a
Exon 5
+
chr2: 60452447-60452472
CUGUCUUCGCACAACGGCU
458







UCUUGG





53335_5_60
BCL11a
Exon 5
+
chr2: 60452478-60452503
CUGUCAGAAAACAUCACAA
459







ACUAGC





53335_5_61
BCL11a
Exon 5
+
chr2: 60452505-60452530
GAUGACAGACCACGCUGAC
460







GUCGAC





53335_5_62
BCL11a
Exon 5
+
chr2: 60452506-60452531
AUGACAGACCACGCUGACG
461







UCGACU





53335_5_63
BCL11a
Exon 5
+
chr2: 60452509-60452534
ACAGACCACGCUGACGUCG
462







ACUGGG





53335_5_64
BCL11a
Exon 5
+
chr2: 60452531-60452556
GGGCGGCACGCGUCCACCC
463







CACCCC





53335_5_65
BCL11a
Exon 5
+
chr2: 60452532-60452557
GGCGGCACGCGUCCACCCC
464







ACCCCU





53335_5_66
BCL11a
Exon 5
+
chr2: 60452533-60452558
GCGGCACGCGUCCACCCCA
465







CCCCUG





53335_5_67
BCL11a
Exon 5
+
chr2: 60452534-60452559
CGGCACGCGUCCACCCCACC
466







CCUGG





53335_5_68
BCL11a
Exon 5
+
chr2: 60452559-60452584
GGGCUUCAAAUUUUCUCAG
467







AACUUA





53335_5_69
BCL11a
Exon 5
+
chr2: 60452560-60452585
GGCUUCAAAUUUUCUCAGA
468







ACUUAA





53335_5_70
BCL11a
Exon 5
+
chr2: 60452607-60452632
AAACUGCCACACAUCUUGA
469







GCUCUC





53335_5_71
BCL11a
Exon 5
+
chr2: 60452608-60452633
AACUGCCACACAUCUUGAG
470







CUCUCU





53335_5_72
BCL11a
Exon 5
+
chr2: 60452623-60452648
UGAGCUCUCUGGGUACUAC
471







GCCGAA





53335_5_73
BCL11a
Exon 5
+
chr2: 60452624-60452649
GAGCUCUCUGGGUACUACG
472







CCGAAU





53335_5_74
BCL11a
Exon 5
+
chr2: 60452625-60452650
AGCUCUCUGGGUACUACGC
473







CGAAUG





53335_5_75
BCL11a
Exon 5
+
chr2: 60452626-60452651
GCUCUCUGGGUACUACGCC
474







GAAUGG





53335_5_76
BCL11a
Exon 5
+
chr2: 60452649-60452674
GGGGGUGUGUGAAGAACCU
475







AGAAAG





53335_5_77
BCL11a
Exon 5
+
chr2: 60452653-60452678
GUGUGUGAAGAACCUAGAA
476







AGAGGU





53335_5_78
BCL11a
Exon 5
+
chr2: 60452662-60452687
GAACCUAGAAAGAGGUUGG
477







AGACAG





53335_5_79
BCL11a
Exon 5

chr2: 60451215-60451240
CUUAGUGAAAAGAUAGCCA
478







AAUAAU





53335_5_80
BCL11a
Exon 5

chr2: 60451256-60451281
GGGAAAAUCCUACCUAUCC
479







ACCUUC





53335_5_81
BCL11a
Exon 5

chr2: 60451281-60451306
CACAUACAGGCCGUGAACC
480







UAAGUG





53335_5_82
BCL11a
Exon 5

chr2: 60451282-60451307
UCACAUACAGGCCGUGAAC
481







CUAAGU





53335_5_83
BCL11a
Exon 5

chr2: 60451283-60451308
UUCACAUACAGGCCGUGAA
482







CCUAAG





53335_5_84
BCL11a
Exon 5

chr2: 60451299-60451324
ACCUGUGUGCUGUAGAUUC
483







ACAUAC





53335_5_85
BCL11a
Exon 5

chr2: 60451350-60451375
UAGAAACAACAUAGCAAAU
484







UAAAAU





53335_5_86
BCL11a
Exon 5

chr2: 60451394-60451419
UCUCAGUUUGGUAUUUUUU
485







ACUGCU





53335_5_87
BCL11a
Exon 5

chr2: 60451411-60451436
AAUUUGCACAGAACUUUUC
486







UCAGUU





53335_5_88
BCL11a
Exon 5

chr2: 60451446-60451471
ACAAACAGGUGGUAAAAAU
487







UCUUUC





53335_5_89
BCL11a
Exon 5

chr2: 60451462-60451487
CAAAUAAGUUACAUCUACA
488







AACAGG





53335_5_90
BCL11a
Exon 5

chr2: 60451465-60451490
CCACAAAUAAGUUACAUCU
489







ACAAAC





53335_5_91
BCL11a
Exon 5

chr2: 60451552-60451577
GAUUUUAGAGGGGGGAAAU
490







UAUAGG





53335_5_92
BCL11a
Exon 5

chr2: 60451555-60451580
GCAGAUUUUAGAGGGGGGA
491







AAUUAU





53335_5_93
BCL11a
Exon 5

chr2: 60451565-60451590
GAAAUUUGGGGCAGAUUUU
492







AGAGGG





53335_5_94
BCL11a
Exon 5

chr2: 60451566-60451591
GGAAAUUUGGGGCAGAUUU
493







UAGAGG





53335_5_95
BCL11a
Exon 5

chr2: 60451567-60451592
AGGAAAUUUGGGGCAGAUU
494







UUAGAG





53335_5_96
BCL11a
Exon 5

chr2: 60451568-60451593
CAGGAAAUUUGGGGCAGAU
495







UUUAGA





53335_5_97
BCL11a
Exon 5

chr2: 60451569-60451594
UCAGGAAAUUUGGGGCAGA
496







UUUUAG





53335_5_98
BCL11a
Exon 5

chr2: 60451582-60451607
UUUAGUACUUACAUCAGGA
497







AAUUUG





53335_5_99
BCL11a
Exon 5

chr2: 60451583-60451608
CUUUAGUACUUACAUCAGG
498







AAAUUU





53335_5_100
BCL11a
Exon 5

chr2: 60451584-60451609
UCUUUAGUACUUACAUCAG
499







GAAAUU





53335_5_101
BCL11a
Exon 5

chr2: 60451592-60451617
AUAAAACUUCUUUAGUACU
500







UACAUC





53335_5_102
BCL11a
Exon 5

chr2: 60451648-60451673
UCUAAUUUUAGGUUCCCAA
501







ACCUUC





53335_5_103
BCL11a
Exon 5

chr2: 60451664-60451689
GUUUCUUAUUAAAUAUUCU
502







AAUUUU





53335_5_104
BCL11a
Exon 5

chr2: 60451707-60451732
CUGGGCGAGCGGUAAAUCC
503







UAAAGA





53335_5_105
BCL11a
Exon 5

chr2: 60451723-60451748
UUAGGAAAGAACAUCACUG
504







GGCGAG





53335_5_106
BCL11a
Exon 5

chr2: 60451730-60451755
AUUUAGCUUAGGAAAGAAC
505







AUCACU





53335_5_107
BCL11a
Exon 5

chr2: 60451731-60451756
AAUUUAGCUUAGGAAAGAA
506







CAUCAC





53335_5_108
BCL11a
Exon 5

chr2: 60451746-60451771
UUGAAUUUGUCUUUUAAUU
507







UAGCUU





53335_5_109
BCL11a
Exon 5

chr2: 60451776-60451801
UAUAUGCUUUUGGUGGCUA
508







CCAUGC





53335_5_110
BCL11a
Exon 5

chr2: 60451788-60451813
CUGUUUUUCAAAUAUAUGC
509







UUUUGG





53335_5_111
BCL11a
Exon 5

chr2: 60451791-60451816
AUCCUGUUUUUCAAAUAUA
510







UGCUUU





53335_5_112
BCL11a
Exon 5

chr2: 60451827-60451852
GCAUACCAUUAAAUAAUGC
511







AUAAUA





53335_5_113
BCL11a
Exon 5

chr2: 60451882-60451907
AUUGCUGUUUAUUAAUGCU
512







GAAGUG





53335_5_114
BCL11a
Exon 5

chr2: 60451949-60451974
CAAGGAGAAUCAAAAUGCA
513







AAACUU





53335_5_115
BCL11a
Exon 5

chr2: 60451950-60451975
UCAAGGAGAAUCAAAAUGC
514







AAAACU





53335_5_116
BCL11a
Exon 5

chr2: 60451972-60451997
GCUUAUCAGAUGGCAUAAA
515







UUUUCA





53335_5_117
BCL11a
Exon 5

chr2: 60451987-60452012
GGGAACUAGGUUACCGCUU
516







AUCAGA





53335_5_118
BCL11a
Exon 5

chr2: 60452005-60452030
GGGCAGGAGAUGUAGGAGG
517







GGAACU





53335_5_119
BCL11a
Exon 5

chr2: 60452012-60452037
GAGAAAUGGGCAGGAGAUG
518







UAGGAG





53335_5_120
BCL11a
Exon 5

chr2: 60452013-60452038
UGAGAAAUGGGCAGGAGAU
519







GUAGGA





53335_5_121
BCL11a
Exon 5

chr2: 60452014-60452039
UUGAGAAAUGGGCAGGAGA
520







UGUAGG





53335_5_122
BCL11a
Exon 5

chr2: 60452017-60452042
GAUUUGAGAAAUGGGCAGG
521







AGAUGU





53335_5_123
BCL11a
Exon 5

chr2: 60452026-60452051
GGAGGAACAGAUUUGAGAA
522







AUGGGC





53335_5_124
BCL11a
Exon 5

chr2: 60452030-60452055
GGUAGGAGGAACAGAUUUG
523







AGAAAU





53335_5_125
BCL11a
Exon 5

chr2: 60452031-60452056
GGGUAGGAGGAACAGAUUU
524







GAGAAA





53335_5_126
BCL11a
Exon 5

chr2: 60452049-60452074
UACAGACACCCAUCGGGUG
525







GGUAGG





53335_5_127
BCL11a
Exon 5

chr2: 60452052-60452077
UCCUACAGACACCCAUCGG
526







GUGGGU





53335_5_128
BCL11a
Exon 5

chr2: 60452056-60452081
UGUUUCCUACAGACACCCA
527







UCGGGU





53335_5_129
BCL11a
Exon 5

chr2: 60452057-60452082
CUGUUUCCUACAGACACCC
528







AUCGGG





53335_5_130
BCL11a
Exon 5

chr2: 60452060-60452085
UACCUGUUUCCUACAGACA
529







CCCAUC





53335_5_131
BCL11a
Exon 5

chr2: 60452061-60452086
GUACCUGUUUCCUACAGAC
530







ACCCAU





53335_5_132
BCL11a
Exon 5

chr2: 60452111-60452136
AAUUUUUAAUGCUUAUAAG
531







ACAAUG





53335_5_133
BCL11a
Exon 5

chr2: 60452155-60452180
ACACAAUAAAUGUUGGAGC
532







UUUAGG





53335_5_134
BCL11a
Exon 5

chr2: 60452158-60452183
UUGACACAAUAAAUGUUGG
533







AGCUUU





53335_5_135
BCL11a
Exon 5

chr2: 60452167-60452192
UGCUUAACAUUGACACAAU
534







AAAUGU





53335_5_136
BCL11a
Exon 5

chr2: 60452256-60452281
CCAGCCAACCUAAUUACCU
535







GUAUUG





53335_5_137
BCL11a
Exon 5

chr2: 60452295-60452320
ACCAUCGCUGUCAUGAGUG
536







AUGCCC





53335_5_138
BCL11a
Exon 5

chr2: 60452323-60452348
GAAUCAGUCCCAUAGAGAG
537







GGCCCG





53335_5_139
BCL11a
Exon 5

chr2: 60452330-60452355
GAACAGUGAAUCAGUCCCA
538







UAGAGA





53335_5_140
BCL11a
Exon 5

chr2: 60452331-60452356
GGAACAGUGAAUCAGUCCC
539







AUAGAG





53335_5_141
BCL11a
Exon 5

chr2: 60452357-60452382
UAAAAACAAAAAAACAGAC
540







CCACAU





53335_5_142
BCL11a
Exon 5

chr2: 60452423-60452448
GAGUCCUGCAGAGUCCUUC
541







CAGCCU





53335_5_143
BCL11a
Exon 5

chr2: 60452517-60452542
GCGUGCCGCCCAGUCGACG
542







UCAGCG





53335_5_144
BCL11a
Exon 5

chr2: 60452547-60452572
AAAUUUGAAGCCCCCAGGG
543







GUGGGG





53335_5_145
BCL11a
Exon 5

chr2: 60452550-60452575
AGAAAAUUUGAAGCCCCCA
544







GGGGUG





53335_5_146
BCL11a
Exon 5

chr2: 60452551-60452576
GAGAAAAUUUGAAGCCCCC
545







AGGGGU





53335_5_147
BCL11a
Exon 5

chr2: 60452552-60452577
UGAGAAAAUUUGAAGCCCC
546







CAGGGG





53335_5_148
BCL11a
Exon 5

chr2: 60452555-60452580
UUCUGAGAAAAUUUGAAGC
547







CCCCAG





53335_5_149
BCL11a
Exon 5

chr2: 60452556-60452581
GUUCUGAGAAAAUUUGAAG
548







CCCCCA





53335_5_150
BCL11a
Exon 5

chr2: 60452557-60452582
AGUUCUGAGAAAAUUUGAA
549







GCCCCC





53335_5_151
BCL11a
Exon 5

chr2: 60452602-60452627
CUCAAGAUGUGUGGCAGUU
550







UUCGGA





53335_5_152
BCL11a
Exon 5

chr2: 60452606-60452631
AGAGCUCAAGAUGUGUGGC
551







AGUUUU





53335_5_153
BCL11a
Exon 5

chr2: 60452616-60452641
UAGUACCCAGAGAGCUCAA
552







GAUGUG





53335_5_154
BCL11a
Exon 5

chr2: 60452646-60452671
UCUAGGUUCUUCACACACC
553







CCCAUU





53335_4_1
BCL11a
Exon 4
+
chr2: 60457199-60457224
UUAAUUUUUUUUAUUUUUU
554







CAAUAA





53335_4_2
BCL11a
Exon 4
+
chr2: 60457200-60457225
UAAUUUUUUUUAUUUUUUC
555







AAUAAA





53335_4_3
BCL11a
Exon 4
+
chr2: 60457209-60457234
UUAUUUUUUCAAUAAAGGG
556







ACAAAA





53335_4_4
BCL11a
Exon 4
+
chr2: 60457210-60457235
UAUUUUUUCAAUAAAGGGA
557







CAAAAU





53335_4_5
BCL11a
Exon 4
+
chr2: 60457222-60457247
AAAGGGACAAAAUGGGUGU
558







AUGAAC





53335_4_6
BCL11a
Exon 4
+
chr2: 60457259-60457284
ACAACUGCCAAAAAAACAC
559







AGACAG





53335_4_7
BCL11a
Exon 4
+
chr2: 60457312-60457337
CCAGAAACAAAUACAAUAA
560







AAAGCC





53335_4_8
BCL11a
Exon 4
+
chr2: 60457328-60457353
UAAAAAGCCAGGUUGUAAU
561







GACCUU





53335_4_9
BCL11a
Exon 4
+
chr2: 60457401-60457426
CAAAUUAAGUGCCUCUGUU
562







UUGAAC





53335_4_10
BCL11a
Exon 4
+
chr2: 60457402-60457427
AAAUUAAGUGCCUCUGUUU
563







UGAACA





53335_4_11
BCL11a
Exon 4
+
chr2: 60457480-60457505
AGUUACGACAAACAGCUUU
564







CAUUAC





53335_4_12
BCL11a
Exon 4
+
chr2: 60457491-60457516
ACAGCUUUCAUUACAGGAA
565







UAGAAA





53335_4_13
BCL11a
Exon 4
+
chr2: 60457545-60457570
AUUUACAAAAAAGUAUUGA
566







CUAAAG





53335_4_14
BCL11a
Exon 4
+
chr2: 60457546-60457571
UUUACAAAAAAGUAUUGAC
567







UAAAGC





53335_4_15
BCL11a
Exon 4
+
chr2: 60457616-60457641
UAAAUAUAAAGCACCAUUU
568







AGUUUU





53335_4_16
BCL11a
Exon 4
+
chr2: 60457642-60457667
GGCAAUGAAAAAAACUGCA
569







AAACAU





53335_4_17
BCL11a
Exon 4
+
chr2: 60457695-60457720
UCUUUCUUUCUUUUACUGC
570







AUAUGA





53335_4_18
BCL11a
Exon 4
+
chr2: 60457706-60457731
UUUACUGCAUAUGAAGGUA
571







AGAUGC





53335_4_19
BCL11a
Exon 4
+
chr2: 60457714-60457739
AUAUGAAGGUAAGAUGCUG
572







GAAUGU





53335_4_20
BCL11a
Exon 4
+
chr2: 60457715-60457740
UAUGAAGGUAAGAUGCUGG
573







AAUGUA





53335_4_21
BCL11a
Exon 4
+
chr2: 60457725-60457750
AGAUGCUGGAAUGUAGGGU
574







GAUAGA





53335_4_22
BCL11a
Exon 4
+
chr2: 60457730-60457755
CUGGAAUGUAGGGUGAUAG
575







AAGGAA





53335_4_23
BCL11a
Exon 4
+
chr2: 60457731-60457756
UGGAAUGUAGGGUGAUAGA
576







AGGAAA





53335_4_24
BCL11a
Exon 4
+
chr2: 60457792-60457817
UUAGCUUGCAGUACUGCAU
577







ACAGUA





53335_4_25
BCL11a
Exon 4
+
chr2: 60457799-60457824
GCAGUACUGCAUACAGUAU
578







GGCAGC





53335_4_26
BCL11a
Exon 4
+
chr2: 60457806-60457831
UGCAUACAGUAUGGCAGCA
579







GGAAAA





53335_4_27
BCL11a
Exon 4
+
chr2: 60457817-60457842
UGGCAGCAGGAAAAAGGAA
580







CAAAAA





53335_4_28
BCL11a
Exon 4
+
chr2: 60457863-60457888
ACAGCCAUCCAUGUGACAU
581







UCUAGC





53335_4_29
BCL11a
Exon 4
+
chr2: 60457887-60457912
CAGGCUCCCCCAAACCGCC
582







AUUAUA





53335_4_30
BCL11a
Exon 4
+
chr2: 60457996-60458021
CCUGCCAAAUUAAAAAAAU
583







AUACUG





53335_4_31
BCL11a
Exon 4
+
chr2: 60458031-60458056
UCUUUUUUUUUUCCACUAC
584







CAAAAA





53335_4_32
BCL11a
Exon 4
+
chr2: 60458178-60458203
AAAGACCAUAAAUGUAUUU
585







UAGCAU





53335_4_33
BCL11a
Exon 4
+
chr2: 60458274-60458299
UUUUUUUUUUUUACAACCU
586







GAAGAG





53335_4_34
BCL11a
Exon 4
+
chr2: 60458287-60458312
CAACCUGAAGAGCGGUGUG
587







UAUCCA





53335_4_35
BCL11a
Exon 4
+
chr2: 60458317-60458342
UAGAAUUUCCACUACCAUU
588







UUUAAA





53335_4_36
BCL11a
Exon 4
+
chr2: 60458350-60458375
AAGUCUUGUAACACCACCA
589







AGACAA





53335_4_37
BCL11a
Exon 4
+
chr2: 60458564-60458589
UAAGUAAGCUCAAUAGUCA
590







AGUAAA





53335_4_38
BCL11a
Exon 4
+
chr2: 60458568-60458593
UAAGCUCAAUAGUCAAGUA
591







AAUGGC





53335_4_39
BCL11a
Exon 4
+
chr2: 60458677-60458702
UUCCCUUAAGUAUAGACCU
592







GUAAAC





53335_4_40
BCL11a
Exon 4
+
chr2: 60458678-60458703
UCCCUUAAGUAUAGACCUG
593







UAAACU





53335_4_41
BCL11a
Exon 4
+
chr2: 60458717-60458742
GUGCACUUAAUUGUCCUAU
594







CUGAGC





53335_4_42
BCL11a
Exon 4
+
chr2: 60458775-60458800
AUUAGAGAAAAGAUACAGA
595







UAUCAC





53335_4_43
BCL11a
Exon 4
+
chr2: 60458806-60458831
AGUCAAGUGCUAUUUGAAC
596







ACCAAC





53335_4_44
BCL11a
Exon 4
+
chr2: 60458807-60458832
GUCAAGUGCUAUUUGAACA
597







CCAACU





53335_4_45
BCL11a
Exon 4
+
chr2: 60458808-60458833
UCAAGUGCUAUUUGAACAC
598







CAACUG





53335_4_46
BCL11a
Exon 4
+
chr2: 60458904-60458929
GUUAACACAAAUAGCACAC
599







AGUGUA





53335_4_47
BCL11a
Exon 4
+
chr2: 60458930-60458955
GGAAAAGAAAUGAAGUACA
600







ACUUUU





53335_4_48
BCL11a
Exon 4
+
chr2: 60458931-60458956
GAAAAGAAAUGAAGUACAA
601







CUUUUA





53335_4_49
BCL11a
Exon 4
+
chr2: 60459074-60459099
CUUAUAUACCUGUUCUAGU
602







UUUAAA





53335_4_50
BCL11a
Exon 4
+
chr2: 60459165-60459190
UAUUGUCAGCCUCUUCCUU
603







UCAAUA





53335_4_51
BCL11a
Exon 4
+
chr2: 60459174-60459199
CCUCUUCCUUUCAAUAUGG
604







UAUACA





53335_4_52
BCL11a
Exon 4
+
chr2: 60459223-60459248
UGUCCACUUGACAACCAAG
605







UAGAUC





53335_4_53
BCL11a
Exon 4
+
chr2: 60459238-60459263
CAAGUAGAUCUGGAUCUAU
606







UUCUUU





53335_4_54
BCL11a
Exon 4
+
chr2: 60459322-60459347
UUACUAGUGUAUUUAAUUG
607







CGUUCC





53335_4_55
BCL11a
Exon 4
+
chr2: 60459323-60459348
UACUAGUGUAUUUAAUUGC
608







GUUCCA





53335_4_56
BCL11a
Exon 4
+
chr2: 60459378-60459403
UCAUUGUUUAAAAAAAAUA
609







AAACUU





53335_4_57
BCL11a
Exon 4
+
chr2: 60459379-60459404
CAUUGUUUAAAAAAAAUAA
610







AACUUU





53335_4_58
BCL11a
Exon 4
+
chr2: 60459413-60459438
AGCCCAUUUCUUUUAAGCU
611







CUCACC





53335_4_59
BCL11a
Exon 4
+
chr2: 60459435-60459460
ACCAGGAGCAAAGUAGCUU
612







UUAUAC





53335_4_60
BCL11a
Exon 4
+
chr2: 60459470-60459495
AGUUUUGUUUAUAAAAUUA
613







AACUAA





53335_4_61
BCL11a
Exon 4
+
chr2: 60459490-60459515
ACUAAAGGAAAAAUGAUGA
614







UUAACU





53335_4_62
BCL11a
Exon 4
+
chr2: 60459499-60459524
AAAAUGAUGAUUAACUAGG
615







ACAUAA





53335_4_63
BCL11a
Exon 4
+
chr2: 60459500-60459525
AAAUGAUGAUUAACUAGGA
616







CAUAAU





53335_4_64
BCL11a
Exon 4
+
chr2: 60459513-60459538
CUAGGACAUAAUGGGUCAU
617







CUUUUU





53335_4_65
BCL11a
Exon 4
+
chr2: 60459564-60459589
AUAUAGAAUUAUAUGCUAG
618







UUCCUA





53335_4_66
BCL11a
Exon 4
+
chr2: 60459632-60459657
UAACAAGUAGAAAGAACCA
619







UCGAUG





53335_4_67
BCL11a
Exon 4
+
chr2: 60459649-60459674
CAUCGAUGUGGUUUUAAUA
620







GAUCCA





53335_4_68
BCL11a
Exon 4
+
chr2: 60459718-60459743
GUUUUUCUGUUAAUUUGUC
621







AAUUCA





53335_4_69
BCL11a
Exon 4
+
chr2: 60459818-60459843
UCAGUGCUAUCUAUUCUGU
622







CUAUAG





53335_4_70
BCL11a
Exon 4
+
chr2: 60459819-60459844
CAGUGCUAUCUAUUCUGUC
623







UAUAGA





53335_4_71
BCL11a
Exon 4
+
chr2: 60459900-60459925
UAUGUAUUACAGAAUGUAU
624







GCAGCA





53335_4_72
BCL11a
Exon 4
+
chr2: 60459937-60459962
CUCUCUCUCUCUUUUUCUC
625







UCAGAA





53335_4_73
BCL11a
Exon 4
+
chr2: 60459943-60459968
CUCUCUUUUUCUCUCAGAA
626







CGGAAC





53335_4_74
BCL11a
Exon 4
+
chr2: 60459977-60460002
CAACAUGUUUGCUCAGCAA
627







CGAAUU





53335_4_75
BCL11a
Exon 4
+
chr2: 60459978-60460003
AACAUGUUUGCUCAGCAAC
628







GAAUUA





53335_4_76
BCL11a
Exon 4
+
chr2: 60460068-60460093
ACAUGUAAAUUAUUGCACA
629







AGAGAA





53335_4_77
BCL11a
Exon 4
+
chr2: 60460126-60460151
GCCCCAUACAGAUCAUGCA
630







UUCAAA





53335_4_78
BCL11a
Exon 4
+
chr2: 60460140-60460165
AUGCAUUCAAACGGUGAGA
631







ACAUAA





53335_4_79
BCL11a
Exon 4
+
chr2: 60460193-60460218
AAAGAAAAAGAAAAAGAAA
632







AAAAAC





53335_4_80
BCL11a
Exon 4
+
chr2: 60460201-60460226
AGAAAAAGAAAAAAAACAG
633







GUGUGC





53335_4_81
BCL11a
Exon 4
+
chr2: 60460269-60460294
UGUUUGUUUGUUUGUUUAA
634







AUCACA





53335_4_82
BCL11a
Exon 4
+
chr2: 60460270-60460295
GUUUGUUUGUUUGUUUAAA
635







UCACAU





53335_4_83
BCL11a
Exon 4
+
chr2: 60460291-60460316
ACAUGGGACUAGAAAAAAA
636







UCCUAC





53335_4_84
BCL11a
Exon 4
+
chr2: 60460292-60460317
CAUGGGACUAGAAAAAAAU
637







CCUACA





53335_4_85
BCL11a
Exon 4
+
chr2: 60460297-60460322
GACUAGAAAAAAAUCCUAC
638







AGGGAG





53335_4_86
BCL11a
Exon 4
+
chr2: 60460298-60460323
ACUAGAAAAAAAUCCUACA
639







GGGAGU





53335_4_87
BCL11a
Exon 4
+
chr2: 60460299-60460324
CUAGAAAAAAAUCCUACAG
640







GGAGUG





53335_4_88
BCL11a
Exon 4
+
chr2: 60460303-60460328
AAAAAAAUCCUACAGGGAG
641







UGGGGC





53335_4_89
BCL11a
Exon 4
+
chr2: 60460306-60460331
AAAAUCCUACAGGGAGUGG
642







GGCUGG





53335_4_90
BCL11a
Exon 4
+
chr2: 60460307-60460332
AAAUCCUACAGGGAGUGGG
643







GCUGGA





53335_4_91
BCL11a
Exon 4
+
chr2: 60460313-60460338
UACAGGGAGUGGGGCUGGA
644







GGGCGA





53335_4_92
BCL11a
Exon 4
+
chr2: 60460314-60460339
ACAGGGAGUGGGGCUGGAG
645







GGCGAU





53335_4_93
BCL11a
Exon 4
+
chr2: 60460315-60460340
CAGGGAGUGGGGCUGGAGG
646







GCGAUG





53335_4_94
BCL11a
Exon 4
+
chr2: 60460319-60460344
GAGUGGGGCUGGAGGGCGA
647







UGGGGA





53335_4_95
BCL11a
Exon 4
+
chr2: 60460320-60460345
AGUGGGGCUGGAGGGCGAU
648







GGGGAA





53335_4_96
BCL11a
Exon 4
+
chr2: 60460321-60460346
GUGGGGCUGGAGGGCGAUG
649







GGGAAG





53335_4_97
BCL11a
Exon 4
+
chr2: 60460326-60460351
GCUGGAGGGCGAUGGGGAA
650







GGGGAG





53335_4_98
BCL11a
Exon 4
+
chr2: 60460335-60460360
CGAUGGGGAAGGGGAGUGG
651







UGAAAA





53335_4_99
BCL11a
Exon 4
+
chr2: 60460336-60460361
GAUGGGGAAGGGGAGUGGU
652







GAAAAA





53335_4_100
BCL11a
Exon 4
+
chr2: 60460337-60460362
AUGGGGAAGGGGAGUGGUG
653







AAAAAG





53335_4_101
BCL11a
Exon 4
+
chr2: 60460338-60460363
UGGGGAAGGGGAGUGGUGA
654







AAAAGG





53335_4_102
BCL11a
Exon 4
+
chr2: 60460345-60460370
GGGGAGUGGUGAAAAAGGG
655







GGUGUC





53335_4_103
BCL11a
Exon 4
+
chr2: 60460348-60460373
GAGUGGUGAAAAAGGGGGU
656







GUCAGG





53335_4_104
BCL11a
Exon 4
+
chr2: 60460349-60460374
AGUGGUGAAAAAGGGGGUG
657







UCAGGU





53335_4_105
BCL11a
Exon 4
+
chr2: 60460356-60460381
AAAAAGGGGGUGUCAGGUG
658







GGAGUG





53335_4_106
BCL11a
Exon 4
+
chr2: 60460357-60460382
AAAAGGGGGUGUCAGGUGG
659







GAGUGA





53335_4_107
BCL11a
Exon 4
+
chr2: 60460360-60460385
AGGGGGUGUCAGGUGGGAG
660







UGAGGG





53335_4_108
BCL11a
Exon 4
+
chr2: 60460361-60460386
GGGGGUGUCAGGUGGGAGU
661







GAGGGA





53335_4_109
BCL11a
Exon 4
+
chr2: 60460362-60460387
GGGGUGUCAGGUGGGAGUG
662







AGGGAG





53335_4_110
BCL11a
Exon 4
+
chr2: 60460442-60460467
GUGCCAUUUUUUCAUGUGU
663







UUCUCC





53335_4_111
BCL11a
Exon 4
+
chr2: 60460443-60460468
UGCCAUUUUUUCAUGUGUU
664







UCUCCA





53335_4_112
BCL11a
Exon 4
+
chr2: 60460462-60460487
UCUCCAGGGUACUGUACAC
665







GCUAAA





53335_4_113
BCL11a
Exon 4
+
chr2: 60460505-60460530
ACAUUUGUAAACGUCCUUC
666







CCCACC





53335_4_114
BCL11a
Exon 4
+
chr2: 60460527-60460552
ACCUGGCCAUGCGUUUUCA
667







UGUGCC





53335_4_115
BCL11a
Exon 4
+
chr2: 60460544-60460569
CAUGUGCCUGGUGAGCUUG
668







CUACUC





53335_4_116
BCL11a
Exon 4
+
chr2: 60460545-60460570
AUGUGCCUGGUGAGCUUGC
669







UACUCU





53335_4_117
BCL11a
Exon 4
+
chr2: 60460551-60460576
CUGGUGAGCUUGCUACUCU
670







GGGCAC





53335_4_118
BCL11a
Exon 4
+
chr2: 60460579-60460604
CAUAGUUGCACAGCUCGCA
671







UUUAUA





53335_4_119
BCL11a
Exon 4
+
chr2: 60460595-60460620
GCAUUUAUAAGGCCUUUCG
672







CCCGUG





53335_4_120
BCL11a
Exon 4
+
chr2: 60460607-60460632
CCUUUCGCCCGUGUGGCUU
673







CUCCUG





53335_4_121
BCL11a
Exon 4
+
chr2: 60460686-60460711
UCGCUGCGUCUGCCCUCUU
674







UUGAGC





53335_4_122
BCL11a
Exon 4
+
chr2: 60460687-60460712
CGCUGCGUCUGCCCUCUUU
675







UGAGCU





53335_4_123
BCL11a
Exon 4
+
chr2: 60460696-60460721
UGCCCUCUUUUGAGCUGGG
676







CCUGCC





53335_4_124
BCL11a
Exon 4
+
chr2: 60460697-60460722
GCCCUCUUUUGAGCUGGGC
677







CUGCCC





53335_4_125
BCL11a
Exon 4
+
chr2: 60460702-60460727
CUUUUGAGCUGGGCCUGCC
678







CGGGCC





53335_4_126
BCL11a
Exon 4
+
chr2: 60460715-60460740
CCUGCCCGGGCCCGGACCA
679







CUAAUA





53335_4_127
BCL11a
Exon 4
+
chr2: 60460716-60460741
CUGCCCGGGCCCGGACCAC
680







UAAUAU





53335_4_128
BCL11a
Exon 4
+
chr2: 60460717-60460742
UGCCCGGGCCCGGACCACU
681







AAUAUG





53335_4_129
BCL11a
Exon 4
+
chr2: 60460776-60460801
CCCGAGAUCCCUCCGUCCA
682







GCUCCC





53335_4_130
BCL11a
Exon 4
+
chr2: 60460777-60460802
CCGAGAUCCCUCCGUCCAG
683







CUCCCC





53335_4_131
BCL11a
Exon 4
+
chr2: 60460780-60460805
AGAUCCCUCCGUCCAGCUC
684







CCCGGG





53335_4_132
BCL11a
Exon 4
+
chr2: 60460785-60460810
CCUCCGUCCAGCUCCCCGG
685







GCGGUG





53335_4_133
BCL11a
Exon 4
+
chr2: 60460812-60460837
GAGAAGCGCAAACUCCCGU
686







UCUCCG





53335_4_134
BCL11a
Exon 4
+
chr2: 60460827-60460852
CCGUUCUCCGAGGAGUGCU
687







CCGACG





53335_4_135
BCL11a
Exon 4
+
chr2: 60460830-60460855
UUCUCCGAGGAGUGCUCCG
688







ACGAGG





53335_4_136
BCL11a
Exon 4
+
chr2: 60460837-60460862
AGGAGUGCUCCGACGAGGA
689







GGCAAA





53335_4_137
BCL11a
Exon 4
+
chr2: 60460848-60460873
GACGAGGAGGCAAAAGGCG
690







AUUGUC





53335_4_138
BCL11a
Exon 4
+
chr2: 60460865-60460890
CGAUUGUCUGGAGUCUCCG
691







AAGCUA





53335_4_139
BCL11a
Exon 4
+
chr2: 60460869-60460894
UGUCUGGAGUCUCCGAAGC
692







UAAGGA





53335_4_140
BCL11a
Exon 4
+
chr2: 60460870-60460895
GUCUGGAGUCUCCGAAGCU
693







AAGGAA





53335_4_141
BCL11a
Exon 4
+
chr2: 60460887-60460912
CUAAGGAAGGGAUCUUUGA
694







GCUGCC





53335_4_142
BCL11a
Exon 4
+
chr2: 60460890-60460915
AGGAAGGGAUCUUUGAGCU
695







GCCUGG





53335_4_143
BCL11a
Exon 4
+
chr2: 60460902-60460927
UUGAGCUGCCUGGAGGCCG
696







CGUAGC





53335_4_144
BCL11a
Exon 4
+
chr2: 60460935-60460960
CACUGCGAGUACACGUUCU
697







CCGUGU





53335_4_145
BCL11a
Exon 4
+
chr2: 60460936-60460961
ACUGCGAGUACACGUUCUC
698







CGUGUU





53335_4_146
BCL11a
Exon 4
+
chr2: 60460944-60460969
UACACGUUCUCCGUGUUGG
699







GCAUCG





53335_4_147
BCL11a
Exon 4
+
chr2: 60460948-60460973
CGUUCUCCGUGUUGGGCAU
700







CGCGGC





53335_4_148
BCL11a
Exon 4
+
chr2: 60460949-60460974
GUUCUCCGUGUUGGGCAUC
701







GCGGCC





53335_4_149
BCL11a
Exon 4
+
chr2: 60460950-60460975
UUCUCCGUGUUGGGCAUCG
702







CGGCCG





53335_4_150
BCL11a
Exon 4
+
chr2: 60460951-60460976
UCUCCGUGUUGGGCAUCGC
703







GGCCGG





53335_4_151
BCL11a
Exon 4
+
chr2: 60460955-60460980
CGUGUUGGGCAUCGCGGCC
704







GGGGGC





53335_4_152
BCL11a
Exon 4
+
chr2: 60460992-60461017
UUCUCGAGCUUGAUGCGCU
705







UAGAGA





53335_4_153
BCL11a
Exon 4
+
chr2: 60460993-60461018
UCUCGAGCUUGAUGCGCUU
706







AGAGAA





53335_4_154
BCL11a
Exon 4
+
chr2: 60460994-60461019
CUCGAGCUUGAUGCGCUUA
707







GAGAAG





53335_4_155
BCL11a
Exon 4
+
chr2: 60461007-60461032
CGCUUAGAGAAGGGGCUCA
708







GCGAGC





53335_4_156
BCL11a
Exon 4
+
chr2: 60461008-60461033
GCUUAGAGAAGGGGCUCAG
709







CGAGCU





53335_4_157
BCL11a
Exon 4
+
chr2: 60461009-60461034
CUUAGAGAAGGGGCUCAGC
710







GAGCUG





53335_4_158
BCL11a
Exon 4
+
chr2: 60461031-60461056
CUGGGGCUGCCCAGCAGCA
711







GCUUUU





53335_4_159
BCL11a
Exon 4
+
chr2: 60461036-60461061
GCUGCCCAGCAGCAGCUUU
712







UUGGAC





53335_4_160
BCL11a
Exon 4
+
chr2: 60461046-60461071
AGCAGCUUUUUGGACAGGC
713







CCCCCG





53335_4_161
BCL11a
Exon 4
+
chr2: 60461059-60461084
ACAGGCCCCCCGAGGCCGA
714







CUCGCC





53335_4_162
BCL11a
Exon 4
+
chr2: 60461060-60461085
CAGGCCCCCCGAGGCCGAC
715







UCGCCC





53335_4_163
BCL11a
Exon 4
+
chr2: 60461061-60461086
AGGCCCCCCGAGGCCGACU
716







CGCCCG





53335_4_164
BCL11a
Exon 4
+
chr2: 60461072-60461097
GGCCGACUCGCCCGGGGAG
717







CAGCCG





53335_4_165
BCL11a
Exon 4
+
chr2: 60461099-60461124
GCCAUUAACAGUGCCAUCG
718







UCUAUG





53335_4_166
BCL11a
Exon 4
+
chr2: 60461112-60461137
CCAUCGUCUAUGCGGUCCG
719







ACUCGC





53335_4_167
BCL11a
Exon 4
+
chr2: 60461144-60461169
CGAGUCUUCGUCGCAAGUG
720







UCCCUG





53335_4_168
BCL11a
Exon 4
+
chr2: 60461151-60461176
UCGUCGCAAGUGUCCCUGU
721







GGCCCU





53335_4_169
BCL11a
Exon 4
+
chr2: 60461157-60461182
CAAGUGUCCCUGUGGCCCU
722







CGGCCU





53335_4_170
BCL11a
Exon 4
+
chr2: 60461162-60461187
GUCCCUGUGGCCCUCGGCC
723







UCGGCC





53335_4_171
BCL11a
Exon 4
+
chr2: 60461165-60461190
CCUGUGGCCCUCGGCCUCG
724







GCCAGG





53335_4_172
BCL11a
Exon 4
+
chr2: 60461189-60461214
GUGGCCGCGCUUAUGCUUC
725







UCGCCC





53335_4_173
BCL11a
Exon 4
+
chr2: 60461195-60461220
GCGCUUAUGCUUCUCGCCC
726







AGGACC





53335_4_174
BCL11a
Exon 4
+
chr2: 60461198-60461223
CUUAUGCUUCUCGCCCAGG
727







ACCUGG





53335_4_175
BCL11a
Exon 4
+
chr2: 60461202-60461227
UGCUUCUCGCCCAGGACCU
728







GGUGGA





53335_4_176
BCL11a
Exon 4
+
chr2: 60461223-60461248
UGGAAGGCCUCGCUGAAGU
729







GCUGCA





53335_4_177
BCL11a
Exon 4
+
chr2: 60461253-60461278
CUGAGCACCAUGCCCUGCA
730







UGACGU





53335_4_178
BCL11a
Exon 4
+
chr2: 60461254-60461279
UGAGCACCAUGCCCUGCAU
731







GACGUC





53335_4_179
BCL11a
Exon 4
+
chr2: 60461258-60461283
CACCAUGCCCUGCAUGACG
732







UCGGGC





53335_4_180
BCL11a
Exon 4
+
chr2: 60461259-60461284
ACCAUGCCCUGCAUGACGU
733







CGGGCA





53335_4_181
BCL11a
Exon 4
+
chr2: 60461264-60461289
GCCCUGCAUGACGUCGGGC
734







AGGGCG





53335_4_182
BCL11a
Exon 4
+
chr2: 60461312-60461337
GACCGCGCCCCGCGAGCUG
735







UUCUCG





53335_4_183
BCL11a
Exon 4
+
chr2: 60461315-60461340
CGCGCCCCGCGAGCUGUUC
736







UCGUGG





53335_4_184
BCL11a
Exon 4
+
chr2: 60461330-60461355
GUUCUCGUGGUGGCGCGCC
737







GCCUCC





53335_4_185
BCL11a
Exon 4
+
chr2: 60461446-60461471
CCUCUUCCUCCUCGUCCCCG
738







UUCUC





53335_4_186
BCL11a
Exon 4
+
chr2: 60461447-60461472
CUCUUCCUCCUCGUCCCCG
739







UUCUCC





53335_4_187
BCL11a
Exon 4
+
chr2: 60461453-60461478
CUCCUCGUCCCCGUUCUCC
740







GGGAUC





53335_4_188
BCL11a
Exon 4
+
chr2: 60461457-60461482
UCGUCCCCGUUCUCCGGGA
741







UCAGGU





53335_4_189
BCL11a
Exon 4
+
chr2: 60461458-60461483
CGUCCCCGUUCUCCGGGAU
742







CAGGUU





53335_4_190
BCL11a
Exon 4
+
chr2: 60461459-60461484
GUCCCCGUUCUCCGGGAUC
743







AGGUUG





53335_4_191
BCL11a
Exon 4
+
chr2: 60461481-60461506
UUGGGGUCGUUCUCGCUCU
744







UGAACU





53335_4_192
BCL11a
Exon 4
+
chr2: 60461490-60461515
UUCUCGCUCUUGAACUUGG
745







CCACCA





53335_4_193
BCL11a
Exon 4
+
chr2: 60461508-60461533
GCCACCACGGACUUGAGCG
746







CGCUGC





53335_4_194
BCL11a
Exon 4
+
chr2: 60461529-60461554
CUGCUGGCGCUGCCCACCA
747







AGUCGC





53335_4_195
BCL11a
Exon 4
+
chr2: 60461535-60461560
GCGCUGCCCACCAAGUCGC
748







UGGUGC





53335_4_196
BCL11a
Exon 4
+
chr2: 60461536-60461561
CGCUGCCCACCAAGUCGCU
749







GGUGCC





53335_4_197
BCL11a
Exon 4
+
chr2: 60461542-60461567
CCACCAAGUCGCUGGUGCC
750







GGGUUC





53335_4_198
BCL11a
Exon 4
+
chr2: 60461543-60461568
CACCAAGUCGCUGGUGCCG
751







GGUUCC





53335_4_199
BCL11a
Exon 4
+
chr2: 60461544-60461569
ACCAAGUCGCUGGUGCCGG
752







GUUCCG





53335_4_200
BCL11a
Exon 4
+
chr2: 60461550-60461575
UCGCUGGUGCCGGGUUCCG
753







GGGAGC





53335_4_201
BCL11a
Exon 4
+
chr2: 60461553-60461578
CUGGUGCCGGGUUCCGGGG
754







AGCUGG





53335_4_202
BCL11a
Exon 4
+
chr2: 60461556-60461581
GUGCCGGGUUCCGGGGAGC
755







UGGCGG





53335_4_203
BCL11a
Exon 4
+
chr2: 60461571-60461596
GAGCUGGCGGUGGAGAGAC
756







CGUCGU





53335_4_204
BCL11a
Exon 4
+
chr2: 60461586-60461611
AGACCGUCGUCGGACUUGA
757







CCGUCA





53335_4_205
BCL11a
Exon 4
+
chr2: 60461587-60461612
GACCGUCGUCGGACUUGAC
758







CGUCAU





53335_4_206
BCL11a
Exon 4
+
chr2: 60461588-60461613
ACCGUCGUCGGACUUGACC
759







GUCAUG





53335_4_207
BCL11a
Exon 4
+
chr2: 60461589-60461614
CCGUCGUCGGACUUGACCG
760







UCAUGG





53335_4_208
BCL11a
Exon 4
+
chr2: 60461618-60461643
CGAUUUGUGCAUGUGCGUC
761







UUCAUG





53335_4_209
BCL11a
Exon 4
+
chr2: 60461634-60461659
GUCUUCAUGUGGCGCUUCA
762







GCUUGC





53335_4_210
BCL11a
Exon 4
+
chr2: 60461639-60461664
CAUGUGGCGCUUCAGCUUG
763







CUGGCC





53335_4_211
BCL11a
Exon 4
+
chr2: 60461640-60461665
AUGUGGCGCUUCAGCUUGC
764







UGGCCU





53335_4_212
BCL11a
Exon 4
+
chr2: 60461651-60461676
CAGCUUGCUGGCCUGGGUG
765







CACGCG





53335_4_213
BCL11a
Exon 4
+
chr2: 60461660-60461685
GGCCUGGGUGCACGCGUGG
766







UCGCAC





53335_4_214
BCL11a
Exon 4
+
chr2: 60461673-60461698
GCGUGGUCGCACAGGUUGC
767







ACUUGU





53335_4_215
BCL11a
Exon 4
+
chr2: 60461674-60461699
CGUGGUCGCACAGGUUGCA
768







CUUGUA





53335_4_216
BCL11a
Exon 4
+
chr2: 60461690-60461715
GCACUUGUAGGGCUUCUCG
769







CCCGUG





53335_4_217
BCL11a
Exon 4
+
chr2: 60461699-60461724
GGGCUUCUCGCCCGUGUGG
770







CUGCGC





53335_4_218
BCL11a
Exon 4
+
chr2: 60461711-60461736
CGUGUGGCUGCGCCGGUGC
771







ACCACC





53335_4_219
BCL11a
Exon 4
+
chr2: 60461757-60461782
GUCUUGCCGCAGAACUCGC
772







AUGACU





53335_4_220
BCL11a
Exon 4
+
chr2: 60461767-60461792
AGAACUCGCAUGACUUGGA
773







CUUGAC





53335_4_221
BCL11a
Exon 4
+
chr2: 60461768-60461793
GAACUCGCAUGACUUGGAC
774







UUGACC





53335_4_222
BCL11a
Exon 4
+
chr2: 60461769-60461794
AACUCGCAUGACUUGGACU
775







UGACCG





53335_4_223
BCL11a
Exon 4
+
chr2: 60461770-60461795
ACUCGCAUGACUUGGACUU
776







GACCGG





53335_4_224
BCL11a
Exon 4
+
chr2: 60461774-60461799
GCAUGACUUGGACUUGACC
777







GGGGGC





53335_4_225
BCL11a
Exon 4
+
chr2: 60461775-60461800
CAUGACUUGGACUUGACCG
778







GGGGCU





53335_4_226
BCL11a
Exon 4
+
chr2: 60461778-60461803
GACUUGGACUUGACCGGGG
779







GCUGGG





53335_4_227
BCL11a
Exon 4
+
chr2: 60461779-60461804
ACUUGGACUUGACCGGGGG
780







CUGGGA





53335_4_228
BCL11a
Exon 4
+
chr2: 60461782-60461807
UGGACUUGACCGGGGGCUG
781







GGAGGG





53335_4_229
BCL11a
Exon 4
+
chr2: 60461785-60461810
ACUUGACCGGGGGCUGGGA
782







GGGAGG





53335_4_230
BCL11a
Exon 4
+
chr2: 60461786-60461811
CUUGACCGGGGGCUGGGAG
783







GGAGGA





53335_4_231
BCL11a
Exon 4
+
chr2: 60461787-60461812
UUGACCGGGGGCUGGGAGG
784







GAGGAG





53335_4_232
BCL11a
Exon 4
+
chr2: 60461790-60461815
ACCGGGGGCUGGGAGGGAG
785







GAGGGG





53335_4_233
BCL11a
Exon 4
+
chr2: 60461800-60461825
GGGAGGGAGGAGGGGCGGA
786







UUGCAG





53335_4_234
BCL11a
Exon 4
+
chr2: 60461803-60461828
AGGGAGGAGGGGCGGAUUG
787







CAGAGG





53335_4_235
BCL11a
Exon 4
+
chr2: 60461804-60461829
GGGAGGAGGGGCGGAUUGC
788







AGAGGA





53335_4_236
BCL11a
Exon 4
+
chr2: 60461807-60461832
AGGAGGGGCGGAUUGCAGA
789







GGAGGG





53335_4_237
BCL11a
Exon 4
+
chr2: 60461808-60461833
GGAGGGGCGGAUUGCAGAG
790







GAGGGA





53335_4_238
BCL11a
Exon 4
+
chr2: 60461809-60461834
GAGGGGCGGAUUGCAGAGG
791







AGGGAG





53335_4_239
BCL11a
Exon 4
+
chr2: 60461810-60461835
AGGGGCGGAUUGCAGAGGA
792







GGGAGG





53335_4_240
BCL11a
Exon 4
+
chr2: 60461811-60461836
GGGGCGGAUUGCAGAGGAG
793







GGAGGG





53335_4_241
BCL11a
Exon 4
+
chr2: 60461812-60461837
GGGCGGAUUGCAGAGGAGG
794







GAGGGG





53335_4_242
BCL11a
Exon 4
+
chr2: 60461822-60461847
CAGAGGAGGGAGGGGGGGC
795







GUCGCC





53335_4_243
BCL11a
Exon 4
+
chr2: 60461826-60461851
GGAGGGAGGGGGGGCGUCG
796







CCAGGA





53335_4_244
BCL11a
Exon 4
+
chr2: 60461827-60461852
GAGGGAGGGGGGGCGUCGC
797







CAGGAA





53335_4_245
BCL11a
Exon 4
+
chr2: 60461830-60461855
GGAGGGGGGGCGUCGCCAG
798







GAAGGG





53335_4_246
BCL11a
Exon 4
+
chr2: 60461842-60461867
UCGCCAGGAAGGGCGGCUU
799







GCUACC





53335_4_247
BCL11a
Exon 4
+
chr2: 60461846-60461871
CAGGAAGGGCGGCUUGCUA
800







CCUGGC





53335_4_248
BCL11a
Exon 4
+
chr2: 60461851-60461876
AGGGCGGCUUGCUACCUGG
801







CUGGAA





53335_4_249
BCL11a
Exon 4
+
chr2: 60461872-60461897
GGAAUGGUUGCAGUAACCU
802







UUGCAU





53335_4_250
BCL11a
Exon 4
+
chr2: 60461873-60461898
GAAUGGUUGCAGUAACCUU
803







UGCAUA





53335_4_251
BCL11a
Exon 4
+
chr2: 60461877-60461902
GGUUGCAGUAACCUUUGCA
804







UAGGGC





53335_4_252
BCL11a
Exon 4
+
chr2: 60461878-60461903
GUUGCAGUAACCUUUGCAU
805







AGGGCU





53335_4_253
BCL11a
Exon 4
+
chr2: 60461882-60461907
CAGUAACCUUUGCAUAGGG
806







CUGGGC





53335_4_254
BCL11a
Exon 4
+
chr2: 60461887-60461912
ACCUUUGCAUAGGGCUGGG
807







CCGGCC





53335_4_255
BCL11a
Exon 4
+
chr2: 60461888-60461913
CCUUUGCAUAGGGCUGGGC
808







CGGCCU





53335_4_256
BCL11a
Exon 4
+
chr2: 60461889-60461914
CUUUGCAUAGGGCUGGGCC
809







GGCCUG





53335_4_257
BCL11a
Exon 4
+
chr2: 60461896-60461921
UAGGGCUGGGCCGGCCUGG
810







GGACAG





53335_4_258
BCL11a
Exon 4
+
chr2: 60461899-60461924
GGCUGGGCCGGCCUGGGGA
811







CAGCGG





53335_4_259
BCL11a
Exon 4
+
chr2: 60461900-60461925
GCUGGGCCGGCCUGGGGAC
812







AGCGGU





53335_4_260
BCL11a
Exon 4
+
chr2: 60461949-60461974
UCUCUAAGUCUCCUAGAGA
813







AAUCCA





53335_4_261
BCL11a
Exon 4
+
chr2: 60461952-60461977
CUAAGUCUCCUAGAGAAAU
814







CCAUGG





53335_4_262
BCL11a
Exon 4
+
chr2: 60461953-60461978
UAAGUCUCCUAGAGAAAUC
815







CAUGGC





53335_4_263
BCL11a
Exon 4
+
chr2: 60461956-60461981
GUCUCCUAGAGAAAUCCAU
816







GGCGGG





53335_4_264
BCL11a
Exon 4
+
chr2: 60461971-60461996
CCAUGGCGGGAGGCUCCAU
817







AGCCAU





53335_4_265
BCL11a
Exon 4
+
chr2: 60461997-60462022
GGAUUCAACCGCAGCACCC
818







UGUCAA





53335_4_266
BCL11a
Exon 4
+
chr2: 60462004-60462029
ACCGCAGCACCCUGUCAAA
819







GGCACU





53335_4_267
BCL11a
Exon 4
+
chr2: 60462005-60462030
CCGCAGCACCCUGUCAAAG
820







GCACUC





53335_4_268
BCL11a
Exon 4
+
chr2: 60462011-60462036
CACCCUGUCAAAGGCACUC
821







GGGUGA





53335_4_269
BCL11a
Exon 4
+
chr2: 60462012-60462037
ACCCUGUCAAAGGCACUCG
822







GGUGAU





53335_4_270
BCL11a
Exon 4
+
chr2: 60462015-60462040
CUGUCAAAGGCACUCGGGU
823







GAUGGG





53335_4_271
BCL11a
Exon 4
+
chr2: 60462020-60462045
AAAGGCACUCGGGUGAUGG
824







GUGGCC





53335_4_272
BCL11a
Exon 4
+
chr2: 60462021-60462046
AAGGCACUCGGGUGAUGGG
825







UGGCCA





53335_4_273
BCL11a
Exon 4
+
chr2: 60462041-60462066
GGCCAGGGCCAUCUCUUCC
826







GCCCCC





53335_4_274
BCL11a
Exon 4
+
chr2: 60462053-60462078
CUCUUCCGCCCCCAGGCGC
827







UCUAUG





53335_4_275
BCL11a
Exon 4
+
chr2: 60462056-60462081
UUCCGCCCCCAGGCGCUCU
828







AUGCGG





53335_4_276
BCL11a
Exon 4
+
chr2: 60462057-60462082
UCCGCCCCCAGGCGCUCUA
829







UGCGGU





53335_4_277
BCL11a
Exon 4
+
chr2: 60462058-60462083
CCGCCCCCAGGCGCUCUAU
830







GCGGUG





53335_4_278
BCL11a
Exon 4
+
chr2: 60462059-60462084
CGCCCCCAGGCGCUCUAUG
831







CGGUGG





53335_4_279
BCL11a
Exon 4
+
chr2: 60462076-60462101
UGCGGUGGGGGUCCAAGUG
832







AUGUCU





53335_4_280
BCL11a
Exon 4
+
chr2: 60462079-60462104
GGUGGGGGUCCAAGUGAUG
833







UCUCGG





53335_4_281
BCL11a
Exon 4
+
chr2: 60462082-60462107
GGGGGUCCAAGUGAUGUCU
834







CGGUGG





53335_4_282
BCL11a
Exon 4
+
chr2: 60462092-60462117
GUGAUGUCUCGGUGGUGGA
835







CUAAAC





53335_4_283
BCL11a
Exon 4
+
chr2: 60462093-60462118
UGAUGUCUCGGUGGUGGAC
836







UAAACA





53335_4_284
BCL11a
Exon 4
+
chr2: 60462094-60462119
GAUGUCUCGGUGGUGGACU
837







AAACAG





53335_4_285
BCL11a
Exon 4
+
chr2: 60462095-60462120
AUGUCUCGGUGGUGGACUA
838







AACAGG





53335_4_286
BCL11a
Exon 4
+
chr2: 60462096-60462121
UGUCUCGGUGGUGGACUAA
839







ACAGGG





53335_4_287
BCL11a
Exon 4
+
chr2: 60462097-60462122
GUCUCGGUGGUGGACUAAA
840







CAGGGG





53335_4_288
BCL11a
Exon 4
+
chr2: 60462102-60462127
GGUGGUGGACUAAACAGGG
841







GGGGAG





53335_4_289
BCL11a
Exon 4
+
chr2: 60462103-60462128
GUGGUGGACUAAACAGGGG
842







GGGAGU





53335_4_290
BCL11a
Exon 4
+
chr2: 60462106-60462131
GUGGACUAAACAGGGGGGG
843







AGUGGG





53335_4_291
BCL11a
Exon 4
+
chr2: 60462125-60462150
AGUGGGUGGAAAGCGCCCU
844







UCUGCC





53335_4_292
BCL11a
Exon 4
+
chr2: 60462129-60462154
GGUGGAAAGCGCCCUUCUG
845







CCAGGC





53335_4_293
BCL11a
Exon 4
+
chr2: 60462154-60462179
CGGAAGCCUCUCUCGAUAC
846







UGAUCC





53335_4_294
BCL11a
Exon 4
+
chr2: 60462167-60462192
CGAUACUGAUCCUGGUAUU
847







CUUAGC





53335_4_295
BCL11a
Exon 4
+
chr2: 60462174-60462199
GAUCCUGGUAUUCUUAGCA
848







GGUUAA





53335_4_296
BCL11a
Exon 4
+
chr2: 60462175-60462200
AUCCUGGUAUUCUUAGCAG
849







GUUAAA





53335_4_297
BCL11a
Exon 4
+
chr2: 60462176-60462201
UCCUGGUAUUCUUAGCAGG
850







UUAAAG





53335_4_298
BCL11a
Exon 4
+
chr2: 60462203-60462228
GUUAUUGUCUGCAAUAUGA
851







AUCCCA





53335_4_299
BCL11a
Exon 4
+
chr2: 60462208-60462233
UGUCUGCAAUAUGAAUCCC
852







AUGGAG





53335_4_300
BCL11a
Exon 4
+
chr2: 60462211-60462236
CUGCAAUAUGAAUCCCAUG
853







GAGAGG





53335_4_301
BCL11a
Exon 4
+
chr2: 60462215-60462240
AAUAUGAAUCCCAUGGAGA
854







GGUGGC





53335_4_302
BCL11a
Exon 4
+
chr2: 60462216-60462241
AUAUGAAUCCCAUGGAGAG
855







GUGGCU





53335_4_303
BCL11a
Exon 4
+
chr2: 60462220-60462245
GAAUCCCAUGGAGAGGUGG
856







CUGGGA





53335_4_304
BCL11a
Exon 4
+
chr2: 60462244-60462269
AAGGACAUUCUGCACCUAG
857







UCCUGA





53335_4_305
BCL11a
Exon 4
+
chr2: 60462245-60462270
AGGACAUUCUGCACCUAGU
858







CCUGAA





53335_4_306
BCL11a
Exon 4
+
chr2: 60462259-60462284
CUAGUCCUGAAGGGAUACC
859







AACCCG





53335_4_307
BCL11a
Exon 4
+
chr2: 60462260-60462285
UAGUCCUGAAGGGAUACCA
860







ACCCGC





53335_4_308
BCL11a
Exon 4
+
chr2: 60462261-60462286
AGUCCUGAAGGGAUACCAA
861







CCCGCG





53335_4_309
BCL11a
Exon 4
+
chr2: 60462266-60462291
UGAAGGGAUACCAACCCGC
862







GGGGUC





53335_4_310
BCL11a
Exon 4
+
chr2: 60462267-60462292
GAAGGGAUACCAACCCGCG
863







GGGUCA





53335_4_311
BCL11a
Exon 4
+
chr2: 60462268-60462293
AAGGGAUACCAACCCGCGG
864







GGUCAG





53335_4_312
BCL11a
Exon 4
+
chr2: 60462345-60462370
GCGUGUUGCAAGAGAAACC
865







AUGCAC





53335_4_313
BCL11a
Exon 4
+
chr2: 60462352-60462377
GCAAGAGAAACCAUGCACU
866







GGUGAA





53335_4_314
BCL11a
Exon 4
+
chr2: 60462384-60462409
UUGCAAGUUGUACAUGUGU
867







AGCUGC





53335_4_315
BCL11a
Exon 4
+
chr2: 60462385-60462410
UGCAAGUUGUACAUGUGUA
868







GCUGCU





53335_4_316
BCL11a
Exon 4

chr2: 60457269-60457294
GGAAAAACCACUGUCUGUG
869







UUUUUU





53335_4_317
BCL11a
Exon 4

chr2: 60457295-60457320
GUUUCUGGUCUUUGUUAAG
870







UUCUAU





53335_4_318
BCL11a
Exon 4

chr2: 60457315-60457340
CCUGGCUUUUUAUUGUAUU
871







UGUUUC





53335_4_319
BCL11a
Exon 4

chr2: 60457338-60457363
AAGAUGACCAAAGGUCAUU
872







ACAACC





53335_4_320
BCL11a
Exon 4

chr2: 60457352-60457377
AAAAAAAAAAAUAAAAGAU
873







GACCAA





53335_4_321
BCL11a
Exon 4

chr2: 60457415-60457440
UGCUUAUGUGCCCUGUUCA
874







AAACAG





53335_4_322
BCL11a
Exon 4

chr2: 60457459-60457484
AACUUGAAAUUUUAUCUUU
875







UACUAU





53335_4_323
BCL11a
Exon 4

chr2: 60457460-60457485
UAACUUGAAAUUUUAUCUU
876







UUACUA





53335_4_324
BCL11a
Exon 4

chr2: 60457522-60457547
AUGGCAAUGCAGAAUAUUU
877







UGUUAU





53335_4_325
BCL11a
Exon 4

chr2: 60457546-60457571
GCUUUAGUCAAUACUUUUU
878







UGUAAA





53335_4_326
BCL11a
Exon 4

chr2: 60457613-60457638
ACUAAAUGGUGCUUUAUAU
879







UUAGAU





53335_4_327
BCL11a
Exon 4

chr2: 60457632-60457657
GUUUUUUUCAUUGCCAAAA
880







ACUAAA





53335_4_328
BCL11a
Exon 4

chr2: 60457786-60457811
AUGCAGUACUGCAAGCUAA
881







UAACGU





53335_4_329
BCL11a
Exon 4

chr2: 60457858-60457883
AAUGUCACAUGGAUGGCUG
882







UCAUAG





53335_4_330
BCL11a
Exon 4

chr2: 60457859-60457884
GAAUGUCACAUGGAUGGCU
883







GUCAUA





53335_4_331
BCL11a
Exon 4

chr2: 60457860-60457885
AGAAUGUCACAUGGAUGGC
884







UGUCAU





53335_4_332
BCL11a
Exon 4

chr2: 60457870-60457895
GGAGCCUGCUAGAAUGUCA
885







CAUGGA





53335_4_333
BCL11a
Exon 4

chr2: 60457874-60457899
UGGGGGAGCCUGCUAGAAU
886







GUCACA





53335_4_334
BCL11a
Exon 4

chr2: 60457896-60457921
GAGAAGCCAUAUAAUGGCG
887







GUUUGG





53335_4_335
BCL11a
Exon 4

chr2: 60457897-60457922
UGAGAAGCCAUAUAAUGGC
888







GGUUUG





53335_4_336
BCL11a
Exon 4

chr2: 60457898-60457923
AUGAGAAGCCAUAUAAUGG
889







CGGUUU





53335_4_337
BCL11a
Exon 4

chr2: 60457899-60457924
GAUGAGAAGCCAUAUAAUG
890







GCGGUU





53335_4_338
BCL11a
Exon 4

chr2: 60457904-60457929
UUACAGAUGAGAAGCCAUA
891







UAAUGG





53335_4_339
BCL11a
Exon 4

chr2: 60457907-60457932
ACAUUACAGAUGAGAAGCC
892







AUAUAA





53335_4_340
BCL11a
Exon 4

chr2: 60457999-60458024
CCACAGUAUAUUUUUUUAA
893







UUUGGC





53335_4_341
BCL11a
Exon 4

chr2: 60458003-60458028
GCUGCCACAGUAUAUUUUU
894







UUAAUU





53335_4_342
BCL11a
Exon 4

chr2: 60458030-60458055
UUUUGGUAGUGGAAAAAAA
895







AAAGAC





53335_4_343
BCL11a
Exon 4

chr2: 60458046-60458071
GGUAUCAAUGUACCUUUUU
896







UGGUAG





53335_4_344
BCL11a
Exon 4

chr2: 60458052-60458077
UUAAAAGGUAUCAAUGUAC
897







CUUUUU





53335_4_345
BCL11a
Exon 4

chr2: 60458072-60458097
UUUAACUGUUGCUUGUUCU
898







CUUAAA





53335_4_346
BCL11a
Exon 4

chr2: 60458130-60458155
UUGAAUUAAAUGUUCAUCU
899







AGUGUU





53335_4_347
BCL11a
Exon 4

chr2: 60458161-60458186
UGGUCUUUUUUCUGUAUUU
900







CUAGAA





53335_4_348
BCL11a
Exon 4

chr2: 60458186-60458211
UGAUUCCUAUGCUAAAAUA
901







CAUUUA





53335_4_349
BCL11a
Exon 4

chr2: 60458231-60458256
UUAAGAUUAUAUAGUACUU
902







AAAUAU





53335_4_350
BCL11a
Exon 4

chr2: 60458260-60458285
AAAAAAAAAAACAUACAUU
903







GGGGAA





53335_4_351
BCL11a
Exon 4

chr2: 60458265-60458290
UUGUAAAAAAAAAAAACAU
904







ACAUUG





53335_4_352
BCL11a
Exon 4

chr2: 60458266-60458291
GUUGUAAAAAAAAAAAACA
905







UACAUU





53335_4_353
BCL11a
Exon 4

chr2: 60458267-60458292
GGUUGUAAAAAAAAAAAAC
906







AUACAU





53335_4_354
BCL11a
Exon 4

chr2: 60458293-60458318
AUGCCUUGGAUACACACCG
907







CUCUUC





53335_4_355
BCL11a
Exon 4

chr2: 60458312-60458337
AAAUGGUAGUGGAAAUUCU
908







AUGCCU





53335_4_356
BCL11a
Exon 4

chr2: 60458328-60458353
CUUGUUAUCCAUUUAAAAA
909







UGGUAG





53335_4_357
BCL11a
Exon 4

chr2: 60458334-60458359
ACAAGACUUGUUAUCCAUU
910







UAAAAA





53335_4_358
BCL11a
Exon 4

chr2: 60458366-60458391
GCAUUUUAGGGUUCCAUUG
911







UCUUGG





53335_4_359
BCL11a
Exon 4

chr2: 60458369-60458394
ACUGCAUUUUAGGGUUCCA
912







UUGUCU





53335_4_360
BCL11a
Exon 4

chr2: 60458383-60458408
AUGUUUAGGGGGGAACUGC
913







AUUUUA





53335_4_361
BCL11a
Exon 4

chr2: 60458384-60458409
UAUGUUUAGGGGGGAACUG
914







CAUUUU





53335_4_362
BCL11a
Exon 4

chr2: 60458398-60458423
AAAAAACACUUCAUUAUGU
915







UUAGGG





53335_4_363
BCL11a
Exon 4

chr2: 60458399-60458424
UAAAAAACACUUCAUUAUG
916







UUUAGG





53335_4_364
BCL11a
Exon 4

chr2: 60458400-60458425
UUAAAAAACACUUCAUUAU
917







GUUUAG





53335_4_365
BCL11a
Exon 4

chr2: 60458401-60458426
UUUAAAAAACACUUCAUUA
918







UGUUUA





53335_4_366
BCL11a
Exon 4

chr2: 60458402-60458427
UUUUAAAAAACACUUCAUU
919







AUGUUU





53335_4_367
BCL11a
Exon 4

chr2: 60458478-60458503
UGAUUGCUUUCGCUUCUAC
920







AGUGCA





53335_4_368
BCL11a
Exon 4

chr2: 60458535-60458560
GACGCAACAUUGCAAGCGC
921







UGUGAA





53335_4_369
BCL11a
Exon 4

chr2: 60458562-60458587
UACUUGACUAUUGAGCUUA
922







CUUACU





53335_4_370
BCL11a
Exon 4

chr2: 60458634-60458659
AAAAAAAUUGAACACAAUC
923







UCAUUG





53335_4_371
BCL11a
Exon 4

chr2: 60458682-60458707
UCCCAGUUUACAGGUCUAU
924







ACUUAA





53335_4_372
BCL11a
Exon 4

chr2: 60458683-60458708
UUCCCAGUUUACAGGUCUA
925







UACUUA





53335_4_373
BCL11a
Exon 4

chr2: 60458696-60458721
GCACUGUACAAUUUUCCCA
926







GUUUAC





53335_4_374
BCL11a
Exon 4

chr2: 60458734-60458759
GAGUAUAAAAUAAACCUGC
927







UCAGAU





53335_4_375
BCL11a
Exon 4

chr2: 60458764-60458789
AUCUUUUCUCUAAUCAGAG
928







AUACAG





53335_4_376
BCL11a
Exon 4

chr2: 60458829-60458854
AAUAAAAGCUAGCAUCUGC
929







CCCAGU





53335_4_377
BCL11a
Exon 4

chr2: 60458897-60458922
UGUGCUAUUUGUGUUAACA
930







UGGAAG





53335_4_378
BCL11a
Exon 4

chr2: 60458903-60458928
ACACUGUGUGCUAUUUGUG
931







UUAACA





53335_4_379
BCL11a
Exon 4

chr2: 60459085-60459110
ACUAUUUGCCAUUUAAAAC
932







UAGAAC





53335_4_380
BCL11a
Exon 4

chr2: 60459114-60459139
AAUAAUAUGAUUUAUUAGC
933







ACAACG





53335_4_381
BCL11a
Exon 4

chr2: 60459152-60459177
AGGCUGACAAUAAGGUUUG
934







ACAGAG





53335_4_382
BCL11a
Exon 4

chr2: 60459153-60459178
GAGGCUGACAAUAAGGUUU
935







GACAGA





53335_4_383
BCL11a
Exon 4

chr2: 60459154-60459179
AGAGGCUGACAAUAAGGUU
936







UGACAG





53335_4_384
BCL11a
Exon 4

chr2: 60459165-60459190
UAUUGAAAGGAAGAGGCUG
937







ACAAUA





53335_4_385
BCL11a
Exon 4

chr2: 60459177-60459202
CCUUGUAUACCAUAUUGAA
938







AGGAAG





53335_4_386
BCL11a
Exon 4

chr2: 60459183-60459208
UUAAGACCUUGUAUACCAU
939







AUUGAA





53335_4_387
BCL11a
Exon 4

chr2: 60459229-60459254
GAUCCAGAUCUACUUGGUU
940







GUCAAG





53335_4_388
BCL11a
Exon 4

chr2: 60459240-60459265
CAAAAGAAAUAGAUCCAGA
941







UCUACU





53335_4_389
BCL11a
Exon 4

chr2: 60459271-60459296
UUUAAUAAUGUCUUUUUAA
942







AAAUAC





53335_4_390
BCL11a
Exon 4

chr2: 60459323-60459348
UGGAACGCAAUUAAAUACA
943







CUAGUA





53335_4_391
BCL11a
Exon 4

chr2: 60459348-60459373
UUGAAUGUGUAAUGUGCAA
944







AAGCCC





53335_4_392
BCL11a
Exon 4

chr2: 60459418-60459443
CUCCUGGUGAGAGCUUAAA
945







AGAAAU





53335_4_393
BCL11a
Exon 4

chr2: 60459419-60459444
GCUCCUGGUGAGAGCUUAA
946







AAGAAA





53335_4_394
BCL11a
Exon 4

chr2: 60459439-60459464
ACCAGUAUAAAAGCUACUU
947







UGCUCC





53335_4_395
BCL11a
Exon 4

chr2: 60459547-60459572
UUCUAUAUUGUAUUUCUCA
948







CAACAA





53335_4_396
BCL11a
Exon 4

chr2: 60459588-60459613
AGCAUUGGGUGAGGUAAUA
949







AACCUU





53335_4_397
BCL11a
Exon 4

chr2: 60459602-60459627
UUGUAGCUUAAUUCAGCAU
950







UGGGUG





53335_4_398
BCL11a
Exon 4

chr2: 60459607-60459632
UAAACUUGUAGCUUAAUUC
951







AGCAUU





53335_4_399
BCL11a
Exon 4

chr2: 60459608-60459633
AUAAACUUGUAGCUUAAUU
952







CAGCAU





53335_4_400
BCL11a
Exon 4

chr2: 60459651-60459676
CUUGGAUCUAUUAAAACCA
953







CAUCGA





53335_4_401
BCL11a
Exon 4

chr2: 60459674-60459699
AUUUGGUUUUAAAAUAUGA
954







GUGCCU





53335_4_402
BCL11a
Exon 4

chr2: 60459696-60459721
AACAGAACAAGUUUAUUCU
955







AUCAUU





53335_4_403
BCL11a
Exon 4

chr2: 60459749-60459774
UGUAUCAAUUGGAAAGGAA
956







GAAAAA





53335_4_404
BCL11a
Exon 4

chr2: 60459760-60459785
AAAGGGUUAAAUGUAUCAA
957







UUGGAA





53335_4_405
BCL11a
Exon 4

chr2: 60459765-60459790
UCUCUAAAGGGUUAAAUGU
958







AUCAAU





53335_4_406
BCL11a
Exon 4

chr2: 60459782-60459807
UAUGAGCUAAAUGUCUGUC
959







UCUAAA





53335_4_407
BCL11a
Exon 4

chr2: 60459783-60459808
CUAUGAGCUAAAUGUCUGU
960







CUCUAA





53335_4_408
BCL11a
Exon 4

chr2: 60459855-60459880
UAACGUGAGGAGGAAAAAC
961







AGUCUU





53335_4_409
BCL11a
Exon 4

chr2: 60459870-60459895
UACAGUUUUAUUUUAUAAC
962







GUGAGG





53335_4_410
BCL11a
Exon 4

chr2: 60459873-60459898
AUGUACAGUUUUAUUUUAU
963







AACGUG





53335_4_411
BCL11a
Exon 4

chr2: 60460023-60460048
CUUAGACAGCAUGUAUGGU
964







AUGUUA





53335_4_412
BCL11a
Exon 4

chr2: 60460033-60460058
UUUUUUUAAACUUAGACAG
965







CAUGUA





53335_4_413
BCL11a
Exon 4

chr2: 60460130-60460155
ACCGUUUGAAUGCAUGAUC
966







UGUAUG





53335_4_414
BCL11a
Exon 4

chr2: 60460131-60460156
CACCGUUUGAAUGCAUGAU
967







CUGUAU





53335_4_415
BCL11a
Exon 4

chr2: 60460132-60460157
UCACCGUUUGAAUGCAUGA
968







UCUGUA





53335_4_416
BCL11a
Exon 4

chr2: 60460314-60460339
AUCGCCCUCCAGCCCCACUC
969







CCUGU





53335_4_417
BCL11a
Exon 4

chr2: 60460403-60460428
GAAUAAUGAUAUAAAAACU
970







GAAUAG





53335_4_418
BCL11a
Exon 4

chr2: 60460448-60460473
UACCCUGGAGAAACACAUG
971







AAAAAA





53335_4_419
BCL11a
Exon 4

chr2: 60460468-60460493
AUGCCUUUUAGCGUGUACA
972







GUACCC





53335_4_420
BCL11a
Exon 4

chr2: 60460522-60460547
AUGAAAACGCAUGGCCAGG
973







UGGGGA





53335_4_421
BCL11a
Exon 4

chr2: 60460526-60460551
GCACAUGAAAACGCAUGGC
974







CAGGUG





53335_4_422
BCL11a
Exon 4

chr2: 60460527-60460552
GGCACAUGAAAACGCAUGG
975







CCAGGU





53335_4_423
BCL11a
Exon 4

chr2: 60460528-60460553
AGGCACAUGAAAACGCAUG
976







GCCAGG





53335_4_424
BCL11a
Exon 4

chr2: 60460531-60460556
ACCAGGCACAUGAAAACGC
977







AUGGCC





53335_4_425
BCL11a
Exon 4

chr2: 60460536-60460561
AGCUCACCAGGCACAUGAA
978







AACGCA





53335_4_426
BCL11a
Exon 4

chr2: 60460553-60460578
CUGUGCCCAGAGUAGCAAG
979







CUCACC





53335_4_427
BCL11a
Exon 4

chr2: 60460610-60460635
CCACAGGAGAAGCCACACG
980







GGCGAA





53335_4_428
BCL11a
Exon 4

chr2: 60460617-60460642
UCACUGUCCACAGGAGAAG
981







CCACAC





53335_4_429
BCL11a
Exon 4

chr2: 60460618-60460643
CUCACUGUCCACAGGAGAA
982







GCCACA





53335_4_430
BCL11a
Exon 4

chr2: 60460631-60460656
GAACUGUAGCAAUCUCACU
983







GUCCAC





53335_4_431
BCL11a
Exon 4

chr2: 60460670-60460695
ACGCAGCGACACUUGUGAG
984







UACUGU





53335_4_432
BCL11a
Exon 4

chr2: 60460671-60460696
GACGCAGCGACACUUGUGA
985







GUACUG





53335_4_433
BCL11a
Exon 4

chr2: 60460701-60460726
GCCCGGGCAGGCCCAGCUC
986







AAAAGA





53335_4_434
BCL11a
Exon 4

chr2: 60460702-60460727
GGCCCGGGCAGGCCCAGCU
987







CAAAAG





53335_4_435
BCL11a
Exon 4

chr2: 60460718-60460743
CCAUAUUAGUGGUCCGGGC
988







CCGGGC





53335_4_436
BCL11a
Exon 4

chr2: 60460722-60460747
CGCCCCAUAUUAGUGGUCC
989







GGGCCC





53335_4_437
BCL11a
Exon 4

chr2: 60460723-60460748
ACGCCCCAUAUUAGUGGUC
990







CGGGCC





53335_4_438
BCL11a
Exon 4

chr2: 60460728-60460753
GGAGCACGCCCCAUAUUAG
991







UGGUCC





53335_4_439
BCL11a
Exon 4

chr2: 60460729-60460754
GGGAGCACGCCCCAUAUUA
992







GUGGUC





53335_4_440
BCL11a
Exon 4

chr2: 60460734-60460759
GUGGAGGGAGCACGCCCCA
993







UAUUAG





53335_4_441
BCL11a
Exon 4

chr2: 60460754-60460779
GGGGCGCAGCGGCACGGGA
994







AGUGGA





53335_4_442
BCL11a
Exon 4

chr2: 60460755-60460780
CGGGGCGCAGCGGCACGGG
995







AAGUGG





53335_4_443
BCL11a
Exon 4

chr2: 60460758-60460783
UCUCGGGGCGCAGCGGCAC
996







GGGAAG





53335_4_444
BCL11a
Exon 4

chr2: 60460764-60460789
GAGGGAUCUCGGGGCGCAG
997







CGGCAC





53335_4_445
BCL11a
Exon 4

chr2: 60460765-60460790
GGAGGGAUCUCGGGGCGCA
998







GCGGCA





53335_4_446
BCL11a
Exon 4

chr2: 60460770-60460795
UGGACGGAGGGAUCUCGGG
999







GCGCAG





53335_4_447
BCL11a
Exon 4

chr2: 60460778-60460803
CGGGGAGCUGGACGGAGGG
1000







AUCUCG





53335_4_448
BCL11a
Exon 4

chr2: 60460779-60460804
CCGGGGAGCUGGACGGAGG
1001







GAUCUC





53335_4_449
BCL11a
Exon 4

chr2: 60460780-60460805
CCCGGGGAGCUGGACGGAG
1002







GGAUCU





53335_4_450
BCL11a
Exon 4

chr2: 60460787-60460812
CACACCGCCCGGGGAGCUG
1003







GACGGA





53335_4_451
BCL11a
Exon 4

chr2: 60460788-60460813
CCACACCGCCCGGGGAGCU
1004







GGACGG





53335_4_452
BCL11a
Exon 4

chr2: 60460791-60460816
UCUCCACACCGCCCGGGGA
1005







GCUGGA





53335_4_453
BCL11a
Exon 4

chr2: 60460795-60460820
CGCUUCUCCACACCGCCCG
1006







GGGAGC





53335_4_454
BCL11a
Exon 4

chr2: 60460801-60460826
AGUUUGCGCUUCUCCACAC
1007







CGCCCG





53335_4_455
BCL11a
Exon 4

chr2: 60460802-60460827
GAGUUUGCGCUUCUCCACA
1008







CCGCCC





53335_4_456
BCL11a
Exon 4

chr2: 60460803-60460828
GGAGUUUGCGCUUCUCCAC
1009







ACCGCC





53335_4_457
BCL11a
Exon 4

chr2: 60460829-60460854
CUCGUCGGAGCACUCCUCG
1010







GAGAAC





53335_4_458
BCL11a
Exon 4

chr2: 60460830-60460855
CCUCGUCGGAGCACUCCUC
1011







GGAGAA





53335_4_459
BCL11a
Exon 4

chr2: 60460837-60460862
UUUGCCUCCUCGUCGGAGC
1012







ACUCCU





53335_4_460
BCL11a
Exon 4

chr2: 60460849-60460874
AGACAAUCGCCUUUUGCCU
1013







CCUCGU





53335_4_461
BCL11a
Exon 4

chr2: 60460884-60460909
AGCUCAAAGAUCCCUUCCU
1014







UAGCUU





53335_4_462
BCL11a
Exon 4

chr2: 60460913-60460938
GUGGCUCGCCGGCUACGCG
1015







GCCUCC





53335_4_463
BCL11a
Exon 4

chr2: 60460921-60460946
UACUCGCAGUGGCUCGCCG
1016







GCUACG





53335_4_464
BCL11a
Exon 4

chr2: 60460929-60460954
AGAACGUGUACUCGCAGUG
1017







GCUCGC





53335_4_465
BCL11a
Exon 4

chr2: 60460937-60460962
CAACACGGAGAACGUGUAC
1018







UCGCAG





53335_4_466
BCL11a
Exon 4

chr2: 60460957-60460982
CUGCCCCCGGCCGCGAUGC
1019







CCAACA





53335_4_467
BCL11a
Exon 4

chr2: 60460975-60461000
CUCGAGAAGGAGUUCGACC
1020







UGCCCC





53335_4_468
BCL11a
Exon 4

chr2: 60460993-60461018
UUCUCUAAGCGCAUCAAGC
1021







UCGAGA





53335_4_469
BCL11a
Exon 4

chr2: 60461043-60461068
GGGGCCUGUCCAAAAAGCU
1022







GCUGCU





53335_4_470
BCL11a
Exon 4

chr2: 60461044-60461069
GGGGGCCUGUCCAAAAAGC
1023







UGCUGC





53335_4_471
BCL11a
Exon 4

chr2: 60461067-60461092
GCUCCCCGGGCGAGUCGGC
1024







CUCGGG





53335_4_472
BCL11a
Exon 4

chr2: 60461068-60461093
UGCUCCCCGGGCGAGUCGG
1025







CCUCGG





53335_4_473
BCL11a
Exon 4

chr2: 60461069-60461094
CUGCUCCCCGGGCGAGUCG
1026







GCCUCG





53335_4_474
BCL11a
Exon 4

chr2: 60461070-60461095
GCUGCUCCCCGGGCGAGUC
1027







GGCCUC





53335_4_475
BCL11a
Exon 4

chr2: 60461071-60461096
GGCUGCUCCCCGGGCGAGU
1028







CGGCCU





53335_4_476
BCL11a
Exon 4

chr2: 60461077-60461102
GGCCGCGGCUGCUCCCCGG
1029







GCGAGU





53335_4_477
BCL11a
Exon 4

chr2: 60461085-60461110
CUGUUAAUGGCCGCGGCUG
1030







CUCCCC





53335_4_478
BCL11a
Exon 4

chr2: 60461086-60461111
ACUGUUAAUGGCCGCGGCU
1031







GCUCCC





53335_4_479
BCL11a
Exon 4

chr2: 60461097-60461122
UAGACGAUGGCACUGUUAA
1032







UGGCCG





53335_4_480
BCL11a
Exon 4

chr2: 60461103-60461128
ACCGCAUAGACGAUGGCAC
1033







UGUUAA





53335_4_481
BCL11a
Exon 4

chr2: 60461115-60461140
CCGGCGAGUCGGACCGCAU
1034







AGACGA





53335_4_482
BCL11a
Exon 4

chr2: 60461131-60461156
GACGAAGACUCGGUGGCCG
1035







GCGAGU





53335_4_483
BCL11a
Exon 4

chr2: 60461139-60461164
ACACUUGCGACGAAGACUC
1036







GGUGGC





53335_4_484
BCL11a
Exon 4

chr2: 60461143-60461168
AGGGACACUUGCGACGAAG
1037







ACUCGG





53335_4_485
BCL11a
Exon 4

chr2: 60461146-60461171
CACAGGGACACUUGCGACG
1038







AAGACU





53335_4_486
BCL11a
Exon 4

chr2: 60461167-60461192
CACCUGGCCGAGGCCGAGG
1039







GCCACA





53335_4_487
BCL11a
Exon 4

chr2: 60461168-60461193
CCACCUGGCCGAGGCCGAG
1040







GGCCAC





53335_4_488
BCL11a
Exon 4

chr2: 60461175-60461200
AGCGCGGCCACCUGGCCGA
1041







GGCCGA





53335_4_489
BCL11a
Exon 4

chr2: 60461176-60461201
AAGCGCGGCCACCUGGCCG
1042







AGGCCG





53335_4_490
BCL11a
Exon 4

chr2: 60461182-60461207
AAGCAUAAGCGCGGCCACC
1043







UGGCCG





53335_4_491
BCL11a
Exon 4

chr2: 60461188-60461213
GGCGAGAAGCAUAAGCGCG
1044







GCCACC





53335_4_492
BCL11a
Exon 4

chr2: 60461196-60461221
AGGUCCUGGGCGAGAAGCA
1045







UAAGCG





53335_4_493
BCL11a
Exon 4

chr2: 60461214-60461239
UCAGCGAGGCCUUCCACCA
1046







GGUCCU





53335_4_494
BCL11a
Exon 4

chr2: 60461215-60461240
UUCAGCGAGGCCUUCCACC
1047







AGGUCC





53335_4_495
BCL11a
Exon 4

chr2: 60461221-60461246
CAGCACUUCAGCGAGGCCU
1048







UCCACC





53335_4_496
BCL11a
Exon 4

chr2: 60461233-60461258
CUCAGCUCCAUGCAGCACU
1049







UCAGCG





53335_4_497
BCL11a
Exon 4

chr2: 60461263-60461288
GCCCUGCCCGACGUCAUGC
1050







AGGGCA





53335_4_498
BCL11a
Exon 4

chr2: 60461268-60461293
GCCGCGCCCUGCCCGACGU
1051







CAUGCA





53335_4_499
BCL11a
Exon 4

chr2: 60461269-60461294
AGCCGCGCCCUGCCCGACG
1052







UCAUGC





53335_4_500
BCL11a
Exon 4

chr2: 60461304-60461329
GCUCGCGGGGCGCGGUCGU
1053







GGGCGU





53335_4_501
BCL11a
Exon 4

chr2: 60461305-60461330
AGCUCGCGGGGCGCGGUCG
1054







UGGGCG





53335_4_502
BCL11a
Exon 4

chr2: 60461310-60461335
AGAACAGCUCGCGGGGCGC
1055







GGUCGU





53335_4_503
BCL11a
Exon 4

chr2: 60461311-60461336
GAGAACAGCUCGCGGGGCG
1056







CGGUCG





53335_4_504
BCL11a
Exon 4

chr2: 60461317-60461342
CACCACGAGAACAGCUCGC
1057







GGGGCG





53335_4_505
BCL11a
Exon 4

chr2: 60461322-60461347
CGCGCCACCACGAGAACAG
1058







CUCGCG





53335_4_506
BCL11a
Exon 4

chr2: 60461323-60461348
GCGCGCCACCACGAGAACA
1059







GCUCGC





53335_4_507
BCL11a
Exon 4

chr2: 60461324-60461349
GGCGCGCCACCACGAGAAC
1060







AGCUCG





53335_4_508
BCL11a
Exon 4

chr2: 60461350-60461375
UACGGCUUCGGGCUGAGCC
1061







UGGAGG





53335_4_509
BCL11a
Exon 4

chr2: 60461353-60461378
GACUACGGCUUCGGGCUGA
1062







GCCUGG





53335_4_510
BCL11a
Exon 4

chr2: 60461356-60461381
CUGGACUACGGCUUCGGGC
1063







UGAGCC





53335_4_511
BCL11a
Exon 4

chr2: 60461366-60461391
CUCGCUCUCCCUGGACUAC
1064







GGCUUC





53335_4_512
BCL11a
Exon 4

chr2: 60461367-60461392
UCUCGCUCUCCCUGGACUA
1065







CGGCUU





53335_4_513
BCL11a
Exon 4

chr2: 60461373-60461398
ACUGCCUCUCGCUCUCCCU
1066







GGACUA





53335_4_514
BCL11a
Exon 4

chr2: 60461380-60461405
CUCCUCGACUGCCUCUCGC
1067







UCUCCC





53335_4_515
BCL11a
Exon 4

chr2: 60461512-60461537
GCCAGCAGCGCGCUCAAGU
1068







CCGUGG





53335_4_516
BCL11a
Exon 4

chr2: 60461515-60461540
AGCGCCAGCAGCGCGCUCA
1069







AGUCCG





53335_4_517
BCL11a
Exon 4

chr2: 60461544-60461569
CGGAACCCGGCACCAGCGA
1070







CUUGGU





53335_4_518
BCL11a
Exon 4

chr2: 60461545-60461570
CCGGAACCCGGCACCAGCG
1071







ACUUGG





53335_4_519
BCL11a
Exon 4

chr2: 60461548-60461573
UCCCCGGAACCCGGCACCA
1072







GCGACU





53335_4_520
BCL11a
Exon 4

chr2: 60461562-60461587
UCUCCACCGCCAGCUCCCCG
1073







GAACC





53335_4_521
BCL11a
Exon 4

chr2: 60461569-60461594
GACGGUCUCUCCACCGCCA
1074







GCUCCC





53335_4_522
BCL11a
Exon 4

chr2: 60461592-60461617
CCCCCAUGACGGUCAAGUC
1075







CGACGA





53335_4_523
BCL11a
Exon 4

chr2: 60461608-60461633
CACAUGCACAAAUCGUCCC
1076







CCAUGA





53335_4_524
BCL11a
Exon 4

chr2: 60461665-60461690
AACCUGUGCGACCACGCGU
1077







GCACCC





53335_4_525
BCL11a
Exon 4

chr2: 60461712-60461737
UGGUGGUGCACCGGCGCAG
1078







CCACAC





53335_4_526
BCL11a
Exon 4

chr2: 60461713-60461738
CUGGUGGUGCACCGGCGCA
1079







GCCACA





53335_4_527
BCL11a
Exon 4

chr2: 60461726-60461751
AUUUCAGAGCAACCUGGUG
1080







GUGCAC





53335_4_528
BCL11a
Exon 4

chr2: 60461734-60461759
ACGUUCAAAUUUCAGAGCA
1081







ACCUGG





53335_4_529
BCL11a
Exon 4

chr2: 60461737-60461762
AAGACGUUCAAAUUUCAGA
1082







GCAACC





53335_4_530
BCL11a
Exon 4

chr2: 60461766-60461791
UCAAGUCCAAGUCAUGCGA
1083







GUUCUG





53335_4_531
BCL11a
Exon 4

chr2: 60461794-60461819
UCCGCCCCUCCUCCCUCCCA
1084







GCCCC





53335_4_532
BCL11a
Exon 4

chr2: 60461848-60461873
CAGCCAGGUAGCAAGCCGC
1085







CCUUCC





53335_4_533
BCL11a
Exon 4

chr2: 60461868-60461893
AAAGGUUACUGCAACCAUU
1086







CCAGCC





53335_4_534
BCL11a
Exon 4

chr2: 60461891-60461916
CCCAGGCCGGCCCAGCCCU
1087







AUGCAA





53335_4_535
BCL11a
Exon 4

chr2: 60461909-60461934
GUCUAGCCCACCGCUGUCC
1088







CCAGGC





53335_4_536
BCL11a
Exon 4

chr2: 60461913-60461938
ACACGUCUAGCCCACCGCU
1089







GUCCCC





53335_4_537
BCL11a
Exon 4

chr2: 60461942-60461967
CUCUAGGAGACUUAGAGAG
1090







CUGGCA





53335_4_538
BCL11a
Exon 4

chr2: 60461943-60461968
UCUCUAGGAGACUUAGAGA
1091







GCUGGC





53335_4_539
BCL11a
Exon 4

chr2: 60461947-60461972
GAUUUCUCUAGGAGACUUA
1092







GAGAGC





53335_4_540
BCL11a
Exon 4

chr2: 60461963-60461988
GGAGCCUCCCGCCAUGGAU
1093







UUCUCU





53335_4_541
BCL11a
Exon 4

chr2: 60461974-60461999
CCAAUGGCUAUGGAGCCUC
1094







CCGCCA





53335_4_542
BCL11a
Exon 4

chr2: 60461989-60462014
GUGCUGCGGUUGAAUCCAA
1095







UGGCUA





53335_4_543
BCL11a
Exon 4

chr2: 60461995-60462020
GACAGGGUGCUGCGGUUGA
1096







AUCCAA





53335_4_544
BCL11a
Exon 4

chr2: 60462008-60462033
CCCGAGUGCCUUUGACAGG
1097







GUGCUG





53335_4_545
BCL11a
Exon 4

chr2: 60462016-60462041
ACCCAUCACCCGAGUGCCU
1098







UUGACA





53335_4_546
BCL11a
Exon 4

chr2: 60462017-60462042
CACCCAUCACCCGAGUGCC
1099







UUUGAC





53335_4_547
BCL11a
Exon 4

chr2: 60462046-60462071
CGCCUGGGGGCGGAAGAGA
1100







UGGCCC





53335_4_548
BCL11a
Exon 4

chr2: 60462052-60462077
AUAGAGCGCCUGGGGGCGG
1101







AAGAGA





53335_4_549
BCL11a
Exon 4

chr2: 60462061-60462086
CCCCACCGCAUAGAGCGCC
1102







UGGGGG





53335_4_550
BCL11a
Exon 4

chr2: 60462064-60462089
GACCCCCACCGCAUAGAGC
1103







GCCUGG





53335_4_551
BCL11a
Exon 4

chr2: 60462065-60462090
GGACCCCCACCGCAUAGAG
1104







CGCCUG





53335_4_552
BCL11a
Exon 4

chr2: 60462066-60462091
UGGACCCCCACCGCAUAGA
1105







GCGCCU





53335_4_553
BCL11a
Exon 4

chr2: 60462067-60462092
UUGGACCCCCACCGCAUAG
1106







AGCGCC





53335_4_554
BCL11a
Exon 4

chr2: 60462091-60462116
UUUAGUCCACCACCGAGAC
1107







AUCACU





53335_4_555
BCL11a
Exon 4

chr2: 60462143-60462168
GAGAGAGGCUUCCGGCCUG
1108







GCAGAA





53335_4_556
BCL11a
Exon 4

chr2: 60462144-60462169
CGAGAGAGGCUUCCGGCCU
1109







GGCAGA





53335_4_557
BCL11a
Exon 4

chr2: 60462151-60462176
UCAGUAUCGAGAGAGGCUU
1110







CCGGCC





53335_4_558
BCL11a
Exon 4

chr2: 60462156-60462181
CAGGAUCAGUAUCGAGAGA
1111







GGCUUC





53335_4_559
BCL11a
Exon 4

chr2: 60462163-60462188
AGAAUACCAGGAUCAGUAU
1112







CGAGAG





53335_4_560
BCL11a
Exon 4

chr2: 60462180-60462205
ACCCCUUUAACCUGCUAAG
1113







AAUACC





53335_4_561
BCL11a
Exon 4

chr2: 60462227-60462252
AUGUCCUUCCCAGCCACCU
1114







CUCCAU





53335_4_562
BCL11a
Exon 4

chr2: 60462228-60462253
AAUGUCCUUCCCAGCCACC
1115







UCUCCA





53335_4_563
BCL11a
Exon 4

chr2: 60462261-60462286
CGCGGGUUGGUAUCCCUUC
1116







AGGACU





53335_4_564
BCL11a
Exon 4

chr2: 60462267-60462292
UGACCCCGCGGGUUGGUAU
1117







CCCUUC





53335_4_565
BCL11a
Exon 4

chr2: 60462279-60462304
ACGGAAGUCCCCUGACCCC
1118







GCGGGU





53335_4_566
BCL11a
Exon 4

chr2: 60462283-60462308
GAACACGGAAGUCCCCUGA
1119







CCCCGC





53335_4_567
BCL11a
Exon 4

chr2: 60462284-60462309
CGAACACGGAAGUCCCCUG
1120







ACCCCG





53335_4_568
BCL11a
Exon 4

chr2: 60462303-60462328
UAAGAAUCUACUUAGAAAG
1121







CGAACA





53335_4_569
BCL11a
Exon 4

chr2: 60462333-60462358
UCUUGCAACACGCACAGAA
1122







CACUCA





53335_4_570
BCL11a
Exon 4

chr2: 60462365-60462390
UUGCAAACAGCCAUUCACC
1123







AGUGCA





53335_3_1
BCL11a
Exon 3
+
chr2: 60468716-60468741
UAAGGCUCAACUUACAAAU
1124







ACCCUG





53335_3_2
BCL11a
Exon 3
+
chr2: 60468717-60468742
AAGGCUCAACUUACAAAUA
1125







CCCUGC





53335_3_3
BCL11a
Exon 3
+
chr2: 60468718-60468743
AGGCUCAACUUACAAAUAC
1126







CCUGCG





53335_3_4
BCL11a
Exon 3
+
chr2: 60468740-60468765
GCGGGGCAUAUUCUGCACU
1127







CAUCCC





53335_3_5
BCL11a
Exon 3
+
chr2: 60468745-60468770
GCAUAUUCUGCACUCAUCC
1128







CAGGCG





53335_3_6
BCL11a
Exon 3
+
chr2: 60468746-60468771
CAUAUUCUGCACUCAUCCC
1129







AGGCGU





53335_3_7
BCL11a
Exon 3
+
chr2: 60468747-60468772
AUAUUCUGCACUCAUCCCA
1130







GGCGUG





53335_3_8
BCL11a
Exon 3
+
chr2: 60468773-60468798
GGAUUAGAGCUCCAUGUGC
1131







AGAACG





53335_3_9
BCL11a
Exon 3
+
chr2: 60468774-60468799
GAUUAGAGCUCCAUGUGCA
1132







GAACGA





53335_3_10
BCL11a
Exon 3
+
chr2: 60468775-60468800
AUUAGAGCUCCAUGUGCAG
1133







AACGAG





53335_3_11
BCL11a
Exon 3
+
chr2: 60468778-60468803
AGAGCUCCAUGUGCAGAAC
1134







GAGGGG





53335_3_12
BCL11a
Exon 3
+
chr2: 60468783-60468808
UCCAUGUGCAGAACGAGGG
1135







GAGGAG





53335_3_13
BCL11a
Exon 3

chr2: 60468739-60468764
GGAUGAGUGCAGAAUAUGC
1136







CCCGCA





53335_3_14
BCL11a
Exon 3

chr2: 60468740-60468765
GGGAUGAGUGCAGAAUAUG
1137







CCCCGC





53335_3_15
BCL11a
Exon 3

chr2: 60468765-60468790
ACAUGGAGCUCUAAUCCCC
1138







ACGCCU





53335_3_16
BCL11a
Exon 3

chr2: 60468766-60468791
CACAUGGAGCUCUAAUCCC
1139







CACGCC





53335_3_17
BCL11a
Exon 3

chr2: 60468787-60468812
GCCUCUCCUCCCCUCGUUC
1140







UGCACA





53335_3_18
BCL11a
Exon 3

chr2: 60468814-60468839
UCACAGAUAAACUUCUGCA
1141







CUGGAG





53335_3_19
BCL11a
Exon 3

chr2: 60468815-60468840
UUCACAGAUAAACUUCUGC
1142







ACUGGA





53335_3_20
BCL11a
Exon 3

chr2: 60468816-60468841
UUUCACAGAUAAACUUCUG
1143







CACUGG





53335_3_21
BCL11a
Exon 3

chr2: 60468819-60468844
UUCUUUCACAGAUAAACUU
1144







CUGCAC





53335_2_1
BCL11a
Exon 2
+
chr2: 60545963-60545988
CAUUUACCUGCUAUGUGUU
1145







CCUGUU





53335_2_2
BCL11a
Exon 2
+
chr2: 60545964-60545989
AUUUACCUGCUAUGUGUUC
1146







CUGUUU





53335_2_3
BCL11a
Exon 2
+
chr2: 60545965-60545990
UUUACCUGCUAUGUGUUCC
1147







UGUUUG





53335_2_4
BCL11a
Exon 2
+
chr2: 60546009-60546034
ACGUUGAUAAACAAUCGUC
1148







AUCCUC





53335_2_5
BCL11a
Exon 2
+
chr2: 60546019-60546044
ACAAUCGUCAUCCUCUGGC
1149







GUGACC





53335_2_6
BCL11a
Exon 2
+
chr2: 60546035-60546060
GGCGUGACCUGGAUGCCAA
1150







CCUCCA





53335_2_7
BCL11a
Exon 2
+
chr2: 60546036-60546061
GCGUGACCUGGAUGCCAAC
1151







CUCCAC





53335_2_8
BCL11a
Exon 2
+
chr2: 60546041-60546066
ACCUGGAUGCCAACCUCCA
1152







CGGGAU





53335_2_9
BCL11a
Exon 2
+
chr2: 60546063-60546088
GAUUGGAUGCUUUUUUCAU
1153







CUCGAU





53335_2_10
BCL11a
Exon 2
+
chr2: 60546069-60546094
AUGCUUUUUUCAUCUCGAU
1154







UGGUGA





53335_2_11
BCL11a
Exon 2
+
chr2: 60546070-60546095
UGCUUUUUUCAUCUCGAUU
1155







GGUGAA





53335_2_12
BCL11a
Exon 2
+
chr2: 60546071-60546096
GCUUUUUUCAUCUCGAUUG
1156







GUGAAG





53335_2_13
BCL11a
Exon 2
+
chr2: 60546075-60546100
UUUUCAUCUCGAUUGGUGA
1157







AGGGGA





53335_2_14
BCL11a
Exon 2
+
chr2: 60546078-60546103
UCAUCUCGAUUGGUGAAGG
1158







GGAAGG





53335_2_15
BCL11a
Exon 2
+
chr2: 60546106-60546131
CUUAUCCACAGCUUUUUCU
1159







AAGCAG





53335_2_16
BCL11a
Exon 2
+
chr2: 60546162-60546187
CGAUAAAAAUAAGAAUGUC
1160







CCCCAA





53335_2_17
BCL11a
Exon 2
+
chr2: 60546163-60546188
GAUAAAAAUAAGAAUGUCC
1161







CCCAAU





53335_2_18
BCL11a
Exon 2
+
chr2: 60546175-60546200
AAUGUCCCCCAAUGGGAAG
1162







UUCAUC





53335_2_19
BCL11a
Exon 2
+
chr2: 60546188-60546213
GGGAAGUUCAUCUGGCACU
1163







GCCCAC





53335_2_20
BCL11a
Exon 2
+
chr2: 60546193-60546218
GUUCAUCUGGCACUGCCCA
1164







CAGGUG





53335_2_21
BCL11a
Exon 2
+
chr2: 60546196-60546221
CAUCUGGCACUGCCCACAG
1165







GUGAGG





53335_2_22
BCL11a
Exon 2
+
chr2: 60546213-60546238
AGGUGAGGAGGUCAUGAUC
1166







CCCUUC





53335_2_23
BCL11a
Exon 2
+
chr2: 60546225-60546250
CAUGAUCCCCUUCUGGAGC
1167







UCCCAA





53335_2_24
BCL11a
Exon 2
+
chr2: 60546226-60546251
AUGAUCCCCUUCUGGAGCU
1168







CCCAAC





53335_2_25
BCL11a
Exon 2
+
chr2: 60546232-60546257
CCCUUCUGGAGCUCCCAAC
1169







GGGCCG





53335_2_26
BCL11a
Exon 2
+
chr2: 60546237-60546262
CUGGAGCUCCCAACGGGCC
1170







GUGGUC





53335_2_27
BCL11a
Exon 2
+
chr2: 60546257-60546282
UGGUCUGGUUCAUCAUCUG
1171







UAAGAA





53335_2_28
BCL11a
Exon 2
+
chr2: 60546267-60546292
CAUCAUCUGUAAGAAUGGC
1172







UUCAAG





53335_2_29
BCL11a
Exon 2
+
chr2: 60546272-60546297
UCUGUAAGAAUGGCUUCAA
1173







GAGGCU





53335_2_30
BCL11a
Exon 2
+
chr2: 60546278-60546303
AGAAUGGCUUCAAGAGGCU
1174







CGGCUG





53335_2_31
BCL11a
Exon 2
+
chr2: 60546282-60546307
UGGCUUCAAGAGGCUCGGC
1175







UGUGGU





53335_2_32
BCL11a
Exon 2

chr2: 60545956-60545981
ACACAUAGCAGGUAAAUGA
1176







GAAGCA





53335_2_33
BCL11a
Exon 2

chr2: 60545972-60545997
UUUGCCCCAAACAGGAACA
1177







CAUAGC





53335_2_34
BCL11a
Exon 2

chr2: 60545985-60546010
UCAUCUAGAGGAAUUUGCC
1178







CCAAAC





53335_2_35
BCL11a
Exon 2

chr2: 60546002-60546027
ACGAUUGUUUAUCAACGUC
1179







AUCUAG





53335_2_36
BCL11a
Exon 2

chr2: 60546033-60546058
GAGGUUGGCAUCCAGGUCA
1180







CGCCAG





53335_2_37
BCL11a
Exon 2

chr2: 60546045-60546070
UCCAAUCCCGUGGAGGUUG
1181







GCAUCC





53335_2_38
BCL11a
Exon 2

chr2: 60546053-60546078
AAAAAGCAUCCAAUCCCGU
1182







GGAGGU





53335_2_39
BCL11a
Exon 2

chr2: 60546057-60546082
AUGAAAAAAGCAUCCAAUC
1183







CCGUGG





53335_2_40
BCL11a
Exon 2

chr2: 60546060-60546085
GAGAUGAAAAAAGCAUCCA
1184







AUCCCG





53335_2_41
BCL11a
Exon 2

chr2: 60546114-60546139
GGCAGCCUCUGCUUAGAAA
1185







AAGCUG





53335_2_42
BCL11a
Exon 2

chr2: 60546140-60546165
UCGAGCACAAACGGAAACA
1186







AUGCAA





53335_2_43
BCL11a
Exon 2

chr2: 60546154-60546179
CAUUCUUAUUUUUAUCGAG
1187







CACAAA





53335_2_44
BCL11a
Exon 2

chr2: 60546183-60546208
CAGUGCCAGAUGAACUUCC
1188







CAUUGG





53335_2_45
BCL11a
Exon 2

chr2: 60546184-60546209
GCAGUGCCAGAUGAACUUC
1189







CCAUUG





53335_2_46
BCL11a
Exon 2

chr2: 60546185-60546210
GGCAGUGCCAGAUGAACUU
1190







CCCAUU





53335_2_47
BCL11a
Exon 2

chr2: 60546186-60546211
GGGCAGUGCCAGAUGAACU
1191







UCCCAU





53335_2_48
BCL11a
Exon 2

chr2: 60546211-60546236
AGGGGAUCAUGACCUCCUC
1192







ACCUGU





53335_2_49
BCL11a
Exon 2

chr2: 60546212-60546237
AAGGGGAUCAUGACCUCCU
1193







CACCUG





53335_2_50
BCL11a
Exon 2

chr2: 60546234-60546259
CACGGCCCGUUGGGAGCUC
1194







CAGAAG





53335_2_51
BCL11a
Exon 2

chr2: 60546235-60546260
CCACGGCCCGUUGGGAGCU
1195







CCAGAA





53335_2_52
BCL11a
Exon 2

chr2: 60546236-60546261
ACCACGGCCCGUUGGGAGC
1196







UCCAGA





53335_2_53
BCL11a
Exon 2

chr2: 60546248-60546273
AUGAUGAACCAGACCACGG
1197







CCCGUU





53335_2_54
BCL11a
Exon 2

chr2: 60546249-60546274
GAUGAUGAACCAGACCACG
1198







GCCCGU





53335_2_55
BCL11a
Exon 2

chr2: 60546257-60546282
UUCUUACAGAUGAUGAACC
1199







AGACCA





53335_1_1
BCL11a
Exon 1
+
chr2: 60553216-60553241
CGAGAAUUCCCGUUUGCUU
1200







AAGUGC





53335_1_2
BCL11a
Exon 1
+
chr2: 60553217-60553242
GAGAAUUCCCGUUUGCUUA
1201







AGUGCU





53335_1_3
BCL11a
Exon 1
+
chr2: 60553218-60553243
AGAAUUCCCGUUUGCUUAA
1202







GUGCUG





53335_1_4
BCL11a
Exon 1
+
chr2: 60553234-60553259
UAAGUGCUGGGGUUUGCCU
1203







UGCUUG





53335_1_5
BCL11a
Exon 1
+
chr2: 60553244-60553269
GGUUUGCCUUGCUUGCGGC
1204







GAGACA





53335_1_6
BCL11a
Exon 1
+
chr2: 60553247-60553272
UUGCCUUGCUUGCGGCGAG
1205







ACAUGG





53335_1_7
BCL11a
Exon 1
+
chr2: 60553248-60553273
UGCCUUGCUUGCGGCGAGA
1206







CAUGGU





53335_1_8
BCL11a
Exon 1
+
chr2: 60553254-60553279
GCUUGCGGCGAGACAUGGU
1207







GGGCUG





53335_1_9
BCL11a
Exon 1
+
chr2: 60553255-60553280
CUUGCGGCGAGACAUGGUG
1208







GGCUGC





53335_1_10
BCL11a
Exon 1
+
chr2: 60553256-60553281
UUGCGGCGAGACAUGGUGG
1209







GCUGCG





53335_1_11
BCL11a
Exon 1
+
chr2: 60553291-60553316
CGGCGGCGGCGGCGGCGGC
1210







GGCGGG





53335_1_12
BCL11a
Exon 1
+
chr2: 60553298-60553323
GGCGGCGGCGGCGGCGGGC
1211







GGACGA





53335_1_13
BCL11a
Exon 1
+
chr2: 60553303-60553328
CGGCGGCGGCGGGCGGACG
1212







ACGGCU





53335_1_14
BCL11a
Exon 1
+
chr2: 60553313-60553338
GGGCGGACGACGGCUCGGU
1213







UCACAU





53335_1_15
BCL11a
Exon 1
+
chr2: 60553314-60553339
GGCGGACGACGGCUCGGUU
1214







CACAUC





53335_1_16
BCL11a
Exon 1
+
chr2: 60553322-60553347
ACGGCUCGGUUCACAUCGG
1215







GAGAGC





53335_1_17
BCL11a
Exon 1
+
chr2: 60553323-60553348
CGGCUCGGUUCACAUCGGG
1216







AGAGCC





53335_1_18
BCL11a
Exon 1
+
chr2: 60553335-60553360
CAUCGGGAGAGCCGGGUUA
1217







GAAAGA





53335_1_19
BCL11a
Exon 1
+
chr2: 60553406-60553431
AAAUAAAUUAGAAAUAAUA
1218







CAAAGA





53335_1_20
BCL11a
Exon 1
+
chr2: 60553412-60553437
AUUAGAAAUAAUACAAAGA
1219







UGGCGC





53335_1_21
BCL11a
Exon 1
+
chr2: 60553413-60553438
UUAGAAAUAAUACAAAGAU
1220







GGCGCA





53335_1_22
BCL11a
Exon 1
+
chr2: 60553427-60553452
AAGAUGGCGCAGGGAAGAU
1221







GAAUUG





53335_1_23
BCL11a
Exon 1
+
chr2: 60553428-60553453
AGAUGGCGCAGGGAAGAUG
1222







AAUUGU





53335_1_24
BCL11a
Exon 1
+
chr2: 60553441-60553466
AAGAUGAAUUGUGGGAGAG
1223







CCGUCA





53335_1_25
BCL11a
Exon 1

chr2: 60553227-60553252
GGCAAACCCCAGCACUUAA
1224







GCAAAC





53335_1_26
BCL11a
Exon 1

chr2: 60553228-60553253
AGGCAAACCCCAGCACUUA
1225







AGCAAA





53335_1_27
BCL11a
Exon 1

chr2: 60553253-60553278
AGCCCACCAUGUCUCGCCG
1226







CAAGCA





53335_1_28
BCL11a
Exon 1

chr2: 60553349-60553374
CUCUGGAGUCUCCUUCUUU
1227







CUAACC





53335_1_29
BCL11a
Exon 1

chr2: 60553371-60553396
AAGGCACUGAUGAAGAUAU
1228







UUUCUC





53335_1_30
BCL11a
Exon 1

chr2: 60553395-60553420
UUUCUAAUUUAUUUUGGAU
1229







GUCAAA





53335_1_31
BCL11a
Exon 1

chr2: 60553406-60553431
UCUUUGUAUUAUUUCUAAU
1230







UUAUUU





53335_1_32
BCL11a
Exon 1

chr2: 60553463-60553488
AAAAAAGCUUAAAAAAAAG
1231







CCAUGA
















TABLE 2







gRNA targeting domains targeting BCL11a Intron 2 (e.g., to a BCL11a Enhancer)



















SEQ




Target

Targeting Site

ID


Id.
Target
Region
Strand
(hg38)
gRNA Targeting Domain
NO:





53335_I2_1
BCL11a
Intron 2
+
chr2: 60494277-60494302
GGGAGUUUGGCUUCUCA
1232







UCUGUGCA





53335_I2_2
BCL11a
Intron 2
+
chr2: 60494289-60494314
UCUCAUCUGUGCAUGGC
1233







CUCUAAAC





53335_I2_3
BCL11a
Intron 2
+
chr2: 60494290-60494315
CUCAUCUGUGCAUGGCC
1234







UCUAAACU





53335_I2_4
BCL11a
Intron 2
+
chr2: 60494302-60494327
UGGCCUCUAAACUGGGC
1235







AGUGACCA





53335_I2_5
BCL11a
Intron 2
+
chr2: 60494307-60494332
UCUAAACUGGGCAGUGA
1236







CCAUGGCC





53335_I2_6
BCL11a
Intron 2
+
chr2: 60494324-60494349
CCAUGGCCUGGUCACCU
1237







CCCCACUC





53335_I2_7
BCL11a
Intron 2
+
chr2: 60494330-60494355
CCUGGUCACCUCCCCACU
1238







CUGGACC





53335_I2_8
BCL11a
Intron 2
+
chr2: 60494331-60494356
CUGGUCACCUCCCCACUC
1239







UGGACCU





53335_I2_9
BCL11a
Intron 2
+
chr2: 60494351-60494376
GACCUGGGUUGCCCCUC
1240







UGUAAACA





53335_I2_10
BCL11a
Intron 2
+
chr2: 60494354-60494379
CUGGGUUGCCCCUCUGU
1241







AAACAAGG





53335_I2_11
BCL11a
Intron 2
+
chr2: 60494418-60494443
AAAUCUUAUGCAAUUUU
1242







UGCCAAGA





53335_I2_12
BCL11a
Intron 2
+
chr2: 60494419-60494444
AAUCUUAUGCAAUUUUU
1243







GCCAAGAU





53335_I2_13
BCL11a
Intron 2
+
chr2: 60494426-60494451
UGCAAUUUUUGCCAAGA
1244







UGGGAGUA





53335_I2_14
BCL11a
Intron 2
+
chr2: 60494427-60494452
GCAAUUUUUGCCAAGAU
1245







GGGAGUAU





53335_I2_15
BCL11a
Intron 2
+
chr2: 60494428-60494453
CAAUUUUUGCCAAGAUG
1246







GGAGUAUG





53335_I2_16
BCL11a
Intron 2
+
chr2: 60494440-60494465
AGAUGGGAGUAUGGGGA
1247







GAGAAGAG





53335_I2_17
BCL11a
Intron 2
+
chr2: 60494446-60494471
GAGUAUGGGGAGAGAAG
1248







AGUGGAAA





53335_I2_18
BCL11a
Intron 2
+
chr2: 60494477-60494502
AGAGCUCAGUGAGAUGA
1249







GAUAUCAA





53335_I2_19
BCL11a
Intron 2
+
chr2: 60494478-60494503
GAGCUCAGUGAGAUGAG
1250







AUAUCAAA





53335_I2_20
BCL11a
Intron 2
+
chr2: 60494479-60494504
AGCUCAGUGAGAUGAGA
1251







UAUCAAAG





53335_I2_21
BCL11a
Intron 2
+
chr2: 60494518-60494543
UCAUUCCAUCUCCCUAA
1252







UCUCCAAU





53335_I2_22
BCL11a
Intron 2
+
chr2: 60494533-60494558
AAUCUCCAAUUGGCAAA
1253







GCCAGACU





53335_I2_23
BCL11a
Intron 2
+
chr2: 60494534-60494559
AUCUCCAAUUGGCAAAG
1254







CCAGACUU





53335_I2_24
BCL11a
Intron 2
+
chr2: 60494535-60494560
UCUCCAAUUGGCAAAGC
1255







CAGACUUG





53335_I2_25
BCL11a
Intron 2
+
chr2: 60494548-60494573
AAGCCAGACUUGGGGCA
1256







AUACAGAC





53335_I2_26
BCL11a
Intron 2
+
chr2: 60494617-60494642
UAUCACCAAAUGUUCUU
1257







UCUUCAGC





53335_I2_27
BCL11a
Intron 2
+
chr2: 60494631-60494656
CUUUCUUCAGCUGGAAU
1258







UUAAAAUA





53335_I2_28
BCL11a
Intron 2
+
chr2: 60494649-60494674
UAAAAUAUGGACUCAUC
1259







CGUAAAAU





53335_I2_29
BCL11a
Intron 2
+
chr2: 60494675-60494700
GGAAUAAUAAUAGUAUA
1260







UGCUUCAU





53335_I2_30
BCL11a
Intron 2
+
chr2: 60494676-60494701
GAAUAAUAAUAGUAUAU
1261







GCUUCAUA





53335_I2_31
BCL11a
Intron 2
+
chr2: 60494766-60494791
GCUUGUGAACUAAAAUG
1262







CUGCCUCC





53335_I2_32
BCL11a
Intron 2
+
chr2: 60494806-60494831
ACACCUCAGCAGAAACA
1263







AAGUUAUC





53335_I2_33
BCL11a
Intron 2
+
chr2: 60494830-60494855
CAGGCCCUUUCCCCAAU
1264







UCCUAGUU





53335_I2_34
BCL11a
Intron 2
+
chr2: 60494831-60494856
AGGCCCUUUCCCCAAUU
1265







CCUAGUUU





53335_I2_35
BCL11a
Intron 2
+
chr2: 60494844-60494869
AAUUCCUAGUUUGGGUC
1266







AGAAGAAA





53335_I2_36
BCL11a
Intron 2
+
chr2: 60494845-60494870
AUUCCUAGUUUGGGUCA
1267







GAAGAAAA





53335_I2_37
BCL11a
Intron 2
+
chr2: 60494851-60494876
AGUUUGGGUCAGAAGAA
1268







AAGGGAAA





53335_I2_38
BCL11a
Intron 2
+
chr2: 60494852-60494877
GUUUGGGUCAGAAGAAA
1269







AGGGAAAA





53335_I2_39
BCL11a
Intron 2
+
chr2: 60494857-60494882
GGUCAGAAGAAAAGGGA
1270







AAAGGGAG





53335_I2_40
BCL11a
Intron 2
+
chr2: 60494864-60494889
AGAAAAGGGAAAAGGGA
1271







GAGGAAAA





53335_I2_41
BCL11a
Intron 2
+
chr2: 60494883-60494908
GGAAAAAGGAAAAGAAU
1272







AUGACGUC





53335_I2_42
BCL11a
Intron 2
+
chr2: 60494884-60494909
GAAAAAGGAAAAGAAUA
1273







UGACGUCA





53335_I2_43
BCL11a
Intron 2
+
chr2: 60494885-60494910
AAAAAGGAAAAGAAUAU
1274







GACGUCAG





53335_I2_44
BCL11a
Intron 2
+
chr2: 60494886-60494911
AAAAGGAAAAGAAUAUG
1275







ACGUCAGG





53335_I2_45
BCL11a
Intron 2
+
chr2: 60494889-60494914
AGGAAAAGAAUAUGACG
1276







UCAGGGGG





53335_I2_46
BCL11a
Intron 2
+
chr2: 60494901-60494926
UGACGUCAGGGGGAGGC
1277







AAGUCAGU





53335_I2_47
BCL11a
Intron 2
+
chr2: 60494902-60494927
GACGUCAGGGGGAGGCA
1278







AGUCAGUU





53335_I2_48
BCL11a
Intron 2
+
chr2: 60494928-60494953
GGAACACAGAUCCUAAC
1279







ACAGUAGC





53335_I2_49
BCL11a
Intron 2
+
chr2: 60494939-60494964
CCUAACACAGUAGCUGG
1280







UACCUGAU





53335_I2_50
BCL11a
Intron 2
+
chr2: 60494955-60494980
GUACCUGAUAGGUGCCU
1281







AUAUGUGA





53335_I2_51
BCL11a
Intron 2
+
chr2: 60494959-60494984
CUGAUAGGUGCCUAUAU
1282







GUGAUGGA





53335_I2_52
BCL11a
Intron 2
+
chr2: 60494960-60494985
UGAUAGGUGCCUAUAUG
1283







UGAUGGAU





53335_I2_53
BCL11a
Intron 2
+
chr2: 60494963-60494988
UAGGUGCCUAUAUGUGA
1284







UGGAUGGG





53335_I2_54
BCL11a
Intron 2
+
chr2: 60494986-60495011
GGUGGACAGCCCGACAG
1285







AUGAAAAA





53335_I2_55
BCL11a
Intron 2
+
chr2: 60494998-60495023
GACAGAUGAAAAAUGGA
1286







CAAUUAUG





53335_I2_56
BCL11a
Intron 2
+
chr2: 60495001-60495026
AGAUGAAAAAUGGACAA
1287







UUAUGAGG





53335_I2_57
BCL11a
Intron 2
+
chr2: 60495002-60495027
GAUGAAAAAUGGACAAU
1288







UAUGAGGA





53335_I2_58
BCL11a
Intron 2
+
chr2: 60495003-60495028
AUGAAAAAUGGACAAUU
1289







AUGAGGAG





53335_I2_59
BCL11a
Intron 2
+
chr2: 60495017-60495042
AUUAUGAGGAGGGGAGA
1290







GUGCAGAC





53335_I2_60
BCL11a
Intron 2
+
chr2: 60495018-60495043
UUAUGAGGAGGGGAGAG
1291







UGCAGACA





53335_I2_61
BCL11a
Intron 2
+
chr2: 60495019-60495044
UAUGAGGAGGGGAGAGU
1292







GCAGACAG





53335_I2_62
BCL11a
Intron 2
+
chr2: 60495045-60495070
GGAAGCUUCACCUCCUU
1293







UACAAUUU





53335_I2_63
BCL11a
Intron 2
+
chr2: 60495046-60495071
GAAGCUUCACCUCCUUU
1294







ACAAUUUU





53335_I2_64
BCL11a
Intron 2
+
chr2: 60495057-60495082
UCCUUUACAAUUUUGGG
1295







AGUCCACA





53335_I2_65
BCL11a
Intron 2
+
chr2: 60495062-60495087
UACAAUUUUGGGAGUCC
1296







ACACGGCA





53335_I2_66
BCL11a
Intron 2
+
chr2: 60495135-60495160
CAUCACCAAGAGAGCCU
1297







UCCGAAAG





53335_I2_67
BCL11a
Intron 2
+
chr2: 60495144-60495169
GAGAGCCUUCCGAAAGA
1298







GGCCCCCC





53335_I2_68
BCL11a
Intron 2
+
chr2: 60495145-60495170
AGAGCCUUCCGAAAGAG
1299







GCCCCCCU





53335_I2_69
BCL11a
Intron 2
+
chr2: 60495152-60495177
UCCGAAAGAGGCCCCCC
1300







UGGGCAAA





53335_I2_70
BCL11a
Intron 2
+
chr2: 60495162-60495187
GCCCCCCUGGGCAAACG
1301







GCCACCGA





53335_I2_71
BCL11a
Intron 2
+
chr2: 60495167-60495192
CCUGGGCAAACGGCCAC
1302







CGAUGGAG





53335_I2_72
BCL11a
Intron 2
+
chr2: 60495215-60495240
CCACCCACGCCCCCACCC
1303







UAAUCAG





53335_I2_73
BCL11a
Intron 2
+
chr2: 60495230-60495255
CCCUAAUCAGAGGCCAA
1304







ACCCUUCC





53335_I2_74
BCL11a
Intron 2
+
chr2: 60495293-60495318
ACUAGCUUCAAAGUUGU
1305







AUUGACCC





53335_I2_75
BCL11a
Intron 2
+
chr2: 60495333-60495358
AAGAGUAGAUGCCAUAU
1306







CUCUUUUC





53335_I2_76
BCL11a
Intron 2
+
chr2: 60495354-60495379
UUUCUGGCCUAUGUUAU
1307







UACCUGUA





53335_I2_77
BCL11a
Intron 2
+
chr2: 60495366-60495391
GUUAUUACCUGUAUGGA
1308







CUUUGCAC





53335_I2_78
BCL11a
Intron 2
+
chr2: 60495400-60495425
CUAUCUGCUCUUACUUA
1309







UGCACACC





53335_I2_79
BCL11a
Intron 2
+
chr2: 60495401-60495426
UAUCUGCUCUUACUUAU
1310







GCACACCU





53335_I2_80
BCL11a
Intron 2
+
chr2: 60495402-60495427
AUCUGCUCUUACUUAUG
1311







CACACCUG





53335_I2_81
BCL11a
Intron 2
+
chr2: 60495486-60495511
CCUGUCUAGCUGCCUUC
1312







CUUAUCAC





53335_I2_82
BCL11a
Intron 2
+
chr2: 60495500-60495525
UUCCUUAUCACAGGAAU
1313







AGCACCCA





53335_I2_83
BCL11a
Intron 2
+
chr2: 60495543-60495568
GAGUAGAACCCCCUAUA
1314







AACUAGUC





53335_I2_84
BCL11a
Intron 2
+
chr2: 60495554-60495579
CCUAUAAACUAGUCUGG
1315







UUUGCCCA





53335_I2_85
BCL11a
Intron 2
+
chr2: 60495555-60495580
CUAUAAACUAGUCUGGU
1316







UUGCCCAU





53335_I2_86
BCL11a
Intron 2
+
chr2: 60495556-60495581
UAUAAACUAGUCUGGUU
1317







UGCCCAUG





53335_I2_87
BCL11a
Intron 2
+
chr2: 60495566-60495591
UCUGGUUUGCCCAUGGG
1318







GCACAGUC





53335_I2_88
BCL11a
Intron 2
+
chr2: 60495578-60495603
AUGGGGCACAGUCAGGC
1319







UGUUUUCC





53335_I2_89
BCL11a
Intron 2
+
chr2: 60495579-60495604
UGGGGCACAGUCAGGCU
1320







GUUUUCCA





53335_I2_90
BCL11a
Intron 2
+
chr2: 60495582-60495607
GGCACAGUCAGGCUGUU
1321







UUCCAGGG





53335_I2_91
BCL11a
Intron 2
+
chr2: 60495583-60495608
GCACAGUCAGGCUGUUU
1322







UCCAGGGU





53335_I2_92
BCL11a
Intron 2
+
chr2: 60495584-60495609
CACAGUCAGGCUGUUUU
1323







CCAGGGUG





53335_I2_93
BCL11a
Intron 2
+
chr2: 60495661-60495686
ACACACGUAUGUGUUGU
1324







GAUCCCUG





53335_I2_94
BCL11a
Intron 2
+
chr2: 60495674-60495699
UUGUGAUCCCUGUGGUU
1325







UGAGAGUU





53335_I2_95
BCL11a
Intron 2
+
chr2: 60495706-60495731
UCCCUAAAAGUCAAAAU
1326







AUUCUCAA





53335_I2_96
BCL11a
Intron 2
+
chr2: 60495707-60495732
CCCUAAAAGUCAAAAUA
1327







UUCUCAAU





53335_I2_97
BCL11a
Intron 2
+
chr2: 60495735-60495760
CCCUCAAUCAGCACAUA
1328







CACACAAA





53335_I2_98
BCL11a
Intron 2
+
chr2: 60495742-60495767
UCAGCACAUACACACAA
1329







AAGGUACC





53335_I2_99
BCL11a
Intron 2
+
chr2: 60495775-60495800
UGUAAUUCUUUUCCUGC
1330







UCAAAGAC





53335_I2_100
BCL11a
Intron 2
+
chr2: 60495820-60495845
CCCCAACCAAAAACCCUU
1331







GCCACCA





53335_I2_101
BCL11a
Intron 2
+
chr2: 60495821-60495846
CCCAACCAAAAACCCUU
1332







GCCACCAU





53335_I2_102
BCL11a
Intron 2
+
chr2: 60495828-60495853
AAAAACCCUUGCCACCA
1333







UGGGAGCC





53335_I2_103
BCL11a
Intron 2
+
chr2: 60495829-60495854
AAAACCCUUGCCACCAU
1334







GGGAGCCU





53335_I2_104
BCL11a
Intron 2
+
chr2: 60495830-60495855
AAACCCUUGCCACCAUG
1335







GGAGCCUG





53335_I2_105
BCL11a
Intron 2
+
chr2: 60495839-60495864
CCACCAUGGGAGCCUGG
1336







GGCAGAGA





53335_I2_106
BCL11a
Intron 2
+
chr2: 60495867-60495892
CACAGUGAAGUCAAACU
1337







GUAAUUCC





53335_I2_107
BCL11a
Intron 2
+
chr2: 60495877-60495902
UCAAACUGUAAUUCCAG
1338







GCUCUAAA





53335_I2_108
BCL11a
Intron 2
+
chr2: 60495913-60495938
UUUUUCUGAGAGUCUCU
1339







AAAUUACA





53335_I2_109
BCL11a
Intron 2
+
chr2: 60495914-60495939
UUUUCUGAGAGUCUCUA
1340







AAUUACAA





53335_I2_110
BCL11a
Intron 2
+
chr2: 60495972-60495997
ACACCUAAGAAACAUAC
1341







UGCAGCUC





53335_I2_111
BCL11a
Intron 2
+
chr2: 60496001-60496026
AAAGAGAACAAACAAAC
1342







CAAAGAGA





53335_I2_112
BCL11a
Intron 2
+
chr2: 60496002-60496027
AAGAGAACAAACAAACC
1343







AAAGAGAA





53335_I2_113
BCL11a
Intron 2
+
chr2: 60496011-60496036
AACAAACCAAAGAGAAG
1344







GGAUCCAG





53335_I2_114
BCL11a
Intron 2
+
chr2: 60496048-60496073
UAUGUGAAAAGUCAAUU
1345







GAUAAUGA





53335_I2_115
BCL11a
Intron 2
+
chr2: 60496055-60496080
AAAGUCAAUUGAUAAUG
1346







AAGGCUUU





53335_I2_116
BCL11a
Intron 2
+
chr2: 60496063-60496088
UUGAUAAUGAAGGCUUU
1347







AGGAUAAC





53335_I2_117
BCL11a
Intron 2
+
chr2: 60496066-60496091
AUAAUGAAGGCUUUAGG
1348







AUAACCGG





53335_I2_118
BCL11a
Intron 2
+
chr2: 60496067-60496092
UAAUGAAGGCUUUAGGA
1349







UAACCGGA





53335_I2_119
BCL11a
Intron 2
+
chr2: 60496068-60496093
AAUGAAGGCUUUAGGAU
1350







AACCGGAG





53335_I2_120
BCL11a
Intron 2
+
chr2: 60496098-60496123
AUGAUUGAAAGCAAUGC
1351







ACCUGUGC





53335_I2_121
BCL11a
Intron 2
+
chr2: 60496104-60496129
GAAAGCAAUGCACCUGU
1352







GCAGGAAA





53335_I2_122
BCL11a
Intron 2
+
chr2: 60496111-60496136
AUGCACCUGUGCAGGAA
1353







AUGGAUUA





53335_I2_123
BCL11a
Intron 2
+
chr2: 60496118-60496143
UGUGCAGGAAAUGGAUU
1354







ACGGAAAC





53335_I2_124
BCL11a
Intron 2
+
chr2: 60496119-60496144
GUGCAGGAAAUGGAUUA
1355







CGGAAACA





53335_I2_125
BCL11a
Intron 2
+
chr2: 60496153-60496178
UCAUGAAAUCCCAGAAA
1356







ACCAGAAC





53335_I2_126
BCL11a
Intron 2
+
chr2: 60496154-60496179
CAUGAAAUCCCAGAAAA
1357







CCAGAACC





53335_I2_127
BCL11a
Intron 2
+
chr2: 60496164-60496189
CAGAAAACCAGAACCGG
1358







GAAAGUUC





53335_I2_128
BCL11a
Intron 2
+
chr2: 60496171-60496196
CCAGAACCGGGAAAGUU
1359







CUGGAAGU





53335_I2_129
BCL11a
Intron 2
+
chr2: 60496198-60496223
GAAAAACAAAUCAUGAC
1360







UUAAGCAA





53335_I2_130
BCL11a
Intron 2
+
chr2: 60496238-60496263
CGUUUACAGAAUGCCUU
1361







GUCCCACG





53335_I2_131
BCL11a
Intron 2

chr2: 60494308-60494333
AGGCCAUGGUCACUGCC
1362







CAGUUUAG





53335_I2_132
BCL11a
Intron 2

chr2: 60494327-60494352
CCAGAGUGGGGAGGUGA
1363







CCAGGCCA





53335_I2_133
BCL11a
Intron 2

chr2: 60494333-60494358
CCAGGUCCAGAGUGGGG
1364







AGGUGACC





53335_I2_134
BCL11a
Intron 2

chr2: 60494341-60494366
GGGGCAACCCAGGUCCA
1365







GAGUGGGG





53335_I2_135
BCL11a
Intron 2

chr2: 60494344-60494369
AGAGGGGCAACCCAGGU
1366







CCAGAGUG





53335_I2_136
BCL11a
Intron 2

chr2: 60494345-60494370
CAGAGGGGCAACCCAGG
1367







UCCAGAGU





53335_I2_137
BCL11a
Intron 2

chr2: 60494346-60494371
ACAGAGGGGCAACCCAG
1368







GUCCAGAG





53335_I2_138
BCL11a
Intron 2

chr2: 60494356-60494381
CUCCUUGUUUACAGAGG
1369







GGCAACCC





53335_I2_139
BCL11a
Intron 2

chr2: 60494365-60494390
UAUUACAACCUCCUUGU
1370







UUACAGAG





53335_I2_140
BCL11a
Intron 2

chr2: 60494366-60494391
UUAUUACAACCUCCUUG
1371







UUUACAGA





53335_I2_141
BCL11a
Intron 2

chr2: 60494367-60494392
UUUAUUACAACCUCCUU
1372







GUUUACAG





53335_I2_142
BCL11a
Intron 2

chr2: 60494401-60494426
UAAGAUUUAUAAGACAU
1373







UAGGGUAU





53335_I2_143
BCL11a
Intron 2

chr2: 60494407-60494432
AUUGCAUAAGAUUUAUA
1374







AGACAUUA





53335_I2_144
BCL11a
Intron 2

chr2: 60494408-60494433
AAUUGCAUAAGAUUUAU
1375







AAGACAUU





53335_I2_145
BCL11a
Intron 2

chr2: 60494440-60494465
CUCUUCUCUCCCCAUACU
1376







CCCAUCU





53335_I2_146
BCL11a
Intron 2

chr2: 60494477-60494502
UUGAUAUCUCAUCUCAC
1377







UGAGCUCU





53335_I2_147
BCL11a
Intron 2

chr2: 60494478-60494503
UUUGAUAUCUCAUCUCA
1378







CUGAGCUC





53335_I2_148
BCL11a
Intron 2

chr2: 60494526-60494551
CUUUGCCAAUUGGAGAU
1379







UAGGGAGA





53335_I2_149
BCL11a
Intron 2

chr2: 60494532-60494557
GUCUGGCUUUGCCAAUU
1380







GGAGAUUA





53335_I2_150
BCL11a
Intron 2

chr2: 60494533-60494558
AGUCUGGCUUUGCCAAU
1381







UGGAGAUU





53335_I2_151
BCL11a
Intron 2

chr2: 60494541-60494566
UUGCCCCAAGUCUGGCU
1382







UUGCCAAU





53335_I2_152
BCL11a
Intron 2

chr2: 60494554-60494579
GAACCAGUCUGUAUUGC
1383







CCCAAGUC





53335_I2_153
BCL11a
Intron 2

chr2: 60494599-60494624
GGUGAUAAAUCAUUAGG
1384







AAUGAGCU





53335_I2_154
BCL11a
Intron 2

chr2: 60494610-60494635
AAAGAACAUUUGGUGAU
1385







AAAUCAUU





53335_I2_155
BCL11a
Intron 2

chr2: 60494625-60494650
AAAUUCCAGCUGAAGAA
1386







AGAACAUU





53335_I2_156
BCL11a
Intron 2

chr2: 60494668-60494693
AUAUACUAUUAUUAUUC
1387







CUAUUUUA





53335_I2_157
BCL11a
Intron 2

chr2: 60494745-60494770
AAGCUCGGAGCACUUAC
1388







UCUGCUCU





53335_I2_158
BCL11a
Intron 2

chr2: 60494765-60494790
GAGGCAGCAUUUUAGUU
1389







CACAAGCU





53335_I2_159
BCL11a
Intron 2

chr2: 60494789-60494814
UGAGGUGUAACUAAUAA
1390







AUACCAGG





53335_I2_160
BCL11a
Intron 2

chr2: 60494792-60494817
UGCUGAGGUGUAACUAA
1391







UAAAUACC





53335_I2_161
BCL11a
Intron 2

chr2: 60494812-60494837
GGGCCUGAUAACUUUGU
1392







UUCUGCUG





53335_I2_162
BCL11a
Intron 2

chr2: 60494837-60494862
UGACCCAAACUAGGAAU
1393







UGGGGAAA





53335_I2_163
BCL11a
Intron 2

chr2: 60494838-60494863
CUGACCCAAACUAGGAA
1394







UUGGGGAA





53335_I2_164
BCL11a
Intron 2

chr2: 60494843-60494868
UUCUUCUGACCCAAACU
1395







AGGAAUUG





53335_I2_165
BCL11a
Intron 2

chr2: 60494844-60494869
UUUCUUCUGACCCAAAC
1396







UAGGAAUU





53335_I2_166
BCL11a
Intron 2

chr2: 60494845-60494870
UUUUCUUCUGACCCAAA
1397







CUAGGAAU





53335_I2_167
BCL11a
Intron 2

chr2: 60494851-60494876
UUUCCCUUUUCUUCUGA
1398







CCCAAACU





53335_I2_168
BCL11a
Intron 2

chr2: 60494942-60494967
CCUAUCAGGUACCAGCU
1399







ACUGUGUU





53335_I2_169
BCL11a
Intron 2

chr2: 60494961-60494986
CAUCCAUCACAUAUAGG
1400







CACCUAUC





53335_I2_170
BCL11a
Intron 2

chr2: 60494972-60494997
GGCUGUCCACCCAUCCA
1401







UCACAUAU





53335_I2_171
BCL11a
Intron 2

chr2: 60494998-60495023
CAUAAUUGUCCAUUUUU
1402







CAUCUGUC





53335_I2_172
BCL11a
Intron 2

chr2: 60494999-60495024
UCAUAAUUGUCCAUUUU
1403







UCAUCUGU





53335_I2_173
BCL11a
Intron 2

chr2: 60495058-60495083
GUGUGGACUCCCAAAAU
1404







UGUAAAGG





53335_I2_174
BCL11a
Intron 2

chr2: 60495061-60495086
GCCGUGUGGACUCCCAA
1405







AAUUGUAA





53335_I2_175
BCL11a
Intron 2

chr2: 60495080-60495105
GAAAUAAUUUGUAUGCC
1406







AUGCCGUG





53335_I2_176
BCL11a
Intron 2

chr2: 60495111-60495136
GGAGAAUUGGAUUUUAU
1407







UUCUCAAU





53335_I2_177
BCL11a
Intron 2

chr2: 60495112-60495137
UGGAGAAUUGGAUUUUA
1408







UUUCUCAA





53335_I2_178
BCL11a
Intron 2

chr2: 60495129-60495154
GAAGGCUCUCUUGGUGA
1409







UGGAGAAU





53335_I2_179
BCL11a
Intron 2

chr2: 60495137-60495162
CUCUUUCGGAAGGCUCU
1410







CUUGGUGA





53335_I2_180
BCL11a
Intron 2

chr2: 60495143-60495168
GGGGGCCUCUUUCGGAA
1411







GGCUCUCU





53335_I2_181
BCL11a
Intron 2

chr2: 60495152-60495177
UUUGCCCAGGGGGGCCU
1412







CUUUCGGA





53335_I2_182
BCL11a
Intron 2

chr2: 60495156-60495181
GCCGUUUGCCCAGGGGG
1413







GCCUCUUU





53335_I2_183
BCL11a
Intron 2

chr2: 60495166-60495191
UCCAUCGGUGGCCGUUU
1414







GCCCAGGG





53335_I2_184
BCL11a
Intron 2

chr2: 60495167-60495192
CUCCAUCGGUGGCCGUU
1415







UGCCCAGG





53335_I2_185
BCL11a
Intron 2

chr2: 60495168-60495193
UCUCCAUCGGUGGCCGU
1416







UUGCCCAG





53335_I2_186
BCL11a
Intron 2

chr2: 60495169-60495194
CUCUCCAUCGGUGGCCG
1417







UUUGCCCA





53335_I2_187
BCL11a
Intron 2

chr2: 60495170-60495195
CCUCUCCAUCGGUGGCC
1418







GUUUGCCC





53335_I2_188
BCL11a
Intron 2

chr2: 60495183-60495208
GAGGACUGGCAGACCUC
1419







UCCAUCGG





53335_I2_189
BCL11a
Intron 2

chr2: 60495186-60495211
GAAGAGGACUGGCAGAC
1420







CUCUCCAU





53335_I2_190
BCL11a
Intron 2

chr2: 60495202-60495227
GGGCGUGGGUGGGGUAG
1421







AAGAGGAC





53335_I2_191
BCL11a
Intron 2

chr2: 60495207-60495232
GGUGGGGGCGUGGGUGG
1422







GGUAGAAG





53335_I2_192
BCL11a
Intron 2

chr2: 60495216-60495241
UCUGAUUAGGGUGGGGG
1423







CGUGGGUG





53335_I2_193
BCL11a
Intron 2

chr2: 60495217-60495242
CUCUGAUUAGGGUGGGG
1424







GCGUGGGU





53335_I2_194
BCL11a
Intron 2

chr2: 60495218-60495243
CCUCUGAUUAGGGUGGG
1425







GGCGUGGG





53335_I2_195
BCL11a
Intron 2

chr2: 60495221-60495246
UGGCCUCUGAUUAGGGU
1426







GGGGGCGU





53335_I2_196
BCL11a
Intron 2

chr2: 60495222-60495247
UUGGCCUCUGAUUAGGG
1427







UGGGGGCG





53335_I2_197
BCL11a
Intron 2

chr2: 60495227-60495252
AGGGUUUGGCCUCUGAU
1428







UAGGGUGG





53335_I2_198
BCL11a
Intron 2

chr2: 60495228-60495253
AAGGGUUUGGCCUCUGA
1429







UUAGGGUG





53335_I2_199
BCL11a
Intron 2

chr2: 60495229-60495254
GAAGGGUUUGGCCUCUG
1430







AUUAGGGU





53335_I2_200
BCL11a
Intron 2

chr2: 60495230-60495255
GGAAGGGUUUGGCCUCU
1431







GAUUAGGG





53335_I2_201
BCL11a
Intron 2

chr2: 60495233-60495258
CCAGGAAGGGUUUGGCC
1432







UCUGAUUA





53335_I2_202
BCL11a
Intron 2

chr2: 60495234-60495259
UCCAGGAAGGGUUUGGC
1433







CUCUGAUU





53335_I2_203
BCL11a
Intron 2

chr2: 60495246-60495271
UUUAUCACAGGCUCCAG
1434







GAAGGGUU





53335_I2_204
BCL11a
Intron 2

chr2: 60495251-60495276
UUGCUUUUAUCACAGGC
1435







UCCAGGAA





53335_I2_205
BCL11a
Intron 2

chr2: 60495252-60495277
GUUGCUUUUAUCACAGG
1436







CUCCAGGA





53335_I2_206
BCL11a
Intron 2

chr2: 60495256-60495281
AACAGUUGCUUUUAUCA
1437







CAGGCUCC





53335_I2_207
BCL11a
Intron 2

chr2: 60495263-60495288
GCAAGCUAACAGUUGCU
1438







UUUAUCAC





53335_I2_208
BCL11a
Intron 2

chr2: 60495318-60495343
AUCUACUCUUAGACAUA
1439







ACACACCA





53335_I2_209
BCL11a
Intron 2

chr2: 60495319-60495344
CAUCUACUCUUAGACAU
1440







AACACACC





53335_I2_210
BCL11a
Intron 2

chr2: 60495347-60495372
AAUAACAUAGGCCAGAA
1441







AAGAGAUA





53335_I2_211
BCL11a
Intron 2

chr2: 60495364-60495389
GCAAAGUCCAUACAGGU
1442







AAUAACAU





53335_I2_212
BCL11a
Intron 2

chr2: 60495376-60495401
GCUGAUUCCAGUGCAAA
1443







GUCCAUAC





53335_I2_213
BCL11a
Intron 2

chr2: 60495426-60495451
CGAUACAGGGCUGGCUC
1444







UAUGCCCC





53335_I2_214
BCL11a
Intron 2

chr2: 60495440-60495465
AGAUGGCUGAAAAGCGA
1445







UACAGGGC





53335_I2_215
BCL11a
Intron 2

chr2: 60495444-60495469
AGUGAGAUGGCUGAAAA
1446







GCGAUACA





53335_I2_216
BCL11a
Intron 2

chr2: 60495445-60495470
UAGUGAGAUGGCUGAAA
1447







AGCGAUAC





53335_I2_217
BCL11a
Intron 2

chr2: 60495462-60495487
GACUUGGGAGUUAUCUG
1448







UAGUGAGA





53335_I2_218
BCL11a
Intron 2

chr2: 60495482-60495507
UAAGGAAGGCAGCUAGA
1449







CAGGACUU





53335_I2_219
BCL11a
Intron 2

chr2: 60495483-60495508
AUAAGGAAGGCAGCUAG
1450







ACAGGACU





53335_I2_220
BCL11a
Intron 2

chr2: 60495489-60495514
CCUGUGAUAAGGAAGGC
1451







AGCUAGAC





53335_I2_221
BCL11a
Intron 2

chr2: 60495501-60495526
UUGGGUGCUAUUCCUGU
1452







GAUAAGGA





53335_I2_222
BCL11a
Intron 2

chr2: 60495505-60495530
GACCUUGGGUGCUAUUC
1453







CUGUGAUA





53335_I2_223
BCL11a
Intron 2

chr2: 60495524-60495549
CUACUCUGAGGUACUGA
1454







UGGACCUU





53335_I2_224
BCL11a
Intron 2

chr2: 60495525-60495550
UCUACUCUGAGGUACUG
1455







AUGGACCU





53335_I2_225
BCL11a
Intron 2

chr2: 60495532-60495557
AGGGGGUUCUACUCUGA
1456







GGUACUGA





53335_I2_226
BCL11a
Intron 2

chr2: 60495541-60495566
CUAGUUUAUAGGGGGUU
1457







CUACUCUG





53335_I2_227
BCL11a
Intron 2

chr2: 60495554-60495579
UGGGCAAACCAGACUAG
1458







UUUAUAGG





53335_I2_228
BCL11a
Intron 2

chr2: 60495555-60495580
AUGGGCAAACCAGACUA
1459







GUUUAUAG





53335_I2_229
BCL11a
Intron 2

chr2: 60495556-60495581
CAUGGGCAAACCAGACU
1460







AGUUUAUA





53335_I2_230
BCL11a
Intron 2

chr2: 60495557-60495582
CCAUGGGCAAACCAGAC
1461







UAGUUUAU





53335_I2_231
BCL11a
Intron 2

chr2: 60495578-60495603
GGAAAACAGCCUGACUG
1462







UGCCCCAU





53335_I2_232
BCL11a
Intron 2

chr2: 60495579-60495604
UGGAAAACAGCCUGACU
1463







GUGCCCCA





53335_I2_233
BCL11a
Intron 2

chr2: 60495604-60495629
GGCAGAGAAUGUCUGCA
1464







CCCCACCC





53335_I2_234
BCL11a
Intron 2

chr2: 60495630-60495655
UGACGUUAUAUGUAAGC
1465







AUCACAAC





53335_I2_235
BCL11a
Intron 2

chr2: 60495684-60495709
GGAAGCUCCAAACUCUC
1466







AAACCACA





53335_I2_236
BCL11a
Intron 2

chr2: 60495685-60495710
GGGAAGCUCCAAACUCU
1467







CAAACCAC





53335_I2_237
BCL11a
Intron 2

chr2: 60495710-60495735
CCCAUUGAGAAUAUUUU
1468







GACUUUUA





53335_I2_238
BCL11a
Intron 2

chr2: 60495711-60495736
GCCCAUUGAGAAUAUUU
1469







UGACUUUU





53335_I2_239
BCL11a
Intron 2

chr2: 60495738-60495763
CCUUUUGUGUGUAUGUG
1470







CUGAUUGA





53335_I2_240
BCL11a
Intron 2

chr2: 60495739-60495764
ACCUUUUGUGUGUAUGU
1471







GCUGAUUG





53335_I2_241
BCL11a
Intron 2

chr2: 60495768-60495793
AGCAGGAAAAGAAUUAC
1472







AGUUUUCC





53335_I2_242
BCL11a
Intron 2

chr2: 60495790-60495815
GGUAUUGAAUUGCCUGU
1473







CUUUGAGC





53335_I2_243
BCL11a
Intron 2

chr2: 60495816-60495841
GGCAAGGGUUUUUGGUU
1474







GGGGGAAG





53335_I2_244
BCL11a
Intron 2

chr2: 60495817-60495842
UGGCAAGGGUUUUUGGU
1475







UGGGGGAA





53335_I2_245
BCL11a
Intron 2

chr2: 60495818-60495843
GUGGCAAGGGUUUUUGG
1476







UUGGGGGA





53335_I2_246
BCL11a
Intron 2

chr2: 60495822-60495847
CAUGGUGGCAAGGGUUU
1477







UUGGUUGG





53335_I2_247
BCL11a
Intron 2

chr2: 60495823-60495848
CCAUGGUGGCAAGGGUU
1478







UUUGGUUG





53335_I2_248
BCL11a
Intron 2

chr2: 60495824-60495849
CCCAUGGUGGCAAGGGU
1479







UUUUGGUU





53335_I2_249
BCL11a
Intron 2

chr2: 60495825-60495850
UCCCAUGGUGGCAAGGG
1480







UUUUUGGU





53335_I2_250
BCL11a
Intron 2

chr2: 60495829-60495854
AGGCUCCCAUGGUGGCA
1481







AGGGUUUU





53335_I2_251
BCL11a
Intron 2

chr2: 60495836-60495861
CUGCCCCAGGCUCCCAUG
1482







GUGGCAA





53335_I2_252
BCL11a
Intron 2

chr2: 60495837-60495862
UCUGCCCCAGGCUCCCAU
1483







GGUGGCA





53335_I2_253
BCL11a
Intron 2

chr2: 60495842-60495867
CCUUCUCUGCCCCAGGCU
1484







CCCAUGG





53335_I2_254
BCL11a
Intron 2

chr2: 60495845-60495870
GUGCCUUCUCUGCCCCA
1485







GGCUCCCA





53335_I2_255
BCL11a
Intron 2

chr2: 60495854-60495879
GACUUCACUGUGCCUUC
1486







UCUGCCCC





53335_I2_256
BCL11a
Intron 2

chr2: 60495893-60495918
AAAAAUGACAGCACCAU
1487







UUAGAGCC





53335_I2_257
BCL11a
Intron 2

chr2: 60495978-60496003
UUUCCAGAGCUGCAGUA
1488







UGUUUCUU





53335_I2_258
BCL11a
Intron 2

chr2: 60496020-60496045
GGGUGACCUCUGGAUCC
1489







CUUCUCUU





53335_I2_259
BCL11a
Intron 2

chr2: 60496035-60496060
ACUUUUCACAUAUGAGG
1490







GUGACCUC





53335_I2_260
BCL11a
Intron 2

chr2: 60496045-60496070
UUAUCAAUUGACUUUUC
1491







ACAUAUGA





53335_I2_261
BCL11a
Intron 2

chr2: 60496046-60496071
AUUAUCAAUUGACUUUU
1492







CACAUAUG





53335_I2_262
BCL11a
Intron 2

chr2: 60496090-60496115
GCAUUGCUUUCAAUCAU
1493







CUCCCCUC





53335_I2_263
BCL11a
Intron 2

chr2: 60496119-60496144
UGUUUCCGUAAUCCAUU
1494







UCCUGCAC





53335_I2_264
BCL11a
Intron 2

chr2: 60496165-60496190
AGAACUUUCCCGGUUCU
1495







GGUUUUCU





53335_I2_265
BCL11a
Intron 2

chr2: 60496166-60496191
CAGAACUUUCCCGGUUC
1496







UGGUUUUC





53335_I2_266
BCL11a
Intron 2

chr2: 60496174-60496199
CCGACUUCCAGAACUUU
1497







CCCGGUUC





53335_I2_267
BCL11a
Intron 2

chr2: 60496180-60496205
GUUUUUCCGACUUCCAG
1498







AACUUUCC





53335_I2_268
BCL11a
Intron 2

chr2: 60496233-60496258
GACAAGGCAUUCUGUAA
1499







ACGUGUAU









In embodiments, the gRNA targeting domain consists of the 20 3′ nt of any one of the sequences in the table above.


Exemplary preferred gRNA targeting domains useful in the compositions and methods of the invention are described in the tables below.









TABLE 5







Preferred Guide RNA Targeting Domains Directed


to Coding Regions of the BCL11a Gene















SEQ ID


Id.
Target
gRNA Targeting Domain
Targeting Site (Chr2)
NO:














CR000044
BCL11a
ACAGGCCGUGAACCUAAGUG
60678414-60678436
1





CR000056
BCL11a
UAGAGGGGGGAAAUUAUAGG
60678685-60678707
2





CR000068
BCL11a
CGAGCGGUAAAUCCUAAAGA
60678840-60678862
3





CR000079
BCL11a
AGACAAAUUCAAAUCCUGCA
60678895-60678917
4





CR000091
BCL11a
GCUUUUGGUGGCUACCAUGC
60678909-60678931
5





CR000102
BCL11a
AAUUUAUGCCAUCUGAUAAG
60679112-60679134
6





CR000033
BCL11a
UGUUCCUCCUACCCACCCGA
60679178-60679200
7





CR000045
BCL11a
AUAAAUGUUGGAGCUUUAGG
60679288-60679310
8





CR000069
BCL11a
CAACCUAAUUACCUGUAUUG
60679389-60679411
9





CR000080
BCL11a
CGCUGUCAUGAGUGAUGCCC
60679428-60679450
10





CR000092
BCL11a
GGCAUCACUCAUGACAGCGA
60679432-60679454
11





CR000103
BCL11a
AGUCCCAUAGAGAGGGCCCG
60679456-60679478
12





CR000115
BCL11a
ACUGAUUCACUGUUCCAAUG
60679476-60679498
13





CR000034
BCL11a
AGGACUCUGUCUUCGCACAA
60679577-60679599
14





CR000058
BCL11a
CCACGCUGACGUCGACUGGG
60679650-60679672
15





CR000070
BCL11a
GUUCUUCACACACCCCCAUU
60679779-60679801
16





CR000081
BCL11a
GCGCUUCUCCACACCGCCCG
60687934-60687956
17





CR000093
BCL11a
GUCUGGAGUCUCCGAAGCUA
60688006-60688028
18





CR000116
BCL11a
AAAGAUCCCUUCCUUAGCUU
60688017-60688039
19





CR000035
BCL11a
UCGCCGGCUACGCGGCCUCC
60688046-60688068
20





CR000047
BCL11a
CGGAGAACGUGUACUCGCAG
60688070-60688092
21





CR000071
BCL11a
GAGCUUGAUGCGCUUAGAGA
60688133-60688155
22





CR000082
BCL11a
CCCCCCGAGGCCGACUCGCC
60688200-60688222
23





CR000094
BCL11a
CACCAUGCCCUGCAUGACGU
60688394-60688416
24





CR000105
BCL11a
GAGAGCGAGAGGGUGGACUA
60688506-60688528
25





CR000117
BCL11a
CACGGACUUGAGCGCGCUGC
60688649-60688671
26





CR000036
BCL11a
GCCCACCAAGUCGCUGGUGC
60688676-60688698
27





CR000048
BCL11a
CCCACCAAGUCGCUGGUGCC
60688677-60688699
28





CR000060
BCL11a
GGCGGUGGAGAGACCGUCGU
60688712-60688734
29





CR000072
BCL11a
GCCGCAGAACUCGCAUGACU
60688898-60688920
30





CR000083
BCL11a
CCGCCCCCAGGCGCUCUAUG
60689194-60689216
31





CR000095
BCL11a
UGGGGGUCCAAGUGAUGUCU
60689217-60689239
32





CR000106
BCL11a
CUCAACUUACAAAUACCCUG
60695857-60695879
33





CR000118
BCL11a
AGUGCAGAAUAUGCCCCGCA
60695872-60695894
34





CR000037
BCL11a
GCAUAUUCUGCACUCAUCCC
60695881-60695903
35





CR000049
BCL11a
GAGCUCUAAUCCCCACGCCU
60695898-60695920
36





CR000061
BCL11a
AGAGCUCCAUGUGCAGAACG
60695914-60695936
37





CR000084
BCL11a
GAUAAACUUCUGCACUGGAG
60695947-60695969
38





CR000096
BCL11a
UAGCUGUAGUGCUUGAUUUU
60695981-60696003
39





CR000107
BCL11a
UAUCCAAAUUCAUACAAUAG
60716451-60716473
40





CR000119
BCL11a
AUGCCCUGAGUAUCCCAACA
60717068-60717090
41





CR000038
BCL11a
UAGUAACAGACCCAUGUGCU
60717232-60717254
42





CR000050
BCL11a
AUACUUCAAGGCCUCAAUGA
60717661-60717683
43





CR000062
BCL11a
GACUAGGUAGACCUUCAUUG
60717672-60717694
44





CR000073
BCL11a
CUGAGCUAGUGGGGGCUCUU
60720773-60720795
45





CR000085
BCL11a
CUGAGCACAUUCUUACGCCU
60721291-60721313
46





CR000097
BCL11a
UUUAUAAGACAUUAGGGUAt
60721534-60721556
47





CR000108
BCL11a
UGAUAGGUGCCUAUAUGUGA
60722096-60722118
48





CR000120
BCL11a
UCCACCCAUCCAUCACAUAU
60722105-60722127
49





CR000039
BCL11a
CUUCAAAGUUGUAUUGACCC
60722434-60722456
50





CR000051
BCL11a
AAACCAGACUAGUUUAUAGG
60722687-60722709
51





CR000063
BCL11a
UUUGAGACAGUUACCCCUUC
60723706-60723728
52





CR000074
BCL11a
AACCUGAGGGCUAGUUUCUA
60724541-60724563
53





CR000086
BCL11a
GCCUGGACCCACCGCUUCAU
60725058-60725080
54





CR000109
BCL11a
AAACCAGUGAGGUCAUCUAU
60725857-60725879
55





CR000121
BCL11a
ACCUGCUAUGUGUUCCUGUU
60773104-60773126
56





CR000040
BCL11a
UAGAGGAAUUUGCCCCAAAC
60773118-60773140
57





CR000052
BCL11a
GAUAAACAAUCGUCAUCCUC
60773150-60773172
58





CR000064
BCL11a
UGGCAUCCAGGUCACGCCAG
60773166-60773188
59





CR000075
BCL11a
GACCUGGAUGCCAACCUCCA
60773176-60773198
60





CR000087
BCL11a
AAAAGCAUCCAAUCCCGUGG
60773190-60773212
61





CR000110
BCL11a
GAUGCUUUUUUCAUCUCGAU
60773204-60773226
62





CR000122
BCL11a
CCACAGCUUUUUCUAAGCAG
60773247-60773269
63





CR000041
BCL11a
CCCCCAAUGGGAAGUUCAUC
60773316-60773338
64





CR000053
BCL11a
AUCAUGACCUCCUCACCUGU
60773344-60773366
65





CR000065
BCL11a
AGGAGGUCAUGAUCCCCUUC
60773354-60773376
66





CR000088
BCL11a
CCCCUUCUGGAGCUCCCAAC
60773367-60773389
67





CR000099
BCL11a
GCUCCCAACGGGCCGUGGUC
60773378-60773400
68





CR000111
BCL11a
ACAGAUGAUGAACCAGACCA
60773390-60773412
69





CR000123
BCL11a
UCUGUAAGAAUGGCUUCAAG
60773408-60773430
70





CR000042
BCL11a
CAAUUAUUAGAGUGCCAGAG
60773459-60773481
71





CR000054
BCL11a
GCCUUGCUUGCGGCGAGACA
60780385-60780407
72





CR000066
BCL11a
ACCAUGUCUCGCCGCAAGCA
60780386-60780408
73





CR000077
BCL11a
GAGUCUCCUUCUUUCUAACC
60780482-60780504
74





CR000089
BCL11a
GAAUUGUGGGAGAGCCGUCA
60780582-60780604
75





CR000100
BCL11a
AAAAUAGAGCGAGAGUGCAC
60781166-60781188
76





CR000112
BCL11a
GCCCCUGGCGUCCACACGCG
60781306-60781328
77





CR000124
BCL11a
CUCCUCGUUCUUUAUUCCUC
60781716-60781738
78





CR000043
BCL11a
GACUGCCCGCGCUUUGUCCU
60781815-60781837
79





CR000055
BCL11a
UUCCCAGGGACUGGGACUCC
60781838-60781860
80





CR000078
BCL11a
UGGCUCCUGGGUGUGCGCCU
60782123-60782145
81





CR000090
BCL11a
UGAAGCCCGCUUUUUGACAG
60782254-60782276
82





CR000101
BCL11a
AGGGUGGAGACGGGUCGCCA
60782526-60782548
83





CR000113
BCL11a
GCUCAGGGUCUCGCGGGCCA
60782543-60782565
84





CR000059
BCL11a
UGAGUCCGAGCAGAAGAAGA
73160981-73161003
85
















TABLE 6







Preferred Guide RNA Targeting Domains directed to the French HPFH


(French HPFH; Sankaran VG et al. A functional element necessary


for fetal hemoglobin silencing. NEJM (2011) 365: 807-814.)

















SEQ



Target


Genomic Target
ID


Id.
Name
Strand
gRNA Targeting Domain
Location
NO:















CR001016
HPFH

UCUUAAACCAACCUGCUCAC
chr11: 5234538-5234558
86





CR001017
HPFH
+
CAGGUUGGUUUAAGAUAAGC
chr11: 5234543-5234563
87





CR001018
HPFH
+
AGGUUGGUUUAAGAUAAGCA
chr11: 5234544-5234564
88





CR001019
HPFH

UUAAGGGAAUAGUGGAAUGA
chr11: 5234600-5234620
89





CR001020
HPFH

AGGGCAAGUUAAGGGAAUAG
chr11: 5234608-5234628
90





CR001021
HPFH
+
CCCUUAACUUGCCCUGAGAU
chr11: 5234613-5234633
91





CR001022
HPFH

CCAAUCUCAGGGCAAGUUAA
chr11: 5234616-5234636
92





CR001023
HPFH

GCCAAUCUCAGGGCAAGUUA
chr11: 5234617-5234637
93





CR001024
HPFH

UGACAGAACAGCCAAUCUCA
chr11: 5234627-5234647
94





CR001025
HPFH

AUGACAGAACAGCCAAUCUC
chr11: 5234628-5234648
95





CR001026
HPFH

GAGAUAUGUAGAGGAGAACA
chr11: 5234670-5234690
96





CR001027
HPFH

GGAGAUAUGUAGAGGAGAAC
chr11: 5234671-5234691
97





CR001028
HPFH

UGCGGUGGGGAGAUAUGUAG
chr11: 5234679-5234699
98





CR001029
HPFH

CUGCUGAAAGAGAUGCGGUG
chr11: 5234692-5234712
99





CR001030
HPFH

ACUGCUGAAAGAGAUGCGGU
chr11: 5234693-5234713
100





CR001031
HPFH

AACUGCUGAAAGAGAUGCGG
chr11: 5234694-5234714
101





CR001032
HPFH

AACAACUGCUGAAAGAGAUG
chr11: 5234697-5234717
102





CR001033
HPFH

UCUGCAAAAAUGAAACUAGG
chr11: 5234731-5234751
103





CR001034
HPFH

ACUUCUGCAAAAAUGAAACU
chr11: 5234734-5234754
104





CR001035
HPFH
+
CAUUUUUGCAGAAGUGUUUU
chr11: 5234739-5234759
105





CR001036
HPFH
+
AGUGUUUUAGGCUAAUAUAG
chr11: 5234751-5234771
106





CR001037
HPFH

UUGGAGACAAAAAUCUCUAG
chr11: 5234883-5234903
107





CR001038
HPFH
+
UCUAGAGAUUUUUGUCUCCA
chr11: 5234882-5234902
108





CR001039
HPFH
+
CUAGAGAUUUUUGUCUCCAA
chr11: 5234883-5234903
109





CR001040
HPFH
+
GUCUCCAAGGGAAUUUUGAG
chr11: 5234895-5234915
110





CR001041
HPFH
+
CCAAGGGAAUUUUGAGAGGU
chr11: 5234899-5234919
111





CR001042
HPFH

CCAACCUCUCAAAAUUCCCU
chr11: 5234902-5234922
112





CR001043
HPFH
+
GGAAUUUUGAGAGGUUGGAA
chr11: 5234904-5234924
113





CR001044
HPFH
+
UGCUUGCUUCCUCCUUCUUU
chr11: 5234953-5234973
114





CR001045
HPFH

AAGAAUUUACCAAAAGAAGG
chr11: 5234965-5234985
115





CR001046
HPFH

AGGAAGAAUUUACCAAAAGA
chr11: 5234968-5234988
116





CR001047
HPFH

AAAAAUUAGAGUUUUAUUAU
chr11: 5234988-5235008
117





CR001048
HPFH

UUUUUUAAAUAUUCUUUUAA
Chr11: 5235023-5235045
118





CR001049
HPFH
+
UAUUUACCAGUUAUUGAAAU
chr11: 5235062-5235082
119





CR001050
HPFH
+
CCAGUUAUUGAAAUAGGUUC
chr11: 5235068-5235088
120





CR001051
HPFH

CCAGAACCUAUUUCAAUAAC
chr11: 5235071-5235091
121





CR001052
HPFH
+
UUCUGGAAACAUGAAUUUUA
chr11: 5235085-5235105
122





CR001053
HPFH
+
AUUUUGAAUGUUUAAAAUUA
chr11: 5235151-5235171
123





CR001054
HPFH

AAAUUUAAUCUGGCUGAAUA
chr11: 5235216-5235236
124





CR001055
HPFH

GAACUUCGUUAAAUUUAAUC
chr11: 5235226-5235246
125





CR001056
HPFH
+
AUUAAAUUUAACGAAGUUCC
chr11: 5235227-5235247
126





CR001057
HPFH
+
UUAAAUUUAACGAAGUUCCU
chr11: 5235228-5235248
127





CR001058
HPFH

UUCUGUACUAGCAUAUUCCC
chr11: 5235248-5235268
128





CR001059
HPFH
+
UGUGUUCUUAAAAAAAAAUG
Chr11: 5235275-5235297
129





CR001060
HPFH
+
AAAAAUGUGGAAUUAGACCC
chr11: 5235293-5235313
130





CR001061
HPFH

CUACUGGGAUCUUCAUUCCU
chr11: 5235313-5235333
131





CR001062
HPFH

ACUACUGGGAUCUUCAUUCC
chr11: 5235314-5235334
132





CR001063
HPFH

GAAAAGAGUGAAAAACUACU
chr11: 5235328-5235348
133





CR001064
HPFH

AGAAAAGAGUGAAAAACUAC
chr11: 5235329-5235349
134





CR001065
HPFH
+
GAAUUCAAAUAAUGCCACAA
chr11: 5235349-5235369
135





CR001066
HPFH

UGUGUAUUUGUCUGCCAUUG
chr11: 5235366-5235386
136





CR001067
HPFH
+
CACCCAUGAGCAUAUCCAAA
chr11: 5235384-5235404
137





CR001068
HPFH

UUCCUUUUGGAUAUGCUCAU
chr11: 5235389-5235409
138





CR001069
HPFH

CUUCCUUUUGGAUAUGCUCA
chr11: 5235390-5235410
139





CR001070
HPFH
+
CAUGAGCAUAUCCAAAAGGA
chr11: 5235388-5235408
140





CR001071
HPFH
+
UAUCCAAAAGGAAGGAUUGA
chr11: 5235396-5235416
141





CR001072
HPFH

UUUCCUUCAAUCCUUCCUUU
chr11: 5235402-5235422
142





CR001073
HPFH
+
AAGGAAGGAUUGAAGGAAAG
chr11: 5235403-5235423
143





CR001074
HPFH
+
GAAGGAUUGAAGGAAAGAGG
chr11: 5235406-5235426
144





CR001075
HPFH
+
GAGGAGGAAGAAAUGGAGAA
chr11: 5235422-5235442
145





CR001076
HPFH
+
AGGAAGAAAUGGAGAAAGGA
chr11: 5235426-5235446
146





CR001077
HPFH
+
GAAGGAAGAGGGGAAGAGAG
chr11: 5235448-5235468
147





CR001078
HPFH
+
GAAGAGGGGAAGAGAGAGGA
chr11: 5235452-5235472
148





CR001079
HPFH
+
AGGGGAAGAGAGAGGAUGGA
chr11: 5235456-5235476
149





CR001080
HPFH
+
GGGGAAGAGAGAGGAUGGAA
chr11: 5235457-5235477
150





CR001081
HPFH
+
AAGAGAGAGGAUGGAAGGGA
chr11: 5235461-5235481
151





CR001082
HPFH
+
AGAGAGGAUGGAAGGGAUGG
chr11: 5235464-5235484
152





CR001083
HPFH
+
GGAAGGGAUGGAGGAGAAGA
chr11: 5235473-5235493
153





CR001084
HPFH
+
GAAGAAGGAAAAAUAAAUAA
Chr11: 5235483-5235505
154





CR001085
HPFH
+
AGGAAAAAUAAAUAAUGGAG
Chr11: 5235488-5235510
155





CR001086
HPFH
+
AAAUAAAUAAUGGAGAGGAG
chr11: 5235498-5235518
156





CR001087
HPFH
+
UGGAGAGGAGAGGAGAAAAA
chr11: 5235508-5235528
157





CR001088
HPFH
+
AGAGGAGAGGAGAAAAAAGG
chr11: 5235511-5235531
158





CR001089
HPFH
+
GAGGAGAGGAGAAAAAAGGA
chr11: 5235512-5235532
159





CR001090
HPFH
+
AGGAGAGGAGAAAAAAGGAG
chr11: 5235513-5235533
160





CR001091
HPFH
+
AGGAGAAAAAAGGAGGGGAG
chr11: 5235518-5235538
161





CR001092
HPFH
+
GAGAGGAGAGGAGAAGGGAU
chr11: 5235535-5235555
162





CR001093
HPFH
+
AGAGGAGAGGAGAAGGGAUA
chr11: 5235536-5235556
163





CR001094
HPFH
+
GAAGAGAAAGAGAAAGGGAA
Chr11: 5235553-5235575
164





CR001095
HPFH
+
AAGAGAGGAAAGAAGAGAAG
chr11: 5235581-5235601
165





CR001096
HPFH
+
GAGAGAAAAGAAACGAAGAG
Chr11: 5235598-5235620
166





CR001097
HPFH
+
AGAGAAAAGAAACGAAGAGA
Chr11: 5235599-5235621
167





CR001098
HPFH
+
GAGAAAAGAAACGAAGAGAG
Chr11: 5235600-5235622
168





CR001099
HPFH
+
AAAGAAACGAAGAGAGGGGA
chr11: 5235609-5235629
169





CR001100
HPFH
+
AAGAAACGAAGAGAGGGGAA
chr11: 5235610-5235630
170





CR001101
HPFH
+
GGAAGGGAAGGAAAAAAAAG
chr11: 5235626-5235646
171





CR001102
HPFH
+
AAGACUGACAGUUCAAAUUU
chr11: 5235672-5235692
172





CR001103
HPFH
+
ACUGACAGUUCAAAUUUUGG
chr11: 5235675-5235695
173





CR001104
HPFH
+
UUCAAAUUUUGGUGGUGAUA
chr11: 5235683-5235703
174





CR001105
HPFH
+
AAUAGAAACUCAAACUCUGU
chr11: 5235709-5235729
175





CR001106
HPFH
+
GUACAAUAGUAUAACCCCUU
chr11: 5235739-5235759
176





CR001107
HPFH

CUAUUAAAGGUUUUCCAAAG
chr11: 5235756-5235776
177





CR001108
HPFH

ACUAUUAAAGGUUUUCCAAA
chr11: 5235757-5235777
178





CR001109
HPFH

UACUAUUAAAGGUUUUCCAA
chr11: 5235758-5235778
179





CR001110
HPFH

GCAUUUGUGGAUACUAUUAA
chr11: 5235769-5235789
180





CR001111
HPFH
+
UUAAUAGUAUCCACAAAUGC
chr11: 5235769-5235789
181





CR001132
HPFH

UAUCAAGCAUCCAGCAUUUG
chr11: 5235782-5235802
1500





CR001133
HPFH

UAUCUAAAAAUGUAAUUGCU
chr11: 5235814-5235834
1501





CR001134
HPFH

AGCAUUUCUAUACAUGUCUU
chr11: 5235862-5235882
1502





CR001135
HPFH
+
UAAUCAUAAAAACCUCAAAC
chr11: 5235893-5235913
1503





CR001136
HPFH

UUUAAGUGGCUACCGGUUUG
chr11: 5235908-5235928
1504





CR001137
HPFH

GUAAGCAUUUAAGUGGCUAC
chr11: 5235915-5235935
1505





CR001138
HPFH

ACUGUUGGUAAGCAUUUAAG
chr11: 5235922-5235942
1506





CR001139
HPFH

UAAUUUAUCAAUUCUACUGU
chr11: 5235937-5235957
1507





CR001140
HPFH
+
ACAGUAGAAUUGAUAAAUUA
chr11: 5235937-5235957
1508





CR001141
HPFH
+
CAAAUGCAUUUUACAGCAUU
chr11: 5236027-5236047
1509





CR001142
HPFH
+
GGUUGAUUAAAAGUAACCAG
chr11: 5236048-5236068
1510





CR001143
HPFH

AUAUAGUUUGAACUCACCUC
Chr11: 5236059-5236081
1511





CR001144
HPFH
+
UUUAUUUGUAUAUAGAAAGA
chr11: 5236090-5236110
1512





CR001145
HPFH
+
UGCCUGAGAUUCUGAUCACA
chr11: 5236119-5236139
1513





CR001146
HPFH
+
GCCUGAGAUUCUGAUCACAA
chr11: 5236120-5236140
1514





CR001147
HPFH
+
CCUGAGAUUCUGAUCACAAG
chr11: 5236121-5236141
1515





CR001148
HPFH

CCCCUUGUGAUCAGAAUCUC
chr11: 5236124-5236144
1516





CR001149
HPFH
+
AAGGGGAAAUGUUAUAAAAU
chr11: 5236138-5236158
1517





CR001150
HPFH
+
AGGGGAAAUGUUAUAAAAUA
chr11: 5236139-5236159
1518





CR001151
HPFH
+
UGUUAUAAAAUAGGGUAGAG
chr11: 5236147-5236167
1519





CR001152
HPFH

CAAAGUUUAAAGGUCAUUCA
chr11: 5236175-5236195
1520





CR001153
HPFH

UAACUUGUAACAAAGUUUAA
chr11: 5236185-5236205
1521





CR001154
HPFH
+
CAAGUUAUUUUUCUGUAACC
chr11: 5236198-5236218
1522





CR001155
HPFH

AAUAUCUUUCGUUGGCUUCC
chr11: 5236219-5236239
1523





CR001156
HPFH

AAUUAUUCAAUAUCUUUCGU
chr11: 5236227-5236247
1524





CR001157
HPFH
+
GAUAUUGAAUAAUUCAAGAA
chr11: 5236233-5236253
1525





CR001158
HPFH
+
AUUGAAUAAUUCAAGAAAGG
chr11: 5236236-5236256
1526





CR001159
HPFH
+
GAAUAAUUCAAGAAAGGUGG
chr11: 5236239-5236259
1527





CR001160
HPFH
+
AUUCAAGAAAGGUGGUGGCA
chr11: 5236244-5236264
1528





CR001161
HPFH
+
UAUUUUAGAAGUAGAGAAAA
chr11: 5236313-5236333
1529





CR001162
HPFH
+
AUUUUAGAAGUAGAGAAAAU
chr11: 5236314-5236334
1530





CR001163
HPFH
+
GAAAAUGGGAGACAAAUAGC
chr11: 5236328-5236348
1531





CR001164
HPFH
+
AAAAUGGGAGACAAAUAGCU
chr11: 5236329-5236349
1532





CR001165
HPFH
+
AGCUGGGCUUCUGUUGCAGU
chr11: 5236345-5236365
1533





CR001166
HPFH
+
GCUGGGCUUCUGUUGCAGUA
chr11: 5236346-5236366
1534





CR001167
HPFH
+
GCCAUUUCUAUUAUCAGACU
chr11: 5236383-5236403
1535





CR001168
HPFH

UCCAAGUCUGAUAAUAGAAA
chr11: 5236387-5236407
1536





CR001169
HPFH
+
UUAUCAGACUUGGACCAUGA
chr11: 5236393-5236413
1537





CR001170
HPFH

CACGACUGACAUCACCGUCA
chr11: 5236410-5236430
1538





CR001171
HPFH
+
UCAGUCGUGAACACAAGAAU
chr11: 5236421-5236441
1539





CR001172
HPFH
+
CAGUCGUGAACACAAGAAUA
chr11: 5236422-5236442
1540





CR001173
HPFH
+
GGCCACAUUUGUGAGUUUAG
chr11: 5236443-5236463
1541





CR001174
HPFH

UACCACUAAACUCACAAAUG
chr11: 5236448-5236468
1542





CR001175
HPFH
+
UAAAAUCAGAAAUACAGUCU
chr11: 5236471-5236491
1543





CR001176
HPFH
+
AAAAGAUGUACUUAGAUAUG
chr11: 5236528-5236548
1544





CR001177
HPFH
+
UGUACUUAGAUAUGUGGAUC
chr11: 5236534-5236554
1545





CR001178
HPFH
+
AGCUCAGAAAGAAUACAACC
chr11: 5236557-5236577
1546





CR001179
HPFH
+
ACCAGGUCAAGAAUACAGAA
chr11: 5236574-5236594
1547





CR001180
HPFH

UCCAUUCUGUAUUCUUGACC
chr11: 5236578-5236598
1548





CR001181
HPFH

CUGUCAUUUUUAACAGGUAG
chr11: 5236646-5236666
1549





CR001182
HPFH

CAUCAUCUGUCAUUUUUAAC
chr11: 5236652-5236672
1550





CR001183
HPFH

AAACACAUUCUAAGAUUUUA
chr11: 5236691-5236711
1551





CR001184
HPFH
+
AAUCUUAGAAUGUGUUUGUG
chr11: 5236694-5236714
1552





CR001185
HPFH
+
AUCUUAGAAUGUGUUUGUGA
chr11: 5236695-5236715
1553





CR001186
HPFH
+
UUAGAAUGUGUUUGUGAGGG
chr11: 5236698-5236718
1554





CR001187
HPFH

CAAUUUUCUUAUAUAUGAAU
chr11: 5236734-5236754
1555





CR001188
HPFH
+
UUGAUUCUAAAAAAAAUGUU
Chr11: 5236746-5236768
1556





CR001189
HPFH
+
AAAUGUUAGGUAAAUUCUUA
chr11: 5236764-5236784
1557





CR001190
HPFH
+
GGUAAAUUCUUAAGGCCAUG
chr11: 5236772-5236792
1558





CR001191
HPFH

AGAUCAAAUAACAGUCCUCA
chr11: 5236790-5236810
1559





CR001192
HPFH
+
GUCUGUUAAUUCCAAAGACU
chr11: 5236812-5236832
1560





CR001193
HPFH

AAAGUGAAAAGCCAAGUCUU
chr11: 5236826-5236846
1561





CR001194
HPFH
+
CCUGAAAUGAUUUUACACAU
chr11: 5236858-5236878
1562





CR001195
HPFH

CCAAUGUGUAAAAUCAUUUC
chr11: 5236861-5236881
1563





CR001196
HPFH
+
CUGAAAUGAUUUUACACAUU
chr11: 5236859-5236879
1564





CR001197
HPFH
+
AUUUUACACAUUGGGAGAUC
chr11: 5236867-5236887
1565





CR001198
HPFH
+
GGUUACAUGUUUAUUCUAUA
chr11: 5236888-5236908
1566





CR001199
HPFH
+
UCUAUAUGGAUUGCAUUGAG
chr11: 5236902-5236922
1567





CR001200
HPFH
+
AGGAUUUGUAUAACAGAAUA
chr11: 5236922-5236942
1568





CR001201
HPFH
+
UUUUCUUUUCUCUUCUGAGA
Chr11: 5236945-5236967
1569





CR001202
HPFH

GCACUCUAGCUUGGGCAAUA
chr11: 5236984-5237004
1570





CR001203
HPFH

UGCACUCUAGCUUGGGCAAU
chr11: 5236985-5237005
1571





CR001204
HPFH

UGCACCAUUGCACUCUAGCU
Chr11: 5236985-5237007
1572





CR001205
HPFH

GCUAUUCAGGUGGCUGAGGC
chr11: 5237061-5237081
1573





CR001206
HPFH
+
ACCUGAAUAGCUGGGACUGC
Chr11: 5237065-5237087
1574





CR001207
HPFH
+
GCAGGCAUGCACCACACGCC
Chr11: 5237083-5237105
1575





CR001208
HPFH

UACAAAAUCAGCCGGGCGUG
chr11: 5237102-5237122
1576





CR001209
HPFH

GGCUUGUAAACCCAGCACUU
chr11: 5237208-5237228
1577





CR001210
HPFH

CUGGCUGGAUGCGGUGGCUC
chr11: 5237229-5237249
1578





CR001211
HPFH
+
CUGAGCCACCGCAUCCAGCC
chr11: 5237227-5237247
1579





CR001212
HPFH

CUUAUCCUGGCUGGAUGCGG
chr11: 5237235-5237255
1580





CR001213
HPFH
+
CACCGCAUCCAGCCAGGAUA
chr11: 5237233-5237253
1581





CR001214
HPFH

GACCUUAUCCUGGCUGGAUG
chr11: 5237238-5237258
1582





CR001215
HPFH

CUUUUAGACCUUAUCCUGGC
chr11: 5237244-5237264
1583





CR001216
HPFH
+
GCCAGGAUAAGGUCUAAAAG
chr11: 5237244-5237264
1584





CR001217
HPFH

UCCACUUUUAGACCUUAUCC
chr11: 5237248-5237268
1585





CR001218
HPFH
+
AAUAGCAUCUACUCUUGUUC
chr11: 5237271-5237291
1586





CR001219
HPFH
+
CUCUUGUUCAGGAAACAAUG
chr11: 5237282-5237302
1587





CR001220
HPFH
+
GGAAACAAUGAGGACCUGAC
chr11: 5237292-5237312
1588





CR001221
HPFH
+
GAAACAAUGAGGACCUGACU
chr11: 5237293-5237313
1589





CR001222
HPFH
+
ACCUGACUGGGCAGUAAGAG
chr11: 5237305-5237325
1590





CR001223
HPFH

ACCACUCUUACUGCCCAGUC
chr11: 5237309-5237329
1591





CR001224
HPFH
+
AAGAGUGGUGAUUAAUAGAU
chr11: 5237320-5237340
1592





CR001225
HPFH
+
AGAGUGGUGAUUAAUAGAUA
chr11: 5237321-5237341
1593





CR001226
HPFH
+
AGAAUCGAACUGUUGAUUAG
chr11: 5237356-5237376
1594





CR001227
HPFH
+
UCGAACUGUUGAUUAGAGGU
chr11: 5237360-5237380
1595





CR003027
HPFH
+
CGAACUGUUGAUUAGAGGUA
chr11: 5237361-5237381
1692





CR003028
HPFH
+
AUGAUUUUAAUCUGUGACCU
chr11: 5237386-5237406
1693





CR003029
HPFH
+
UAAUCUGUGACCUUGGUGAA
chr11: 5237393-5237413
1694





CR003030
HPFH
+
AAUCUGUGACCUUGGUGAAU
chr11: 5237394-5237414
1695





CR003031
HPFH

AGCUACUUGCCCAUUCACCA
chr11: 5237406-5237426
1696





CR003032
HPFH
+
UAGCUAUCUAAUGACUAAAA
chr11: 5237421-5237441
1697





CR003033
HPFH
+
AUGACUAAAAUGGAAAACAC
chr11: 5237431-5237451
1698





CR003034
HPFH
+
AAAUACCCAUGCUGAGUCUG
chr11: 5237482-5237502
1699





CR003035
HPFH

AGGCACCUCAGACUCAGCAU
chr11: 5237490-5237510
1700





CR003036
HPFH

UAGGCACCUCAGACUCAGCA
chr11: 5237491-5237511
1701





CR003037
HPFH
+
GCUGAGUCUGAGGUGCCUAU
chr11: 5237492-5237512
1702





CR003038
HPFH

UAUUUAUAUAGAUGUCCUAU
chr11: 5237510-5237530
1703





CR003039
HPFH

CAUAUAUCAAACAAUGUACU
chr11: 5237535-5237555
1704





CR003040
HPFH
+
CCAGUACAUUGUUUGAUAUA
chr11: 5237533-5237553
1705





CR003041
HPFH

CCAUAUAUCAAACAAUGUAC
chr11: 5237536-5237556
1706





CR003042
HPFH
+
CAGUACAUUGUUUGAUAUAU
chr11: 5237534-5237554
1707





CR003043
HPFH
+
CAUUGUUUGAUAUAUGGGUU
chr11: 5237539-5237559
1708





CR003044
HPFH
+
GAUAUAUGGGUUUGGCACUG
chr11: 5237547-5237567
1709





CR003045
HPFH
+
UAUGGGUUUGGCACUGAGGU
chr11: 5237551-5237571
1710





CR003046
HPFH
+
GGGUUUGGCACUGAGGUUGG
chr11: 5237554-5237574
1711





CR003047
HPFH
+
GCACUGAGGUUGGAGGUCAG
chr11: 5237561-5237581
1712





CR003048
HPFH
+
CAGAGGUUAGAAAUCAGAGU
chr11: 5237578-5237598
1713





CR003049
HPFH
+
AGAGGUUAGAAAUCAGAGUU
chr11: 5237579-5237599
1714





CR003050
HPFH
+
UAGAAAUCAGAGUUGGGAAU
chr11: 5237585-5237605
1715





CR003051
HPFH
+
AGAAAUCAGAGUUGGGAAUU
chr11: 5237586-5237606
1716





CR003052
HPFH
+
GUUGGGAAUUGGGAUUAUAC
chr11: 5237596-5237616
1717





CR003053
HPFH

CUUUGUAUUCAUCACACUCU
chr11: 5237654-5237674
1718





CR003054
HPFH
+
AUGAAUACAAAGUUAAAUGA
chr11: 5237662-5237682
1719





CR003055
HPFH

UAAAUGUUGGUGUUCAUUAA
chr11: 5237689-5237709
1720





CR003056
HPFH

UGAGAUUUCACAUUAAAUGU
chr11: 5237702-5237722
1721





CR003057
HPFH
+
ACAUUUAAUGUGAAAUCUCA
chr11: 5237702-5237722
1722





CR003058
HPFH

UAAAAUCAUCGGGGAUUUUG
chr11: 5237749-5237769
1723





CR003059
HPFH

CUAAAAUCAUCGGGGAUUUU
chr11: 5237750-5237770
1724





CR003060
HPFH

UCUAAAAUCAUCGGGGAUUU
chr11: 5237751-5237771
1725





CR003061
HPFH

ACUGAGUUCUAAAAUCAUCG
chr11: 5237758-5237778
1726





CR003062
HPFH

UACUGAGUUCUAAAAUCAUC
chr11: 5237759-5237779
1727





CR003063
HPFH

AUACUGAGUUCUAAAAUCAU
chr11: 5237760-5237780
1728





CR003064
HPFH
+
UAAUUAGUGUAAUGCCAAUG
chr11: 5237786-5237806
1729





CR003065
HPFH
+
AAUUAGUGUAAUGCCAAUGU
chr11: 5237787-5237807
1730





CR003066
HPFH
+
AAUGCCAAUGUGGGUUAGAA
chr11: 5237796-5237816
1731





CR003067
HPFH

ACUUCCAUUCUAACCCACAU
chr11: 5237803-5237823
1732





CR003068
HPFH
+
AAUGGAAGUCAACUUGCUGU
chr11: 5237814-5237834
1733





CR003069
HPFH
+
CUUGCUGUUGGUUUCAGAGC
chr11: 5237826-5237846
1734





CR003070
HPFH
+
CUGUUGGUUUCAGAGCAGGU
chr11: 5237830-5237850
1735





CR003071
HPFH
+
UUCAGAGCAGGUAGGAGAUA
chr11: 5237838-5237858
1736





CR003072
HPFH
+
AGUGAAAAGCUGAAACAAAA
chr11: 5237877-5237897
1737





CR003073
HPFH
+
AAGCUGAAACAAAAAGGAAA
chr11: 5237883-5237903
1738





CR003074
HPFH
+
UGAAACAAAAAGGAAAAGGU
chr11: 5237887-5237907
1739





CR003075
HPFH
+
GAAACAAAAAGGAAAAGGUA
chr11: 5237888-5237908
1740





CR003076
HPFH
+
GGAAAAGGUAGGGUGAAAGA
chr11: 5237898-5237918
1741





CR003077
HPFH
+
GAAAAGGUAGGGUGAAAGAU
chr11: 5237899-5237919
1742





CR003078
HPFH
+
AAAGAUGGGAAAUGUAUGUA
chr11: 5237913-5237933
1743





CR003079
HPFH
+
GAUGGGAAAUGUAUGUAAGG
chr11: 5237916-5237936
1744





CR003080
HPFH
+
UGUAAGGAGGAUGAGCCACA
chr11: 5237929-5237949
1745





CR003081
HPFH
+
GGAGGAUGAGCCACAUGGUA
chr11: 5237934-5237954
1746





CR003082
HPFH
+
GAGGAUGAGCCACAUGGUAU
chr11: 5237935-5237955
1747





CR003083
HPFH
+
GAUGAGCCACAUGGUAUGGG
chr11: 5237938-5237958
1748





CR003084
HPFH

AGUAUACCUCCCAUACCAUG
chr11: 5237947-5237967
1749





CR003085
HPFH
+
AUGGUAUGGGAGGUAUACUA
chr11: 5237948-5237968
1750





CR003086
HPFH
+
GGAGGUAUACUAAGGACUCU
chr11: 5237956-5237976
1751





CR003087
HPFH
+
GAGGUAUACUAAGGACUCUA
chr11: 5237957-5237977
1752





CR003088
HPFH
+
ACUCUAGGGUCAGAGAAAUA
chr11: 5237971-5237991
1753





CR003089
HPFH
+
CUCUAGGGUCAGAGAAAUAU
chr11: 5237972-5237992
1754





CR003090
HPFH

AAGAAUGUGAAUUUUGUAGA
chr11: 5238004-5238024
1755





CR003091
HPFH
+
UUCUACAAAAUUCACAUUCU
chr11: 5238003-5238023
1756





CR003092
HPFH
+
ACAAAAUUCACAUUCUUGGC
chr11: 5238007-5238027
1757





CR003093
HPFH
+
CAAAAUUCACAUUCUUGGCU
chr11: 5238008-5238028
1758





CR003094
HPFH
+
UUCACAUUCUUGGCUGGGUG
chr11: 5238013-5238033
1759





CR003095
HPFH
+
AGGGUGGAUCACCUGAUGUU
chr11: 5238071-5238093
1760





CR003096
HPFH

GAUCUCGAACUCCUAACAUC
chr11: 5238090-5238110
1761









In some aspects of the invention, it is preferred that the gRNA molecule to an HPFH region comprise, e.g., consist of, a targeting domain of a gRNA capable of producing at least about a 20% increase in F cells relative to control, e.g., in an assay described in Example 4. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 113. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 99. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 112. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 98. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 1580. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 106. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 1589. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 1503. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 160. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 1537. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 159. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 101. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 162. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 104. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 138. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 1536. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 1539. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 1585.


In some aspects of the invention, e.g., as indicated herein, it may be beneficial to include gRNA molecules targeting more than one, e.g., two, target sites (e.g., a first gRNA molecule and a second gRNA molecule). In some embodiments, the two target sites are both located in an HPFH region. In such aspects, any combination of more than one, e.g., two, gRNA molecules (e.g., a first gRNA molecule and a second gRNA molecule) comprising targeting domains listed in Table 6 may be used. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 100 and SEQ ID NO: 165, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 100 and SEQ ID NO: 113, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 100 and SEQ ID NO: 99, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 100 and SEQ ID NO: 112, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 100 and SEQ ID NO: 98, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 100 and SEQ ID NO: 1580, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 100 and SEQ ID NO: 106, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 100 and SEQ ID NO: 1503, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 100 and SEQ ID NO: 1589, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 100 and SEQ ID NO: 160, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 100 and SEQ ID NO: 1537, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 100 and SEQ ID NO: 159, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 100 and SEQ ID NO: 101, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 100 and SEQ ID NO: 162, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 100 and SEQ ID NO: 104, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 100 and SEQ ID NO: 138, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 100 and SEQ ID NO: 1536, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 100 and SEQ ID NO: 1539, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 100 and SEQ ID NO: 1585, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 165 and SEQ ID NO: 113, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 165 and SEQ ID NO: 99, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 165 and SEQ ID NO: 112, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 165 and SEQ ID NO: 98, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 165 and SEQ ID NO: 1580, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 165 and SEQ ID NO: 106, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 165 and SEQ ID NO: 1503, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 165 and SEQ ID NO: 1589, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 165 and SEQ ID NO: 160, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 165 and SEQ ID NO: 1537, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 165 and SEQ ID NO: 159, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 165 and SEQ ID NO: 101, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 165 and SEQ ID NO: 162, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 165 and SEQ ID NO: 104, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 165 and SEQ ID NO: 138, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 165 and SEQ ID NO: 1536, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 165 and SEQ ID NO: 1539, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 165 and SEQ ID NO: 1585, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 113 and SEQ ID NO: 165, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 113 and SEQ ID NO: 99, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 113 and SEQ ID NO: 112, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 113 and SEQ ID NO: 98, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 113 and SEQ ID NO: 1580, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 113 and SEQ ID NO: 106, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 113 and SEQ ID NO: 1503, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 113 and SEQ ID NO: 1589, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 113 and SEQ ID NO: 160, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 113 and SEQ ID NO: 1537, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 113 and SEQ ID NO: 159, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 113 and SEQ ID NO: 101, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 113 and SEQ ID NO: 162, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 113 and SEQ ID NO: 104, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 113 and SEQ ID NO: 138, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 113 and SEQ ID NO: 1536, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 113 and SEQ ID NO: 1539, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 113 and SEQ ID NO: 1585, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 99 and SEQ ID NO: 165, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 99 and SEQ ID NO: 113, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 99 and SEQ ID NO: 112, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 99 and SEQ ID NO: 98, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 99 and SEQ ID NO: 1580, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 99 and SEQ ID NO: 106, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 99 and SEQ ID NO: 1503, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 99 and SEQ ID NO: 1589, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 99 and SEQ ID NO: 160, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 99 and SEQ ID NO: 1537, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 99 and SEQ ID NO: 159, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 99 and SEQ ID NO: 101, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 99 and SEQ ID NO: 162, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 99 and SEQ ID NO: 104, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 99 and SEQ ID NO: 138, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 99 and SEQ ID NO: 1536, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 99 and SEQ ID NO: 1539, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 99 and SEQ ID NO: 1585, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 112 and SEQ ID NO: 165, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 112 and SEQ ID NO: 113, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 112 and SEQ ID NO: 99, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 112 and SEQ ID NO: 98, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 112 and SEQ ID NO: 1580, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 112 and SEQ ID NO: 106, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 112 and SEQ ID NO: 1503, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 112 and SEQ ID NO: 1589, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 112 and SEQ ID NO: 160, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 112 and SEQ ID NO: 1537, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 112 and SEQ ID NO: 159, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 112 and SEQ ID NO: 101, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 112 and SEQ ID NO: 162, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 112 and SEQ ID NO: 104, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 112 and SEQ ID NO: 138, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 112 and SEQ ID NO: 1536, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 112 and SEQ ID NO: 1539, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 112 and SEQ ID NO: 1585, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 98 and SEQ ID NO: 165, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 98 and SEQ ID NO: 113, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 98 and SEQ ID NO: 99, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 98 and SEQ ID NO: 112, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 98 and SEQ ID NO: 1580, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 98 and SEQ ID NO: 106, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 98 and SEQ ID NO: 1503, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 98 and SEQ ID NO: 1589, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 98 and SEQ ID NO: 160, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 98 and SEQ ID NO: 1537, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 98 and SEQ ID NO: 159, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 98 and SEQ ID NO: 101, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 98 and SEQ ID NO: 162, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 98 and SEQ ID NO: 104, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 98 and SEQ ID NO: 138, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 98 and SEQ ID NO: 1536, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 98 and SEQ ID NO: 1539, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 98 and SEQ ID NO: 1585, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1580 and SEQ ID NO: 165, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1580 and SEQ ID NO: 113, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1580 and SEQ ID NO: 99, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1580 and SEQ ID NO: 112, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1580 and SEQ ID NO: 98, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1580 and SEQ ID NO: 106, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1580 and SEQ ID NO: 1503, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1580 and SEQ ID NO: 1589, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1580 and SEQ ID NO: 160, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1580 and SEQ ID NO: 1537, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1580 and SEQ ID NO: 159, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1580 and SEQ ID NO: 101, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1580 and SEQ ID NO: 162, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1580 and SEQ ID NO: 104, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1580 and SEQ ID NO: 138, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1580 and SEQ ID NO: 1536, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1580 and SEQ ID NO: 1539, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1580 and SEQ ID NO: 1585, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 106 and SEQ ID NO: 165, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 106 and SEQ ID NO: 113, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 106 and SEQ ID NO: 99, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 106 and SEQ ID NO: 112, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 106 and SEQ ID NO: 98, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 106 and SEQ ID NO: 1580, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 106 and SEQ ID NO: 1503, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 106 and SEQ ID NO: 1589, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 106 and SEQ ID NO: 160, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 106 and SEQ ID NO: 1537, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 106 and SEQ ID NO: 159, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 106 and SEQ ID NO: 101, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 106 and SEQ ID NO: 162, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 106 and SEQ ID NO: 104, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 106 and SEQ ID NO: 138, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 106 and SEQ ID NO: 1536, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 106 and SEQ ID NO: 1539, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 106 and SEQ ID NO: 1585, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1503 and SEQ ID NO: 165, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1503 and SEQ ID NO: 113, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1503 and SEQ ID NO: 99, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1503 and SEQ ID NO: 112, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1503 and SEQ ID NO: 98, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1503 and SEQ ID NO: 1580, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1503 and SEQ ID NO: 106, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1503 and SEQ ID NO: 1589, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1503 and SEQ ID NO: 160, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1503 and SEQ ID NO: 1537, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1503 and SEQ ID NO: 159, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1503 and SEQ ID NO: 101, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1503 and SEQ ID NO: 162, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1503 and SEQ ID NO: 104, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1503 and SEQ ID NO: 138, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1503 and SEQ ID NO: 1536, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1503 and SEQ ID NO: 1539, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1503 and SEQ ID NO: 1585, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1589 and SEQ ID NO: 165, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1589 and SEQ ID NO: 113, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1589 and SEQ ID NO: 99, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1589 and SEQ ID NO: 112, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1589 and SEQ ID NO: 98, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1589 and SEQ ID NO: 1580, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1589 and SEQ ID NO: 106, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1589 and SEQ ID NO: 1503, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1589 and SEQ ID NO: 160, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1589 and SEQ ID NO: 1537, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1589 and SEQ ID NO: 159, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1589 and SEQ ID NO: 101, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1589 and SEQ ID NO: 162, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1589 and SEQ ID NO: 104, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1589 and SEQ ID NO: 138, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1589 and SEQ ID NO: 1536, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1589 and SEQ ID NO: 1539, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1589 and SEQ ID NO: 1585, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 160 and SEQ ID NO: 165, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 160 and SEQ ID NO: 113, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 160 and SEQ ID NO: 99, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 160 and SEQ ID NO: 112, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 160 and SEQ ID NO: 98, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 160 and SEQ ID NO: 1580, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 160 and SEQ ID NO: 106, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 160 and SEQ ID NO: 1503, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 160 and SEQ ID NO: 1589, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 160 and SEQ ID NO: 1537, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 160 and SEQ ID NO: 159, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 160 and SEQ ID NO: 101, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 160 and SEQ ID NO: 162, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 160 and SEQ ID NO: 104, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 160 and SEQ ID NO: 138, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 160 and SEQ ID NO: 1536, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 160 and SEQ ID NO: 1539, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 160 and SEQ ID NO: 1585, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1537 and SEQ ID NO: 165, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1537 and SEQ ID NO: 113, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1537 and SEQ ID NO: 99, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1537 and SEQ ID NO: 112, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1537 and SEQ ID NO: 98, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1537 and SEQ ID NO: 1580, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1537 and SEQ ID NO: 106, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1537 and SEQ ID NO: 1503, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1537 and SEQ ID NO: 1589, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1537 and SEQ ID NO: 160, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1537 and SEQ ID NO: 159, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1537 and SEQ ID NO: 101, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1537 and SEQ ID NO: 162, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1537 and SEQ ID NO: 104, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1537 and SEQ ID NO: 138, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1537 and SEQ ID NO: 1536, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1537 and SEQ ID NO: 1539, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1537 and SEQ ID NO: 1585, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 159 and SEQ ID NO: 165, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 159 and SEQ ID NO: 113, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 159 and SEQ ID NO: 99, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 159 and SEQ ID NO: 112, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 159 and SEQ ID NO: 98, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 159 and SEQ ID NO: 1580, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 159 and SEQ ID NO: 106, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 159 and SEQ ID NO: 1503, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 159 and SEQ ID NO: 1589, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 159 and SEQ ID NO: 160, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 159 and SEQ ID NO: 1537, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 159 and SEQ ID NO: 101, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 159 and SEQ ID NO: 162, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 159 and SEQ ID NO: 104, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 159 and SEQ ID NO: 138, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 159 and SEQ ID NO: 1536, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 159 and SEQ ID NO: 1539, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 159 and SEQ ID NO: 1585, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 101 and SEQ ID NO: 165, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 101 and SEQ ID NO: 113, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 101 and SEQ ID NO: 99, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 101 and SEQ ID NO: 112, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 101 and SEQ ID NO: 98, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 101 and SEQ ID NO: 1580, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 101 and SEQ ID NO: 106, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 101 and SEQ ID NO: 1503, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 101 and SEQ ID NO: 1589, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 101 and SEQ ID NO: 160, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 101 and SEQ ID NO: 1537, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 101 and SEQ ID NO: 159, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 101 and SEQ ID NO: 162, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 101 and SEQ ID NO: 104, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 101 and SEQ ID NO: 138, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 101 and SEQ ID NO: 1536, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 101 and SEQ ID NO: 1539, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 101 and SEQ ID NO: 1585, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 162 and SEQ ID NO: 165, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 162 and SEQ ID NO: 113, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 162 and SEQ ID NO: 99, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 162 and SEQ ID NO: 112, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 162 and SEQ ID NO: 98, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 162 and SEQ ID NO: 1580, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 162 and SEQ ID NO: 106, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 162 and SEQ ID NO: 1503, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 162 and SEQ ID NO: 1589, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 162 and SEQ ID NO: 160, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 162 and SEQ ID NO: 1537, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 162 and SEQ ID NO: 159, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 162 and SEQ ID NO: 101, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 104 and SEQ ID NO: 165, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 104 and SEQ ID NO: 113, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 104 and SEQ ID NO: 99, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 104 and SEQ ID NO: 112, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 104 and SEQ ID NO: 98, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 104 and SEQ ID NO: 1580, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 104 and SEQ ID NO: 106, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 104 and SEQ ID NO: 1503, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 104 and SEQ ID NO: 1589, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 104 and SEQ ID NO: 160, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 104 and SEQ ID NO: 1537, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 104 and SEQ ID NO: 159, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 104 and SEQ ID NO: 101, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 104 and SEQ ID NO: 162, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 104 and SEQ ID NO: 138, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 104 and SEQ ID NO: 1536, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 104 and SEQ ID NO: 1539, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 104 and SEQ ID NO: 1585, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 138 and SEQ ID NO: 165, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 138 and SEQ ID NO: 113, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 138 and SEQ ID NO: 99, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 138 and SEQ ID NO: 112, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 138 and SEQ ID NO: 98, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 138 and SEQ ID NO: 1580, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 138 and SEQ ID NO: 106, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 138 and SEQ ID NO: 1503, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 138 and SEQ ID NO: 1589, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 138 and SEQ ID NO: 160, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 138 and SEQ ID NO: 1537, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 138 and SEQ ID NO: 159, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 138 and SEQ ID NO: 101, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 138 and SEQ ID NO: 162, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 138 and SEQ ID NO: 104, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 138 and SEQ ID NO: 1536, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 138 and SEQ ID NO: 1539, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 138 and SEQ ID NO: 1585, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1536 and SEQ ID NO: 165, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1536 and SEQ ID NO: 113, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1536 and SEQ ID NO: 99, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1536 and SEQ ID NO: 112, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1536 and SEQ ID NO: 98, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1536 and SEQ ID NO: 1580, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1536 and SEQ ID NO: 106, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1536 and SEQ ID NO: 1503, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1536 and SEQ ID NO: 1589, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1536 and SEQ ID NO: 160, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1536 and SEQ ID NO: 1537, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1536 and SEQ ID NO: 159, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1536 and SEQ ID NO: 101, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1536 and SEQ ID NO: 162, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1536 and SEQ ID NO: 104, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1536 and SEQ ID NO: 138, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1536 and SEQ ID NO: 1539, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1536 and SEQ ID NO: 1585, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1539 and SEQ ID NO: 165, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1539 and SEQ ID NO: 113, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1539 and SEQ ID NO: 99, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1539 and SEQ ID NO: 112, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1539 and SEQ ID NO: 98, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1539 and SEQ ID NO: 1580, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1539 and SEQ ID NO: 106, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1539 and SEQ ID NO: 1503, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1539 and SEQ ID NO: 1589, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1539 and SEQ ID NO: 160, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1539 and SEQ ID NO: 1537, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1539 and SEQ ID NO: 159, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1539 and SEQ ID NO: 101, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1539 and SEQ ID NO: 162, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1539 and SEQ ID NO: 104, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1539 and SEQ ID NO: 138, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1539 and SEQ ID NO: 1536, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1539 and SEQ ID NO: 1585, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1585 and SEQ ID NO: 165, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1585 and SEQ ID NO: 113, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1585 and SEQ ID NO: 99, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1585 and SEQ ID NO: 112, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1585 and SEQ ID NO: 98, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1585 and SEQ ID NO: 1580, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1585 and SEQ ID NO: 106, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1585 and SEQ ID NO: 1503, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1585 and SEQ ID NO: 1589, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1585 and SEQ ID NO: 160, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1585 and SEQ ID NO: 1537, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1585 and SEQ ID NO: 159, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1585 and SEQ ID NO: 101, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1585 and SEQ ID NO: 162, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1585 and SEQ ID NO: 104, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1585 and SEQ ID NO: 138, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1585 and SEQ ID NO: 1536, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1585 and SEQ ID NO: 1539, respectively.









TABLE 7







Preferred Guide RNA Targeting Domains directed to the +58


Enhancer Region of the BCL11a Gene (i.e., to a BCL11a Enhancer)













Exon/



SEQ ID


Id.
Feature
Strand
Targeting domain
Locations
NO:





CR00242
58
+
UAUGCAAUUUUUGCCAAGAU
Chr2: 60494419-60494441
182





CR00243
58
+
UUUUGCCAAGAUGGGAGUAU
Chr2: 60494427-60494449
183





CR00244
58
+
UUUGCCAAGAUGGGAGUAUG
Chr2: 60494428-60494450
184





CR00245
58
+
UCAGUGAGAUGAGAUAUCAA
Chr2: 60494477-60494499
185





CR00246
58
+
CAGUGAGAUGAGAUAUCAAA
Chr2: 60494478-60494500
186





CR00247
58
+
CCAUCUCCCUAAUCUCCAAU
Chr2: 60494518-60494540
187





CR00248
58

CCAAUUGGAGAUUAGGGAGA
Chr2: 60494518-60494540
188





CR00249
58

GCUUUGCCAAUUGGAGAUUA
Chr2: 60494524-60494546
189





CR00250
58

GGCUUUGCCAAUUGGAGAUU
Chr2: 60494525-60494547
190





CR00251
58
+
AAUUGGCAAAGCCAGACUUG
Chr2: 60494535-60494557
191





CR00252
58

AGUCUGUAUUGCCCCAAGUC
Chr2: 60494546-60494568
192





CR00253
58
+
AGACUUGGGGCAAUACAGAC
Chr2: 60494548-60494570
193





CR00255
58

ACAUUUGGUGAUAAAUCAUU
Chr2: 60494602-60494624
194





CR00256
58
+
CCAAAUGUUCUUUCUUCAGC
Chr2: 60494617-60494639
195





CR00257
58
+
AUAAUAGUAUAUGCUUCAUA
Chr2: 60494676-60494698
196





CR00258
58

CGGAGCACUUACUCUGCUCU
Chr2: 60494737-60494759
197





CR00259
58

AGCAUUUUAGUUCACAAGCU
Chr2: 60494757-60494779
198





CR00260
58

UGUAACUAAUAAAUACCAGG
Chr2: 60494781-60494803
199





CR00261
58

AGGUGUAACUAAUAAAUACC
Chr2: 60494784-60494806
200





CR00264
58

UCUGACCCAAACUAGGAAUU
Chr2: 60494836-60494858
201





CR00266
58
+
AAGGAAAAGAAUAUGACGUC
Chr2: 60494883-60494905
202





CR00267
58
+
AGGAAAAGAAUAUGACGUCA
Chr2: 60494884-60494906
203





CR00268
58
+
GGAAAAGAAUAUGACGUCAG
Chr2: 60494885-60494907
204





CR00269
58
+
GAAAAGAAUAUGACGUCAGG
Chr2: 60494886-60494908
205





CR00270
58
+
UCAGGGGGAGGCAAGUCAGU
Chr2: 60494901-60494923
206





CR00271
58
+
CAGGGGGAGGCAAGUCAGUU
Chr2: 60494902-60494924
207





CR00272
58

AUCACAUAUAGGCACCUAUC
Chr2: 60494939-60494961
208





CR00273
58

CAGGUACCAGCUACUGUGUU
Chr2: 60494939-60494961
209





CR00274
58

ACUAUCCACGGAUAUACACU
Chr2: 60494939-60494961
210





CR00275
58
+
CACAGUAGCUGGUACCUGAU
Chr2: 60494939-60494961
211





CR00276
58

AUCACAUAUAGGCACCUAUC
Chr2: 60494953-60494975
212





CR00277
58
+
UGAUAGGUGCCUAUAUGUGA
Chr2: 60494955-60494977
213





CR00278
58
+
AGGUGCCUAUAUGUGAUGGA
Chr2: 60494959-60494981
214





CR00279
58
+
GGUGCCUAUAUGUGAUGGAU
Chr2: 60494960-60494982
215





CR00280
58

UCCACCCAUCCAUCACAUAU
Chr2: 60494964-60494986
216





CR00281
58
+
ACAGCCCGACAGAUGAAAAA
Chr2: 60494986-60495008
217





CR00282
58
+
AUGAAAAAUGGACAAUUAUG
Chr2: 60494998-60495020
218





CR00283
58
+
AAAAAUGGACAAUUAUGAGG
Chr2: 60495001-60495023
219





CR00284
58
+
AAAAUGGACAAUUAUGAGGA
Chr2: 60495002-60495024
220





CR00285
58
+
AAAUGGACAAUUAUGAGGAG
Chr2: 60495003-60495025
221





CR00286
58
+
GAGGAGGGGAGAGUGCAGAC
Chr2: 60495017-60495039
222





CR00287
58
+
AGGAGGGGAGAGUGCAGACA
Chr2: 60495018-60495040
223





CR00288
58
+
CUUCACCUCCUUUACAAUUU
Chr2: 60495045-60495067
224





CR00289
58
+
UUCACCUCCUUUACAAUUUU
Chr2: 60495046-60495068
225





CR00290
58

GACUCCCAAAAUUGUAAAGG
Chr2: 60495050-60495072
226





CR00291
58

GUGGACUCCCAAAAUUGUAA
Chr2: 60495053-60495075
227





CR00292
58
+
UUUUGGGAGUCCACACGGCA
Chr2: 60495062-60495084
228





CR00293
58

AAUUUGUAUGCCAUGCCGUG
Chr2: 60495072-60495094
229





CR00294
58
+
CCAAGAGAGCCUUCCGAAAG
Chr2: 60495135-60495157
230





CR00295
58

CCAGGGGGGCCUCUUUCGGA
Chr2: 60495144-60495166
231





CR00296
58
+
CCUUCCGAAAGAGGCCCCCC
Chr2: 60495144-60495166
232





CR00297
58
+
CUUCCGAAAGAGGCCCCCCU
Chr2: 60495145-60495167
233





CR00298
58
+
AAGAGGCCCCCCUGGGCAAA
Chr2: 60495152-60495174
234





CR00299
58

CGGUGGCCGUUUGCCCAGGG
Chr2: 60495158-60495180
235





CR00300
58

UCGGUGGCCGUUUGCCCAGG
Chr2: 60495159-60495181
236





CR00301
58

AUCGGUGGCCGUUUGCCCAG
Chr2: 60495160-60495182
237





CR00302
58

CAUCGGUGGCCGUUUGCCCA
Chr2: 60495161-60495183
238





CR00303
58
+
CCUGGGCAAACGGCCACCGA
Chr2: 60495162-60495184
239





CR00304
58

CCAUCGGUGGCCGUUUGCCC
Chr2: 60495162-60495184
240





CR00305
58
+
GCAAACGGCCACCGAUGGAG
Chr2: 60495167-60495189
241





CR00306
58

CUGGCAGACCUCUCCAUCGG
Chr2: 60495175-60495197
242





CR00307
58

GGACUGGCAGACCUCUCCAU
Chr2: 60495178-60495200
243





CR00308
58

UCUGAUUAGGGUGGGGGCGU
Chr2: 60495213-60495235
244





CR00309
58
+
CACGCCCCCACCCUAAUCAG
Chr2: 60495215-60495237
245





CR00310
58

UUGGCCUCUGAUUAGGGUGG
Chr2: 60495219-60495241
246





CR00311
58

UUUGGCCUCUGAUUAGGGUG
Chr2: 60495220-60495242
247





CR00312
58

GUUUGGCCUCUGAUUAGGGU
Chr2: 60495221-60495243
248





CR00313
58

GGUUUGGCCUCUGAUUAGGG
Chr2: 60495222-60495244
249





CR00314
58

AAGGGUUUGGCCUCUGAUUA
Chr2: 60495225-60495247
250





CR00315
58

GAAGGGUUUGGCCUCUGAUU
Chr2: 60495226-60495248
251





CR00316
58

UUGCUUUUAUCACAGGCUCC
Chr2: 60495248-60495270
252





CR00317
58

CUAACAGUUGCUUUUAUCAC
Chr2: 60495255-60495277
253





CR00318
58
+
CUUCAAAGUUGUAUUGACCC
Chr2: 60495293-60495315
254





CR00319
58

ACUCUUAGACAUAACACACC
Chr2: 60495311-60495333
255





CR00320
58
+
UAGAUGCCAUAUCUCUUUUC
Chr2: 60495333-60495355
256





CR00321
58

CAUAGGCCAGAAAAGAGAUA
Chr2: 60495339-60495361
257





CR00322
58
+
GGCCUAUGUUAUUACCUGUA
Chr2: 60495354-60495376
258





CR00323
58

GUCCAUACAGGUAAUAACAU
Chr2: 60495356-60495378
259





CR00324
58
+
UACCUGUAUGGACUUUGCAC
Chr2: 60495366-60495388
260





CR00325
58

UUCCAGUGCAAAGUCCAUAC
Chr2: 60495368-60495390
261





CR00326
58
+
UGCUCUUACUUAUGCACACC
Chr2: 60495400-60495422
262





CR00327
58
+
GCUCUUACUUAUGCACACCU
Chr2: 60495401-60495423
263





CR00328
58
+
CUCUUACUUAUGCACACCUG
Chr2: 60495402-60495424
264





CR00329
58

CAGGGCUGGCUCUAUGCCCC
Chr2: 60495418-60495440
265





CR00330
58

GCUGAAAAGCGAUACAGGGC
Chr2: 60495432-60495454
266





CR00331
58

GAUGGCUGAAAAGCGAUACA
Chr2: 60495436-60495458
267





CR00332
58

AGAUGGCUGAAAAGCGAUAC
Chr2: 60495437-60495459
268





CR00333
58

GGGAGUUAUCUGUAGUGAGA
Chr2: 60495454-60495476
269





CR00334
58

AAGGCAGCUAGACAGGACUU
Chr2: 60495474-60495496
270





CR00335
58

GAAGGCAGCUAGACAGGACU
Chr2: 60495475-60495497
271





CR00336
58

GAUAAGGAAGGCAGCUAGAC
Chr2: 60495481-60495503
272





CR00337
58
+
CUAGCUGCCUUCCUUAUCAC
Chr2: 60495486-60495508
273





CR00338
58

UGGGUGCUAUUCCUGUGAUA
Chr2: 60495497-60495519
274





CR00339
58
+
UAUCACAGGAAUAGCACCCA
Chr2: 60495500-60495522
275





CR00340
58

CUGAGGUACUGAUGGACCUU
Chr2: 60495516-60495538
276





CR00341
58

UCUGAGGUACUGAUGGACCU
Chr2: 60495517-60495539
277





CR001124
58

UUAGGGUGGGGGCGUGGGUG
Chr2: 60495214-60495236
334





CR001125
58

UUUUAUCACAGGCUCCAGGA
Chr2: 60495215-60495237
335





CR001126
58

UUUAUCACAGGCUCCAGGAA
Chr2: 60495216-60495238
336





CR001127
58

CACAGGCUCCAGGAAGGGUU
Chr2: 60495220-60495242
337





CR001128
58
+
AUCAGAGGCCAAACCCUUCC
Chr2: 60495236-60495258
338





CR001129
58

CUCUGAUUAGGGUGGGGGCG
Chr2: 60495244-60495266
339





CR001130
58

GAUUAGGGUGGGGGCGUGGG
Chr2: 60495249-60495271
340





CR001131
58

AUUAGGGUGGGGGCGUGGGU
Chr2: 60495250-60495272
341









In some aspects of the invention, it is preferred that the gRNA molecule to the +58 Enhancer region of BCL11a comprise a targeting domain of a gRNA listed in FIG. 11. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 341. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 246. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 248. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 247. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 245. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 249. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 244. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 199. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 251. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 250. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 334. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 185. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 186. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 336. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 337.


In some aspects of the invention, e.g., as indicated herein, it may be beneficial to include gRNA moleucles targeting more than one, e.g., two, target sites (e.g., a first gRNA molecule and a second gRNA molecule). In some embodiments, the two target sites are both located in the +58 BCL11a enhancer region. In such aspects, any combination of more than one, e.g., two, gRNA molecules (e.g., a first gRNA molecule and a second gRNA molecule) comprising targeting domains listed in Table 7 may be used. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 341 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 341 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 341 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 341 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 341 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 341 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 341 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 341 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 341 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 341 and SEQ ID NO: 246, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 341 and SEQ ID NO: 248, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 341 and SEQ ID NO: 247, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 341 and SEQ ID NO: 245, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 341 and SEQ ID NO: 249, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 341 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 341 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 341 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 341 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 341 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 341 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 341 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 341 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 341 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 246 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 246 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 246 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 246 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 246 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 246 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 246 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 246 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 246 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 246 and SEQ ID NO: 248, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 246 and SEQ ID NO: 247, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 246 and SEQ ID NO: 245, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 246 and SEQ ID NO: 249, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 246 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 246 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 246 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 246 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 246 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 246 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 246 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 246 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 246 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 248 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 248 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 248 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 248 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 248 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 248 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 248 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 248 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 248 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 248 and SEQ ID NO: 246, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 248 and SEQ ID NO: 247, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 248 and SEQ ID NO: 245, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 248 and SEQ ID NO: 249, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 248 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 248 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 248 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 248 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 248 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 248 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 248 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 248 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 248 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 247 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 247 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 247 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 247 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 247 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 247 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 247 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 247 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 247 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 247 and SEQ ID NO: 246, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 247 and SEQ ID NO: 248, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 247 and SEQ ID NO: 245, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 247 and SEQ ID NO: 249, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 247 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 247 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 247 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 247 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 247 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 247 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 247 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 247 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 247 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 245 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 245 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 245 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 245 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 245 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 245 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 245 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 245 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 245 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 245 and SEQ ID NO: 246, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 245 and SEQ ID NO: 248, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 245 and SEQ ID NO: 247, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 245 and SEQ ID NO: 249, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 245 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 245 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 245 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 245 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 245 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 245 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 245 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 245 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 245 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 249 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 249 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 249 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 249 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 249 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 249 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 249 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 249 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 249 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 249 and SEQ ID NO: 246, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 249 and SEQ ID NO: 248, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 249 and SEQ ID NO: 247, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 249 and SEQ ID NO: 245, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 249 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 249 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 249 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 249 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 249 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 249 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 249 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 249 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 249 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 244 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 244 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 244 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 244 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 244 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 244 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 244 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 244 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 244 and SEQ ID NO: 246, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 244 and SEQ ID NO: 248, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 244 and SEQ ID NO: 247, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 244 and SEQ ID NO: 245, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 244 and SEQ ID NO: 249, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 244 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 244 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 244 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 244 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 244 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 244 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 244 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 244 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 199 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 199 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 199 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 199 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 199 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 199 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 199 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 199 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 199 and SEQ ID NO: 246, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 199 and SEQ ID NO: 248, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 199 and SEQ ID NO: 247, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 199 and SEQ ID NO: 245, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 199 and SEQ ID NO: 249, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 199 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 199 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 199 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 199 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 199 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 199 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 199 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 199 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 251 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 251 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 251 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 251 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 251 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 251 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 251 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 251 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 251 and SEQ ID NO: 246, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 251 and SEQ ID NO: 248, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 251 and SEQ ID NO: 247, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 251 and SEQ ID NO: 245, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 251 and SEQ ID NO: 249, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 251 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 251 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 251 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 251 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 251 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 251 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 251 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 251 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 250 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 250 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 250 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 250 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 250 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 250 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 250 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 250 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 250 and SEQ ID NO: 246, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 250 and SEQ ID NO: 248, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 250 and SEQ ID NO: 247, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 250 and SEQ ID NO: 245, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 250 and SEQ ID NO: 249, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 250 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 250 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 250 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 250 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 250 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 250 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 250 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 250 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 334 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 334 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 334 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 334 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 334 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 334 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 334 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 334 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 334 and SEQ ID NO: 246, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 334 and SEQ ID NO: 248, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 334 and SEQ ID NO: 247, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 334 and SEQ ID NO: 245, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 334 and SEQ ID NO: 249, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 334 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 334 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 334 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 334 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 334 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 334 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 334 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 334 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 185 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 185 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 185 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 185 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 185 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 185 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 185 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 185 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 185 and SEQ ID NO: 246, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 185 and SEQ ID NO: 248, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 185 and SEQ ID NO: 247, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 185 and SEQ ID NO: 245, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 185 and SEQ ID NO: 249, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 185 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 185 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 185 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 185 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 185 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 185 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 185 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 185 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 186 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 186 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 186 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 186 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 186 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 186 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 186 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 186 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 186 and SEQ ID NO: 246, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 186 and SEQ ID NO: 248, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 186 and SEQ ID NO: 247, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 186 and SEQ ID NO: 245, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 186 and SEQ ID NO: 249, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 186 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 186 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 186 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 186 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 186 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 186 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 186 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 186 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 336 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 336 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 336 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 336 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 336 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 336 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 336 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 336 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 336 and SEQ ID NO: 246, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 336 and SEQ ID NO: 248, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 336 and SEQ ID NO: 247, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 336 and SEQ ID NO: 245, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 336 and SEQ ID NO: 249, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 336 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 336 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 336 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 336 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 336 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 336 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 336 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 336 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 337 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 337 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 337 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 337 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 337 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 337 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 337 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 337 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 337 and SEQ ID NO: 246, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 337 and SEQ ID NO: 248, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 337 and SEQ ID NO: 247, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 337 and SEQ ID NO: 245, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 337 and SEQ ID NO: 249, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 337 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 337 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 337 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 337 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 337 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 337 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 337 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 337 and SEQ ID NO: 336, respectively.


In embodiments, the aspects of the invention relate to or incorporate a gRNA molecule that is complementary to a target sequence within the +58 enhancer region of the BCL11a gene which is disposed 3′ to the GATA-1 binding site, e.g., 3′ to the GATA1 binding site and TAL-1 binding site. In embodiments, the CRISPR system comprising a gRNA molecule described herein induces one or more indels at or near the target site. In embodiments, the indel does not comprise a nucleotide of a GATA-1 binding site and/or does not comprise a nucleotide of a TAL-1 binding site. In embodiments, the CRISPR system induces one or more frameshift indels at or near the target site, e.g., at an overall frameshift indel rate of at least about 10%, at least about 20%, at least about 30%, at least about 40%, or at least about 50%, e.g., as measured by NGS. In embodiments, the overall indel rate is at least about 70%, at least about 80%, at least about 90%, or at least about 95%, e.g., as measured by NGS.









TABLE 8







Preferred Guide RNA Targeting Domains directed to the +62 Enhancer


Region of the BCL11a Gene (i.e., to a BCL11a Enhancer)













Exon/



SEQ ID


Id.
Feature
Strand
Targeting domain
Locations
NO:





CR00171
62

AGCUCUGGAAUGAUGGCUUA
Chr2: 60490354-60490376
278





CR00172
62

AUUGUGGAGCUCUGGAAUGA
Chr2: 60490361-60490383
279





CR00173
62

CUGGAAUAGAAAAUUGGAGU
Chr2: 60490384-60490406
280





CR00174
62

UGGGUACGGGGAACUAAGAC
Chr2: 60490403-60490425
281





CR00175
62
+
UUAGUUCCCCGUACCCAUCA
Chr2: 60490409-60490431
282





CR00176
62

UAUUUUCCUUGAUGGGUACG
Chr2: 60490415-60490437
283





CR00177
62

AUAUUUUCCUUGAUGGGUAC
Chr2: 60490416-60490438
284





CR00178
62

AAUAUUUUCCUUGAUGGGUA
Chr2: 60490417-60490439
285





CR00179
62

GGAAGGAAAUGAGAACGGAA
Chr2: 60490456-60490478
286





CR00180
62

AGGAAGGAAAUGAGAACGGA
Chr2: 60490457-60490479
287





CR00181
62
+
AUACUUCAAGGCCUCAAUGA
Chr2: 60490520-60490542
288





CR00182
62

GACUAGGUAGACCUUCAUUG
Chr2: 60490531-60490553
289





CR00183
62

UUCUUCUUGCUAAGGUGACU
Chr2: 60490547-60490569
290





CR00184
62

GAGAUUGAUUCUUCUUGCUA
Chr2: 60490555-60490577
291





CR00185
62

GUGUUCUAUGAGGUUGGAGA
Chr2: 60490580-60490602
292





CR00186
62

GGAUGAGUGUUCUAUGAGGU
Chr2: 60490586-60490608
293





CR00187
62

CAUGGGAUGAGUGUUCUAUG
Chr2: 60490590-60490612
294





CR00188
62

UGAGUCAGGGAGUGGUGCAU
Chr2: 60490607-60490629
295





CR00189
62

AUGAGUCAGGGAGUGGUGCA
Chr2: 60490608-60490630
296





CR00190
62
+
CCACUCCCUGACUCAUAUCU
Chr2: 60490615-60490637
297





CR00191
62

UAAGGCCUAGAUAUGAGUCA
Chr2: 60490620-60490642
298





CR00192
62

GUAAGGCCUAGAUAUGAGUC
Chr2: 60490621-60490643
299





CR00193
62
+
AUAUCUAGGCCUUACAUUGC
Chr2: 60490629-60490651
300





CR00194
62

AAAUUAAUUAGAGGCAUAGA
Chr2: 60490656-60490678
301





CR00195
62

GAAAUUAAUUAGAGGCAUAG
Chr2: 60490657-60490679
302





CR00196
62

GAACACAUGAAAUUAAUUAG
Chr2: 60490665-60490687
303





CR00197
62
+
CCAAUGAGUUUCUUCAAUAC
Chr2: 60490688-60490710
304





CR00198
62

CAAAUAUAAUAGAAGCAAGU
Chr2: 60490721-60490743
305





CR00199
62

AAAUAACUUCCCUUUUAGGA
Chr2: 60490821-60490843
306





CR00200
62

GGAAAAAUAACUUCCCUUUU
Chr2: 60490825-60490847
307





CR00201
62

UUUUGAACAGAAAUGAUAUU
Chr2: 60490846-60490868
308





CR00202
62

AGUUCAAGUAGAUAUCAGAA
Chr2: 60490905-60490927
309





CR00203
62

AAGUUCAAGUAGAUAUCAGA
Chr2: 60490906-60490928
310





CR00204
62

GGGUGGCUGUUUAAAGAGGG
Chr2: 60490994-60491016
311





CR00205
62

GUGGGGUGGCUGUUUAAAGA
Chr2: 60490997-60491019
312





CR00206
62

UGUGGGGUGGCUGUUUAAAG
Chr2: 60490998-60491020
313





CR00207
62
+
UGCCAACCAGACUGUGCGCC
Chr2: 60491051-60491073
314





CR00208
62

AACCUGGCGCACAGUCUGGU
Chr2: 60491053-60491075
315





CR00209
62
+
AACCAGACUGUGCGCCAGGU
Chr2: 60491055-60491077
316





CR00210
62

UACCAACCUGGCGCACAGUC
Chr2: 60491057-60491079
317





CR00211
62

UCUGUCAGACUUUACCAACC
Chr2: 60491069-60491091
318





CR00212
62
+
AUAUGUGAAGCCCAACUACG
Chr2: 60491118-60491140
319





CR00213
62

AGUUGCACAACCACGUAGUU
Chr2: 60491128-60491150
320





CR00214
62

GAGUUGCACAACCACGUAGU
Chr2: 60491129-60491151
321





CR00215
62
+
CUAUAGCUGACUUUCAACCA
Chr2: 60491151-60491173
322





CR00216
62

AACUUCUUUGCAGAUGACCA
Chr2: 60491168-60491190
323





CR00217
62

UUGCAUUGAGGAUGCGCAGG
Chr2: 60491199-60491221
324





CR00218
62

UUUUUGCAUUGAGGAUGCGC
Chr2: 60491202-60491224
325





CR00221
62
+
GACCUCAUUUUGAUGCCAGA
Chr2: 60491281-60491303
326





CR00222
62

UGCCCUCUGGCAUCAAAAUG
Chr2: 60491283-60491305
327





CR00223
62
+
AUGCCAGAGGGCAGCAAACA
Chr2: 60491293-60491315
328





CR00224
62

CUGUACUUAAUAGCUGAAGG
Chr2: 60491326-60491348
329





CR00225
62

ACUGUACUUAAUAGCUGAAG
Chr2: 60491327-60491349
330





CR00227
62
+
CAGCUAUUAAGUACAGUAAA
Chr2: 60491333-60491355
331





CR00228
62

GAGCAUUUCAAAUGAUAGUU
Chr2: 60491360-60491382
332





CR00229
62
+
CAUUUGAAAUGCUCCCGGCC
Chr2: 60491369-60491391
333









In some aspects of the invention, it is preferred that the gRNA molecule to the +62 Enhancer region of BCL11a comprise a targeting domain of a gRNA listed in FIG. 12. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 318. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 312. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 313. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 294. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 310. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 319. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 298. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 322. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 311. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 315. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 290. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 317. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 309. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 289. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 281.


In some aspects of the invention, e.g., as indicated herein, it may be beneficial to include gRNA moleucles targeting more than one, e.g., two, target sites (e.g., a first gRNA molecule and a second gRNA molecule). In some embodiments, the two target sites are both located in the +62 BCL11a enhancer region. In such aspects, any combination of more than one, e.g., two, gRNA molecules (e.g., a first gRNA molecule and a second gRNA molecule) comprising targeting domains listed in Table 8 may be used. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 318 and SEQ ID NO: 312, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 318 and SEQ ID NO: 313, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 318 and SEQ ID NO: 294, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 318 and SEQ ID NO: 310, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 318 and SEQ ID NO: 319, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 318 and SEQ ID NO: 298, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 318 and SEQ ID NO: 322, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 318 and SEQ ID NO: 311, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 318 and SEQ ID NO: 315, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 318 and SEQ ID NO: 290, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 318 and SEQ ID NO: 317, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 318 and SEQ ID NO: 309, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 318 and SEQ ID NO: 289, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 318 and SEQ ID NO: 281, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 312 and SEQ ID NO: 313, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 312 and SEQ ID NO: 294, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 312 and SEQ ID NO: 310, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 312 and SEQ ID NO: 319, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 312 and SEQ ID NO: 298, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 312 and SEQ ID NO: 322, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 312 and SEQ ID NO: 311, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 312 and SEQ ID NO: 315, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 312 and SEQ ID NO: 290, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 312 and SEQ ID NO: 317, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 312 and SEQ ID NO: 309, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 312 and SEQ ID NO: 289, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 312 and SEQ ID NO: 281, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 313 and SEQ ID NO: 312, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 313 and SEQ ID NO: 294, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 313 and SEQ ID NO: 310, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 313 and SEQ ID NO: 319, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 313 and SEQ ID NO: 298, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 313 and SEQ ID NO: 322, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 313 and SEQ ID NO: 311, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 313 and SEQ ID NO: 315, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 313 and SEQ ID NO: 290, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 313 and SEQ ID NO: 317, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 313 and SEQ ID NO: 309, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 313 and SEQ ID NO: 289, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 313 and SEQ ID NO: 281, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 294 and SEQ ID NO: 312, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 294 and SEQ ID NO: 313, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 294 and SEQ ID NO: 310, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 294 and SEQ ID NO: 319, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 294 and SEQ ID NO: 298, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 294 and SEQ ID NO: 322, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 294 and SEQ ID NO: 311, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 294 and SEQ ID NO: 315, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 294 and SEQ ID NO: 290, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 294 and SEQ ID NO: 317, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 294 and SEQ ID NO: 309, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 294 and SEQ ID NO: 289, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 294 and SEQ ID NO: 281, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 310 and SEQ ID NO: 312, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 310 and SEQ ID NO: 313, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 310 and SEQ ID NO: 294, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 310 and SEQ ID NO: 319, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 310 and SEQ ID NO: 298, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 310 and SEQ ID NO: 322, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 310 and SEQ ID NO: 311, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 310 and SEQ ID NO: 315, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 310 and SEQ ID NO: 290, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 310 and SEQ ID NO: 317, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 310 and SEQ ID NO: 309, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 310 and SEQ ID NO: 289, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 310 and SEQ ID NO: 281, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 319 and SEQ ID NO: 312, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 319 and SEQ ID NO: 313, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 319 and SEQ ID NO: 294, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 319 and SEQ ID NO: 310, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 319 and SEQ ID NO: 298, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 319 and SEQ ID NO: 322, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 319 and SEQ ID NO: 311, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 319 and SEQ ID NO: 315, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 319 and SEQ ID NO: 290, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 319 and SEQ ID NO: 317, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 319 and SEQ ID NO: 309, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 319 and SEQ ID NO: 289, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 319 and SEQ ID NO: 281, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 298 and SEQ ID NO: 312, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 298 and SEQ ID NO: 313, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 298 and SEQ ID NO: 294, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 298 and SEQ ID NO: 310, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 298 and SEQ ID NO: 319, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 298 and SEQ ID NO: 322, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 298 and SEQ ID NO: 311, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 298 and SEQ ID NO: 315, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 298 and SEQ ID NO: 290, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 298 and SEQ ID NO: 317, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 298 and SEQ ID NO: 309, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 298 and SEQ ID NO: 289, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 298 and SEQ ID NO: 281, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 322 and SEQ ID NO: 312, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 322 and SEQ ID NO: 313, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 322 and SEQ ID NO: 294, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 322 and SEQ ID NO: 310, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 322 and SEQ ID NO: 319, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 322 and SEQ ID NO: 298, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 322 and SEQ ID NO: 311, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 322 and SEQ ID NO: 315, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 322 and SEQ ID NO: 290, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 322 and SEQ ID NO: 317, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 322 and SEQ ID NO: 309, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 322 and SEQ ID NO: 289, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 322 and SEQ ID NO: 281, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 311 and SEQ ID NO: 312, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 311 and SEQ ID NO: 313, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 311 and SEQ ID NO: 294, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 311 and SEQ ID NO: 310, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 311 and SEQ ID NO: 319, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 311 and SEQ ID NO: 298, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 311 and SEQ ID NO: 322, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 311 and SEQ ID NO: 315, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 311 and SEQ ID NO: 290, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 311 and SEQ ID NO: 317, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 311 and SEQ ID NO: 309, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 311 and SEQ ID NO: 289, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 311 and SEQ ID NO: 281, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 315 and SEQ ID NO: 312, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 315 and SEQ ID NO: 313, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 315 and SEQ ID NO: 294, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 315 and SEQ ID NO: 310, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 315 and SEQ ID NO: 319, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 315 and SEQ ID NO: 298, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 315 and SEQ ID NO: 322, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 315 and SEQ ID NO: 311, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 315 and SEQ ID NO: 290, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 315 and SEQ ID NO: 317, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 315 and SEQ ID NO: 309, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 315 and SEQ ID NO: 289, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 315 and SEQ ID NO: 281, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 290 and SEQ ID NO: 312, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 290 and SEQ ID NO: 313, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 290 and SEQ ID NO: 294, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 290 and SEQ ID NO: 310, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 290 and SEQ ID NO: 319, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 290 and SEQ ID NO: 298, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 290 and SEQ ID NO: 322, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 290 and SEQ ID NO: 311, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 290 and SEQ ID NO: 315, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 290 and SEQ ID NO: 317, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 290 and SEQ ID NO: 309, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 290 and SEQ ID NO: 289, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 290 and SEQ ID NO: 281, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 317 and SEQ ID NO: 312, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 317 and SEQ ID NO: 313, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 317 and SEQ ID NO: 294, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 317 and SEQ ID NO: 310, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 317 and SEQ ID NO: 319, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 317 and SEQ ID NO: 298, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 317 and SEQ ID NO: 322, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 317 and SEQ ID NO: 311, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 317 and SEQ ID NO: 315, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 317 and SEQ ID NO: 290, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 317 and SEQ ID NO: 309, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 317 and SEQ ID NO: 289, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 317 and SEQ ID NO: 281, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 309 and SEQ ID NO: 312, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 309 and SEQ ID NO: 313, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 309 and SEQ ID NO: 294, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 309 and SEQ ID NO: 310, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 309 and SEQ ID NO: 319, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 309 and SEQ ID NO: 298, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 309 and SEQ ID NO: 322, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 309 and SEQ ID NO: 311, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 309 and SEQ ID NO: 315, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 309 and SEQ ID NO: 290, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 309 and SEQ ID NO: 317, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 309 and SEQ ID NO: 289, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 309 and SEQ ID NO: 281, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 289 and SEQ ID NO: 312, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 289 and SEQ ID NO: 313, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 289 and SEQ ID NO: 294, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 289 and SEQ ID NO: 310, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 289 and SEQ ID NO: 319, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 289 and SEQ ID NO: 298, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 289 and SEQ ID NO: 322, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 289 and SEQ ID NO: 311, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 289 and SEQ ID NO: 315, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 289 and SEQ ID NO: 290, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 289 and SEQ ID NO: 317, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 289 and SEQ ID NO: 309, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 289 and SEQ ID NO: 281, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 281 and SEQ ID NO: 312, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 281 and SEQ ID NO: 313, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 281 and SEQ ID NO: 294, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 281 and SEQ ID NO: 310, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 281 and SEQ ID NO: 319, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 281 and SEQ ID NO: 298, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 281 and SEQ ID NO: 322, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 281 and SEQ ID NO: 311, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 281 and SEQ ID NO: 315, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 281 and SEQ ID NO: 290, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 281 and SEQ ID NO: 317, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 281 and SEQ ID NO: 309, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 281 and SEQ ID NO: 289, respectively.









TABLE 9







Preferred Guide RNA Targeting Domains directed to the +55


Enhancer Region of the BCL11a Gene (i.e., to a BCL11a Enhancer)

















SEQ ID


ID
Species
Strand
Location
Targeting Domain Sequence
NO:





CR002142
h
+
Chr2: 60498031-60498053
CCUGGCAGACCCUCAAGAGC
1596





CR002143
h

Chr2: 60498031-60498053
CCUGGCAGACCCUCAAGAGC
1597





CR002144
h
+
Chr2: 60498032-60498054
CUGGCAGACCCUCAAGAGCA
1598





CR002145
h
+
Chr2: 60498033-60498055
UGGCAGACCCUCAAGAGCAG
1599





CR002146
h

Chr2: 60498040-60498062
CCCUCAAGAGCAGGGGUCUU
1600





CR002147
h

Chr2: 60498041-60498063
CCUCAAGAGCAGGGGUCUUC
1601





CR001262
h
+
Chr1: 55039155-55039177
UAAGGCCAGUGGAAAGAAUU
1602





CR002148
h
+
Chr2: 60498045-60498067
AAGAGCAGGGGUCUUCUCUU
1603





CR002149
h
+
Chr2: 60498046-60498068
AGAGCAGGGGUCUUCUCUUU
1604





CR002150
h
+
Chr2: 60498047-60498069
GAGCAGGGGUCUUCUCUUUG
1605





CR002151
h
+
Chr2: 60498048-60498070
AGCAGGGGUCUUCUCUUUGG
1606





CR002152
h
+
Chr2: 60498051-60498073
AGGGGUCUUCUCUUUGGGGG
1607





CR002153
h
+
Chr2: 60498068-60498090
GGGAGGACAUCACUCUUAGC
1608





CR002154
h
+
Chr2: 60498069-60498091
GGAGGACAUCACUCUUAGCA
1609





CR001261
h

Chr1: 55039269-55039291
GCCAGACUCCAAGUUCUGCC
1610





CR002155
h
+
Chr2: 60498073-60498095
GACAUCACUCUUAGCAGGGC
1611





CR002156
h
+
Chr2: 60498074-60498096
ACAUCACUCUUAGCAGGGCU
1612





CR002157
h
+
Chr2: 60498075-60498097
CAUCACUCUUAGCAGGGCUG
1613





CR002158
h
+
Chr2: 60498091-60498113
GCUGGGGUGAGUCAAAAGUC
1614





CR002159
h
+
Chr2: 60498092-60498114
CUGGGGUGAGUCAAAAGUCU
1615





CR002160
h
+
Chr2: 60498099-60498121
GAGUCAAAAGUCUGGGAGAA
1616





CR002161
h
+
Chr2: 60498102-60498124
UCAAAAGUCUGGGAGAAUGG
1617





CR002162
h
+
Chr2: 60498107-60498129
AGUCUGGGAGAAUGGAGGUG
1618





CR002163
h
+
Chr2: 60498110-60498132
CUGGGAGAAUGGAGGUGUGG
1619





CR002164
h
+
Chr2: 60498111-60498133
UGGGAGAAUGGAGGUGUGGA
1620





CR002165
h
+
Chr2: 60498112-60498134
GGGAGAAUGGAGGUGUGGAG
1621





CR002166
h
+
Chr2: 60498120-60498142
GGAGGUGUGGAGGGGAUAAC
1622





CR001263
h
+
Chr1: 55039180-55039202
GGCAGCGAGGAGUCCACAGU
1623





CR002167
h
+
Chr2: 60498121-60498143
GAGGUGUGGAGGGGAUAACU
1624





CR002168
h
+
Chr2: 60498137-60498159
AACUGGGUCAGACCCCAAGC
1625





CR002169
h
+
Chr2: 60498141-60498163
GGGUCAGACCCCAAGCAGGA
1626





CR002170
h
+
Chr2: 60498142-60498164
GGUCAGACCCCAAGCAGGAA
1627





CR002171
h

Chr2: 60498149-60498171
CCCCAAGCAGGAAGGGCCUC
1628





CR002172
h

Chr2: 60498150-60498172
CCCAAGCAGGAAGGGCCUCU
1629





CR002173
h

Chr2: 60498151-60498173
CCAAGCAGGAAGGGCCUCUA
1630





CR002174
h
+
Chr2: 60498157-60498179
AGGAAGGGCCUCUAUGUAGA
1631





CR002175
h
+
Chr2: 60498158-60498180
GGAAGGGCCUCUAUGUAGAC
1632





CR002176
h
+
Chr2: 60498165-60498187
CCUCUAUGUAGACGGGUGUG
1633





CR002177
h

Chr2: 60498165-60498187
CCUCUAUGUAGACGGGUGUG
1634





CR002178
h
+
Chr2: 60498175-60498197
GACGGGUGUGUGGCUCCUUA
1635





CR002179
h

Chr2: 60498190-60498212
CCUUAAGGUGACCCAGCAGC
1636





CR002180
h
+
Chr2: 60498192-60498214
UUAAGGUGACCCAGCAGCCC
1637





CR002181
h
+
Chr2: 60498193-60498215
UAAGGUGACCCAGCAGCCCU
1638





CR002182
h

Chr2: 60498201-60498223
CCCAGCAGCCCUGGGCACAG
1639





CR002183
h

Chr2: 60498202-60498224
CCAGCAGCCCUGGGCACAGA
1640





CR001261
h

Chr1: 55039269-55039291
GCCAGACUCCAAGUUCUGCC
1641





CR002184
h
+
Chr2: 60498204-60498226
AGCAGCCCUGGGCACAGAAG
1642





CR002185
h

Chr2: 60498209-60498231
CCCUGGGCACAGAAGUGGUG
1643





CR002186
h

Chr2: 60498210-60498232
CCUGGGCACAGAAGUGGUGC
1644





CR002187
h
+
Chr2: 60498211-60498233
CUGGGCACAGAAGUGGUGCG
1645





CR002188
h
+
Chr2: 60498240-60498262
UGCCAACAGUGAUAACCAGC
1646





CR002189
h
+
Chr2: 60498241-60498263
GCCAACAGUGAUAACCAGCA
1647





CR001262
h
+
Chr1: 55039155-55039177
UAAGGCCAGUGGAAAGAAUU
1648





CR002190
h

Chr2: 60498242-60498264
CCAACAGUGAUAACCAGCAG
1649





CR002191
h
+
Chr2: 60498255-60498277
CCAGCAGGGCCUGUCAGAAG
1650





CR002192
h

Chr2: 60498255-60498277
CCAGCAGGGCCUGUCAGAAG
1651





CR002193
h
+
Chr2: 60498261-60498283
GGGCCUGUCAGAAGAGGCCC
1652





CR002194
h

Chr2: 60498264-60498286
CCUGUCAGAAGAGGCCCUGG
1653





CR002195
h
+
Chr2: 60498271-60498293
GAAGAGGCCCUGGACACUGA
1654





CR002196
h
+
Chr2: 60498275-60498297
AGGCCCUGGACACUGAAGGC
1655





CR002197
h
+
Chr2: 60498276-60498298
GGCCCUGGACACUGAAGGCU
1656





CR001264
h

Chr1: 55039149-55039171
UCUUUCCACUGGCCUUAACC
1657





CR002198
h

Chr2: 60498278-60498300
CCCUGGACACUGAAGGCUGG
1658





CR002199
h

Chr2: 60498279-60498301
CCUGGACACUGAAGGCUGGG
1659





CR002200
h
+
Chr2: 60498287-60498309
CUGAAGGCUGGGCACAGCCU
1660





CR002201
h
+
Chr2: 60498288-60498310
UGAAGGCUGGGCACAGCCUU
1661





CR002202
h
+
Chr2: 60498289-60498311
GAAGGCUGGGCACAGCCUUG
1662





CR002203
h
+
Chr2: 60498301-60498323
CAGCCUUGGGGACCGCUCAC
1663





CR002204
h

Chr2: 60498304-60498326
CCUUGGGGACCGCUCACAGG
1664





CR002205
h

Chr2: 60498313-60498335
CCGCUCACAGGACAUGCAGC
1665





CR002206
h

Chr2: 60498341-60498363
CCGACAACUCCCUACCGCGA
1666





CR002207
h

Chr2: 60498350-60498372
CCCUACCGCGACCCCUAUCA
1667





CR002208
h

Chr2: 60498351-60498373
CCUACCGCGACCCCUAUCAG
1668





CR002209
h

Chr2: 60498355-60498377
CCGCGACCCCUAUCAGUGCC
1669





CR002210
h

Chr2: 60498361-60498383
CCCCUAUCAGUGCCGACCAA
1670





CR002211
h

Chr2: 60498362-60498384
CCCUAUCAGUGCCGACCAAG
1671





CR002212
h

Chr2: 60498363-60498385
CCUAUCAGUGCCGACCAAGC
1672





CR002213
h

Chr2: 60498373-60498395
CCGACCAAGCACACAAGAUG
1673





CR002214
h

Chr2: 60498377-60498399
CCAAGCACACAAGAUGCACA
1674





CR002215
h
+
Chr2: 60498380-60498402
AGCACACAAGAUGCACACCC
1675





CR002216
h
+
Chr2: 60498384-60498406
CACAAGAUGCACACCCAGGC
1676





CR002217
h
+
Chr2: 60498385-60498407
ACAAGAUGCACACCCAGGCU
1677





CR001264
h

Chr1: 55039149-55039171
UCUUUCCACUGGCCUUAACC
1678





CR002218
h
+
Chr2: 60498389-60498411
GAUGCACACCCAGGCUGGGC
1679





CR002219
h
+
Chr2: 60498396-60498418
ACCCAGGCUGGGCUGGACAG
1680





CR002220
h
+
Chr2: 60498397-60498419
CCCAGGCUGGGCUGGACAGA
1681





CR002221
h

Chr2: 60498397-60498419
CCCAGGCUGGGCUGGACAGA
1682





CR002222
h
+
Chr2: 60498398-60498420
CCAGGCUGGGCUGGACAGAG
1683





CR002223
h

Chr2: 60498398-60498420
CCAGGCUGGGCUGGACAGAG
1684





CR002224
h
+
Chr2: 60498415-60498437
GAGGGGUCCCACAAGAUCAC
1685





CR002225
h
+
Chr2: 60498416-60498438
AGGGGUCCCACAAGAUCACA
1686





CR002226
h

Chr2: 60498422-60498444
CCCACAAGAUCACAGGGUGU
1687





CR001263
h
+
Chr1: 55039180-55039202
GGCAGCGAGGAGUCCACAGU
1688





CR002227
h

Chr2: 60498423-60498445
CCACAAGAUCACAGGGUGUG
1689





CR002228
h
+
Chr2: 60498431-60498453
UCACAGGGUGUGCCCUGAGA
1690





CR002229
h
+
Chr2: 60498434-60498456
CAGGGUGUGCCCUGAGAAGG
1691









In some aspects of the invention, it is preferred that the gRNA molecule to the +55 Enhancer region of BCL11a comprise a targeting domain comprising, e.g., consisting of a targeting domain sequence selected from SEQ ID NO: 1683, SEQ ID NO: 1638, SEQ ID NO: 1647, SEQ ID NO: 1609, SEQ ID NO: 1621, SEQ ID NO: 1617, SEQ ID NO: 1654, SEQ ID NO: 1631, SEQ ID NO: 1620, SEQ ID NO: 1637, SEQ ID NO: 1612, SEQ ID NO: 1656, SEQ ID NO: 1619, SEQ ID NO: 1675, SEQ ID NO: 1645, SEQ ID NO: 1598, SEQ ID NO: 1599, SEQ ID NO: 1663, SEQ ID NO: 1677, and SEQ ID NO: 1626.


In some aspects of the invention, e.g., as indicated herein, it may be beneficial to include gRNA moleucles targeting more than one, e.g., two, target sites (e.g., a first gRNA molecule and a second gRNA molecule). In some embodiments, the two target sites are both located in the +55 BCL11a enhancer region. In such aspects, any combination of more than one, e.g., two, gRNA molecules (e.g., a first gRNA molecule and a second gRNA molecule) comprising, e.g., consisting of, targeting domains listed in Table 9 may be used, that target different target sites of the +55 BCL11a enhancer region. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1683 and SEQ ID NO: 1638, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1683 and SEQ ID NO: 1647, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1683 and SEQ ID NO: 1609, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1683 and SEQ ID NO: 1621, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1683 and SEQ ID NO: 1617, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1683 and SEQ ID NO: 1654, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1683 and SEQ ID NO: 1631, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1683 and SEQ ID NO: 1620, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1683 and SEQ ID NO: 1637, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1683 and SEQ ID NO: 1612, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1683 and SEQ ID NO: 1656, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1683 and SEQ ID NO: 1619, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1683 and SEQ ID NO: 1675, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1683 and SEQ ID NO: 1645, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1683 and SEQ ID NO: 1598, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1683 and SEQ ID NO: 1599, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1683 and SEQ ID NO: 1663, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1683 and SEQ ID NO: 1677, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1683 and SEQ ID NO: 1626, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1638 and SEQ ID NO: 1647, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1638 and SEQ ID NO: 1609, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1638 and SEQ ID NO: 1621, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1638 and SEQ ID NO: 1617, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1638 and SEQ ID NO: 1654, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1638 and SEQ ID NO: 1631, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1638 and SEQ ID NO: 1620, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1638 and SEQ ID NO: 1637, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1638 and SEQ ID NO: 1612, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1638 and SEQ ID NO: 1656, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1638 and SEQ ID NO: 1619, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1638 and SEQ ID NO: 1675, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1638 and SEQ ID NO: 1645, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1638 and SEQ ID NO: 1598, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1638 and SEQ ID NO: 1599, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1638 and SEQ ID NO: 1663, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1638 and SEQ ID NO: 1677, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1638 and SEQ ID NO: 1626, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1647 and SEQ ID NO: 1638, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1647 and SEQ ID NO: 1609, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1647 and SEQ ID NO: 1621, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1647 and SEQ ID NO: 1617, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1647 and SEQ ID NO: 1654, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1647 and SEQ ID NO: 1631, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1647 and SEQ ID NO: 1620, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1647 and SEQ ID NO: 1637, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1647 and SEQ ID NO: 1612, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1647 and SEQ ID NO: 1656, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1647 and SEQ ID NO: 1619, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1647 and SEQ ID NO: 1675, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1647 and SEQ ID NO: 1645, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1647 and SEQ ID NO: 1598, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1647 and SEQ ID NO: 1599, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1647 and SEQ ID NO: 1663, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1647 and SEQ ID NO: 1677, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1647 and SEQ ID NO: 1626, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1609 and SEQ ID NO: 1638, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1609 and SEQ ID NO: 1647, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1609 and SEQ ID NO: 1621, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1609 and SEQ ID NO: 1617, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1609 and SEQ ID NO: 1654, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1609 and SEQ ID NO: 1631, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1609 and SEQ ID NO: 1620, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1609 and SEQ ID NO: 1637, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1609 and SEQ ID NO: 1612, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1609 and SEQ ID NO: 1656, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1609 and SEQ ID NO: 1619, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1609 and SEQ ID NO: 1675, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1609 and SEQ ID NO: 1645, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1609 and SEQ ID NO: 1598, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1609 and SEQ ID NO: 1599, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1609 and SEQ ID NO: 1663, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1609 and SEQ ID NO: 1677, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1609 and SEQ ID NO: 1626, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1621 and SEQ ID NO: 1638, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1621 and SEQ ID NO: 1647, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1621 and SEQ ID NO: 1609, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1621 and SEQ ID NO: 1617, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1621 and SEQ ID NO: 1654, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1621 and SEQ ID NO: 1631, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1621 and SEQ ID NO: 1620, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1621 and SEQ ID NO: 1637, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1621 and SEQ ID NO: 1612, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1621 and SEQ ID NO: 1656, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1621 and SEQ ID NO: 1619, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1621 and SEQ ID NO: 1675, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1621 and SEQ ID NO: 1645, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1621 and SEQ ID NO: 1598, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1621 and SEQ ID NO: 1599, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1621 and SEQ ID NO: 1663, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1621 and SEQ ID NO: 1677, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1621 and SEQ ID NO: 1626, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1617 and SEQ ID NO: 1638, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1617 and SEQ ID NO: 1647, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1617 and SEQ ID NO: 1609, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1617 and SEQ ID NO: 1621, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1617 and SEQ ID NO: 1654, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1617 and SEQ ID NO: 1631, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1617 and SEQ ID NO: 1620, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1617 and SEQ ID NO: 1637, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1617 and SEQ ID NO: 1612, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1617 and SEQ ID NO: 1656, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1617 and SEQ ID NO: 1619, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1617 and SEQ ID NO: 1675, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1617 and SEQ ID NO: 1645, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1617 and SEQ ID NO: 1598, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1617 and SEQ ID NO: 1599, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1617 and SEQ ID NO: 1663, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1617 and SEQ ID NO: 1677, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1617 and SEQ ID NO: 1626, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1654 and SEQ ID NO: 1638, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1654 and SEQ ID NO: 1647, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1654 and SEQ ID NO: 1609, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1654 and SEQ ID NO: 1621, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1654 and SEQ ID NO: 1617, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1654 and SEQ ID NO: 1631, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1654 and SEQ ID NO: 1620, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1654 and SEQ ID NO: 1637, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1654 and SEQ ID NO: 1612, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1654 and SEQ ID NO: 1656, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1654 and SEQ ID NO: 1619, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1654 and SEQ ID NO: 1675, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1654 and SEQ ID NO: 1645, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1654 and SEQ ID NO: 1598, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1654 and SEQ ID NO: 1599, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1654 and SEQ ID NO: 1663, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1654 and SEQ ID NO: 1677, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1654 and SEQ ID NO: 1626, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1631 and SEQ ID NO: 1638, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1631 and SEQ ID NO: 1647, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1631 and SEQ ID NO: 1609, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1631 and SEQ ID NO: 1621, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1631 and SEQ ID NO: 1617, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1631 and SEQ ID NO: 1654, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1631 and SEQ ID NO: 1620, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1631 and SEQ ID NO: 1637, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1631 and SEQ ID NO: 1612, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1631 and SEQ ID NO: 1656, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1631 and SEQ ID NO: 1619, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1631 and SEQ ID NO: 1675, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1631 and SEQ ID NO: 1645, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1631 and SEQ ID NO: 1598, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1631 and SEQ ID NO: 1599, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1631 and SEQ ID NO: 1663, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1631 and SEQ ID NO: 1677, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1631 and SEQ ID NO: 1626, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1620 and SEQ ID NO: 1638, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1620 and SEQ ID NO: 1647, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1620 and SEQ ID NO: 1609, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1620 and SEQ ID NO: 1621, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1620 and SEQ ID NO: 1617, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1620 and SEQ ID NO: 1654, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1620 and SEQ ID NO: 1631, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1620 and SEQ ID NO: 1637, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1620 and SEQ ID NO: 1612, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1620 and SEQ ID NO: 1656, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1620 and SEQ ID NO: 1619, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1620 and SEQ ID NO: 1675, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1620 and SEQ ID NO: 1645, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1620 and SEQ ID NO: 1598, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1620 and SEQ ID NO: 1599, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1620 and SEQ ID NO: 1663, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1620 and SEQ ID NO: 1677, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1620 and SEQ ID NO: 1626, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1637 and SEQ ID NO: 1638, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1637 and SEQ ID NO: 1647, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1637 and SEQ ID NO: 1609, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1637 and SEQ ID NO: 1621, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1637 and SEQ ID NO: 1617, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1637 and SEQ ID NO: 1654, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1637 and SEQ ID NO: 1631, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1637 and SEQ ID NO: 1620, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1637 and SEQ ID NO: 1612, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1637 and SEQ ID NO: 1656, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1637 and SEQ ID NO: 1619, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1637 and SEQ ID NO: 1675, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1637 and SEQ ID NO: 1645, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1637 and SEQ ID NO: 1598, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1637 and SEQ ID NO: 1599, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1637 and SEQ ID NO: 1663, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1637 and SEQ ID NO: 1677, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1637 and SEQ ID NO: 1626, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1612 and SEQ ID NO: 1638, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1612 and SEQ ID NO: 1647, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1612 and SEQ ID NO: 1609, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1612 and SEQ ID NO: 1621, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1612 and SEQ ID NO: 1617, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1612 and SEQ ID NO: 1654, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1612 and SEQ ID NO: 1631, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1612 and SEQ ID NO: 1620, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1612 and SEQ ID NO: 1637, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1612 and SEQ ID NO: 1656, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1612 and SEQ ID NO: 1619, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1612 and SEQ ID NO: 1675, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1612 and SEQ ID NO: 1645, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1612 and SEQ ID NO: 1598, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1612 and SEQ ID NO: 1599, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1612 and SEQ ID NO: 1663, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1612 and SEQ ID NO: 1677, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1612 and SEQ ID NO: 1626, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1656 and SEQ ID NO: 1638, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1656 and SEQ ID NO: 1647, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1656 and SEQ ID NO: 1609, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1656 and SEQ ID NO: 1621, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1656 and SEQ ID NO: 1617, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1656 and SEQ ID NO: 1654, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1656 and SEQ ID NO: 1631, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1656 and SEQ ID NO: 1620, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1656 and SEQ ID NO: 1637, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1656 and SEQ ID NO: 1612, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1656 and SEQ ID NO: 1619, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1656 and SEQ ID NO: 1675, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1656 and SEQ ID NO: 1645, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1656 and SEQ ID NO: 1598, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1656 and SEQ ID NO: 1599, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1656 and SEQ ID NO: 1663, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1656 and SEQ ID NO: 1677, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1656 and SEQ ID NO: 1626, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1619 and SEQ ID NO: 1638, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1619 and SEQ ID NO: 1647, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1619 and SEQ ID NO: 1609, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1619 and SEQ ID NO: 1621, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1619 and SEQ ID NO: 1617, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1619 and SEQ ID NO: 1654, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1619 and SEQ ID NO: 1631, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1619 and SEQ ID NO: 1620, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1619 and SEQ ID NO: 1637, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1619 and SEQ ID NO: 1612, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1619 and SEQ ID NO: 1656, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1619 and SEQ ID NO: 1675, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1619 and SEQ ID NO: 1645, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1619 and SEQ ID NO: 1598, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1619 and SEQ ID NO: 1599, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1619 and SEQ ID NO: 1663, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1619 and SEQ ID NO: 1677, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1619 and SEQ ID NO: 1626, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1675 and SEQ ID NO: 1638, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1675 and SEQ ID NO: 1647, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1675 and SEQ ID NO: 1609, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1675 and SEQ ID NO: 1621, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1675 and SEQ ID NO: 1617, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1675 and SEQ ID NO: 1654, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1675 and SEQ ID NO: 1631, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1675 and SEQ ID NO: 1620, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1675 and SEQ ID NO: 1637, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1675 and SEQ ID NO: 1612, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1675 and SEQ ID NO: 1656, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1675 and SEQ ID NO: 1619, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1675 and SEQ ID NO: 1645, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1675 and SEQ ID NO: 1598, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1675 and SEQ ID NO: 1599, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1675 and SEQ ID NO: 1663, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1675 and SEQ ID NO: 1677, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1675 and SEQ ID NO: 1626, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1645 and SEQ ID NO: 1638, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1645 and SEQ ID NO: 1647, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1645 and SEQ ID NO: 1609, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1645 and SEQ ID NO: 1621, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1645 and SEQ ID NO: 1617, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1645 and SEQ ID NO: 1654, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1645 and SEQ ID NO: 1631, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1645 and SEQ ID NO: 1620, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1645 and SEQ ID NO: 1637, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1645 and SEQ ID NO: 1612, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1645 and SEQ ID NO: 1656, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1645 and SEQ ID NO: 1619, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1645 and SEQ ID NO: 1675, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1598 and SEQ ID NO: 1638, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1598 and SEQ ID NO: 1647, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1598 and SEQ ID NO: 1609, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1598 and SEQ ID NO: 1621, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1598 and SEQ ID NO: 1617, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1598 and SEQ ID NO: 1654, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1598 and SEQ ID NO: 1631, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1598 and SEQ ID NO: 1620, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1598 and SEQ ID NO: 1637, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1598 and SEQ ID NO: 1612, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1598 and SEQ ID NO: 1656, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1598 and SEQ ID NO: 1619, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1598 and SEQ ID NO: 1675, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1598 and SEQ ID NO: 1645, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1598 and SEQ ID NO: 1599, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1598 and SEQ ID NO: 1663, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1598 and SEQ ID NO: 1677, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1598 and SEQ ID NO: 1626, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1599 and SEQ ID NO: 1638, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1599 and SEQ ID NO: 1647, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1599 and SEQ ID NO: 1609, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1599 and SEQ ID NO: 1621, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1599 and SEQ ID NO: 1617, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1599 and SEQ ID NO: 1654, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1599 and SEQ ID NO: 1631, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1599 and SEQ ID NO: 1620, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1599 and SEQ ID NO: 1637, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1599 and SEQ ID NO: 1612, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1599 and SEQ ID NO: 1656, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1599 and SEQ ID NO: 1619, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1599 and SEQ ID NO: 1675, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1599 and SEQ ID NO: 1645, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1599 and SEQ ID NO: 1598, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1599 and SEQ ID NO: 1663, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1599 and SEQ ID NO: 1677, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1599 and SEQ ID NO: 1626, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1663 and SEQ ID NO: 1638, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1663 and SEQ ID NO: 1647, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1663 and SEQ ID NO: 1609, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1663 and SEQ ID NO: 1621, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1663 and SEQ ID NO: 1617, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1663 and SEQ ID NO: 1654, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1663 and SEQ ID NO: 1631, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1663 and SEQ ID NO: 1620, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1663 and SEQ ID NO: 1637, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1663 and SEQ ID NO: 1612, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1663 and SEQ ID NO: 1656, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1663 and SEQ ID NO: 1619, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1663 and SEQ ID NO: 1675, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1663 and SEQ ID NO: 1645, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1663 and SEQ ID NO: 1598, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1663 and SEQ ID NO: 1599, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1663 and SEQ ID NO: 1677, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1663 and SEQ ID NO: 1626, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1677 and SEQ ID NO: 1638, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1677 and SEQ ID NO: 1647, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1677 and SEQ ID NO: 1609, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1677 and SEQ ID NO: 1621, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1677 and SEQ ID NO: 1617, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1677 and SEQ ID NO: 1654, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1677 and SEQ ID NO: 1631, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1677 and SEQ ID NO: 1620, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1677 and SEQ ID NO: 1637, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1677 and SEQ ID NO: 1612, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1677 and SEQ ID NO: 1656, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1677 and SEQ ID NO: 1619, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1677 and SEQ ID NO: 1675, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1677 and SEQ ID NO: 1645, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1677 and SEQ ID NO: 1598, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1677 and SEQ ID NO: 1599, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1677 and SEQ ID NO: 1663, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1677 and SEQ ID NO: 1626, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1626 and SEQ ID NO: 1638, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1626 and SEQ ID NO: 1647, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1626 and SEQ ID NO: 1609, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1626 and SEQ ID NO: 1621, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1626 and SEQ ID NO: 1617, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1626 and SEQ ID NO: 1654, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1626 and SEQ ID NO: 1631, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1626 and SEQ ID NO: 1620, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1626 and SEQ ID NO: 1637, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1626 and SEQ ID NO: 1612, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1626 and SEQ ID NO: 1656, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1626 and SEQ ID NO: 1619, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1626 and SEQ ID NO: 1675, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1626 and SEQ ID NO: 1645, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1626 and SEQ ID NO: 1598, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1626 and SEQ ID NO: 1599, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1626 and SEQ ID NO: 1663, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1626 and SEQ ID NO: 1677, respectively.


III. Methods for Designing gRNAs

Methods for designing gRNAs are described herein, including methods for selecting, designing and validating target sequences. Exemplary targeting domains are also provided herein. Targeting Domains discussed herein can be incorporated into the gRNAs described herein.


Methods for selection and validation of target sequences as well as off-target analyses are described, e.g., in. Mali el al., 2013 SCIENCE 339(6121): 823-826; Hsu et al, 2013 NAT BIOTECHNOL, 31 (9): 827-32; Fu et al, 2014 NAT BIOTECHNOL, doi: 10.1038/nbt.2808. PubMed PM ID: 24463574; Heigwer et al, 2014 NAT METHODS 11(2): 122-3. doi: 10.1038/nmeth.2812. PubMed PMID: 24481216; Bae el al, 2014 BIOINFORMATICS PubMed PMID: 24463181; Xiao A el al, 2014 BIOINFORMATICS PubMed PMID: 24389662.


For example, a software tool can be used to optimize the choice of gRNA within a user's target sequence, e.g., to minimize total off-target activity across the genome. Off target activity may be other than cleavage. For each possible gRNA choice e.g., using S. pyogenes Cas9, the tool can identify all off-target sequences (e.g., preceding either NAG or NGG PAMs) across the genome that contain up to certain number (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10) of mismatched base-pairs. The cleavage efficiency at each off-target sequence can be predicted, e.g., using an experimentally-derived weighting scheme. Each possible gRNA is then ranked according to its total predicted off-target cleavage; the top-ranked gRNAs represent those that are likely to have the greatest on-target and the least off-target cleavage. Other functions, e.g., automated reagent design for CRISPR construction, primer design for the on-target Surveyor assay, and primer design for high-throughput detection and quantification of off-target cleavage via next-gen sequencing, can also be included in the tool. Candidate gRNA molecules can be evaluated by art-known methods or as described herein.


Although software algorithms may be used to generate an initial list of potential gRNA molecules, cutting efficiency and specificity will not necessarily reflect the predicted values, and gRNA molecules typically require screening in specific cell lines, e.g., primary human cell lines, e.g., human HSPCs, e.g., human CD34+ cells, to determine, for example, cutting efficiency, indel formation, cutting specificity and change in desired phenotype. These properties may be assayed by the methods described herein.


In aspects of the invention, a gRNA comprising the targeting domain of CR00312 (SEQ ID NO: 248, underlined below), e.g., one of the gRNA molecules described below, is useful in the CRISPR systems, methods, cells and other aspects and embodiments of the invention, including in aspects involving more than one gRNA molecule, e.g., described herein:









sgRNA CR00312 #1:







(SEQ ID NO: 342)








GUUUGGCCUCUGAUUAGGGUGUUUUAGAGCUAGAAAUAGCAAGUUAAAAU






AAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUU





sgRNA CR00312 #2:







(SEQ ID NO: 343)








mG*mU*mU*UGGCCUCUGAUUAGGGUGUUUUAGAGCUAGAAAUAGCAAGU






UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU





GCU*mU*mU*mU





sgRNA CR00312 #3:







(SEQ ID NO: 1762))








mG*mU*mU*UGGCCUCUGAUUAGGGUGUUUUAGAGCUAGAAAUAGCAAGU






UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU





GCmU*mU*mU*U





dgRNA CR00312 #1:


crRNA:







(SEQ ID NO: 344)








GUUUGGCCUCUGAUUAGGGUGUUUUAGAGCUAUGCUGUUUUG






tracr:







(SEQ ID NO: 6660)







AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG





UGGCACCGAGUCGGUGCUUUUUUU





dgRNA CR00312 #2:


crRNA:







(SEQ ID NO: 345)








mG*mU*mU*UGGCCUCUGAUUAGGGUGUUUUAGAGCUAUGCUGUU*mU*m






U*mG





tracr:







(SEQ ID NO: 346)







mA*mA*mC*AGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUG





AAAAAGUGGCACCGAGUCGGUGCUUUU*mU*mU*mU





dgRNA CR00312 #3:


crRNA:







(SEQ ID NO: 345)








mG*mU*mU*UGGCCUCUGAUUAGGGUGUUUUAGAGCUAUGCUGUU*mU*m






U*mG





tracr:







(SEQ ID NO: 6660)







AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG





UGGCACCGAGUCGGUGCUUUUUUU.






In aspects of the invention, a gRNA comprising the targeting domain of CR001128 (SEQ ID NO: 338, underlined below), e.g., one of the gRNA molecules described below, is useful in the CRISPR systems, methods, cells and other aspects and embodiments of the invention, including in aspects involving more than one gRNA molecule, e.g., described herein:









sgRNA CR001128 #1:







(SEQ ID NO: 347)








AUCAGAGGCCAAACCCUUCCGUUUUAGAGCUAGAAAUAGCAAGUUAAAAU






AAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUU





sgRNA CR001128 #2:







(SEQ ID NO: 348)








mA*mU*mC*AGAGGCCAAACCCUUCCGUUUUAGAGCUAGAAAUAGCAAGU






UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU





GCU*mU*mU*mU





sgRNA CR001128 #3:







(SEQ ID NO: 1763)








mA*mU*mC*AGAGGCCAAACCCUUCCGUUUUAGAGCUAGAAAUAGCAAGU






UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU





GCmU*mU*mU*U





dgRNA CR001128 #1:


crRNA:







(SEQ ID NO: 349)








AUCAGAGGCCAAACCCUUCCGUUUUAGAGCUAUGCUGUUUUG






tracr:







(SEQ ID NO: 6660)







AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG





UGGCACCGAGUCGGUGCUUUUUUU





dgRNA CR001128 #2:


crRNA:







(SEQ ID NO: 350)








mA*mU*mC*AGAGGCCAAACCCUUCCGUUUUAGAGCUAUGCUGUU*mU*m



U*mG





tracr:







(SEQ ID NO: 346)







mA*mA*mC*AGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUG





AAAAAGUGGCACCGAGUCGGUGCUUUU*mU*mU*mU





dgRNA CR001128 #3:


crRNA:







(SEQ ID NO: 350)








mA*mU*mC*AGAGGCCAAACCCUUCCGUUUUAGAGCUAUGCUGUU*mU*m






U*mG





tracr:







(SEQ ID NO: 6660)







AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG





UGGCACCGAGUCGGUGCUUUUUUU.






In aspects of the invention, a gRNA comprising the targeting domain of CR001126 (SEQ ID NO: 336, underlined below), e.g., one of the gRNA molecules described below, is useful in the CRISPR systems, methods, cells and other aspects and embodiments of the invention, including in aspects involving more than one gRNA molecule, e.g., described herein:









sgRNA CR001126 #1:







(SEQ ID NO: 351)








UUUAUCACAGGCUCCAGGAAGUUUUAGAGCUAGAAAUAGCAAGUUAAAAU






AAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUU





sgRNA CR001126 #2:







(SEQ ID NO: 352)








mU*mU*mU*AUCACAGGCUCCAGGAAGUUUUAGAGCUAGAAAUAGCAAGU






UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU





GCU*mU*mU*mU





sgRNA CR001126 #3:







(SEQ ID NO: 1764)








mU*mU*mU*AUCACAGGCUCCAGGAAGUUUUAGAGCUAGAAAUAGCAAGU






UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU





GCmU*mU*mU*U





dgRNA CR001126 #1:


crRNA:







(SEQ ID NO: 353)








UUUAUCACAGGCUCCAGGAAGUUUUAGAGCUAUGCUGUUUUG






tracr:







(SEQ ID NO: 6660)







AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG





UGGCACCGAGUCGGUGCUUUUUUU





dgRNA CR001126 #2:


crRNA:







(SEQ ID NO: 354)








mU*mU*mU*AUCACAGGCUCCAGGAAGUUUUAGAGCUAUGCUGUU*mU*m






U*mG





tracr:







(SEQ ID NO: 346)







mA*mA*mC*AGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUG





AAAAAGUGGCACCGAGUCGGUGCUUUU*mU*mU*mU





dgRNA CR001126 #3:


crRNA:







(SEQ ID NO: 354)








mU*mU*mU*AUCACAGGCUCCAGGAAGUUUUAGAGCUAUGCUGUU*mU*m






U*mG





tracr:







(SEQ ID NO: 6660)







AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG





UGGCACCGAGUCGGUGCUUUUUUU.






In aspects of the invention, a gRNA comprising the targeting domain of CR00311 (SEQ ID NO: 247, underlined below), e.g., one of the gRNA molecules described below, is useful in the CRISPR systems, methods, cells and other aspects and embodiments of the invention, including in aspects involving more than one gRNA molecule, e.g., described herein:









sgRNA CR00311 #1:







(SEQ ID NO: 355)








UUUGGCCUCUGAUUAGGGUGGUUUUAGAGCUAGAAAUAGCAAGUUAAAAU






AAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUU





sgRNA CR00311 #2:







(SEQ ID NO: 356)








mU*mU*mU*GGCCUCUGAUUAGGGUGGUUUUAGAGCUAGAAAUAGCAAGU






UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU





GCU*mU*mU*mU





sgRNA CR00311 #3:







(SEQ ID NO: 1765)








mU*mU*mU*GGCCUCUGAUUAGGGUGGUUUUAGAGCUAGAAAUAGCAAGU






UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU





GCmU*mU*mU*U





dgRNA CR00311 #1:


crRNA:







(SEQ ID NO: 357)








UUUGGCCUCUGAUUAGGGUGGUUUUAGAGCUAUGCUGUUUUG






tracr:







(SEQ ID NO: 6660)







AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG





UGGCACCGAGUCGGUGCUUUUUUU





dgRNA CR00311 #2:


crRNA:







(SEQ ID NO: 358)








mU*mU*mU*GGCCUCUGAUUAGGGUGGUUUUAGAGCUAUGCUGUU*mU*m






U*mG





tracr:







(SEQ ID NO: 346)







mA*mA*mC*AGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUG





AAAAAGUGGCACCGAGUCGGUGCUUUU*mU*mU*mU





dgRNA CR00311 #3:


crRNA:







(SEQ ID NO: 358)








mU*mU*mU*GGCCUCUGAUUAGGGUGGUUUUAGAGCUAUGCUGUU*mU*m






U*mG





tracr:







(SEQ ID NO: 6660)







AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG





UGGCACCGAGUCGGUGCUUUUUUU.






In aspects of the invention, a gRNA comprising the targeting domain of CR00309 (SEQ ID NO: 245, underlined below), e.g., one of the gRNA molecules described below, is useful in the CRISPR systems, methods, cells and other aspects and embodiments of the invention, including in aspects involving more than one gRNA molecule, e.g., described herein:









sgRNA CR00309 #1:







(SEQ ID NO: 359)








CACGCCCCCACCCUAAUCAGGUUUUAGAGCUAGAAAUAGCAAGUUAAAAU






AAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUU





sgRNA CR00309 #2:







(SEQ ID NO: 360)








mC*mA*mC*GCCCCCACCCUAAUCAGGUUUUAGAGCUAGAAAUAGCAAGU






UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU





GCU*mU*mU*mU





sgRNA CR00309 #3:







(SEQ ID NO: 1766)








mC*mA*mC*GCCCCCACCCUAAUCAGGUUUUAGAGCUAGAAAUAGCAAGU






UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU





GCmU*mU*mU*U





dgRNA CR00309 #1:


crRNA:







(SEQ ID NO: 361)








CACGCCCCCACCCUAAUCAGGUUUUAGAGCUAUGCUGUUUUG






tracr:







(SEQ ID NO: 6660)







AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG





UGGCACCGAGUCGGUGCUUUUUUU





dgRNA CR00309 #2:


crRNA:







(SEQ ID NO: 362)








mC*mA*mC*GCCCCCACCCUAAUCAGGUUUUAGAGCUAUGCUGUU*mU*m






U*mG





tracr:







(SEQ ID NO: 346)







mA*mA*mC*AGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUG





AAAAAGUGGCACCGAGUCGGUGCUUUU*mU*mU*mU





dgRNA CR00309 #3:


crRNA:







(SEQ ID NO: 362)








mC*mA*mC*GCCCCCACCCUAAUCAGGUUUUAGAGCUAUGCUGUU*mU*m






U*mG





tracr:







(SEQ ID NO: 6660)







AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG





UGGCACCGAGUCGGUGCUUUUUUU.






In aspects of the invention, a gRNA comprising the targeting domain of CR001127 (SEQ ID NO: 337, underlined below), e.g., one of the gRNA molecules described below, is useful in the CRISPR systems, methods, cells and other aspects and embodiments of the invention, including in aspects involving more than one gRNA molecule, e.g., described herein:









sgRNA CR001127 #1:







(SEQ ID NO: 363)








CACAGGCUCCAGGAAGGGUUGUUUUAGAGCUAGAAAUAGCAAGUUAAAAU






AAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUU





sgRNA CR001127 #2:







(SEQ ID NO: 364)








mC*mA*mC*AGGCUCCAGGAAGGGUUGUUUUAGAGCUAGAAAUAGCAAGU






UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU





GCU*mU*mU*mU





sgRNA CR001127 #3:







(SEQ ID NO: 1767)








mC*mA*mC*AGGCUCCAGGAAGGGUUGUUUUAGAGCUAGAAAUAGCAAGU






UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU





GCmU*mU*mU*U





dgRNA CR001127 #1:


crRNA:







(SEQ ID NO: 365)








CACAGGCUCCAGGAAGGGUUGUUUUAGAGCUAUGCUGUUUUG






tracr:







(SEQ ID NO: 6660)







AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG





UGGCACCGAGUCGGUGCUUUUUUU





dgRNA CR001127 #2:


crRNA:







(SEQ ID NO: 366)








mC*mA*mC*AGGCUCCAGGAAGGGUUGUUUUAGAGCUAUGCUGUU*mU*m






U*mG





tracr:







(SEQ ID NO: 346)







mA*mA*mC*AGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUG





AAAAAGUGGCACCGAGUCGGUGCUUUU*mU*mU*mU





dgRNA CR001127 #3:


crRNA:







(SEQ ID NO: 366)








mC*mA*mC*AGGCUCCAGGAAGGGUUGUUUUAGAGCUAUGCUGUU*mU*m






U*mG





tracr:







(SEQ ID NO: 6660)







AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG





UGGCACCGAGUCGGUGCUUUUUUU.






In aspects of the invention, a gRNA comprising the targeting domain of CR00316 (SEQ ID NO: 252, underlined below), e.g., one of the gRNA molecules described below, is useful in the CRISPR systems, methods, cells and other aspects and embodiments of the invention, including in aspects involving more than one gRNA molecule, e.g., described herein:









sgRNA CR00316 #1:







(SEQ ID NO: 367)








UUGCUUUUAUCACAGGCUCCGUUUUAGAGCUAGAAAUAGCAAGUUAAAAU






AAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUU





sgRNA CR00316 #2:







(SEQ ID NO: 368)








mU*mU*mG*CUUUUAUCACAGGCUCCGUUUUAGAGCUAGAAAUAGCAAGU






UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU





GCU*mU*mU*mU





sgRNA CR00316 #3:







(SEQ ID NO: 1768)








mU*mU*mG*CUUUUAUCACAGGCUCCGUUUUAGAGCUAGAAAUAGCAAGU






UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU





GCmU*mU*mU*U





dgRNA CR00316 #1:


crRNA:







(SEQ ID NO: 369)








UUGCUUUUAUCACAGGCUCCGUUUUAGAGCUAUGCUGUUUUG






tracr:







(SEQ ID NO: 6660)







AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG





UGGCACCGAGUCGGUGCUUUUUUU





dgRNA CR00316 #2:


crRNA:







(SEQ ID NO: 370)








mU*mU*mG*CUUUUAUCACAGGCUCCGUUUUAGAGCUAUGCUGUU*mU*m






U*mG





tracr:







(SEQ ID NO: 346)







mA*mA*mC*AGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUG





AAAAAGUGGCACCGAGUCGGUGCUUUU*mU*mU*mU





dgRNA CR00316 #3:


crRNA:







(SEQ ID NO: 370)








mU*mU*mG*CUUUUAUCACAGGCUCCGUUUUAGAGCUAUGCUGUU*mU*m






U*mG





tracr:







(SEQ ID NO: 6660)







AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG





UGGCACCGAGUCGGUGCUUUUUUU.






In aspects of the invention, a gRNA comprising the targeting domain of CR001125 (SEQ ID NO: 335, underlined below), e.g., one of the gRNA molecules described below, is useful in the CRISPR systems, methods, cells and other aspects and embodiments of the invention, including in aspects involving more than one gRNA molecule, e.g., described herein:









sgRNA CR001125 #1:







(SEQ ID NO: 371)








UUUUAUCACAGGCUCCAGGAGUUUUAGAGCUAGAAAUAGCAAGUUAAAAU






AAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUU





sgRNA CR001125 #2:







(SEQ ID NO: 372)








mU*mU*mU*UAUCACAGGCUCCAGGAGUUUUAGAGCUAGAAAUAGCAAGU






UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU





GCU*mU*mU*mU





sgRNA CR001125 #3:







(SEQ ID NO: 1769)








mU*mU*mU*UAUCACAGGCUCCAGGAGUUUUAGAGCUAGAAAUAGCAAGU






UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU





GCmU*mU*mU*U





dgRNA CR001125 #1:


crRNA:







(SEQ ID NO: 373)








UUUUAUCACAGGCUCCAGGAGUUUUAGAGCUAUGCUGUUUUG






tracr:







(SEQ ID NO: 6660)







AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG





UGGCACCGAGUCGGUGCUUUUUUU





dgRNA CR001125 #2:


crRNA:







(SEQ ID NO: 374)








mU*mU*mU*UAUCACAGGCUCCAGGAGUUUUAGAGCUAUGCUGUU*mU*m






U*mG





tracr:







(SEQ ID NO: 346)







mA*mA*mC*AGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUG





AAAAAGUGGCACCGAGUCGGUGCUUUU*mU*mU*mU





dgRNA CR001125 #3:


crRNA:







(SEQ ID NO: 374)








mU*mU*mU*UAUCACAGGCUCCAGGAGUUUUAGAGCUAUGCUGUU*mU*m






U*mG





tracr:







(SEQ ID NO: 6660)







AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG





UGGCACCGAGUCGGUGCUUUUUUU.






In aspects of the invention, a gRNA comprising the targeting domain of CR001030 (SEQ ID NO: 100, underlined below), e.g., one of the gRNA molecules described below, is useful in the CRISPR systems, methods, cells and other aspects and embodiments of the invention, including in aspects involving more than one gRNA molecule, e.g., described herein:









sgRNA CR001030 #1:







(SEQ ID NO: 375)








ACUGCUGAAAGAGAUGCGGUGUUUUAGAGCUAGAAAUAGCAAGUUAAAAU






AAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUU





sgRNA CR001030 #2:







(SEQ ID NO: 376)








mA*mC*mU*GCUGAAAGAGAUGCGGUGUUUUAGAGCUAGAAAUAGCAAGU






UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU





GCU*mU*mU*mU





sgRNA CR001030 #3:







(SEQ ID NO: 1770)








mA*mC*mU*GCUGAAAGAGAUGCGGUGUUUUAGAGCUAGAAAUAGCAAGU






UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU





GCmU*mU*mU*U





dgRNA CR001030 #1:







(SEQ ID NO: 377)







crRNA: ACUGCUGAAAGAGAUGCGGUGUUUUAGAGCUAUGCUGUUUUG





tracr:







(SEQ ID NO: 6660)







AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG





UGGCACCGAGUCGGUGCUUUUUUU





dgRNA CR001030 #2:


crRNA:







(SEQ ID NO: 378)








mA*mC*mU*GCUGAAAGAGAUGCGGUGUUUUAGAGCUAUGCUGUU*mU*m






U*mG





tracr:







(SEQ ID NO: 346)







mA*mA*mC*AGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUG





AAAAAGUGGCACCGAGUCGGUGCUUUU*mU*mU*mU





dgRNA CR001030 #3:


crRNA:







(SEQ ID NO: 378)








mA*mC*mU*GCUGAAAGAGAUGCGGUGUUUUAGAGCUAUGCUGUU*mU*m






U*mG





tracr:







(SEQ ID NO: 6660)







AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG





UGGCACCGAGUCGGUGCUUUUUUU.






In aspects of the invention, a gRNA comprising the targeting domain of CR001028 (SEQ ID NO: 98, underlined below), e.g., one of the gRNA molecules described below, is useful in the CRISPR systems, methods, cells and other aspects and embodiments of the invention, including in aspects involving more than one gRNA molecule, e.g., described herein:









sgRNA CR001028 #1:







(SEQ ID NO: 379)








UGCGGUGGGGAGAUAUGUAGGUUUUAGAGCUAGAAAUAGCAAGUUAAAAU






AAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUU





sgRNA CR001028 #2:







(SEQ ID NO: 380)








mU*mG*mC*GGUGGGGAGAUAUGUAGGUUUUAGAGCUAGAAAUAGCAAGU






UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU





GCU*mU*mU*mU





sgRNA CR001028 #3:







(SEQ ID NO: 1771)








mU*mG*mC*GGUGGGGAGAUAUGUAGGUUUUAGAGCUAGAAAUAGCAAGU






UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU





GCmU*mU*mU*U





dgRNA CR001028 #1:







(SEQ ID NO: 381)







crRNA: UGCGGUGGGGAGAUAUGUAGGUUUUAGAGCUAUGCUGUUUUG





tracr:







(SEQ ID NO: 6660)







AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG





UGGCACCGAGUCGGUGCUUUUUUU





dgRNA CR001028 #2:


crRNA:







(SEQ ID NO: 382)








mU*mG*mC*GGUGGGGAGAUAUGUAGGUUUUAGAGCUAUGCUGUU*mU*m






U*mG





tracr:







(SEQ ID NO: 346)







mA*mA*mC*AGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUG





AAAAAGUGGCACCGAGUCGGUGCUUUU*mU*mU*mU





dgRNA CR001028 #3:


crRNA:







(SEQ ID NO: 382)








mU*mG*mC*GGUGGGGAGAUAUGUAGGUUUUAGAGCUAUGCUGUU*mU*m






U*mG





tracr:







(SEQ ID NO: 6660)







AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG





UGGCACCGAGUCGGUGCUUUUUUU.






In aspects of the invention, a gRNA comprising the targeting domain of CR001221 (SEQ ID NO: 1589, underlined below), e.g., one of the gRNA molecules described below, is useful in the CRISPR systems, methods, cells and other aspects and embodiments of the invention, including in aspects involving more than one gRNA molecule, e.g., described herein:









sgRNA CR001221 #1:







(SEQ ID NO: 383)








GAAACAAUGAGGACCUGACUGUUUUAGAGCUAGAAAUAGCAAGUUAAAAU






AAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUU





sgRNA CR001221 #2:







(SEQ ID NO: 384)








mG*mA*mA*ACAAUGAGGACCUGACUGUUUUAGAGCUAGAAAUAGCAAGU






UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU





GCU*mU*mU*mU





sgRNA CR001221 #3:







(SEQ ID NO: 1772)








mG*mA*mA*ACAAUGAGGACCUGACUGUUUUAGAGCUAGAAAUAGCAAGU






UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU





GCmU*mU*mU*U





dgRNA CR001221 #1:







(SEQ ID NO: 385)







crRNA: GAAACAAUGAGGACCUGACUGUUUUAGAGCUAUGCUGUUUUG





tracr:







(SEQ ID NO: 6660)







AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG





UGGCACCGAGUCGGUGCUUUUUUU





dgRNA CR001221 #2:


crRNA:







(SEQ ID NO: 386)








mG*mA*mA*ACAAUGAGGACCUGACUGUUUUAGAGCUAUGCUGUU*mU*m






U*mG





tracr:







(SEQ ID NO: 346)







mA*mA*mC*AGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUG





AAAAAGUGGCACCGAGUCGGUGCUUUU*mU*mU*mU





dgRNA CR001221 #3:


crRNA:







(SEQ ID NO: 386)








mG*mA*mA*ACAAUGAGGACCUGACUGUUUUAGAGCUAUGCUGUU*mU*m






U*mG





tracr:







(SEQ ID NO: 6660)







AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG





UGGCACCGAGUCGGUGCUUUUUUU.






In aspects of the invention, a gRNA comprising the targeting domain of CR001137 (SEQ ID NO: 1505, underlined below), e.g., one of the gRNA molecules described below, is useful in the CRISPR systems, methods, cells and other aspects and embodiments of the invention, including in aspects involving more than one gRNA molecule, e.g., described herein:









sgRNA CR001137 #1:







(SEQ ID NO: 387)








GUAAGCAUUUAAGUGGCUACGUUUUAGAGCUAGAAAUAGCAAGUUAAAAU






AAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUU





sgRNA CR001137 #2:







(SEQ ID NO: 388)








mG*mU*mA*AGCAUUUAAGUGGCUACGUUUUAGAGCUAGAAAUAGCAAGU






UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU





GCU*mU*mU*mU





sgRNA CR001137 #3:







(SEQ ID NO: 1773)








mG*mU*mA*AGCAUUUAAGUGGCUACGUUUUAGAGCUAGAAAUAGCAAGU






UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU





GCmU*mU*mU*U





dgRNA CR001137 #1:







(SEQ ID NO: 389)







crRNA: GUAAGCAUUUAAGUGGCUACGUUUUAGAGCUAUGCUGUUUUG





tracr:







(SEQ ID NO: 6660)







AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG





UGGCACCGAGUCGGUGCUUUUUUU





dgRNA CR001137 #2:


crRNA:







(SEQ ID NO: 390)








mG*mU*mA*AGCAUUUAAGUGGCUACGUUUUAGAGCUAUGCUGUU*mU*m






U*mG





tracr:







(SEQ ID NO: 346)







mA*mA*mC*AGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUG





AAAAAGUG





GCACCGAGUCGGUGCUUUU*mU*mU*mU





dgRNA CR001137 #3:


crRNA:







(SEQ ID NO: 390)








mG*mU*mA*AGCAUUUAAGUGGCUACGUUUUAGAGCUAUGCUGUU*mU*m






U*mG





tracr:







(SEQ ID NO: 6660)







AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG





UGGCACCGAGUCGGUGCUUUUUUU.






In aspects of the invention, a gRNA comprising the targeting domain of CR003035 (SEQ ID NO: 1505, underlined below), e.g., one of the gRNA molecules described below, is useful in the CRISPR systems, methods, cells and other aspects and embodiments of the invention, including in aspects involving more than one gRNA molecule, e.g., described herein:









sgRNA CR003035 #1:







(SEQ ID NO: 391)








AGGCACCUCAGACUCAGCAUGUUUUAGAGCUAGAAAUAGCAAGUUAAAAU






AAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUU





sgRNA CR003035 #2:







(SEQ ID NO: 392)








mA*mG*mG*CACCUCAGACUCAGCAGUUUUAGAGCUAGAAAUAGCAAGU






UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU





GCU*mU*mU*mU





sgRNA CR003035 #3:







(SEQ ID NO: 1774)








mA*mG*mG*CACCUCAGACUCAGCAUGUUUUAGAGCUAGAAAUAGCAAGU






UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU





GCmU*mU*mU*U





dgRNA CR003035 #1:







(SEQ ID NO: 393)







crRNA: AGGCACCUCAGACUCAGCAUGUUUUAGAGCUAUGCUGUUUUG





tracr:







(SEQ ID NO: 6660)







AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG





UGGCACCGAGUCGGUGCUUUUUUU





dgRNA CR003035 #2:







(SEQ ID NO: 394)







crRNA: mA*mG*mG*CACCUCAGACUCAGCAUGUUUUAGAGCUAUGCUG





UU*mU*mU*mG





tracr:







(SEQ ID NO: 346)







mA*mA*mC*AGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUG





AAAAAGUGGCACCGAGUCGGUGCUUUU*mU*mU*mU





dgRNA CR003035 #3:







(SEQ ID NO: 394)







crRNA: mA*mG*mG*CACCUCAGACUCAGCAUGUUUUAGAGCUAUGCUG





UU*mU*mU*mG





tracr:







(SEQ ID NO: 6660)







AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG





UGGCACCGAGUCGGUGCUUUUUUU.






In aspects of the invention, a gRNA comprising the targeting domain of CR003085 (SEQ ID NO: 1750, underlined below), e.g., one of the gRNA molecules described below, is useful in the CRISPR systems, methods, cells and other aspects and embodiments of the invention, including in aspects involving more than one gRNA molecule, e.g., described herein:









sgRNA CR003085 #1:







(SEQ ID NO: 395)








AUGGUAUGGGAGGUAUACUAGUUUUAGAGCUAGAAAUAGCAAGUUAAAAU






AAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUU





sgRNA CR003085 #2:







(SEQ ID NO: 396)








mA*mU*mG*GUAUGGGAGGUAUACUAGUUUUAGAGCUAGAAAUAGCAAGU






UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU





GCU*mU*mU*mU





sgRNA CR003085 #3:







(SEQ ID NO: 1775)








mA*mU*mG*GUAUGGGAGGUAUACUAGUUUUAGAGCUAGAAAUAGCAAGU






UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU





GCmU*mU*mU*U





dgRNA CR003085 #1:







(SEQ ID NO: 397)







crRNA: AUGGUAUGGGAGGUAUACUAGUUUUAGAGCUAUGCUGUUUUG





tracr:







(SEQ ID NO: 6660)







AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG





UGGCACCGAGUCGGUGCUUUUUUU





dgRNA CR003085 #2:


crRNA:







(SEQ ID NO: 398)








mA*mU*mG*GUAUGGGAGGUAUACUAGUUUUAGAGCUAUGCUGUU*mU*m






U*mG





tracr:







(SEQ ID NO: 346)







mA*mA*mC*AGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUG





AAAAAGUGGCACCGAGUCGGUGCUUUU*mU*mU*mU





dgRNA CR003085 #3:


crRNA:







(SEQ ID NO: 398)








mA*mU*mG*GUAUGGGAGGUAUACUAGUUUUAGAGCUAUGCUGUU*mU*m






U*mG





tracr:







(SEQ ID NO: 6660)







AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG





UGGCACCGAGUCGGUGCUUUUUUU.






In each of the gRNA molecules described above, a “*” denotes a phosphorothioate bond between the adjacent nucleotides, and “mN” (where N=A, G, C or U) denotes a 2′-OMe modified nucleotide. In embodiments, any of the gRNA molecules described herein, e.g., described above, is complexed with a Cas9 molecule, e.g., as described herein, to form a ribonuclear protein complex (RNP). Such RNPs are particularly useful in the methods, cells, and other aspects and embodiments of the invention, e.g., described herein.


IV. Cas Molecules
Cas9 Molecules

In preferred embodiments, the Cas molecule is a Cas9 molecule. Cas9 molecules of a variety of species can be used in the methods and compositions described herein. While the S. pyogenes Cas9 molecule are the subject of much of the disclosure herein, Cas9 molecules of, derived from, or based on the Cas9 proteins of other species listed herein can be used as well. In other words, other Cas9 molecules, e.g., S. thermophilus, Staphylococcus aureus and/or Neisseria meningitidis Cas9 molecules, may be used in the systems, methods and compositions described herein. Additional Cas9 species include: Acidovorax avenae, Actinobacillus pleuropneumoniae, Actinobacillus succinogenes, Actinobacillus suis, Actinomyces sp., cycliphilus denitrificans, Aminomonas paucivorans, Bacillus cereus, Bacillus smithii, Bacillus thuringiensis, Bacteroides sp., Blastopirellula marina, Bradyrhiz obium sp., Brevibacillus latemsporus, Campylobacter coli, Campylobacter jejuni, Campylobacter lad, Candidatus Puniceispirillum, Clostridiu cellulolyticum, Clostridium perfringens, Corynebacterium accolens, Corynebacterium diphtheria, Corynebacterium matruchotii, Dinoroseobacter sliibae, Eubacterium dolichum, gamma proteobacterium, Gluconacetobacler diazotrophicus, Haemophilus parainfluenzae, Haemophilus sputorum, Helicobacter canadensis, Helicobacter cinaedi, Helicobacter mustelae, Ilyobacler polytropus, Kingella kingae, Lactobacillus crispatus, Listeria ivanovii, Listeria monocytogenes, Listeriaceae bacterium, Methylocystis sp., Methylosinus trichosporium, Mobiluncus mulieris, Neisseria bacilliformis, Neisseria cinerea, Neisseria flavescens, Neisseria lactamica. Neisseria sp., Neisseria wadsworthii, Nitrosomonas sp., Parvibaculum lavamentivorans, Pasteurella multocida, Phascolarctobacterium succinatutens, Ralstonia syzygii, Rhodopseudomonas palustris, Rhodovulum sp., Simonsiella muelleri, Sphingomonas sp., Sporolactobacillus vineae, Staphylococcus lugdunensis, Streptococcus sp., Subdoligranulum sp., Tislrella mobilis, Treponema sp., or Verminephrobacter eiseniae.


A Cas9 molecule, as that term is used herein, refers to a molecule that can interact with a gRNA molecule (e.g., sequence of a domain of a tracr) and, in concert with the gRNA molecule, localize (e.g., target or home) to a site which comprises a target sequence and PAM sequence.


In an embodiment, the Cas9 molecule is capable of cleaving a target nucleic acid molecule, which may be referred to herein as an active Cas9 molecule. In an embodiment, an active Cas9 molecule, comprises one or more of the following activities: a nickase activity, i.e., the ability to cleave a single strand, e.g., the non-complementary strand or the complementary strand, of a nucleic acid molecule; a double stranded nuclease activity, i.e., the ability to cleave both strands of a double stranded nucleic acid and create a double stranded break, which in an embodiment is the presence of two nickase activities; an endonuclease activity; an exonuclease activity; and a helicase activity, i.e., the ability to unwind the helical structure of a double stranded nucleic acid.


In an embodiment, an enzymatically active Cas9 molecule cleaves both DNA strands and results in a double stranded break. In an embodiment, a Cas9 molecule cleaves only one strand, e.g., the strand to which the gRNA hybridizes to, or the strand complementary to the strand the gRNA hybridizes with. In an embodiment, an active Cas9 molecule comprises cleavage activity associated with an HNH-like domain. In an embodiment, an active Cas9 molecule comprises cleavage activity associated with an N-terminal RuvC-like domain. In an embodiment, an active Cas9 molecule comprises cleavage activity associated with an HNH-like domain and cleavage activity associated with an N-terminal RuvC-like domain. In an embodiment, an active Cas9 molecule comprises an active, or cleavage competent, HNH-like domain and an inactive, or cleavage incompetent, N-terminal RuvC-like domain. In an embodiment, an active Cas9 molecule comprises an inactive, or cleavage incompetent, HNH-like domain and an active, or cleavage competent, N-terminal RuvC-like domain.


In an embodiment, the ability of an active Cas9 molecule to interact with and cleave a target nucleic acid is PAM sequence dependent. A PAM sequence is a sequence in the target nucleic acid. In an embodiment, cleavage of the target nucleic acid occurs upstream from the PAM sequence. Active Cas9 molecules from different bacterial species can recognize different sequence motifs (e.g., PAM sequences). In an embodiment, an active Cas9 molecule of S. pyogenes recognizes the sequence motif NGG and directs cleavage of a target nucleic acid sequence 1 to 10, e.g., 3 to 5, base pairs upstream from that sequence. See, e.g., Mali el ai, SCIENCE 2013; 339(6121): 823-826. In an embodiment, an active Cas9 molecule of S. thermophilus recognizes the sequence motif NGGNG and NNAG AAW (W=A or T) and directs cleavage of a core target nucleic acid sequence 1 to 10, e.g., 3 to 5, base pairs upstream from these sequences. See, e.g., Horvath et al., SCIENCE 2010; 327(5962): 167-170, and Deveau et al, J BACTERIOL 2008; 190(4): 1390-1400. In an embodiment, an active Cas9 molecule of S mulans recognizes the sequence motif NGG or NAAR (R-A or G) and directs cleavage of a core target nucleic acid sequence 1 to 10, e.g., 3 to 5 base pairs, upstream from this sequence. See, e.g., Deveau et al., J BACTERIOL 2008; 190(4): 1390-1400.


In an embodiment, an active Cas9 molecule of S. aureus recognizes the sequence motif NNGRR (R=A or G) and directs cleavage of a target nucleic acid sequence 1 to 10, e.g., 3 to 5, base pairs upstream from that sequence. See, e.g., Ran F. et al., NATURE, vol. 520, 2015, pp. 186-191. In an embodiment, an active Cas9 molecule of N. meningitidis recognizes the sequence motif NNNNGATT and directs cleavage of a target nucleic acid sequence 1 to 10, e.g., 3 to 5, base pairs upstream from that sequence. See, e.g., Hou et al., PNAS EARLY EDITION 2013, 1-6. The ability of a Cas9 molecule to recognize a PAM sequence can be determined, e.g., using a transformation assay described in Jinek et al, SCIENCE 2012, 337:816.


Some Cas9 molecules have the ability to interact with a gRNA molecule, and in conjunction with the gRNA molecule home (e.g., targeted or localized) to a core target domain, but are incapable of cleaving the target nucleic acid, or incapable of cleaving at efficient rates. Cas9 molecules having no, or no substantial, cleavage activity may be referred to herein as an inactive Cas9 (an enzymatically inactive Cas9), a dead Cas9, or a dCas9 molecule. For example, an inactive Cas9 molecule can lack cleavage activity or have substantially less, e.g., less than 20, 10, 5, 1 or 0.1% of the cleavage activity of a reference Cas9 molecule, as measured by an assay described herein.


Exemplary naturally occurring Cas9 molecules are described in Chylinski et al, RNA Biology 2013; 10:5, 727-737. Such Cas9 molecules include Cas9 molecules of a cluster 1 bacterial family, cluster 2 bacterial family, cluster 3 bacterial family, cluster 4 bacterial family, cluster 5 bacterial family, cluster 6 bacterial family, a cluster 7 bacterial family, a cluster 8 bacterial family, a cluster 9 bacterial family, a cluster 10 bacterial family, a cluster 11 bacterial family, a cluster 12 bacterial family, a cluster 13 bacterial family, a cluster 14 bacterial family, a cluster 1 bacterial family, a cluster 16 bacterial family, a cluster 17 bacterial family, a cluster 18 bacterial family, a cluster 19 bacterial family, a cluster 20 bacterial family, a cluster 21 bacterial family, a cluster 22 bacterial family, a cluster 23 bacterial family, a cluster 24 bacterial family, a cluster 25 bacterial family, a cluster 26 bacterial family, a cluster 27 bacterial family, a cluster 28 bacterial family, a cluster 29 bacterial family, a cluster 30 bacterial family, a cluster 31 bacterial family, a cluster 32 bacterial family, a cluster 33 bacterial family, a cluster 34 bacterial family, a cluster 35 bacterial family, a cluster 36 bacterial family, a cluster 37 bacterial family, a cluster 38 bacterial family, a cluster 39 bacterial family, a cluster 40 bacterial family, a cluster 41 bacterial family, a cluster 42 bacterial family, a cluster 43 bacterial family, a cluster 44 bacterial family, a cluster 45 bacterial family, a cluster 46 bacterial family, a cluster 47 bacterial family, a cluster 48 bacterial family, a cluster 49 bacterial family, a cluster 50 bacterial family, a cluster 51 bacterial family, a cluster 52 bacterial family, a cluster 53 bacterial family, a cluster 54 bacterial family, a cluster 55 bacterial family, a cluster 56 bacterial family, a cluster 57 bacterial family, a cluster 58 bacterial family, a cluster 59 bacterial family, a cluster 60 bacterial family, a cluster 61 bacterial family, a cluster 62 bacterial family, a cluster 63 bacterial family, a cluster 64 bacterial family, a cluster 65 bacterial family, a cluster 66 bacterial family, a cluster 67 bacterial family, a cluster 68 bacterial family, a cluster 69 bacterial family, a cluster 70 bacterial family, a cluster 71 bacterial family, a cluster 72 bacterial family, a cluster 73 bacterial family, a cluster 74 bacterial family, a cluster 75 bacterial family, a cluster 76 bacterial family, a cluster 77 bacterial family, or a cluster 78 bacterial family.


Exemplary naturally occurring Cas9 molecules include a Cas9 molecule of a cluster 1 bacterial family. Examples include a Cas9 molecule of: S. pyogenes (e.g., strain SF370, MGAS 10270, MGAS 10750, MGAS2096, MGAS315, MGAS5005, MGAS6180, MGAS9429, NZ131 and SSI-1), S. thermophilus (e.g., strain LMD-9), S. pseudoporcinus (e.g., strain SPIN 20026), S. mutans (e.g., strain UA 159, NN2025), S. macacae (e.g., strain NCTC1 1558), S. gallolylicus (e.g., strain UCN34, ATCC BAA-2069), S. equines (e.g., strain ATCC 9812, MGCS 124), S. dysdalactiae (e.g., strain GGS 124), S. bovis (e.g., strain ATCC 700338), S. cmginosus (e.g.; strain F0211), S. agalactia* (e.g., strain NEM316, A909), Listeria monocytogenes (e.g., strain F6854), Listeria innocua (L. innocua, e.g., strain Clip 1 1262), EtUerococcus italicus (e.g., strain DSM 15952), or Enterococcus faecium (e.g., strain 1,231,408). Additional exemplary Cas9 molecules are a Cas9 molecule of Neisseria meningitidis (Hou et al. PNAS Early Edition 2013, 1-6) and a S. aureus Cas9 molecule.


In an embodiment, a Cas9 molecule, e.g., an active Cas9 molecule or inactive Cas9 molecule, comprises an amino acid sequence: having 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% homology with; differs at no more than 1%, 2%, 5%, 10%, 15%, 20%, 30%, or 40% of the amino acid residues when compared with; differs by at least 1, 2, 5, 10 or 20 amino acids but by no more than 100, 80, 70, 60, 50, 40 or 30 amino acids from; or is identical to; any Cas9 molecule sequence described herein or a naturally occurring Cas9 molecule sequence, e.g., a Cas9 molecule from a species listed herein or described in Chylinski et al., RNA Biology 2013, 10:5, ′I2′I-T,1 Hou et al. PNAS Early Edition 2013, 1-6.


In an embodiment, a Cas9 molecule comprises an amino acid sequence having 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% homology with; differs at no more than 1%, 2%, 5%, 10%, 15%, 20%, 30%, or 40% of the amino acid residues when compared with; differs by at least 1, 2, 5, 10 or 20 amino acids but by no more than 100, 80, 70, 60, 50, 40 or 30 amino acids from; or is identical to; S. pyogenes Cas9:










(SEQ ID NO: 6611)









Met Asp Lys Lys Tyr Ser Ile Gly Leu Asp Ile Gly Thr Asn Ser Val



1               5                   10                  15





Gly Trp Ala Val Ile Thr Asp Glu Tyr Lys Val Pro Ser Lys Lys Phe


            20                  25                  30





Lys Val Leu Gly Asn Thr Asp Arg His Ser Ile Lys Lys Asn Leu Ile


        35                  40                  45





Gly Ala Leu Leu Phe Asp Ser Gly Glu Thr Ala Glu Ala Thr Arg Leu


    50                  55                  60





Lys Arg Thr Ala Arg Arg Arg Tyr Thr Arg Arg Lys Asn Arg Ile Cys


65                  70                  75                  80





Tyr Leu Gln Glu Ile Phe Ser Asn Glu Met Ala Lys Val Asp Asp Ser


                85                  90                  95





Phe Phe His Arg Leu Glu Glu Ser Phe Leu Val Glu Glu Asp Lys Lys


            100                 105                 110





His Glu Arg His Pro Ile Phe Gly Asn Ile Val Asp Glu Val Ala Tyr


        115                 120                 125





His Glu Lys Tyr Pro Thr Ile Tyr His Leu Arg Lys Lys Leu Val Asp


    130                 135                 140





Ser Thr Asp Lys Ala Asp Leu Arg Leu Ile Tyr Leu Ala Leu Ala His


145                 150                 155                 160





Met Ile Lys Phe Arg Gly His Phe Leu Ile Glu Gly Asp Leu Asn Pro


                165                 170                 175





Asp Asn Ser Asp Val Asp Lys Leu Phe Ile Gln Leu Val Gln Thr Tyr


            180                 185                 190





Asn Gln Leu Phe Glu Glu Asn Pro Ile Asn Ala Ser Gly Val Asp Ala


        195                 200                 205





Lys Ala Ile Leu Ser Ala Arg Leu Ser Lys Ser Arg Arg Leu Glu Asn


    210                 215                 220





Leu Ile Ala Gln Leu Pro Gly Glu Lys Lys Asn Gly Leu Phe Gly Asn


225                 230                 235                 240





Leu Ile Ala Leu Ser Leu Gly Leu Thr Pro Asn Phe Lys Ser Asn Phe


                245                 250                 255





Asp Leu Ala Glu Asp Ala Lys Leu Gln Leu Ser Lys Asp Thr Tyr Asp


            260                 265                 270





Asp Asp Leu Asp Asn Leu Leu Ala Gln Ile Gly Asp Gln Tyr Ala Asp


        275                 280                 285





Leu Phe Leu Ala Ala Lys Asn Leu Ser Asp Ala Ile Leu Leu Ser Asp


    290                 295                 300





Ile Leu Arg Val Asn Thr Glu Ile Thr Lys Ala Pro Leu Ser Ala Ser


305                 310                 315                 320





Met Ile Lys Arg Tyr Asp Glu His His Gln Asp Leu Thr Leu Leu Lys


                325                 330                 335





Ala Leu Val Arg Gln Gln Leu Pro Glu Lys Tyr Lys Glu Ile Phe Phe


            340                 345                 350





Asp Gln Ser Lys Asn Gly Tyr Ala Gly Tyr Ile Asp Gly Gly Ala Ser


        355                 360                 365





Gln Glu Glu Phe Tyr Lys Phe Ile Lys Pro Ile Leu Glu Lys Met Asp


    370                 375                 380





Gly Thr Glu Glu Leu Leu Val Lys Leu Asn Arg Glu Asp Leu Leu Arg


385                 390                 395                 400





Lys Gln Arg Thr Phe Asp Asn Gly Ser Ile Pro His Gln Ile His Leu


                405                 410                 415





Gly Glu Leu His Ala Ile Leu Arg Arg Gln Glu Asp Phe Tyr Pro Phe


            420                 425                 430





Leu Lys Asp Asn Arg Glu Lys Ile Glu Lys Ile Leu Thr Phe Arg Ile


        435                 440                 445





Pro Tyr Tyr Val Gly Pro Leu Ala Arg Gly Asn Ser Arg Phe Ala Trp


    450                 455                 460





Met Thr Arg Lys Ser Glu Glu Thr Ile Thr Pro Trp Asn Phe Glu Glu


465                 470                 475                 480





Val Val Asp Lys Gly Ala Ser Ala Gln Ser Phe Ile Glu Arg Met Thr


                485                 490                 495





Asn Phe Asp Lys Asn Leu Pro Asn Glu Lys Val Leu Pro Lys His Ser


            500                 505                 510





Leu Leu Tyr Glu Tyr Phe Thr Val Tyr Asn Glu Leu Thr Lys Val Lys


        515                 520                 525





Tyr Val Thr Glu Gly Met Arg Lys Pro Ala Phe Leu Ser Gly Glu Gln


    530                 535                 540





Lys Lys Ala Ile Val Asp Leu Leu Phe Lys Thr Asn Arg Lys Val Thr


545                 550                 555                 560





Val Lys Gln Leu Lys Glu Asp Tyr Phe Lys Lys Ile Glu Cys Phe Asp


                565                 570                 575





Ser Val Glu Ile Ser Gly Val Glu Asp Arg Phe Asn Ala Ser Leu Gly


            580                 585                 590





Thr Tyr His Asp Leu Leu Lys Ile Ile Lys Asp Lys Asp Phe Leu Asp


        595                 600                 605





Asn Glu Glu Asn Glu Asp Ile Leu Glu Asp Ile Val Leu Thr Leu Thr


    610                 615                 620





Leu Phe Glu Asp Arg Glu Met Ile Glu Glu Arg Leu Lys Thr Tyr Ala


625                 630                 635                 640





His Leu Phe Asp Asp Lys Val Met Lys Gln Leu Lys Arg Arg Arg Tyr


                645                 650                 655





Thr Gly Trp Gly Arg Leu Ser Arg Lys Leu Ile Asn Gly Ile Arg Asp


            660                 665                 670





Lys Gln Ser Gly Lys Thr Ile Leu Asp Phe Leu Lys Ser Asp Gly Phe


        675                 680                 685





Ala Asn Arg Asn Phe Met Gln Leu Ile His Asp Asp Ser Leu Thr Phe


    690                 695                 700





Lys Glu Asp Ile Gln Lys Ala Gln Val Ser Gly Gln Gly Asp Ser Leu


705                 710                 715                 720





His Glu His Ile Ala Asn Leu Ala Gly Ser Pro Ala Ile Lys Lys Gly


                725                 730                 735





Ile Leu Gln Thr Val Lys Val Val Asp Glu Leu Val Lys Val Met Gly


            740                 745                 750





Arg His Lys Pro Glu Asn Ile Val Ile Glu Met Ala Arg Glu Asn Gln


        755                 760                 765





Thr Thr Gln Lys Gly Gln Lys Asn Ser Arg Glu Arg Met Lys Arg Ile


    770                 775                 780





Glu Glu Gly Ile Lys Glu Leu Gly Ser Gln Ile Leu Lys Glu His Pro


785                 790                 795                 800





Val Glu Asn Thr Gln Leu Gln Asn Glu Lys Leu Tyr Leu Tyr Tyr Leu


                805                 810                 815





Gln Asn Gly Arg Asp Met Tyr Val Asp Gln Glu Leu Asp Ile Asn Arg


            820                 825                 830





Leu Ser Asp Tyr Asp Val Asp His Ile Val Pro Gln Ser Phe Leu Lys


        835                 840                 845





Asp Asp Ser Ile Asp Asn Lys Val Leu Thr Arg Ser Asp Lys Asn Arg


    850                 855                 860





Gly Lys Ser Asp Asn Val Pro Ser Glu Glu Val Val Lys Lys Met Lys


865                 870                 875                 880





Asn Tyr Trp Arg Gln Leu Leu Asn Ala Lys Leu Ile Thr Gln Arg Lys


                885                 890                 895





Phe Asp Asn Leu Thr Lys Ala Glu Arg Gly Gly Leu Ser Glu Leu Asp


            900                 905                 910





Lys Ala Gly Phe Ile Lys Arg Gln Leu Val Glu Thr Arg Gln Ile Thr


        915                 920                 925





Lys His Val Ala Gln Ile Leu Asp Ser Arg Met Asn Thr Lys Tyr Asp


    930                 935                 940





Glu Asn Asp Lys Leu Ile Arg Glu Val Lys Val Ile Thr Leu Lys Ser


945                 950                 955                 960





Lys Leu Val Ser Asp Phe Arg Lys Asp Phe Gln Phe Tyr Lys Val Arg


                965                 970                 975





Glu Ile Asn Asn Tyr His His Ala His Asp Ala Tyr Leu Asn Ala Val


            980                 985                 990





Val Gly Thr Ala Leu Ile Lys Lys Tyr Pro Lys Leu Glu Ser Glu Phe


        995                 1000                1005





Val Tyr Gly Asp Tyr Lys Val Tyr Asp Val Arg Lys Met Ile Ala Lys


    1010                1015                1020





Ser Glu Gln Glu Ile Gly Lys Ala Thr Ala Lys Tyr Phe Phe Tyr Ser


1025                1030                1035                1040





Asn Ile Met Asn Phe Phe Lys Thr Glu Ile Thr Leu Ala Asn Gly Glu


                1045                1050                1055





Ile Arg Lys Arg Pro Leu Ile Glu Thr Asn Gly Glu Thr Gly Glu Ile


            1060                1065                1070





Val Trp Asp Lys Gly Arg Asp Phe Ala Thr Val Arg Lys Val Leu Ser


        1075                1080                1085





Met Pro Gln Val Asn Ile Val Lys Lys Thr Glu Val Gln Thr Gly Gly


    1090                1095                1100





Phe Ser Lys Glu Ser Ile Leu Pro Lys Arg Asn Ser Asp Lys Leu Ile


1105                1110                1115                1120





Ala Arg Lys Lys Asp Trp Asp Pro Lys Lys Tyr Gly Gly Phe Asp Ser


                1125                1130                1135





Pro Thr Val Ala Tyr Ser Val Leu Val Val Ala Lys Val Glu Lys Gly


            1140                1145                1150





Lys Ser Lys Lys Leu Lys Ser Val Lys Glu Leu Leu Gly Ile Thr Ile


        1155                1160                1165





Met Glu Arg Ser Ser Phe Glu Lys Asn Pro Ile Asp Phe Leu Glu Ala


    1170                1175                1180





Lys Gly Tyr Lys Glu Val Lys Lys Asp Leu Ile Ile Lys Leu Pro Lys


1185                1190                1195                1200





Tyr Ser Leu Phe Glu Leu Glu Asn Gly Arg Lys Arg Met Leu Ala Ser


                1205                1210                1215





Ala Gly Glu Leu Gln Lys Gly Asn Glu Leu Ala Leu Pro Ser Lys Tyr


            1220                1225                1230





Val Asn Phe Leu Tyr Leu Ala Ser His Tyr Glu Lys Leu Lys Gly Ser


        1235                1240                1245





Pro Glu Asp Asn Glu Gln Lys Gln Leu Phe Val Glu Gln His Lys His


    1250                1255                1260





Tyr Leu Asp Glu Ile Ile Glu Gln Ile Ser Glu Phe Ser Lys Arg Val


1265                1270                1275                1280





Ile Leu Ala Asp Ala Asn Leu Asp Lys Val Leu Ser Ala Tyr Asn Lys


                1285                1290                1295





His Arg Asp Lys Pro Ile Arg Glu Gln Ala Glu Asn Ile Ile His Leu


            1300                1305                1310





Phe Thr Leu Thr Asn Leu Gly Ala Pro Ala Ala Phe Lys Tyr Phe Asp


        1315                1320                1325





Thr Thr Ile Asp Arg Lys Arg Tyr Thr Ser Thr Lys Glu Val Leu Asp


    1330                1335                1340





Ala Thr Leu Ile His Gln Ser Ile Thr Gly Leu Tyr Glu Thr Arg Ile


1345                1350                1355                1360





Asp Leu Ser Gln Leu Gly Gly Asp


                1365






In embodiments, the Cas9 molecule is a S. pyogenes Cas9 variant of SEQ ID NO: 6611 that includes one or more mutations to positively charged amino acids (e.g., lysine, arginine or histidine) that introduce an uncharged or nonpolar amino acid, e.g., alanine, at said position. In embodiments, the mutation is to one or more positively charged amino acids in the nt-groove of Cas9. In embodiments, the Cas9 molecule is a S. pyogenes Cas9 variant of SEQ ID NO: 6611 that includes a mutation at position 855 of SEQ ID NO: 6611, for example a mutation to an uncharged amino acid, e.g., alanine, at position 855 of SEQ ID NO: 6611. In embodiments, the Cas9 molecule has a mutation only at position 855 of SEQ ID NO: 6611, relative to SEQ ID NO: 6611, e.g., to an uncharged amino acid, e.g., alanine. In embodiments, the Cas9 molecule is a S. pyogenes Cas9 variant of SEQ ID NO: 6611 that includes a mutation at position 810, a mutation at position 1003, and/or a mutation at position 1060 of SEQ ID NO: 6611, for example a mutation to alanine at position 810, position 1003, and/or position 1060 of SEQ ID NO: 6611. In embodiments, the Cas9 molecule has a mutation only at position 810, position 1003, and position 1060 of SEQ ID NO: 6611, relative to SEQ ID NO: 6611, e.g., where each mutation is to an uncharged amino acid, for example, alanine. In embodiments, the Cas9 molecule is a S. pyogenes Cas9 variant of SEQ ID NO: 6611 that includes a mutation at position 848, a mutation at position 1003, and/or a mutation at position 1060 of SEQ ID NO: 6611, for example a mutation to alanine at position 848, position 1003, and/or position 1060 of SEQ ID NO: 6611. In embodiments, the Cas9 molecule has a mutation only at position 848, position 1003, and position 1060 of SEQ ID NO: 6611, relative to SEQ ID NO: 6611, e.g., where each mutation is to an uncharged amino acid, for example, alanine. In embodiments, the Cas9 molecule is a Cas9 molecule as described in Slaymaker et al., Science Express, available online Dec. 1, 2015 at Science DOI: 10.1126/science.aad5227.


In embodiments, the Cas9 molecule is a S. pyogenes Cas9 variant of SEQ ID NO: 6611 that includes one or more mutations. In embodiments, the Cas9 variant comprises a mutation at position 80 of SEQ ID NO: 6611, e.g., includes a leucine at position 80 of SEQ ID NO: 6611 (i.e., comprises, e.g., consists of, SEQ ID NO: 6611 with a C80L mutation). In embodiments, the Cas9 variant comprises a mutation at position 574 of SEQ ID NO: 6611, e.g., includes a glutamic acid at position 574 of SEQ ID NO: 6611 (i.e., comprises, e.g., consists of, SEQ ID NO: 6611 with a C574E mutation). In embodiments, the Cas9 variant comprises a mutation at position 80 and a mutation at position 574 of SEQ ID NO: 6611, e.g., includes a leucine at position 80 of SEQ ID NO: 6611, and a glutamic acid at position 574 of SEQ ID NO: 6611 (i.e., comprises, e.g., consists of, SEQ ID NO: 6611 with a C80L mutation and a C574E mutation). Without being bound by theory, it is believed that such mutations improve the solution properties of the Cas9 molecule.


In embodiments, the Cas9 molecule is a S. pyogenes Cas9 variant of SEQ ID NO: 6611 that includes one or more mutations. In embodiments, the Cas9 variant comprises a mutation at position 147 of SEQ ID NO: 6611, e.g., includes a tyrosine at position 147 of SEQ ID NO: 6611 (i.e., comprises, e.g., consists of, SEQ ID NO: 6611 with a D147Y mutation). In embodiments, the Cas9 variant comprises a mutation at position 411 of SEQ ID NO: 6611, e.g., includes a threonine at position 411 of SEQ ID NO: 6611 (i.e., comprises, e.g., consists of, SEQ ID NO: 6611 with a P411T mutation). In embodiments, the Cas9 variant comprises a mutation at position 147 and a mutation at position 411 of SEQ ID NO: 6611, e.g., includes a tyrosine at position 147 of SEQ ID NO: 6611, and a threonine at position 411 of SEQ ID NO: 6611 (i.e., comprises, e.g., consists of, SEQ ID NO: 6611 with a D147Y mutation and a P411T mutation). Without being bound by theory, it is believed that such mutations improve the targeting efficiency of the Cas9 molecule, e.g., in yeast.


In embodiments, the Cas9 molecule is a S. pyogenes Cas9 variant of SEQ ID NO: 6611 that includes one or more mutations. In embodiments, the Cas9 variant comprises a mutation at position 1135 of SEQ ID NO: 6611, e.g., includes a glutamic acid at position 1135 of SEQ ID NO: 6611 (i.e., comprises, e.g., consists of, SEQ ID NO: 6611 with a D1135E mutation). Without being bound by theory, it is believed that such mutations improve the selectivity of the Cas9 molecule for the NGG PAM sequence versus the NAG PAM sequence.


In embodiments, the Cas9 molecule is a S. pyogenes Cas9 variant of SEQ ID NO: 6611 that includes one or more mutations that introduce an uncharged or nonpolar amino acid, e.g., alanine, at certain positions. In embodiments, the Cas9 molecule is a S. pyogenes Cas9 variant of SEQ ID NO: 6611 that includes a mutation at position 497, a mutation at position 661, a mutation at position 695 and/or a mutation at position 926 of SEQ ID NO: 6611, for example a mutation to alanine at position 497, position 661, position 695 and/or position 926 of SEQ ID NO: 6611. In embodiments, the Cas9 molecule has a mutation only at position 497, position 661, position 695, and position 926 of SEQ ID NO: 6611, relative to SEQ ID NO: 6611, e.g., where each mutation is to an uncharged amino acid, for example, alanine Without being bound by theory, it is believed that such mutations reduce the cutting by the Cas9 molecule at off-target sites


It will be understood that the mutations described herein to the Cas9 molecule may be combined, and may be combined with any of the fusions or other modifications described herein, and the Cas9 molecule tested in the assays described herein.


Various types of Cas molecules can be used to practice the inventions disclosed herein. In some embodiments, Cas molecules of Type II Cas systems are used. In other embodiments, Cas molecules of other Cas systems are used. For example, Type I or Type III Cas molecules may be used. Exemplary Cas molecules (and Cas systems) are described, e.g., in Haft et ai, PLoS COMPUTATIONAL BIOLOGY 2005, 1(6): e60 and Makarova et al, NATURE REVIEW MICROBIOLOGY 2011, 9:467-477, the contents of both references are incorporated herein by reference in their entirety.


In an embodiment, the Cas9 molecule comprises one or more of the following activities: a nickase activity; a double stranded cleavage activity (e.g., an endonuclease and/or exonuclease activity); a helicase activity; or the ability, together with a gRNA molecule, to localize to a target nucleic acid.


Altered Cas9 Molecules

Naturally occurring Cas9 molecules possess a number of properties, including: nickase activity, nuclease activity (e.g., endonuclease and/or exonuclease activity); helicase activity; the ability to associate functionally with a gRNA molecule; and the ability to target (or localize to) a site on a nucleic acid (e.g., PAM recognition and specificity). In an embodiment, a Cas9 molecules can include all or a subset of these properties. In typical embodiments, Cas9 molecules have the ability to interact with a gRNA molecule and, in concert with the gRNA molecule, localize to a site in a nucleic acid. Other activities, e.g., PAM specificity, cleavage activity, or helicase activity can vary more widely in Cas9 molecules.


Cas9 molecules with desired properties can be made in a number of ways, e.g., by alteration of a parental, e.g., naturally occurring Cas9 molecules to provide an altered Cas9 molecule having a desired property. For example, one or more mutations or differences relative to a parental Cas9 molecule can be introduced. Such mutations and differences comprise: substitutions (e.g., conservative substitutions or substitutions of non-essential amino acids); insertions; or deletions. In an embodiment, a Cas9 molecule can comprises one or more mutations or differences, e.g., at least 1, 2, 3, 4, 5, 10, 15, 20, 30, 40 or 50 mutations but less than 200, 100, or 80 mutations relative to a reference Cas9 molecule.


In an embodiment, a mutation or mutations do not have a substantial effect on a Cas9 activity, e.g. a Cas9 activity described herein. In an embodiment, a mutation or mutations have a substantial effect on a Cas9 activity, e.g. a Cas9 activity described herein. In an embodiment, exemplary activities comprise one or more of PAM specificity, cleavage activity, and helicase activity. A mutation(s) can be present, e.g., in: one or more RuvC-like domain, e.g., an N-terminal RuvC-like domain; an HNH-like domain; a region outside the RuvC-like domains and the HNH-like domain. In some embodiments, a mutation(s) is present in an N-terminal RuvC-like domain. In some embodiments, a mutation(s) is present in an HNH-like domain. In some embodiments, mutations are present in both an N-terminal RuvC-like domain and an HNH-like domain.


Whether or not a particular sequence, e.g., a substitution, may affect one or more activity, such as targeting activity, cleavage activity, etc, can be evaluated or predicted, e.g., by evaluating whether the mutation is conservative or by the method described in Section III. In an embodiment, a “non-essential” amino acid residue, as used in the context of a Cas9 molecule, is a residue that can be altered from the wild-type sequence of a Cas9 molecule, e.g., a naturally occurring Cas9 molecule, e.g., an active Cas9 molecule, without abolishing or more preferably, without substantially altering a Cas9 activity (e.g., cleavage activity), whereas changing an “essential” amino acid residue results in a substantial loss of activity (e.g., cleavage activity).


Cas9 Molecules with Altered PAM Recognition or No PAM Recognition


Naturally occurring Cas9 molecules can recognize specific PAM sequences, for example the PAM recognition sequences described above for S. pyogenes, S. thermophilus, S. mutans, S. aureus and N. meningitidis.


In an embodiment, a Cas9 molecule has the same PAM specificities as a naturally occurring Cas9 molecule. In other embodiments, a Cas9 molecule has a PAM specificity not associated with a naturally occurring Cas9 molecule, or a PAM specificity not associated with the naturally occurring Cas9 molecule to which it has the closest sequence homology. For example, a naturally occurring Cas9 molecule can be altered, e.g., to alter PAM recognition, e.g., to alter the PAM sequence that the Cas9 molecule recognizes to decrease off target sites and/or improve specificity; or eliminate a PAM recognition requirement. In an embodiment, a Cas9 molecule can be altered, e.g., to increase length of PAM recognition sequence and/or improve Cas9 specificity to high level of identity to decrease off target sites and increase specificity. In an embodiment, the length of the PAM recognition sequence is at least 4, 5, 6, 7, 8, 9, 10 or 15 amino acids in length. Cas9 molecules that recognize different PAM sequences and/or have reduced off-target activity can be generated using directed evolution. Exemplary methods and systems that can be used for directed evolution of Cas9 molecules are described, e.g., in Esvelt el al, Nature 2011, 472(7344): 499-503. Candidate Cas9 molecules can be evaluated, e.g., by methods described herein.


Non-Cleaving and Modified-Cleavage Cas9 Molecules

In an embodiment, a Cas9 molecule comprises a cleavage property that differs from naturally occurring Cas9 molecules, e.g., that differs from the naturally occurring Cas9 molecule having the closest homology. For example, a Cas9 molecule can differ from naturally occurring Cas9 molecules, e.g., a Cas9 molecule of S. pyogenes, as follows: its ability to modulate, e.g., decreased or increased, cleavage of a double stranded break (endonuclease and/or exonuclease activity), e.g., as compared to a naturally occurring Cas9 molecule (e.g., a Cas9 molecule of S. pyogenes); its ability to modulate, e.g., decreased or increased, cleavage of a single strand of a nucleic acid, e.g., a non-complimentary strand of a nucleic acid molecule or a complementary strand of a nucleic acid molecule (nickase activity), e.g., as compared to a naturally occurring Cas9 molecule (e.g., a Cas9 molecule of S. pyogenes); or the ability to cleave a nucleic acid molecule, e.g., a double stranded or single stranded nucleic acid molecule, can be eliminated.


Modified Cleavage Active Cas9 Molecules

In an embodiment, an active Cas9 molecule comprises one or more of the following activities: cleavage activity associated with an N-terminal RuvC-like domain; cleavage activity associated with an HNH-like domain; cleavage activity associated with an HNH domain and cleavage activity associated with an N-terminal RuvC-like domain.


In an embodiment, the Cas9 molecule is a Cas9 nickase, e.g., cleaves only a single strand of DNA. In an embodiment, the Cas9 nickase includes a mutation at position 10 and/or a mutation at position 840 of SEQ ID NO: 6611, e.g., comprises a D10A and/or H840A mutation to SEQ ID NO: 6611.


Non-Cleaving Inactive Cas9 Molecules

In an embodiment, the altered Cas9 molecule is an inactive Cas9 molecule which does not cleave a nucleic acid molecule (either double stranded or single stranded nucleic acid molecules) or cleaves a nucleic acid molecule with significantly less efficiency, e.g., less than 20, 10, 5, 1 or 0.1% of the cleavage activity of a reference Cas9 molecule, e.g., as measured by an assay described herein. The reference Cas9 molecule can by a naturally occurring unmodified Cas9 molecule, e.g., a naturally occurring Cas9 molecule such as a Cas9 molecule of S. pyogenes, S. thermophilus, S. aureus or N. meningitidis. In an embodiment, the reference Cas9 molecule is the naturally occurring Cas9 molecule having the closest sequence identity or homology. In an embodiment, the inactive Cas9 molecule lacks substantial cleavage activity associated with an N-terminal RuvC-like domain and cleavage activity associated with an HNH-like domain.


In an embodiment, the Cas9 molecule is dCas9. Tsai et al. (2014), Nat. Biotech. 32:569-577.


A catalytically inactive Cas9 molecule may be fused with a transcription repressor. An inactive Cas9 fusion protein complexes with a gRNA and localizes to a DNA sequence specified by gRNA's targeting domain, but, unlike an active Cas9, it will not cleave the target DNA. Fusion of an effector domain, such as a transcriptional repression domain, to an inactive Cas9 enables recruitment of the effector to any DNA site specified by the gRNA. Site specific targeting of a Cas9 fusion protein to a promoter region of a gene can block or affect polymerase binding to the promoter region, for example, a Cas9 fusion with a transcription factor (e.g., a transcription activator) and/or a transcriptional enhancer binding to the nucleic acid to increase or inhibit transcription activation. Alternatively, site specific targeting of a a Cas9-fusion to a transcription repressor to a promoter region of a gene can be used to decrease transcription activation.


Transcription repressors or transcription repressor domains that may be fused to an inactive Cas9 molecule can include ruppel associated box (KRAB or SKD), the Mad mSIN3 interaction domain (SID) or the ERF repressor domain (ERD).


In another embodiment, an inactive Cas9 molecule may be fused with a protein that modifies chromatin. For example, an inactive Cas9 molecule may be fused to heterochromatin protein 1 (HP1), a histone lysine methyltransferase (e.g., SUV39H 1, SUV39H2, G9A, ESET/SETDB 1, Pr-SET7/8, SUV4-20H 1,RIZ1), a histone lysine demethylates (e.g., LSD1/BHC1 10, SpLsdl/Sw, 1/Safl 10, Su(var)3-3, JMJD2A/JHDM3A, JMJD2B, JMJD2C/GASC1, JMJD2D, Rph1, JARID 1 A/RBP2, JARI DIB/PLU-I, JAR1D 1C/SMCX, JARID1 D/SMCY, Lid, Jhn2, Jmj2), a histone lysine deacetylases (e.g., HDAC1, HDAC2, HDAC3, HDAC8, Rpd3, Hos 1, Cir6, HDAC4, HDAC5, HDAC7, HDAC9, Hda1, Cir3, SIRT 1, SIRT2, Sir2, Hst 1, Hst2, Hst3, Hst4, HDAC 11) and a DNA methylases (DNMT1,DNMT2a/DMNT3b, MET1). An inactive Cas9-chomatin modifying molecule fusion protein can be used to alter chromatin status to reduce expression a target gene.


The heterologous sequence (e.g., the transcription repressor domain) may be fused to the N- or C-terminus of the inactive Cas9 protein. In an alternative embodiment, the heterologous sequence (e.g., the transcription repressor domain) may be fused to an internal portion (i.e., a portion other than the N-terminus or C-terminus) of the inactive Cas9 protein.


The ability of a Cas9 molecule/gRNA molecule complex to bind to and cleave a target nucleic acid can be evaluated, e.g., by the methods described herein in Section III. The activity of a Cas9 molecule, e.g., either an active Cas9 or a inactive Cas9, alone or in a complex with a gRNA molecule may also be evaluated by methods well-known in the art, including, gene expression assays and chromatin-based assays, e.g., chromatin immunoprecipitation (ChiP) and chromatin in vivo assay (CiA).


Other Cas9 Molecule Fusions

In embodiments, the Cas9 molecule, e.g, a Cas9 of S. pyogenes, may additionally comprise one or more amino acid sequences that confer additional activity.


In some aspects, the Cas9 molecule may comprise one or more nuclear localization sequences (NLSs), such as at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more NLSs. In some embodiments, the Cas9 molecule comprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more NLSs at or near the amino-terminus, at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more NLSs at or near the carboxy-terminus, or a combination of these (e.g. one or more NLS at the amino-terminus and one or more NLS at the carboxy terminus). When more than one NLS is present, each may be selected independently of the others, such that a single NLS may be present in more than one copy and/or in combination with one or more other NLSs present in one or more copies. In some embodiments, an NLS is considered near the N- or C-terminus when the nearest amino acid of the NLS is within about 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 40, 50, or more amino acids along the polypeptide chain from the N- or C-terminus. Typically, an NLS consists of one or more short sequences of positively charged lysines or arginines exposed on the protein surface, but other types of NLS are known. Non-limiting examples of NLSs include an NLS sequence comprising or derived from: the NLS of the SV40 virus large T-antigen, having the amino acid sequence PKKKRKV (SEQ ID NO: 6612); the NLS from nucleoplasmin (e.g. the nucleoplasmin bipartite NLS with the sequence KRPAATKKAGQAKKKK (SEQ ID NO: 6613); the c-myc NLS having the amino acid sequence PAAKRVKLD (SEQ ID NO: 6614) or RQRRNELKRSP (SEQ ID NO: 6615); the hRNPA1 M9 NLS having the sequence NQSSNFGPMKGGNFGGRSSGPYGGGGQYFAKPRNQGGY (SEQ ID NO: 6616); the sequence RMRIZFKNKGKDTAELRRRRVEVSVELRKAKKDEQILKRRNV (SEQ ID NO: 6617) of the IBB domain from importin-alpha; the sequences VSRKRPRP (SEQ ID NO: 6618) and PPKKARED (SEQ ID NO: 6619) of the myoma T protein; the sequence PQPKKKPL (SEQ ID NO: 6620) of human p53; the sequence SALIKKKKKMAP (SEQ ID NO: 6621) of mouse c-ab1 IV; the sequences DRLRR (SEQ ID NO: 6622) and PKQKKRK (SEQ ID NO: 6623) of the influenza virus NS1; the sequence RKLKKKIKKL (SEQ ID NO: 6624) of the Hepatitis virus delta antigen; the sequence REKKKFLKRR (SEQ ID NO: 6625) of the mouse Mxl protein; the sequence KRKGDEVDGVDEVAKKKSKK (SEQ ID NO: 6626) of the human poly(ADP-ribose) polymerase; and the sequence RKCLQAGMNLEARKTKK (SEQ ID NO: 6627) of the steroid hormone receptors (human) glucocorticoid. Other suitable NLS sequences are known in the art (e.g., Sorokin, Biochemistry (Moscow) (2007) 72:13, 1439-1457; Lange J Biol Chem. (2007) 282:8, 5101-5).


In an embodiment, the Cas9 molecule, e.g., S. pyogenes Cas9 molecule, comprises a NLS sequence of SV40, e.g., disposed N terminal to the Cas9 molecule. In an embodiment, the Cas9 molecule, e.g., S. pyogenes Cas9 molecule, comprises a NLS sequence of SV40 disposed N-terminal to the Cas9 molecule and a NLS sequence of SV40 disposed C terminal to the Cas9 molecule. In an embodiment, the Cas9 molecule, e.g., S. pyogenes Cas9 molecule, comprises a NLS sequence of SV40 disposed N-terminal to the Cas9 molecule and a NLS sequence of nucleoplasmin disposed C-terminal to the Cas9 molecule. In any of the aforementioned embodiments, the molecule may additionally comprise a tag, e.g., a His tag, e.g., a His(6) tag or His(8) tag, e.g., at the N terminus or the C terminus.


In some aspects, the Cas9 molecule may comprise one or more amino acid sequences that allow the Cas9 molecule to be specifically recognized, for example a tag. In one embodiment, the tag is a Histidine tag, e.g., a histidine tag comprising at least 3, 4, 5, 6, 7, 8, 9, 10 or more histidine amino acids. In embodiments, the histidine tag is a His6 tag (six histidines). In other embodiments, the histidine tag is a His8 tag (eight histidines). In embodiments, the histidine tag may be separated from one or more other portions of the Cas9 molecule by a linker. In embodiments, the linker is GGS. An example of such a fusion is the Cas9 molecule iProt106520.


In some aspects, the Cas9 molecule may comprise one or more amino acid sequences that are recognized by a protease (e.g., comprise a protease cleavage site). In embodiments, the cleavage site is the tobacco etch virus (TEV) cleavage site, e.g., comprises the sequence ENLYFQG (SEQ ID NO: 7810). In some aspects the protease cleavage site, e.g., the TEV cleavage site is disposed between a tag, e.g., a His tag, e.g., a His6 or His8 tag, and the remainder of the Cas9 molecule. Without being bound by theory it is believed that such introduction will allow for the use of the tag for, e.g., purification of the Cas9 molecule, and then subsequent cleavage so the tag does not interfere with the Cas9 molecule function.


In embodiments, the Cas9 molecule (e.g., a Cas9 molecule as described herein) comprises an N-terminal NLS, and a C-terminal NLS (e.g., comprises, from N- to C-terminal NLS-Cas9-NLS), e.g., wherein each NLS is an SV40 NLS (PKKKRKV (SEQ ID NO: 6612)). In embodiments, the Cas9 molecule (e.g., a Cas9 molecule as described herein) comprises an N-terminal NLS, a C-terminal NLS, and a C-terminal His6 tag (e.g., comprises, from N- to C-terminal NLS-Cas9-NLS-His tag), e.g., wherein each NLS is an SV40 NLS (PKKKRKV (SEQ ID NO: 6612)). In embodiments, the Cas9 molecule (e.g., a Cas9 molecule as described herein) comprises an N-terminal His tag (e.g., His6 tag), an N-terminal NLS, and a C-terminal NLS (e.g., comprises, from N- to C-terminal His tag-NLS-Cas9-NLS), e.g., wherein each NLS is an SV40 NLS (PKKKRKV (SEQ ID NO: 6612)). In embodiments, the Cas9 molecule (e.g., a Cas9 molecule as described herein) comprises an N-terminal NLS and a C-terminal His tag (e.g., His6 tag) (e.g., comprises from N- to C-terminal His tag-Cas9-NLS), e.g., wherein the NLS is an SV40 NLS (PKKKRKV (SEQ ID NO: 6612)). In embodiments, the Cas9 molecule (e.g., a Cas9 molecule as described herein) comprises an N-terminal NLS and a C-terminal His tag (e.g., His6 tag) (e.g., comprises from N- to C-terminal NLS-Cas9-His tag), e.g., wherein the NLS is an SV40 NLS (PKKKRKV (SEQ ID NO: 6612)). In embodiments, the Cas9 molecule (e.g., a Cas9 molecule as described herein) comprises an N-terminal His tag (e.g., His8 tag), an N-terminal cleavage domain (e.g., a tobacco etch virus (TEV) cleavage domain (e.g., comprises the sequence ENLYFQG (SEQ ID NO: 7810))), an N-terminal NLS (e.g., an SV40 NLS; SEQ ID NO: 6612), and a C-terminal NLS (e.g., an SV40 NLS; SEQ ID NO: 6612) (e.g., comprises from N- to C-terminal His tag-TEV-NLS-Cas9-NLS). In any of the aforementioned embodiments the Cas9 has the sequence of SEQ ID NO: 6611. Alternatively, in any of the aforementioned embodiments, the Cas9 has a sequence of a Cas9 variant of SEQ ID NO: 6611, e.g., as described herein. In any of the aforementioned embodiments, the Cas9 molecule comprises a linker between the His tag and another portion of the molecule, e.g., a GGS linker. Amino acid sequences of exemplary Cas9 molecules described above are provided below. “iProt” identifiers match those in FIG. 60.










iProt105026 (also referred to as iProt106154, iProt106331,



iProt106545, and PID426303, depending on the preparation of the


protein) (SEQ ID NO: 7821):


MAPKKKRKVD KKYSIGLDIG TNSVGWAVIT DEYKVPSKKF KVLGNTDRHS IKKNLIGALL





FDSGETAEAT RLKRTARRRY TRRKNRICYL QEIFSNEMAK VDDSFFHRLE ESFLVEEDKK





HERHPIFGNI VDEVAYHEKY PTIYHLRKKL VDSTDKADLR LIYLALAHMI KFRGHFLIEG





DLNPDNSDVD KLFIQLVQTY NQLFEENPIN ASGVDAKAIL SARLSKSRRL ENLIAQLPGE





KKNGLFGNLI ALSLGLTPNF KSNFDLAEDA KLQLSKDTYD DDLDNLLAQI GDQYADLFLA





AKNLSDAILL SDILRVNTEI TKAPLSASMI KRYDEHHQDL TLLKALVRQQ LPEKYKEIFF





DQSKNGYAGY IDGGASQEEF YKFIKPILEK MDGTEELLVK LNREDLLRKQ RTFDNGSIPH





QIHLGELHAI LRRQEDFYPF LKDNREKIEK ILTFRIPYYV GPLARGNSRF AWMTRKSEET





ITPWNFEEVV DKGASAQSFI ERMTNFDKNL PNEKVLPKHS LLYEYFTVYN ELTKVKYVTE





GMRKPAFLSG EQKKAIVDLL FKTNRKVTVK QLKEDYFKKI ECFDSVEISG VEDRFNASLG





TYHDLLKIIK DKDFLDNEEN EDILEDIVLT LTLFEDREMI EERLKTYAHL FDDKVMKQLK





RRRYTGWGRL SRKLINGIRD KQSGKTILDF LKSDGFANRN FMQLIHDDSL TFKEDIQKAQ





VSGQGDSLHE HIANLAGSPA IKKGILQTVK VVDELVKVMG RHKPENIVIE MARENQTTQK





GQKNSRERMK RIEEGIKELG SQILKEHPVE NTQLQNEKLY LYYLQNGRDM YVDQELDINR





LSDYDVDHIV PQSFLKDDSI DNKVLTRSDK NRGKSDNVPS EEVVKKMKNY





WRQLLNAKLI TQRKFDNLTK AERGGLSELD KAGFIKRQLV ETRQITKHVA QILDSRMNTK





YDENDKLIRE VKVITLKSKL VSDFRKDFQF YKVREINNYH HAHDAYLNAV VGTALIKKYP





KLESEFVYGD YKVYDVRKMI AKSEQEIGKA TAKYFFYSNI MNFFKTEITL ANGEIRKRPL





IETNGETGEI VWDKGRDFAT VRKVLSMPQV NIVKKTEVQT GGFSKESILP KRNSDKLIAR





KKDWDPKKYG GFDSPTVAYS VLVVAKVEKG KSKKLKSVKE LLGITIMERS SFEKNPIDFL





EAKGYKEVKK DLIIKLPKYS LFELENGRKR MLASAGELQK GNELALPSKY VNFLYLASHY





EKLKGSPEDN EQKQLFVEQH KHYLDEIIEQ ISEFSKRVIL ADANLDKVLS AYNKHRDKPI





REQAENIIHL FTLTNLGAPA AFKYFDTTID RKRYTSTKEV LDATLIHQSI TGLYETRIDL





SQLGGDSRAD PKKKRKVHHH HHH





iProt106518 (SEQ ID NO: 7822):


MAPKKKRKVD KKYSIGLDIG TNSVGWAVIT DEYKVPSKKF KVLGNTDRHS IKKNLIGALL





FDSGETAEAT RLKRTARRRY TRRKNRILYL QEIFSNEMAK VDDSFFHRLE ESFLVEEDKK





HERHPIFGNI VDEVAYHEKY PTIYHLRKKL VDSTDKADLR LIYLALAHMI KFRGHFLIEG





DLNPDNSDVD KLFIQLVQTY NQLFEENPIN ASGVDAKAIL SARLSKSRRL ENLIAQLPGE





KKNGLFGNLI ALSLGLTPNF KSNFDLAEDA KLQLSKDTYD DDLDNLLAQI GDQYADLFLA





AKNLSDAILL SDILRVNTEI TKAPLSASMI KRYDEHHQDL TLLKALVRQQ LPEKYKEIFF





DQSKNGYAGY IDGGASQEEF YKFIKPILEK MDGTEELLVK LNREDLLRKQ RTFDNGSIPH





QIHLGELHAI LRRQEDFYPF LKDNREKIEK ILTFRIPYYV GPLARGNSRF AWMTRKSEET





ITPWNFEEVV DKGASAQSFI ERMTNFDKNL PNEKVLPKHS LLYEYFTVYN ELTKVKYVTE





GMRKPAFLSG EQKKAIVDLL FKTNRKVTVK QLKEDYFKKI EEFDSVEISG VEDRFNASLG





TYHDLLKIIK DKDFLDNEEN EDILEDIVLT LTLFEDREMI EERLKTYAHL FDDKVMKQLK





RRRYTGWGRL SRKLINGIRD KQSGKTILDF LKSDGFANRN FMQLIHDDSL TFKEDIQKAQ





VSGQGDSLHE HIANLAGSPA IKKGILQTVK VVDELVKVMG RHKPENIVIE MARENQTTQK





GQKNSRERMK RIEEGIKELG SQILKEHPVE NTQLQNEKLY LYYLQNGRDM YVDQELDINR





LSDYDVDHIV PQSFLKDDSI DNKVLTRSDK NRGKSDNVPS EEVVKKMKNY





WRQLLNAKLI TQRKFDNLTK AERGGLSELD KAGFIKRQLV ETRQITKHVA QILDSRMNTK





YDENDKLIRE VKVITLKSKL VSDFRKDFQF YKVREINNYH HAHDAYLNAV VGTALIKKYP





KLESEFVYGD YKVYDVRKMI AKSEQEIGKA TAKYFFYSNI MNFFKTEITL ANGEIRKRPL





IETNGETGEI VWDKGRDFAT VRKVLSMPQV NIVKKTEVQT GGFSKESILP KRNSDKLIAR





KKDWDPKKYG GFDSPTVAYS VLVVAKVEKG KSKKLKSVKE LLGITIMERS SFEKNPIDFL





EAKGYKEVKK DLIIKLPKYS LFELENGRKR MLASAGELQK GNELALPSKY VNFLYLASHY





EKLKGSPEDN EQKQLFVEQH KHYLDEIIEQ ISEFSKRVIL ADANLDKVLS AYNKHRDKPI





REQAENIIHL FTLTNLGAPA AFKYFDTTID RKRYTSTKEV LDATLIHQSI TGLYETRIDL





SQLGGDSRAD PKKKRKVHHH HHH





iProt106519 (SEQ ID NO: 7823):


MGSSHHHHHH HHENLYFQGS MDKKYSIGLD IGTNSVGWAV ITDEYKVPSK





KFKVLGNTDR HSIKKNLIGA LLFDSGETAE ATRLKRTARR RYTRRKNRIC YLQEIFSNEM





AKVDDSFFHR LEESFLVEED KKHERHPIFG NIVDEVAYHE KYPTIYHLRK KLVDSTDKAD





LRLIYLALAH MIKFRGHFLI EGDLNPDNSD VDKLFIQLVQ TYNQLFEENP INASGVDAKA





ILSARLSKSR RLENLIAQLP GEKKNGLFGN LIALSLGLTP NFKSNFDLAE DAKLQLSKDT





YDDDLDNLLA QIGDQYADLF LAAKNLSDAI LLSDILRVNT EITKAPLSAS MIKRYDEHHQ





DLTLLKALVR QQLPEKYKEI FFDQSKNGYA GYIDGGASQE EFYKFIKPIL EKMDGTEELL





VKLNREDLLR KQRTFDNGSI PHQIHLGELH AILRRQEDFY PFLKDNREKI EKILTFRIPY





YVGPLARGNS RFAWMTRKSE ETITPWNFEE VVDKGASAQS FIERMTNFDK NLPNEKVLPK





HSLLYEYFTV YNELTKVKYV TEGMRKPAFL SGEQKKAIVD LLFKTNRKVT





VKQLKEDYFK KIECFDSVEI SGVEDRFNAS LGTYHDLLKI IKDKDFLDNE ENEDILEDIV





LTLTLFEDRE MIEERLKTYA HLFDDKVMKQ LKRRRYTGWG RLSRKLINGI RDKQSGKTIL





DFLKSDGFAN RNFMQLIHDD SLTFKEDIQK AQVSGQGDSL HEHIANLAGS PAIKKGILQT





VKVVDELVKV MGRHKPENIV IEMARENQTT QKGQKNSRER MKRIEEGIKE LGSQILKEHP





VENTQLQNEK LYLYYLQNGR DMYVDQELDI NRLSDYDVDH IVPQSFLKDD SIDNKVLTRS





DKNRGKSDNV PSEEVVKKMK NYWRQLLNAK LITQRKFDNL TKAERGGLSE





LDKAGFIKRQ LVETRQITKH VAQILDSRMN TKYDENDKLI REVKVITLKS KLVSDFRKDF





QFYKVREINN YHHAHDAYLN AVVGTALIKK YPKLESEFVY GDYKVYDVRK





MIAKSEQEIG KATAKYFFYS NIMNFFKTEI TLANGEIRKR PLIETNGETG EIVWDKGRDF





ATVRKVLSMP QVNIVKKTEV QTGGFSKESI LPKRNSDKLI ARKKDWDPKK YGGFDSPTVA





YSVLVVAKVE KGKSKKLKSV KELLGITIME RSSFEKNPID FLEAKGYKEV KKDLIIKLPK





YSLFELENGR KRMLASAGEL QKGNELALPS KYVNFLYLAS HYEKLKGSPE DNEQKQLFVE





QHKHYLDEII EQISEFSKRV ILADANLDKV LSAYNKHRDK PIREQAENII HLFTLTNLGA





PAAFKYFDTT IDRKRYTSTK EVLDATLIHQ SITGLYETRI DLSQLGGDGG GSPKKKRKV





iProt106520 (SEQ ID NO: 7824):


MAHHHHHHGG SPKKKRKVDK KYSIGLDIGT NSVGWAVITD EYKVPSKKFK





VLGNTDRHSI KKNLIGALLF DSGETAEATR LKRTARRRYT RRKNRICYLQ EIFSNEMAKV





DDSFFHRLEE SFLVEEDKKH ERHPIFGNIV DEVAYHEKYP TIYHLRKKLV DSTDKADLRL





IYLALAHMIK FRGHFLIEGD LNPDNSDVDK LFIQLVQTYN QLFEENPINA SGVDAKAILS





ARLSKSRRLE NLIAQLPGEK KNGLFGNLIA LSLGLTPNFK SNFDLAEDAK LQLSKDTYDD





DLDNLLAQIG DQYADLFLAA KNLSDAILLS DILRVNTEIT KAPLSASMIK RYDEHHQDLT





LLKALVRQQL PEKYKEIFFD QSKNGYAGYI DGGASQEEFY KFIKPILEKM DGTEELLVKL





NREDLLRKQR TFDNGSIPHQ IHLGELHAIL RRQEDFYPFL KDNREKIEKI LTFRIPYYVG





PLARGNSRFA WMTRKSEETI TPWNFEEVVD KGASAQSFIE RMTNFDKNLP NEKVLPKHSL





LYEYFTVYNE LTKVKYVTEG MRKPAFLSGE QKKAIVDLLF KTNRKVTVKQ LKEDYFKKIE





CFDSVEISGV EDRFNASLGT YHDLLKIIKD KDFLDNEENE DILEDIVLTL TLFEDREMIE





ERLKTYAHLF DDKVMKQLKR RRYTGWGRLS RKLINGIRDK QSGKTILDFL KSDGFANRNF





MQLIHDDSLT FKEDIQKAQV SGQGDSLHEH IANLAGSPAI KKGILQTVKV VDELVKVMGR





HKPENIVIEM ARENQTTQKG QKNSRERMKR IEEGIKELGS QILKEHPVEN TQLQNEKLYL





YYLQNGRDMY VDQELDINRL SDYDVDHIVP QSFLKDDSID NKVLTRSDKN RGKSDNVPSE





EVVKKMKNYW RQLLNAKLIT QRKFDNLTKA ERGGLSELDK AGFIKRQLVE





TRQITKHVAQ ILDSRMNTKY DENDKLIREV KVITLKSKLV SDFRKDFQFY KVREINNYHH





AHDAYLNAVV GTALIKKYPK LESEFVYGDY KVYDVRKMIA KSEQEIGKAT





AKYFFYSNIM NFFKTEITLA NGEIRKRPLI ETNGETGEIV WDKGRDFATV RKVLSMPQVN





IVKKTEVQTG GFSKESILPK RNSDKLIARK KDWDPKKYGG FDSPTVAYSV LVVAKVEKGK





SKKLKSVKEL LGITIMERSS FEKNPIDFLE AKGYKEVKKD LIIKLPKYSL FELENGRKRM





LASAGELQKG NELALPSKYV NFLYLASHYE KLKGSPEDNE QKQLFVEQHK HYLDEIIEQI





SEFSKRVILA DANLDKVLSA YNKHRDKPIR EQAENIIHLF TLTNLGAPAA FKYFDTTIDR





KRYTSTKEVL DATLIHQSIT GLYETRIDLS QLGGDSRADP KKKRKV





iProt106521 (SEQ ID NO: 7825):


MAPKKKRKVD KKYSIGLDIG TNSVGWAVIT DEYKVPSKKF KVLGNTDRHS IKKNLIGALL





FDSGETAEAT RLKRTARRRY TRRKNRICYL QEIFSNEMAK VDDSFFHRLE ESFLVEEDKK





HERHPIFGNI VDEVAYHEKY PTIYHLRKKL VDSTDKADLR LIYLALAHMI KFRGHFLIEG





DLNPDNSDVD KLFIQLVQTY NQLFEENPIN ASGVDAKAIL SARLSKSRRL ENLIAQLPGE





KKNGLFGNLI ALSLGLTPNF KSNFDLAEDA KLQLSKDTYD DDLDNLLAQI GDQYADLFLA





AKNLSDAILL SDILRVNTEI TKAPLSASMI KRYDEHHQDL TLLKALVRQQ LPEKYKEIFF





DQSKNGYAGY IDGGASQEEF YKFIKPILEK MDGTEELLVK LNREDLLRKQ RTFDNGSIPH





QIHLGELHAI LRRQEDFYPF LKDNREKIEK ILTFRIPYYV GPLARGNSRF AWMTRKSEET





ITPWNFEEVV DKGASAQSFI ERMTNFDKNL PNEKVLPKHS LLYEYFTVYN ELTKVKYVTE





GMRKPAFLSG EQKKAIVDLL FKTNRKVTVK QLKEDYFKKI ECFDSVEISG VEDRFNASLG





TYHDLLKIIK DKDFLDNEEN EDILEDIVLT LTLFEDREMI EERLKTYAHL FDDKVMKQLK





RRRYTGWGRL SRKLINGIRD KQSGKTILDF LKSDGFANRN FMQLIHDDSL TFKEDIQKAQ





VSGQGDSLHE HIANLAGSPA IKKGILQTVK VVDELVKVMG RHKPENIVIE MARENQTTQK





GQKNSRERMK RIEEGIKELG SQILKEHPVE NTQLQNEKLY LYYLQNGRDM YVDQELDINR





LSDYDVDHIV PQSFLKDDSI DNKVLTRSDK NRGKSDNVPS EEVVKKMKNY





WRQLLNAKLI TQRKFDNLTK AERGGLSELD KAGFIKRQLV ETRQITKHVA QILDSRMNTK





YDENDKLIRE VKVITLKSKL VSDFRKDFQF YKVREINNYH HAHDAYLNAV VGTALIKKYP





KLESEFVYGD YKVYDVRKMI AKSEQEIGKA TAKYFFYSNI MNFFKTEITL ANGEIRKRPL





IETNGETGEI VWDKGRDFAT VRKVLSMPQV NIVKKTEVQT GGFSKESILP KRNSDKLIAR





KKDWDPKKYG GFDSPTVAYS VLVVAKVEKG KSKKLKSVKE LLGITIMERS SFEKNPIDFL





EAKGYKEVKK DLIIKLPKYS LFELENGRKR MLASAGELQK GNELALPSKY VNFLYLASHY





EKLKGSPEDN EQKQLFVEQH KHYLDEIIEQ ISEFSKRVIL ADANLDKVLS AYNKHRDKPI





REQAENIIHL FTLTNLGAPA AFKYFDTTID RKRYTSTKEV LDATLIHQSI TGLYETRIDL





SQLGGDSRAD HHHHHH





iProt106522 (SEQ ID NO: 7826):


MAHHHHHHGG SDKKYSIGLD IGTNSVGWAV ITDEYKVPSK KFKVLGNTDR HSIKKNLIGA





LLFDSGETAE ATRLKRTARR RYTRRKNRIC YLQEIFSNEM AKVDDSFFHR LEESFLVEED





KKHERHPIFG NIVDEVAYHE KYPTIYHLRK KLVDSTDKAD LRLIYLALAH MIKFRGHFLI





EGDLNPDNSD VDKLFIQLVQ TYNQLFEENP INASGVDAKA ILSARLSKSR RLENLIAQLP





GEKKNGLFGN LIALSLGLTP NFKSNFDLAE DAKLQLSKDT YDDDLDNLLA QIGDQYADLF





LAAKNLSDAI LLSDILRVNT EITKAPLSAS MIKRYDEHHQ DLTLLKALVR QQLPEKYKEI





FFDQSKNGYA GYIDGGASQE EFYKFIKPIL EKMDGTEELL VKLNREDLLR KQRTFDNGSI





PHQIHLGELH AILRRQEDFY PFLKDNREKI EKILTFRIPY YVGPLARGNS RFAWMTRKSE





ETITPWNFEE VVDKGASAQS FIERMTNFDK NLPNEKVLPK HSLLYEYFTV YNELTKVKYV





TEGMRKPAFL SGEQKKAIVD LLFKTNRKVT VKQLKEDYFK KIECFDSVEI SGVEDRFNAS





LGTYHDLLKI IKDKDFLDNE ENEDILEDIV LTLTLFEDRE MIEERLKTYA HLFDDKVMKQ





LKRRRYTGWG RLSRKLINGI RDKQSGKTIL DFLKSDGFAN RNFMQLIHDD SLTFKEDIQK





AQVSGQGDSL HEHIANLAGS PAIKKGILQT VKVVDELVKV MGRHKPENIV IEMARENQTT





QKGQKNSRER MKRIEEGIKE LGSQILKEHP VENTQLQNEK LYLYYLQNGR DMYVDQELDI





NRLSDYDVDH IVPQSFLKDD SIDNKVLTRS DKNRGKSDNV PSEEVVKKMK





NYWRQLLNAK LITQRKFDNL TKAERGGLSE LDKAGFIKRQ LVETRQITKH VAQILDSRMN





TKYDENDKLI REVKVITLKS KLVSDFRKDF QFYKVREINN YHHAHDAYLN AVVGTALIKK





YPKLESEFVY GDYKVYDVRK MIAKSEQEIG KATAKYFFYS NIMNFFKTEI TLANGEIRKR





PLIETNGETG EIVWDKGRDF ATVRKVLSMP QVNIVKKTEV QTGGFSKESI LPKRNSDKLI





ARKKDWDPKK YGGFDSPTVA YSVLVVAKVE KGKSKKLKSV KELLGITIME RSSFEKNPID





FLEAKGYKEV KKDLIIKLPK YSLFELENGR KRMLASAGEL QKGNELALPS KYVNFLYLAS





HYEKLKGSPE DNEQKQLFVE QHKHYLDEII EQISEFSKRV ILADANLDKV LSAYNKHRDK





PIREQAENII HLFTLTNLGA PAAFKYFDTT IDRKRYTSTK EVLDATLIHQ SITGLYETRI





DLSQLGGDSR ADPKKKRKV





iProt106658 (SEQ ID NO: 7827):


MGSSHHHHHH HHENLYFQGS MDKKYSIGLD IGTNSVGWAV ITDEYKVPSK





KFKVLGNTDR HSIKKNLIGA LLFDSGETAE ATRLKRTARR RYTRRKNRIC YLQEIFSNEM





AKVDDSFFHR LEESFLVEED KKHERHPIFG NIVDEVAYHE KYPTIYHLRK KLVDSTDKAD





LRLIYLALAH MIKFRGHFLI EGDLNPDNSD VDKLFIQLVQ TYNQLFEENP INASGVDAKA





ILSARLSKSR RLENLIAQLP GEKKNGLFGN LIALSLGLTP NFKSNFDLAE DAKLQLSKDT





YDDDLDNLLA QIGDQYADLF LAAKNLSDAI LLSDILRVNT EITKAPLSAS MIKRYDEHHQ





DLTLLKALVR QQLPEKYKEI FFDQSKNGYA GYIDGGASQE EFYKFIKPIL EKMDGTEELL





VKLNREDLLR KQRTFDNGSI PHQIHLGELH AILRRQEDFY PFLKDNREKI EKILTFRIPY





YVGPLARGNS RFAWMTRKSE ETITPWNFEE VVDKGASAQS FIERMTNFDK NLPNEKVLPK





HSLLYEYFTV YNELTKVKYV TEGMRKPAFL SGEQKKAIVD LLFKTNRKVT





VKQLKEDYFK KIECFDSVEI SGVEDRFNAS LGTYHDLLKI IKDKDFLDNE ENEDILEDIV





LTLTLFEDRE MIEERLKTYA HLFDDKVMKQ LKRRRYTGWG RLSRKLINGI RDKQSGKTIL





DFLKSDGFAN RNFMQLIHDD SLTFKEDIQK AQVSGQGDSL HEHIANLAGS PAIKKGILQT





VKVVDELVKV MGRHKPENIV IEMARENQTT QKGQKNSRER MKRIEEGIKE LGSQILKEHP





VENTQLQNEK LYLYYLQNGR DMYVDQELDI NRLSDYDVDH IVPQSFLKDD SIDNKVLTRS





DKNRGKSDNV PSEEVVKKMK NYWRQLLNAK LITQRKFDNL TKAERGGLSE





LDKAGFIKRQ LVETRQITKH VAQILDSRMN TKYDENDKLI REVKVITLKS KLVSDFRKDF





QFYKVREINN YHHAHDAYLN AVVGTALIKK YPKLESEFVY GDYKVYDVRK





MIAKSEQEIG KATAKYFFYS NIMNFFKTEI TLANGEIRKR PLIETNGETG EIVWDKGRDF





ATVRKVLSMP QVNIVKKTEV QTGGFSKESI LPKRNSDKLI ARKKDWDPKK YGGFDSPTVA





YSVLVVAKVE KGKSKKLKSV KELLGITIME RSSFEKNPID FLEAKGYKEV KKDLIIKLPK





YSLFELENGR KRMLASAGEL QKGNELALPS KYVNFLYLAS HYEKLKGSPE DNEQKQLFVE





QHKHYLDEII EQISEFSKRV ILADANLDKV LSAYNKHRDK PIREQAENII HLFTLTNLGA





PAAFKYFDTT IDRKRYTSTK EVLDATLIHQ SITGLYETRI DLSQLGGDGG GSPKKKRKV





iProt106745 (SEQ ID NO: 7828):


MAPKKKRKVD KKYSIGLDIG TNSVGWAVIT DEYKVPSKKF KVLGNTDRHS IKKNLIGALL





FDSGETAEAT RLKRTARRRY TRRKNRICYL QEIFSNEMAK VDDSFFHRLE ESFLVEEDKK





HERHPIFGNI VDEVAYHEKY PTIYHLRKKL VDSTDKADLR LIYLALAHMI KFRGHFLIEG





DLNPDNSDVD KLFIQLVQTY NQLFEENPIN ASGVDAKAIL SARLSKSRRL ENLIAQLPGE





KKNGLFGNLI ALSLGLTPNF KSNFDLAEDA KLQLSKDTYD DDLDNLLAQI GDQYADLFLA





AKNLSDAILL SDILRVNTEI TKAPLSASMI KRYDEHHQDL TLLKALVRQQ LPEKYKEIFF





DQSKNGYAGY IDGGASQEEF YKFIKPILEK MDGTEELLVK LNREDLLRKQ RTFDNGSIPH





QIHLGELHAI LRRQEDFYPF LKDNREKIEK ILTFRIPYYV GPLARGNSRF AWMTRKSEET





ITPWNFEEVV DKGASAQSFI ERMTNFDKNL PNEKVLPKHS LLYEYFTVYN ELTKVKYVTE





GMRKPAFLSG EQKKAIVDLL FKTNRKVTVK QLKEDYFKKI ECFDSVEISG VEDRFNASLG





TYHDLLKIIK DKDFLDNEEN EDILEDIVLT LTLFEDREMI EERLKTYAHL FDDKVMKQLK





RRRYTGWGRL SRKLINGIRD KQSGKTILDF LKSDGFANRN FMQLIHDDSL TFKEDIQKAQ





VSGQGDSLHE HIANLAGSPA IKKGILQTVK VVDELVKVMG RHKPENIVIE MARENQTTQK





GQKNSRERMK RIEEGIKELG SQILKEHPVE NTQLQNEKLY LYYLQNGRDM YVDQELDINR





LSDYDVDHIV PQSFLKDDSI DNAVLTRSDK NRGKSDNVPS EEVVKKMKNY





WRQLLNAKLI TQRKFDNLTK AERGGLSELD KAGFIKRQLV ETRQITKHVA QILDSRMNTK





YDENDKLIRE VKVITLKSKL VSDFRKDFQF YKVREINNYH HAHDAYLNAV VGTALIKKYP





KLESEFVYGD YKVYDVRKMI AKSEQEIGKA TAKYFFYSNI MNFFKTEITL ANGEIRKRPL





IETNGETGEI VWDKGRDFAT VRKVLSMPQV NIVKKTEVQT GGFSKESILP KRNSDKLIAR





KKDWDPKKYG GFDSPTVAYS VLVVAKVEKG KSKKLKSVKE LLGITIMERS SFEKNPIDFL





EAKGYKEVKK DLIIKLPKYS LFELENGRKR MLASAGELQK GNELALPSKY VNFLYLASHY





EKLKGSPEDN EQKQLFVEQH KHYLDEIIEQ ISEFSKRVIL ADANLDKVLS AYNKHRDKPI





REQAENIIHL FTLTNLGAPA AFKYFDTTID RKRYTSTKEV LDATLIHQSI TGLYETRIDL





SQLGGDSRAD PKKKRKVHHH HHH





iProt106746 (SEQ ID NO: 7829):


MAPKKKRKVD KKYSIGLDIG TNSVGWAVIT DEYKVPSKKF KVLGNTDRHS IKKNLIGALL





FDSGETAEAT RLKRTARRRY TRRKNRICYL QEIFSNEMAK VDDSFFHRLE ESFLVEEDKK





HERHPIFGNI VDEVAYHEKY PTIYHLRKKL VDSTDKADLR LIYLALAHMI KFRGHFLIEG





DLNPDNSDVD KLFIQLVQTY NQLFEENPIN ASGVDAKAIL SARLSKSRRL ENLIAQLPGE





KKNGLFGNLI ALSLGLTPNF KSNFDLAEDA KLQLSKDTYD DDLDNLLAQI GDQYADLFLA





AKNLSDAILL SDILRVNTEI TKAPLSASMI KRYDEHHQDL TLLKALVRQQ LPEKYKEIFF





DQSKNGYAGY IDGGASQEEF YKFIKPILEK MDGTEELLVK LNREDLLRKQ RTFDNGSIPH





QIHLGELHAI LRRQEDFYPF LKDNREKIEK ILTFRIPYYV GPLARGNSRF AWMTRKSEET





ITPWNFEEVV DKGASAQSFI ERMTNFDKNL PNEKVLPKHS LLYEYFTVYN ELTKVKYVTE





GMRKPAFLSG EQKKAIVDLL FKTNRKVTVK QLKEDYFKKI ECFDSVEISG VEDRFNASLG





TYHDLLKIIK DKDFLDNEEN EDILEDIVLT LTLFEDREMI EERLKTYAHL FDDKVMKQLK





RRRYTGWGRL SRKLINGIRD KQSGKTILDF LKSDGFANRN FMQLIHDDSL TFKEDIQKAQ





VSGQGDSLHE HIANLAGSPA IKKGILQTVK VVDELVKVMG RHKPENIVIE MARENQTTQK





GQKNSRERMK RIEEGIKELG SQILKEHPVE NTQLQNEALY LYYLQNGRDM YVDQELDINR





LSDYDVDHIV PQSFLKDDSI DNKVLTRSDK NRGKSDNVPS EEVVKKMKNY





WRQLLNAKLI TQRKFDNLTK AERGGLSELD KAGFIKRQLV ETRQITKHVA QILDSRMNTK





YDENDKLIRE VKVITLKSKL VSDFRKDFQF YKVREINNYH HAHDAYLNAV VGTALIKKYP





ALESEFVYGD YKVYDVRKMI AKSEQEIGKA TAKYFFYSNI MNFFKTEITL ANGEIRKAPL





IETNGETGEI VWDKGRDFAT VRKVLSMPQV NIVKKTEVQT GGFSKESILP KRNSDKLIAR





KKDWDPKKYG GFDSPTVAYS VLVVAKVEKG KSKKLKSVKE LLGITIMERS SFEKNPIDFL





EAKGYKEVKK DLIIKLPKYS LFELENGRKR MLASAGELQK GNELALPSKY VNFLYLASHY





EKLKGSPEDN EQKQLFVEQH KHYLDEIIEQ ISEFSKRVIL ADANLDKVLS AYNKHRDKPI





REQAENIIHL FTLTNLGAPA AFKYFDTTID RKRYTSTKEV LDATLIHQSI TGLYETRIDL





SQLGGDSRAD PKKKRKVHHH HHH





iProt106747 (SEQ ID NO: 7830):


MAPKKKRKVD KKYSIGLDIG TNSVGWAVIT DEYKVPSKKF KVLGNTDRHS IKKNLIGALL





FDSGETAEAT RLKRTARRRY TRRKNRICYL QEIFSNEMAK VDDSFFHRLE ESFLVEEDKK





HERHPIFGNI VDEVAYHEKY PTIYHLRKKL VDSTDKADLR LIYLALAHMI KFRGHFLIEG





DLNPDNSDVD KLFIQLVQTY NQLFEENPIN ASGVDAKAIL SARLSKSRRL ENLIAQLPGE





KKNGLFGNLI ALSLGLTPNF KSNFDLAEDA KLQLSKDTYD DDLDNLLAQI GDQYADLFLA





AKNLSDAILL SDILRVNTEI TKAPLSASMI KRYDEHHQDL TLLKALVRQQ LPEKYKEIFF





DQSKNGYAGY IDGGASQEEF YKFIKPILEK MDGTEELLVK LNREDLLRKQ RTFDNGSIPH





QIHLGELHAI LRRQEDFYPF LKDNREKIEK ILTFRIPYYV GPLARGNSRF AWMTRKSEET





ITPWNFEEVV DKGASAQSFI ERMTNFDKNL PNEKVLPKHS LLYEYFTVYN ELTKVKYVTE





GMRKPAFLSG EQKKAIVDLL FKTNRKVTVK QLKEDYFKKI ECFDSVEISG VEDRFNASLG





TYHDLLKIIK DKDFLDNEEN EDILEDIVLT LTLFEDREMI EERLKTYAHL FDDKVMKQLK





RRRYTGWGRL SRKLINGIRD KQSGKTILDF LKSDGFANRN FMQLIHDDSL TFKEDIQKAQ





VSGQGDSLHE HIANLAGSPA IKKGILQTVK VVDELVKVMG RHKPENIVIE MARENQTTQK





GQKNSRERMK RIEEGIKELG SQILKEHPVE NTQLQNEKLY LYYLQNGRDM YVDQELDINR





LSDYDVDHIV PQSFLADDSI DNKVLTRSDK NRGKSDNVPS EEVVKKMKNY





WRQLLNAKLI TQRKFDNLTK AERGGLSELD KAGFIKRQLV ETRQITKHVA QILDSRMNTK





YDENDKLIRE VKVITLKSKL VSDFRKDFQF YKVREINNYH HAHDAYLNAV VGTALIKKYP





ALESEFVYGD YKVYDVRKMI AKSEQEIGKA TAKYFFYSNI MNFFKTEITL ANGEIRKAPL





IETNGETGEI VWDKGRDFAT VRKVLSMPQV NIVKKTEVQT GGFSKESILP KRNSDKLIAR





KKDWDPKKYG GFDSPTVAYS VLVVAKVEKG KSKKLKSVKE LLGITIMERS SFEKNPIDFL





EAKGYKEVKK DLIIKLPKYS LFELENGRKR MLASAGELQK GNELALPSKY VNFLYLASHY





EKLKGSPEDN EQKQLFVEQH KHYLDEIIEQ ISEFSKRVIL ADANLDKVLS AYNKHRDKPI





REQAENIIHL FTLTNLGAPA AFKYFDTTID RKRYTSTKEV LDATLIHQSI TGLYETRIDL





SQLGGDSRAD PKKKRKVHHH HHH





iProt106884 (SEQ ID NO: 7831):


MAPKKKRKVD KKYSIGLDIG TNSVGWAVIT DEYKVPSKKF KVLGNTDRHS IKKNLIGALL





FDSGETAEAT RLKRTARRRY TRRKNRICYL QEIFSNEMAK VDDSFFHRLE ESFLVEEDKK





HERHPIFGNI VDEVAYHEKY PTIYHLRKKL VDSTDKADLR LIYLALAHMI KFRGHFLIEG





DLNPDNSDVD KLFIQLVQTY NQLFEENPIN ASGVDAKAIL SARLSKSRRL ENLIAQLPGE





KKNGLFGNLI ALSLGLTPNF KSNFDLAEDA KLQLSKDTYD DDLDNLLAQI GDQYADLFLA





AKNLSDAILL SDILRVNTEI TKAPLSASMI KRYDEHHQDL TLLKALVRQQ LPEKYKEIFF





DQSKNGYAGY IDGGASQEEF YKFIKPILEK MDGTEELLVK LNREDLLRKQ RTFDNGSIPH





QIHLGELHAI LRRQEDFYPF LKDNREKIEK ILTFRIPYYV GPLARGNSRF AWMTRKSEET





ITPWNFEEVV DKGASAQSFI ERMTAFDKNL PNEKVLPKHS LLYEYFTVYN ELTKVKYVTE





GMRKPAFLSG EQKKAIVDLL FKTNRKVTVK QLKEDYFKKI ECFDSVEISG VEDRFNASLG





TYHDLLKIIK DKDFLDNEEN EDILEDIVLT LTLFEDREMI EERLKTYAHL FDDKVMKQLK





RRRYTGWGAL SRKLINGIRD KQSGKTILDF LKSDGFANRN FMALIHDDSL TFKEDIQKAQ





VSGQGDSLHE HIANLAGSPA IKKGILQTVK VVDELVKVMG RHKPENIVIE MARENQTTQK





GQKNSRERMK RIEEGIKELG SQILKEHPVE NTQLQNEKLY LYYLQNGRDM YVDQELDINR





LSDYDVDHIV PQSFLKDDSI DNKVLTRSDK NRGKSDNVPS EEVVKKMKNY





WRQLLNAKLI TQRKFDNLTK AERGGLSELD KAGFIKRQLV ETRAITKHVA QILDSRMNTK





YDENDKLIRE VKVITLKSKL VSDFRKDFQF YKVREINNYH HAHDAYLNAV VGTALIKKYP





KLESEFVYGD YKVYDVRKMI AKSEQEIGKA TAKYFFYSNI MNFFKTEITL ANGEIRKRPL





IETNGETGEI VWDKGRDFAT VRKVLSMPQV NIVKKTEVQT GGFSKESILP KRNSDKLIAR





KKDWDPKKYG GFDSPTVAYS VLVVAKVEKG KSKKLKSVKE LLGITIMERS SFEKNPIDFL





EAKGYKEVKK DLIIKLPKYS LFELENGRKR MLASAGELQK GNELALPSKY VNFLYLASHY





EKLKGSPEDN EQKQLFVEQH KHYLDEIIEQ ISEFSKRVIL ADANLDKVLS AYNKHRDKPI





REQAENIIHL FTLTNLGAPA AFKYFDTTID RKRYTSTKEV LDATLIHQSI TGLYETRIDL





SQLGGDSRAD PKKKRKVHHH HHH






Nucleic Acids Encoding Cas9 Molecules

Nucleic acids encoding the Cas9 molecules, e.g., an active Cas9 molecule or an inactive Cas9 molecule are provided herein.


Exemplary nucleic acids encoding Cas9 molecules are described in Cong et al, SCIENCE 2013, 399(6121):819-823; Wang et al, CELL 2013, 153(4):910-918; Mali et al., SCIENCE 2013, 399(6121):823-826; Jinek et al, SCIENCE 2012, 337(6096):816-821.


In an embodiment, a nucleic acid encoding a Cas9 molecule can be a synthetic nucleic acid sequence. For example, the synthetic nucleic acid molecule can be chemically modified, e.g., as described in Section XIII. In an embodiment, the Cas9 mRNA has one or more of, e.g., all of the following properties: it is capped, polyadenylated, substituted with 5-methylcytidine and/or pseudouridine.


In addition or alternatively, the synthetic nucleic acid sequence can be codon optimized, e.g., at least one non-common codon or less-common codon has been replaced by a common codon. For example, the synthetic nucleic acid can direct the synthesis of an optimized messenger mRNA, e.g., optimized for expression in a mammalian expression system, e.g., described herein.


Provided below is an exemplary codon optimized nucleic acid sequence encoding a Cas9 molecule of S. pyogenes.










(SEQ ID NO: 6628)










atggataaaa agtacagcat cgggctggac atcggtacaa actcagtggg gtgggccgtg
60






attacggacg agtacaaggt accctccaaa aaatttaaag tgctgggtaa cacggacaga
120





cactctataa agaaaaatct tattggagcc ttgctgttcg actcaggcga gacagccgaa
180





gccacaaggt tgaagcggac cgccaggagg cggtatacca ggagaaagaa ccgcatatgc
240





tacctgcaag aaatcttcag taacgagatg gcaaaggttg acgatagctt tttccatcgc
300





ctggaagaat cctttcttgt tgaggaagac aagaagcacg aacggcaccc catctttggc
360





aatattgtcg acgaagtggc atatcacgaa aagtacccga ctatctacca cctcaggaag
420





aagctggtgg actctaccga taaggcggac ctcagactta tttatttggc actcgcccac
480





atgattaaat ttagaggaca tttcttgatc gagggcgacc tgaacccgga caacagtgac
540





gtcgataagc tgttcatcca acttgtgcag acctacaatc aactgttcga agaaaaccct
600





ataaatgctt caggagtcga cgctaaagca atcctgtccg cgcgcctctc aaaatctaga
660





agacttgaga atctgattgc tcagttgccc ggggaaaaga aaaatggatt gtttggcaac
720





ctgatcgccc tcagtctcgg actgacccca aatttcaaaa gtaacttcga cctggccgaa
780





gacgctaagc tccagctgtc caaggacaca tacgatgacg acctcgacaa tctgctggcc
840





cagattgggg atcagtacgc cgatctcttt ttggcagcaa agaacctgtc cgacgccatc
900





ctgttgagcg atatcttgag agtgaacacc gaaattacta aagcacccct tagcgcatct
960





atgatcaagc ggtacgacga gcatcatcag gatctgaccc tgctgaaggc tcttgtgagg
1020





caacagctcc ccgaaaaata caaggaaatc ttctttgacc agagcaaaaa cggctacgct
1080





ggctatatag atggtggggc cagtcaggag gaattctata aattcatcaa gcccattctc
1140





gagaaaatgg acggcacaga ggagttgctg gtcaaactta acagggagga cctgctgcgg
1200





aagcagcgga cctttgacaa cgggtctatc ccccaccaga ttcatctggg cgaactgcac
1260





gcaatcctga ggaggcagga ggatttttat ccttttctta aagataaccg cgagaaaata
1320





gaaaagattc ttacattcag gatcccgtac tacgtgggac ctctcgcccg gggcaattca
1380





cggtttgcct ggatgacaag gaagtcagag gagactatta caccttggaa cttcgaagaa
1440





gtggtggaca agggtgcatc tgcccagtct ttcatcgagc ggatgacaaa ttttgacaag
1500





aacctcccta atgagaaggt gctgcccaaa cattctctgc tctacgagta ctttaccgtc
1560





tacaatgaac tgactaaagt caagtacgtc accgagggaa tgaggaagcc ggcattcctt
1620





agtggagaac agaagaaggc gattgtagac ctgttgttca agaccaacag gaaggtgact
1680





gtgaagcaac ttaaagaaga ctactttaag aagatcgaat gttttgacag tgtggaaatt
1740





tcaggggttg aagaccgctt caatgcgtca ttggggactt accatgatct tctcaagatc
1800





ataaaggaca aagacttcct ggacaacgaa gaaaatgagg atattctcga agacatcgtc
1860





ctcaccctga ccctgttcga agacagggaa atgatagaag agcgcttgaa aacctatgcc
1920





cacctcttcg acgataaagt tatgaagcag ctgaagcgca ggagatacac aggatgggga
1980





agattgtcaa ggaagctgat caatggaatt agggataaac agagtggcaa gaccatactg
2040





gatttcctca aatctgatgg cttcgccaat aggaacttca tgcaactgat tcacgatgac
2100





tctcttacct tcaaggagga cattcaaaag gctcaggtga gcgggcaggg agactccctt
2160





catgaacaca tcgcgaattt ggcaggttcc cccgctatta aaaagggcat ccttcaaact
2220





gtcaaggtgg tggatgaatt ggtcaaggta atgggcagac ataagccaga aaatattgtg
2280





atcgagatgg cccgcgaaaa ccagaccaca cagaagggcc agaaaaatag tagagagcgg
2340





atgaagagga tcgaggaggg catcaaagag ctgggatctc agattctcaa agaacacccc
2400





gtagaaaaca cacagctgca gaacgaaaaa ttgtacttgt actatctgca gaacggcaga
2460





gacatgtacg tcgaccaaga acttgatatt aatagactgt ccgactatga cgtagaccat
2520





atcgtgcccc agtccttcct gaaggacgac tccattgata acaaagtctt gacaagaagc
2580





gacaagaaca ggggtaaaag tgataatgtg cctagcgagg aggtggtgaa aaaaatgaag
2640





aactactggc gacagctgct taatgcaaag ctcattacac aacggaagtt cgataatctg
2700





acgaaagcag agagaggtgg cttgtctgag ttggacaagg cagggtttat taagcggcag
2760





ctggtggaaa ctaggcagat cacaaagcac gtggcgcaga ttttggacag ccggatgaac
2820





acaaaatacg acgaaaatga taaactgata cgagaggtca aagttatcac gctgaaaagc
2880





aagctggtgt ccgattttcg gaaagacttc cagttctaca aagttcgcga gattaataac
2940





taccatcatg ctcacgatgc gtacctgaac gctgttgtcg ggaccgcctt gataaagaag
3000





tacccaaagc tggaatccga gttcgtatac ggggattaca aagtgtacga tgtgaggaaa
3060





atgatagcca agtccgagca ggagattgga aaggccacag ctaagtactt cttttattct
3120





aacatcatga atttttttaa gacggaaatt accctggcca acggagagat cagaaagcgg
3180





ccccttatag agacaaatgg tgaaacaggt gaaatcgtct gggataaggg cagggatttc
3240





gctactgtga ggaaggtgct gagtatgcca caggtaaata tcgtgaaaaa aaccgaagta
3300





cagaccggag gattttccaa ggaaagcatt ttgcctaaaa gaaactcaga caagctcatc
3360





gcccgcaaga aagattggga ccctaagaaa tacgggggat ttgactcacc caccgtagcc
3420





tattctgtgc tggtggtagc taaggtggaa aaaggaaagt ctaagaagct gaagtccgtg
3480





aaggaactct tgggaatcac tatcatggaa agatcatcct ttgaaaagaa ccctatcgat
3540





ttcctggagg ctaagggtta caaggaggtc aagaaagacc tcatcattaa actgccaaaa
3600





tactctctct tcgagctgga aaatggcagg aagagaatgt tggccagcgc cggagagctg
3660





caaaagggaa acgagcttgc tctgccctcc aaatatgtta attttctcta tctcgcttcc
3720





cactatgaaa agctgaaagg gtctcccgaa gataacgagc agaagcagct gttcgtcgaa
3780





cagcacaagc actatctgga tgaaataatc gaacaaataa gcgagttcag caaaagggtt
3840





atcctggcgg atgctaattt ggacaaagta ctgtctgctt ataacaagca ccgggataag
3900





cctattaggg aacaagccga gaatataatt cacctcttta cactcacgaa tctcggagcc
3960





cccgccgcct tcaaatactt tgatacgact atcgaccgga aacggtatac cagtaccaaa
4020





gaggtcctcg atgccaccct catccaccag tcaattactg gcctgtacga aacacggatc
4080





gacctctctc aactgggcgg cgactag
4107






If the above Cas9 sequences are fused with a peptide or polypeptide at the C-terminus (e.g., an inactive Cas9 fused with a transcription repressor at the C-terminus), it is understood that the stop codon will be removed.


VI. Functional Analysis of Candidate Molecules

Candidate Cas9 molecules, candidate gRNA molecules, candidate Cas9 molecule/gRNA molecule complexes, can be evaluated by art-known methods or as described herein. For example, exemplary methods for evaluating the endonuclease activity of Cas9 molecule are described, e.g., in Jinek el al., SCIENCE 2012; 337(6096):816-821.


VII. Template Nucleic Acids (For Introduction of Nucleic Acids)

The term “template nucleic acid” or “donor template” as used herein refers to a nucleic acid to be inserted at or near a target sequence that has been modified, e.g., cleaved, by a CRISPR system of the present invention. In an embodiment, nucleic acid sequence at or near the target sequence is modified to have some or all of the sequence of the template nucleic acid, typically at or near cleavage site(s). In an embodiment, the template nucleic acid is single stranded. In an alternate embodiment, the template nucleic acid is double stranded. In an embodiment, the template nucleic acid is DNA, e.g., double stranded DNA. In an alternate embodiment, the template nucleic acid is single stranded DNA.


In embodiments, the template nucleic acid comprises sequence encoding a globin protein, e.g., a beta globin, e.g., comprises a beta globin gene. In an embodiment, the beta globin encoded by the nucleic acid comprises one or more mutations, e.g., anti-sickling mutations. In an embodiment, the beta globin encoded by the nucleic acid comprises the mutation T87Q. In an embodiment, the beta globin encoded by the nucleic acid comprises the mutation G16D. In an embodiment, the beta globin encoded by the nucleic acid comprises the mutation E22A. In an embodiment, the beta globin gene comprises the mutations G16D, E22A and T87Q. In embodiments, the template nucleic acid further comprises one or more regulatory elements, e.g., a promoter (e.g., a human beta globin promoter), a 3′ enhancer, and/or at least a portion of a globin locus control region (e.g., one or more DNAseI hypersensitivity sites (e.g., HS2, HS3 and/or HS4 of the human globin locus)).


In other embodiments, the template nucleic acid comprises sequence encoding a gamma globin, e.g., comprises a gamma globin gene. In embodiments, the template nucleic acid comprises sequence encoding more than one copy of a gamma globin protein, e.g., comprises two or more, e.g., two, gamma globin gene sequences. In embodiments, the template nucleic acid further comprises one or more regulatory elements, e.g., a promotor and/or enhancer.


In an embodiment, the template nucleic acid alters the structure of the target position by participating in a homology directed repair event. In an embodiment, the template nucleic acid alters the sequence of the target position. In an embodiment, the template nucleic acid results in the incorporation of a modified, or non-naturally occurring base into the target nucleic acid.


Mutations in a gene or pathway described herein may be corrected using one of the approaches discussed herein. In an embodiment, a mutation in a gene or pathway described herein is corrected by homology directed repair (HDR) using a template nucleic acid. In an embodiment, a mutation in a gene or pathway described herein is corrected by homologous recombination (HR) using a template nucleic acid. In an embodiment, a mutation in a gene or pathway described herein is corrected by Non-Homologous End Joining (NHEJ) repair using a template nucleic acid. In other embodiments, nucleic acid encoding molecules of interest may be inserted at or near a site modified by a CRISPR system of the present invention. In embodiments, the template nucleic acid comprises regulatory elements, e.g., one or more promotors and/or enhancers, operably linked to the nucleic acid sequence encoding a molecule of interest, e.g., as described herein.


HDR or HR Repair and Template Nucleic Acids

As described herein, nuclease-induced homology directed repair (HDR) or homologous recombination (HR) can be used to alter a target sequence and correct (e.g., repair or edit) a mutation in the genome. While not wishing to be bound by theory, it is believed that alteration of the target sequence occurs by repair based on a donor template or template nucleic acid. For example, the donor template or the template nucleic acid provides for alteration of the target sequence. It is contemplated that a plasmid donor or linear double stranded template can be used as a template for homologous recombination. It is further contemplated that a single stranded donor template can be used as a template for alteration of the target sequence by alternate methods of homology directed repair (e.g., single strand annealing) between the target sequence and the donor template. Donor template-effected alteration of a target sequence may depend on cleavage by a Cas9 molecule. Cleavage by Cas9 can comprise a double strand break, one single strand break, or two single strand breaks.


In an embodiment, a mutation can be corrected by either a single double-strand break or two single strand breaks. In an embodiment, a mutation can be corrected by providing a template and a CRISPR/Cas9 system that creates (1) one double strand break, (2) two single strand breaks, (3) two double stranded breaks with a break occurring on each side of the target sequence, (4) one double stranded break and two single strand breaks with the double strand break and two single strand breaks occurring on each side of the target sequence, (5) four single stranded breaks with a pair of single stranded breaks occurring on each side of the target sequence, or (6) one single strand break.


Double Strand Break Mediated Correction

In an embodiment, double strand cleavage is effected by a Cas9 molecule having cleavage activity associated with an HNH-like domain and cleavage activity associated with a RuvC-like domain, e.g., an N-terminal RuvC-like domain, e.g., a wild type Cas9. Such embodiments require only a single gRNA.


Single Strand Break Mediated Correction

In other embodiments, two single strand breaks, or nicks, are effected by a Cas9 molecule having nickase activity, e.g., cleavage activity associated with an HNH-like domain or cleavage activity associated with an N-terminal RuvC-like domain Such embodiments require two gRNAs, one for placement of each single strand break. In an embodiment, the Cas9 molecule having nickase activity cleaves the strand to which the gRNA hybridizes, but not the strand that is complementary to the strand to which the gRNA hybridizes. In an embodiment, the Cas9 molecule having nickase activity does not cleave the strand to which the gRNA hybridizes, but rather cleaves the strand that is complementary to the strand to which the gRNA hybridizes.


In an embodiment, the nickase has HNH activity, e.g., a Cas9 molecule having the RuvC activity inactivated, e.g., a Cas9 molecule having a mutation at D10, e.g., the D10A mutation. D10A inactivates RuvC; therefore, the Cas9 nickase has (only) HN H activity and will cut on the strand to which the gRNA hybridizes (e.g., the complementary strand, which does not have the NGG PAM on it). In other embodiments, a Cas9 molecule having an H840, e.g., an H840A, mutation can be used as a nickase. H840A inactivates HNH; therefore, the Cas9 nickase has (only) RuvC activity and cuts on the non-complementary strand (e.g., the strand that has the NGG PAM and whose sequence is identical to the gRNA).


In an embodiment, in which a nickase and two gRNAs are used to position two single strand nicks, one nick is on the + strand and one nick is on the − strand of the target nucleic acid. The PAMs are outwardly facing. The gRNAs can be selected such that the gRNAs are separated by, from about 0-50, 0-100, or 0-200 nucleotides. In an embodiment, there is no overlap between the target sequence that is complementary to the targeting domains of the two gRNAs. In an embodiment, the gRNAs do not overlap and are separated by as much as 50, 100, or 200 nucleotides. In an embodiment, the use of two gRNAs can increase specificity, e.g., by decreasing off-target binding (Ran el cil., CELL 2013).


In an embodiment, a single nick can be used to induce HDR. It is contemplated herein that a single nick can be used to increase the ratio of HDR, HR or NHEJ at a given cleavage site.


Placement of the Double Strand Break or a Single Strand Break Relative to Target Position

The double strand break or single strand break in one of the strands should be sufficiently close to target position such that correction occurs. In an embodiment, the distance is not more than 50, 100, 200, 300, 350 or 400 nucleotides. While not wishing to be bound by theory, it is believed that the break should be sufficiently close to target position such that the break is within the region that is subject to exonuclease-mediated removal during end resection. If the distance between the target position and a break is too great, the mutation may not be included in the end resection and, therefore, may not be corrected, as donor sequence may only be used to correct sequence within the end resection region.


In an embodiment, in which a gRNA (unimolecular (or chimeric) or modular gRNA) and Cas9 nuclease induce a double strand break for the purpose of inducing HDR- or HR-mediated correction, the cleavage site is between 0-200 bp (e.g., 0 to 175, 0 to 150, 0 to 125, 0 to 100, 0 to 75, 0 to 50, 0 to 25, 25 to 200, 25 to 175, 25 to 150, 25 to 125, 25 to 100, 25 to 75, 25 to 50, 50 to 200, 50 to 175, 50 to 150, 50 to 125, 50 to 100, 50 to 75, 75 to 200, 75 to 175, 75 to 150, 75 to 125, 75 to 100 bp) away from the target position. In an embodiment, the cleavage site is between 0-100 bp (e.g., 0 to 75, 0 to 50, 0 to 25, 25 to 100, 25 to 75, 25 to 50, 50 to 100, 50 to 75 or 75 to 100 bp) away from the target position.


In an embodiment, in which two gRNAs (independently, unimolecular (or chimeric) or modular gRNA) complexing with Cas9 nickases induce two single strand breaks for the purpose of inducing HDR-mediated correction, the closer nick is between 0-200 bp (e.g., 0 to 175, 0 to 150, 0 to 125, 0 to 100, 0 to 75, 0 to 50, 0 to 25, 25 to 200, 25 to 175, 25 to 150, 25 to 125, 25 to 100, 25 to 75, 25 to 50, 50 to 200, 50 to 175, 50 to 150, 50 to 125, 50 to 100, 50 to 75, 75 to 200, 75 to 175, 75 to 150, 75 to 125, 75 to 100 bp) away from the target position and the two nicks will ideally be within 25-55 bp of each other (e.g., 25 to 50, 25 to 45, 25 to 40, 25 to 35, 25 to 30, 30 to 55, 30 to 50, 30 to 45, 30 to 40, 30 to 35, 35 to 55, 35 to 50, 35 to 45, 35 to 40, 40 to 55, 40 to 50, 40 to 45 bp) and no more than 100 bp away from each other (e.g., no more than 90, 80, 70, 60, 50, 40, 30, 20, 10 or 5 bp away from each other). In an embodiment, the cleavage site is between 0-100 bp (e.g., 0 to 75, 0 to 50, 0 to 25, 25 to 100, 25 to 75, 25 to 50, 50 to 100, 50 to 75 or 75 to 100 bp) away from the target position.


In one embodiment, two gRNAs, e.g., independently, unimolecular (or chimeric) or modular gRNA, are configured to position a double-strand break on both sides of a target position. In an alternate embodiment, three gRNAs, e.g., independently, unimolecular (or chimeric) or modular gRNA, are configured to position a double strand break (i.e., one gRNA complexes with a Cas9 nuclease) and two single strand breaks or paired single stranded breaks (i.e., two gRNAs complex with Cas9 nickases) on either side of the target position (e.g., the first gRNA is used to target upstream (i.e., 5′) of the target position and the second gRNA is used to target downstream (i.e., 3′) of the target position). In another embodiment, four gRNAs, e.g., independently, unimolecular (or chimeric) or modular gRNA, are configured to generate two pairs of single stranded breaks (i.e., two pairs of two gRNAs complex with Cas9 nickases) on either side of the target position (e.g., the first gRNA is used to target upstream (i.e., 5′) of the target position and the second gRNA is used to target downstream (i.e., 3′) of the target position). The double strand break(s) or the closer of the two single strand nicks in a pair will ideally be within 0-500 bp of the target position (e.g., no more than 450, 400, 350, 300, 250, 200, 150, 100, 50 or 25 bp from the target position). When nickases are used, the two nicks in a pair are within 25-55 bp of each other (e.g., between 25 to 50, 25 to 45, 25 to 40, 25 to 35, 25 to 30, 50 to 55, 45 to 55, 40 to 55, 35 to 55, 30 to 55, 30 to 50, 35. to 50, 40 to 50, 45 to 50, 35 to 45, or 40 to 45 bp) and no more than 100 bp away from each other (e.g., no more than 90, 80, 70, 60, 50, 40, 30, 20 or 10 bp).


In one embodiment, two gRNAs, e.g., independently, unimolecular (or chimeric) or modular gRNA, are configured to position a double-strand break on both sides of a target position. In an alternate embodiment, three gRNAs, e.g., independently, unimolecular (or chimeric) or modular gRNA, are configured to position a double strand break (i.e., one gRNA complexes with a Cas9 nuclease) and two single strand breaks or paired single stranded breaks (i.e., two gRNAs complex with Cas9 nickases) on two target sequences (e.g., the first gRNA is used to target an upstream (i.e., 5′) target sequence and the second gRNA is used to target a downstream (i.e., 3′) target sequence of an insertion site. In another embodiment, four gRNAs, e.g., independently, unimolecular (or chimeric) or modular gRNA, are configured to generate two pairs of single stranded breaks (i.e., two pairs of two gRNAs complex with Cas9 nickases) on either side of an insertion site (e.g., the first gRNA is used to target an upstream (i.e., 5′) target sequence described herein, and the second gRNA is used to target a downstream (i.e., 3′) target sequence described herein). The double strand break(s) or the closer of the two single strand nicks in a pair will ideally be within 0-500 bp of the target position (e.g., no more than 450, 400, 350, 300, 250, 200, 150, 100, 50 or 25 bp from the target position). When nickases are used, the two nicks in a pair are within 25-55 bp of each other (e.g., between 25 to 50, 25 to 45, 25 to 40, 25 to 35, 25 to 30, 50 to 55, 45 to 55, 40 to 55, 35 to 55, 30 to 55, 30 to 50, 35 to 50, 40 to 50, 45 to 50, 35 to 45, or 40 to 45 bp) and no more than 100 bp away from each other (e.g., no more than 90, 80, 70, 60, 50, 40, 30, 20 or 10 bp).


Length of the Homology Arms

The homology arm should extend at least as far as the region in which end resection may occur, e.g., in order to allow the resected single stranded overhang to find a complementary region within the donor template. The overall length could be limited by parameters such as plasmid size or viral packaging limits. In an embodiment, a homology arm does not extend into repeated elements, e.g., ALU repeats, LINE repeats. A template may have two homology arms of the same or different lengths.


Exemplary Homology Arm Lengths Include at Least 25, 50, 100, 250, 500, 750 or 1000 Nucleotides.

Target position, as used herein, refers to a site on a target nucleic acid (e.g., the chromosome) that is modified by a Cas9 molecule-dependent process. For example, the target position can be a modified Cas9 molecule cleavage of the target nucleic acid and template nucleic acid directed modification, e.g., correction, of the target position. In an embodiment, a target position can be a site between two nucleotides, e.g., adjacent nucleotides, on the target nucleic acid into which one or more nucleotides is added. The target position may comprise one or more nucleotides that are altered, e.g., corrected, by a template nucleic acid. In an embodiment, the target position is within a target sequence (e.g., the sequence to which the gRN A binds) In an embodiment, a target position is upstream or downstream of a target sequence (e.g., the sequence to which the gRNA binds).


Typically, the template sequence undergoes a breakage mediated or catalyzed recombination with the target sequence. In an embodiment, the template nucleic acid includes sequence that corresponds to a site on the target sequence that is cleaved by a Cas9 mediated cleavage event. In an embodiment, the template nucleic acid includes sequence that corresponds to both, a first site on the target sequence that is cleaved in a first Cas9 mediated event, and a second site on the target sequence that is cleaved in a second Cas9 mediated event.


In an embodiment, the template nucleic acid can include sequence which results in an alteration in the coding sequence of a translated sequence, e.g., one which results in the substitution of one amino acid for another in a protein product, e.g., transforming a mutant allele into a wild type allele, transforming a wild type allele into a mutant allele, and/or introducing a stop codon, insertion of an amino acid residue, deletion of an amino acid residue, or a nonsense mutation.


In other embodiments, the template nucleic acid can include sequence which results in an alteration in a non-coding sequence, e.g., an alteration in an exon or in a 5′ or 3′ non-translated or non-transcribed region. Such alterations include an alteration in a control element, e.g., a promoter, enhancer, and an alteration in a cis-acting or trans-acting control element.


The template nucleic acid can include sequence which, when integrated, results in:


decreasing the activity of a positive control element;


increasing the activity of a positive control element;


decreasing the activity of a negative control element;


increasing the activity of a negative control element;


decreasing the expression of a gene;


increasing the expression of a gene;


increasing resistance to a disorder or disease;


increasing resistance to viral entry;


correcting a mutation or altering an unwanted amino acid residue;


conferring, increasing, abolishing or decreasing a biological property of a gene product, e.g., increasing the enzymatic activity of an enzyme, or increasing the ability of a gene product to interact with another molecule.


The template nucleic acid can include sequence which results in:


a change in sequence of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 or more nucleotides of the target sequence.


In an embodiment, the template nucleic acid is 20+/−10, 30+/−10, 40+/−10, 50+/−10, 60+/−10, 70+/−10, 80+/−10, 90+/−10, 100+/−10, 110+/−10, 120+/−10, 130+/−10, 140+/−10, 150+/−10, 160+/−10, 170+/−10, 180+/−10, 190+/−10, 200+/−10, 210+/−10, 220+/−10, 200-300, 300-400, 400-500, 500-600, 600-700, 700-800, 800-900, 900-1000, 1000-2000, 2000-3000 or more than 3000 nucleotides in length.


A template nucleic acid comprises the following components:


[5′ homology arm]-[insertion sequence]-[3′ homology arm].


The homology arms provide for recombination into the chromosome, which can replace the undesired element, e.g., a mutation or signature, with the replacement sequence. In an embodiment, the homology arms flank the most distal cleavage sites.


In an embodiment, the 3′ end of the 5′ homology arm is the position next to the 5′ end of the replacement sequence. In an embodiment, the 5′ homology arm can extend at least 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 120, 150, 180, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1500, or 2000 nucleotides 5′ from the 5′ end of the replacement sequence.


In an embodiment, the 5′ end of the 3′ homology arm is the position next to the 3′ end of the replacement sequence. In an embodiment, the 3′ homology arm can extend at least 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 120, 150, 180, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1500, or 2000 nucleotides 3′ from the 3′ end of the replacement sequence.


It is contemplated herein that one or both homology arms may be shortened to avoid including certain sequence repeat elements, e.g., Alu repeats, LINE elements. For example, a 5′ homology arm may be shortened to avoid a sequence repeat element. In other embodiments, a 3′ homology arm may be shortened to avoid a sequence repeat element. In some embodiments, both the 5′ and the 3′ homology arms may be shortened to avoid including certain sequence repeat elements.


It is contemplated herein that template nucleic acids for correcting a mutation may designed for use as a single-stranded oligonucleotide (ssODN). When using a ssODN, 5′ and 3′ homology arms may range up to about 200 base pairs (bp) in length, e.g., at least 25, 50, 75, 100, 125, 150, 175, or 200 bp in length. Longer homology arms are also contemplated for ssODNs as improvements in oligonucleotide synthesis continue to be made.


NHEJ Approaches for Gene Targeting

As described herein, nuclease-induced non-homologous end-joining (NHEJ) can be used to target gene-specific knockouts. Nuclease-induced NHEJ can also be used to remove (e.g., delete) sequence in a gene of interest.


While not wishing to be bound by theory, it is believed that, in an embodiment, the genomic alterations associated with the methods described herein rely on nuclease-induced NHEJ and the error-prone nature of the NHEJ repair pathway. NHEJ repairs a double-strand break in the DNA by joining together the two ends; however, generally, the original sequence is restored only if two compatible ends, exactly as they were formed by the double-strand break, are perfectly ligated. The DNA ends of the double-strand break are frequently the subject of enzymatic processing, resulting in the addition or removal of nucleotides, at one or both strands, prior to rejoining of the ends. This results in the presence of insertion and/or deletion (indel) mutations in the DNA sequence at the site of the NHEJ repair. Two-thirds of these mutations may alter the reading frame and, therefore, produce a non-functional protein. Additionally, mutations that maintain the reading frame, but which insert or delete a significant amount of sequence, can destroy functionality of the protein. This is locus dependent as mutations in critical functional domains are likely less tolerable than mutations in non-critical regions of the protein.


The indel mutations generated by NHEJ are unpredictable in nature; however, at a given break site certain indel sequences are favored and are over represented in the population. The lengths of deletions can vary widely; most commonly in the 1-50 bp range, but they can easily reach greater than 100-200 bp. Insertions tend to be shorter and often include short duplications of the sequence immediately surrounding the break site. However, it is possible to obtain large insertions, and in these cases, the inserted sequence has often been traced to other regions of the genome or to plasmid DNA present in the cells.


Because NHEJ is a mutagenic process, it can also be used to delete small sequence motifs as long as the generation of a specific final sequence is not required. If a double-strand break is targeted near to a short target sequence, the deletion mutations caused by the NHEJ repair often span, and therefore remove, the unwanted nucleotides. For the deletion of larger DNA segments, introducing two double-strand breaks, one on each side of the sequence, can result in NHEJ between the ends with removal of the entire intervening sequence. Both of these approaches can be used to delete specific DNA sequences; however, the error-prone nature of NHEJ may still produce indel mutations at the site of repair.


Both double strand cleaving Cas9 molecules and single strand, or nickase, Cas9 molecules can be used in the methods and compositions described herein to generate NHEJ-mediated indels. NHEJ-mediated indels targeted to the gene, e.g., a coding region, e.g., an early coding region of a gene of interest can be used to knockout (i.e., eliminate expression of) a gene of interest. For example, early coding region of a gene of interest includes sequence immediately following a transcription start site, within a first exon of the coding sequence, or within 500 bp of the transcription start site (e.g., less than 500, 450, 400, 350, 300, 250, 200, 150, 100 or 50 bp).


Placement of Double Strand or Single Strand Breaks Relative to the Target Position

In an embodiment, in which a gRNA and Cas9 nuclease generate a double strand break for the purpose of inducing NHEJ-mediated indels, a gRNA, e.g., a unimolecular (or chimeric) or modular gRNA molecule, is configured to position one double-strand break in close proximity to a nucleotide of the target position. In an embodiment, the cleavage site is between 0-500 bp away from the target position (e.g., less than 500, 400, 300, 200, 100, 50, 40, 30, 25, 20, 15, 10, 9, 8, 7, 6, 5, 4, 3, 2 or 1 bp from the target position).


In an embodiment, in which two gRNAs complexing with Cas9 nickases induce two single strand breaks for the purpose of inducing NHEJ-mediated indels, two gRNAs, e.g., independently, unimolecular (or chimeric) or modular gRNA, are configured to position two single-strand breaks to provide for NHEJ repair a nucleotide of the target position. In an embodiment, the gRNAs are configured to position cuts at the same position, or within a few nucleotides of one another, on different strands, essentially mimicking a double strand break. In an embodiment, the closer nick is between 0-30 bp away from the target position (e.g., less than 30, 25, 20, 1, 10, 9, 8, 7, 6, 5, 4, 3, 2 or 1 bp from the target position), and the two nicks are within 25-55 bp of each other (e.g., between 25 to 50, 25 to 45, 25 to 40, 25 to 35, 25 to 30, 50 to 55, 45 to 55, 40 to 55, 35 to 55, 30 to 55, 30 to 50, 35 to 50, 40 to 50, 45 to 50, 35 to 45, or 40 to 45 bp) and no more than 100 bp away from each other (e.g., no more than 90, 80, 70, 60, 50, 40, 30, 20 or 10 bp). In an embodiment, the gRNAs are configured to place a single strand break on either side of a nucleotide of the target position.


Both double strand cleaving Cas9 molecules and single strand, or nickase, Cas9 molecules can be used in the methods and compositions described herein to generate breaks both sides of a target position. Double strand or paired single strand breaks may be generated on both sides of a target position to remove the nucleic acid sequence between the two cuts (e.g., the region between the two breaks is deleted). In one embodiment, two gRNAs, e.g., independently, unimolecular (or chimeric) or modular gRNA, are configured to position a double-strand break on both sides of a target position (e.g., the first gRNA is used to target upstream (i.e., 5′) of the mutation in a gene or pathway described herein, and the second gRNA is used to target downstream (i.e., 3′) of the mutation in a gene or pathway described herein). In an alternate embodiment, three gRNAs, e.g., independently, unimolecular (or chimeric) or modular gRNA, are configured to position a double strand break (i.e., one gRNA complexes with a Cas9 nuclease) and two single strand breaks or paired single stranded breaks (i.e., two gRNAs complex with Cas9 nickases) on either side of a target position (e.g., the fu st gRNA is used to target upstream (i.e., 5′) of the mutation in a gene or pathway described herein, and the second gRNA is used to target downstream (i.e., 3′) of the mutation in a gene or pathway described herein). In another embodiment, four gRNAs, e.g., independently, unimolecular (or chimeric) or modular gRNA, are configured to generate two pairs of single stranded breaks (i.e., two pairs of two gRNAs complex with Cas9 nickases) on either side of the target position (e.g., the first gRNA is used to target upstream (i.e., 5′) of the mutation in a gene or pathway described herein, and the second gRNA is used to target downstream (i.e., 3′) of the mutation in a gene or pathway described herein). The double strand break(s) or the closer of the two single strand nicks in a pair will ideally be within 0-500 bp of the target position (e.g., no more than 450, 400, 350, 300, 250, 200, 150, 100, 50 or 25 bp from the target position). When nickases are used, the two nicks in a pair are within 25-55 bp of each other (e.g., between 25 to 50, 25 to 45, 25 to 40, 25 to 35, 25 to 30, 50 to 55, 45 to 55, 40 to 55, 35 to 55, 30 to 55, 30 to 50, 35 to 50, 40 to 50, 45 to 50, 35 to 45, or 40 to 45 bp) and no more than 100 bp away from each other (e.g., no more than 90, 80, 70, 60, 50, 40, 30, 20 or 10 bp).


In other embodiments, the insertion of template nucleic acid may be mediated by microhomology end joining (MMEJ). See, e.g., Saksuma et al., “MMEJ-assisted gene knock-in using TALENs and CRISPR-Cas9 with the PITCh systems.” Nature Protocols 11, 118-133 (2016) doi:10.1038/nprot.2015.140 Published online 17 Dec. 2015, the contents of which are incorporated by reference in their entirety.


VIII. Systems Comprising More Than One gRNA Molecule

While not intending to be bound by theory, it has been surprisingly shown herein that the targeting of two target sequences (e.g., by two gRNA molecule/Cas9 molecule complexes which each induce a single- or double-strand break at or near their respective target sequences) located in close proximity on a continuous nucleic acid induces excision (e.g., deletion) of the nucleic acid sequence (or at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% of the nucleic acid sequence) located between the two target sequences. In some aspects, the present disclosure provides for the use of two or more gRNA molecules that comprise targeting domains targeting target sequences in close proximity on a continuous nucleic acid, e.g., a chromosome, e.g., a gene or gene locus, including its introns, exons and regulatory elements. The use may be, for example, by introduction of the two or more gRNA molecules, together with one or more Cas9 molecules (or nucleic acid encoding the two or more gRNA molecules and/or the one or more Cas9 molecules) into a cell.


In some aspects, the target sequences of the two or more gRNA molecules are located at least 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 2000, 3000, 4000, 5000, 6000, 7000, 8000, 9000, 10,000, 11,000, 12,000, 13,000, 14,000, or 15,000 nucleotides apart on a continuous nucleic acid, but not more than 25,000 nucleotides apart on a continuous nucleic acid. In an embodiment, the target sequences are located about 4000 nucleotides apart. In an embodiment, the target sequences are located about 6000 nucleotides apart.


In some aspects, the plurality of gRNA molecules each target sequences within the same gene or gene locus. In another aspect, the plurality of gRNA molecules each target sequences within 2 or more different genes.


In some aspects, the invention provides compositions and cells comprising a plurality, for example, 2 or more, for example, 2, gRNA molecules of the invention, wherein the plurality of gRNA molecules target sequences less than 15,000, less than 14,000, less than 13,000, less than 12,000, less than 11,000, less than 10,000, less than 9,000, less than 8,000, less than 7,000, less than 6,000, less than 5,000, less than 4,000, less than 3,000, less than 2,000, less than 1,000, less than 900, less than 800, less than 700, less than 600, less than 500, less than 400, less than 300, less than 200, less than 100, less than 90, less than 80, less than 70, less than 60, less than 50, less than 40, or less than 30 nucleotides apart. In an embodiment, the target sequences are on the same strand of duplex nucleic acid. In an embodiment, the target sequences are on different strands of duplex nucleic acid.


In one embodiment, the invention provides a method for excising (e.g., deleting) nucleic acid disposed between two gRNA binding sites disposed less than 25,000, less than 20,000, less than 15,000, less than 14,000, less than 13,000, less than 12,000, less than 11,000, less than 10,000, less than 9,000, less than 8,000, less than 7,000, less than 6,000, less than 5,000, less than 4,000, less than 3,000, less than 2,000, less than 1,000, less than 900, less than 800, less than 700, less than 600, less than 500, less than 400, less than 300, less than 200, less than 100, less than 90, less than 80, less than 70, less than 60, less than 50, less than 40, or less than 30 nucleotides apart on the same or different strands of duplex nucleic acid. In an embodiment, the method provides for deletion of more than 50%, more than 60%, more than 70%, more than 80%, more than 85%, more than 86%, more than 87%, more than 88%, more than 89%, more than 90%, more than 91%, more than 92%, more than 93%, more than 94%, more than 95%, more than 96%, more than 97%, more than 98%, more than 99%, or 100% of the nucleotides disposed between the PAM sites associated with each gRNA binding site. In embodiments, the deletion further comprises of one or more nucleotides within one or more of the PAM sites associated with each gRNA binding site. In embodiments, the deletion also comprises one or more nucleotides outside of the region between the PAM sites associated with each gRNA binding site.


In one aspect, the two or more gRNA molecules comprise targeting domains targeting target sequences flanking a gene regulatory element, e.g., a promotor binding site, an enhancer region, or a repressor region, such that excision of the intervening sequence (or a portion of the intervening sequence) causes up- or down-regulation of a gene of interest.


In an embodiment, the two or more gRNA molecules include targeting domains comprising, e.g., consisting of, a targeting domain sequence of Table 1 or Table 5. In aspects, the two or more gRNA molecules comprise targeting domains that are complementary with sequences in the same gene. In aspects, the two or more gRNA molecules comprise targeting domains that are complementary with sequences of different genes. In an embodiment, the two or more gRNA molecules include targeting domains comprising, e.g., consisting of, a targeting domain sequence of Table 6. In an embodiment, the two or more gRNA molecules include targeting domains comprising, e.g., consisting of, a targeting domain sequence of Table 2, Table 7, Table 8 and/or Table 9. In aspects, the two or more gRNA molecules comprise targeting domains that are complementary with sequences in the same gene. In aspects, the two or more gRNA molecules comprise targeting domains that are complementary with sequences of different genes. In an embodiment, the two or more gRNA molecules are selected from the gRNA molecules of Table 7, Table 8 and/or Table 9. In an embodiment, the first and second gRNA molecules comprise targeting domains comprising, e.g., consisting of, targeting domain sequences selected from Tables 1-9, and are selected from different tables, e.g., and comprise targeting domains that are complementary with sequences of different genes.


In one aspect, the two or more gRNA molecules comprise targeting domains targeting target sequences flanking a gene regulatory element, e.g., a promotor binding site, an enhancer region, or a repressor region, such that excision of the intervening sequence (or a portion of the intervening sequence) causes up- or down-regulation of a gene of interest. By way of example, the two or more gRNA molecules comprise targeting domains targeting target sequences flanking a GATA1 binding site (or portion thereof) or TAL1 binding site (or portion thereof) of the erythroid enhancer region of the BCL11a gene (e.g., within the +55, +58 or +62 region). In other embodiments, the gRNA molecule or molecules do not result in a disruption of the GATA1 binding site or TAL1 binding site within the BCL11a Enhancer.


In an embodiment, the two or more gRNA molecules comprise targeting domains that comprise, e.g., consist of, targeting domains selected from Table 1. In an embodiment, the two or more gRNA molecules comprise targeting domains that comprise, e.g., consist of, targeting domains selected from Table 2. In an embodiment, the two or more gRNA molecules comprise targeting domains that comprise, e.g., consist of, targeting domains selected from Table 3. In an embodiment, the two or more gRNA molecules comprise targeting domains that comprise, e.g., consist of, targeting domains selected from Table 4. In an embodiment, the two or more gRNA molecules comprise targeting domains that comprise, e.g., consist of, targeting domains selected from Table 5. In an embodiment, the two or more gRNA molecules comprise targeting domains that comprise, e.g., consist of, targeting domains selected from Table 6. In an embodiment, the two or more gRNA molecules comprise targeting domains that comprise, e.g., consist of, targeting domains selected from Table 7. In an embodiment, the two or more gRNA molecules comprise targeting domains that comprise, e.g., consist of, targeting domains selected from Table 8. In an embodiment, the two or more gRNA molecules comprise targeting domains that comprise, e.g., consist of, targeting domains selected from Table 9.


In aspects, the two or more gRNA molecules comprise targeting domains comprising, e.g., consisting of the targeting domain sequence pairs listed in section II, above.


Without being bound by theory, it is believed that increasing the expression of fetal hemoglobin (e.g., gamma globin) while simultaneously reducing or eliminating expression of beta globin (e.g., beta globin comprising a sickling mutation), will result in increased efficacy in treating a hemoglobinopathy, e.g., sickle cell disease. Thus, in one aspect, the two or more gRNA molecules comprise a first gRNA molecule that causes an increase in gamma globin expression and a second gRNA molecule that reduces or eliminates expression of beta globin, e.g., beta globin carrying a sickle cell mutation. In embodiments, the two or more gRNA molecules comprise a first gRNA molecule that targets a sequence within a BCL11a enhancer region, e.g., as described herein, e.g., a gRNA molecule comprising a targeting domain comprising, e.g., consisting of, a targeting domain of Table 7, Table 8 or Table 9, and a second gRNA molecule that targets a sequence of a sickle globin gene (e.g., a beta globin gene comprising a sickling mutation).


IX. Properties of the gRNA

It has further been surprisingly shown herein that gRNA molecules and CRISPR systems comprising said gRNA molecules produce similar or identical indel patterns across multiple experiments using the same cell type, method of delivery and crRNA/tracr components. Without being bound by theory, it is believed that some indel patterns may be more advantageous than others. For example, indels which predominantly include insertions and/or deletions which result in a “frameshift mutation” (e.g., 1- or 2-base pair insertion or deletions, or any insertion or deletion where n/3 is not a whole number (where n=the number of nucleotides in the insertion or deletion)) may be beneficial in reducing or eliminating expression of a functional protein. Likewise, indels which predominantly include “large deletions” (deletions of more than 10, 11, 12, 13, 14, 15, 20, 25, or 30 nucleotides) may also be beneficial in, for example, removing critical regulatory sequences such as promoter binding sites, which may similarly have an improved effect on expression of functional protein. While the indel patterns induced by a given gRNA/CRISPR system have surprisingly been found to be consistently reproduced across cell types, as described herein, not any single indel structure will inevitably be produced in a given cell upon introduction of a gRNA/CRISPR system.


The invention thus provides for gRNA molecules which create a beneficial indel pattern or structure, for example, which have indel patterns or structures predominantly composed of frameshift mutation(s) and/or large deletions. Such gRNA molecules may be selected by assessing the indel pattern or structure created by a candidate gRNA molecule in a test cell (for example, a HEK293 cell) or in the cell of interest, e.g., a HSPC cell by NGS, as described herein. As shown in the Examples, gRNA molecules have been discovered, which, when introduced into the desired cell population, result in a population of cells comprising a significant fraction of the cells having a frameshift mutation in the targeted gene. In some cases, the rate of frameshift mutation is as high as 75%, 80%, 85%, 90% or more. The invention thus provides for populations of cells which comprise at least about 40% of cells (e.g., at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or at least about 99%) having a frameshift mutation, e.g., as described herein, at or near the target site of a gRNA moleucle described herein. The invention also provides for populations of cells which comprise at least about 50% of cells (e.g., at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or at least about 99%) having a frameshift mutation, e.g., as described herein, at or near the target site of a gRNA moleucle described herein.


The invention thus provides methods of selecting gRNA molecules for use in the therapeutic methods of the invention comprising: 1) providing a plurality of gRNA molecules to a target of interest, 2) assessing the indel pattern or structure created by use of said gRNA molecules, 3) selecting a gRNA molecule that forms an indel pattern or structure composed predominantly of frameshift mutations, large deletions or a combination thereof, and 4) using said selected gRNA in a methods of the invention.


The invention further provides methods of altering cells, and altered cells, wherein a particular indel pattern is consistently produced with a given gRNA/CRISPR system in that cell type. The indel patterns, including the top 5 most frequently occurring indels observed with the gRNA/CRISPR systems described herein are disclosed, for example, in the Examples. As shown in the examples, populations of cells are generated, wherein a significant fraction of the cells comprises one of the top 5 indels (for example, populations of cells wherein one of the top 5 indels is present in more than 30%, more than 40%, more than 50%, more than 60% or more of the cells of the population. Thus, the invention provides cells, e.g., HSPCs (as described herein), which comprise an indel of any one of the top 5 indels observed with a given gRNA/CRISPR system. Further, the invention provides populations of cells, e.g., HSPCs (as described herein), which when assessed by, for example, NGS, comprise a high percentage of cells comprising one of the top 5 indels described herein for a given gRNA/CRISPR system. When used in connection with indel pattern analysis, a “high percentage” refers to at least about 50% (e.g., at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or at least about 99%) of the cells of the population comprising one of the top 5 indels described herein for a given gRNA/CRISPR system. In other embodiments, the population of cells comprises at least about 25% (e.g., from about 25% to about 60%, e.g., from about 25% to about 50%, e.g., from about 25% to about 40%, e.g., from about 25% to about 35%) of cells which have one of the top 5 indels described herein for a given gRNA/CRISPR system. In embodiments, the top indels, e.g., top 5 indels for a given gRNA/CRISPR system which targets a +58 region of the BCL11a enhancer are provided in Table 15, FIG. 25, and Table 37. In embodiments, the top indels, e.g., top 5 indels for a given gRNA/CRISPR system which targets a HPFH region are provided in Table 26, Table 27 and Table 37.


It has also been discovered that certain gRNA molecules do not create indels at off-target sequences within the genome of the target cell type, or produce indels at off target sites at very low frequencies (e.g., <5% of cells within a population) relative to the frequency of indel creation at the target site. Thus, the invention provides for gRNA molecules and CRISPR systems which do not exhibit off-target indel formation in the target cell type, or which produce a frequency of off-target indel formation of <5%. In embodiments, the invention provides gRNA molecules and CRISPR systems which do not exhibit any off target indel formation in the target cell type. Thus, the invention further provides a cell, e.g., a population of cells, e.g., HSPCs, e.g., as described herein, which comprise an indel at or near a target site of a gRNA molecule described herein (e.g., a frameshift indel, or any one of the top 5 indels produced by a given gRNA/CRISPR system, e.g., as described herein), but does not comprise an indel at any off-target site of the gRNA molecule. In other embodiments, the invention further provides a a population of cells, e.g., HSPCs, e.g., as described herein, which comprises >50% of cells which have an indel at or near a target site of a gRNA molecule described herein (e.g., a frameshift indel, or any one of the top 5 indels produced by a given gRNA/CRISPR system, e.g., as described herein), but which comprises less than 5%, e.g., less than 4%, less than 3%, less than 2% or less than 1%, of cells comprising an indel at any off-target site of the gRNA molecule.


In embodiments, the indel produced by a CRISPR system described herein (e.g., a CRISPR system comprising a gRNA molecule described herein), does not comprise a nucleotide of a GATA-1 binding site and/or does not comprise a nucleotide of a TAL-1 binding site (e.g., does not comprise a nucleotide of a GATA-1 binding site and/or TAL-1 binding site described in FIG. 25).


X. Delivery/Constructs

The components, e.g., a Cas9 molecule or gRNA molecule, or both, can be delivered, formulated, or administered in a variety of forms. As a non-limiting example, the gRNA molecule and Cas9 molecule can be formulated (in one or more compositions), directly delivered or administered to a cell in which a genome editing event is desired. Alternatively, nucleic acid encoding one or more components, e.g., a Cas9 molecule or gRNA molecule, or both, can be formulated (in one or more compositions), delivered or administered. In one aspect, the gRNA molecule is provided as DNA encoding the gRNA molecule and the Cas9 molecule is provided as DNA encoding the Cas9 molecule. In one embodiment, the gRNA molecule and Cas9 molecule are encoded on separate nucleic acid molecules. In one embodiment, the gRNA molecule and Cas9 molecule are encoded on the same nucleic acid molecule. In one aspect, the gRNA molecule is provided as RNA and the Cas9 molecule is provided as DNA encoding the Cas9 molecule. In one embodiment, the gRNA molecule is provided with one or more modifications, e.g., as described herein. In one aspect, the gRNA molecule is provided as RNA and the Cas9 molecule is provided as mRNA encoding the Cas9 molecule. In one aspect, the gRNA molecule is provided as RNA and the Cas9 molecule is provided as a protein. In one embodiment, the gRNA and Cas9 molecule are provided as a ribonuclear protein complex (RNP). In one aspect, the gRNA molecule is provided as DNA encoding the gRNA molecule and the Cas9 molecule is provided as a protein.


Delivery, e.g., delivery of the RNP, (e.g., to HSPC cells as described herein) may be accomplished by, for example, electroporation (e.g., as known in the art) or other method that renders the cell membrane permeable to nucleic acid and/or polypeptide molecules. In embodiments, the CRISPR system, e.g., the RNP as described herein, is delivered by electroporation using a 4D-Nucleofector (Lonza), for example, using program CM-137 on the 4D-Nucleofector (Lonza). In embodiments, the CRISPR system, e.g., the RNP as described herein, is delivered by electroporation using a voltage from about 800 volts to about 2000 volts, e.g., from about 1000 volts to about 1800 volts, e.g., from about 1200 volts to about 1800 volts, e.g., from about 1400 volts to about 1800 volts, e.g., from about 1600 volts to about 1800 volts, e.g., about 1700 volts, e.g., at a voltage of 1700 volts. In embodiments, the pulse width/length is from about 10 ms to about 50 ms, e.g., from about 10 ms to about 40 ms, e.g., from about 10 ms to about 30 ms, e.g., from about 15 ms to about 25 ms, e.g., about 20 ms, e.g., 20 ms. In embodiments, 1, 2, 3, 4, 5, or more, e.g., 2, e.g., 1 pulses are used. In an embodiment, the CRISPR system, e.g., the RNP as described herein, is delivered by electroporation using a voltage of about 1700 volts (e.g., 1700 volts), a pulse width of about 20 ms (e.g., 20 ms), using a single (1) pulse. In embodiments, electroporation is accomplished using a Neon electroporator. Additional techniques for rendering the membrane permeable are known in the art and include, for example, cell squeezing (e.g., as described in WO2015/023982 and WO2013/059343, the contents of which are hereby incorporated by reference in their entirety), nanoneedles (e.g., as described in Chiappini et al., Nat. Mat., 14; 532-39, or US2014/0295558, the contents of which are hereby incorporated by reference in their entirety) and nanostraws (e.g., as described in Xie, ACS Nano, 7(5); 4351-58, the contents of which are hereby incorporated by reference in their entirety).


When a component is delivered encoded in DNA the DNA will typically include a control region, e.g., comprising a promoter, to effect expression. Useful promoters for Cas9 molecule sequences include CMV, EF-1alpha, MSCV, PGK, CAG control promoters. Useful promoters for gRNAs include H1, EF-1a and U6 promoters. Promoters with similar or dissimilar strengths can be selected to tune the expression of components. Sequences encoding a Cas9 molecule can comprise a nuclear localization signal (NLS), e.g., an SV40 NLS. In an embodiment, a promoter for a Cas9 molecule or a gRNA molecule can be, independently, inducible, tissue specific, or cell specific.


DNA-Based Delivery of a Cas9 Molecule and or a gRNA Molecule


DNA encoding Cas9 molecules and/or gRNA molecules, can be administered to subjects or delivered into cells by art-known methods or as described herein. For example, Cas9-encoding and/or gRNA-encoding DNA can be delivered, e.g., by vectors (e.g., viral or non-viral vectors), non-vector based methods (e.g., using naked DNA or DNA complexes), or a combination thereof.


In some embodiments, the Cas9- and/or gRNA-encoding DNA is delivered by a vector (e.g., viral vector/virus, plasmid, minicircle or nanoplasmid).


A vector can comprise a sequence that encodes a Cas9 molecule and/or a gRNA molecule. A vector can also comprise a sequence encoding a signal peptide (e.g., for nuclear localization, nucleolar localization, mitochondrial localization), fused, e.g., to a Cas9 molecule sequence. For example, a vector can comprise one or more nuclear localization sequence (e.g., from SV40) fused to the sequence encoding the Cas9 molecule.


One or more regulatory/control elements, e.g., a promoter, an enhancer, an intron, a polyadenylation signal, a Kozak consensus sequence, internal ribosome entry sites (IRES), a 2A sequence, and a splice acceptor or donor can be included in the vectors. In some embodiments, the promoter is recognized by RNA polymerase II (e.g., a CMV promoter). In other embodiments, the promoter is recognized by RNA polymerase III (e.g., a U6 promoter). In some embodiments, the promoter is a regulated promoter (e.g., inducible promoter). In other embodiments, the promoter is a constitutive promoter. In some embodiments, the promoter is a tissue specific promoter. In some embodiments, the promoter is a viral promoter. In other embodiments, the promoter is a non-viral promoter.


In some embodiments, the vector or delivery vehicle is a minicircle. In some embodiments, the vector or delivery vehicle is a nanoplasmid.


In some embodiments, the vector or delivery vehicle is a viral vector (e.g., for generation of recombinant viruses). In some embodiments, the virus is a DNA virus (e.g., dsDNA or ssDNA virus). In other embodiments, the virus is an RNA virus (e.g., an ssRNA virus).


Exemplary viral vectors/viruses include, e.g., retroviruses, lentiviruses, adenovirus, adeno-associated virus (AAV), vaccinia viruses, poxviruses, and herpes simplex viruses. Viral vector technology is well known in the art and is described, for example, in Sambrook et al., 2012, MOLECULAR CLONING: A LABORATORY MANUAL, volumes 1-4, Cold Spring Harbor Press, NY), and in other virology and molecular biology manuals.


In some embodiments, the virus infects dividing cells. In other embodiments, the virus infects non-dividing cells. In some embodiments, the virus infects both dividing and non-dividing cells. In some embodiments, the virus can integrate into the host genome. In some embodiments, the virus is engineered to have reduced immunity, e.g., in human. In some embodiments, the virus is replication-competent. In other embodiments, the virus is replication-defective, e.g., having one or more coding regions for the genes necessary for additional rounds of virion replication and/or packaging replaced with other genes or deleted. In some embodiments, the virus causes transient expression of the Cas9 molecule and/or the gRNA molecule. In other embodiments, the virus causes long-lasting, e.g., at least 1 week, 2 weeks, 1 month, 2 months, 3 months, 6 months, 9 months, 1 year, 2 years, or permanent expression, of the Cas9 molecule and/or the gRNA molecule. The packaging capacity of the viruses may vary, e.g., from at least about 4 kb to at least about 30 kb, e.g., at least about 5 kb, 10 kb, 15 kb, 20 kb, 25 kb, 30 kb, 35 kb, 40 kb, 45 kb, or 50 kb.


In some embodiments, the Cas9- and/or gRNA-encoding DNA is delivered by a recombinant retrovirus. In some embodiments, the retrovirus (e.g., Moloney murine leukemia virus) comprises a reverse transcriptase, e.g., that allows integration into the host genome. In some embodiments, the retrovirus is replication-competent. In other embodiments, the retrovirus is replication-defective, e.g., having one of more coding regions for the genes necessary for additional rounds of virion replication and packaging replaced with other genes, or deleted.


In some embodiments, the Cas9- and/or gRNA-encoding DNA is delivered by a recombinant lentivirus. For example, the lentivirus is replication-defective, e.g., does not comprise one or more genes required for viral replication.


In some embodiments, the Cas9- and/or gRNA-encoding DNA is delivered by a recombinant adenovirus. In some embodiments, the adenovirus is engineered to have reduced immunity in human.


In some embodiments, the Cas9- and/or gRNA-encoding DNA is delivered by a recombinant AAV. In some embodiments, the AAV can incorporate its genome into that of a host cell, e.g., a target cell as described herein. In some embodiments, the AAV is a self-complementary adeno-associated virus (scAAV), e.g., a scAAV that packages both strands which anneal together to form double stranded DNA. AAV serotypes that may be used in the disclosed methods include, e.g., AAV 1, AAV2, modified AAV2 (e.g., modifications at Y444F, Y500F, Y730F and/or S662V), AAV3, modified AAV3 (e.g., modifications at Y705F, Y731F and/or. T492V), AAV4, AAVS, AAV6, modified AAV6 (e.g., modifications at S663V and/or T492V), AAV8. AAV 8.2, AAV9, AAV rh 10, and pseudotyped AAV, such as AAV2/8, AAV2/5 and AAV2/6 can also be used in the disclosed methods.


In some embodiments, the Cas9- and/or gRNA-encoding DNA is delivered by a hybrid virus, e.g., a hybrid of one or more of the viruses described herein.


A Packaging cell is used to form a virus particle that is capable of infecting a host or target cell. Such a cell includes a 293 cell, which can package adenovirus, and a w2 cell or a PA317 cell, which can package retrovirus. A viral vector used in gene therapy is usually generated by a producer cell line that packages a nucleic acid vector into a viral particle. The vector typically contains the minimal viral sequences required for packaging and subsequent integration into a host or target cell (if applicable), with other viral sequences being replaced by an expression cassette encoding the protein to be expressed. For example, an AAV vector used in gene therapy typically only possesses inverted terminal repeat (ITR) sequences from the AAV genome which are required for packaging and gene expression in the host or target cell. The missing viral functions are supplied in trans by the packaging cell line. Henceforth, the viral DNA is packaged in a cell line, which contains a helper plasmid encoding the other AAV genes, namely rep and cap, but lacking ITR sequences. The cell line is also infected with adenovirus as a helper. The helper virus promotes replication of the AAV vector and expression of AAV genes from the helper plasmid. The helper plasmid is not packaged in significant amounts due to a lack of ITR sequences. Contamination with adenovirus can be reduced by, e.g., heat treatment to which adenovirus is more sensitive than AAV.


In an embodiment, the viral vector has the ability of cell type and/or tissue type recognition. For example, the viral vector can be pseudotyped with a different/alternative viral envelope glycoprotein; engineered with a cell type-specific receptor (e.g., genetic modification of the viral envelope glycoproteins to incorporate targeting ligands such as a peptide ligand, a single chain antibody, a growth factor); and/or engineered to have a molecular bridge with dual specificities with one end recognizing a viral glycoprotein and the other end recognizing a moiety of the target cell surface (e.g., ligand-receptor, monoclonal antibody, avidin-biotin and chemical conjugation).


In an embodiment, the viral vector achieves cell type specific expression. For example, a tissue-specific promoter can be constructed to restrict expression of the transgene (Cas 9 and gRNA) in only the target cell. The specificity of the vector can also be mediated by microRNA-dependent control of transgene expression. In an embodiment, the viral vector has increased efficiency of fusion of the viral vector and a target cell membrane. For example, a fusion protein such as fusion-competent hemagglutin (HA) can be incorporated to increase viral uptake into cells. In an embodiment, the viral vector has the ability of nuclear localization. For example, a virus that requires the breakdown of the cell wall (during cell division) and therefore will not infect a non-diving cell can be altered to incorporate a nuclear localization peptide in the matrix protein of the virus thereby enabling the transduction of non-proliferating cells.


In some embodiments, the Cas9- and/or gRNA-encoding DNA is delivered by a non-vector based method (e.g., using naked DNA or DNA complexes). For example, the DNA can be delivered, e.g., by organically modified silica or silicate (Ormosil), electroporation, gene gun, sonoporation, magnetofection, lipid-mediated transfection, dendrimers, inorganic nanoparticles, calcium phosphates, or a combination thereof.


In some embodiments, the Cas9- and/or gRNA-encoding DNA is delivered by a combination of a vector and a non-vector based method. For example, a virosome comprises a liposome combined with an inactivated virus (e.g., HIV or influenza virus), which can result in more efficient gene transfer, e.g., in a respiratory epithelial cell than either a viral or a liposomal method alone.


In an embodiment, the delivery vehicle is a non-viral vector. In an embodiment, the non-viral vector is an inorganic nanoparticle (e.g., attached to the payload to the surface of the nanoparticle).


Exemplary inorganic nanoparticles include, e.g., magnetic nanoparticles (e.g., Fe lvln02), or silica. The outer surface of the nanoparticle can be conjugated with a positively charged polymer (e.g., polyethylenimine, polylysine, polyserine) which allows for attachment (e.g., conjugation or entrapment) of payload. In an embodiment, the non-viral vector is an organic nanoparticle (e.g., entrapment of the payload inside the nanoparticle). Exemplary organic nanoparticles include, e.g., SNALP liposomes that contain cationic lipids together with neutral helper lipids which are coated with polyethylene glycol (PEG) and protamine and nucleic acid complex coated with lipid coating.


Exemplary lipids and/or polymers for for transfer of CRISPR systems or nucleic acid, e.g., vectors, encoding CRISPR systems or components thereof include, for example, those described in WO2011/076807, WO2014/136086, WO2005/060697, WO2014/140211, WO2012/031046, WO2013/103467, WO2013/006825, WO2012/006378, WO2015/095340, and WO2015/095346, the contents of each of the foregoing are hereby incorporated by reference in their entirety. In an embodiment, the vehicle has targeting modifications to increase target cell update of nanoparticles and liposomes, e.g., cell specific antigens, monoclonal antibodies, single chain antibodies, aptamers, polymers, sugars, and cell penetrating peptides. In an embodiment, the vehicle uses fusogenic and endosome-destabilizing peptides/polymers. In an embodiment, the vehicle undergoes acid-triggered conformational changes (e.g., to accelerate endosomal escape of the cargo). In an embodiment, a stimuli-cleavable polymer is used, e.g., for release in a cellular compartment. For example, disulfide-based cationic polymers that are cleaved in the reducing cellular environment can be used.


In an embodiment, the delivery vehicle is a biological non-viral delivery vehicle. In an embodiment, the vehicle is an attenuated bacterium (e.g., naturally or artificially engineered to be invasive but attenuated to prevent pathogenesis and expressing the transgene (e.g., Listeria monocytogenes, certain Salmonella strains, Bifidobacterium longum, and modified Escherichia coli), bacteria having nutritional and tissue-specific tropism to target specific tissues, bacteria having modified surface proteins to alter target tissue specificity). In an embodiment, the vehicle is a genetically modified bacteriophage (e.g., engineered phages having large packaging capacity, less immunogenic, containing mammalian plasmid maintenance sequences and having incorporated targeting ligands) In an embodiment, the vehicle is a mammalian virus-like particle. For example, modified viral particles can be generated (e.g., by purification of the “empty” particles followed by ex vivo assembly of the virus with the desired cargo). The vehicle can also be engineered to incorporate targeting ligands to alter target tissue specificity. In an embodiment, the vehicle is a biological liposome. For example, the biological liposome is a phospholipid-based particle derived from human cells (e.g., erythrocyte ghosts, which are red blood cells broken down into spherical structures derived from the subject (e.g., tissue targeting can be achieved by attachment of various tissue or cell-specific ligands), or secretory exosomes—subject (i.e., patient) derived membrane-bound nanovescicle (30-100 nm) of endocytic origin (e.g., can be produced from various cell types and can therefore be taken up by cells without the need of for targeting ligands).


In an embodiment, one or more nucleic acid molecules (e.g., DNA molecules) other than the components of a Cas system, e.g., the Cas9 molecule component and/or the gRNA molecule component described herein, are delivered. In an embodiment, the nucleic acid molecule is delivered at the same time as one or more of the components of the Cas system are delivered. In an embodiment, the nucleic acid molecule is delivered before or after (e.g., less than about 30 minutes, 1 hour, 2 hours, 3 hours, 6 hours, 9 hours, 12 hours, 1 day, 2 days, 3 days, 1 week, 2 weeks, or 4 weeks) one or more of the components of the Cas9 system are delivered. In an embodiment, the nucleic acid molecule is delivered by a different means than one or more of the components of the Cas9 system, e.g., the Cas9 molecule component and/or the gRNA molecule component, are delivered. The nucleic acid molecule can be delivered by any of the delivery methods described herein. For example, the nucleic acid molecule can be delivered by a viral vector, e.g., an integration-deficient lentivirus, and the Cas9 molecule component and/or the gRNA molecule component can be delivered by electroporation, e.g., such that the toxicity caused by nucleic acids (e.g., DNAs) can be reduced. In an embodiment, the nucleic acid molecule encodes a therapeutic protein, e.g., a protein described herein. In an embodiment, the nucleic acid molecule encodes an RNA molecule, e.g., an RNA molecule described herein. Delivery of RNA encoding a Cas9 molecule


RNA encoding Cas9 molecules (e.g., active Cas9 molecules, inactive Cas9 molecules or inactive Cas9 fusion proteins) and/or gRNA molecules, can be delivered into cells, e.g., target cells described herein, by art-known methods or as described herein. For example, Cas9-encoding and/or gRNA-encoding RNA can be delivered, e.g., by microinjection, electroporation, lipid-mediated transfection, peptide-mediated delivery, or a combination thereof.


Delivery of Cas9 Molecule as Protein

Cas9 molecules (e.g., active Cas9 molecules, inactive Cas9 molecules or inactive Cas9 fusion proteins) can be delivered into cells by art-known methods or as described herein. For example, Cas9 protein molecules can be delivered, e.g., by microinjection, electroporation, lipid-mediated transfection, peptide-mediated delivery, cell squeezing or abrasion (e.g., by nanoneedles) or a combination thereof. Delivery can be accompanied by DNA encoding a gRNA or by a gRNA, e.g., by precomplexing the gRNA and the Cas9 protein in a ribonuclear protein complex (RNP).


In an aspect the Cas9 molecule, e.g., as described herein, is delivered as a protein and the gRNA molecule is delivered as one or more RNAs (e.g., as a dgRNA or sgRNA, as described herein). In embodiments, the Cas9 protein is complexed with the gRNA molecule prior to delivery to a cell, e.g., as described herein, as a ribonuclear protein complex (“RNP”). In embodiments, the RNP can be delivered into cells, e.g., described herein, by any art-known method, e.g., electroporation. As described herein, and without being bound by theory, it can be preferable to use a gRNA moleucle and Cas9 molecule which result in high % editing at the target sequence (e.g., >85%, >90%, >95%, >98%, or >99%) in the target cell, e.g., described herein, even when the concentration of RNP delivered to the cell is reduced. Again, without being bound by theory, delivering a reduced or low concentration of RNP comprising a gRNA moleucle that produces a high % editing at the target sequence in the target cell (including at the low RNP concentration), can be beneficial because it may reduce the frequency and number of off-target editing events. In one aspect, where a low or reduced concentration of RNP is to be used, the following exemplary procedure can be used to generate the RNP with a dgRNA molecule:

    • 1. Provide the Cas9 molecule and the tracr in solution at a high concentration (e.g., a concentration higher than the final RNP concentration to be delivered to the cell), and allow the two components to equilibrate;
    • 2. Provide the crRNA molecule, and allow the components to equilibrate (thereby forming a high-concentration solution of the RNP);
    • 3. Dilute the RNP solution to the desired concentration;
    • 4. Deliver said RNP at said desired concentration to the target cells, e.g., by electroporation.


The above procedure may be modified for use with sgRNA molecules by omitting step 2, above, and in step 1, providing the Cas9 molecule and the sgRNA molecule in solution at high concentraiton, and allowing the components to equilibrate. In embodiments, the Cas9 moleucle and each gRNA component are provided in solution at a 1:2 ratio (Cas9:gRNA), e.g., a 1:2 molar ratio of Cas9:gRNA molecule. Where dgRNA molecules are used, the ratio, e.g., molar rato, is 1:2:2 (Cas9:tracr:crRNA). In embodiments, the RNP is formed at a concentration of 20 uM or higher, e.g., a concentration from about 20 uM to about 50 uM. In embodiments, the RNP is formed at a concentration of 10 uM or higher, e.g., a concentration from about 10 uM to about 30 uM. In embodiments, the RNP is diluted to a final concentration of 10 uM or less (e.g., a concentration from about 0.01 uM to about 10 uM) in a solution comprising the target cell (e.g., described herein) for delivery to said target cell. In embodiments, the RNP is diluted to a final concentration of 3 uM or less (e.g., a concentration from about 0.01 uM to about 3 uM) in a solution comprising the target cell (e.g., described herein) for delivery to said target cell. In embodiments, the RNP is diluted to a final concentration of 1 uM or less (e.g., a concentration from about 0.01 uM to about 1 uM) in a solution comprising the target cell (e.g., described herein) for delivery to said target cell. In embodiments, the RNP is diluted to a final concentration of 0.3 uM or less (e.g., a concentration from about 0.01 uM to about 0.3 uM) in a solution comprising the target cell (e.g., described herein) for delivery to said target cell. In embodiments, the RNP is provided at a final concentration of about 3 uM in a solution comprising the target cell (e.g., described herein) for delivery to said target cell. In embodiments, the RNP is provided at a final concentration of about 1 uM in a solution comprising the target cell (e.g., described herein) for delivery to said target cell. In embodiments, the RNP is provided at a final concentration of about 0.3 uM in a solution comprising the target cell (e.g., described herein) for delivery to said target cell. In embodiments, the RNP is provided at a final concentration of about 0.1 uM in a solution comprising the target cell (e.g., described herein) for delivery to said target cell. In embodiments, the RNP is provided at a final concentration of about 0.05 uM in a solution comprising the target cell (e.g., described herein) for delivery to said target cell. In embodiments, the RNP is provided at a final concentration of about 0.03 uM in a solution comprising the target cell (e.g., described herein) for delivery to said target cell. In embodiments, the RNP is provided at a final concentration of about 0.01 uM in a solution comprising the target cell (e.g., described herein) for delivery to said target cell. In embodiments, the RNP is formulated in a medium suitable for electroporation. In embodiments, the RNP is delivered to cells, e.g., HSPC cells, e.g., as described herein, by electroporation, e.g., using electroporation conditions described herein.


Bi-Modal or Differential Delivery of Components

Separate delivery of the components of a Cas system, e.g., the Cas9 molecule component and the gRNA molecule component, and more particularly, delivery of the components by differing modes, can enhance performance, e.g., by improving tissue specificity and safety.


In an embodiment, the Cas9 molecule and the gRNA molecule are delivered by different modes, or as sometimes referred to herein as differential modes. Different or differential modes, as used herein, refer modes of delivery that confer different pharmacodynamic or pharmacokinetic properties on the subject component molecule, e.g., a Cas9 molecule, gRNA molecule, or template nucleic acid. For example, the modes of delivery can result in different tissue distribution, different half-life, or different temporal distribution, e.g., in a selected compartment, tissue, or organ.


Some modes of delivery, e.g., delivery by a nucleic acid vector that persists in a cell, or in progeny of a cell, e.g., by autonomous replication or insertion into cellular nucleic acid, result-in more persistent expression of and presence of a component.


XI. Methods of Treatment

The Cas9 systems, e.g., one or more gRNA molecules and one or more Cas9 molecules, described herein are useful for the treatment of disease in a mammal, e.g., in a human. The terms “treat,” “treated,” “treating,” and “treatment,” include the administration of cas9 systems, e.g., one or more gRNA molecules and one or more cas9 molecules, to cells to prevent or delay the onset of the symptoms, complications, or biochemical indicia of a disease, alleviating the symptoms or arresting or inhibiting further development of the disease, condition, or disorder. Treatment may also include the administration of one or more (e.g., a population of) cells, e.g., HSPCs, that have been modified by the introduction of a gRNA molecule (or more than one gRNA molecule) of the present invention, or by the introduction of a CRISPR system as described herein, or by any of the methods of preparing said cells described herein, to prevent or delay the onset of the symptoms, complications, or biochemical indicia of a disease, alleviating the symptoms or arresting or inhibiting further development of the disease, condition, or disorder. Treatment may be prophylactic (to prevent or delay the onset of the disease, or to prevent the manifestation of clinical or subclinical symptoms thereof) or therapeutic suppression or alleviation of symptoms after the manifestation of the disease. Treatment can be measured by the therapeutic measures described hererin. Thus, the methods of “treatment” of the present invention also include administration of cells altered by the introduction of a cas9 system (e.g., one or more gRNA molecules and one or more Cas9 molecules) into said cells to a subject in order to cure, reduce the severity of, or ameliorate one or more symptoms of a disease or condition, in order to prolong the health or survival of a subject beyond that expected in the absence of such treatment. For example, “treatment” includes the alleviation of a disease symptom in a subject by at least 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or more.


Cas9 systems comprising gRNA molecules comprising the targeting domains described herein, e.g., in Tables 1, 2, 3, 4, 5, 6, 7, 8, and/or 9, are useful for the treatment of hemoglobinopathies.


Hemoglobinopathies

Hemoglobinopathies encompass a number of anemias of genetic origin in which there is a decreased production and/or increased destruction (hemolysis) of red blood cells (RBCs). These also include genetic defects that result in the production of abnormal hemoglobins with a concomitant impaired ability to maintain oxygen concentration. Some such disorders involve the failure to produce normal β-globin in sufficient amounts, while others involve the failure to produce normal β-globin entirely. These disorders associated with the β-globin protein are referred to generally as β-hemoglobinopathies. For example, β-thalassemias result from a partial or complete defect in the expression of the β-globin gene, leading to deficient or absent HbA. Sickle cell anemia results from a point mutation in the β-globin structural gene, leading to the production of an abnormal (sickle) hemoglobin (HbS). HbS is prone to polymerization, particularly under deoxygenated conditions. HbS RBCs are more fragile than normal RBCs and undergo hemolysis more readily, leading eventually to anemia.


In an embodiment, a genetic defect in alpha globin or beta globin is corrected, e.g., by homologous recombination, using the Cas9 molecules and gRNA molecules, e.g., CRISPR systems, described herein.


In an embodiment, a gene encoding a wild type (e.g., non-mutated) copy of alpha globin or beta globin is inserted into the genome of the cell, e.g., at a safe harbor site, e.g., at an AAVS1 safe harbor site, by homologous recombination, using a CRISPR system and methods described herein.


In an embodiment, a hemoglobinopathies-associated gene is targeted, using the Cas9 molecule and gRNA molecule described herein. Exemplary targets include, e.g., genes associated with control of the gamma-globin genes. In an embodiment, the target is BCL11A. In an embodiment, the target is a BCL11a enhancer. In an embodiment, the target is a HPFH region.


Fetal hemoglobin (also hemoglobin F or HbF or α2γ2) is a tetramer of two adult alpha-globin polypeptides and two fetal beta-like gamma-globin polypeptides. HbF is the main oxygen transport protein in the human fetus during the last seven months of development in the uterus and in the newborn until roughly 6 months old. Functionally, fetal hemoglobin differs most from adult hemoglobin in that it is able to bind oxygen with greater affinity than the adult form, giving the developing fetus better access to oxygen from the mother's bloodstream.


In newborns, fetal hemoglobin is nearly completely replaced by adult hemoglobin by approximately 6 months postnatally. In adults, fetal hemoglobin production can be reactivated pharmacologically, which is useful in the treatment of diseases such as hemoglobinopathies. For example, in certain patients with hemoglobinopathies, higher levels of gamma-globin expression can partially compensate for defective or impaired beta-globin gene production, which can ameliorate the clinical severity in these diseases. Increased HbF levels or F-cell (HbF containing erythrocyte) numbers can ameliorate the disease severity of hemoglobinopathies, e.g., beta-thalassemia major and sickle cell anemia.


Increased HbF levels or F-cell can be associated reduced BCL11A expression in cells. The BCL11A gene encodes a multi-zinc finger transcription factor. In an embodiment, the expression of BCL11A is modulated, e.g., down-regulated. In an embodiment, the BCL11A gene is edited. In an embodiment, the function of BCL11a, e.g., in an enrythroid lineage cell, is impaired or down-regulated. In an embodiment, the cell is a hemopoietic stem cell or progenitor cell.


Sickle Cell Diseases

Sickle cell disease is a group of disorders that affects hemoglobin. People with this disorder have atypical hemoglobin molecules (hemoglobin S), which can distort red blood cells into a sickle, or crescent, shape. Characteristic features of this disorder include a low number of red blood cells (anemia), repeated infections, and periodic episodes of pain.


Mutations in the HBB gene cause sickle cell disease. T e HBB gene provides instructions for making beta-globin. Various versions of beta-globin result from different mutations in the HBB gene. One particular HBB gene mutation produces an abnormal version of beta-globin known as hemoglobin S (HbS). Other mutations in the HBB gene lead to additional abnormal versions of beta-globin such as hemoglobin C (HbC) and hemoglobin E (HbE). HBB gene mutations can also result in an unusually low level of beta-globin, i.e., beta thalassemia.


In people with sickle cell disease, at least one of the beta-globin subunits in hemoglobin is replaced with hemoglobin S. In sickle cell anemia, which is a common form of sickle cell disease, hemoglobin S replaces both beta-globin subunits in hemoglobin. In other types of sickle cell disease, just one beta-globin subunit in hemoglobin is replaced with hemoglobin S. The other beta-globin subunit is replaced with a different abnormal variant, such as hemoglobin C. For example, people with sickle-hemoglobin C (HbSC) disease have hemoglobin molecules with hemoglobin S and hemoglobin C instead of beta-globin. If mutations that produce hemoglobin S and beta thalassemia occur together, individuals have hemoglobin S-beta thalassemia (HbSBetaThal) disease.


Beta Thalassemia

Beta thalassemia is a blood disorder that reduces the production of hemoglobin. In people with beta thalassemia, low levels of hemoglobin lead to a lack of oxygen in many parts of the body. Affected individuals also have a shortage of red blood cells (anemia), which can cause pale skin, weakness, fatigue, and more serious complications. People with beta thalassemia are at an increased risk of developing abnormal blood clots.


Beta thalassemia is classified into two types depending on the severity of symptoms: thalassemia major (also known as Cooley's anemia) and thalassemia intermedia. Of the two types, thalassemia major is more severe.


Mutations in the HBB gene cause beta thalassemia. The HBB gene provides instructions for making beta-globin. Some mutations in the HBB gene prevent the production of any beta-globin. The absence of beta-globin is referred to as beta-zero (Bº) thalassemia. Other HBB gene mutations allow some beta-globin to be produced but in reduced amounts, i.e., beta-plus (B+) thalassemia. People with both types have been diagnosed with thalassemia major and thalassemia intermedia.


In an embodiment, a Cas9 molecule/gRNA molecule complex targeting a first gene is used to treat a disorder characterized by second gene, e.g., a mutation in a second gene. By way of example, targeting of the first gene, e.g., by editing or payload delivery, can compensate for, or inhibit further damage from, the affect of a second gene, e.g., a mutant second gene. In an embodiment the allele(s) of the first gene carried by the subject is not causative of the disorder.


In one aspect, the invention relates to the treatment of a mammal, e.g., a human, in need of increased fetal hemoglobin (HbF).


In one aspect, the invention relates to the treatment of a mammal, e.g., a human, that has been diagnosed with, or is at risk of developing, a hemoglobinopathy.


In one aspect, the hemoglobinopathy is a β-hemoglobinopathy. In one aspect, the hemoglobinopathy is sickle cell disease. In one aspect, the hemoglobinopathy is beta thalassemia.


Methods of Treatment of Hemoglobinopathies

In another aspect the invention provides methods of treatment. In aspects, the gRNA molecules, CRISPR systems and/or cells of the invention are used to treat a patient in need thereof. In aspects, the patient is a mammal, e.g., a human. In aspects, the patient has a hemoglobinopathy. In embodiments, the patient has sickle cell disease. In embodiments, the patient has beta thalassemia.


In one aspect, the method of treatment comprises administering to a mammal, e.g., a human, one or more gRNA molecules, e.g., one or more gRNA molecules comprising a targeting domain described in Table 1, 2, 3, 4, 5, 6, 7, 8, or 9, and one or more cas9 molecules described herein.


In one aspect, the method of treatment comprises administering to a mammal a cell population, wherein the cell population is a cell population from a mammal, e.g., a human, that has been administered one or more gRNA molecules, e.g., one or more gRNA molecules comprising a targeting domain described in Table 1, 2, 3, 4, 5, 6, 7, 8, or 9, and one or more cas9 molecules described herein, e.g., a CRISPR system as described herein. In one embodiment, the administration of the one or more gRNA molecules or CRISPR systems to the cell is accomplished in vivo. In one embodiment the administration of the one or more gRNA molecules or CRISPR systems to the cell is accomplished ex vivo.


In one aspect, the method of treatment comprises administering to the mammal, e.g., the human, an effective amount of a cell population comprising cells which comprise or at one time comprised one or more gRNA molecules, e.g., one or more gRNA molecules comprising a targeting domain described in Table 1, 2, 3, 4, 5, 6, 7, 8, or 9, and one or more cas9 molecules described herein, or the progeny of said cells. In one embodiment, the cells are allogeneic to the mammal. In one embodiment, the cells are autologous to the mammal. In one embodiment the cells are harvested from the mammal, manipulated ex vivo, and returned to the mammal.


In aspects, the cells comprising or which at one time comprised one or more gRNA molecules, e.g., one or more gRNA molecules comprising a targeting domain described in Table 1, 2, 3, 4, 5, 6, 7, 8, or 9, and one or more cas9 molecules described herein, or the progeny of said cells, comprise stem cells or progenitor cells. In one aspect, the stem cells are hematopoietic stem cells. In one aspect, the progenitor cells are hematopoietic progenitor cells. In one aspect, the cells comprise both hematopoietic stem cells and hematopoietic progenitor cells, e.g., are HSPCs. In one aspect, the cells comprise, e.g., consist of, CD34+ cells. In one aspect the cells are substantially free of CD34− cells. In one aspect, the cells comprise, e.g., consist of, CD34+/CD90+ stem cells. In one aspect, the cells comprise, e.g., consist of, CD34+/CD90− cells. In an aspect, the cells are a population comprising one or more of the cell types described above or described herein.


In one embodiment, the disclosure provides a method for treating a hemoglobinopathy, e.g., sickle cell disease or beta-thalassemia, or a method for increasing fetal hemoglobin expression in a mammal, e.g., a human, in need thereof, the method comprising:


a) providing, e.g., harvesting or isolating, a population of HSPCs (e.g., CD34+ cells) from a mammal;


b) providing said cells ex vivo, e.g., in a cell culture medium, optionally in the presence of an effective amount of a composition comprising at least one stem cell expander, whereby said population of HSPCs (e.g., CD34+ cells) expands to a greater degree than an untreated population;


c) contacting the population of HSPCs (e.g., CD34+ cells) with an effective amount of: a composition comprising at least one gRNA molecule comprising a targeting domain described herein, e.g., a targeting domain described in Tables 1, 2, 3, 4, 5, 6, 7, 8, or 9, or a nucleic acid encoding said gRNA molecule, and at least one cas9 molecule, e.g., described herein, or a nucleic acid encoding said cas9 molecule, e.g., one or more RNPs as described herein, e.g., with a CRISPR system described herein;


d) causing at least one modification in at least a portion of the cells of the population (e.g., at least a portion of the HSPCs, e.g., CD34+ cells, of the population), whereby, e.g., when said HSPCs are differentiated into cells of an erythroid lineage, e.g., red blood cells, fetal hemoglobin expression is increased, e.g., relative to cells not contacted according to step c); and


f) returning a population of cells comprising said modified HSPCs (e.g., CD34+ cells) to the mammal.


In an aspect, the HSPCs are allogeneic to the mammal to which they are returned. In an aspect, the HSPCs are autologous to the mammal to which they are returned. In aspects, the HSPCs are isolated from bone marrow. In aspects, the HSPCs are isolated from peripheral blood, e.g., mobilized peripheral blood. In aspects, the moblized peripheral blood is isolated from a subject who has been administered a G-CSF. In aspects, the moblized peripheral blood is isolated from a subject who has been administered a moblization agent other than G-CSF, for example, Plerixafor® (AMD3100). In aspects, the HSPCs are isolated from umbilical cord blood.


In further embodiments of the method, the method further comprises, after providing a population of HSPCs (e.g., CD34+ cells), e.g., from a source described above, the step of enriching the population of cells for HSPCs (e.g., CD34+ cells). In embodiments of the method, after said enriching, the population of cells, e.g., HSPCs, is substantially free of CD34− cells.


In embodiments, the population of cells which is returned to the mammal includes at least 70% viable cells. In embodiments, the population of cells which is returned to the mammal includes at least 75% viable cells. In embodiments, the population of cells which is returned to the mammal includes at least 80% viable cells. In embodiments, the population of cells which is returned to the mammal includes at least 85% viable cells. In embodiments, the population of cells which is returned to the mammal includes at least 90% viable cells. In embodiments, the population of cells which is returned to the mammal includes at least 95% viable cells. In embodiments, the population of cells which is returned to the mammal includes at least 99% viable cells. Viability can be determined by staining a representative portion of the population of cells for a cell viability marker, e.g., as known in the art.


In another embodiment, the disclosure provides a method for treating a hemoglobinopathy, e.g., sickle cell disease or beta-thalassemia, or a method for increasing fetal hemoglobin expression in a mammal, e.g., a human, in need thereof, the method comprising the steps of:


a) providing, e.g., harvesting or isolating, a population of HSPCs (e.g., CD34+ cells) of a mammal, e.g., from the bone marrow of a mammal;


b) isolating the CD34+ cells from the population of cells of step a);


c) providing said CD34+ cells ex vivo, and culturing said cells, e.g., in a cell culture medium, in the presence of an effective amount of a composition comprising at least one stem cell expander, e.g., Compound 4, e.g., Compound 4 at a concentration of about 0.5 to about 0.75 micromolar, whereby said population of CD34+ cells expands to a greater degree than an untreated population;


d) introducing into the cells of the population CD34+ cells an effective amount of: a composition comprising a Cas9 molecule, e.g., as described herein, and a gRNA molecule, e.g., as described herein, e.g., optionally where the Cas9 molecule and the gRNA molecule are in the form of an RNP, e.g., as described herein, and optionally where said introduction is by electroporation, e.g., as described herein, of said RNP into said cells;


e) causing at least one genetic modification in at least a portion of the cells of the population (e.g., at least a portion of the HSPCs, e.g., CD34+ cells, of the population), whereby an indel, e.g., as described herein, is created at or near the genomic site complementary to the targeting domain of the gRNA introduced in step d);


f) optionally, additionally culturing said cells after said introducing, e.g., in a cell culture medium, in the presence of an effective amount of a composition comprising at least one stem cell expander, e.g., Compound 4, e.g., Compound 4 at a concentration of about 0.5 to about 0.75 micromolar, such that the cells expand at least 2-fold, e.g., at least 4-fold, e.g., at least 5-fold;


g) cryopreserving said cells; and


h) returning the cells to the mammal, wherein,

    • the cells returned to the mammal comprise cells that 1) maintain the ability to differentiate into cells of the erythroid lineage, e.g., red blood cells; 2) when differentiated into red blood cells, produce an increased level of fetal hemoglobin, e.g., relative to cells unmodified by the gRNA of step e), e.g., produce at least 6 picograms fetal hemoglobin per cell.


In an aspect, the HSPCs are allogeneic to the mammal to which they are returned. In an aspect, the HSPCs are autologous to the mammal to which they are returned. In aspects, the HSPCs are isolated from bone marrow. In aspects, the HSPCs are isolated from peripheral blood, e.g., mobilized peripheral blood. In aspects, the moblized peripheral blood is isolated from a subject who has been administered a G-CSF. In aspects, the moblized peripheral blood is isolated from a subject who has been administered a moblization agent other than G-CSF, for example, Plerixafor® (AMD3100). In aspects, the HSPCs are isolated from umbilical cord blood.


In embodiments of the method above, the recited step b) results in a population of cells which is substantially free of CD34− cells.


In further embodiments of the method, the method further comprises, after providing a population of HSPCs (e.g., CD34+ cells), e.g., from a source described above, the population of cells is enriched for HSPCs (e.g., CD34+ cells).


In a further embodiments of these methods, the population of modified HSPCs (e.g., CD34+ stem cells) having the ability to differentiate increased fetal hemoglobin expression is cryopreserved and stored prior to being reintroduced into the mammal. In embodiments, the cryopreserved population of HSPCs having the ability to differentiate into cells of the erythroid lineage, e.g., red blood cells, and/or when differentiated into cells of the erythroid lineage, e.g., red blood cells, produce an increased level of fetal hemoglobin is thawed and then reintroduced into the mammal. In a further embodiment of these methods, the method comprises chemotherapy and/or radiation therapy to remove or reduce the endogenous hematopoietic progenitor or stem cells in the mammal. In a further embodiment of these methods, the method does not comprise a step of chemotherapy and/or radiation therapy to remove or reduce the endogenous hematopoietic progenitor or stem cells in the mammal. In a further embodiment of these methods, the method comprises a chemotherapy and/or radiation therapy to reduce partially (e.g., partial lymphodepletion) the endogenous hematopoietic progenitor or stem cells in the mammal. In embodiments the patient is treated with a fully lymphodepleting dose of busulfan prior to reintroduction of the modified HSPCs to the mammal. In embodiments, the patient is treated with a partially lymphodepleting dose of busulfan prior to reintroduction of the modified HSPCs to the mammal.


In embodiments, the cells are contacted with RNP comprising a Cas9 molecule, e.g., as described herein, complexed with a gRNA to the +58 BCL11a enhancer region. In embodiments, the gRNA comprises the targeting domain of CR000312. In embodiments, the gRNA comprises the targeting domain of CR000311. In embodiments, the gRNA comprises the targeting domain of CR001128. In embodiments, the gRNA comprises the targeting domain of CR001125. In embodiments, the gRNA comprises the targeting domain of CR001126. In embodiments, the gRNA comprises the targeting domain of CR001127. In embodiments the gRNA is a dual guide RNA comprising a crRNA comprising, e.g., consisting of, [SEQ ID NO: 248]-[SEQ ID NO: 6607], and a tracr comprising, e.g., consisting of, [SEQ ID NO: 7812], optionally with 1, 2, 3, 4, 5, 6, or 7 additional 3′ uracil nucleotides, e.g., SEQ ID NO: 6660. In embodiments, the gRNA is a sgRNA comprising, e.g., consisting of, [SEQ ID NO: 248]-[SEQ ID NO: 6601, optionally with 1, 2, 3, 4, 5, 6, or 7 additional 3′ uracil nucleotides, e.g., [SEQ ID NO: 248]-[SEQ ID NO: 7811]. In embodiments the gRNA is a dual guide RNA comprising a crRNA comprising, e.g., consisting of, [SEQ ID NO: 247]-[SEQ ID NO: 6607], and a tracr comprising, e.g., consisting of, SEQ ID NO: 7812, optionally with 1, 2, 3, 4, 5, 6, or 7 additional 3′ uracil nucleotides, e.g., SEQ ID NO: 6660. In embodiments, the gRNA is a sgRNA comprising, e.g., consisting of, [SEQ ID NO: 247]-[SEQ ID NO: 6601, optionally with 1, 2, 3, 4, 5, 6, or 7 additional 3′ uracil nucleotides, e.g., [SEQ ID NO: 247]-[SEQ ID NO: 7811]. In embodiments the gRNA is a dual guide RNA comprising a crRNA comprising, e.g., consisting of, [SEQ ID NO: 338]-[SEQ ID NO: 6607], and a tracr comprising, e.g., consisting of, SEQ ID NO: 7812, optionally with 1, 2, 3, 4, 5, 6, or 7 additional 3′ uracil nucleotides, e.g., SEQ ID NO: 6660. In embodiments, the gRNA is a sgRNA comprising, e.g., consisting of, [SEQ ID NO: 338]-[SEQ ID NO: 6601], optionally with 1, 2, 3, 4, 5, 6, or 7 additional 3′ uracil nucleotides, e.g., [SEQ ID NO: 338]-[SEQ ID NO: 7811]. In embodiments the gRNA is a dual guide RNA comprising a crRNA comprising, e.g., consisting of, [SEQ ID NO: 335]-[SEQ ID NO: 6607], and a tracr comprising, e.g., consisting of, SEQ ID NO: 7812, optionally with 1, 2, 3, 4, 5, 6, or 7 additional 3′ uracil nucleotides, e.g., SEQ ID NO: 6660. In embodiments, the gRNA is a sgRNA comprising, e.g., consisting of, [SEQ ID NO: 335]-[SEQ ID NO: 6601], optionally with 1, 2, 3, 4, 5, 6, or 7 additional 3′ uracil nucleotides, e.g., [SEQ ID NO: 335]-[SEQ ID NO: 7811]. In embodiments the gRNA is a dual guide RNA comprising a crRNA comprising, e.g., consisting of, [SEQ ID NO: 336]-[SEQ ID NO: 6607], and a tracr comprising, e.g., consisting of, SEQ ID NO: 7812, optionally with 1, 2, 3, 4, 5, 6, or 7 additional 3′ uracil nucleotides, e.g., SEQ ID NO: 6660. In embodiments, the gRNA is a sgRNA comprising, e.g., consisting of, [SEQ ID NO: 336]-[SEQ ID NO: 6601], optionally with 1, 2, 3, 4, 5, 6, or 7 additional 3′ uracil nucleotides, e.g., [SEQ ID NO: 336]-[SEQ ID NO: 7811]. In embodiments the gRNA is a dual guide RNA comprising a crRNA comprising, e.g., consisting of, [SEQ ID NO: 337]-[SEQ ID NO: 6607], and a tracr comprising, e.g., consisting of, SEQ ID NO: 7812, optionally with 1, 2, 3, 4, 5, 6, or 7 additional 3′ uracil nucleotides, e.g., SEQ ID NO: 6660. In embodiments, the gRNA is a sgRNA comprising, e.g., consisting of, [SEQ ID NO: 337]-[SEQ ID NO: 6601], optionally with 1, 2, 3, 4, 5, 6, or 7 additional 3′ uracil nucleotides, e.g., [SEQ ID NO: 337]-[SEQ ID NO: 7811]. In any of the aforementioned embodiments, any or all of the RNA components of the gRNA may be modified at one or more nucleotides, e.g., as described herein. In embodiments, the gRNA molecule is SEQ ID NO: 342. In embodiments, the gRNA molecule is SEQ ID NO: 343. In embodiments, the gRNA molecule is SEQ ID NO: 1762. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 344 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 344 and SEQ ID NO: 346. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 345 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 345 and SEQ ID NO: 346. In embodiments, the gRNA molecule is SEQ ID NO: 347. In embodiments, the gRNA molecule is SEQ ID NO: 348. In embodiments, the gRNA molecule is SEQ ID NO: 1763. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 349 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 349 and SEQ ID NO: 346. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 350 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 350 and SEQ ID NO: 346. In embodiments, the gRNA molecule is SEQ ID NO: 351. In embodiments, the gRNA molecule is SEQ ID NO: 352. In embodiments, the gRNA molecule is SEQ ID NO: 1764. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 353 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 353 and SEQ ID NO: 346. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 354 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 354 and SEQ ID NO: 346. In embodiments, the gRNA molecule is SEQ ID NO: 355. In embodiments, the gRNA molecule is SEQ ID NO: 356. In embodiments, the gRNA molecule is SEQ ID NO: 1765. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 357 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 357 and SEQ ID NO: 346. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 358 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 358 and SEQ ID NO: 346. In embodiments, the gRNA molecule is SEQ ID NO: 359. In embodiments, the gRNA molecule is SEQ ID NO: 360. In embodiments, the gRNA molecule is SEQ ID NO: 1766. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 361 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 361 and SEQ ID NO: 346. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 362 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 362 and SEQ ID NO: 346. In embodiments, the gRNA molecule is SEQ ID NO: 363. In embodiments, the gRNA molecule is SEQ ID NO: 364. In embodiments, the gRNA molecule is SEQ ID NO: 1767. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 365 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 365 and SEQ ID NO: 346. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 366 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 366 and SEQ ID NO: 346. In embodiments, the gRNA molecule is SEQ ID NO: 367. In embodiments, the gRNA molecule is SEQ ID NO: 368. In embodiments, the gRNA molecule is SEQ ID NO: 1768. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 369 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 369 and SEQ ID NO: 346. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 370 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 370 and SEQ ID NO: 346. In embodiments, the gRNA molecule is SEQ ID NO: 371. In embodiments, the gRNA molecule is SEQ ID NO: 372. In embodiments, the gRNA molecule is SEQ ID NO: 1769. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 373 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 373 and SEQ ID NO: 346. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 374 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 374 and SEQ ID NO: 346.


In embodiments, the cells are contacted with RNP comprising a Cas9 molecule, e.g., as described herein, complexed with a gRNA to the HPFH region. In embodiments, the gRNA comprises the targeting domain of CR001030. In embodiments, the gRNA comprises the targeting domain of CR001028. In embodiments, the gRNA comprises the targeting domain of CR001221. In embodiments, the gRNA comprises the targeting domain of CR001137. In embodiments, the gRNA comprises the targeting domain of CR003035. In embodiments, the gRNA comprises the targeting domain of CR003085. In embodiments the gRNA is a dual guide RNA comprising a crRNA comprising, e.g., consisting of, [SEQ ID NO: 98]-[SEQ ID NO: 6607], and a tracr comprising, e.g., consisting of, SEQ ID NO: 7812, optionally with 1, 2, 3, 4, 5, 6, or 7 additional 3′ uracil nucleotides, e.g., SEQ ID NO: 6660. In embodiments, the gRNA is a sgRNA comprising, e.g., consisting of, [SEQ ID NO: 98]-[SEQ ID NO: 6601], optionally with 1, 2, 3, 4, 5, 6, or 7 additional 3′ uracil nucleotides, e.g., [SEQ ID NO: 98]-[SEQ ID NO: 7811]. In embodiments the gRNA is a dual guide RNA comprising a crRNA comprising, e.g., consisting of, [SEQ ID NO: 100]-[SEQ ID NO: 6607], and a tracr comprising, e.g., consisting of, SEQ ID NO: 7812, optionally with 1, 2, 3, 4, 5, 6, or 7 additional 3′ uracil nucleotides, e.g., SEQ ID NO: 6660. In embodiments, the gRNA is a sgRNA comprising, e.g., consisting of, [SEQ ID NO: 100]-[SEQ ID NO: 6601], optionally with 1, 2, 3, 4, 5, 6, or 7 additional 3′ uracil nucleotides, e.g., [SEQ ID NO: 100]-[SEQ ID NO: 7811]. In embodiments the gRNA is a dual guide RNA comprising a crRNA comprising, e.g., consisting of, [SEQ ID NO: 1589]-[SEQ ID NO: 6607], and a tracr comprising, e.g., consisting of, SEQ ID NO: 7812, optionally with 1, 2, 3, 4, 5, 6, or 7 additional 3′ uracil nucleotides, e.g., SEQ ID NO: 6660. In embodiments, the gRNA is a sgRNA comprising, e.g., consisting of, [SEQ ID NO: 1589]-[SEQ ID NO: 6601], optionally with 1, 2, 3, 4, 5, 6, or 7 additional 3′ uracil nucleotides, e.g., [SEQ ID NO: 1589]-[SEQ ID NO: 7811]. In embodiments the gRNA is a dual guide RNA comprising a crRNA comprising, e.g., consisting of, [SEQ ID NO: 1505]-[SEQ ID NO: 6607], and a tracr comprising, e.g., consisting of, SEQ ID NO: 7812, optionally with 1, 2, 3, 4, 5, 6, or 7 additional 3′ uracil nucleotides, e.g., SEQ ID NO: 6660. In embodiments, the gRNA is a sgRNA comprising, e.g., consisting of, [SEQ ID NO: 1505]-[SEQ ID NO: 6601], optionally with 1, 2, 3, 4, 5, 6, or 7 additional 3′ uracil nucleotides, e.g., [SEQ ID NO: 1505]-[SEQ ID NO: 7811]. In embodiments the gRNA is a dual guide RNA comprising a crRNA comprising, e.g., consisting of, [SEQ ID NO: 1700]-[SEQ ID NO: 6607], and a tracr comprising, e.g., consisting of, SEQ ID NO: 7812, optionally with 1, 2, 3, 4, 5, 6, or 7 additional 3′ uracil nucleotides, e.g., SEQ ID NO: 6660. In embodiments, the gRNA is a sgRNA comprising, e.g., consisting of, [SEQ ID NO: 1700]-[SEQ ID NO: 6601], optionally with 1, 2, 3, 4, 5, 6, or 7 additional 3′ uracil nucleotides, e.g., [SEQ ID NO: 1700]-[SEQ ID NO: 7811]. In embodiments the gRNA is a dual guide RNA comprising a crRNA comprising, e.g., consisting of, [SEQ ID NO: 1750]-[SEQ ID NO: 6607], and a tracr comprising, e.g., consisting of, SEQ ID NO: 7812, optionally with 1, 2, 3, 4, 5, 6, or 7 additional 3′ uracil nucleotides, e.g., SEQ ID NO: 6660. In embodiments, the gRNA is a sgRNA comprising, e.g., consisting of, [SEQ ID NO: 1750]-[SEQ ID NO: 6601], optionally with 1, 2, 3, 4, 5, 6, or 7 additional 3′ uracil nucleotides, e.g., [SEQ ID NO: 1750]-[SEQ ID NO: 7811]. In embodiments, the gRNA molecule is SEQ ID NO: 375. In embodiments, the gRNA molecule is SEQ ID NO: 376. In embodiments, the gRNA molecule is SEQ ID NO: 1770. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 377 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 377 and SEQ ID NO: 346. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 378 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 378 and SEQ ID NO: 346. In embodiments, the gRNA molecule is SEQ ID NO: 379. In embodiments, the gRNA molecule is SEQ ID NO: 380. In embodiments, the gRNA molecule is SEQ ID NO: 1771. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 381 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 381 and SEQ ID NO: 346. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 382 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 382 and SEQ ID NO: 346. In embodiments, the gRNA molecule is SEQ ID NO: 383. In embodiments, the gRNA molecule is SEQ ID NO: 384. In embodiments, the gRNA molecule is SEQ ID NO: 1772. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 385 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 385 and SEQ ID NO: 346. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 386 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 386 and SEQ ID NO: 346. In embodiments, the gRNA molecule is SEQ ID NO: 387. In embodiments, the gRNA molecule is SEQ ID NO: 388. In embodiments, the gRNA molecule is SEQ ID NO: 1773. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 389 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 389 and SEQ ID NO: 346. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 390 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 390 and SEQ ID NO: 346. In embodiments, the gRNA molecule is SEQ ID NO: 391. In embodiments, the gRNA molecule is SEQ ID NO: 392. In embodiments, the gRNA molecule is SEQ ID NO: 1774. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 393 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 393 and SEQ ID NO: 346. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 394 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 394 and SEQ ID NO: 346. In embodiments, the gRNA molecule is SEQ ID NO: 395. In embodiments, the gRNA molecule is SEQ ID NO: 396. In embodiments, the gRNA molecule is SEQ ID NO: 1775. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 397 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 397 and SEQ ID NO: 346. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 398 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 398 and SEQ ID NO: 346.


In embodiments, the stem cell expander is Compound 1. In embodiments, the stem cell expander is Compound 2. In embodiments, the stem cell expander is Compound 3. In embodiments, the stem cell expander is Compound 4. In embodiments, the stem cell expander is Compound 4 and is present at a concentration of 2-0.1 micromolar, e.g., 1-0.25 micromolar, e.g., 0.75-0.5 micromolar. In embodiments, the stem cell expander is a molecule described in WO2010/059401 (e.g., the molecule described in Example 1 of WO2010/059401).


In embodiments, the cells, e.g., HSPCs, e.g., as described herein, are cultured ex vivo for a period of about 1 hour to about 15 days, e.g., a period of about 12 hours to about 12 days, e.g., a period of about 12 hours to 4 days, e.g., a period of about 1 day to about 4 days, e.g., a period of about 1 day to about 2 days, e.g., a period of about 1 day or a period of about 2 days, prior to the step of contacting the cells with a CRISPR system, e.g., described herein. In embodiments, said culturing prior to said contacting step is in a composition (e.g., a cell culture medium) comprising a stem cell expander, e.g., described herein, e.g., compound 4, e.g., compound 4 at a concentration of about 0.25 uM to about 1 uM, e.g., compound 4 at a concentration of about 0.75-0.5 micromolar. In embodiments, the cells are cultured ex vivo for a period of no more than about about 1 day, e.g., no more than about 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 hour(s) after the step of contacting the cells with a CRISPR system, e.g., described herein, e.g., in a cell culture medium which comprises a stem cell expander, e.g., described herein, e.g., compound 4, e.g., compound 4 at a concentration of about 0.25 uM to about 1 uM, e.g., compound 4 at a concentration of about 0.75-0.5 micromolar. In other embodiments, the cells are cultured ex vivo for a period of about 1 hour to about 15 days, e.g., a period of about 12 hours to about 10 days, e.g., a period of about 1 day to about 10 days, e.g., a period of about 1 day to about 5 days, e.g., a period of about 1 thy to about 4 days, e.g., a period of about 2 days to about 4 days, e.g., a period of about 2 days, about 3 days or about 4 days, after the step of contacting the cells with a CRISPR system, e.g., described herein, in a cell culture medium, e.g., which comprises a stem cell expander, e.g., described herein, e.g., compound 4, e.g., compound 4 at a concentration of about 0.25 uM to about 1 uM, e.g., compound 4 at a concentration of about 0.75-0.5 micromolar. In embodiments, the cells are cultured ex vivo (e.g., cultured prior to said contacting step and/or cultured after said contacting step) for a period of about 1 hour to about 20 days, e.g., a period of about 6-12 days, e.g., a period of about 6, about 7, about 8, about 9, about 10, about 11, or about 12 days.


In embodiments, the population of cells comprising the modified HSPCs returned to the mammal comprises at least about 1 million cells (e.g., at least about 1 million CD34+ cells) per kg. In embodiments, the population of cells comprising the modified HSPCs returned to the mammal comprises at least about 2 million cells (e.g., at least about 2 million CD34+ cells) per kg. In embodiments, the population of cells comprising the modified HSPCs returned to the mammal comprises at least about 3 million cells (e.g., at least about 3 million CD34+ cells) per kg. In embodiments, the population of cells comprising the modified HSPCs returned to the mammal comprises at least about 4 million cells (e.g., at least about 4 million CD34+ cells) per kg. In embodiments, the population of cells comprising the modified HSPCs returned to the mammal comprises at least about 5 million cells (e.g., at least about 5 million CD34+ cells) per kg. In embodiments, the population of cells comprising the modified HSPCs returned to the mammal comprises at least about 6 million cells (e.g., at least about 6 million CD34+ cells) per kg. In embodiments, the population of cells comprising the modified HSPCs returned to the mammal comprises at least 1 million cells (e.g., at least 1 million CD34+ cells) per kg. In embodiments, the population of cells comprising the modified HSPCs returned to the mammal comprises at least 2 million cells (e.g., at least 2 million CD34+ cells) per kg. In embodiments, the population of cells comprising the modified HSPCs returned to the mammal comprises at least 3 million cells (e.g., at least 3 million CD34+ cells) per kg. In embodiments, the population of cells comprising the modified HSPCs returned to the mammal comprises at least 4 million cells (e.g., at least 4 million CD34+ cells) per kg. In embodiments, the population of cells comprising the modified HSPCs returned to the mammal comprises at least 5 million cells (e.g., at least 5 million CD34+ cells) per kg. In embodiments, the population of cells comprising the modified HSPCs returned to the mammal comprises at least 6 million cells (e.g., at least 6 million CD34+ cells) per kg. In embodiments, the population of cells comprising the modified HSPCs returned to the mammal comprises about 1 million cells (e.g., about 1 million CD34+ cells) per kg. In embodiments, the population of cells comprising the modified HSPCs returned to the mammal comprises about 2 million cells (e.g., about 2 million CD34+ cells) per kg. In embodiments, the population of cells comprising the modified HSPCs returned to the mammal comprises about 3 million cells (e.g., about 3 million CD34+ cells) per kg. In embodiments, the population of cells comprising the modified HSPCs returned to the mammal comprises about 4 million cells (e.g., about 4 million CD34+ cells) per kg. In embodiments, the population of cells comprising the modified HSPCs returned to the mammal comprises about 5 million cells (e.g., about 5 million CD34+ cells) per kg. In embodiments, the population of cells comprising the modified HSPCs returned to the mammal comprises about 6 million cells (e.g., about 6 million CD34+ cells) per kg. In embodiments, the population of cells comprising the modified HSPCs returned to the mammal comprises about 2×106 cells per kg body weight of the patient. In embodiments, the population of cells comprising the modified HSPCs returned to the mammal comprises at least 2×106 cells per kg body weight of the patient.


In embodiments, any of the methods described above results in the patient having at least 80% of its circulating CD34+ cells comprising an indel at or near the genomic site complementary to the targeting domain of the gRNA molecule used in the method, e.g., as measured at least 15 days, e.g., at least 20, at least 30, at least 40 at least 50 or at least 60 days after reintroduction of the cells into the mammal.


In embodiments, any of the methods described above results in the patient having at least 20% of its bone marrow CD34+ cells comprising an indel at or near the genomic site complementary to the targeting domain of the gRNA molecule used in the method, e.g., as measured at least 15 days, e.g., at least 20, at least 30, at least 40 at least 50 or at least 60 days after reintroduction of the cells into the mammal.


In embodiments, the HSPCs that are reintroduced into the mammal are able to differentiate in vivo into cells of the erythroid lineage, e.g., red blood cells, and said differentiated cells exhibit increased fetal hemoglobin levels, e.g., produce at least 6 picograms fetal hemoglobin per cell, e.g., at least 7 picograms fetal hemoglobin per cell, at least 8 picograms fetal hemoglobin per cell, at least 9 picograms fetal hemoglobin per cell, at least 10 picograms fetal hemoglobin per cell, e.g., between about 9 and about 10 picograms fetal hemoglobin per cell, e.g., such that the hemoglobinopathy is treated the mammal.


It will be understood that when a cell is characterized as having increased fetal hemoglobin, that includes embodiments in which a progeny, e.g., a differentiated progeny, of that cell exhibits increased fetal hemoglobin. For example, in the methods described herein, the altered or modified CD34+ cell (or cell population) may not express increased fetal hemoglobin, but when differentiated into cells of erythroid lineage, e.g., red blood cells, the cells express increased fetal hemoglobin, e.g., increased fetal hemoglobin relative to an unmodified or unaltered cell under similar conditions.


XII. Culture Methods and Methods of Manufacturing Cells

The disclosure provides methods of culturing cells, e.g., HSPCs, e.g., hematopoietic stem cells, e.g., CD34+ cells modified, or to be modified, with the gRNA molecules described herein.


DNA Repair Pathway Inhibitors

Without being bound by theory, it is believed that the pattern of indels produced by a given gRNA molecule at a particular target sequence is a product of each of the active DNA repair mechamisms within the cell (e.g., non-homologous end joining, microhomology-mediated end joining, etc.). Wihtout being bound by theory, it is believed that a particularly favorable indel may be selected for or enriched for by contacting the cells to be edited with an inhibitor of a DNA repair pathway that does not produce the desired indel. Thus, the gRNA molecules, CRISPR systems, methods and other aspects of the invention may be performed in combination with such inhibitors. Examples of such inhibitors include those described in, e.g., WO2014/130955, the contents of which are hereby incorporated by reference in their entirety. In embodiment, the inhibitor is a DNAPKc inhibitor, e.g., NU7441.


Stem Cell Expanders

In one aspect the invention relates to culturing the cells, e.g., HSPCs, e.g., CD34+ cells modified, or to be modified, with the gRNA molecules described herein, with one or more agents that result in an increased expansion rate, increased expansion level, or increased engraftment relative to cells not treated with the agent. Such agents are referred to herein as stem cell expanders.


In an aspect, the one or more agents that result in an increased expansion rate or increased expansion level, relative to cells not treated with the agent, e.g., the stem cell expander, comprises an agent that is an inhibitor of the aryl hydrocarbon receptor (AHR) pathway. In aspects, the stem cell expander is a compound disclosed in WO2013/110198 or a compound disclosed in WO2010/059401, the contents of which are incorporated by reference in their entirety.


In one aspect, the one or more agents that result in an increased expansion rate or increased expansion level, relative to cells not treated with the agent, is a pyrimido[4,5-b]indole derivative, e.g., as disclosed in WO2013/110198, the contents of which are hereby incorporated by reference in their entirety. In one embodiment the agent is compound 1 ((1r,4r)-N1-(2-benzyl-7-(2-methyl-2H-tetrazol-5-yl)-9H-pyrimido[4,5-b]indol-4-yl)cyclohexane-1,4-diamine):


Compound 1



embedded image


In another aspect, the agent is Compound 2 (methyl 4-(3-piperidin-1-ylpropylamino)-9H-pyrimido[4,5-b]indole-7-carboxylate):


Compound 2:



embedded image


In another aspect, the one or more agents that result in an increased expansion rate or increased expansion level, relative to cells not treated with the agent, is an agent disclosed in WO2010/059401, the contents of which are hereby incorporated by reference in their entirety.


In one embodiment, the stem cell expander is 4-(2-(2-(benzo[b]thiophen-3-yl)-9-isopropyl-9H-purin-6-ylamino)ethyl)phenol, i.e., is the compound from example 1 of WO2010/059401, having the following structure:


Compound 3:



embedded image


In another aspect, the stem cell expander is compound 4 ((S)-2-(6-(2-(1H-indol-3-yl)ethylamino)-2-(5-fluoropyridin-3-yl)-9H-purin-9-yl)propan-1-ol, i.e., is the compound 157S according to WO2010/059401), having the following structure:


Compound 4:



embedded image


In embodiments the population of HSPCs is contacted with the stem cell expander, e.g., compound 1, compound 2, compound 3, compound 4, or combinations thereof (e.g., a combination of compound 1 and compound 4) before introduction of the CRISPR system (e.g., gRNA molecule and/or Cas9 molecule of the invention) to said HSPCs. In embodiments, the population of HSPCs is contacted with the stem cell expander, e.g., compound 1, compound 2, compound 3, compound 4, or combinations thereof (e.g., a combination of compound 1 and compound 4), after introduction of the CRISPR system (e.g., gRNA molecule and/or Cas9 molecule of the invention) to said HSPCs. In embodiments, the population of HSPCs is contacted with the stem cell expander, e.g., compound 1, compound 2, compound 3, compound 4, or combinations thereof (e.g., a combination of compound 1 and compound 4), both before and after introduction of the CRISPR system (e.g., gRNA molecule and/or Cas9 molecule of the invention) to said HSPCs.


In embodiments, the stem cell expander is present in an effective amount to increase the expansion level of the HSPCs, relative to HSPCs in the same media but for the absence of the stem cell expander. In embodiments, the stem cell expander is present at a concentration ranging from about 0.01 to about 10 uM, e.g., from about 0.1 uM to about 1 uM. In embodiments, the stem cell expander is present in the cell culture medium at a concentration of about 1 uM, about 950 nM, about 900 nM, about 850 nM, about 800 nM, about 750 nM, about 700 nM, about 650 nM, about 600 nM, about 550 nM, about 500 nM, about 450 nM, about 400 nM, about 350 nM, about 300 nM, about 250 nM, about 200 nM, about 150 nM, about 100 nM, about 50 nM, about 25 nM, or about 10 nM. In embodiments, the stem cell expander is present at a concentration ranging from about 500 nM to about 750 nM.


In embodiments, the stem cell expander is compound 4, which is present in the cell culture medium at a concentration ranging from about 0.01 to about 10 micromolar (uM). In embodiments, the stem cell expander is compound 4, which is present in the cell culture medium at a concentration ranging from about 0.1 to about 1 micromolar (uM). In embodiments, the stem cell expander is compound 4, which is present in the cell culture medium at a concentration of about 0.75 micromolar (uM). In embodiments, the stem cell expander is compound 4, which is present in the cell culture medium at a concentration of about 0.5 micromolar (uM). In embodiments of any of the foregoing, the cell culture medium additionally comprises compound 1.


In embodiments, the stem cell expander is a mixture of compound 1 and compound 4.


In embodiments, the cells of the invention are contacted with one or more stem cell expander molecules for a sufficient time and in a sufficient amount to cause a 2 to 10,000-fold expansion of CD34+ cells, e.g., a 2-1000-fold expansion of CD34+ cells, e.g., a 2-100-fold expansion of CD34+ cells, e.g., a 20-200-fold expansion of CD34+ cells. As described herein, the contacting with the one or more stem cell expanders may be before the cells are contacted with a CRISPR system, e.g., as described herein, after the cells are contacted with a CRISPR system, e.g., as described herein, or a combination thereof. In an embodiment, the cells are contacted with one or more stem cell expander molecules, e.g., Compound 4, for a sufficient time and in a sufficient amount to cause at least a 2-fold expansion of CD34+ cells, e.g., CD34+ cells comprising an indel at or near the target site having complementarity to the targeting domain of the gRNA of the CRISPR/Cas9 system introduced into said cell. In an embodiment, the cells are contacted with one or more stem cell expander molecules, e.g., Compound 4, for a sufficient time and in a sufficient amount to cause at least a 4-fold expansion of CD34+ cells, e.g., CD34+ cells comprising an indel at or near the target site having complementarity to the targeting domain of the gRNA of the CRISPR/Cas9 system introduced into said cell. In an embodiment, the cells are contacted with one or more stem cell expander molecules, e.g., Compound 4, for a sufficient time and in a sufficient amount to cause at least a 5-fold expansion of CD34+ cells, e.g., CD34+ cells comprising an indel at or near the target site having complementarity to the targeting domain of the gRNA of the CRISPR/Cas9 system introduced into said cell. In an embodiment, the cells are contacted with one or more stem cell expander molecules for a sufficient time and in a sufficient amount to cause at least a 10-fold expansion of CD34+ cells. In an embodiment, the cells are contacted with one or more stem cell expander molecules for a sufficient time and in a sufficient amount to cause at least a 20-fold expansion of CD34+ cells. In an embodiment, the cells are contacted with one or more stem cell expander molecules for a sufficient time and in a sufficient amount to cause at least a 30-fold expansion of CD34+ cells. In an embodiment, the cells are contacted with one or more stem cell expander molecules for a sufficient time and in a sufficient amount to cause at least a 40-fold expansion of CD34+ cells. In an embodiment, the cells are contacted with one or more stem cell expander molecules for a sufficient time and in a sufficient amount to cause at least a 50-fold expansion of CD34+ cells. In an embodiment, the cells are contacted with one or more stem cell expander molecules for a sufficient time and in a sufficient amount to cause at least a 60-fold expansion of CD34+ cells. In embodiments, the cells are contacted with the one or more stem cell expanders for a period of about 1-60 days, e.g., about 1-50 days, e.g., about 1-40 days, e.g., about 1-30 days, e.g., 1-20 days, e.g., about 1-10 days, e.g., about 7 days, e.g., about 1-5 days, e.g., about 2-5 days, e.g., about 2-4 days, e.g., about 2 days or, e.g., about 4 days.


In embodiments, the cells, e.g., HSPCs, e.g., as described herein, are cultured ex vivo for a period of about 1 hour to about 10 days, e.g., a period of about 12 hours to about 5 days, e.g., a period of about 12 hours to 4 days, e.g., a period of about 1 day to about 4 days, e.g., a period of about 1 day to about 2 days, e.g., a period of about 1 day or a period of about 2 days, prior to the step of contacting the cells with a CRISPR system, e.g., described herein. In embodiments, said culturing prior to said contacting step is in a composition (e.g., a cell culture medium) comprising a stem cell expander, e.g., described herein, e.g., compound 4, e.g., compound 4 at a concentration of about 0.25 uM to about 1 uM, e.g., compound 4 at a concentration of about 0.75-0.5 micromolar. In embodiments, the cells are cultured ex vivo for a period of no more than about about 1 day, e.g., no more than about 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 hour(s) after the step of contacting the cells with a CRISPR system, e.g., described herein, e.g., in a cell culture medium which comprises a stem cell expander, e.g., described herein, e.g., compound 4, e.g., compound 4 at a concentration of about 0.25 uM to about 1 uM, e.g., compound 4 at a concentration of about 0.75-0.5 micromolar. In other embodiments, the cells are cultured ex vivo for a period of about 1 hour to about 14 days, e.g., a period of about 12 hours to about 10 days, e.g., a period of about 1 day to about 10 days, e.g., a period of about 1 day to about 5 days, e.g., a period of about 1 day to about 4 days, e.g., a period of about 2 days to about 4 days, e.g., a period of about 2 days, about 3 days or about 4 days, after the step of contacting the cells with a CRISPR system, e.g., described herein, in a cell culture medium, e.g., which comprises a stem cell expander, e.g., described herein, e.g., compound 4, e.g., compound 4 at a concentration of about 0.25 uM to about 1 uM, e.g., compound 4 at a concentration of about 0.75-0.5 micromolar.


In embodiments, the cell culture medium is a chemically defined medium. In embodiments, the cell culture medium may additionally contain, for example, StemSpan SFEM (StemCell Technologies; Cat no. 09650). In embodiments, the cell culture medium may alternatively or additionally contain, for example, HSC Brew, GMP (Miltenyi). In embodiments, the media may be supplemented with thrombopoietin (TPO), human Flt3 ligand (Flt-3L), human stem cell factor (SCF), human interleukin-6, L-glutamine, and/or penicillin/streptomycin. In embodiments, the media is supplemented with thrombopoietin (TPO), human Flt3 ligand (Flt-3L), human stem cell factor (SCF), human interleukin-6, and L-glutamine. In other embodiments, the media is supplemented with thrombopoietin (TPO), human Flt3 ligand (Flt-3L), human stem cell factor (SCF), and human interleukin-6. In other embodiments the media is supplemented with thrombopoietin (TPO), human Flt3 ligand (Flt-3L), and human stem cell factor (SCF), but not human interleukin-6. When present in the medium, the thrombopoietin (TPO), human Flt3 ligand (Flt-3L), human stem cell factor (SCF), human interleukin-6, and/or L-glutamine are each present in a concentration ranging from about 1 ng/mL to about 1000 ng/mL, e.g., a concentration ranging from about 10 ng/mL to about 500 ng/mL, e.g., a concentration ranging from about 10 ng/mL to about 100 ng/mL, e.g., a concentration ranging from about 25 ng/mL to about 75 ng/mL, e.g., a concentration of about 50 ng/mL. In embodiments, each of the supplemented components is at the same concentration. In other embodiments, each of the supplemented components is at a different concentration. In an embodiment, the medium comprises StemSpan SFEM (StemCell Technologies; Cat no. 09650), 50 ng/mL of thrombopoietin (Tpo), 50 ng/mL of human Flt3 ligand (Flt-3L), 50 ng/mL of human stem cell factor (SCF), and 50 ng/mL of human interleukin-6 (IL-6). In an embodiment, the medium comprises StemSpan SFEM (StemCell Technologies; Cat no. 09650), 50 ng/mL of thrombopoietin (Tpo), 50 ng/mL of human Flt3 ligand (Flt-3L), and 50 ng/mL of human stem cell factor (SCF), and does not comprise IL-6. In embodiments, the media further comprises a stem cell expander, e.g., compound 4, e.g., compound 4 at a concentration of 0.75 μM. In embodiments, the media further comprises a stem cell expander, e.g., compound 4, e.g., compound 4 at a concentration of 0.5 μM. In embodiments, the media further comprises 1% L-glutamine and 2% penicillin/streptomycin. In embodiments, the cell culture medium is serum free.


XII. Combination Therapy

The present disclosure contemplates the use of the gRNA molecules described herein, or cells (e.g., hematopoietic stem cells, e.g., CD34+ cells) modified with the gRNA molecules described herein, in combination with one or more other therapeutic modalities and/or agents agents. Thus, in addition to the use of the gRNA molecules or cells modified with the gRNA molecules described herein, one may also administer to the subject one or more “standard” therapies for treating hemoglobinopathies.


The one or more additional therapies for treating hemoglobinopathies may include, for example, additional stem cell transplantation, e.g., hematopoietic stem cell transplantation. The stem cell transplantation may be allogeneic or autologous.


The one or more additional therapies for treating hemoglobinopathies may include, for example, blood transfusion and/or iron chealation (e.g., removal) therapy. Known iron chealation agents include, for example, deferoxamine and deferasirox.


The one or more additional therapies for treating hemoglobinopathies may include, for example, folic acid supplements, or hydroxyurea (e.g., 5-hydroxyurea). The one or more additional therapies for treating hemoglobinopathies may be hydroxyurea. In embodiments, the hydroxyurea may be administered at a dose of, for example, 10-35 mg/kg per day, e.g., 10-20 mg/kg per day. In embodiments, the hydroxyurea is adminstered at a dose of 10 mg/kg per day. In embodiments, the hydroxyurea is adminstered at a dose of 10 mg/kg per day. In embodiments, the hydroxyurea is adminstered at a dose of 20 mg/kg per day. In embodiments, the hydroxyurea is administered before and/or after the cell (or population of cells), e.g., CD34+ cell (or population of cells) of the invention, e.g., as described herein.


The one or more additional therapeutic agents may include, for example, an anti-p-selectin antibody, e.g., SelG1 (Selexys). P-selectin antibodies are described in, for example, PCT publication WO1993/021956, PCT publication WO1995/034324, PCT publication WO2005/100402, PCT publication WO2008/069999, US patent application publication US2011/0293617, U.S. Pat. No. 5,800,815, U.S. Pat. No. 6,667,036, U.S. Pat. No. 8,945,565, U.S. Pat. No. 8,377,440 and U.S. Pat. No. 9,068,001, the contents of each of which are incorporated herein in their entirety.


The one or more additional agents may include, for example, a small molecule which upregulates fetal hemoglobin. Examples of such molecules include TN1 (e.g., as described in Nam, T. et al., ChemMedChem 2011, 6, 777-780, DOI: 10.1002/cmdc.201000505, herein incorporated by reference).


The one or more additional therapies may also include irradiation or other bone marrow ablation therapies known in the art. An example of such a therapy is busulfan. Such additional therapy may be performed prior to introduction of the cells of the invention into the subject. In an embodiment the methods of treatment described herein (e.g., the methods of treatment that include administration of cells (e.g., HSPCs) modified by the methods described herein (e.g., modified with a CRISPR system described herein, e.g., to increase HbF production)), the method does not include the step of bone marrow ablation. In embodiments, the methods include a partial bone marrow ablation step.


The therapies described herein (e.g., comprising administering a population of HSPCs, e.g., HSPCs modified using a CRISPR system described herein) may also be combined with an additional therapeutic agent. In an embodiment, the additional therapeutic agent is an HDAC inhibitor, e.g., panobinostat. In an embodiment, the additional therapeutic is a compound described in PCT Publication No. WO2014/150256, e.g., a compound described in Table 1 of WO2014/150256, e.g., GBT440. Other examples of HDAC inhibitors include, for example, suberoylanilide hydroxamic acid (SAHA). The one or more additional agents may include, for example, a DNA methylation inhibitor. Such agents have been shown to increase the HbF induction in cells having reduced BCL11a activity (e.g., Jian Xu et al, Science 334, 993 (2011); DOI: 0.1126/science.1211053, herein incorporated by reference). Other HDAC inhibitors include any HDAC inhibitor known in the art, for example, trichostatin A, HC toxin, DACI-2, FK228, DACI-14, depudicin, DACI-16, tubacin, NK57, MAZ1536, NK125, Scriptaid, Pyroxamide, MS-275, ITF-2357, MCG-D0103, CRA-024781, CI-994, and LBH589 (see, e.g., Bradner J E, et al., PNAS, 2010 (vol. 107:28), 12617-12622, herein incorporated by reference in its entirety).


The gRNA molecules described herein, or cells (e.g., hematopoietic stem cells, e.g., CD34+ cells) modified with the gRNA molecules described herein, and the co-therapeutic agent or co-therapy can be administered in the same formulation or separately. In the case of separate administration, the gRNA molecules described herein, or cells modified with the gRNA molecules described herein, can be administered before, after or concurrently with the co-therapeutic or co-therapy. One agent may precede or follow administration of the other agent by intervals ranging from minutes to weeks. In embodiments where two or more different kinds of therapeutic agents are applied separately to a subject, one would generally ensure that a significant period of time did not expire between the time of each delivery, such that these different kinds of agents would still be able to exert an advantageously combined effect on the target tissues or cells.


XIII. Modified Nucleosides, Nucleotides, and Nucleic Acids

Modified nucleosides and modified nucleotides can be present in nucleic acids, e.g., particularly gRNA, but also other forms of RNA, e.g., mRNA, RNAi, or siRNA. As described herein “nucleoside” is defined as a compound containing a five-carbon sugar molecule (a pentose or ribose) or derivative thereof, and an organic base, purine or pyrimidine, or a derivative thereof. As described herein, “nucleotide” is defined as a nucleoside further comprising a phosphate group.


Modified nucleosides and nucleotides can include one or more of:


(i) alteration, e.g., replacement, of one or both of the non-linking phosphate oxygens and/or of one or more of the linking phosphate oxygens in the phosphodiester backbone linkage;


(ii) alteration, e.g., replacement, of a constituent of the ribose sugar, e.g., of the 2′ hydroxyl on the ribose sugar;


(iii) wholesale replacement of the phosphate moiety with “dephospho” linkers;


(iv) modification or replacement of a naturally occurring nucleobase, including with a non-canonical nucleobase;


(v) replacement or modification of the ribose-phosphate backbone;


(vi) modification of the 3′ end or 5′ end of the oligonucleotide, e.g., removal, modification or replacement of a terminal phosphate group or conjugation of a moiety, cap or linker; and


(vii) modification or replacement of the sugar.


The modifications listed above can be combined to provide modified nucleosides and nucleotides that can have two, three, four, or more modifications. For example, a modified nucleoside or nucleotide can have a modified sugar and a modified nucleobase. In an embodiment, every base of a gRNA is modified, e.g., all bases have a modified phosphate group, e.g., all are phosphorothioate groups. In an embodiment, all, or substantially all, of the phosphate groups of a unimolecular or modular gRNA molecule are replaced with phosphorothioate groups. In embodiments, one or more of the five 3′-terminal bases and/or one or more of the five 5′-terminal bases of the gRNA are modified with a phosphorothioate group.


In an embodiment, modified nucleotides, e.g., nucleotides having modifications as described herein, can be incorporated into a nucleic acid, e.g., a “modified nucleic acid.” In some embodiments, the modified nucleic acids comprise one, two, three or more modified nucleotides. In some embodiments, at least 5% (e.g., at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or about 100%) of the positions in a modified nucleic acid are a modified nucleotides.


Unmodified nucleic acids can be prone to degradation by, e.g., cellular nucleases. For example, nucleases can hydrolyze nucleic acid phosphodiester bonds. Accordingly, in one aspect the modified nucleic acids described herein can contain one or more modified nucleosides or nucleotides, e.g., to introduce stability toward nucleases.


In some embodiments, the modified nucleosides, modified nucleotides, and modified nucleic acids described herein can exhibit a reduced innate immune response when introduced into a population of cells, both in vivo and ex vivo. The term “innate immune response” includes a cellular response to exogenous nucleic acids, including single stranded nucleic acids, generally of viral or bacterial origin, which involves the induction of cytokine expression and release, particularly the interferons, and cell death. In some embodiments, the modified nucleosides, modified nucleotides, and modified nucleic acids described herein can disrupt binding of a major groove interacting partner with the nucleic acid.


In some embodiments, the modified nucleosides, modified nucleotides, and modified nucleic acids described herein can exhibit a reduced innate immune response when introduced into a population of cells, both in vivo and ex vivo, and also disrupt binding of a major groove interacting partner with the nucleic acid.


Definitions of Chemical Groups

As used herein, “alkyl” is meant to refer to a saturated hydrocarbon group which is straight-chained or branched. Example alkyl groups include methyl (Me), ethyl (Et), propyl (e.g., n-propyl and isopropyl), butyl (e.g., n-butyl, isobutyl, t-butyl), pentyl (e.g., n-pentyl, isopentyl, neopentyl), and the like. An alkyl group can contain from 1 to about 20, from 2 to about 20, from 1 to about 12, from 1 to about 8, from 1 to about 6, from 1 to about 4, or from 1 to about 3 carbon atoms.


As used herein, “aryl” refers to monocyclic or polycyclic (e.g., having 2, 3 or 4 fused rings) aromatic hydrocarbons such as, for example, phenyl, naphthyl, anthracenyl, phenanthrenyl, indanyl, indenyl, and the like. In some embodiments, aryl groups have from 6 to about 20 carbon atoms.


As used herein, “alkenyl” refers to an aliphatic group containing at least one double bond. As used herein, “alkynyl” refers to a straight or branched hydrocarbon chain containing 2-12 carbon atoms and characterized in having one or more triple bonds. Examples of alkynyl groups include, but are not limited to, ethynyl, propargyl, and 3-hexynyl.


As used herein, “arylalkyl” or “aralkyl” refers to an alkyl moiety in which an alkyl hydrogen atom is replaced by an aryl group. Aralkyl includes groups in which more than one hydrogen atom has been replaced by an aryl group. Examples of “arylalkyl” or “aralkyl” include benzyl, 2-phenylethyl, 3-phenylpropyl, 9-fluorenyl, benzhydryl, and trityl groups.


As used herein, “cycloalkyl” refers to a cyclic, bicyclic, tricyclic, or polycyclic non-aromatic hydrocarbon groups having 3 to 12 carbons. Examples of cycloalkyl moieties include, but are not limited to, cyclopropyl, cyclopentyl, and cyclohexyl.


As used herein, “heterocyclyl” refers to a monovalent radical of a heterocyclic ring system. Representative heterocyclyls include, without limitation, tetrahydrofuranyl, tetrahydrothienyl, pyrrolidinyl, pyrrolidonyl, piperidinyl, pyrrolinyl, piperazinyl, dioxanyl, dioxolanyl, diazepinyl, oxazepinyl, thiazepinyl, and morpholinyl.


As used herein, “heteroaryl” refers to a monovalent radical of a heteroaromatic ring system. Examples of heteroaryl moieties include, but are not limited to, imidazolyl, oxazolyl, thiazolyl, triazolyl, pyrrolyl, furanyl, indolyl, thiophenyl pyrazolyl, pyridinyl, pyrazinyl, pyridazinyl, pyrimidinyl, indolizinyl, purinyl, naphthyridinyl, quinolyl, and pteridinyl.


Phosphate Backbone Modifications
The Phosphate Group

In some embodiments, the phosphate group of a modified nucleotide can be modified by replacing one or more of the oxygens with a different substituent. Further, the modified nucleotide, e.g., modified nucleotide present in a modified nucleic acid, can include the wholesale replacement of an unmodified phosphate moiety with a modified phosphate as described herein. In some embodiments, the modification of the phosphate backbone can include alterations that result in either an uncharged linker or a charged linker with unsymmetrical charge distribution.


Examples of modified phosphate groups include, phosphorothioate, phosphoroselenates, borano phosphates, borano phosphate esters, hydrogen phosphonates, phosphoroamidates, alkyl or aryl phosphonates and phosphotriesters. In some embodiments, one of the non-bridging phosphate oxygen atoms in the phosphate backbone moiety can be replaced by any of the following groups: sulfur (S), selenium (Se), BR3 (wherein R can be, e.g., hydrogen, alkyl, or aryl), C (e.g., an alkyl group, an aryl group, and the like), H, NR2 (wherein R can be, e.g., hydrogen, alkyl, or aryl), or OR (wherein R can be, e.g., alkyl or aryl). The phosphorous atom in an unmodified phosphate group is achiral. However, replacement of one of the non-bridging oxygens with one of the above atoms or groups of atoms can render the phosphorous atom chiral; that is to say that a phosphorous atom in a phosphate group modified in this way is a stereogenic center. The stereogenic phosphorous atom can possess either the “R” configuration (herein Rp) or the “S” configuration (herein Sp).


Phosphorodithioates have both non-bridging oxygens replaced by sulfur. The phosphorus center in the phosphorodithioates is achiral which precludes the formation of oligoribonucleotide diastereomers. In some embodiments, modifications to one or both non-bridging oxygens can also include the replacement of the non-bridging oxygens with a group independently selected from S, Se, B, C, H, N, and OR (R can be, e.g., alkyl or aryl).


The phosphate linker can also be modified by replacement of a bridging oxygen, (i.e., the oxygen that links the phosphate to the nucleoside), with nitrogen (bridged phosphoroamidates), sulfur (bridged phosphorothioates) and carbon (bridged methylenephosphonates). The replacement can occur at either linking oxygen or at both of the linking oxygens.


Replacement of the Phosphate Group

The phosphate group can be replaced by non-phosphorus containing connectors. In some embodiments, the charge phosphate group can be replaced by a neutral moiety.


Examples of moieties which can replace the phosphate group can include, without limitation, e.g., methyl phosphonate, hydroxylamino, siloxane, carbonate, carboxymethyl, carbamate, amide, thioether, ethylene oxide linker, sulfonate, sulfonamide, thioformacetal, formacetal, oxime, methyleneimino, methylenemethylimino, methylenehydrazo, methylenedimethylhydrazo and methyleneoxymethylimino.


Replacement of the Ribophosphate Backbone

Scaffolds that can mimic nucleic acids can also be constructed wherein the phosphate linker and ribose sugar are replaced by nuclease resistant nucleoside or nucleotide surrogates. In some embodiments, the nucleobases can be tethered by a surrogate backbone. Examples can include, without limitation, the morpholino, cyclobutyl, pyrrolidine and peptide nucleic acid (PNA) nucleoside surrogates.


Sugar Modifications

The modified nucleosides and modified nucleotides can include one or more modifications to the sugar group. For example, the 2′ hydroxyl group (OH) can be modified or replaced with a number of different “oxy” or “deoxy” substituents. In some embodiments, modifications to the 2′ hydroxyl group can enhance the stability of the nucleic acid since the hydroxyl can no longer be deprotonated to form a 2′-alkoxide ion. The 2′-alkoxide can catalyze degradation by intramolecular nucleophilic attack on the linker phosphorus atom.


Examples of “oxy”-2′ hydroxyl group modifications can include alkoxy or aryloxy (OR, wherein “R” can be, e.g., alkyl, cycloalkyl, aryl, aralkyl, heteroaryl or a sugar); polyethyleneglycols (PEG), 0(CH2CH20)nCH2CH2OR wherein R can be, e.g., H or optionally substituted alkyl, and n can be an integer from 0 to 20 (e.g., from 0 to 4, from 0 to 8, from 0 to 10, from 0 to 16, from 1 to 4, from 1 to 8, from 1 to 10, from 1 to 16, from 1 to 20, from 2 to 4, from 2 to 8, from 2 to 10, from 2 to 16, from 2 to 20, from 4 to 8, from 4 to 10, from 4 to 16, and from 4 to 20). In some embodiments, the “oxy”-2′ hydroxyl group modification can include “locked” nucleic acids (LNA) in which the 2′ hydroxyl can be connected, e.g., by a Ci-6 alkylene or Cj-6 heteroalkylene bridge, to the 4′ carbon of the same ribose sugar, where exemplary bridges can include methylene, propylene, ether, or amino bridges; O-amino (wherein amino can be, e.g., NH2; alkylamino, dialkylamino, heterocyclyl, arylamino, diarylamino, heteroarylamino, or diheteroarylamino, ethylenediamine, or polyamino) and aminoalkoxy, 0(CH2)n-amino, (wherein amino can be, e.g., NH2; alkylamino, dialkylamino, heterocyclyl, arylamino, diarylamino, heteroarylamino, or diheteroarylamino, ethylenediamine, or polyamino). In some embodiments, the “oxy”-2′ hydroxyl group modification can include the methoxyethyl group (MOE), (OCH2CH2OCH3, e.g., a PEG derivative).


“Deoxy” modifications can include hydrogen (i.e. deoxyribose sugars, e.g., at the overhang portions of partially ds RNA); halo (e.g., bromo, chloro, fluoro, or iodo); amino (wherein amino can be, e.g., NH2; alkylamino, dialkylamino, heterocyclyl, arylamino, diarylamino, heteroarylamino, diheteroarylamino, or amino acid); NH(CH2CH2NH)nCH2CH2— amino (wherein amino can be, e.g., as described herein), —NHC(0)R (wherein R can be, e.g., alkyl, cycloalkyl, aryl, aralkyl, heteroaryl or sugar), cyano; mercapto; alkyl-thio-alkyl; thioalkoxy; and alkyl, cycloalkyl, aryl, alkenyl and alkynyl, which may be optionally substituted with e.g., an amino as described herein.


The sugar group can also contain one or more carbons that possess the opposite stereochemical configuration than that of the corresponding carbon in ribose. Thus, a modified nucleic acid can include nucleotides containing e.g., arabinose, as the sugar. The nucleotide “monomer” can have an alpha linkage at the F position on the sugar, e.g., alpha-nucleosides. The modified nucleic acids can also include “abasic” sugars, which lack a nucleobase at C—. These abasic sugars can also be further modified at one or more of the constituent sugar atoms. The modified nucleic acids can also include one or more sugars that are in the L form, e.g. L-nucleosides.


Generally, RNA includes the sugar group ribose, which is a 5-membered ring having an oxygen. Exemplary modified nucleosides and modified nucleotides can include, without limitation, replacement of the oxygen in ribose (e.g., with sulfur (S), selenium (Se), or alkylene, such as, e.g., methylene or ethylene); addition of a double bond (e.g., to replace ribose with cyclopentenyl or cyclohexenyl); ring contraction of ribose (e.g., to form a 4-membered ring of cyclobutane or oxetane); ring expansion of ribose (e.g., to form a 6- or 7-membered ring having an additional carbon or heteroatom, such as for example, anhydrohexitol, altritol, mannitol, cyclohexanyl, cyclohexenyl, and morpholino that also has a phosphoramidate backbone). In some embodiments, the modified nucleotides can include multicyclic forms (e.g., tricyclo; and “unlocked” forms, such as glycol nucleic acid (GNA) (e.g., R-GNA or S-GNA, where ribose is replaced by glycol units attached to phosphodiester bonds), threose nucleic acid (TNA, where ribose is replaced with a-L-threofuranosyl-(3′-→2′)).


Modifications on the Nucleobase


The modified nucleosides and modified nucleotides described herein, which can be incorporated into a modified nucleic acid, can include a modified nucleobase. Examples of nucleobases include, but are not limited to, adenine (A), guanine (G), cytosine (C), and uracil (U). These nucleobases can be modified or wholly replaced to provide modified nucleosides and modified nucleotides that can be incorporated into modified nucleic acids. The nucleobase of the nucleotide can be independently selected from a purine, a pyrimidine, a purine or pyrimidine analog. In some embodiments, the nucleobase can include, for example, naturally-occurring and synthetic derivatives of a base.


Uracil


In some embodiments, the modified nucleobase is a modified uracil. Exemplary nucleobases and nucleosides having a modified uracil include without limitation pseudouridine (ψ), pyridin-4-one ribonucleoside, 5-aza-uridine, 6-aza-uridine, 2-thio-5-aza-uridine, 2-thio-uridine (s2U), 4-thio-uridine (s4U), 4-thio-pseudouridine, 2-thio-pseudouridine, 5-hydroxy-u,ridine (ho5U), 5-aminoallyl-uridine, 5-halo-uridine (e.g., 5-iodo-uridine or 5-bromo-uridine), 3-methyl-uridine (m3U), 5-methoxy-uridine (mo5U), uridine 5-oxyacetic acid (cmo5U), uridine 5-oxyacetic acid methyl ester (mcmôU), 5-carboxymethyl-uridine (cmsU), 1-carboxymethyl-pseudouridine, 5-carboxyhydroxymethyl-uridine (chm5U), 5-carboxyhydroxymethyl-uridine methyl ester (mchm5U), 5-methoxycarbonylmethyl-uridine (mcm5U), 5-methoxycarbonylmethyl-2-thio-uridine (mcm5s2U), 5-aminomethyl-2-thio-uridine (nm5s2U), 5-methylaminomethyl-uridine (mnm5U), 5-methylaminomethyl-2-thio-uridine (mnm5s2U), 5-methylaminomethyl-2-seleno-uridine (mnm5se2U), 5-carbamoylmethyl-uridine (ncm5U), 5-carboxymethylaminomethyl-uridine (cmnm5U), 5-carboxymethylaminomethyl-2-thio-uridine (cmnm \s2U), 5-propynyl-uridine, 1-propynyl-pseudouridine, 5-taurinomethyl-uridine (xcm5U), 1-taurinomethyl-pseudouridine, 5-taurinomethyl-2-thio-uridine(Trn5s2U), 1-taurinomethyl-4-thio-pseudouridine, 5-methyl-uridine (m5U, i.e., having the nucleobase deoxythymine), 1-methyl-pseudouridine (ιτι′ψ). 5-methyl-2-thio-uridine (m5s2U), l-methyl-4-thio-pseudouridine (m's \|/), 4-thio-1-methyl-pseudouridine, 3-methyl-pseudouridine (m′V), 2-thio-1-methyl-pseudouridine, 1-methyl-1-deaza-pseudouridine, 2-thio-1-methyl-1-deaza-pseudouridine, dihydroundine (D), dihydropseudoundine, 5,6-dihydrouridine, 5-methyl-dihydrouridine (m5D), 2-thio-dihydrouridine, 2-thio-dihydropseudouridine, 2-methoxy-uridine, 2-methoxy-4-thio-uridine, 4-methoxy-pseudouridine, 4-methoxy-2-thio-pseudouridine, N1-methyl-pseudouridine, 3-(3-amino-3-carboxypropyl)uridine (acp3U), 1-methyl-3-(3-amino-3-carboxypropy pseudouridine 5-(isopentenylaminomethyl)uridine (inm5U), 5-(isopentenylaminomethyp-2-thio-uridine (inm5s2U), a-thio-uridine, 2′-0-methyl-uridine (Urn), 5,2′-0-dimethyl-uridine (m5Um), 2′-0-methyl-pseudouridine (ψπι), 2-thio-2′-0-methyl-uridine (s2Um), 5-methoxycarbonylmethyl-2′-0-methyl-uridine (mcm 5Um), 5-carbamoylmethyl-2′-0-methyl-uridine (ncm 5Um), 5-carboxymethylaminomethyl-2′-0-methyl-uridine (cmnm 5Um), 3,2′-0-dimethyl-uridine (m3Um), 5-(isopentenylaminomethyl)-2′-0-methyl-uridine (inm5Um), 1-thio-uridine, deoxythymidine, 2′-F-ara-uridine, 2′-F-uridine, 2′-OH-ara-uridine, 5-(2-carbomethoxyvinyl) uridine, 5-[3-(1-E-propenylamino)uridine, pyrazolo[3,4-d]pyrimidines, xanthine, and hypoxanthine.


Cytosine

In some embodiments, the modified nucleobase is a modified cytosine. Exemplary nucleobases and nucleosides having a modified cytosine include without limitation 5-aza-cytidine, 6-aza-cytidine, pseudoisocytidine, 3-methyl-cytidine (m3C), N4-acetyl-cytidine (act), 5-formyl-cytidine (f5C), N4-methyl-cytidine (m4C), 5-methyl-cytidine (m5C), 5-halo-cytidine (e.g., 5-iodo-cytidine), 5-hydroxymethyl-cytidine (hm5C), 1-methyl-pseudoisocytidine, pyrrolo-cytidine, pyrrolo-pseudoisocytidine, 2-thio-cytidine (s2C), 2-thio-5-methyl-cytidine, 4-thio-pseudoisocytidine, 4-thio-1-methyl-pseudoisocytidine, 4-thio-1-methyl-1-deaza-pseudoisocytidine, 1-methyl-1-deaza-pseudoisocytidine, zebularine, 5-aza-zebularine, 5-methyl-zebularine, 5-aza-2-thio-zebularine, 2-thio-zebularine, 2-methoxy-cytidine, 2-methoxy-5-methyl-cytidine, 4-methoxy-pseudoisocytidine, 4-methoxy-1-methyl-pseudoisocytidine, lysidine (k2C), a-thio-cytidine, 2′-0-methyl-cytidine (Cm), 5,2′-0-dimethyl-cytidine (m5Cm), N4-acetyl-2′-0-methyl-cytidine (ac4Cm), N4,2′-0-dimethyl-cytidine (m4Cm), 5-formyl-2′-0-methyl-cytidine (f 5Cm), N4,N4,2′-0-trimethyl-cytidine (m42Cm), 1-thio-cytidine, 2′-F-ara-cytidine, 2′-F-cytidine, and 2′-OH-ara-cytidine.


Adenine

In some embodiments, the modified nucleobase is a modified adenine. Exemplary nucleobases and nucleosides having a modified adenine include without limitation 2-amino-purine, 2,6-diaminopurine, 2-amino-6-halo-purine (e.g., 2-amino-6-chloro-purine), 6-halo-purine (e.g., 6-chloi-purine), 2-amino-6-methyl-purine, 8-azido-adenosine, 7-deaza-adenine, 7-deaza-8-aza-adenine, 7-deaza-2-amino-purine, 7-deaza-8-aza-2-amino-purine, 7-deaza-2,6-diaminopurine, 7-deaza-8-aza-2,6-diaminopurine, 1-methyl-adenosine (m′A), 2-methyl-adenine (m A), N6-methyl-adenosine (m6A), 2-methylthio-N6-methyl-adenosine (ms2 m6A), N6-isopentenyl-adenosine 2-methylthio-N6-isopentenyl-adenosine (ms2i6A), N6-(cis-hydroxyisopentenyl)adenosine (io6A), 2-methylthio-N6-(cis-hydroxyisopentenyl)adenosine (ms2io6A), N6-glycinylcarbamoyl-adenosine (g6A), N6-threonylcarbamoyl-adenosine (t6A), N6-methyl-N6-threonylcarbamoyl-adenosine (m6t6A), 2-methylthio-N6-threonylcarbamoyl-adenosine (ms2g6A), N6,N6-dimethyl-adenosine (m62A), N6-hydroxynorvalylcarbamoyl-adenosine (hn6A), 2-methylthio-N6-hydroxynorvalylcarbamoyl-adenosine (ms2hn6A), N6-acetyl-adenosine (ac6A), 7-methyl-adenine, 2-methylthio-adenine, 2-methoxy-adenine, a-thio-adenosine, 2′-0-methyl-adenosine (Am), N6,2′-0-dimethyl-adenosine (m5Am), N6-Methyl-2′-deoxyadenosine, N6,N6,2′-0-trimethyl-adenosine (m62Am), 1,2′-0-dimethyl-adenosine (m′ Am), 2′-0-ribosyladenosine (phosphate) (Ar(p)), 2-amino-N6-methyl-purine, 1-thio-adenosine, 8-azido-adenosine, 2′-F-ara-adenosine, 2′-F-adenosine, 2′-OH-ara-adenosine, and N6-(19-amino-pentaoxanonadecyl)-adenosine.


Guanine

In some embodiments, the modified nucleobase is a modified guanine. Exemplary nucleobases and nucleosides having a modified guanine include without limitation inosine (I), 1-methyl-inosine (m′l), wyosine (imG), methylwyosine (mimG), 4-demethyl-wyo″sine (imG-14), isowyosine (imG2), wybutosine (yW), peroxywybutosine (o2yW), hydroxywybutosine (OHyW), undemriodified hydroxywybutosine (OHyW*), 7-deaza-guanosine, queuosine (Q), epoxyqueuosine (oQ), galactosyl-queuosine (galQ), mannosyl-queuosine (manQ), 7-cyano-7-deaza-guanosine (preQ0), 7-aminomethyl-7-deaza-guanosine (preQi), archaeosine (G+), 7-deaza-8-aza-guanosine, 6-thio-guanosine, 6-thio-7-deaza-guanosine, 6-thio-7-deaza-8-aza-guanosine, 7-methyl-guanosine (m7G), 6-thio-7-methyl-guanosine, 7-methyl-inosine, 6-methoxy-guanosine, 1-methyl-guanosine (m′G), N2-methyl-guanosine (m2G), N2,N2-dimethyl-guanosine (m22G), N2,7-dimethyl-guanosine (m2,7G), N2, N2,7-dimethyl-guanosine (m2,2,7G), 8-oxo-guanosine, 7-methyl-8-oxo-guanosine, 1-meth thio-guanosine, N2-methyl-6-thio-guanosine, N2,N2-dimethyl-6-thio-guanosine, a-thio-guanosine, 2′-0-methyl-guanosine (Gm), N2-methyl-2′-0-methyl-guanosine (m¾m), N2,N2-dimethyl-2′-0-methyl-guanosine (m22Gm), 1-methyl-2′-0-methyl-guanosine (m′Gm), N2,7-dimethyl-2′-0-methyl-guanosine (m2,7Gm), 2′-0-methyl-inosine (Im), 1,2′-0-dimethyl-inosine (m′lm), 06-phenyl-2′-deoxyinosine, 2′-0-ribosylguanosine (phosphate) (Gr(p)), 1-thio-guanosine, 06-methy]-guanosine, 06-Methyl-2′-deoxyguanosine, 2′-F-ara-guanosine, and 2′-F-guanosine.


Modified gRNAs


In some embodiments, the modified nucleic acids can be modified gRNAs. In some embodiments, gRNAs can be modified at the 3′ end. In this embodiment, the gRNAs can be modified at the 3′ terminal U ribose. For example, the two terminal hydroxyl groups of the U ribose can be oxidized to aldehyde groups and a concomitant opening of the ribose ring to afford a modified nucleoside, wherein U can be an unmodified or modified uridine.


In another embodiment, the 3′ terminal U can be modified with a 2′ 3′ cyclic phosphate, wherein U can be an unmodified or modified uridine. In some embodiments, the gRNA molecules may contain 3′ nucleotides which can be stabilized against degradation, e.g., by incorporating one or more of the modified nucleotides described herein. In this embodiment, e.g., uridines can be replaced with modified uridines, e.g., 5-(2-amino)propyl uridine, and 5-bromo uridine, or with any of the modified uridines described herein; adenosines and guanosines can be replaced with modified adenosines and guanosines, e.g., with modifications at the 8-position, e.g., 8-bromo guanosine, or with any of the modified adenosines or guanosines described herein. In some embodiments, deaza nucleotides, e.g., 7-deaza-adenosine, can be incorporated into the gRNA. In some embodiments, O- and N-alkylated nucleotides, e.g., N6-methyl andenosine, can be incorporated into the gRNA. In some embodiments, sugar-modified ribonucleotides can be incorporated, e.g., wherein the 2′ OH— group is replaced by a group selected from H, —OR, —R (wherein R can be, e.g., methyl, alkyl, cycloalkyl, aryl, aralkyl, heteroaryl or sugar), halo, —SH, —SR (wherein R can be, e.g., alkyl, cycloalkyl, aryl, aralkyl, heteroaryl or sugar), amino (wherein amino can be, e.g., NH2; alkylamino, dialkylamino, heterocyclyl, arylamino, diarylamino, heteroarylamino, diheteroarylamino, or amino acid); or cyano (—CN). In some embodiments, the phosphate backbone can be modified as described herein, e.g., with a phosphothioate group. In some embodiments, the nucleotides in the overhang region of the gRNA can each independently be a modified or unmodified nucleotide including, but not limited to 2′-sugar modified, such as, 2-F 2′-0-methyl, thymidine (T), 2′-O-methoxyethyl-5-methyluridine (Teo), 2′-O-methoxyethyladenosine (Aeo), 2′-O-methoxyethyl-5-methylcytidine (m5Ceo), and any combinations thereof.


In an embodiment, a one or more or all of the nucleotides in single stranded overhang of an RNA molecule, e.g., a gRNA molecule, are deoxynucleotides.


Pharmaceutical Compositions

Pharmaceutical compositions of the present invention may comprise a gRNA molecule described herein, e.g., a plurality of gRNA molecules as described herein, or a cell (e.g., a population of cells, e.g., a population of hematopoietic stem cells, e.g., of CD34+ cells) comprising one or more cells modified with one or more gRNA molecules described herein, in combination with one or more pharmaceutically or physiologically acceptable carriers, diluents or excipients. Such compositions may comprise buffers such as neutral buffered saline, phosphate buffered saline and the like; carbohydrates such as glucose, mannose, sucrose or dextrans, mannitol; proteins; polypeptides or amino acids such as glycine; antioxidants; chelating agents such as EDTA or glutathione; adjuvants (e.g., aluminum hydroxide); and preservatives. Compositions of the present invention are in one aspect formulated for intravenous administration.


Pharmaceutical compositions of the present invention may be administered in a manner appropriate to the disease to be treated (or prevented). The quantity and frequency of administration will be determined by such factors as the condition of the patient, and the type and severity of the patient's disease, although appropriate dosages may be determined by clinical trials.


In one embodiment, the pharmaceutical composition is substantially free of, e.g., there are no detectable levels of a contaminant, e.g., selected from the group consisting of endotoxin, mycoplasma, mouse antibodies, pooled human serum, bovine serum albumin, bovine serum, culture media components, unwanted CRISPR system components, a bacterium and a fungus. In one embodiment, the bacterium is at least one selected from the group consisting of Alcaligenes faecalis, Candida albicans, Escherichia coli, Haemophilus influenza, Neisseria meningitides, Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus pneumonia, and Streptococcus pyogenes group A.


The administration of the subject compositions may be carried out in any convenient manner, including by aerosol inhalation, injection, ingestion, transfusion, implantation or transplantation. The compositions described herein may be administered to a patient transarterially, subcutaneously, intradermally, intratumorally, intranodally, intramedullary, intramuscularly, by intravenous (i.v.) injection, or intraperitoneally. In one aspect, the compositions of the present invention are administered to a patient by intradermal or subcutaneous injection. In one aspect, the cell compositions of the present invention are administered by i.v. injection.


The dosage of the above treatments to be administered to a patient will vary with the precise nature of the condition being treated and the recipient of the treatment. The scaling of dosages for human administration can be performed according to art-accepted practices.


Cells

The invention also relates to cells comprising a gRNA molecule of the invention, or nucleic acid encoding said gRNA molecules.


In an aspect the cells are cells made by a process described herein.


In embodiments, the cells are hematopoietic stem cells (e.g., hematopoietic stem and progenitor cells; HSPCs), for example, CD34+ stem cells. In embodiments, the cells are CD34+/CD90+ stem cells. In embodiments, the cells are CD34+/CD90− stem cells. In embodiments, the cells are human hematopoietic stem cells. In embodiments, the cells are autologous. In embodiments, the cells are allogeneic.


In embodiments, the cells are derived from bone marrow, e.g., autologous bone marrow. In embodiments, the cells are derived from peripheral blood, e.g., mobilized peripheral blood, e.g., autologous mobilized peripheral blood. In embodiments employing moblized peripheral blood, the cells are isoalted from patients who have been administered a mobilization agent. In embodiments, the mobilization agent is G-CSF. In embodiments, the mobilization agent is Plerixafor® (AMD3100). In embodiments, the cells are derived from umbilical cord blood, e.g., allogeneic umbilical cord blood.


In embodiments, the cells are mammalian. In embodiments, the cells are human.


In an aspect, the invention provides a cell comprising a modification or alteration, e.g., an indel, at or near (e.g., within 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2 or 1 nucleotides of) a nucleic acid sequence having complementarity to a gRNA molecule or gRNA molecules, e.g., as described herein, introduced into said cells, e.g., as part of a CRISPR system as described herein. In embodiments, the cell is a CD34+ cell. In embodiments, the altered or modified cell, e.g., CD34+ cell, maintains the ability to differentiate into cells of multiple lineages, e.g., maintains the ability to differentiate into cells of the erythroid lineage. In embodiments, the altered or modified cell, e.g., CD34+ cell, has undergone or is able to undergo at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9 or at least 10 or more doublings in culture, e.g., in culture comprising a stem cell expander, e.g., Compound 4. In embodiments, the altered or modified cell, e.g., CD34+ cell, has undergone or is able to undergo at least 5, e.g., about 5, doublings in culture, e.g., in culture comprising a stem cell expander molecule, e.g., as described herein, e.g., Compound 4. In embodiments the altered or modified cell, e.g., CD34+ cell, exhibits and/or is able to differentiate into a cell, e.g., into a cell of the erythroid lineage, e.g., into a red blood cell, that exhibits increased fetal hemoglobin level (e.g., expression level and/or protein level), e.g., at least a 20% increase in fetal hemoglobin protein level, relative to a similar unmodified or unaltered cell. In embodiments the altered or modified cell, e.g., CD34+ cell, exhibits and/or is able to differentiate into a cell, e.g., into a cell of the erythroid lineage, e.g., into a red blood cell, that exhibits increased fetal hemoglobin level (e.g., expression level and/or protein level), relative to a similar unmodified or unaltered cell, e.g., produces at least 6 picograms, e.g., at least 7 picograms, at least 8 picograms, at least 9 picograms, or at least 10 picograms of fetal hemoglobin. In embodiments the altered or modified cell, e.g., CD34+ cell, exhibits and/or is able to differentiate into a cell, e.g., into a cell of the erythroid lineage, e.g., into a red blood cell, that exhibits increased fetal hemoglobin level (e.g., expression level and/or protein level), relative to a similar unmodified or unaltered cell, e.g., produces about 6 to about 12, about about 6 to about 7, about 7 to about 8, about 8 to about 9, about 9 to about 10, about 10 to about 11 or about 11 to about 12 picograms of fetal hemoglobin.


In an aspect, the invention provides a population of cells comprising cells having a modification or alteration, e.g., an indel, at or near (e.g., within 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2 or 1 nucleotides of) a nucleic acid sequence having complementarity to a gRNA molecule or gRNA molecules, e.g., as described herein, introduced into said cells, e.g., as part of a CRISPR system as described herein. In embodiments, at least 50%, e.g., at least 60%, at least 70%, at least 80% or at least 90% of the cells of the population have the modification or alteration (e.g., have at least one modification or alteration), e.g., as measured by NGS, e.g., as described herein, e.g., at day two following introduction of the gRNA and/or CRISPR system of the invention. In embodiments, at least 90%, e.g., at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of the cells of the population have the modification or alteration (e.g., have at least one modification or alteration), e.g., as measured by NGS, e.g., as described herein, e.g., at day two following introduction of the gRNA and/or CRISPR system of the invention. In embodiments, the population of cells comprise CD34+ cells, e.g., comprise at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 95% or at least about 98% CD34+ cells. In embodiments, the population of cells comprising the altered or modified cells, e.g., CD34+ cells, maintain the ability to produce, e.g., differentiate into, cells of multiple lineages, e.g., maintains the ability to produce, e.g., differentiate into, cells of the erythroid lineage. In embodiments, the population of cells, e.g., population of CD34+ cells, has undergone or is able to undergo at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9 or at least 10 or more population doublings in culture, e.g., in culture comprising a stem cell expander, e.g., Compound 4. In embodiments, the population of altered or modified cells, e.g., population of CD34+ cells, has undergone or is capable of undergoing at least 5, e.g., about 5, population doublings in culture, e.g., in culture comprising a stem cell expander molecule, e.g., as described herein, e.g., Compound 4. In embodiments the population of cells comprising altered or modified cells, e.g., CD34+ cells, exhibits and/or is able to differentiate into a population of cells, e.g., into a population of cells of the erythroid lineage, e.g., into a population of red blood cells, that exhibits increased fetal hemoglobin level (e.g., expression level and/or protein level), e.g., at least a 20% increase in fetal hemoglobin protein level, relative to a similar unmodified or unaltered cells. In embodiments the population of cells comprising altered or modified cells, e.g., CD34+ cells, exhibits and/or is able to differentiate into a population of cells, e.g., into a population of cells of the erythroid lineage, e.g., into a population of red blood cells, that exhibits increased fetal hemoglobin level (e.g., expression level and/or protein level), relative to a similar unmodified or unaltered cells, e.g., comprises cells that produce at least 6 picograms, e.g., at least 7 picograms, at least 8 picograms, at least 9 picograms, or at least 10 picograms of fetal hemoglobin per cell. In embodiments the population of altered or modified cells, e.g., CD34+ cells, exhibits and/or is able to differentiate into a population of cells, e.g., into a population of cells of the erythroid lineage, e.g., into a population of red blood cells, that exhibits increased fetal hemoglobin level (e.g., expression level and/or protein level), relative to a similar unmodified or unaltered cell, e.g., comprises cells that produce about 6 to about 12, about about 6 to about 7, about 7 to about 8, about 8 to about 9, about 9 to about 10, about 10 to about 11 or about 11 to about 12 picograms of fetal hemoglobin per cell.


In embodiments, the population of cells, e.g., as described herein, comprises at least about 1e3 cells.


In embodiments, the population of cells, e.g., as described herein, comprises at least about 1e4 cells.


In embodiments, the population of cells, e.g., as described herein, comprises at least about 1e5 cells.


In embodiments, the population of cells, e.g., as described herein, comprises at least about 1e6 cells.


In embodiments, the population of cells, e.g., as described herein, comprises at least about 1e7 cells.


In embodiments, the population of cells, e.g., as described herein, comprises at least about 1e8 cells.


In embodiments, the population of cells, e.g., as described herein, comprises at least about 1e9 cells.


In embodiments, the population of cells, e.g., as described herein, comprises at least about 1e10 cells.


In embodiments, the population of cells, e.g., as described herein, comprises at least about 1e11 cells.


In embodiments, the population of cells, e.g., as described herein, comprises at least about 1e12 cells.


In embodiments, the population of cells, e.g., as described herein, comprises at least about 1e13 cells per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 1e6 cells per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 2e6 cells per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 3e6 cells per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 4e6 cells per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 5e6 cells per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 6e6 cells per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 7e6 cells per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 8e6 cells per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 9e6 cells per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 1e7 cells per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 2e7 cells per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 3e7 cells per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 4e7 cells per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 5e7 cells per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 6e7 cells per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 7e7 cells per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 8e7 cells per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 9e7 cells per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 1e8 cells per kilogram body weight of the patient to which they are to be administered. In any of the aforementioned embodiments, the population of cells may comprise at least about 50% (for example, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 95% or at least about 99%) HSPCs, e.g., CD34+ cells. In any of the aforementioned embodiments, the population of cells may comprise about 60% HSPCs, e.g., CD34+ cells. In an embodiment, the population of cells, e.g., as described herein, comprises about 3e7 cells and comprises about 2e7 HSPCs, e.g., CD34+ cells.


In embodiments, the population of cells, e.g., as described herein, comprises at least about 1e6 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 1.5e6 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 2e6 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 3e6 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 4e6 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 5e6 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 6e6 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 7e6 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 8e6 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 9e6 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 1e7 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 2e7 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 3e7 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 4e7 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 5e7 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 6e7 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 7e7 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 8e7 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 9e7 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 1e8 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 2e8 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 3e8 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 4e8 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 5e8 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered.


In embodiments, the population of cells, e.g., as described herein, comprises about 1e6 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises about 1.5e6 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises about 2e6 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises about 3e6 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises about 4e6 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises about 5e6 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises about 6e6 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises about 7e6 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises about 8e6 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises about 9e6 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises about 1e7 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises about 2e7 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises about 3e7 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises about 4e7 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises about 5e7 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises about 6e7 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises about 7e7 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises about 8e7 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises about 9e7 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises about 1e8 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises about 2e8 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises about 3e8 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises about 4e8 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises about 5e8 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered.


In embodiments, the population of cells, e.g., as described herein, comprises from about 2e6 to about 10e6 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises from 2e6 to 10e6 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered.


The cells of the invention may comprise a gRNA molecule of the present invention, or nucleic acid encoding said gRNA molecule, and a Cas9 molecule of the present invention, or nucleic acid encoding said Cas9 molecule. In an embodiment, the cells of the invention may comprise a ribonuclear protein (RNP) complex which comprises a gRNA molecule of the invention and a Cas9 molecule of the invention.


The cells of the invention are preferrably modified to comprise a gRNA molecule of the invention ex vivo, for example by a method described herein, e.g., by electroporation.


The cells of the invention include cells in which expression of one or more genes has been altered, for example, reduced or inhibited, by introduction of a CRISPR system comprising a gRNA of the invention. For example, the cells of the present invention may have a reduced level of BCL11a expression relative to unmodified cells. As another example, the cells of the present invention may have an increased level of fetal hemoglobin expression relative to unmodified cells. As another example, the cells of the present invention may have reduced level of beta globin expression relative to unmodified cells. Alternatively, or in addition, a cell of the invention may give rise, e.g., differentiate into, another type of cell, e.g., an erythrocyte, that has a reduced level of BCL11a expression relative to cells differentiated from unmodified cells. Alternatively, or in addition, a cell of the invention may give rise, e.g., differentiate into, another type of cell, e.g., an erythrocyte, that has an increased level of fetal hemoglobin expression relative to cells differentiated from unmodified cells. Alternatively, or in addition, a cell of the invention may give rise, e.g., differentiate into, another type of cell, e.g., an erythrocyte, that has a reduced level of beta globin expression relative to cells differentiated from unmodified cells.


The cells of the invention include cells in which expression of one or more genes has been altered, for example, reduced or inhibited, by introduction of a CRISPR system comprising a gRNA of the invention. For example, the cells of the present invention may have a reduced level of hemeoglobin beta, for example a mutated or wild-type hemoglobin beta, expression relative to unmodified cells. In another aspect, the invention provides cells which are derived from, e.g., differentiated from, cells in which a CRISPR system comprising a gRNA of the invention has been introduced. In such aspects, the cells in which the CRISPR system comprising the gRNA of the invention has been introduced may not exhibit the reduced level of hemoglobin beta, for example a mutated or wild-type hemoglobin beta, but the cells derived from, e.g., differentiated from, said cells exhibit the reduced level of hemoglobin beta, for example a mutated or wild-type hemoglobin beta. In embodiments, the derivation, e.g., differentiation, is accomplished in vivo (e.g., in a patient). In embodiments the cells in which the CRISPR system comprising the gRNA of the invention has been introduced are CD34+ cells and the cells derived, e.g., differentiated, therefrom are of the erythroid lineage, e.g., red blood cells.


The cells of the invention include cells in which expression of one or more genes has been altered, for example, increased or promoted, by introduction of a CRISPR system comprising a gRNA of the invention. For example, the cells of the present invention may have an increased level of fetal hemoglobin expression relative to unmodified cells. In another aspect, the invention provides cells which are derived from, e.g., differentiated from, cells in which a CRISPR system comprising a gRNA of the invention has been introduced. In such aspects, the cells in which the CRISPR system comprising the gRNA of the invention has been introduced may not exhibit the increased level of fetal hemoglobin but the cells derived from, e.g., differentiated from, said cells exhibit the increased level of fetal hemoglobin. In embodiments, the derivation, e.g., differentiation, is accomplished in vivo (e.g., in a patient). In embodiments the cells in which the CRISPR system comprising the gRNA of the invention has been introduced are CD34+ cells and the cells derived, e.g., differentiated, therefrom are of the erythroid lineage, e.g., red blood cells.


In another aspect, the invention relates to cells which include an indel at (e.g., within) or near (e.g., within 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2 or 1 nucleotides of) a nucleic acid sequence having complementarity to the gRNA molecule or gRNA molecules introduced into said cells. In embodiments, the indel is a frameshift indel. In embodiments, the indel is an indel listed in Table 15. In embodiments, the indel is an indel listed in Table 26, Table 27 or Table 37. In embodiments the invention pertains to a population of cells, e.g., as described herein, wherein the population of cells comprises cells having an indel listed in Table 15. In embodiments the invention pertains to a population of cells, e.g., as described herein, wherein the population of cells comprises cells having an indel listed in Table 26, Table 27 or Table 37.


In an aspect, the invention relates to a population of cells, e.g., a population of HSPCs, which comprises cells which include an indel, e.g., as described herein, e.g., an indel or pattern of indels described in FIG. 25, Table 15, Table 26, Table 27 or Table 37, at or near (e.g., within 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2 or 1 nucleotides of) a nucleic acid sequence having complementarity to a gRNA molecule or gRNA molecules, e.g., as described herein, introduced into said cells, e.g., as described herein. In embodiments, the indel is a frameshift indel. In embodiments, 20%-100% of the cells of the population include said indel or indels. In embodiments, 30%-100% of the cells of the population include said indel or indels. In embodiments, 40%-100% of the cells of the population include said indel or indels. In embodiments, 50%-100% of the cells of the population include said indel or indels. In embodiments, 60%-100% of the cells of the population include said indel or indels. In embodiments, 70%-100% of the cells of the population include said indel or indels. In embodiments, 80%-100% of the cells of the population include said indel or indels. In embodiments, 90%-100% of the cells of the population include said indel or indels. In embodiments, the population of cells retains the ability to differentiate into multiple cell types, e.g., maintains the ability to differentiate into cells of erythroid lineage, e.g., red blood cells. In embodiments, the edited and differentiated cells (e.g., red blood cells) maintain the ability to proliferate, e.g., proliferate at least 5-fold, at least 10-fold, at least 15-fold, at least 20-fold, at least 25-fold, at least 30-fold, at least 35-fold, at least 40-fold, at least 45-fold, at least 50-fold or more after 7 days in erythroid differentiation medium (EDM), e.g., as described in the Examples, and/or, proliferate at least 30-fold, at least 35-fold, at least 40-fold, at least 45-fold, at least 50-fold, at least 55-fold, at least 60-fold, at least 65-fold, at least 70-fold, at least 75-fold, at least 80-fold, at least 85-fold, at least 90-fold, at least 95-fold, at least 100-fold, at least 110-fold, at least 120-fold, at least 130-fold, at least 140-fold, at least 150-fold, at least 200-fold, at least 300-fold, at least 400-fold, at least 500-fold, at least 600-fold, at least 700-fold, at least 800-fold, at least 900-fold, at least 1000-fold, at least 1100-fold, at least 1200-fold, at least 1300-fold, at least 1400-fold, at least 1500-fold or more after 21 days in erythroid differentiation medium (EDM), e.g., as described in the Examples,


In an embodiment, the invention provides a population of cells, e.g., CD34+ cells, of which at least 90%, e.g., at least 95%, e.g., at least 98%, of the cells of the population comprise an indel, e.g., as described herein (without being bound by theory, it is believed that introduction of a gRNA molecule or CRISPR system as described herein into a population of cells produces a pattern of indels in said population, and thus, each cell of the population which comprises an indel may not exhibit the same indel), at or near a site complementary to the targeting domain of a gRNA molecule described herein; wherein said cells maintain the ability to differentiate into cells of an erythroid lineage, e.g., red blood cells; and/or wherein said cells differentiated from the population of cells have an increased level of fetal hemoglobin (e.g., the population has a higher % F cells) relative to cells differentiated from a similar population of unmodified cells. In embodiments, the population of cells has undergone at least a 5-fold expansion ex vivo, e.g., in the media comprising Compound 4.


In embodiments, the indel is less than about 50 nucleotides, e.g., less than about 45, less than about 40, less than about 35, less than about 30 or less than about 25 nucleotides. In embodiments, the indel is less than about 25 nucleotides. In embodiments, the indel is less than about 20 nucleotides. In embodiments, the indel is less than about 15 nucleotides. In embodiments, the indel is less than about 10 nucleotides. In embodiments, the indel is less than about 9 nucleotides. In embodiments, the indel is less than about 9 nucleotides. In embodiments, the indel is less than about 7 nucleotides. In embodiments, the indel is less than about 6 nucleotides. In embodiments, the indel is less than about 5 nucleotides. In embodiments, the indel is less than about 4 nucleotides. In embodiments, the indel is less than about 3 nucleotides. In embodiments, the indel is less than about 2 nucleotides. In any of the aforementioned embodiments, the indel is at least 1 nucleotide. In embodiments, the indel is 1 nucleotide.


In an aspect, the invention provides a population of modified HSPCs or erythroid cells differentiated from said HSPCs (e.g., differentiated ex vivo or in a patient), e.g., as described herein, wherein at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% of the cells are F cells. In embodiments, the population of cells contains (or is capable of differentiating, e.g., in vivo, into a population of erythrocytes that contains) a higher percent of F cells than a similar population of cells which have not had a gRNA molecule or gRNA molecules, e.g., as described herein, introduced into said cells. In embodiments, the population of cells has (or is capable of differentiating, e.g., in vivo, into a population of erythrocytes that has) at least a 20% increase, e.g, at least 21% increase, at least 22% increase, at least 23% increase, at least 24% increase, at least 25% increase, at least 26% increase, at least 27% increase, at least 28% increase, or at least 29% increase, in F cells relative to the similar population of cells which have not had a gRNA molecule or gRNA molecules, e.g., as described herein, introduced into said cells. In embodiments, the population of cells has (or is capable of differentiating, e.g., in vivo, into a population of erythrocytes that has) at least a 30% increase, e.g., at least a 35% increase, at least a 40% increase, at least a 45% increase, at least a 50% increase, at least a 55% increase, at least a 60% increase, at least a 65% increase, at least a 70% increase, at least a 75% increase, at least a 80% increase, at least a 85% increase, at least a 90% increase or at least a 95% increase, in F cells relative to the similar population of cells which have not had a gRNA molecule or gRNA molecules, e.g., as described herein, introduced into said cells. In embodiments, the population of cells has (or is capable of differentiating, e.g., in vivo, into a population of erythrocytes that has) at a 10-90%, a 20%-80%, a 20%-70%, a 20%-60%, a 20%-50%, a 20%-40%, a 20%-30%, a 25%-80%, a 25%-70%, a 25%-60%, a 25%-50%, a 25%-40%, a 25%-35%, a 25%-30%, a 30%-80%, a 30%-70%, a 30%-60%, a 30%-50%, a 30%-40%, or a 30%-35% increase in F cells relative to the similar population of cells which have not had a gRNA molecule or gRNA molecules, e.g., as described herein, introduced into said cells. In embodiments, the population of cells, e.g., as produced by a method described herein, comprises a sufficient number or cells and/or a sufficient increase in % F cells to treat a hemoglobinopathy, e.g., as described herein, e.g., sickle cell disease and/or beta thalassemia, in a patient in need thereof when introduced into said patient, e.g., in a therapeutically effective amount. In embodiments, the increase in F cells is as measured in an erythroid differentiation assay, e.g., as described herein.


In embodiments, including in any of the embodiments and aspects described herein, the invention relates to a cell, e.g., a population of cells, e.g., as modified by any of the gRNA, methods and/or CRISPR systems described herein, comprising F cells that produce at least 6 picograms fetal hemoglobin per cell. In embodiments, the F cells produce at least 7 picograms fetal hemoglobin per cell. In embodiments, the F cells produce at least 8 picograms fetal hemoglobin per cell. In embodiments, the F cells produce at least 9 picograms fetal hemoglobin per cell. In embodiments, the F cells produce at least 10 picograms fetal hemoglobin per cell. In embodiments, the F cells produce an average of between 6.0 and 7.0 picograms, between 7.0 and 8.0, between 8.0 and 9.0, between 9.0 and 10.0, between 10.0 and 11.0, or between 11.0 and 12.0 picograms of fetal hemoglobin per cell.


In embodiments, including in any of the aforementioned embodiments, the cell and/or population of cells of the invention includes, e.g., consists of, cells which do not comprise nucleic acid encoding a Cas9 molecule.


Methods of Treatment
Delivery Timing

In an embodiment, one or more nucleic acid molecules (e.g., DNA molecules) other than the components of a Cas system, e.g., the Cas9 molecule component and/or the gRNA molecule component described herein, are delivered. In an embodiment, the nucleic acid molecule is delivered at the same time as one or more of the components of the Cas system are delivered. In an embodiment, the nucleic acid molecule is delivered before or after (e.g., less than about 30 minutes, 1 hour, 2 hours, 3 hours, 6 hours, 9 hours, 12 hours, 1 day, 2 days, 3 days, 1 week, 2 weeks, or 4 weeks) one or more of the components of the Cas system are delivered. In an embodiment, the nucleic acid molecule is delivered by a different means than one or more of the components of the Cas system, e.g., the Cas9 molecule component and/or the gRNA molecule component, are delivered. The nucleic acid molecule can be delivered by any of the delivery methods described herein. For example, the nucleic acid molecule can be delivered by a viral vector, e.g., an integration-deficient lentivirus, and the Cas9 molecule component and/or the gRNA molecule component can be delivered by electroporation, e.g., such that the toxicity caused by nucleic acids (e.g., DNAs) can be reduced. In an embodiment, the nucleic acid molecule encodes a therapeutic protein, e.g., a protein described herein. In an embodiment, the nucleic acid molecule encodes an RNA molecule, e.g, an RNA molecule described herein.


Bi-Modal or Differential Delivery of Components

Separate delivery of the components of a Cas system, e.g., the Cas9 molecule component and the gRNA molecule component, and more particularly, delivery of the components by differing modes, can enhance performance, e.g., by improving tissue specificity and safety. In an embodiment, the Cas9 molecule and the gRNA molecule are delivered by different modes, or as sometimes referred to herein as differential modes. Different or differential modes, as used herein, refer modes of delivery, that confer different pharmacodynamic or pharmacokinetic properties on the subject component molecule, e.g., a Cas9 molecule, gRNA molecule, template nucleic acid, or payload. E.g., the modes of delivery can result in different tissue distribution, different half-life, or different temporal distribution, e.g., in a selected compartment, tissue, or organ.


Some modes of delivery, e.g., delivery by a nucleic acid vector that persists in a cell, or in progeny of a cell, e.g., by autonomous replication or insertion into cellular nucleic acid, result in more persistent expression of and presence of a component. Examples include viral, e.g., adeno associated virus or lentivirus, delivery.


By way of example, the components, e.g., a Cas9 molecule and a gRNA molecule, can be delivered by modes that differ in terms of resulting half life or persistent of the delivered component the body, or in a particular compartment, tissue or organ. In an embodiment, a gRNA molecule can be delivered by such modes. The Cas9 molecule component can be delivered by a mode which results in less persistence or less exposure of its to the body or a particular compartment or tissue or organ.


More generally, in an embodiment, a first mode of delivery is used to deliver a first component and a second mode of delivery is used to deliver a second component. The first mode of delivery confers a first pharmacodynamic or pharmacokinetic property. The first pharmacodynamic property can be, e.g., distribution, persistence, or exposure, of the component, or of a nucleic acid that encodes the component, in the body, a compartment, tissue or organ. The second mode of delivery confers a second pharmacodynamic or pharmacokinetic property. The second pharmacodynamic property can be, e.g., distribution, persistence, or exposure, of the component, or of a nucleic acid that encodes the component, in the body, a compartment, tissue or organ.


In an embodiment, the first pharmacodynamic or pharmacokinetic property, e.g., distribution, persistence or exposure, is more limited than the second pharmacodynamic or pharmacokinetic property.


In an embodiment, the first mode of delivery is selected to optimize, e.g., minimize, a pharmacodynamic or pharmacokinetic property, e.g., distribution, persistence or exposure.


In an embodiment, the second mode of delivery is selected to optimize, e.g., maximize, a pharmacodynamic or pharmcokinetic property, e.g., distribution, persistence or exposure.


In an embodiment, the first mode of delivery comprises the use of a relatively persistent element, e.g., a nucleic acid, e.g., a plasmid or viral vector, e.g., an AAV or lentivirus. As such vectors are relatively persistent product transcribed from them would be relatively persistent.


In an embodiment, the second mode of delivery comprises a relatively transient element, e.g., an RNA or protein.


In an embodiment, the first component comprises gRNA, and the delivery mode is relatively persistent, e.g., the gRNA is transcribed from a plasmid or viral vector, e.g., an AAV or lentivirus. Transcription of these genes would be of little physiological consequence because the genes do not encode for a protein product, and the gR As are incapable of acting in isolation. The second component, a Cas9 molecule, is delivered in a transient manner, for example as mRNA or as protein, ensuring that the full Cas9 molecule/gRNA molecule complex is only present and active for a short period of time.


Furthermore, the components can be delivered in different molecular form or with different delivery vectors that complement one another to enhance safety and tissue specificity.


Use of differential delivery modes can enhance performance,’ safety and efficacy. For example, the likelihood of an eventual off-target modification can be reduced. Delivery of immunogenic components, e.g., Cas9 molecules, by less persistent modes can reduce immunogenicity, as peptides from the bacterially-derived Cas enzyme are displayed on the surface of the cell by MHC molecules. A two-part delivery system can alleviate these drawbacks.


Differential delivery modes can be used to deliver components to different, but overlapping target regions. The formation active complex is minimized outside the overlap of the target regions. Thus, in an embodiment, a first component, e.g., a gRNA molecule is delivered by a first delivery mode that results in a first spatial, e.g., tissue, distribution. A second component, e.g., a Cas9 molecule is delivered by a second delivery mode that results in a second spatial, e.g., tissue, distribution. In an embodiment, the first mode comprises a first element selected from a liposome, nanoparticle, e.g., polymeric nanoparticle, and a nucleic acid, e.g., viral vector. The second mode comprises a second element selected from the group. In an embodiment, the first mode of delivery comprises a first targeting element, e.g., a cell specific receptor or an antibody, and the second mode of delivery does not include that element. In an embodiment, the second mode of delivery comprises a second targeting element, e.g., a second cell specific receptor or second antibody.


When the Cas9 molecule is delivered in a virus delivery vector, a liposome, or polymeric nanoparticle, there is the potential for delivery to and therapeutic activity in multiple tissues, when it may be desirable to only target a single tissue. A two-part delivery system can resolve this challenge and enhance tissue specificity. If the gRNA molecule and the Cas9 molecule are packaged in separated delivery vehicles with distinct but overlapping tissue tropism, the fully functional complex is only be formed in the tissue that is targeted by both vectors.


Candidate Cas molecules, e.g., Cas9 molecules, candidate gRNA molecules, candidate Cas9 molecule/gRNA molecule complexes, and candidate CRISPR systems, can be evaluated by art-known methods or as described herein. For example, exemplary methods for evaluating the endonuclease activity of Cas9 molecule are described, e.g., in Jinek el al., SCIENCE 2012; 337(6096):816-821.


EXAMPLES
Example 1
Guide Selection and Design

Initial guide selection was performed in silico using a human reference genome and user defined genomic regions of interest (e.g., a gene, an exon of a gene, non-coding regulatory region, etc), for identifying PAMs in the regions of interest. For each identified PAM, analyses were performed and statistics reported. gRNA molecules were further selected and rank-ordered based on a number of methods for determining efficiency and efficacy, e.g., as described herein.


Throughout the Examples, in the experiments below, either sgRNA molecules or dgRNA molecules were used. Unless indicated otherwise, where dgRNA molecules were used, the gRNA includes the following:











crRNA: [targeting domain]-[SEQ ID NO: 6607]







tracr (trRNA): SEQ ID NO: 6660






Unless indicated otherwise, in experiments employing a sgRNA molecule, the following sequence was used:











[targeting domain]-[SEQ ID NO: 6601]-UUUU






Unless indicated otherwise, in experiments employing a sgRNA molecule labeled “BC”, the following sequence was used:











[targeting domain]-[SEQ ID NO: 6604]-UUUU






Transfection of HEK-293 Cas9GFP Cells for Primary Guide Screening

Transfection of Cas9GFP-expressing HEK293 cells (HEK-293_Cas9GFP) was used for primary screening of target specific crRNAs. In this example, target specific crRNAs were designed and selected for primary screening using defined criteria including in silico off-target detection, e.g., as described herein. Selected crRNAs were chemically synthesized and delivered in a 96 well format. HEK-293-Cas9GFP cells were transfected with target crRNAs in a 1:1 ratio with stock trRNA. The transfection was mediated using lipofection technology according to manufacturer's protocol (Lipofectamine 2000, Life Technologies). Transfected cells were lysed 24 h following lipofection and editing (e.g., cleavage) was detected within lysates with the T7E1 assay and/or next generation sequencing (NGS; below).


T7E1 Assay

The T7E1 assay was used to detect mutation events in genomic DNA such as insertions, deletions and substitutions created through non-homologous end joining (NHEJ) following DNA cleavage by Cas9 (See Cho et al., Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease. Nature Biotechnology. 2013; 31, 230-232).


Genomic DNA regions that have been targeted for cutting by CRISPR/Cas9 were amplified by PCR, denatured at 95° C. for 10 minutes, and then re-annealed by ramping down from 95° C. to 25° C. at 0.5° C. per second. If mutations were present within the amplified region, the DNA combined to form heteroduplexes. The re-annealed heteroduplexes were then digested with T7E1 (New England Biolabs) at 37° C. for 25 minutes or longer. T7E1 endonuclease recognizes DNA mismatches, heteroduplexes and nicked double stranded DNA and generates a double stranded break at these sites. The resulting DNA fragments were analyzed using a Fragment Analyzer and quantified to determine cleavage efficiency.


Next-Generation Sequencing (NGS) and Analysis for On-Target Cleavage Efficiency and Indel Formation

To determine the efficiency of editing (e.g., cleaving) the target location in the genome, deep sequencing was utilized to identify the presence of insertions and deletions introduced by non-homologous end joining.


PCR primers were first designed around the target site, and the genomic area of interest PCR amplified. Additional PCR was performed according to manufacturer's protocols (Illumina) to add the necessary chemistry for sequencing. The amplicons were then sequenced on an Illumina MiSeq instrument. The reads were then aligned to the human reference genome (e.g., hg38) after eliminating those having low quality scores. From the resulting files containing the reads mapped to the reference genome (BAM files), reads which overlap the target region of interest were selected and the number of wild type reads versus the number of reads which contain an insertion or deletion was calculated. The editing percentage was then defined as the total number of reads with insertions or deletions over the total number of reads, including wild type. To determine the pattern of insertions and/or deletions that resulted from the edit, the aligned reads with indels were selected and the number of a reads with a given indel were summed. This information was then displayed as a list as well as visualized in the form on histograms which represent the frequency of each indel.


RNP Generation

The addition of crRNA and trRNA to Cas9 protein results in the formation of the active Cas9 ribonucleoprotein complex (RNP), which mediates binding to the target region specified by the crRNA and specific cleavage of the targeted genomic DNA. This complex was formed by loading trRNA and crRNA into Cas9, which is believed to cause conformational changes to Cas9 allowing it to bind and cleave dsDNA.


The crRNA and trRNA were separately denatured at 95° C. for 2 minutes, and allowed to come to room temperature. Cas9 protein (10 mg/ml) was added to 5×CCE buffer (20 mM HEPES, 100 mM KCl, 5 mM MgCl2, 1 mM DTT, 5% glycerol), to which trRNA and the various crRNAs were then added (in separate reactions) and incubated at 37° C. for 10 minutes, thereby forming the active RNP complex. The complex was delivered by electroporation and other methods into a wide variety of cells, including HEK-293 and CD34+ hematopoietic cells.


Delivery of RNPs to CD34+ HSCs

Cas9 RNPs were delivered into CD34+ HSCs.


CD34+ HSCs were thawed and cultured (at 500,000 cells/ml) overnight in StemSpan SFEM (StemCell Technologies) media with IL12, SCF, TPO, Flt3L and Pen/Strep added. Roughly 90,000 cells were aliquoted and pelleted per each RNP delivery reaction. The cells were then resuspended in 60 ul P3 nucleofection buffer (Lonza), to which active RNP was subsequently added. The HSCs were then electroporated (e.g., nucleofected using program CA-137 on a Lonza Nucleofector) in triplicate (20 uL/electroporation). Immediately following electroporation, StemSpan SFEM media (with IL12, SCF, TPO, Flt3L and Pen/Strep) was added to the HSCs, which were cultured for at least 24 hours. HSCs were then harvested and subjected to T7E1, NGS, and/or surface marker expression analyses.


HSC Functional Assay

CD34+ HSCs may be assayed for stem cell phenotype using known techniques such as flow cytometry or the in vitro colony forming assay. By way of example, cells were assayed by the in vitro colony forming assay (CFC) using the Methocult H4034 Optimum kit (StemCell Technologies) using the manufacturer's protocol. Briefly, 500-2000 CD34+ cells in <=100 ul volume are added to 1-1.25 ml methocult. The mixture was vortexed vigorously for 4-5 seconds to mix thoroughly, then allowed to rest at room temperature for at least 5 minutes. Using a syringe, 1-1.25 ml of MethoCult+ cells was transferred to a 35 mm dish or well of a 6-well plate. Colony number and morphology was assessed after 12-14 days as per the manufacturer's protocol.


In Vivo Xeno-Transplantation

HSCs are functionally defined by their ability to self-renew and for multi-lineage differentiation. This functionality can only be assessed in vivo. The gold-standard for determining human HSC function is through xeno-transplantation into the NOD-SCID gamma mouse (NSG) that through a series of mutations is severely immunocompromised and thus can act as a recipient for human cells. HSCs following editing will be transplanted into NSG mice to validate that the induced edit does not impact HSC function. Monthly peripheral blood analysis will be used to assess human chimerism and lineage development and secondary transplantation following 20 weeks will be used to establish the presence of functional HSCs.


Results

The results of editing using gRNA molecules (e.g., dgRNA molecules as describe above) described herein, in HEK293_Cas9GFP cells, as assayed by T7E1 (“T7”) and/or NGS are summarized in FIG. 1 (gRNAs molecules to +58 BCL11a enhancer region) and FIG. 2 (gRNA moleucles to +62 BCL11a enhancer region), and in the tables below, as indicated. Average editing in CD34+ HSPCs are reported in, for example, Table 10 (gRNAs molecules to +58 BCL11a enhancer region), Table 11 (gRNAs molecules to +62 BCL11a enhancer region), Table 12B (gRNAs molecules to +55 BCL11a enhancer region), and Table 13 (gRNAs molecules to the French HPFH region), below. Where T7E1 assay results are reported, “2” indicates high efficiency cutting; “1” indicates low efficiency cutting, and “0” indicates no cutting. In general, T7E1 results correlate with the quantitative cutting assayed by NGS. Top 15 gRNAs (as ranked by highest % editing in CD34+ cells) are shown in FIG. 11 (+58 BCL11a enhancer region) and FIG. 12 (+62 BCL11a enhancer region).









TABLE 10







Bcl11a +58 enhancer region crRNA 1° Screen results in


CD34+ HSPCs (by NGS, n = 3).












Average %




Targeting Domain
Editing



ID
(n = 3)
StDev















CR000242
1.4%
0.3%



CR000243
n/a
n/a



CR000244
3.7%
1.0%



CR000245
24.7%
1.4%



CR000246
24.2%
0.3%



CR000247
3.6%
0.6%



CR000248
6.4%
0.5%



CR000249
13.3%
0.6%



CR000250
4.8%
0.5%



CR000251
4.7%
0.5%



CR000252
2.7%
0.5%



CR000253
9.0%
0.6%



CR000255
n/a
n/a



CR000256
1.3%
0.2%



CR000257
2.4%
0.4%



CR000258
2.0%
0.0%



CR000259
3.9%
0.4%



CR000260
32.7%
2.3%



CR000261
17.9%
0.9%



CR000264
2.1%
0.2%



CR000266
2.9%
0.1%



CR000267
3.9%
0.1%



CR000268
6.3%
0.6%



CR000269
4.4%
0.2%



CR000270
2.7%
0.9%



CR000271
7.2%
1.4%



CR000272
11.9%
2.9%



CR000273
3.1%
0.2%



CR000274
1.4%
0.1%



CR000275
9.6%
0.6%



CR000276
14.5%
0.5%



CR000277
8.6%
0.5%



CR000278
4.8%
0.6%



CR000279
6.5%
0.9%



CR000280
7.9%
0.8%



CR000281
3.3%
0.7%



CR000282
10.1%
1.2%



CR000283
4.7%
0.2%



CR000284
5.8%
0.1%



CR000285
8.9%
1.2%



CR000286
20.2%
1.1%



CR000287
10.1%
1.0%



CR000288
1.6%
0.1%



CR000289
3.0%
0.4%



CR000290
2.3%
0.4%



CR000291
2.8%
0.1%



CR000292
9.9%
0.9%



CR000293
n/a
n/a



CR000294
2.7%
0.5%



CR000295
1.9%
0.4%



CR000296
2.8%
0.4%



CR000297
5.7%
0.4%



CR000298
2.2%
0.2%



CR000299
2.9%
0.2%



CR000300
2.3%
0.2%



CR000301
10.2%
0.8%



CR000302
5.0%
0.6%



CR000303
3.7%
0.3%



CR000304
6.2%
0.8%



CR000305
7.7%
2.2%



CR000306
4.0%
2.2%



CR000307
8.8%
3.6%



CR000308
39.9%
1.7%



CR000309
38.3%
8.2%



CR000310
56.8%
1.0%



CR000311
46.0%
1.2%



CR000312
48.5%
1.7%



CR000313
41.2%
4.4%



CR000314
29.9%
0.9%



CR000315
32.0%
2.9%



CR000316
3.9%
1.0%



CR000317
2.8%
0.3%



CR000318
2.6%
0.2%



CR000319
7.9%
1.8%



CR000320
1.9%
0.1%



CR000321
13.2%
1.7%



CR000322
5.2%
0.8%



CR000323
20.3%
2.1%



CR000324
2.2%
0.4%



CR000325
8.4%
0.9%



CR000326
1.4%
0.2%



CR000327
6.9%
1.7%



CR000328
2.6%
0.4%



CR000329
1.1%
0.1%



CR000330
1.7%
0.2%



CR000331
22.0%
0.9%



CR000332
3.2%
1.0%



CR000333
3.8%
0.7%



CR000334
3.2%
0.1%



CR000335
2.7%
0.3%



CR000336
2.2%
0.2%



CR000337
7.2%
1.0%



CR000338
10.3%
1.8%



CR000339
4.2%
0.2%



CR000340
4.6%
0.6%



CR000341
7.5%
1.4%



CR001124
26.1%
2.0%



CR001125
8.4%
1.6%



CR001126
17.2%
5.8%



CR001127
7.4%
2.3%



CR001128
9.0%
0.9%



CR001129
16.5%
6.0%



CR001130
11.1%
8.3%



CR001131
54.1%
4.9%

















TABLE 11







Bcl11a +62 enhancer region crRNA 1° Screen results in CD34+ HSPCs


(by NGS, n = 3).












Average %




Targeting Domain ID
Edit (n = 3)
StDev















CR000171
4.4
0.7



CR000172
4.6
2.4



CR000173
3.1
0.7



CR000174
27.6
6.5



CR000175
14.7
1.0



CR000176
2.1
0.6



CR000177
7.6
2.3



CR000178
7.1
1.7



CR000179
7.7
1.8



CR000180
2.8
0.5



CR000181
25.6
3.8



CR000182
27.6
3.5



CR000183
30.5
6.9



CR000184
4.2
1.9



CR000185
11.4
0.7



CR000186
7.2
3.7



CR000187
46.3
2.2



CR000188
21.0
6.0



CR000189
22.3
2.1



CR000190
20.2
5.7



CR000191
38.2
7.9



CR000192
5.4
1.8



CR000193
14.7
2.0



CR000194
13.5
0.7



CR000195
8.2
1.2



CR000196
27.0
6.4



CR000197
6.6
0.6



CR000198
8.7
3.2



CR000199
3.3
1.3



CR000200
6.9
0.5



CR000201
1.6
0.5



CR000202
28.1
5.6



CR000203
43.7
0.5



CR000204
35.1
2.2



CR000205
53.6
0.8



CR000206
52.8
6.0



CR000207
2.5
0.3



CR000208
31.5
7.5



CR000209
13.5
2.9



CR000210
28.7
6.6



CR000211
59.3
5.5



CR000212
40.0
1.6



CR000213
13.6
7.1



CR000214
9.4
0.7



CR000215
37.0
6.9



CR000216
25.3
2.6



CR000217
7.6
1.6



CR000218
5.1
1.3



CR000221
12.4
3.5



CR000222
7.2
2.6



CR000223
8.4
2.1



CR000224
13.9
5.3



CR000225
10.3
4.4



CR000227
12.6
1.8



CR000228
13.5
4.8



CR000229
3.2
0.8

















TABLE 12A







Bcl11a +55 enhancer region crRNA 1° Screen results


in HEK-293-Cas9 Cells











Targeting Domain
Average % Edit




ID
(n = 3)
StDev







CR002142
25.0
2.0



CR002143
n/a
n/a



CR002144
51.2
8.3



CR002145
51.0
3.3



CR002146
n/a
n/a



CR002147
n/a
n/a



CR002148
13.7
4.3



CR002149
22.3
4.5



CR002150
43.8
9.0



CR002151
31.1
0.6



CR002152
33.2
8.7



CR002153
24.5
7.8



CR002154
62.1
3.9



CR002155
48.2
10.9 



CR002156
57.4
8.5



CR002157
46.6
4.3



CR002158
11.0
1.7



CR002159
13.7
2.3



CR002160
37.8
0.8



CR002161
61.5
4.6



CR002162
47.0
14.0 



CR002163
52.2
9.6



CR002164
58.5
4.4



CR002165
61.5
6.8



CR002166
42.6
11.3 



CR002167
37.8
4.7



CR002168
32.0
12.9 



CR002169
48.5
6.3



CR002170
44.8
2.9



CR002171
n/a
n/a



CR002172
n/a
n/a



CR002173
n/a
n/a



CR002174
59.8
3.8



CR002175
22.1
1.3



CR002176
35.4
5.9



CR002177
n/a
n/a



CR002178
25.9
3.2



CR002179
n/a
n/a



CR002180
57.6
6.4



CR002181
63.8
3.9



CR002182
n/a
n/a



CR002183
n/a
n/a



CR002184
30.0
4.0



CR002185
n/a
n/a



CR002186
n/a
n/a



CR002187
51.6
2.9



CR002188
35.8
8.7



CR002189
62.7
6.0



CR002190
n/a
n/a



CR002191
37.4
7.4



CR002192
n/a
n/a



CR002193
6.1
1.7



CR002194
n/a
n/a



CR002195
60.0
9.4



CR002196
42.9
13.7 



CR002197
52.2
2.8



CR002198
n/a
n/a



CR002199
n/a
n/a



CR002200
 4.3
1.0



CR002201
 1.8
0.3



CR002202
 2.6
0.3



CR002203
50.7
5.3



CR002204
n/a
n/a



CR002205
n/a
n/a



CR002206
n/a
n/a



CR002207
n/a
n/a



CR002208
n/a
n/a



CR002209
n/a
n/a



CR002210
n/a
n/a



CR002211
n/a
n/a



CR002212
n/a
n/a



CR002213
n/a
n/a



CR002214
n/a
n/a



CR002215
51.7
8.9



CR002216
14.1
8.3



CR002217
50.1
10.5 



CR002218
45.0
19.4 



CR002219
30.7
14.7 



CR002220
44.7
13.3 



CR002221
n/a
n/a



CR002222
64.0
3.9



CR002223
n/a
n/a



CR002224
n/a
n/a



CR002225
n/a
n/a



CR002226
n/a
n/a



CR002227
n/a
n/a



CR002228
10.4
5.6



CR002229
n/a
n/a







n/a = not assessed






After the experiment above, the same guide RNA molecules were tested again in triplicate in both HEK-293-Cas9 cells and in CD34+ cells using a newly designed set of primers for the NGS analysis. The results are reported below in Table 12B.









TABLE 12B







Bcl11a +55 enhancer region crRNA screen results in


HEK-293-Cas9 Cells and in CD34+ HSPCs (by NGS, n = 3).












Editing % HEK-
Editing %




293-Cas9 Cells
CD34+ HSPCs



ID
(n = 3)
(n = 3)















CR002142
2.1
2.07



CR002143
39.6
2.31



CR002144
74.3
4.70



CR002145
72.1
11.46



CR002146
77.2
5.18



CR002147
37.3
3.13



CR002148
34.6
2.02



CR002149
40.7
3.16



CR002150
64.4
4.01



CR002151
70.5
5.05



CR002152
63.6
6.59



CR002153
42.2
2.82



CR002154
71.0
17.89



CR002155
60.3
6.01



CR002156
62.3
9.43



CR002157
38.5
4.72



CR002158
12.4
2.16



CR002159
14.8
3.64



CR002160
72.8
7.97



CR002161
74.5
18.12



CR002162
64.8
4.53



CR002163
86.7
13.92



CR002164
3.2
10.23



CR002165
78.3
9.74



CR002166
67.2
7.78



CR002167
51.6
29.26



CR002168
29.9
4.15



CR002169
80.2
9.11



CR002170
83.0
16.17



CR002171
67.8
4.83



CR002172
64.3
7.59



CR002173
80.7
6.00



CR002174
78.2
26.89



CR002175
79.4
27.08



CR002176
39.5
5.14



CR002177
66.7
21.45



CR002178
52.5
12.74



CR002179
83.1
38.88



CR002180
51.3
5.46



CR002181
54.0
12.54



CR002182
67.9
28.01



CR002183
30.3
3.52



CR002184
67.1
21.31



CR002185
65.6
8.18



CR002186
58.9
8.16



CR002187
70.2
10.05



CR002188
56.6
9.92



CR002189
71.9
31.14



CR002190
27.4
6.84



CR002191
70.0
17.54



CR002192
62.6
6.92



CR002193
1.6
0.67



CR002194
82.5
24.52



CR002195
64.4
36.32



CR002196
2.1
0.96



CR002197
63.8
37.29



CR002198
67.8
16.45



CR002199
61.3
9.78



CR002200
3.1
1.10



CR002201
1.2
0.84



CR002202
2.8
0.82



CR002203
49.9
0.84



CR002204
43.2
17.48



CR002205
60.6
11.06



CR002206
48.5
9.02



CR002207
49.4
12.29



CR002208
61.7
16.56



CR002209
61.2
9.36



CR002210
57.6
27.77



CR002211
45.4
30.93



CR002212
56.0
31.55



CR002213
34.4
10.40



CR002214
11.1
1.77



CR002215
49.3
40.23



CR002216
22.1
1.80



CR002217
52.3
11.29



CR002218
73.7
11.17



CR002219
34.2
7.94



CR002220
64.8
8.63



CR002221
20.7
5.66



CR002222
78.9
30.01



CR002223
8.2
1.21



CR002224
7.8
n.d



CR002225
n.d
n.d



CR002226
2.6
n.d



CR002227
n.d
n.d



CR002228
23.2
3.65



CR002229
39.0
n.d







n.d. = not determined













TABLE 13







French HPFH region crRNA 1° Screen results in


HEK-293-Cas9 Cells and in CD34+ HSPCs (by NGS, n = 3).











Average Edit %
Average Edit %
StDev (%) for


Targeting
HEK-293-Cas9
CD34+ HSPCs
% Edit in


Domain ID
(n = 3)
(n = 3)
CD34+ HSPCs













CR001016
33.1
24.0
1.2


CR001017
30.4
19.5
1.5


CR001018
46.5
53.0
3.4


CR001019
45.9
57.6
2.3


CR001020
62.1
47.7
9.3


CR001021
29.1
34.2
1.8


CR001022
66.1
66.2
2.3


CR001023
27.3
46.0
6.1


CR001024
62.5
73.4
6.9


CR001025
25.5
24.5
1.6


CR001026
61.4
72.1
2.9


CR001027
23.3
33.2
2.2


CR001028
47.7
72.1
4.9


CR001029
53.9
61.2
5.7


CR001030
49.2
49.9
29.0


CR001031
42.7
65.0
9.3


CR001032
67.6
50.1
9.7


CR001033
15.3
44.5
3.2


CR001034
28.5
52.9
2.7


CR001035
16.9
28.5
16.4


CR001036
28.0
68.3
3.7


CR001037
52.7
53.2
4.2


CR001038
1.9
23.7
20.6


CR001039
2.2
35.8
2.8


CR001040
nd
n/a
0.0


CR001041
nd
n/a
0.0


CR001042
2.7
n/a
0.0


CR001043
nd
n/a
0.0


CR001044
4.9
1.5
0.4


CR001045
38.1
31.2
2.0


CR001046
18.4
28.4
3.9


CR001047
nd
n/a
0.0


CR001048
1.6
0.2
0.3


CR001049
nd
n/a
0.0


CR001050
nd
n/a
0.0


CR001051
nd
n/a
0.0


CR001052
nd
n/a
0.0


CR001053
5.8
4.4
0.7


CR001054
9.0
4.1
0.4


CR001055
5.2
0.1
0.1


CR001056
7.7
5.0
0.3


CR001057
25.2
7.8
0.8


CR001058
41.6
29.5
6.7


CR001059
5.2
4.9
0.1


CR001060
43.5
18.7
5.2


CR001061
21.7
4.7
0.8


CR001062
12.2
5.2
1.1


CR001063
16.6
21.5
1.6


CR001064
6.0
4.2
0.7


CR001065
43.0
20.0
1.4


CR001066
11.1
4.2
0.4


CR001067
25.7
7.9
3.5


CR001068
11.3
5.9
1.6


CR001069
15.1
2.9
0.2


CR001070
38.2
11.1
3.1


CR001071
34.6
8.5
0.2


CR001072
22.8
3.5
0.4


CR001073
45.2
18.1
4.1


CR001074
40.1
38.1
2.5


CR001075
53.0
29.2
1.8


CR001076
25.6
1.8
0.1


CR001077
8.9
12.2
0.4


CR001078
10.9
17.7
3.3


CR001079
18.3
7.8
0.9


CR001080
21.3
17.4
5.6


CR001081
22.0
21.4
0.5


CR001082
5.4
8.5
0.6


CR001083
12.3
11.6
0.5


CR001084
25.4
9.5
4.5


CR001085
18.3
12.4
1.7


CR001086
25.3
4.4
2.0


CR001087
16.4
6.9
0.9


CR001088
9.6
18.4
1.9


CR001089
nd
15.8
12.9


CR001090
16.9
30.1
3.5


CR001091
11.4
0.8
0.5


CR001092
17.4
17.0
9.8


CR001093
23.0
13.0
4.5


CR001094
10.0
24.9
5.4


CR001095
22.1
34.8
3.6


CR001096
29.8
20.4
2.0


CR001097
17.9
20.5
0.5


CR001098
49.8
34.7
5.1


CR001099
24.7
39.9
1.8


CR001100
nd
33.2
2.8


CR001101
16.9
24.7
2.1


CR001102
29.4
13.9
0.7


CR001103
9.9
8.6
2.2


CR001104
11.3
3.3
0.7


CR001105
5.0
3.6
0.9


CR001106
15.7
13.1
1.6


CR001107
31.2
8.5
4.5


CR001108
16.1
3.2
0.5


CR001109
12.1
4.6
2.1


CR001110
23.5
6.0
3.0


CR001111
12.3
2.6
1.3


CR001132
18.7
3.4
0.4


CR001133
35.4
27.0
4.2


CR001134
12.3
0.3
0.2


CR001135
57.8
16.2
2.7


CR001136
7.1
1.7
0.5


CR001137
31.2
6.2
2.7


CR001138
45.4
9.6
1.2


CR001139
nd
3.3
0.3


CR001140
28.7
11.2
1.2


CR001141
3.6
1.5
0.5


CR001142
56.7
9.7
1.2


CR001143
58.4
4.6
1.3


CR001144
23.2
4.3
2.5


CR001145
4.9
0.1
0.0


CR001146
38.2
0.2
0.0


CR001147
16.0
0.1
0.1


CR001148
22.3
3.0
1.6


CR001149
19.4
6.0
3.9


CR001150
30.8
30.4
17.9


CR001151
35.8
0.8
0.2


CR001152
24.6
0.3
0.1


CR001153
5.4
0.3
0.4


CR001154
6.3
3.6
2.1


CR001155
nd
2.1
0.6


CR001156
19.6
4.8
0.8


CR001157
16.4
2.7
0.6


CR001158
36.5
5.1
3.2


CR001159
42.9
7.7
1.0


CR001160
32.5
8.5
1.9


CR001161
20.5
10.3
1.9


CR001162
35.0
30.5
4.5


CR001163
9.9
3.3
0.5


CR001164
23.3
14.4
8.8


CR001165
5.5
1.5
0.4


CR001166
49.8
27.1
4.4


CR001167
13.8
6.0
0.8


CR001168
nd
6.4
4.7


CR001169
43.9
n/a
0.0


CR001170
28.5
10.7
6.4


CR001171
37.5
2.7
2.6


CR001172
41.5
14.8
3.5


CR001173
49.5
16.7
3.9


CR001174
36.6
4.4
0.7


CR001175
17.0
5.3
1.7


CR001176
7.7
3.6
2.8


CR001177
4.0
4.1
2.3


CR001178
nd
27.0
15.6


CR001179
59.0
27.9
1.5


CR001180
nd
8.5
5.3


CR001181
30.9
5.7
0.8


CR001182
34.5
13.6
7.8


CR001183
6.9
0.4
0.3


CR001184
15.7
5.2
2.7


CR001185
18.2
7.6
1.2


CR001186
12.0
5.0
0.6


CR001187
8.3
4.1
0.3


CR001188
16.8
7.1
2.0


CR001189
13.3
3.7
1.3


CR001190
nd
5.6
1.1


CR001191
39.5
4.8
1.0


CR001192
27.5
3.9
1.3


CR001193
17.1
1.5
1.9


CR001194
17.8
5.9
4.1


CR001195
nd
16.4
9.5


CR001196
5.8
2.2
0.7


CR001197
32.4
8.1
3.1


CR001198
28.4
18.2
5.8


CR001199
40.8
7.9
4.0


CR001200
24.4
1.2
0.7


CR001201
1.7
0.3
0.1


CR001202
46.0
39.3
22.7


CR001203
11.9
3.1
1.6


CR001204
1.2
0.8
0.1


CR001205
3.0
0.2
0.1


CR001206
3.9
0.5
0.2


CR001207
7.6
2.4
1.2


CR001208
5.5
1.5
0.7


CR001209
4.4
1.7
0.2


CR001210
10.8
3.9
2.5


CR001211
6.8
3.4
2.0


CR001212
32.7
11.1
6.5


CR001213
21.6
6.2
1.5


CR001214
28.4
5.7
0.8


CR001215
9.0
1.5
0.5


CR001216
nd
2.5
1.4


CR001217
nd
n/a
0.0


CR001218
7.7
4.1
1.0


CR001219
40.0
20.3
0.6


CR001220
33.8
n/a
0.0


CR001221
41.3
n/a
0.0


CR001222
39.1
18.9
10.9


CR001223
35.9
n/a
0.0


CR001224
34.9
16.5
7.1


CR001225
55.0
24.6
1.1


CR001226
34.1
4.7
4.1


CR001227
46.4
6.4
0.6


CR003027
50.2
4.5
nd


CR003028
3.0
2.2
nd


CR003029
14.4
3.4
nd


CR003030
20.2
5.8
nd


CR003031
31.3
9.7
nd


CR003032
15.1
4.4
nd


CR003033
46.5
25.2
nd


CR003034
55.2
11.8
nd


CR003035
42.4
15.9
nd


CR003036
17.4
6.1
nd


CR003037
38.6
19.6
nd


CR003038
47.1
24.6
nd


CR003039
53.8
21.1
nd


CR003040
35.9
6.1
nd


CR003041
23.7
9.9
nd


CR003042
35.5
8.7
nd


CR003043
24.4
4.3
nd


CR003044
54.1
16.2
nd


CR003045
33.7
6.6
nd


CR003046
34.8
3.6
nd


CR003047
46.9
9.8
nd


CR003048
12.6
1.7
nd


CR003049
24.4
4.9
nd


CR003050
19.6
2.9
nd


CR003051
15.4
1.8
nd


CR003052
15.7
7.8
nd


CR003053
10.8
0.9
nd


CR003054
16.7
2.9
nd


CR003055
17.3
4.4
nd


CR003056
46.3
19.3
nd


CR003057
40.9
11.3
nd


CR003058
40.0
8.9
nd


CR003059
23.7
<2%
nd


CR003060
16.8
<2%
nd


CR003061
27.6
<2%
nd


CR003062
3.9
<2%
nd


CR003063
19.8
2.5
nd


CR003064
19.6
<2%
nd


CR003065
42.3
0.1
nd


CR003066
36.5
0.0
nd


CR003067
53.1
0.1
nd


CR003068
11.5
<2%
nd


CR003069
42.7
0.0
nd


CR003070
49.0
0.1
nd


CR003071
41.8
<2%
nd


CR003072
27.2
<2%
nd


CR003073
45.1
0.1
nd


CR003074
40.2
0.1
nd


CR003075
58.5
0.1
nd


CR003076
28.5
<2%
nd


CR003077
44.9
0.0
nd


CR003078
43.9
<2%
nd


CR003079
31.1
<2%
nd


CR003080
41.1
<2%
nd


CR003081
29.4
<2%
nd


CR003082
30.8
<2%
nd


CR003083
26.5
0.0
nd


CR003084
32.3
<2%
nd


CR003085
24.0
0.1
nd


CR003086
40.8
10.8
nd


CR003087
51.0
45.0
nd


CR003088
25.5
9.7
nd


CR003089
26.0
11.5
nd


CR003090
15.2
<2%
nd


CR003091
26.4
5.5
nd


CR003092
4.9
2.1
nd


CR003093
16.7
2.9
nd


CR003094
39.5
4.7
nd


CR003095
12.0
1.7
nd


CR003096
22.9
4.0
nd





n/a = not assayed;


nd = not determined






Genome Editing at the BCL11a Enhancer Site

Synthetic sgRNA molecules containing targeting domains specific for genomic DNA within the +58 or +62 erythroid enhancer region of BCL11a were ordered. FIG. 5 shows the genomic DNA targeted by the sgRNAs, which were named sgEH1 through sgEH9.











sgEH1 Targeting Domain (CR00276):







(SEQ ID NO: 212)









AUCACAUAUAGGCACCUAUC







sgEH2 Targeting Domain (CR00275):







(SEQ ID NO: 211)









CACAGUAGCUGGUACCUGAU







sgEH8 Targeting Domain (CR00273):







(SEQ ID NO: 209)









CAGGUACCAGCUACUGUGUU







sgEH9 (CR00277) Targeting Domain:







(SEQ ID NO: 213)









UGAUAGGUGCCUAUAUGUGA






RNPs containing sgEH[X] precomplexed with Cas9 were introduced into CD34+ bone marrow cells (Bone Marrow CD34+ cells ordered from Lonza, Cat #2M-101C, Lot#466977, 30y, F, B (96.8%)) using electroporation (NEON electroporator). Cutting was determined in CD34+ stem cells using T7E1 and NGS. The results are summarized in FIG. 6A-D, which shows overall indel formation across four experiments (two experiments from two different donors), as well as the top indel patterns. sgEH1, 2 and 9 were able to direct cutting with high efficiency.


It was surprisingly found that across multiple experiments, including those using cells from different donors, the indel pattern remained constant (See FIG. 6A-D). That is, each gRNA gave a consistent pattern of indel formation. As well, deletions appeared to correlate with regions of microhomology near the cutting site.


To further investigate this phenomenon, gRNAs to the BCL11a locus were designed at tested using different biological samples as well as different delivery methods, and gRNA scaffolds. For this experiment, gRNAs with the following targeting domains were used:











G7 (also referred to as g7) Targeting domain:



GUGCCAGAUGAACUUCCCAU



(e.g., the 3′ 20 nt of SEQ ID NO: 1191)







G8 (also referred to as g8) Targeting domain:



CACAAACGGAAACAAUGCAA



(e.g., the 3′ 20 nt of SEQ ID NO: 1186)






In a first experiment, g7 and g8 were tested across two different biological samples. As shown in FIG. 7, the pattern of top 3 most prevalent indels for each gRNA was identical. Next, gRNA molecules comprising the G7 and G8 targeting domains were tested with a different tracrRNA component. In the previous experiments, SEQ ID NO: 6601, followed by -UUUU, was directly appended to the gRNA targeting domain to form the sgRNA. In the next set of experiments, SEQ ID NO: 6604, followed by -UUUU, was directly appended to the gRNA targeting domains of g7 and g8 to create sgRNA molecules with a different scaffold (gRNAs called g7BC or g8BC). As shown in FIG. 8, the indel pattern remained constant even when different sgRNA scaffolds are used. Finally, the indel pattern was compared using different delivery methods. Delivery of g7 to 293 cells via either RNP electroporation or by delivery of a g7-encoding plasmid via lipofectamine 2000 was investigated and the results reported in FIG. 9. As shown, the indel pattern remained the same.


Together, these results strongly suggest that indel pattern formation is sequence-dependent. gRNA molecules that target sequences where cutting results in large deletions and/or frameshift deletions may be beneficial for loss of function.


Excision with Multiple Guides


G7 and g8, above, target genomic DNA at proximal sites (PAM sequences are within 50 nucleotides of each other within the BCL11a gene). To investigate the effect of simultaneously targeting two proximal sites, CD34+ cells were transfected with RNPs comprising gRNAs with the targeting domain of G7 as well as RNPs comprising gRNAs with the targeting domain of G8. Cutting efficiency and indel pattern was assessed by NGS. As shown in FIG. 10, the primary indel is a delection of the nucleotides between the two gRNA binding sites. These results demonstrate that a plurality, e.g., 2, guides that bind in proximity may be used to effect an excision of the DNA located between the two binding sites.


Genome Editing in CD34+ Stem Cells

Genome editing at the BCL11a locus was demonstrated in CD34+ primary hematopoietic stem cells. Briefly, CD34+ cells were isolated from G-CSF mobilized peripheral blood from adult donors (AllCells) using immunoselection (Miltenyi) according to the manufacturer's instructions. Cell gating is shown in FIG. 3. Cells were aliquotted and cryopreserved. Thawed cells were seeded at 2×105/ml in SFEM (StemCell Technologies)+1× antibiotic/antimycotic+50 ng/ml each cytokine (TPO, FLT3L, IL6 and SCF)+500 nM compound 4 and cultured for 5 days at 37 C, 5% CO2 in a humidified incubator. Cell concentration after 5 days was 1×106/ml.


Preincubated RNP complex consisting of 150 ng each Cas9 (Genscript #265425-7) and sgRNA (TriLink, comprising the sgBCL11A_7 Targeting Domain (i.e., the targeting domain of g7): GTGCCAGATGAACTTCCCATGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAAT AAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGCTTTT) (SEQ ID NO: 2000) was added to 2×105 cells and electroporated on the Neon system (Lifetechnologies) with pulse parameters: 1600 V, 20 ms, 1 pulse, according to manufacturer's protocols. Duplicate electroporation were performed. Mock electroporation were also performed in the absence of RNP complex. After electroporation, cells were seeded into 1 ml media to recover overnight.


The day following electroporation, 1/20 of the unsorted culture was seeded in SFEM (StemCell Technologies)+1× antibiotic/antimycotic+50 ng/ml each TPO, FLT3L, IL6, SCF, IL3 and GCSF for 6 days. The remaining cells were stained with antibodies to human CD34 and human CD90 and sorted by flow cytometry for CD34+CD90+ and CD34+CD90− populations. CD34+CD90+ cells are known to contain hematopoietic stem cells, as defined by long-term multi-lineage engraftment in immunodeficient mice (see Majeti et al. 2007 Cell Stem Cell 1, 635-645). Cell populations selected for sorting are indicated by the gates in the representative dot plot of FIG. 3. Sorted cells were cultured in SFEM (StemCell Technologies)+1× antibiotic/antimycotic+50 ng/ml each TPO, FLT3L, IL6, SCF, IL3 and GCSF for 6 days, at which point all cultures were harvested for analysis of genome editing.


Genomic DNA was purified from harvested cells and the targeted region was amplified with the following primers: BCL11A-7 F, gcttggctacagcacctctga; BCL11A-7 R, ggcatggggttgagatgtgct. PCR product was denatured and reannealed, followed by incubation with T7E1 (New England Biolabs) as per the manufacturer's recommendations. The reaction was then analyzed by agarose gel electrophoresis (FIG. 4). The upper band represents uncleaved homoduplex DNA and the lower bands indicate cleavage products resulting from heteroduplex DNA. The far left lane is a DNA ladder. Band intensity was calculated by peak integration of unprocessed images by ImageJ software. % gene modification (indel) was calculated as follows: % gene modification=100×(1−(1−fraction cleaved)1/2), and is indicated below each corresponding lane of the gel.


The results are shown in FIG. 4. Gene editing efficiency in the hematopoietic stem cell-containing CD34+CD90+ population was equivalent to CD34+CD90− cells or unsorted. These experiments demonstrate that gene editing can be accomplished in CD34+ HSPCs and CD34+CD90+ cells that are further enriched in HSCs.


Example 3. BCL11A Erythroid Enhancer Editing in Hematopoietic Stem and Progenitor Cells (HSPCs) Using CRISPR-Cas9 for Derepression of Fetal Globin Expression in Adult Erythroid Cells
Methods:

Human CD34+ cell culture. Human bone marrow CD34+ cells were purchased from either AllCells (Cat#: ABM017F) or Lonza (Cat#: 2M-101C) and expanded for 2 to 3 days using StemSpan SFEM (StemCell Technologies; Cat no. 09650) supplemented with 50 ng/mL of thrombopoietin (Tpo, Peprotech; Cat#300-18), 50 ng/mL of human Flt3 ligand (Flt-3L, Peprotech; Cat#300-19), 50 ng/mL of human stem cell factor (SCF, Peprotech; Cat#300-07), human interleukin-6 (IL-6, Peprotech; Cat#200-06), 1% L-glutamine; 2% penicillin/streptomycin, and Compound 4 (0.75 μM). After 2 to 3 days of expansion, the culture had expanded 2- to 3-fold relative to starting cell numbers purchased from AllCells and 1- to 1.5-fold from Lonza. These culture conditions were used for all CD34+ expansion steps, including both before and after introduction of the CRISPR/Cas systems as described herein.


Assembly of Cas9 and guide RNA ribonucleoprotein (RNP) complexes, preparation of HSC, and electroporation of RNP into HSC. Cas9-guide RNA ribonucleoprotein complexes (RNPs) were prepared immediately prior to electroporation. For formation of RNP using dual guide RNAs (dgRNAs), 3 μg of each of crRNA (in 2.24 μL) and tracr (in 1.25 μL) are first denatured at 95° C. for 2 min in separate tubes and then cooled to room temperature. For preparation of Cas9 protein, 7.3 μg of CAS9 protein (in 1.21 μL) was mixed with 0.52 μL of 5×CCE buffer (20 mM HEPES, 100 mM KCL, 5 mM MgCL2, 5% Glycerol and freshly added 1 mM DTT). Tracr was first mixed with the Cas9 preparation and incubated at 37° C. for 5 min. The crRNA was then added to Tracr/CAS9 complexes and incubated for 5 min at 37° C. The HSC were collected by centrifugation at 200×g for 15 min and resuspended in T buffer that comes with Neon electroporation kit (Invitrogen; Cat#: MPK1096) at a cell density of 2×107/mL. The RNP mixed with 12 μL of cells by pipetting up and down 3 times gently. To prepare single guide RNA (sgRNA) and Cas9 complexes, 2.25 μg sgRNA (in 1.5 μL) was mixed with 2.25 μg Cas9 protein (in 3 μL) and incubated at RT for 5 min. The sgRNA/Cas9 complex was then mixed with 10.5 μL of 2×107/mL cells by pipetting up and down several times gently and incubated at RT for 2 min. The RNP/cell mixture (10 μL) was transferred into Neon electroporation probe. The electroporation was performed with Neon transfection system (Invitrogen; MPK5000S) using 1700 volts/20 milliseconds and 1 pulse. After electroporation, the cells were transferred into 0.5 mL pre-warmed StemSpan SFEM medium supplemented with growth factors and cytokines as described above and cultured at 37° C. for 2 days.


Genomic DNA preparation. Genomic DNA was prepared from edited and unedited HSC at 48 hours post-electroporation. The cells were lysed in 10 mM Tris-HCL, pH 8.0; 0.05% SDS and freshly added Protease K of 25 μg/mL and incubated at 37° C. for 1 hour followed by additional incubation at 85° C. for 15 min to inactivate protease K.


T7E1 assay. To determine editing efficiency of HSCs, T7E1 and assay was performed. PCR was performed using Phusion Hot Start II High-Fidelity kit (Thermo Scientific; Cat#: F-549L) with the following cycling condition: 98° C. for 30″; 35 cycles of 98° C. for 5″, 68° C. for 20′, 72° C. for 30″; 72° C. for 5 min. The following primers were used: forward primer: 5′-AGCTCCAAACTCTCAAACCACAGGG-3′ (SEQ ID NO: 2001) and reverse primer: 5′-TACAATTTTGGGAGTCCACACGGCA-3′ (SEQ ID NO: 2002). The PCR products were denatured and re-annealed using the following condition: 95° C. for 5 min, 95-85° C. at −2° C./s, 85-25° C. at −0.1° C./s, 4° C. hold. After annealing, 1 μL of mismatch-sensitive T7 E1 nuclease (NEB, Cat# M0302L) was added into 10 μL of PCR product above and further incubated at 37° C. for 15 min for digestion of hetero duplexes, and the resulting DNA fragments were analyzed by agarose gel (2%) electrophoresis. The editing efficiency was quantified using ImageJ software (http://rsb.info.nih.gov/ij/).


Next generation sequencing (NGS). To determine editing efficiency more precisely and patterns of insertions and deletions (indels), the PCR products were subjected to next generation sequencing (NGS). The PCR were performed in duplicate using Titanium Taq PCR kit (Clontech Laboratories; Cat#: 639210) with the following cycling condition: 98° C. for 5 min; 30 cycles of 95° C. for 15 seconds, 68° C. for 15 seconds, 72° C. 1 min; 72° C. for 7 min. The following primers were used: forward primer: 5′-AGCTCCAAACTCTCAAACCACAGGG-3′ (SEQ ID NO: 2001) and reverse primer: 5′-TACAATTTTGGGAGTCCACACGGCA-3′ (SEQ ID NO: 2002). The PCR products were analyzed by 2% agarose gel electrophoresis and submitted for deep sequencing.


Flow cytometry analysis of HSPC culture. The HSPC were subjected to flow cytometry to characterize stem and progenitor cell populations. The percentage of CD34+, CD34+CD90+ cell subsets, prior to and after genome editing was determined on aliquots of the cell cultures. The cells were incubated with anti-CD34 (BD Biosciences, Cat#555824), anti-CD90 (Biolegend, Cat#328109) in staining buffer, containing PBS supplemented with 0.5% BSA, at 4° C., in dark for 30 min. The cell viability is determined by 7AAD. The cells were washed with staining buffer and Multicolor FACS analysis was performed on a FACSCanto (Becton Dickinson). Flow cytometry results analyzed using Flowjo and the data were presented as percent CD34+, CD34+CD90+ of the total cell population. Absolute numbers of each cell type population in the culture were calculated from the total number of cells multiplied by the percentage of each population.


In vitro erythropoiesis and FACS analysis for HbF containing erythroid cells. The genome edited HSC were subjected to in vitro erythroid differentiation 48 hours post-electroporation. Briefly, the edited HSC were cultured in erythroid differentiation medium (EDM) consisting of IMDM (Invitrogen, Cat#31980-097) supplemented with 330 μg/mL human holo-transferrin (Sigma, Cat# T0665), 10 μg/mL recombinant human insulin (Sigma, Cat#13536), 2 IU/mL heparin (Sigma, Cat # H3149), 5% human plasma (Sigma, Cat# P9523), 3 IU/mL human erythropoietin (R&D, Cat#287-TC), 1% L-glutamine, and 2% penicillin/streptomycin. During days 0-7 of culture, EDM was further supplemented with 10−6M hydrocortisone (Sigma, Cat# H0888), 100 ng/mL human SCF (Peprotech, Cat#300-07), and 5 ng/mL human IL-3 (Peprotech, Cat#200-03) for 7-days. During days 7-11 of culture, EDM was supplemented with 100 ng/mL of human SCF only. During days 11-21 of culture, EDM has no additional supplements. On days 7, 14 and 21 of the culture, the cells (2-10×105) were analyzed by intracellular staining for HbF expression. Briefly, the cells were collected by centrifugation at 350×g for 5 min and washed once with staining buffer (Biolegend, Cat#420201). The cells were then fixed with 0.5 mL of fixation buffer (Biolegend, Cat#420801) and washed three times with 2 mL of 1× intracellular staining permeabilization wash buffer (Biolegend, Cat#421002) by centrifugation at 350×g for 5 min. The cells were then incubated with 5 μL of anti-HbF antibody (Life technologies, Cat# MHFH01) in 100 μL of 1× intracellular staining perm wash buffer for 20 min at room temperature. The cells were washed twice with 2 mL of 1× intracellular staining Perm wash buffer and resuspend in 200 μL staining buffer and analyzed on FACS Canto (Becton Dickinson) for HbF expression. The results analyzed using Flowjo and data were presented as % of HbF positive cells (F-cells) in total cell population.


Gene expression assays. ˜1×106 cells were used to purify RNA using RNeasy mini kit (Qiagen. Cat#74104). 200 to 400 ng RNA was used for 1st strand synthesize using qScript cDNA synthesis kit (Quanta, Cat#95047-500). Taq-man PCR was performed using Taq-Man Fast Advance PR Mix (Life technologies, Cat#4444963) and GAPDH (Life technologies, ID# Hs02758991_g1), HbB (Life technologies, ID#: Hs00747223_g1), HbG2/HbG1 (Life technologies, ID# Hs00361131_g1) and BCL11A (Life technologies, ID#: Hs01093197_m1) according to suppliers protocol. The relative expression of each gene was normalized to GAPDH expression.


Colony forming unit cell assay. For colony forming unit (CFU) assay, 300 cells per 1.1 mL Methocult/35 mm dish in duplicate were plated in Methocult H4434 methylcellulose medium containing SCF, GM-CSF, IL-3, and erythropoietin (StemCell Technologies). Pen/Strep was added into the Methocult. The culture dishes were incubated in a humidified incubator at 37° C. Colonies containing at least 30 cells were counted at day 14 post-plating using StemVision (StemCell Technologies) to take the image of entire plate. The total number of colonies, number of CFU-GEMM (Granulocyte, Erythrocyte, Macrophage, Megakaryocyte), CFU-GM (Granulocyte, Macrophage), CFU-M (Macrophage), CFU-E (erythroid) and BFU-E (Burst-forming unit-erythroid) were then counted StemVision image analyzer software and confirmed by manually using StemVision Colony Marker software.


In vivo engraftment study. In vivo engraftment studies are conducted under protocol approved by IACUC. A fraction of final culture of genome edited HSC equivalent to 30,000 starting cells are injected intravenously via the tail vein into sub-lethally irradiated (200 cGY) 6- to 8-week old NSG mice. Engraftment is performed within 24 h after irradiation. Engraftment is monitored by flow cytometric analysis of blood collected at 4, 8, and 12 weeks post-infusion using anti-human CD45 and anti-mouse CD45 antibodies. The mice are sacrificed 13 weeks post-transplantation and bone marrow, spleen and thymus collected for analysis by flow cytometry and colony forming cell unit assay. For secondary engraftment, 50% of the bone marrow from each recipient mouse is transplanted into one secondary sub-lethally irradiated NSG mouse. Engraftment is monitored by flow cytometric analysis of blood collected at 4, 8, and 12 weeks post-infusion using panleukocyte marker, CD45 using anti-human CD45 and anti-mouse CD45 antibodies. Fifteen weeks after transplantation, bone marrow and spleen were harvested from the secondary mice and analyzed by flow cytometry and colony forming cell unit assay.


Results:

Without being bound by theory, it is believed that targeted genetic disruption of BCL11A erythroid enhancer in HSC will down regulate the expression of BCL11A selectively in erythroid cell lineage and relieve repression of γ-globin expression, allowing production of the red blood cells containing elevated HbF protein, F-cells. The elevated HbF prevents sickling of the red blood cells under deoxygenated conditions and will be therapeutic/curative for the patients of both β-thalassemia and SCD. Autologous hematopoietic stem cell transplantation (HSCT) with ex vivo genome edited HSC from SCD patients was also combined with stem cell expansion enhancing technology, e.g., an aryl hydrocarbon receptor (AHR) inhibitor, e.g., as described in WO2010/059401 (the contents of which are incorporated by reference in their entirety), e.g., Compound 4 to improve ex vivo expansion and increase the dose of gene modified HSC delivered.


For efficient genome editing via programmable nuclease, Cas9, the successful delivery of guide RNA (gRNA) and Cas9 protein into target cells and tissues is essential. Recent reports demonstrated that Cas9 ribonucleoprotein (RNP) complexes when delivered into target cells by electroporation can accomplish efficient and specific genome editing in several different cell types. Cas9-RNP complexes cleave chromosomal DNA almost immediately after delivery and are degraded rapidly in cells, reducing off-target effects. In contrast, use of plasmid and viral vector systems used to deliver Cas9 results in prolonged expression of the enzyme aggravating off-target effects associated with the system. Additionally, delivery of RNPs into the target cells requires no additional tools which would greatly facilitate translation of genome editing for therapeutic purposes in the clinic. Purified recombinant Cas9 protein and gRNA complexes (RNPs) were delivered into cultured HSPC and an overview experiments used are shown in FIG. 17.


Recombinant Cas9 protein was purified from Escherichia coli and complexed with synthetic dual gRNAs (dgRNA) that consist of crRNA and tracr or full-length single guide RNA (sgRNA) to generate ribonucleoprotein (RNP) complexes. The list and sequences of gRNAs used in the study are shown in Table 14. The RNP complexes were electroporated into healthy or SCD patient derived bone marrow CD34+ HSPC via electroporation as described under materials and methods. The cells were expanded for 2-days in HSC expansion medium containing Compound 4 prior to the delivery of RNP complexes. Actively dividing cells may facilitate uptake of RNP complexes delivered by electroporation. To facilitate recovery from transfection process, the cells were cultured for two additional days in the modified expansion medium containing compound 4. Viability of the cells 48 hours after electroporation was determined by flow cytometry using 7AAD. The viability was relatively high with >80% of the cells viable (FIG. 18) suggesting that the HSPC tolerated electroporation of the RNP complexes relatively well compared to other methods of Cas9 and gRNA delivery systems reported in the literature.









TABLE 14







List of gRNAs targeting BCL11A erythroid specific enhancer


used in the current study.












Guide RNA







targeting
Region/
dgRNA
sgRNA


domain ID
strand
tested
tested
Target Sequence
Coordinates (hg38)





CR000245
+58/+
x

tcagtgagatgagatatcaa
chr2: 60494483-60494502





CR000246
+58/+
x

cagtgagatgagatatcaaa
chr2: 60494484-60494503





CR000260
+58/−
x

tgtaactaataaataccagg
chr2: 60494790-60494809





CR001124
+58/−
x

ttagggtgggggcgtgggtg
chr2: 60495217-60495236





CR001131
+58/−
x

attagggtgggggcgtgggt
chr2: 60495218-60495237





CR000309
+58/+
x
X
cacgcccccaccctaatcag
chr2: 60495221-60495240





CR000308
+58/−
x
X
tctgattagggtgggggcgt
chr2: 60495222-60495241





CR000310
+58/−
x
X
ttggcctctgattagggtgg
chr2: 60495228-60495247





CR000311
+58/−
x
X
tttggcctctgattagggtg
chr2: 60495229-60495248





CR000312
+58/−
x
X
gtttggcctctgattagggt
chr2: 60495230-60495249





CR000313
+58/−
x
X
ggtttggcctctgattaggg
chr2: 60495231-60495250





CR000314
+58/−
x
X
aagggtttggcctctgatta
chr2: 60495234-60495253





CR000315
+58/−
x
X
gaagggtttggcctctgatt
chr2: 60495235-60495254





CR001128/
+58/+

X
atcagaggccaaacccttcc
chr2: 60495236-60495255


sgEH15





CR001127/
+58/−

X
cacaggctccaggaagggtt
chr2: 60495247-60495266


sgEH14





CR001126/
+58/−
x
X
tttatcacaggctccaggaa
chr2: 60495252-60495271


sgEH13





CR001125/
+58/−

X
ttttatcacaggctccagga
chr2: 60495253-60495272


sgEH12





CR000316/
+58/−

X
ttgcttttatcacaggctcc
chr2: 60495257-60495276


sgEH11





CR000317/
+58/−


ctaacagttgcttttatcac
chr2: 60495264-60495283


sgEH4









The T7E1 assay is a convenient method to assess editing at specific sites in the genome. The genomic DNA was extracted from the HSPC 2-days post-electroporation. The targeted BCL11A erythroid enhancer region was amplified by polymerase chain reaction (PCR). The PCR products were subjected to T7E1 assay. The end products of T7E1 assay were subjected to 2% agarose gel electrophoresis and the percent edited alleles quantified by imageJ (http://rsb.info.nih.gov/ij/). Expected PCR product sizes and approximate expected sizes of T7E1-digested fragments are shown in FIG. 19. The total editing frequencies are indicated as percentage of total edits below the agarose gel image. The genome editing at the BCL11A locus was observed in the cells treated with BCL11A Cas9 RNPs but not in mock electroporated control cells (FIG. 19).


The genomic PCR products of the +58 erythroid enhancer region of BCL11A were also subjected to next generation sequencing (NGS). The NGS facilitates simultaneous monitoring of a large number of samples giving a global view of the alleles. Moreover, it provides information on the heterogeneity of insertions and deletions (indels). The sequences were compared with the sequences from control (mock) treated cells. The results of sequence analysis showed that CRISPR-Cas9 induced double stranded breaks were repaired by NHEJ resulting in variable frequencies of small deletions and insertions (indels) near Cas9 cleavage site located in +58 BCL11A erythroid enhancer region (FIG. 20 and Table 15). Overall, the observed editing efficiencies was higher for sgRNAs compared to dgRNAs targeting the same sequence, with 12 out 14 sgRNA producing editing at more than 50% alleles (FIG. 20 and Table 15), though (without being bound by theory) the differences in efficiency between sgRNA and dgRNA may be affected by the source of the materials.









TABLE 15







Genotypes identified by NGS in HSPCs edited with Cas9-RNP. The nucleotide sequence


for each population is given. The target sequence targeted by each gRNA is indicated


above each indel population, with the PAM sequences indicated in lower case. Dashes


denote deleted bases and lowercase letters denote insertions. In the description of the


gRNA, dgRNA refers to dual gRNA molecules comprising the indicated targeting domain


sgRNA indicates single gRNA molecules comprising the indicated targeting domain.


Where multiple experiments were run with the same dgRNA or sgRNA, successive


experiments are labeled “dgRNA,” “d1gRNA”, “d2gRNA,” etc.












%
Indel


gRNA
Variant
Allele
length














CTAACAGTTGCTTTTATCACagg




CR00317-
TAGTGCAAGCTAACAG---------------GCTCCAGGAAGGGTTTGGCCTCTGATTAG
5.96%
−15


dgRNA





CR00317-
TAGTGCAAGCTAACAGTTGCTTTTATtCACAGGCTCCAGGAAGGGTTTGGCCTCTGATTAG
5.77%
1


dgRNA





CR00317-
TAGTGCAAGCTAACAGTTGCT-------------CCAGGAAGGGTTTGGCCTCTGATTAG
4.69%
−13


dgRNA





CR00317-
TAGTGCAAGCTAACAGTTGCTTTTATCA--GGCTCCAGGAAGGGTTTGGCCTCTGATTAG
0.90%
−2


dgRNA





CR00317-
TAGTGCAAGCTAACAGTTGCTTTTA-CACAGGCTCCAGGAAGGGTTTGGCCTCTGATTAG
0.88%
−1


dgRNA





CR00317-
TAGTGCAAGCTAACAGTTGCTTTT--CACAGGCTCCAGGAAGGGTTTGGCCTCTGATTAG
0.77%
−2


dgRNA





CR00317-
TAGTGCAAGCT-----------------------CCAGGAAGGGTTTGGCCTCTGATTAG
0.67%
−23


dgRNA






ATCAGAGGCCAAACCCTTCCacc


CR001128-
AGCTAACAGTTGCTTTTATCACAGGCTCCAGGA-GGGTTTGGCCTCTGATTAGGGTGGGG
20.07%
−1


dgRNA





CR001128-
AGCTAACAGTTGCTTTTATCACAGGCTCCAGG-----TTTGGCCTCTGATTAGGGTGGGG
5.00%
−5


dgRNA





CR001128-
AGCTAACAGTTGCTTTTATCACAGGCTCCAGGAAaGGGTTTGGCCTCTGATTAGGGTGGGG
4.84%
1


dgRNA





CR001128-
AGCTAACAGTTGCTTTTATCACAGGCTCCAGG----GTTTGGCCTCTGATTAGGGTGGGG
4.01%
−4


dgRNA





CR001128-
AGCTAACAGTTGCTTTTATCACAGGCTCCAGGA--GGTTTGGCCTCTGATTAGGGTGGGG
2.99%
−2


dgRNA





CR001128-
AGCTAACAGTTGCTTTTATCACAGGCTCCAGGA-GGGTTTGGCCTCTGATTAGGGTGGGG
23.33%
−1


sgRNA





CR001128-
AGCTAACAGTTGCTTTTATCACAGGCTCCAGGAAGG-TTTGGCCTCTGATTAGGGTGGGG
5.77%
−1


sgRNA





CR001128-
AGCTAACAGTTGCTTTTATCACAGGCTCCAGGAAaGGGTTTGGCCTCTGATTAGGGTGGGG
5.77%
1


sgRNA





CR001128-
AGCTAACAGTTGCTTTTATCACAGGCTCCAGGA--GGTTTGGCCTCTGATTAGGGTGGGG
5.37%
−2


sgRNA





CR001128-
AGCTAACAGTTGCTTTTATCACAGGCTCCAGGAAG--TTTGGCCTCTGATTAGGGTGGGG
3.70%
−2


sgRNA





CR001128-
AGCTAACAGTTGCTTTTATCACAGGCTCCAGG----------CCTCTGATTAGGGTGGGG
3.62%
−10


sgRNA





CR001128-
AGCTAACAGTTGCTTTTATCACAGGC-----------------CTCTGATTAGGGTGGGG
3.54%
−17


sgRNA





CR001128-
AGCTAACAGTTGCTTTTATCACAGGCTCCAGGA---GTTTGGCCTCTGATTAGGGTGGGG
2.97%
−3


sgRNA






TTGCTTTTATCACAGGCTCCagg


CR00316-
AGCTAACAGTTGCTTTTATCACAGG-------AAGGGTTTGGCCTCTGATTAGGGTGGGG
16.03%
−7


sgRNA





CR00316-
AGCTAACAGTTGCTTTTATCACAGGCTtCCAGGAAGGGTTTGGCCTCTGATTAGGGTGGGG
8.25%
1


sgRNA





CR00316-
AGCTAACAGTTGCTTTTATC--------CAGGAAGGGTTTGGCCTCTGATTAGGGTGGGG
8.04%
−8


sgRNA





CR00316-
AGCTAACAGTTGCTTTTATCACAGGCcTCCAGGAAGGGTTTGGCCTCTGATTAGGGTGGGG
4.07%
1


sgRNA





CR00316-
AGCTAACAGTTGCTTTTATCACAGGC-CCAGGAAGGGTTTGGCCTCTGATTAGGGTGGGG
3.55%
−1


sgRNA





CR00316-
AGCTAACAGTTGCTTTTATCACAGGC--CAGGAAGGGTTTGGCCTCTGATTAGGGTGGGG
2.37%
−2


sgRNA





CR00316-
AGCTAACAGTTGCTTTTATCACAGG-------AAGGGTTTGGCCTCTGATTAGGGTGGGG
2.49%
−7


dgRNA





CR00316-
AGCTAACAGTTGCTTTTATCACAGGCTtCCAGGAAGGGTTTGGCCTCTGATTAGGGTGGGG
1.78%
1


dgRNA





CR00316-
AGCTAACAGTTGCTTTTATC--------CAGGAAGGGTTTGGCCTCTGATTAGGGTGGGG
1.32%
−8


dgRNA





CR00316-
AGCTAACAGTTGCTTTTATCACAGGCcTCCAGGAAGGGTTTGGCCTCTGATTAGGGTGGGG
1.26%
1


dgRNA





CR00316-
AGCTAACAGTTGCTTTTATCACAGG-------AAGGGTTTGGCCTCTGATTAGGGTGGGG
6.94%
−7


d1gRNA





CR00316-
AGCTAACAGTTGCTTTTATC--------CAGGAAGGGTTTGGCCTCTGATTAGGGTGGGG
4.99%
−8


d1gRNA





CR00316-
AGCTAACAGTTGCTTTTATCACAGGCTtCCAGGAAGGGTTTGGCCTCTGATTAGGGTGGGG
4.69%
1


d1gRNA





CR00316-
AGCTAACAGT-------------------------------------GATTAGGGTGGGG
2.90%
−37


d1gRNA





CR00316-
AGCTAACAGTTGCTTTTATCACAGGC-CCAGGAAGGGTTTGGCCTCTGATTAGGGTGGGG
1.54%
−1


d1gRNA





CR00316-
AGCTAACAGTTGCTTTTATCACAGG-------AAGGGTTTGGCCTCTGATTAGGGTGGGG
11.64%
−7


d2gRNA





CR00316-
AGCTAACAGTTGCTTTTATC--------CAGGAAGGGTTTGGCCTCTGATTAGGGTGGGG
6.04%
−8


d2gRNA





CR00316-
AGCTAACAGTTGCTTTTATCACAGGCTtCCAGGAAGGGTTTGGCCTCTGATTAGGGTGGGG
5.40%
1


d2gRNA





CR00316-
AGCTAACAGTTGCTTTTATCACAGGCcTCCAGGAAGGGTTTGGCCTCTGATTAGGGTGGGG
1.80%
1


d2gRNA





CR00316-
AGCTAACAGTTGCTTTTATCACAGGC-----GAAGGGTTTGGCCTCTGATTAGGGTGGGG
1.43%
−5


d2gRNA






TTTTATCACAGGCTCCAGGAagg


CR001125-
AACAGTTGCTTTTATCACAGGCTCCAaGGAAGGGTTTGGCCTCTGATTAGGGTGGGGGCGT
13.50%
1


dgRNA





CR001125-
AACAGTTGCTTTTATCACAGGC-----------------CTCTGATTAGGGTGGGGGCGT
1.82%
−17


dgRNA





CR001125-
AACAGTTGCTTTTATCACAGG-----------GTTTGGCCTCTGATTAGGGTGGGGGCGT
1.76%
−11


dgRNA





CR001125-
AACAGTTGCTTTTATCACAGG-------AAGGGTTTGGCCTCTGATTAGGGTGGGGGCGT
1.59%
−7


dgRNA





CR001125-
AACAGTTGCTTTT------------------------------------GGTGGGGGCGT
1.33%
−36


dgRNA





CR001125-
AACAGTTGCTTTTATCACAGGCTCCAaGGAAGGGTTTGGCCTCTGATTAGGGTGGGGGCGT
26.27%
1


sgRNA





CR001125-
AACAGTTGCTTTTATCACAGG-----------GTTTGGCCTCTGATTAGGGTGGGGGCGT
4.64%
−11


sgRNA





CR001125-
AACAGTTGCTTTTATCACAGG-------AAGGGTTTGGCCTCTGATTAGGGTGGGGGCGT
4.11%
−7


sgRNA





CR001125-
AACAGTTGCTTTTATCACAGGC-----------------CTCTGATTAGGGTGGGGGCGT
2.66%
−17


sgRNA





CR001125-
AACAGTTGCTTTTATCACAGGCT------------TGGCCTCTGATTAGGGTGGGGGCGT
2.58%
−12


sgRNA





CR001125-
AACAGTTGCTTTTATCACAGGCTCC-GGAAGGGTTTGGCCTCTGATTAGGGTGGGGGCGT
1.84%
−1


sgRNA






TTTATCACAGGCTCCAGGAAggg


CR001126-
ACAGTTGCTTTTATCACAGGCTCCAG-AAGGGTTTGGCCTCTGATTAGGGTGGGGGCGTG
9.38%
−1


dgRNA





CR001126-
ACAGTTGCTTTTATCACAGG-----------GTTTGGCCTCTGATTAGGGTGGGGGCGTG
3.28%
−11


dgRNA





CR001126-
ACAGTTGCTTTTATCACAGGCTCCAGGgAAGGGTTTGGCCTCTGATTAGGGTGGGGGCGTG
2.91%
1


dgRNA





CR001126-
ACAGTTGCTTTTATCACAGGC-----------------CTCTGATTAGGGTGGGGGCGTG
2.82%
−17


dgRNA





CR001126-
ACAGTTGCTTTT---------------------------------------GGGGGCGTG
1.61%
−39


dgRNA





CR001126-
ACAGTTGCTTT----------------------------------------GGGGGCGTG
1.12%
−40


dgRNA





CR001126-
ACAGTTGCTTTTATCACAGGCTCCAG-AAGGGTTTGGCCTCTGATTAGGGTGGGGGCGTG
12.70%
−1


sgRNA





CR001126-
ACAGTTGCTTTTATCACAGG-----------GTTTGGCCTCTGATTAGGGTGGGGGCGTG
4.37%
−11


sgRNA





CR001126-
ACAGTTGCTTTTATCACAGGCTCCAGGgAAGGGTTTGGCCTCTGATTAGGGTGGGGGCGTG
3.22%
1


sgRNA





CR001126-
ACAGTTGCTTTTATCACAGGCTCCAGaT------------------AAGGTGGGGGCGTG
2.96%
−18


sgRNA





CR001126-
ACAGTTGCTTTTATCACAGGC-----------------CTCTGATTAGGGTGGGGGCGTG
2.68%
−17


sgRNA





CR001126-
ACAGTTGCTTTTATCACAGGCTCCAGG----GTTTGGCCTCTGATTAGGGTGGGGGCGTG
2.59%
−4


sgRNA





CR001126-
ACAGTTGCTTTTATCACAGGCTCCAGcGAAGGGTTTGGCCTCTGATTAGGGTGGGGGCGTG
1.80%
1


sgRNA





CR001126-
ACAGTTGCTTTTATCACAGGCTCC-GGAAGGGTTTGGCCTCTGATTAGGGTGGGGGCGTG
1.74%
−1


sgRNA






CACAGGCTCCAGGAAGGGTTtgg


CR001127-
TGCTTTTATCACAGGCTCCAGGAAGG-TTTGGCCTCTGATTAGGGTGGGGGCGTGGGTGG
4.00%
−1


dgRNA





CR001127-
TGCTTTTATCACAGGCcT-----------------------------GGGGCGTGGGTGG
2.35%
−29


dgRNA





CR001127-
TGCTTTTATCACAGGC------------------------------------GTGGGTGG
2.19%
−36


dgRNA





CR001127-
TGCTTTTATCACAGGC-----------------CTCTGATTAGGGTGGGGGCGTGGGTGG
1.59%
−17


dgRNA





CR001127-
TGCTTTTATCACAGGCTCCAGGAAGG------CCTCTGATTAGGGTGGGGGCGTGGGTGG
1.48%
−6


dgRNA





CR001127-
TGCTTTTATCACAGGCTCCAGGA-GGGTTTGGCCTCTGATTAGGGTGGGGGCGTGGGTGG
23.21%
−1


sgRNA





CR001127-
TGCTTTTATCACAGGCTCCAGGAAGG-TTTGGCCTCTGATTAGGGTGGGGGCGTGGGTGG
6.65%
−1


sgRNA





CR001127-
TGCTTTTATCACAGGC-----------------CTCTGATTAGGGTGGGGGCGTGGGTGG
5.20%
−17


sgRNA





CR001127-
TGCTTTTATCACAGGCTCCAGGAAaGGGTTTGGCCTCTGATTAGGGTGGGGGCGTGGGTGG
4.89%
1


sgRNA





CR001127-
TGCTTTTATCACAGGCTCCAGG----------------------------GCGTGGGTGG
4.30%
−28


sgRNA





CR001127-
TGCTTTTATCACAGGCTCCAGG-----TTTGGCCTCTGATTAGGGTGGGGGCGTGGGTGG
3.72%
−5


sgRNA





CR001127-
TGCTTTTATCACAGGC------------------------------------GTGGGTGG
3.71%
−36


sgRNA





CR001127-
TGCTTTTATCACAGGCTCCAGGAAG--TTTGGCCTCTGATTAGGGTGGGGGCGTGGGTGG
3.53%
−2


sgRNA





CR001127-
TGCTTTTATCACAGGCTCCAGGAAGGtC-----------------CGTTTGCGTGGGTGG
2.29%
−17


sgRNA






CACGCCCCCACCCTAATCAGagg


CR00309-
TATCACAGGCTCCAGGAAGGGTTTGGC-------------------GTGGGTGGGGTAGA
11.56%
−19


sgRNA





CR00309-
TATCACAGGCTCCAGGAAGGGTTTGGCCTCTGAaTTAGGGTGGGGGCGTGGGTGGGGTAGA
7.29%
1


sgRNA





CR00309-
TATCACAGGCTCCAGGAAGGG------------------------CGTGGGTGGGGTAGA
6.16%
−24


sgRNA





CR00309-
TATCACAGGCTCCAGGAAGGG----------------------GGCGTGGGTGGGGTAGA
4.74%
−22


sgRNA





CR00309-
TATCACAGGCTCCAGGAAGGGTTTGG------------------GCGTGGGTGGGGTAGA
4.34%
−18


sgRNA





CR00309-
TATCACAGGCTCCAGGAAGGGTTTGG------------------------GTGGGGTAGA
3.45%
−24


sgRNA





CR00309-
TATCACAGGCTCCAGG---------------------------GGCGTGGGTGGGGTAGA
1.87%
−27


sgRNA






GAAGGGTTTGGCCTCTGATTagg


CR00313-
TCCAGGAAGGGTTTGG------------------------GTGGGGTAGAAGAGGACTGG
3.36%
−24


sgRNA





CR00313-
TCCAGGAAGGGTTTGGCCTCTGATTAGG-TGGGGGCGTGGGTGGGGTAGAAGAGGACTGG
3.31%
−1


sgRNA





CR00313-
TCCAGGAAGGGTT-----------------------------GGGGTAGAAGAGGACTGG
2.83%
−29


sgRNA





CR00313-
TCCAGGAAGGGTTTGGCCT-------------------GGGTGGGGTAGAAGAGGACTGG
2.76%
−19


sgRNA





CR00313-
TCCAGGAAGGGTTTGG------------------------------TAGAAGAGGACTGG
2.31%
−30


sgRNA






GTTTGGCCTCTGATTAGGGTggg


CR00312-
CCAGGAAGGGTTTGGCCTCTGATTAGG-TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGC
16.87%
−1


dgRNA





CR00312-
CCAGGAAGGGTTTGGC-------------------GTGGGTGGGGTAGAAGAGGACTGGC
9.86%
−19


dgRNA





CR00312-
CCAGGAAGGGTTTGGCCTCTGATT--GGTGGGGGCGTGGGTGGGGTAGAAGAGGACTGGC
5.65%
−2


dgRNA





CR00312-
CCAGGAAGGG------------------------CGTGGGTGGGGTAGAAGAGGACTGGC
3.83%
−24


dgRNA





CR00312-
CCAGGAAGGG----------------------GGCGTGGGTGGGGTAGAAGAGGACTGGC
3.42%
−22


dgRNA





CR00312-
CCAGGAAGGGTTTGG------------------------GTGGGGTAGAAGAGGACTGGC
2.10%
−24


dgRNA





CR00312-
CCAGGAAGGGTTTGGCCTCTGA----GGTGGGGGCGTGGGTGGGGTAGAAGAGGACTGGC
1.85%
−4


dgRNA





CR00312-
CCAGGAAGGGTTTGGCCTCTGATTAGG-TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGC
13.35%
−1


sgRNA





CR00312-
CCAGGAAGGGTTTGGC-------------------GTGGGTGGGGTAGAAGAGGACTGGC
7.85%
−19


sgRNA





CR00312-
CCAGGAAGGGTTTGG------------------------GTGGGGTAGAAGAGGACTGGC
4.19%
−24


sgRNA





CR00312-
CCAGGAAGGGTTTGGCCTCTGATT--GGTGGGGGCGTGGGTGGGGTAGAAGAGGACTGGC
3.98%
−2


sgRNA





CR00312-
CCAGGAAGGGTTTGGCCTCTGATTAGGG-----GCGTGGGTGGGGTAGAAGAGGACTGGC
2.95%
−5


sgRNA





CR00312-
CCAGGAAGGG------------------------CGTGGGTGGGGTAGAAGAGGACTGGC
2.29%
−24


sgRNA





CR00312-
CCAGGAAGGGTTTGGCCTCTGATTAGaGGTGGGGGCGTGGGTGGGGTAGAAGAGGACTGGC
2.09%
1


sgRNA





CR00312-
CCAGGAAGGGTTTGGCCTCTGATTAGG-TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGC
19.22%
−1


d1gRNA





CR00312-
CCAGGAAGGGTTTGGCCTCTGATT--GGTGGGGGCGTGGGTGGGGTAGAAGAGGACTGGC
6.28%
−2


d1gRNA





CR00312-
CCAGGAAGGGTTTGG------------------------GTGGGGTAGAAGAGGACTGGC
5.31%
−24


d1gRNA





CR00312-
CCAGGAAGGGTTTGGC-------------------GTGGGTGGGGTAGAAGAGGACTGGC
4.22%
−19


d1gRNA





CR00312-
CCAGGAAGGGTTTGG----------------GGGCGTGGGTGGGGTAGAAGAGGACTGGC
3.10%
−16


d1gRNA





CR00312-
CCAGGAAGGGTTTGGCCTCTGATTAG--TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGC
2.85%
−2


d1gRNA





CR00312-
CCAGGAAGGG------------------------CGTGGGTGGGGTAGAAGAGGACTGGC
2.74%
−24


d1gRNA





CR00312-
CCAGGAAGGGTTTGGCCTCTGATTAGG-TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGC
23.15%
−1


d2gRNA





CR00312-
CCAGGAAGGGTTTGGC-------------------GTGGGTGGGGTAGAAGAGGACTGGC
8.99%
−19


d2gRNA





CR00312-
CCAGGAAGGGTTTGGCCTCTGATT--GGTGGGGGCGTGGGTGGGGTAGAAGAGGACTGGC
6.82%
−2


d2gRNA





CR00312-
CCAGGAAGGG-----------------------GCGTGGGTGGGGTAGAAGAGGACTGGC
2.69%
−23


d2gRNA





CR00312-
CCAGGAAGGG------------------------CGTGGGTGGGGTAGAAGAGGACTGGC
2.29%
−24


d2gRNA





CR00312-
CCAGGAAGGGTTTGGCCTCTGATTAG--TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGC
2.25%
−2


d2gRNA





CR00312-
CCAGGAAGGGTTTGG----------------GGGCGTGGGTGGGGTAGAAGAGGACTGGC
2.13%
−16


d2gRNA






TTTGGCCTCTGATTAGGGTGggg


CR00311-
CAGGAAGGGTTTGGCCTCTGATTAGG-TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCA
19.62%
−1


dgRNA





CR00311-
CAGGAAGGGTTTGGC-------------------GTGGGTGGGGTAGAAGAGGACTGGCA
3.01%
−19


dgRNA





CR00311-
CAGGAAGGGTTTGGCCTCTGATTAG--TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCA
2.77%
−2


dgRNA





CR00311-
CAGGAAGGGTTTGGCCTCTGATTAGGG-----GCGTGGGTGGGGTAGAAGAGGACTGGCA
2.23%
−5


dgRNA





CR00311-
CAGGAAGGGTTTGG------------------------GTGGGGTAGAAGAGGACTGGCA
2.21%
−24


dgRNA





CR00311-
CAGGAAGGGTTTGG-------------TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCA
2.05%
−13


dgRNA





CR00311-
CAGGAAGGGTTTGGCCTCTG-------TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCA
1.88%
−7


dgRNA





CR00311-
CAGGAAGGGT------------------------------GGGGTAGAAGAGGACTGGCA
1.76%
−30


dgRNA





CR00311-
CAGGAAGGGTTTGGCCTCTGATTAGG-TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCA
28.21%
−1


sgRNA





CR00311-
CAGGAAGGGTTTGGC-------------------GTGGGTGGGGTAGAAGAGGACTGGCA
4.88%
−19


sgRNA





CR00311-
CAGGAAGGGT------------------------------GGGGTAGAAGAGGACTGGCA
2.72%
−30


sgRNA





CR00311-
CAGGAAGGGTTTGGCCTCTGATTAG--TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCA
2.62%
−2


sgRNA





CR00311-
CAGGAAGGGTTTGGCCTCTGATTAGGG----GGCGTGGGTGGGGTAGAAGAGGACTGGCA
2.35%
−4


sgRNA





CR00311-
CAGGAAGGGTTTGGCCTCTGATTAGGG-----GCGTGGGTGGGGTAGAAGAGGACTGGCA
2.06%
−5


sgRNA





CR00311-
CAGGAAGGGTTTGGCCTCTGATTAGG-TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCA
31.34%
−1


d1gRNA





CR00311-
CAGGAAGGGTTTGGCCTCTGATTAG--TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCA
4.00%
−2


d1gRNA





CR00311-
CAGGAAGGGTTTGGCCT------------------------------AAGAGGACTGGCA
2.84%
−30


d1gRNA





CR00311-
CAGGAAGGGTTTGG-----------------------------------GAGGACTGGCA
2.41%
−35


d1gRNA





CR00311-
CAGGAAGGGTTT---------------------------------AGAAGAGGACTGGCA
2.35%
−33


d1gRNA





CR00311-
CAGGAAGGGTTTGGCCTC-------------------------------GAGGACTGGCA
2.11%
−31


d1gRNA





CR00311-
CAGGAAGGGTTTGGCCTCTGATTAGGG----GGCGTGGGTGGGGTAGAAGAGGACTGGCA
2.03%
−4


d1gRNA





CR00311-
CAGGAAGGGTTTGGCCTCTGATTAGGG---GGGCGTGGGTGGGGTAGAAGAGGACTGGCA
1.71%
−3


d1gRNA





CR00311-
CAGGAAGGGTTTGGCCTCTGATTAGG-TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCA
30.20%
−1


d2gRNA





CR00311-
CAGGAAGGGTTTGGC-------------------GTGGGTGGGGTAGAAGAGGACTGGCA
7.57%
−19


d2gRNA





CR00311-
CAGGAAGGGTTTGGCCTCTGATTAG--TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCA
3.57%
−2


d2gRNA





CR00311-
CAGGAAGGGTTTGG----------------------------GGTAGAAGAGGACTGGCA
2.39%
−28


d2gRNA





CR00311-
CAGGAAGGGTTTGGCCTCTGATTAGGG-----GCGTGGGTGGGGTAGAAGAGGACTGGCA
2.10%
−5


d2gRNA





CR00311-
CAGGAAGGGTTTGGCCTCTGATTAGGG----GGCGTGGGTGGGGTAGAAGAGGACTGGCA
1.50%
−4


d2gRNA





CR00311-
CAGGAAGGGTTTGG----------------GGGCGTGGGTGGGGTAGAAGAGGACTGGCA
1.49%
−16


d2gRNA






TTGGCCTCTGATTAGGGTGGggg


CR00310-
AGGAAGGGTTTGGCCTCTGATTAGGG----GGCGTGGGTGGGGTAGAAGAGGACTGGCAG
7.70%
−4


sgRNA





CR00310-
AGGAAGGGTTTGGCCTCTGATTAGGG------CGTGGGTGGGGTAGAAGAGGACTGGCAG
7.13%
−6


sgRNA





CR00310-
AGGAAGGGTTTGGCCTCTGATTAGGG-----GCGTGGGTGGGGTAGAAGAGGACTGGCAG
6.34%
−5


sgRNA





CR00310-
AGGAAGGGTTTGGCCTCTGATTAGG-TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCAG
5.38%
−1


sgRNA





CR00310-
AGGAAGGGTTTGGCCTCTGATTAG--TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCAG
3.73%
−2


sgRNA





CR00310-
AGGAAGGGTTTGGCCTCTGATT-----GGGGGCGTGGGTGGGGTAGAAGAGGACTGGCAG
3.54%
−5


sgRNA





CR00310-
AGGAAGGGTTTGGCCTCTGATTAGGGTGGGGGCGTGGGTGGG-TAGAAGAGGACTGGCAG
0.67%
−1


dgRNA






TCTGATTAGGGTGGGGGCGTggg


CR00308-
GGTTTGGCCTCTGATTAGGGTGGGG------------TAGAAGAGGACTGGCAGACCTCT
16.28%
−12


sgRNA





CR00308-
GGTTTGGCCTCTGATTAGGGTGGGGG-----------TAGAAGAGGACTGGCAGACCTCT
5.59%
−11


sgRNA





CR00308-
GGTTTGGCCTCTGATTAGGGTGGG--------TGGGGTAGAAGAGGACTGGCAGACCTCT
4.51%
−8


sgRNA





CR00308-
GGTTTGGCCTCTGAT------------------GGGGTAGAAGAGGACTGGCAGACCTCT
3.54%
−18


sgRNA





CR00308-
GGTTTGGCCTCTGATTtA-----------------------------CTGGCAGACCTCT
2.76%
−29


sgRNA





CR00308-
GGTTTGGCCTCTGATTgG-------CCGTGGGTGGGGTAGAAGAGGACTGGCAGACCTCT
2.27%
−7


sgRNA





CR00308-
GGTTTGGCCTCTGATTAGGG----------------GTAGAAGAGGACTGGCAGACCTCT
2.26%
−16


sgRNA





CR00308-
GGTTTGGCCTCTGATcC--AAGAGCCCGTGGGTGGGGTAGAAGAGGACTGGCAGACCTCT
1.99%
−2


sgRNA





CR00308-
GGTTTGGCCTCTGATTAGGGTGGGGGCGTGGGTGGG-TAGAAGAGGACTGGCAGACCTCT
0.42%
−1


dgRNA






ATTAGGGTGGGGGCGTGGGTggg


CR001131-
TGGCCTCTGATTAGGGTGGGG------------TAGAAGAGGACTGGCAGACCTCTCCAT
44.62%
−12


dgRNA





CR001131-
TGGCCTCTGATTAGGGTGGGGG-----------TAGAAGAGGACTGGCAGACCTCTCCAT
3.19%
−11


dgRNA





CR001131-
TGGCCTCTGATTAGGGTGGGGGCGTGG-TGGGGTAGAAGAGGACTGGCAGACCTCTCCAT
1.72%
−1


dgRNA





CR001131-
TGGCCTCTGATTAGGGTGGGGGCG------------AAGAGGACTGGCAGACCTCTCCAT
1.04%
−12


dgRNA






TTAGGGTGGGGGCGTGGGTGggg


CR001124-
GGCCTCTGATTAGGGTGGGG------------TAGAAGAGGACTGGCAGACCTCTCCATC
8.52%
−12


dgRNA





CR001124-
GGCCTCTGATTAGGGTGGGGGCGTGG-TGGGGTAGAAGAGGACTGGCAGACCTCTCCATC
2.12%
−1


dgRNA





CR001124-
GGCCTCTGATTAGGGTGGGGG-----------TAGAAGAGGACTGGCAGACCTCTCCATC
1.33%
−11


dgRNA






TGTAACTAATAAATACCagg


CR00260-
CTGCTGAGGTGTAACTAATAAATACC-GGAGGCAGCATTTTAGTTCACAAGCTCGGAGCA
26.54%
−1


dgRNA





CR00260-
CTGCTGAGGTGTAACTAATAAATAC-AGGAGGCAGCATTTTAGTTCACAAGCTCGGAGCA
12.39%
−1


dgRNA





CR00260-
CTGCTGAGGTGTAACTAATAAATACCcAGGAGGCAGCATTTTAGTTCACAAGCTCGGAGCA
12.32%
1


dgRNA





CR00260-
CTGCTGAGGTGTAACTAATAAATACC--GAGGCAGCATTTTAGTTCACAAGCTCGGAGCA
2.37%
−2


dgRNA





CR00260-
CTGCTGAGGTGTAACTAATAAAT--CAGGAGGCAGCATTTTAGTTCACAAGCTCGGAGCA
1.89%
−2


dgRNA





CR00260-
CTGCTGAGGTGTAACTAATAAATA---GGAGGCAGCATTTTAGTTCACAAGCTCGGAGCA
1.28%
−3


dgRNA






CAGTGAGATGAGATATCAAAggg


CR00246-
GGGAGATGGAATGAACACTTTTCGTCCCCTTTGgATATCTCATCTCACTGAGCTCTGGGCC
7.56%
1


dgRNA





CR00246-
GGGAGATGGAATGAACACTTTTCGTCCCCTTTGAT--CTCATCTCACTGAGCTCTGGGCC
4.46%
−2


dgRNA





CR00246-
GGGAGATGGAATGAACACTTTTCGTCCCCTTTG------CATCTCACTGAGCTCTGGGCC
3.50%
−6


dgRNA





CR00246-
GGGAGATGGAATGAACACTTTTCGTCCCCTTT-----CTCATCTCACTGAGCTCTGGGCC
2.98%
−5


dgRNA





CR00246-
GGGAGATGGAATGAACACTTTTCGTCCCCTTT-ATATCTCATCTCACTGAGCTCTGGGCC
2.97%
−1


dgRNA





CR00246-
GGGAGATGGAATGAACACTTTTCGTCCCCTTTG---TCTCATCTCACTGAGCTCTGGGCC
2.96%
−3


dgRNA





CR00246-
GGGAGATGGAATGAACACTTTTCGTCCCCTTT--TATCTCATCTCACTGAGCTCTGGGCC
2.93%
−2


dgRNA





CR00246-
GGGAGATGGAATGAACACTTTTCGTCCCCTTTG-TATCTCATCTCACTGAGCTCTGGGCC
2.70%
−1


dgRNA






TCAGTGAGATGAGATATCAAagg


CR00245-
GGAGATGGAATGAACACTTTTCGTCCCCTTTGAaTATCTCATCTCACTGAGCTCTGGGCCG
22.36%
1


dgRNA





CR00245-
GGAGATGGAATGAACACTTTTCGTCCCCTTTGA-ATCTCATCTCACTGAGCTCTGGGCCG
8.97%
−1


dgRNA





CR00245-
GGAGATGGAATGAACACTTTTCGTCCCCTTTGAT--CTCATCTCACTGAGCTCTGGGCCG
4.03%
−2


dgRNA





CR00245-
GGAGATGGAATGAACACTTTTCGTCCCCTTTG-TATCTCATCTCACTGAGCTCTGGGCCG
2.45%
−1


dgRNA





CR00245-
GGAGATGGAATGAACACTTTTCGTCCCCTT--ATATCTCATCTCACTGAGCTCTGGGCCG
1.85%
−2


dgRNA





CR00245-
GGAGATGGAATGAACACTTTTCGTCCCCTTTGA-----CATCTCACTGAGCTCTGGGCCG
1.38%
−5


dgRNA






GTGCCAGATGAACTTCCCATtgg


g7BCL11a-BC-
CTGTGGGCAGTGCCAGATGAACTTCC-ATTGGGGGACATTCTTATTTTTATCGAGCACAA
15.63%
−1


1sgRNA





g7BCL11a-BC-
CTGTGGGCAGTGCCAGATGAACTTC--ATTGGGGGACATTCTTATTTTTATCGAGCACAA
7.36%
−2


1sgRNA





g7BCL11a-BC-
CTGTGGGCAGTGCCAGATGAACTTCCCcATTGGGGGACATTCTTATTTTTATCGAGCACAA
6.88%
1


1sgRNA





g7BCL11a-BC-
CTGTGGGCAGTGCCAGATGAAC-----ATTGGGGGACATTCTTATTTTTATCGAGCACAA
2.81%
−5


1sgRNA





g7BCL11a-BC-
CTGTGGGCAGTGCCAGATGAACTTCC--TTGGGGGACATTCTTATTTTTATCGAGCACAA
2.59%
−2


1sgRNA





g7BCL11a-BC-
CTGTGGGCAGTGCCAGATGAACTTCC-ATTGGGGGACATTCTTATTTTTATCGAGCACAA
18.89%
−1


2sgRNA





g7BCL11a-BC-
CTGTGGGCAGTGCCAGATGAACTTC--ATTGGGGGACATTCTTATTTTTATCGAGCACAA
9.14%
−2


2sgRNA





g7BCL11a-BC-
CTGTGGGCAGTGCCAGATGAACTTCCCcATTGGGGGACATTCTTATTTTTATCGAGCACAA
5.52%
1


2sgRNA





g7BCL11a-BC-
CTGTGGGCAGTGCCAGATGAACTTCC--TTGGGGGACATTCTTATTTTTATCGAGCACAA
4.39%
−2


2sgRNA





g7BCL11a-BC-
CTGTGGGCAGTGCCAGATGAACT---CATTGGGGGACATTCTTATTTTTATCGAGCACAA
3.18%
−3


2sgRNA









To determine whether CD34+ HSPC have retained their multilineage potential to differentiate into effector cells after ex vivo manipulations including genome editing, in vitro colony forming cell (CFC) unit assays were performed for select gRNAs. The genome edited cells were suspended in cytokine-supplemented methylcellulose and maintained for 14 days at 37° C. in a humidified atmosphere of 5% CO2. Discrete colonies developed which were classified and counted based on the number and types of mature cells using morphological and phenotypic criteria (STEMvision) that they contain and scored for contribution to colony forming unit-erythroid (CFU-E), burst forming unit-erythroid (BFU-E), colony-forming unit-granulocyte/macrophage (CFU-GM) and colony-forming unit-granulocyte/erythrocyte/macrophage/megakaryocyte (CFU-GEMM; FIG. 21). The colony forming potential of mock transfected cells was the highest followed by gRNAs targeting +58 erythroid enhancer of BCL11A. A similar number and types of colonies were observed for gRNAs targeting BCL11A erythroid enhancer. The guide RNA targeting exon 2 of BCL11A gave the least number of colonies (FIG. 22).


Relative mRNA expression levels of BCL11A, gamma- and beta-globin chains in unilineage erythroid cultures were quantified by Real-Time PCR. The transcript levels were normalized against human GAPDH transcript levels. The BCL11A mRNA levels were reduced in genome edited HSPC. In contrast, BCL11A mRNA levels remained the same in unedited or edited HSPC at the exon 2 of BCL11A on days 7 and 14 of erythroid differentiation (FIG. 23). Gamma globin mRNA levels increased and correspondingly beta-globin mRNA decreased gradually in edited HSPC during erythroid differentiation (FIG. 23). Increase in HbF and decrease in beta-globin (sickled globin) levels in erythrocytes derived from genome edited cells likely to have therapeutic implications by reduced sickling.


The genome edited and unedited HSPC at various stages (day 7, 14 and 21) of erythroid differentiation were analyzed by flow cytometry for expression levels of fetal globin and two erythroid cell surface markers, transferrin receptor (CD71) and glycophorin A (CD235a) using antibodies conjugated to fluorescent dyes. The live cells were identified and gated by exclusion of 7AAD. Genome editing did not adversely affect erythroid differentiation as the cultured cells showed similar levels of CD71 and CD235A positivity consistent with late stage erythroblasts. Genome editing of +58 erythroid enhancer region resulted in a larger increase in HbF containing cells (up to 67%) than other gRNAs and the mock electroporated cells (FIG. 24). Very high induction of HbF positive cells by g7 gRNA targeting exon 2 of BCL11A was observed. However, the cell proliferation and colony forming potential of exon 2 targeted cells was dramatically reduced (FIGS. 21 and 22).


Upon deep sequencing of the targeted region, we noticed that GATA1 and TAL1 binding motifs were intact in the genome edited target region (FIG. 25). Recent literature demonstrated the importance of GATA1 binding site in regulation of BCL11A expression and derepression of fetal globin. Viestra et al., Nature Methods. 2015, 12:927. In contrast to the literature reports, which showed the importance of the two motifs for maintenance of BCL11A levels in adult erythroid cells, our findings demonstrate that sequences upstream of the two transcription factor binding sites are also important in regulation of BCL11a gene expression, and genome editing exclusively at these upstream sites leads to upregulation of HbF, even when the GATA1 and TAL1 binding sites remain intact.


Example 3.1
Methods:

Human CD34+ cell culture. Human CD34+ cells were isolated from G-CSF mobilized peripheral blood from adult donors (AllCells) using immunoselection (Miltenyi) according to the manufacturer's instructions and expanded for 3 days using StemSpan SFEM (StemCell Technologies; Cat no. 09650) supplemented with 50 ng/mL each of thrombopoietin (Tpo), Flt3 ligand (Flt-3L, Life Technologies, Cat. #PHC9413), human stem cell factor (SCF, Life Technologies, Cat. #PHC2113) and human interleukin-6 (IL-6, Life Technologies, Cat. #PHC0063), as well as 1× antibiotic/antimycotic (Gibco, Cat. #10378-016) and 500 nM compound 4.


Assembly of Cas9 and guide RNA ribonucleoprotein (RNP) complexes, preparation of HSPC, and electroporation of RNP into HSPC. Cas9-guide RNA ribonucleoprotein complexes (RNPs) were prepared immediately prior to electroporation. For formation of RNP using dual guide RNAs (dgRNAs), 3 μg of each of crRNA (in 2.24 μL) and tracr (in 1.25 μL) are first denatured at 95° C. for 2 min in separate tubes and then cooled to room temperature. For preparation of Cas9 protein, 6 μg of CAS9 protein (in 1 μL) was mixed with 0.5 μL of 5×CCE buffer (20 mM HEPES, 100 mM KCL, 5 mM MgCL2, 5% Glycerol and freshly added 1 mM DTT). Tracr was first mixed with the Cas9 preparation and incubated at 37° C. for 5 min. The crRNA was then added to Tracr/CAS9 complexes and incubated for 5 min at 37° C. For the None/control condition, vehicle rather than crRNA was added to the Tracr/CAS9 complexes. The HSPC were collected by centrifugation and resuspended in P3 Primary Cell Solution (Lonza cat. No. PBP3-00675) at a cell density of 2.5×106/mL. The RNP was mixed with 20 μL of cells by pipetting up and down and incubated at RT for 2 min. The RNP/cell mixture (20 μL) was electroporated using code CM-137 on the 4D-Nucleofector (Lonza). Duplicate 20 μL electroporations were performed. For the experiments in this Example 3.1, the tracr used was SEQ ID NO: 7808, and the crRNA had the following format and sequence, with 2′O-Methyl (m) and Phosphorothioate Bond (*) modifications indicated: mN*mN*mN*rNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrGrUrUrUrUrArGrArGrCrUrArU*mG*m C*mU, where N's are the nucleotides of the indicated targeting domain (e.g., as indicated by the CRxxxxx identifier).


In vitro erythropoiesis and FACS analysis for HbF containing erythroid cells. After electroporation, the cells were immediately transferred into 250 μL pre-warmed erythroid differentiation medium (EDM) consisting of IMDM (Hyclone, Cat. #SH30228.01), 330 μg/mL human holo-transferrin (Invitria Cat#777TRF029), 10 μg/mL recombinant human insulin (Gibco Cat#A1138211), 2 IU/mL heparin (Sigma, part #H3393), 5% human AB serum (Sigma, Cat# H4522), 125 ng/mL human erythropoietin (Peprotech #10779-058), and 1× antibiotic/antimycotic (Gibco, Cat. #10378-016). EDM was further supplemented with 1 μM hydrocortisone (Sigma H8672), 100 ng/mL human SCF (Life Technologies, Cat. #PHC2113), and 5 ng/mL human IL-3 (Peprotech #10779-598). After 2 days, the cell culture was diluted in fresh medium. Cultures were maintained for a total of 7 days, at which time the cells were analyzed by intracellular staining for HbF expression. Briefly, the cells were washed once with PBS, resuspended in LIVE/DEAD® Fixable Violet Dead Cell Stain (ThermoFisher L34963; 1:1000 in PBS) and incubated for 30 min. Cell were then washed and stained with anti-CD71-BV711 (Fisher Scientific Company Llc. BDB563767) and anti-CD235a-APC (BD 551336) antibodies for 30 min. The cells were then washed, followed by fixation with fixation buffer (Biolegend, Cat#420801) and permeabilized with 1× intracellular staining permeabilization wash buffer (Biolegend, Cat#421002) according to the manufacturer's instructions. The cells were then incubated with 0.5 μL of anti-HbF-PE antibody (Life Technologies, part #MHFH04) in 50 μL of 1× intracellular staining perm wash buffer for 20 min at room temperature. The cells were washed twice with 2 mL of 1× intracellular staining Perm wash buffer and resuspend in staining buffer and analyzed on an LSRFortessa flow cytometer (BD Biosciences) for HbF expression. The results were analyzed using Flowjo and data were presented as % of HbF positive cells (F-cells) in the viable CD71 positive erythroid cell population.


Genomic DNA preparation and next generation sequencing (NGS). Genomic DNA was prepared from edited and unedited HSPC at 48 hours post-electroporation using Quick Extract DNA Extraction Solution (Epicentre Cat # QE09050). To determine editing efficiency and patterns of insertions and deletions (indels), PCR products were generated using primers flanking the target sites, which were then subjected to next generation sequencing (NGS). Percent editing of corresponding sequences in unedited samples was typically less than 1% and never exceeded 3%.


Results:

Without being bound by theory, it is believed that targeted genetic disruption of the BCL11A erythroid enhancer region will relieve repression of γ-globin expression, allowing production of the red blood cells containing elevated HbF protein, (cells expressing fetal hemoglobin, e.g., expressing elevated levels of fetal hemoglobin, are sometimes referred to herein as “F-cells.” In embodiments, a cell is considered an F-cell if it produces as least 6 picograms fetal hemoglobin per cell). The elevated HbF prevents sickling of the red blood cells under deoxygenated conditions and will be therapeutic/curative for the patients of both β-thalassemia and SCD. Autologous hematopoietic stem cell transplantation (HSCT) with ex vivo genome edited HSC from SCD patients was also combined with stem cell expansion enhancing technology, e.g., an aryl hydrocarbon receptor (AHR) inhibitor, e.g., as described in WO2010/059401 (the contents of which are incorporated by reference in their entirety), e.g., Compound 4, to improve ex vivo expansion and increase the dose of gene modified HSC delivered.


For efficient genome editing via programmable nuclease, Cas9, the successful delivery of guide RNA (gRNA) and Cas9 protein into target cells and tissues is essential. Recent reports demonstrated that Cas9 ribonucleoprotein (RNP) complexes when delivered into target cells by electroporation can accomplish efficient and specific genome editing in several different cell types. Cas9-RNP complexes cleave chromosomal DNA almost immediately after delivery and are degraded rapidly in cells, reducing off-target effects. In contrast, use of plasmid and viral vector systems used to deliver Cas9 results in prolonged expression of the enzyme aggravating off-target effects associated with the system. Additionally, delivery of RNPs into the target cells requires no additional tools which would greatly facilitate translation of genome editing for therapeutic purposes in the clinic. Purified recombinant Cas9 protein and gRNA complexes (RNPs) were delivered into cultured HSPC and an overview experiments used are shown in FIG. 17.


Recombinant Cas9 protein was purified from Escherichia coli and complexed with synthetic dual gRNAs (dgRNA) that consist of crRNA and tracr to generate ribonucleoprotein (RNP) complexes. The list and of gRNAs used in the study are shown in Table 17 (e.g., gRNAs comprising the targeting domain of the indicated CRxxxxxx identifier). The RNP complexes were electroporated into CD34+ HSPC via electroporation as described under materials and methods. The cells were expanded prior to the delivery of RNP complexes. Actively dividing cells may facilitate uptake of RNP complexes delivered by electroporation.









TABLE 17







List of gRNAs targeting the BCL11A erythroid specific enhancer region


used in the current study. All gRNA molecules were tested in duplicate


in the dgRNA format as described in the materials and methods.












% HbF+ (F
% HbF+ (F




Guide RNA
cells),
cells),
% edited,
% edited,


targeting domain
average of
standard
average of
standard


ID
replicates
deviation
replicates
deviation














CR000308
27.7
0.5
52.8
0.7


CR000309
43.1
1.4
74.8
7.5


CR000310
28.6
0.1
65.1
3.6


CR000311
27.2
0.7
50.5
1.9


CR000312
47.9
1.0
87.8
0.9


CR000313
36.8
1.2
66.6
2.7


CR000314
32.7
0.1
39.8
0.5


CR000316_EH11
34.4
0.8
52.9
1.3


CR000317_EH4
50.7
0.4
82.7
2.5


CR001124
28.6
0.1
2.5
0.1


CR001125_EH12
42.3
0.4
94.0
0.9


CR001126_EH13
44.6
1.7
76.7
6.1


CR001127_EH14
33.3
0.1
26.1
3.3


CR001128_EH15
46.4
1.2
84.6
5.6


CR001129
25.3
0.8
3.6
0.4


CR001130
27.1
0.8
11.8
1.7


CR001131
28.6
0.0
35.6
8.5


None/control
22.4
0.6
n/a
n/a


g8
66.3
0.7
94.2
1.1









The genome edited and unedited HSPC were analyzed by flow cytometry for expression levels of fetal globin and two erythroid cell surface markers, transferrin receptor (CD71) and glycophorin A (CD235a) using antibodies conjugated to fluorescent dyes. The live cells were identified and gated by exclusion of Live Dead Violet. BCL11A erythroid specific enhancer region targeting resulted in increased percentage of erythroid cells containing HbF (up to 50.7%) compared to mock electroporated cells (22.4%) (Table 17). Induction of HbF positive cells by dgRNA including the targeting domain of g8 targeting exon 2 of BCL11A was also observed in parallel. Genomic PCR products of the BCL11A erythroid enhancer region were also subjected to next generation sequencing (NGS) to determine the percentage of edited alleles in the cell population. The dgRNA treatments that resulted in greater than 40% HbF+ cells had a range of 74.8% to 94.0% editing (Table 17). For the same targeting domain, the dgRNA in this Example differed in tracr and crRNA sequence from that in Example 3; however, the editing and HbF induction were similar across dgRNA formats for most targeting domains. Of note, CR000317_EH4 in the dgRNA format in the current study resulted in a high HbF induction to 50.7% HbF+ cells. An increase in HbF-containing erythrocytes derived from genome edited cells is likely to have positive therapeutic implications by reduced sickling.


Example 3.2. Optimization of gRNA Editing and Fetal Hemoglobin Upregulation Using gRNAs Targeting the +58 Region of the BCL11a Enhancer in HSPCs

Based on the % editing results from the comprehensive screen of gRNAs targeting the +58 region of the BCL11a Enhancer, 8 gRNA targeting domains were selected for further study and optimization. To test the effect of modifications to the gRNA molecules on % editing, erythroid differentiation, and fetal hemoglobin expression, different versions of the eight gRNA molecules targeting sites within the +58 region of the BCL11a enhancer region were designed. The following versions of of gRNAs comprising the targeting domain of CR00309, CR00311, CR00312, CR00316, CR01125, CR01126, CR01127, and CR01128 were made:


dgRNA (all Sequences Other than Those of the Targeting Domain as Described in Example 1):

    • 1. Unmodified crRNA and unmodified tracr (“Unmodified” or “Unmod”)
    • 2. Unmodified crRNA and unmodified tracr, but with only the 5′-18nt of the indicated targeting domain (not the full 20 nt) (“18nt”)
    • 3. Three 3′ nt and three 5′ nt of crRNA modified with phosphorothioate linkages, and unmodified tracr (“PS”)
    • 4. Additional inverted abasic residue at both 5′- and 3′-end of crRNA, and unmodified tracr (“Invd”)
    • 5. Three 3′ nt and three 5′ nt of crRNA modified with phosphorothioate linkages and with 2′-Omethyl groups, and unmodified tracr (“OMePS”)
    • 6. Three 3′ nt and three 5′ nt of crRNA modified with 2′-fluoro group, and unmodified tmcr (“F”)
    • 7. Three 3′ nt and three 5′ nt of crRNA modified with phosphorothioate linkages and with 2′-fluoro group, and unmodified tracr (“F—PS”)


      sgRNA (all Sequences Other than Targeting Domain are as Described in Example 1):
    • 1. Unmodified sgRNA (“Unmodified” or “Unmod”)
    • 2. Targeting domain consisting of only the 5′-18nt of the indicated targeting domain (not the full 20 nt) (“18nt”)
    • 3. Three 3′ nt and three 5′ nt of sgRNA modified with phosphorothioate linkages (“PS”)
    • 4. Additional inverted abasic residue at both 5′- and 3′-end of sgRNA (“Invd”)
    • 5. Three 3′ nt and three 5′ nt of sgRNA modified with phosphorothioate linkages and with 2′-Omethyl groups (“OMePS”)
    • 6. Three 3′ nt and three 5′ nt of sgRNA modified with 2′-fluoro group (“F”)
    • 7. Three 3′ nt and three 5′ nt of sgRNA modified with phosphorothioate linkages and with 2′-fluoro group (“F—PS”)


All other reagents and methods were as described in Example 3. All results were run in duplicate, and the results are reported in FIGS. 28-32. FIG. 28A and FIG. 28B show the % editing, as measured by NGS, in CD34+ cells 2 days after electroporation of RNP comprising the indicated dual guide RNAs (dgRNAs). FIG. 29 shows the % editing, as measured by NGS, in CD34+ cells 2 days after electroporation of RNP comprising the indicated single guide RNAs (sgRNAs). FIG. 30 shows the % HbF positive cells as measured by flow cytometry at day 14 following transfer of edited CD34+ cells to erythroid differentiation medium, after electroporation of RNP comprising the indicated dual guide RNAs (dgRNAs). FIG. 31 shows the % HbF positive cells as measured by flow cytometry at day 14 following transfer of edited CD34+ cells to erythroid differentiation medium, after electroporation of RNP comprising the indicated single guide RNAs (sgRNAs). FIG. 32 shows the fold-expansion of edited cells after 14 days in the erythroid differentiation medium. These results indicate that many of the selected gRNA molecules, in both dgRNA and sgRNA formats, are capable of achieving genome editing at the target site with greater than 90% efficiency, and in some cases, with greater than 98% efficiency, when delivered to CD34+ cells as RNP via electroporation. As well, many of the selected gRNAs were able to achieve a greater than 20% increase in % F cells relative to unmodified cells (“mock”). Finally, although genome editing of BCL11A erythroid enhancer in HSPC lowered the expansion capabilities of erythroid cells, with the effect more pronounced with some gRNAs (e.g., CR00309) than other gRNAs (e.g., CR00312), most edited cell populations differentiated into erythrocytes were non-the-less capable of achieving between 500-1500 population doublings in 14 days in erythroid differentiation medium ex vivo, indicating that the edited cells may be therapeutically useful in treating hemoglobinopathies such as sickle cell disease or beta thalassemia in patients.


Example 4. HPFH Region Editing in Hematopoietic Stem and Progenitor Cells (HSPCs) Using CRISPR-Cas9 for Derepression of Fetal Globin Expression in Adult Erythroid Cells
Methods:

Human CD34+ cell culture. Human CD34+ cells were isolated from G-CSF mobilized peripheral blood from adult donors (AllCells) using immunoselection (Miltenyi) according to the manufacturer's instructions and expanded for 4 to 6 days using StemSpan SFEM (StemCell Technologies; Cat no. 09650) supplemented with 50 ng/mL each of thrombopoietin (Tpo), Flt3 ligand (Flt-3L, Life Technologies, Cat. #PHC9413), human stem cell factor (SCF, Life Technologies, Cat. #PHC2113) and human interleukin-6 (IL-6, Life Technologies, Cat. #PHC0063), as well as 1× antibiotic/antimycotic (Gibco, Cat. #10378-016) and 500 nM compound 4. Throughout this example (including its subexamples), where the protocol indicates that cells were “expanded,” this medium was used. This medium is also referred to as “stem cell expansion medium,” or “expansion medium” throughout this example (including its subexamples).


Assembly of Cas9 and guide RNA ribonucleoprotein (RNP) complexes, preparation of HSPC, and electroporation of RNP into HSPC. Cas9-guide RNA ribonucleoprotein complexes (RNPs) were prepared immediately prior to electroporation. For formation of RNP using dual guide RNAs (dgRNAs), 3 μg of each of crRNA (in 2.24 μL) and tracr (in 1.25 μL) are first denatured at 95° C. for 2 min in separate tubes and then cooled to room temperature. For preparation of Cas9 protein, 6 μg of CAS9 protein (in 0.8 to 1 μL) was mixed with 0.5 μL of 5×CCE buffer (20 mM HEPES, 100 mM KCL, 5 mM MgCL2, 5% Glycerol and freshly added 1 mM DTT). Tracr was first mixed with the Cas9 preparation and incubated at 37° C. for 5 min. The crRNA was then added to Tracr/CAS9 complexes and incubated for 5 min at 37° C. For the None/control condition, vehicle rather than crRNA was added to the Tracr/CAS9 complexes. The HSPC were collected by centrifugation and resuspended in T buffer that comes with Neon electroporation kit (Invitrogen; Cat#: MPK1096) at a cell density of 5×106/mL. The RNP was mixed with 20 μL of cells by pipetting up and down and incubated at RT for 2 min. The RNP/cell mixture (10 μL) was transferred into Neon electroporation probe. The electroporation was performed with Neon transfection system (Invitrogen; MPK5000S) using 1700 volts/20 milliseconds and 1 pulse. Duplicate 10 μL electroporations were performed.


In vitro erythropoiesis and FACS analysis for HbF containing erythroid cells. After electroporation, the cells were immediately transferred into 250 μL pre-warmed erythroid differentiation medium (EDM) consisting of IMDM (Hyclone, Cat. #SH30228.01), 330 μg/mL human holo-transferrin (Invitria Cat#777TRF029), 10 μg/mL recombinant human insulin (Gibco Cat#A1138211), 2 IU/mL heparin (Sigma, part #H3393), 5% human AB serum (Sigma, Cat# H4522), 125 ng/mL human erythropoietin (Peprotech #10779-058), and 1× antibiotic/antimycotic (Gibco, Cat. #10378-016). EDM was further supplemented with 1 μM hydrocortisone (Sigma H8672), 100 ng/mL human SCF (Life Technologies, Cat. #PHC2113), and 5 ng/mL human IL-3 (Peprotech #10779-598). After 2 days, the cell culture was diluted in fresh medium. Cultures were maintained for a total of 7 days, at which time the cells were analyzed by intracellular staining for HbF expression. Briefly, the cells were washed once with PBS, resuspended in LIVE/DEAD® Fixable Violet Dead Cell Stain (ThermoFisher L34963; 1:1000 in PBS) and incubated for 30 min. Cell were then washed and stained with anti-CD71-BV711 (Fisher Scientific Company Llc. BDB563767) and anti-CD235a-APC (BD 551336) antibodies for 30 min. The cells were then washed, followed by fixation with fixation buffer (Biolegend, Cat#420801) and permeabilized with 1× intracellular staining permeabilization wash buffer (Biolegend, Cat#421002) according to the manufacturers instructions. The cells were then incubated with 0.5 μL of anti-HbF-PE antibody (Life Technologies, part #MHFH04) in 50 μL of 1× intracellular staining perm wash buffer for 20 min at room temperature. The cells were washed twice with 2 mL of 1× intracellular staining Perm wash buffer and resuspend in staining buffer and analyzed on an LSRFortessa flow cytometer (BD Biosciences) for HbF expression. The results were analyzed using Flowjo and data were presented as % of HbF positive cells (F-cells) in the viable CD71 positive erythroid cell population.


Gene expression analysis. After 7 days of in vitro erythropoiesis as described, approximately 1×105 cells were used to purify RNA using the Zymo Research ZR-96 quick RNA Kit (Zymo Cat# R1053). Up to 1 μg RNA was used for 1st strand synthesis using Quantiscript Reverse Transcription Kit (Qiagen, Cat#205313). Taq-man quantitative real-time PCR was performed using the 2× Taq-Man Fast Advance PR Mix (Life technologies, Cat#4444963) and Taq-Man Gene Expression Assays for GAPDH (Life technologies, ID# Hs02758991_g1, VIC), HBB (Life technologies, ID# Hs00747223_g1, VIC) and HBG2/HBG1 (Life technologies, ID# Hs00361131_g1, FAM), according to the suppliers protocol. The relative expression of each gene was normalized to GAPDH expression and reported as fold of None/control RNP-delivered samples by the ΔΔCt method. Alternatively, after conversion to a GAPDH normalized relative quantity of transcript (2̂-ΔCt), the HBG2/HBG1 expression level was calculated as a percentage of the sum of HBB and HBG2/HBG1 expression.


Genomic DNA preparation and next generation sequencing (NGS). Genomic DNA was prepared from edited and unedited HSPC at 48 hours post-electroporation using Quick Extract DNA Extraction Solution (Epicentre Cat # QE09050). To determine editing efficiency and patterns of insertions and deletions (indels), PCR products were generated using primers flanking the target sites, which were then subjected to next generation sequencing (NGS) as described in the literature. Percent editing of corresponding sequences in unedited samples (electroporated with RNPs consisting of Cas9 and Tracr only) was typically less than 1% and never exceeded 3%.


Results:

Without being bound by theory, it is believed that targeted genetic disruption of the HPFH region will relieve repression of γ-globin expression, allowing production of the red blood cells containing elevated HbF protein, (cells expressing fetal hemoglobin are sometimes referred to herein as “F-cells”). The elevated HbF prevents sickling of the red blood cells under deoxygenated conditions and will be therapeutic/curative for the patients of both β-thalassemia and SCD. Autologous hematopoietic stem cell transplantation (HSCT) with ex vivo genome edited HSC from SCD patients was also combined with stem cell expansion enhancing technology, e.g., an aryl hydrocarbon receptor (AHR) inhibitor, e.g., as described in WO2010/059401 (the contents of which are incorporated by reference in their entirety), e.g., Compound 4 to improve ex vivo expansion and increase the dose of gene modified HSC delivered.


For efficient genome editing via programmable nuclease, Cas9, the successful delivery of guide RNA (gRNA) and Cas9 protein into target cells and tissues is essential. Recent reports demonstrated that Cas9 ribonucleoprotein (RNP) complexes when delivered into target cells by electroporation can accomplish efficient and specific genome editing in several different cell types. Cas9-RNP complexes cleave chromosomal DNA almost immediately after delivery and are degraded rapidly in cells, reducing off-target effects. In contrast, use of plasmid and viral vector systems used to deliver Cas9 results in prolonged expression of the enzyme aggravating off-target effects associated with the system. Additionally, delivery of RNPs into the target cells requires no additional tools which would greatly facilitate translation of genome editing for therapeutic purposes in the clinic. Purified recombinant Cas9 protein and gRNA complexes (RNPs) were delivered into cultured HSPC and an overview experiments used are shown in FIG. 17.


Recombinant Cas9 protein was purified from Escherichia coli and complexed with synthetic dual gRNAs (dgRNA) that consist of crRNA and tracr to generate ribonucleoprotein (RNP) complexes. The list and sequences of gRNAs used in the study are shown in Table 16. The RNP complexes were electroporated into CD34+ HSPC via electroporation as described under materials and methods. The cells were expanded prior to the delivery of RNP complexes. Actively dividing cells may facilitate uptake of RNP complexes delivered by electroporation.









TABLE 16







List of gRNAs targeting the HPFH region used in the current study. All gRNA


molecules were tested in duplicate in the dgRNA format described above,


except for g8 (crRNA consisting of mN*mN*mN*rNrNrNrNrNrNrNrNrNrNr-


NrNrNrNrNrNrNrGrUrUrUrUrArGrArGrCrUrArU*mG*m C*mU, where N's are


the residues of the targeting domain, and modifications are indicated


as follows: 2′O-Methyl (m) and Phosphorothioate Bond (*); with the


tracr sequence SEQ ID NO: 7808) and None/control. The g8 and None/


control were tested in 16 replicates each.














% HbF+ (F
% HbF+ (F






Guide RNA
cells),
cells),
% CD71+,
% CD71+,
% edited,
% edited,


targeting
average of
standard
average of
standard
average of
standard


domain ID
replicates
deviation
replicates
deviation
replicates
deviation
















CR001030
51.4
5.2
84.4
0.6
84.5
1.6


CR001095
49.3
1.8
82.7
2.5
66.1
1.4


CR001043
44.8
2.0
84.1
0.8
80.0
0.7


CR001029
43.7
1.3
82.2
0.7
86.6
2.7


CR001142
43.4
0.6
83.9
0.1
76.9
0.4


CR001028
42.9
1.3
84.8
0.5
91.7
0.5


CR001212
42.6
5.8
83.1
0.9
81.6
1.5


CR001036
42.4
1.3
82.6
0.6
91.5
5.0


CR001135
42.4
0.7
83.7
0.1
84.4
13.3


CR001221
41.8
1.7
80.8
0.4
83.9
1.4


CR001158
41.7
1.3
81.7
0.2
72.4
2.7


CR001090
41.3
0.1
85.5
0.8
87.2
1.2


CR001169
41.3
1.5
82.4
2.6
80.2
2.5


CR001089
40.9
0.6
82.8
6.6
81.7
0.3


CR001031
40.8
0.1
81.5
1.8
90.7
1.8


CR001092
40.8
2.2
84.1
0.1
43.0
1.1


CR001034
40.7
1.0
84.5
0.0
72.7
3.8


CR001068
40.7
2.3
85.7
0.4
90.5
0.9


CR001168
40.2
3.4
82.6
0.1
74.2
7.1


CR001171
40.1
1.6
83.4
0.4
63.8
1.6


CR001217
40.1
0.8
81.9
0.1
80.9
0.8


CR001023
39.6
3.2
82.2
0.8
90.2
0.7


CR001093
39.3
0.3
86
1.1
38.3
14.5


CR001080
39.2
3.4
87.1
1.1
32.4
1.1


CR001164
38.6
2.0
84.4
0.4
92.0
0.7


CR001178
38.6
1.2
82.6
2.4
61.1
0.6


CR001032
38.4
9.2
82.4
0.6
57.6
32.9


CR001100
38.4
1.8
81.7
0.2
29.6
2.4


CR001156
38.4
1.2
81.6
0.3
91.2
3.6


CR001159
38.4
1.8
81.8
0.2
65.5
0.7


CR001042
38.2
0.4
83.1
1.0
90.8
0.3


CR001065
38.2
0.0
85.2
2.0
86.5
0.2


CR001133
38.1
0.0
83.6
0.5
92.1
0.8


CR001173
38
1.5
81.7
1.1
72.5
5.0


CR001161
37.7
4.6
82.3
1.7
54.8
10.7


CR001138
37.6
7.6
83.7
0.7
69.4
28.9


CR001037
37.4
1.3
81.2
0.8
90.5
1.5


CR001098
37.4
1.2
85.6
1.5
95.0
0.2


CR001150
37.3
2.0
84.8
0.4
52.8
7.5


CR001160
37.3
0.5
81.4
1.5
65.9
1.6


CR001197
37.3
1.1
83.3
1.6
83.8
2.8


CR001170
37.2
1.3
83.7
1.2
47.3
0.3


CR001226
37
1.0
82.5
1.3
65.3
2.0


CR001018
36.9
0.8
80.9
0.8
97.2
0.0


CR001109
36.8
0.3
84.7
1.4
91.0
2.4


CR001219
36.8
0.6
82.5
0.1
75.9
0.2


CR001047
36.7
0.6
83.2
0.3
70.8
1.5


CR001101
36.6
3.3
81.7
0.1
50.6
3.8


CR001046
36.5
1.0
84
0.3
76.9
4.2


CR001021
36.4
0.3
82.2
0.4
79.5
2.9


CR001060
36.3
3.2
84.1
1.1
50.0
0.4


CR001074
36.3
1.6
87.3
1.8
56.5
4.9


CR001097
36.3
0.2
87.1
1.3
58.5
2.1


CR001099
36.1
4.0
85.8
1.8
89.8
0.3


CR001172
36.1
1.7
82.2
0.7
71.1
3.7


CR001195
36.1
0.8
83.4
0.2
67.2
2.7


CR001075
36
1.9
87.2
0.1
56.8
2.6


CR001143
35.9
3.7
83.5
0.4
56.7
9.2


CR001063
35.8
1.3
84.3
0.4
71.7
1.9


CR001225
35.5
0.4
83.1
0.5
81.1
4.2


CR001027
35.4
0.9
81.9
0.8
71.1
0.5


CR001073
35.4
1.6
86.5
1.6
56.3
5.9


CR001180
35.3
1.1
79.6
1.4
86.2
4.0


CR001182
35.3
0.8
81.8
0.2
72.5
3.9


CR001162
35.2
9.1
85
0.0
62.6
35.7


CR001026
35.1
1.0
82.4
0.2
97.0
0.3


CR001078
35
1.1
85
1.7
12.7
1.8


CR001025
34.9
0.3
81.9
1.5
55.5
3.8


CR001187
34.9
2.5
79.4
2.3
70.1
3.7


CR001081
34.8
1.4
87.5
4.0
27.0
0.7


CR001137
34.8
13.6
83.8
1.6
41.5
39.8


CR001174
34.8
0.5
81.8
0.6
34.1
3.2


CR001058
34.6
1.0
83.3
1.5
71.4
6.2


CR001188
34.6
1.3
82.6
1.2
64.0
2.2


CR001079
34.4
2.5
89.2
0.2
12.8
2.0


CR001179
34.4
3.2
82
0.4
81.4
4.3


CR001214
34
2.2
82.1
1.5
58.1
1.0


CR001139
33.9
1.9
83
2.5
70.3
0.4


CR001222
33.9
1.6
80.6
0.8
35.5
1.4


CR001096
33.8
0.1
85.6
2.2
77.5
1.0


CR001148
33.6
2.1
84.5
0.4
50.9
4.0


CR001140
33.5
0.4
84
1.4
66.3
1.5


CR001191
33.5
2.5
83.2
0.3
83.4
5.1


CR001227
33.5
2.3
79
0.2
56.3
0.1


CR001110
33.4
0.4
85.2
0.1
70.3
0.1


CR001220
33.4
1.7
81.4
0.4
72.4
3.3


CR001224
33.4
3.1
82.2
1.3
71.3
2.3


CR001033
33.2
0.3
81.9
0.6
63.6
8.1


CR001051
33.2
0.6
82.2
0.6
42.2
0.5


CR001106
33.2
0.2
82.6
3.0
46.9
2.0


CR001020
32.9
8.9
81.9
1.3
67.7
29.4


CR001022
32.9
0.8
82.4
1.6
91.5
0.3


CR001045
32.9
0.4
80.5
0.0
88.5
0.4


CR001198
32.9
0.5
81.3
1.8
96.8
0.5


CR001084
32.8
1.7
87.5
0.1
55.1
5.4


CR001111
32.6
1.0
84.2
2.5
78.1
1.4


CR001087
32.5
0.1
87.6
0.7
89.6
2.6


CR001107
32.5
0.4
83.3
1.8
46.5
2.2


CR001108
31.8
1.8
84.7
0.6
75.2
3.3


CR001205
31.7
2.3
81.3
6.2
2.7
1.7


CR001085
31.6
2.1
86
0.3
31.2
1.2


CR001166
31.5
0.5
83.6
0.8
86.9
0.3


CR001019
31.3
2.3
80.6
0.9
35.1
4.0


CR001076
31.3
0.5
86.6
0.2
96.3
0.3


CR001016
31.2
1.2
80.2
0.7
95.0
1.9


CR001035
31.1
1.8
83.5
1.3
80.0
0.9


CR001192
31
2.5
79.9
0.7
60.4
5.1


CR001091
30.7
2.8
85.3
0.6
72.4
7.6


CR001105
30.7
0.1
84.8
0.1
12.1
1.1


CR001185
30.7
0.7
82.7
0.4
36.7
0.2


CR001190
30.7
0.1
82.4
0.7
53.2
0.8


CR001024
30.6
0.4
81.8
0.7
97.0
0.6


CR001132
30.5
2.3
84.6
0.1
26.4
2.2


CR001189
30.4
1.9
83.1
0.3
42.0
0.6


CR001040
30.1
8.3
77.5
2.2
73.6
33.6


CR001146
30.1
1.5
83.8
0.1
88.1
2.1


CR001070
29.8
0.9
82.7
0.4
44.9
0.8


CR001213
29.8
1.8
81.9
0.2
48.4
4.4


CR001017
29.6
11.8
81.3
1.5
44.3
36.8


CR001077
29.5
0.9
87.2
2.5
14.3
0.5


CR001083
29.4
1.1
84.3
9.1
26.6
10.6


CR001082
29
0.7
87.6
1.5
17.7
0.0


CR001175
29
1.1
81.7
0.1
6.3
0.7


CR001144
28.9
0.4
82.6
0.9
38.8
1.1


CR001194
28.8
4.3
81.8
0.6
70.2
1.9


CR001157
28.5
1.1
81
1.3
29.2
4.2


CR001163
28.4
0.6
83.5
0.7
13.4
3.0


CR001151
28.2
0.6
84.6
1.6
51.8
2.3


CR001181
28.2
0.2
80.3
0.8
46.0
0.5


CR001061
28
2.9
82.6
0.4
53.6
5.8


CR001152
27.8
0.8
84.9
0.2
37.0
1.9


CR001094
27.7
9.2
74.6
12.7
85.2
2.1


CR001202
27.7
6.3
84
2.3
61.7
8.4


CR001149
27.6
1.7
84.1
0.6
10.8
1.3


CR001207
27.6
5.7
83.3
0.1
31.5
17.5


CR001134
27.2
1.6
83.2
1.3
2.3
0.2


CR001206
27.2
1.8
84.4
0.2
11.1
0.4


CR001067
27
18.4
84.2
2.6
6.0
0.8


CR001167
27
0.5
81.7
0.2
32.3
0.1


CR001209
27
0.8
81.5
2.5
14.8
0.2


CR001165
26.9
0.5
81.6
1.3
12.9
2.1


CR001044
26.8
7.2
78.2
4.3
28.5
20.7


CR001052
26.6
0.3
82.5
1.5
26.5
0.9


CR001062
26.6
0.7
78.7
2.8
39.1
5.3


CR001071
26.6
1.0
84.2
0.4
15.1
1.1


CR001210
26.6
2.1
80.1
3.3
58.6
2.2


CR001223
26.6
0.9
80.2
0.8
40.3
1.9


CR001057
26.5
6.5
82.4
0.1
25.0
18.9


CR001147
26.5
1.3
83.5
0.4
33.1
2.7


CR001186
26.4
2.1
79.6
3.8
40.5
2.1


CR001103
26.1
0.2
84.3
0.0
51.2
3.6


CR001199
25.9
0.8
80.9
1.5
89.3
1.4


CR001216
25.7
1.0
77.7
0.0
43.2
2.7


CR001041
25.6
1.8
78.9
4.8
22.4
2.1


CR001053
25.5
1.4
82.4
1.9
38.4
0.3


CR001086
25.4
0.6
84.4
0.9
30.4
0.6


CR001050
25.1
0.4
80.6
1.1
4.9
0.2


CR001136
25.1
0.7
82.3
1.0
9.1
1.1


CR001203
25.1
4.0
83.4
1.8
22.0
13.1


CR001211
24.8
1.1
83.3
0.4
5.0
1.0


CR001066
24.4
0.4
86.1
0.1
15.2
1.8


CR001145
24.4
1.0
83.5
0.9
16.4
8.9


CR001049
24.3
0.3
83.9
1.9
3.7
0.0


CR001176
24.3
0.6
81.9
0.6
29.0
1.4


CR001218
24.1
0.2
81.9
0.1
21.6
2.4


CR001141
23.8
0.5
82.8
0.4
4.1
0.8


CR001196
23.6
0.8
82.5
0.6
18.2
2.9


CR001184
23.5
0.4
81.1
0.4
43.5
1.6


CR001204
23.3
1.1
81.5
0.7
0.5
0.2


CR001069
23.1
1.1
85
0.0
16.2
0.3


CR001072
23
0.3
84.2
0.7
15.6
0.3


CR001102
22.8
1.7
84.7
1.6
58.1
4.8


CR001153
22.8
1.3
82.8
0.1
17.2
2.6


CR001177
22.8
0.5
82.2
0.9
2.0
0.2


CR001104
22.7
1.7
84.8
1.1
29.4
5.0


CR001064
22.6
1.1
82.1
1.0
35.8
5.2


CR001200
22.6
0.1
82
0.0
9.8
0.7


CR001154
22.4
0.0
82.2
1.3
8.0
1.1


CR001055
22.3
1.0
83.4
1.1
19.0
0.8


CR001054
22
1.1
83.5
1.0
11.3
1.4


CR001039
21.9
0.2
80.8
0.2
16.6
1.5


CR001183
21.6
0.7
81.4
0.8
13.3
0.1


CR001155
21.4
0.0
81.6
0.8
5.0
1.0


CR001059
21.1
0.6
82.5
1.2
4.6
0.3


CR001056
20.8
0.9
83.2
0.2
3.7
0.9


CR001193
20.5
0.9
80.4
0.9
4.8
0.2


CR001208
20.5
0.1
81.1
0.9
12.6
3.0


CR001201
20.1
1.7
81.7
0.6
10.7
0.7


CR001048
19.3
3.0
82.3
1.1
0.4
0.3


CR001215
19.2
0.2
81.2
2.3
5.6
2.2


CR001038
19.1
0.1
80.8
1.3
6.5
1.1


CR001088
18.8
5.9
67.3
2.7
74.6
2.3


None/control
21.0
2.0
82.9
1.9
n/a
n/a


g8
59.2
3.0
74.3
4.4
95.1
1.8









The genome edited and unedited HSPC were analyzed by flow cytometry for expression levels of fetal globin and two erythroid cell surface markers, transferrin receptor (CD71) and glycophorin A (CD235a) using antibodies conjugated to fluorescent dyes. The live cells were identified and gated by exclusion of Live Dead Violet. Genome editing did not adversely affect erythroid differentiation as the cultured cells showed percentages of CD71+ cells consistent with erythroblasts similar to uneditied cells. HPFH region targeting resulted in increased percentage of erythroid cells containing HbF (up to 51.4%) compared to mock electroporated cells (21.0%) (Table 16). Induction of HbF positive cells by dgRNA including the targeting domain of g8 targeting exon 2 of BCL11A was also observed in parallel. Genomic PCR products of the HPFH region were also subjected to next generation sequencing (NGS) to determine the percentage of edited alleles in the cell population. High genome editing percentages at the HFPH locus was observed in many of the cell cultures electroporated with RNPs containing Cas9, crRNA of the given targeting domain and Tracr (Table 16), but not in control cells with no targeting domain delivered (RNPs containing only Cas9 and Tracr). In particular, the dgRNA treatments that resulted in greater than 40% HbF+ cells had a range of 43.0% to 91.7% edited alleles (Table 16).









TABLE 18







Gene expression analysis of select cultures edited with gRNAs targeting


the HPFH region in the current study. All gRNA molecules were tested in


duplicate in the dgRNA format. Fetal gamma-globin (γ-globin, HBG2/


HBG1 genes), adult beta-globin (β-globin, HBB gene) and


Glyceraldehyde- 3-Phosphate Dehydrogenase (GAPDH gene)


expression were determined and reported as described


in Materials and Methods.













γ-globin
β-globin





expression,
expression,
% globin




fold over
fold over
expression,


Guide RNA
Number of
control
control
γ/(γ + β)


targeting
electroporation
(average of
(average of
(average of


domain ID
replicates
replicates)
replicates)
replicates)














CR001030
2
3.8
0.91
26.6


CR001142
2
1.6
0.76
20.0


CR001212
2
2.2
0.58
18.6


CR001036
2
2.6
0.91
19.7


CR001221
2
2.3
0.79
15.2


CR001217
2
1.9
0.72
13.8


None/control
5
1
1
7.7









Some cultures in this study were also analyzed for hemoglobin gene expression. Of these targeting domains, fetal gamma-globin gene expression was induced 1.6 to 3.8-fold over None/control, which was accompanied by a modest reduction in adult beta-globin expression (0.58 to 0.91-fold of None/control) (Table 18). These effects together resulted in gamma-globin expression levels ranging from 13.8% to 26.6% of the total beta-type globins (γ/[γ+β]) in the cell population (Table 17), with relative fetal globin induction across targeting domains similar to that observed for HbF protein induction (Table 16). Either an increase in HbF/gamma-globin or an increase in HbF/gamma-globin together with a decrease in beta-globin (sickled globin) levels in erythrocytes derived from genome edited cells is likely to have therapeutic implications by reduced sickling.


Example 4.2

Methods: Methods are as in Example 4, with the Following Exceptions.


Assembly of Cas9 and guide RNA ribonucleoprotein (RNP) complexes, preparation of HSPC, and electroporation of RNP into HSPC. The HSPC collected by centrifugation were resuspended in P3 Primary Cell Solution (Lonza cat. No. PBP3-00675) at a cell density of 2.5×106/mL. The RNP was mixed with 20 μL of cells by pipetting up and down and incubated at RT for 2 min. The RNP/cell mixture (20 μL) was electroporated using code CM-137 on the 4D-Nucleofector (Lonza).


Results:

Without being bound by theory, it is believed that targeted genetic disruption of the HPFH region will relieve repression of γ-globin expression, allowing production of the red blood cells containing elevated HbF protein, (cells expressing fetal hemoglobin are sometimes referred to herein as “F-cells”). The elevated HbF prevents sickling of the red blood cells under deoxygenated conditions and will be therapeutic/curative for the patients of both β-thalassemia and SCD. Autologous hematopoietic stem cell transplantation (HSCT) with ex vivo genome edited HSC from SCD patients was also combined with stem cell expansion enhancing technology, e.g., an aryl hydrocarbon receptor (AHR) inhibitor, e.g., as described in WO2010/059401 (the contents of which are incorporated by reference in their entirety), e.g., Compound 4 to improve ex vivo expansion and increase the dose of gene modified HSC delivered.


For efficient genome editing via programmable nuclease, Cas9, the successful delivery of guide RNA (gRNA) and Cas9 protein into target cells and tissues is essential. Recent reports demonstrated that Cas9 ribonucleoprotein (RNP) complexes when delivered into target cells by electroporation can accomplish efficient and specific genome editing in several different cell types. Cas9-RNP complexes cleave chromosomal DNA almost immediately after delivery and are degraded rapidly in cells, reducing off-target effects. In contrast, use of plasmid and viral vector systems used to deliver Cas9 results in prolonged expression of the enzyme aggravating off-target effects associated with the system. Additionally, delivery of RNPs into the target cells requires no additional tools which would greatly facilitate translation of genome editing for therapeutic purposes in the clinic. Purified recombinant Cas9 protein and gRNA complexes (RNPs) were delivered into cultured HSPC and an overview experiments used are shown in FIG. 17.


Recombinant Cas9 protein was purified from Escherichia coli and complexed with synthetic dual gRNAs (dgRNA) that consist of crRNA and tracr to generate ribonucleoprotein (RNP) complexes. The list of gRNAs used in the study are shown in Table 19. The RNP complexes were electroporated into CD34+ HSPC via electroporation as described under materials and methods. The cells were expanded prior to the delivery of RNP complexes. Actively dividing cells may facilitate uptake of RNP complexes delivered by electroporation.









TABLE 19







List of gRNAs targeting the HPFH region used in the current study. All


gRNA molecules were tested in the dgRNA format (except for g8 which


was tested in the dgRNA format using: crRNA consisting of


mN*mN*mN*rNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrGrUrUrUr


UrArGrArGrCrUrArU*mG*mC*mU, where N's are the residues


of the targeting domain, and modifications are indicated as


follows: 2′O-Methyl (m) and Phosphorothioate Bond (*); with the


tracr sequence SEQ ID NO: 7808).











Guide RNA





targeting
% HbF+ (F



domain ID
cells)
% CD71+















CR003037
46.6
80.3



CR003033
45.4
75.9



CR003038
42.9
77.6



CR003035
42.1
77.8



CR003087
42.1
76.7



CR003085
41.8
77.6



CR003052
39.9
80.5



CR003080
38.0
80.1



CR003081
35.3
80.6



CR003031
34.8
77.7



CR003056
34.3
78.3



CR003070
33.9
81.2



CR003089
33.8
77.8



CR003065
33.0
76.4



CR003075
33.0
75.2



CR003088
33.0
77.3



CR003041
32.1
76.2



CR003039
31.9
75.7



CR003044
30.6
77.7



CR003084
29.7
77.2



CR003073
29.5
76.9



CR003066
29.3
77.9



CR003082
29.3
78.6



CR003067
29.2
78.1



CR003074
29.1
77.5



CR003095
28.8
80.4



CR003083
28.3
76.6



CR003030
27.9
78.4



CR003069
27.7
78.9



CR003055
27.6
78.9



CR003058
27.6
78.8



CR003054
27.5
79.0



CR003029
27.1
78.4



CR003086
27.1
76.6



CR003063
27.0
76.0



CR003071
26.5
79.5



CR003079
26.5
78.0



CR003042
26.4
77.0



CR003045
26.3
78.0



CR003034
25.9
76.8



CR003027
25.7
79.2



CR003043
25.0
76.0



CR003032
24.9
77.9



CR003040
24.9
75.7



CR003028
24.8
78.6



CR003048
24.8
80.4



CR003057
24.7
79.0



CR003096
24.6
78.9



CR003077
24.4
77.7



CR003036
24.3
76.8



CR003049
24.3
78.4



CR003047
24.0
78.2



CR003059
23.9
80.2



CR003051
23.7
77.2



CR003053
23.7
76.9



CR003091
23.7
80.2



CR003093
23.7
79.2



CR003060
23.6
78.9



CR003072
23.6
77.7



CR003076
23.6
78.0



CR003078
23.6
78.0



CR003064
23.4
75.9



CR003046
23.3
80.5



CR003092
22.9
81.7



CR003090
22.7
79.7



CR003050
22.6
77.2



CR003062
22.1
76.5



CR003061
21.5
76.3



CR003068
21.5
78.8



CR003094
21.0
79.6



None/control
18.9
77.0



replicate 1



None/control
21.1
79.7



replicate 2



g8 replicate 1
56.8
65.4



g8 replicate 2
56.4
65.8










The genome edited and unedited HSPC were analyzed by flow cytometry for expression levels of fetal globin and two erythroid cell surface markers, transferrin receptor (CD71) and glycophorin A (CD235a) using antibodies conjugated to fluorescent dyes. The live cells were identified and gated by exclusion of Live Dead Violet. Genome editing did not adversely affect erythroid differentiation as the cultured cells showed percentages of CD71+ cells consistent with erythroblasts similar to uneditied cells. HPFH region targeting resulted in increased percentage of erythroid cells containing HbF (up to 46.6%) compared to mock electroporated cells (18.9 and 21.1%) (Table 19). Induction of HbF positive cells by dgRNA including the targeting domain of g8 targeting exon 2 of BCL11A was also observed in parallel.


Finally, the indel pattern created at or near the target site for dgRNAs comprising the targeting domains of CR003031, CR003033, CR003035, CR003037, CR003038, CR003052, CR003085 were assessed by NGS. The top 5 most frequent indels at each location are shown in Table 27.









TABLE 27







5 most frequent indels at each taget sequence after exposure to RNP


comprising the indicated gRNA molecule. Each gRNA was tested in dgRNA.


Capital letters are the naturally occurring nucleotides at and near the target


sequence. Deletions relative to the unmodified target sequence are shown


as “—”; insertions are shown as lowercase letters.










dgRNA





targeting

% of all
Indel


domain
Variant Read (Genomic Sequence)
reads
Length













CR003031
ACTGTTGATTAGAGGTAGGGAAATGATTTTAATCTGTGACCTTGG-------
9.74%
−7



GCAAGTAGCTATCTAATGACTAAAATGG





CR003031
ACTGTTGATTAGAGGTAGGGAAATGATTTTAATCTGTGACCTTGGTtGAATGGGC
7.82%
1



AAGTAGCTATCTAATGACTAAAATGG





CR003031
ACTGTTGATTAGAGGTAGGGAAATGATTTTAATCTGTGACCTTG---
2.19%
−3



AATGGGCAAGTAGCTATCTAATGACTAAAATGG





CR003031
ACTGTTGATTAGAGGTAGGGAAATGATTTTAATCTGTGACCTTG-
1.37%
−1



TGAATGGGCAAGTAGCTATCTAATGACTAAAATGG





CR003031
ACTGTTGATTAGAGGTAGGGAAATGATTTTAATCTGTGA---------
1.33%
−9



ATGGGCAAGTAGCTATCTAATGACTAAAATGG





CR003031

. . .
. . .





CR003033
ATGGGCAAGTAGCTATCTAATGACTAAAATGGAA----------
25.21%
−10



GAGAAACAGTTTTAGTATAACAAGTGAAATACCCAT





CR003033
ATGGGCAAGTAGCTATCTAATGACTAAAATGGAAAAaCACTGGAAGAGAAACAGT
7.77%
1



TTTAGTATAACAAGTGAAATACCCAT





CR003033
ATGGGCAAGTAGCTATCTAATGACTAAAATGGAA--
5.72%
−2



CACTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACCCAT





CR003033
ATGGGCAAGTAGCTATCTAATGACTAAAATGGAAAAC--
2.94%
−2



TGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACCCAT





CR003033
ATGGGCAAGTAGCTATCTAATGACTAAAATGGAAAACcACTGGAAGAGAAACAGT
1.68%
1



TTTAGTATAACAAGTGAAATACCCAT





CR003033

. . .
. . .





CR003035
CACTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACCCATG---
10.87%
−3



AGTCTGAGGTGCCTATAGGACATCTATATAAA





CR003035
CACTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACCCAT-
2.62%
−1



CTGAGTCTGAGGTGCCTATAGGACATCTATATAAA





CR003035
CACTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACCCA--
2.04%
−2



CTGAGTCTGAGGTGCCTATAGGACATCTATATAAA





CR003035
CACTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACCCATG--
1.79%
−2



GAGTCTGAGGTGCCTATAGGACATCTATATAAA





CR003035
CACTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACCC----
1.77%
−4



TGAGTCTGAGGTGCCTATAGGACATCTATATAAA





CR003035

. . .
. . .





CR003037
TAACAAGTGAAATACCCATGCTGAGTCTGAGG----------
7.19%
−10



ACATCTATATAAATAAGCCCAGTACATTGTTTGATATA





CR003037
TAACAAGTGAAATACCCATGCTGAGTCTGAGGTGCC-
6.13%
−1



ATAGGACATCTATATAAATAAGCCCAGTACATTGTTTGATATA





CR003037
TAACAAGTGAAATACCCATGCTGAGTCTGAGGTGCCcTATAGGACATCTATATAA
4.17%
1



ATAAGCCCAGTACATTGTTTGATATA





CR003037
TAACAAGTGAAATACCCATGCTGAGTCTGAGGTGCCTtATAGGACATCTATATAA
3.89%
1



ATAAGCCCAGTACATTGTTTGATATA





CR003037
TAACAAGTGAAATACCCATGCTGAGTCTGAGGTGC-
3.72%
−1



TATAGGACATCTATATAAATAAGCCCAGTACATTGTTTGATATA





CR003037

. . .
. . .





CR003038
TAGTATAACAAGTGAAATACCCATGCTGAGTCTGAGGTGCCTATA----------
14.85%
−11



-TAAATAAGCCCAGTACATTGTTTG





CR003038
TAGTATAACAAGTGAAATACCCATGCTGAGTCTGAGGTGCCTATAG-
6.25%
−1



ACATCTATATAAATAAGCCCAGTACATTGTTTG





CR003038
TAGTATAACAAGTGAAATACCCATGCTGAGTCTGAGGTGCCTAT-
3.99%
−1



GGACATCTATATAAATAAGCCCAGTACATTGTTTG





CR003038
TAGTATAACAAGTGAAATACCCATGCTGAGTCTGAGGTGCCTATAGGgACATCTA
2.83%
1



TATAAATAAGCCCAGTACATTGTTTG





CR003038
TAGTATAACAAGTGAAATACCCATGCTGAGTCTGAGGTGCCTATAaGGACATCTA
2.76%
1



TATAAATAAGCCCAGTACATTGTTTG





CR003038

. . .
. . .





CR003052
TCAGAGGTTAGAAATCAGAGTTGGGAATTGGGATTA--
14.04%
−2



CAGGCTGTATTTAAGAGTTTAGATATAACTGTGAATCCAAGA





CR003052
TCAGAGGTTAGAAATCAGAGTTGGGAATTGGGATTAaTACAGGCTGTATTTAAGA
2.94%
1



GTTTAGATATAACTGTGAATCCAAGA





CR003052
TCAGAGGTTAGAAATCAGAGTTGGGAATTGGGATT-
2.41%
−1



TACAGGCTGTATTTAAGAGTTTAGATATAACTGTGAATCCAAGA





CR003052
TCAGAGGTTAGAAATCAGAGTTGGGAATTGGGATTATtACAGGCTGTATTTAAGA
2.37%
1



GTTTAGATATAACTGTGAATCCAAGA





CR003052
TCAGAGGTTAGAAATCAGAGTTGGGAATTGGGATTAaaTACAGGCTGTATTTAAG
2.28%
2



AGTTTAGATATAACTGTGAATCCAAGA





CR003052

. . .
. . .





CR003085
TGTAAGGAGGATGAGCCACATGGTATGGGAGGTAT-
12.03%
−1



CTAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTAC





CR003085
TGTAAGGAGGATGAGCCACATGGTATGGGAGG----------
8.70%
−10



ACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTAC





CR003085
TGTAAGGAGGATGAGCCACATGGTATGGGA-------------
4.42%
−13



CTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTAC





CR003085
TGTAAGGAGGATGAGCCACATGGTATGGGAGGTATAaCTAAGGACTCTAGGGTCA
4.38%
1



GAGAAATATGGGTTATATCCTTCTAC





CR003085
TGTAAGGAGGATGAGCCACATGGTATGGGAGGTA-----
3.41%
−5



AGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTAC





CR003085

. . .
. . .





CR003087
GATGAGCCACATGGTATGGGAGGTATACTAAGGACTtCTAGGGTCAGAGAAATAT
24.73%
1



GGGTTATATCCTTCTACAAAATTCAC





CR003087
GATGAGCCACATGGTATGGGAGGTATACTA---------
15.83%
−9



GGGTCAGAGAAATATGGGTTATATCCTTCTACAAAATTCAC





CR003087
GATGAGCCACATGGTATGGGAGGTATACTAAGG--------
8.50%
−8



GTCAGAGAAATATGGGTTATATCCTTCTACAAAATTCAC





CR003087
GATGAGCCACATGGTATGGGAGGTATACTAAGGACT--
7.07%
−2



AGGGTCAGAGAAATATGGGTTATATCCTTCTACAAAATTCAC





CR003087
GATGAGCCACATGGTATGGGAGGTATACTAAGG---------
1.75%
−9



TCAGAGAAATATGGGTTATATCCTTCTACAAAATTCAC





CR003087

. . .
. . .









These results support the conclusion from earlier experiments described herein that small indels (e.g., in this case, indels from 1-20 nucleotides) in the HPFH region targeted by the indicated gRNA molecule can have a significant impact on expression and production of HbF. An increase in HbF-containing erythrocytes derived from genome edited cells is likely to have therapeutic implications by reduced sickling.


Example 4.3

Methods: Methods are as in Example 4, with the Following Exceptions.


Human CD34+ cell culture. Human CD34+ cells were expanded for 3 days prior to RNP delivery in expansion medium.


Assembly of Cas9 and guide RNA ribonucleoprotein (RNP) complexes, preparation of HSPC, and electroporation of RNP into HSPC. The HSPC collected by centrifugation were resuspended in P3 Primary Cell Solution (Lonza cat. No. PBP3-00675) at a cell density of 6.4×106/mL. The RNP was mixed with 20 μL of cells by pipetting up and down and incubated at RT for 2 min. The RNP/cell mixture (20 μL) was electroporated using code CM-137 on the 4D-Nucleofector (Lonza). Electroporations were performed in duplicate. The Tracr was SEQ ID NO: 7808 and the crRNA had the following format with 2′O-Methyl (m) and Phosphorothioate Bond (*) modifications indicated: mN*mN*mN*rNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrGrUrUrUrUrArGrArGrCrUrArU*mG*m C*mU, where N's are the nucleotides of the targeting domain.


In vitro erythropoiesis and FACS analysis for HbF containing erythroid cells. After electroporation, the cells were immediately transferred into pre-warmed medium consisting of EDM and supplements. During days 0-7 of culture, EDM was further supplemented with 1 μM hydrocortisone (Sigma. H8672), 100 ng/mL human SCF (Life Technologies, Cat. #PHC2113), and 5 ng/mL human IL-3 (Peprotech #10779-598). During days 7-11 of culture, EDM was supplemented with 100 ng/mL of human SCF only. During days 11-21 of culture, EDM had no additional supplements. Cell cultures were initiated at 2.6×104 cells per ml on day 0, adjusted to 4.0×104 cells per ml on day 7, and adjusted to 1.0×106 cells per ml on day 11. On days 14 and 19, the media was replenished. Viable cells were counted at 1, 4, 7, 11, 14 and 21 days post-RNP delivery. All viable cell counts were determined by flow cytometry using AccuCheck Counting Beads (ThermoFisher cat. No. PCB100) with inviable cells discriminated by DAPI (4′,6-Diamidino-2-Phenylindole) staining. On days 7, 16 and 21 of the culture, the cells (1×105) were analyzed by intracellular staining for HbF expression. On days 16 and 21 intracellular staining for HbF expression did not include anti-CD71 and anti-CD235a antibodies, and % of HbF positive cells (F-cells) in the entire viable cell population was reported. On day 21 LIVE/DEAD® Fixable Near-IR Dead Cell Stain (ThermoFisher L34975) was used as the viability dye.


Genomic DNA preparation and next generation sequencing (NGS). Genomic DNA was prepared from edited and unedited HSPC at 7 days post-electroporation using Quick Extract DNA Extraction Solution (Epicentre Cat # QE09050).


Results:

Without being bound by theory, it is believed that targeted genetic disruption of the HPFH region will relieve repression of γ-globin expression, allowing production of the red blood cells containing elevated HbF protein, (cells expressing fetal hemoglobin are sometimes referred to herein as “F-cells”). The elevated HbF prevents sickling of the red blood cells under deoxygenated conditions and will be therapeutic/curative for the patients of both β-thalassemia and SCD. Autologous hematopoietic stem cell transplantation (HSCT) with ex vivo genome edited HSC from SCD patients was also combined with stem cell expansion enhancing technology, e.g., an aryl hydrocarbon receptor (AHR) inhibitor, e.g., as described in WO2010/059401 (the contents of which are incorporated by reference in their entirety), e.g., Compound 4 to improve ex vivo expansion and increase the dose of gene modified HSC delivered.


For efficient genome editing via programmable nuclease, Cas9, the successful delivery of guide RNA (gRNA) and Cas9 protein into target cells and tissues is essential. Recent reports demonstrated that Cas9 ribonucleoprotein (RNP) complexes when delivered into target cells by electroporation can accomplish efficient and specific genome editing in several different cell types. Cas9-RNP complexes cleave chromosomal DNA almost immediately after delivery and are degraded rapidly in cells, reducing off-target effects. In contrast, use of plasmid and viral vector systems used to deliver Cas9 results in prolonged expression of the enzyme aggravating off-target effects associated with the system. Additionally, delivery of RNPs into the target cells requires no additional tools which would greatly facilitate translation of genome editing for therapeutic purposes in the clinic. Purified recombinant Cas9 protein and gRNA complexes (RNPs) were delivered into cultured HSPC and an overview experiments used are shown in FIG. 17.


Recombinant Cas9 protein was purified from Escherichia coli and complexed with synthetic dual gRNAs (dgRNA) that consist of crRNA and tracr to generate ribonucleoprotein (RNP) complexes. The list of gRNAs used in the study are shown in Table 20. The RNP complexes were electroporated into CD34+ HSPC via electroporation as described under materials and methods. The cells were expanded prior to the delivery of RNP complexes. Actively dividing cells may facilitate uptake of RNP complexes delivered by electroporation.









TABLE 20







Relative viable cell proliferation in the current study. Individual


electroporation replicates are shown. All gRNA molecules were


tested in the dgRNA format using the tracr SEQ ID NO: 7808,


and the crRNA had the following format with 2′O-Methyl (m)


and Phosphorothioate Bond (*) modifications indicated:


mN*mN*mN*rNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrGrUrUr-


UrUrArGrArGrCrUrArU*mG*m C*mU, where N's are the nucleotides


of the targeting domain. (n.d. not determined)














Guide RNA targeting









domain ID and replicate
Day 0
Day 1
Day 4
Day 7
Day 11
Day 14
Day 21

















CR001030 replicate 1
1
0.66
4.3
43.1
627
680
772


CR001030 replicate 2
1
0.65
4.0
38.4
651
694
880


CR001028 replicate 1
1
0.61
4.0
33.2
588
509
742


CR001028 replicate 2
1
0.77
6.1
44.9
724
759
838


CR001095 replicate 1
1
0.66
4.0
40.7
665
503
835


CR001095 replicate 2
1
0.96
5.2
42.2
651
777
n.d.


CR001212 replicate 1
1
0.58
3.4
33.6
465
414
495


CR001212 replicate 2
1
0.74
3.6
32.4
490
519
572


g8 replicate 1
1
0.61
4.4
31.8
221
341
91


g8 replicate 2
1
0.60
5.2
33.2
269
270
103


None/control replicate 1
1
0.79
7.6
58.5
741
862
707


None/control replicate 2
1
0.71
8.2
51.4
923
1204
1075









The genome edited and unedited HSPC were analyzed for proliferation in a three-stage erythroid differentiation cell culture protocol. Percent cell recovery at 1 day after electroporation ranged from 58% to 96% and was similar across conditions, including the unedited but electroporated control (Table 20). Proliferation was suppressed in the cells edited by dgRNA including the targeting domain of g8 targeting exon 2 of BCL11A (10-12% of unedited control at day 21, Table 20), but proliferation of cells edited with the included HPFH region targeting dgRNAs was similar to control (47-99% of unedited control at day 21, Table 20).









TABLE 21







HbF induction in the current study. Individual electroporation replicates


are shown. All gRNA molecules were tested in the dgRNA format. All


gRNA molecules were tested in the dgRNA format using the tracr


SEQ ID NO: 7808, and the crRNA had the following format with 2′O-


Methyl (m) and Phosphorothioate Bond (*) modifications indicated:


mN*mN*mN*rNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrGrUrUrUr


UrArGrArGrCrUrArU*mG*mC*mU, where N's are the nucleotides of


the targeting domain. (n.d. not determined)












Guide RNA







targeting
%
%
% HbF+
% HbF+
% HbF+


domain
edited,
CD71+,
(F cells),
(F cells),
(F cells),


ID and replicate
Day 7
Day 7
Day 7
Day 16
Day 21





CR001030
90.7
91.2
61.0
45.4
53.7


replicate 1


CR001030
90.1
91.1
63.9
44.3
55.9


replicate 2


CR001028
91.9
90.0
61.6
40.9
52.0


replicate 1


CR001028
87.6
90.7
56.3
46.6
45.8


replicate 2


CR001095
25.7
91.4
51.3
36.8
43.7


replicate 1


CR001095
30.5
91.1
52.5
42.7
n.d.


replicate 2


CR001212
86.2
90.8
57.5
38.7
45.2


replicate 1


CR001212
80.9
90.4
54.7
36.5
42.7


replicate 2


g8 replicate 1
95.3
84.6
70.7
71.9
63.4


g8 replicate 2
94.3
82.6
70.0
72.6
54.8


None/control
n/a
94.0
27.1
24.4
22.8


replicate 1


None/control
n/a
93.8
26.2
25.7
21.1


replicate 2









The genome edited and unedited HSPC were analyzed by flow cytometry for expression levels of fetal globin and two erythroid cell surface markers, transferrin receptor (CD71) and glycophorin A (CD235a) using antibodies conjugated to fluorescent dyes. The live cells were identified and gated by exclusion of Live/Dead Fixable Dead Cell Stain. Genome editing did not adversely affect erythroid differentiation as the cultured cells showed percentages of CD71+ cells consistent with erythroblasts similar to uneditied cells at day 7 of differentiation. Cultures treated with the included HPFH region targeting dgRNAs resulted in increased percentage of erythroid cells containing HbF compared to mock electroporated cells throughout the 21 day culture period (Table 21). Induction of HbF positive cells by dgRNA including the targeting domain of g8 targeting exon 2 of BCL11A was also observed in parallel. Genomic PCR products of the HPFH region were also subjected to next generation sequencing (NGS) to determine the percentage of edited alleles in the cell population. Genome editing at the HFPH locus was observed in cell cultures electroporated with RNPs containing Cas9, crRNA of the given targeting domain and Tracr (Table 21), but not in control cells with no targeting domain delivered (RNPs containing only Cas9 and Tmcr). An increase in HbF-containing erythrocytes derived from genome edited cells is likely to have therapeutic implications by reduced sickling.


Example 4.4

Methods: Methods are as in Example 4, with the Following Exceptions.


Human CD34+ cell culture Human CD34+ cells were expanded for 3 to 6 days prior to RNP delivery in expansion medium, depending on study.


Assembly of Cas9 and guide RNA ribonucleoprotein (RNP) complexes, preparation of HSPC, and electroporation of RNP into HSPC. For some studies, the RNP complexes were delivered using the 4D-Nucleofector (Lonza). In those studies, the HSPC collected by centrifugation were resuspended in P3 Primary Cell Solution (Lonza cat. No. PBP3-00675) at a cell density of 2.2×106/mL to 6.4×106/mL, depending on study. The RNP was mixed with 20 μL of cells by pipetting up and down and incubated at RT for 2 min. The RNP/cell mixture (20 μL) was electroporated using code CM-137 on the 4D-Nucleofector (Lonza). Electroporations were performed in duplicate. The dgRNA format varied between studies and is indicated in Table 22 by the following notation. Form A is the dgRNA format described above in Example 1, with the targeting domain sequence indicated. Form B is a dgRNA format using a crRNA of rNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrGrUrUrUrUrArGrArGrCrUrArUrGrCrU, where r indicates an RNA base and the N's correspond to the indicated targeting domain sequence, and a tracr consisting of SEQ ID NO: 7808. Form C is a dgRNA format using crRNA of the sequence mN*mN*mN*rNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrGrUrUrUrUrArGrArGrCrUrArU*mG*m C*mU, where r indicates an RNA base, N's corresponds to the indicated targeting domain sequence, m indicates a base with 20-Methyl modification, and * indicates a phosphorothioate bond, and the tracr consists of SEQ ID NO: 7808.


In vitro erythropoiesis and FACS analysis for HbF containing erythroid cells. In one study, cell cultures were initiated at 2.6×104 cells per ml on day 0. For those initiated by seeding directly into 250 μl (as described in Example 4), the cell culture was diluted in fresh medium after 1 to 3 days, depending on the study.


Genomic DNA preparation and next generation sequencing (NGS). Genomic DNA was prepared from edited and unedited HSPC at 24 hours to 7 days post-electroporation, depending on the study, using Quick Extract DNA Extraction Solution (Epicentre Cat # QE09050).


Results:

Without being bound by theory, it is believed that targeted genetic disruption of the HPFH region will relieve repression of γ-globin expression, allowing production of the red blood cells containing elevated HbF protein, (cells expressing fetal hemoglobin are sometimes referred to herein as “F-cells”). The elevated HbF prevents sickling of the red blood cells under deoxygenated conditions and will be therapeutic/curative for the patients of both β-thalassemia and SCD. Autologous hematopoietic stem cell transplantation (HSCT) with ex vivo genome edited HSC from SCD patients was also combined with stem cell expansion enhancing technology, e.g., an aryl hydrocarbon receptor (AHR) inhibitor, e.g., as described in WO2010/059401 (the contents of which are incorporated by reference in their entirety), e.g., Compound 4 to improve ex vivo expansion and increase the dose of gene modified HSC delivered.


For efficient genome editing via programmable nuclease, Cas9, the successful delivery of guide RNA (gRNA) and Cas9 protein into target cells and tissues is essential. Recent reports demonstrated that Cas9 ribonucleoprotein (RNP) complexes when delivered into target cells by electroporation can accomplish efficient and specific genome editing in several different cell types. Cas9-RNP complexes cleave chromosomal DNA almost immediately after delivery and are degraded rapidly in cells, reducing off-target effects. In contrast, use of plasmid and viral vector systems used to deliver Cas9 results in prolonged expression of the enzyme aggravating off-target effects associated with the system. Additionally, delivery of RNPs into the target cells requires no additional tools which would greatly facilitate translation of genome editing for therapeutic purposes in the clinic. Purified recombinant Cas9 protein and gRNA complexes (RNPs) were delivered into cultured HSPC and an overview experiments used are shown in FIG. 17.


Recombinant Cas9 protein was purified from Escherichia coli and complexed with synthetic dual gRNAs (dgRNA) that consist of crRNA and tracr to generate ribonucleoprotein (RNP) complexes. The list of gRNAs used in the studies are shown in Table 22. The RNP complexes were electroporated into CD34+ HSPC via electroporation as described under materials and methods. The cells were expanded prior to the delivery of RNP complexes. Actively dividing cells may facilitate uptake of RNP complexes delivered by electroporation.









TABLE 22







Summary data for multiple studies evaluating indicated


gRNAs targeting the HPFH region and controls. All gRNA


molecules were tested in dgRNA formats. Details of the


dgRNA formats in the indicated studies are specified as


described above. Note that evaluations 4 and 5 were


performed in parallel and thus share control conditions.








Guide RNA



targeting
Evaluation number
















domain ID

1
2
3
4
5
6
7
8





CR001028
Format
A
A
B
B
C


C



Replicates
2
2
2
2
2


2



% HbF+ (F cells),
42.9
39.7
47.4
51.1
55.3


59.0



average of replicates



% edited, average of
91.7
78.0
87.5
90.9
84.6


89.8



replicates


CR001030
Format
A
A
B
B
C
C
C
C



Replicates
2
2
2
2
2
2
2
2



% HbF+ (F cells),
51.4
48.7
50.9
51.8
58.0
39.7
50.6
62.5



average of replicates



% edited, average of
84.5
61.8
74.3
75.0
85.6
94.1
85.4
90.4



replicates


CR001036
Format
A
A
B



Replicates
2
2
2



% HbF+ (F cells),
42.4
40.8
43.3



average of replicates



% edited, average of
84.4
78.3
92.6



replicates


CR001043
Format
A
A
B



Replicates
2
2
2



% HbF+ (F cells),
44.8
33.0
42.9



average of replicates



% edited, average of
80.0
42.7
87.7



replicates


CR001080
Format
A
A


C



Replicates
2
2


2



% HbF+ (F cells),
39.2
34.9


49.3



average of replicates



% edited, average of
32.4
24.0


41.6



replicates


CR001095
Format
A
A
B
B
C
C
C
C



Replicates
2
2
1
2
2
2
2
2



% HbF+ (F cells),
49.3
41.5
47
51.8
51.8
32.9
46.8
51.9



average of replicates



% edited, average of
66.1
49.8
65.1
64.6
64.2
66.8
56.1
28.1



replicates


CR001137
Format
A
A



C
C



Replicates
2
2



2
2



% HbF+ (F cells),
34.8
45.6



31.0
40.8



average of replicates



% edited, average of
41.5
46.9



69.0
57.9



replicates


CR001142
Format
A
A


C



Replicates
2
2


2



% HbF+ (F cells),
43.4
45.5


48.1



average of replicates



% edited, average of
76.9
63.7


89.2



replicates


CR001158
Format
A
A


C



Replicates
2
2


2



% HbF+ (F cells),
41.7
36.9


44.6



average of replicates



% edited, average of
72.4
43.9


78.4



replicates


CR001212
Format
A
A
B
B
C
C
C
C



Replicates
2
2
2
2
2
2
2
2



% HbF+ (F cells),
42.6
46.9
43.8
44.5
53.5
39.4
47.1
56.1



average of replicates



% edited, average of
81.6
58.1
48.6
47.5
69.2
82.0
67.0
83.6



replicates


CR001217
Format
A
A



C
C



Replicates
2
2



2
2



% HbF+ (F cells),
40.1
41.5



29.9
45.9



average of replicates



% edited, average of
80.9
50.3



89.0
82.1



replicates


CR001221
Format
A
A
B
B
C



Replicates
2
2
1
2
2



% HbF+ (F cells),
41.8
45.2
44.6
46.2
48.6



average of replicates



% edited, average of
83.9
71.1
73.6
70.7
92.1



replicates


g8
Format
C
C
C
C
C

C
C



Replicates
16
2
2
2
2

2
2



% HbF+ (F cells),
59.2
60.0
66.3
64.7
64.7

55.8
70.4



average of replicates



% edited, average of
95.1
85.4
94.2
94.6
94.6

91.7
94.8



replicates


None/control
Format
n/a
n/a
n/a
n/a
n/a
n/a
n/a
n/a



Replicates
16
2
2
2
2
2
2
2



% HbF+ (F cells),
21.0
20.3
22.4
22.4
22.4
13.9
24.0
26.7



average of replicates



% edited, average of
n/a
n/a
n/a
n/a
n/a
n/a
n/a
n/a



replicates









The genome edited and unedited HSPC were analyzed by flow cytometry for expression levels of fetal globin and two erythroid cell surface markers, transferrin receptor (CD71) and glycophorin A (CD235a) using antibodies conjugated to fluorescent dyes. The live cells were identified and gated by exclusion of Live Dead Violet. HPFH region targeting resulted in increased percentage of erythroid cells containing HbF compared to mock electroporated cells, a consistent result across multiple evaluations and dgRNA formats (Table 22). In some instances, an increase in % HbF+ cells was associated with a particular dgRNA form, for example Form C for CR001028 (Table 22). Induction of HbF positive cells by dgRNA including the targeting domain of g8 targeting exon 2 of BCL11A was also observed in parallel. Genomic PCR products of the HPFH region were also subjected to next generation sequencing (NGS) to determine the percentage of edited alleles in the cell population. Genome editing at the HFPH locus was observed in cell cultures electroporated with RNPs containing Cas9, crRNA of the given targeting domain and Tracr (Table 22), but not in control cells with no targeting domain delivered (RNPs containing only Cas9 and Tracr).


Finally, the indel pattern as well as frequency of each indel was assessed for each gRNA by NGS. The most frequently occurring indels at each target site are shown in Table 26.









TABLE 26







5 most frequent indels at each taget sequence after exposure to RNP comprising the


indicated gRNA molecule. Each gRNA was tested in dgRNA format in two separate experiments,


and the results are shown seperately for each experiment. Capital letters are the naturally


occurring nucleotides at and near the target sequence. Deletions relative to the unmodified


target sequence are shown as “—”; insertions are shown as lowercase letters.












dgRNA





Experiment
targeting

% of all
Indel


Number
domain
Variant Read (Genomic Sequence)
reads
Length














1
CR001028
TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTCTA-
13.26%
−1




ATATCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC





1
CR001028
TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCC-------------
12.48%
−13




CCACCGCATCTCTTTCAGCAGTTGTTTC





1
CR001028
TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTCTA----
6.04%
−4




TCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC





1
CR001028
TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTCTA--
3.94%
−2




TATCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC





1
CR001028
TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC-------------
3.65%
−13




ACCGCATCTCTTTCAGCAGTTGTTTC





1
CR001028

. . .
. . .





2
CR001028
TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCC-------------
14.30%
−13




CCACCGCATCTCTTTCAGCAGTTGTTTC





2
CR001028
TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTCTA-
11.51%
−1




ATATCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC





2
CR001028
TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTCTA--
5.63%
−2




TATCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC





2
CR001028
TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTCTA----
4.98%
−4




TCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC





2
CR001028
TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC-------------
4.91%
−13




ACCGCATCTCTTTCAGCAGTTGTTTC





2
CR001028

. . .
. . .





1
CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTC-------------
9.10%
−13




TTTCAGCAGTTGTTTCTAAAAATATCCTCC





1
CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCCACC-
4.77%
−1




CATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC





1
CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCCACC--
3.54%
−2




ATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC





1
CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCCACCGgCATCTCTTTCA
2.51%
1




GCAGTTGTTTCTAAAAATATCCTCC





1
CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCCA-----
2.39%
−5




TCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC





1
CR001030

. . .
. . .





2
CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTC-------------
9.67%
−13




TTTCAGCAGTTGTTTCTAAAAATATCCTCC





2
CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCCACC-
4.87%
−1




CATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC





2
CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCCACC--
3.33%
−2




ATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC





2
CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCCACCGgCATCTCTTTCA
2.93%
1




GCAGTTGTTTCTAAAAATATCCTCC





2
CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCCAC-
1.85%
−1




GCATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC





2
CR001030

. . .
. . .





1
CR001036
CCTAGTTTCATTTTTGCAGAAGTGTTTTAGGCTAAT-
19.08%
−1




TAGTGGAATGTATCTTAGAGTTTAACTTATTTGTTTCTGTCAC





1
CR001036
CCTAGTTTCATTTTTGCAGAAGTGTTTTAGGCTAATA--
17.13%
−2




GTGGAATGTATCTTAGAGTTTAACTTATTTGTTTCTGTCAC





1
CR001036
CCTAGTTTCATTTTTGCAGAAGTGTTTTAG----------
3.55%
−10




TGGAATGTATCTTAGAGTTTAACTTATTTGTTTCTGTCAC





1
CR001036
CCTAGTTTCATTTTTGCAGAAGTGTTTTAGGCTAATAaTAGTGGAATGTATCTTAG
2.42%
1




AGTTTAACTTATTTGTTTCTGTCAC





1
CR001036
CCTAGTTTCATTTTTGCAGAAGTGTTTTAGGCTAATA-
2.38%
−1




AGTGGAATGTATCTTAGAGTTTAACTTATTTGTTTCTGTCAC





1
CR001036

. . .
. . .





2
CR001036
CCTAGTTTCATTTTTGCAGAAGTGTTTTAGGCTAATA--
22.26%
−2




GTGGAATGTATCTTAGAGTTTAACTTATTTGTTTCTGTCAC





2
CR001036
CCTAGTTTCATTTTTGCAGAAGTGTTTTAGGCTAAT-
19.77%
−1




TAGTGGAATGTATCTTAGAGTTTAACTTATTTGTTTCTGTCAC





2
CR001036
CCTAGTTTCATTTTTGCAGAAGTGTTTTAG----------
6.25%
−10




TGGAATGTATCTTAGAGTTTAACTTATTTGTTTCTGTCAC





2
CR001036
CCTAGTTTCATTTTTGCAGAAGTGTTTTAGGCTAATA-
1.96%
−1




AGTGGAATGTATCTTAGAGTTTAACTTATTTGTTTCTGTCAC





2
CR001036
CCTAGTTTCATTTTTGCAGAAGTGTTTTAGG------------
1.41%
−12




AATGTATCTTAGAGTTTAACTTATTTGTTTCTGTCAC





2
CR001036

. . .
. . .





1
CR001043
TAGAGATTTTTGTCTCCAAGGGAATTTTGAGAGGTTG-
5.28%
−1




AATGGACAAATCTATTGCTGCAGTTTAAACTTGCTTGCTTCC





1
CR001043
TAGAGATTTTTGTCTCCAAGGGAATTTTGAGAGGTTGGA-----
2.67%
−5




CAAATCTATTGCTGCAGTTTAAACTTGCTTGCTTCC





1
CR001043
TAGAGATTTTTGTCTCCAAGGGAATTTTGA---------
2.62%
−9




ATGGACAAATCTATTGCTGCAGTTTAAACTTGCTTGCTTCC





1
CR001043
TAGAGATTTTTGTCTCCAAGGGAATTTTGAGAGG---------
2.22%
−9




ACAAATCTATTGCTGCAGTTTAAACTTGCTTGCTTCC





1
CR001043
TAGAGATTTTTGTCTCCAAGGGAATTTTGAGAGGTTGGgAATGGACAAATCTATTG
2.06%
1




CTGCAGTTTAAACTTGCTTGCTTCC





1
CR001043

. . .
. . .





2
CR001043
TAGAGATTTTTGTCTCCAAGGGAATTTTGAGAGGTTG-
5.87%
−1




AATGGACAAATCTATTGCTGCAGTTTAAACTTGCTTGCTTCC





2
CR001043
TAGAGATTTTTGTCTCCAAGGGAATTTTGAGAGG---------
3.11%
−9




ACAAATCTATTGCTGCAGTTTAAACTTGCTTGCTTCC





2
CR001043
TAGAGATTTTTGTCTCCAAGGGAATTTTGAGAGGTTGGA-----
2.42%
−5




CAAATCTATTGCTGCAGTTTAAACTTGCTTGCTTCC





2
CR001043
TAGAGATTTTTGTCTCCAAGGGAATTTTGAGAGGTTGGgAATGGACAAATCTATTG
1.90%
1




CTGCAGTTTAAACTTGCTTGCTTCC





2
CR001043
TAGAGATTTTTGTCTCCAAGGGAATTTTGA---------
1.72%
−9




ATGGACAAATCTATTGCTGCAGTTTAAACTTGCTTGCTTCC





2
CR001043

. . .
. . .





1
CR001080
GAGAAAGGAAGGAAGGAAGAGGGGAAGAGAGAGGATG-
2.72%
−1




AAGGGATGGAGGAGAAGAAGGAAAAATAAATAATGGAGAGGA





1
CR001080
GAGAAAGGAAGGAAGGAAGAGGGGAAGAGAGAGGATGGA---------
2.22%
−9




GGAGAAGAAGGAAAAATAAATAATGGAGAGGA





1
CR001080
GAGAAAGGAAGGAAGGAAGAGGGGAAGAGAGAGG--------
1.44%
−8




GATGGAGGAGAAGAAGGAAAAATAAATAATGGAGAGGA





1
CR001080
GAGAAAGGAAGGAAGGAAGAGGGGAAGAGAGAGGATGGgAAGGGATGGAGGAGAAG
1.41%
1




AAGGAAAAATAAATAATGGAGAGGA





1
CR001080
GAGAAAGGAAGGAAGGAAGAGGGGAAGAGAGAGGA----
1.11%
−4




AGGGATGGAGGAGAAGAAGGAAAAATAAATAATGGAGAGGA





1
CR001080

. . .
. . .





2
CR001080
GAGAAAGGAAGGAAGGAAGAGGGGAAGAGAGAGGATGGA---------
3.43%
−9




GGAGAAGAAGGAAAAATAAATAATGGAGAGGA





2
CR001080
GAGAAAGGAAGGAAGGAAGAGGGGAAGAGAGAGGATG-
3.17%
−1




AAGGGATGGAGGAGAAGAAGGAAAAATAAATAATGGAGAGGA





2
CR001080
GAGAAAGGAAGGAAGGAAGAGGGGAAGAGA---------
1.61%
−9




AGGGATGGAGGAGAAGAAGGAAAAATAAATAATGGAGAGGA





2
CR001080
GAGAAAGGAAGGAAGGAAGAGGGGAAGAGAGAGGA----
1.28%
−4




AGGGATGGAGGAGAAGAAGGAAAAATAAATAATGGAGAGGA





2
CR001080
GAGAAAGGAAGGAAGGAAGAGGGGAAGAGAGAGG--------
1.16%
−8




GATGGAGGAGAAGAAGGAAAAATAAATAATGGAGAGGA





2
CR001080

. . .
. . .





1
CR001095
GAGAAAGAGAAAGGGAAGGGAAGAGAGGAAAGAAGA--
5.94%
−2




AGAGGAGAGAAAAGAAACGAAGAGAGGGGAAGGGAAGGAAAA





1
CR001095
GAGAAAGAGAAAGGGAAGGGAAGAGAGGAAAGAAGAG-----
5.54%
−5




GAGAGAAAAGAAACGAAGAGAGGGGAAGGGAAGGAAAA





1
CR001095
GAGAAAGAGAAAGGGAAGGGAAGAGAGGA---------------
4.02%
−15




GAGAAAAGAAACGAAGAGAGGGGAAGGGAAGGAAAA





1
CR001095
GAGAAAGAGAAAGGGAAGGGAAGAGAGGAAAGAA--------------------
3.23%
−20




ACGAAGAGAGGGGAAGGGAAGGAAAA





1
CR001095
GAGAAAGAGAAAGGGAAGGGAAGAGAGGAAAGA--------
2.49%
−8




GGAGAGAAAAGAAACGAAGAGAGGGGAAGGGAAGGAAAA





1
CR001095

. . .
. . .





2
CR001095
GAGAAAGAGAAAGGGAAGGGAAGAGAGGAAAGAAGAG-----
7.89%
−5




GAGAGAAAAGAAACGAAGAGAGGGGAAGGGAAGGAAAA





2
CR001095
GAGAAAGAGAAAGGGAAGGGAAGAGAGGAAAGAAGA--
6.18%
−2




AGAGGAGAGAAAAGAAACGAAGAGAGGGGAAGGGAAGGAAAA





2
CR001095
GAGAAAGAGAAAGGGAAGGGAAGAGAGGA---------------
4.16%
−15




GAGAAAAGAAACGAAGAGAGGGGAAGGGAAGGAAAA





2
CR001095
GAGAAAGAGAAAGGGAAGGGAAGAGAGGAAAGAAGAGgAAGAGGAGAGAAAAGAAA
2.77%
1




CGAAGAGAGGGGAAGGGAAGGAAAA





2
CR001095
GAGAAAGAGAAAGGGAAGGGA--------------------
1.98%
−20




GGAGAGAAAAGAAACGAAGAGAGGGGAAGGGAAGGAAAA





2
CR001095

. . .
. . .





1
CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC-------
6.73%
−7




ACTTAAATGCTTACCAACAGTAGAATTGATAAAT





1
CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACCGGTAGgCCACTTAAATG
4.02%
1




CTTACCAACAGTAGAATTGATAAAT





1
CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACCGGTAaGCCACTTAAATG
2.87%
1




CTTACCAACAGTAGAATTGATAAAT





1
CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCA--------
1.71%
−8




GCCACTTAAATGCTTACCAACAGTAGAATTGATAAAT





1
CR001137
AAATGCTTATGACAGCAATAATCATAAAAACC--------------
0.95%
−14




ACTTAAATGCTTACCAACAGTAGAATTGATAAAT





1
CR001137

. . .
. . .





2
CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC-------
7.25%
−7




ACTTAAATGCTTACCAACAGTAGAATTGATAAAT





2
CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACCGGTAGgCCACTTAAATG
3.44%
1




CTTACCAACAGTAGAATTGATAAAT





2
CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACCGGTAaGCCACTTAAATG
2.50%
1




CTTACCAACAGTAGAATTGATAAAT





2
CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACCGGTA--------
1.37%
−8




AATGCTTACCAACAGTAGAATTGATAAAT





2
CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACCGGT-------
1.11%
−7




TAAATGCTTACCAACAGTAGAATTGATAAAT





2
CR001137

. . .
. . .





1
CR001142
AAATGCATTTTACAGCATTTGGTTGATTAAAAGTAACCcAGAGGTGAGTTCAAACT
8.00%
1




ATATGACTTTATTTGTATATAGAAA





1
CR001142
AAATGCATTTTACAGCATTTGGTTGATTAAAAG-------
6.63%
−7




AGGTGAGTTCAAACTATATGACTTTATTTGTATATAGAAA





1
CR001142
AAATGCATTTTACAGCATTTGGTTGATTAAAAGTAAC-
2.86%
−1




AGAGGTGAGTTCAAACTATATGACTTTATTTGTATATAGAAA





1
CR001142
AAATGCATTTTACAGCATTTGGTTGATTAAAAG---------
2.03%
−9




GTGAGTTCAAACTATATGACTTTATTTGTATATAGAAA





1
CR001142
AAATGCATTTTACAGCATTTGGTTGA--------------------
1.71%
−20




GTTCAAACTATATGACTTTATTTGTATATAGAAA





1
CR001142

. . .
. . .





2
CR001142
AAATGCATTTTACAGCATTTGGTTGATTAAAAGTAACCcAGAGGTGAGTTCAAACT
9.94%
1




ATATGACTTTATTTGTATATAGAAA





2
CR001142
AAATGCATTTTACAGCATTTGGTTGATTAAAAG-------
5.81%
−7




AGGTGAGTTCAAACTATATGACTTTATTTGTATATAGAAA





2
CR001142
AAATGCATTTTACAGCATTTGGTTGATTAAAAGTAAC-
4.19%
−1




AGAGGTGAGTTCAAACTATATGACTTTATTTGTATATAGAAA





2
CR001142
AAATGCATTTTACAGCATTTGGTTGATTAAAAG---------
2.59%
−9




GTGAGTTCAAACTATATGACTTTATTTGTATATAGAAA





2
CR001142
AAATGCATTTTACAGCATTTGGTTGA--------------------
2.26%
−20




GTTCAAACTATATGACTTTATTTGTATATAGAAA





2
CR001142

. . .
. . .





1
CR001158
CCTGGAAGCCAACGAAAGATATTGAATAATTCAAGAAAaGGTGGTGGCATGGTTTG
10.94%
1




ATTTGTGTCTTTAAAAGATTATTCT





1
CR001158
CCTGGAAGCCAACGAAAGATATTGAATAATTCAAG----
10.03%
−4




GTGGTGGCATGGTTTGATTTGTGTCTTTAAAAGATTATTCT





1
CR001158
CCTGGAAGCCAACGAAAGATATTGAATAATTCAAGAA-
3.80%
−1




GGTGGTGGCATGGTTTGATTTGTGTCTTTAAAAGATTATTCT





1
CR001158
CCTGGAAGCCAACGAAAGATATTGAATAATTCAAGA--
1.19%
−2




GGTGGTGGCATGGTTTGATTTGTGTCTTTAAAAGATTATTCT





1
CR001158
CCTGGAAGCCAACGAAAGATATTGAATAATTCA-----
0.78%
−5




GGTGGTGGCATGGTTTGATTTGTGTCTTTAAAAGATTATTCT





1
CR001158

. . .
. . .





2
CR001158
CCTGGAAGCCAACGAAAGATATTGAATAATTCAAGAAAaGGTGGTGGCATGGTTTG
11.89%
1




ATTTGTGTCTTTAAAAGATTATTCT





2
CR001158
CCTGGAAGCCAACGAAAGATATTGAATAATTCAAG----
9.97%
−4




GTGGTGGCATGGTTTGATTTGTGTCTTTAAAAGATTATTCT





2
CR001158
CCTGGAAGCCAACGAAAGATATTGAATAATTCAAGAA-
3.45%
−1




GGTGGTGGCATGGTTTGATTTGTGTCTTTAAAAGATTATTCT





2
CR001158
CCTGGAAGCCAACGAAAGATATTGAATAATTCAAGA--
0.86%
−2




GGTGGTGGCATGGTTTGATTTGTGTCTTTAAAAGATTATTCT





2
CR001158
CCTGGAAGCCAACGAAAGATATTGAATAATTCAAGAAcaAGGTGGTGGCATGGTTT
0.49%
2




GATTTGTGTCTTTAAAAGATTATTCT





2
CR001158

. . .
. . .





1
CR001212
CCTTGGCCTCCCAAAGTGCTGGGTTTACAAGCCTGAGCCA-------------
11.38%
−13




GGATAAGGTCTAAAAGTGGAAAGAATA





1
CR001212
CCTTGGCCTCCCAAAGTGCTGGGTTTACAAGCCTGAGCCACC-
3.98%
−1




CATCCAGCCAGGATAAGGTCTAAAAGTGGAAAGAATA





1
CR001212
CCTTGGCCTCCCAAAGTGCTGGGTTTACAAGCCTGAGCCA-----
3.05%
−5




TCCAGCCAGGATAAGGTCTAAAAGTGGAAAGAATA





1
CR001212
CCTTGGCCTCCCAAAGTGCTGGGTTTACAAGCCTGAGCCACCG-
2.94%
−1




ATCCAGCCAGGATAAGGTCTAAAAGTGGAAAGAATA





1
CR001212
CCTTGGCCTCCCAAAGTGCTGGGTTTACAAGCCTGAGCCACC------
2.82%
−6




AGCCAGGATAAGGTCTAAAAGTGGAAAGAATA





1
CR001212

. . .
. . .





2
CR001212
CCTTGGCCTCCCAAAGTGCTGGGTTTACAAGCCTGAGCCA-------------
11.42%
−13




GGATAAGGTCTAAAAGTGGAAAGAATA





2
CR001212
CCTTGGCCTCCCAAAGTGCTGGGTTTACAAGCCTGAGCCACC-
6.41%
−1




CATCCAGCCAGGATAAGGTCTAAAAGTGGAAAGAATA





2
CR001212
CCTTGGCCTCCCAAAGTGCTGGGTTTACAAGCCTGAGCCACCG-
5.61%
−1




ATCCAGCCAGGATAAGGTCTAAAAGTGGAAAGAATA





2
CR001212
CCTTGGCCTCCCAAAGTGCTGGGTTTACAAGCCTGAGCCACCG--
2.85%
−2




TCCAGCCAGGATAAGGTCTAAAAGTGGAAAGAATA





2
CR001212
CCTTGGCCTCCCAAAGTGCTGGGTTTACAAGCCTGAGCCACC------
1.96%
−6




AGCCAGGATAAGGTCTAAAAGTGGAAAGAATA





2
CR001212

. . .
. . .





1
CR001217
AAGTGCTGGGTTTACAAGCCTGAGCCACCGCATCCAGCCAGG------
17.75%
−6




TCTAAAAGTGGAAAGAATAGCATCTACTCTTG





1
CR001217
AAGTGCTGGGTTTACAAGCCTGAGCCACCGCATCCAGCCAGGATtAAGGTCTAAAA
4.06%
1




GTGGAAAGAATAGCATCTACTCTTG





1
CR001217
AAGTGCTGGGTTTACAAGCCTGAGCCACCGCATCCAGCCAGGAaTAAGGTCTAAAA
2.38%
1




GTGGAAAGAATAGCATCTACTCTTG





1
CR001217
AAGTGCTGGGTTTACAAGCCTGAGCCACCGCATCCAGCCAGGA-
1.35%
−1




AAGGTCTAAAAGTGGAAAGAATAGCATCTACTCTTG





1
CR001217
AAGTGCTGGGTTTACAAGCCTGAGCCACCGCATCCAGCCAGGAT-----
1.10%
−5




CTAAAAGTGGAAAGAATAGCATCTACTCTTG





1
CR001217

. . .
. . .





2
CR001217
AAGTGCTGGGTTTACAAGCCTGAGCCACCGCATCCAGCCAGG------
18.91%
−6




TCTAAAAGTGGAAAGAATAGCATCTACTCTTG





2
CR001217
AAGTGCTGGGTTTACAAGCCTGAGCCACCGCATCCAGCCAGGATtAAGGTCTAAAA
5.59%
1




GTGGAAAGAATAGCATCTACTCTTG





2
CR001217
AAGTGCTGGGTTTACAAGCCTGAGCCACCGCATCCAGCCAGGAaTAAGGTCTAAAA
1.42%
1




GTGGAAAGAATAGCATCTACTCTTG





2
CR001217
AAGTGCTGGGTTTACAAGCCTGAGCCACCGCATCCAGCCAGGA-
1.38%
−1




AAGGTCTAAAAGTGGAAAGAATAGCATCTACTCTTG





2
CR001217
AAGTGCTGGGTTTACAAGCCTGAGCCACCGCATCCAGCCAGGAT-----
1.26%
−5




CTAAAAGTGGAAAGAATAGCATCTACTCTTG





2
CR001217

. . .
. . .





1
CR001221
TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCTG----
28.78%
−4




GGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA





1
CR001221
TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCT-
9.51%
−1




ACTGGGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA





1
CR001221
TAGCATCTACTCTTGTTCAGGAAACAATGAGGAC-----
4.35%
−5




TGGGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA





1
CR001221
TAGCATCTACTCTTGTTCAGGAAACAATGAGG-----------
1.87%
−11




CAGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA





1
CR001221
TAGCATCTACTCTTGTTCAGGAAACAATG------------
1.71%
−12




GGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA





1
CR001221

. . .
. . .





2
CR001221
TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCTG----
29.12%
−4




GGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA





2
CR001221
TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCT-
10.32%
−1




ACTGGGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA





2
CR001221
TAGCATCTACTCTTGTTCAGGAAACAATGAGGAC-----
4.26%
−5




TGGGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA





2
CR001221
TAGCATCTACTCTTGTTCAGGAAACAATGAGGAC----------
1.89%
−10




AGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA





2
CR001221
TAGCATCTACTCTTGTTCAGGAAACAATGAGG-----------
1.67%
−11




CAGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA





2
CR001221

. . .
. . .









Although in some cases, the relative abundance of the most frequent indels varied from experiment to experiment, the top indels were largely the same across both experiments for any given gRNA. This indicates that for these dgRNAs, the indel pattern created in HSC cells was consistent. As well, these results support the surprising finding from earlier experiments that small indels (e.g., in this case, indels from 1-20 nucleotides) in the HPFH regions targeted by these gRNAs could result in significant upregulation of fetal hemoglobin. An increase in HbF-containing erythrocytes derived from genome edited cells is likely to have therapeutic implications by reduced sickling.


Example 4.5

Methods: Methods are as in Sub-Example 4.1, with the Following Exceptions.


Human CD34+ cell culture. Human CD34+ cells were derived from bone marrow (Hemacare Corporation, Cat. No. BM34C-3). CD34+ cells were thawed and expanded in expansion medium for 1 day prior to RNP delivery. After RNP delivery, cells were immediately transferred back into 200 μl expansion medium and allowed to recover overnight. The following day, the cultures were counted and adjusted to 2.0×105 viable cells per ml. Percent recovery was calculated as the viable cell count 1 day after RNP delivery as a percentage of the viable cells electroporated. After an additional 7 days in expansion medium (8 days following RNP delivery), the viable cell count was again determined. Fold proliferation was calculated as the viable cell count after 7 days in expansion medium divided by 2.0×105 cells per ml. All viable cell counts were measured by flow cytometry using AccuCheck Counting Beads (ThermoFisher cat. No. PCB100) with inviable cells discriminated by DAPI (4′,6-Diamidino-2-Phenylindole) staining After an additional 1 day in expansion medium (9 days following RNP delivery), the cell cultures were phenotyped by flow cytometry as described under Cell phenotyping.


Assembly of Cas9 and guide RNA ribonucleoprotein (RNP) complexes, preparation of HSPC, and electroporation of RNP into HSPC. The HSPC collected by centrifugation were resuspended in P3 Primary Cell Solution (Lonza cat. No. PBP3-00675) at a cell density of 5.4×106/mL. The RNP was mixed with 20 μL of cells by pipetting up and down and incubated at RT for 2 min. The RNP/cell mixture (20 μL) was electroporated using code CM-137 on the 4D-Nucleofector (Lonza). Electroporations were performed in duplicate. The crRNAs used were of the sequence mN*mN*mN*rNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrGrUrUrUrUrArGrArGrCrUrArU*mG*m C*mU, where r indicates an RNA base, m indicates a base with 2′O-Methyl modification, and * indicates a Phosphorothioate Bond. N's indicate the residues of the indicated targeting domain. The tracr sequence used was SEQ ID NO: 7808.


Colony forming unit cell assay. The day following RNP delivery, viable cells were counted as described in Human CD34+ cell culture. For the granulocyte/macrophage progenitor colony forming unit (CFU) assay, 227 cells per 1 mL Methocult H4035 methylcellulose medium (StemCell Technologies) was plated in duplicate. 1× antibiotic/antimycotic (Gibco, Cat. #10378-016) was added into the Methocult. The culture dishes were incubated in a humidified incubator at 37° C. Colonies containing at least 50 cells were counted at day 15 post-plating. Colony number per ml of Methocult was divided by 227 and multiplied by 1000 to obtain the CFU frequency per 1000 cells.


Cell phenotyping. Cells were analyzed for surface marker expression after staining with the following antibody panels. Panel 1: Antibodies specific for CD38 (FITC-conjugate, BD Biosciences #340926, clone HB7), CD133 epitope 1 (PE-conjugate, Miltenyi #130-080-801, clone AC133), CD34 (PerCP-conjugate, BD Biosciences #340666, clone 8G12), CD90 (APC-conjugate, BD Biosciences #598695, clone E10), CD45RA (Pe-Cy7-conjugate, eBioscience #25-0458-42, clone HI100). Panel 2: CD34 (PerCP-conjugate, BD Biosciences #340666, clone 8G12), CD33 (PE-Cy7-conjugate, BD Biosciences #333946, clone P67.6), CD14 (APC-H7-conjugate, BD Biosciences #560270, clone MφP9), CD15 (PE-conjugate, Biolegend #301905, clone HI98). Panel 3: CD34 (PerCP-conjugate, BD Biosciences #340666, clone 8G12), CD41a (APC-H7-conjugate, BD Biosciences #561422, clone HIPS), CD71 (FITC-conjugate, BD Biosciences #555536, clone M-A712), CD19 (PE-conjugate, BD Biosciences #340720, clone SJ25C1), CD56 (APC-conjugate, Biolegend #318310, clone HCD56). Corresponding isotype control antibody panels were used to stain cultures in parallel, except that anti-CD45RA was included instead of its isotype control. Inviable cells were discriminated by DAPI (4′,6-Diamidino-2-Phenylindole) staining Stained samples were analyzed on an LSRFortessa flow cytometer (BD Biosciences) for cell surface protein expression. The results were analyzed using Flowjo, and data were presented as % of the DAPI negative viable cell population.


Genomic DNA preparation and next generation sequencing (NGS). Genomic DNA was prepared from edited and unedited HSPC at 1 and 8 days post-electroporation using Quick Extract DNA Extraction Solution (Epicentre Cat # QE09050).


Results:

Without being bound by theory, it is believed that targeted genetic disruption of the HPFH or BCL11A erythroid enhancer region will relieve repression of γ-globin expression, allowing production of the red blood cells containing elevated HbF protein, (cells expressing fetal hemoglobin are sometimes referred to herein as “F-cells”). The elevated HbF prevents sickling of the red blood cells under deoxygenated conditions and will be therapeutic/curative for the patients of both β-thalassemia and SCD. Autologous hematopoietic stem cell transplantation (HSCT) with ex vivo genome edited HSC from SCD patients was also combined with stem cell expansion enhancing technology, e.g., an aryl hydrocarbon receptor (AHR) inhibitor, e.g., as described in WO2010/059401 (the contents of which are incorporated by reference in their entirety), e.g., Compound 4 to improve ex vivo expansion and increase the dose of gene modified HSC delivered.


For efficient genome editing via programmable nuclease, Cas9, the successful delivery of guide RNA (gRNA) and Cas9 protein into target cells and tissues is essential. Recent reports demonstrated that Cas9 ribonucleoprotein (RNP) complexes when delivered into target cells by electroporation can accomplish efficient and specific genome editing in several different cell types. Cas9-RNP complexes cleave chromosomal DNA almost immediately after delivery and are degraded rapidly in cells, reducing off-target effects. In contrast, use of plasmid and viral vector systems used to deliver Cas9 results in prolonged expression of the enzyme aggravating off-target effects associated with the system. Additionally, delivery of RNPs into the target cells requires no additional tools which would greatly facilitate translation of genome editing for therapeutic purposes in the clinic. Purified recombinant Cas9 protein and gRNA complexes (RNPs) were delivered into cultured HSPC and an overview experiments used are shown in FIG. 17.


Recombinant Cas9 protein was purified from Escherichia coli and complexed with synthetic dual gRNAs (dgRNA) that consist of crRNA and tracr to generate ribonucleoprotein (RNP) complexes. The list of gRNAs used in the study are shown in Table 23. The RNP complexes were electroporated into CD34+ HSPC via electroporation as described under materials and methods. The cells were expanded prior to the delivery of RNP complexes. Actively dividing cells may facilitate uptake of RNP complexes delivered by electroporation.









TABLE 23







Relative viable cell recovery, proliferation in CD34+ medium, and


granulocyte/macrophage progenitor colony forming unit (CFU) frequency


for edited and unedited cell cultures in the current study. Percent


recovery, Fold proliferation and CFU frequency were calculated as


described in Materials and Methods. Individual electroporation replicates


are shown. All gRNA molecules were tested in the dgRNA format. The


Tracr sequence was SEQ ID NO: 7808, and the crRNA had the following


format with 2′O-Methyl (m) and Phosphorothioate Bond (*)


modifications indicated: mN*mN*mN*rNrNrNrNrNrNrNrNrNrNrNrNr


NrNrNrNrNrGrUrUrUrUrArGrArGrCrUrArU*mG*m C*mU, where N's


are the residues of the indicated targeting domain












Fold



Guide RNA targeting
%
proliferation
CFU (per


domain ID and replicate
recovery
(7 days)
1000 cells)













CR001030 replicate 1
77.7
7.1
117


CR001030 replicate 2
87.9
4.8
95


CR001028 replicate 1
85.3
10.6
176


CR001028 replicate 2
82.1
10.9
141


CR001095 replicate 1
72.5
7.3
121


CR001095 replicate 2
73.3
7.3
126


CR001212 replicate 1
75.6
7.7
123


CR001212 replicate 2
75.5
8.2
97


CR000312 replicate 1
77.7
12.2
145


CR000312 replicate 2
81.0
9.0
143


g8 replicate 1
80.0
16.6
145


g8 replicate 2
84.6
17.3
145


None/control replicate 1
89.8
19.3
185


None/control replicate 2
81.2
20.5
154









Percent cell recovery at 1 day after electroporation ranged from 72.5% to 89.8% and was similar across conditions, including the unedited but electroporated control (Table 23). The genome edited and unedited HSPC were analyzed for proliferation in CD34+ cell expansion medium. Proliferation ranged from 4.8-fold to 17.3-fold over 7 days for edited cell cultures, and ranged from 19.3 to 20.5-fold for unedited cells (Table 22). Editing by dgRNAs in this study targeting the HPFH or BCL11A erythroid enhancer regions did not alter the composition of cell types in the culture compared to unedited control, as determined by surface marker expression, indicating that targeting these sites does not alter HSPC fate under these conditions (FIG. 26A-B). In contrast, editing with dgRNA targeting g8 in the BCL11A exon resulted in a modest reduction in proliferation but a marked shift in cell composition, specifically a decrease in the percentage of all CD34+ HSPC sub-types as well as of the CD71+ erythroid population and an increase in the percentage of CD14+ monocyte and CD15+ granulocyte populations (Table 23 and FIG. 26A-B). The frequency of granulocyte/macrophage progenitor colony forming units (CFU) was similar across edited cultures, with only a modest CFU reduction in edited cultures (ranging from 95 to 145 CFU per 1000 cells) compared with unedited cultures (154 to 185 CFU per 1000 cells), suggesting that granulocyte/macrophage progenitor function is not grossly altered by targeting these sites (Table 23).


Example 4.6

Methods: Methods are as in Example 4, with the Following Exceptions.


Assembly of Cas9 and guide RNA ribonucleoprotein (RNP) complexes, preparation of HSPC, and electroporation of RNP into HSPC. In some instances, crRNAs containing two different targeting domains were delivered into the same cell culture. In these instances, the total RNP delivered to cells contained 6 μg of Cas9, 3 μg of crRNA and 3 μg of Tracr, as in sub-example 4.1; however, the two crRNAs containing 1.5 μg each were independently complexed Tracr/CAS9 mixtures containing 1.5 μg Tracr and 3 μg Cas9 and only combined when added to the cells. The HSPC collected by centrifugation were resuspended in P3 Primary Cell Solution (Lonza cat. No. PBP3-00675) at a cell density of 2.5×106/mL. The RNP was mixed with 20 μL of cells by pipetting up and down and incubated at RT for 2 min. The RNP/cell mixture (20 μL) was electroporated using code CM-137 on the 4D-Nucleofector (Lonza). Electroporations were performed in duplicate. The dgRNA format used a tracr having SEQ ID NO: 7808, and a crRNA of the sequence mN*mN*mN*rNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrGrUrUrUrUrArGrArGrCrUrArU*mG*m C*mU, where r indicates an RNA base, m indicates a base with 20-Methyl modification, and * indicates a Phosphorothioate Bond, and N's indicate the residues of the indicated targeting domain.


In vitro erythropoiesis and FACS analysis for HbF containing erythroid cells. The cell culture was diluted in fresh medium after 3 days.


Genomic DNA preparation and next generation sequencing (NGS). Genomic DNA was prepared from edited and unedited HSPC at 3 days post-electroporation using Quick Extract DNA Extraction Solution (Epicentre Cat # QE09050).


Results:

Without being bound by theory, it is believed that targeted genetic disruption of the HPFH or BCL11A erythroid enhancer region will relieve repression of γ-globin expression, allowing production of the red blood cells containing elevated HbF protein, (cells expressing fetal hemoglobin are sometimes referred to herein as “F-cells”). The elevated HbF prevents sickling of the red blood cells under deoxygenated conditions and will be therapeutic/curative for the patients of both β-thalassemia and SCD. Autologous hematopoietic stem cell transplantation (HSCT) with ex vivo genome edited HSC from SCD patients was also combined with stem cell expansion enhancing technology, e.g., an aryl hydrocarbon receptor (AHR) inhibitor, e.g., as described in WO2010/059401 (the contents of which are incorporated by reference in their entirety), e.g., Compound 4 to improve ex vivo expansion and increase the dose of gene modified HSC delivered.


For efficient genome editing via programmable nuclease, Cas9, the successful delivery of guide RNA (gRNA) and Cas9 protein into target cells and tissues is essential. Recent reports demonstrated that Cas9 ribonucleoprotein (RNP) complexes when delivered into target cells by electroporation can accomplish efficient and specific genome editing in several different cell types. Cas9-RNP complexes cleave chromosomal DNA almost immediately after delivery and are degraded rapidly in cells, reducing off-target effects. In contrast, use of plasmid and viral vector systems used to deliver Cas9 results in prolonged expression of the enzyme aggravating off-target effects associated with the system. Additionally, delivery of RNPs into the target cells requires no additional tools which would greatly facilitate translation of genome editing for therapeutic purposes in the clinic. Purified recombinant Cas9 protein and gRNA complexes (RNPs) were delivered into cultured HSPC and an overview experiments used are shown in FIG. 17.


Recombinant Cas9 protein was purified from Escherichia coli and complexed with synthetic dual gRNAs (dgRNA) that consist of crRNA and tracr to generate ribonucleoprotein (RNP) complexes. The list of gRNAs used in the study are shown in Table 24. The RNP complexes were electroporated into CD34+ HSPC via electroporation as described under materials and methods. The cells were expanded prior to the delivery of RNP complexes. Actively dividing cells may facilitate uptake of RNP complexes delivered by electroporation.









TABLE 24







HbF induction by simultaneous targeting of both the BCL11A erythroid


enhancer and HPFH regions. All gRNA molecules were tested in the


dgRNA format in duplicate. The tracr used has the sequence of SEQ


ID NO: 7808, and the crRNA had the following format with 2′O-Methyl


(m) and Phosphorothioate Bond (*) modifications indicated:


mN*mN*mN*rNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrGrUrUrUrUr


ArGrArGrCrUrArU*mG*mC*mU, where N's are the residues of


the indicated targeting domain.












Guide

% edited at
% edited at



RNA
% HbF+
targeting
targeting


Guide RNA
targeting
(F cells),
site #1,
site #2,


targeting domain
domain
average of
average of
average of


ID #1
ID #2
replicates
replicates
replicates





CR000312
n/a
41.3
91.3
n/a


CR001128_EH15
n/a
43.7
77.5
n/a


n/a
CR001030
58.0
n/a
85.6


n/a
CR001221
48.6
n/a
92.1


CR000312
CR001030
66.8
58.3
81.2


CR000312
CR001221
60.6
64.2
85.0


CR001128_EH15
CR001030
69.1
49.8
82.9


CR001128_EH15
CR001221
62.7
58.5
84.8


g8
n/a
64.7
94.6
n/a


None/control
n/a
23.8
n/a
n/a









The genome edited and unedited HSPC were analyzed by flow cytometry for expression levels of fetal globin and two erythroid cell surface markers, transferrin receptor (CD71) and glycophorin A (CD235a) using antibodies conjugated to fluorescent dyes. The live cells were identified and gated by exclusion of Live Dead Violet. HPFH region or BCL11A erythroid enhancer targeting resulted in increased percentage of erythroid cells containing HbF compared to mock electroporated cells (Table 24). Induction of HbF positive cells by dgRNA including the targeting domain of g8 targeting exon 2 of BCL11A was also observed in parallel. When the HPFH region and BCL11A erythroid enhancer were targeted simultaneously in the same cell population, the percentage of HbF containing cells was increased beyond that of targeting either region independently (Table 24). Thus, an increase in HbF-containing erythrocytes derived from edited cells can be achieved by targeting either the HPFH region or BCL erythroid enhancer, as well as to a greater extent by simultaneous targeting of both regions.


Genomic PCR products of both regions were independently subjected to next generation sequencing (NGS) to determine the percentage of edited alleles in the cell population. Genome editing was observed in cell cultures electroporated with RNPs containing Cas9, crRNA of the given targeting domain and Tracr (Table 24), but not in control cells with no targeting domain delivered (RNPs containing only Cas9 and Tracr). When RNPs targeting two sites were delivered into the same cell population, editing at both sites was observed (Table 24). In some instances, the percent edited cells at a given site was modestly reduced when two RNPs were delivered compared with when only one RNP was delivered (Table 24), possibly due to the lower RNP concentration targeting a given site in the former instance. Higher editing percentages and potentially higher percentages of HbF containing cells may be achieved by increasing the each individual RNP concentration when two RNPs are delivered simultaneously. An increase in HbF-containing erythrocytes derived from genome edited cells is likely to have therapeutic implications by reduced sickling.


Example 4.7

Methods: Methods are as in Example 4, with the Following Exceptions.


Human CD34+ cell culture. Human CD34+ cells were derived from bone marrow (Lonza, Cat. No. 2M-101D). CD34+ cells were thawed and expanded for 2 days in expansion medium prior to RNP delivery.


Assembly of Cas9 and guide RNA ribonucleoprotein (RNP) complexes, preparation of HSPC, and electroporation of RNP into HSPC. For formation of RNP using single guide RNAs (sgRNAs), 6 μg of sgRNA was added to 6 μg of CAS9 protein (in 0.8 to 1 μL) and 0.5 μL of 5×CCE buffer (20 mM HEPES, 100 mM KCL, 5 mM MgCL2, 5% Glycerol and freshly added 1 mM DTT) in a total volume of 5 μL and incubated for 5 min at 37° C. The HSPC were collected by centrifugation were resuspended in P3 Primary Cell Solution (Lonza cat. No. PBP3-00675) at a cell density of 6.4×106/mL. The RNP was mixed with 20 μL of cells by pipetting up and down and incubated at RT for 2 min. The RNP/cell mixture (20 μL) was electroporated using code CM-137 on the 4D-Nucleofector (Lonza). Electroporations were performed in duplicate. For dgRNA, dgRNA-PS and dgRNA-OMePS the Tracr was SEQ ID NO: 6660, with the exception of g8 which was used with Tracr SEQ ID NO: 7808. The formats for all gRNAs used in this experiment are shown in Table 36, with the exception of the dgRNA g8 OMePS, which included a crRNA having the sequence mC*mA*mC*AAACGGAAACAAUGCAAGUUUUAGAGCUAU*mG*mC*mU. and a tracr having the sequence of SEQ ID NO: 7808.


In vitro erythropoiesis and FACS analysis for HbF containing erythroid cells. After RNP delivery, cells were maintained as per Protocol 1 or Protocol 2. For Protocol 1, the cells were immediately transferred into pre-warmed medium consisting of EDM and supplements. During days 0-7 of culture, EDM was further supplemented with 1 μM hydrocortisone (Sigma H8672), 100 ng/mL human SCF (Life Technologies, Cat. #PHC2113), and 5 ng/mL human IL-3 (Peprotech #10779-598). During days 7-11 of culture, EDM was supplemented with 100 ng/mL of human SCF only. During days 11-21 of culture, EDM had no additional supplements. Cell cultures were adjusted to 4.0×104 cells per ml on day 7. On days 11, 14 and 19, the media was replenished. For Protocol 2, cells were immediately transferred back into 200 al expansion medium and allowed to expand for an additional 2 days. The cultures were counted at 2 days after RNP delivery. The cells were then pelleted and resuspended in pre-warmed medium consisting of EDM and supplements. During days 0-7 of EDM culture, EDM was further supplemented with 1 μM hydrocortisone (Sigma H8672), 100 ng/mL human SCF (Life Technologies, Cat. #PHC2113), and 5 ng/mL human IL-3 (Peprotech #10779-598). During days 7-11 of culture, EDM was supplemented with 100 ng/mL of human SCF only. During days 11-21 of culture, EDM had no additional supplements. Cell cultures were initiated at 4.0×104 cells per ml on day 0, diluted 4-fold with fresh medium on day 4, and adjusted to 2.0×105 cells per ml on day 7. On days 11, 14 and 19, the media was replenished. Viable cells were counted at 7, 18 and 21 days in EDM culture. All viable cell counts were determined by flow cytometry using AccuCheck Counting Beads (ThermoFisher cat. No. PCB100) with inviable cells discriminated by DAPI (4′,6-Diamidino-2-Phenylindole) staining. For both protocols, on days 7, 14 and 21 of the erythroid differentiation culture, the cells were analyzed by intracellular staining for HbF expression. On days 14 and 21 intracellular staining for HbF expression did not include anti-CD71 and anti-CD235a antibodies, and % of HbF positive cells (F-cells) in the entire viable cell population was reported. LIVE/DEAD® Fixable Near-IR Dead Cell Stain (ThermoFisher L34975) was used as the viability dye.


Genomic DNA preparation and next generation sequencing (NGS). Genomic DNA was prepared at 2 and 6 days post-electroporation from edited and unedited HSPC cultured by Protocol 2 using Quick Extract DNA Extraction Solution (Epicentre Cat # QE09050).


Results:

Without being bound by theory, it is believed that targeted genetic disruption of the HPFH region will relieve repression of γ-globin expression, allowing production of the red blood cells containing elevated HbF protein, (cells expressing fetal hemoglobin are sometimes referred to herein as “F-cells”). The elevated HbF prevents sickling of the red blood cells under deoxygenated conditions and will be therapeutic/curative for the patients of both β-thalassemia and SCD. Autologous hematopoietic stem cell transplantation (HSCT) with ex vivo genome edited HSC from SCD patients was also combined with stem cell expansion enhancing technology, e.g., an aryl hydrocarbon receptor (AHR) inhibitor, e.g., as described in WO2010/059401 (the contents of which are incorporated by reference in their entirety), e.g., Compound 4 to improve ex vivo expansion and increase the dose of gene modified HSC delivered.


For efficient genome editing via programmable nuclease, Cas9, the successful delivery of guide RNA (gRNA) and Cas9 protein into target cells and tissues is essential. Recent reports demonstrated that Cas9 ribonucleoprotein (RNP) complexes when delivered into target cells by electroporation can accomplish efficient and specific genome editing in several different cell types. Cas9-RNP complexes cleave chromosomal DNA almost immediately after delivery and are degraded rapidly in cells, reducing off-target effects. In contrast, use of plasmid and viral vector systems used to deliver Cas9 results in prolonged expression of the enzyme aggravating off-target effects associated with the system. Additionally, delivery of RNPs into the target cells requires no additional tools which would greatly facilitate translation of genome editing for therapeutic purposes in the clinic. Purified recombinant Cas9 protein and gRNA complexes (RNPs) were delivered into cultured HSPC and an overview experiments used are shown in FIG. 17.


Recombinant Cas9 protein was purified from Escherichia coli and complexed with synthetic single gRNAs (sgRNA) or dual gRNAs (dgRNA) that consist of crRNA and tracr to generate ribonucleoprotein (RNP) complexes. The formats of gRNAs used in the study are shown in Table 36. The RNP complexes were electroporated into CD34+ HSPC via electroporation as described under materials and methods. The cells were expanded prior to the delivery of RNP complexes and, in some cases (Protocol 2) also after electroporation. Actively dividing cells may facilitate uptake of RNP complexes delivered by electroporation.


Genomic PCR products of the HPFH region were subjected to next generation sequencing (NGS) to determine the percentage of edited alleles in the cell population. Genome editing at the HFPH locus was observed in cell cultures electroporated with RNPs containing Cas9, crRNA of the given targeting domain and Tracr (FIG. 43), but not in control cells with no targeting domain delivered (RNPs containing only Cas9 and Tracr). In some instances, editing was greater at a given target site using modified sgRNAs relative to the other gRNA formats (FIG. 43). Finally, the indel pattern as well as frequency of each indel was assessed for each gRNA by NGS. Indel pattern across multiple replicates using the same gRNA/Cas9 were similar Representative most frequently occurring indels at each target site are shown in Table 37.









TABLE 36







gRNA sequences used in the experiments described in


this sub-example. N indicates the residues of the indicated


targeting domain; mN indicates a 2′-OMe-modified


nucleic acid; *indicates a phosphorothioate modification.









Label
Format
Sequence





CRxxxxxx
sgRNA
NNNNNNNNNNNNNNNNNNNNGUUUUAGAGCUAGAAAUAGCAAGU


sg

UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGA




GUCGGUGCUUUU





CRxxxxxx
sgRNA
mN*mN*mN*NNNNNNNNNNNNNNNNNGUUUUAGAGCUAGAAAUA


OMePS sg

GCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGG


or

CACCGAGUCGGUGCmU*mU*mU*U


CRxxxxxx


sg OMePS





CRxxxxxx
sgRNA
N*N*N*NNNNNNNNNNNNNNNNNGUUUUAGAGCUAGAAAUAGCAA


PS sg or

GUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACC


CRxxxxxx

GAGUCGGUGCU*U*U*U


sg PS





CRxxxxxx
dgRNA
NNNNNNNNNNNNNNNNNNNNGUUUUAGAGCUAUGCUGUUUUG




and




AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUG




AAAAAGUGGCACCGAGUCGGUGCUUUUUUU (SEQ ID NO: 6660)





CRxxxxxx
dgRNA
mN*mN*mN*NNNNNNNNNNNNNNNNNGUUUUAGAGCUAUGCUGU


OMePS

U*mU*mU*mG




and




AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUG




AAAAAGUGGCACCGAGUCGGUGCUUUUUUU (SEQ ID NO: 6660)





CRxxxxxx
dgRNA
N*N*N*NNNNNNNNNNNNNNNNNGUUUUAGAGCUAUGCUGUU*U*


PS

U*G




and




AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUG




AAAAAGUGGCACCGAGUCGGUGCUUUUUUU (SEQ ID NO: 6660)
















TABLE 37







Top indels observed for each gRNA (targeting domain and format) from NGS


sequencing at Day 6 post-RNP introduction. gRNA sequences are as indicated


in Table 36. Capital letters are the naturally occurring nucleotides at and near


the target sequence. Deletions relative to the unmodified target sequence


are shown as “-”; insertions are shown as lowercase letters.










gRNA





targeting

% of


domain ID

all
Indel


and format
Variant Read (Genomic Sequence)
reads
length













g8 dgRNA
ACATTCTTATTTTTATCGAGCACAAACGGAAACAATG-----
47.57%
−5


OMePS
GCAGCCTCTGCTTAGAAAAAGCTGTGGATAAGCCACCT





g8 dgRNA
ACATTCTTATTTTTATCGAGCACAAACGGAAACAATG-
13.92%
−1


OMePS
AATGGCAGCCTCTGCTTAGAAAAAGCTGTGGATAAGCCA



CCT





g8 dgRNA
ACATTCTTATTTTTATCGAGCACAAACGGAAACAATG--
2.89%
−2


OMePS
ATGGCAGCCTCTGCTTAGAAAAAGCTGTGGATAAGCCAC



CT





g8 dgRNA
ACATTCTTATTTTTATCGAGCACAAACGGAAACAATGCA--
2.01%
−6


OMePS
----GCCTCTGCTTAGAAAAAGCTGTGGATAAGCCACCT





g8 dgRNA
ACATTCTTATTTTTATCGAGCACAAACGGAAACAAT-
1.65%
−1


OMePS
CAATGGCAGCCTCTGCTTAGAAAAAGCTGTGGATAAGCC



ACCT





g8 dgRNA
ACATTCTTATTTTTATCGAGCACAAACGGAAACAAaTGCA
1.53%
1


OMePS
ATGGCAGCCTCTGCTTAGAAAAAGCTGTGGATAAGCCAC



CT





CR001028
TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCC----
14.45%
−13



---------CCACCGCATCTCTTTCAGCAGTTGTTTC





CR001028
TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC
7.55%
0



TgCATATCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC





CR001028
TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC
7.49%
−1



TA-ATATCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC





CR001028
TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC
4.94%
−13



-------------ACCGCATCTCTTTCAGCAGTTGTTTC





CR001028
TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC
4.33%
−4



TA----TCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC





CR001028
TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC
2.83%
−2



TA--TATCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC





CR001028
TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCC----
19.29%
−13


OMePS sg
---------CCACCGCATCTCTTTCAGCAGTTGTTTC





CR001028
TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC
7.11%
0


OMePS sg
TgCATATCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC





CR001028
TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC
6.26%
−13


OMePS sg
-------------ACCGCATCTCTTTCAGCAGTTGTTTC





CR001028
TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC
6.19%
−1


OMePS sg
TA-ATATCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC





CR001028
TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC
5.44%
−4


OMePS sg
TA----TCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC





CR001028
TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC
2.89%
−2


OMePS sg
TA--TATCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC





CR001028
TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCC----
15.91%
−13


OMePS
---------CCACCGCATCTCTTTCAGCAGTTGTTTC





CR001028
TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC
8.91%
0


OMePS
TgCATATCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC





CR001028
TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC
4.80%
−4


OMePS
TA----TCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC





CR001028
TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC
4.59%
−13


OMePS
-------------ACCGCATCTCTTTCAGCAGTTGTTTC





CR001028
TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC
2.92%
−1


OMePS
TA-ATATCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC





CR001028
TTCTGTCATGTGTGTCTTGACTCAGAAACCtTGTTCTCCTC
1.75%
0


OMePS
TACATATCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC





CR001028
TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCC----
13.02%
−13


PS
---------CCACCGCATCTCTTTCAGCAGTTGTTTC





CR001028
TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC
8.11%
0


PS
TgCATATCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC





CR001028
TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC
6.08%
−1


PS
TA-ATATCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC





CR001028
TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC
4.43%
−13


PS
-------------ACCGCATCTCTTTCAGCAGTTGTTTC





CR001028
TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC
3.86%
−4


PS
TA----TCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC





CR001028
TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC
2.96%
−2


PS
TA--TATCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC





CR001028
TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCC----
17.48%
−13


PS sg
---------CCACCGCATCTCTTTCAGCAGTTGTTTC





CR001028
TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC
7.01%
−13


PS sg
-------------ACCGCATCTCTTTCAGCAGTTGTTTC





CR001028
TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC
6.84%
0


PS sg
TgCATATCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC





CR001028
TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC
6.05%
−4


PS sg
TA----TCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC





CR001028
TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC
4.59%
−2


PS sg
TA--TATCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC





CR001028
TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC
3.53%
−1


PS sg
TA-ATATCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC





CR001028
TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCC----
10.58%
−13


sg
---------CCACCGCATCTCTTTCAGCAGTTGTTTC





CR001028
TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC
9.11%
0


sg
TgCATATCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC





CR001028
TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC
6.47%
−1


sg
TA-ATATCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC





CR001028
TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC
4.78%
−2


sg
TA--TATCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC





CR001028
TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC
4.06%
−13


sg
-------------ACCGCATCTCTTTCAGCAGTTGTTTC





CR001028
TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC
3.41%
−4


sg
TA----TCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC





CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTC--------
8.30%
−13



------TTTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTgCATATCTCCCCA
4.39%
0



CCGCATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC
2.61%
−5



A-----TCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC
2.18%
−1



ACC-CATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001030
TCTTGACTCAGAAACCtTGTTCTCCTCTACATATCTCCCCA
2.12%
0



CCGCATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC
2.10%
−2



ACC--ATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTC--------
10.40%
−13


IDT
-----TTTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC
4.56%
1


IDT
ACCGgCATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC
3.83%
−1


IDT
AC-GCATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC
3.68%
−2


IDT
ACC--ATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC
2.87%
−5


IDT
A-----TCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCT----------
2.54%
−15


IDT
-----TTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTC--------
9.90%
−13



-----TTTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC
4.63%
1



ACCGgCATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC
3.71%
−1



ACC-CATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC
2.39%
−2



ACC--ATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTgCATATCTCCCCA
2.03%
0



CCGCATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC
1.95%
−5



A-----TCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTC--------
19.91%
−13


OMePS sg
-----TTTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC
5.76%
−1


OMePS sg
ACC-CATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC
3.09%
1


OMePS sg
ACCGgCATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC
3.03%
−4


OMePS sg
ACCG----TCTTTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC
2.98%
−6


OMePS sg
AC------TCTTTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTgCATATCT----------
2.81%
−15


OMePS sg
-----TTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTC--------
8.52%
−13


OMePS
-----TTTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTgCATATCTCCCCA
5.21%
0


OMePS
CCGCATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC
2.63%
1


OMePS
ACCGgCATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC
2.25%
−1


OMePS
AC-GCATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC
1.81%
−5


OMePS
A-----TCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC
1.77%
−1


OMePS
ACC-CATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTC--------
5.99%
−13


PS
-----TTTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTgCATATCTCCCCA
4.09%
0


PS
CCGCATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC
3.90%
1


PS
ACCGgCATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC
3.59%
−5


PS
A-----TCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC
2.86%
−1


PS
ACC-CATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC
2.39%
−2


PS
ACC--ATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTC--------
11.86%
−13


PS sg
-----TTTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC
5.20%
−1


PS sg
ACC-CATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC
3.65%
1


PS sg
ACCGgCATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC
3.33%
−2


PS sg
ACC--ATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC
2.92%
−5


PS sg
A-----TCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACAT---------------
2.14%
−15


PS sg
CTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001030
TCTTGACTCAGAAACCCTGTTCTC--------------------------
2.08%
−26


PS sg
TTTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTC--------
11.22%
−13


sg
-----TTTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC
4.64%
−1


sg
ACC-CATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC
2.78%
1


sg
ACCGgCATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC
2.73%
−5


sg
A-----TCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC
2.34%
−1


sg
AC-GCATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001030
TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC
2.29%
−6


sg
AC------TCTTTCAGCAGTTGTTTCTAAAAATATCCTCC





CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC
4.26%
1



GGTAGgCCACTTAAATGCTTACCAACAGTAGAATTGATAA



AT





CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC-
3.80%
−7



------ACTTAAATGCTTACCAACAGTAGAATTGATAAAT





CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC
1.32%
1



GGTAaGCCACTTAAATGCTTACCAACAGTAGAATTGATAA



AT





CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC
0.98%
−8



GGTA--------AATGCTTACCAACAGTAGAATTGATAAAT





CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC
0.97%
−7



GGT-------TAAATGCTTACCAACAGTAGAATTGATAAAT





CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCAAA-----
0.85%
−6



-GCCACTTAAATGCTTACCAACAGTAGAATTGATAAAT





CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC
0.73%
−1



GGT-



GCCACTTAAATGCTTACCAACAGTAGAATTGATAAAT





CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC
19.40%
1


OMePS sg
GGTAGgCCACTTAAATGCTTACCAACAGTAGAATTGATAA



AT





CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC-
7.73%
−7


OMePS sg
------ACTTAAATGCTTACCAACAGTAGAATTGATAAAT





CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCAA-------
2.97%
−7


OMePS sg
GCCACTTAAATGCTTACCAACAGTAGAATTGATAAAT





CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC
2.78%
−8


OMePS sg
GGTA--------AATGCTTACCAACAGTAGAATTGATAAAT





CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC
2.27%
1


OMePS sg
GGTAaGCCACTTAAATGCTTACCAACAGTAGAATTGATAA



AT





CR001137
AAATGCTTATGACAGCAATAAT-----------------------------------
2.06%
−35


OMePS sg
TACCAACAGTAGAATTGATAAAT





CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCAAA-----
2.04%
−16


OMePS sg
-----------TGCTTACCAACAGTAGAATTGATAAAT





CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC
5.27%
1


OMePS
GGTAGgCCACTTAAATGCTTACCAACAGTAGAATTGATAA



AT





CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC-
4.66%
−7


OMePS
------ACTTAAATGCTTACCAACAGTAGAATTGATAAAT





CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC
2.38%
−8


OMePS
GGTA--------AATGCTTACCAACAGTAGAATTGATAAAT





CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC
1.91%
−7


OMePS
GGT-------TAAATGCTTACCAACAGTAGAATTGATAAAT





CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC
1.72%
1


OMePS
GGTAaGCCACTTAAATGCTTACCAACAGTAGAATTGATAA



AT





CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCAA-------
1.03%
−7


OMePS
GCCACTTAAATGCTTACCAACAGTAGAATTGATAAAT





CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCA--------
0.82%
−8


OMePS
GCCACTTAAATGCTTACCAACAGTAGAATTGATAAAT





CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC-
7.49%
−7


PS
------ACTTAAATGCTTACCAACAGTAGAATTGATAAAT





CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC
6.85%
1


PS
GGTAGgCCACTTAAATGCTTACCAACAGTAGAATTGATAA



AT





CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC
2.64%
−8


PS
GGTA--------AATGCTTACCAACAGTAGAATTGATAAAT





CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC
2.11%
1


PS
GGTAaGCCACTTAAATGCTTACCAACAGTAGAATTGATAA



AT





CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC
1.91%
−3


PS
GG---CCACTTAAATGCTTACCAACAGTAGAATTGATAAAT





CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCAAAC---
1.81%
−10


PS
-------TTAAATGCTTACCAACAGTAGAATTGATAAAT





CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC
1.28%
−7


PS
GGT-------TAAATGCTTACCAACAGTAGAATTGATAAAT





CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC
11.90%
1


PS sg
GGTAGgCCACTTAAATGCTTACCAACAGTAGAATTGATAA



AT





CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC-
7.45%
−7


PS sg
------ACTTAAATGCTTACCAACAGTAGAATTGATAAAT





CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC
4.87%
−25


PS sg
GGTAG-------------------------AATTGATAAAT





CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC
3.82%
−1


PS sg
GGT-



GCCACTTAAATGCTTACCAACAGTAGAATTGATAAAT





CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC
3.57%
1


PS sg
GGTAaGCCACTTAAATGCTTACCAACAGTAGAATTGATAA



AT





CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC
2.81%
−1


PS sg
GGTA-



CCACTTAAATGCTTACCAACAGTAGAATTGATAAAT





CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC
2.35%
−3


PS sg
GGTA---ACTTAAATGCTTACCAACAGTAGAATTGATAAAT





CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC-
6.84%
−7


sg
------ACTTAAATGCTTACCAACAGTAGAATTGATAAAT





CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC
4.54%
1


sg
GGTAGgCCACTTAAATGCTTACCAACAGTAGAATTGATAA



AT





CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC
2.46%
1


sg
GGTAaGCCACTTAAATGCTTACCAACAGTAGAATTGATAA



AT





CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC
1.83%
−7


sg
GGT-------TAAATGCTTACCAACAGTAGAATTGATAAAT





CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC
1.11%
−8


sg
GGTA--------AATGCTTACCAACAGTAGAATTGATAAAT





CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC
0.78%
−4


sg
GGTA----CTTAAATGCTTACCAACAGTAGAATTGATAAAT





CR001137
AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC
0.72%
1


sg
GGTAtGCCACTTAAATGCTTACCAACAGTAGAATTGATAA



AT





CR001221
TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCTG----
29.13%
−4



GGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA





CR001221
TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCT-
4.65%
−1



ACTGGGCAGTAAGAGTGGTGATTAATAGATAGGGACAAA



TTGA





CR001221
TAGCATCTACTCTTGTTCAGGAAACAATGAGGAC-----
4.27%
−5



TGGGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATT



GA





CR001221
TAGCATCTACTCTTGTTCAGGAAACAATGAGG----------
1.47%
−10



GCAGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA





CR001221
TAGCATCTACTCTTGTTCAGGAAACAATGAGGAC----------
1.14%
−10



AGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA





CR001221
TAGCATCTACTCTTGTTCAGG-------------------------
1.04%
−25



TAAGAGTGGTGATTAATAGATAGGGACAAATTGA





CR001221
TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCTtACT
0.86%
0



GGGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA





CR001221
TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCTG----
26.33%
−4


OMePS sg
GGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA





CR001221
TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCT-
15.83%
−1


OMePS sg
ACTGGGCAGTAAGAGTGGTGATTAATAGATAGGGACAAA



TTGA





CR001221
TAGCATCTACTCTTGTTCAGGAAACAATGAGGAC-----
6.26%
−5


OMePS sg
TGGGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATT



GA





CR001221
TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCTG--
3.75%
−2


OMePS sg
TGGGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATT



GA





CR001221
TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCTGtAC
2.61%
1


OMePS sg
TGGGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATT



GA





CR001221
TAGCATCTACTCTTGTTCAGGAAACAATGAGGAC----------
2.15%
−10


OMePS sg
AGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA





CR001221
TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCTGAaC
1.82%
1


OMePS sg
TGGGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATT



GA





CR001221
TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCTG----
32.73%
−4


OMePS
GGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA





CR001221
TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCT-
6.46%
−1


OMePS
ACTGGGCAGTAAGAGTGGTGATTAATAGATAGGGACAAA



TTGA





CR001221
TAGCATCTACTCTTGTTCAGGAAACAATGAGGAC-----
5.49%
−5


OMePS
TGGGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATT



GA





CR001221
TAGCATCTACTCTTGTTCAGGAAACAATGAGG-----------
3.16%
−11


OMePS
CAGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA





CR001221
TAGCATCTACTCTTGTTCAGGAAACAATGAGG----------
2.03%
−10


OMePS
GCAGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA





CR001221
TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCTGtAC
1.53%
1


OMePS
TGGGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATT



GA





CR001221
TAGCATCTACTCTTGTTCAGGAAACAATG------------
1.05%
−12


OMePS
GGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA





CR001221
TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCTG----
33.94%
−4


PS
GGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA





CR001221
TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCT-
7.39%
−1


PS
ACTGGGCAGTAAGAGTGGTGATTAATAGATAGGGACAAA



TTGA





CR001221
TAGCATCTACTCTTGTTCAGGAAACAATGAGGAC-----
5.05%
−5


PS
TGGGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATT



GA





CR001221
TAGCATCTACTCTTGTTCAGGAAACAATGAGGAC----------
4.03%
−10


PS
AGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA





CR001221
TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCTGtAC
1.52%
1


PS
TGGGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATT



GA





CR001221
TAGCATCTACTCTTGTTCAGGAAACAATG------------
1.48%
−12


PS
GGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA





CR001221
TAGCATCTACTCTTGTTCAGGAAACAATGAGG-----------
1.43%
−11


PS
CAGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA





CR001221
TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCTG----
27.00%
−4


PS sg
GGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA





CR001221
TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCT-
13.43%
−1


PS sg
ACTGGGCAGTAAGAGTGGTGATTAATAGATAGGGACAAA



TTGA





CR001221
TAGCATCTACTCTTGTTCAGGAAACAATGAGGAC-----
6.57%
−5


PS sg
TGGGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATT



GA





CR001221
TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCTGtAC
4.28%
1


PS sg
TGGGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATT



GA





CR001221
TAGCATCTACTCTTGTTCAGGAAACAATGAGGACC--
3.13%
−2


PS sg
ACTGGGCAGTAAGAGTGGTGATTAATAGATAGGGACAAA



TTGA





CR001221
TAGCATCTACTCTTGTTCAGGAAACAATGAGGAC----------
2.40%
−10


PS sg
AGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA





CR001221
TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCTG------
2.13%
−8


PS sg
--GTAAGAGTGGTGATTAATAGATAGGGACAAATTGA





CR001221
TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCTG----
26.35%
−4


sg
GGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA





CR001221
TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCT-
8.55%
−1


sg
ACTGGGCAGTAAGAGTGGTGATTAATAGATAGGGACAAA



TTGA





CR001221
TAGCATCTACTCTTGTTCAGGAAACAATGAGGAC-----
7.25%
−5


sg
TGGGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATT



GA





CR001221
TAGCATCTACTCTTGTTCAGGAAACAATGAGGAC----------
2.41%
−10


sg
AGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA





CR001221
TAGCATCTACTCTTGTTCAGGAAACAATGAGG-----------
1.90%
−11


sg
CAGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA





CR001221
TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCTG------
1.82%
−9


sg
---TAAGAGTGGTGATTAATAGATAGGGACAAATTGA





CR001221
TAGCATCTACTCTTGTTCAGGAAACAATG------------
1.81%
−12


sg
GGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA





CR003035
CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC
12.23%
−3



CATG---AGTCTGAGGTGCCTATAGGACATCTATATAAATA





CR003035
CTGGAAGAGAAAtAGTTTTAGTATAACAAGTGAAATACCC
8.25%
0



ATGCTGAGTCTGAGGTGCCTATAGGACATCTATATAAATA





CR003035
CTGGAAGAGAAAtAGTTTTAGTATAACAAGTGAAATACCC
4.47%
−3



ATG---AGTCTGAGGTGCCTATAGGACATCTATATAAATA





CR003035
CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC
3.60%
−1



CAT-



CTGAGTCTGAGGTGCCTATAGGACATCTATATAAATA





CR003035
CTGGAAGAGAAACAGTTTTAGTATAACAAGTGA-------------
2.79%
−14



-GTCTGAGGTGCCTATAGGACATCTATATAAATA





CR003035
CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC
2.55%
−2



CATG--



GAGTCTGAGGTGCCTATAGGACATCTATATAAATA





CR003035
CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATAC---
1.68%
−6



---TGAGTCTGAGGTGCCTATAGGACATCTATATAAATA





CR003035
CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC
13.59%
−3


OMePS sg
CATG---AGTCTGAGGTGCCTATAGGACATCTATATAAATA





CR003035
CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC
5.56%
−2


OMePS sg
CA--CTGAGTCTGAGGTGCCTATAGGACATCTATATAAATA





CR003035
CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC
5.34%
−1


OMePS sg
CAT-



CTGAGTCTGAGGTGCCTATAGGACATCTATATAAATA





CR003035
CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC
5.30%
−2


OMePS sg
CATG--



GAGTCTGAGGTGCCTATAGGACATCTATATAAATA





CR003035
CTGGAAGAGAAACAGTTTTAGTATAACAAGTGA-------------
4.70%
−14


OMePS sg
-GTCTGAGGTGCCTATAGGACATCTATATAAATA





CR003035
CTGGAAGAGAAAtAGTTTTAGTATAACAAGTGAAATACCC
4.44%
−3


OMePS sg
ATG---AGTCTGAGGTGCCTATAGGACATCTATATAAATA





CR003035
CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC
2.05%
−1


OMePS sg
CATG-



TGAGTCTGAGGTGCCTATAGGACATCTATATAAATA





CR003035
CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC
9.22%
−3


OMePS
CATG---AGTCTGAGGTGCCTATAGGACATCTATATAAATA





CR003035
CTGGAAGAGAAAtAGTTTTAGTATAACAAGTGAAATACCC
7.81%
0


OMePS
ATGCTGAGTCTGAGGTGCCTATAGGACATCTATATAAATA





CR003035
CTGGAAGAGAAAtAGTTTTAGTATAACAAGTGAAATACCC
3.79%
−3


OMePS
ATG---AGTCTGAGGTGCCTATAGGACATCTATATAAATA





CR003035
CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC
2.63%
−1


OMePS
CAT-



CTGAGTCTGAGGTGCCTATAGGACATCTATATAAATA





CR003035
CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC
2.00%
−2


OMePS
CA--CTGAGTCTGAGGTGCCTATAGGACATCTATATAAATA





CR003035
CTGGAAGAGAAACAGTTTTAGTATAACAAGTGA-------------
1.92%
−14


OMePS
-GTCTGAGGTGCCTATAGGACATCTATATAAATA





CR003035
CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC-
1.69%
−5


OMePS
----TGAGTCTGAGGTGCCTATAGGACATCTATATAAATA





CR003035
CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC
13.91%
−3


PS
CATG---AGTCTGAGGTGCCTATAGGACATCTATATAAATA





CR003035
CTGGAAGAGAAAtAGTTTTAGTATAACAAGTGAAATACCC
6.11%
−3


PS
ATG---AGTCTGAGGTGCCTATAGGACATCTATATAAATA





CR003035
CTGGAAGAGAAAtAGTTTTAGTATAACAAGTGAAATACCC
3.77%
0


PS
ATGCTGAGTCTGAGGTGCCTATAGGACATCTATATAAATA





CR003035
CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC
3.64%
−1


PS
CAT-



CTGAGTCTGAGGTGCCTATAGGACATCTATATAAATA





CR003035
CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC
2.39%
−2


PS
CATG--



GAGTCTGAGGTGCCTATAGGACATCTATATAAATA





CR003035
CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC
2.16%
−2


PS
CA--CTGAGTCTGAGGTGCCTATAGGACATCTATATAAATA





CR003035
CTGGAAGAGAAAtAGTTTTAGTATAACAAGTGAAATACCC
1.87%
−1


PS
AT-CTGAGTCTGAGGTGCCTATAGGACATCTATATAAATA





CR003035
CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC
8.32%
−1


PS sg
CAT-



CTGAGTCTGAGGTGCCTATAGGACATCTATATAAATA





CR003035
CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC
6.41%
−3


PS sg
CATG---AGTCTGAGGTGCCTATAGGACATCTATATAAATA





CR003035
CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC
4.19%
−2


PS sg
CATG--



GAGTCTGAGGTGCCTATAGGACATCTATATAAATA





CR003035
CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC
4.08%
−2


PS sg
CA--CTGAGTCTGAGGTGCCTATAGGACATCTATATAAATA





CR003035
CTGGAAGAGAAAtAGTTTTAGTATAACAAGTGAAATACCC
3.31%
−1


PS sg
AT-CTGAGTCTGAGGTGCCTATAGGACATCTATATAAATA





CR003035
CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC
2.99%
−4


PS sg
C----TGAGTCTGAGGTGCCTATAGGACATCTATATAAATA





CR003035
CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC-
2.23%
−5


PS sg
----TGAGTCTGAGGTGCCTATAGGACATCTATATAAATA





CR003035
CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC
10.92%
−3


sg
CATG---AGTCTGAGGTGCCTATAGGACATCTATATAAATA





CR003035
CTGGAAGAGAAAtAGTTTTAGTATAACAAGTGAAATACCC
6.05%
−3


sg
ATG---AGTCTGAGGTGCCTATAGGACATCTATATAAATA





CR003035
CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC
5.42%
−1


sg
CAT-



CTGAGTCTGAGGTGCCTATAGGACATCTATATAAATA





CR003035
CTGGAAGAGAAAtAGTTTTAGTATAACAAGTGAAATACCC
4.55%
0


sg
ATGCTGAGTCTGAGGTGCCTATAGGACATCTATATAAATA





CR003035
CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC
4.53%
−2


sg
CA--CTGAGTCTGAGGTGCCTATAGGACATCTATATAAATA





CR003035
CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC
3.59%
−2


sg
CATG--



GAGTCTGAGGTGCCTATAGGACATCTATATAAATA





CR003035
CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC
2.30%
−4


sg
C----TGAGTCTGAGGTGCCTATAGGACATCTATATAAATA





CR001128
GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGCTCCA
10.38%
−1



GGA-GGGTTTGGCCTCTGATTAGGGTGGGGGCGTGGGTGG





CR001128
GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGCTCCA
5.87%
−4



GG----GTTTGGCCTCTGATTAGGGTGGGGGCGTGGGTGG





CR001128
GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGCTCCA
5.50%
1



GGAAaGGGTTTGGCCTCTGATTAGGGTGGGGGCGTGGGT



GG





CR001128
GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGCTCCA
4.87%
−5



GG-----TTTGGCCTCTGATTAGGGTGGGGGCGTGGGTGG





CR001128
GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGC--------
4.61%
−36



----------------------------GTGGGTGG





CR001128
GTCTAGTGCAAGCTAACAaC----------------------------
2.38%
−28



ATCACAGGCTCCAGGATAGGGGGCGTGGGTGG





CR001128
GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGCTCCA
2.00%
−2



GGA--GGTTTGGCCTCTGATTAGGGTGGGGGCGTGGGTGG





CR001128
GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGCTCCA
7.56%
−23


OMePS
GG-----------------------TGGGGGCGTGGGTGG





CR001128
GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGCTCCA
6.53%
−4


OMePS
GG----GTTTGGCCTCTGATTAGGGTGGGGGCGTGGGTGG





CR001128
GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGCTCCA
6.18%
−5


OMePS
GG-----TTTGGCCTCTGATTAGGGTGGGGGCGTGGGTGG





CR001128
GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGCTCCA
6.06%
−1


OMePS
GGA-GGGTTTGGCCTCTGATTAGGGTGGGGGCGTGGGTGG





CR001128
GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGCTCCA
3.92%
1


OMePS
GGAAaGGGTTTGGCCTCTGATTAGGGTGGGGGCGTGGGT



GG





CR001128
GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGCTCCA
2.55%
−10


OMePS
GG----------CCTCTGATTAGGGTGGGGGCGTGGGTGG





CR001128
GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGCTCCA
10.12%
−1


sg
GGA-GGGTTTGGCCTCTGATTAGGGTGGGGGCGTGGGTGG





CR001128
GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGCTCCA
7.05%
−5


sg
GG-----TTTGGCCTCTGATTAGGGTGGGGGCGTGGGTGG





CR001128
GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGCTCCA
4.59%
−4


sg
GG----GTTTGGCCTCTGATTAGGGTGGGGGCGTGGGTGG





CR001128
GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGCTCCA
4.24%
1


sg
GGAAaGGGTTTGGCCTCTGATTAGGGTGGGGGCGTGGGT



GG





CR001128
GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGCTCCA
2.21%
−27


sg
GG---------------------------GGCGTGGGTGG





CR001128
GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGCTCCA
1.66%
−30


sg
G------------------------------CGTGGGTGG





CR001128
GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGC--------
1.48%
−17


sg
---------CTCTGATTAGGGTGGGGGCGTGGGTGG





CR001128
GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGCTCCA
10.59%
−5


sg OMePS
GG-----TTTGGCCTCTGATTAGGGTGGGGGCGTGGGTGG





CR001128
GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGCTCCA
7.59%
−4


sg OMePS
GG----GTTTGGCCTCTGATTAGGGTGGGGGCGTGGGTGG





CR001128
GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGCTCCA
5.92%
−1


sg OMePS
GGA-GGGTTTGGCCTCTGATTAGGGTGGGGGCGTGGGTGG





CR001128
GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGCTCCA
3.38%
1


sg OMePS
GGAAaGGGTTTGGCCTCTGATTAGGGTGGGGGCGTGGGT



GG





CR001128
GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGCTCCA
2.49%
2


sg OMePS
GGAAGagGGTTTGGCCTCTGATTAGGGTGGGGGCGTGGGT



GG





CR001128
GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGCTCCA
1.95%
−16


sg OMePS
GGA----------------TTAGGGTGGGGGCGTGGGTGG





CR001128
GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGCTCCA
1.85%
−2


sg OMePS
GGA--GGTTTGGCCTCTGATTAGGGTGGGGGCGTGGGTGG





CR000312
TATCACAGGCTCCAGGAAGGGTTTGGCCTCTGATTAGG-
11.83%
−1



TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCAGACCTC



TC





CR000312
TATCACAGGCTCCAGGAAGGGTTTGG----------------
5.11%
−16



GGGCGTGGGTGGGGTAGAAGAGGACTGGCAGACCTCTC





CR000312
TATCACAGGCTCCAGGAAGGGTTTGGC-------------------
4.33%
−19



GTGGGTGGGGTAGAAGAGGACTGGCAGACCTCTC





CR000312
TATCACAGGCTCCAGGAAGGGTTTGGCCTCTGATT--
3.63%
−2



GGTGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCAGAC



CTCTC





CR000312
TATCACAGGCTCCAGGAAGGG-----------------------
2.50%
−23



GCGTGGGTGGGGTAGAAGAGGACTGGCAGACCTCTC





CR000312
TATCACAGGCTCCAGGAAGGGTTTGGCCTCTG------
2.47%
−6



GTGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCAGACCT



CTC





CR000312
TATCACAGGCTCCAGGAAGGGTTTGGCCTCTG---------
2.35%
−9



GGGGCGTGGGTGGGGTAGAAGAGGACTGGCAGACCTCTC





CR000312
TATCACAGGCTCCAGGAAGGGTTTGGCCTCTGATTAGG-
12.06%
−1


OMePS
TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCAGACCTC



TC





CR000312
TATCACAGGCTCCAGGAAGGGTTTGG-------------
4.75%
−13


OMePS
TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCAGACCTC



TC





CR000312
TATCACAGGCTCCAGGAAGGGTTTGGCCTCTGATT--
4.32%
−2


OMePS
GGTGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCAGAC



CTCTC





CR000312
TATCACAGGCTCCAGGAAGGGTTTGGC-------------------
3.97%
−19


OMePS
GTGGGTGGGGTAGAAGAGGACTGGCAGACCTCTC





CR000312
TATCACAGGCTCCAGGAAGGGTTTGG----------------
3.28%
−16


OMePS
GGGCGTGGGTGGGGTAGAAGAGGACTGGCAGACCTCTC





CR000312
TATCACAGGCTCCAGGAAGGGTTTGGCCTCTGATTAGaGG
3.25%
1


OMePS
TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCAGACCTC



TC





CR000312
TATCACAGGCTCCAGGAAGGGTTTGGCCTCTGATTAG--
1.91%
−2


OMePS
TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCAGACCTC



TC





CR000312
TATCACAGGCTCCAGGAAGGGTTTGGCCTCTGATTAG--
6.69%
−2


sg
TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCAGACCTC



TC





CR000312
TATCACAGGCTCCAGGAAGGGTTTGGCCTCTGATTAGG-
6.28%
−1


sg
TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCAGACCTC



TC





CR000312
TATCACAGGCTCCAGGAAGGGTTTGGCCTCTGA--------------
4.58%
−29


sg
---------------AGGACTGGCAGACCTCTC





CR000312
TATCACAGGCTCCAGGAAGGGTTTGGCCTCTGATTAGaGG
3.83%
1


sg
TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCAGACCTC



TC





CR000312
TATCACAGGCTCCAGGAAGGGTTTGG----------------
3.74%
−16


sg
GGGCGTGGGTGGGGTAGAAGAGGACTGGCAGACCTCTC





CR000312
TATCACAGGCTCCAGGAAGGGTTTGGCCTCTG---------
3.66%
−9


sg
GGGGCGTGGGTGGGGTAGAAGAGGACTGGCAGACCTCTC





CR000312
TATCACAGGCTCCAGGAAGGGTTTGGCCTCTGATTAGGG-
3.19%
−6


sg
-----CGTGGGTGGGGTAGAAGAGGACTGGCAGACCTCTC





CR000312
TATCACAGGCTCCAGGAAGGGTTTGG-------------
3.18%
−13


sg
TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCAGACCTC



TC





CR000312
TATCACAGGCTCCAGGAAGGGTTTGGCCTCTGATTAGG-
12.59%
−1


sg OMePS
TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCAGACCTC



TC





CR000312
TATCACAGGCTCCAGGAAGGGTTTGGCCTCTGATT--
7.73%
−2


sg OMePS
GGTGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCAGAC



CTCTC





CR000312
TATCACAGGCTCCAGGAAGGGTTTGGCCTCTG---------
6.49%
−9


sg OMePS
GGGGCGTGGGTGGGGTAGAAGAGGACTGGCAGACCTCTC





CR000312
TATCACAGGCTCCAGGAAGGGTTTGG----------------
5.32%
−16


sg OMePS
GGGCGTGGGTGGGGTAGAAGAGGACTGGCAGACCTCTC





CR000312
TATCACAGGCTCCAGGAAGGGTTTGGC-------------------
3.89%
−19


sg OMePS
GTGGGTGGGGTAGAAGAGGACTGGCAGACCTCTC





CR000312
TATCACAGGCTCCAGGAAGGG----------------------
2.50%
−22


sg OMePS
GGCGTGGGTGGGGTAGAAGAGGACTGGCAGACCTCTC





CR000312
TATCACAGGCTCCAGGAAGGGTTTGG-------------
2.50%
−13


sg OMePS
TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCAGACCTC



TC





CR000312
TATCACAGGCTCCAGGAAGGGTTTGGCCTCTGATTAG--
2.25%
−2


sg OMePS
TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCAGACCTC



TC





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGAGG----------
12.51%
−10



ACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTAT-
8.89%
−1



CTAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTT



CTA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTATAaC
7.30%
1



TAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTC



TA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGA-------------
6.20%
−13



CTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA





CR003085
ATGTAAGGAGGATGAGCCACATGGTA--------------
3.50%
−14



AGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTA-----
3.09%
−5



AGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTATA---
2.29%
−3



AGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTATA-
1.64%
−1



TAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTC



TA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGG---------
1.43%
−9



TAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTC



TA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTATA--
1.39%
−2



AAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTATAaC
13.65%
1


OMePS sg
TAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTC



TA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGAGG----------
10.96%
−10


OMePS sg
ACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGA-------------
8.21%
−13


OMePS sg
CTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTAT-
8.15%
−1


OMePS sg
CTAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTT



CTA





CR003085
ATGTAAGGAGGATGAGCCACATGGTA--------------
6.29%
−14


OMePS sg
AGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTA-----
4.53%
−5


OMePS sg
AGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTATA---
3.60%
−3


OMePS sg
AGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTA--
3.47%
−2


OMePS sg
CTAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTT



CTA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTATA-
1.30%
−1


OMePS sg
TAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTC



TA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGG-------------------
1.00%
−37


OMePS sg
------------------TTATATCCTTCTA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTATAaC
10.09%
1


OMePS
TAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTC



TA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGAGG----------
9.05%
−10


OMePS
ACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTAT-
6.52%
−1


OMePS
CTAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTT



CTA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGA-------------
4.94%
−13


OMePS
CTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA





CR003085
ATGTAAGGAGGATGAGCCACATGGTA--------------
4.55%
−14


OMePS
AGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTA-----
2.40%
−5


OMePS
AGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTA--
2.00%
−2


OMePS
CTAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTT



CTA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTATA---
1.82%
−3


OMePS
AGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTATA-
1.57%
−1


OMePS
TAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTC



TA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGAGGT----------
1.16%
−34


OMePS
------------------------TATATCCTTCTA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGAGG----------
15.06%
−10


PS
ACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTAT-
11.15%
−1


PS
CTAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTT



CTA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTATAaC
8.37%
1


PS
TAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTC



TA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGA-------------
7.44%
−13


PS
CTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA





CR003085
ATGTAAGGAGGATGAGCCACATGGTA--------------
5.33%
−14


PS
AGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTA-----
3.58%
−5


PS
AGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTATA---
3.50%
−3


PS
AGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTA--
2.05%
−2


PS
CTAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTT



CTA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGG--------------
1.39%
−14


PS
ACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTATA-
0.86%
−1


PS
TAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTC



TA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTAT-
12.62%
−1


PS sg
CTAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTT



CTA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTATAaC
11.73%
1


PS sg
TAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTC



TA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGAGG----------
8.86%
−10


PS sg
ACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGA-------------
6.59%
−13


PS sg
CTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA





CR003085
ATGTAAGGAGGATGAGCCACATGGTA-------------
4.88%
−14


PS sg
AGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTATA---
3.68%
−3


PS sg
AGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTA--
3.62%
−2


PS sg
CTAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTT



CTA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTATA-
3.48%
−1


PS sg
TAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTC



TA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTA-----
2.90%
−5


PS sg
AGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA





CR003085
ATGTAAGGAGGATGAGCCACATGGTAT------------
1.10%
−12


PS sg
AAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGAGG----------
11.79%
−10


sg
ACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTAT-
9.21%
−1


sg
CTAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTT



CTA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTATAaC
6.84%
1


sg
TAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTC



TA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGA-------------
6.44%
−13


sg
CTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA





CR003085
ATGTAAGGAGGATGAGCCACATGGTA--------------
4.12%
−14


sg
AGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTA-----
3.46%
−5


sg
AGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTATA---
3.22%
−3


sg
AGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTA--
1.65%
−2


sg
CTAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTT



CTA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTATA-
1.07%
−1


sg
TAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTC



TA





CR003085
ATGTAAGGAGGATGAGCCACATGGTATGG--------------
0.95%
−14


sg
ACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA









The genome edited and unedited HSPC were analyzed for proliferation and HbF upregulation in a three-stage erythroid differentiation cell culture protocol. The genome edited and unedited HSPC were analyzed by flow cytometry for expression levels of fetal globin and at day 7 for two erythroid cell surface markers, transferrin receptor (CD71) and glycophorin A (CD235a) using antibodies conjugated to fluorescent dyes. The live cells were identified and gated by exclusion of Live/Dead Fixable Dead Cell Stain. Genome editing with the included HPFH region targeting and BCL11A erythroid enhancer targeting gRNAs did not adversely affect erythroid differentiation as the cultured cells showed percentages of CD71+ cells consistent with erythroblasts similar to unedited cells at day 7 of differentiation, although Protocol 1 and Protocol 2 differed in percentages of CD71+ across conditions (FIG. 44). Cultures treated with the included HPFH region targeting and BCL11A erythroid enhancer targeting gRNAs resulted in similar patterns of relative changes in the percentage of erythroid cells containing HbF compared to mock electroporated cells throughout the 21 day culture period and between the two protocols (FIG. 45, FIG. 46 and FIG. 47). HbF was induced in cells exposed of RNPs and maintained in either Protocol 1 or Protocol 2, however, the percentage of cells that were HbF positive tended to be lower across conditions and timepoints with Protocol 2 (FIG. 45, FIG. 46 and FIG. 47). Induction of HbF was most pronounced with gRNAs consisting of target domains CR001030, CR00312 and CR001128, particularly at the later timepoints (FIG. 45, FIG. 46 and FIG. 47). Across targeting domains, sgRNAs trended to higher induction of HbF than dgRNAs, particularly OMePS modified sgRNAs (FIG. 45, FIG. 46 and FIG. 47). Relatively low induction of HbF with targeting domain CR001137 may be explained by the lower level of editing at this target site (FIG. 43, FIG. 45-FIG. 47). Induction of HbF positive cells by dgRNA including the targeting domain of g8 targeting exon 2 of BCL11A was also observed in parallel (FIG. 45-FIG. 47). An increase in HbF-containing erythrocytes derived from genome edited cells is likely to have therapeutic implications by reduced sickling. Edited cells were capable of proliferating in erythroid differentiation conditions (9 to 53-fold at day 7 and 36 to 143-fold at day 21, FIG. 48), however, in some cases, proliferation was suppressed relative to unedited control cells (14-83% of unedited control at day 7 and 18-95% of unedited control at day 21) (FIG. 48). Lowest proliferation was observed with the cells edited by dgRNA including the targeting domain of g8 targeting exon 2 of BCL11A (30% of unedited control at day 7 and 18% of unedited control at day 21) and with many of the OMePS modified sgRNAs (FIG. 48).


Example 5 Excision Using Two gRNAs to the HPFH Region

Primary human CD34+ HSPCs were electroporated with RNP containing two different gRNA molecules to different sites within the HPFH region. For each RNP, dgRNA molecules as described above, were used. Briefly, RNP comprising a dgRNA targeting a first site within the French HPFH region and RNP comprising a dgRNA targeting a second site within the French HPFH region were combined, and electroporated into CD34+ HSPCs in the following ratios: 0.5× first dgRNA RNP+0.5× second dgRNA RNP; 1.0×g2 dgRNA (“g2”=positive control comprising a targeting domain of CR000088, which targets a coding sequence of the BCL11a gene); no RNPs (“control”). Cells were cultured as described above, and differentiated into erythrocytes using the protocol described above (see FIG. 17). Fetal hemoglobin expression was assessed. The results are shown in FIG. 27 and Table 25. Without being bound by theory, it is believed that simultaneous introduction of RNPs comprising gRNA molecules to two target sequences will cause the deletion (i.e., excision) of the DNA between the two cut sites (e.g., all or most of the DNA between the two cut sites), including any regulatory or coding sequences contained within that region. These results show that RNPs targeting two separate regions within the HPFH region could be delivered simultaneously to CD34+ HSPCs by electroporation and induce fetal hemoglobin expression in edited cells differentiated into erythrocytes.












TABLE 25







Guide RNA targeting




domain ID 1/Guide RNA
% HbF+ (F cells), average



targeting domain ID 2
of replicates



















CR001016/CR001021
50.9



CR001021/CR001034
53.4



CR001034/CR001037
56.1



CR001037/CR001045
50.6



CR001045/CR001058
45.2



CR001058/CR001065
42.6



CR001065/CR001075
43.3



CR001075/CR001086
40.4



CR001086/CR001096
39.3



CR001096/CR001107
41.6



CR001107/CR001135
45.6



CR001143/CR001151
40.1



CR001151/CR001159
40.9



CR001159/CR001166
42.0



CR001166/CR001173
44.8



CR001173/CR001179
43.1



CR001179/CR001191
41.9



CR001191/CR001199
42.7



CR001199/CR001212
48.3



CR001212/CR001227
45.6



CR001016/CR001034
53.4



CR001034/CR001045
50.0



CR001045/CR001065
44.2



CR001065/CR001086
39.1



CR001086/CR001107
43.4



CR001107/CR001143
44.8



CR001143/CR001159
45.0



CR001159/CR001173
46.6



CR001173/CR001191
44.8



CR001191/CR001212
51.7



CR001021/CR001037
56.9



CR001037/CR001058
48.0



CR001058/CR001075
41.7



CR001075/CR001096
41.5



CR001096/CR001135
44.3



CR001135/CR001151
42.9



CR001151/CR001166
41.9



CR001166/CR001179
40.4



CR001179/CR001199
38.5



CR001199/CR001227
40.0



g2
54.0



ctrl
34.5










Example 6. Potential Off-Target Editing Assessment of gRNAs Targeting the BCL11a Enhancer

An oligo insertion based assay (See, e.g., Tsai et al., Nature Biotechnology. 33, 187-197; 2015) was used to determine potential off-target genomic sites cleaved by Cas9 targeting the BCL11a enhancer.


A total of 28 guides (dual guide RNAs comprising the indicated targeting domain) targeting the BCL11a enhancer and 10 gRNAs targeting the HPFH region were screened in the Cas9-expressing HEK293 cells described above, and the results are plotted in FIG. 33 (BCL11a enhancer) and FIG. 49 (HPFH). With respect to the gRNAs targeting the BCL11a enhancer, the assay identified potential off-target sites for some guides, however targeted deep sequencing was used to determine whether the potential sites were bona fide off-target sites cleaved by Cas9. Using primers that flanked the potential off-target sites, isolated genomic DNA was amplified and the amplicons were sequenced. If the potential off-target site was cleaved by Cas9, indels should be detected at the site. From these follow-on interrogations of the potential off-target sites, no indels were detected at the potential off-target sites for at least three of the guide RNAs: CR000311, CR000312, CR001128. With respect to the gRNAs targeting the BCL11a enhancer, the assay did not identify any potential off-target sites for at least gRNAs CR001137, CR001212, and CR001221. Targeted deep sequencing will be performed to determine whether the potential off target sites identified for the other gRNA molecules are bona-fide off target sites cleaved by Cas9.


Example 7: Evaluation of Cas9 Variants
Evaluation in CD34+ Hematopoietic Stem Cells

We evaluated 14 purified Streptococcus pyogenes Cas9 (SPyCas9) proteins by measuring their efficiency of knocking out the beta-2-microglobulin (B2M) gene in primary human hematopoietic stem cells (HSCs). These proteins were divided into 3 groups: the first group consisted of SPyCas9 variants with improved selectivity (Slaymaker et al. 2015, Science 351: 84 (e1.0, e1.1 and K855A); Kleinstiver et al. 2016, Nature 529: 490 (HF)). The second group consisted of wild type SPyCas9 with different numbers and/or positions of the SV40 nuclear localization signal (NLS) and the 6×Histidine (His6) or 8×Histidine (His8) tag with or without a cleavable 1EV site, and a SPyCas9 protein with two cysteine substitutions (C80L, C574E), which have been reported to stabilize Cas9 for structural studies (Nishimasu et al. 2014, Cell 156:935). The third group consisted of the same recombinant SPyCas9 produced by different processes (FIG. 60). B2M knockout was determined by FACS and next generation sequencing (NGS).


Methods
Materials



  • 1. Neon electroporation instrument (Invitrogen, MPK5000)

  • 2. Neon electroporation kit (Invitrogen, MPK1025)

  • 3. crRNA (targeting domain sequence of GGCCACGGAGCGAGACAUCU, complementary to a sequence in the B2M gene, fused to SEQ ID NO: 6607)

  • 4. tracrRNA (SEQ ID NO: 6660)

  • 5. Cas9 storage buffer: 20 mM Tris-Cl, pH 8.0, 200 mM KCl, 10 mM MgCl2

  • 6. Bone marrow derived CD34+ HSCs (Lonza, 2M-101C)

  • 7. Cell culture media (Stemcell Technologies, StemSpam SFEM II with StemSpam CC-100)

  • 8. FACS wash buffer: 2% FCS in PBS

  • 9. FACS block buffer: per mL PBS, add 0.5 ug mouse IgG, 150 ug Fc block, 20 uL FCS

  • 10. Chelex suspension: 10% Chelex 100 (bioRad, Cat#142-1253) in H2O

  • 11. Anti-B2M antibody: Biolegend, cat#316304



Process

Thaw and grow the cells following Lonza's recommendations, add media every 2-3 days. On day 5, pellet the cells at 200×g for 15 min, wash once with PBS, resuspend the cells with T-buffer from NEON kit at 2×104/uL, put on ice. Dilute Cas 9 protein with Cas9 storage buffer to 5 mg/ml. Reconstitute crRNA and tracrRNA to 100 uM with H2O. The ribonucleoprotein (RNP) complex is made by mixing 0.8 uL each of CAS 9 protein, crRNA and tracrRNA with 0.6 uL of Cas9 storage buffer, incubate at room temperature for 10 min. Mix 7 uL of HSCs with RNP complex for two minutes and transfer the entire 10 uL into a Neon pipette tip, electroporate at 1700v, 20 ms and 1 pulse. After electroporation, immediately transfer cells into a well of 24-well plate containing 1 ml media pre-calibrated at 37° C., 5% CO2. Harvest cells 72 hrs post-electroporation for FACS and NGS analysis.


FACS: take 250 uL of the cells from each well of 24-well plate, to wells of 96-well U-bottom plate and pellet the cells. Wash once with 2% FCS (fetal calf serum)-PBS. Add 50 uL FACS block buffer to the cells and incubate on ice for 10 minutes, add 1 uL FITC labeled B2M antibody and incubate for 30 minutes. Wash with 150 uL FACS wash buffer once followed by once more with 200 uL FACS wash buffer once. Cells were resuspended in 200 uL FACS buffer FACS analysis.


NGS sample prep: transfer 250 uL of cell suspension from each well of the 24-well plate to a 1.5 ml Eppendorf tube, add 1 mL PBS and pellet the cells. Add 100 uL of Chelex suspension, incubate at 99° C. for 8 minutes and vortex 10 seconds followed by incubating at 99° C. for 8 minutes, vortex 10 seconds. Pellet down the resin by centrifuging at 10,000×g for 3 minutes and the supernatant lysate is used for PCR. Take 4 uL lysate and do PCR reaction with the b2m primers (b2mg67F: CAGACAGCAAACTCACCCAGT, b2mg67R: CTGACGCTTATCGACGCCCT) using Titanium kit (Clonetech, cat#639208) and follow the manufacturer's instruction. The following PCR conditions are used: 5 minutes at 98° C. for 1 cycle; 15 seconds at 95° C., 15 seconds at 62° C., and 1 minute at 72° C. for 30 cycles; and finally 3 minutes at 72° C. for 1 cycle. The PCR product was used for NGS.


Statistics: The percentage of B2M KO cells by FACS and the percentage of indels by NGS are used to evaluate the CAS 9 cleavage efficiency. The experiment was designed with Cas9 as fixed effect. Each experiment is nested within donors, as nested random effects. Therefore, the mixed linear model was applied for the analysis of FACS and NGS data.


Results

In order to normalize the experimental and donor variations, we graphed the relative activity of each protein to iProt105026, the original design with two SV40 NLS flanking the wild type SPyCas9 and the His6 tag at the C-terminal of the protein (FIG. 34). The statistical analysis shows that compared with the reference Cas9 protein iProt105026, iProt106331, iProt106518, iProt106520 and iProt106521 are not significantly different in knocking out B2M in HSCs, while the other variants tested (PID426303, iProt106519, iProt106522, iProt106545, iProt106658, iProt106745, iProt106746, iProt106747, iProt106884) are highly significantly different from the reference iProt105026 in knocking out B2M in HSCs. We found that moving the His6 tag from the C-terminal to N-terminal (iProt106520) did not affect the activity of the protein (FIG. 34). One NLS was sufficient to maintain activity only when it was placed at the C-terminal of the protein (iProt106521 vs. iProt106522, FIG. 34). Proteins purified from process 1 had consistent higher knockout efficiency than those from processes 2 and 3 (iProt106331 vs. iProt106545 & PID426303, FIG. 34). In general, the SPyCas9 variants with a reported improved selectivity were not as active as the wild type SPyCas9 (iProt106745, iProt106746 and iProt106747, FIG. 34). Interestingly iProt106884 did not cut the targeting site. This is consistent with the report by Kleinstiver et al that this variant failed to cut up to 20% of the legitimate targeting sites in mammalian cells (Kleinstiver et al. 2016, Nature 529: 490). Finally, the Cas9 variant with two cysteine substitutions (iProt106518) maintained high levels of enzymatic activity (FIG. 34).


Next, editing efficiency of RNPs comprising different Cas9 variants were tested with either modified or unmodified gRNAs targeting the +58 enhancer region. sgRNA molecules comprising the targeting domains of cr00312 and cr1128 were tested in either unmodified (CR00312=SEQ ID NO: 342; CR001128=SEQ ID NO: 347) or modified (OMePS CR00312=SEQ ID NO: 1762; OMePS CR001128=SEQ ID NO: 1763), and were precomplexed with Cas9 variants shown in Table 35.









TABLE 35







Cas9 variants tested for biological function with +58 enhancer region-


targeting gRNA molecules.










iProt Code
Construct







iProt106518
NLS-Cas9(C80L/C574E)-NLS-His6



iProt106331
NLS-Cas9-NLS-His6



iProt106745
NLS-Cas9(K855A)-NLS-His6



iProt106884
NLS-Cas9(HF)-NLS-His6










RNP formed as described above were delivered to HSPC cells as described above, and the cells assessed for % editing (by NGS) and % HbF induction upon erythroid differentiation, as described in these Examples. The results are shown in FIG. 42A (% editing) and FIG. 42B (HbF induction). The results show that varying the Cas9 component between those variants tested did not alter the gene editing efficiency of both unmodified and modified versions of sgRNA CR00312 and CR001128, nor did the Cas9 variants impact the ability of the erythroid-differentiated gene edited cells to produce HbF.


Example 8: Ex Vivo Expansion of Gene Edited HSPCs, and Editing Analysis in HSPC Subsets
Expansion of Cells Prior to Gene-Editing

Human bone marrow CD34+ cells were purchased from either AllCells (Cat#: ABM017F) or Lonza (Cat#: 2M-101C) and expanded for 2 to 3 days using StemSpan SFEM (StemCell Technologies; Cat no. 09650) supplemented with 50 ng/mL of thrombopoietin (Tpo, Peprotech; Cat#300-18), 50 ng/mL of human Flt3 ligand (Flt-3L, Peprotech; Cat#300-19), 50 ng/mL of human stem cell factor (SCF, Peprotech; Cat#300-07), human interleukin-6 (IL-6, Peprotech; Cat#200-06), 1% L-glutamine; 2% penicillin/streptomycin, and Compound 4 (0.75 μM).


Electroporation of Cas9 and Guide RNA Ribonucleoprotein (RNP) Complexes into Cells


Cas9-guide RNA ribonucleoprotein complexes (RNPs) were prepared immediately prior to electroporation. For formation of RNP using dual guide RNAs, 3 μg of each of crRNA (in 2.24 μL) and tracrRNA (in 1.25 μL) were first denatured at 95° C. for 2 min in separate tubes and then cooled to room temperature. For preparation of Cas9 protein, 7.3 μg of CAS9 protein (in 1.21 μL) was mixed with 0.52 μL of 5×CCE buffer (20 mM HEPES, 100 mM KCL, 5 mM MgCL2, 5% Glycerol and freshly added 1 mM DTT). TracrRNA was first mixed with the Cas9 preparation and incubated at 37° C. for 5 min. The CrRNA was then added to TracrRNA/CAS9 complexes and incubated for 5 min at 37° C. The HSPC were collected by centrifugation at 200×g for 15 min and resuspended in T buffer affiliated with the Neon electroporation kit (Invitrogen; Cat#: MPK1096) at a cell density of 2×107/mL. RNP was mixed with 12 μL of cells by pipetting up and down 3 times gently. To prepare single guide RNA (sgRNA) and Cas9 complexes, 2.25 μg sgRNA (in 1.5 μL) was mixed with 2.25 μg Cas9 protein (in 3 μL) and incubated at RT for 5 min. The sgRNA/Cas9 complex was then mixed with 10.5 μL of 2×107/mL cells by pipetting up and down several times gently and incubated at RT for 2 min. The RNP/cell mixture (10 μL) was transferred into a Neon electroporation probe. Electroporation was performed with Neon transfection system (Invitrogen; MPK5000S) using 1700 volts/20 milliseconds and 1 pulse.


Expansion of Cells after Gene-Editing


After electroporation, the cells were transferred into 0.5 mL pre-warmed StemSpan SFEM medium supplemented with growth factors, cytokines and Compound 4 as described above and cultured at 37° C. for 3 days. After a total of 10 days of cell expansion, 3 days before electroporation and 7 days after electroporation, the total cell number increased 2-7 fold relative to the starting cell number (FIG. 35).


Genomic DNA Preparation

Genomic DNA was prepared from edited and unedited HSPC at 48 hours post-electroporation. Cells were lysed in 10 mM Tris-HCL, pH 8.0; 0.05% SDS and freshly added Protease K of 25 μg/mL and incubated at 37° C. for 1 hour followed by additional incubation at 85° C. for 15 min to inactivate protease K.


T7E1 Assay

To determine editing efficiency of HSPCs, T7E1 assay was performed. PCR was performed using Phusion Hot Start II High-Fidelity kit (Thermo Scientific; Cat#: F-549L) with the following cycling condition: 98° C. for 30″; 35 cycles of 98° C. for 5″, 68° C. for 20′, 72° C. for 30″; 72° C. for 5 min. The following primers were used: forward primer: 5′-AGCTCCAAACTCTCAAACCACAGGG-3′ and reverse primer: 5′-TACAATTTTGGGAGTCCACACGGCA-3′. PCR products were denatured and re-annealed using the following condition: 95° C. for 5 min, 95-85° C. at −2° C./s, 85-25° C. at −0.1° C./s, 4° C. hold. After annealing, 1 μL of mismatch-sensitive T7 E1 nuclease (NEB, Cat# M0302L) was added into 10 μL of PCR product above and further incubated at 37° C. for 15 min for digestion of hetero duplexes, and the resulting DNA fragments were analyzed by agarose gel (2%) electrophoresis. Editing efficiency was quantified using ImageJ software (http://rsb.info.nih.gov/ij/).


PCR Preparation for Next Generation Sequencing (NGS)

To determine editing efficiency more precisely and patterns of insertions and deletions (indels), the PCR products were subjected to next generation sequencing (NGS). The PCR were performed in duplicate using Titanium Taq PCR kit (Clontech Laboratories; Cat#: 639210) with the following cycling condition: 98° C. for 5 min; 30 cycles of 95° C. for 15 seconds, 68° C. for 15 seconds, 72° C. 1 min; 72° C. for 7 min. The following primers were used: forward primer: 5′-AGCTCCAAACTCTCAAACCACAGGG-3′ and reverse primer: 5′-TACAATTTTGGGAGTCCACACGGCA-3′. The PCR products were analyzed by 2% agarose gel electrophoresis and submitted for deep sequencing.


Flow Cytometry Analysis of Editing Efficiency in Hematopoietic Stem and Progenitor Subpopulations.

Cells were subjected to flow cytometry to characterize editing efficiency in stem and progenitor cell (HSPC) subpopulations. The frequencies of HSPC subsets, including CD34+ cells, CD34+CD90+ cells, CD34+CD90+CD45RA− cells, and CD34+CD9O+CD45RA−CD49f+ cells, prior to (48 hours in culture) and after genome editing (10 days in culture; 3 days after genome editing) was determined from sampling aliquots of cell cultures (FIG. 36, FIG. 37, FIG. 38). Cells were incubated with anti-CD34 (BD Biosciences, Cat#555824), anti-CD38 (BD Biosciences, Cat#560677), anti-CD90 (BD Biosciences, Cat#555596), anti-CD45RA (BD Biosciences, Cat#563963), anti-CD49f (BD Biosciences, Cat#562582) in modified FACS buffer, containing PBS supplemented with 0.5% BSA, 2 mM EDTA pH7.4, at 4° C., in dark for 30 min. Cell viability was determined by 7AAD. Cells were washed with modified FACS buffer and multicolor FACS analysis was performed on a Fortessa (BD Biosciences). Flow cytometry results were analyzed using Flowjo software. Genome edited cells grown in the presence of Compound 4 (alone) exhibited detectible levels of all HSPC subsets assessed, including CD34+, CD34+CD90+, CD34+CD9O+CD45RA−, and CD34+CD9O+CD45RA−CD49f+ subsets, indicating that long-term HSC populations persist in cell culture in the presence of Compound 4 (alone) after genome editing (FIG. 38).


Four hours after gene editing, aliquots of cell cultures were sampled and cells were sorted into HSPC subsets (CD34+, CD34+CD38+, CD34+CD38−, CD34+CD38−CD45RA−, CD34+CD38−CD45RA−CD9O+CD49f−, CD34+CD38−CD45RA−CD9O−CD49f−, and CD34+CD38−CD45RA−CD9O−CD49f+ cells) and subjected to NGS to measure the editing efficiency (Table 28). It is important to note that all hematopoietic subsets, including the subsets enriched in long-term HSCs, displayed similarly high gene editing efficiencies (>95%). This high gene editing efficiency in long-term HSCs has significant therapeutic impact as these cells are capable of engrafting patients in the long-term and sustain life-long hematopoietic multi-lineage regeneration.









TABLE 28







Editing efficiency in each HSPC subset measured by NGS.









gRNA
HSPC subsets
Avg (% Indels)





Dg CR00312
Total (singlets)
97.98%



CD34+CD38−CD45RA−
98.66%



CD34+CD38−CD45RA−CD90+CD49f−
98.19%



CD34+CD38−CD45RA−CD90−CD49f−
98.70%



CD34+CD38−CD45RA−CD90−CD49f+
98.81%


Dg
Total (singlets)
97.62%


CR001128
CD34+CD38−CD45RA−
95.93%



CD34+CD38−CD45RA−CD90−CD49f−
98.00%



CD34+CD38−CD45RA−CD90−CD49f+
99.01%









Example 9 Evaluation of Potential Off-Target Editing
HSPC Culture and CRISPR/Cas9 Genome Editing

Methods for RNP generation and cell manipulation are as in Example 4, with the following exceptions. Human CD34+ cell culture Human CD34+ cells were either isolated from G-CSF mobilized peripheral blood from adult donors (AllCells, Cat. No. mPB025-Reg.E) using immunoselection (Miltenyi) according to the manufacturer's instructions or derived from bone marrow (Hemacare Corporation, Cat. No. BM34C-3). CD34+ cells were thawed and expanded for 2 days or 5 days prior to RNP delivery. After RNP delivery, cells were either cultured for an additional 13 days in expansion medium or cultured in erythroid differentiation medium for 7 or 11 days as follows. During days 0-7 of culture, EDM was further supplemented with 1 μM hydrocortisone (Sigma H8672), 100 ng/mL human SCF (Life Technologies, Cat. #PHC2113), and 5 ng/mL human IL-3 (Peprotech #10779-598). During days 7-11 of culture, EDM was supplemented with 100 ng/mL of human SCF only. At the conclusion of the culture period, cells were harvested for genomic DNA preparation and analysis.


Assembly of Cas9 and guide RNA ribonucleoprotein (RNP) complexes, preparation of HSPC, and electroporation of RNP into HSPC. The HSPC collected by centrifugation were resuspended in P3 Primary Cell Solution (Lonza cat. No. PBP3-00675). The RNP was mixed with 20 μL of cells by pipetting up and down and incubated at RT for 2 min. The RNP/cell mixture (20 μL) was electroporated using code CM-137 on the 4D-Nucleofector (Lonza). dgRNAs comprising a crRNA having the sequence NNNNNNNNNNNNNNNNNNNNGUUUUAGAGCUAUGCUGUUUUG (where N indicates a residue of the indicated targeting domain) and a tracr having the sequence of SEQ ID NO: 6660 were used.


Genomic DNA Extraction

Genomic DNA was isolated from RNP treated and untreated HSPC using the DNeasy Blood & Tissue Kit (Qiagen, Cat #69506) following the manufacturer's recommendations.


In Silico Identification of Potential gRNA Off-Target Loci


Potential off-target loci for the BCL11A+58 region gRNAs CR00309, CR00311, CR00312, CR00316, CR001125, CR001126, CR001127, and CR001128, and the HPFH region gRNAs CR001028, CR001030, CR001137, CR001221, CR003035, and CR003085 were identified as follows. For each gRNA, the 20 nucleotide gRNA protospacer sequence was aligned to the human genome reference sequence (build GRCh38) using the BFAST sequence aligner (version 0.6.4f, Homer et al, PLoS One, 2009, 4(11), e7767, PMID: 19907642) using standard parameters allowing up to 5 nucleotide mismatches. Loci identified were filtered to only contain sites that are 5′ adjacent to the Cas9 canonical 5′-NGG-3′ PAM sequence (i.e. 5′-off-target locus-PAM-3′). Using the BEDTools script (version 2.11.2, Quinlan and Hall, Bioinformatics, 2010 26(6):841-2, PMID: 20110278) sites with 5 nucleotide mismatches were further filtered against RefSeq gene annotations (Pruitt et al, Nucleic Acids Res., 2014 42(Database issue):D756-63, PMID: 24259432) to only contain loci annotated as exons. Counts of the potential off-target loci identified for the BCL11A+58 region and the HPFH region gRNAs are shown in Tables 1 and 2 respectively.









TABLE 29







Counts of in silico off-target loci identified for the


BCL11A +58 region gRNAs CR00309, CR00311, CR00312,


CR00316, CR001125, CR001126, CR001127, and CR001128


with 0, 1, 2, 3 and 4 nucleotide mismatches and 5 nucleotide


mismatches within RefSeq exons are shown.








gRNA



targeting
Number of off-targets with N mismatches














domain ID
0
1
2
3
4
5 RefSeq exons
Total sites

















CR00309
0
0
2
9
77
52
140


CR00311
0
0
3
13
213
38
267


CR00312
0
0
0
6
126
33
165


CR00316
0
0
0
22
234
90
346


CR001125
0
0
1
16
221
83
321


CR001126
0
0
2
26
235
86
349


CR001127
0
0
1
35
331
157
524


CR001128
0
0
0
9
156
42
207
















TABLE 30







Counts of in silico off-target loci identified for the


HPFH region gRNAs CR001028, CR001030, CR001137,


CR001221, CR003035, and CR003085 with 0, 1, 2, 3


and 4 nucleotide mismatches and 5 nucleotide mismatches


within RefSeq exons are shown.








gRNA



targeting
Number of off-targets with N mismatches














domain ID
0
1
2
3
4
5 RefSeq exons
Total sites

















CR001028
0
0
1
11
154
67
233


CR001030
0
0
0
14
125
85
224


CR001137
0
0
1
6
85
21
113


CR001221
0
0
2
17
166
44
229


CR003035
0
0
4
10
158
77
249


CR003085
0
0
0
5
75
16
96









PCR Primer Design for Targeted Amplification of Potential Off-Target Sites

PCR amplicons targeting potential off-target loci (and the on-target locus) identified for the BCL11A +58 region gRNAs (CR00309, CR00311, CR00312, CR00316, CR001125, CR001126, CR001127, and CR001128) and the HPFH region gRNAs (CR001028, CR001030, CR001137, CR001221, CR003035, and CR003085) were design using Primer3 (version 2.3.6, Untergasser et al, Nucleic Acids Res., 2012 40(15):e115, PMID: 22730293) using default parameters aiming for an amplicon size range of approximately 160-300 base pairs in length with the gRNA protospacer sequence located in the center of the amplicon. For gRNA CR001127 PCR primers were only designed for sites with 0-4 nucleotide mismatches, no primers were designed for sites with 5 nucleotide mismatches within RefSeq exons. Resulting PCR primer pairs and amplicon sequences were checked for uniqueness by BLAST searching (version 2.2.19, Altschul et al, J Mol Biol., 1990, 215(3):403-10, PMID: 2231712) sequences against the human genome reference sequence (build GRCh38). Primer pairs resulting in more than one amplicon sequence were discarded and redesigned. Tables 3 and 5 show counts of successful PCR primer pairs designed for the BCL11A+58 region and the HPFH region gRNAs respectively.


Illumina Sequencing Library Preparation, Quantification and Sequencing

Genomic DNA from RNP treated (2 replicates per gRNA) and untreated (1 replicate per gRNA) HSPC samples was quantified using the Quant-iT PicoGreen dsDNA kit (Thermo Fisher, Cat # P7581) using manufacture's recommendations. Illumina sequencing libraries targeting individual off-target loci (and the on-target locus) were generated for each sample using two sequential PCR reactions. The first PCR amplified the target locus using target specific PCR primers (designed above) that were tailed with universal Illumina sequencing compatible sequences. The second PCR added additional Illumina sequencing compatible sequences to the first PCR amplicon, including sample barcodes to enable multiplexing during sequencing. PCR 1 was performed in a final volume of 10 μL with each reaction containing 3-6 ng of gDNA (equivalent to approximately 500-1000 cells), PCR 1 primer pairs (Integrated DNA Technologies) at a final concentration of 0.25 μM and 1× final concentration of Q5 Hot Start Master Mix (New England BioLabs, Cat #102500-140). PCR 1 left primers were 5′ tailed (i.e. 5′-tail-target specific left primer-3′) with sequence 5′-TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG-3′ and right primers were 5′ tailed (i.e. 5′-tail-target specific right primer-3′) with sequence 5′-GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG-3′. PCR 1 was performed on a thermocycler using the following cycling conditions: 1 cycle of 98° C. for 1 min; 25 cycles of 98° C. for 10 sec, 63° C. for 20 sec, and 72° C. for 30 sec; 1 cycle at 72° C. for 2 min. PCR 1 was then diluted 1 in 100 using nuclease free water (Ambion, Cat # AM9932) and used as input into PCR 2. PCR 2 was performed in a final volume of 10 μL with each reaction containing 2 μL of diluted PCR 1 product, PCR 2 primer pairs (Integrated DNA Technologies) at a final concentration of 0.5 μM and 1× final concentration of Q5 Hot Start Master Mix (New England BioLabs, Cat #102500-140). PCR 2 left primer sequence used was 5′-AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTC-3′ and PCR 2 right primer sequence used was 5′-CAAGCAGAAGACGGCATACGAGATNNNNNNNNGTCTCGTGGGCTCGG-3′ where the NNNNNNNN denote an 8 nucleotide barcode sequence used for sample multiplexing as part of the standard Illumina sequencing process. PCR 2 was performed on a thermocycler using the following cycling conditions: 1 cycle of 72° C. for 3 min; 1 cycle of 98° C. for 2 min; 15 cycles of 98° C. for 10 sec, 63° C. for 30 sec, and 72° C. for 2 min. PCR 2 amplicons, now viable Illumina sequencing libraries, were cleaned up using Agencourt AMPure XP beads (Beckman Coulter, Cat # A63882) following the manufacture's recommendations. The cleaned Illumina sequencing libraries were then quantified using standard qPCR quantification methods using Power SYBR Green PCR master mix (Life Technologies, Cat #4367660) and primers specific to the Illumina sequencing library ends (forward primer sequence 5′-CAAGCAGAAGACGGCATACGA-3′ and reverse primer sequence 5′-AATGATACGGCGACCACCGAGA-3′) Illumina sequencing libraries were then pooled equimolar and subjected to Illumina sequencing on a MiSeq instrument (Illumina, Cat # SY-410-1003) with 300 base paired-end reads using a MiSeq Reagent Kit v3 (Illumina, Cat # MS-102-3003) following the manufacture's recommendations. A minimum of 1000-fold sequence coverage was generated for each locus for at least one treated replicate. PCR, cleanup, pooling and sequencing of treated and untreated samples were performed separately to avoid any possibility of cross contamination between treated and untreated samples or PCR amplicons generated therefrom.


Illumina Sequencing Data QC and Variant Analysis

Using default parameters, the Illumina MiSeq analysis software (MiSeq reporter, version 2.6.2, Illumina) was used to generate amplicon specific FASTQ sequencing data files (Cock et al, Nucleic Acids Res. 2010, 38(6):1767-71, PMID: 20015970). FASTQ files were then processed through an internally developed variant analysis pipeline consisting of a series of public domain software packages joined together using a standard Perl script wrapper. The workflow used was divided into five stages.


Stage 1, PCR Primer and On- and Off-Target Sequence QC:

For both on- and off-target sites the 20 nucleotide gRNA protospacer sequence plus PAM sequence and target specific PCR primer sequences (left and right without the additional Illumina sequences) were aligned to the human genome reference sequence (build GRCh38) using a BLAST search (version 2.2.29+, Altschul et al, J Mol Biol., 1990, 215(3):403-10, PMID: 2231712). On- and off-target sites with multiple genomic locations were flagged.


Stage 2, Sequencer File Decompression:

Illumina sequencer generated FASTQ.GZ files were decompressed to FASTQ files using the gzip script (version 1.3.12) and number of reads per file was calculated. Files with no reads were excluded from further analysis.


Stage 3, Sequence Read Alignment and Quality Trimming:

Sequencing reads in FASTQ files were aligned to the human genome reference sequence (build GRCh38) using the BWA-MEM aligner (version 0.7.4-r385, Li and Durbin, Bioinformatics, 2009, 25(14):1754-60, PMID: 19451168) using ‘hard-clipping’ to trim 3′ ends of reads of Illumina sequences and low quality bases. Resulting aligned reads, in the BAM file format (Li et al, Bioinformatics, 2009 25(16):2078-9, PMID: 19505943), were converted to FASTQ files using the SAMtools script (version 0.1.19-44428cd, Li et al, Bioinformatics, 2009 25(16):2078-9, PMID: 19505943). FASTQ files were then aligned again to the human genome reference sequence (build GRCh38) using the BWA-MEM aligner, this time without ‘hard-clipping’.


Stage 4, Variant (SNP and INDEL) Analysis:

BAM files of aligned reads were processed using the VarDict variant caller (version 1.0 ‘Cas9 aware’ modified by developer ZhangWu Lia, Lai et al, Nucleic Acids Res., 2016, 44(11):e108, PMID: 27060149) with allele frequency detection limit set at >=0.0001 to identify variants (SNPs and INDELs). The Cas9 aware VarDict caller is based on a public domain package but able to move ambiguous variant calls, generated due to repetitive sequences in the alignment region of the variant events, toward the potential Cas9 nuclease cut site in the gRNA protospacer sequence located 3 bases 5′ of the PAM sequence. The SAMtools script was used to calculate read coverage per sample amplicon to determine whether the on- and off-target sites were covered at >1000-fold sequence coverage. Sites with <1000-fold sequence coverage were flagged.


Stage 5, dbSNP Filtering and Treated/Untreated Differential Analysis:


Variants identified were filtered for known variants (SNPs and INDELs) found in dbSNP (build 142, Shery et al, Nucleic Acids Res. 2001, 29(1):308-11, PMID: 11125122). Variants in the treated samples were further filtered to exclude: 1) variants identified in the untreated control samples; 2) variants with a VarDict strand bias of 2:1 (where forward and reverse read counts supporting the reference sequence are balanced but imbalanced for the non-reference variant call); 3) variants located outside a 100 bp window around the potential Cas9 cut site; 4) single nucleotide variants within a 100 bp window around the potential Cas9 cut site. Finally only sites with a combined INDEL frequency of >2% (editing in more than approximately 10-20 cell) in a 100 bp window of the potential Cas9 cut site were considered. Potential active editing sites were further examined at the read alignment level using the Integrative Genome Viewer (IGV version 2.3, Robinson et al, Nat Biotechnol. 2011, 9(1):24-6, PMID: 21221095) that allows for visual inspection of read alignments to the genome reference sequence.


On- and Off-Target Analysis Results

On-target sites for the BCL11A+58 region and the HPFH region gRNAs showed robust editing at the intended Cas9 cut site in treated samples with an INDEL frequency greater than 88% for all gRNAs. Tables 3 and 5 show number of off-target sites characterized in at least one biological replicate. Uncharacterized sites failed PCR primer design or PCR amplification and remain under investigation.


BCL11A+58 Region in Silico Targeted Analysis Results

gRNA CR00309:


The on-target site for gRNA CR00309 showed robust editing at the intended Cas9 cut site with an average INDEL frequency of approximately 92%. Table 31 shows the number of off-target sites characterized. Uncharacterized sites failed in PCR primer design or PCR amplification and remain under investigation. Characterization of potential off-target sites identified four off-target sites in the 100 bp window around the proposed Cas9 cut site in both treated replicates. Site 1 has an average INDEL frequency approximately 18%, has 3 mismatches relative to the on-target gRNA protospacer sequence (5′-CtCaCCtCCACCCTAATCAG-PAM-3′, PAM=AGG) and is located in intron 1 of the Anoctamin 5 gene (ANO5), on chromosome 11 at base pair position 22,195,800-22,195,819, approximately 2.3 kb away from exon 1. Site 2 has an average INDEL frequency of approximately 18%, has 2 mismatches relative to the on-target gRNA protospacer sequence (5′-CACGCCCaCACCtTAATCAG-PAM-3′, PAM=GGG) and is located in an intergenic region of chromosome 12 at base pair position 3,311,901-3,311,926. Site 3 has an average INDEL frequency approximately 80%, has 2 mismatches relative to the on-target gRNA protospacer sequence (5′-CACGaCCCaACCCTAATCAG-PAM-3′, PAM=AGG) and is located in a GenBank (Clark et al., Nucleic Acids Res. 2016 Jan. 4; 44(Database issue): D67-D72, PMID: 26590407) transcript (BC012501 not annotated in RefSeq) on chromosome 1 at base pair position 236,065,415-236,065,434. Site 4 has an average INDEL frequency of approximately 2%, has 4 mismatches relative to the on-target gRNA protospacer sequence (5′-CtaGCCCCtACCCTAATaAG-3′, PAM=TGG) and is located in intron 1 of a GenBank annotated transcript called polyhomeotic 2 protein (not annotated in RefSeq) on chromosome 1 at base pair position 33,412,659-33,412,678.


gRNA CR00311:


The on-target site for gRNA CR00311 showed robust editing at the intended Cas9 cut site with an average INDEL frequency of approximately 95%. Table 31 shows the number of off-target sites successfully characterized. Uncharacterized sites failed in PCR primer design or PCR amplification and remain under investigation. To date no significant off-target activity was observed at sites examined.


gRNA CR000312:


The on-target site for gRNA CR000312 showed robust editing at the intended Cas9 cut site with an average INDEL frequency of approximately 98%. Table 31 shows the number of off-target sites successfully characterized. Uncharacterized sites failed in PCR primer design or PCR amplification and remain under investigation. To date no significant off-target activity was observed at sites examined.


gRNA CR000316:


The on-target site for gRNA CR000316 showed robust editing at the intended Cas9 cut site in with an average INDEL frequency of approximately 91%, however the majority of off-target sites remain to be characterized.


gRNA CR001125:


The on-target site for gRNA CR0001125 showed robust editing at the intended Cas9 cut site with an average INDEL frequency of approximately 91%. Table 31 shows the number of off-target sites successfully characterized. Uncharacterized sites failed in PCR primer design or PCR amplification and remain under investigation. To date no significant off-target activity was observed at sites examined.


gRNA CR001126:


The on-target site for gRNA CR0001126 showed robust editing at the intended Cas9 cut site with an average INDEL frequency of approximately 92%. Table 31 shows the number of off-target sites successfully characterized. Uncharacterized sites failed in PCR primer design or PCR amplification and remain under investigation. Characterization of potential off-target sites identified two off-target sites to date in the 100 bp window around the proposed Cas9 cut site in both treated replicates. The first site has an average INDEL frequency approximately 2%, has 2 mismatches relative to the on-target gRNA protospacer sequence (5′-TTTATaACAGGCTCCAGaAA-PAM-3′, PAM=TGG) and is located in an intergenic region on chromosome 4 at base pair position 35,881,815-35,881,834, approximately 9.5 kb away from the nearest GenBank transcript (not annotated in RefSeq). The second site has an average INDEL frequency of approximately 1.7%, has 4 mismatches relative to the on-target gRNA protospacer sequence (5′ caTATCACAGGCcCCAGGAg-PAM-3′, PAM=GGG) and is located in intron 6 of the Ataxin 1 gene (ATXN1), on chromosome 6 at base pair position 16,519,907-16,519,926, approximately 2.7 kb away from exon 6.


gRNA CR001127:


The on-target site for gRNA CR0001127 showed robust editing at the intended Cas9 cut site with an average INDEL frequency of approximately 97%. Table 31 shows the number of off-target sites successfully characterized. Uncharacterized sites failed in PCR primer design or PCR amplification and remain under investigation. To date no significant off-target activity was observed at sites examined.


gRNA CR001128:


The on-target site for gRNA CR0001128 showed robust editing at the intended Cas9 cut site with an average INDEL frequency of approximately 94%. Table 31 shows the number of off-target sites successfully characterized. Uncharacterized sites failed in PCR primer design or PCR amplification and remain under investigation. To date no significant off-target activity was observed at sites examined.


Manual inspection of all actively edited BCL11 +58 region off-target sites identified showed typical INDEL patterns surrounding the proposed Cas9 cut site typical of Cas9 mediated double stranded break non homologous end joining DNA repair. It is unclear whether editing at the sites identified has any detrimental effect on gene expression or cell viability, further analysis is required.









TABLE 31







Counts of in silico off-target sites identified, sites successfully


characterized in at least one treated replicate and sites that show


editing for the BCL11A +58 region gRNAs CR00309, CR00311,


CR00312, CR00316, CR001125, CR001126, CR001127, and


CR001128 are shown.











Total
Number of in




number of
silico off-
Number



in silico
target sites
of active in silico


gRNA name
off-target sites
characterized
off-target sites identified





CR00309
141
140
4


CR00311
267
245
0


CR00312
165
163
0


CR00316
346
TBD
TBD


CR001125
321
319
0


CR001126
349
348
2


CR001127*
367
365
0


CR001128
207
194
0





*only sites with 0-4 nucleotide mismatches were examined.






BCL11A+58 Region GUIDE-Seq Hit Validation Results

Potential off-target hits identified by GUIDE-seq (Tsai et al, Nat Biotechnol. 2015, 33(2):187-97, PMID: 25513782) were characterized in RNP treated and untreated HSPC using targeted sequencing methods described above for in silico defined sites. GUIDE-seq potential hits were identified for gRNAs CR00312, CR00316, CR001125, CR001126, CR001127 and CR001128. No potential hits were identified for gRNA CR00311 and CR001128. When the potential hits were interrogated in HSPCs using targeted sequencing, none of the potential hits validated in treated HSPC for gRNA CR00312, CR001125 and CR001127. One potential hit validated for gRNA CR001126, the same site that was identified by the in silico directed method in intron 6 of ATXN1 (chromosome 6:16,519,907-16,519,926 base pairs).Validation of potential hits for gRNAs CR00309 and CR00316 is still in progress.


HPFH Region in Silico Targeted Analysis Results

gRNA CR001028:


The on-target site for gRNA CR0001028 showed robust editing at the intended Cas9 cut site with an average INDEL frequency of approximately 91%. Table 32 shows the number of off-target sites successfully characterized. Uncharacterized sites failed in PCR primer design or PCR amplification and remain under investigation. Characterization of potential off-target sites identified two off-target sites to date in the 100 bp window around the proposed Cas9 cut site in both treated replicates. Site 1 has an average INDEL frequency approximately 2.8%, has 2 mismatches relative to the on-target gRNA protospacer sequence (5′-TGgGGTGGGGAGATATGaAG-PAM-3′, PAM=AGG) and is located in intron 2 of a non-coding RNA (LF330410, not annotated in RefSeq) located on chromosome 4 at base pair position 58,169,308-58,169,327. Site 2 has an average INDEL frequency approximately 3.5%, has 3 mismatches relative to the on-target gRNA protospacer sequence (5′-gGaGGTGGGGAGAgATGTAG-PAM-3′, PAM=AGG) and is located in intron 1 of the Butyrophilin subfamily 3 member A2 gene (BTN3A2) located on chromosome 6 at base pair position 26,366,733-26,366,752, approximately 1.3 kb from exon 2.


gRNA CR001030:


The on-target site for gRNA CR0001030 showed robust editing at the intended Cas9 cut site with an average INDEL frequency of approximately 89%. Table 32 shows the number of off-target sites successfully characterized. Uncharacterized sites failed in PCR primer design or PCR amplification and remain under investigation. Characterization of potential off-target sites identified one off-target sites to date with average INDEL frequency of 57% in the 100 bp window around the proposed Cas9 cut site in both treated replicates. The site has 3 mismatches relative to the on-target gRNA protospacer sequence (5′-caTGCgGAAAGAGATGCGGT-PAM-3′, PAM=TGG) and is located in exon 4 of the Pyruvate Dehydrogenase Kinase 3 gene (PDK3) located on the X chromosome at base pair position 24,503,476-24,503,495.


gRNA CR001137:


The on-target site for gRNA CR0001037 showed robust editing at the intended Cas9 cut site with an average INDEL frequency of approximately 84%. Table 32 shows the number of off-target sites successfully characterized. Uncharacterized sites failed in PCR primer design or PCR amplification and remain under investigation. To date no significant off-target activity was observed at sites examined.


gRNA CR001221:


The on-target site for gRNA CR0001221 showed robust editing at the intended Cas9 cut site with an average INDEL frequency of approximately 95%. Table 32 shows the number of off-target sites successfully characterized. Uncharacterized sites failed in PCR primer design or PCR amplification and remain under investigation. To date no significant off-target activity was observed at sites examined.


gRNA CR003035:


The on-target site for gRNA CR0003035 showed robust editing at the intended Cas9 cut site with an average INDEL frequency of approximately 89%. Table 32 shows the number of off-target sites successfully characterized. Uncharacterized sites failed in PCR primer design or PCR amplification and remain under investigation. Characterization of potential off-target sites identified two off-target sites to date in the 100 bp window around the proposed Cas9 cut site in both treated replicates. Site 1 has an average INDEL frequency of approximately 20%, has 2 mismatches relative to the on-target gRNA protospacer sequence (5′-AGGtACCTCAaACTCAGCAT-PAM-3′, PAM=AGG) and is located in an intergenic region on chromosome 2 at base pair position 66,281,781-66,281,800 and is approximately 7.1 kb from the nearest transcript (JD432564, not annotated in RefSeq). Site 2 has an average INDEL frequency approximately 2.5%, has 3 mismatches relative to the on-target gRNA protospacer sequence (5′-AGagACCcCAGACTCAGCAT-PAM-3′, PAM=AGG) and is located in an intergenic region on chromosome 10 at base pair position 42,997,289-42,997,308, and is approximately 0.3 kb from MicroRNA 5100 (MIR5100).


gRNA CR003085:


The on-target site for gRNA CR0003038 showed robust editing at the intended Cas9 cut site with an average INDEL frequency of approximately 94%. Table 32 shows the number of off-target sites successfully characterized. Uncharacterized sites failed in PCR primer design or PCR amplification and remain under investigation. Characterization of potential off-target sites identified one off-target sites to date with average INDEL frequency of approximately 2% in the 100 bp window around the proposed Cas9 cut site in both treated replicates. The site has 3 mismatches relative to the on-target gRNA protospacer sequence (5′-ATGGTATGaGAaaTATACTA-PAM-3′, PAM=TGG) and is located in intron 2 of the Solute Carrier Family 25 Member 12 gene (SLC25A12) located on chromosome 2 at base pair position 171,872,630-171,872,649, and is approximately 3.8 kb from exon 3.


Manual inspection of all actively edited HPFH region off-target sites identified showed typical INDEL patterns surrounding the proposed Cas9 cut site typical of Cas9 mediated double stranded break non homologous end joining DNA repair. It is unclear whether editing at the sites identified has any detrimental effect on gene expression or cell viability, further analysis is required.









TABLE 32







Counts of potential in silico off-target sites identified, sites successfully


characterized in at least one treated replicate and sites that show


editing for the HPFH region gRNAs CR001028, CR001030,


CR001137, CR001221, CR003035 and CR003085 are shown.












Number of in




Total number
silico off-
Number of



of in silico
target sites
active in silico


gRNA name
off-target sites
characterized
off-target sites identified













CR001028
233
217
2


CR001030
224
219
1


CR001137
113
109
0


CR001221
229
224
0


CR003035
249
243
2


CR003085
96
95
1









HPFH Region GUIDE-Seq Hit Validation Results

Potential off-target hits identified using GUIDE-seq (Tsai et al, Nat Biotechnol. 2015, 33(2):187-97, PMID: 25513782) were interrogated in RNP treated and untreated HSPC using the same methods described for in silico sites. GUIDE-seq potential off-target hits were identified for gRNA CR001028, CR001030, CR003035 and CR003085 (to date). No hits were identified for gRNAs CR001137 and CR001221 to date. One hit for gRNA CR001028 validated in HSPC, the same site that was identified by the in silico directed method on chromosome 4 at base pair position 58,169,308-58,169,327. One hit validated for gRNA CR001030 in HSPC, the same site that was identified by the in silico directed method in exon 4 of the PDK3 gene. One hit validated for gRNA CR003035 in HSPC, the same site that was identified by the in silico directed method in the intergenic region of chromosome 2 at base pair position 66,281,781-66,281,800. One hit validated for gRNA CR003085 in HSPC, the same site as was identified by the in silico directed method on chromosome 2 at base pair position 171,872,630-171,872,649.


On-Target Analysis for gRNA Editing Efficiency Screening


PCR amplicons targeting the gRNA on-target site were cleaned up using Agencourt AMPure XP beads (Beckman Coulter, Cat # A63882) following the manufacture's recommendations. Samples were quantified using the Quant-iT PicoGreen dsDNA kit (Thermo Fisher, Cat # P7581) using manufacture's recommendations. Amplicons were transformed into Illumina sequencing libraries using the Nextera DNA Library Preparation Kit (Illumina, Cat# FC-121-1031) following the manufacture's recommendations. Resulting sequencing libraries were AMPure bead cleaned up, qPCR quantified, pooled and sequenced with an Illumina MiSeq instrument using 150 base (Illumina, Cat# MS-102-2002) or 250 base (Illumina, Cat# MS-102-2003) paired-end reads as described in the off-target analysis section. For each library a minimum of a 1000-fold sequencing coverage was generated and variants were called using a series of in house scripts. In short, sequencing reads spanning an 80-100 base pair window centered on the gRNA sequence were identified using a string based sequence search, compared to the amplicon sequence, binned by sequence differences and variant frequencies were calculated. Additionally, sequencing reads were aligned to the amplicon sequence using the Illumina MiSeq reporter software (Illumina version 2.6.1) and resulting read alignments were examined using the Integrative Genome Viewer (IGV version 2.3, Robinson et al, Nat Biotechnol. 2011, 9(1):24-6, PMID: 21221095).


Example 10: Evaluation of RNP Concentration On Gene Editing and HbF Induction
RNP Dilution Assay to Determine Optimal RNP Concentration for Gene Editing

Gene editing was performed using a serial dilution of Cas9 (iProt: 106331) and guide ribonucleotide complexes (RNP) concentrations (Table 33). Various gRNA used, their formats, and modification applied in this assay are listed in Table 34.









TABLE 33







RNP dilution used to investigate RNP concentration effect


on gene editing and HbF induction.















RNP
RNP
RNP
RNP
RNP


gRNA
RNP
Conc
Conc
Conc
Conc
Conc


Format
Components
RNP-1
RNP-2
RNP-3
RNP-4
RNP-5
















Single
crRNA (ug)
3
1.5
0.75
0.37
0.18


gRNA
Cas9 (ug)
3
1.5
0.75
0.37
0.18



RNP (uM)
1.94
0.97
0.48
0.24
0.12


Dual
crRNA (ug)
3.86
1.93
0.97
0.48
0.24


gRNA
tracrRNA (ug)
3.86
1.93
0.97
0.48
0.24



Cas9 (ug)
3.86
1.93
0.97
0.48
0.24



RNP (uM)
5.89
2.94
1.47
0.74
0.37
















TABLE 34







List of gRNAs, in single or dual guide format, with or without chemical


modification used in the RNP dilution assay. “OMePS” modification,


with respect to dgRNA format, refers to modified crRNA having


the following structure:


mN*mN*mN*NNNNNNNNNNNNNNNNNGUUUUAGAGCUAUGC


UGUU*mU*mU*mG paired with unmodified tracr (i.e., tracrRNA)


of SEQ ID NO: 6660; and with respect to sgRNA, refers to a


gRNA having the following structure:


mN*mN*mN*NNNNNNNNNNNNNNNNNGUUUUAGAGCUAGAAA


UAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAA


AAGUGGCACCGAGUCGGUGCmU*mU*mU*U, where


N = a nucleotide


of the targeting domain, mN refers to a 2′-OMe-modified nucelotide, and *


refers to a phosphorothioate bond. “Unmodified” refers to a gRNA


having no RNA modifications: dgRNA consist of NNNNNNNNNNNNN


NNNNNNNGUUUUAGAGCUAUGCUGUUUUG paired with SEQ ID


NO: 6660; sgRNA refer to


NNNNNNNNNNNNNNNNNNNNGUUUUAGAGCUAGAAAUAGCA


AGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUG


GCACCGAGUCGGUGCUUUU, where N = the


nucleotides of the indicated targeting domain










gRNA

gRNA Targeting



Format
Sample ID
Domain ID
gRNA Modification





Dual gRNA
1
CR00312
Unmodified



2
CR001128
Unmodified



3
CR00312
OMePS



4
CR001128
OMePS


Single gRNA
5
CR00312
Unmodified



6
CR001128
Unmodified



7
CR00312
OMePS



8
CR001128
OMePS



9
Mock electroporation
N/A




control









CD34+ cells were electroporated as described previously, and subjected to measurement of cell viability, gene editing efficiency, and ability to produce HbF. When assessing cell viability, the results showed that varying RNP concentration had no impact on cell viability upon electroporation, either when single or dual guide format is used (FIG. 39A and FIG. 39B). Upon gene editing of CD34+ cells, NGS data showed that RNP concentrations down to 1.47 uM achieved maximum % gene editing efficiency for unmodified CR00312 and CR001128, and modified CR00312, while maximum % gene editing efficiency for modified CR001228 was achieved at RNP concentrations as low as 2.94 uM (FIG. 40A). For sgRNA formats, all gRNAs tested achieved maximum % editing at RNP concentrations down to 0.48 uM (FIG. 40B). In measuring the ability of gene edited cells to differentiate into erythroid lineage and produce HbF, our data showed that the RNP concentration down to 2.94 uM for dgRNA-containing RNP (FIG. 41A) and down to 0.97 uM for sgRNA-containing RNP (FIG. 41B) resulted in maximum levels of HbF induction.


This application is being filed with a sequence listing. To the extent there are any discrepancies between the sequence listing and any sequence recited in the specification, the sequence recited in the specification should be considered the correct sequence. Unless otherwise indicated, all genomic locations are according to hg38.


INCORPORATION BY REFERENCE

All publications, patents, and patent applications mentioned herein are hereby incorporated by reference in their entirety as if each individual publication, patent or patent application was specifically and individually indicated to be incorporated by reference. In case of conflict, the present application, including any definitions herein, will control.


EQUIVALENTS

Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described herein. While this invention has been disclosed with reference to specific aspects, it is apparent that other aspects and variations of this invention may be devised by others skilled in the art without departing from the true spirit and scope of the invention. The appended claims are intended to be construed to include all such aspects and equivalent variations.

Claims
  • 1. A gRNA molecule comprising a tracr and crRNA, wherein the crRNA comprises a targeting domain that is complementary with a target sequence of a BCL11A gene (e.g., a human BCL11a gene), a BCL11a enhancer (e.g., a human BCL11a enhancer), or a HFPH region (e.g., a human HPFH region).
  • 2. A gRNA molecule of claim 1, wherein the target sequence is of the BCL11A gene, and the targeting domain comprises, e.g., consists of, any one of SEQ ID NO: 1 to SEQ ID NO: 85 or SEQ ID NO: 400 to SEQ ID NO: 1231.
  • 3. A gRNA molecule of claim 1, wherein the target sequence is of a BCL11a enhancer, and the targeting domain comprises, e.g., consists of, any one of SEQ ID NO: 1232 to SEQ ID NO: 1499.
  • 4. A gRNA molecule of claim 1, wherein the target sequence is of a BCL11a enhancer, and the targeting domain comprises, e.g., consists of, any one of SEQ ID NO: 182 to SEQ ID NO: 277 or SEQ ID NO: 334 to SEQ ID NO: 341.
  • 5. A gRNA molecule of claim 4, wherein the targeting domain comprises, e.g., consists of, any one of SEQ ID NO: 341, SEQ ID NO: 246, SEQ ID NO: 248, SEQ ID NO: 247, SEQ ID NO: 245, SEQ ID NO: 249, SEQ ID NO: 244, SEQ ID NO: 199, SEQ ID NO: 251, SEQ ID NO: 250, SEQ ID NO: 334, SEQ ID NO: 185, SEQ ID NO: 186, SEQ ID NO: 336, or SEQ ID NO: 337.
  • 6. A gRNA molecule of claim 4, wherein the targeting domain comprises, e.g., consists of, any one of SEQ ID NO: 247, SEQ ID NO: 248, SEQ ID NO: 335, SEQ ID NO: 336, SEQ ID NO: 337, or SEQ ID NO: 338.
  • 7. A gRNA molecule of claim 4, wherein the targeting domain comprises, e.g., consists of, any one of SEQ ID NO: 248 or SEQ ID NO: 338.
  • 8. A gRNA molecule of claim 4, wherein the targeting domain comprises, e.g., consists of, SEQ ID NO: 248.
  • 9. A gRNA molecule of claim 4, wherein the targeting domain comprises, e.g., consists of, SEQ ID NO: 338.
  • 10. A gRNA molecule of claim 1, wherein the target sequence is of a BCL11a enhancer, and the targeting domain comprises, e.g., consists of, any one of SEQ ID NO: 278 to SEQ ID NO: 333.
  • 11. A gRNA molecule of claim 10, wherein the targeting domain comprises, e.g., consists of, any one of SEQ ID NO: 318, SEQ ID NO: 312, SEQ ID NO: 313, SEQ ID NO: 294, SEQ ID NO: 310, SEQ ID NO: 319, SEQ ID NO: 298, SEQ ID NO: 322, SEQ ID NO: 311, SEQ ID NO: 315, SEQ ID NO: 290, SEQ ID NO: 317, SEQ ID NO: 309, SEQ ID NO: 289, or SEQ ID NO: 281.
  • 12. A gRNA molecule of claim 10, wherein the targeting domain comprises, e.g., consists of, SEQ ID NO: 318.
  • 13. A gRNA molecule of claim 1, wherein the target sequence is of a BCL11a enhancer, and the targeting domain comprises, e.g., consists of, any one of SEQ ID NO: 1596 to SEQ ID NO: 1691.
  • 14. A gRNA molecule of claim 13, wherein the targeting domain comprises, e.g., consists of, any one of SEQ ID NO: 1683, SEQ ID NO: 1638, SEQ ID NO: 1647, SEQ ID NO: 1609, SEQ ID NO: 1621, SEQ ID NO: 1617, SEQ ID NO: 1654, SEQ ID NO: 1631, SEQ ID NO: 1620, SEQ ID NO: 1637, SEQ ID NO: 1612, SEQ ID NO: 1656, SEQ ID NO: 1619, SEQ ID NO: 1675, SEQ ID NO: 1645, SEQ ID NO: 1598, SEQ ID NO: 1599, SEQ ID NO: 1663, SEQ ID NO: 1677, or SEQ ID NO: 1626.
  • 15. A gRNA molecule of claim 1, wherein the target sequence is of a HFPH region (e.g., a French HPFH region), and the targeting domain comprises, e.g., consists of, any one of SEQ ID NO: 86 to SEQ ID NO: 181, SEQ ID NO: 1500 to SEQ ID NO: 1595, or SEQ ID NO: 1692 to SEQ ID NO: 1761.
  • 16. A gRNA molecule of claim 15, wherein the targeting domain comprises, e.g., consists of, any one of SEQ ID NO: 100, SEQ ID NO: 165, SEQ ID NO: 113, SEQ ID NO: 99, SEQ ID NO: 112, SEQ ID NO: 98, SEQ ID NO: 1580, SEQ ID NO: 106, SEQ ID NO: 1503, SEQ ID NO: 1589, SEQ ID NO: 160, SEQ ID NO: 1537, SEQ ID NO: 159, SEQ ID NO: 101, SEQ ID NO: 162, SEQ ID NO: 104, SEQ ID NO: 138, SEQ ID NO: 1536, SEQ ID NO: 1539, SEQ ID NO: 1585.
  • 17. A gRNA molecule of claim 15, wherein the targeting domain comprises, e.g., consists of, any one of SEQ ID NO: 98, SEQ ID NO: 100, SEQ ID NO: 1505, SEQ ID NO: 1589, SEQ ID NO: 1700, or SEQ ID NO: 1750.
  • 18. A gRNA molecule of claim 15, wherein the targeting domain comprises, e.g., consists of, any one of SEQ ID NO: 100, SEQ ID NO: 165, or SEQ ID NO: 113.
  • 19. The gRNA molecule of any of claims 2-18, wherein the targeting domain comprises, e.g., consists of, 17, 18, 19, 20, 21, 22, 23, or 24 consecutive nucleic acids of any one of the recited targeting domain sequences.
  • 20. The gRNA molecule of claim 16, wherein the 17, 18, 19, 20, 21, 22, 23, or 24 consecutive nucleic acids of any one of the recited targeting domain sequences are the 17, 18, 19, 20, 21, 22, 23, or 24 consecutive nucleic acids disposed at the 3′ end of the recited targeting domain sequence.
  • 21. The gRNA molecule of claim 16, wherein the 17, 18, 19, 20, 21, 22, 23, or 24 consecutive nucleic acids of any one of the recited targeting domain sequences are the 17, 18, 19, 20, 21, 22, 23, or 24 consecutive nucleic acids disposed at the 5′ end of the recited targeting domain sequence.
  • 22. The gRNA molecule of claim 16, wherein the 17, 18, 19, 20, 21, 22, 23, or 24 consecutive nucleic acids of any one of the recited targeting domain sequences do not comprise either the 5′ or 3′ nucleic acid of the recited targeting domain sequence.
  • 23. The gRNA molecule of any of claims 2-22, wherein the targeting domain consists of the recited targeting domain sequence.
  • 24. The gRNA molecule of any of the previous claims, wherein a portion of the crRNA and a portion of the tracr hybridize to form a flagpole comprising SEQ ID NO: 6584 or 6585.
  • 25. The gRNA molecule of claim 24, wherein the flagpole further comprises a first flagpole extension, located 3′ to the crRNA portion of the flagpole, wherein said first flagpole extension comprises SEQ ID NO: 6586.
  • 26. The gRNA molecule of claim 24 or 25, wherein the flagpole further comprises a second flagpole extension located 3′ to the crRNA portion of the flagpole and, if present, the first flagpole extension, wherein said second flagpole extension comprises SEQ ID NO: 6587.
  • 27. The gRNA molecule of any of claims 1-26, wherein the tracr comprises SEQ ID NO: 6660 or SEQ ID NO: 6661.
  • 28. The gRNA molecule of any of claims 1-26, wherein the tracr comprises SEQ ID NO: 7812, optionally further comprising, at the 3′ end, an additional 1, 2, 3, 4, 5, 6, or 7 uracil (U) nucleotides.
  • 29. The gRNA molecule of any of claims 1-28, wherein the crRNA comprises, from 5′ to 3′, [targeting domain]-: a) SEQ ID NO: 6584;b) SEQ ID NO: 6585;c) SEQ ID NO: 6605;d) SEQ ID NO: 6606;e) SEQ ID NO: 6607;f) SEQ ID NO: 6608; org) SEQ ID NO: 7806.
  • 30. The gRNA molecule of any of claim 1-23 or 29, wherein the tracr comprises, from 5′ to 3′: a) SEQ ID NO: 6589;b) SEQ ID NO: 6590;c) SEQ ID NO: 6609;d) SEQ ID NO: 6610;e) SEQ ID NO: 6660;f) SEQ ID NO: 6661;g) SEQ ID NO: 7812;h) SEQ ID NO: 7807;i) (SEQ ID NO: 7808;j) SEQ ID NO: 7809;k) any of a) to j), above, further comprising, at the 3′ end, at least 1, 2, 3, 4, 5, 6 or 7 uracil (U) nucleotides, e.g., 1, 2, 3, 4, 5, 6, or 7 uracil (U) nucleotides;l) any of a) to k), above, further comprising, at the 3′ end, at least 1, 2, 3, 4, 5, 6 or 7 adenine (A) nucleotides, e.g., 1, 2, 3, 4, 5, 6, or 7 adenine (A) nucleotides; orm) any of a) to l), above, further comprising, at the 5′ end (e.g., at the 5′ terminus), at least 1, 2, 3, 4, 5, 6 or 7 adenine (A) nucleotides, e.g., 1, 2, 3, 4, 5, 6, or 7 adenine (A) nucleotides.
  • 31. The gRNA molecule of any of claims 1-23, wherein the targeting domain and the tracr are disposed on separate nucleic acid molecules, and wherein the nucleic acid molecule comprising the targeting domain comprises SEQ ID NO: 6607, optionally disposed immediately 3′ to the targeting domain, and the nucleic acid molecule comprising the tracr comprises, e.g., consists of, SEQ ID NO: 6660.
  • 32. The gRNA molecule of any of claims 27-28, wherein the crRNA portion of the flagpole comprises SEQ ID NO: 6607 or SEQ ID NO: 6608.
  • 33. The gRNA molecule of any of claims 1-26, wherein the tracr comprises SEQ ID NO: 6589 or 6590, and optionally, if a first flagpole extension is present, a first tracr extension, disposed 5′ to SEQ ID NO: 6589 or 6590, said first tracr extension comprising SEQ ID NO: 6591.
  • 34. The gRNA molecule of any of claims 1-33, wherein the targeting domain and the tracr are disposed on separate nucleic acid molecules.
  • 35. The gRNA molecule of any of claims 1-33, wherein the targeting domain and the tracr are disposed on a single nucleic acid molecule, and wherein the tracr is disposed 3′ to the targeting domain.
  • 36. The gRNA molecule of claim 35, further comprising a loop, disposed 3′ to the targeting domain and 5′ to the tracr.
  • 37. The gRNA molecule of claim 36, wherein the loop comprises SEQ ID NO: 6588.
  • 38. The gRNA molecule of any of claims 1-23, comprising, from 5′ to 3′, [targeting domain]-: (a) SEQ ID NO: 6601;(b) SEQ ID NO: 6602;(c) SEQ ID NO: 6603;(d) SEQ ID NO: 6604;(e) SEQ ID NO: 7811; or(f) any of (a) to (e), above, further comprising, at the 3′ end, 1, 2, 3, 4, 5, 6 or 7 uracil (U) nucleotides.
  • 39. The gRNA molecule of any of claims 1-40, wherein the targeting domain and the tracr are disposed on a single nucleic acid molecule, and wherein said nucleic acid molecule comprises, e.g., consists of, said targeting domain and SEQ ID NO: 7811, optionally disposed immediately 3′ to said targeting domain.
  • 40. The gRNA molecule of any of claims 1-39 wherein one, or optionally more than one, of the nucleic acid molecules comprising the gRNA molecule comprises: a) one or more, e.g., three, phosphorothioate modifications at the 3′ end of said nucleic acid molecule or molecules;b) one or more, e.g., three, phosphorothioate modifications at the 5′ end of said nucleic acid molecule or molecules;c) one or more, e.g., three, 2′-O-methyl modifications at the 3′ end of said nucleic acid molecule or molecules;d) one or more, e.g., three, 2′-O-methyl modifications at the 5′ end of said nucleic acid molecule or molecules;e) a 2′ O-methyl modification at each of the 4th-to-terminal, 3rd-to-terminal, and 2nd-to-terminal 3′ residues of said nucleic acid molecule or molecules;f) a 2′ O-methyl modification at each of the 4th-to-terminal, 3rd-to-terminal, and 2nd-to-terminal 5′ residues of said nucleic acid molecule or molecules; orf) any combination thereof.
  • 41. A gRNA molecule of claim 1, comprising, e.g., consisting of, the sequence: (a) SEQ ID NO: 342;(b) SEQ ID NO: 343; or(c) SEQ ID NO: 1762.
  • 42. A gRNA molecule of claim 1, comprising, e.g., consisting of: (a) a crRNA comprising, e.g., consisting of, SEQ ID NO: 344, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660;(b) a crRNA comprising, e.g., consisting of, SEQ ID NO: 344, and a tracr comprising, e.g., consisting of, SEQ ID NO: 346;(c) a crRNA comprising, e.g., consisting of, SEQ ID NO: 345, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660; or(d) a crRNA comprising, e.g., consisting of, SEQ ID NO: 345, and a tracr comprising, e.g., consisting of, SEQ ID NO: 346.
  • 43. A gRNA molecule of claim 1, comprising, e.g., consisting of, the sequence: (a) SEQ ID NO: 347;(b) SEQ ID NO: 348; or(c) SEQ ID NO: 1763.
  • 44. A gRNA molecule of claim 1, comprising, e.g., consisting of: (a) a crRNA comprising, e.g., consisting of, SEQ ID NO: 349, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660;(b) a crRNA comprising, e.g., consisting of, SEQ ID NO: 349, and a tracr comprising, e.g., consisting of, SEQ ID NO: 346;(c) a crRNA comprising, e.g., consisting of, SEQ ID NO: 350, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660; or(d) a crRNA comprising, e.g., consisting of, SEQ ID NO: 350, and a tracr comprising, e.g., consisting of, SEQ ID NO: 346.
  • 45. A gRNA molecule of claim 1, comprising, e.g., consisting of, the sequence: (a) SEQ ID NO: 351;(b) SEQ ID NO: 352; or(c) SEQ ID NO: 1764.
  • 46. A gRNA molecule of claim 1, comprising, e.g., consisting of: (a) a crRNA comprising, e.g., consisting of, SEQ ID NO: 353, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660;(b) a crRNA comprising, e.g., consisting of, SEQ ID NO: 353, and a tracr comprising, e.g., consisting of, SEQ ID NO: 346;(c) a crRNA comprising, e.g., consisting of, SEQ ID NO: 354, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660; or(d) a crRNA comprising, e.g., consisting of, SEQ ID NO: 354, and a tracr comprising, e.g., consisting of, SEQ ID NO: 346.
  • 47. A gRNA molecule of claim 1, comprising, e.g., consisting of, the sequence: (a) SEQ ID NO: 355;(b) SEQ ID NO: 356; or(c) SEQ ID NO: 1765.
  • 48. A gRNA molecule of claim 1, comprising, e.g., consisting of: (a) a crRNA comprising, e.g., consisting of, SEQ ID NO: 357, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660;(b) a crRNA comprising, e.g., consisting of, SEQ ID NO: 357, and a tracr comprising, e.g., consisting of, SEQ ID NO: 346;(c) a crRNA comprising, e.g., consisting of, SEQ ID NO: 358, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660; or(d) a crRNA comprising, e.g., consisting of, SEQ ID NO: 358, and a tracr comprising, e.g., consisting of, SEQ ID NO: 346.
  • 49. A gRNA molecule of claim 1, comprising, e.g., consisting of, the sequence: (a) SEQ ID NO: 359;(b) SEQ ID NO: 360; or(c) SEQ ID NO: 1766.
  • 50. A gRNA molecule of claim 1, comprising, e.g., consisting of: (a) a crRNA comprising, e.g., consisting of, SEQ ID NO: 361, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660;(b) a crRNA comprising, e.g., consisting of, SEQ ID NO: 361, and a tracr comprising, e.g., consisting of, SEQ ID NO: 346;(c) a crRNA comprising, e.g., consisting of, SEQ ID NO: 362, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660; or(d) a crRNA comprising, e.g., consisting of, SEQ ID NO: 362, and a tracr comprising, e.g., consisting of, SEQ ID NO: 346.
  • 51. A gRNA molecule of claim 1, comprising, e.g., consisting of, the sequence: (a) SEQ ID NO: 363;(b) SEQ ID NO: 364; or(c) SEQ ID NO: 1767.
  • 52. A gRNA molecule of claim 1, comprising, e.g., consisting of: (a) a crRNA comprising, e.g., consisting of, SEQ ID NO: 365, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660;(b) a crRNA comprising, e.g., consisting of, SEQ ID NO: 365, and a tracr comprising, e.g., consisting of, SEQ ID NO: 346;(c) a crRNA comprising, e.g., consisting of, SEQ ID NO: 366, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660; or(d) a crRNA comprising, e.g., consisting of, SEQ ID NO: 366, and a tracr comprising, e.g., consisting of, SEQ ID NO: 346.
  • 53. A gRNA molecule of claim 1, comprising, e.g., consisting of, the sequence: (a) SEQ ID NO: 367;(b) SEQ ID NO: 368; or(c) SEQ ID NO: 1768.
  • 54. A gRNA molecule of claim 1, comprising, e.g., consisting of: (a) a crRNA comprising, e.g., consisting of, SEQ ID NO: 369, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660;(b) a crRNA comprising, e.g., consisting of, SEQ ID NO: 369, and a tracr comprising, e.g., consisting of, SEQ ID NO: 346;(c) a crRNA comprising, e.g., consisting of, SEQ ID NO: 370, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660; or(d) a crRNA comprising, e.g., consisting of, SEQ ID NO: 370, and a tracr comprising, e.g., consisting of, SEQ ID NO: 346.
  • 55. A gRNA molecule of claim 1, comprising, e.g., consisting of, the sequence: (a) SEQ ID NO: 371;(b) SEQ ID NO: 372; or(c) SEQ ID NO: 1769.
  • 56. A gRNA molecule of claim 1, comprising, e.g., consisting of: (a) a crRNA comprising, e.g., consisting of, SEQ ID NO: 373, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660;(b) a crRNA comprising, e.g., consisting of, SEQ ID NO: 373, and a tracr comprising, e.g., consisting of, SEQ ID NO: 346;(c) a crRNA comprising, e.g., consisting of, SEQ ID NO: 374, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660; or(d) a crRNA comprising, e.g., consisting of, SEQ ID NO: 374, and a tracr comprising, e.g., consisting of, SEQ ID NO: 346.
  • 57. A gRNA molecule of claim 1, comprising, e.g., consisting of, the sequence: (a) SEQ ID NO: 375;(b) SEQ ID NO: 376; or(c) SEQ ID NO: 1770.
  • 58. A gRNA molecule of claim 1, comprising, e.g., consisting of: (a) a crRNA comprising, e.g., consisting of, SEQ ID NO: 377, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660;(b) a crRNA comprising, e.g., consisting of, SEQ ID NO: 377, and a tracr comprising, e.g., consisting of, SEQ ID NO: 346;(c) a crRNA comprising, e.g., consisting of, SEQ ID NO: 378, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660; or(d) a crRNA comprising, e.g., consisting of, SEQ ID NO: 378, and a tracr comprising, e.g., consisting of, SEQ ID NO: 346.
  • 59. A gRNA molecule of claim 1, comprising, e.g., consisting of, the sequence: (a) SEQ ID NO: 379;(b) SEQ ID NO: 380; or(c) SEQ ID NO: 1771.
  • 60. A gRNA molecule of claim 1, comprising, e.g., consisting of: (a) a crRNA comprising, e.g., consisting of, SEQ ID NO: 381, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660;(b) a crRNA comprising, e.g., consisting of, SEQ ID NO: 381, and a tracr comprising, e.g., consisting of, SEQ ID NO: 346;(c) a crRNA comprising, e.g., consisting of, SEQ ID NO: 382, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660; or(d) a crRNA comprising, e.g., consisting of, SEQ ID NO: 382, and a tracr comprising, e.g., consisting of, SEQ ID NO: 346.
  • 61. A gRNA molecule of claim 1, comprising, e.g., consisting of, the sequence: (a) SEQ ID NO: 383;(b) SEQ ID NO: 384; or(c) SEQ ID NO: 1772.
  • 62. A gRNA molecule of claim 1, comprising, e.g., consisting of: (a) a crRNA comprising, e.g., consisting of, SEQ ID NO: 385, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660;(b) a crRNA comprising, e.g., consisting of, SEQ ID NO: 385, and a tracr comprising, e.g., consisting of, SEQ ID NO: 346;(c) a crRNA comprising, e.g., consisting of, SEQ ID NO: 386, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660; or(d) a crRNA comprising, e.g., consisting of, SEQ ID NO: 386, and a tracr comprising, e.g., consisting of, SEQ ID NO: 346.
  • 63. A gRNA molecule of claim 1, comprising, e.g., consisting of, the sequence: (a) SEQ ID NO: 387;(b) SEQ ID NO: 388; or(c) SEQ ID NO: 1773.
  • 64. A gRNA molecule of claim 1, comprising, e.g., consisting of: (a) a crRNA comprising, e.g., consisting of, SEQ ID NO: 389, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660;(b) a crRNA comprising, e.g., consisting of, SEQ ID NO: 389, and a tracr comprising, e.g., consisting of, SEQ ID NO: 346;(c) a crRNA comprising, e.g., consisting of, SEQ ID NO: 390, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660; or(d) a crRNA comprising, e.g., consisting of, SEQ ID NO: 390, and a tracr comprising, e.g., consisting of, SEQ ID NO: 346.
  • 65. A gRNA molecule of claim 1, comprising, e.g., consisting of, the sequence: (a) SEQ ID NO: 391;(b) SEQ ID NO: 392; or(c) SEQ ID NO: 1774.
  • 66. A gRNA molecule of claim 1, comprising, e.g., consisting of: (a) a crRNA comprising, e.g., consisting of, SEQ ID NO: 393, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660;(b) a crRNA comprising, e.g., consisting of, SEQ ID NO: 393, and a tracr comprising, e.g., consisting of, SEQ ID NO: 346;(c) a crRNA comprising, e.g., consisting of, SEQ ID NO: 394, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660; or(d) a crRNA comprising, e.g., consisting of, SEQ ID NO: 394, and a tracr comprising, e.g., consisting of, SEQ ID NO: 346.
  • 67. A gRNA molecule of claim 1, comprising, e.g., consisting of, the sequence: (a) SEQ ID NO: 395;(b) SEQ ID NO: 396; or(c) SEQ ID NO: 1775.
  • 68. A gRNA molecule of claim 1, comprising, e.g., consisting of: (a) a crRNA comprising, e.g., consisting of, SEQ ID NO: 397, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660;(b) a crRNA comprising, e.g., consisting of, SEQ ID NO: 397, and a tracr comprising, e.g., consisting of, SEQ ID NO: 346;(c) a crRNA comprising, e.g., consisting of, SEQ ID NO: 398, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660; or(d) a crRNA comprising, e.g., consisting of, SEQ ID NO: 398, and a tracr comprising, e.g., consisting of, SEQ ID NO: 346.
  • 69. A gRNA molecule of any of claims 1-68, wherein when a CRISPR system (e.g., an RNP as described herein) comprising the gRNA molecule is introduced into a cell, an indel is formed at or near the target sequence complementary to the targeting domain of the gRNA molecule.
  • 70. The gRNA molecule of claim 69, wherein the indel does not comprise a nucleotide of a GATA-1 or TAL-1 binding site.
  • 71. A gRNA molecule of any of claims 1-70, wherein when a CRISPR system (e.g., an RNP as described herein) comprising the gRNA molecule is introduced into a population of cells, an indel is formed at or near the target sequence complementary to the targeting domain of the gRNA molecule in at least about 40%, e.g., at least about 50%, e.g., at least about 60%, e.g., at least about 70%, e.g., at least about 80%, e.g., at least about 90%, e.g., at least about 95%, e.g., at least about 96%, e.g., at least about 97%, e.g., at least about 98%, e.g., at least about 99%, of the cells of the population.
  • 72. A gRNA molecule of any of claims 1-68, wherein when a CRISPR system (e.g., an RNP as described herein) comprising the gRNA molecule is introduced into a population of cells, an indel that does not comprise a nucleotide of a GATA-1 or TAL-1 binding site is formed at or near the target sequence complementary to the targeting domain of the gRNA molecule in at least about 20%, e.g., at least about 30%, e.g., at least about 35%, e.g., at least about 40%, e.g., at least about 45%, e.g., at least about 50%, e.g., at least about 55%, e.g., at least about 60%, e.g., at least about 65%, e.g., at least about 70%, e.g., at least about 75%, e.g., at least about 80%, e.g., at least about 85%, e.g., at least about 90%, e.g., at least about 95%, e.g., at least about 99%, of the cells of the population.
  • 73. The gRNA molecule of any of claims 71-72, wherein in at least about 30%, e.g., least about 40%, e.g., at least about 50%, e.g., at least about 60%, e.g., at least about 70%, e.g., at least about 80%, e.g., at least about 90%, e.g., at least about 95%, e.g., at least about 96%, e.g., at least about 97%, e.g., at least about 98%, e.g., at least about 99%, of the cells of the population, the indel is an indel listed in any of FIG. 25, Table 15, Table 26, Table 27 or Table 37.
  • 74. The gRNA molecule of any of claims 71-73, wherein the three most frequently detected indels in said population of cells comprise the indels associated with any gRNA molecule listed in any of FIG. 25, Table 15, Table 26, Table 27 or Table 37.
  • 75. The gRNA molecule of any of claims 69-74, wherein the indel is as measured by next generation sequencing (NGS).
  • 76. A gRNA molecule of any of claims 1-75, wherein when a CRISPR system (e.g., an RNP as described herein) comprising the gRNA molecule is introduced into a cell, expression of fetal hemoglobin is increased in said cell or its progeny, e.g., its erythroid progeny, e.g., its red blood cell progeny.
  • 77. A gRNA molecule of claim 76, wherein expression of fetal hemoglobin is increased in said cell or its progeny, e.g., its erythroid progeny, e.g., its red blood cell progeny, by at least about 20%, e.g., at least about 30%, e.g., at least about 40%, e.g., at least about 50%, e.g., at least about 60%, e.g., at least about 70%, e.g., at least about 80%, e.g., at least about 90%, e.g., at least about 95%, e.g., at least about 96%, e.g., at least about 97%, e.g., at least about 98%, e.g., at least about 99%.
  • 78. A gRNA molecule of any of claims 76-77, wherein said cell or its progeny, e.g., its erythroid progeny, e.g., its red blood cell progeny, produces at least about 6 picograms (e.g., at least about 7 picograms, at least about 8 picograms, at least about 9 picograms, at least about 10 picograms, or from about 8 to about 9 picograms, or from about 9 to about 10 picograms) fetal hemoglobin per cell.
  • 79. The gRNA molecule of any of claims 1-78, wherein when a CRISPR system (e.g., an RNP as described herein) comprising the gRNA molecule is introduced into a cell, no off-target indels are formed in said cell, e.g., as detectible by next generation sequencing and/or a nucleotide insertional assay.
  • 80. The gRNA molecule of any of claims 1-78, wherein when a CRISPR system (e.g., an RNP as described herein) comprising the gRNA molecule is introduced into a population of cells, no off-target indel is detected in more than about 5%, e.g., more than about 1%, e.g., more than about 0.1%, e.g., more than about 0.01%, of the cells of the population of cells, e.g., as detectible by next generation sequencing and/or a nucleotide insertional assay.
  • 81. The gRNA molecule of any of claims 69-80, wherein the cell is (or population of cells comprises) a mammalian, primate, or human cell, e.g., is a human cell.
  • 82. The gRNA molecule of claim 81, wherein the cell is (or population of cells comprises) an HSPC.
  • 83. The gRNA molecule of claim 82, wherein the HSPC is CD34+.
  • 84. The gRNA molecule of claim 83, wherein the HSPC is CD34+CD90+.
  • 85. The gRNA molecule of any of claims 69-84, wherein the cell is autologous with respect to a patient to be administered said cell.
  • 86. The gRNA molecule of any of claims 69-84, wherein the cell is allogeneic with respect to a patient to be administered said cell.
  • 87. A composition comprising: 1) one or more gRNA molecules (including a first gRNA molecule) of any of claims 1-86 and a Cas9 molecule;2) one or more gRNA molecules (including a first gRNA molecule) of any of claims 1-86 and nucleic acid encoding a Cas9 molecule;3) nucleic acid encoding one or more gRNA molecules (including a first gRNA molecule) of any of claims 1-86 and a Cas9 molecule;4) nucleic acid encoding one or more gRNA molecules (including a first gRNA molecule) of any of claims 1-86 and nucleic acid encoding a Cas9 molecule; or5) any of 1) to 4), above, and a template nucleic acid; or6) any of 1) to 4) above, and nucleic acid comprising sequence encoding a template nucleic acid.
  • 88. A composition comprising a first gRNA molecule of any of claims 1-86, further comprising a Cas9 molecule.
  • 89. The composition of claim 87 or 88, wherein the Cas9 molecule is an active or inactive s. pyogenes Cas9.
  • 90. The composition of claim 87-89, wherein the Cas9 molecule comprises SEQ ID NO: 6611.
  • 91. The composition of claim 87-89, wherein the Cas9 molecule comprises, e.g., consists of: (a) SEQ ID NO: 7821;(b) SEQ ID NO: 7822;(c) SEQ ID NO: 7823;(d) SEQ ID NO: 7824;(e) SEQ ID NO: 7825;(f) SEQ ID NO: 7826;(g) SEQ ID NO: 7827;(h) SEQ ID NO: 7828;(i) SEQ ID NO: 7829;(j) SEQ ID NO: 7830; or(k) SEQ ID NO: 7831.
  • 92. The composition of any of claims 88-91, wherein the first gRNA molecule and Cas9 molecule are present in a ribonuclear protein complex (RNP).
  • 93. The composition of any of claims 87-92, further comprising a second gRNA molecule; a second gRNA molecule and a third gRNA molecule; or a second gRNA molecule, optionally, a third gRNA molecule, and, optionally, a fourth gRNA molecule, wherein the second gRNA molecule, the optional third gRNA molecule, and the optional fourth gRNA molecule are a gRNA molecule of any of claims 1-68, and wherein each gRNA molecule of the composition is complementary to a different target sequence.
  • 94. The composition of claim 93, wherein two or more of the first gRNA molecule, the second gRNA molecule, the optional third gRNA molecule, and the optional fourth gRNA molecule are complementary to target sequences within the same gene or region.
  • 95. The composition of claim 93 or 94, wherein the first gRNA molecule, the second gRNA molecule, the optional third gRNA molecule, and the optional fourth gRNA molecule are complementary to target sequences not more than 20000 nucleotides, not more than 10000 nucleotides, not more than 6000, not more than 5000 nucleotides, not more than 4000, not more than 1000 nucleotides, not more than 500 nucleotides, not more than 400 nucleotides, not more than 300 nucleotides, not more than 200 nucleotides, not more than 100 nucleotides, not more than 90 nucleotides, not more than 80 nucleotides, not more than 70 nucleotides, not more than 60 nucleotides, not more than 50 nucleotides, not more than 40 nucleotides, not more than 30 nucleotides, not more than 20 nucleotides or not more than 10 nucleotides apart.
  • 96. The composition of claim 93, wherein two or more of the first gRNA molecule, the second gRNA molecule, the optional third gRNA molecule, and the optional fourth gRNA molecule are complementary to target sequence within different genes or regions.
  • 97. The composition of any of claims 94-95, comprising a first gRNA molecule and a second gRNA molecule, wherein the first gRNA molecule and second gRNA molecule are: (a) independently selected from the gRNA molecules of claim 4, and are complementary to different target sequences;(b) independently selected from the gRNA molecules of claim 5, and are complementary to different target sequences;c) independently selected from the gRNA molecules of claim 6, and are complementary to different target sequences; or(d) independently selected from the gRNA molecules of claim 7, and are complementary to different target sequences; or(e) independently selected from the gRNA molecules of any of claims 41-56, and are complementary to different target sequences.
  • 98. The composition of any of claims 94-95, comprising a first gRNA molecule and a second gRNA molecule, wherein the first gRNA molecule and second gRNA molecule are: (a) independently selected from the gRNA molecules of claim 10, and are complementary to different target sequences; or(b) independently selected from the gRNA molecules of claim 11, and are complementary to different target sequences.
  • 99. The composition of any of claims 94-95, comprising a first gRNA molecule and a second gRNA molecule, wherein the first gRNA molecule and second gRNA molecule are: (a) independently selected from the gRNA molecules of claim 13, and are complementary to different target sequences; or(b) independently selected from the gRNA molecules of claim 14, and are complementary to different target sequences.
  • 100. The composition of any of claims 94-96, comprising a first gRNA molecule and a second gRNA molecule, wherein the first gRNA molecule and second gRNA molecule are: (a) independently selected from the gRNA molecules of claim 16, and are complementary to different target sequences;(b) independently selected from the gRNA molecules of claim 17, and are complementary to different target sequences;(c) independently selected from the gRNA molecules of claim 18, and are complementary to different target sequences; or(d) independently selected from the gRNA molecules of any of claims 57-68, and are complementary to different target sequences.
  • 101. The composition of any of claims 94-96, comprising a first gRNA molecule and a second gRNA molecule, wherein: (1) the first gRNA molecule is: (a) selected from the gRNA molecules of claim 4, (b) selected from the gRNA molecules of claim 5, (c) selected from the gRNA molecules of claim 6, (d) selected from the gRNA molecules of claim 7, or (e) selected from the gRNA molecules of any of claims 41-56; and(2) the second gRNA molecule is: (a) selected from the gRNA molecules of claim 10, or (b) selected from the gRNA molecules of claim 11.
  • 102. The composition of any of claims 94-96, comprising a first gRNA molecule and a second gRNA molecule, wherein: (1) the first gRNA molecule is: (a) selected from the gRNA molecules of claim 4, (b) selected from the gRNA molecules of claim 5, (c) selected from the gRNA molecules of claim 6, (d) selected from the gRNA molecules of claim 7, or (e) selected from the gRNA molecules of any of claims 41-56; and(2) the second gRNA molecule is: (a) selected from the gRNA molecules of claim 13, (b) selected from the gRNA molecules of claim 14.
  • 103. The composition of any of claims 94-96, comprising a first gRNA molecule and a second gRNA molecule, wherein: (1) the first gRNA molecule is: (a) selected from the gRNA molecules of claim 4, (b) selected from the gRNA molecules of claim 5, (c) selected from the gRNA molecules of claim 6, (d) selected from the gRNA molecules of claim 7, or (e) selected from the gRNA molecules of any of claims 41-56; and(2) the second gRNA molecule is: (a) selected from the gRNA molecules of claim 16, (b) selected from the gRNA molecules of claim 17, (c) selected from the gRNA molecules of claim 18, or (d) selected from the gRNA molecules of any of claims 57-68.
  • 104. The composition of any of claims 94-96, comprising a first gRNA molecule and a second gRNA molecule, wherein: (1) the first gRNA molecule is: (a) selected from the gRNA molecules of claim 10, or (b) selected from the gRNA molecules of claim 11; and(2) the second gRNA molecule is: (a) selected from the gRNA molecules of claim 13, (b) selected from the gRNA molecules of claim 14.
  • 105. The composition of any of claims 94-96, comprising a first gRNA molecule and a second gRNA molecule, wherein: (1) the first gRNA molecule is: (a) selected from the gRNA molecules of claim 10, or (b) selected from the gRNA molecules of claim 11; and(2) the second gRNA molecule is: (a) selected from the gRNA molecules of claim 16, (b) selected from the gRNA molecules of claim 17, (c) selected from the gRNA molecules of claim 18, or (d) selected from the gRNA molecules of any of claims 57-68.
  • 106. The composition of any of claims 94-96, comprising a first gRNA molecule and a second gRNA molecule, wherein: (1) the first gRNA molecule is: (a) selected from the gRNA molecules of claim 13, (b) selected from the gRNA molecules of claim 14; and(2) the second gRNA molecule is: (a) selected from the gRNA molecules of claim 16, (b) selected from the gRNA molecules of claim 17, (c) selected from the gRNA molecules of claim 18, or (d) selected from the gRNA molecules of any of claims 57-68.
  • 107. The composition of claim 96, comprising a first gRNA molecule and a second gRNA molecule, wherein: (1) the first gRNA molecule is: (a) selected from the gRNA molecules of claim 16, (b) selected from the gRNA molecules of claim 17, (c) selected from the gRNA molecules of claim 18, or (d) selected from the gRNA molecules of any of claims 57-68; and (2) the second gRNA molecule comprises a targeting domain that is complementary to a target sequence of the beta globin gene; or(1) the first gRNA molecule is: (a) selected from the gRNA molecules of claim 4, (b) selected from the gRNA molecules of claim 5, (c) selected from the gRNA molecules of claim 6, (d) selected from the gRNA molecules of claim 7, (e) selected from the gRNA molecules of any of claims 41-56, (f) selected from the gRNA molecules of claim 10, (g) selected from the gRNA molecules of claim 11, (h) selected from the gRNA molecules of claim 13, or (i) selected from the gRNA molecules of claim 14; and (2) the second gRNA molecule comprises a targeting domain that is complementary to a target sequence of the beta globin gene.
  • 108. The composition of claim 94-96, wherein the first gRNA molecule and the second gRNA molecule are independently selected from the gRNA molecules of any of claims 41-68.
  • 109. The composition of any of claims 87-108, wherein with respect to the gRNA molecule components of the composition, the composition consists of a first gRNA molecule and a second gRNA molecule.
  • 110. The composition of any one of claims 87-109, wherein each of said gRNA molecules is in a ribonuclear protein complex (RNP) with a Cas9 molecule described herein, e.g., a Cas9 molecule of any of claim 90 or 91.
  • 111. The composition of any of claims 87-110, comprising a template nucleic acid, wherein the template nucleic acid comprises a nucleotide that corresponds to a nucleotide at or near the target sequence of the first gRNA molecule.
  • 112. The composition of any of claim 111, wherein the template nucleic acid comprises nucleic acid encoding: (a) human beta globin, e.g., human beta globin comprising one or more of the mutations G16D, E22A and T87Q, or fragment thereof; or(b) human gamma globin, or fragment thereof.
  • 113. The composition of any of claims 87-112, formulated in a medium suitable for electroporation.
  • 114. The composition of any of claims 87-113, wherein each of said gRNA molecules is in a RNP with a Cas9 molecule described herein, and wherein each of said RNP is at a concentration of less than about 10 uM, e.g., less than about 3 uM, e.g., less than about 1 uM, e.g., less than about 0.5 uM, e.g., less than about 0.3 uM, e.g., less than about 0.1 uM.
  • 115. A nucleic acid sequence that encodes one or more gRNA molecules of any of claims 1-68.
  • 116. The nucleic acid sequence of claim 115, wherein the nucleic acid comprises a promoter operably linked to the sequence that encodes the one or more gRNA molecules.
  • 117. The nucleic acid sequence of claim 116, wherein the promoter is a promoter recognized by an RNA polymerase II or RNA polymerase III.
  • 118. The nucleic acid sequence of claim 117, wherein the promoter is a U6 promoter or an HI promoter.
  • 119. The nucleic acid sequence of any of claims 115-118, wherein the nucleic acid further encodes a Cas9 molecule.
  • 120. The nucleic acid sequence of claim 119, wherein the Cas9 molecule comprises any of SEQ ID NO: 6611, SEQ ID NO: 7821, SEQ ID NO: 7822, SEQ ID NO: 7823, SEQ ID NO: 7824, SEQ ID NO: 7825, SEQ ID NO: 7826, SEQ ID NO: 7827, SEQ ID NO: 7828, SEQ ID NO: 7829, SEQ ID NO: 7830, or SEQ ID NO: 7831.
  • 121. The nucleic acid sequence of any of claims 119-120, wherein said nucleic acid comprises a promoter operably linked to the sequence that encodes a Cas9 molecule.
  • 122. The nucleic acid sequence of claim 121, wherein the promoter is an EF-1 promoter, a CMV IE gene promoter, an EF-1α promoter, an ubiquitin C promoter, or a phosphoglycerate kinase (PGK) promoter.
  • 123. A vector comprising the nucleic acid of any of claims 115-122.
  • 124. The vector of claim 123, wherein in the vector is selected from the group consisting of a lentiviral vector, an adenoviral vector, an adeno-associated viral (AAV) vector, a herpes simplex virus (HSV) vector, a plasmid, a minicircle, a nanoplasmid, and an RNA vector.
  • 125. A method of altering a cell (e.g., a population of cells), (e.g., altering the structure (e.g., sequence) of nucleic acid) at or near a target sequence within said cell, comprising contacting (e.g., introducing into) said cell (e.g., population of cells) with: 1) one or more gRNA molecules of any of claims 1-68 and a Cas9 molecule;2) one or more gRNA molecules of any of claims 1-68 and nucleic acid encoding a Cas9 molecule;3) nucleic acid encoding one or more gRNA molecules of any of claims 1-68 and a Cas9 molecule;4) nucleic acid encoding one or more gRNA molecules of any of claims 1-68 and nucleic acid encoding a Cas9 molecule;5) any of 1) to 4), above, and a template nucleic acid;6) any of 1) to 4) above, and nucleic acid comprising sequence encoding a template nucleic acid;7) the composition of any of claims 87-114; or8) the vector of any of claims 123-124.
  • 126. The method of claim 125, wherein the gRNA molecule or nucleic acid encoding the gRNA molecule, and the Cas9 molecule or nucleic acid encoding the Cas9 molecule, are formulated in a single composition.
  • 127. The method of claim 125, wherein the gRNA molecule or nucleic acid encoding the gRNA molecule, and the Cas9 molecule or nucleic acid encoding the Cas9 molecule, are formulated in more than one composition.
  • 128. The method of claim 127, wherein the more than one composition are delivered simultaneously or sequentially.
  • 129. The method of any of claims 125-128, wherein the cell is an animal cell.
  • 130. The method of any of claims 125-128, wherein the cell is a mammalian, primate, or human cell.
  • 131. The method of claim 130, wherein the cell is a hematopoietic stem or progenitor cell (HSPC) (e.g., a population of HSPCs).
  • 132. The method of any of claims 125-131, wherein the cell is a CD34+ cell.
  • 133. The method of any of claims 125-132, wherein the cell is a CD34+CD90+ cell.
  • 134. The method of any of claims 125-133, wherein the cell is disposed in a composition comprising a population of cells that has been enriched for CD34+ cells.
  • 135. The method of any of claims 125-134, wherein the cell (e.g. population of cells) has been isolated from bone marrow, mobilized peripheral blood, or umbilical cord blood.
  • 136. The method of any of claims 125-135, wherein the cell is autologous or allogeneic with respect to a patient to be administered said cell.
  • 137. The method of any of claims 125-136, wherein the altering results in an indel at or near a genomic DNA sequence complementary to the targeting domain of the one or more gRNA molecules.
  • 138. The method of claim 137, wherein the indel is an indel shown on FIG. 25, Table 15, Table 26, Table 27 or Table 37.
  • 139. The method of claim 137-138, wherein the indel is an insertion or deletion of less than about 40 nucleotides, e.g., less than 30 nucleotides, e.g., less than 20 nucleotides, e.g., less than 10 nucleotides.
  • 140. The method of claim 139, wherein the indel is a single nucleotide deletion.
  • 141. The method of any of claims 137-140, wherein the method results in a population of cells wherein at least about 50%, e.g., at least about 60%, e.g., at least about 70%, e.g., at least about 80%, e.g., at least about 90% (e.g., at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99%) of the cells of the population have been altered, e.g., comprise an indel.
  • 142. The method of any of claims 125-141, wherein the altering results in a cell (e.g., population of cells) that is capable of differentiating into a differentiated cell of an erythroid lineage (e.g., a red blood cell), and wherein said differentiated cell exhibits an increased level of fetal hemoglobin, e.g., relative to an unaltered cell (e.g., population of cells).
  • 143. The method of any of claims 125-142, wherein the altering results in a population of cells that is capable of differentiating into a population of differentiated cells, e.g., a population of cells of an erythroid lineage (e.g., a population of red blood cells), and wherein said population of differentiated cells has an increased fraction of F cells (e.g., at least about 15%, at least about 20%, at least about 25%, at least about 30%, or at least about 40% higher) e.g., relative to a population of unaltered cells.
  • 144. The method of any of claims 125-142, wherein the altering results in a cell that is capable of differentiating into a differentiated cell, e.g., a cell of an erythroid lineage (e.g., a red blood cell), and wherein said differentiated cell produces at least about 6 picograms (e.g., at least about 7 picograms, at least about 8 picograms, at least about 9 picograms, at least about 10 picograms, or from about 8 to about 9 picograms, or from about 9 to about 10 picograms) fetal hemoglobin per cell.
  • 145. A cell, altered by the method of any of claims 125-144.
  • 146. A cell, obtainable by the method of any of claims 125-144.
  • 147. A cell, comprising a first gRNA molecule of any of claims 1-68, or a composition of any of claims 87-114, a nucleic acid of any of claims 115-122, or a vector of any of claims 123-124.
  • 148. The cell of claim 147, comprising a Cas9 molecule.
  • 149. The cell of claim 148, wherein the Cas9 molecule comprises any of SEQ ID NO: 6611, SEQ ID NO: 7821, SEQ ID NO: 7822, SEQ ID NO: 7823, SEQ ID NO: 7824, SEQ ID NO: 7825, SEQ ID NO: 7826, SEQ ID NO: 7827, SEQ ID NO: 7828, SEQ ID NO: 7829, SEQ ID NO: 7830, or SEQ ID NO: 7831.
  • 150. The cell of any of claims 145-149, wherein the cell comprises, has comprised, or will comprise a second gRNA molecule of any of claims 1-68, or a nucleic acid encoding a second gRNA molecule of any of claims 1-68, wherein the first gRNA molecule and second gRNA molecule comprise nonidentical targeting domains.
  • 151. The cell of any of claims 145-150, wherein expression of fetal hemoglobin is increased in said cell or its progeny (e.g., its erythroid progeny, e.g., its red blood cell progeny) relative to a cell or its progeny of the same cell type that has not been modified to comprise a gRNA molecule.
  • 152. The cell of any of claims 145-150, wherein the cell is capable of differentiating into a differentiated cell, e.g., a cell of an erythroid lineage (e.g., a red blood cell), and wherein said differentiated cell exhibits an increased level of fetal hemoglobin, e.g., relative to a cell of the same type that has not been modified to comprise a gRNA molecule.
  • 153. The cell of claim 152, wherein the differentiated cell (e.g., cell of an erythroid lineage, e.g., red blood cell) produces at least about 6 picograms (e.g., at least about 7 picograms, at least about 8 picograms, at least about 9 picograms, at least about 10 picograms, or from about 8 to about 9 picograms, or from about 9 to about 10 picograms) fetal hemoglobin, e.g., relative to a cell of the same type that has not been modified to comprise a gRNA molecule.
  • 154. The cell of any of claims 145-153, that has been contacted with a stem cell expander.
  • 155. The cell of claim 154, wherein the stem cell expander is compound 1, compound 2, compound 3, compound 4, or a combination thereof (e.g., compound 1 and compound 4).
  • 156. The cell of claim 155, wherein the stem cell expander is compound 4.
  • 157. A cell, e.g., a cell of any of claims 145-156, comprising an indel at or near a genomic DNA sequence complementary to the targeting domain of a gRNA molecule of any of claims 1-68.
  • 158. The cell of claim 157, wherein the indel is an indel shown on FIG. 25, Table 15, Table 26, Table 27 or Table 37.
  • 159. The cell of any of claims 157-158, wherein the indel is an insertion or deletion of less than about 40 nucleotides, e.g., less than 30 nucleotides, e.g., less than 20 nucleotides, e.g., less than 10 nucleotides.
  • 160. The cell of any of claims 157-159, wherein the indel is a single nucleotide deletion.
  • 161. The cell of any of claims 145-160, wherein the cell is an animal cell.
  • 162. The cell of claim 161, wherein the cell is a mammalian, a primate, or a human cell.
  • 163. The cell of any of claims 145-162, wherein the cell is a hematopoietic stem or progenitor cell (HSPC) (e.g., a population of HSPCs).
  • 164. The cell of any of claims 145-163, wherein the cell is a CD34+ cell.
  • 165. The cell of claim 164, wherein the cell is a CD34+CD90+ cell.
  • 166. The cell of any of claims 145-165, wherein the cell (e.g. population of cells) has been isolated from bone marrow, mobilized peripheral blood, or umbilical cord blood.
  • 167. The cell of any of claims 145-166, wherein the cell is autologous with respect to a patient to be administered said cell.
  • 168. The cell of any of claims 145-166, wherein the cell is allogeneic with respect to a patient to be administered said cell.
  • 169. A population of cells comprising the cell of any of claims 145-168.
  • 170. The population of cells of claim 169, wherein at least about 50%, e.g., at least about 60%, e.g., at least about 70%, e.g., at least about 80%, e.g., at least about 90% (e.g., at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99%) of the cells of the population are a cell according to any one of claims 145-168.
  • 171. The population of cells of any of claims 169-170, wherein the population of cells is capable of differentiating into a population of differentiated cells, e.g., a population of cells of an erythroid lineage (e.g., a population of red blood cells), and wherein said population of differentiated cells has an increased fraction of F cells (e.g., at least about 15%, at least about 20%, at least about 25%, at least about 30%, or at least about 40% higher) e.g., relative to a population of unmodified cells of the same type.
  • 172. The population of cells of claim 171, wherein the F cells of the population of differentiated cells produce an average of at least about 6 picograms (e.g., at least about 7 picograms, at least about 8 picograms, at least about 9 picograms, at least about 10 picograms, or from about 8 to about 9 picograms, or from about 9 to about 10 picograms) fetal hemoglobin per cell.
  • 173. The population of cells of any of claims 169-172, comprising: 1) at least 1e6 CD34+ cells/kg body weight of the patient to whom the cells are to be administered;2) at least 2e6 CD34+ cells/kg body weight of the patient to whom the cells are to be administered;3) at least 3e6 CD34+ cells/kg body weight of the patient to whom the cells are to be administered;4) at least 4e6 CD34+ cells/kg body weight of the patient to whom the cells are to be administered; or5) from 2e6 to 10e6 CD34+ cells/kg body weight of the patient to whom the cells are to be administered.
  • 174. The population of cells of any of claims 169-173, wherein at least about 40%, e.g., at least about 50%, (e.g., at least about 60%, at least about 70%, at least about 80%, or at least about 90%) of the cells of the population are CD34+ cells.
  • 175. The population of cells of claim 174, wherein at least about 10%, e.g., at least about 15%, e.g., at least about 20%, e.g., at least about 30% of the cells of the population are CD34+CD90+ cells.
  • 176. The population of cells of any of claims 169-175, wherein the population of cells is derived from bone marrow.
  • 177. The population of cells of any of claims 169-176, wherein the population of cells comprises, e.g., consists of, mammalian cells, e.g., human cells.
  • 178. The population of cells of any of claims 169-177, wherein the population of cells is autologous relative to a patient to which it is to be administered.
  • 179. The population of cells of any of claims 169-177, wherein the population of cells is allogeneic relative to a patient to which it is to be administered.
  • 180. A composition comprising a cell of any of claims 145-168, or the population of cells of any of claims 169-179.
  • 181. The composition of claim 180, comprising a pharmaceutically acceptable medium, e.g., a pharmaceutically acceptable medium suitable for cryopreservation.
  • 182. A method of treating a hemoglobinopathy, comprising administering to a patient a cell of any of claims 145-168, a population of cells of any of claims 169-179, or a composition of any of claims 180-181.
  • 183. A method of increasing fetal hemoglobin expression in a mammal, comprising administering to a patient a cell of any of claims 145-168, a population of cells of any of claims 169-179, or a composition of any of claims 180-181.
  • 184. The method of claim 182, wherein the hemoglobinopathy is beta-thalassemia or sickle cell disease.
  • 185. A method of preparing a cell (e.g., a population of cells) comprising: (a) providing a cell (e.g., a population of cells) (e.g., a HSPC (e.g., a population of HSPCs));(b) culturing said cell (e.g., said population of cells) ex vivo in a cell culture medium comprising a stem cell expander; and(c) introducing into said cell a first gRNA molecule of any of claims 1-68, a nucleic acid molecule encoding a first gRNA molecule of any of claims 1-68, a composition of any of claims 87-114, a nucleic acid of any of claims 115-122, or a vector of any of claims 123-124.
  • 186. The method of claim 185, wherein after said introducing of step (c), said cell (e.g., population of cells) is capable of differentiating into a differentiated cell (e.g., population of differentiated cells), e.g., a cell of an erythroid lineage (e.g., population of cells of an erythroid lineage), e.g., a red blood cell (e.g., a population of red blood cells), and wherein said differentiated cell (e.g., population of differentiated cells) produces increased fetal hemoglobin, e.g., relative to the same cells which have not been subjected to step (c).
  • 187. The method of any of claims 185-186, wherein the stem cell expander is compound 1, compound 2, compound 3, compound 4 or a combination thereof (e.g., compound 1 and compound 4).
  • 188. The method of claim 187, wherein the stem cell expander is compound 4.
  • 189. The method of any of claims 185-188, wherein the cell culture medium comprises thrombopoietin (Tpo), Flt3 ligand (Flt-3L), and human stem cell factor (SCF).
  • 190. The method of claim 189, wherein the cell culture medium further comprises human interleukin-6 (IL-6).
  • 191. The method of claim 189-190, wherein the cell culture medium comprises thrombopoietin (Tpo), Flt3 ligand (Flt-3L), and human stem cell factor (SCF) each at a concentration ranging from about 10 ng/mL to about 1000 ng/mL.
  • 192. The method of claim 191, wherein the cell culture medium comprises thrombopoietin (Tpo), Flt3 ligand (Flt-3L), and human stem cell factor (SCF) each at a concentration of about 50 ng/mL, e.g, at a concentration of 50 ng/mL.
  • 193. The method of any of claims 190-192, wherein the cell culture medium comprises human interleukin-6 (IL-6) at a concentration ranging from about 10 ng/mL to about 1000 ng/mL.
  • 194. The method of claim 193, wherein the cell culture medium comprises human interleukin-6 (IL-6) at a concentration of about 50 ng/mL, e.g, at a concentration of 50 ng/mL.
  • 195. The method of any of claims 185-194, wherein the cell culture medium comprises a stem cell expander at a concentration ranging from about 1 nM to about 1 mM.
  • 196. The method of claim 195, wherein the cell culture medium comprises a stem cell expander at a concentration ranging from about 1 uM to about 100 uM.
  • 197. The method of claim 196, wherein the cell culture medium comprises a stem cell expander at a concentration ranging from about 50 uM to about 75 uM.
  • 198. The method of claim 197, wherein the cell culture medium comprises a stem cell expander at a concentration of about 50 uM, e.g., at a concentration of 50 uM.
  • 199. The method of claim 197, wherein the cell culture medium comprises a stem cell expander at a concentration of about 75 uM, e.g., at a concentration of 75 uM.
  • 200. The method of any of claims 185-199, wherein the culturing of step (b) comprises a period of culturing before the introducing of step (c).
  • 201. The method of claim 200, wherein the period of culturing before the introducing of step (c) is at least 12 hours, e.g., is for a period of about 1 day to about 3 days, e.g., is for a period of about 1 day to about 2 days, e.g., is for a period of about 2 days.
  • 202. The method of any of claims 185-201, wherein the culturing of step (b) comprises a period of culturing after the introducing of step (c).
  • 203. The method of claim 202, wherein the period of culturing after the introducing of step (c) is at least 12 hours, e.g., is for a period of about 1 day to about 10 days, e.g., is for a period of about 1 day to about 5 days, e.g., is for a period of about 2 days to about 4 days, e.g., is for a period of about 2 days or is for a period of about 3 days or is for a period of about 4 days.
  • 204. The method of any of claims 185-203, wherein the population of cells is expanded at least 4-fold, e.g., at least 5-fold, e.g, at least 10-fold, e.g., relative to cells which are not cultured according to step (b).
  • 205. The method of any of claims 185-204, wherein the introducing of step (c) comprises an electroporation.
  • 206. The method of claim 205, wherein the electroporation comprises 1 to 5 pulses, e.g., 1 pulse, and wherein each pulse is at a pulse voltage ranging from 700 volts to 2000 volts and has a pulse duration ranging from 10 ms to 100 ms.
  • 207. The method of claim 206, wherein the electroporation comprises 1 pulse.
  • 208. The method of any of claims 206-207, wherein the pulse voltage ranges from 1500 to 1900 volts, e.g., is 1700 volts.
  • 209. The method of any of claims 206-208, wherein the pulse duration ranges from 10 ms to 40 ms, e.g., is 20 ms.
  • 210. The method of any of claims 185-209, wherein the cell (e.g., population of cells) provided in step (a) is a human cell (e.g., a population of human cells).
  • 211. The method of claim 210, wherein the cell (e.g., population of cells) provided in step (a) is isolated from bone marrow, peripheral blood (e.g., mobilized peripheral blood) or umbilical cord blood.
  • 212. The method of claim 211, wherein the cell (e.g., population of cells) provided in step (a) is isolated from bone marrow, e.g., is isolated from bone marrow of a patient suffering from a hemoglobinopathy.
  • 213. The method of any of claims 185-212, wherein the population of cells provided in step (a) is enriched for CD34+ cells.
  • 214. The method of any of claims 185-213, wherein subsequent to the introducing of step (c), the cell (e.g., population of cells) is cryopreserved.
  • 215. The method of any of claims 185-214, wherein subsequent to the introducing of step (c), the cell (e.g., population of cells) comprises an indel at or near a genomic DNA sequence complementary to the targeting domain of the first gRNA molecule.
  • 216. The method of any of claim 132, wherein the indel is an indel shown on FIG. 25, Table 15, Table 26, Table 27 or Table 37.
  • 217. The method of any of claims 185-216, wherein after the introducing of step (c), at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98% or at least about 99% of the cells of the population of cells comprise an indel at or near a genomic DNA sequence complementary to the targeting domain of the first gRNA molecule.
  • 218. The method of claim 217, wherein the indel in each of said cells of the population of cells is an indel shown in FIG. 25, Table 15, Table 26, Table 27 or Table 37.
  • 219. A cell (e.g., population of cells), obtainable by the method of any of claims 185-218.
  • 220. A method of treating a hemoglobinopathy, comprising administering to a human patient a composition comprising a cell (e.g., a population of cells) of claim 219.
  • 221. A method of increasing fetal hemoglobin expression in a human patient, comprising administering to said human patient a composition comprising a cell (e.g., a population of cells) of claim 219.
  • 222. The method of claim 220, wherein the hemoglobinopathy is beta-thalassemia or sickle cell disease.
  • 223. The method of any of claims 220-222, wherein the human patient is administered a composition comprising at least about 1e6 cells of claim 219 per kg body weight of the human patient, e.g., at least about 1e6 CD34+ cells of claim 219 per kg body weight of the human patient.
  • 224. The method claim 223, wherein the human patient is administered a composition comprising at least about 2e6 cells of claim 219 per kg body weight of the human patient, e.g., at least about 2e6 CD34+ cells of claim 219 per kg body weight of the human patient.
  • 225. The method claim 223, wherein the human patient is administered a composition comprising from about 2e6 to about 10e6 cells of claim 219 per kg body weight of the human patient, e.g., at least about 2e6 to about 10e6 CD34+ cells of claim 219 per kg body weight of the human patient.
  • 226. A gRNA molecule of any of claims 1-86, a composition of any of claim 87-114 or 180-181, a nucleic acid of any of claims 115-122, a vector of any of claims 123-124, a cell of any of claim 145-168 or 219, or a population of cells of any of claims 169-179, for use as a medicament.
  • 227. A gRNA molecule of any of claims 1-86, a composition of any of claim 87-114 or 180-181, a nucleic acid of any of claims 115-122, a vector of any of claims 123-124, a cell of any of claim 145-168 or 219, or a population of cells of any of claims 169-179, for use in the manufacture of a medicament.
  • 228. A gRNA molecule of any of claims 1-86, a composition of any of claim 87-114 or 180-181, a nucleic acid of any of claims 115-122, a vector of any of claims 123-124, a cell of any of claim 145-168 or 219, or a population of cells of any of claims 169-179, for use in the treatment of a disease.
  • 229. A gRNA molecule of any of claims 1-86, a composition of any of claim 87-114 or 180-181, a nucleic acid of any of claims 115-122, a vector of any of claims 123-124, a cell of any of claim 145-168 or 219, or a population of cells of any of claims 169-179, for use in the treatment of a disease, wherein the disease is a hemoglobinopathy.
  • 230. A gRNA molecule of any of claims 1-86, a composition of any of claim 87-114 or 180-181, a nucleic acid of any of claims 115-122, a vector of any of claims 123-124, a cell of any of claim 145-168 or 219, or a population of cells of any of claims 169-179, for use in the treatment of a disease, wherein the hemoglobinopathy is beta-thalassemia or sickle cell disease.
RELATED APPLICATIONS

This application claims priority to U.S. Provisional patent application No. 62/271,968, filed Dec. 28, 2015, and U.S. Provisional patent application No. 62/347,484, filed Jun. 8, 2016. The entire contents of these applications are incorporated herein by reference.

PCT Information
Filing Document Filing Date Country Kind
PCT/IB2016/058007 12/26/2016 WO 00
Provisional Applications (2)
Number Date Country
62347484 Jun 2016 US
62271968 Dec 2015 US