Patent Application
20230365996
The present invention relates to methods for gene-editing cells to introduce a RAG1 polypeptide, for example as a treatment for severe combined immunodeficiency. The present invention also relates to polynucleotides, vectors, guide RNAs, kits, compositions, and gene editing systems for use in said methods. The present invention also relates to genomes and cells obtained or obtainable by said methods.
The RAG1 and RAG2 proteins initiate V(D)J recombination, allowing generation of a diverse repertoire of T and B cells (Teng G, Schatz DG. Advances in Immunology. 2015;128:1-39). RAG mutations in humans cause a broad spectrum of phenotypes, including T- B- SCID, Omenn syndrome (OS), atypical SCID (AS) and combined immunodeficiency with granuloma/autoimmunity (CID-G/AI) (Notarangelo LD, et al. Nat Rev Immunol. 2016; 16(4):234-246).
Hematopoietic stem cell transplantation (HSCT) is the mainstay for severe forms of RAG1 deficiency, including T- B- SCID, OS and AS with an overall survival of ~80% after transplantation from donors other than matched siblings (Haddad E, et al. Blood. 2018;132(17):1737-49). However, overall survival rate is lower in non-matched-sibling donors and a high rate of graft failure and poor T and B cell immune reconstitution are observed in the absence of myeloablative or reduced intensity conditioning. Besides donor type and conditioning, other factors associated with worse outcomes after HSCT include age (>3.5 months of life) and infections at the time of transplantation.
An alternative approach to overcome the obstacles with HSCT is represented by gene therapy. Selective advantage of gene-corrected hematopoietic stem cells (HSCs) to overcome the block of T and B cells that occur in the absence of RAG activity represents the rationale for developing such a strategy. In recent years, lentiviral vectors have become the strategy of choice to deliver the transgene of interest, and allow its expression under the control of suitable promoters (Naldini L, Nature. 2015;526:351-360). In the case of RAG1 deficiency, the observation that endogenous RAG1 gene expression is tightly regulated during cell cycle and during lymphoid development, may expose to the risk that ectopic or dysregulated gene expression could lead to immune dysregulation or leukemia (Lagresle-Peyrou C, et al. Blood. 2006;107(1):63-72; Pike-Overzet K, et al. Leukemia. 2011;25(9):1471-83; and Pike-Overzet K, et al. Journal of Allergy and Clinical Immunology . 2014;134:242-243). Several groups have examined the safety and efficacy of lentivirus-mediated gene therapy for RAG deficiency in preclinical models showing poor immune reconstitution or severe signs of inflammation, with cellular infiltrates in the skin, lung, liver, kidney, and presence of circulating anti-double strand DNA (van Til NP, et al. J Allergy Clin Immunol. 2014;133(4):1116-23).
Overall, these data raise significant concerns on the clinical use of conventional RAG1 gene therapy vectors that allow suboptimal levels and deregulated pattern of gene expression.
Thus, there is a demand for improved treatments for RAG1 deficiency.
The present inventors have developed a gene editing strategy to correct mutations in the RAG1 gene by targeting the genomic region located at the 5′ of the second exon, which contains the entire coding sequence of the gene.
The present inventors have designed and selected a panel of CRISPR-Cas9 nucleases and identified specific sites in non-repeated regions of the first intron of the human RAG1 gene. The present inventors have identified guide RNAs and optimal conditions for the delivery of the CRISPR-Cas9 nuclease ribonucleoprotein complexes. In parallel, the present inventors have developed a donor DNA carrying the human RAG1 cDNA.
The gene editing strategy allows a high level of activity (measured as frequency of NHEJ-mutagenesis) and targeting efficiency (measured as GFP expression), both in a surrogate cell line deficient in RAG1 expression and expressing a recombination cassette, and in humans CD34+ HSCs obtained from mobilized peripheral blood (mPB). High editing efficiencies were reached in mobilized peripheral blood (mPB) CD34+ cells using the gene editing strategy.
In one aspect, the present invention provides a polynucleotide comprising from 5′ to 3′: a first homology region, a splice acceptor sequence, a nucleotide sequence encoding a RAG1 polypeptide, and a second homology region.
In another aspect, the present invention provides a polynucleotide comprising from 5′ to 3′: a first homology region, a nucleotide sequence encoding a RAG1 polypeptide, and a second homology region.
In some embodiments:
In some embodiments, the first homology region is homologous to a first region of the RAG1 intron 1 and the second homology region is homologous to a second region of the RAG1 intron 1.
In some embodiments, the first homology region is homologous to a first region of the RAG1 intron 1 and the second homology region is homologous to a second region of the RAG1 exon 2.
In some embodiments, the first homology region is homologous to a first region of the RAG1 exon 2 and the second homology region is homologous to a second region of the RAG1 exon 2.
In some embodiments:
In some embodiments:
In preferred embodiments, the first homology region is homologous to a region upstream of chr 11: 36569295 and the second homology region is homologous to a region downstream of chr 11: 36569298.
In some embodiments, the first homology region is homologous to a region upstream of chr 11: 36573790 and the second homology region is homologous to a region downstream of chr 11: 36573793.
In some embodiments, the first homology region is homologous to a region upstream of chr 11: 36573641 and the second homology region is homologous to a region downstream of chr 11: 36573644.
In some embodiments, the first homology region is homologous to a region upstream of chr 11: 36573351 and the second homology region is homologous to a region downstream of chr 11: 36573354.
In some embodiments, the first homology region is homologous to a region upstream of chr 11: 36569080 and the second homology region is homologous to a region downstream of chr 11: 36569083.
In some embodiments, the first homology region is homologous to a region upstream of chr 11: 36572472 and the second homology region is homologous to a region downstream of chr 11: 36572475.
In some embodiments, the first homology region is homologous to a region upstream of chr 11: 36571458 and the second homology region is homologous to a region downstream of chr 11: 36571461.
In some embodiments, the first homology region is homologous to a region upstream of chr 11: 36571366 and the second homology region is homologous to a region downstream of chr 11: 36571369.
In some embodiments, the first homology region is homologous to a region upstream of chr 11: 36572859 and the second homology region is homologous to a region downstream of chr 11: 36572862.
In some embodiments, the first homology region is homologous to a region upstream of chr 11: 36571457 and the second homology region is homologous to a region downstream of chr 11: 36571460.
In some embodiments, the first homology region is homologous to a region upstream of chr 11: 36569351 and the second homology region is homologous to a region downstream of chr 11: 36569354.
In some embodiments, the first homology region is homologous to a region upstream of chr 11: 36572375 and the second homology region is homologous to a region downstream of chr 11: 36572378.
In preferred embodiments, the first homology region is homologous to a region comprising chr 11: 36569245-chr 11: 36569294 and/or the second homology region is homologous to a region comprising chr 11: 36569299-chr 11: 36569348.
In some embodiments, the 3′ terminal sequence of the first homology region comprises or consists of a nucleotide sequence that has at least 70% identity to SEQ ID NO: 7 and/or the 5′ terminal sequence of the second homology region comprises or consists of a nucleotide sequence that has at least 70% identity to SEQ ID NO: 19.
In some embodiments, the first homology region comprises or consists of a nucleotide sequence that has at least 70% identity to SEQ ID NO: 31, or a fragment thereof and/or the second homology region comprises or consists of a nucleotide sequence that has at least 70% identity to SEQ ID NO: 32, or a fragment thereof.
In some embodiments, the first and second homology regions are each 50-1000 bp in length, 100-500 bp in length, or 200-400 bp in length.
In some embodiments, the nucleotide sequence encoding a RAG1 polypeptide comprises or consists of a nucleotide sequence encoding an amino acid sequence that has at least 70% identity to SEQ ID NO: 4 or SEQ ID NO: 5.
In some embodiments, the nucleotide sequence encoding a RAG1 polypeptide comprises or consists of a nucleotide sequence that has at least 70% identity to SEQ ID NO: 6.
In some embodiments, the splice acceptor site comprises or consists of a nucleotide sequence that has at least 70% identity to SEQ ID NO: 33.
In preferred embodiments, the nucleotide sequence encoding a RAG1 polypeptide is operably linked to a polyadenylation sequence, optionally wherein the polyadenylation sequence is a bGH polyadenylation sequence.
In some embodiments, the nucleotide sequence encoding a RAG1 polypeptide is operably linked to a polyadenylation sequence comprising or consisting of a nucleotide sequence that has at least 70% identity to SEQ ID NO: 35.
In some embodiments, the nucleotide sequence encoding a RAG1 polypeptide is operably linked a Kozak sequence, optionally wherein the Kozak sequence comprises or consists of a nucleotide sequence that has at least 70% identity to SEQ ID NO: 36.
In some embodiments, the polynucleotide comprises or consists of a nucleotide sequence that has at least 70% identity to SEQ ID NO: 39.
In another aspect, the present invention provides a vector comprising the polynucleotide of the invention.
In some embodiments, the vector is a viral vector, optionally an adeno-associated viral (AAV) vector such as an AAV6 vector. In some embodiments, the vector is a lentiviral vector, such as an integration-defective lentiviral vector (IDLV).
In another aspect, the present invention provides a guide RNA comprising or consisting of a nucleotide sequence that has at least 90% identity to any of SEQ ID NOs: 41-52.
In another aspect, the present invention provides a guide RNA comprising or consisting of a nucleotide sequence that has at least 90% identity to any of SEQ ID NOs: 53-55.
In preferred embodiments, the guide RNA comprises or consists of a nucleotide sequence that has at least 90% identity to SEQ ID NO: 41. In preferred embodiments, the guide RNA comprises or consists of a nucleotide sequence that has at least 90% identity to SEQ ID NO: 53. In some embodiments, the guide RNA comprises or consists of a nucleotide sequence that has at least 90% identity to SEQ ID NO: 42. In some embodiments, the guide RNA comprises or consists of a nucleotide sequence that has at least 90% identity to SEQ ID NO: 43. In some embodiments, the guide RNA comprises or consists of a nucleotide sequence that has at least 90% identity to SEQ ID NO: 44. In some embodiments, the guide RNA comprises or consists of a nucleotide sequence that has at least 90% identity to SEQ ID NO: 45. In some embodiments, the guide RNA comprises or consists of a nucleotide sequence that has at least 90% identity to SEQ ID NO: 46. In some embodiments, the guide RNA comprises or consists of a nucleotide sequence that has at least 90% identity to SEQ ID NO: 47. In some embodiments, the guide RNA comprises or consists of a nucleotide sequence that has at least 90% identity to SEQ ID NO: 48. In some embodiments, the guide RNA comprises or consists of a nucleotide sequence that has at least 90% identity to SEQ ID NO: 49. In some embodiments, the guide RNA comprises or consists of a nucleotide sequence that has at least 90% identity to SEQ ID NO: 50. In some embodiments, the guide RNA comprises or consists of a nucleotide sequence that has at least 90% identity to SEQ ID NO: 51. In some embodiments, the guide RNA comprises or consists of a nucleotide sequence that has at least 90% identity to SEQ ID NO: 52. In some embodiments, the guide RNA comprises or consists of a nucleotide sequence that has at least 90% identity to SEQ ID NO: 54. In some embodiments, the guide RNA comprises or consists of a nucleotide sequence that has at least 90% identity to SEQ ID NO: 55.
In some embodiments, from one to five of the terminal nucleotides at 5′ end and/or 3′ end of the guide RNA are chemically modified to enhance stability, optionally wherein three terminal nucleotides at 5′ end and/or 3′ end if the guide RNA are chemically modified to enhance stability, optionally wherein the chemical modification is modification with 2′-O-methyl 3′phosphorothioate.
In another aspect, the present invention provides a kit comprising the polynucleotide or the vector of the invention.
In another aspect, the present invention provides a composition comprising the polynucleotide or the vector of the invention.
In another aspect, the present invention provides a gene-editing system comprising the polynucleotide or the vector of the invention.
In some embodiments, the kit, composition, or gene-editing system further comprises a guide RNA of the invention. In some embodiments, the kit, composition, or gene-editing system further comprises a RNA-guided nuclease, optionally wherein the RNA-guided nuclease is a Cas9 endonuclease
In another aspect, the present invention provides for use of the polynucleotide, the vector, the kit, the composition, or the gene-editing system, for gene editing a cell or a population of cells. In some embodiments, the use is ex vivo or in vitro use.
In another aspect, the present invention provides a genome comprising the polynucleotide of the invention.
In another aspect, the present invention provides a genome comprising a splice acceptor sequence and a nucleotide sequence encoding a RAG1 polypeptide located in the RAG1 intron 1 or RAG1 exon 2. In some embodiments, the splice acceptor sequence and the nucleotide sequence encoding RAG1 are located in the RAG1 intron 1.
In some embodiments:
In some embodiments:
In some embodiments, the splice acceptor sequence and the nucleotide sequence encoding RAG1 replace chr 11: 36569295 to chr 11: 36569298.
In another aspect, the present invention provides a cell comprising the polynucleotide, the vector, or the genome of the invention.
In another aspect, the present invention provides a population of cells comprising one or more cells of the present invention.
In another aspect, the present invention provides a method of gene editing a population of cells comprising delivering the polynucleotide or the vector of the invention to a population of cells to obtain a population of gene-edited cells. In some embodiments, the method is an ex vivo or in vitro method.
In another aspect, the present invention provides a method of treating immunodeficiency in a subject in need thereof, comprising delivering the polynucleotide or the vector of the invention to a population of cells to obtain a population of gene-edited cells and administering the population of gene-edited cells to the subject.
In another aspect, the present invention provides a population of gene-edited cells obtainable by the method of the invention.
In another aspect, the present invention provides the polynucleotide, the vector, the guide RNA, the kit, the composition, or the gene-editing system, for use in treating immunodeficiency in a subject.
In another aspect, the present invention provides a method of treating a subject comprising administering a cell, a population of cells, or a population of gene edited cells of the present invention to the subject.
In another aspect, the present invention provides a method of treating immunodeficiency in a subject in need thereof comprising administering a cell, a population of cells, or a population of gene edited cells of the present invention to the subject.
In another aspect, the present invention provides a cell, a population of cells, or a population of gene edited cells of the present invention for use as a medicament.
In another aspect, the present invention provides a cell, a population of cells, or a population of gene edited cells of the present invention for use in treating immunodeficiency in a subject.
It must be noted that as used herein and in the appended claims, the singular forms “a”, “an”, and “the” include plural referents unless the context clearly dictates otherwise.
The terms “comprising”, “comprises” and “comprised of′ as used herein are synonymous with “including”, “includes” or “containing”, “contains”, and are inclusive or open-ended and do not exclude additional, non-recited members, elements or method steps. The terms “comprising”, “comprises” and “comprised of” also include the term “consisting of”.
Numeric ranges are inclusive of the numbers defining the range. Unless otherwise indicated, any nucleic acid sequences are written left to right in 5′ to 3′ orientation; amino acid sequences are written left to right in amino to carboxy orientation, respectively.
All recited genomic locations are based on human genome assembly GRCh38.p13 (GCF_000001405.39). One of skill in the art will be able to identify the corresponding genome locations in alternative genome assemblies and convert the recited genomic location accordingly. For example, RAG1 is located at chr 11: 36510353 to 36579762 in assembly GRCh38.p13 and at chr 11: 36532053 to 36601312 in assembly GRCh37.p13.
The publications discussed herein are provided solely for their disclosure prior to the filing date of the present application. Nothing herein is to be construed as an admission that such publications constitute prior art to the claims appended hereto.
The present invention relates to methods for gene-editing cells to introduce a RAG1 polypeptide, for example as a treatment for severe combined immunodeficiency. The present invention also relates to polynucleotides, vectors, guide RNAs, kits, compositions, and gene editing systems for use in said methods, and genomes and cells obtained or obtainable by said methods.
“RAG1” is the abbreviated name of the polypeptide encoded by recombination activating gene 1 and is also known as RAG-1, RNF74, and recombination activating 1.
RAG1 is the catalytic component of the RAG complex, a multiprotein complex that mediates the DNA cleavage phase during V(D)J recombination. V(D)J recombination assembles a diverse repertoire of immunoglobulin and T-cell receptor genes in developing B and T-lymphocytes through rearrangement of different V (variable), in some cases D (diversity), and J (joining) gene segments. In the RAG complex, RAG1 mediates the DNA-binding to the conserved recombination signal sequences (RSS) and catalyses the DNA cleavage activities by introducing a double-strand break between the RSS and the adjacent coding segment. RAG2 is not a catalytic component but is required for all known catalytic activities.
A “RAG1 polypeptide” is a polypeptide having RAG1 activity, for example a polypeptide which is able to form a RAG complex, mediate DNA-binding to the RSS, and introduce a double-strand break between the RSS and the adjacent coding segment. Suitably, a RAG1 polypeptide may have the same or similar activity to a wild-type RAG1, e.g. may have at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 100%, at least 110%, at least 120%, at least 130%, at least 140%, or at least 150% of the activity of a wild-type RAG1 polypeptide.
The RAG1 polypeptide may be a fragment of RAG1 and/or a RAG1 variant.
A “fragment of RAG1” may refer to a portion or region of a full-length RAG1 polypeptide that has the same of similar activity as a full-length RAG1 polypeptide, i.e. the fragment may be a functional fragment. The fragment may have at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, or 100% of the activity of a full-length RAG1 polypeptide. A person skilled in the art would be able to generate fragments based on the known structural and functional features of RAG1. These are described, for instance, in Arbuckle, J.L., et al., 2011. BMC biochemistry, 12(1), p.23; Ru, H., et al., 2015. Cell, 163(5), pp.1138-1152; and Kim, M.S., et al., 2015. Nature, 518(7540), pp.507-511.
The minimal regions of RAG1 required for catalysis have been identified. These regions are referred to as the core proteins. Core RAG1 consists of multiple structural domains, termed the nonamer binding domain (NBD; residues 389-464), the central domain (residues 528-760), and the C-terminal domain (residues 761-980) domains. Besides the ability to recognize the RSS nonamer and heptamer through the NBD and the central domain, respectively, core RAG1 contains the essential acidic active site residues (Arbuckle, J.L., et al., 2011. BMC biochemistry, 12(1), p.23). Suitably, a fragment of RAG1 comprises the nonamer binding domain, the central domain, and/or the C-terminal domain.
A “RAG1 variant” may include an amino acid sequence or a nucleotide sequence which may be at least 50%, at least 55%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85% or at least 90% identical, optionally at least 95% or at least 97% or at least 99% identical to a wild-type RAG1 polypeptide. RAG1 variants may have the same or similar activity to a wild-type RAG1 polypeptide, e.g. may have at least at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 100%, at least 110%, at least 120%, at least 130%, at least 140%, or at least 150% of the activity of a wild-type RAG1 polypeptide. A person skilled in the art would be able to generate RAG1 variants based on the known structural and functional features of RAG1 and/or using conservative substitutions.
The gene encoding RAG1 (NCBI gene ID: 5896) is located in the human genome at chr 11: 36510353 to 36579762.
Several alternative mRNAs are transcribed from the RAG1 gene. Transcript variant 1 (NM_000448) has two exons and one intron. As used herein, the region of the RAG1 gene corresponding to the first exon of transcript variant 1 is called the “RAG1 exon 1”, the region of the RAG1 gene corresponding to the intron of transcript variant 1 is called the “RAG1 intron 1”, and the region of the RAG1 gene corresponding to the second exon (which encodes a RAG1 polypeptide) is called the “RAG1 exon 2”.
Suitably, the RAG1 exon 1 is from chr 11: 36568006 to chr 11: 36568122; the RAG1 intron 1 is from chr 11: 36568123 to chr 11: 36573290; and/or the RAG1 exon 2 is from chr 11: 36573291 to chr 11: 36579762.
Suitably, the RAG1 exon 1 consists of the nucleotide sequence of SEQ ID NO: 1, or variants thereof; the RAG1 intron 1 consists of the nucleotide sequence of SEQ ID NO: 2, or variants thereof; and/or the RAG1 exon 2 consists of the nucleotide sequence of SEQ ID NO: 3, or variants thereof.
Illustrative RAG1 exon 1 (SEQ ID NO: 1)
Illustrative RAG1 intron 1 (SEQ ID NO: 2)
Illustrative RAG1 exon 2 (SEQ ID NO: 3)
In the illustrative RAG1 exon 2 (SEQ ID NO: 3), upper case letters indicate a nucleotide sequence which encodes a RAG1 polypeptide.
The RAG1 polypeptide may be a human RAG1 polypeptide. Suitably, the RAG1 polypeptide may comprise or consist of a polypeptide sequence of UniProtKB accession P15918, or a fragment or variant thereof.
In some embodiments of the invention, the RAG1 polypeptide comprises or consists of an amino acid sequence which is at least 70% identical to SEQ ID NO: 4 or a fragment thereof. Suitably, the RAG1 polypeptide comprises or consists of an amino acid sequence which is at least 80%, at least 85%, at least 90%, at least 95%, at least 98% or at least 99% identical to SEQ ID NO: 4 or a fragment thereof.
In some embodiments, the RAG1 polypeptide comprises or consists of SEQ ID NO: 4 or a fragment thereof.
RAG1 polypeptide isoform 1, UniProtKB accession P15918 (SEQ ID NO: 4)
In some embodiments of the invention, the RAG1 polypeptide comprises or consists of an amino acid sequence which is at least 70% identical to SEQ ID NO: 5 or a fragment thereof. Suitably, the RAG1 polypeptide comprises or consists of an amino acid sequence which is at least 80%, at least 85%, at least 90%, at least 95%, at least 98% or at least 99% identical to SEQ ID NO: 5 or a fragment thereof.
In some embodiments, the RAG1 polypeptide comprises or consists of SEQ ID NO: 5 or a fragment thereof.
RAG1 polypeptide isoform 2, UniProtKB accession P15918 (SEQ ID NO: 5)
The nucleotide sequence encoding a RAG1 polypeptide may be codon-optimised. Suitably, the nucleotide sequence encoding a RAG1 polypeptide may be codon optimised for expression in a human cell.
Different cells differ in their usage of particular codons. This codon bias corresponds to a bias in the relative abundance of particular tRNAs in the cell type. By altering the codons in the sequence so that they are tailored to match with the relative abundance of corresponding tRNAs, it is possible to increase expression. By the same token, it is possible to decrease expression by deliberately choosing codons for which the corresponding tRNAs are known to be rare in the particular cell type. Thus, an additional degree of translational control is available. Codon usage tables are known in the art for mammalian cells (e.g. humans), as well as for a variety of other organisms.
In some embodiments of the invention, the nucleotide sequence encoding a RAG1 polypeptide comprises or consists of a nucleotide sequence which is at least 70% identical to SEQ ID NO: 6 or a fragment thereof. Suitably, the nucleotide sequence encoding a RAG1 polypeptide comprises or consists of a nucleotide sequence which is at least 80%, at least 85%, at least 90%, at least 95%, at least 98% or at least 99% identical to SEQ ID NO: 6 or a fragment thereof.
In some embodiments of the invention, the nucleotide sequence encoding a RAG1 polypeptide comprises or consists of the nucleotide sequence SEQ ID NO: 6 or a fragment thereof.
Exemplary nucleotide sequence encoding a RAG1 polypeptide (SEQ ID NO: 6)
In one aspect, the present invention provides a polynucleotide comprising from 5′ to 3′: a first homology region, a splice acceptor sequence, a nucleotide sequence encoding a RAG1 polypeptide, and a second homology region. The polynucleotide may be an isolated polynucleotide. The polynucleotide may be a DNA molecule, e.g. a double-stranded DNA molecule.
Suitably, the polynucleotide of the invention may be limited to a size suitable to be inserted into a vector (e.g. an adeno-associated viral (AAV) vector, such as AAV6). Suitably, the polynucleotide of the invention may be 5.0 kb or less, 4.9 kb or less, 4.8 kb or less, 4.7 kb or less, 4.6 kb or less, 4.5 kb or less, 4.4 kb or less, 4.3 kb or less, 4.2 kb or less, 4.1 kb or less, 4.0 kb or less in total size. In some embodiments, the polynucleotide of the invention is 4.1 kb or less or 4.0 kb or less in size.
In another aspect, the present invention provides a genome comprising a splice acceptor sequence and a nucleotide sequence encoding a RAG1 polypeptide. Suitably, the genome may comprise the polynucleotide of the present invention. The genome may be an isolated genome. The genome may be a mammalian genome, e.g. a human genome.
A “homology region” (also known as “homology arm”) is a nucleotide sequence which is located upstream or downstream of a nucleotide sequence to be inserted (a “nucleotide sequence insert” e.g. a splice acceptor sequence and a nucleotide sequence encoding a RAG1 polypeptide). The polynucleotide of the present invention comprises two homology regions, one upstream of the nucleotide sequence insert (the “first homology region”) and one downstream of the nucleotide insert (the “second homology region”).
Each “homology region” is designed such that the nucleotide sequence insert can be introduced into a genome at a site of a double strand break (DSB) by homology-directed repair (HDR). One of skill in the art will be able to design homology arms depending on the desired insertion site (i.e. the site of the DSB) (see e.g. Ran, F.A., et al., 2013. Nature protocols, 8(11), pp.2281-2308). Each “homology region” is homologous to a region either side of the DSB. For example, the first homology region may be homologous to a region upstream of the DSB and the second homology region may be homologous to a region downstream of the DSB.
As used herein, the term “homologous” means that the nucleotide sequences are similar or identical. For example, the nucleotide sequences may be at least 70% identical, at least 75% identical, at least 80% identical, at least 85% identical, at least 90% identical, at least 95% identical, at least 98% identical, at least 99% identical, or 100% identical.
As used herein, “upstream” and “downstream” both refer to relative positions in DNA or RNA. Each strand of DNA or RNA has a 5′ end and a 3′ end and, by convention, “upstream” and “downstream” relate to the 5′ to 3′ direction respectively in which RNA transcription takes place. For example, when considering double-stranded DNA, “upstream” is toward the 5′ end of the coding strand for the gene in question (e.g. RAG1) and downstream is toward the 3′ end of the coding strand for the gene in question (e.g. RAG1).
The homology regions may be any length suitable for HDR. The homology regions may be the same or different lengths. Suitably, the homology regions are each independently 50-1000 bp in length, 100-500 bp in length, or 200-400 bp in length. For example, the first homology may be 50-1000 bp in length and homologous to a region upstream of a DSB and the second homology region may be 50-1000 bp in length and homologous to a region downstream of the DSB.
In some embodiments:
In some embodiments, the first homology region is homologous to a first region of the RAG1 intron 1 and the second homology region is homologous to a second region of the RAG1 intron 1.
In some embodiments:
In some embodiments:
In some embodiments, the first homology region is homologous to a region upstream of chr 11: 36569295 and the second homology region is homologous to a region downstream of chr 11: 36569298.
In some embodiments:
In some embodiments:
In some embodiments, the first homology region is homologous to a region comprising chr 11: 36569245-36569294 and the second homology region is homologous to a region comprising chr 11: 36569299-36569348.
In some embodiments, the first homology region is homologous to a region comprising chr 11: 36573740-36573789 and the second homology region is homologous to a region comprising chr 11: 36573794-36573843.
In some embodiments, the first homology region is homologous to a region comprising chr 11: 36573591-36573640 and the second homology region is homologous to a region comprising chr 11: 36573645-36573694.
In some embodiments, the first homology region is homologous to a region comprising chr 11: 36573301-36573350 and the second homology region is homologous to a region comprising chr 11: 36573355-36573404.
In some embodiments, the first homology region is homologous to a region comprising chr 11: 36569030-36569079 and the second homology region is homologous to a region comprising chr 11: 36569084-36569133.
In some embodiments, the first homology region is homologous to a region comprising chr 11: 36572422-36572471 and the second homology region is homologous to a region comprising chr 11: 36572476-36572525.
In some embodiments, the first homology region is homologous to a region comprising chr 11: 36571408-36571457 and the second homology region is homologous to a region comprising chr 11: 36571462-36571511.
In some embodiments, the first homology region is homologous to a region comprising chr 11: 36571316-36571365 and the second homology region is homologous to a region comprising chr 11: 36571370-36571419.
In some embodiments, the first homology region is homologous to a region comprising chr 11: 36572809-36572858 and the second homology region is homologous to a region comprising chr 11: 36572863-36572912.
In some embodiments, the first homology region is homologous to a region comprising chr 11: 36571407-36571456 and the second homology region is homologous to a region comprising chr 11: 36571461-36571510.
In some embodiments, the first homology region is homologous to a region comprising chr 11: 36569301-36569350 and the second homology region is homologous to a region comprising chr 11: 36569355-36569404.
In some embodiments, the first homology region is homologous to a region comprising chr 11: 36572325-36572374 and the second homology region is homologous to a region comprising chr 11: 36572379-36572428.
Exemplary homology regions are shown below in Table 1.
In some embodiments, the first homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to any of SEQ ID NOs: 7-18 and/or the second homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to any of SEQ ID NOs: 19-30.
Preferably, the first and second homology regions comprise or consist of nucleotide sequences that have at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to first and second homology regions in the same row of Table 1. Suitably, the first homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to any of SEQ ID NOs: 7-18 and the second homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to the corresponding nucleotide sequence in Table 1 (i.e. SEQ ID NOs: 19-30). For example, in some embodiments:
In some embodiments:
In some embodiments, the first homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 7 and the second homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 19.
In some embodiments, the first homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 8 and the second homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 20.
In some embodiments, the first homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 9 and the second homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 21.
In some embodiments, the first homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 10 and the second homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 22.
In some embodiments, the first homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 11 and the second homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 23.
In some embodiments, the first homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 12 and the second homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 24.
In some embodiments, the first homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 13 and the second homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 25.
In some embodiments, the first homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 14 and the second homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 26.
In some embodiments, the first homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 15 and the second homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 27.
In some embodiments, the first homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 16 and the second homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 28.
In some embodiments, the first homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 17 and the second homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 29.
In some embodiments, the first homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 18 and the second homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 30.
In some embodiments, the first homology region comprises or consists of a nucleotide sequence that has at least 98% identity to SEQ ID NO: 7 and the second homology region comprises or consists of a nucleotide sequence that has at least 98% identity to SEQ ID NO: 19.
In some embodiments, the first homology region comprises or consists of the nucleotide sequence of SEQ ID NO: 7 and the second homology region comprises or consists of the nucleotide sequence of SEQ ID NO: 19.
In some embodiments, the 3′ terminal sequence of the first homology region consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to any of SEQ ID NOs: 7-18 and/or the 5′ terminal sequence of the second homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to any of SEQ ID NOs: 19-30.
Suitably, the 3′ terminal sequence of the first homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to any of SEQ ID NOs: 7-18 and the 5′ terminal sequence of the second homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to the corresponding nucleotide sequence in Table 1 (i.e. SEQ ID NOs: 19-30).
For example, in some embodiments:
In some embodiments:
In some embodiments, the 3′ terminal sequence of the first homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 7 and the 5′ terminal sequence of the second homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 19.
In some embodiments, the 3′ terminal sequence of the first homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 8 and the 5′ terminal sequence of the second homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 20.
In some embodiments, the 3′ terminal sequence of the first homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 9 and the 5′ terminal sequence of the second homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 21.
In some embodiments, the 3′ terminal sequence of the first homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 10 and the 5′ terminal sequence of the second homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 22.
In some embodiments, the 3′ terminal sequence of the first homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 11 and the 5′ terminal sequence of the second homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 23.
In some embodiments, the 3′ terminal sequence of the first homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 12 and the 5′ terminal sequence of the second homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 24.
In some embodiments, the 3′ terminal sequence of the first homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 13 and the 5′ terminal sequence of the second homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 25.
In some embodiments, the 3′ terminal sequence of the first homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 14 and the 5′ terminal sequence of the second homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 26.
In some embodiments, the 3′ terminal sequence of the first homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 15 and the 5′ terminal sequence of the second homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 27.
In some embodiments, the 3′ terminal sequence of the first homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 16 and the 5′ terminal sequence of the second homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 28.
In some embodiments, the 3′ terminal sequence of the first homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 17 and the 5′ terminal sequence of the second homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 29.
In some embodiments, the 3′ terminal sequence of the first homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 18 and the 5′ terminal sequence of the second homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 30.
In some embodiments, the 3′ terminal sequence of the first homology region comprises or consists of a nucleotide sequence that has at least 98% identity to SEQ ID NO: 7 and the 5′ terminal sequence of the second homology region comprises or consists of a nucleotide sequence that has at least 98% identity to SEQ ID NO: 19.
In some embodiments, the 3′ terminal sequence of the first homology region comprises or consists of the nucleotide sequence of SEQ ID NO: 7 and the 5′ terminal sequence of the second homology region comprises or consists of the nucleotide sequence of SEQ ID NO: 19.
In some embodiments, the first homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 31, or a fragment thereof; and the second homology region comprises or consists of a nucleotide sequence that has at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity, or 100% identity to SEQ ID NO: 32, or a fragment thereof. Suitably, the fragments are at least 50 bp in length, for example 50-250 bp or 100-200 bp in length.
In some embodiments, the first homology region comprises or consists of a nucleotide sequence that has at least 98% identity to SEQ ID NO: 31, or a fragment thereof; and the second homology region comprises or consists of a nucleotide sequence that has at least 98% identity to SEQ ID NO: 32, or a fragment thereof.
In some embodiments, the first homology region comprises or consists of the nucleotide of SEQ ID NO: 31, or a fragment thereof, and the second homology region comprises or consists of the nucleotide sequence of SEQ ID NO: 32, or a fragment thereof.
Illustrative first homology region for guide RNA 9 (SEQ ID NO: 31)
Illustrative second homology region for guide RNA 9 (SEQ ID NO: 32)
The site of the double-strand break (DSB) can be introduced specifically by any suitable technique, for example using a CRISPR/Cas9 system and the guide RNAs disclosed herein. In the present invention, the DSB is introduced into the RAG1 intron 1 or RAG1 exon 2. For example, a DSB may be introduced at any of the sites recited in Table 2 below. Optionally, a DSB is introduced into the RAG1 intron 1.
Suitably, each homology region is homologous to a fragment of the RAG1 intron 1 and/or RAG1 exon 2 either side of the DSB. For example, the first homology region may be homologous to a region in the RAG1 intron 1 and/or RAG1 exon 2 upstream of the DSB and the second homology region may be homologous to a region downstream of the DSB.
In the present invention, the nucleotide sequence insert (e.g. a splice acceptor sequence and a nucleotide sequence encoding a RAG1 polypeptide) may be introduced at the DSB site by homology-directed repair (HDR). Thus, the nucleotide insert (e.g. a splice acceptor sequence and a nucleotide sequence encoding a RAG1 polypeptide) may replace the region of the genome flanked by the homology regions and comprising the DSB.
As used herein, the “nucleotide sequence insert” may consist of the region of the polynucleotide flanked by the first homology region and the second homology region. For example, the nucleotide sequence insert may comprise a splice acceptor sequence and a nucleotide sequence encoding a RAG1 polypeptide.
The nucleotide sequence insert may be introduced into a genome at any of the sites recited in Table 2 above. In other words, the genome of the present invention may comprise the nucleotide sequence insert at any of the sites recited in Table 2 above.
In some embodiments, the nucleotide sequence insert is introduced:
In some embodiments, the nucleotide sequence insert is introduced between chr 11: 36569296 and 36569297.
In some embodiments, the genome of the present invention comprises a nucleotide sequence comprising a splice acceptor sequence and a nucleotide sequence encoding a RAG1 polypeptide, which is introduced:
In some embodiments, the genome of the present invention comprises a nucleotide sequence comprising a splice acceptor sequence and a nucleotide sequence encoding a RAG1 polypeptide, which is introduced between chr 11: 36569296 and 36569297.
The nucleotide sequence insert may replace any of the regions recited in Table 3 below. In other words, the genome of the present invention may comprise the nucleotide sequence insert replacing any of the regions recited in Table 3.
In some embodiments, the nucleotide sequence insert replaces:
In some embodiments, the nucleotide sequence insert replaces chr 11: 36569295 to 36569298.
In some embodiments, the genome of the present invention comprises a nucleotide sequence comprising a splice acceptor sequence and a nucleotide sequence encoding a RAG1 polypeptide, which replaces:
In some embodiments, the genome of the present invention comprises a nucleotide sequence comprising a splice acceptor sequence and a nucleotide sequence encoding a RAG1 polypeptide, which replaces chr 11: 36569295 to 36569298.
RNA splicing is a form of RNA processing in which a newly made precursor messenger RNA (pre-mRNA) transcript is transformed into a mature messenger RNA (mRNA). During splicing, introns (non-coding regions) are removed and exons (coding regions) are joined together.
Within introns, a donor site (5′ end of the intron), a branch site (near the 3′ end of the intron) and an acceptor site (3′ end of the intron) are required for splicing. The splice donor site includes an almost invariant sequence GU at the 5′ end of the intron, within a larger, less highly conserved region. The splice acceptor site at the 3′ end of the intron terminates the intron with an almost invariant AG sequence. Upstream (5′-ward) from the AG there is a region high in pyrimidines (C and U), or polypyrimidine tract. Further upstream from the polypyrimidine tract is the branchpoint.
A “splice acceptor sequence” is a nucleotide sequence which can function as an acceptor site at the 3′ end of the intron. Consensus sequences and frequencies of human splice site regions are described in Ma, S.L., et al., 2015. PLoS One, 10(6), p.e0130729.
Suitably, the splice acceptor sequence may comprise the nucleotide sequence (Y)nNYAG, where n is 10-20, or a variant with at least 90% or at least 95% sequence identity. Suitably, the splice acceptor sequence may comprise the sequence (Y)nNCAG, where n is 10-20, or a variant with at least 90% or at least 95% sequence identity.
In some embodiments of the invention, the splice acceptor sequence comprises or consists of a nucleotide sequence which is at least 70% identical to SEQ ID NO: 33 or a fragment thereof. Suitably, the splice acceptor sequence comprises or consists of a nucleotide sequence which is at least 80%, at least 85%, at least 90%, at least 95%, at least 98% or at least 99% identical to SEQ ID NO: 33 or a fragment thereof.
In some embodiments of the invention, the splice acceptor sequence comprises or consists of the nucleotide sequence SEQ ID NO: 33 or a fragment thereof.
Exemplary splice acceptor sequence (SEQ ID NO: 33)
The polynucleotide of the invention may comprise a splice donor sequence. The genome may comprise a splice donor sequence in the RAG1 intron 1. Suitably, the splice donor sequence nucleotide sequence is 3′ of the nucleotide sequence encoding a RAG1 polypeptide. The splice donor sequence may be used to provide an mRNA comprising the RAG1 polypeptide and RAG1 exon 2.
A “splice donor sequence” is a nucleotide sequence which can function as a donor site at the 5′ end of the intron. Consensus sequences and frequencies of human splice site regions are describe in Ma, S.L., et al., 2015. PLoS One, 10(6), p.e0130729.
In some embodiments of the invention, the splice donor sequence comprises or consists of a nucleotide sequence which is at least 85% identical to SEQ ID NO: 34 or a fragment thereof. In some embodiments of the invention, the splice donor sequence comprises or consists of the nucleotide sequence SEQ ID NO: 34 or a fragment thereof.
Exemplary splice donor sequence (SEQ ID NO: 34)
In some embodiments of the invention, the polynucleotide of the invention does not comprise a splice donor sequence.
The polynucleotide of the invention may comprise one or more regulatory elements which may act pre- or post-transcriptionally. Suitably, the nucleotide sequence encoding a RAG1 polypeptide is operably linked to one or more regulatory elements which may act pre- or post-transcriptionally. The one or more regulatory elements may facilitate expression of the RAG1 polypeptide in the cells of the invention.
A “regulatory element” is any nucleotide sequence which facilitates expression of a polypeptide, e.g. acts to increase expression of a transcript or to enhance mRNA stability. Suitable regulatory elements include for example promoters, enhancer elements, post-transcriptional regulatory elements and polyadenylation sites.
The polynucleotide of the invention may comprise a polyadenylation sequence. Suitably, the nucleotide sequence encoding a RAG1 polypeptide is operably linked to a polyadenylation sequence. The polyadenylation sequence may improve gene expression.
Suitable polyadenylation sequences will be well known to those of skill in the art. Suitable polyadenylation sequences include a bovine growth hormone (BGH) polyadenylation sequence or an early SV40 polyadenylation signal. In some embodiments of the invention, the polyadenylation sequence is a BGH polyadenylation sequence.
In some embodiments of the invention, the polyadenylation sequence comprises or consists of a nucleotide sequence which is at least 70% identical to SEQ ID NO: 35, 62 or 65 or a fragment thereof. Suitably, the polyadenylation sequence comprises or consists of a nucleotide sequence which is at least 80%, at least 85%, at least 90%, at least 95%, at least 98% or at least 99% identical to SEQ ID NO: 35, 62 or 65 or a fragment thereof.
In some embodiments of the invention, the polyadenylation sequence comprises or consists of the nucleotide sequence SEQ ID NO: 35, 62 or 65 or a fragment thereof.
Exemplary BGH polyadenylation sequence (SEQ ID NO: 35)
Exemplary BGH polyadenylation sequence (SEQ ID NO: 62)
Exemplary BGH polyadenylation sequence (SEQ ID NO: 65)
The polynucleotide of the invention may comprise a Kozak sequence. Suitably, the nucleotide sequence encoding a RAG1 polypeptide is operably linked to a Kozak sequence. A Kozak sequence may be inserted before the start codon of the RAG1 polypeptide to improve the initiation of translation.
Suitable Kozak sequences will be well known to those of skill in the art.
In some embodiments of the invention, the Kozak sequence comprises or consists of a nucleotide sequence which is at least 70% identical to SEQ ID NO: 36 or a fragment thereof. Suitably, the Kozak sequence comprises or consists of a nucleotide sequence which is at least 80%, or at least 90% identical to SEQ ID NO: 36 or a fragment thereof.
In some embodiments of the invention, the Kozak sequence comprises or consists of the nucleotide sequence SEQ ID NO: 36 or a fragment thereof.
Exemplary Kozak sequence (SEQ ID NO: 36)
The polynucleotide of the invention may comprise a post-transcriptional regulatory element. Suitably, the nucleotide sequence encoding a RAG1 polypeptide is operably linked to a post-transcriptional regulatory element. The post-transcriptional regulatory element may improve gene expression.
Suitable post-transcriptional regulatory elements will be well known to those of skill in the art.
The polynucleotide of the invention may comprise a Woodchuck Hepatitis Virus Post-transcriptional Regulatory Element (WPRE). Suitably, the nucleotide sequence encoding a RAG1 polypeptide is operably linked to a WPRE.
In some embodiments of the invention, the WPRE comprises or consists of a nucleotide sequence which is at least 70% identical to SEQ ID NO: 37 or a fragment thereof. Suitably, the WPRE comprises or consists of a nucleotide sequence which is at least 80%, or at least 90% identical to SEQ ID NO: 37 or a fragment thereof.
In some embodiments of the invention, the WPRE comprises or consists of the nucleotide sequence SEQ ID NO: 37 or a fragment thereof.
Exemplary WPRE (SEQ ID NO: 37)
In some embodiments of the invention, the RAG1 polypeptide is not operably linked to a post-transcriptional regulatory element. In some embodiments of the invention, the RAG1 polypeptide is not operably linked to a WPRE.
The polynucleotide of the invention may comprise an endogenous RAG1 3′UTR. Suitably, the nucleotide sequence encoding a RAG1 polypeptide is operably linked to an endogenous RAG1 3′UTR.
In some embodiments of the invention, the RAG1 3′UTR comprises or consists of a nucleotide sequence which is at least 70% identical to SEQ ID NO: 38 or a fragment thereof. Suitably, the RAG1 3′UTR comprises or consists of a nucleotide sequence which is at least 80%, or at least 90% identical to SEQ ID NO: 38 or a fragment thereof.
In some embodiments of the invention, the RAG1 3′UTR comprises or consists of the nucleotide sequence SEQ ID NO: 38 or a fragment thereof.
Exemplary RAG1 3′UTR (SEQ ID NO: 38)
In some embodiments of the invention, the RAG1 polypeptide is not operably linked to a RAG1 3′UTR.
The polynucleotide of the invention may comprise a further coding sequence. The polynucleotide of the invention may comprise an internal ribosome entry site sequence (IRES). The IRES may increase or allow expression of the further coding sequence. The IRES may be operably linked to the further coding sequence.
In some embodiments of the invention, the IRES comprises or consists of a nucleotide sequence which is at least 70% identical to SEQ ID NO: 63 or a fragment thereof. Suitably, the IRES comprises or consists of a nucleotide sequence which is at least 80%, or at least 90% identical to SEQ ID NO: 63 or a fragment thereof.
In some embodiments of the invention, the IRES comprises or consists of the nucleotide sequence SEQ ID NO: 63 or a fragment thereof.
Exemplary IRES (SEQ ID NO: 63)
The further coding sequence may encode a selector, for example a NGFR receptor, e.g. a low affinity NGFR, such as a C-terminal truncated low affinity NGFR. The selector may be used for enrichment of cells.
In some embodiments of the invention, the NGFR-encoding sequence comprises or consists of a nucleotide sequence which is at least 70% identical to SEQ ID NO: 64 or a fragment thereof. Suitably, the NGFR-encoding sequence comprises or consists of a nucleotide sequence which is at least 80%, or at least 90% identical to SEQ ID NO: 64 or a fragment thereof.
In some embodiments of the invention, the NGFR-encoding sequence comprises or consists of the nucleotide sequence SEQ ID NO: 64 or a fragment thereof.
Exemplary NGFR-encoding sequence (SEQ ID NO: 64)
The further coding sequence may encode a destabilisation domain, for example a peptide sequence rich in proline (P), glutamic acid (E), serine (S), and threonine (T) (PEST). Endogenous RAG1 protein may be destabilized by the destabilisation domain, e.g. PEST signal peptide via proteasome degradation.
In some embodiments of the invention, the PEST-encoding sequence comprises or consists of a nucleotide sequence which is at least 70% identical to SEQ ID NO: 66 or a fragment thereof. Suitably, the PEST-encoding sequence comprises or consists of a nucleotide sequence which is at least 80%, or at least 90% identical to SEQ ID NO: 66 or a fragment thereof.
In some embodiments of the invention, the PEST-encoding sequence comprises or consists of the nucleotide sequence SEQ ID NO: 66 or a fragment thereof.
Exemplary PEST-encoding sequence (SEQ ID NO: 66)
Suitably, the nucleotide sequence encoding a RAG1 polypeptide is operably linked to a promoter and/or enhancer element.
A “promoter” is a region of DNA that leads to initiation of transcription of a gene. Promoters are located near the transcription start sites of genes, upstream on the DNA (towards the 5′ region of the sense strand). Any suitable promoter may be used, the selection of which may be readily made by the skilled person.
An “enhancer” is a region of DNA that can be bound by proteins (activators) to increase the likelihood that transcription of a particular gene will occur. Enhancers are cis-acting. They can be located up to 1 Mbp (1,000,000 bp) away from the gene, upstream or downstream from the start site. Any suitable enhancer may be used, the selection of which may be readily made by the skilled person.
Transcription of the nucleotide sequence encoding a RAG1 polypeptide may be driven by an endogenous promoter. For example, if the polynucleotide of the present invention is inserted into the RAG1 intron 1, transcription of the nucleotide sequence encoding a RAG1 polypeptide may be driven by the endogenous RAG1 promoter.
In some embodiments of the invention, the polynucleotide of the invention does not comprise a promoter and/or enhancer element. In some embodiments of the invention, the genome of the invention does not comprise a promoter and/or enhancer element (e.g. an exogenous promoter and/or enhancer element) in the RAG1 intron 1.
In some embodiments, the polynucleotide of the invention comprises, essentially consists of, or consists of from 5′ to 3′: a first homology region, a splice acceptor sequence, a nucleotide sequence encoding a RAG1 polypeptide, a polyadenylation sequence and a second homology region.
In some embodiments, the polynucleotide of the invention comprises, essentially consists of, or consists of from 5′ to 3′: a first homology region, a splice acceptor sequence, a kozak sequence, a nucleotide sequence encoding a RAG1 polypeptide, a polyadenylation sequence and a second homology region.
In some embodiments, the polynucleotide of the invention comprises, essentially consists of, or consists of from 5′ to 3′: a first homology region, a splice acceptor sequence, a nucleotide sequence encoding a RAG1 polypeptide, a WPRE, a polyadenylation sequence and a second homology region.
In some embodiments, the polynucleotide of the invention comprises, essentially consists of, or consists of from 5′ to 3′: a first homology region, a splice acceptor sequence, a kozak sequence, a nucleotide sequence encoding a RAG1 polypeptide, a WPRE, a polyadenylation sequence and a second homology region.
In some embodiments, the polynucleotide of the invention comprises, essentially consists of, or consists of from 5′ to 3′: a first homology region, a splice acceptor sequence, a kozak sequence, a nucleotide sequence encoding a RAG1 polypeptide, a 3′ UTR, a polyadenylation sequence and a second homology region.
In some embodiments, the polynucleotide of the invention comprises, essentially consists of, or consists of from 5′ to 3′: a first homology region, a splice acceptor sequence, a kozak sequence, a nucleotide sequence encoding a RAG1 polypeptide, an IRES, a nucleotide sequence encoding a selector (e.g. NGFR), a polyadenylation sequence and a second homology region.
In some embodiments, the polynucleotide of the invention comprises, essentially consists of, or consists of from 5′ to 3′: a first homology region, a splice acceptor sequence, a kozak sequence, a nucleotide sequence encoding a RAG1 polypeptide, an IRES, a nucleotide sequence encoding a destabilisation domain (e.g. a PEST sequence), a splice donor sequence, and a second homology region.
In some embodiments, the polynucleotide of the invention comprises, essentially consists of, or consists of from 5′ to 3′: a first homology region, a splice acceptor sequence, a nucleotide sequence encoding a RAG1 polypeptide, a splice donor sequence and a second homology region.
In some embodiments, the polynucleotide of the invention comprises or consists of a nucleotide sequence that has at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% identity to SEQ ID NO: 39.
In some embodiments, the polynucleotide of the invention comprises or consists of the nucleotide sequence of SEQ ID NO: 39.
In some embodiments, the genome of the invention comprises a nucleotide sequence that has at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% identity to SEQ ID NO: 39.
In some embodiments, the genome of the invention comprises the nucleotide sequence of SEQ ID NO: 39.
In some embodiments, the genome of the invention comprises a nucleotide sequence that has at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% identity to nucleotides 297-3687 of SEQ ID NO: 39 or nucleotides 291-3693 of SEQ ID NO: 39.
In some embodiments, the genome of the invention comprises the nucleotide sequence of nucleotides 297-3687 of SEQ ID NO: 39 or nucleotides 291-3693 of SEQ ID NO: 39.
Exemplary polynucleotide (SEQ ID NO: 39)
In some embodiments, the genome of the invention comprises a nucleotide sequence that has at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% identity to SEQ ID NO: 40.
In some embodiments, the genome of the invention comprises the nucleotide sequence of SEQ ID NO: 40.
Exemplary nucleotide sequence insert (SEQ ID NO: 40)
In addition to the specific proteins and nucleotides mentioned herein, the invention also encompasses variants, derivatives, and fragments thereof.
In the context of the invention, a “variant” of any given sequence is a sequence in which the specific sequence of residues (whether amino acid or nucleic acid residues) has been modified in such a manner that the polypeptide or polynucleotide in question retains at least one of its endogenous functions. For example, a variant of RAG1 may retain the ability to form a RAG complex, mediate DNA-binding to the RSS, and introduce a double-strand break between the RSS and the adjacent coding segment. A variant sequence can be obtained by addition, deletion, substitution, modification, replacement and/or variation of at least one residue present in the naturally occurring polypeptide or polynucleotide.
The term “derivative” as used herein in relation to proteins or polypeptides of the invention includes any substitution of, variation of, modification of, replacement of, deletion of and/or addition of one (or more) amino acid residues from or to the sequence, providing that the resultant protein or polypeptide retains at least one of its endogenous functions. For example, a derivative of RAG1 may retain the ability to form a RAG complex, mediate DNA-binding to the RSS, and introduce a double-strand break between the RSS and the adjacent coding segment.
Typically, amino acid substitutions may be made, for example from 1, 2 or 3, to 10 or 20 substitutions, provided that the modified sequence retains the required activity or ability. Amino acid substitutions may include the use of non-naturally occurring analogues.
Proteins used in the invention may also have deletions, insertions or substitutions of amino acid residues which produce a silent change and result in a functionally equivalent protein. Deliberate amino acid substitutions may be made on the basis of similarity in polarity, charge, solubility, hydrophobicity, hydrophilicity and/or the amphipathic nature of the residues as long as the endogenous function is retained. For example, negatively charged amino acids include aspartic acid and glutamic acid; positively charged amino acids include lysine and arginine; and amino acids with uncharged polar head groups having similar hydrophilicity values include asparagine, glutamine, serine, threonine and tyrosine.
Conservative substitutions may be made, for example according to the table below. Amino acids in the same block in the second column and in the same line in the third column may be substituted for each other:
Typically, a variant may have a certain identity with the wild type amino acid sequence or the wild type nucleotide sequence.
In the present context, a variant sequence is taken to include an amino acid sequence which may be at least 50%, 55%, 65%, 75%, 85% or 90% identical, suitably at least 95%, 96% or 97% or 98% or 99% identical to the subject sequence. Although a variant can also be considered in terms of similarity (i.e. amino acid residues having similar chemical properties/functions), in the context of the present invention it is preferred to express in terms of sequence identity.
In the present context, a variant sequence is taken to include a nucleotide sequence which may be at least 50%, 55%, 65%, 75%, 85% or 90% identical, suitably at least 95%, 96% or 97% or 98% or 99% identical to the subject sequence. Although a variant can also be considered in terms of similarity, in the context of the present invention it is preferred to express it in terms of sequence identity.
Suitably, reference to a sequence which has a percent identity to any one of the SEQ ID NOs detailed herein refers to a sequence which has the stated percent identity over the entire length of the SEQ ID NO referred to.
Sequence identity comparisons can be conducted by eye, or more usually, with the aid of readily available sequence comparison programs. These commercially available computer programs can calculate percent identity between two or more sequences.
Percent identity may be calculated over contiguous sequences, i.e. one sequence is aligned with the other sequence and each amino acid or nucleotide in one sequence is directly compared with the corresponding amino acid or nucleotide in the other sequence, one residue at a time. This is called an “ungapped” alignment. Typically, such ungapped alignments are performed only over a relatively short number of residues.
Although this is a very simple and consistent method, it fails to take into consideration that, for example, in an otherwise identical pair of sequences, one insertion or deletion in the amino acid or nucleotide sequence may cause the following residues or codons to be put out of alignment, thus potentially resulting in a large reduction in percent identity when a global alignment is performed. Consequently, most sequence comparison methods are designed to produce optimal alignments that take into consideration possible insertions and deletions without penalising unduly the overall identity score. This is achieved by inserting “gaps” in the sequence alignment to try to maximise local identity.
However, these more complex methods assign “gap penalties” to each gap that occurs in the alignment so that, for the same number of identical amino acids or nucleotides, a sequence alignment with as few gaps as possible, reflecting higher relatedness between the two compared sequences, will achieve a higher score than one with many gaps. “Affine gap costs” are typically used that charge a relatively high cost for the existence of a gap and a smaller penalty for each subsequent residue in the gap. This is the most commonly used gap scoring system. High gap penalties will of course produce optimised alignments with fewer gaps. Most alignment programs allow the gap penalties to be modified. However, it is preferred to use the default values when using such software for sequence comparisons. For example when using the GCG Wisconsin Bestfit package the default gap penalty for amino acid sequences is -12 for a gap and -4 for each extension.
Calculation of maximum percent identity therefore firstly requires the production of an optimal alignment, taking into consideration gap penalties. A suitable computer program for carrying out such an alignment is the GCG Wisconsin Bestfit package (University of Wisconsin, USA; Devereux et al. (1984) Nucleic Acids Research 12: 387). Examples of other software that can perform sequence comparisons include, but are not limited to, the BLAST package (see Ausubel et al. (1999) ibid - Ch. 18), FASTA (Atschul et al. (1990) J. Mol. Biol. 403-410), EMBOSS Needle (Madeira, F., et al., 2019. Nucleic acids research, 47(W1), pp.W636-W641) and the GENEWORKS suite of comparison tools. Both BLAST and FASTA are available for offline and online searching (see Ausubel et al. (1999) ibid, pages 7-58 to 7-60). However, for some applications, it is preferred to use the GCG Bestfit program. Another tool, BLAST 2 Sequences, is also available for comparing protein and nucleotide sequences (FEMS Microbiol. Lett. (1999) 174(2):247-50; FEMS Microbiol. Lett. (1999) 177(1):187-8).
Although the final percent identity can be measured, the alignment process itself is typically not based on an all-or-nothing pair comparison. Instead, a scaled similarity score matrix is generally used that assigns scores to each pairwise comparison based on chemical similarity or evolutionary distance. An example of such a matrix commonly used is the BLOSUM62 matrix (the default matrix for the BLAST suite of programs). GCG Wisconsin programs generally use either the public default values or a custom symbol comparison table if supplied (see the user manual for further details). For some applications, it is preferred to use the public default values for the GCG package, or in the case of other software, the default matrix, such as BLOSUM62.
Once the software has produced an optimal alignment, it is possible to calculate percent sequence identity. The software typically does this as part of the sequence comparison and generates a numerical result. The percent sequence identity may be calculated as the number of identical residues as a percentage of the total residues in the SEQ ID NO referred to.
“Fragments” are also variants and the term typically refers to a selected region of the polypeptide or polynucleotide that is of interest either functionally or, for example, in an assay.
“Fragment” thus refers to an amino acid or nucleic acid sequence that is a portion of a full-length polypeptide or polynucleotide.
Such variants, derivatives, and fragments may be prepared using standard recombinant DNA techniques such as site-directed mutagenesis. Where insertions are to be made, synthetic DNA encoding the insertion together with 5′ and 3′ flanking regions corresponding to the naturally-occurring sequence either side of the insertion site may be made. The flanking regions will contain convenient restriction sites corresponding to sites in the naturally-occurring sequence so that the sequence may be cut with the appropriate enzyme(s) and the synthetic DNA ligated into the cut. The DNA is then expressed in accordance with the invention to make the encoded protein. These methods are only illustrative of the numerous standard techniques known in the art for manipulation of DNA sequences and other known techniques may also be used.
In one aspect, the present invention provides a vector comprising the polynucleotide of the invention.
The vector may be suitable for editing a genome using the polynucleotide of the invention. The vector may be used to deliver the polynucleotide into the cell. Subsequently, the nucleotide sequence insert can be introduced into a genome at a site of a double strand break (DSB) by homology-directed repair (HDR).
The vector of the present invention may be capable of transducing mammalian cells, for example human cells. Suitably, the vector of the present invention is capable of transducing HSCs, HPCs, and/or LPCs. Suitably, the vector of the present invention is capable of transducing CD34+ cells. Suitably, the vector of the present invention is capable of transducing NALM6, K562, and/or other human cell lines (e.g. Molt4, U937, etc.). Suitably, the vector of the present invention is capable of transducing T cells.
Suitably, the vector of the present invention is a viral vector. The vector of the invention may be an adeno-associated viral (AAV) vector, although it is contemplated that other viral vectors may be used e.g. lentiviral vectors (e.g. IDLV vectors), or single or double stranded DNA.
The vector of the present invention may be in the form of a viral vector particle. Suitably, the viral vector of the present invention is in the form of an AAV vector particle. Suitably, the viral vector of the present invention is in the form of a lentiviral vector particle, for example an IDLV vector particle.
Methods of preparing and modifying viral vectors and viral vector particles, such as those derived from AAV, are well known in the art. Suitable methods are described in Ayuso, E., et al., 2010. Current gene therapy, 10(6), pp.423-436, Merten, O.W., et al., 2016. Molecular Therapy-Methods & Clinical Development, 3, p.16017; and Nadeau, I. and Kamen, A., 2003. Biotechnology advances, 20(7-8), pp.475-489.
The vector of the present invention may be an adeno-associated viral (AAV) vector. Optionally, the vector is an AAV6 vector. The vector of the present invention may be in the form of an AAV vector particle. Optionally, the vector is in the form of an AAV6 vector particle.
The AAV vector or AAV vector particle may comprise an AAV genome or a fragment or derivative thereof. An AAV genome is a polynucleotide sequence, which may encode functions needed for production of an AAV particle. These functions include those operating in the replication and packaging cycle of AAV in a host cell, including encapsidation of the AAV genome into an AAV particle. Naturally occurring AAVs are replication-deficient and rely on the provision of helper functions in trans for completion of a replication and packaging cycle. Accordingly, the AAV genome of the AAV vector of the invention is typically replication-deficient.
The AAV genome may be in single-stranded form, either positive or negative-sense, or alternatively in double-stranded form. The use of a double-stranded form allows bypass of the DNA replication step in the target cell and so can accelerate transgene expression.
AAVs occurring in nature may be classified according to various biological systems. The AAV genome may be from any naturally derived serotype, isolate or clade of AAV.
AAV may be referred to in terms of their serotype. A serotype corresponds to a variant subspecies of AAV which, owing to its profile of expression of capsid surface antigens, has a distinctive reactivity which can be used to distinguish it from other variant subspecies. Typically, an AAV vector particle having a particular AAV serotype does not efficiently cross-react with neutralising antibodies specific for any other AAV serotype. AAV serotypes include AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10 and AAV11. The AAV vector of the invention may be an AAV6 serotype.
AAV may also be referred to in terms of clades or clones. This refers to the phylogenetic relationship of naturally derived AAVs, and typically to a phylogenetic group of AAVs which can be traced back to a common ancestor, and includes all descendants thereof. Additionally, AAVs may be referred to in terms of a specific isolate, i.e. a genetic isolate of a specific AAV found in nature. The term genetic isolate describes a population of AAVs which has undergone limited genetic mixing with other naturally occurring AAVs, thereby defining a recognisably distinct population at a genetic level.
Typically, the AAV genome of a naturally derived serotype, isolate or clade of AAV comprises at least one inverted terminal repeat sequence (ITR). An ITR sequence acts in cis to provide a functional origin of replication and allows for integration and excision of the vector from the genome of a cell. ITRs may be the only sequences required in cis next to the therapeutic gene. Suitably, one or more ITR sequences flank the polynucleotide of the invention.
The AAV genome may also comprise packaging genes, such as rep and/or cap genes which encode packaging functions for an AAV particle. A promoter may be operably linked to each of the packaging genes. Specific examples of such promoters include the p5, p19 and p40 promoters. For example, the p5 and p19 promoters are generally used to express the rep gene, while the p40 promoter is generally used to express the cap gene. The rep gene encodes one or more of the proteins Rep78, Rep68, Rep52 and Rep40 or variants thereof. The cap gene encodes one or more capsid proteins such as VP1, VP2 and VP3 or variants thereof.
The AAV genome may be the full genome of a naturally occurring AAV. For example, a vector comprising a full AAV genome may be used to prepare an AAV vector or vector particle.
Suitably, the AAV genome is derivatised for the purpose of administration to patients. Such derivatisation is standard in the art and the invention encompasses the use of any known derivative of an AAV genome, and derivatives which could be generated by applying techniques known in the art. The AAV genome may be a derivative of any naturally occurring AAV. Suitably, the AAV genome is a derivative of AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, or AAV11. Suitably, the AAV genome is a derivative of AAV6.
Derivatives of an AAV genome include any truncated or modified forms of an AAV genome which allow for expression of a transgene from an AAV vector of the invention in vivo. Typically, it is possible to truncate the AAV genome significantly to include minimal viral sequence yet retain the above function. This may reduce the risk of recombination of the vector with wild-type virus, and avoid triggering a cellular immune response by the presence of viral gene proteins in the target cell.
Typically, a derivative will include at least one inverted terminal repeat sequence (ITR), optionally more than one ITR, such as two ITRs or more. One or more of the ITRs may be derived from AAV genomes having different serotypes, or may be a chimeric or mutant ITR.
A suitable mutant ITR is one having a deletion of a trs (terminal resolution site). This deletion allows for continued replication of the genome to generate a single-stranded genome which contains both coding and complementary sequences, i.e. a self-complementary AAV genome. This allows for bypass of DNA replication in the target cell, and so enables accelerated transgene expression.
The AAV genome may comprise one or more ITR sequences from any naturally derived serotype, isolate or clade of AAV or a variant thereof. The AAV genome may comprise at least one, such as two, AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, or AAV11 ITRs, or variants thereof.
The one or more ITRs may flank the nucleotide sequence of the invention at either end. The inclusion of one or more ITRs is can aid concatamer formation of the AAV vector in the nucleus of a host cell, for example following the conversion of single-stranded vector DNA into double-stranded DNA by the action of host cell DNA polymerases. The formation of such episomal concatamers protects the AAV vector during the life of the host cell, thereby allowing for prolonged expression of the transgene in vivo.
Suitably, ITR elements will be the only sequences retained from the native AAV genome in the derivative. Suitably, a derivative may not include the rep and/or cap genes of the native genome and any other sequences of the native genome. This may reduce the possibility of integration of the vector into the host cell genome. Additionally, reducing the size of the AAV genome allows for increased flexibility in incorporating other sequence elements (such as regulatory elements) within the vector in addition to the transgene.
The following portions could therefore be removed in a derivative of the invention: one inverted terminal repeat (ITR) sequence, the replication (rep) and capsid (cap) genes. However, derivatives may additionally include one or more rep and/or cap genes or other viral sequences of an AAV genome. Naturally occurring AAV integrates with a high frequency at a specific site on human chromosome 19, and shows a negligible frequency of random integration, such that retention of an integrative capacity in the AAV vector may be tolerated in a therapeutic setting.
The invention additionally encompasses the provision of sequences of an AAV genome in a different order and configuration to that of a native AAV genome. The invention also encompasses the replacement of one or more AAV sequences or genes with sequences from another virus or with chimeric genes composed of sequences from more than one virus. Such chimeric genes may be composed of sequences from two or more related viral proteins of different viral species.
The AAV vector particle may be encapsidated by capsid proteins. Suitably, the AAV vector particles may be transcapsidated forms wherein an AAV genome or derivative having an ITR of one serotype is packaged in the capsid of a different serotype. The AAV vector particle also includes mosaic forms wherein a mixture of unmodified capsid proteins from two or more different serotypes makes up the viral capsid. The AAV vector particle also includes chemically modified forms bearing ligands adsorbed to the capsid surface. For example, such ligands may include antibodies for targeting a particular cell surface receptor.
Where a derivative comprises capsid proteins i.e. VP1, VP2 and/or VP3, the derivative may be a chimeric, shuffled or capsid-modified derivative of one or more naturally occurring AAVs. In particular, the invention encompasses the provision of capsid protein sequences from different serotypes, clades, clones, or isolates of AAV within the same vector (i.e. a pseudotyped vector). The AAV vector may be in the form of a pseudotyped AAV vector particle.
Chimeric, shuffled or capsid-modified derivatives will be typically selected to provide one or more desired functionalities for the AAV vector. Thus, these derivatives may display increased efficiency of gene delivery and/or decreased immunogenicity (humoral or cellular) compared to an AAV vector comprising a naturally occurring AAV genome. Increased efficiency of gene delivery, for example, may be effected by improved receptor or co-receptor binding at the cell surface, improved internalisation, improved trafficking within the cell and into the nucleus, improved uncoating of the viral particle and improved conversion of a single-stranded genome to double-stranded form.
Chimeric capsid proteins include those generated by recombination between two or more capsid coding sequences of naturally occurring AAV serotypes. This may be performed for example by a marker rescue approach in which non-infectious capsid sequences of one serotype are co-transfected with capsid sequences of a different serotype, and directed selection is used to select for capsid sequences having desired properties. The capsid sequences of the different serotypes can be altered by homologous recombination within the cell to produce novel chimeric capsid proteins.
Chimeric capsid proteins also include those generated by engineering of capsid protein sequences to transfer specific capsid protein domains, surface loops or specific amino acid residues between two or more capsid proteins, for example between two or more capsid proteins of different serotypes.
Shuffled or chimeric capsid proteins may also be generated by DNA shuffling or by error-prone PCR. Hybrid AAV capsid genes can be created by randomly fragmenting the sequences of related AAV genes e.g. those encoding capsid proteins of multiple different serotypes and then subsequently reassembling the fragments in a self-priming polymerase reaction, which may also cause crossovers in regions of sequence homology. A library of hybrid AAV genes created in this way by shuffling the capsid genes of several serotypes can be screened to identify viral clones having a desired functionality. Similarly, error prone PCR may be used to randomly mutate AAV capsid genes to create a diverse library of variants which may then be selected for a desired property.
The sequences of the capsid genes may also be genetically modified to introduce specific deletions, substitutions or insertions with respect to the native wild-type sequence. In particular, capsid genes may be modified by the insertion of a sequence of an unrelated protein or peptide within an open reading frame of a capsid coding sequence, or at the N-and/or C-terminus of a capsid coding sequence. The unrelated protein or peptide may advantageously be one which acts as a ligand for a particular cell type, thereby conferring improved binding to a target cell or improving the specificity of targeting of the vector to a particular cell population. The unrelated protein may also be one which assists purification of the viral particle as part of the production process, i.e. an epitope or affinity tag. The site of insertion will typically be selected so as not to interfere with other functions of the viral particle e.g. internalisation, trafficking of the viral particle.
The capsid protein may be an artificial or mutant capsid protein. The term “artificial capsid” as used herein means that the capsid particle comprises an amino acid sequence which does not occur in nature or which comprises an amino acid sequence which has been engineered (e.g. modified) from a naturally occurring capsid amino acid sequence. In other words the artificial capsid protein comprises a mutation or a variation in the amino acid sequence compared to the sequence of the parent capsid from which it is derived where the artificial capsid amino acid sequence and the parent capsid amino acid sequences are aligned. The AAV vector particle may comprise an AAV6 capsid protein.
The vector of the present invention may be a retroviral vector or a lentiviral vector. The vector of the present invention may be a retroviral vector particle or a lentiviral vector particle.
A retroviral vector may be derived from or may be derivable from any suitable retrovirus. A large number of different retroviruses have been identified. Examples include murine leukaemia virus (MLV), human T-cell leukaemia virus (HTLV), mouse mammary tumour virus (MMTV), Rous sarcoma virus (RSV), Fujinami sarcoma virus (FuSV), Moloney murine leukaemia virus (Mo-MLV), FBR murine osteosarcoma virus (FBR MSV), Moloney murine sarcoma virus (Mo-MSV), Abelson murine leukaemia virus (A-MLV), avian myelocytomatosis virus-29 (MC29) and avian erythroblastosis virus (AEV).
Retroviruses may be broadly divided into two categories, “simple” and “complex”. Retroviruses may be even further divided into seven groups. Five of these groups represent retroviruses with oncogenic potential. The remaining two groups are the lentiviruses and the spumaviruses.
The basic structure of retrovirus and lentivirus genomes share many common features such as a 5′ LTR and a 3′ LTR. Between or within these are located a packaging signal to enable the genome to be packaged, a primer binding site, integration sites to enable integration into a host cell genome, and gag, pol and env genes encoding the packaging components - these are polypeptides required for the assembly of viral particles. Lentiviruses have additional features, such as rev and RRE sequences in HIV, which enable the efficient export of RNA transcripts of the integrated provirus from the nucleus to the cytoplasm of an infected target cell.
In the provirus, these genes are flanked at both ends by regions called long terminal repeats (LTRs). The LTRs are responsible for proviral integration and transcription. LTRs also serve as enhancer-promoter sequences and can control the expression of the viral genes.
The LTRs themselves are identical sequences that can be divided into three elements: U3, R and U5. U3 is derived from the sequence unique to the 3′ end of the RNA. R is derived from a sequence repeated at both ends of the RNA. U5 is derived from the sequence unique to the 5′ end of the RNA. The sizes of the three elements can vary considerably among different retroviruses.
In a defective retroviral vector genome gag, pol and env may be absent or not functional.
In a typical retroviral vector, at least part of one or more protein coding regions essential for replication may be removed from the virus. This makes the viral vector replication-defective. Portions of the viral genome may also be replaced by a library encoding candidate modulating moieties operably linked to a regulatory control region and a reporter moiety in the vector genome in order to generate a vector comprising candidate modulating moieties which is capable of transducing a target host cell and/or integrating its genome into a host genome.
Lentivirus vectors are part of the larger group of retroviral vectors. In brief, lentiviruses can be divided into primate and non-primate groups. Examples of primate lentiviruses include but are not limited to human immunodeficiency virus (HIV), the causative agent of human acquired immunodeficiency syndrome (AIDS); and simian immunodeficiency virus (SIV). Examples of non-primate lentiviruses include the prototype “slow virus” visna/maedi virus (VMV), as well as the related caprine arthritis-encephalitis virus (CAEV), equine infectious anaemia virus (EIAV), and the more recently described feline immunodeficiency virus (FIV) and bovine immunodeficiency virus (BIV).
The lentivirus family differs from retroviruses in that lentiviruses have the capability to infect both dividing and non-dividing cells. In contrast, other retroviruses, such as MLV, are unable to infect non-dividing or slowly dividing cells such as those that make up, for example, muscle, brain, lung and liver tissue.
A lentiviral vector, as used herein, is a vector which comprises at least one component part derivable from a lentivirus. Suitably, that component part is involved in the biological mechanisms by which the vector infects cells, expresses genes or is replicated.
The lentiviral vector may be a “primate” vector. The lentiviral vector may be a “non-primate” vector (i.e. derived from a virus which does not primarily infect primates, especially humans). Examples of non-primate lentiviruses may be any member of the family of lentiviridae which does not naturally infect a primate.
As examples of lentivirus-based vectors, HIV-1- and HIV-2-based vectors are described below.
The HIV-1 vector contains cis-acting elements that are also found in simple retroviruses. It has been shown that sequences that extend into the gag open reading frame are important for packaging of HIV-1. Therefore, HIV-1 vectors often contain the relevant portion of gag in which the translational initiation codon has been mutated. In addition, most HIV-1 vectors also contain a portion of the env gene that includes the RRE. Rev binds to RRE, which permits the transport of full-length or singly spliced mRNAs from the nucleus to the cytoplasm. In the absence of Rev and/or RRE, full-length HIV-1 RNAs accumulate in the nucleus. Alternatively, a constitutive transport element from certain simple retroviruses such as Mason-Pfizer monkey virus can be used to relieve the requirement for Rev and RRE. Efficient transcription from the HIV-1 LTR promoter requires the viral protein Tat.
Most HIV-2-based vectors are structurally very similar to HIV-1 vectors. Similar to HIV-1-based vectors, HIV-2 vectors also require RRE for efficient transport of the full-length or singly spliced viral RNAs.
Optionally, the viral vector used in the present invention has a minimal viral genome.
By “minimal viral genome” it is to be understood that the viral vector has been manipulated so as to remove the non-essential elements and to retain the essential elements in order to provide the required functionality to infect, transduce and deliver a nucleotide sequence of interest to a target host cell. Further details of this strategy can be found in WO 1998/017815.
Optionally, the plasmid vector used to produce the viral genome within a host cell/packaging cell will have sufficient lentiviral genetic information to allow packaging of an RNA genome, in the presence of packaging components, into a viral particle which is capable of infecting a target cell, but is incapable of independent replication to produce infectious viral particles within the final target cell. Optionally, the vector lacks a functional gag-pol and/or env gene and/or other genes essential for replication.
However, the plasmid vector used to produce the viral genome within a host cell/packaging cell will also include transcriptional regulatory control sequences operably linked to the lentiviral genome to direct transcription of the genome in a host cell/packaging cell. These regulatory sequences may be the natural sequences associated with the transcribed viral sequence (i.e. the 5′ U3 region), or they may be a heterologous promoter, such as another viral promoter (e.g. the CMV promoter).
The vectors may be self-inactivating (SIN) vectors in which the viral enhancer and promoter sequences have been deleted. SIN vectors can be generated and transduce non-dividing cells in vivo with an efficacy similar to that of wild-type vectors. The transcriptional inactivation of the long terminal repeat (LTR) in the SIN provirus should prevent mobilisation by replication-competent virus. This should also enable the regulated expression of genes from internal promoters by eliminating any cis-acting effects of the LTR.
The vectors may be integration-defective. Integration defective lentiviral vectors (IDLVs) can be produced, for example, either by packaging the vector with catalytically inactive integrase (such as an HIV integrase bearing the D64V mutation in the catalytic site) or by modifying or deleting essential att sequences from the vector LTR, or by a combination of the above.
The vector of the present invention may be an adenoviral vector. The vector of the present invention may be an adenoviral vector particle.
The adenovirus is a double-stranded, linear DNA virus that does not go through an RNA intermediate. There are over 50 different human serotypes of adenovirus divided into 6 subgroups based on the genetic sequence homology. The natural targets of adenovirus are the respiratory and gastrointestinal epithelia, generally giving rise to only mild symptoms. Serotypes 2 and 5 (with 95% sequence homology) are most commonly used in adenoviral vector systems and are normally associated with upper respiratory tract infections in the young.
Adenoviruses have been used as vectors for gene therapy and for expression of heterologous genes. The large (36 kb) genome can accommodate up to 8 kb of foreign insert DNA and is able to replicate efficiently in complementing cell lines to produce very high titres of up to 1012. Adenovirus is thus one of the best systems to study the expression of genes in primary non-replicative cells.
The expression of viral or foreign genes from the adenovirus genome does not require a replicating cell. Adenoviral vectors enter cells by receptor mediated endocytosis. Once inside the cell, adenovirus vectors rarely integrate into the host chromosome. Instead, they function episomally (independently from the host genome) as a linear genome in the host nucleus. Hence the use of recombinant adenovirus alleviates the problems associated with random integration into the host genome.
The vector of the present invention may be a herpes simplex viral vector. The vector of the present invention may be a herpes simplex viral vector particle.
Herpes simplex virus (HSV) is a neurotropic DNA virus with favorable properties as a gene delivery vector. HSV is highly infectious, so HSV vectors are efficient vehicles for the delivery of exogenous genetic material to cells. Viral replication is readily disrupted by null mutations in immediate early genes that in vitro can be complemented in trans, enabling straightforward production of high-titre pure preparations of non-pathogenic vector. The genome is large (152 Kb) and many of the viral genes are dispensable for replication in vitro, allowing their replacement with large or multiple transgenes. Latent infection with wild-type virus results in episomal viral persistence in sensory neuronal nuclei for the duration of the host lifetime. The vectors are non-pathogenic, unable to reactivate and persist long-term. The latency active promoter complex can be exploited in vector design to achieve long-term stable transgene expression in the nervous system. HSV vectors transduce a broad range of tissues because of the wide expression pattern of the cellular receptors recognized by the virus. Increasing understanding of the processes involved in cellular entry has allowed targeting the tropism of HSV vectors.
The vector of the present invention may be a vaccinia viral vector. The vector of the present invention may be a vaccinia viral vector particle.
Vaccinia virus is large enveloped virus that has an approximately 190 kb linear, double-stranded DNA genome. Vaccinia virus can accommodate up to approximately 25 kb of foreign DNA, which also makes it useful for the delivery of large genes.
A number of attenuated vaccinia virus strains are known in the art that are suitable for gene therapy applications, for example the MVA and NYVAC strains.
The vector of the present invention may be used to deliver a polynucleotide into a cell. Subsequently, a nucleotide sequence insert can be introduced into the cell’s genome at a site of a double strand break (DSB) by homology-directed repair (HDR). The site of the double-strand break (DSB) can be introduced specifically by any suitable technique, for example by using an RNA-guided gene editing system.
An “RNA-guided gene editing system” can be used to introduce a DSB and typically comprises a guide RNA and a RNA-guided nuclease. A CRISPR/Cas9 system is an example of a commonly used RNA-guided gene editing system, but other RNA-guided gene editing systems may also be used.
A “guide RNA” (gRNA) confers target sequence specificity to a RNA-guided nuclease. Guide RNAs are non-coding short RNA sequences which bind to the complementary target DNA sequences. For example, in the CRISPR/Cas9 system, guide RNA first binds to the Cas9 enzyme and the gRNA sequence guides the resulting complex via base-pairing to a specific location on the DNA, where Cas9 performs its nuclease activity by cutting the target DNA strand.
The term “guide RNA” encompasses any suitable gRNA that can be used with any RNA-guided nuclease, and not only those gRNAs that are compatible with a particular nuclease such as Cas9.
The guide RNA may comprise a trans-activating CRISPR RNA (tracrRNA) that provides the stem loop structure and a target-specific CRISPR RNA (crRNA) designed to cleave the gene target site of interest. The tracrRNA and crRNA may be annealed, for example by heating them at 95° C. for 5 minutes and letting them slowly cool down to room temperature for 10 minutes. Alternatively, the guide RNA may be a single guide RNA (sgRNA) that consists of both the crRNA and tracrRNA as a single construct.
The guide RNA may comprise of a 3′-end, which forms a scaffold for nuclease binding, and a 5′-end which is programmable to target different DNA sites. For example, the targeting specificity of CRISPR-Cas9 may be determined by the 15-25 bp sequence at the 5′ end of the guide RNA. The desired target sequence typically precedes a protospacer adjacent motif (PAM) which is a short DNA sequence usually 2-6 bp in length that follows the DNA region targeted for cleavage by the CRISPR system, such as CRISPR-Cas9. The PAM is required for a Cas nuclease to cut and is typically found 3-4 bp downstream from the cut site. After base pairing of the guide RNA to the target, Cas9 mediates a double strand break about 3-nt upstream of PAM.
Numerous tools exist for designing guide RNAs (e.g. Cui, Y., et al., 2018. Interdisciplinary Sciences: Computational Life Sciences, 10(2), pp.455-465). For example, COSMID is a web-based tool for identifying and validating guide RNAs (Cradick TJ, et al. Mol Ther - Nucleic Acids. 2014;3(12):e214).
A list of exemplary guide RNAs for use in the present invention is provided below in Table 4.
In one aspect, the present invention provides a guide RNA comprising or consisting of a nucleotide sequence that has at least 90% identity or at least 95% identity to any of SEQ ID NOs: 41-52, optionally wherein the guide RNA comprises or consists of a nucleotide sequence that has at least 90% identity or at least 95% identity to SEQ ID NO: 41.
In some embodiments, the guide RNA comprises or consists of the nucleotide sequence of any of SEQ ID NOs: 41-52, optionally wherein the guide RNA comprises or consists of the nucleotide sequence of SEQ ID NO: 41.
For example, sequences for guides 9, 3 and 7 may be extended as shown below, for example when used as crRNA:
In one aspect, the present invention provides a guide RNA comprising or consisting of a nucleotide sequence that has at least 90% identity or at least 95% identity to any of SEQ ID NOs: 53-55, optionally wherein the guide RNA comprises or consists of a nucleotide sequence that has at least 90% identity or at least 95% identity to SEQ ID NO: 53.
In some embodiments, the guide RNA comprises or consists of the nucleotide sequence of any of SEQ ID NOs: 53-55, optionally wherein the guide RNA comprises or consists of the nucleotide sequence of SEQ ID NO: 53.
Suitably, the guide RNA is chemically modified. The chemical modification may enhance the stability of the guide RNA. For example, from one to five (e.g. three) of the terminal nucleotides at 5′ end and/or 3′ end of the guide RNA may be chemically modified to enhance stability.
Any chemical modification which enhances the stability of the guide RNA may be used. For example, the chemical modification may be modification with 2′-O-methyl 3′-phosphorothioate, as described in Hendel A, et al. Nat Biotechnol. 2015;33(9):985-9.
A “nuclease” is an enzyme that can cleave the phosphodiester bond present within a polynucleotide chain. Suitably, the nuclease is an endonuclease. Endonucleases are capable of breaking the bond from the middle of a chain.
An “RNA-guided nuclease” is a nuclease which can be directed to a specific site by a guide RNA. The present invention can be implemented using any suitable RNA-guided nuclease, for example any RNA-guided nuclease described in Murugan, K., et al., 2017. Molecular cell, 68(1), pp.15-25. RNA-guided nucleases include, but are not limited to, Type II CRISPR nucleases such as Cas9, and Type V CRISPR nucleases such as Cas12a and Cas12b, as well as other nucleases derived therefrom. RNA-guided nucleases can be defined, in broad terms, by their PAM specificity and cleavage activity.
Suitably, the RNA-guided nuclease is a Type II CRISPR nuclease, for example a Cas9 nuclease. Cas9 is a dual RNA-guided endonuclease enzyme associated with the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) adaptive immune system. Cas9 nucleases include the well-characterized ortholog from Streptococcus pyogenes (SpCas9). SpCas9 and other orthologs (including SaCas9, FnCa9, and AnaCas9) have been reviewed by Jiang, F. and Doudna, J.A., 2017. Annual review of biophysics, 46, pp.505-529.
The RNA-guided nuclease may be in a complex with the guide RNA, i.e. the guide RNA and the RNA-guided nuclease may together form a ribonucleoprotein (RNP). Suitably, the RNP is a Cas9 RNP. A RNP may be formed by any method known in the art, for example by incubating a RNA-guided nuclease with a guide RNA for 5-30 minutes at room temperature. Delivering Cas9 as a preassembled RNP can protect the guide RNA from intracellular degradation thus improving stability and activity of the RNA-guided nuclease (Kim S, et al. Genome Res. 2014;24(6):1012-9).
In one aspect, the present invention provides a kit, composition, or gene-editing system comprising the polynucleotide of the invention, the vector of the invention, and/or the guide RNA of the invention.
As used herein, a “gene-editing system” is a system which comprises all components necessary to edit a genome using the polynucleotide of the invention.
In some embodiments, the kit, composition, or gene-editing system comprises a polynucleotide and/or vector of the invention and a guide RNA. The guide RNA may correspond to the same DSB site targeted by the homology arms. For example, in some embodiments the kit, composition, or gene-editing system comprises:
In some embodiments, the kit, composition, or gene-editing system comprises:
In some embodiments, the kit, composition, or gene-editing system comprises:
In some embodiments, the kit, composition, or gene-editing system comprises:
In some embodiments, the kit, composition, or gene-editing system comprises:
The kit, composition, or gene-editing system may further comprise an RNA-guided nuclease. Suitably, the RNA-guided nuclease corresponds to the guide RNA used. For example, if the guide RNA comprises or consists of a nucleotide sequence that has at least 90% identity, at least 95% identity or 100% identity to any one of SEQ ID NOs: 41-52, the RNA-guided nuclease is suitably a Cas9 endonuclease. For example, if the guide RNA comprises or consists of a nucleotide sequence that has at least 90% identity, at least 95% identity or 100% identity to any one of SEQ ID NOs: 53-55, the RNA-guided nuclease is suitably a Cas9 endonuclease.
The RNA-guided nuclease may be in a complex with the guide RNA, i.e. the guide RNA and the RNA-guided nuclease together form a ribonucleoprotein (RNP).
In one aspect, the present invention provides a cell which has been edited using the polynucleotide, vector, kit, composition, or gene-editing system of the present invention.
In a related aspect, the present invention provides a cell comprising the polynucleotide, vector and/or genome of the present invention.
Suitably, the cell is an isolated cell. Suitably, the cell is a mammalian cell, for example a human cell.
Suitably, the cell is a hematopoietic stem cell (HSC), a hematopoietic progenitor cell (HPC), or a lymphoid progenitor cell (LPC). In some embodiments, the cell is a HSC or a HPC, optionally the cell is a HSC.
As used herein “hematopoietic stem cells” are stem cells that have no differentiation potential to cells other than hematopoietic cells, “hematopoietic progenitor cells” are progenitor cells that have no differentiation potential to cells other than hematopoietic cells, and “lymphoid progenitor cells” are progenitor cells that have no differentiation potential to cells other than lymphocytes.
The cell can be obtained from any source. The cell may be autologous or allogeneic. The cell may be obtained or obtainable from any biological sample, such as peripheral blood or cord blood. Peripheral blood may be treated with mobilising agent, i.e. may be mobilised peripheral blood. The cell may be a universal cell.
The cell may be isolated or isolatable using commercially available antibodies that bind to cell surface antigens, e.g. CD34, using methods known to those of skill in the art. For example, the antibodies may be conjugated to magnetic beads and immunological procedures utilized to recover the desired cell type. Suitably, the cell is identified by the presence or absence of one or more antigenic markers. Suitable antigenic markers include CD34, CD133, CD90, CD45, CD4, CD19, CD13, CD3, CD56, CD14, CD61/41, CD135, CD45RA, CD33, CD66b, CD38, CD45, CD10, CD11c, CD19, CD7, and CD71.
Suitably, the cell is identified by the presence of the antigenic marker CD34 (CD34+), i.e. the cell is a CD34+ cell. For example, the cell may be a cord blood CD34+ cell or a (mobilised) peripheral blood CD34+ cell. The cell may be a CD34+ HSC, a CD34+ HPC, or a CD34+ LPC, optionally the cell is a CD34+ HSC.
In some embodiments, the cell is identified by the presence of CD34 and the presence or absence or one or more further antigenic markers. The further antigenic markers may be selected from one or more of CD133, CD90, CD3, CD56, CD14, CD61/41, CD135, CD45RA, CD33, CD66b, CD38, CD45, CD10, CD11c, CD19, CD7, and CD71. For example, the cell may be a CD34+CD133+CD90+ cell, a CD34+CD133+CD90- cell, or a CD34+CD133-CD90-cell.
Suitably, the cell is a NALM6 cell, a K562 cell, or other human cell (e.g. a Molt4 cell, a U937 cell, etc.). Suitably, the cell is a T cell.
In one aspect, the present invention provides a population or cells comprising the cell of the present invention. Suitably, at least 1%, at least 2%, at least 5%, at least 10%, or at least 20% of the cells in the population of cells are cells of the present invention. Suitably, the population of cells comprises at least 10×105, at least 50×105, or at least 100×105 cells of the present invention.
In a related aspect, the present invention provides a population of cells which have been edited using the polynucleotide, vector, kit, composition, or gene-editing system of the present invention. Suitably, at least 1%, at least 2%, at least 5%, at least 10%, or at least 20% of the cells in the population of cells are cells which have been edited using the polynucleotide, vector, kit, composition, or gene-editing system of the present invention. Suitably, the population of cells comprises at least 10×105, at least 50×105, or at least 100×105 cells which have been edited using the polynucleotide, vector, kit, composition, or gene-editing system of the present invention.
In a related aspect, the present invention provides a population of cells comprising the polynucleotide, vector and/or genome of the present invention. Suitably, at least 1%, at least 2%, at least 5%, at least 10%, or at least 20% of the cells in the population of cells are cells comprising the polynucleotide, vector and/or genome of the present invention. Suitably, the population of cells comprises at least 10×105, at least 50×105, or at least 100×105 cells comprising the polynucleotide, vector and/or genome of the present invention.
Suitably, the population of cells are mammalian cells, for example human cells. The population of cells may be autologous or allogeneic. Suitably, the population of cells are obtained or obtainable from (mobilised) peripheral blood or cord blood. The population of cells may be universal cells.
Suitably, at least 50%, at least 60%, at least 70%, or at least 80% of the population of cells are HSCs, HPCs, and/or LPCs. Suitably, at least 50%, at least 60%, at least 70%, or at least 80% of the population of cells are CD34+ cells.
In some embodiments, at least 1%, at least 2%, at least 5%, at least 10%, or at least 20% of the population of cells are CD34+ cells comprising the polynucleotide, vector and/or genome of the present invention. For example, in some embodiments at least 20% of the population of cells are CD34+ cells comprising the genome of the present invention.
In some embodiments, the population of cells comprises at least 10×105, at least 50×105, or at least 100×105 CD34+ cells comprising the polynucleotide, vector and/or genome of the present invention. For example, in some embodiments the population of cells comprises at least 100×105 CD34+ cells comprising the genome of the present invention.
In one aspect, the present invention provides a method of gene editing a cell or a population of cells using polynucleotides, vectors, guide RNAs, kits, compositions and/or gene-editing system of the present invention. The present invention also provide a population of gene-edited cells obtained or obtainable by said methods.
In another aspect the present invention provides use of a polynucleotide, vector, guide RNA, kit, composition, and/or gene-editing system of the present invention for gene editing a cell or a population of cells.
Suitably, the method of gene editing a cell or a population of cells comprises:
For example, the method of gene editing a cell or a population of cells comprises:
The gene-edited cell or population of gene-edited cells may be as defined herein. The present invention also provides a gene-edited cell or population of gene-edited cells obtained or obtainable by said method.
The population of cells may be obtained or obtainable from any suitable source. Suitably, the population of cells are obtained or obtainable from (mobilised) peripheral blood or cord blood. The population of cells may be obtained or obtainable from a subject, e.g. a subject to be treated. Suitably, the population of cells may be isolated and/or enriched from a biological sample by any method known in the art, for example by FACS and/or magnetic bead sorting.
Suitably, the population of cells are mammalian cells, for example human cells. The population of cells may be, for example, autologous or allogeneic. The population of cells may be, for example, universal cells.
Suitably, the population of cells comprises about 1 × 105 cells per well to about 10 × 105 cells per well, e.g. about 2 × 105 cells per well, or about 5 × 105 cells per well.
The population of cells may comprise HSCs, HPCs, and/or LPCs. Suitably, at least 50%, at least 60%, at least 70%, or at least 80% of the population of cells are HSCs, HPCs, and/or LPCs. In some embodiments, the population of cells consists essentially of HSCs, HPCs, and/or LPCs, or consists of HSCs, HPCs, and/or LPCs.
The population of cells may comprise CD34+ cells, e.g. CD34+ HSCs, HPCs, and/or LPCs. Suitably, at least 50%, at least 60%, at least 70%, or at least 80% of the population of cells are CD34+ cells, e.g. CD34+ HSCs, HPCs, and/or LPCs. In some embodiments, the population of cells consists essentially of CD34+ cells, e.g. CD34+ HSCs, HPCs, and/or LPCs, or consists of CD34+ cells, e.g. CD34+ HSCs, HPCs, and/or LPCs.
The population of cells may comprise CD34+CD133+CD90+ cells, CD34+CD133+CD90-cells, and/or CD34+CD133-CD90-. Suitably, at least 50%, at least 60%, at least 70%, or at least 80% of the population of cells are CD34+CD133+CD90+ cells, CD34+CD133+CD90-cells, and/or CD34+CD133-CD90- cells. In some embodiments, the population of cells consists essentially of CD34+CD133+CD90+ cells, CD34+CD133+CD90- cells, and/or CD34+CD133-CD90- cells, or consists of CD34+CD133+CD90+ cells, CD34+CD133+CD90-cells, and/or CD34+CD133-CD90- cells.
The cell or population of cells may be cultured prior to step (b). The pre-culturing step may comprise a pre-activation step and/or a pre-expansion step, optionally the pre-culturing step is a pre-activation step.
As used herein, a “pre-culturing step” refers to a culturing step which occurs prior to genetic modification of the cells. As used herein, a “pre-activating step” refers to an activation step or stimulation step which occurs prior to genetic modification of the cells. As used herein, a “pre-expansion step” refers to an expansion step which occurs prior to genetic modification of the cells.
Suitably, the method may comprise:
The pre-culturing step (e.g. pre-activation step and/or pre-expansion step) may be carried out using any suitable conditions.
During the pre-culturing step (e.g. pre-activation step and/or pre-expansion step) the population of cells may be seeded at a concentration of about 1 × 105 cells/ml to about 10 × 105 cells/ml, e.g. about 2 × 105 cells/ml, or about 5 × 105 cells/ml.
Suitably, the pre-culturing step (e.g. pre-activation step and/or pre-expansion step) is at least 1 day, at least 2 days, or at least 3 days. Suitably, the population of cells are pre-cultured (e.g. pre-activated and/or pre-expanded) for about 3 days. Suitably, the population of cells are pre-cultured in a 5% CO2 humidified atmosphere at 37° C.
Any suitable culture medium may be used. For example, commercially available medium such as StemSpan medium may be used, which contains bovine serum albumin, insulin, transferrin, and supplements in Iscove’s MDM. The culture medium may be supplemented with one or more antibiotic (e.g. penicillin, streptomycin).
The pre-culturing step (e.g. pre-activation step and/or pre-expansion step) may be carried out in the presence in of one or more cytokines and/or growth factors. As used herein, a “cytokine” is any cell signalling substance and includes chemokines, interferons, interleukins, lymphokines, and tumour necrosis factors. As used herein, a “growth factor” is any substance capable of stimulating cell proliferation, wound healing, or cellular differentiation. The terms “cytokine” and “growth factor” may overlap.
The pre-culturing step (e.g. pre-activation step and/or pre-expansion step) may be carried out in the presence of one or more early-acting cytokine, one or more transduction enhancer, and/or one or more expansion enhancer.
As used herein, an “early-acting cytokine” is a cytokine which stimulates HSCs, HPCS, and/or LPCs or CD34+ cells. Early-acting cytokines include thrombopoietin (TPO), stem cell factor (SCF), Flt3-ligand (FLT3-L), interleukin (IL)-3, and IL-6. In some embodiments, the pre-culturing step (e.g. pre-activation step and/or pre-expansion step) is carried out in the presence of at least one early-acting cytokine. Any suitable concentration of early-acting cytokine may be used. For example, 1-1000 ng/ml, or 10-1000 ng/ml, or 10-500 ng/ml.
In some embodiments, the pre-culturing step (e.g. pre-activation step and/or pre-expansion step) is carried out in the presence of SCF. The concentration of SCF may be about 10-1000 ng/ml, about 50-500 ng/ml, or about 100-300 ng/ml.
In some embodiments, the pre-culturing step (e.g. pre-activation step and/or pre-expansion step) is carried out in the presence of FLT3-L. The concentration of FLT3-L may be about 10-1000 ng/ml, about 50-500 ng/ml, or about 100-300 ng/ml.
In some embodiments, the pre-culturing step (e.g. pre-activation step and/or pre-expansion step) is carried out in the presence of TPO. The concentration of TPO may be about 5-500 ng/ml, about 10-200 ng/ml, or about 20-100 ng/ml.
In some embodiments, the pre-culturing step (e.g. pre-activation step and/or pre-expansion step) is carried out in the presence of IL-3. The concentration of IL-3 may be about 10-200 ng/ml, about 20-100 ng/ml, or about 60 ng/ml.
In some embodiments, the pre-culturing step (e.g. pre-activation step and/or pre-expansion step) is carried out in the presence of IL-6. The concentration of IL-6 may be about 5-100 ng/ml, about 10-50 ng/ml, or about 20 ng/ml.
In some embodiments, the pre-culturing step (e.g. pre-activation step and/or pre-expansion step) is carried out in the presence of SCF (e.g. in a concentration of about 100 ng/ml), FLT3-L (e.g. in a concentration of about 100 ng/ml), TPO (e.g. in a concentration of about 20 ng/ml) and IL-6 (e.g. in a concentration of about 20 ng/ml), in particular when the population of cells are cord-blood CD34+ cells.
In some embodiments, the pre-culturing step (e.g. pre-activation step and/or pre-expansion step) is carried out in the presence of SCF (e.g. in a concentration of about 300 ng/ml), FLT3-L (e.g. in a concentration of about 300 ng/ml), TPO (e.g. in a concentration of about 100 ng/ml) and IL-3 (e.g. in a concentration of about 60 ng/ml), in particular when the population of cells are (mobilised) peripheral blood CD34+ cells.
As used herein, a “transduction enhancer” is a substance that is capable of improving viral transduction of HSCs, HPCS, and/or LPCs or CD34+ cells. Suitable transduction enhancers include LentiBOOST, prostaglandin E2 (PGE2), protamine sulfate (PS), Vectofusin-1, ViraDuctin, RetroNectin, staurosporine (Stauro), 7-hydroxy-stauro, human serum albumin, polyvinyl alcohol, and cyclosporin H (CsH). In some embodiments, the pre-culturing step (e.g. pre-activation step and/or pre-expansion step) is carried out in the presence of at least one transduction enhancer. Any suitable concentration of transduction enhancer may be used, for example as described in Schott, J.W., et al., 2019. Molecular Therapy-Methods & Clinical Development, 14, pp.134-147 or Yang, H., et al., 2020. Molecular Therapy-Nucleic Acids, 20, pp. 451-458.
In some embodiments, the pre-culturing step (e.g. pre-activation step and/or pre-expansion step) is carried out in the presence of PGE2. Suitably, the PGE2 is 16,16-dimethyl prostaglandin E2 (dmPGE2). The concentration of PGE2 may be about 1-100 µM, about 5-20 µM, or about 10 µM.
In some embodiments, the pre-culturing step (e.g. pre-activation step and/or pre-expansion step) is carried out in the presence of CsH. The concentration of CsH may be about 1-50 µM, 5-50 µM, about 10-50 µM, or about 10 µM.
As used herein, an “expansion enhancer” is a substance that is capable of improving expansion of HSCs, HPCS, and/or LPCs or CD34+ cells. Suitable expansion enhancers include UM171, UM729, StemRegenin1 (SR1), diethylaminobenzaldehyde (DEAB), LG1506, BIO (GSK3β inhibitor), NR-101, trichostatin A (TSA), garcinol (GAR), valproic acid (VPA), copper chelator, tetraethylenepentamine, and nicotinamide. In some embodiments, the pre-culturing step (e.g. pre-activation step and/or pre-expansion step) is carried out in the presence of at least one expansion enhancer. Any suitable concentration of expansion enhancer may be used, for example as described in Huang, X., et al., 2019. F1000Research, 8, 1833.
In some embodiments, the pre-culturing step (e.g. pre-activation step and/or pre-expansion step) is carried out in the presence of UM171 or UM729. The concentration of UM171 may be about 10-200 nM, about 20-100 nM, or about 50 nM.
In some embodiments, the pre-culturing step (e.g. pre-activation step and/or pre-expansion step) is carried out in the presence of SR1. The concentration of SR1 may be about 0.1-10 µM, about 0.5-5 µM, or about 1 µM.
In some embodiments, the pre-culturing step (e.g. pre-activation step and/or pre-expansion step) is carried out in the presence of UM171 (e.g. in a concentration of about 50 nM) or UM729 and SR1 (e.g. in a concentration of about 1 µM).
In some embodiments, the pre-culturing step (e.g. pre-activation step and/or pre-expansion step) is carried out in the presence of SCF (e.g. in a concentration of about 100 ng/ml), FLT3-L (e.g. in a concentration of about 100 ng/ml), TPO (e.g. in a concentration of about 20 ng/ml), IL-6 (e.g. in a concentration of about 20 ng/ml), PGE2 (e.g. in a concentration of about 10 µM), UM171 (e.g. in a concentration of about 50 nM), and SR1 (e.g. in a concentration of about 1 µM), in particular when the population of cells are cord-blood CD34+ cells.
In some embodiments, the pre-culturing step (e.g. pre-activation step and/or pre-expansion step) is carried out in the presence of SCF (e.g. in a concentration of about 300 ng/ml), FLT3-L (e.g. in a concentration of about 300 ng/ml), TPO (e.g. in a concentration of about 100 ng/ml), IL-3 (e.g. in a concentration of about 60 ng/ml), PGE2 (e.g. in a concentration of about 10 µM), UM171 (e.g. in a concentration of about 50 nM), and SR1 (e.g. in a concentration of about 1 µM), in particular when the population of cells are (mobilised) peripheral blood CD34+ cells.
A kit, composition, and/or gene-editing system comprising an RNA-guided nuclease, a guide RNA, and/or a polynucleotide or vector of the present invention may, for example, be used to obtain the gene-edited cell or a population of gene-edited cells.
The RNA-guided nuclease, guide RNA, and/or polynucleotide or vector may be any suitable combination described herein. The guide RNA may correspond to the same DSB site targeted by the homology arms. The RNA-guided nuclease may correspond to the guide RNA used. For example:
In some embodiments:
The RNA-guided nuclease, guide RNA, and/or polynucleotide or vector may be delivered to the cell by any suitable technique. For example, the RNA-guided nuclease may be delivered directly using electroporation, microinjection, bead loading or the like, or indirectly via transfection and/or transduction. The guide RNA, and/or polynucleotide or vector may be introduced by transfection and/or transduction.
As used herein “transfection” is a process using a non-viral vector to deliver a polypeptide and/or polynucleotide to a target cell. Typical transfection methods include electroporation, DNA biolistics, lipid-mediated transfection, compacted DNA-mediated transfection, liposomes, immunoliposomes, lipofectin, cationic agent-mediated transfection, cationic facial amphiphiles (CFAs) and combinations thereof.
As used herein “transduction” is a process using a viral vector to deliver a polynucleotide to a target cell. Typical transduction methods include infection with recombinant viral vectors, such as adeno-associated viral, retroviral, lentiviral, adenoviral, baculoviral and herpes simplex viral vectors.
The RNA-guided nuclease and the guide RNA may be delivered by any suitable method, for instance any method described in Wilbie, D., et al., 2019. Accounts of chemical research, 52(6), pp.1555-1564. Suitably, the RNA-guided nuclease and the guide RNA are delivered together preassembled as in the form of a RNP complex. The RNP complex may be delivered by electroporation.
Any suitable dose of the RNA-guided nuclease and/or the guide RNA may be used. For example, the guide RNA may be delivered at a dose of about 10-100 pmol/well, optionally about 50 pmol/well. For example, the RNP may be delivered at a dose of about 1-10 µM, optionally 1-2.5 µM.
The RNA-guided nuclease and/or the guide RNA may be delivered prior to the vector and/or simultaneously with the polynucleotide or vector of the invention. Suitably, the RNA-guided nuclease and/or the guide RNA are delivered prior to the polynucleotide or vector. For example, the RNA-guided nuclease and/or the guide RNA may be delivered about 1-100 minutes, about 5-30, or about 15 minutes, prior to the polynucleotide or vector.
The polynucleotide or vector of the invention may be delivered by any suitable method. For example, when the polynucleotide may be in a viral vector or the vector may be a viral vector and delivered by transduction.
Any suitable dose of the polynucleotide or vector may be used. For example, the vector may be delivered at a MOI of about 104 to 105 vg/cell, optionally about 104 vg/cell.
The method may further comprise a step of delivering a p53 inhibitor and/or HDR enhancer. The p53 inhibitor and/or HDR enhancer may be delivered simultaneously. The p53 inhibitor and/or HDR enhancer may be delivered simultaneously with or after the RNA-guided nuclease and/or the guide RNA.
As used herein, a “p53 inhibitor” is a substance which inhibits activation of the p53 pathway. The p53 pathway plays a role in regulation or progression through the cell cycle, apoptosis, and genomic stability by means of several mechanisms including: activation of DNA repair proteins, arrest of the cell cycle; and initiation of apoptosis. Inhibition of this p53 response by delivery during editing has been shown to increase hematopoietic repopulation by treated cells (Schiroli, G. et al. 2019. Cell Stem Cell 24, 551-565). Suitably, the p53 inhibitors is a dominant-negative p53 mutant protein, e.g. GSE56.
GSE56 may have the amino acid sequence:
(SEQ ID NO: 67)
In one embodiment, the p53 dominant negative peptide is a variant of GSE56 comprising 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 amino acid substitutions, additions or deletions, while retaining the activity of GSE56, for example in reducing or preventing p53 signalling.
In one embodiment, the p53 dominant negative peptide comprises an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identity to SEQ ID NO: 67.
As used herein, an “HDR enhancer” is a substance that is capable of improving HDR efficiency in HSCs, HPCS, and/or LPCs or CD34+ cells. HDR is constrained in long-term-repopulating HSCs. Any suitable HDR enhancer may be used, for example as described in Ferrari, S., et al., 2020. Nature Biotechnology, pp.1-11. Suitably, the HDR enhancer is the adenovirus 5 E4orf6/7 protein. Adenovirus 5 E4orf6/7 proteins may be as disclosed in WO 2020/002380 (incorporated herein by reference).
The p53 inhibitor and the HDR enhancer may be delivered by any suitable method. The p53 inhibitor and/or the HDR enhancer may be transiently expressed, for example the p53 inhibitor and/or the HDR enhancer may delivered via mRNA. The p53 inhibitor and the HDR enhancer may be delivered by separate mRNAs or on a single mRNA encoding a fusion protein, optionally with a self-cleaving peptide (e.g. P2A). Any suitable dose of the p53 inhibitor and/or the HDR enhancer may be used, for example mRNA be delivered at a concentration of about 10-1000 µg/ml, about 50-500 µg/ml, or about 150 µg/ml.
In some embodiments, step (b) comprises:
The method may further comprise a step of culturing the population of gene-edited cells. This may be an expansion step, i.e. the method may further comprises a step of expanding the population of gene-edited cells.
The culturing step (e.g. expansion step) may be carried out using any suitable conditions.
During the culturing step (e.g. expansion step) the population of cells may be seeded at a concentration of about 1 × 105 cells/ml to about 10 × 105 cells/ml, e.g. about 2 × 105 cells/ml, or about 5 × 105 cells/ml. Suitably, the culturing step (e.g. expansion step) is for at least one day, or one to five days. For example, the culturing step (e.g. expansion step) may be for about one day. Suitably, the population of cells are cultured in a 5% CO2 humidified atmosphere at 37° C.
Any suitable culture medium may be used. For example, commercially available medium such as StemSpan medium may be used, which contains bovine serum albumin, insulin, transferrin, and supplements in Iscove’s MDM. The culture medium may be supplemented with one or more antibiotic (e.g. penicillin, streptomycin). The culturing step (e.g. expansion step) may be carried out in the presence in of one or more cytokines and/or growth factors.
In some embodiments, step (b) comprises:
In one aspect the present invention provides a method of treating a subject using polynucleotides, vectors, guide RNAs, kits, compositions, gene-editing systems, cells and/or populations of cells of the present invention. Suitably, the method of treating a subject may comprise administering a cell or population of cells of the present the invention.
In a related aspect the present invention provides a polynucleotide, vector, guide RNA, kit, composition, gene-editing system, cell and/or populations of cells of the present invention for use as a medicament. Suitably, the cell or population of cells of the present the invention may be used as a medicament.
In a related aspect, the present invention provides use of a polynucleotide, vector, guide RNA, kit, composition, gene-editing system, cell and/or populations of cells of the present invention for the manufacture of a medicament. Suitably, the cell or population of cells of the present the invention may be used for the manufacture of a medicament.
Suitably, a method of treating a subject may comprise:
For example, a method of treating a subject may comprise:
Steps (a) and (b) may be identical to the steps described in the section above.
Suitably, the cell of population of cells may be isolated and/or enriched from the subject to be treated, e.g. the population of cells may be an autologous population of CD34+ cells. Suitably, the population of cells are isolated from (mobilised) peripheral blood or cord blood of the subject to be treated and subsequently enriched (e.g. by FACS and/or magnetic bead sorting).
The subject may be immunocompromised and/or the disease to be treated may be an immunodeficiency, i.e. the medicament may be for treating an immunodeficiency. As used herein, an “immunodeficiency” is a disease in which the immune system’s ability to fight infectious disease and cancer is compromised or entirely absent. A subject who has an immunodeficiency is said to be “immunocompromised”. An immunocompromised person may be particularly vulnerable to opportunistic infections, in addition to normal infections that could affect everyone.
The subject may have RAG deficiency, e.g. a RAG1 deficiency. A RAG1 deficiency may be due to a loss-of-function mutation in the RAG1 gene, optionally a loss-of-function mutation in the RAG1 exon 2.
The immunodeficiency may be a RAG deficient-immunodeficiency. As used herein, a “RAG deficient-immunodeficiency” is an immunodeficiency characterised by loss of RAG1/RAG2 activity. A RAG deficient-immunodeficiency may, for example be caused by a mutation in RAG genes.
Suitably, the RAG deficient-immunodeficiency may be a RAG1 deficiency. A RAG1 deficiency may be due to a loss-of-function mutation in the RAG1 gene, optionally a loss-of-function mutation in the RAG1 exon 2.
Mutations of the RAG genes in humans are associated with distinct clinical phenotypes, which are characterized by variable association of infections and autoimmunity. In some cases, environmental factors have been shown to contribute to such phenotypic heterogeneity. In humans, RAG1 deficiency can cause a broad spectrum of phenotypes, including T- B- SCID, Omenn syndrome (OS), atypical SCID (AS) and combined immunodeficiency with granuloma/autoimmunity (CID-G/Al). (Notarangelo, L.D., et al., 2016. Nature Reviews Immunology, 16(4), pp.234-246 and Delmonte, O.M., et al., 2018. Journal of clinical immunology, 38(6), pp.646-655).
In some embodiments, the RAG deficient-immunodeficiency is T- B- SCID, Omenn syndrome, atypical SCID, or CID-G/Al.
Severe combined immunodeficiency (SCID) comprises a heterogeneous group of disorders that are characterized by profound abnormalities in the development and function of T cells (and also B cells in some forms of SCID), and are associated with early-onset severe infections. This condition is inevitably fatal early in life, unless immune reconstitution is achieved, usually with HSCT. Following the introduction of newborn screening for SCID in the United States, it has become possible to establish that RAG mutations account for 19% of all cases of SCID and SCID-related conditions, and are a prominent cause of atypical SCID and Omenn syndrome in particular. (Notarangelo, L.D., et al., 2016. Nature Reviews Immunology, 16(4), pp.234-246).
In 1996, RAG mutations were identified as the main cause of T-B- SCID with normal cellular radiosensitivity. A distinct phenotype characterizes Omenn syndrome, which was first described in 1965. These patients manifest early-onset generalized erythroderma, lymphadenopathy, hepatosplenomegaly, eosinophilia and severe hypogammaglobulinaemia with increased IgE levels, which are associated with the presence of autologous, oligoclonal and activated T cells that infiltrate multiple organs. In some patients with hypomorphic RAG mutations, a residual presence of autologous T cells was demonstrated without clinical manifestations of Omenn syndrome. This condition is referred to as ‘atypical’ or ‘leaky’ SCID. A distinct SCID phenotype involving the oligoclonal expansion of autologous γδ T cells (referred to here as γδ T+ SCID) has been reported in infants with RAG deficiency and disseminated cytomegalovirus (CMV) infection. (Notarangelo, L.D., et al., 2016. Nature Reviews Immunology, 16(4), pp.234-246).
Whereas SCID, atypical SCID and Omenn syndrome are inevitably fatal early in life if untreated, several forms of RAG deficiency with a milder clinical course and delayed presentation have been reported in recent years. In particular, the occurrence of CID-G/Al was reported in three unrelated girls with RAG mutations who manifested granulomas in the skin, mucous membranes and internal organs, and had severe complications after viral infections, including B cell lymphoma. Following this description, several other cases of CID-G/Al with various autoimmune manifestations (such as cytopaenias, vitiligo, psoriasis, myasthenia gravis and Guillain-Barré syndrome) have been reported. (Notarangelo, L.D., et al., 2016. Nature Reviews Immunology, 16(4), pp.234-246).
Additional phenotypes that are associated with RAG deficiency include idiopathic CD4+ T cell lymphopaenia, common variable immunodeficiency, IgA deficiency, selective deficiency of polysaccharide-specific antibody responses, hyper-lgM syndrome and sterile chronic multifocal osteomyelitis. (Notarangelo, L.D., et al., 2016. Nature Reviews Immunology, 16(4), pp.234-246).
The skilled person will understand that they can combine all features of the invention disclosed herein without departing from the scope of the invention as disclosed.
Preferred features and embodiments of the invention will now be described by way of nonlimiting examples.
The practice of the present invention will employ, unless otherwise indicated, conventional techniques of chemistry, biochemistry, molecular biology, microbiology and immunology, which are within the capabilities of a person of ordinary skill in the art. Such techniques are explained in the literature. See, for example, Sambrook, J., Fritsch, E.F. and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual, 2nd Edition, Cold Spring Harbor Laboratory Press; Ausubel, F.M. et al. (1995 and periodic supplements) Current Protocols in Molecular Biology, Ch. 9, 13 and 16, John Wiley & Sons; Roe, B., Crabtree, J. and Kahn, A. (1996) DNA Isolation and Sequencing: Essential Techniques, John Wiley & Sons; Polak, J.M. and McGee, J.O’D. (1990) In Situ Hybridization: Principles and Practice, Oxford University Press; Gait, M.J. (1984) Oligonucleotide Synthesis: A Practical Approach, IRL Press; and Lilley, D.M. and Dahlberg, J.E. (1992) Methods in Enzymology: DNA Structures Part A: Synthesis and Physical Analysis of DNA, Academic Press. Each of these general texts is herein incorporated by reference.
We have developed a platform to correct CD34+ hematopoietic stem cells by exploiting a gene targeting approach.
In the approach described herein, we deliver by nucleofection a Cas9 ribonucleoprotein (RNP) that introduces a DNA double strand break (DSB) in the first intron of RAG1 gene. Following the DNA DSB, the corrective donor DNA, delivered by AAV6 vector, is integrated by homology directed repair (HDR), thanks to the presence of two sequences, flanking the corrective donor, that are homologous to the Cas9 cutting site. An alternative splicing acceptor (SA) upstream of the corrective DNA allows the endogenous promoter of RAG1 to control the expression of the transgene (
First, to test our panel of Cas9 guide RNAs we generated two cell lines with inducible Cas9 expression. NALM6 and K562 cell lines were transduced with a lentiviral vector carrying the Cas9 cassette under the control of a TET-inducible promoter and a cassette that confers resistance to puromycin. After transduction with MOI 20 the two cell lines were kept in culture with puromycin 1.5 µg/ml for one week to select the transduced cells (
A panel of nine guides was first identified to target three non-repeated loci of RAG1 intron 1. In addition, three guides (gRNA 1,2,3) targeting the first 200 bp of RAG1 exon 2 were designed with the final aim to integrate the corrective RAG1 coding sequence in frame with the endogenous ATG. This strategy would exploit the endogenous splice acceptor thus preserving any putative endogenous splicing regulations (
Guides were electroporated as plasmid DNAs in K562 Cas9 and NALM6 Cas9 cell lines considering two different doses (100 ng/well and 200 ng/well.) Cas9 expression was induced the day before the electroporation and for the two following days by adding doxycycline (1 µg/ml) to the medium. Genomic DNA was extracted at day 7 and cutting frequency was evaluated measuring the percentage of NHEJ-mediated indel mutations by T7 nuclease assay (scheme shown in
The majority of the tested guides had good cutting frequency showing similar results in both cell lines. In particular, Guide 9 was the best performing guide targeting the intron with a cutting frequency up to 72.7% in K562 Cas9 and 78.5% in NALM6 Cas9. Similar cutting frequencies were also achieved by Guide 7, that showed a cutting frequency up to 67.5% in K562 Cas9 and 70.5% in NALM6 Cas9 cell lines. Guide 3 was the best performing guide targeting the exon with a cutting frequency up to 58.9% in K562 Cas9 (
Guide 9 was further tested in NALM6 Cas9 and K562 Cas9 cell lines to verify the correct integration of the PGK_GFP reporter cassette flanked by two homology arms.
We also assessed the ability of the endogenous RAG1 promoter to induce the expression of the GFP in the absence of the PGK promoter using a donor plasmid containing splice acceptor (SA) SA_GFP cassette. RAG1 expression occurs only during lymphocytes differentiation at DN2 T and pro-B cell stages. To assess whether the endogenous promoter of RAG1 was able to induce the expression of the GFP cassette, we exploited NALM6 cell line, a Pre-B cell line that constitutively expresses RAG1 (
To assess whether the 3′UTR of RAG1 is necessary for the efficient expression of our corrective donor, we generated four different SA_GFP donor DNAs (
NALM6 Cas 9 and K562 Cas9 cell lines, previously stimulated with doxycycline to induce Cas9, were transfected with guide 9 plasmid DNA (100 ng/well) and of various linearized DNA donors (1600 ng/well). Stable integration of the donor DNA was verified by flow cytometry as GFP expression.
The PGK_GFP positive control was stably integrated in both cell lines. In particular, ten days after transfection, 14% K562 Cas9 and 1.8% of NALM6 Cas9 were GFP positive (
The effect of constructs carrying different 3′UTR was evaluated in NALM6 Cas9 cell line by fluorescence intensity (MFI) of GFP+ events at flow cytometry. The analysis suggested that the endogenous RAG1 3′UTR negatively affects the expression of the transgene. GFP MFI obtained upon transfection with SA_GFP_SD and SA_GFP_3′UTR constructs was significantly lower than MFI obtained by SA_GFP_BGH (
Preliminary in silico analysis demonstrated a promising off-target profile of guide 9 and showed that most likely off-targets fall in intronic regions thus suggesting a low risk of off-target related gene disruption events (
The editing procedure was then optimized in human CD34+ cells from cord blood (hCB-CD34). To this end, hCB-CD34 cells were thawed at day 0 and prestimulated for three days seeding 1×106 cells/ml in StemSpan enriched with cytokines (hTPO 20 ng/ml, hlL6 20 ng/ml, hSCF 100 ng/ml, hFlt3-L 100 ng/ml, SR1 1 uM, UM171 50 nM).
At day 3, guides 3 and 9 were delivered by electroporation as in vitro preassembled RNPs and two doses were considered 25 and 50 pmol/well. To enhance cellular stability, chemical modification consisting in 2′-O-methyl 3′phosphorothioate were added at the last three terminal nucleotides at 5′ and 3′ ends of the guide RNAs. After 15′, AAV6 vectors were added to the medium using three (104, 5×104, 105) MOI doses (
Guide 9 retained an activity comparable to that verified in NALM6 and K562 cell lines, 73.9% cutting frequency was observed with 25 pmol/well and 80.1% with 50 pmol/well. Guide 3 displayed a lower activity in hCB-CD34 with a cutting frequency of 16.9% and 19.3% with 25 and 50 pmol/well respectively (
Guide 9 promoted a highly efficient targeted integration of the PGK_GFP cassette. Apoptosis analysis showed a low toxicity associated with the editing procedure, and viability (7AAD- AnnexinV- cells) was above 70% the day after the editing for all the conditions tested (
Analysis of integration frequency showed that that the most primitive subpopulation (CD34+CD133+CD90+) was the less permissive fraction. The highest editing frequency in this subpopulation was obtained using 25 pmol of Cas9 and the MOI 105 (52.8%). At lower MOI, the higher Cas9 dose (50 pmol) enhanced the editing efficiency particularly in the most primitive subpopulation, indeed, with a MOI 104, editing frequency was 24.6% and 40.5% with 25 and 50 pmol of Cas9 respectively (
Overall, these data suggest that using this platform, we were able to obtain efficient targeting even in the most primitive CD34+ subpopulation. The editing protocol does not affect the phenotype of the cells (both in terms of total CD34+ cells and in terms of subpopulation distribution). In particular, we identified a guide RNA promoting high frequency of targeted integration and set up editing conditions (50 pmol/well Cas9 and MOI 104 Vg/cell) that allow the best compromise between toxicity and targeting frequency (
In order to assess if our procedure allows targeted integration in HSCs while preserving their long-term repopulating activity, edited CD34+ cells were transplanted into sublethally irradiated NOD-scid IL2Rgnull mice (NSG) mice. Following the same protocol used in the previous experiment, after 3 days of stimulation, hCB-CD34+ cells were electroporated with 50 pmol/well of guide 9 RNP and 15 minutes later transduced with AAV6 at MOI 104 Vg/cell. In this experiment two distinct AAV6 vectors were used. The first AAV6 vector carrying the PGK_GFP_BGH was used as a positive control to easily follow engraftment of edited cells. The second donor carrying a SA_GFP_BGH was used to assess the in vivo expression of GFP gene under the control of RAG1 endogenous promoter. The day following the editing procedure, treated hCB-CD34+ 350,000 cells/mouse were injected in 4-5 NSG mice per group, 6 hours after sublethal total body irradiation (120 rad). In order to assess the levels of gene targeting efficiency after the treatment, few cells were maintained in culture for 4 more days. Using both the AAV6 vectors we measured ~80% of targeted integration by ddPCR (
In the group of mice receiving cells treated with PGK_GFP_BGH vector, edited hCD45+ GFP+ cells were maintained over time at high percentage (-40-50%), thus suggesting that the treatment was tolerated from the most primitive cells and confirming their long-term survival in vivo (
At sacrifice, analysis of the bone marrow confirmed the engraftment of treated CD34+ stem cells. Moreover, in the PGK_GFP_BGH group, a high frequency of GFP+ targeted cells (~38%) was observed among the CD34+ cells further suggesting efficient engraftment of long-term repopulating stem cells (
Taken together these observations suggest that we have established an efficient protocol for the editing of long-term repopulating stem cells without affecting their engraftment and multilineage differentiation capacity. Our data further suggest an in vivo controlled expression pattern of the transgene, in the absence of exogenous promoters, highlighting that the expression is lymphoid specific and limited to immature lymphocytes.
Next we designed and tested the corrective AAV6 vector carrying RAG1 coding sequence. In particular, the corrective donor included the two homology arms at the 3′ and 5′ extremities, a splice acceptor followed by the Kozak sequence, the RAG1 coding sequence and the BGH PolyA for a total length of 4.1 Kb (
MPB-CD34+ cells from normal donors (commercially purchased by AllCells California, US) were thawed and prestimulated for three days. We adjusted the editing protocol as follows: Stem cell factor (SCF) 300 ng/ml, Flt3 ligand (Flt-3L) 300 ng/ml, Thrombopoietin (TPO) 100 ng/ml, Interleukin 3 (IL-3) 60 ng/ml, StemRegenin1 (SR1, 1 uM) and 16,16-dimethyl prostaglandin E2 (dmPGE2, 10 uM), UM171 35 nM.
Cas9 was electroporated as in vitro preassembled RNP at two doses (25 pmol/well and 50 pmol/well). Since our previous observation suggested that high AAV6 vector MOI could impair cell fitness, we considered two low MOI (104 and 2*104).
Impact of the editing procedure was evaluated considering cell growth and cell phenotype by flow cytometry. Since the corrective donor does not include any reporter gene, we assessed the integration by molecular assays. Four days after editing, cells were sorted based on the expression of CD34, CD133, and CD90 to identify and analyze primitive, early and committed progenitor subpopulations. Genomic DNA from sorted subpopulations was extracted, and targeted integration of the corrective donor was verified by ddPCR assay, using a set of primers specific for the on-target integration and for the codon optimized donor sequence (
To assess whether our gene editing procedure may affect engraftment capability, edited hMPB-CD34+ cells were transplanted into sub-lethally irradiated NSG mice. Following the same protocol used in the previous experiment, after 3 days of stimulation, hMPB-CD34+ cells were electroporated with 50pmol/well of guide 9 RNP and 15 minutes later transduced with corrective AAV6 at MOI 104 Vg/cell. To dampen the previously reported editing-induced p53 response, which decreases hematopoietic reconstitution by edited HSPCs, we added to the electroporation mixture an mRNA encoding for the dominant-negative p53 inhibitor GSE56 (Schiroli G, et al. Cell Stem Cell. 2019;24(4):551-565.e8).
To evaluate in vivo gene correction, we had access to hMPB-CD34+ cells obtained from a patient (NIHPID0021) carrying hypomorphic mutations in RAG1 gene. Of note NIHPID0021 is an adult patient with CID-G/Al due to missense RAG1 mutations (C1228T; G1520A) allowing residual development of B and T cells. The patient presented B cells 23/uL, T cells 665/uL (8% naïve), normal NK counts. Of note, the very low B cell counts in the periphery was also due to the treatment with anti-CD20 mAb to control severe autoimmune manifestations.
RAG1 patients received G-CSF/Plerixafor, and CD34+ cells were collected by the NIH clinical facility and their purity was verified by flow cytometry (>97% CD34+).
hMPB-CD34+ cells from two independent healthy donors (commercially purchased) were used in parallel. The day following the editing, 1×106 of treated or untreated cells were injected in sublethally irradiated mice (120 rad) (
Flow cytometric analysis on the peripheral blood was performed 5, 8, 12 weeks after transplantation, and mice were sacrificed at 15 weeks.
The analysis of the peripheral blood showed that engraftment of hMPB-CD34+ was significantly lower than hCB-CD34+. Frequency of hCD45+ cells from HDs assessed in the blood was between 4.4% and 8.7% in all time points, and engraftment of the two batches was superimposable. Conversely, in CID/AG NIHPID002 patient the frequency of hCD45+ cells in PB was generally lower (between 2.1 and 5.2% at the first two time points) and decreased at later time points suggesting exhaustion of the engraftment. Of note, in both cases (CID/AG Patient and HD cells) no differences between treated and untreated cells were noticed in terms of frequency of hCD45+ cells in PB, confirming that engraftment capability was not affected by the editing protocol (
Molecular analysis performed by ddPCR assay revealed a targeting frequency of 35.3% in human cells obtained from peripheral blood of mice receiving gene edited MPB-CD34+ HD cells, thus recapitulating previous observations obtained with the reporter gene and further confirming that targeting procedure does not affect the engraftment (
With regard to peripheral blood composition, NSG mice transplanted with treated HD cells showed no major skewing in the subpopulation composition and a comparable frequency of B, T and myeloid cells was observed in mice receiving treated or untreated cells, confirming that multilineage differentiation was not impaired (
Mice were sacrificed 17 weeks after the transplant to analyze the engraftment of edited cells in bone marrow, thymus and spleen. In the bone marrow and spleen, frequencies of human CD45+ cells were higher than those retrieved mice peripheral blood (
HDR targeting efficiency assessed by ddPCR on DNA samples extracted from bone marrow and spleen showed a range from 1.1% to 19.6% in edited cells from the bone marrow, while 2.1% to 8.5% in the case of patient cells (
Overall, these findings confirmed the feasibility of gene editing approach to target the human RAG1 locus in HSCs derived from HD and patient with RAG1 mutation. The GE procedure did not affect the engraftment capability and the multilineage differentiation of HSCs.
Classical gene-addition based gene therapy strategies rely upon the use of integrating vectors. The introduction of new generation vectors, whose improved design confers a safer integration profile, alleviated but did not abolish the risk of insertional mutagenesis caused by vector semi-random integration into the genome (Doi K, Takeuchi Y. Vol. 65, Uirusu. 2015. p. 27-36). Furthermore, the use of ubiquitous promoters dramatically hampers the physiological expression of therapeutic transgene whose expression is cell specific or tightly controlled during cell cycle.
RAG1 molecule mediates the site-specific DNA double stranded breaks necessary for initiating V(D)J recombination (Oettinger MA, et al. Science. 1990;248(4962):1517-23). DNA double strand breaks are per se dangerous lesions that can result in pathological genome rearrangements or chromosomal translocations. An important mechanism that ensures the fidelity of V(D)J recombination resides in the fine control of RAG1 expression that is restricted to specific target cells at specific developmental stages. RAG1 expression regulation is also indispensable for the selection of functional, non-self-reactive lymphocyte through complex mechanisms of “allelic exclusion” or BCR and TCR receptor editing (Ten Boekel E, et al. Immunity. 1998;8(2):199-207).
In the past, several attempts to correct RAG1 deficiency by retrovirus or lentivirus-mediated gene transfer have led to variable T and B cell reconstitution with development of inflammatory infiltrates and autoimmunity when suboptimal immune reconstitution is achieved (Pike-Overzet K, et al. Leukemia. 2011;25(9):1471-83; Pike-Overzet K, et al. Vol. 134, Journal of Allergy and Clinical Immunology. 2014. p. 242-3; Lagresle-Peyrou C, et al. Blood. 2006;107(1):63-72; and van Til NP, et al. J Allergy Clin Immunol. 2014;133(4):1116-23). In parallel, use of exogenous and ubiquitous promoters may lead to genotoxicity (Zhang Y, et al. Advances in Immunology. 2010. p. 93-133; and Papaemmanuil E, et al. Nat Genet. 2014;46(2):116-25).
The development of a gene editing platform represents a strategy to overcome several issues raised by conventional gene addition protocol. We have been focusing on HSC-based genome editing strategy to correct the broad spectrum of RAG1 deficiencies. To this end, we designed a strategy targeting the first RAG1 intron thus replacing the RAG1 coding sequence entirely contained in the exon 2. Our strategy has the advantage to cure most of disease-causing RAG1 mutations, while conserving the expression of the gene driven by its own promoter. To this purpose, we identified the best combination of nuclease reagents and corrective cDNA donors in NALM6 and K562 cell lines. Cas9 was electroporated as in vitro preassembled RNP in order to ensure a robust and short-term persistence in cells as prolonged persistence of Cas9 protein in primary cells could lead to off-target cleavage, potentially affecting cell homeostasis and functionality (Kim S, et al. Genome Res. 2014;24(6):1012-9). Delivering Cas9 as preassembled RNP is well tolerated and partially protect the gRNA from intracellular degradation thus improving stability and activity of the nuclease (Hendel A, et al. Nat Biotechnol. 2015;33(9):985-9). To further improve Cas9 activity profile, chemically modified gRNAs were used to enhance the stability, together with High Fidelity Cas9 variant in order to reduce off-target related toxicity (Vakulskas CA, et al. Nat Med. 2018;24(8):1216-24).
Prediction analysis of gRNA activity using Cas9 expressing cell line revealed reliable results for the guide targeting the intron (guide 9).
Next, we turned to hCB-CD34+ cells. HSPC were prestimulated to favour the transit through S/G2 phases when HDR preferably occurs (Genovese P, et al. Nature. 2014;510(7504):235-40; and Kass EM, Jasin M. Vol. 584, FEBS Letters. 2010. p. 3703-8) resulting in a moderate cell expansion while preserving original stemness phenotype considering expression of CD34, CD133 and CD90 markers.
Using guide 9 (50 pmol/well), Cas9 RNP and AAV6 vector (MOI 104) carrying the PGK_GFP reporter cassette, we obtained good levels of targeting frequency (40.5%) in CD34+CD133+CD90+ the most primitive cell subpopulation. Molecular analysis assessed by ddPCR analysis showed that the majority of the integration was on target. Notably, during Cas9 and AAV6 dosage optimization, we noticed that high MOI of AAV6 had a strong impact on cell fitness. In vivo experiments further confirmed in vitro data. Transplantation of treated hCB-CD34+ cells in sublethally irradiated NSG mice showed long-term engraftment both in the bone marrow and peripheral blood, confirming multi-lineage differentiation capacity and long-term engraftment of targeted cells. We also tested SA_GFP cassette in which GFP expression is controlled by RAG1 endogenous promoter. In vivo data in NSG mice indicated a controlled lymphoid specific expression pattern of the transgene, that was restricted to immature lymphocytes in which RAG1 is physiologically expressed. To assess the impact of the endogenous RAG1 3′UTR in the donor DNA, we tested different donor constructs carrying GFP reporter gene. Analysis of donor AAV6 carrying endogenous RAG1-3′UTR indicates a reduction of GFP expression as compared to the level obtained using a donor with BGH_PolyA. These data associated with the lack of clinically relevant mutations in the RAG1 3′UTR so far reported in literature, suggest that this region could be dispensable in the design of the corrective donor. Finally, SA_GFP_ WPRE did not show advantage in GFP expression suggesting that WPRE-mediated expression enhancement could be promoter and cell line dependent. Based on this evidence, BGH PolyA sequence that allows the highest transgene expression level was cloned in the donor DNA. Furthermore, to further enhance protein translation, human RAG1 coding sequence was codon optimized replacing more “rare” codons with more frequent ones without changing the final amino acid sequence.
The newly designed donor AAV6 vector (including a SA sequence followed by the Kozak sequence, the RAG1 codon optimized followed by BGH_PolyA) was tested also in hMPB-CD34+ cells. We observed the same efficiency obtained with the previous donors, confirming that our protocol is reproducible using several donors and several HSPC sources. Moreover, the multiparametric analysis of HSPC composition in untreated and edited HD cells showed a redistribution of HSPC subtypes in cultured cells as compared to cells analyzed before the expansion phase (
Notably, ddPCR analysis showed more than 80% HDR in total CD34+ cells and 45% of targeting frequency was observed in the most primitive (CD133+ CD90+) subpopulation subset. In vivo experiments in NSG mice transplanted with treated hMPB-CD34+ cells showed good level of engraftment and multilineage differentiation capability as those treated with unedited cells.
We had access to hMPB-CD34+ cells from a CID-G/Al RAG1 patient carrying hypomorphic mutations and presenting with a combined immunodeficiency associated to severe inflammation and autoimmune signs. We confirmed that the editing procedure did not affect the HSPC composition in RAG1-deficient cells (
Overall, we have established an efficient and promising genome editing platform for the correction of RAG1 deficiency.
LVs were produced by transient transfection of 293T cells. 24 hours before transfection 9×106 cells were plated in a 15 cm dish, 2 hours before transfection Iscove’s Modified Dulbecco’s (IMDM) medium was changed. The required transfer vector (34 µg) was mixed with 9 µg of VSV-G envelope encoding plasmid, 12.5 µg pMDLg/pRRE, 6.25 µg of REV plasmid and 15 µg of pADVANTAGE per 15 cm dish. This mixture was added to 293T cells by calcium phosphate precipitation. After 12-14 hours the medium was replaced with fresh complete IMDM supplemented with 1 mM of sodium butyrate. Collection and filtration of the supernatant took place 30 hours after this medium change. Following collection, the LV was concentrated 500 times by ultracentrifugation (2 hr, 20.000 rpm, 20°). A serial dilution was made of a known amount of 293T cells infected by the LV. After 3 days genomic DNA (gDNA) of the different dilutions was isolated with the DNeasy® Blood and Tissue Kit. Vector copy number (VCN) of the LV was measured by ddPCR. Titer was calculated by using the following formula: Titer = VCN x dilution factor x number of infected 293T cells. p24 HIV protein by ELISA assay (Abcam 218268) in order to estimate the amount of vector particles and calculate the relative infectivity of the vector preparation.
NALM6 Cas9 cell line was generated by transducing NALM6 cells with a lentiviral vector expressing Cas9 protein under the control of a TET-inducible promoter and with a vector that constitutively expresses the TET transactivator (Clackson T. Vol. 7, Gene Therapy. 2000. p. 120-5). When doxycycline is administered to the culture media, the TET transactivator can bind the promoter of the Cas9 and induce its expression in the cells. K562 Cas9 cell line was generated with the same vector. Doxycycline was administered 24 h before electroporation of the nuclease. Cell lines were maintained in RPMI 1640 medium supplemented with 10% FBS, glutamine and penicillin/streptomycin antibiotics (complete medium).
Cas9 protein and custom RNA guides were purchased from Integrated DNA Technologies (IDT) and assembled following the manufacturer protocol. To enhance cellular stability, chemically modified guide RNAs were used. Briefly crRNA and trRNA were annealed heating them at 95° C. for 5 minutes and letting them slowly cool down at RT for 10 minutes. Cas9 protein was then incubated for 15 minutes at room temperature with the annealed guide RNA fragments, to assemble the ribonucleoprotein (RNP).
Guide sequences are shown in the table below:
When used directly as RNA, the following guide sequences for guides 3, 7, 9 and RAG1KO may be used:
A T7 endonuclease (T7E1) assay was used to measure indels induced by NHEJ. Briefly, gDNA of gene edited cells was extracted and amplified by PCR with primers flanking the Cas9 RNP target site. The PCR product was denatured, slowly re- annealed and digested with T7 endonuclease (New England BioLabs) for 1 h, 37°. T7 nuclease only cut DNA at sites where there is a mismatch between the DNA strands, thus between re-annealed wild type and mutant alleles. Fragments were separated on LabChip GXII Touch High Resolution DNA Chip (PerkinElmer®) and analysed by the provided software. The ratio of the uncleaved parental fragment versus cleaved fragments was calculated and it gives a good estimation of NHEJ efficiency of the artificial nuclease. Calculation of % NHEJ: (sum cleaved fragment)/(sum cleaved fragments + parental fragment) x 100. Primer used for NHEJ assay:
In silico prediction of off-target profile was performed with COSMID (CRISPR Off-target Sites with Mismatches, Insertions, and Deletions) (Cradick TJ, et al. Mol Ther - Nucleic Acids. 2014;3(12):e214) to search genomes for potential CRISPR off-target sites. For GUIDE-Seq analysis K562 cells were electroporated with 50 pmol of High Fidelity Cas9 Nuclease V3 guide7 or guide 9 (as RNP) and dsODN to tag the breaks via an end-joining process consistent with NHEJ. dsODN integration sites in genomic DNA were precisely mapped at the nucleotide level using unbiased amplification and next-generation sequencing (Tsai SQ, et al. Nat Biotechnol. 2015;33(2):187-97). Library construction and GUIDE-Seq sequencing were performed by Creative Biogen Biotechnology (NY, USA) using Unique Molecular Identifier (UMI) for tracking PCR duplicates. Quality checking and trimming were performed on the sequencing reads, using FastQC and Trim_galore, respectively. High quality reads were aligned against the human reference genome (GRCh38), using Bowtie2 (Langmead B, Salzberg SL. Nat Methods. 2012;9(4):357-9) in the “very-sensitive-local” mode, in order to achieve optimal alignments. GUIDE-Seq data analysis was performed employing the R/Bioconductor package GUIDE-seq (Zhu LJ, et al. BMC Genomics. 2017;18(1)), and using UMI to deduplicate reads.
The cloning of plasmids was performed using basic molecular biology techniques. In short, plasmids were digested using restriction enzymes (New England BioLabs) and correct fragments were separated and purified by agarose gel electrophoresis. Fragments were inserted into a dephosphorylated linearized backbone with either Quick Ligase or T4 Ligase after purification with QIAquick PCR Purification Kit (QIAGEN). After ligation, TOP10 chemically competent E. Coli bacteria were transformed and plated on plates containing antibiotics. Plasmid DNA was extracted and purified with Wizard Plus SV Minipreps DNA Purification System (Promega) and EndoFree Plasmid Maxi Kit (QIAGEN). Colonies were screened with control digestions and sequenced. Sequences of vector inserts with main features are reported below:
INSERT
HA Left
Splice Acceptor
KOZAK
GFP
PolyA
HA Right
INSERT
HA Left
Splice Acceptor
KOZAK
GFP
WPRE
PolyA
HA Right
INSERT
HA Left
Splice Acceptor
KOZAZ
GFP
Splice Donor
HA Right
INSERT
HA Left
PGK promoter
KOZAK
GFP
PolyA
HA Right
INSERT
HA Left
Splice Acceptor
KOZAK
GFP
3′UTR
HA Right
INSERT
HA Left
SA
KOZAK
RAG1-CDS
PolyA
HA Right
INSERT
HA Left
PGK promoter
KOZAK
GFP
PolyA
HA Right
INSERT
Cas9
PGK promoter
Puromycin
rTTA
WPRE
The analysis was performed to assess integration of the GFP cassette in different cell types and cell populations. Unstained and single-stained cells or compensation beads were used as negative and positive controls. For apoptosis/necrosis detection cells were stained with 7-Aminoactinomycin D (7-AAD, BD Pharming) and Pacific Blue (PB) Annexin V (Biolegend). HSCs were stained with phycoerythrin cyanine 7 (PECy7) CD34 (Clone: AC136, Miltenyi Biotec), phycoerythrin (PE) CD133 (Miltenyi Biotec) allophycocyanin (APC) CD90 (BD Biosciences). Cell sorting on CD133/CD90 edited cells was performed using MoFlo XDP Cell Sorter (Beckman Coulter).
For mice analysis single-cell suspensions were obtained from bone marrow, spleen, thymus and peripheral blood and stained with the following anti-human antibodies: CD45 (clone REA757), CD3(clone REA613) (Miltenyi biotech), CD19 (clone SJ25C1), CD13 (clone WM15) (BD Biosciences). Human and murine Fc blocking was performed before each staining using human F-Block and murine CD16/CD32 from BD Pharmingen. Live/Dead Fixable Yellow (Thermo Fisher Scientific, Waltham, MA) was added to the antibody mix to exclude dead cells. Samples were acquired on a FACSCanto II (BD) and analyzed with FlowJo software (TreeStar, Ashland, Ore).
Analysis of HSPC composition of MPB-CD34+ cells was performed according to the protocol described in Basso-Ricci L, et al. Cytom Part A. 2017; 91(10):952-65. Briefly, 1.5×105 cells were labeled with fluorescent antibodies against CD3, CD56, CD14, CD61/41, CD135, CD34, CD45RA (Biolegend) and CD33, CD66b, CD38, CD45, CD90, CD10, CD11c, CD19, CD7, and CD71 (BD Biosciences). All samples were acquired through BD LSR-Fortessa (BD Bioscience) cytofluorimeter after Rainbow beads (Spherotech) calibration and raw data were collected through DIVA software (BD Biosciences). The data were subsequently analyzed with FlowJo software Version 9.3.2 (TreeStar) and the graphical output was automatically generated through Prism 6.0c (GraphPad software).
AAV vectors were produced by transient triple transfection of HEK293 cells by calcium phosphate. The following day, the medium was changed with serum-free DMEM and cells were harvested 72 hours after transfection. Cells were lysed by three rounds of freeze-thaw to release the viral particles and the lysate was incubated with DNAsel and RNAse I to eliminate nucleic acids. AAV vector was then purified by two sequential rounds of Cesium Cloride (CsCI2) gradient. For each viral preparation, physical titres (genome copies/mL) were determined by PCR quantification using TaqMan.
2×105 / 5×105 cells per well were electroporated (Lonza, SF Cell line 4D Nucleofector X Kit, program FF120 for K562 or program DC100 for NALM6) with either plasmids or RNPs. Fifteen minutes after electroporation, cells were infected with AAV6 at different MOl: 104; 5×104; 105 Vector Genome/cell, Vg/cell.
Human cord blood CD34+ cells (CB CD34+ cells) were obtained from Lonza (PoieticsTM cat# 2C 101). CB CD34+ cells/ml were stimulated in StemSpan medium supplemented with penicillin/streptomycin antibiotics and early-acting cytokines: Stem cell factor (SCF) 100 ng/ml, Flt3 ligand (Flts-L) 100 ng/ml, Thrombopoietin (TPO) 20 ng/ml, Interleukin 6 (IL- 6) 20 ng/ml, StemRegenin1 (SR1) (1 uM) and 16,16-dimethyl prostaglandin E2 (dmPGE2) (10 uM), UM171 50 nM. Patient mobilized peripheral blood CD34+ cells (CB CD34+ cells) were kindly provided by Dr. Luigi Notarangelo (Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States). MPB CD34+ cells/ml were stimulated in StemSpan medium supplemented with penicillin/streptomycin antibiotics and early-acting cytokines: Stem cell factor (SCF) 300 ng/ml, Flt3 ligand (Flts-L) 300 ng/ml, Thrombopoietin (TPO) 100 ng/ml, Interleukin 3 (IL- 3) 60 ng/ml, StemRegenin1 (SR1) (1 uM) and 16,16-dimethyl prostaglandin E2 (dmPGE2) (10 uM), UM171 50 nM.
After 3 days of expansion 2×105 CD34+ cells per condition were electroporated (Lonza, P3 Primary Cell 4DNucleofectorX Kit, CD34+ program) with RNPs, GSE56 mRNA (p53 inhibitor) was added at a dose of 150 µg/ml when cells were aimed at being transplanted. 15 minutes after electroporation, CD34+ cells were infected with AAV6 at different MOl: 104; 5×104; 105 Vg/cell.
Digital PCR (ddPCR) was performed to assess targeted integration. In short, gDNA was quantified using Nanodrop, and diluted in H2O to reach 5-10 ng per reaction (1-2 ng/ul). It is possible to increase the gDNA quantity per reaction but it is important to remain below the saturation limit of the system. ddPCR master mix was prepared by adding 11 ul ddPCR Supermix for Probes (no dUTP; BioRad), 1.1 ul primer mix Primer forward + Primer reverse (final concentration 0.9 uM) + Probe (final concentration 0.25 uM), 1.1 ul normalizer primer mix, 4.9 ul H2O per reaction. Finally, 17 ul of ddPCR master mix and 5 ul of diluted gDNA were added to each well (we included UT and H2O as negative controls, and mono- or bi allelic clone as positive control to validate the system). Droplets were prepared on the BioRad AutoDG Automated Droplet Generator and the droplet plate was sealed with foil using BioRad PX1 PCR Plate Sealer. The sealed plate was placed into BioRad T100 Thermal Cycler and we ran the appropriate PCR program. The run was read in BioRad QX200 Droplet Reader.
Calculation copies per genome: concentration (copies/µl) gene of interest / concentration (copies/µl) normalizer gene x 2 Calculation percentage of HDR: copies per genome x 100.
Optimized PCR program (40 cycles):
Primers and Probes used for ddPCR assay are the following:
NOD-scid IL2Rgnull mice (NSG; Charles River) were purchased from Charles River Laboratories Inc. (Calco, Italy) and were maintained in specific pathogen-free (SPF) conditions. Mice were transplanted at 8-10 weeks approximately 6 hours after sublethal total body irradiation (120 rad), via intravenous injection of treated HSCPs in phosphate-buffered saline. Gentamicin sulfate (Italfarmaco, Milan, Italy) was administered in drinking water (8 mg/mL) for the first 2 weeks after transplantation to prevent infections. Mice were followed until the sacrifice and then euthanized for ex vivo analyses.
When normality assumptions were not met, non-parametric statistical tests were performed. Kruskal-Wallis test with multiple comparison post-test was performed when comparing more groups. When normality assumptions were met, two-way analysis of variance (ANOVA) was used. For repeated measures over time, two-way ANOVA with Bonferroni’s multiple comparison post-test was utilized. Values are expressed as Mean ± SD.
To further explore the role of the 3′UTR and the selection strategy, further corrective donor sequences numbered 5-8 below were designed and compared with the sequences numbered 1-4 below (
To screen the donors described above, NALM6 cells were transfected with guide 9 and Cas9 as an RNP (25 pmol) and donors as linearized DNA fragments (1600 ng), and then kept in culture with RPMI and 10% FBS. To synchronize cell cycles at G0/G1 phase when the RAG1 gene is mainly expressed, cells were serum starved 16 days after the transfection (
We evaluated GFP expression as the percentage of GFP+ cells and GFP mean fluorescence intensity (MFI) by flow cytometry over time. The proportion of GFP+ cells was low in all conditions as expected because NALM6 are poorly permissive to the editing. We confirmed data described in
We analyzed the GFP expression 4, 5 and 7 days after serum starvation to evaluate the modulation of transgene expression when regulated by the RAG1 promoter. We found that all the donors carrying the 3′UTR or using the endogenous 3′UTR (by SD sequence) resulted in a modulation of GFP expression upon starvation (
To further understand the efficacy of the gene editing approach to correct RAG1 defects, we exploited a novel organoid platform, referred to as artificial thymic organoid (ATO) based on the aggregation of DLL4 expressing stromal cell line (MS5-hDLL4) with CD34+ cells isolated from bone marrow or mobilized peripheral blood. The ATO platform (Seet et al. (2017) Nat Methods) is a suitable tool to study the first steps of human T cell differentiation. We adopted this platform to assess the impact of the gene editing procedure on T cell differentiation and to evaluate the extent to which precise correction allows the overcoming of a T cell differentiation block.
To this end, we set up and optimized the ATO system using CD34+ cells obtained from healthy donor (HD) mobilized peripheral blood (MPB) or bone marrow (BM). One day after editing, CD34+ cells were aggregated with MS5-hDLL4 cells and kept in culture for 4 to 7 weeks to assess the T cell differentiation potential and the editing efficiency (
To overcome the high toxicity likely caused by the exacerbated p53 response and at the same time to enhance HDR efficiency, we tested the effect of gene editing enhancer compounds: to this end we exploited the messenger RNA for the dominant negative p53 GSE56 with or without Ad5-E4orf6/7, or Ad5-E4orf6/7 alone during the editing procedure. Ad5-E4orf6/7 is an adenoviral protein known as a helper in Ad-AAV co-infection, which interacts with several components involved in survival and cell cycle.
We electroporated CD34+ cells in the presence of gene editing enhancers: GSE56 or Ad5-E4orf6/7 alone or the combination of GSE56 and Ad5-E4orf6/7 (COMBO). Cells were then transduced with AAV6 vectors: the corrective donor vector carrying the codon optimized RAG1 downstream of the splice acceptor (SA) and followed by the BGH polyA (SA_coRAG1_BGH polyA) or the AAV6 vector carrying the PGK_GFP_BGHpolyA to track edited cells in HPSC cell subsets (
Moreover, we performed multiparametric analysis of MPB or BM HSPC compositions before (day 0) and after gene editing (day 4) (
After 24 hours from gene editing (at day 4), CD34+ cells were washed, counted and seeded in the presence of MS5-hDLL4 to form thymic organoids to follow T cell differentiation for 4-7 weeks. Starting from the fourth week after the seeding, ATOs were dissociated, and bulk cells edited with the corrective donor were analyzed for HDR efficiency by molecular analysis (ddPCR), while cells edited with pGK_GFP_BGHpolyA AAV6 vector were analyzed by flow cytometry to detect the frequency of GFP+ cells in different T cell subsets. Evaluation of ATOs, showed an improvement of organoid morphology in the presence of the combined action of GSE56+E4orf6/7 (
The molecular analysis of HDR frequency in T cells differentiated from CD34+ edited with SA_coRAG1_BGHpolyA further confirmed the synergistic effect of GSE56+Ad5-E4orf6/7 revealing the higher proportion of edited alleles in the COMBO condition as compared to others (
Overall, these data indicate that the use of gene editing enhancers dramatically enhance HDR editing efficiency in CD34+ cells while preserving their ability to differentiate towards T cell lineage.
The cloning of plasmids was performed using general molecular biology techniques. Briefly, plasmids were digested using restriction enzymes (New England BioLabs) and correct fragments were separated and purified by agarose gel electrophoresis. Fragments were inserted into a dephosphorylated linearized backbone with either Quick Ligase or T4 Ligase after purification with QIAquick PCR Purification Kit (QIAGEN). After ligation, TOP10 chemically competent E. Coli bacteria were transformed and plated on plates containing antibiotics. Plasmid DNA was extracted and purified with Wizard Plus SV Minipreps DNA Purification System (Promega) and EndoFree Plasmid Maxi Kit (QIAGEN). Colonies were screened with control digestions and sequenced. Sequences of the further inserts are shown below:
INSERT
HA Left
Splice Acceptor
KOZAK
GFP
3′UTR
BGH
HA Right
INSERT
HA Left
Splice Acceptor
KOZAK
GFP
IRES
NGFR
BGH
HA Right
INSERT
HA Left
Splice Acceptor
KOZAK
GFP
IRES
PEST
Splice Donor
HA Right
5×105 cells per well were electroporated (Lonza, SF Cell line 4D Nucleofector X Kit, program FF120 for K562 or program DS100 for NALM6) with either plasmids or RNPs. Donor DNA was delivered by electroporation as fragment plasmid spanning the region between the left and right homology arms at a dose of 1600 ng.
Human MPB or BM CD34+ cells were obtained from Lonza and stimulated in StemSpan medium supplemented with penicillin/streptomycin antibiotics and early-acting cytokines: Stem cell factor (SCF) 300 ng/ml, Flt3 ligand (Flt3-L) 300 ng/ml, Thrombopoietin (TPO) 100 ng/ml, StemRegenin1 (SR1) (1 µM) and 16,16-dimethyl prostaglandin E2 (dmPGE2) (10 µM), UM171 35 nM.
After 3 days of expansion, 2-5×105 CD34+ cells per condition were electroporated (Lonza, P3 Primary Cell 4DNucleofector X Kit, CD34+ program) with RNPs, GSE56 mRNA (3 ug/test), Ad5-E4orf6/7 (1.5 ug/test) or GSE56+Ad5-E4orf6/7 as fusion protein with P2A self cleaving peptide (5 ug/test). 15 minutes after electroporation, CD34+ cells were infected with AAV6 at 104 Vg/cell and kept in culture with StemSpan medium supplemented with penicillin/streptomycin antibiotics and early-acting cytokines: Stem cell factor (SCF) 300 ng/ml, Flt3 ligand (Flt3-L) 300 ng/ml, Thrombopoietin (TPO) 100 ng/ml, StemRegenin1 (SR1) (1 µM) and UM171 35 nM.
For the analysis of GFP expression, unstained and single-stained cells or compensation beads were used as negative and positive controls. For apoptosis/necrosis detection, cells were stained with 7-Aminoactinomycin D (7-AAD, BD Pharming). CD34+ cells were stained with phycoerythrin cyanine 7 (PECy7) CD34 (Clone: AC136, Miltenyi Biotec), phycoerythrin (PE) CD133 (Miltenyi Biotec) allophycocyanin (APC) CD90 (BD Biosciences). Cell sorting on CD133/CD90 edited cells was performed using MoFlo XDP Cell Sorter (Beckman Coulter).
Analysis of HSPC composition of MPB/BM-CD34+ cells was performed according to the protocol in (Basso-Ricci et al. (2017) Cytom Part A. 91: 952-65). Briefly, 1.5×105 cells were labeled with fluorescent antibodies against CD3, CD56, CD14, CD61/41, CD135, CD34, CD45RA (Biolegend) and CD33, CD66b, CD38, CD45, CD90, CD10, CD11c, CD19, CD7, and CD71 (BD Biosciences). All samples were acquired through BD LSR-Fortessa (BD Bioscience) cytofluorimeter after Rainbow bead (Spherotech) calibration and raw data were collected through DIVA software (BD Biosciences).
T cell differentiation was analyzed after cell harvesting from ATOs by flow cytometry using the following mAb: TCRab APC (cl. IP26, eBioscience), CD4 Alexa Fluor 700 (cl. OKT4, eBioscience), CD19 PerCP-Cy5.5 (cl. HIB19, Biolegend), CD56 FITC (cl. MEM-188, Biolegend), CD8a PE/Dazzle (cl. RPA-T8, Biolegend), CD45 V500 (cl. HI30, BD Biosciences), CD3 BV421 (cl. UCHT1, BD Biosciences), CD8b PE (cl. 2ST8.5H7, BD Biosciences) LIVE/DEAD™ Fixable Yellow Dead Cell Stain Kit (Invitrogen). All samples were acquired through BD Cantoll (BD Bioscience) cytofluorimeter after Rainbow bead (Spherotech) calibration and raw data were collected through DIVA software (BD Biosciences).
The data were subsequently analyzed with FlowJo software Version 9.3.2 (TreeStar) and the graphical output was automatically generated through Prism 6.0c (GraphPad software).
CFU-C assay was performed 24 h after editing procedure by plating 600 cells in methylcellulose-based medium (MethoCult H4434, StemCell Technologies) supplemented with 100 IU/ml penicillin and 100 µg/ml streptomycin. Three technical replicates were performed for each condition. Two weeks after plating, colonies were counted and identified according to morphological criteria.
ATOs were generated as described in Seet et al (Seet et al. (2017) Nat Methods). Briefly, one day after the editing procedure 5000-10000 CD34+ from BM or MPB samples (commercially available, Lonza) were combined with 150000 MS5-hDLL4 cells per ATO. We normalized the number of “true” live CD34+ cells according to the flow cytometry analysis excluding dead and CD34- cells. Each ATO (5 µI) was then plated in a 0.4 µM Millicell Transwell insert, placed on a well of a 6-well plate containing 1 ml complete RB27 medium supplemented with rhlL-7 (5 ng/ml), rhFlt3-L (5 ng/ml) and 30 µM I-ascorbic acid 2-phosphate sesquimagnesium salt hydrate. Each insert contained a maximum of two ATOs. Medium was changed every 3-4 days. From weeks 4 to 9, ATOs were collected by adding MACS buffer (PBS with 7.5% BSA and 0.5 M EDTA) to each well and pipetting to dissociate the ATOs. Cells were then resuspended in FACS Buffer (PBS 2% FBS), counted and stained with the following antibodies: CD14 PE, CD45 PerCP-Cy5.5, CD1a APC, CD7 Alexa Fluor 700, CD5 PE-Cy7, CD34 VioBlue, CD56 FITC, CD8a APC, TCRab PerCP-Cy5.5, CD3 APC, CD4 PeVio770, CD8b PE. Yellow live dead was used to exclude dead cells. Samples were analyzed using FlowJo software version 10.5.2 (FlowJo, LLC, Ashland, OR).
Digital PCR (ddPCR) was performed to assess targeted integration. Briefly, gDNA was quantified using Nanodrop, and diluted in H2O to reach 5-10 ng per reaction (1-2 ng/ul). It is possible to increase the gDNA quantity per reaction but it is important to remain below the saturation limit of the system. ddPCR master mix was prepared by adding 11 ul ddPCR Supermix for Probes (no dUTP; BioRad), 1.1 ul primer mix Primer forward + Primer reverse (final concentration 0.9 uM) + Probe (final concentration 0.25 uM), 1.1 ul normalizer primer mix, 4.9 ul H2O per reaction. Finally, 17 ul of ddPCR master mix and 5 ul of diluted gDNA were added to each well (we included UT and H2O as negative controls, and mono- or bi allelic clone as positive control to validate the system). Droplets were prepared on the BioRad AutoDG Automated Droplet Generator and the droplet plate was sealed with foil using BioRad PX1 PCR Plate Sealer. The sealed plate was placed into BioRad T100 Thermal Cycler and we ran the appropriate PCR program. The run was read in BioRad QX200 Droplet Reader.
Calculation copies per genome: concentration (copies/µl) gene of interest / concentration (copies/µl) normalizer gene x 2 Calculation percentage of HDR: copies per genome x 100.
Optimized PCR program (40 cycles):
Primers and Probes used for the ddPCR assay are the following:
For gene expression analyses, total RNA was extracted using RNeasy Plus Micro Kit (QIAGEN), according to the manufacturer’s instructions and DNase treatment was performed using RNase-free DNase Set (QIAGEN). cDNA was synthetized with the High Capacity cDNA Reverse Transcription kit (Applied Biosystem). cDNA was then used for qPCR in a Viia7 Real-time PCR thermal cycler using Power Syber Green PCR Master Mix (Applied Biosystems). Data were analyzed with Viia7 Real-Time PCR software (Applied Biosystem). Relative expression of each target gene was represented as fold changes (2-ΔCt) relative to the beta-actin normalizer.
Two further donor constructs were designed and generated:
To test the two corrective donors, NALM6.Rag1KO cells were transfected with guide 9 and Cas9 as RNP (50pmol) and transduced with SA_coRAG1 CDS_BGHpA or SA_coRAG1 CDS_SD AAV6 donor at two doses (104 and 5×104) (
To compare the correction efficiency of the two donors into the selected edited clones, we analyzed the RAG1 CDS expression by RT-qPCR and the recombination activity assessed by the transduction of cells with a LV carrying an inverted GFP cassette which is recombined in presence of a functional RAG1 protein (Liang HE, et al. Immunity. 2002;17:639-651; Bredemeyer AL, et al. Nature. 2006;442(7101):466-470; De Ravin SS, et al. Blood. 2010;116:1263-1271; Lee YN, et al., J Allergy Clin Immunol. 2014;133(4):1099-10).
We observed the increase of RAG1 CDS expression (
To compare the two donors in terms of impact on hematopoietic stem and progenitor cells (HSPC), we edited HSPC derived from the mobilized peripheral blood of HD with guide 9 and Cas9 as RNP (50pmol) in presence of the combination of editing enhancers (GSE56 and Ad5-E4orf6/7) followed by the transduction with SA_coRAG1 CDS_BGHpA or SA_coRAG1 CDS_SD AAV6 donor at three different doses.
We observed comparable editing efficiencies between HSPC edited by SA_coRAG1 CDS_BGHpA or SA_coRAG1 CDS_SD AAV6 donor, increasing according to the dose (
To further compare the two AAV6 donor constructs, we exploited the artificial thymic organoid (ATO) platform to differentiate edited HSPC towards the T cell lineage by applying the protocol previously described (
Overall, these data indicate that both corrective donors are able to obtain efficient targeting while preserving the most primitive CD34+ CD133+ CD90+ cells subpopulation.
All publications mentioned in the above specification are herein incorporated by reference. Various modifications and variations of the disclosed polynucleotides, vectors, RNAs, methods, cells, kits, compositions, systems and uses of the invention will be apparent to the skilled person without departing from the scope and spirit of the invention. Although the invention has been disclosed in connection with specific preferred embodiments, it should be understood that the invention as claimed should not be unduly limited to such specific embodiments. Indeed, various modifications of the disclosed modes for carrying out the invention, which are obvious to the skilled person are intended to be within the scope of the following claims.
| Number | Date | Country | Kind |
|---|---|---|---|
| 2016139.4 | Oct 2020 | GB | national |
| 2021202657 | Apr 2021 | AU | national |
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/EP2021/078222 | 10/12/2021 | WO |
