Patent Application
20230399635
Disclosed herein are engineered guide RNAs. In some embodiments, an engineered guide RNA, upon hybridization to a target RNA implicated in a disease or condition, can form a guide-target RNA scaffold comprising a structural feature selected from the group consisting of a bulge, an internal loop, a hairpin, and any combination thereof. In some embodiments, the structural feature can substantially form upon hybridization to the target RNA. In some embodiments, an engineered guide RNA is configured to hybridize to a target RNA implicated in a disease or condition. In some embodiments, the guide-target RNA scaffold further comprises a mismatch. In some embodiments, the mismatch is an adenosine/cytosine (A/C) mismatch, wherein the adenosine (A) is present in the target RNA and the cytosine (C) is present in the engineered guide RNA. In some embodiments, the guide-target RNA scaffold comprises a wobble base pair. In some embodiments, the guide-target RNA scaffold can be a substrate for an RNA editing entity that chemically modifies a base of a nucleotide in the target RNA. In some embodiments, the RNA editing entity chemically modifies the adenosine in the target RNA to an inosine. In some embodiments, the guide-target RNA scaffold comprises a structured motif comprising two or more structural features selected from the group consisting of a bulge, an internal loop, a hairpin, and any combination thereof. In some embodiments, the guide-target RNA scaffold comprises at least two, three, four, five, six, seven, eight, nine, or 10 structural features selected from the group consisting of a bulge, an internal loop, a hairpin, and any combination thereof. In some embodiments, the structural feature is a bulge. In some embodiments, the bulge is an asymmetric bulge. In some embodiments, the bulge is a symmetric bulge. In some embodiments, the bulge comprises from 1 to 4 nucleotides of the engineered guide RNA and from 0 to 4 nucleotides of the target RNA. In some embodiments, the bulge comprises from 0 to 4 nucleotides of the engineered guide RNA and from 1 to 4 nucleotides of the target RNA. In some embodiments, the asymmetric bulge is an X1/X2 asymmetric bulge, wherein X1 is the number of nucleotides of the target RNA in the asymmetric bulge and X2 is the number of nucleotides of the engineered guide RNA in the asymmetric bulge, wherein the X1/X2 asymmetric bulge is a 0/1 asymmetric bulge, a 1/0 asymmetric bulge, a 0/2 asymmetric bulge, a 2/0 asymmetric bulge, a 0/3 asymmetric bulge, a 3/0 asymmetric bulge, a 0/4 asymmetric bulge, a 4/0 asymmetric bulge, a 1/2 asymmetric bulge, a 2/1 asymmetric bulge, a 1/3 asymmetric bulge, a 3/1 asymmetric bulge, a 1/4 asymmetric bulge, a 4/1 asymmetric bulge, a 2/3 asymmetric bulge, a 3/2 asymmetric bulge, a 2/4 asymmetric bulge, a 4/2 asymmetric bulge, a 3/4 asymmetric bulge, or a 4/3 asymmetric bulge. In some embodiments, the symmetric bulge is an X1/X2 symmetric bulge, wherein X1 is the number of nucleotides of the target RNA in the symmetric bulge and X2 is the number of nucleotides of the engineered guide RNA in the symmetric bulge, and wherein the X1/X2 symmetric bulge a 2/2 symmetric bulge, a 3/3 symmetric bulge, or a 4/4 symmetric bulge. In some embodiments, the structural feature comprises an internal loop. In some embodiments, the internal loop comprises an asymmetric internal loop. In some embodiments, the internal loop comprises a symmetric internal loop. In some embodiments, the asymmetric internal loop is an X1/X2 asymmetric internal loop, wherein X1 is the number of nucleotides of the target RNA in the asymmetric internal loop and X2 is the number of nucleotides of the engineered guide RNA in the asymmetric internal loop, and wherein the X1/X2 asymmetric internal loop is a 5/6 asymmetric internal loop, a 6/5 asymmetric internal loop, a 5/7 asymmetric internal loop, a 7/5 asymmetric internal loop, a 5/8 asymmetric internal loop, a 8/5 asymmetric internal loop, a 5/9 asymmetric internal loop, a 9/5 asymmetric internal loop, a 5/10 asymmetric internal loop, a 10/5 asymmetric internal loop, a 6/7 asymmetric internal loop, a 7/6 asymmetric internal loop, a 6/8 asymmetric internal loop, a 8/6 asymmetric internal loop, a 6/9 asymmetric internal loop, a 9/6 asymmetric internal loop, a 6/10 asymmetric internal loop, a 10/6 asymmetric internal loop, a 7/8 asymmetric internal loop, a 8/7 asymmetric internal loop, a 7/9 asymmetric internal loop, a 9/7 asymmetric internal loop, a 7/10 asymmetric internal loop, a 10/7 asymmetric internal loop, a 8/9 asymmetric internal loop, a 9/8 asymmetric internal loop, a 8/10 asymmetric internal loop, a 10/8 asymmetric internal loop, or a 9/10 asymmetric internal loop, or a 10/9 asymmetric internal loop. In some embodiments, the symmetric internal loop is an X1/X2 symmetric internal loop, wherein X1 is the number of nucleotides of the target RNA in the symmetric internal loop and X2 is the number of nucleotides of the engineered guide RNA in the symmetric internal loop, and wherein the X1/X2 symmetric internal loop is a 5/5 symmetric internal loop, a 6/6 symmetric internal loop, a 7/7 symmetric internal loop, a 8/8 symmetric internal loop, a 9/9 symmetric internal loop, a 10/10 symmetric internal loop, a 12/12 symmetric internal loop, a 15/15 symmetric internal loop, or a 20/20 symmetric internal loop. In some embodiments, the internal loop is formed by at least 5 nucleotides on either the engineered guide RNA or the target RNA. In some embodiments, the internal loop is formed by from 5 to 1000 nucleotides of either the engineered guide RNA or the target RNA. In some embodiments, the internal loop is formed by from 5 to 50 nucleotides of either the engineered guide RNA or the target RNA. In some embodiments, the internal loop is formed by from 5 to 20 nucleotides of either the engineered guide RNA or the target RNA. In some embodiments, the structural feature comprises a hairpin. In some embodiments, the hairpin comprises a non-recruitment hairpin. In some embodiments, a loop portion of the hairpin comprises from about 3 to about 15 nucleotides in length. In some embodiments, the engineered guide RNA further comprises at least two additional structural features that comprise at least two mismatches. In some embodiments, at least one of the at least two mismatches is a G/G mismatch. In some embodiments, the engineered guide RNA further comprises an additional structural feature that comprises a wobble base pair. In some embodiments, the wobble base pair comprises a guanine paired with a uracil. In some embodiments, the target RNA comprises a 5′ guanosine adjacent to the adenosine in the target RNA that is chemically modified to an inosine by the RNA editing entity. In some embodiments, the engineered guide RNA comprises a 5′ guanosine adjacent to the cytosine of the A/C mismatch. In some embodiments, the RNA editing entity is: (a) an adenosine deaminase acting on RNA (ADAR); (b) a catalytically active fragment of (a); (c) a fusion polypeptide comprising (a) or (b); or (d) any combination of these. In some embodiments, the RNA editing entity is endogenous to a cell. In some embodiments, the RNA editing entity comprises an ADAR. In some embodiments, the ADAR comprises human ADAR (hADAR). In some embodiments, the ADAR comprises ADAR1, ADAR2, ADAR3, or any combination thereof. In some embodiments, the ADAR1 comprises ADAR1p110, ADAR1p150, or a combination thereof. In some embodiments, the engineered guide RNA comprises a modified RNA base, an unmodified RNA base, or a combination thereof. In some embodiments, the target RNA is an mRNA molecule. In some embodiments, the target RNA is a pre-mRNA molecule. In some embodiments, the target RNA is APP, ABCA4, SERPINA1, HEXA, LRRK2, CFTR, SNCA, MAPT, or LIPA, a fragment any of these, or any combination thereof. In some embodiments, the target RNA encodes amyloid precursor polypeptide, ATP-binding cassette, sub-family A, member 4 (ABCA4) polypeptide, alpha-1 antitrypsin (AAT) polypeptide, hexosaminidase A enzyme, leucine-rich repeat kinase 2 (LRRK2) polypeptide, CFTR polypeptide, alpha synuclein polypeptide, Tau polypeptide, or lysosomal acid lipase polypeptide. In some embodiments, the target RNA encodes ABCA4 polypeptide. In some embodiments, the target RNA comprises a G to A substitution at position 5882, 6320, or 5714, relative to a wildtype ABCA4 gene sequence of accession number NC_000001.11:c94121149-93992837. In some embodiments, the guide-target RNA scaffold comprises one or more structural features selected from TABLE 7, TABLE, 9, TABLE 10, TABLE 11, TABLE 18, or TABLE 19. In some embodiments, the guide-target RNA scaffold comprises a structural features selected from the group consisting of: (i) one or more X1/X2 bulges, wherein X1 is the number of nucleotides of the target RNA in the bulge and X2 is the number of nucleotides of the engineered guide RNA in the bulge, and wherein the one or more bulges is a 2/1 asymmetric bulge, a 1/0 asymmetric bulge, a 2/2 symmetric bulge, a 3/3 symmetric bulge, or a 4/4 symmetric bulge; (ii) an X1/X2 internal loop, wherein X1 is the number of nucleotides of the target RNA in the internal loop and X2 is the number of nucleotides of the engineered guide RNA in the internal loop, and wherein the internal loop is a 5/5 symmetric loop (iii) one or more mismatches, wherein the one or more mismatches is a G/G mismatch, an A/C mismatch, or a G/A mismatch, (iv) a G/U wobble base pair or a U/G wobble base pair, and (v) any combination thereof. In some embodiments, the guide-target RNA scaffold comprises a 2/1 asymmetric bulge, a 1/0 asymmetric bulge, a G/G mismatch, an A/C mismatch, and a 3/3 symmetric bulge. In some embodiments, the engineered guide RNA has a length of from 80 to 175 nucleotides. In some embodiments, the engineered guide RNA comprises a polynucleotide having at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, at least 99%, or 100% sequence identity to SEQ ID NO: 21, SEQ ID NO: 29, SEQ ID NO: 11, SEQ ID NO: 22, SEQ ID NO: 30, SEQ ID NO: 12, SEQ ID NO: 339-SEQ ID NO: 341, or SEQ ID NO: 292-SEQ ID NO: 296. In some embodiments, the engineered guide RNA comprises a polynucleotide at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, at least 99%, or 100% sequence identity to any one of SEQ ID NO: 11-34, 58, 218-289, 291-296, or 328-343. In some embodiments, the target RNA encodes LRRK2 polypeptide. In some embodiments, the LRRK2 polypeptide comprises a mutation selected from the group consisting of: E10L, A30P, S52F, E46K, A53T, L119P, A211V, C228S, E334K, N363S, V366M, A419V, R506Q, N544E, N551K, A716V, M712V, I723V, P755L, R793M, I810V, K871E, Q923H, Q930R, R1067Q, S1096C, Q1111H, I1122V, A1151T, L1165P, I1192V, H1216R, S1228T, P1262A, R1325Q, I1371V, R1398H, T1410M, D1420N, R1441G, R1441H, A1442P, P1446L, V1450I, K1468E, R1483Q, R1514Q, P1542S, V1613A, R1628P, M1646T, S1647T, Y1699C, R1728H, R1728L, L1795F, M1869V, M1869T, L1870F, E1874X, R1941H, Y2006H, I2012T, G2019S, I2020T, T2031S, N2081D, T2141M, R2143H, Y2189C, T2356I, G2385R, V2390M, E2395K, M2397T, L2466H, or Q2490NfsX3. In some embodiments, the guide-target RNA scaffold comprises one or more structural features selected from TABLE 12, TABLE 15, TABLE 25, TABLE 26, TABLE 27, TABLE 17, or TABLE 20. In some embodiments, the guide-target RNA scaffold comprises one or more structural features selected from the group consisting of: (i) one or more X1/X2 bulges, wherein X1 is the number of nucleotides of the target RNA in the bulge and X2 is the number of nucleotides of the engineered guide RNA in the bulge, and wherein the one or more bulges is a 0/1 asymmetric bulge, a 2/2 symmetric bulge, a 3/3 symmetric bulge, or a 4/4 symmetric bulge; (ii) one or more X1/X2 internal loops, wherein X1 is the number of nucleotides of the target RNA in the internal loop and X2 is the number of nucleotides of the engineered guide RNA in the internal loop, and wherein the one or more internal loops is a 5/0 asymmetric internal loop, a 5/4 asymmetric internal loop, a 5/5 symmetric internal loop, a 6/6 symmetric internal loop, a 7/7 symmetric internal loop, or a 10/10 symmetric internal loop; (iii) one or more mismatches, wherein the one or more mismatches is an A/C mismatch, an A/G mismatch, a C/U mismatch, a G/A mismatch, or a C/C mismatch, (iv) a G/U wobble base pair or a U/G wobble base pair, and (v) any combination thereof. In some embodiments, the guide-target RNA scaffold comprises a 6/6 symmetrical internal loop, an A/C mismatch, an A/G mismatch, and a C/U mismatch. In some embodiments, the engineered guide RNA has a length of from 80 to 175 nucleotides. In some embodiments, the engineered guide RNA comprises a polynucleotide having at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, at least 99%, or 100% sequence identity to SEQ ID NO: 30, SEQ ID NO: 344, or SEQ ID NO: 345. In some embodiments, the engineered guide RNA comprises a polynucleotide having at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, at least 99%, or 100% sequence identity to any one of SEQ ID NO: 35-42, 46-52, 111-207, or 344-345. In some embodiments, the target RNA encodes SNCA polypeptide. In some embodiments, the engineered guide RNA hybridizes to a sequence of the target RNA selected from the group consisting of: a 5′ untranslated region (UTR), a 3′ UTR, and a translation initiation site of an SNCA gene. In some embodiments, the guide-target RNA scaffold comprises one or more structural features selected from TABLE 21, TABLE 23, or TABLE 28. In some embodiments, the guide-target RNA scaffold comprises one or more structural features selected from the group consisting of: (i) an X1/X2 bulge, wherein X1 is the number of nucleotides of the target RNA in the bulge and X2 is the number of nucleotides of the engineered guide RNA in the bulge, and wherein the bulge is a 4/4 symmetric bulge; (ii) one or more X1/X2 internal loops, wherein X1 is the number of nucleotides of the target RNA in the internal loop and X2 is the number of nucleotides of the engineered guide RNA in the internal loop, and wherein the one or more internal loop is a 5/5 symmetric loop, an 8/8 symmetric loop, or a 49/4 asymmetric loop; (iii) one or more mismatches, wherein the one or more mismatches is an A/C mismatch, a G/G mismatch, a G/A mismatch, a U/C mismatch, or an A/A mismatch, (iv) any combination thereof. In some embodiments, the engineered guide RNA has a length of from 80 to 175 nucleotides. In some embodiments, the engineered guide RNA comprises a polynucleotide having at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, at least 99%, or 100% sequence identity to any one of SEQ ID NO: 59-101, 104-108, and 208-217. In some embodiments, the target RNA encodes SERPINA1. In some embodiments, the target RNA comprises a G to A substitution at position 9989, relative to a wildtype SERPINA1 gene sequence of accession number NC_000014.9:c94390654-94376747. In some embodiments, the guide-target RNA scaffold comprises one or more structural features selected from TABLE 5, TABLE 29, TABLE 30, TABLE 31, TABLE 32, TABLE 33, TABLE 34, TABLE 35, or TABLE 36. In some embodiments, the guide-target RNA scaffold comprises one or more structural features selected from the group consisting of: (i) one or more X1/X2 bulges, wherein X1 is the number of nucleotides of the target RNA in the bulge and X2 is the number of nucleotides of the engineered guide RNA in the bulge, and wherein the bulge is a 0/2 asymmetric bulge, a 0/3 asymmetric bulge, a 1/0 asymmetric bulge, a 2/0 asymmetric bulge, a 2/2 symmetric bulge, a 3/0 asymmetric bulge, a 2/2 symmetric bulge, or a 3/3 symmetric bulge; (ii) an X1/X2 internal loop, wherein X1 is the number of nucleotides of the target RNA in the internal loop and X2 is the number of nucleotides of the engineered guide RNA in the internal loop, and wherein the internal loop is a 5/5 symmetric internal loop; (iii) one or more mismatches, wherein the one or more mismatches is an A/C mismatch, an A/A mismatch, and a G/A mismatch, (iv) a G/U wobble base pair, or a U/G wobble base pair; and (v) any combination thereof. In some embodiments, the engineered guide RNA has a length of from 80 to 175 nucleotides. In some embodiments, the engineered guide RNA comprises a polynucleotide having at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, at least 99%, or 100% sequence identity to any one of SEQ ID NO: 6-10, 102-103 or 297-327. In some embodiments, the base of the nucleotide of the target RNA that is modified by the RNA editing entity is comprised in a point mutation of the target RNA. In some embodiments, the point mutation comprises a missense mutation. In some embodiments, the point mutation is a nonsense mutation. In some embodiments, the nonsense mutation is a premature UAA stop codon. In some embodiments, the structural feature increases selectivity of editing a target adenosine in the target RNA relative to an otherwise comparable guide RNA lacking the structural feature. In some embodiments, the structural feature decreases an amount of RNA editing of local off-target adenosines within 200, within 100, within 50, within 25, within 10, within 5, within 2, or 1 within 1 nucleotide 5′ or 3′ of a target adenosine in the target RNA by the RNA editing entity, relative to an otherwise comparable guide RNA lacking the structural feature.
Also disclosed herein are engineered RNAs comprising (a) an engineered guide RNA as described herein, and (b) a U7 snRNA hairpin sequence, a SmOPT sequence, or a combination thereof. In some embodiments, the U7 hairpin has a sequence of TAGGCTTTCTGGCTTTTTACCGGAAAGCCCCT (SEQ ID NO: 389) or CAGGTTTTCTGACTTCGGTCGGAAAACCCCT (SEQ ID NO: 394). In some embodiments, the SmOPT sequence has a sequence of AATTTTTGGAG (SEQ ID NO: 390).
Also disclosed herein are polynucleotides encoding an engineered guide RNA as described herein or an engineered RNA as described herein.
Also disclosed herein are delivery vectors comprising an engineered guide RNA as described herein, an engineered RNA as described herein, or a polynucleotide as described herein (encoding an engineered guide RNA or an engineered RNA). In some embodiments, the delivery vector is a viral vector. In some embodiments, the viral vector is an adeno-associated viral (AAV) vector or a derivative thereof. In some embodiments, the AAV vector is from an adeno-associated virus having a serotype selected from AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, AAV 11, AAV 12, AAV13, AAV 14, AAV 15, AAV 16, AAV.rh8, AAV.rh10, AAV.rh20, AAV.rh39, AAV.Rh74, AAV.RHM4-1, AAV.hu37, AAV.Anc80, AAV.Anc80L65, AAV.7m8, AAV.PHP.B, AAV2.5, AAV2tYF, AAV3B, AAV.LK03, AAV.HSC1, AAV.HSC2, AAV.HSC3, AAV.HSC4, AAV.HSC5, AAV.HSC6, AAV.HSC7, AAV.HSC8, AAV.HSC9, AAV.HSC10, AAV.HSC11, AAV.HSC12, AAV.HSC13, AAV.HSC14, AAV.HSC15, AAV.HSC16 and AAVhu68. In some embodiments, the AAV vector is a recombinant AAV (rAAV) vector, a hybrid AAV vector, a chimeric AAV vector, a self-complementary AAV (scAAV) vector, a single-stranded AAV or any combination thereof. In some embodiments, the AAV vector comprises a genome comprising a replication gene and inverted terminal repeats from a first AAV serotype and a capsid protein from a second AAV serotype. In some embodiments, the AAV vector is an AAV 2/5 vector, an AAV 2/6 vector, an AAV 2/7 vector, an AAV2/8 vector, or an AAV 2/9 vector. In some embodiments, the inverted terminal repeats comprise a 5′ inverted terminal repeat, a 3′ inverted terminal repeat, and a mutated inverted terminal repeat. In some embodiments, the mutated inverted terminal repeat lacks a terminal resolution site.
Also disclosed herein are pharmaceutical compositions comprising: (a) an engineered guide RNA as described herein, an engineered RNA as described herein, a polynucleotide as described herein, or a delivery vector as described herein, and (b) a pharmaceutically acceptable: excipient, carrier, or diluent. In some embodiments, the pharmaceutical composition is in unit dose form. In some embodiments, the pharmaceutical composition further comprises an additional therapeutic agent. In some embodiments, the additional therapeutic agent comprises an ammonia reducer, a beta blocker, a synthetic hormone, an antibiotic, or an antiviral drug, a vascular endothelial growth factor (VEGF) inhibitor, a stem cell treatment, a vitamin or modified form thereof, or any combination thereof.
Also disclosed herein are methods of editing a target RNA in a cell. In some embodiments, the method comprises: administering to the cell an effective amount of an engineered guide RNA as described herein, an engineered RNA as described herein, a polynucleotide as described herein, a delivery vector as described herein, or a pharmaceutical composition as described herein.
Also disclosed herein are methods of treating a disease in a subject. In some embodiments, the method comprises administering to the subject an effective amount of an engineered guide RNA as described herein, an engineered RNA as described herein, a polynucleotide as described herein, a delivery vector as described herein, or a pharmaceutical composition as described herein. In some embodiments, the engineered guide RNA is administered as a unit dose. In some embodiments, the unit dose is an amount sufficient to treat the subject. In some embodiments, the administering is intrathecal, intraocular, intravitreal, retinal, intravenous, intramuscular, intraventricular, intracerebral, intracerebellar, intracerebroventricular, intraperenchymal, subcutaneous, or a combination thereof. In some embodiments, the disease comprises a neurological disease. In some embodiments, the neurological disease comprises Parkinson's disease, Alzheimer's disease, a Tauopathy, or dementia. In some embodiments, the neurological disease is associated with elevated levels of SNCA polypeptide, relative to a healthy subject that does not have the neurological disease or condition. In some embodiments, the engineered guide RNA hybridizes to a sequence of a target RNA encoding the SNCA polypeptide selected from the group consisting of: a 5′ untranslated region (UTR), a 3′ UTR, and a translation initiation site of SNCA; wherein hybridization produces a guide-target RNA scaffold that is a substrate for an RNA editing entity that chemically modifies a base of a nucleotide in the sequence of the target RNA, thereby reducing levels of the SNCA polypeptide. In some embodiments, the engineered guide RNA hybridizes to a sequence of a target RNA encoding the translation initiation site of SNCA. In some embodiments, the engineered guide RNA comprises a polynucleotide having at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, at least 99%, or 100% sequence identity to any one of SEQ ID NO: 59-101, 104-108, and 208-217. In some embodiments, the engineered guide RNA comprises has a percent on-target editing for ADAR2 of at least about 90%. In some embodiments, the neurological disease is associated with a mutation of an LRRK2 polypeptide encoded by the target RNA, wherein the mutation is selected from the group consisting of: E10L, A30P, S52F, E46K, A53T, L119P, A211V, C228S, E334K, N363S, V366M, A419V, R506Q, N544E, N551K, A716V, M712V, 1723V, P755L, R793M, 1810V, K871E, Q923H, Q930R, R1067Q, S1096C, Q1111H, I1122V, A1151T, L1165P, I1192V, H1216R, S1228T, P1262A, R1325Q, I1371V, R1398H, T1410M, D1420N, R1441G, R1441H, A1442P, P1446L, V1450I, K1468E, R1483Q, R1514Q, P1542S, V1613A, R1628P, M1646T, S1647T, Y1699C, R1728H, R1728L, L1795F, M1869V, M1869T, L1870F, E1874X, R1941H, Y2006H, I2012T, G2019S, I2020T, T2031S, N2081D, T2141M, R2143H, Y2189C, T2356I, G2385R, V2390M, E2395K, M2397T, L2466H, or Q2490NfsX3. In some embodiments, the neurological disease is associated with a mutation of an LRRK2 polypeptide encoded by the target RNA, wherein the mutation is a G2019S mutation. In some embodiments, the engineered guide RNA comprises a polynucleotide having at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, at least 99%, or 100% sequence identity to any one of SEQ ID NO: 35-42, 46-52, 111-207, or 344-345. In some embodiments, the engineered guide RNA comprises has a percent on-target editing for ADAR1 of at least about 60% or a percent on-target editing for ADAR2 of at least about 90%. In some embodiments, the disease comprises a liver disease. In some embodiments, the liver disease comprises liver cirrhosis. In some embodiments, the liver disease is alpha-1 antitrypsin (AAT) deficiency. In some embodiments, the AAT deficiency is associated with a G to A substitution at position 9989 of a wildtype SERPINA1 gene sequence of accession number NC_000014.9:c94390654-94376747. In some embodiments, the engineered latent wherein the engineered guide RNA comprises a polynucleotide having at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, at least 99%, or 100% sequence identity to any one of SEQ ID NO: 6-10, 102-103 or 297-327. In some embodiments, the engineered guide RNA comprises has a percent on-target editing for ADAR1 of at least about 60% or a percent on-target editing for ADAR2 of at least about 90%. In some embodiments, the disease is a macular degeneration. In some embodiments, the macular degeneration is Stargardt Disease. In some embodiments, the Stargardt disease is associated with a G to A substitution at position 5882, 6320, or 5714 of a wildtype ABCA4 gene sequence of accession number NC_000001.11:c94121149-93992837. In some embodiments, the Stargardt disease is associated with a G to A substitution at position 5882. In some embodiments, the engineered guide RNA comprises a polynucleotide having at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, at least 99%, or 100% sequence identity to any one of SEQ ID NO: 11-34, 58, 218-289, 291-296, or 328-343. In some embodiments, the engineered guide RNA comprises has a percent on-target editing for ADAR1 of at least about 70% or a percent on-target editing for ADAR2 of at least about 80%. In some embodiments, the subject is diagnosed with the disease or the condition.
Also disclosed herein is an engineered guide RNA as described herein, an engineered RNA as described herein, a polynucleotide as described herein, a delivery vector as described herein, or a pharmaceutical composition as described herein, for use as a medicament.
Also disclosed herein is an engineered guide RNA as described herein, an engineered RNA as described herein, a polynucleotide as described herein, a delivery vector as described herein, or a pharmaceutical composition as described herein, for use in treatment of a neurological disease. In some embodiments, the neurological disease is Parkinson's disease, Alzheimer's disease, a Tauopathy, or dementia.
Also disclosed herein is an engineered guide RNA as described herein, an engineered RNA as described herein, a polynucleotide as described herein, a delivery vector as described herein, or a pharmaceutical composition as described herein, for use in treatment of a liver disease. In some embodiments, the liver disease comprises liver cirrhosis. In some embodiments, the liver disease is alpha-1 antitrypsin (AAT) deficiency.
Also disclosed herein is an engineered guide RNA as described herein, an engineered RNA as described herein, a polynucleotide as described herein, a delivery vector as described herein, or a pharmaceutical composition as described herein, for use in treatment of macular degeneration. In some embodiments, the macular degeneration is Stargardt disease.
Also disclosed herein is the use of an engineered guide RNA as described herein, an engineered RNA as described herein, a polynucleotide as described herein, a delivery vector as described herein, or a pharmaceutical composition as described herein, for the manufacture of a medicament.
Also disclosed herein is the use of an engineered guide RNA as described herein, an engineered RNA as described herein, a polynucleotide as described herein, a delivery vector as described herein, or a pharmaceutical composition as described herein, for the manufacture of a medicament for the treatment of a neurological disease, a liver disease or macular degeneration.
All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference.
The novel features of the present disclosure are set forth with particularity in the appended claims. A better understanding of the features and advantages of embodiments of the present disclosure will be obtained by reference to the following detailed description that sets forth illustrative embodiments, and the accompanying drawings of which:
RNA editing refers to a process by which RNA can be enzymatically modified post synthesis on specific nucleosides. RNA editing can comprise any one of an insertion, deletion, or substitution of a nucleotide(s). Examples of RNA editing include pseudouridylation (the isomerization of uridine residues) and deamination (removal of an amine group from cytidine to give rise to uridine or C-to-U editing through recruitment of an APOBEC enzyme described herein, or from adenosine to inosine or A-to-I editing through recruitment of an adenosine deaminase such as ADAR). Editing of RNA can be a way to modulate expression of a polypeptide, for example, through modulation of polypeptide-encoding double stranded RNA (“dsRNA” herein) substrates that enter the RNA interference (RNAi) pathway. This modulation can then act at the chromatin level to modulate expression of the polypeptide. Editing of RNA can also be a way to regulate gene translation. RNA editing can be a mechanism in which to regulate transcript recoding by regulating the triplet codon to introduce silent mutations and/or non-synonymous mutations.
Provided herein, in certain embodiments, are compositions that comprise engineered guide RNAs and engineered polynucleotides encoding the same that facilitate RNA editing via an RNA editing entity or a biologically active fragment thereof and methods of using the same. In an aspect, an RNA editing entity can comprise an adenosine Deaminase Acting on RNA (ADAR) and biologically active fragments thereof. In some instances, ADARs are enzymes that catalyze the chemical conversion of adenosines to inosines in RNA. Because the properties of inosine mimic those of guanosine (inosine will form two hydrogen bonds with cytosine, for example), inosine can be recognized as guanosine by the translational cellular machinery. “Adenosine-to-inosine (A-to-I) RNA editing”, therefore, effectively changes the primary sequence of RNA targets. In general, ADAR enzymes share a common domain architecture comprising a variable number of amino-terminal dsRNA binding domains (dsRBDs) and a single carboxy-terminal catalytic deaminase domain. Human ADARs possess two or three dsRBDs. Evidence suggests that ADARs can form homodimer as well as heterodimer with other ADARs when bound to double-stranded RNA, however it can be currently inconclusive if dimerization is needed for editing to occur.
Three human ADAR genes have been identified (ADARs 1-3) with ADAR1 (official symbol ADAR) and ADAR2 (ADARB1) proteins having well-characterized adenosine deamination activity. ADARs have a typical modular domain organization that includes at least two copies of a dsRNA binding domain (dsRBD; ADAR1 with three dsRBDs; ADAR2 and ADAR3 each with two dsRBDs) in their N-terminal region followed by a C-terminal deaminase domain.
Specific RNA editing can lead to transcript recoding. Because inosine shares the base pairing properties of guanosine, the translational machinery interprets edited adenosines as guanosine, altering the triplet codon, which can result in amino acid substitutions in protein products. More than half the triplet codons in the genetic code could be reassigned through RNA editing. Due to the degeneracy of the genetic code, RNA editing can cause both silent and non-synonymous amino acid substitutions.
In some cases, targeting an RNA can affect splicing. Adenosines targeted for editing can be disproportionately localized near splice junctions in pre-mRNA. Therefore, during formation of a dsRNA ADAR substrate, intronic cis-acting sequences can form RNA duplexes encompassing splicing sites and potentially obscuring them from the splicing machinery. Furthermore, through modification of select adenosines, ADARs can create or eliminate splicing sites, broadly affecting later splicing of the transcript. Similar to the translational machinery, the spliceosome interprets inosine as guanosine, and therefore, a canonical GU 5′ splice site and AG 3′ acceptor site can be created via the deamination of AU (IU=GU) and AA (AI=AG), respectively. Correspondingly, RNA editing can destroy a canonical AG 3′ splice site (IG=GG).
In some cases, targeting an RNA can affect microRNA (miRNA) production and function. For example, RNA editing of a pre-miRNA precursor can affect the abundance of a miRNA, RNA editing in the seed of the miRNA can redirect it to another target for translational repression, or RNA editing of a miRNA binding site in an RNA can interfere with miRNA complementarity, and thus interfere with suppression via RNAi.
In an aspect, an RNA editing entity can be recruited by a guide RNA of the present disclosure. In some examples, a guide RNA can recruit an RNA editing entity that, when associated with the guide RNA and a target RNA as described herein, facilitates: an editing of a base of a nucleotide of the target RNA, a modulation of the expression of a polypeptide encoded by a subject target RNA (such as LRRK2, SNCA, PINK1, Tau, and others described herein); or a combination thereof. A guide RNA can optionally contain an RNA editing entity recruiting domain capable of recruiting an RNA editing entity. In some embodiments, a guide RNA can lack an RNA editing entity recruiting domain and still be capable of binding an RNA editing entity, or be bound by it.
Disclosed herein are engineered guide RNAs and engineered polynucleotides encoding the same for site-specific, selective editing of a target RNA via an RNA editing entity or a biologically active fragment thereof. An engineered guide RNA of the present disclosure can comprise latent structures, such that when the engineered guide RNA is hybridized to the target RNA to form a guide-target RNA scaffold, at least a portion of the latent structure manifests as at least a portion of a structural feature as described herein.
An engineered guide RNA as described herein comprises a targeting domain with complementarity to a target RNA described herein. As such, a guide RNA can be engineered to site-specifically/selectively target and hybridize to a particular target RNA, thus facilitating editing of a specific target RNA via an RNA editing entity or a biologically active fragment thereof. The targeting domain can include a nucleotide that is positioned such that, when the guide RNA is hybridized to the target RNA, the nucleotide opposes a base to be edited by the RNA editing entity or biologically active fragment thereof and does not base pair, or does not fully base pair, with the base to be edited. This mismatch can help to localize editing of the RNA editing entity to the desired base of the target RNA. However, in some instances there can be some, and in some cases significant, off target editing in addition to the desired edit.
Hybridization of the target RNA and the targeting domain of the guide RNA produces specific secondary and tertiary structures in the guide-target RNA scaffold that manifest upon hybridization, which are referred to herein as “latent structures.” Latent structures when manifested become structural features described herein, including mismatches, bulges, internal loops, and hairpins. Without wishing to be bound by theory, the presence of structural features described herein that are produced upon hybridization of the guide RNA with the target RNA configure the guide RNA to facilitate a specific, or selective, targeted edit of the target RNA via the RNA editing entity or biologically active fragment thereof. Further, the structural features in combination with the mismatch described above generally facilitate an increased amount of editing of a target adenosine, fewer off target edits, or both, as compared to a construct comprising the mismatch alone or a construct having perfect complementarity to a target RNA. Accordingly, rational design of latent structures in engineered guide RNAs of the present disclosure to produce specific structural features in a guide-target RNA scaffold can be a powerful tool to promote editing of a target RNA with high specificity, selectivity, and robust activity.
In some embodiments, the engineered guide RNAs of the present disclosure can be provided in an engineered RNA construct comprising other RNA elements, such as snRNA sequences, snRNA hairpins, or both. For example, an engineered RNA may comprise any engineered guide RNA disclosed herein and an SmOPT sequence, a U7 hairpin, or both. An SmOPT sequence, a U7 hairpin, or both may be positioned 5′ or 3′ of the engineered guide RNA.
Provided herein are engineered guide RNAs with one or more latent structures (“latent structure guide RNAs”) that manifest as one or more structural features upon hybridization of the engineered guide RNA to a target RNA (for example, an RNA implicated in a disease or condition) and compositions comprising said engineered guide RNAs. As disclosed herein, the structural features in combination described herein generally facilitate an increased amount of editing of a target adenosine of the target RNA, fewer off target edits, or both, as compared to a construct comprising lacking the structural features. As used herein, the term “engineered” in reference to a guide RNA or polynucleotide encoding the same refers to a non-naturally occurring guide RNA or polynucleotide encoding the same. Such an engineered guide or engineered polynucleotide encoding an engineered guide, when administered to a subject, can be referred to as a heterologous guide RNA or heterologous polynucleotide. In some examples, the engineered guide RNA can be encoded by an engineered polynucleotide. In some instances, the engineered guide can be an RNA engineered guide. In some instances, the engineered guide can comprise RNA and can further comprise at least on deoxyribonucleotide. In some examples, the engineered guide RNA comprises a DNA base. In some examples, the engineered guide RNA comprises RNA bases exclusively. In some examples, the engineered guide RNA comprises modified DNA bases or unmodified DNA bases. In some examples, the engineered guide RNA comprises modified RNA bases or unmodified RNA bases. In some examples, the engineered guide RNA comprises both DNA and RNA bases. In some examples, an engineered guide of the disclosure can be utilized for RNA editing, for example to prevent or treat a disease or condition. In some cases, an engineered guide RNA can be used in association with a subject RNA editing entity to edit a target RNA or modulate expression of a polypeptide encoded by the target RNA. In some examples, compositions disclosed herein can include engineered guide RNAs capable of facilitating editing by subject RNA editing entities such as ADAR polypeptides or biologically active fragments thereof.
In some examples, provided herein are engineered latent guide RNAs that, upon hybridization to a target RNA implicated in a disease or condition, form a guide-target RNA scaffold comprising a structural feature selected from the group consisting of a bulge, an internal loop, a hairpin, and any combination thereof, wherein the structural feature substantially forms upon hybridization to the target RNA.
In some examples, an engineered guide RNA disclosed herein comprise: (a) at least one RNA editing enzyme recruiting domain; (b) at least one structural feature; or (c) any combination thereof, where the engineered guide RNA is configured to facilitate editing of a nucleotide base of a nucleotide of a target RNA molecule to modulate an expression level of a protein (e.g., ABCA4, APP, SERPINA1, HEXA, LRRK2, SNCA, CFTR, APP, GBA, PINK1 or LIPA) expressed from said target RNA molecule.
In some examples, chemical modification of the base of the nucleotide in the target RNA molecules (e.g., an adenosine to inosine edit) can be confirmed by sequencing (e.g., Sanger sequencing or next generating sequencing). In some examples, confirming that chemical modification has occurred comprises isolating one or more target RNA molecules to which an engineered guide has been administered and then converting the target RNA to cDNA by reverse transcriptase prior to sequencing. In some examples, the sequencing employed can be Sanger sequencing, next generation sequencing, or a combination thereof.
A. Targeting Domain
Engineered guide RNAs disclosed herein can be engineered in any way suitable for RNA editing. In some examples, an engineered guide RNA generally comprises at least a targeting sequence that allows it to hybridize to a region of a target RNA molecule. A targeting sequence can also be referred to as a “targeting domain” or a “targeting region”.
In some cases, a targeting sequence of an engineered guide RNA allows the engineered guide RNA to target an RNA sequence through base pairing, such as Watson Crick base pairing. In some examples, the targeting sequence can be located at either the N-terminus or C-terminus of the engineered guide RNA. In some cases, the targeting sequence can be located at both termini. The targeting sequence can be of any length. In some cases, the targeting sequence can be at least about: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 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, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, or up to about 200 nucleotides in length. In some cases, the targeting sequence can be no greater than about: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 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, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, or 200 nucleotides in length. In some examples, an engineered guide RNA comprises a targeting sequence that can be about 75-100, 80-110, 90-120, or 95-115 nucleotides in length. In some examples, an engineered guide comprises a targeting sequence that can be about 100 nucleotides in length.
In some examples, the target RNA sequence can be an mRNA molecule or a pre-mRNA molecule.
In some examples, the target RNA sequence can be an mRNA molecule. In some examples, the mRNA molecule comprises a premature stop codon. In some examples, the mRNA comprises 1, 2, 3, 4 or 5 premature stop codons. In some examples, the stop codon can be an amber stop codon (UAG), an ochre stop codon (UAA), or an opal stop codon (UGA), or a combination thereof. In some examples, the premature stop codon can be a consequence of a point mutation. In some examples, the premature stop codon causes translation termination of an expression product expressed by the mRNA molecule. In some examples, the premature stop codon can be produced by a point mutation on an mRNA molecule in combination with two additional nucleotides. In some examples, the two additional nucleotides can be (i) a U and (ii) an A or a G, on a 5′ and a 3′ end of the point mutation.
In some examples, the target RNA sequence can be a pre-mRNA molecule. In some examples, the pre-mRNA molecule comprises a splice site mutation. In some examples, the splice site mutation facilitates unintended splicing of a pre-mRNA molecule. In some examples, the splice site mutation results in mistranslation and/or truncation of a protein encoded by the pre-mRNA molecule.
In some examples, the target RNA molecule can be a pre-mRNA or mRNA molecule encoded by an ABCA4, APP, SERPINA1, HEXA, LRRK2, SNCA, CFTR, APP, GBA, PINK1 or LIPA gene, a fragment of any of these, or any combination thereof. In some examples, the target RNA molecule can be a encoded by gene selected from ABCA4, AAT, SERPINA1, SERPINA1 E342K, HEXA, LRRK2, SNCA, APP, Tau, GBA, PINK1, RAB7A, CFTR, ALAS1, ATP7B, ATP7B G1226R, HFE C282Y, LIPA c.894 G>A, PCSK9 start site, or SCNN1A start site, a fragment any of these, or any combination thereof. In some examples, the target RNA molecule encodes an ABCA4, APP, SERPINA1, HEXA, LRRK2, SNCA, CFTR, APP, GBA, PINK1, Tau, or LIPA protein, a fragment of any of these, or a combination thereof. In some examples, the target RNA molecule encodes ABCA4, AAT, SERPINA1, SERPINA1 E342K, HEXA, LRRK2, SNCA, APP, Tau, GBA, PINK1, RAB7A, CFTR, ALAS1, ATP7B, ATP7B G1226R, HFE C282Y, LIPA c.894 G>A, a fragment any of these, or any combination thereof. In some examples, the DNA encoding the RNA molecule comprises a mutation relative to an otherwise identical reference DNA molecule. In some examples, the RNA molecule comprises a mutation relative to an otherwise identical reference RNA molecule. In some examples, the protein encoded for by the target RNA molecule comprises a mutation relative to an otherwise identical reference protein.
In some examples, the target RNA molecule can be encoded by, at least in part, a SERPINA1 gene. In some examples, the SERPINA1 gene comprises a mutation. In some examples, the mutation can be a substitution of a G with an A at nucleotide position 9989 within a wildtype SERPINA1 gene (such as accession number NC_000014.9:c94390654-94376747). In some examples, the mutation causes or contributes to an antitrypsin (AAT) deficiency, such as alpha-1 antitrypsin deficiency (AATD) in a subject to which the engineered guide RNA can be administered to treat the AATD.
In some examples, the target RNA molecule can be encoded by, at least in part, an ABCA4 gene. In some examples, the ABCA4 gene comprises a mutation. In some examples, the mutation comprises a substitution of a G with an A at nucleotide position 5882 in a wildtype ABCA4 gene (such as accession number NC_000001.11:c94121149-93992837). In some examples, the mutation comprises a G with an A at nucleotide position 5714 in a wildtype ABCA4 gene (such as accession number NC_000001.11:c94121149-93992837). In some examples, the mutation comprises a substitution of a G with an A at nucleotide position 6320 in a wildtype ABCA4 gene (such as accession number NC_000001.11:c94121149-93992837). In some examples, the mutation causes or contributes to macular degeneration in a subject to which the engineered guide RNA is administered. In some examples, the macular degeneration can be Stargardt macular degeneration. In some examples the target RNA molecule comprises an adenosine with a 5′ G. In some examples, the adenosine with the 5′ G can be the base intended for chemical modification by the RNA editing entity. In some examples, the RNA editing entity can be an ADAR, and the ADAR chemically modifies the adenosine with the 5′ G after recruitment by the double stranded substrate.
In some examples, the target RNA molecule encodes, at least in part, an amyloid precursor protein (APP). In some examples, the target RNA molecule encodes, at least in part, an APP cleavage site. In some examples, the target RNA molecule encodes, at least in part, a beta secretase (BACE) or gamma secretase cleavage site of an APP protein. In some examples, the target RNA molecule encodes, at least in part, a beta secretase (BACE) cleavage site of an APP protein. In some examples, the target RNA molecule encodes, at least in part, an APP start site. In some examples, cleavage of the APP protein at the cleavage cite causes or contributes to Amyloid beta (AD or Abeta) peptide deposition in the brain or blood vessels. In some examples, the Abeta deposition causes or contributes to a neurodegenerative disease. In some examples, the disease comprises Alzheimer's disease, Parkinson's disease, corticobasal degeneration, dementia with Lewy bodies, Lewy body variant of Alzheimer's disease, Parkinson's disease with dementia, Pick's disease, progressive supranuclear palsy, dementia, fronto-temporal dementia with Parkinsonism linked to tau mutations on chromosome 17, or any combination thereof.
In some cases, a targeting sequence comprises 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 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence complementarity to a target RNA. In some cases, a targeting sequence comprises less than 100% complementarity to a target RNA sequence. For example, a targeting sequence and a region of a target RNA that is bound by the targeting sequence can have a single base mismatch. In other cases, the targeting sequence of an engineered guide RNA comprises at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, or up to about 200 unpaired bases, wherein the unpaired bases are apart of a structural feature disclosed herein. In other cases, the targeting sequence of an engineered guide RNA comprises no more than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, or up to about 200 unpaired bases, wherein the unpaired bases are part of a structural feature disclosed herein. In some examples, unpaired bases are associated with structural features provided herein. In some examples, a targeting sequence comprises at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or up to about 15 nucleotides that differ relative to an RNA sequence with perfect complementarity to a subject target RNA. In some examples, a targeting sequence comprises no more than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 nucleotides that differ in complementarity from a wildtype RNA of a subject target RNA. In some cases, a targeting sequence comprises at least 50 nucleotides having complementarity to a target RNA. In some cases, a targeting sequence comprises from 50 to 150 nucleotides having complementarity to a target RNA. In some cases, a targeting sequence comprises from 50 to 200 nucleotides having complementarity to a target RNA. In some cases, a targeting sequence comprises from 50 to 250 nucleotides having complementarity to a target RNA. In some cases, a targeting sequence comprises from 50 to 300 nucleotides having complementarity to a target RNA. In some cases, a targeting sequence comprises 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 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, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, or 300 nucleotides having complementarity to a target RNA. In some cases, a targeting sequence comprises more than 50 nucleotides total and has at least 50 nucleotides having complementarity to a target RNA. In some cases, a targeting sequence comprises from 50 to 400 nucleotides total and has from 50 to 150 nucleotides having complementarity to a target RNA. In some cases, a targeting sequence comprises from 50 to 400 nucleotides total and has from 50 to 200 nucleotides having complementarity to a target RNA. In some cases, a targeting sequence comprises from 50 to 400 nucleotides total and has from 50 to 250 nucleotides having complementarity to a target RNA. In some cases, a targeting sequence comprises from 50 to 400 nucleotides total and has from 50 to 300 nucleotides having complementarity to a target RNA. In some cases, the at least 50 nucleotides having complementarity to a target RNA are separated by a structural feature described herein (e.g. one or more mismatches, one or more bulges, or one or more loops, one or more hairpins, or any combination thereof). In some cases, the 50 to 150 nucleotides having complementarity to a target RNA are separated by a structural feature described herein (e.g. one or more mismatches, one or more bulges, or one or more loops, one or more hairpins, or any combination thereof). In some cases, the 50 to 200 nucleotides having complementarity to a target RNA are separated by a structural feature described herein (e.g. one or more mismatches, one or more bulges, or one or more loops, one or more hairpins, or any combination thereof). In some cases, the 50 to 250 nucleotides having complementarity to a target RNA are separated by a structural feature described herein (e.g. one or more mismatches, one or more bulges, or one or more loops, one or more hairpins, or any combination thereof). In some cases, the 50 to 300 nucleotides having complementarity to a target RNA are separated by a structural feature described herein (e.g. one or more mismatches, one or more bulges, or one or more loops, one or more hairpins, or any combination thereof). For example, a targeting sequence can comprise a total of 54 nucleotides wherein, sequentially, 25 nucleotides are complementarity to a target RNA, 4 nucleotides form a bulge, and 25 nucleotides are complementarity to a target RNA. As another example, a targeting sequence comprises a total of 118 nucleotides wherein, sequentially, 25 nucleotides are complementarity to a target RNA, 4 nucleotides form a bulge, 25 nucleotides are complementarity to a target RNA, 14 nucleotides form an internal loop, and 50 nucleotides are complementary to a target RNA.
In some cases, an engineered guide RNA can comprise multiple targeting sequences. In some instances, one or more target sequence domains in the engineered guide RNA can bind to one or more regions of a target RNA. For example, a first targeting sequence can be configured to be at least partially complementary to a first region of a target RNA (e.g., a first exon of a pre-mRNA), while a second targeting sequence can be configured to be at least partially complementary to a second region of a target RNA (e.g. a second exon of a pre-mRNA). In some instances, multiple target sequences can be operatively linked to provide continuous hybridization of multiple regions of a target RNA. In some instances, multiple target sequences can provide non-continuous hybridization of multiple regions of a target RNA. A “non-continuous” overlap or hybridization refers to hybridization of a first region of a target RNA by a first targeting sequence, along with hybridization of a second region of a target RNA by a second targeting sequence, where the first region and the second region of the target RNA are discontinuous (e.g., where there is intervening sequence between the first and the second region of the target RNA). For example, a targeting sequence can be configured to bind to a portion of a first exon and can comprise an internal asymmetric loop (e.g., an oligo tether) that is configured to bind to a portion of a second exon, while the intervening sequence between the portion of exon 1 and the portion of exon 2 is not hybridized by either the targeting sequence or the oligo tether. Use of an engineered guide RNA as described herein configured for non-continuous hybridization can provide a number of benefits. For instance, such a guide can potentially target pre-mRNA during transcription (or shortly thereafter), which can then facilitate chemical modification using a deaminase (e.g., ADAR) co-transcriptionally and thus increase the overall efficiency of the chemical modification. Further, the use of oligo tethers to provide non-continuous hybridization while skipping intervening sequence can result in shorter, more specific guide RNA with fewer off-target editing.
In some instances, an engineered guide RNA configured for non-continuous hybridization to a target RNA (e.g., an engineered guide RNA comprising a targeting sequence with an oligo tether) can be configured to bind distinct regions or a target RNA separated by intervening sequence. In some instances, the intervening sequence can be at least: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 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, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320, 330, 340, 350, 360, 370, 380, 390, 400, 410, 420, 430, 440, 450, 460, 470, 480, 490, 500, 510, 520, 530, 540, 550, 560, 570, 580, 590, 600, 610, 620, 630, 640, 650, 660, 670, 680, 690, 700, 710, 720, 730, 740, 750, 760, 770, 780, 790, 800, 810, 820, 830, 840, 850, 860, 870, 880, 890, 900, 910, 920, 930, 940, 950, 960, 970, 980, 990, 1000, 1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, 1900, 2000, 2100, 2200, 2300, 2400, 2500, 2600, 2700, 2800, 2900, 3000, 3100, 3200, 3300, 3400, 3500, 3600, 3700, 3800, 3900, 4000, 4100, 4200, 4300, 4400, 4500, 4600, 4700, 4800, 4900, 5000, 5100, 5200, 5300, 5400, 5500, 5600, 5700, 5800, 5900, 6000, 6100, 6200, 6300, 6400, 6500, 6600, 6700, 6800, 6900, 7000, 7100, 7200, 7300, 7400, 7500, 7600, 7700, 7800, 7900, 8000, 8100, 8200, 8300, 8400, 8500, 8600, 8700, 8800, 8900, 9000, 9100, 9200, 9300, 9400, 9500, 9600, 9700, 9800, 9900, or 10000 nucleotides. In some instances, the targeting sequence and oligo tether can target distinct non-continuous regions of the same intron or exon. In some instances, the targeting sequence and oligo tether can target distinct non-continuous regions of adjacent exons or introns. In some instances, the targeting sequence and oligo tether can target distinct non-continuous regions of distal exons or introns.
B. Engineered Guide RNAs Having a Recruiting Domain
In some examples, an engineered guide RNA can comprise an RNA editing entity recruiting domain formed and present in the absence of binding to a target RNA. An RNA editing entity can be recruited by an RNA editing entity recruiting domain on an engineered guide RNA. In some examples, an engineered guide RNA comprising an RNA editing entity recruiting domain can be configured to facilitate editing of a base of a nucleotide of a polynucleotide of a region of a subject target RNA, modulation expression of a polypeptide encoded by the subject target RNA, or both. In some cases, an engineered guide RNA can be configured to facilitate an editing of a base of a nucleotide or polynucleotide of a region of an RNA by a subject RNA editing entity. In order to facilitate editing, an engineered guide RNA of the disclosure can recruit an RNA editing entity.
Various RNA editing entity recruiting domains can be utilized. In some examples, a recruiting domain comprises: Glutamate ionotropic receptor AMPA type subunit 2 (GluR2), APOBEC, MS2-bacteriophage-coat-protein-recruiting domain, Alu, a TALEN recruiting domain, a Zn-finger polypeptide recruiting domain, a mega-TAL recruiting domain, or a Cas13 recruiting domain, combinations thereof, or modified versions thereof. In some examples, more than one recruiting domain can be included in an engineered guide of the disclosure. In examples where a recruiting sequence is present, the recruiting sequence can be utilized to position the RNA editing entity to effectively react with a subject target RNA after the targeting sequence, for example an antisense sequence, hybridizes to a target RNA. In some cases, a recruiting sequence can allow for transient binding of the RNA editing entity to the engineered guide RNA. In some examples, the recruiting sequence allows for permanent binding of the RNA editing entity to the engineered guide. A recruiting sequence can be of any length. In some cases, a recruiting sequence can be from about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, up to about 80 nucleotides in length. In some cases, a recruiting sequence can be no more than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, or 80 nucleotides in length. In some cases, a recruiting sequence can be about 45 nucleotides in length. In some cases, at least a portion of a recruiting sequence comprises at least 1 to about 75 nucleotides. In some cases, at least a portion of a recruiting sequence comprises about 45 nucleotides to about 60 nucleotides. In some aspects, an RNA editing entity recruiting domain can form a recruitment hairpin, as disclosed herein. A recruitment hairpin can recruit an RNA editing entity, such as ADAR. In some embodiments, a recruitment hairpin comprises a GluR2 domain. In some embodiments, a recruitment hairpin comprises an Alu domain.
In an embodiment, an RNA editing entity recruiting domain comprises a GluR2 sequence or functional fragment thereof. In some cases, a GluR2 sequence can be recognized by an RNA editing entity, such as an ADAR or biologically active fragment thereof. In some embodiments, a GluR2 sequence can be a non-naturally occurring sequence. In some cases, a GluR2 sequence can be modified, for example for enhanced recruitment. In some embodiments, a GluR2 sequence can comprise a portion of a naturally occurring GluR2 sequence and a synthetic sequence.
In some examples, a recruiting domain comprises a GluR2 sequence, or a sequence having at least about 70%, 80%, 85%, 90%, 95%, 98%, 99%, or 100% identity and/or length to: GUGGAAUAGUAUAACAAUAUGCUAAAUGUUGUUAUAGUAUCCCAC (SEQ ID NO: 3). In some cases, a recruiting domain can comprise at least about 80% sequence homology to at least about 10, 15, 20, 25, or 30 nucleotides of SEQ ID NO: 3. In some examples, a recruiting domain can comprise at least about 90%, 95%, 96%, 97%, 98%, or 99% sequence homology and/or length to SEQ ID NO: 3.
Additional RNA editing entity recruiting domains are also contemplated. In an embodiment, a recruiting domain comprises an apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like (APOBEC) domain. In some cases, an APOBEC domain can comprise a non-naturally occurring sequence or naturally occurring sequence. In some embodiments, an APOBEC-domain-encoding sequence can comprise a modified portion. In some cases, an APOBEC-domain-encoding sequence can comprise a portion of a naturally occurring APOBEC-domain-encoding-sequence. In some examples, a recruiting domain can be from an MS2-bacteriophage-coat-protein-recruiting domain. In another embodiment, a recruiting domain can be from an Alu domain. In some examples, a recruiting domain can comprise at least about: 70%, 80%, 85%, 90%, or 95% sequence homology and/or length to at least about: 15, 20, 25, 30, or 35 nucleotides of an APOBEC, MS2-bacteriophage-coat-protein-recruiting domain, or Alu domain.
Any number of recruiting sequences can be found in an engineered guide RNA of the present disclosure. In some examples, at least about 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or up to about 10 recruiting sequences can be included in an engineered guide. Recruiting sequences can be located at any position of guide RNAs. In some cases, a recruiting sequence can be on an N-terminus, middle, or C-terminus of a polynucleotide. A recruiting sequence can be upstream or downstream of a targeting sequence. In some cases, a recruiting sequence flanks a targeting sequence of a guide RNA. A recruiting sequence can comprise all ribonucleotides or deoxyribonucleotides, although a recruiting sequence comprising both ribo- and deoxyribonucleotides may in some cases not be excluded.
In some examples, a double stranded RNA (dsRNA) substrate (a guide-target RNA scaffold) is formed upon hybridization of an engineered guide RNA of the present disclosure to a target RNA. In some examples, the target RNA forming the double stranded substrate comprises a portion of an mRNA molecule encoded by a SERPINA1 gene. In some examples the targeting region of the engineered guide forming the double stranded substrate is, at least in part, complementary to a portion of an mRNA molecule encoded by a SERPINA1 gene. In some examples the double stranded substrate comprises a single mismatch. In some examples, the mismatch comprised any two nucleotides that do not base pair. In some examples, the engineered guide RNA comprises an RNA editing entity recruiting domain that comprises a hairpin. In some examples, the hairpin comprises an ADAR recruiting domain. In some examples, the double stranded substrate can be formed by a target RNA comprising an mRNA encoded by the SERPINA1 gene and an engineered guide RNA complementary to a portion of the mRNA encoded by the SERPINA1 gene, wherein the double stranded substrate comprises a single mismatch and an RNA editing entity recruiting domain that comprises a hairpin.
In certain examples, the engineered guide RNA targeting SERPINA1 mRNA and having an RNA editing entity recruiting domain comprises a polynucleotide of the following sequence:
C
GUCGAUGGUC
AGCACAGCCUUAUGCACGGCCUUGGAGAGCUU
the C in bold and underlined text indicates the base that produces a mismatch with the target A to be edited; the GluR2 hairpin recruiting domain is indicated by bold, italicized, and underlined). In some examples, the engineered guide RNA comprises a polynucleotide having at least 99% identity, at least 95% identity, at least 90% identity, at least 85% identity, at least 80% identity, or at least 70% identity to the above SEQ ID NO: 4. In some examples, the engineered guide comprises a polynucleotide having at least 99% length, at least 95% length, at least 90% length, at least 85% length, at least 80% length, or at least 70% length to the above SEQ ID NO: 4.
In some examples, the target RNA forming the double stranded substrate (the guide-target RNA complex) comprises a portion of a pre-mRNA molecule encoded by a SERPINA1 gene. In some examples the targeting region of the engineered guide RNA forming the double stranded substrate is, at least in part, complementary to a portion of a pre-mRNA molecule encoded by the SERPINA1 gene. In some examples the double stranded substrate comprises a single mismatch. In some examples, the mismatch comprised any two nucleotides that do not base pair. In some examples, the engineered substrate comprises an RNA editing entity recruiting domain that comprises a hairpin. In some examples, the hairpin functions as an ADAR recruiting domain. In some examples, the double stranded substrate can be formed by a target RNA comprising a pre-mRNA encoded by the SERPINA1 gene and an engineered guide complementary to a portion of the pre-mRNA encoded by the SERPINA1 gene, wherein the double stranded substrate comprises a single mismatch and a hairpin.
In certain examples, an engineered guide RNA targeting SERPINA1 pre-mRNA and having an RNA editing entity recruiting domain comprises a polynucleotide of the following sequence:
C
GUC
AUGCACGGCcUggaggggagagaagCaga;
the C in bold and underlined text indicates the base that produces a mismatch with the target A to be edited; the GluR2 hairpin recruiting domain is indicated in bold, italicized, and underlined text). In some examples, the engineered guide comprises a polynucleotide having at least 99% identity, at least 95% identity, at least 90% identity, at least 85% identity, at least 80% identity, or at least 70% identity to the above SEQ ID NO: 5. In some examples, the engineered guide RNA comprises a polynucleotide having at least 99% length, at least 95% length, at least 90% length, at least 85% length, at least 80% length, or at least 70% length to the above SEQ ID NO: 5.
In some examples, the engineered guide RNAs disclosed herein comprise a polynucleotide having at least 99% identity, at least 95% identity, at least 90% identity, at least 85% identity, at least 80% identity, or at least 70% identity to the sequences listed below in TABLE 1. In some examples, the engineered guide RNA comprises a polynucleotide having at least 99% length, at least 95% length, at least 90% length, at least 85% length, at least 80% length, or at least 70% length to the sequences listed below in TABLE 1. In some examples the engineered guides disclosed herein comprises a polynucleotide of any of the sequences listed below in TABLE 1.
C. Engineered Guides with Latent Structure
In some embodiments, the present disclosure provides for engineered guide RNAs with latent structure, also referred to as “latent guide RNAs”. Latent structure refers to a structural feature that forms only upon hybridization of a guide RNA to a target RNA, within the guide-target RNA scaffold. For example, the sequence of a guide RNA provides one or more latent structural features, but these latent structural features only form upon hybridization of the latent guide RNA to the target RNA. Thus, the one or more latent structural features manifest as structural features upon hybridization of the latent guide RNA to the target RNA. Upon hybridization of the latent guide RNA to the target RNA, the structural feature is formed and the latent structure provided in the guide RNA is, thus, unmasked. An engineered latent guide RNA can comprise a portion of sequence that, upon hybridization to a target RNA, forms at least a portion of a structural feature, other than a single A/C mismatch feature at the target adenosine to be edited. In some embodiments, a latent structural feature formed upon hybridization to a target RNA includes at least two contiguous nucleotides of the guide RNA. In some instances, a latent structural feature can include any structural feature disclosed herein in addition to an A/C mismatch at the target adenosine to be edited, with these additional structural features providing an increase in an amount of editing of the target adenosine by an RNA editing entity, a decrease in an amount of editing of local off-target adenosines by an RNA editing entity, or both relative to an otherwise comparable guide RNA lacking the additional structural features. Thus, the engineered latent guide RNAs of the present disclosure comprise latent structural features that manifest more than one structural feature upon hybridization to a target RNA within the guide-target RNA scaffold. The presence of multiple structural features within the guide-target RNA scaffold provides for secondary and tertiary, three-dimensional structures that serve as superior substrates for ADAR and drive unexpectedly high editing efficiency of the target adenosine and highly selective editing of the target adenosine (reduced editing of local off-target adenosines) by an otherwise promiscuous enzyme. The latent structures of the engineered latent guide RNAs described herein, which substantially form structural features upon hybridization to a target RNA within the guide-target RNA scaffold can also, upon editing by ADAR, drive improved translation and increased protein production. In some embodiments, the engineered guide RNAs disclosed herein having latent structure can be administered to a cell and result in superior on-target editing, reduced local off-target editing, increased translation, increased protein production, or any combination thereof, all in comparison to a guide RNA lacking latent structures. In some embodiments, the engineered latent guide RNAs disclosed herein have latent structure and also lack an RNA editing entity recruiting domain that is formed and present in the absence of binding to the target RNA. A double stranded RNA (dsRNA) substrate can also be referred to herein as a guide-target RNA scaffold. A guide-target RNA scaffold, as disclosed herein, can be a resulting double stranded RNA duplex formed upon hybridization of a guide RNA to a target RNA, where the guide RNA prior to hybridizing to the target RNA comprise a portion of sequence that, upon hybridization to a target RNA, forms at least a portion of a structural feature, other than a single A/C mismatch feature at the target adenosine to be edited. Accordingly, a guide-target RNA scaffold has structural features formed within the double stranded RNA duplex. For example, the guide-target RNA scaffold can have two or more features selected from a bulge, mismatch, internal loop, hairpin, or wobble base pair. In some embodiments, engineered guide RNAs with latent structure lack an RNA editing entity recruiting domain that is formed and present in the absence of binding to the target RNA. In some embodiments, engineered guide RNAs with latent structure further comprise a recruiting domain that is formed and present in the absence of binding to the target RNA.
In some examples, an engineered guide RNA disclosed herein, when present in an aqueous solution and not bound to the target RNA molecule, does not recruit an RNA editing entity. In some examples, (i) the engineered guide RNA, when present in an aqueous solution and not bound to the target RNA molecule, does not comprise any bulges, internal loops, or hairpins; (ii) the engineered guide RNA, when present in an aqueous solution and not bound to the target RNA molecule, does not comprise any bulges, internal loops, or hairpins that recruit a human ADAR1 with a dissociation constant lower than about 100 nM, 200 nM, 300 nM, 400 nM, 500 nM, 600 nM, 700 nM, 800 nM, 900 nM, or 1,000 nM as determined by an in vitro assay; (iii) the engineered guide RNA, upon at least partially binding to the target RNA molecule and thereby forming a guide-target RNA scaffold, is configured to adopt a structural feature (along with the target RNA) that recruits an RNA editing entity; or (iv) any combination thereof. In some examples, the engineered guide RNA, when present in an aqueous solution and not bound to the target RNA molecule, if it binds to the RNA editing entity, does so with a dissociation constant of about greater than or equal to about 100 nM, 200 nM, 300 nM, 400 nM, 500 nM, 600 nM, 700 nM, 800 nM, 900 nM, or 1,000 nM. In some examples, the engineered guide RNA, when present in an aqueous solution and not bound to the target RNA molecule, if it binds to the RNA editing entity, does so with a dissociation constant of about greater than or equal to about 500 nM. In some examples, the engineered guide RNAs disclosed herein, when present in an aqueous solution and not bound to the target RNA molecule, lack a structural feature described herein. In some examples, the engineered guide RNAs disclosed herein, when present in an aqueous solution and not bound to the target RNA molecule does not comprise any bulges, internal loops, or hairpins. In some examples, the engineered guide RNAs disclosed herein, when present in an aqueous solution and not bound to the target RNA molecule, may be linear and do not comprise any structural features.
In some examples, an engineered guide RNA can be configured to facilitate an editing of a base of a nucleotide or polynucleotide of a region of a target RNA by a subject RNA editing entity. In order to facilitate editing, an engineered guide RNA of the disclosure can recruit an RNA editing entity.
In cases where an RNA editing entity recruiting domain formed and present in the absence of binding to a target RNA is not included in an engineered guide RNA, the engineered guide RNA can be still capable of associating with a subject RNA editing entity (e.g., ADAR) to facilitate editing of a target RNA and/or modulate expression of a polypeptide encoded by a subject target RNA. This can be achieved through the presence of structural features that manifest from latent structures formed upon hybridization of the guide RNA and target RNA. Structural features can comprise any one of a: mismatch, symmetrical bulge, asymmetrical bulge, symmetrical internal loop, asymmetrical internal loop, hairpins, wobble base pairs, a structured motif, circularized RNA, chemical modification, or any combination thereof. In an aspect, a double stranded RNA (dsRNA) substrate (a guide-target RNA scaffold), can be formed upon hybridization of an engineered guide RNA of the present disclosure to a target RNA. Described herein is a feature, which corresponds to one of several structural features that can be present in a dsRNA substrate of the present disclosure. Examples of features include a mismatch, a bulge (symmetrical bulge or asymmetrical bulge), an internal loop (symmetrical internal loop or asymmetrical internal loop), or a hairpin (a hairpin comprising a non-targeting domain). Engineered guide RNAs of the present disclosure can have from 1 to 50 features. For example, engineered guide RNAs of the present disclosure can have from 1 to 5, from 5 to 10, from 10 to 15, from 15 to 20, from 20 to 25, from 25 to 30, from 30 to 35, from 35 to 40, from 40 to 45, from 45 to 50, from 5 to 20, from 5 to 25, from 5 to 30, from 5 to 35, from 5 to 40, from 5 to 45, from 5 to 50, from 1 to 2, from 1 to 3, from 1 to 4, from 1 to 5, from 1 to 6, from 1 to 7, from 1 to 8, from 1 to 9, from 1 to 10, from 1 to 11, from 1 to 12, from 1 to 13, from 1 to 14, from 1 to 15, from 1 to 16, from 1 to 17, from 1 to 18, from 1 to 19, from 1 to 20, from 1 to 21, from 1 to 22, from 1 to 23, from 1 to 24, from 1 to 25, from 1 to 26, from 1 to 27, from 1 to 28, from 1 to 29, from 1 to 30, from 1 to 31, from 1 to 32, from 1 to 33, from 1 to 34, from 1 to 35, from 1 to 36, from 1 to 37, from 1 to 38, from 1 to 39, from 1 to 40, from 1 to 41, from 1 to 42, from 1 to 43, from 1 to 44, from 1 to 45, from 1 to 46, from 1 to 47, from 1 to 48, from 1 to 49, from 4 to 5, from 2 to 10, from 20 to 40, from 10 to 40, from 20 to 50, from 30 to 50, from 4 to 7, or from 8 to 10 features. In some instances, an engineered guide RNA can have at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 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 features.
As disclosed herein, a “structured motif” comprises two or more features in a dsRNA substrate (a guide-target RNA scaffold).
A double stranded RNA (dsRNA) substrate (a guide-target RNA scaffold) is formed upon hybridization of an engineered guide RNA of the present disclosure to a target RNA. As disclosed herein, a “mismatch” refers to a nucleotide in a guide RNA that can be unpaired or fully unpaired to an opposing nucleotide in a target RNA within the dsRNA. A mismatch can comprise any two nucleotides that do not base pair, are not complementary, or both. In some embodiments, a mismatch can be an A/C mismatch. An A/C mismatch can comprise a C in an engineered guide RNA of the present disclosure opposite an A in a target RNA. An A/C mismatch can comprise an A in an engineered guide RNA of the present disclosure opposite an C in a target RNA. In an embodiment, a G/G mismatch can comprise a G in an engineered guide RNA of the present disclosure opposite a G in a target RNA. In some embodiments, a mismatch positioned 5′ of the edit site can facilitate base-flipping of the target A to be edited. A mismatch can also help confer sequence specificity. In an embodiment, a mismatch comprises a G/G mismatch. In an embodiment, a mismatch comprises an A/C mismatch, wherein the A can be in the target RNA and the C can be in the targeting sequence of the engineered guide RNA. In another embodiment, the A in the A/C mismatch can be the base of the nucleotide in the target RNA edited by a subject RNA editing entity.
In an aspect, a structural feature can include both latent structures as described above, as well as non-latent structures. As described herein, a “non-latent structure” refers to a structure that can form in an engineered RNA independent of binding to a target RNA. For example, a recruitment hairpin (e.g., the GluR2 recruitment domain) may not be a latent structure, but rather may form in an engineered RNA independently. In some cases, a structural feature can form when an engineered RNA binds to a target RNA and is, thus, latent structure. A structural feature can also form when an engineered RNA associates with other molecules such as a peptide, a nucleotide, or a small molecule. In certain embodiments, a structural feature is present when an engineered guide RNA is in association with a target RNA.
In some examples, a structural feature is present when an engineered guide RNA is in association with a target RNA. A structural feature of an engineered guide RNA can form a substantially linear two-dimensional structure. A structural feature of an engineered guide RNA can comprise a linear region, a stem-loop, a cruciform, a toe hold, a mismatch bulge, or any combination thereof. In some instances, a structural feature can comprise a stem, a hairpin loop, a pseudoknot, a bulge, an internal loop, a multiloop, a G-quadruplex, or any combination thereof. In some examples, an engineered guide RNA can adopt an A-form, a B-form, a Z-form, or any combination thereof.
In some cases, a structural feature can be a hairpin. In some cases, an engineered guide RNA can lack a hairpin domain (for instance, the engineered guide RNA does not form an intramolecular hairpin in the absence of hybridization to a target RNA). In other cases, an engineered guide RNA can contain a hairpin domain or more than one hairpin domain. A hairpin can be located anywhere in a guide RNA. As disclosed herein, a “hairpin” is an RNA duplex wherein a single RNA strand has folded in upon itself to form the RNA duplex. The single RNA strand folds upon itself due to having nucleotide sequences upstream and downstream of the folding region base pairs to each other. A hairpin can have from 10 to 500 nucleotides in length of the entire duplex structure. The stem-loop structure of a hairpin can be from 3 to 15 nucleotides long. A hairpin can be present in any of the engineered guide RNAs disclosed herein. The engineered guide RNAs disclosed herein can have from 1 to 10 hairpins. In some embodiments, the engineered guide RNAs disclosed herein have 1 hairpin. In some embodiments, the engineered guide RNAs disclosed herein have 2 hairpins. As disclosed herein, a hairpin can be a recruitment hairpin or a non-recruitment hairpin. A hairpin can be located anywhere within the engineered guide RNAs of the present disclosure. In some embodiments, one or more hairpins can be present at the 3′ end of an engineered guide RNAs of the present disclosure, at the 5′ end of an engineered guide RNAs of the present disclosure or within the targeting sequence of an engineered guide RNAs of the present disclosure, or any combination thereof.
In yet another aspect, a structural feature comprises a non-recruitment hairpin. A non-recruitment hairpin, as disclosed herein, can exhibit functionality that improves localization of the engineered guide RNAs to the target RNA. In some embodiments, a non-recruitment hairpin exhibits functionality that improves localization of the engineered guide RNAs to the region of the target RNA for hybridization. In some embodiments, the non-recruitment hairpin improves nuclear retention. In some embodiments, structural features are not formed from latent structures and are, instead, pre-formed structures (e.g., a GluR2 recruitment hairpin or a hairpin from U7 snRNA). In some embodiments, a non-recruitment hairpin that is preformed (is not a latent structure) is a hairpin from U7 snRNA.
In another aspect, a structural feature comprises a wobble base. A “wobble base pair” refers to two bases that weakly pair. For example, a wobble base pair of the present disclosure can refer to a G paired with a U.
A hairpin of the present disclosure can be of any length. In an aspect, a hairpin can be from about 5-200 or more nucleotides. In some cases, a hairpin can comprise about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 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, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398, 399, or 400 or more nucleotides. In other cases, a hairpin can also comprise 5 to 10, 5 to 20, 5 to 30, 5 to 40, 5 to 50, 5 to 60, 5 to 70, 5 to 80, 5 to 90, 5 to 100, 5 to 110, 5 to 120, 5 to 130, 5 to 140, 5 to 150, 5 to 160, 5 to 170, 5 to 180, 5 to 190, 5 to 200, 5 to 210, 5 to 220, 5 to 230, 5 to 240, 5 to 250, 5 to 260, 5 to 270, 5 to 280, 5 to 290, 5 to 300, 5 to 310, 5 to 320, 5 to 330, 5 to 340, 5 to 350, 5 to 360, 5 to 370, 5 to 380, 5 to 390, or 5 to 400 nucleotides.
In some cases, a structural feature can be a bulge. A bulge can comprise 1 to 4 (intentional) nucleic acid mismatch(s) between the target strand and an engineered guide RNA strand. In some cases, 1 to 4 consecutive mismatch(s) between strands constitutes a bulge as long as the bulge region, mismatched stretch of nucleotides, is flanked on both sides with hybridized, complementary dsRNA regions. A bulge can be located at any location of a guide RNA other than the last nucleotides of either the 5′ end or the 3′ end. In some cases, a bulge is be located from about 30 to about 70 nucleotides from a 5′ hydroxyl or the 3′ hydroxyl.
In an embodiment, a double stranded RNA (dsRNA) substrate (guide-target RNA scaffold) is formed upon hybridization of an engineered guide RNA of the present disclosure to a target RNA. As disclosed herein, a bulge refers to the structure substantially formed only upon formation of the guide-target RNA scaffold, where contiguous nucleotides in either the engineered guide RNA or the target RNA are not complementary to their positional counterparts on the opposite strand. A bulge can change the secondary or tertiary structure of the guide-target RNA scaffold. A bulge can independently have from 0 to 4 contiguous nucleotides on the guide RNA side of the guide-target RNA scaffold and 1 to 4 contiguous nucleotides on the target RNA side of the guide-target RNA scaffold or a bulge can independently have from 0 to 4 nucleotides on the target RNA side of the guide-target RNA scaffold and 1 to 4 contiguous nucleotides on the guide RNA side of the guide-target RNA scaffold. However, a bulge, as used herein, does not refer to a structure where a single participating nucleotide of the engineered guide RNA and a single participating nucleotide of the target RNA do not base pair—a single participating nucleotide of the engineered guide RNA and a single participating nucleotide of the target RNA that do not base pair is referred to herein as a mismatch. Further, where the number of participating nucleotides on either the guide RNA side or the target RNA side exceeds 4, the resulting structure is no longer considered a bulge, but rather, is considered an internal loop. In some embodiments, the guide-target RNA scaffold of the present disclosure has 2 bulges. In some embodiments, the guide-target RNA scaffold of the present disclosure has 3 bulges. In some embodiments, the guide-target RNA scaffold of the present disclosure has 4 bulges. Thus, a bulge can be a structural feature formed from latent structure provided by an engineered latent guide RNA.
In some embodiments, the presence of a bulge in a guide-target RNA scaffold can position or can help to position ADAR to selectively edit the target A in the target RNA and reduce off-target editing of non-target A(s) in the target RNA. In some embodiments, the presence of a bulge in a guide-target RNA scaffold can recruit or help recruit additional amounts of ADAR. Bulges in guide-target RNA scaffolds disclosed herein can recruit other proteins, such as other RNA editing entities. In some embodiments, a bulge positioned 5′ of the edit site can facilitate base-flipping of the target A to be edited. A bulge can also help confer sequence specificity for the A of the target RNA to be edited, relative to other A(s) present in the target RNA. For example, a bulge can help direct ADAR editing by constraining it in an orientation that yields selective editing of the target A. In some embodiments, selective editing of the target A is achieved by positioning the target A between two bulges (e.g., positioned between a 5′ end bulge and a 3′ end bulge, based on the engineered guide RNA). In some embodiments, the two bulges are both symmetrical bulges. In some embodiments, the two bulges each are formed by 2 nucleotides on the engineered guide RNA side of the guide-RNA scaffold and 2 nucleotides on the target RNA side of the guide-RNA scaffold. In some embodiments, the two bulges each are formed by 3 nucleotides on the engineered guide RNA side of the guide-RNA scaffold and 3 nucleotides on the target RNA side of the guide-RNA scaffold. In some embodiments, the two bulges each are formed by 4 nucleotides on the engineered guide RNA side of the guide-RNA scaffold and 4 nucleotides on the target RNA side of the guide-RNA scaffold. In some embodiments, the target A is position between the two bulges, and is at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 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, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398, 399, or 400 nucleotides from a bulge (e.g., from a 5′ end bulge or a 3′ end bulge). In some embodiments, additional structural features are located between the bulges (e.g., between the 5′ end bulge and the 3′ end bulge). In some embodiments, a mismatch in a bulge comprises a nucleotide base for editing in the target RNA (e.g., an A/C mismatch in the bulge, wherein part of the bulge in the engineered guide RNA comprises a C mismatched to an A in the part of the bulge in the target RNA, and the A is edited).
In an aspect, a double stranded RNA (dsRNA) substrate (guide-target RNA scaffold) is formed upon hybridization of an engineered guide RNA of the present disclosure to a target RNA. A bulge can be a symmetrical bulge or an asymmetrical bulge. For illustrative purposes, examples of a symmetrical bulge and an asymmetrical bulge in a guide-target RNA scaffold are depicted in
In some cases, a double stranded RNA (dsRNA) substrate (guide-target RNA scaffold) can be formed upon hybridization of an engineered guide RNA of the present disclosure to a target RNA. A bulge can be a symmetrical bulge or an asymmetrical bulge. An asymmetrical bulge is formed when a different number of nucleotides is present on each side of the bulge. For example, an asymmetrical bulge in a guide-target RNA scaffold of the present disclosure can have different numbers of nucleotides on the engineered guide RNA side and the target RNA side of the guide-target RNA scaffold. An asymmetrical bulge of the present disclosure can be formed by 0 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold and 1 nucleotide on the target RNA side of the guide-target RNA scaffold. An asymmetrical bulge of the present disclosure can be formed by 0 nucleotides on the target RNA side of the guide-target RNA scaffold and 1 nucleotide on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical bulge of the present disclosure can be formed by 0 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold and 2 nucleotides on the target RNA side of the guide-target RNA scaffold. An asymmetrical bulge of the present disclosure can be formed by 0 nucleotides on the target RNA side of the guide-target RNA scaffold and 2 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical bulge of the present disclosure can be formed by 0 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold and 3 nucleotides on the target RNA side of the guide-target RNA scaffold. An asymmetrical bulge of the present disclosure can be formed by 0 nucleotides on the target RNA side of the guide-target RNA scaffold and 3 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical bulge of the present disclosure can be formed by 0 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold and 4 nucleotides on the target RNA side of the guide-target RNA scaffold. An asymmetrical bulge of the present disclosure can be formed by 0 nucleotides on the target RNA side of the guide-target RNA scaffold and 4 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical bulge of the present disclosure can be formed by 1 nucleotide on the engineered guide RNA side of the guide-target RNA scaffold and 2 nucleotides on the target RNA side of the guide-target RNA scaffold. An asymmetrical bulge of the present disclosure can be formed by 1 nucleotide on the target RNA side of the guide-target RNA scaffold and 2 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical bulge of the present disclosure can be formed by 1 nucleotide on the engineered guide RNA side of the guide-target RNA scaffold and 3 nucleotides on the target RNA side of the guide-target RNA scaffold. An asymmetrical bulge of the present disclosure can be formed by 1 nucleotide on the target RNA side of the guide-target RNA scaffold and 3 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical bulge of the present disclosure can be formed by 1 nucleotide on the engineered guide RNA side of the guide-target RNA scaffold and 4 nucleotides on the target RNA side of the guide-target RNA scaffold. An asymmetrical bulge of the present disclosure can be formed by 1 nucleotide on the target RNA side of the guide-target RNA scaffold and 4 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical bulge of the present disclosure can be formed by 2 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold and 3 nucleotides on the target RNA side of the guide-target RNA scaffold. An asymmetrical bulge of the present disclosure can be formed by 2 nucleotides on the target RNA side of the guide-target RNA scaffold and 3 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical bulge of the present disclosure can be formed by 2 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold and 4 nucleotides on the target RNA side of the guide-target RNA scaffold. An asymmetrical bulge of the present disclosure can be formed by 2 nucleotides on the target RNA side of the guide-target RNA scaffold and 4 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical bulge of the present disclosure can be formed by 3 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold and 4 nucleotides on the target RNA side of the guide-target RNA scaffold. An asymmetrical bulge of the present disclosure can be formed by 3 nucleotides on the target RNA side of the guide-target RNA scaffold and 4 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. Thus, an asymmetrical bulge can be a structural feature formed from latent structure provided by an engineered latent guide RNA.
In an aspect, a double stranded RNA (dsRNA) substrate (guide-target RNA scaffold) can be formed upon hybridization of an engineered guide RNA of the present disclosure to a target RNA. As disclosed herein, an internal loop refers to the structure substantially formed only upon formation of the guide-target RNA scaffold, where nucleotides in either the engineered guide RNA or the target RNA are not complementary to their positional counterparts on the opposite strand and where one side of the internal loop, either on the target RNA side or the engineered guide RNA side of the guide-target RNA scaffold, has 5 nucleotides or more. Where the number of participating nucleotides on both the guide RNA side and the target RNA side drops below 5, the resulting structure is no longer considered an internal loop, but rather, is considered a bulge or a mismatch, depending on the size of the structural feature. An internal loop can be a symmetrical internal loop or an asymmetrical internal loop. For illustrative purposes, examples of a symmetrical bulge and an asymmetrical bulge in a guide-target RNA scaffold are depicted in
An internal loop can be a symmetrical internal loop or an asymmetrical internal loop. In some embodiments, selective editing of the target A is achieved by positioning the target A between two loops (e.g., positioned between a 5′ end loop and a 3′ end loop, based on the engineered guide RNA). In some embodiments, the two loops are both symmetrical loops. In some embodiments, the two loops each are formed by 5 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold and 5 nucleotides on the target RNA side of the guide-target RNA scaffold. In some embodiments, the two loops each are formed by 6 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold and 6 nucleotides on the target RNA side of the guide-target RNA scaffold. In some embodiments, the two loops each are formed by 7 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold and 7 nucleotides on the target RNA side of the guide-target RNA scaffold. In some embodiments, the two loops each are formed by 8 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold and 8 nucleotides on the target RNA side of the guide-target RNA scaffold. In some embodiments, the two loops each are formed by 9 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold and 9 nucleotides on the target RNA side of the guide-target RNA scaffold. In some embodiments, the two loops each are formed by 10 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold and 10 nucleotides on the target RNA side of the guide-target RNA scaffold. In some embodiments, the target A is position between the two loops, and is at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 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, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398, 399, or 400 nucleotides from a loop (e.g., from a 5′ end loop or a 3′ end loop). In some embodiments, additional structural features are located between the loops (e.g., between the 5′ end loop and the 3′ end loop).
A symmetrical internal loop is formed when the same number of nucleotides is present on each side of the internal loop. For example, a symmetrical internal loop in a guide-target RNA scaffold of the present disclosure can have the same number of nucleotides on the engineered guide RNA side and the target RNA side of the guide-target RNA scaffold. A symmetrical internal loop of the present disclosure can be formed by 5 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold target and 5 nucleotides on the target RNA side of the guide-target RNA scaffold. A symmetrical internal loop of the present disclosure can be formed by 6 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold target and 6 nucleotides on the target RNA side of the guide-target RNA scaffold. A symmetrical internal loop of the present disclosure can be formed by 7 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold target and 7 nucleotides on the target RNA side of the guide-target RNA scaffold. A symmetrical internal loop of the present disclosure can be formed by 8 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold target and 8 nucleotides on the target RNA side of the guide-target RNA scaffold. A symmetrical internal loop of the present disclosure can be formed by 9 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold target and 9 nucleotides on the target RNA side of the guide-target RNA scaffold. A symmetrical internal loop of the present disclosure can be formed by 10 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold target and 10 nucleotides on the target RNA side of the guide-target RNA scaffold. A symmetrical internal loop of the present disclosure can be formed by 15 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold target and 15 nucleotides on the target RNA side of the guide-target RNA scaffold. A symmetrical internal loop of the present disclosure can be formed by 20 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold target and 20 nucleotides on the target RNA side of the guide-target RNA scaffold. A symmetrical internal loop of the present disclosure can be formed by 30 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold target and 30 nucleotides on the target RNA side of the guide-target RNA scaffold. A symmetrical internal loop of the present disclosure can be formed by 40 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold target and 40 nucleotides on the target RNA side of the guide-target RNA scaffold. A symmetrical internal loop of the present disclosure can be formed by 50 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold target and 50 nucleotides on the target RNA side of the guide-target RNA scaffold. A symmetrical internal loop of the present disclosure can be formed by 60 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold target and 60 nucleotides on the target RNA side of the guide-target RNA scaffold. A symmetrical internal loop of the present disclosure can be formed by 70 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold target and 70 nucleotides on the target RNA side of the guide-target RNA scaffold. A symmetrical internal loop of the present disclosure can be formed by 80 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold target and 80 nucleotides on the target RNA side of the guide-target RNA scaffold. A symmetrical internal loop of the present disclosure can be formed by 90 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold target and 90 nucleotides on the target RNA side of the guide-target RNA scaffold. A symmetrical internal loop of the present disclosure can be formed by 100 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold target and 100 nucleotides on the target RNA side of the guide-target RNA scaffold. A symmetrical internal loop of the present disclosure can be formed by 110 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold target and 110 nucleotides on the target RNA side of the guide-target RNA scaffold. A symmetrical internal loop of the present disclosure can be formed by 120 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold target and 120 nucleotides on the target RNA side of the guide-target RNA scaffold. A symmetrical internal loop of the present disclosure can be formed by 130 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold target and 130 nucleotides on the target RNA side of the guide-target RNA scaffold. A symmetrical internal loop of the present disclosure can be formed by 140 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold target and 140 nucleotides on the target RNA side of the guide-target RNA scaffold. A symmetrical internal loop of the present disclosure can be formed by 150 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold target and 150 nucleotides on the target RNA side of the guide-target RNA scaffold. A symmetrical internal loop of the present disclosure can be formed by 200 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold target and 200 nucleotides on the target RNA side of the guide-target RNA scaffold. A symmetrical internal loop of the present disclosure can be formed by 250 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold target and 250 nucleotides on the target RNA side of the guide-target RNA scaffold. A symmetrical internal loop of the present disclosure can be formed by 300 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold target and 300 nucleotides on the target RNA side of the guide-target RNA scaffold. A symmetrical internal loop of the present disclosure can be formed by 350 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold target and 350 nucleotides on the target RNA side of the guide-target RNA scaffold. A symmetrical internal loop of the present disclosure can be formed by 400 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold target and 400 nucleotides on the target RNA side of the guide-target RNA scaffold. A symmetrical internal loop of the present disclosure can be formed by 450 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold target and 450 nucleotides on the target RNA side of the guide-target RNA scaffold. A symmetrical internal loop of the present disclosure can be formed by 500 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold target and 500 nucleotides on the target RNA side of the guide-target RNA scaffold. A symmetrical internal loop of the present disclosure can be formed by 600 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold target and 600 nucleotides on the target RNA side of the guide-target RNA scaffold. A symmetrical internal loop of the present disclosure can be formed by 700 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold target and 700 nucleotides on the target RNA side of the guide-target RNA scaffold. A symmetrical internal loop of the present disclosure can be formed by 800 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold target and 800 nucleotides on the target RNA side of the guide-target RNA scaffold. A symmetrical internal loop of the present disclosure can be formed by 900 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold target and 900 nucleotides on the target RNA side of the guide-target RNA scaffold. A symmetrical internal loop of the present disclosure can be formed by 1000 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold target and 1000 nucleotides on the target RNA side of the guide-target RNA scaffold. Thus, a symmetrical internal loop can be a structural feature formed from latent structure provided by an engineered latent guide RNA.
An asymmetrical internal loop is formed when a different number of nucleotides is present on each side of the internal loop. For example, an asymmetrical internal loop in a guide-target RNA scaffold of the present disclosure can have different numbers of nucleotides on the engineered guide RNA side and the target RNA side of the guide-target RNA scaffold.
An asymmetrical internal loop of the present disclosure can be formed by from 5 to 150 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold and from 5 to 150 nucleotides on the target RNA side of the guide-target RNA scaffold, wherein the number of nucleotides is the different on the engineered side of the guide-target RNA scaffold target than the number of nucleotides on the target RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by from 5 to 1000 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold and from 5 to 1000 nucleotides on the target RNA side of the guide-target RNA scaffold, wherein the number of nucleotides is the different on the engineered side of the guide-target RNA scaffold target than the number of nucleotides on the target RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 5 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold and 6 nucleotides on the target RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 5 nucleotides on the target RNA side of the guide-target RNA scaffold and 6 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 5 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold and 7 nucleotides on the target RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 5 nucleotides on the target RNA side of the guide-target RNA scaffold and 7 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 5 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold and 8 nucleotides internal loop the target RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 5 nucleotides on the target RNA side of the guide-target RNA scaffold and 8 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 5 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold and 9 nucleotides internal loop the target RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 5 nucleotides on the target RNA side of the guide-target RNA scaffold and 9 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 5 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold and 10 nucleotides internal loop the target RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 5 nucleotides on the target RNA side of the guide-target RNA scaffold and 10 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 6 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold and 7 nucleotides internal loop the target RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 6 nucleotides on the target RNA side of the guide-target RNA scaffold and 7 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 6 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold and 8 nucleotides internal loop the target RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 6 nucleotides on the target RNA side of the guide-target RNA scaffold and 8 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 6 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold and 9 nucleotides internal loop the target RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 6 nucleotides on the target RNA side of the guide-target RNA scaffold and 9 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 6 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold and 10 nucleotides internal loop the target RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 6 nucleotides on the target RNA side of the guide-target RNA scaffold and 10 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 7 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold and 8 nucleotides internal loop the target RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 7 nucleotides on the target RNA side of the guide-target RNA scaffold and 8 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 7 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold and 9 nucleotides internal loop the target RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 7 nucleotides on the target RNA side of the guide-target RNA scaffold and 9 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 7 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold and 10 nucleotides internal loop the target RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 7 nucleotides on the target RNA side of the guide-target RNA scaffold and 10 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 8 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold and 9 nucleotides internal loop the target RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 8 nucleotides on the target RNA side of the guide-target RNA scaffold and 9 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 8 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold and 10 nucleotides internal loop the target RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 8 nucleotides on the target RNA side of the guide-target RNA scaffold and 10 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 9 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold and 10 nucleotides internal loop the target RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 9 nucleotides on the target RNA side of the guide-target RNA scaffold and 10 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 5 nucleotides on the target RNA side of the guide-target RNA scaffold and 50 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 5 nucleotides on the target RNA side of the guide-target RNA scaffold and 100 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 5 nucleotides on the target RNA side of the guide-target RNA scaffold and 150 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 5 nucleotides on the target RNA side of the guide-target RNA scaffold and 200 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 5 nucleotides on the target RNA side of the guide-target RNA scaffold and 300 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 5 nucleotides on the target RNA side of the guide-target RNA scaffold and 400 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 5 nucleotides on the target RNA side of the guide-target RNA scaffold and 500 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 5 nucleotides on the target RNA side of the guide-target RNA scaffold and 1000 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 1000 nucleotides on the target RNA side of the guide-target RNA scaffold and 5 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 500 nucleotides on the target RNA side of the guide-target RNA scaffold and 5 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 400 nucleotides on the target RNA side of the guide-target RNA scaffold and 5 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 300 nucleotides on the target RNA side of the guide-target RNA scaffold and 5 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 200 nucleotides on the target RNA side of the guide-target RNA scaffold and 5 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 150 nucleotides on the target RNA side of the guide-target RNA scaffold and 5 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 100 nucleotides on the target RNA side of the guide-target RNA scaffold and 5 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 50 nucleotides on the target RNA side of the guide-target RNA scaffold and 5 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 50 nucleotides on the target RNA side of the guide-target RNA scaffold and 100 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 50 nucleotides on the target RNA side of the guide-target RNA scaffold and 150 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 50 nucleotides on the target RNA side of the guide-target RNA scaffold and 200 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 50 nucleotides on the target RNA side of the guide-target RNA scaffold and 300 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 50 nucleotides on the target RNA side of the guide-target RNA scaffold and 400 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 50 nucleotides on the target RNA side of the guide-target RNA scaffold and 500 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 50 nucleotides on the target RNA side of the guide-target RNA scaffold and 1000 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 1000 nucleotides on the target RNA side of the guide-target RNA scaffold and 50 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 500 nucleotides on the target RNA side of the guide-target RNA scaffold and 50 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 400 nucleotides on the target RNA side of the guide-target RNA scaffold and 50 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 300 nucleotides on the target RNA side of the guide-target RNA scaffold and 50 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 200 nucleotides on the target RNA side of the guide-target RNA scaffold and 50 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 150 nucleotides on the target RNA side of the guide-target RNA scaffold and 50 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 100 nucleotides on the target RNA side of the guide-target RNA scaffold and 50 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 100 nucleotides on the target RNA side of the guide-target RNA scaffold and 150 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 100 nucleotides on the target RNA side of the guide-target RNA scaffold and 200 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 100 nucleotides on the target RNA side of the guide-target RNA scaffold and 300 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 100 nucleotides on the target RNA side of the guide-target RNA scaffold and 400 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 100 nucleotides on the target RNA side of the guide-target RNA scaffold and 500 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 100 nucleotides on the target RNA side of the guide-target RNA scaffold and 1000 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 1000 nucleotides on the target RNA side of the guide-target RNA scaffold and 100 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 500 nucleotides on the target RNA side of the guide-target RNA scaffold and 100 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 400 nucleotides on the target RNA side of the guide-target RNA scaffold and 100 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 300 nucleotides on the target RNA side of the guide-target RNA scaffold and 100 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 200 nucleotides on the target RNA side of the guide-target RNA scaffold and 100 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 150 nucleotides on the target RNA side of the guide-target RNA scaffold and 100 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 150 nucleotides on the target RNA side of the guide-target RNA scaffold and 200 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 150 nucleotides on the target RNA side of the guide-target RNA scaffold and 300 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 150 nucleotides on the target RNA side of the guide-target RNA scaffold and 400 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 150 nucleotides on the target RNA side of the guide-target RNA scaffold and 500 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 150 nucleotides on the target RNA side of the guide-target RNA scaffold and 1000 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 1000 nucleotides on the target RNA side of the guide-target RNA scaffold and 150 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 500 nucleotides on the target RNA side of the guide-target RNA scaffold and 5 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 400 nucleotides on the target RNA side of the guide-target RNA scaffold and 150 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 300 nucleotides on the target RNA side of the guide-target RNA scaffold and 150 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 200 nucleotides on the target RNA side of the guide-target RNA scaffold and 300 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 200 nucleotides on the target RNA side of the guide-target RNA scaffold and 400 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 200 nucleotides on the target RNA side of the guide-target RNA scaffold and 500 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 200 nucleotides on the target RNA side of the guide-target RNA scaffold and 1000 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 1000 nucleotides on the target RNA side of the guide-target RNA scaffold and 200 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 500 nucleotides on the target RNA side of the guide-target RNA scaffold and 200 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 400 nucleotides on the target RNA side of the guide-target RNA scaffold and 200 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 300 nucleotides on the target RNA side of the guide-target RNA scaffold and 200 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 300 nucleotides on the target RNA side of the guide-target RNA scaffold and 400 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 300 nucleotides on the target RNA side of the guide-target RNA scaffold and 500 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 300 nucleotides on the target RNA side of the guide-target RNA scaffold and 1000 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 1000 nucleotides on the target RNA side of the guide-target RNA scaffold and 300 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 500 nucleotides on the target RNA side of the guide-target RNA scaffold and 300 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 400 nucleotides on the target RNA side of the guide-target RNA scaffold and 300 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 400 nucleotides on the target RNA side of the guide-target RNA scaffold and 500 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 400 nucleotides on the target RNA side of the guide-target RNA scaffold and 1000 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 1000 nucleotides on the target RNA side of the guide-target RNA scaffold and 400 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 500 nucleotides on the target RNA side of the guide-target RNA scaffold and 400 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 500 nucleotides on the target RNA side of the guide-target RNA scaffold and 1000 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. An asymmetrical internal loop of the present disclosure can be formed by 1000 nucleotides on the target RNA side of the guide-target RNA scaffold and 500 nucleotides on the engineered guide RNA side of the guide-target RNA scaffold. Thus, an asymmetrical internal loop can be a structural feature formed from latent structure provided by an engineered latent guide RNA.
Structural features that comprise an internal loop can be of any size greater than 5 nucleotides. In some cases, an internal loop comprise at least: 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 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, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, or 1000 nucleotides. In some cases, an internal loop comprise at least about 5-10, 5-15, 10-20, 15-25, 20-30, 5-30, 5-40, 5-50, 5-60, 5-70, 5-80, 5-90, 5-100, 5-110, 5-120, 5-130, 5-140, 5-150, 5-200, 5-250, 5-300, 5-350, 5-400, 5-450, 5-500, 5-600, 5-700, 5-800, 5-900, 5-1000, 20-50, 20-60, 20-70, 20-80, 20-90, 20-100, 20-110, 20-120, 20-130, 20-140, 20-150, 30-40, 30-50, 30-60, 30-70, 30-80, 30-90, 30-100, 30-110, 30-120, 30-130, 30-140, 30-150, 30-200, 30-250, 30-300, 30-350, 30-400, 30-450, 30-500, 30-600, 30-700, 30-800, 30-900, 30-1000, 40-50, 40-60, 40-70, 40-80, 40-90, 40-100, 40-110, 40-120, 40-130, 40-140, 40-150, 40-200, 40-250, 40-300, 40-350, 40-400, 40-450, 40-500, 40-600, 40-700, 40-800, 40-900, 40-1000, 50-60, 50-70, 50-80, 50-90, 50-100, 50-110, 50-120, 50-130, 50-140, 50-150, 50-200, 50-250, 50-300, 50-350, 50-400, 50-450, 50-500, 50-600, 50-700, 50-800, 50-900, 50-1000, 60-70, 60-80, 60-90, 60-100, 60-110, 60-120, 60-130, 60-140, 60-150, 60-200, 60-250, 60-300, 60-350, 60-400, 60-450, 60-500, 60-600, 60-700, 60-800, 60-900, 60-1000, 70-80, 70-90, 70-100, 70-110, 70-120, 70-130, 70-140, 70-150, 70-200, 70-250, 70-300, 70-350, 70-400, 70-450, 70-500, 70-600, 70-700, 70-800, 70-900, 70-1000, 80-90, 80-100, 80-110, 80-120, 80-130, 80-140, 80-150, 80-200, 80-250, 80-300, 80-350, 80-400, 80-450, 80-500, 80-600, 80-700, 80-800, 80-900, 80-1000, 90-100, 90-110, 90-120, 90-130, 90-140, 90-150, 90-200, 90-250, 90-300, 90-350, 90-400, 90-450, 90-500, 90-600, 90-700, 90-800, 90-900, 90-1000, 100-110, 100-120, 100-130, 100-140, 100-150, 100-200, 100-250, 100-300, 100-350, 100-400, 100-450, 100-500, 100-600, 100-700, 100-800, 100-900, 100-1000, 110-120, 110-130, 110-140, 110-150, 110-200, 110-250, 110-300, 110-350, 110-400, 110-450, 110-500, 110-600, 110-700, 110-800, 110-900, 110-1000, 120-130, 120-140, 120-150, 120-200, 120-250, 120-300, 120-350, 120-400, 120-450, 120-500, 120-600, 120-700, 120-800, 120-900, 120-1000, 130-140, 130-150, 130-200, 130-250, 130-300, 130-350, 130-400, 130-450, 130-500, 130-600, 130-700, 130-800, 130-900, 130-1000, 140-150, 140-200, 140-250, 140-300, 140-350, 140-400, 140-450, 140-500, 140-600, 140-700, 140-800, 140-900, 140-1000, 150-200, 150-250, 150-300, 150-350, 150-400, 150-450, 150-500, 150-600, 150-700, 150-800, 150-900, 150-1000, 200-250, 200-300, 200-350, 200-400, 200-450, 200-500, 200-600, 200-700, 200-800, 200-900, 200-1000, 250-300, 250-350, 250-400, 250-450, 250-500, 250-600, 250-700, 250-800, 250-900, 250-1000, 300-350, 300-400, 300-450, 300-500, 300-600, 300-700, 300-800, 300-900, 300-1000, 350-400, 350-450, 350-500, 350-600, 350-700, 350-800, 350-900, 350-1000, 400-450, 400-500, 400-600, 400-700, 400-800, 400-900, 400-1000, 500-600, 500-700, 500-800, 500-900, 500-1000, 600-700, 600-800, 600-900, 600-1000, 700-800, 700-900, 700-1000, 800-900, 800-1000, or 900-1000 nucleotides in total.
In some embodiments, a double stranded RNA (dsRNA) substrate (a guide-target RNA scaffold) comprises a base paired region. As disclosed herein, a base paired (bp) region refers to a stretch of the guide-target RNA scaffold in which the bases in the guide RNA are paired with opposing bases in the target RNA. Base paired regions can extend from one end of the guide-target RNA scaffold to the other end of the guide-target RNA scaffold. Base paired regions can extend between two structural features. Base paired regions can extend from one end of the guide-target RNA scaffold to a structural feature. Base paired regions can extend from a structural feature to the other end of the guide-target RNA scaffold. In some embodiments, a base paired region has from 1 bp to 100 bp, from 1 bp to 90 bp, from 1 bp to 80 bp, from 1 bp to 70 bp, from 1 bp to 60 bp, from 1 bp to 50 bp, from 1 bp to 45 bp, from 1 bp to 40 bp, from 1 bp to 35 bp, from 1 bp to 30 bp, from 1 bp to 25 bp, from 1 bp to 20 bp, from 1 bp to 15 bp, from 1 bp to 10 bp, from 1 bp to 5 bp, from 5 bp to 10 bp, from 5 bp to 20 bp, from 10 bp to 20 bp, from 10 bp to 50 bp, from 5 bp to 50 bp, at least 1 bp, at least 2 bp, at least 3 bp, at least 4 bp, at least 5 bp, at least 6 bp, at least 7 bp, at least 8 bp, at least 9 bp, at least 10 bp, at least 12 bp, at least 14 bp, at least 16 bp, at least 18 bp, at least 20 bp, at least 25 bp, at least 30 bp, at least 35 bp, at least 40 bp, at least 45 bp, at least 50 bp, at least 60 bp, at least 70 bp, at least 80 bp, at least 90 bp, at least 100 bp.
In some examples, a double stranded RNA (dsRNA) substrate (a guide-target RNA scaffold) is formed upon hybridization of an engineered guide of the present disclosure to a target RNA. In some examples, the double stranded substrate comprises structural features mimicking the structural features of a naturally occurring ADAR substrate. In some examples, the naturally occurring ADAR substrate can be a drosophila ADAR substrate. In some examples, the naturally occurring drosophila ADAR substrate can be as depicted in
Some examples of mimicry and related features are included in
In some cases, a structural feature can be a structured motif. As disclosed herein, a structured motif comprises two or more structural features in a dsRNA substrate. A structured motif can comprise any combination of structural features, such as in the above claims, to generate an ideal substrate for ADAR editing at a precise location(s). These structural motifs could be artificially engineered to maximized ADAR editing, and/or these structural motifs can be modeled to recapitulate known ADAR substrates.
In some cases, an engineered guide RNA can be circularized. In some cases, an engineered guide RNA provided herein can be circularized or in a circular configuration. In some aspects, an at least partially circular guide RNA lacks a 5′ hydroxyl or a 3′ hydroxyl.
In some examples, an engineered guide RNA can comprise a backbone comprising a plurality of sugar and phosphate moieties covalently linked together. In some examples, a backbone of an engineered guide RNA can comprise a phosphodiester bond linkage between a first hydroxyl group in a phosphate group on a 5′ carbon of a deoxyribose in DNA or ribose in RNA and a second hydroxyl group on a 3′ carbon of a deoxyribose in DNA or ribose in RNA.
In some embodiments, a backbone of an engineered guide RNA can lack a 5′ reducing hydroxyl, a 3′ reducing hydroxyl, or both, capable of being exposed to a solvent. In some embodiments, a backbone of an engineered guide can lack a 5′ reducing hydroxyl, a 3′ reducing hydroxyl, or both, capable of being exposed to nucleases. In some embodiments, a backbone of an engineered guide can lack a 5′ reducing hydroxyl, a 3′ reducing hydroxyl, or both, capable of being exposed to hydrolytic enzymes. In some instances, a backbone of an engineered guide can be represented as a polynucleotide sequence in a circular 2-dimensional format with one nucleotide after the other. In some instances, a backbone of an engineered guide can be represented as a polynucleotide sequence in a looped 2-dimensional format with one nucleotide after the other. In some cases, a 5′ hydroxyl, a 3′ hydroxyl, or both, can be joined through a phosphorus-oxygen bond. In some cases, a 5′ hydroxyl, a 3′ hydroxyl, or both, can be modified into a phosphoester with a phosphorus-containing moiety.
In some embodiments, the present disclosure provides for split guide RNA systems, where an engineered guide RNA of the present disclosure comprising a recruiting domain (e.g., GluR2) may be delivered as a split guide RNA system.
In some embodiments, a split guide RNA system can comprise two segments—an ADAR recruiting domain (e.g., GluR2 or Alu) and at least one targeting domain. The targeting domain can be at the 5′ and/or 3′ end of the recruiting domain. At least one targeting domain has a sequence that is only partially complementary to the sequence of segment of the target RNA. Binding of the two segments to the target RNA forms a trimolecular complex which recruits ADAR enzymes to deaminate one or more mismatched adenosine residues in the guide-target RNA scaffold.
In some embodiments, a split guide RNA system can comprise two segments—a first segment comprising a first portion of a recruiting domain (e.g., GluR2 or Alu) and, optionally, a part of a targeting domain and a second segment comprising a second portion of the recruiting domain and optionally, a part of a targeting domain. For example, a recruiting domain (e.g., a GluR2 hairpin) may be placed internally, within the targeting domain. The internal recruiting domain can be split into two asymmetric 5′ and 3′ segments, with the 5′ GluR2 segment located within the first guide RNA and the 3′ GluR2 segment located within the second guide RNA. Upon hybridization of the two segments of the engineered guide RNA to the target RNA, the GluR2 hairpin is re-constituted. The binding of the two segments to the target RNA, thus, forms a trimolecular complex, which contains a reconstituted GluR2 hairpin capable of recruiting ADAR for target-specific RNA-editing.
In some embodiments, an engineered guide RNA described herein can comprise modifications. A modification can be a substitution, insertion, deletion, chemical modification, physical modification, stabilization, purification, or any combination thereof. In some cases, a modification can be a chemical modification. Suitable chemical modifications comprise any one of. 5′adenylate, 5′ guanosine-triphosphate cap, 5′N7-Methylguanosine-triphosphate cap, 5′triphosphate cap, 3′phosphate, 3′thiophosphate, 5′phosphate, 5′thiophosphate, Cis-Syn thymidine dimer, trimers, C12 spacer, C3 spacer, C6 spacer, dSpacer, PC spacer, rSpacer, Spacer 18, Spacer 9,3′-3′ modifications, 5′-5′ modifications, abasic, acridine, azobenzene, biotin, biotin BB, biotin TEG, cholesteryl TEG, desthiobiotin TEG, DNP TEG, DNP-X, DOTA, dT-Biotin, dual biotin, PC biotin, psoralen C2, psoralen C6, TINA, 3′DABCYL, black hole quencher 1, black hole quencher 2, DABCYL SE, dT-DABCYL, IRDye QC-1, QSY-21, QSY-35, QSY-7, QSY-9, carboxyl linker, thiol linkers, 2′deoxyribonucleoside analog purine, 2′deoxyribonucleoside analog pyrimidine, ribonucleoside analog, 2′-O-methyl ribonucleoside analog, sugar modified analogs, wobble/universal bases, fluorescent dye label, 2′fluoro RNA, 2′O-methyl RNA, methylphosphonate, phosphodiester DNA, phosphodiester RNA, phosphothioate DNA, phosphorothioate RNA, UNA, pseudouridine-5′-triphosphate, 5-methylcytidine-5′-triphosphate, 2-O-methyl 3phosphorothioate or any combinations thereof. In some embodiments, an engineered guide RNA described herein does not comprise modifications.
In some embodiments, an engineered guide RNA can be selected by a high throughput guide screening assay. A high throughput guide screening assay for selecting engineered guide RNAs was completed with ABCA4, LRRK2, and Serpina1 target RNA and the results are shown in TABLE 2. TABLE 2 shows the disease associated with the target RNA, the tissue expression pattern of the target RNA, the in vivo ADAR type used in the editing, the target motif in the target RNA, the target nucleotide in the target motif for the target RNA, the codon change with a successful editing of the target nucleotide, the associated amino acid change in the protein encoded by the edited target RNA, and the total number of guide RNA designs screened in the high throughput assay are shown for each target RNA.
AGC −>
GGC
AAG −>
GAG
In some examples, the guide-target RNA scaffold produced upon hybridization of the guide RNA and target RNA recruits an RNA editing entity. In some examples, an RNA editing entity comprises an ADAR. In some examples, an ADAR comprises any one of: ADAR1, ADAR1p110, ADAR1p150, ADAR2, ADAR3, APOBEC protein, or any combination thereof. In some examples, the ADAR RNA editing entity can be ADAR1. In some examples, additionally, or alternatively, the ADAR RNA editing entity can be ADAR2. In some examples, additionally, or alternatively, the ADAR RNA editing entity can be ADAR3. In an aspect, an RNA editing entity can be a non-ADAR. In some examples, the RNA editing entity can be an APOBEC protein. In some examples, the RNA editing entity can be APOBEC1, APOBEC2, APOBEC3A, APOBEC3B, APOBEC3C, APOBEC3E, APOBEC3F, APOBEC3G, APOBEC3H, APOBEC4, or any combination thereof. In some examples, the ADAR or APOBEC can be mammalian. In some examples, the ADAR or APOBEC protein can be human. In some examples, the ADAR or APOBEC protein can be recombinant (e.g., an exogenously delivered recombinant ADAR or APOBEC protein), modified (e.g., an exogenously delivered modified ADAR or APOBEC protein), endogenous, or any combination thereof. In some examples, the RNA editing entity can be a fusion protein. In some examples, the RNA editing entity can be a functional portion of an RNA editing entity, such as any of the RNA editing proteins provided herein. In some instances, an RNA editing entity can comprise at least about 70% sequence homology and/or length to APOBEC1, APOBEC2, ADAR1, ADAR1p110, ADAR1p150, ADAR2, ADAR3, or any combination thereof.
Other RNA editing entities are also contemplated. In some examples, the RNA editing entity comprises a clustered regularly interspaced short palindromic repeats (CRISPR) system. In some cases, an RNA editing entity can be a virus-encoded RNA-dependent RNA polymerase. In some cases, an RNA editing entity can be a virus-encoded RNA-dependent RNA polymerase from measles, mumps, or parainfluenza. In some instances, an RNA editing entity can be an enzyme from Trypanosoma brucei capable of adding or deleting a nucleotide or nucleotides in a target RNA. In some instances, an RNA editing entity can be an enzyme from Trypanosoma brucei capable of adding or deleting an Uracil or more than one Uracil in a target RNA. In some instances, an RNA editing entity comprises a recombinant enzyme. In some cases, an RNA editing entity comprises a fusion polypeptide. In some cases, an RNA editing entity does not comprise a fusion polypeptide.
Disclosed herein are methods of delivering any engineered guide disclosed herein (e.g., an engineered guide, a vector encoding or comprising an engineered guide, and any pharmaceutical formulations thereof) to a cell. In some examples, methods of delivering an engineered guide to a cell comprise delivering directly or indirectly to the cell an engineered guide that at least partially hybridizes to and forms, at least in part, a double stranded substrate with at least a portion of a target RNA molecule, wherein the double stranded substrate comprises at least one structural feature, and wherein the double stranded substrate recruits an RNA editing entity and facilitates a chemical modification of a base of a nucleotide in the target RNA molecule by the RNA editing entity. In some examples, the chemical modification of the base of the nucleotide in the target RNA molecules can be confirmed by sequencing. In some examples, confirming that chemical modification has occurred comprises isolating one or more target RNA molecules to which an engineered guide has been administered and then converting the target RNA to cDNA by reverse transcriptase prior to sequencing. In some examples, the sequencing employed can be Sanger sequencing, next generation sequencing, or a combination thereof. In some examples, in any of the methods disclosed herein, the engineered guide can be encoded by a polynucleotide or a vector disclosed herein or can be comprised in a composition, pharmaceutical composition, isolated cell, or plurality of cells disclosed herein.
Also disclosed herein are methods of treating a disease or condition in a subject in need thereof comprising administering to the subject any engineered guide (e.g., an engineered guide, a vector encoding or comprising an engineered guide) disclosed herein. In some examples, the methods of treating or preventing a disease or a condition in a subject in need thereof comprise administering to the subject having the disease or the condition an engineered guide, thereby treating or preventing the disease or the condition in the subject, wherein the engineered guide: (a) at least in part associates with at least a portion of a target RNA molecule; (b) in association with the target RNA molecule, forms a double stranded substrate comprising at least one structural feature, and wherein the double stranded substrate recruits an RNA editing entity; and (c) facilitates a chemical modification of a base of a nucleotide in the target RNA molecule by the RNA editing entity. In some examples, chemical modification of the base can be confirmed by sequencing. In some examples, confirming that chemical modification has occurred comprises isolating one or more target RNA molecules to which an engineered guide has been administered and then converting the target RNA to cDNA by reverse transcriptase prior to sequencing. In some examples, the sequencing employed can be Sanger sequencing, next generation sequencing, or a combination thereof. In some examples, in any of the methods disclosed herein, the engineered guide can be encoded by a polynucleotide or a vector disclosed herein or can be comprised in a composition, pharmaceutical composition, isolated cell, or plurality of cells disclosed herein.
Compositions and methods provided herein can be utilized to modulate expression of a target. Modulation can refer to altering the expression of a gene or portion thereof at one of various stages, with a view to alleviate a disease or condition associated with the gene or a mutation in the gene. Modulation can be mediated at the level of transcription or post-transcriptionally. Modulating transcription can correct aberrant expression of splice variants generated by a mutation in a gene. In some cases, compositions and methods provided herein can be utilized to regulate gene translation of a target. Modulation can refer to decreasing or knocking down the expression of a gene or portion thereof by decreasing the abundance of a transcript. The decreasing the abundance of a transcript can be mediated by decreasing the processing, splicing, turnover or stability of the transcript; or by decreasing the accessibility of the transcript by translational machinery such as ribosome. In some cases, an engineered guide described herein can facilitate a knockdown. A knockdown can reduce the expression of a target RNA. In some cases, a knockdown can be accompanied by editing of an mRNA. In some cases, a knockdown can occur with substantially little to no editing of an mRNA. In some instances, a knockdown can occur by targeting an untranslated region of the target RNA, such as a 3′ UTR, a 5′ UTR or both. In some cases, a knockdown can occur by targeting a coding region of the target RNA. In some instances, a knockdown can be mediated by an RNA editing enzyme (e.g., ADAR). In some instances, an RNA editing enzyme can cause a knockdown by hydrolytic deamination of multiple adenosines in an RNA. Hydrolytic deamination of multiple adenosines in an RNA can be referred to as hyper-editing. In some cases, hyper-editing can occur in cis (e.g. in an Alu element) or in trans (e.g. in a target RNA by an engineered guide).). In some instances, an RNA editing enzyme can cause a knockdown by editing a target RNA to comprise a premature stop codon or prevent initiation of translation of the target RNA due to an edit in the target RNA.
In some examples, the disease or condition can be associated with a mutation in a DNA molecule or RNA molecule encoding ABCA4, APP, SERPINA1, HEXA, LRRK2, SNCA, CFTR, or LIPA, a fragment of any of these, or any combination thereof. In some examples, a protein encoded for by a mutated DNA molecule or RNA molecule encoding ABCA4, APP, SERPINA1, HEXA, LRRK2, SNCA, CFTR, or LIPA contributes to, at least in part, the pathogenesis or progression of a disease. In some examples, the disease or condition can be associated with a mutation in a DNA molecule or RNA molecule encoding ABCA4, AAT, SERPINA1, SERPINA1 E342K, HEXA, LRRK2, SNCA, APP, Tau, GBA, PINK1, RAB7A, CFTR, ALAS1, ATP7B, ATP7B G1226R, HFE C282Y, LIPA c.894 G>A, PCSK9 start site, or SCNN1A start site, a fragment any of these, or any combination thereof. In some examples, a protein encoded for by a mutated DNA molecule or RNA molecule encoding ABCA4, AAT, SERPINA1, SERPINA1 E342K, HEXA, LRRK2, SNCA, APP, Tau, GBA, PINK1, RAB7A, CFTR, ALAS1, ATP7B, ATP7B G1226R, HFE C282Y, LIPA c.894 G>A, PCSK9 start site, or SCNN1A start site, a fragment any of these, or any combination thereof contributes to, at least in part, the pathogenesis or progression of a disease. In some examples, the mutation in the DNA or RNA molecule can be relative to an otherwise identical reference DNA or RNA molecule. In some examples, the mutation in the DNA or RNA molecule can be relative to an otherwise identical reference DNA or RNA molecule.
SERPINA1. In some embodiments, the present disclosure provides compositions and methods of use thereof of guide RNAs that are capable of facilitating RNA editing of serpin family A member 1 (SERPINA1). In some examples, the disease or condition can be an AAT deficiency or an associated lung or liver pathology (e.g., chronic obstructive pulmonary disease, cirrhosis, hepatocellular carcinoma) caused, at least in part, by a mutation in a SERPINA1 gene. In some examples, the mutation can be a substitution of a G with an A at nucleotide position 9989 within a wildtype SERPINA1 gene (such as accession number NC_000011:c94121149-93992837). In some examples, administration of the engineered guides disclosed herein restores expression of a normal AAT protein (e.g., as compared to an inactive or defective AAT protein) in a subject with an AAT deficiency. In some examples, a double stranded RNA (dsRNA) substrate (a guide-target RNA scaffold) is formed upon hybridization of an engineered guide of the present disclosure to a target RNA. In some examples, the target RNA forming the double stranded substrate comprises a portion of an mRNA or pre-mRNA molecule encoded by the SERPINA1 gene. In some examples the targeting region of the engineered guide forming the double stranded substrate is, at least in part, complementary to a portion of an mRNA or pre-mRNA molecule encoded by the SERPINA1 gene. In some examples the double stranded substrate comprises a single mismatch. In some examples, the engineered substrate additionally comprises one or two bulges. In some examples, the double stranded substrate can be formed by a target RNA comprising an mRNA or pre-mRNA encoded by the SERPINA1 gene and an engineered guide complementary to a portion of the mRNA encoded by the SERPINA1 gene, wherein the engineered substrate comprises a single mismatch. In some examples, the double stranded substrate can be formed by a target RNA comprising an mRNA or pre-mRNA encoded by the SERPINA1 gene and an engineered guide complementary to a portion of the mRNA or pre-mRNA encoded by the SERPINA1 gene, wherein the engineered substrate comprises a single mismatch, and wherein the engineered substrate comprises two additional bulges.
Guide RNAs can facilitate correction of a G to A mutation at nucleotide position 9989 of a SERPINA1 gene. In some embodiments, a guide RNA of the present disclosure can target, for example, E342K of SERPINA1. Said guide RNAs targeting a site in SERPINA1 can be encoded for by an engineered polynucleotide construct of the present disclosure. An engineered guide RNA targeting SERPINA1 can comprise a polynucleotide of any of the following sequences recited in TABLE 3:
The C in bold and italicized text indicates the base that produces a mismatch with the target A to be edited, the nucleotide sequence which form the additional bulges in the double stranded substrate are underlined, and the lowercase text signifies regions of the guide that hybridize to intronic target pre-mRNA. Further, a guide RNA targeting SERPINA1 can comprise any one of SEQ ID NO: 102-SEQ ID NO: 103 or SEQ ID NO: 297-SEQ ID NO: 327. In some examples, the engineered guide (including a latent guide RNA having latent structure) comprises a polynucleotide having at least 99% identity, at least 95% identity, at least 90% identity, at least 85% identity, at least 80% identity, or at least 70% identity to any one of SEQ ID NOS: 6-10, 102-103 or 297-327. In some examples, the engineered guide (including a latent guide RNA having latent structure) comprises a polynucleotide having at least 99% length, at least 95% length, at least 90% length, at least 85% length, at least 80% length, or at least 70% length to the above SEQ ID NOS: 6-10, 102-103 or 297-327. In some examples, hybridization of a latent guide RNA targeting SERPINA1 to a target SERPINA1 mRNA produces a guide-target RNA scaffold that comprises a structural features selected from the group consisting of: (i) one or more X1/X2 bulges, wherein X1 is the number of nucleotides of the target RNA in the bulge and X2 is the number of nucleotides of the engineered guide RNA in the bulge, and wherein the bulge is a 0/2 asymmetric bulge, a 0/3 asymmetric bulge, a 1/0 asymmetric bulge, a 2/0 asymmetric bulge, a 2/2 symmetric bulge, a 3/0 asymmetric bulge, a 2/2 symmetric bulge, or a 3/3 symmetric bulge; (ii) an X1/X2 internal loop, wherein X1 is the number of nucleotides of the target RNA in the internal loop and X2 is the number of nucleotides of the engineered guide RNA in the internal loop, and wherein the internal loop is a 5/5 symmetric internal loop; (iii) one or more mismatches, wherein the one or more mismatches is an A/C mismatch, an A/A mismatch, and a G/A mismatch, (iv) a G/U wobble base pair, or a U/G wobble base pair; and (v) any combination thereof. Said engineered guide RNA can be delivered via viral vector (e.g., encoded for and delivered via AAV) as disclosed herein and can be administered via any route of administration disclosed herein to a subject in need thereof. The subject may be human and may be at risk of developing or has developed alpha-1 antitrypsin deficiency. Such alpha-1 antitrypsin deficiency can be at least partially caused by a mutation of SERPINA1, for which an engineered guide RNA described herein can facilitate editing in, thus correcting the mutation in SERPINA1 and reducing the incidence of alpha-1 antitrypsin deficiency in the subject. Thus, the guide RNAs of the present disclosure can be used in a method of treatment of alpha-1 antitrypsin deficiency.
ABCA4. In some embodiments, the present disclosure provides compositions and methods of use thereof of guide RNAs that are capable of facilitating RNA editing of ATP binding cassette subfamily A member 4 (ABCA4). In some examples, the disease or condition can be associated with a mutation in an ABCA4 gene. In some examples, the disease or condition can be Stargardt macular degeneration. In some examples, the Stargardt macular degeneration can be caused, at least in part, by a mutation in an ABCA4 gene. In some examples, the mutation comprises a substitution of a G with an A at nucleotide position 5882 in a wildtype ABCA4 gene (such as accession number NC_000001.11:c94121149-93992837). In some examples, the mutation comprises a G with an A at nucleotide position 5714 in a wildtype ABCA4 gene (such as accession number NC_000001.11:c94121149-93992837). In some examples, the mutation comprises a substitution of a G with an A at nucleotide position 6320 in a wildtype ABCA4 gene (such as accession number NC_000001.11:c94121149-93992837). In some examples, the double stranded substrate mimics one or more structural features of the naturally occurring ADAR substrate and comprises a target mRNA molecule encoded by the ABCA4 gene and an engineered guide that can be complementary, at least in part, to a portion of the target mRNA molecule.
In some examples, the engineered guide targeting ABCA4 mRNA (including a latent guide RNA having latent structure) comprises a polynucleotide of any one of SEQ ID NO: 11-34, 58, 218-289, 291-296, or 328-343. In some examples, the engineered guide targeting ABCA4 mRNA (including a latent guide RNA having latent structure) comprises a polynucleotide having at least 99% identity, at least 95% identity, at least 90% identity, at least 85% identity, at least 80% identity, or at least 70% identity to any one of SEQ ID NO: 11-34, 58, 218-289, 291-296, or 328-343. In some examples, the engineered guide (including a latent guide RNA having latent structure) comprises a polynucleotide having at least 99% length, at least 95% length, at least 90% length, at least 85% length, at least 80% length, or at least 70% length to any one of SEQ ID NO: 11-34, 58, 218-289, 291-296, or 328-343. In some examples, hybridization of a latent guide RNA targeting ABCA4 to a target ABCA4 mRNA produces a guide-target RNA scaffold that comprises a structural features selected from the group consisting of: (i) one or more X1/X2 bulges, wherein X1 is the number of nucleotides of the target RNA in the bulge and X2 is the number of nucleotides of the engineered guide RNA in the bulge, and wherein the one or more bulges is a 2/1 asymmetric bulge, a 1/0 asymmetric bulge, a 2/2 symmetric bulge, a 3/3 symmetric bulge, or a 4/4 symmetric bulge; (ii) an X1/X2 internal loop, wherein X1 is the number of nucleotides of the target RNA in the internal loop and X2 is the number of nucleotides of the engineered guide RNA in the internal loop, and wherein the internal loop is a 5/5 symmetric loop (iii) one or more mismatches, wherein the one or more mismatches is a G/G mismatch, an A/C mismatch, or a G/A mismatch, (iv) a G/U wobble base pair or a U/G wobble base pair, and (v) any combination thereof. In some embodiments, the guide-target RNA scaffold comprises a 2/1 asymmetric bulge, a 1/0 asymmetric bulge, a G/G mismatch, an A/C mismatch, and a 3/3 symmetric bulge. In some instances, the engineered latent guide RNA targeting ABCA4 is the engineered latent guide RNA of SEQ ID NO: 291. In some instances, the engineered latent guide RNA targeting ABCA4 is the engineered latent guide RNA of SEQ ID NO: 291. In some instances, the engineered latent guide RNA targeting ABCA4 comprises a G/G mismatch, a U/U mismatch, and a G/G mismatch. Said engineered guide RNAs can be delivered via viral vector (e.g., encoded for and delivered via AAV) as disclosed herein and can be administered via any route of administration disclosed herein to a subject in need thereof. The subject can be human and may be at risk of developing or has developed Stargardt macular degeneration (or Stargardt's disease). Such Stargardt macular degeneration can be at least partially caused by a mutation of ABCA4, for which an engineered guide RNA described herein can facilitate editing in, thus correcting the mutation in ABCA4 and reducing the incidence of Stargardt macular degeneration in the subject. Thus, the guide RNAs of the present disclosure can be used in a method of treatment of Stargardt macular degeneration.
APP. In some embodiments, the present disclosure provides compositions and methods of use thereof of guide RNAs that are capable of facilitating RNA editing of an amyloid precursor protein (APP). In some examples, the disease or condition can be associated with expression of or cleavage products of an amyloid precursor protein (APP). In some examples, the disease or condition associated with Amyloid beta (AD or Abeta) peptide deposition in the brain or blood vessels. In some examples, the Abeta deposition can be produced by the cleavage of APP by beta secretase (BACE) or gamma secretase. In some examples, the disease can be a neurodegenerative disease. In some examples, the disease comprises Alzheimer's disease, Parkinson's disease, corticobasal degeneration, dementia with Lewy bodies, Lewy body variant of Alzheimer's disease, Parkinson's disease with dementia, Pick's disease, progressive supranuclear palsy, dementia, fronto-temporal dementia with Parkinsonism linked to tau mutations on chromosome 17, or any combination thereof. In some examples, the engineered guides (including latent guide RNAs having latent structure) can be administered to knockdown expression of APP or to edit a cut site to prevent Abeta fragment formation from APP.
Guide RNAs of the present disclosure can facilitate editing of the cleavage site in APP, so that beta/gamma secretases exhibit reduced cleavage of APP or can no longer cut APP and, therefore, reduced levels of Abeta 40/42 or no Abetas can be produced. In some embodiments, a guide RNA of the present disclosure can target any one of or any combination of the following sites in APP for RNA editing: K670E, K670R, K670G, M671V, A673V, A673T, D672G, E682G, H684R, K687R, K687E, or K687G, I712X, or T714X. Said guide RNAs targeting a site in APP can be encoded by an engineered polynucleotide construct of the present disclosure. Said engineered guide RNAs may be delivered via viral vector (e.g., encoded for and delivered via AAV) as disclosed herein and may be administered via any route of administration disclosed herein to a subject in need thereof. The subject may be human and may be at risk of developing or has developed Alzheimer's disease. The subject may be human and may be at risk of developing or has developed a neurological disease in which APP impacts disease pathology. Thus, the guide RNAs of the present disclosure having latent structure can be used in a method of treatment of neurological diseases (e.g., Alzheimer's disease).
Alpha-synuclein (SNCA). The Alpha-synuclein gene is made up of 5 exons and encodes a 140 amino-acid protein with a predicted molecular mass of ˜14.5 kDa. The encoded product is an intrinsically disordered protein with unknown functions. Usually, Alpha-synuclein is a monomer. Under certain stress conditions or other unknown causes, α-synuclein self-aggregates into oligomers. Lewy-related pathology (LRP), primarily comprised of Alpha-synuclein in more than 50% of autopsy-confirmed Alzheimer's disease patients' brains. While the molecular mechanism of how Alpha-synuclein affects the development of Alzheimer's disease is unclear, experimental evidence has shown that Alpha-synuclein interacts with Tau-p and may seed the intracellular aggregation of Tau-p. Moreover, Alpha-synuclein could regulate the activity of GSK3β, which can mediate Tau-hyperphosphorylation. Alpha-synuclein can also self-assemble into pathogenic aggregates (Lewy bodies). Both Tau and α-synuclein can be released into the extracellular space and spread to other cells. Vascular abnormalities impair the supply of nutrients and removal of metabolic byproducts, cause microinfarcts, and promote the activation of glial cells. Therefore, a multiplex strategy to substantially reduce Tau formation, alpha-synuclein formation, or a combination thereof can be important in effectively treating neurodegenerative diseases.
The domain structure of Alpha-synuclein comprises an N-terminal A2 lipid-binding alpha-helix domain, a Non-amyloid R component (NAC) domain, and a C-terminal acidic domain. The lipid-binding domain consists of five KXKEGV imperfect repeats. The NAC domain consists of a GAV motif with a VGGAVVTGV consensus sequence and three GXXX sub-motifs—where X is any of Gly, Ala, Val, Ile, Leu, Phe, Tyr, Trp, Thr, Ser or Met. The C-terminal acidic domain contains a copper-binding motif with a DPDNEA consensus sequence. Molecularly, Alpha-synuclein is suggested to play a role in neuronal transmission and DNA repair.
In some cases, a region of Alpha-synuclein can be targeted utilizing guide RNAs provided herein. In some cases, a region of the Alpha-synuclein mRNA can be targeted with the engineered guide RNAs disclosed herein for knockdown. In some cases, a region of the exon or intron of the Alpha-synuclein mRNA can be targeted. In some embodiments, a region of the non-coding sequence of the Alpha-synuclein mRNA, such as the 5′ UTR and 3′ UTR, can be targeted. In other cases, a region of the coding sequence of the Alpha-synuclein mRNA can be targeted. Suitable regions include but are not limited to a N-terminal A2 lipid-binding alpha-helix domain, a Non-amyloid R component (NAC) domain, or a C-terminal acidic domain.
In some aspects, an alpha-synuclein mRNA sequence is targeted. In some cases, any one of the 3,177 residues of the sequence may be targeted utilizing the guide RNAs provided herein. In some cases, a target residue may be located among residues 1-100, 101-200, 201-300, 301-400, 401-500, 501-600, 601-700, 701-800, 801-900, 901-1000, 1001-1100, 1101-1200, 1201-1300, 1301-1400, 1401-1500, 1501-1600, 1601-1700, 1701-1800, 1801-1900, 1901-2000, 2001-2100, 2101-2200, 2201-2300, 2301-2400, 2401-2500, 2501-2600, 2601-2700, 2701-2800, 2801-2900, 2901-3000, 3001-3100, and/or 3101-3177.
In some embodiments, the present disclosure provides compositions and methods of use thereof of guide RNAs that are capable of facilitating RNA editing of SNCA. In some embodiments, a guide RNA of the present disclosure can knock down expression of SNCA, for example, by facilitating editing at a 3′ UTR of an SNCA gene. Said guide RNAs targeting a site in SNCA can be encoded by an engineered polynucleotide construct of the present disclosure.
In some examples, the engineered guide targeting SNCA mRNA (including a latent guide RNA having latent structure) comprises a polynucleotide of any one of SEQ ID NO: 59-101, 104-108, and 208-217. In some examples, the engineered guide targeting SNCA mRNA (including a latent guide RNA having latent structure) comprises a polynucleotide having at least 99% identity, at least 95% identity, at least 90% identity, at least 85% identity, at least 80% identity, or at least 70% identity to any one of SEQ ID NO: 59-101, 104-108, and 208-217. In some examples, the engineered guide (including a latent guide RNA having latent structure) comprises a polynucleotide having at least 99% length, at least 95% length, at least 90% length, at least 85% length, at least 80% length, or at least 70% length to any one of SEQ ID NO: 59-101, 104-108, and 208-217. In some examples, hybridization of a latent guide RNA targeting SNCA to a target SNCA mRNA produces a guide-target RNA scaffold that comprises a structural features selected from the group consisting of: (i) an X1/X2 bulge, wherein X1 is the number of nucleotides of the target RNA in the bulge and X2 is the number of nucleotides of the engineered guide RNA in the bulge, and wherein the bulge is a 4/4 symmetric bulge; (ii) one or more X1/X2 internal loops, wherein X1 is the number of nucleotides of the target RNA in the internal loop and X2 is the number of nucleotides of the engineered guide RNA in the internal loop, and wherein the one or more internal loop is a 5/5 symmetric loop, an 8/8 symmetric loop, or a 49/4 asymmetric loop; (iii) one or more mismatches, wherein the one or more mismatches is an A/C mismatch, a G/G mismatch, a G/A mismatch, a U/C mismatch, or an A/A mismatch, (iv) any combination thereof. Said engineered guide RNA can be delivered via viral vector (e.g., encoded for and delivered via AAV) as disclosed herein and can be administered via any route of administration disclosed herein to a subject in need thereof. The subject can be human and may be at risk of developing or has developed Alzheimer's disease or Parkinson's disease. The subject can be human and may be at risk of developing or has developed a neurological disease in which overexpression of SNCA impacts disease pathology. Thus, the guide RNAs of the present disclosure can be used in a method of treatment of neurological diseases (e.g., Alzheimer's disease).
LRRK2. Leucine-rich repeat kinase 2 (LRRK2) has been associated with familial and sporadic cases of Parkinson's Disease and immune-related disorders like Crohn's disease. Its aliases include LRRK2, AURA17, DARDARIN, PARK8, RIPK7, ROCO2, or leucine-rich repeat kinase 2. The LRRK2 gene is made up of 51 exons and encodes a 2527 amino-acid protein with a predicted molecular mass of about 286 kDa. The encoded product is a multi-domain protein with kinase and GTPase activities. LRRK2 can be found in various tissues and organs including but not limited to adrenal, appendix, bone marrow, brain, colon, duodenum, endometrium, esophagus, fat, gall bladder, heart, kidney, liver, lung, lymph node, ovary, pancreas, placenta, prostate, salivary gland, skin, small intestine, spleen, stomach, testis, thyroid, and urinary bladder. LRRK2 can be ubiquitously expressed but is generally more abundant in the brain, kidney, and lung tissue. Cellularly, LRRK2 has been found in astrocytes, endothelial cells, microglia, neurons, and peripheral immune cells.
Over 100 mutations have been identified in LRRK2; six of them-G2019S, R1441C/G/H, Y1699C, and I2020T—have been shown to cause Parkinson's Disease through segregation analysis. G2019S and R1441C are the most common disease-causing mutations in inherited cases. In sporadic cases, these mutations have shown age-dependent penetrance: The percentage of individuals carrying the G2019S mutation that develops the disease jumps from 17% to 85% when the age increases from 50 to 70 years old. In some cases, mutation-carrying individuals never develop the disease.
At its catalytic core, LRRK2 contains the Ras of complex proteins (Roc), C-terminal of ROC (COR), and kinase domains. Multiple protein-protein interaction domains flank this core: an armadillo repeats (ARM) region, an ankyrin repeat (ANK) region, a leucine-rich repeat (LRR) domain are found in the N-terminus joined by a C-terminal WD40 domain. The G2019S mutation is located within the kinase domain. It has been shown to increase the kinase activity; for R1441C/G/H and Y1699C, these mutations can decrease the GTPase activity of the Roc domain. Genome-wide association study has found that common variations in LRRK2 increase the risk of developing sporadic Parkinson's Disease. While some of these variations are nonconservative mutations that affect the protein's binding or catalytic activities, others modulate its expression. These results suggest that specific alleles or haplotypes can regulate LRRK2 expression.
Pro-inflammatory signals upregulate LRRK2 expression in various immune cell types, suggesting that LRRK2 is a critical regulator in the immune response. Studies have found that both systemic and central nervous system (CNS) inflammation are involved in Parkinson's Disease's symptoms. Moreover, LRRK2 mutations associated with Parkinson's Disease modulate its expression levels in response to inflammatory stimuli. Many mutations in LRRK2 are associated with immune-related disorders such as inflammatory bowel disease such as Crohn's Disease. For example, both G2019S and N2081D increase LRRK2's kinase activity and are over-represented in Crohn's Disease patients in specific populations. Because of its critical role in these disorders, LRRK2 is an important therapeutic target for Parkinson's Disease and Crohn's Disease. In particular, many mutations, such as point mutations including G2019S, play roles in developing these diseases, making LRRK2 an attractive for therapeutic strategy such as RNA editing.
In some embodiments, the present disclosure provides compositions and methods of use thereof of guide RNAs that are capable of facilitating RNA editing of LRRK2. In some embodiments, a guide RNA of the present disclosure can target the following mutations in LRRK2: E10L, A30P, S52F, E46K, A53T, L119P, A211V, C228S, E334K, N363S, V366M, A419V, R506Q, N544E, N551K, A716V, M712V, I723V, P755L, R793M, I810V, K871E, Q923H, Q930R, R1067Q, S1096C, Q1111H, I1122V, A1151T, L1165P, I1192V, H1216R, S1228T, P1262A, R1325Q, I1371V, R1398H, T1410M, D1420N, R1441G, R1441H, A1442P, P1446L, V1450I, K1468E, R1483Q, R1514Q, P1542S, V1613A, R1628P, M1646T, 51647T, Y1699C, R1728H, R1728L, L1795F, M1869V, M1869T, L1870F, E1874X, R1941H, Y2006H, I2012T, G2019S, I2020T, T2031S, N2081D, T2141M, R2143H, Y2189C, T2356I, G2385R, V2390M, E2395K, M2397T, L2466H, or Q2490NfsX3. Said guide RNAs targeting a site in LRRK2 can be encoded by an engineered polynucleotide construct of the present disclosure.
In some examples, the engineered guide targeting LRRK2 mRNA (including a latent guide RNA having latent structure) comprises a polynucleotide of any one of SEQ ID NO: 35-42, 46-52, 111-207, or 344-345. In some examples, the engineered guide targeting LRRK2 mRNA (including a latent guide RNA having latent structure) comprises a polynucleotide having at least 99% identity, at least 95% identity, at least 90% identity, at least 85% identity, at least 80% identity, or at least 70% identity to any one of SEQ ID NO: 35-42, 46-52, 111-207, or 344-345. In some examples, the engineered guide (including a latent guide RNA having latent structure) comprises a polynucleotide having at least 99% length, at least 95% length, at least 90% length, at least 85% length, at least 80% length, or at least 70% length to any one of SEQ ID NO: 35-42, 46-52, 111-207, or 344-345. In some examples, hybridization of a latent guide RNA targeting LRRK2 to a target LRRK2 mRNA produces a guide-target RNA scaffold that comprises a structural features selected from the group consisting of: (i) one or more X1/X2 bulges, wherein X1 is the number of nucleotides of the target RNA in the bulge and X2 is the number of nucleotides of the engineered guide RNA in the bulge, and wherein the one or more bulges is a 0/1 asymmetric bulge, a 2/2 symmetric bulge, a 3/3 symmetric bulge, or a 4/4 symmetric bulge; (ii) one or more X1/X2 internal loops, wherein X1 is the number of nucleotides of the target RNA in the internal loop and X2 is the number of nucleotides of the engineered guide RNA in the internal loop, and wherein the one or more internal loops is a 5/0 asymmetric internal loop, a 5/4 asymmetric internal loop, a 5/5 symmetric internal loop, a 6/6 symmetric internal loop, a 7/7 symmetric internal loop, or a 10/10 symmetric internal loop; (iii) one or more mismatches, wherein the one or more mismatches is an A/C mismatch, an A/G mismatch, a C/U mismatch, a G/A mismatch, or a C/C mismatch, (iv) a G/U wobble base pair or a U/G wobble base pair, and (v) any combination thereof. Said engineered guide RNAs can be delivered via viral vector (e.g., encoded for and delivered via AAV) as disclosed herein and can be administered via any route of administration disclosed herein to a subject in need thereof. The subject can be human and may be at risk of developing or has developed a disease or condition associated with mutations in LRRK2 (e.g. diseases of the central nervous system (CNS) or gastrointestinal (GI) tract). For example, such diseases of conditions can include Crohn's disease or Parkinson's disease. Such CNS or GI tract diseases (e.g. Crohn's disease or Parkinson's disease) can be at least partially caused by a mutation of LRRK2, for which an engineered guide RNA described herein can facilitate editing in, thus correcting the mutation in LRRK2 and reducing the incidence of the CNS or GI tract disease in the subject. Thus, the guide RNAs of the present disclosure can be used in a method of treatment of diseases such as Crohn's disease or Parkinson's disease.
An engineered guide RNA of the present disclosure containing latent structures can have increased on-target editing via an RNA editing entity, relative to an otherwise comparable guide RNA lacking latent structures. In some embodiments, an engineered guide RNA of the present disclosure has at least about 1-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 11-fold, 12-fold, 13-fold, 14-fold, 15-fold, 16-fold, 17-fold, 18-fold, 19-fold, 20-fold, 21-fold, 22-fold, 23-fold, 24-fold, 25-fold, 26-fold, 27-fold, 28-fold, 29-fold, 30-fold, 31-fold, 32-fold, 33-fold, 34-fold, 35-fold, 36-fold, 37-fold, 38-fold, 39-fold, 40-fold, 41-fold, 42-fold, 43-fold, 44-fold, 45-fold, 46-fold, 47-fold, 48-fold, 49-fold, 50-fold, 51-fold, 52-fold, 53-fold, 54-fold, 55-fold, 56-fold, 57-fold, 58-fold, 59-fold, 60-fold, 61-fold, 62-fold, 63-fold, 64-fold, 65-fold, 66-fold, 67-fold, 68-fold, 69-fold, 70-fold, 71-fold, 72-fold, 73-fold, 74-fold, 75-fold, 76-fold, 77-fold, 78-fold, 79-fold, 80-fold, 81-fold, 82-fold, 83-fold, 84-fold, 85-fold, 86-fold, 87-fold, 88-fold, 89-fold, 90-fold, 91-fold, 92-fold, 93-fold, 94-fold, 95-fold, 96-fold, 97-fold, 98-fold, 99-fold, or 100-fold improvement in on-target editing via an RNA editing entity, relative to the otherwise comparable guide RNA lacking the latent structures. In some instances, an engineered guide RNA of the present disclosure containing latent structures has an on-target editing of at least about 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 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%, or greater than 99% for ADAR1. In some instances, an engineered guide RNA of the present disclosure containing latent structures has an on-target editing of at least about 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 1%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 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%, or greater than 99% for ADAR2. In some instances, an engineered guide RNA of the present disclosure containing latent structures has an on-target specificity for ADAR1 of at least about 1.00, 1.01, 1.02, 1.03, 1.04, 1.05, 1.06, 1.07, 1.08, 1.09, 1.1, 1.11, 1.12, 1.13, 1.14, 1.15, 1.16, 1.17, 1.18, 1.19, 1.2, 1.21, 1.22, 1.23, 1.24, 1.25, 1.26, 1.27, 1.28, 1.29, 1.3, 1.31, 1.32, 1.33, 1.34, 1.35, 1.36, 1.37, 1.38, 1.39, 1.4, 1.41, 1.42, 1.43, 1.44, 1.45, 1.46, 1.47, 1.48, 1.49, 1.5, 1.51, 1.52, 1.53, 1.54, 1.55, 1.56, 1.57, 1.58, 1.59, 1.6, 1.61, 1.62, 1.63, 1.64, 1.65, 1.66, 1.67, 1.68, 1.69, 1.7, 1.71, 1.72, 1.73, 1.74, 1.75, 1.76, 1.77, 1.78, 1.79, 1.8, 1.81, 1.82, 1.83, 1.84, 1.85, 1.86, 1.87, 1.88, 1.89, 1.9, 1.91, 1.92, 1.93, 1.94, 1.95, 1.96, 1.97, 1.98, 1.99, or greater than 2.00. In some instances, an engineered guide RNA of the present disclosure containing latent structures has an on-target specificity for ADAR2 of at least about 1.00, 1.01, 1.02, 1.03, 1.04, 1.05, 1.06, 1.07, 1.08, 1.09, 1.1, 1.11, 1.12, 1.13, 1.14, 1.15, 1.16, 1.17, 1.18, 1.19, 1.2, 1.21, 1.22, 1.23, 1.24, 1.25, 1.26, 1.27, 1.28, 1.29, 1.3, 1.31, 1.32, 1.33, 1.34, 1.35, 1.36, 1.37, 1.38, 1.39, 1.4, 1.41, 1.42, 1.43, 1.44, 1.45, 1.46, 1.47, 1.48, 1.49, 1.5, 1.51, 1.52, 1.53, 1.54, 1.55, 1.56, 1.57, 1.58, 1.59, 1.6, 1.61, 1.62, 1.63, 1.64, 1.65, 1.66, 1.67, 1.68, 1.69, 1.7, 1.71, 1.72, 1.73, 1.74, 1.75, 1.76, 1.77, 1.78, 1.79, 1.8, 1.81, 1.82, 1.83, 1.84, 1.85, 1.86, 1.87, 1.88, 1.89, 1.9, 1.91, 1.92, 1.93, 1.94, 1.95, 1.96, 1.97, 1.98, 1.99, or greater than 2.00.
Indications
An engineered guide RNA or engineered polynucleotide encoding the same can be administered to a subject to treat a disease or condition described herein. In some cases, a disease or condition comprises a neurodegenerative disease, a muscular disorder, a metabolic disorder, an ocular disorder (e.g. an ocular disease), a cancer, a liver disease (e.g., Alpha-1 antitrypsin (AAT) deficiency), or any combination thereof. In some examples, the disease comprises cystic fibrosis, albinism, alpha-1-antitrypsin deficiency, Alzheimer disease, Amyotrophic lateral sclerosis, Asthma, 0-thalassemia, Cadasil syndrome, Charcot-Marie-Tooth disease, Chronic Obstructive Pulmonary Disease (COPD), dementia, Distal Spinal Muscular Atrophy (DSMA), Duchenne/Becker muscular dystrophy, Dystrophic Epidermolysis bullosa, Epidermylosis bullosa, Fabry disease, Factor V Leiden associated disorders, Familial Adenomatous, Polyposis, Galactosemia, Gaucher's Disease, Glucose-6-phosphate dehydrogenase, Haemophilia, Hereditary Hematochromatosis, Hunter Syndrome, Huntington's disease, Hurler Syndrome, Inflammatory Bowel Disease (IBD), Inherited polyagglutination syndrome, Leber congenital amaurosis, Lesch-Nyhan syndrome, Lynch syndrome, Marfan syndrome, Mucopolysaccharidosis, Muscular Dystrophy, Myotonic dystrophy types I and II, neurofibromatosis, Niemann-Pick disease type A, B and C, NY-esol related cancer, Parkinson's disease, Peutz-Jeghers Syndrome, Phenylketonuria, Pompe's disease, Primary Ciliary Disease, Prothrombin mutation related disorders, such as the Prothrombin G20210A mutation, Pulmonary Hypertension, Retinitis Pigmentosa, Sandhoff Disease, Severe Combined Immune Deficiency Syndrome (SCID), Sickle Cell Anemia, Spinal Muscular Atrophy, Stargardt's Disease, Tay-Sachs Disease, Usher syndrome, Wolman disease, X-linked immunodeficiency, various forms of cancer (e.g., BRCA1 and 2 linked breast cancer and ovarian cancer). In some cases, a treatment of a disease or condition such as a neurodegenerative disease (e.g. Alzheimer's, Parkinson's) can comprise producing an edit, a knockdown or both of amyloid precursor protein (APP), tau, alpha-synuclein, or any combination thereof. In some cases, APP, tau, and alpha-synuclein can comprise a pathogenic variant. In some instances, APP can comprise a pathogenic variant such as A673V mutation or A673T mutation. In some cases, a treatment of a disease or condition such as a neurodegenerative disease (Parkinson's) can comprise producing an edit, a knockdown or both of a pathogenic variant of LRRK2. In some cases, a pathogenic variant of LRRK can comprise a G2019S mutation. The disease or condition can comprise a muscular dystrophy, an omithine transcarbamylase deficiency, a retinitis pigmentosa, a breast cancer, an ovarian cancer, Alzheimer's disease, pain, Stargardt macular dystrophy, Charcot-Marie-Tooth disease, Rett syndrome, or any combination thereof.
In some examples, the disease or condition can be caused or contributed to, at least in part, by a protein encoded by an mRNA comprising a premature stop codon. In some cases, the premature stop codon results in a truncated version of the polypeptide or protein. In some cases, the disease, disorder, or condition can be caused by an increased level of a truncated version of the polypeptide, or a decreased level of substantially full-length polypeptide. In some examples, the premature stop codon can be created by a point mutation. In some examples, the premature stop codon can be produced by a point mutation on an mRNA molecule in combination with two additional nucleotides. In some examples, the mRNA molecule comprises one, two, three, or for premature stop codons. In some examples, the disease or condition can be caused or contributed to, at least in part, by a splice site mutation on a pre-mRNA molecule. In some examples, the splice site mutation facilitates unintended splicing of a pre-mRNA molecule. In some examples, the splice site mutation results in mistranslation and/or truncation of a protein caused by incorrect delineation of a pre-mRNA splice site.
In some examples, in methods disclosed herein, the subject can be diagnosed with the disease or condition. In some examples, the subject can be diagnosed with the disease or condition by an in vitro assay.
In some examples, administration of a composition or engineered guide disclosed herein: (a) decreases expression of a gene relative to an expression of the gene prior to administration; (b) edits at least one point mutation in a subject, such as a subject in need thereof; (c) edits at least one stop codon in the subject to produce a readthrough of a stop codon; (d) produces an exon skip in the subject, or (e) any combination thereof.
Methods described herein can comprise administration to a subject one or more engineered guide RNAs, engineered polynucleotides encoding the same, as well as compositions, pharmaceutical compositions, vectors, cells and isolated cells containing the same as described herein. Methods of determining the most effective means and dosage of administration can vary with the composition used for therapy, the purpose of the therapy, the target cell being treated, and the subject being treated.
In some examples, administration of the engineered guide RNA, engineered polynucleotide, composition, pharmaceutical composition, vector, or cell disclosed herein can be performed for a treatment duration of at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 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 days consecutive or nonconsecutive days. In some examples, administration of the engineered guide RNA, engineered polynucleotide, composition, pharmaceutical composition, vector, or cell disclosed herein can be performed for a treatment duration of no more than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 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 days consecutive or nonconsecutive days.
In some cases, a treatment duration can be from about 1 to about 30 days, from about 2 to about 30 days, from about 3 to about 30 days, from about 4 to about 30 days, from about 5 to about 30 days, from about 6 to about 30 days, from about 7 to about 30 days, from about 8 to about 30 days, from about 9 to about 30 days, from about 10 to about 30 days, from about 11 to about 30 days, from about 12 to about 30 days, from about 13 to about 30 days, from about 14 to about 30 days, from about 15 to about 30 days, from about 16 to about 30 days, from about 17 to about 30 days, from about 18 to about 30 days, from about 19 to about 30 days, from about 20 to about 30 days, from about 21 to about 30 days, from about 22 to about 30 days, from about 23 to about 30 days, from about 24 to about 30 days, from about 25 to about 30 days, from about 26 to about 30 days, from about 27 to about 30 days, from about 28 to about 30 days, or from about 29 to about 30 days.
In some examples, administration of the engineered guide RNA, engineered polynucleotide, composition, pharmaceutical composition, vector, or cell disclosed herein can be performed for a treatment duration of at least about 1 week, at least about 1 month, at least about 1 year, at least about 2 years, at least about 3 years, at least about 4 years, at least about 5 years, at least about 6 years, at least about 7 years, at least about 8 years, at least about 9 years, at least about 10 years, at least about 15 years, at least about 20 years, or more. In some examples, administration can be performed repeatedly over a lifetime of a subject, such as once a month or once a year for the lifetime of a subject. In some examples, administration can be performed repeatedly over a substantial portion of a subject's life, such as once a month or once a year for at least about 1 year, 5 years, 10 years, 15 years, 20 years, 25 years, 30 years, or more.
In some examples, administration of the engineered guide RNA, engineered polynucleotide, composition, pharmaceutical composition, vector, or cell disclosed herein can be performed at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, or 24 times a day. In some examples, administration or application of composition disclosed herein can be performed at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or 21 times a week. In some examples, administration of an engineered guide RNA disclosed herein can be performed at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, or 90 times a month.
In some examples, an engineered guide RNA, engineered polynucleotide, composition, pharmaceutical composition, vector, or cell disclosed herein can be administered/applied as a single dose or as divided doses. In some examples, engineered guides RNA disclosed herein can be administered at a first time point and a second time point. In some examples, an engineered guide RNA disclosed herein can be administered such that a first administration can be administered before the other with a difference in administration time of 1 hour, 2 hours, 4 hours, 8 hours, 12 hours, 16 hours, 20 hours, 1 day, 2 days, 4 days, 7 days, 2 weeks, 4 weeks, 2 months, 3 months, 4 months, 5 months, 6 months, 7 months, 8 months, 9 months, 10 months, 11 months, 1 year or more.
A method of administration can be by inhalation, otic, buccal, conjunctival, dental, endocervical, endosinusial, endotracheal, enteral, epidural, extra-amniotic, extracorporeal, hemodialysis, infiltration, interstitial, intraabdominal, intraamniotic, intraarterial, intraarticular, intrabiliary, intrabronchial, intrabursal, intracardiac, intracartilaginous, intracaudal, intracavemous, intracavitary, intracerebroventricular, intracistemal, intracomeal, intracoronal, intracoronary, intracorpous cavemaosum, intradermal, intradiscal, intraductal, intraduodenal, intradural, intraepidermal, intraesophageal, intragastric, intragingival, intrahippocampal, intraileal, intralesional, intraluminal, intralymphatic, intramedullary, intrameningeal, intramuscular, intraocular, intraovarian, intrapericardial, intraperitoneal, intrapleural, intraprostatic, intrapulmonary, intrasinal, intraspinal, intrasynovial, intratendinous, intratesticular, intrathoracic, intratubular, intratumor, intratympanic, intrauterine, intravascular, intravenous, intravenous bolus, intravenous drip, intravesical, intravitreal, iontophoresis, irrigation, laryngeal, nasal, nasogastric, ophthalmic, oral, oropharyngeal, parenteral, percutaneous, periarticular, peridural, perineural, periodontal, rectal, retrobulbar, subarachnoid, subconjunctival, subcutaneous, sublingual, submucosal, topical, transdermal, transmucosal, transplacental, transtracheal, transtympanic, ureteral, urethral, vaginal, infraorbital, intraparenchymal, intrathecal, intraventricular, stereotactic, or any combination thereof. Delivery can include parenteral administration (including intravenous, subcutaneous, intrathecal, intraperitoneal, intramuscular, intravascular or infusion), oral administration, inhalation administration, intraduodenal administration, rectal administration. Delivery can include topical administration (such as a lotion, a cream, an ointment) to an external surface of a surface, such as a skin. In some cases, administration is by parenchymal injection, intra-thecal injection, intra-ventricular injection, intra-cisternal injection, intravenous injection, or intranasal administration or any combination thereof. In some instances, a subject can administer the composition in the absence of supervision. In some instances, a subject can administer the composition under the supervision of a medical professional (e.g., a physician, nurse, physician's assistant, orderly, hospice worker, etc.). A medical professional can administer the composition. In some cases, a cosmetic professional can administer the composition.
In some examples, a pharmaceutical composition disclosed herein can be administered at dosage levels sufficient to deliver from about 0.0001 mg/kg to about 100 mg/kg, from about 0.001 mg/kg to about 0.05 mg/kg, from about 0.005 mg/kg to about 0.05 mg/kg, from about 0.001 mg/kg to about 0.005 mg/kg, from about 0.05 mg/kg to about 0.5 mg/kg, from about 0.01 mg/kg to about 50 mg/kg, from about 0.1 mg/kg to about 40 mg/kg, from about 0.5 mg/kg to about 30 mg/kg, from about 0.01 mg/kg to about 10 mg/kg, from about 0.1 mg/kg to about 10 mg/kg, or from about 1 mg/kg to about 25 mg/kg, of subject body weight per day, one or more times a day, to obtain the desired therapeutic, diagnostic, or prophylactic, effect.
In some examples, methods described herein can comprise administering a co-therapy. In some examples. a co-therapy can comprise a cancer treatment (e.g. radiotherapy, chemotherapy, CAR-T therapy, immunotherapy, hormony therapy, cryoablation). In some examples, a co-therapy can comprise surgery. In some example, a co-therapy can comprise a laser therapy.
In some examples, the pharmaceutical composition comprises a first active ingredient (e.g., an engineered guide RNA disclosed herein, a composition disclosed herein, an isolated cell disclosed herein, or an isolated plurality of cells disclosed herein). In some examples, the pharmaceutical can comprise a second, third or fourth active ingredient. In some examples, the pharmaceutical composition comprises an additional therapeutic agent. In some examples, the second, third, or fourth active ingredient can be the additional therapeutic agent. In some examples, the additional therapeutic agent treats macular degeneration. In some examples, the additional therapeutic agent can be for treating a neurological disease or disorder (e.g., Parkinson's disease, Alzheimer's disease, or dementia). In some examples, the additional therapeutic agent can be for treating a liver disease or disorder (e.g., liver cirrhosis or alpha-1 antitrypsin deficiency). In some instances, amyloid-beta aggregation (Abeta plaques) contribute to the pathology of Alzheimer's disease. Abeta can be derived from sequential proteolysis of amyloid precursor protein (APP) as variable-length fragments. In some examples, the additional therapeutic agent can be for preventing beta-amyloid from clumping into plaques or remove beta-amyloid plaques that have formed.
In some examples, the additional therapeutic agent can be a 5-HT 6 antagonist, a 5-HT2A inverse agonist, an AB42 lowering agent, an acetylcholinesterase inhibitor, an alpha secretase enhancer, an alpha-1 adrenoreceptor antagonist, an ammonia reducer, an angiotensin II receptor blocker, an alpha-2 adrenergic agonist, an anti-amyloid antibody, an anti-aggregation agent, an anti-amyloid immunotherapy, an anti-inflammatory agent, a glial cell modulator, an antioxidant, anti-tau antibody, an anti-tau immunotherapy, an anti-VEGF agent, an antiviral drug, a BACE inhibitor, a beta-adrenergic blocking agents, a beta-2 andrenergic receptor agonist, an arginase inhibitor, a beta blocker, a beta-HSD1 inhibitor, a calcium channel blocker, a cannabinoid, a CBT or CB2 endocannabinoid receptor agonist, a cholesterol lowering agent, a D2 receptor agonist, a dopamine-norepinephrine reuptake inhibitor, a FLNA inhibitor, a gamma secretase inhibitor, a GABA receptor modulator, a glucagon-like peptide 1 receptor agonist, a glutamate modulator, a glutamate receptor antagonist, a glycine transporter 1 inhibitor, a gonadotropin-releasing hormone receptor agonist, a GSK-3B inhibitor, a hepatocyte growth factor, a histone deacetylase inhibitor, a IgG1-Fc-GAIM fusion protein, an ion channel modulator, an iron chelating agent, a meukotriene receptor antagonist, a MAPT RNA inhibitor, a mast cell stabilizer, a melatonin receptor agonist, a microtubule protein modulator, a mitochondrial ATP synthase inhibitor, a monoamine oxidase B inhibitor, a muscarinic agonist, a nicotinic acetylcholine receptor agonist, an NMDA antagonist, an NMDA receptor modulator, a nonhormonal estrogen receptor B agonist, a nonnucleoside reverse transcriptase inhibitor, a nonsteroidal anti-inflammatory agent, an omega-3 fatty acid, a P38 MAPK inhibitor, a P75 neurotrophin receptor ligand, a PDE 5 inhibitor, a PDE-3 inhibitor, a PDE4D inhibitor, a positive allosteric modulator of GABA-A receptors, a PPAR-gamma agonist, a protein kinase C modulator, a RIPK1 inhibitor, a secretase inhibitor, a selective inhibitor of APP production, a selective norepinephrine reuptake inhibitor, a selective serotonin reuptake inhibitor, a selective tyrosine kinase inhibitor, a SGLT2 inhibitor, a SIGLEC-3 inhibitor, a sigma-1 receptor agonist, a sigma-2 receptor antagonist, a stem cell therapy, an SV2A modulator, a synthetic hormone, a synthetic granulocyte colony stimulator, synthetic thiamine, a tau protein aggregation inhibitor, a telomerase reverse transcriptase vaccine, a thrombin inhibitor, a transport protein ABCC1 activator, a TREM2 inhibitor, a vascular endothelial growth factor (VEGF) inhibitor, a vitamin or any combination thereof.
In some examples, the additional therapeutic agent can be an ammonia reducer, a beta blocker, a synthetic hormone, an antibiotic, or an antiviral drug, a vascular endothelial growth factor (VEGF) inhibitor, a stem cell treatment, a vitamin or modified form thereof, or any combination thereof.
In some examples, the additional therapeutic agent can be AADvac1, AAVrh.10hAPOE2, ABBV-8E12, ABvac40, AD-35, aducanumab, aflibercept, AGB101, AL002, AL003, allopregnanolone, amlopidine, AMX0035, ANAVEX 2-73, APH-1105, AR1001, AstroStem, atorvastatin, AVP-786, AXS-05, BAC, benfotiamine, BHV4157, BI425809, BIIB092, BIIP06, bioactive dietary polyphenol preparation, BPN14770, brexpiprazole, brolucizumab, byrostatin, CAD106, candesartan, CERE-110, cilostazol, CKD-355, CNP520, COR388, crenezumab, cromolyn, CT1812, curcumin, dabigatran, DAOI, dapagliflozin, deferiprone, DHA, DHP1401, DNL747, dronabinol, efavirenz, elderberry juice, elenbecestat, escitalopram, formoterol, gantenerumab, Ginkgo biloba, grapeseed extract, GRF6019, guanfacine, GV1001, hUCB-MSCs, ibuprofen, icosapent ethyl, ID1201, insulin aspart, insulin glulisine, IONIS MAPTRx, J147, JNJ-63733657, lactulose, lactitol, lemborexant, leuprolide acetate depot, levetiracetam, liraglutide, lithium, LM11A-31-BHS, losartan, L-serine, L-ornithine phenylacetate, Lu AF20513, LY3002813, LY3303560, LY3372993, masitinib, methylene blue, methylphenidate, metronidazole, mirtazapine, ML-4334, MLC901, montelukast, MP-101, nabilone, NDX-1017, neflamapimod, neomycin, nicotinamide, nicotine, nilotinib, nitazoxanide, NPT08, octagam 10%, octohydroaminoacridine succinate, omega-3 PUFA, perindopril, pimavanserin, piromelatine, posiphen, prazosin, PTI-125, ranibizumab rasagiline, rifaximin, riluzole, R07105705, RPh201, sagramostim, salsalate, S-equol, sodium benzoate, sodium phenylacetate, solanezumab, SUVN-502, telmisartan, TEP, THN201, TPI-287, traneurocin, TRx0237, UB-311, valacyclovir, venlafaxine hMSCs (human mesenchymal stem cells), vorinostat, xanamem, zolpidem, or any combination thereof.
In some examples, the delivery vehicle comprises a delivery vector. In some examples, the delivery vector comprises DNA, such as double stranded or single stranded DNA. In some examples, the vector comprises RNA. In some examples, the delivery vehicle comprises one or more delivery vectors. In some examples, the one or more delivery vectors comprise an engineered guide disclosed herein. In some examples, the one or more delivery vectors comprises a polynucleotide encoding an engineered guide disclosed herein. In some examples, one delivery vector comprises a polynucleotide encoding an engineered guide RNA disclosed herein. In some examples, one delivery vector comprises a polynucleotide encoding a portion of an engineered guide RNA disclosed herein and a second delivery vector encodes a portion of an engineered guide RNA disclosed herein.
In some examples, the delivery vector can be a eukaryotic vector, a prokaryotic vector (e.g., a bacterial vector) a viral vector, or any combination thereof. In some examples, the delivery vector can be a viral vector. In some examples, the viral vector can be a retroviral vector, an adenoviral vector, an adeno-associated viral vector, an alphavirus vector, a lentivirus vector (e.g., human or porcine), a Herpes virus vector, an Epstein-Barr virus vector, an SV40 virus vectors, a pox virus vector, or a combination thereof. In some examples, the viral vector can be a recombinant vector, a hybrid vector, a chimeric vector, a self-complementary vector, a single-stranded vector or any combination thereof.
In some examples, the viral vector can be as adeno-associated virus (AAV). In some examples, the viral vector can be of a specific serotype. In some examples, the viral vector can be an AAV1 serotype, an AAV2 serotype, AAV3 serotype, an AAV4 serotype, AAV5 serotype, an AAV6 serotype, AAV7 serotype, an AAV8 serotype, an AAV9 serotype, an AAV10 serotype, an AAV11 serotype, AAV 12 serotype, AAV13 serotype, AAV 14 serotype, AAV 15 serotype, AAV 16 serotype, AAV.rh8 serotype, AAV.rh10 serotype, AAV.rh20 serotype, AAV.rh39 serotype, AAV.Rh74 serotype, AAV.RHM4-1 serotype, AAV.hu37 serotype, AAV.Anc80 serotype, AAV.Anc80L65 serotype, AAV.7m8 serotype, AAV.PHP.B serotype, AAV2.5 serotype, AAV2tYF serotype, AAV3B serotype, AAV.LK03 serotype, AAV.HSC1 serotype, AAV.HSC2 serotype, AAV.HSC3 serotype, AAV.HSC4 serotype, AAV.HSC5 serotype, AAV.HSC6 serotype, AAV.HSC7 serotype, AAV.HSC8 serotype, AAV.HSC9 serotype, AAV.HSC10 serotype, AAV.HSC11 serotype, AAV.HSC12 serotype, AAV.HSC13 serotype, AAV.HSC14 serotype, AAV.HSC15 serotype, AAV.HSC16 serotype or AAVhu68 serotype a derivative of any of these, or any combination thereof.
In some examples, the AAV vector can be a recombinant vector, a hybrid AAV vector, a chimeric AAV vector, a self-complementary AAV (scAAV) vector, a single-stranded AAV or any combination thereof.
In some examples, the AAV vector can be a recombinant AAV (rAAV) vector. Methods of producing recombinant AAV vectors generally involve, in some cases, introducing into a producer cell line: (1) DNA necessary for AAV replication and synthesis of an AAV capsid, (b) one or more helper constructs comprising the viral functions missing from the AAV vector (c) a helper virus, and (d) the plasmid construct containing the genome of the AAV vector, e.g., ITRs, promoter and transgene (e.g., an engineered guide disclosed herein) sequences, etc. In some examples, the viral vectors described herein can be engineered through synthetic or other suitable means by references to published sequences, such as can be available in the literature. For example, the genomic and protein sequences of various serotypes of AAV, as well as the sequences of the native terminal repeats (TRs), Rep proteins, and capsid subunits can be found in the literature or in public databases such as GenBank or Protein Data Bank (PDB).
In some examples, methods of producing delivery vectors herein comprising packaging an engineered guide disclosed herein in an AAV vector. In some examples, methods of producing the delivery vectors described herein comprise, (a) introducing into a cell: (i) a polynucleotide encoding any engineered guide RNA disclosed herein; and (ii) a viral genome comprising a Replication (Rep) gene and Capsid (Cap) gene that encodes a wild-type AAV capsid protein or modified version thereof; (b) expressing in the cell the wild-type AAV capsid protein or modified version thereof; (c) assembling an AAV particle; and (d) packaging the polynucleotide encoding the engineered guide RNA in the AAV particle, thereby generating an AAV delivery vector. In some examples, any engineered guide RNA disclosed herein, promoters, stuffer sequences, and any combination thereof can be packaged in the AAV vector. In some examples, the AAV vector can package 1, 2, 3, 4, or 5 copies of the engineered guide RNA. In some examples, the recombinant vectors comprise one or more inverted terminal repeats and the inverted terminal repeats comprise a 5′ inverted terminal repeat, a 3′ inverted terminal repeat, and a mutated inverted terminal repeat. In some examples, the mutated terminal repeat lacks a terminal resolution site.
In some examples, a hybrid AAV vector can be produced by transcapsidation, e.g., packaging an inverted terminal repeat (ITR) from a first serotype into a capsid of a second serotype, wherein the first and second serotypes can be not the same. In some examples, the Rep gene and ITR from a first AAV serotype (e.g., AAV2) can be used in a capsid from a second AAV serotype (e.g., AAV9), wherein the first and second AAV serotypes may not be the same. As a non-limiting example, a hybrid AAV serotype comprising the AAV2 ITRs and AAV9 capsid protein can be indicated AAV2/9. In some examples, the hybrid AAV delivery vector comprises an AAV2/1, AAV2/2, AAV 2/4, AAV2/5, AAV2/8, or AAV2/9 vector.
In some examples, the AAV vector can be a chimeric AAV vector. In some examples, the chimeric AAV vector comprises an exogenous amino acid or an amino acid substitution, or capsid proteins from two or more serotypes. In some examples, a chimeric AAV vector can be genetically engineered to increase transduction efficiency, selectivity, or a combination thereof.
In some examples, the AAV vector comprises a self-complementary AAV genome. Self-complementary AAV genomes can contain both DNA strands which can anneal together to form double-stranded DNA.
In some examples, the delivery vector can be a retroviral vector. In some examples, the retroviral vector can be a Moloney Murine Leukemia Virus vector, a spleen necrosis virus vector, or a vector derived from the Rous Sarcoma Virus, Harvey Sarcoma Virus, avian leukosis virus, human immunodeficiency virus, myeloproliferative sarcoma virus, or mammary tumor virus, or a combination thereof. In some examples, the retroviral vector can be transfected such that the majority of sequences coding for the structural genes of the virus (e.g., gag, pol, and env) can be deleted and replaced by the gene(s) of interest.
In some examples, the delivery vehicle can be a non-viral vector. In some examples, the delivery vehicle can be a plasmid. In some embodiments, the plasmid comprises DNA. In some embodiments, the plasmid comprises RNA. In some examples, the plasmid comprises circular double-stranded DNA. In some examples, the plasmid can be linear. In some examples, the plasmid comprises one or more genes of interest and one or more regulatory elements. In some examples, the plasmid comprises a bacterial backbone containing an origin of replication and an antibiotic resistance gene or other selectable marker for plasmid amplification in bacteria. In some examples, the plasmid can be a minicircle plasmid. In some examples, the plasmid contains one or more genes that provide a selective marker to induce a target cell to retain the plasmid. In some examples, the plasmid can be formulated for delivery through injection by a needle carrying syringe. In some examples, the plasmid can be formulated for delivery via electroporation. In some examples, the plasmids can be engineered through synthetic or other suitable means known in the art. For example, in some cases, the genetic elements can be assembled by restriction digest of the desired genetic sequence from a donor plasmid or organism to produce ends of the DNA which can then be readily ligated to another genetic sequence.
In some examples, an isolated cell or cells comprise any of the engineered guides or delivery vectors disclosed herein. In some examples, the isolated cell or cells comprise one or more human cells. In some examples, the isolated cell or cells comprise one or more T-Cells. In some examples, the isolated cell or cells comprise one or more HEK293 cells.
Disclosed herein, in certain embodiments, are pharmaceutical compositions comprising an engineered guide RNA disclosed herein, a composition disclosed herein, an isolated cell disclosed herein, or an isolated plurality of cells disclosed herein and a pharmaceutically acceptable excipient, carrier or diluent. In some examples, the pharmaceutical composition comprises an engineered guide RNA disclosed herein and a pharmaceutically acceptable excipient, carrier or diluent. In some examples, the pharmaceutical composition comprises an engineered polynucleotide encoding an engineered guide RNA disclosed herein and a pharmaceutically acceptable excipient, carrier or diluent. In some examples, the pharmaceutical composition comprises a delivery vector disclosed herein and a pharmaceutically acceptable excipient, carrier or diluent. In some examples, the pharmaceutical composition comprises an isolated cell (e.g. comprising a delivery vector disclosed herein) or plurality of cells disclosed herein and a pharmaceutically acceptable excipient, carrier or diluent.
In some examples, the pharmaceutical composition comprises a first active ingredient (e.g., an engineered guide disclosed herein, a composition disclosed herein, an isolated cell disclosed herein, or an isolated plurality of cells disclosed herein). In some examples, the pharmaceutical can comprise a second, third or fourth active ingredient. In some examples, the pharmaceutical composition comprises an additional therapeutic agent. In some examples, the second, third, or fourth active ingredient can be the additional therapeutic agent. In some examples, the additional therapeutic agent treats macular degeneration. In some examples, the additional therapeutic agent comprises. In some examples, the additional therapeutic agent can be for treating a neurological disease or disorder (e.g., Parkinson's disease, Alzheimer's disease, or dementia). In some examples, the additional therapeutic agent can be for treating a liver disease or disorder (e.g., liver cirrhosis or alpha-1 antitrypsin deficiency). In some instances, amyloid-beta aggregation (Abeta plaques) contribute to the pathology of Alzheimer's disease. Abeta can be derived from sequential proteolysis of amyloid precursor protein (APP) as variable-length fragments. In some examples, the additional therapeutic agent can be for preventing beta-amyloid from clumping into plaques or remove beta-amyloid plaques that have formed.
In some examples, the additional therapeutic agent can be a 5-HT 6 antagonist, a 5-HT2A inverse agonist, an AB42 lowering agent, an acetylcholinesterase inhibitor, an alpha secretase enhancer, an alpha-1 adrenoreceptor antagonist, an ammonia reducer, an angiotensin II receptor blocker, an alpha-2 adrenergic agonist, an anti-amyloid antibody, an anti-aggregation agent, an anti-amyloid immunotherapy, an anti-inflammatory agent, a glial cell modulator, an antioxidant, anti-tau antibody, an anti-tau immunotherapy, an anti-VEGF agent, an antiviral drug, a BACE inhibitor, a beta-adrenergic blocking agents, a beta-2 andrenergic receptor agonist, an arginase inhibitor, a beta blocker, a beta-HSD1 inhibitor, a calcium channel blocker, a cannabinoid, a CB1 or CB2 endocannabinoid receptor agonist, a cholesterol lowering agent, a D2 receptor agonist, a dopamine-norepinephrine reuptake inhibitor, a FLNA inhibitor, a gamma secretase inhibitor, a GABA receptor modulator, a glucagon-like peptide 1 receptor agonist, a glutamate modulator, a glutamate receptor antagonist, a glycine transporter 1 inhibitor, a gonadotropin-releasing hormone receptor agonist, a GSK-3B inhibitor, a hepatocyte growth factor, a histone deacetylase inhibitor, a IgG1-Fc-GAIM fusion protein, an ion channel modulator, an iron chelating agent, a meukotriene receptor antagonist, a MAPT RNA inhibitor, a mast cell stabilizer, a melatonin receptor agonist, a microtubule protein modulator, a mitochondrial ATP synthase inhibitor, a monoamine oxidase B inhibitor, a muscarinic agonist, a nicotinic acetylcholine receptor agonist, an NMDA antagonist, an NMDA receptor modulator, a nonhormonal estrogen receptor B agonist, a nonnucleoside reverse transcriptase inhibitor, a nonsteroidal anti-inflammatory agent, an omega-3 fatty acid, a P38 MAPK inhibitor, a P75 neurotrophin receptor ligand, a PDE 5 inhibitor, a PDE-3 inhibitor, a PDE4D inhibitor, a positive allosteric modulator of GABA-A receptors, a PPAR-gamma agonist, a protein kinase C modulator, a RIPK1 inhibitor, a secretase inhibitor, a selective inhibitor of APP production, a selective norepinephrine reuptake inhibitor, a selective serotonin reuptake inhibitor, a selective tyrosine kinase inhibitor, a SGLT2 inhibitor, a SIGLEC-3 inhibitor, a sigma-1 receptor agonist, a sigma-2 receptor antagonist, a stem cell therapy, an SV2A modulator, a synthetic hormone, a synthetic granulocyte colony stimulator, synthetic thiamine, a tau protein aggregation inhibitor, a telomerase reverse transcriptase vaccine, a thrombin inhibitor, a transport protein ABCC1 activator, a TREM2 inhibitor, a vascular endothelial growth factor (VEGF) inhibitor, a vitamin or any combination thereof.
In some examples, the additional therapeutic agent can be an ammonia reducer, a beta blocker, a synthetic hormone, an antibiotic, or an antiviral drug, a vascular endothelial growth factor (VEGF) inhibitor, a stem cell treatment, a vitamin or modified form thereof, or any combination thereof.
In some examples, the additional therapeutic agent can be AADvac1, AAVrh.10hAPOE2, ABBV-8E12, ABvac40, AD-35, aducanumab, aflibercept, AGB101, AL002, AL003, allopregnanolone, amlopidine, AMX0035, ANAVEX 2-73, APH-1105, AR1001, AstroStem, atorvastatin, AVP-786, AXS-05, BAC, benfotiamine, BHV4157, BI425809, BIIB092, BIIP06, bioactive dietary polyphenol preparation, BPN14770, brexpiprazole, brolucizumab, byrostatin, CAD106, candesartan, CERE-110, cilostazol, CKD-355, CNP520, COR388, crenezumab, cromolyn, CT1812, curcumin, dabigatran, DAOI, dapagliflozin, deferiprone, DHA, DHP1401, DNL747, dronabinol, efavirenz, elderberry juice, elenbecestat, escitalopram, formoterol, gantenerumab, Ginkgo biloba, grapeseed extract, GRF6019, guanfacine, GV1001, hUCB-MSCs, ibuprofen, icosapent ethyl, ID1201, insulin aspart, insulin glulisine, IONIS MAPTRx, J147, JNJ-63733657, lactulose, lactitol, lemborexant, leuprolide acetate depot, levetiracetam, liraglutide, lithium, LM11A-31-BHS, losartan, L-serine, L-ornithine phenylacetate, Lu AF20513, LY3002813, LY3303560, LY3372993, masitinib, methylene blue, methylphenidate, metronidazole, mirtazapine, ML-4334, MLC901, montelukast, MP-101, nabilone, NDX-1017, neflamapimod, neomycin, nicotinamide, nicotine, nilotinib, nitazoxanide, NPT08, octagam 10%, octohydroaminoacridine succinate, omega-3 PUFA, perindopril, pimavanserin, piromelatine, posiphen, prazosin, PTI-125, ranibizumab rasagiline, rifaximin, riluzole, R07105705, RPh201, sagramostim, salsalate, S-equol, sodium benzoate, sodium phenylacetate, solanezumab, SUVN-502, telmisartan, TEP, THN201, TPI-287, traneurocin, TRx0237, UB-311, valacyclovir, venlafaxine hMSCs (human mesenchymal stem cells), vorinostat, xanamem, zolpidem, or any combination thereof.
In some examples, the pharmaceutical composition can be formulated in unit dose forms or multiple-dose forms. In some examples, the unit dose forms can be physically discrete units suitable for administration to human or non-human subjects (e.g., animals). In some examples, the unit dose forms can be packaged individually. In some examples, each unit dose contains a predetermined quantity of an active ingredient(s) that can be sufficient to produce the desired therapeutic effect in association with pharmaceutical carriers, diluents, excipients, or any combination thereof. In some examples, the unit dose forms comprise ampules, syringes, or individually packaged tablets and capsules, or any combination thereof. In some instances, a unit dose form can be comprised in a disposable syringe. In some instances, unit-dosage forms can be administered in fractions or multiples thereof. In some examples, a multiple-dose form comprises a plurality of identical unit dose forms packaged in a single container, which can be administered in segregated a unit dose form. In some examples, multiple dose forms comprise vials, bottles of tablets or capsules, or bottles of pints or gallons. In some instances, a multiple-dose forms comprise the same pharmaceutically active agents. In some instances, a multiple-dose forms comprise different pharmaceutically active agents.
In some examples, the pharmaceutical composition comprises a pharmaceutically acceptable excipient. In some examples, the excipient comprises a buffering agent, a cryopreservative, a preservative, a stabilizer, a binder, a compaction agent, a lubricant, a chelator, a dispersion enhancer, a disintegration agent, a flavoring agent, a sweetener, or a coloring agent, or any combination thereof.
In some examples, an excipient comprises a buffering agent. In some examples, the buffering agent comprises sodium citrate, magnesium carbonate, magnesium bicarbonate, calcium carbonate, calcium bicarbonate, or any combination thereof. In some examples, the buffering agent comprises sodium bicarbonate, potassium bicarbonate, magnesium hydroxide, magnesium lactate, magnesium glucomate, aluminum hydroxide, sodium citrate, sodium tartrate, sodium acetate, sodium carbonate, sodium polyphosphate, potassium polyphosphate, sodium pyrophosphate, potassium pyrophosphate, disodium hydrogen phosphate, dipotassium hydrogen phosphate, trisodium phosphate, tripotassium phosphate, potassium metaphosphate, magnesium oxide, magnesium hydroxide, magnesium carbonate, magnesium silicate, calcium acetate, calcium glycerophosphate, calcium chloride, or calcium hydroxide and other calcium salts, or any combination thereof.
In some examples, an excipient comprises a cryopreservative. In some examples, the cryopreservative comprises DMSO, glycerol, polyvinylpyrrolidone (PVP), or any combination thereof. In some examples, a cryopreservative comprises a sucrose, a trehalose, a starch, a salt of any of these, a derivative of any of these, or any combination thereof. In some examples, an excipient comprises a pH agent (to minimize oxidation or degradation of a component of the composition), a stabilizing agent (to prevent modification or degradation of a component of the composition), a buffering agent (to enhance temperature stability), a solubilizing agent (to increase protein solubility), or any combination thereof. In some examples, an excipient comprises a surfactant, a sugar, an amino acid, an antioxidant, a salt, a non-ionic surfactant, a solubilizer, a triglyceride, an alcohol, or any combination thereof. In some examples, an excipient comprises sodium carbonate, acetate, citrate, phosphate, poly-ethylene glycol (PEG), human serum albumin (HSA), sorbitol, sucrose, trehalose, polysorbate 80, sodium phosphate, sucrose, disodium phosphate, mannitol, polysorbate 20, histidine, citrate, albumin, sodium hydroxide, glycine, sodium citrate, trehalose, arginine, sodium acetate, acetate, HCl, disodium edetate, lecithin, glycerin, xanthan rubber, soy isoflavones, polysorbate 80, ethyl alcohol, water, teprenone, or any combination thereof. In some examples, the excipient can be an excipient described in the Handbook of Pharmaceutical Excipients, American Pharmaceutical Association (1986).
In some examples, the excipient comprises a preservative. In some examples, the preservative comprises an antioxidant, such as alpha-tocopherol and ascorbate, an antimicrobial, such as parabens, chlorobutanol, and phenol, or any combination thereof. In some examples, the antioxidant comprises EDTA, citric acid, ascorbic acid, butylated hydroxytoluene (BHT), butylated hydroxy anisole (BHA), sodium sulfite, p-amino benzoic acid, glutathione, propyl gallate, cysteine, methionine, ethanol or N-acetyl cysteine, or any combination thereof. In some examples, the preservative comprises validamycin A, TL-3, sodium ortho vanadate, sodium fluoride, N-a-tosyl-Phe-chloromethylketone, N-a-tosyl-Lys-chloromethylketone, aprotinin, phenylmethylsulfonyl fluoride, diisopropylfluorophosphate, kinase inhibitor, phosphatase inhibitor, caspase inhibitor, granzyme inhibitor, cell adhesion inhibitor, cell division inhibitor, cell cycle inhibitor, lipid signaling inhibitor, protease inhibitor, reducing agent, alkylating agent, antimicrobial agent, oxidase inhibitor, or other inhibitors, or any combination thereof.
In some examples, the excipient comprises a binder. In some examples, the binder comprises starches, pregelatinized starches, gelatin, polyvinylpyrolidone, cellulose, methylcellulose, sodium carboxymethylcellulose, ethylcellulose, polyacrylamides, polyvinyloxoazolidone, polyvinylalcohols, C12-C18 fatty acid alcohol, polyethylene glycol, polyols, saccharides, oligosaccharides, or any combination thereof.
In some examples, the binder can be a starch, for example a potato starch, corn starch, or wheat starch; a sugar such as sucrose, glucose, dextrose, lactose, or maltodextrin; a natural and/or synthetic gum; a gelatin; a cellulose derivative such as microcrystalline cellulose, hydroxypropyl cellulose, hydroxyethyl cellulose, hydroxypropyl methyl cellulose, carboxymethyl cellulose, methyl cellulose, or ethyl cellulose; polyvinylpyrrolidone (povidone); polyethylene glycol (PEG); a wax; calcium carbonate; calcium phosphate; an alcohol such as sorbitol, xylitol, mannitol, or water, or any combination thereof.
In some examples, the excipient comprises a lubricant. In some examples, the lubricant comprises magnesium stearate, calcium stearate, zinc stearate, hydrogenated vegetable oils, sterotex, polyoxyethylene monostearate, talc, polyethyleneglycol, sodium benzoate, sodium lauryl sulfate, magnesium lauryl sulfate, or light mineral oil, or any combination thereof. In some examples, the lubricant comprises metallic stearates (such as magnesium stearate, calcium stearate, aluminum stearate), fatty acid esters (such as sodium stearyl fumarate), fatty acids (such as stearic acid), fatty alcohols, glyceryl behenate, mineral oil, paraffins, hydrogenated vegetable oils, leucine, polyethylene glycols (PEG), metallic lauryl sulphates (such as sodium lauryl sulphate, magnesium lauryl sulphate), sodium chloride, sodium benzoate, sodium acetate or talc or a combination thereof.
In some examples, the excipient comprises a dispersion enhancer. In some examples, the dispersion enhancer comprises starch, alginic acid, polyvinylpyrrolidones, guar gum, kaolin, bentonite, purified wood cellulose, sodium starch glycolate, isomorphous silicate, or microcrystalline cellulose, or any combination thereof as high HLB emulsifier surfactants.
In some examples, the excipient comprises a disintegrant. In some examples, a disintegrant comprises a non-effervescent disintegrant. In some examples, a non-effervescent disintegrants comprises starches such as corn starch, potato starch, pregelatinized and modified starches thereof, sweeteners, clays, such as bentonite, micro-crystalline cellulose, alginates, sodium starch glycolate, or gums such as agar, guar, locust bean, karaya, pectin, and tragacanth, or any combination thereof. In some examples, a disintegrant comprises an effervescent disintegrant. In some examples, a suitable effervescent disintegrant comprises bicarbonate in combination with citric acid, and sodium bicarbonate in combination with tartaric acid.
In some examples, the excipient comprises a sweetener, a flavoring agent or both. In some examples, a sweetener comprises glucose (corn syrup), dextrose, invert sugar, fructose, and mixtures thereof (when not used as a carrier); saccharin and its various salts such as a sodium salt; dipeptide sweeteners such as aspartame; dihydrochalcone compounds, glycyrrhizin; Stevia Rebaudiana (Stevioside); chloro derivatives of sucrose such as sucralose; and sugar alcohols such as sorbitol, mannitol, sylitol, and the like, or any combination thereof. In some cases, flavoring agents incorporated into a composition comprise synthetic flavor oils and flavoring aromatics; natural oils; extracts from plants, leaves, flowers, and fruits; or any combination thereof. In some embodiments, a flavoring agent comprises a cinnamon oils; oil of wintergreen; peppermint oils; clover oil; hay oil; anise oil; eucalyptus; vanilla; citrus oil such as lemon oil, orange oil, grape and grapefruit oil; and fruit essences including apple, peach, pear, strawberry, raspberry, cherry, plum, pineapple, and apricot, or any combination thereof.
In some examples, the excipient comprises a pH agent (e.g., to minimize oxidation or degradation of a component of the composition), a stabilizing agent (e.g., to prevent modification or degradation of a component of the composition), a buffering agent (e.g., to enhance temperature stability), a solubilizing agent (e.g., to increase protein solubility), or any combination thereof. In some examples, the excipient comprises a surfactant, a sugar, an amino acid, an antioxidant, a salt, a non-ionic surfactant, a solubilizer, a triglyceride, an alcohol, or any combination thereof. In some examples, the excipient comprises sodium carbonate, acetate, citrate, phosphate, poly-ethylene glycol (PEG), human serum albumin (HSA), sorbitol, sucrose, trehalose, polysorbate 80, sodium phosphate, sucrose, disodium phosphate, mannitol, polysorbate 20, histidine, citrate, albumin, sodium hydroxide, glycine, sodium citrate, trehalose, arginine, sodium acetate, acetate, HCl, disodium edetate, lecithin, glycerine, xanthan rubber, soy isoflavones, polysorbate 80, ethyl alcohol, water, teprenone, or any combination thereof. In some examples, the excipient comprises a cryo-preservative. In some examples, the excipient comprises DMSO, glycerol, polyvinylpyrrolidone (PVP), or any combination thereof. In some examples, the excipient comprises a sucrose, a trehalose, a starch, a salt of any of these, a derivative of any of these, or any combination thereof.
In some examples, the pharmaceutical composition comprises a diluent. In some examples, the diluent comprises water, glycerol, methanol, ethanol, or other similar biocompatible diluents, or any combination thereof. In some examples, a diluent comprises an aqueous acid such as acetic acid, citric acid, maleic acid, hydrochloric acid, phosphoric acid, nitric acid, sulfuric acid, or any combination thereof. In some examples, a diluent comprises an alkaline metal carbonates such as calcium carbonate; alkaline metal phosphates such as calcium phosphate; alkaline metal sulphates such as calcium sulphate; cellulose derivatives such as cellulose, microcrystalline cellulose, cellulose acetate; magnesium oxide, dextrin, fructose, dextrose, glyceryl palmitostearate, lactitol, choline, lactose, maltose, mannitol, simethicone, sorbitol, starch, pregelatinized starch, talc, xylitol and/or anhydrates, hydrates and/or pharmaceutically acceptable derivatives thereof or combinations thereof.
In some examples, the pharmaceutical composition comprises a carrier. In some examples, the carrier comprises a liquid or solid filler, solvent, or encapsulating material. In some examples, the carrier comprises additives proteins, peptides, amino acids, lipids, and carbohydrates (e.g., sugars, including monosaccharides, di-, tri-, tetra-oligosaccharides, and oligosaccharides; derivatized sugars such as alditols, aldolic acids, esterified sugars and the like; and polysaccharides or sugar polymers), alone or in combination.
In some examples, the pharmaceutical composition can be administered to a subject by any means which will contact the gRNA and/or ADAR (or a vector encoding the gRNA and/or ADAR) with a target cell. In some examples, the specific route will depend upon certain variables such as the target cell and can be determined by the skilled practitioner. In some examples, the pharmaceutical composition can be administered by intravenous administration, intraperitoneal administration, intramuscular administration, intracoronary administration, intraarterial administration (e.g., into a carotid artery), subcutaneous administration, transdermal delivery, intratracheal administration, subcutaneous administration, intraarticular administration, intraventricular administration, inhalation (e.g., aerosol), intracerebral, nasal, oral, pulmonary administration, impregnation of a catheter, or direct injection into a tissue, or any combination thereof. In some examples, the target cells can be in or near a tumor and administration can be by direct injection into the tumor or tissue surrounding the tumor. In some examples, the tumor can be a breast tumor and administration comprises impregnation of a catheter and direct injection into the tumor. In some examples, aerosol (inhalation) delivery can be performed using methods known in the art, such as methods described in, for example, Stribling et al., Proc. Natl. Acad. Sci. USA 189: 11277-11281, 1992. In some examples, oral delivery can be performed by complexing an engineered guide (or a vector encoding an engineered guide) to a carrier capable of withstanding degradation by digestive enzymes in the gut of an animal. Examples of such carriers, include plastic capsules or tablets, such as those known in the art.
In some examples, direct injection techniques can be used for administering the gRNA and/or ADAR (or a vector encoding the gRNA and/or ADAR) to a cell or tissue that can be accessible by surgery, and on or near the surface of the body. In some examples, administration of a composition locally within the area of a target cell comprises injecting the composition centimeters and preferably, millimeters from the target cell or tissue.
The appropriate dosage and treatment regimen for the methods of treatment described herein vary with respect to the particular disease being treated, the gRNA and/or ADAR (or a vector encoding the gRNA and/or ADAR) being delivered, and the specific condition of the subject. In some examples, the administration can be over a period of time until the desired effect (e.g., reduction in symptoms is achieved). In some examples, administration can be 1, 2, 3, 4, 5, 6, or 7 times per week. In some examples, administration or application of a composition disclosed herein can be performed for a treatment duration of at least about 1 week, at least about 1 month, at least about 1 year, at least about 2 years, at least about 3 years, at least about 4 years, at least about 5 years, at least about 6 years, at least about 7 years, at least about 8 years, at least about 9 years, at least about 10 years, at least about 15 years, at least about 20 years, or more. In some examples, administration can be over a period of 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 weeks. In some examples, administration can be over a period of 2, 3, 4, 5, 6 or more months. In some examples, administration can be performed repeatedly over a lifetime of a subject, such as once a month or once a year for the lifetime of a subject. In some examples, administration can be performed repeatedly over a substantial portion of a subject's life, such as once a month or once a year for at least about 1 year, 5 years, 10 years, 15 years, 20 years, 25 years, 30 years, or more. In some examples, treatment can be resumed following a period of remission.
Disclosed herein are kits comprising guide RNAs, polynucleotides encoding the same, compositions, pharmaceutical compositions, and isolated cells disclosed herein. In some examples, a kit comprises one or more guide RNAs, polynucleotides encoding the same, compositions, pharmaceutical compositions, or isolated cells disclosed herein and a container. In some examples, the kit comprises a pharmaceutical composition disclosed herein, which comprises an engineered guide RNA disclosed herein or a polynucleotide encoding the engineered guide RNA disclosed herein and a pharmaceutically acceptable excipient, carrier, or diluent. In some examples, the kit comprises one or more delivery vectors disclosed herein which comprise the polynucleotide encoding the engineered guide RNA. In some examples, the kit comprises one or more isolated cells described herein. In some instances, the container can be plastic, glass, metal, or any combination thereof. In some examples, the container can be compartmentalized to receive one or more containers such as vials, tubes, and the like, each of the container(s) comprising one of the separate elements to be used in a method described herein. In some example, the container can be a bottle, a vial, a syringe, or a test tube.
In some examples, in addition to the composition, pharmaceutical composition, or isolated cell disclosed herein, a kit disclosed herein further comprises an additional therapeutic agent disclosed herein. In some examples, the additional therapeutic agent comprises a vascular endothelial growth factor (VEGF) inhibitor, a stem cell treatment, or a vitamin or modified form thereof, or any combination thereof.
In some examples, a kit comprises instructions for use, such as instructions for administration to a subject in need thereof.
In some instances, the kit comprises packaging for a composition or pharmaceutical composition described herein. In some examples, the packaging can be properly labeled. In some instances, the pharmaceutical composition described herein can be manufactured according to good manufacturing practice (cGMP) and labeling regulations.
Also disclosed herein are methods of making a kit disclosed herein. In some examples methods of making the kits herein comprises contacting any of the engineered guides, compositions, pharmaceutical compositions, isolated cells, or isolated plurality of cells disclosed herein with a container. In some examples, methods of making a kit disclosed herein comprising placing an engineered guide RNA, composition, pharmaceutical composition or isolated cell or plurality of cells disclosed herein in a container disclosed herein. In some examples, such methods further comprise placing instructions for use in the container.
Unless defined otherwise, all terms of art, notations and other technical and scientific terms or terminology used herein may be intended to have the same meaning as may be commonly understood by one of ordinary skill in the art to which the claimed subject matter pertains. In some cases, terms with commonly understood meanings may be defined herein for clarity and/or for ready reference, and the inclusion of such definitions herein should not necessarily be construed to represent a substantial difference over what may be generally understood in the art.
Throughout this application, various embodiments may be presented in a range format. It should be understood that the description in range format may be merely for convenience and brevity and should not be construed as an inflexible limitation on the scope of the disclosure. 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, 3, 4, 5, and 6. This applies regardless of the breadth of the range.
As used in the specification and claims, the singular forms “a”, “an” and “the” include plural references unless the context clearly dictates otherwise. For example, the term “a sample” includes a plurality of samples, including mixtures thereof.
As used herein, the term “about” a number can refer to that number plus or minus 10% of that number.
As disclosed herein, a “bulge” refers to the structure substantially formed only upon formation of the guide-target RNA scaffold, where contiguous nucleotides in either the engineered guide RNA or the target RNA are not complementary to their positional counterparts on the opposite strand. A bulge can independently have from 0 to 4 contiguous nucleotides on the guide RNA side of the guide-target RNA scaffold and 1 to 4 contiguous nucleotides on the target RNA side of the guide-target RNA scaffold or a bulge can independently have from 0 to 4 nucleotides on the target RNA side of the guide-target RNA scaffold and 1 to 4 contiguous nucleotides on the guide RNA side of the guide-target RNA scaffold. However, a bulge, as used herein, does not refer to a structure where a single participating nucleotide of the engineered guide RNA and a single participating nucleotide of the target RNA do not base pair—a single participating nucleotide of the engineered guide RNA and a single participating nucleotide of the target RNA that do not base pair is referred to herein as a “mismatch.” Further, where the number of participating nucleotides on either the guide RNA side or the target RNA side exceeds 4, the resulting structure is no longer considered a bulge, but rather, is considered an “internal loop.” A “symmetrical bulge” refers to a bulge where the same number of nucleotides is present on each side of the bulge. An “asymmetrical bulge” refers to a bulge where a different number of nucleotides are present on each side of the bulge.
“Canonical amino acids” refer to those 20 amino acids that occur in nature, including for example, the amino acids shown in TABLE 4.
The term “complementary” or “complementarity” refers to the ability of a nucleic acid to form one or more bonds with a corresponding nucleic acid sequence by, for example, hydrogen bonding (e.g., traditional Watson-Crick), covalent bonding, or other similar methods. In Watson-Crick base pairing, a double hydrogen bond forms between nucleobases T and A, whereas a triple hydrogen bond forms between nucleobases C and G. For example, the sequence A-G-T can be complementary to the sequence T-C-A. A percent complementarity indicates the percentage of residues in a nucleic acid molecule which can form hydrogen bonds (e.g., Watson-Crick base pairing) with a second nucleic acid sequence (e.g., 5, 6, 7, 8, 9, 10 out of 10 being 50%, 60%, 70%, 80%, 90%, and 100% complementary, respectively). “Perfectly complementary” can mean that all the contiguous residues of a nucleic acid sequence will hydrogen bond with the same number of contiguous residues in a second nucleic acid sequence. “Substantially complementary” as used herein can refer to a degree of complementarity that can be at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%. 97%, 98%, 99%, or 100% over a region of 10, 15, 20, 25, 30, 35, 40, 45, 50, or more nucleotides, or can refer to two nucleic acids that hybridize under stringent conditions (e.g., stringent hybridization conditions). Nucleic acids can include nonspecific sequences. As used herein, the term “nonspecific sequence” or “not specific” can refer to a nucleic acid sequence that contains a series of residues that can be not designed to be complementary to or can be only partially complementary to any other nucleic acid sequence.
The terms “determining,” “measuring,” “evaluating,” “assessing,” “assaying,” and “analyzing” can be used interchangeably herein to refer to forms of measurement. The terms include determining if an element may be present or not (for example, detection). These terms can include quantitative, qualitative or quantitative and qualitative determinations. Assessing can be relative or absolute. “Detecting the presence of” can include determining the amount of something present in addition to determining whether it may be present or absent depending on the context.
The term “encode,” as used herein, refers to an ability of a polynucleotide to provide information or instructions sequence sufficient to produce a corresponding gene expression product. In a non-limiting example, mRNA can encode a polypeptide during translation, whereas DNA can encode an mRNA molecule during transcription.
An “engineered latent guide RNA” refers to an engineered guide RNA that comprises a portion of sequence that, upon hybridization or only upon hybridization to a target RNA, substantially forms at least a portion of a structural feature, other than a single A/C mismatch feature at the target adenosine to be edited.
As used herein, the term “facilitates RNA editing” by an engineered guide RNA refers to the ability of the engineered guide RNA when associated with an RNA editing entity and a target RNA to provide a targeted edit of the target RNA by the RNA edited entity. In some instances, the engineered guide RNA can directly recruit or position/orient the RNA editing entity to the proper location for editing of the target RNA. In other instances, the engineered guide RNA when hybridized to the target RNA forms a guide-target RNA scaffold with one or more structural features as described herein, where the guide-target RNA scaffold with structural features recruits or positions/orients the RNA editing entity to the proper location for editing of the target RNA.
A “guide-target RNA scaffold,” as disclosed herein, is the resulting double stranded RNA formed upon hybridization of a guide RNA, with latent structure, to a target RNA. A guide-target RNA scaffold has one or more structural features formed within the double stranded RNA duplex upon hybridization. For example, the guide-target RNA scaffold can have one or more structural features selected from a bulge, mismatch, internal loop, hairpin, or wobble base pair.
As disclosed herein, a “hairpin” includes an RNA duplex wherein a portion of a single RNA strand has folded in upon itself to form the RNA duplex. The portion of the single RNA strand folds upon itself due to having nucleotide sequences that base pair to each other, where the nucleotide sequences are separated by an intervening sequence that does not base pair with itself, thus forming a base-paired portion and non-base paired, intervening loop portion.
“Homology” or “identity” or “similarity” can refer to sequence similarity between two peptides or between two nucleic acid molecules. Homology can be determined by comparing a position in each sequence which can be aligned for purposes of comparison. When a position in the compared sequence can be occupied by the same base or amino acid, then the molecules can be homologous at that position. A degree of homology between sequences can be a function of the number of matching or homologous positions shared by the sequences. An “unrelated” or “non-homologous” sequence shares less than 40% identity, or alternatively less than 25% identity, with one of the sequences of the disclosure. Sequence homology can refer to a % identity of a sequence to a reference sequence. As a practical matter, whether any particular sequence can be at least 50%, 60%, 70%, 80%, 85%, 90%, 92%, 95%, 96%, 97%, 98% or 99% identical to any sequence described herein (which can correspond with a particular nucleic acid sequence described herein), such particular polypeptide sequence can be determined conventionally using known computer programs such the Bestfit program (Wisconsin Sequence Analysis Package, Version 8 for Unix, Genetics Computer Group, University Research Park, 575 Science Drive, Madison, Wis. 53711). When using Bestfit or any other sequence alignment program to determine whether a particular sequence is, for instance, 95% identical to a reference sequence, the parameters can be set such that the percentage of identity can be calculated over the full length of the reference sequence and that gaps in sequence homology of up to 5% of the total reference sequence can be allowed.
In some cases, the identity between a reference sequence (query sequence, e.g., a sequence of the disclosure) and a subject sequence, also referred to as a global sequence alignment, can be determined using the FASTDB computer program based son the algorithm of Brutlag et al. (Comp. App. Biosci. 6:237-245 (1990)). In some embodiments, parameters for a particular embodiment in which identity can be narrowly construed, used in a FASTDB amino acid alignment, can include: Scoring Scheme=PAM (Percent Accepted Mutations) 0, k-tuple=2, Mismatch Penalty=1, Joining Penalty=20, Randomization Group Length=0, Cutoff Score=1, Window Size=sequence length, Gap Penalty=5, Gap Size Penalty=0.05, Window Size=500 or the length of the subject sequence, whichever can be shorter. According to this embodiment, if the subject sequence can be shorter than the query sequence due to N- or C-terminal deletions, not because of internal deletions, a manual correction can be made to the results to take into consideration the fact that the FASTDB program does not account for N- and C-terminal truncations of the subject sequence when calculating global percent identity. For subject sequences truncated at the N- and C-termini, relative to the query sequence, the percent identity can be corrected by calculating the number of residues of the query sequence that can be lateral to the N- and C-terminal of the subject sequence, which can be not matched/aligned with a corresponding subject residue, as a percent of the total bases of the query sequence. A determination of whether a residue can be matched/aligned can be determined by results of the FASTDB sequence alignment. This percentage can be then subtracted from the percent identity, calculated by the FASTDB program using the specified parameters, to arrive at a final percent identity score. This final percent identity score can be used for the purposes of this embodiment. In some cases, only residues to the N- and C-termini of the subject sequence, which can be not matched/aligned with the query sequence, can be considered for the purposes of manually adjusting the percent identity score. That is, only query residue positions outside the farthest N- and C-terminal residues of the subject sequence can be considered for this manual correction. For example, a 90-residue subject sequence can be aligned with a 100-residue query sequence to determine percent identity. The deletion occurs at the N-terminus of the subject sequence, and therefore, the FASTDB alignment does not show a matching/alignment of the first 10 residues at the N-terminus. The 10 unpaired residues represent 10% of the sequence (number of residues at the N- and C-termini not matched/total number of residues in the query sequence) so 10% can be subtracted from the percent identity score calculated by the FASTDB program. If the remaining 90 residues were perfectly matched, the final percent identity can be 90%. In another example, a 90-residue subject sequence can be compared with a 100-residue query sequence. This time the deletions can be internal deletions, so there can be no residues at the N- or C-termini of the subject sequence which can be not matched/aligned with the query. In this case, the percent identity calculated by FASTDB can be not manually corrected. Once again, only residue positions outside the N- and C-terminal ends of the subject sequence, as displayed in the FASTDB alignment, which can be not matched/aligned with the query sequence can be manually corrected for.
In some cases, the identity between a reference sequence (query sequence, e.g., a sequence of the disclosure) and a subject sequence, also referred to as a global sequence alignment, can be determined using the FASTDB computer program based on the algorithm of Brutlag et al. (Comp. App. Biosci. 6:237-245 (1990)). In some embodiments, parameters for a particular embodiment in which identity can be narrowly construed, used in a FASTDB amino acid alignment, can include: Scoring Scheme=PAM (Percent Accepted Mutations) 0, k-tuple=2, Mismatch Penalty=1, Joining Penalty=20, Randomization Group Length=0, Cutoff Score=1, Window Size=sequence length, Gap Penalty=5, Gap Size Penalty=0.05, Window Size=500 or the length of the subject sequence, whichever can be shorter. According to this embodiment, if the subject sequence can be shorter than the query sequence due to N- or C-terminal deletions, not because of internal deletions, a manual correction can be made to the results to take into consideration the fact that the FASTDB program does not account for N- and C-terminal truncations of the subject sequence when calculating global percent identity. For subject sequences truncated at the N- and C-termini, relative to the query sequence, the percent identity can be corrected by calculating the number of residues of the query sequence that can be lateral to the N- and C-terminal of the subject sequence, which can be not matched/aligned with a corresponding subject residue, as a percent of the total bases of the query sequence. A determination of whether a residue can be matched/aligned can be determined by results of the FASTDB sequence alignment. This percentage can be then subtracted from the percent identity, calculated by the FASTDB program using the specified parameters, to arrive at a final percent identity score. This final percent identity score can be used for the purposes of this embodiment. In some cases, only residues to the N- and C-termini of the subject sequence, which can be not matched/aligned with the query sequence, can be considered for the purposes of manually adjusting the percent identity score. That is, only query residue positions outside the farthest N- and C-terminal residues of the subject sequence can be considered for this manual correction. For example, a 90-residue subject sequence can be aligned with a 100-residue query sequence to determine percent identity. The deletion occurs at the N-terminus of the subject sequence, and therefore, the FASTDB alignment does not show a matching/alignment of the first 10 residues at the N-terminus. The 10 unpaired residues represent 10% of the sequence (number of residues at the N- and C-termini not matched/total number of residues in the query sequence) so 10% can be subtracted from the percent identity score calculated by the FASTDB program. If the remaining 90 residues were perfectly matched, the final percent identity can be 90%. In another example, a 90-residue subject sequence can be compared with a 100-residue query sequence. This time the deletions can be internal deletions, so there can be no residues at the N- or C-termini of the subject sequence which can be not matched/aligned with the query. In this case, the percent identity calculated by FASTDB can be not manually corrected. Once again, only residue positions outside the N- and C-terminal ends of the subject sequence, as displayed in the FASTDB alignment, which can be not matched/aligned with the query sequence can be manually corrected for.
As disclosed herein, an “internal loop” refers to the structure substantially formed only upon formation of the guide-target RNA scaffold, where nucleotides in either the engineered guide RNA or the target RNA are not complementary to their positional counterparts on the opposite strand and where one side of the internal loop, either on the target RNA side or the engineered guide RNA side of the guide-target RNA scaffold, has 5 nucleotides or more. Where the number of participating nucleotides on both the guide RNA side and the target RNA side drops below 5, the resulting structure is no longer considered an internal loop, but rather, is considered a “bulge” or a “mismatch,” depending on the size of the structural feature. A “symmetrical internal loop” is formed when the same number of nucleotides is present on each side of the internal loop. An “asymmetrical internal loop” is formed when a different number of nucleotides is present on each side of the internal loop.
“Latent structure” refers to a structural feature that substantially forms only upon hybridization of a guide RNA to a target RNA. For example, the sequence of a guide RNA provides one or more structural features, but these structural features substantially form only upon hybridization to the target RNA, and thus the one or more latent structural features manifest as structural features upon hybridization to the target RNA. Upon hybridization of the guide RNA to the target RNA, the structural feature is formed and the latent structure provided in the guide RNA is, thus, unmasked.
“Messenger RNA” or “mRNA” are RNA molecules comprising a sequence that encodes a polypeptide or protein. In general, RNA can be transcribed from DNA. In some cases, precursor mRNA containing non-protein coding regions in the sequence can be transcribed from DNA and then processed to remove all or a portion of the non-coding regions (introns) to produce mature mRNA. As used herein, the term “pre-mRNA” can refer to the RNA molecule transcribed from DNA before undergoing processing to remove the non-protein coding regions.
As disclosed herein, a “mismatch” refers to a single nucleotide in a guide RNA that is unpaired to an opposing single nucleotide in a target RNA within the guide-target RNA scaffold. A mismatch can comprise any two single nucleotides that do not base pair. Where the number of participating nucleotides on the guide RNA side and the target RNA side exceeds 1, the resulting structure is no longer considered a mismatch, but rather, is considered a “bulge” or an “internal loop,” depending on the size of the structural feature.
The term “mutation” as used herein, can refer to an alteration to a nucleic acid sequence or a polypeptide sequence that can be relative to a reference sequence. A mutation can occur in a DNA molecule, an RNA molecule (e.g., tRNA, mRNA), or in a polypeptide or protein, or any combination thereof. The reference sequence can be obtained from a database such as the NCBI Reference Sequence Database (RefSeq) database. Specific changes that can constitute a mutation can include a substitution, a deletion, an insertion, an inversion, or a conversion in one or more nucleotides or one or more amino acids. Non-limiting examples of mutations in a nucleic acid sequence that, without the mutation, encodes for a polypeptide sequence, include: “missense” mutations that can result in the substitution of one codon for another, a “nonsense” mutations that can change a codon from one encoding a particular amino acid to a stop codon (which can result in truncated translation of proteins), or a “silent” mutations that can be those which have no effect on the resulting protein. The mutation can be a “point mutation,” which can refer to a mutation affecting only one nucleotide in a DNA or RNA sequence. The mutation can be a “splice site mutations,” which can be present pre-mRNA (prior to processing to remove introns) resulting in mistranslation and often truncation of proteins from incorrect delineation of the splice site. The mutation can be a fusion gene. A fusion pair or a fusion gene can result from a mutation, such as a translocation, an interstitial deletion, a chromosomal inversion, or any combination thereof. A mutation can constitute variability in the number of repeated sequences, such as triplications, quadruplications, or others. For example, a mutation can be an increase or a decrease in a copy number associated with a given sequence (e.g., copy number variation, or CNV). A mutation can include two or more sequence changes in different alleles or two or more sequence changes in one allele. A mutation can include two different nucleotides at one position in one allele, such as a mosaic. A mutation can include two different nucleotides at one position in one allele, such as a chimeric. A mutation can be present in a malignant tissue. A mutation can comprise a single nucleotide variation (SNV). A mutation can comprise a sequence variant, a sequence variation, a sequence alteration, or an allelic variant.
A presence or an absence of a mutation can indicate an increased risk to develop a disease or condition. A presence or an absence of a mutation can indicate a presence of a disease or condition. A mutation can be present in a benign tissue. Absence of a mutation can indicate that a tissue or sample can be benign. As an alternative, absence of a mutation may not indicate that a tissue or sample can be benign. Methods as described herein can comprise identifying a presence of a mutation in a sample.
The terms “polynucleotide” and “oligonucleotide” can be used interchangeably and can refer to a polymeric form of nucleotides of any length, either deoxyribonucleotides or ribonucleotides or analogs thereof. Polynucleotides can have any three-dimensional structure and can perform any function, known or unknown. The following may be non-limiting examples of polynucleotides: a gene or gene fragment (for example, a probe, primer, EST or SAGE tag), exons, introns, messenger RNA (mRNA), transfer RNA, ribosomal RNA, RNAi, ribozymes, cDNA, recombinant polynucleotides, branched polynucleotides, plasmids, vectors, isolated DNA of any sequence, isolated RNA of any sequence, nucleic acid probes and primers. A polynucleotide can comprise modified nucleotides, such as methylated nucleotides and nucleotide analogs. If present, modifications to the nucleotide structure can be imparted before or after assembly of the polynucleotide. The sequence of nucleotides can be interrupted by non-nucleotide components. A polynucleotide can be further modified after polymerization, such as by conjugation with a labeling component. The term can also refer to both double- and single-stranded molecules. Unless otherwise specified or required, any embodiment of this disclosure that can be a polynucleotide encompasses both the double-stranded form and each of two complementary single-stranded forms known or predicted to make up the double-stranded form.
A polynucleotide can be composed of a specific sequence of nucleotides. A nucleotide comprises a nucleoside and a phosphate group. A nucleotide comprises a sugar (e.g., ribose or 2′deoxyribose) and a nucleobase, such as a nitrogenous base. Non-limiting examples of nucleobases include adenine (A), cytosine (C), guanine (G), thymine (T), uracil (U), and inosine (I). In some embodiments, I can be formed when hypoxanthine can be attached to ribofuranose via a P-N9-glycosidic bond, resulting in the chemical structure:
Some polynucleotide embodiments refer to a DNA sequence. In some embodiments, the DNA sequence can be interchangeable with a similar RNA sequence. Some embodiments refer to an RNA sequence. In some embodiments, the RNA sequence can be interchangeable with a similar DNA sequence. In some embodiments, Us and Ts can be interchanged in a sequence provided herein.
The term “protein”, “peptide” and “polypeptide” can be used interchangeably and in their broadest sense can refer to a compound of two or more subunit amino acids, amino acid analogs or peptidomimetics. The subunits can be linked by peptide bonds. In another embodiment, the subunit can be linked by other bonds, e.g., ester, ether, etc. A protein or peptide can contain at least two amino acids and no limitation can be placed on the maximum number of amino acids which can comprise a protein's or peptide's sequence. As used herein the term “amino acid” can refer to either natural amino acids, unnatural amino acids, or synthetic amino acids, including glycine and both the D and L optical isomers, amino acid analogs and peptidomimetics. As used herein, the term “fusion protein” can refer to a protein comprised of domains from more than one naturally occurring or recombinantly produced protein, where generally each domain serves a different function. In this regard, the term “linker” can refer to a protein fragment that can be used to link these domains together—optionally to preserve the conformation of the fused protein domains, prevent unfavorable interactions between the fused protein domains which can compromise their respective functions, or both.
The term “stop codon” can refer to a three nucleotide contiguous sequence within messenger RNA that signals a termination of translation. Non-limiting examples include in RNA, UAG (amber), UAA (ochre), UGA (umber, also known as opal) and in DNA TAG, TAA or TGA. Unless otherwise noted, the term can also include nonsense mutations within DNA or RNA that introduce a premature stop codon, causing any resulting protein to be abnormally shortened.
The term “structured motif” refers to a combination of two or more structural features in a guide-target RNA scaffold.
The terms “subject,” “individual,” or “patient” can be used interchangeably herein. A “subject” refers to a biological entity containing expressed genetic materials. The biological entity can be a plant, animal, or microorganism, including, for example, bacteria, viruses, fungi, and protozoa. The subject can be tissues, cells and their progeny of a biological entity obtained in vivo or cultured in vitro. The subject can be a mammal. The mammal can be a human. The subject can be diagnosed or suspected of being at high risk for a disease. In some cases, the subject is not necessarily diagnosed or suspected of being at high risk for the disease
The term “in vivo” refers to an event that takes place in a subject's body.
The term “ex vivo” refers to an event that takes place outside of a subject's body. An ex vivo assay may not be performed on a subject. Rather, it can be performed upon a sample separate from a subject. An example of an ex vivo assay performed on a sample can be an “in vitro” assay.
The term “in vitro” refers to an event that takes places contained in a container for holding laboratory reagent such that it can be separated from the biological source from which the material can be obtained. In vitro assays can encompass cell-based assays in which living or dead cells can be employed. In vitro assays can also encompass a cell-free assay in which no intact cells can be employed.
The term “wobble base pair” refers to two bases that weakly pair. For example, a wobble base pair can refer to a G paired with a U.
The term “substantially forms” as described herein, when referring to a particular secondary or tertiary structure, refers to formation of at least 80% of the structure under physiological conditions (e.g. physiological pH, physiological temperature, physiological salt concentration, etc.).
As used herein, the terms “treatment” or “treating” can be used in reference to a pharmaceutical or other intervention regimen for obtaining beneficial or desired results in the recipient. Beneficial or desired results include but are not limited to a therapeutic benefit and/or a prophylactic benefit. A therapeutic benefit can refer to eradication or amelioration of one or more symptoms of an underlying disorder being treated. Also, a therapeutic benefit can be achieved with the eradication or amelioration of one or more of the physiological symptoms associated with the underlying disorder such that an improvement can be observed in the subject, notwithstanding that the subject can still be afflicted with the underlying disorder. A prophylactic effect includes delaying, preventing, or eliminating the appearance of a disease or condition, delaying or eliminating the onset of one or more symptoms of a disease or condition, slowing, halting, or reversing the progression of a disease or condition, or any combination thereof. For prophylactic benefit, a subject at risk of developing a particular disease, or to a subject reporting one or more of the physiological symptoms of a disease can undergo treatment, even though a diagnosis of this disease may not have been made.
The section headings used herein is for organizational purposes only and is not to be construed as limiting the subject matter described.
A number of compositions, and methods are disclosed herein. Specific exemplary embodiments of these compositions and methods are disclosed below. The following embodiments recite non-limiting permutations of combinations of features disclosed herein. Other permutations of combinations of features are also contemplated. In particular, each of these numbered embodiments is contemplated as depending from or relating to every previous or subsequent numbered embodiment, independent of their order as listed.
The following examples are included for illustrative purposes only and are not intended to limit the scope of the present disclosure.
An example of a workflow according to the methods described herein is illustrated in
This example describes editing of the SERPINA1 E342K mutation in fibroblasts from a patient carrying the homozygous mutation. Guide RNAs (gRNAs) targeting both mRNA and pre-mRNA were recombinantly produced. gRNAs tested comprised a C at a position opposite the target A in SERPINA1 to be edited, thus yielding a mismatch upon hybridization of the gRNA to the target sequence and formation of a double stranded substrate. gRNAs tested were all linear gRNAs. A summary of the gRNAs tested is provided in TABLE 5 below. The column in TABLE 5 titled “Structural Features” describes structural features in the double stranded RNA substrate formed upon hybridization of the gRNA to the target RNA. For the 1.100.50 gRNA, the internal GluR2 is a pre-formed hairpin (or a recruitment domain) in the gRNA itself. For the engineered guide RNA sequences shown in TABLE 5, lower case letters indicate regions of the guide RNA that target intronic sequence and upper case letters indicate regions of the guide RNA that target exonic sequence.
CCTATGATATTGTTGTAAATCGTATAACAA
TATGATAAGGTGAGCACAGCCTTATGCACGG
CCTATGATATTGTTGTAAATCGTATAACAA
TATGATAAGGTGAGCACAGCCTTATGCACGG
Immortalized cells (fibroblasts) from patients carrying the E342K mutation were grown in culture. The mRNA expression of the mutant isoform of the alpha-1 antitrypsin (AAT) protein from the mutated SERPINA1 gene in the patient was verified using RT-PCR or a suitable antibody that can recognize the mutated isoform. An engineered gRNA against Rab7a (“control gRNA”; negative control), and the engineered gRNAs against SERPINA1 were nucleofected in the fibroblasts. 2×10{circumflex over ( )}5 cells were used per transfection and cells were transfected with 60 pmoles of the engineered gRNAs. cDNA synthesized from the isolated RNA was PCR amplified, followed by Sanger sequencing. Percent editing was quantified using the quantification software.
This example describes the effect on ADAR-mediated RNA editing from changing guide RNA length and A/C mismatch placement in ABCA4 targeting engineered guide RNAs of the present disclosure. Fold change luciferase assays in a broken luciferase screen were performed to assess the impact of altering guide length and mismatch placement on RNA editing of ABCA4. A faux ABCA4 mini-gene carrying ABCA4 mutations of interested were introduced into cells. To generate a faux ABCA4 mini-gene, five nucleotides of the original transcript were modified. These changes are summarized in TABLE 6 below. The GAA to TAG mutation introduced a premature stop codon and the A within the TAG sequence in the target RNA was targeted for RNA editing using the engineered guide RNAs disclosed herein.
Guides of various lengths and having various mismatch placements were recombinantly produced. gRNAs tested were all linear gRNAs. A summary of the gRNAs tested is provided in TABLE 7 below. The column in TABLE 7 titled “Structural Features” describes structural features in the double stranded RNA substrate formed upon hybridization of the gRNA to the target RNA.
As shown in
Engineered guides 150.125, 150.75, and 100.80 were selected to move forward into the experiments detailed below.
This example describes engineered guide RNAs of the present disclosure designed to target mutations in ABCA4 RNA for correction. Stargardt disease may be caused by loss-of-function genetic mutations in the ABCA4 gene. The most common mutations present in Stargardt's disease patients are detailed below in TABLE 8, with mutations amenable to correction by ADAR listed in bold text. The most common missense mutations in Stargardt disease include G>A mutation (e.g., the c.5882 G>A mutation), which can be corrected by ADAR. However, ADARs may be generally disinclined to deaminate adenosines with an upstream 5′G, as is the case with targeting the c.5882G>A mutation.
Experiments described herein were conducted to assess the ability of engineered guide RNAs that, upon hybridization to a target ABCA4 sequence, form structural features in the resulting double stranded RNA substrate, as disclosed herein, to correct the c.5882G>A mutations expressed in ABCA4 miniaturized genes (minigenes). Without being bound by any theory, the steric hindrance produced by the structural features may have improved ADAR deamination of adenosines with a 5′G, as compared to ADAR deamination of adenosines facilitated by engineered guide RNAs that do not form said structural features upon hybridization to the target ABCA4 RNA.
Wild type HEK293 cells expressing a minigene containing exons 40-48, in frame, of ABCA4 with a downstream P2A-mCherry were produced. As illustrated in
Engineered guide RNAs of different lengths and different A/C mismatch positioning—150.125, 150.75. and 100.80—were recombinantly produced. Each of these guide RNAs was further engineered to form structural features upon hybridization to the target ABCA4 RNA. The resulting double stranded substrates formed upon hybridization of the engineered guide RNAs and the target ABCA4 RNA produced an engineered guide-target RNA scaffold that mimicked a drosophila substrate—shown in
A summary of the gRNAs tested is provided in TABLE 9 below. The column in TABLE 9 titled “Structural Features” describes structural features in the double stranded RNA substrate formed upon hybridization of the gRNA to the target RNA. In TABLE 9, % RNA editing of ABCA4 was determined in HEK293 cells expressing ADAR1 and ADAR2 48 hours after engineered guide RNA transfection.
HEK293 cells were transfected with plasmids containing the engineered guide RNAs. The 150.125 and 150.75 engineered guide RNAs were transfected in biological triplicate. The 100.80 engineered guide RNAs were transfected in biological duplicate. The target RNA was isolated and collected within 48 hours of transfection, converted into cDNA, and then sequenced via Sanger Sequencing.
An initial set of experiments demonstrated the improvement in RNA editing of ABCA4 observed in engineered guide RNAs incorporating an SmOPT sequence (AATTTTTGGAG; SEQ ID NO: 390) and a U7 hairpin sequence (CAGGTTTTCTGACTTCGGTCGGAAAACCCCT; SEQ ID NO: 389), depicted below as SEQ ID NO: 339-341 of TABLE 10. HEK293 cells naturally expressing ADAR1 were transfected with a piggyBac vector carrying an ABCA4 minigene having the 5882 G->A mutation and ADAR2. Engineered guide RNAs tested included two U6 driven engineered guide RNAs (“U6 Full mimicry 0.100250” and “U6 Full mimicry 0.10080”) and a driven engineered guide RNA containing the SmOPT sequence and U7 hairpin sequence (“UT Full mimicry 0.100.80”). Negative controls included a circular guide RNA to a different gene (Rab7A), GFP plasmid alone, and no transfection. As shown in
A summary of each engineered guide RNA is described below in TABLE 10. The column in TABLE 10 titled “Structural Features” describes structural features in the double stranded RNA substrate formed upon hybridization of the gRNA to the target RNA.
Subsequent experiments evaluated the dose dependence of engineered guide RNAs targeting the ABCA4 5882 G->A mutation, where polynucleotides encoding the engineered guide RNA also encoded for a SmOPT sequence and a U7 hairpin sequence.
Further Modification with Internal Loops
CCCCAGTGAGCATCTT
GAATGTGGTTGTATTG
CCGGCACCATTCACTC
CCAGGAGGCCAAAGCA
CTCTCCAGTGAGAACT
CGGACCACAGCCTCCC
GCTgtgg
AATTTTTGGAG
CCCCAGTGAGCATCTT
GAATGTGGTTGTTTTG
CCGGCACCATTCACTC
CCAGGAGGCCAAAGCA
CTCTCCTCTGAGAACT
CGGACCACAGCCTCCC
GCTGgtgg
AATTTTTGGAG
CCCCAGTGAGCATCTT
GAATGTGGTTGTTTTG
CCGGCACCATTCAGAG
GCAGGAGGCCAAAGC
ACTCTCCTCTGAGAAC
TCGGACCACAGCCTCC
CGCTGgtgg
AATTTTTGGAG
CCCCAGTGAGCATCTT
GAATGTGGTTGTTTTG
CGCCGACCATTCAGAG
GCAGGAGGCCAAAGC
ACTCTCCTCTGAGAAC
TCGGACCACAGCCTCC
CGCTGgtgg
AATTTTTGGAG
CCCCAGTGAGCATCTT
GAATGTCCATGTTTTGC
GCCGACCATTCAGAGG
CAGGAGGCCAAAGCAC
TCTCCTCTGAGAACTC
GGACCACAGCCTCCCG
CTGgtgg
AATTTTTGGAG
This example describes in vitro transcribed (IVT) LRRK2-targeting engineered guide RNAs. gBlocks™ Gene Fragments were purchased from IDT and used to generate IVT engineered guide RNAs (TABLE 12). Formatting of sequences in TABLE 12 indicates various elements of each DNA construct including non-transcribed T7 promoter elements (lowercase), primer binding sequence (underlined); GluR2 recruiting domain (italicized). A denotes a nucleotide mismatch; * denotes a nucleotide that will form a bulge; # denotes a nucleotide that will form an internal loop; underlining denotes a nucleotide that will form part of a hairpin. The column in TABLE 12 titled “Structural Features” describes structural features in the double stranded RNA substrate formed upon hybridization of the gRNA to the target RNA.
g)GTGCCCTCTGATG
g)GTGCCCTCTGATG
ACAATATGCTAAATG
TTGTTATAGTATCCCA
C
GTGGAATAGTATAAC
AATATGCTAAATGTT
GTTATAGTATCCCAC
CAATATGCTAAATGTT
GTTATAGTATCCCAC
CACCCTATGATATTG
TTGTAAATCGTATAAC
AATATGATAAGGTGG
GTGGAATAGTATAAC
AATATGCTAAATGTT
GTTATAGTATCCCAC
The IVT was carried out using the reagents, quantities, and concentrations described in TABLE 13. IVT templates were made for all engineered guide RNAs following Q5 PCR protocol (60C annealing) followed by confirmation via gel electrophoresis (
In brief, the IVT protocol shown in TABLE 13 was utilized to generate IVT guide RNA. Reagents were mixed and incubated at 37° C. overnight (overnight IVT generally gives a great yield). For DNase treatment, 70 μl nuclease-free water, 10 μl of 10× DNase I Buffer, and 2 μl of DNase I (RNase-free) were mixed and incubated for 30 minutes at 37° C. Purified IVT produced polynucleotide RNA was adjusted to 1 μg/ul (˜25 nmol).
Engineered guide RNAs are shown in TABLE 15. These engineered guide RNAs can revert a single base pair mutation at position 6190 of the LRRK2 mRNA sequence. The formatting of the sequences in TABLE 15 indicated various elements of each construct: Recruiting sequences (GluR2) are italicized. {circumflex over ( )} denotes a nucleotide mismatch; * denotes a nucleotide that will form a bulge; # denotes a nucleotide that will form an internal loop; underlining denotes a nucleotide that will form part of a hairpin. The column in TABLE 15 titled “Structural Features” describes structural features in the double stranded RNA substrate formed upon hybridization of the gRNA to the target RNA.
GUAUAACAAUAUG
CUAAAUGUUGUUA
UAGUAUCCCAC
GUGGAAUAGUAUA
ACAAUAUGCUAAA
UGUUGUUAUAGU
AUCCCAC
GUGCCC
GGAAUAGUAUAAC
AAUAUGCUAAAUG
UUGUUAUAGUAU
CCCAC
CUAUGAUAUUGU
UGUAAAUCGUAUA
ACAAUAUGAUAAG
GUG
GCAAUCUUC
EBV transformed B cells (LRRK2 G2019S patient-derived lymphoblastoid cell lines; LCLs) encoding one mutant allele of the G2019S mutation in LRRK2 (heterozygous) from a donor were procured and used throughout these experiments to assess ADAR-mediated RNA editing from A to G and reversion to the wild-type LRRK2 allele.
7 IVT generated engineered guide RNAs (from EXAMPLE 5) were tested against LRRK2 as well as 1 IVT engineered guide RNA against RAB7A (as a control). All engineered guide RNAs were nucleofected in LCL cells using the Lonza X nucleofector with program EH100. Reaction conditions included approximately 40 nmol or 60 nmol of each IVT engineered guide RNA and about 2×10{circumflex over ( )}5 LCL cells per reaction. The reaction was split into 2 wells each containing 1×10{circumflex over ( )}5 cells and cells collected for RNA isolation at either 3 hours or 7 hours. At collection, cells were spun at 1,500×g for 1 min, media was then removed, and 180 μl of RLT lysis buffer+beta-mercaptoethanol (BMe) was added to each well. A Qiagen RNeasy protocol and kit were used to isolate RNA, followed by a New England Biolabs (NEB) ProtoScript II First-Strand cDNA synthesis kit.
LRRK2 mRNA specific primers, outside of the target regions, were used to amplify the region that the IVT engineered guide RNAs were targeting (TABLE 16). The primers had no sequence overlap with any of the engineered guide RNAs. LRRK2 primers 1 and 2 were used to amplify the mRNA, and primer 4 was used for sequencing of the target region. Sanger traces were analyzed to assess editing efficiency of each IVT guide.
This example describes treatment of Parkinson's disease in patients having the G2019S mutation in LRRK2 using the guide RNAs of the present disclosure. Parkinson patients diagnosed with the G2019S mutation are administered any of the guide RNAs described herein (e.g., those listed in TABLE 15). Guide RNAs are prepared, for example, by PCR and IVT (as described in EXAMPLE 6 and EXAMPLE 7) or are genetically encoded in a DNA construct encapsidated in an AAV. Guide RNAs are administered to a subject by any route of administration disclosed herein, such as intravenous injection, intracerebroventricular, intraparenchymal, intracisternal, or intrathecal injection. The subject is a human or non-human animal.
For genetically encoded guide RNAs, the coding sequence of the guide RNA (e.g., such as those listed in TABLE 12) with their T7 promoter sequence replaced with a U7, a U1, a U6, an H1, or a 7SK promoter sequence, is cloned into a viral vector, such as an adenoviral vector, an adeno-associated viral vector (AAV), a lentiviral vector, or a retroviral vector. Alternatively, the coding sequence of the guide RNA (e.g., such as those listed in TABLE 12) with their T7 promoter sequence replaced with a U7, a U1, a U6, an H1, or a 7SK promoter sequence is prepared by PCR or gBlocks™ Gene Fragments and the coding sequence is formulated in a pharmaceutical formulation, a nanoparticle, or a dendrimer (e.g., via encapsulation or direct attachment).
RNA editing is monitored as follows: ˜1×10{circumflex over ( )}5 cells are collected for RNA isolation after a week. At collection, cells are spun at 1,500×g for 1 min. The media is removed. 180 ul of RLT buffer+BMe is added to each well. RNA is isolated from the cells and cDNA is synthesized and sequenced (e.g., via Sanger sequencing or NGS). Percent on-target editing, percent off-targeting editing, or a combination of both is quantified. In particular, the ability of each guide RNA to facilitate ADAR-mediated the RNA editing of the A to G LRRK2 to correct the G2019S mutation is calculated (e.g., by quantitating the difference of trace signal of the LRRK2 mRNA with a G (edited) and an A (unedited) at the 6055th nucleotide).
Because polymorphisms in either LRRK2 (G2019S) or SNCA may be associated with increased risk of idiopathic Parkinson's Disease, simultaneous manipulation of the expression of the two genes can be a useful treatment. RNA editing, as illustrated in the current disclosure, is modular; the RNA editing enzyme and the RNA targeting guide are two different entities. Therefore, engineered guide RNAs can be multiplexed to achieve simultaneous correction of more than one distinct targets. For example, to treat idiopathic Parkinson's Disease patients with contributing polymorphisms in LRRK2 (G2019S) and SNCA, two engineered guide RNAs are designed. The first engineered guide RNA is selected from any of the LRRK2-targeting engineered guide RNAs disclosed herein (e.g., those disclosed in TABLE 15) and targets the LRRK2 G2019S mutation for ADAR-mediated editing of an A to a G at the 6055th nucleotide (e.g., see EXAMPLE 7). The second engineered guide RNA is selected from any of the SNCA-targeting engineered guide RNAs disclosed herein and targets the ATG start codon of SNCA for ADAR-mediated editing of an A to a G. Upon editing of the start site, expression of the alpha-synuclein protein is decreased. Expression of each of these engineered guide RNAs can be independently or together driven under an upstream U7, U1, U6, H1, 7SK promoter and cloned into a single viral vector or two separate viral vectors, such as an adenoviral vector, an adeno-associated viral vector (AAV), a lentiviral vector, or a retroviral vector. Guide RNAs are administered to a subject by any route of administration disclosed herein, such as intravenous injection, intracerebroventricular, intraparenchymal, intracisternal, or intrathecal injection. The subject is a human or non-human animal.
In particular, the ability of each guide RNA to facilitate ADAR-mediated the RNA editing of the A to G LRRK2 to correct the N2081D mutation is calculated (e.g., by quantitating the difference of trace signal of the LRRK2 mRNA with a G (edited) and an A (unedited) at the 6055th nucleotide).
The expression level of SNCA is monitored as follows: knockdown of alpha-synuclein protein is assessed using Western Blot, ELISA, or Meso Scale Discovery (MSD) analysis.
High throughput screening (HTS) of 2,540 gRNA sequences against the LRRK2*G2019S mutation identified designs with superior on-target activity and specificity. Data and results are shown in
This example describes engineered guide RNAs of the present disclosure targeting LRRK2 mRNA. The region of the LRRK2 mRNA that was targeted was an A at position 6055 of a LRRK2 mRNA, which encodes for a pathogenic G2019S mutant protein.
Self-annealing RNA structures comprising the engineered polynucleotide sequences of TABLE 25 (and control engineered polynucleotide sequences) and the sequences of the regions targeted by the guide RNAs were contacted with an RNA editing entity (e.g., a recombinant ADAR1 and/or ADAR2) under conditions that allow for the editing of the regions targeted by the guide RNAs. The regions targeted by the guide RNAs were subsequently assessed for editing using next generation sequencing (NGS).
Exemplary guide RNA sequences corresponding to
This example describes engineered guide RNAs of the present disclosure targeting the ABCA4 G1961E mutation, an ABCA4 missense mutation, implicated in Stargardt disease. The G1961E mutation includes a 5′G upstream of the A to be edited. This editing context is especially difficult to target as it can be refractory to endogenous ADAR editing.
High throughput screening (HTS) of 2,500 guide designs were generated and screen for targeting the ABCA4 G1961E mutation, as shown in
Self-annealing RNA structures comprising the engineered polynucleotide sequences of TABLE 18 and the sequences of the regions targeted by the guide RNAs were contacted with ADAR1 and/or ADAR2 under conditions that allow for the editing of the regions targeted by the guide RNAs (“in cis-editing”). The regions targeted by the guide RNAs were subsequently assessed for editing using next generation sequencing (NGS).
Shown in
Select engineered guide RNAs discovered from the high throughput screen described above were further adapted (e.g., the main segment of the guide RNA that forms the structural features upon hybridization was trimmed and/or elongated to a ˜100mer guide RNA) for in trans editing of ABCA4. The elongated 100mer guide RNAs tested in cells were engineered such that the structural features in the guide target RNA scaffold would be positioned asymmetrically (towards the 5′ end of the target and the 3′ end of the guide RNA). In these cellular experiments, the target adenosine was positioned to be across from around the 80th nucleotide of the guide RNA.
HEK293 cells naturally expressing ADAR1 were transfected with a piggyBac vector carrying the ABCA4 minigene and ADAR2. Engineered guide RNAs were administered to cells and RNA editing was quantified 48 hours post transfection. As shown in
Polynucleotide sequences encoding engineered guide RNAs targeting ABCA4 are provided below in TABLE 19. The column in TABLE 19 titled “Structural Features” describes structural features in the double stranded RNA substrate formed upon hybridization of the gRNA to the target RNA. The italicized sequence is the sequence of the 100mer engineered guide RNA.
TGCCGGCACCATTCACTCC
CAGGAGGCCAAAGCACTCT
CCGGGACGAACTCGGACA
ACAGATGTCCACTGCTGGG
CTGGAGGTGCCTGGATAAA
TCTTGGGgtgg
AATTTTTGGAG
CCCAGTGAGCATCTTGAAT
GTGGTTGTTTTGCCGGCAC
CATTCACTCCCAGGAGGCC
AAAGCACTCTCCGGGACGA
ACTCGGACAACAGATGTCC
ACTGCgtgg
AATTTTTGGAG
TGCCGGCACCATTCACTCC
CAGGAGGCCAAAGCACTCT
CCGGGACGAACTCGGACA
CACAGGCTGTCCACTGCTG
GGCTGGAGGTGCCTGGAT
AAATCTTgtgg
AATTTTTGGAG
CCCAGTGAGCATCTTGAAT
GTGGTTGTTTTGCCGGCAC
CATTCACTCCCAGGAGGCC
AAAGCACTCTCCGGGACGA
ACTCGGACACACAGGCTGT
CCACTgtgg
AATTTTTGGAG
TGCCGGCACCATTCACTCC
CAGGAGGCCAAAGCACTCT
TCAGGGCGAACTTGGACAC
ACAGCCTGTCCACTGCTGG
GCTGGAGGTGCCTGGATA
AATCTTgtgg
AATTTTTGGAG
CCCAGTGAGCATCTTGAAT
GTGGTTGTTTTGCCGGCAC
CATTCACTCCCAGGAGGCC
AAAGCACTCTTCAGGGCGA
ACTTGGACACACAGCCTGT
CCACTgtgg
AATTTTTGGAG
TGCCGGCACCATTCACTCC
CAGGAGGCCAAAGCACTCT
TCAGGGCGATCTTGGACAC
ACAGCCTGTCCACTGCTGG
GCTGGAGGTGCCTGGATA
AATCTTgtgg
AATTTTTGGAG
CCCAGTGAGCATCTTGAAT
GTGGTTGTTTTGCCGGCAC
CATTCACTCCCAGGAGGCC
AAAGCACTCTTCAGGGCGA
TCTTGGACACACAGCCTGT
CCACTgtgg
AATTTTTGGAG
AATTTTTGGAG
AATTTTTGGAG
TGCCGGCACCATTCACTCC
CAGGAGGCCAAAGCACTCT
CCAGGGCGAACTTGGTCAT
ACAGCCTGTCCACTGCTGG
GCTGGAGGTGCCTGGATA
AATCTTgtgg
AATTTTTGGAG
CCCAGTGAGCATCTTGAAT
GTGGTTGTTTTGCCGGCAC
CATTCACTCCCAGGAGGCC
AAAGCACTCTCCAGGGCGA
ACTTGGTCATACAGCCTGT
CCACTgtgg
AATTTTTGGAG
CCCAGTGAGCATCTTGAAT
GTGGTTGTTTTGCCGGCAC
CATTCACTCCCAGGAGGCC
AAAGCACTCTCCGGGACGA
ACTCGGACAACAGTTGTCC
ACTGCgtgg
AATTTTTGGAG
CCCAGTGAGCATCTTGAAT
GTGGTTGTTTTGCCGGCAC
CATTCACTCCCAGGAGGCC
AAAGCACTCTCCGGGACGA
ACTCGGACAACAGCTGTCC
ACTGCgtgg
AATTTTTGGAG
CCCAGTGAGCATCTTGAAT
GTGGTTGTTTTGCCGGCAC
CATTCACTCCCAGGAGGCC
AAAGCACTCTCCAGGACGA
ACTCGGACAACAGATGTCC
ACTGCgtgg
AATTTTTGGAG
CCCAGTGAGCATCTTGAAT
GTGGTTGTTTTGCCGGCAC
CATTCACTCCCAGGAGGCC
AAAGCACTCTCCAGGACGA
ACTCGGACAACAGCTGTCC
ACTGCgtgg
AATTTTTGGAG
CCCAGTGAGCATCTTGAAT
GTGGTTGTTTTGCCGGCAC
CATTCACTCCCAGGAGGCC
AAAGCACTCTCCAGGGCGA
ACTTGGACACACAGCCTGT
CCACTgtgg
AATTTTTGGAG
CCCAGTGAGCATCTTGAAT
GTGGTTGTTTTGCCGGCAC
CATTCACTCCCAGGAGGCC
AAAGCACGCTCCAGGGCG
AATTTGGACACACAGCCTG
TCCACTgtgg
AATTTTTGGAG
CCCAGTGAGCATCTTGAAT
GTGGTTGTTTTGCCGGCAC
CATTCACTCCCAGGAGGCC
AAAGCACGCTCCAGGGCG
AACTTGGTCACACAGCCTG
TCCACTgtgg
AATTTTTGGAG
CCCAGTGAGCATCTTGAAT
GTGGTTGTTTTGCCGGCAC
CATTCACTCCCAGGAGGCC
AAAGCACGCTCCAGGGCG
AATTTGGTCATACAGCCTG
TCCACTgtgg
AATTTTTGGAG
CCCAGTGAGCATCTTGAAT
GTGGTTGTTTTGCCGGCAC
CATTCACTCCCAGGAGGCC
AAAGCACTCTCCAGGGCGA
ATTTGGTCATACAGCCTGT
CCACTgtgg
AATTTTTGGAG
CCCAGTGAGCATCTTGAAT
GTGGTTGTTTTGCCGGCAC
CATTCACTCCCAGGAGGCC
AAAGCACTCTCCAGGGCGA
ACTTGGACATACAGCCTGT
CCACTgtgg
AATTTTTGGAG
CCCAGTGAGCATCTTGAAT
GTGGTTGTTTTGCCGGCAC
CATTCACTCCCAGGAGGCC
AAAGCACTCTCCAGGGCGA
ATTTGGACACACAGCCTGT
CCACTgtgg
AATTTTTGGAG
CCCAGTGAGCATCTTGAAT
GTGGTTGTTTTGCCGGCAC
CATTCACTCCCAGGAGGCC
AAAGCACGCTCCAGGGCG
AACTTGGTCATACAGCCTG
TCCACTgtgg
AATTTTTGGAG
CCCACCTCTTCAGGGCGAT
CTTGGACACACAGCCTGTC
CACTGCTgtgg
AATTTTTGGAG
CCCACCTCTTCAGGGCGAT
CTTGGACACACAACCTGTC
CACTGCTgtgg
AATTTTTGGAG
CCGACCTCTTCAGGGCGAT
CTTGGACACACAACCTGTC
CACTGCTgtgg
AATTTTTGGAG
CCCAGTGAGCATCTTGAAT
GTGGTTGTTTTGCCGGCAC
CATTCACTCCCAGGAGGCC
AAAGCACTCTCCGGGGCG
AACTCGGACAACAGTTGTC
CACTGCgtgg
AATTTTTGGAG
CCCAGTGAGCATCTTGAAT
GTGGTTGTTTTGCCGGCAC
CATTCACTCCCAGGAGGCC
AAAGCACTCTCCGGGACGA
ACTCGGACAACAGATGTCC
ACTGCgtgg
AATTTTTGGAG
CCCAGTGAGCATCTTGAAT
GTGGTTGTTTTGCCGGCAC
CATTCACTCCCAGGAGGCC
AAAGCACTCTCCAGGACGA
ACTCGGACAACAGTTGTCC
ACTGCgtgg
AATTTTTGGAG
CCCAGTGAGCATCTTGAAT
GTGGTTGTTTTGCCGGCAC
CATTCACTCCCAGGAGGCC
AAAGCACTCTCCAGGACGA
ACTCGGACACACAGGCTGT
CCACTgtgg
AATTTTTGGAG
CCCAGTGAGCATCTTGAAT
GTGGTTGTTTTGCCGGCAC
CATTCACTCCCAGGAGGCC
AAAGCACGCTCCAGGGCG
AATTTGGACATACAGCCTG
TCCACTgtgg
AATTTTTGGAG
CCCAGTGAGCATCTTGAAT
GTGGTTGTTTTGCCGGCAC
CATTCACTCCCAGGAGGCC
AAAGCACGCTCCAGGGCG
AACTTATCACATACAGCCT
GTCCACgtgg
AATTTTTGGAG
CCCAGTGAGCATCTTGAAT
GTGGTTGTTTTGCCGGCAC
CATTCACTCCCAGGAGGCC
AAAGCACGCTCCAGGGCG
AATTTGGTCACACAGCCTG
TCCACTgtgg
AATTTTTGGAG
CCCAGTGAGCATCTTGAAT
GTGGTTGTTTTGCCGGCAC
CATTCACTCCCAGGAGGCC
AAAGCACTCTCCAGGGCGA
ATTTGGTCACACAGCCTGT
CCACTgtgg
AATTTTTGGAG
CCCAGTGAGCATCTTGAAT
GTGGTTGTTTTGCCGGCAC
CATTCACTCCCAGGAGGCC
AAAGCACTCTCCAGGGCGA
ATTTGGACATACAGCCTGT
CCACTgtgg
CCCAGTGAGCATCTTGAAT
GTGGTTGTTTTGCCGGCAC
CATTCACTCCCAGGAGGCC
AAAGCACTCTCCAGGGCGA
TCTTGGACACACAGCCTGT
CCACTgtgg
This example describes in cell ADAR-mediated RNA editing of LRRK2, facilitated by engineered guide RNA of the present disclosure. Select engineered guide RNAs discovered from a high throughput screen described in EXAMPLE 9 were further adapted (e.g., the main segment of the guide RNA that forms the structural features upon hybridization was trimmed and/or elongated to a ˜100mer guide RNA) for in trans editing of LRRK2 in cells. Two guide RNA designs targeting the LRRK2 G2019S mutation were tested, both with a SmOPT sequence and a U7 hairpin (SEQ ID NO: 344 and SEQ ID NO: 345). The first engineered guide RNA (“V0118 0.100.50”) contained 100 nucleotides with the target A in LRRK2 to be edited across from the nucleotide at position 50 in the engineered guide RNA. The second engineered guide RNA (“V0118 0.100.80”) contained 100 nucleotides with the target A in LRRK2 to be edited across from the nucleotide at position 80 in the guide. The elongated 100mer guide RNAs tested in cells were engineered such that the structural features in the guide target RNA scaffold would be positioned symmetrically (towards the middle of the guide-target RNA scaffold; v0118 0.100.50) or asymmetrically (towards the 5′ end of the target and the 3′ end of the guide RNA; v0118 0.100.80). Both engineered guide RNAs further formed a 6/6 symmetrical internal loop and 2 other mismatches (an A/G mismatch and a C/U mismatch) apart from the A/C mismatch at the target adenosine. A summary of each engineered guide RNA is described below in TABLE 20. The column in TABLE 20 titled “Structural Features” describes structural features in the double stranded RNA substrate formed upon hybridization of the gRNA to the target RNA.
Engineered guide RNAs were tested for their ability to facilitate ADAR-mediated RNA editing of the G2019S LRRK2 mutation in WT HEK293 cells transfected with a piggyBac vector carrying a LRRK2 minigene. WT HEK293 cells naturally express ADAR1. In experiments in which RNA editing mediated via ADAR1 and ADAR2 was tested, ADAR2 was overexpressed in cells via the same piggyBac vector carrying the LRRK2 minigene. Schematics of the piggyBac constructs are shown in
This example describes constructs of the present disclosure encoding engineered guide RNAs designed to target a start site, or translation initiation site (TIS) (also referred to as translation start site (TSS)) in the SNCA gene. Engineered guide constructs were designed to target SNCA TIS adenosine at nucleotide position 26 of Exon 2 (corresponding to nucleotide position 264 of most SNCA variants, including Exon 1 and Exon 2).
HEK293 cells were transfected with a plasmid encoding a guide RNA of interest and RNA editing was assessed 48 hours post-transfection. RNA editing was assessed for ADAR1 only, which is naturally expressed by HEK293 cells, and ADAR1 and ADAR2. In the latter experiment, HEK293 cells were co-transfected with a piggybac vector encoding ADAR2. Levels of RNA editing were quantified by Sanger sequencing and analyzed using a sequencing analysis script (EditADAR).
Sequences of guides shown in
CAGGTTTTCTGACTTCGGTCG
GAAAACCCCTCC
TCTGACTTCGGTCGGAAAACC
CCTCC
TTGGAGCAGGTTTTCTGACTT
CGGTCGGAAAACCCCTCC
CAGGTTTTCTGACTTCGGTCG
GAAAACCCCTCC
GGTTTTCTGACTTCGGTCGGA
AAACCCCTCC
GGAGCAGGTTTTCTGACTTCG
GTCGGAAAACCCCTCC
ATTTTTGGAGCAGGTTTTCTG
ACTTCGGTCGGAAAACCCCTC
C
CTGACTTCGGTCGGAAAACCC
CTCC
TTCTGACTTCGGTCGGAAAAC
CCCTCC
GGAGCAGGTTTTCTGACTTCG
GTCGGAAAACCCCTCC
GGAGCAGGTTTTCTGACTTCG
GTCGGAAAACCCCTCC
GGAGCAGGTTTTCTGACTTCG
GTCGGAAAACCCCTCC
GGAGCAGGTTTTCTGACTTCG
GTCGGAAAACCCCTCC
TTTTGGAGCAGGTTTTCTGAC
TTCGGTCGGAAAACCCCTCC
TTTTGGAGCAGGTTTTCTGAC
TTCGGTCGGAAAACCCCTCC
TTTTCTGACTTCGGTCGGAAA
ACCCCTCC
TTTGGAGCAGGTTTTCTGACT
TCGGTCGGAAAACCCCTCC
GGTTTTCTGACTTCGGTCGGA
AAACCCCTCC
TTTCTGACTTCGGTCGGAAAA
CCCCTCC
TTTTGGAGCAGGTTTTCTGAC
TTCGGTCGGAAAACCCCTCC
TTCTGACTTCGGTCGGAAAAC
CCCTCC
TCTGACTTCGGTCGGAAAACC
CCTCC
GCAGGTTTTCTGACTTCGGTC
GGAAAACCCCTCC
TTTCTGACTTCGGTCGGAAAA
CCCCTCC
TTGGAGCAGGTTTTCTGACTT
CGGTCGGAAAACCCCTCC
TTTTGGAGCAGGTTTTCTGAC
TTCGGTCGGAAAACCCCTCC
TTTTGGAGCAGGTTTTCTGAC
TTCGGTCGGAAAACCCCTCC
TTTTTGGAGCAGGTTTTCTGA
CTTCGGTCGGAAAACCCCTCC
TTTTTGGAGCAGGTTTTCTGA
CTTCGGTCGGAAAACCCCTCC
AATTTTTGGAGCAGGTTTTCT
GACTTCGGTCGGAAAACCCCT
CC
GGTTTTCTGACTTCGGTCGGA
AAACCCCTCC
AATTTTTGGAGCAGGTTTTCT
GACTTCGGTCGGAAAACCCCT
CC
TTTTTGGAGCAGGTTTTCTGA
CTTCGGTCGGAAAACCCCTCC
AGGTTTTCTGACTTCGGTCGG
AAAACCCCTCC
CAGGTTTTCTGACTTCGGTCG
GAAAACCCCTCC
TTTTTGGAGCAGGTTTTCTGA
CTTCGGTCGGAAAACCCCTCC
ATTTTTGGAGCAGGTTTTCTG
ACTTCGGTCGGAAAACCCCTC
C
TTTTGGAGCAGGTTTTCTGAC
TTCGGTCGGAAAACCCCTCC
AATTTTTGGAGCAGGTTTTCT
GACTTCGGTCGGAAAACCCCT
CC
AGGTTTTCTGACTTCGGTCGG
AAAACCCCTCC
GAGCAGGTTTTCTGACTTCGG
TCGGAAAACCCCTCC
ATTTTTGGAGCAGGTTTTCTG
ACTTCGGTCGGAAAACCCCTC
C
TGACTTCGGTCGGAAAACCCC
TCC
This example describes constructs of the present disclosure encoding guide RNAs designed to target a SERPINA1 missense mutation (SERPINA1, G to A mutation at position 9989 yielding the SERPINA1 E342K mutation), implicated in Alpha-1 antitrypsin deficiency.
Briefly, SERPINA1 minigenes are transfected into K562 cells expressing endogenous ADAR1 via a piggyBac vector and cells were selected via puromycin selection. SERPINA1 minigenes integrated into K562 cells included a SERPINA1 minigene1 having a full length 3′ UTR or a SERPINA1 minigene2 having a truncated 3′ UTR. Both minigenes carried the G to A 9989 mutation of interest. K562 cells (2×10{circumflex over ( )}5 cells) were electroporated with plasmids encoding a guide RNA operably linked to the U7 hairpin and an SmOPT sequence. Expression was driven under a mouse U7 promoter. 24 hours post-electroporation, RNA was isolated, cDNA was synthesized via RT-PCR and RT-PCR products were sequenced via Sanger sequencing to quantify percent RNA editing. Control guide RNAs lacked the U7 hairpin and the SmOPT sequence and expression was driven under a U6 promoter. Guide RNA sequences are summarized in the table below.
This example describes constructs of the present disclosure encoding circular engineered guide RNAs with latent structure that manifest structural features, under the control of a U6 promoter, where the engineered guide RNA is designed to target a start site, or translation initiation site (TIS) (also referred to as translation start site (TSS)) in the SNCA gene. Engineered guide RNA constructs were designed to target SNCA TIS adenosine at nucleotide position 26 of Exon 2 (corresponding to nucleotide position 264 of most SNCA variants, including Exon 1 and Exon 2).
HEK293 cells were transfected with a plasmid encoding a guide RNA of interest and RNA editing was assessed post-transfection. RNA editing was assessed for ADAR1 only, which is naturally expressed by HEK293 cells, and ADAR1 and ADAR2. In the latter experiment, HEK293 cells were co-transfected with a piggybac vector encoding ADAR2. Levels of RNA editing were quantified by sequencing and analyzed.
Sequences of guides shown in
TAGGGATAGGGATAGGGA
CAACTCCCTC
CTTGGCCTTTGAAAGTCCTTTCATGAAT
ACATCCACGGCTAATGAATTCCTTTACA
CCACACTGTCGTCGAATGGCCACTCCC
AGTTCTC
TAGGGATAGGGATAGGGA
CAACTCCCTC
CTTGGCCTTTGAAAGTCCTTTCATGAAT
ACATCCACGGCTAAT
GAATTCCTTTACACCACA
CAACTCCCTCCTTGGCCTTTGAAAGTC
CTTTCATGAATA
C
ATCCACGGCTAATGAATTCCTTTACACC
ACACTGTCGTCGAATGGCCACTCCCAG
TTCTCA
TAGGGATAGGGATAGGGA
CAACTCCCTC
CTTGGCCTTTGAAAGTCCTTTCATGAAT
ACATCCATAGCTAATGAATTCCTTTACA
CCACACTGTCGTCGAATGGCCACTCCC
AGTTCTCA
TAGGGATAGGGATAGGGA
CCCTGTTTGG
TTCTCTCAGCAGCAGCCACAACTCCCT
CCTTGGCCTTTGAAAGTCCTTTCATGAA
TACATCCATAGCTAATGAATTCCTTTAC
ACCACA
This example describes LRRK2 editing with guide RNAs of the present disclosure. Self-annealing RNA structures comprising the guide RNA sequences of TABLE 25 and the sequences of the regions targeted by the engineered guide RNAs were contacted with an RNA editing entity (e.g., a recombinant ADAR1 and/or ADAR2) under conditions that allow for the editing of the regions targeted by the guide RNAs. The regions targeted by the guide RNAs were subsequently assessed for editing using next generation sequencing (NGS).
Exemplary full guide sequences corresponding to
TABLE 25 below depicts the resulting editing for each guide. Each Percent on-target editing is calculated by the following formula: the number of reads containing “G” at the target/the total number of reads. Specificity is calculated by the following formula: (percent on target editing+100)/(sum of off target editing percentage at selected off-targets sites+100).
This example describes engineered guide RNA comprising a dumbbell design and targeting LRRK2 mRNA. A dumbbell design in an engineered guide RNA comprises two symmetrical internal loops, wherein the target A to be edited is positioned between the two symmetrical loops for selective editing of the target A. The two symmetrical internal loops are each formed by 6 nucleotides on the guide RNA side of the dsRNA substrate and 6 nucleotides on the target RNA side of the dsRNA substrate. In this example, the target A is an A at position 6055 of a LRRK2 mRNA, which encodes for a pathogenic G2019S mutant protein. Exemplary engineered guide RNAs with a dumbbell design and targeting LRRK2 mRNA are shown in TABLE 26 and
AATTTTTGGAG
AATTTTTGGAG
This example describes guide RNAs that target LRRK2 mRNA. Self-annealing RNA structures comprising the guide RNA sequences of TABLE 27 and the sequences of the regions targeted by the guide RNAs were contacted with an RNA editing entity (e.g., a recombinant ADAR1 and/or ADAR2) for 30 minutes under conditions that allow for the editing of the regions targeted by the guide RNAs. The regions targeted by the guide RNAs were subsequently assessed for editing using next generation sequencing (NGS). The guide RNAs of TABLE 27 showed specific editing of the A nucleotide at position 6055 of the mRNA encoding the LRRK2 G2019S. Percent on-target editing is calculated by the following formula: the number of reads containing “G” at the target/the total number of reads. Specificity is calculated by the following formula: (percent on target editing+100)/(sum of off target editing percentage at selected off-targets sites+100).
This example describes engineered guide RNAs that target SNCA mRNA. Self-annealing RNA structures comprising the engineered guide RNA sequences of TABLE 28 and the sequences of the regions targeted by the guide RNAs were contacted with an RNA editing entity (e.g., a recombinant ADAR1 and/or ADAR2) under conditions that allow for the editing of the regions targeted by the guide RNAs. The regions targeted by the guide RNAs were subsequently assessed for editing using next generation sequencing (NGS). The guide RNAs of TABLE 28 showed specific editing of the A nucleotide at translation initiation start site (TIS; the A in the ATG start coding with genomic coordinates: hg38 chr4: 89835667 strand −1) of SNCA mRNA. Percent on-target editing is calculated by the following formula: the number of reads containing “G” at the target/the total number of reads. Specificity is calculated by the following formula: (percent on target editing+100)/(sum of off target editing percentage at selected off-targets sites+100).
This example describes editing in vitro in induced pluripotent stem cell (iPSC)-derived neurons that can express LRRK2-G2019S mutant protein. Culturing, induction, maturation, and transfection or transduction of iPSC neurons are optimized for screening of editing facilitated by guide RNAs. Each dopaminergic neuronal phenotype is characterized and validated via TaqMan qPCR, flow cytometry, and immunofluorescence. iPSCs, neural stem cells (NSCs), neural progenitor cell (NPCs), or derived neuronal cells are then transfected or transduced with guide RNAs targeting a nucleotide of the codon encoding the LRRK2-G2019S mutation, and editing efficiency is quantified using Sanger sequencing, ddPCR, and amplicon next generation sequencing of the sequence encoding the LRRK2-G2019S locus. In vitro biochemical editing of LRRK2 mRNA that is translated into LRRK2 protein is assessed using LC-MS/MS of the LRRK2 protein, and Western Blot and Meso Scale Discovery (MSD) analysis of LRRK2 substrates (e.g., phospho-Rab (−8,−10,−35), LRRK2 autophosphorylation).
This example describes editing of the nucleotide of the codon encoding the LRRK2-G2019S mutation ex vivo in primary cortical neurons isolated from hLRRK2-G2019S mice. Primary microdissection and culturing of the primary neurons from the hLRRK2-G2019S mice are optimized prior to transfection or transduction of the guide RNAs. The isolated cortical neurons are then transfected with guide RNAs targeting the mRNA encoding the LRRK2-G2019S mutation, and editing efficiency is quantified using Sanger sequencing, ddPCR, and amplicon next generation sequencing of the LRRK2-G2019S encoding locus. Further, the ex vivo biochemical editing of LRRK2 mRNA that is translated into LRRK2 protein is assessed using LC-MS/MS of the LRRK2 protein, Western Blot and MSD analysis of LRRK2 substrates (e.g., phospho-Rab (−8,−10,−35), LRRK2 autophosphorylation).
This example describes editing of mRNA encoding LRRK2-G2019S in vivo in hLRRK2-G2019S mice. Guide RNAs targeting mRNA encoding the LRRK2-G2019S mutation are administered to the brain of the hLRRK2-G2019S mice via intracerebroventricular, intraparenchymal, intracisternal, or intrathecal injection. Brain tissue is then isolated from the hLRRK2-G2019S mice and processed to isolate LRRK2 nucleic acid and protein. Editing efficiency is quantified using ddPCR and amplicon next generation sequencing of the locus encoding LRRK2-G2019S. Further, the in vivo biochemical editing of LRRK2 mRNA that is translated into LRRK2 protein is assessed using LC-MS/MS of the LRRK2 protein, Western Blot and MSD analysis of LRRK2 substrates (e.g., phospho-Rab (−8,−10,−35), LRRK2 autophosphorylation).
This example describes SNCA editing in vitro in LUHMES and iPSC-derived dopaminergic neurons. Culturing, induction, differentiation, and transfection and transduction of LUHMES and iPSC-derived neurons are optimized for screening of editing facilitated by guide RNAs. Each dopaminergic neuronal phenotype is characterized and validated via TaqMan qPCR, flow cytometry, and immunofluorescence. Neurons are then transfected or transduced with guide RNAs targeting SNCA, and editing efficiency is quantified using qPCR, ddPCR and amplicon next generation sequencing of the SNCA locus. The in vitro biochemical knockdown of SNCA protein is assessed using Western Blot, ELISA, and MSD analysis of SNCA protein levels.
This example describes SNCA mRNA editing and SNCA protein knockdown ex vivo in primary cortical neurons isolated from hSNCA mice. Primary microdissection and culturing of the primary neurons from the SNCA mice are optimized prior to transfection or transduction of the guide RNAs. The isolated cortical neurons are then transfected or transduced with guide RNAs targeting SNCA, and editing efficiency is quantified using qPCR<ddPCR, and amplicon next generation sequencing of the SNCA locus. Further, the ex vivo biochemical knockdown of SNCA protein is assessed using Western Blot, ELISA, and MSD analysis of SNCA protein levels.
This example describes SNCA editing in vivo in hSNCA mice. Guide RNAs targeting SNCA are administered to the brain of the hSNCA mice via intracerebroventricular, intraparenchymal, intracisternal, or intrathecal injection. Brain tissue is then isolated from the hSNCA mice and processed to isolate SNCA nucleic acid and protein. Editing efficiency is quantified using qPCR, ddPCR, and amplicon next generation sequencing of the SNCA locus. Further, the in vivo biochemical knockdown of SNCA protein is assessed from the isolated SNCA protein using Western Blot, ELISA, and MSD analysis of SNCA protein levels.
This example describes engineered guide RNAs that target SERPINA1 mRNA. High throughput screening (HTS) of gRNA sequences against the SERPINA1 E342K mutation identified designs with superior on-target activity and specificity.
Self-annealing RNA structures comprising the engineered guide RNA sequences of TABLE 29 and the sequences of the regions targeted by the guide RNAs were contacted with an RNA editing entity (e.g., a recombinant ADAR1 and/or ADAR2) for 30 minutes under conditions that allow for the editing of the regions targeted by the guide RNAs. The regions targeted by the guide RNAs were subsequently assessed for editing using next generation sequencing (NGS). The guide RNAs of TABLE 29 showed specific editing of the A nucleotide. Percent on-target editing is calculated by the following formula: the number of reads containing “G” at the target/the total number of reads. Specificity is calculated by the following formula: (percent on target editing+100)/(sum of off target editing percentage at selected off-targets sites+100).
This example describes engineered guide RNAs that target SERPINA1 mRNA. A SERPINA1 guide RNA was identified from a high throughput screen for engineered guide RNAs against SERPINA1, similar to the screen described in EXAMPLE 25. Self-annealing RNA structures comprising engineered guide RNA sequences and the sequences of the regions targeted by the guide RNAs were contacted with an RNA editing entity (e.g., a recombinant ADAR1 and/or ADAR2) for 30 minutes under conditions that allow for the editing of the regions targeted by the guide RNAs. The regions targeted by the guide RNAs were subsequently assessed for editing using next generation sequencing (NGS).
The engineered guide RNA sequences in TABLE 30 were adapted for in vitro testing in cells. The engineered guide RNA sequences in TABLE 30 were adapted to 100mer sequences, as disclosed in TABLE 31. K562 cells were stably transfected with a Piggybac vector containing one of two SERPINA1 minigene constructs containing the E342K mutation. Engineered guide RNA sequences were plasmid transfected (2 μg) into 2×10{circumflex over ( )}5 K562 cells. Plasmids encoded for the engineered guide RNA sequence plus a downstream mouse U7 hairpin (CAGGTTTTCTGACTTCGGTCGGAAAACCCCT; SEQ ID NO: 389) and SmOPT sequence (AATTTTTGGAG; SEQ ID NO: 390) and expression was driven under a U6 promoter (no U7 hairpin or SmOPT sequence) or a U7 promoter. 24 hours post-transfection, RNA was isolated, converted to cDNA and Sanger sequenced.
The engineered guide RNA sequence of SEQ ID NO: 349 in TABLE 31 was carried forward into further experiments where the structural features of the A/C mismatch and A/A mismatch were preserved, but the overall engineered guide RNA length was shortened to 95, 85, 80, 75, 70, 65, and 60 nucleotides long. Sequences of the engineered guide RNA sequences used in this experiment are described in TABLE 32. Cell experiments were run as described above, but with RNA editing assessed at 24 hours and 48 hours post-transfection. As demonstrated in
The engineered guide RNAs that were 95 nucleotides in length were carried forward into further experiments in cells. Cell experiments were run as described above, but with RNA editing assessed at 24 hours post-transfection. To examine the ability to reduce local off-target editing, guide RNAs were further engineered to form a symmetric, an asymmetric bulge, or an asymmetric internal loop at sites of local off-target editing (−20 and −21 positions relative to the target adenosine). Sequences of the engineered guide RNA sequences used in this experiment are described in TABLE 33. As shown in
The engineered guide RNAs that formed the asymmetric internal loop described above and in TABLE 33 were carried forward into further experiments in cells where guide length was once again modulated. Cell experiments were run as described above, but with RNA editing assessed at 24 hours post-transfection. Sequences of the engineered guide RNA sequences used in this experiment are described in TABLE 34. As shown in
The engineered guide RNAs that were 107, 111, and 119 nucleotides long (see above and in TABLE 34) were carried forward into further experiments in cell where an additional bulge was placed at the +35 position relative to the target adenosine to be edited. Cell experiments were run as described above, but with RNA editing assessed at 24 hours post-transfection. Sequences of the engineered guide RNA sequences used in this experiment are described in TABLE 35. As shown in
Polynucleotides encoding engineered guide RNAs and oligo tethers were tested for SERPINA1 RNA editing of the E342K. Cell experiments were run as described above, but with RNA editing assessed at 24 hours post-transfection. Sequences of the engineered guide RNA sequences used in this experiment are described in TABLE 36.
While preferred embodiments of the present disclosure have been shown and described herein, such embodiments are provided by way of example only. Numerous variations, changes, and substitutions can occur without departing from the present disclosure. It should be understood that various alternatives to the embodiments described herein may be employed.
This application claims priority under 35 U.S.C. § 119 from Provisional Application Ser. No. 63/112,452, filed Nov. 11, 2020, Provisional Application Ser. No. 63/119,754, filed Dec. 1, 2020, Provisional Application Ser. No. 63/153,070, filed Feb. 24, 2021, Provisional Application Ser. No. 63/178,159, filed Apr. 22, 2021, and Provisional Application Ser. No. 63/193,373, filed May 26, 2021, the disclosures of which are incorporated herein by reference in their entirety.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/US2021/058799 | 11/10/2021 | WO |
| Number | Date | Country | |
|---|---|---|---|
| 63112452 | Nov 2020 | US | |
| 63119754 | Dec 2020 | US | |
| 63153070 | Feb 2021 | US | |
| 63178159 | Apr 2021 | US | |
| 63193373 | May 2021 | US |
