WO2017112895A1

WO2017112895A1 - F8 gene repair

Info

Publication number: WO2017112895A1
Application number: PCT/US2016/068402
Authority: WO
Inventors: Tom E. HOWARD; David Bennett
Original assignee: Haplomics, Inc.
Priority date: 2015-12-23
Filing date: 2016-12-22
Publication date: 2017-06-29

Abstract

Provided herein are methods and systems and related cDNA, polynucleotides, vehicles and compositions which allow, in several embodiments, to selectively target and repair one or more mutations in the DNA sequence of a given F8 of a specific subject, and, in particular, the one or more mutations of the F8 gene resulting in HA.

Description

F8 GENE REPAIR

CROSS REFERENCE TO RELATED APPLICATIONS

[0001] This application claims the benefit of United States Provisional Application Serial No. 62/387,497, filed December 23, 2015, the full disclosure of which is herein incorporated by reference.

FIELD

[0002] The present disclosure relates to gene mutation repairs and related materials, methods and systems, and in particular relates to Factor VIII mutation repair and tolerance induction and related cDNAs compositions, methods and systems.

BACKGROUND

[0003] Factor VIII (FVIII) is a blood-clotting protein, also known as anti-hemophilic factor (AHF), encoded by a FVIII gene (F8 gene or F8). Certain mutations in the F8 gene (F8) cause hemophilia A (HA) in subjects by resulting in the production of an insufficient amount of the FVIII protein (quantitative deficiency) and/or a dysfunctional version of the FVIII protein (qualitative deficiency). Despite developments of various options to manage HA patients, prophylaxis and treatment of individual patients with HA remains challenging.

SUMMARY

[0004] Provided herein are methods and systems and related cDNA, polynucleotides, vehicles and compositions which allow, in several embodiments, to selectively target and repair one or more mutations in the DNA sequence of a given F8 of a specific subject, and, in particular, the one or more mutations of the F8 gene resulting in HA.

[0005] The F8 gene repair method and systems herein described and related cDNA, polynucleotides, vehicles and compositions herein described, are based on a combined use of one or more DNA scission enzyme(s), DNA-SE(s), such as a nuclease or nickase, with one or more of a homologous recombination (HR)-mediated process repair vehicle (RV) and/or the related use. [0006] The one or more DNA-SE(s), are capable of targeting a specific portion of the F8 gene in a subject to create either one double stranded-DNA break (ds-DB) in the F8 gene or two appropriately oriented and spaced single stranded-DNA breaks (ss-DBs) in opposite strands of the F8 gene.

[0007] The one or more RV comprises one or more cDNA-repair sequences (RS) flanked by an upstream flanking sequence (uFS) and a downstream flanking sequence (dFS) (also called homology arms) to form a DNA donor within the RV. The upstream flanking sequence (uFS) is homologous to a nucleic acid sequence located 5' to the break in the one strand of the F8 gene and the downstream flanking sequence (dFS) is homologous to a nucleic acid sequence located 5' to the break in the other strand of the F8 gene. The RV is configured to include the one or more cDNA-RS, the uFS and the dFS in a configuration to allow insertion of the cDNA-RS through homologous recombination of the upstream flanking sequence (uFS) and the downstream flanking sequence (dFS) with a subject's F8 gene (sF8) to provide a repaired F8 gene.

[0008] In some embodiments of methods and systems herein described and related cDNA, polynucleotides, vehicles and compositions the repaired F8 gene upon expression produces functional FVIII protein that induces immune tolerance to FVIII in the subject and/or confers improved coagulation functionality to the FVIII protein encoded by the repaired F8 gene relative to the unrepaired F8. The RV comprises cDNA-RS comprising wild-type exons corresponding to the F8 exons upstream (5') of the DNA-SE target site.

BRIEF DESCRIPTION OF THE DRAWINGS

[0009] The accompanying drawings, which are incorporated into and constitute a part of this specification, illustrate one or more embodiments of the present disclosure and, together with the detailed description and the examples, serve to explain the principles and implementations of the disclosure.

[0010] FIG. 1 illustrates the CRISPR/Cas9-mediated F8 repair strategy targeting exon 1. [0011] FIG. 2 illustrates the CRISPR/Cas9-mediated F8 repair strategy targeting exon 2. [0012] FIG. 3 is a schematic showing the genomic DNA, spliced mRNA and proteins in normal F8 and F8 that has been repaired by two variations of the present 5' gene repair strategy.

DETAILED DESCRIPTION

[0013] The term "Factor VIII" or "FVIII" as used herein indicates an essential cofactor in the blood coagulation pathway provided by a large plasma glycoprotein that functions in the blood coagulation cascade as a cofactor for the factor IXa-dependent activation of factor X. Factor VIII is tightly associated in the blood with von Willebrand factor (VWF), which serves as a protective carrier protein for factor VIII. In particular Factor VIII circulates in the bloodstream in an inactive form, bound to von Willebrand factor (VWF). Upon injury, FVIII is activated. The activated protein (FVIIIa) interacts with coagulation factor IX, leading to clotting as will be understood by a skilled person.

[0014] FVIII is encoded in a subject by a F8 gene containing 26 exons and spanning 186 kb (Gitschier, et al. Nature 314: 738-740, 1985). In humans the F8 gene is located in the X chromosome. In some subjects (e.g. humans, monkeys, rats) the sequences F8 gene also contains an F8A gene and an F8B gene within intron 22. The F8A gene is intron-less, is contained entirely in intron 22 of the F8 gene in reverse orientation to the F8 gene, and is therefore transcribed in the opposite direction to F8. The F8B gene is also located in intron 22 and is transcribed in opposite direction from F8A gene; its first exon lies within intron 22 and is spliced to exons 23-26.

[0015] The term "orientation" with reference to a gene indicates the direction of the 5'→ 3' DNA strand which provides the sense strand in the double stranded polynucleotide comprising the gene. Accordingly, 5'->3' DNA strand is designated, for a given gene, as 'sense', 'plus' or 'coding' strand when its sequence is identical to the sequence of the premessenger (premRNA), except for uracil (U) in RNA, instead of thymine (T) in DNA. An anti sense strand is instead the 3'->5' strand complementary to the sense strand in a double stranded polynucleotide coding for the gene. The antisense transcribed by the RNA polymerase and is also designated as "template" DNA. Accordingly two genes or sequences thereof within the F8 genomic locus encoded by a same polynucleotide are in a same orientation when their respective sense strands are located on a same strand of the polynucleotide and are in in reverse or opposite orientation when respective sense strands are located on different strand of the polynucleotide. Accordingly two genes or coding sequences within the F8 genomic locus encoded by a same polynucleotide are in a same orientation when their respective sense strands are located on a same strand of the polynucleotide. Two genes or coding sequences within the F8 genomic locus are in reverse or opposite orientation when their respective sense strands are located on the opposing strand of the polynucleotide.

[0016] FVIII is synthesized primarily in the liver of a subject and the primary translation product of 2332 amino acids undergoes extensive post-translational modification, including Island O-linked glycosylation, sulfation, and proteolytic cleavage. FVIII contains Arg-X-X-Arg motifs recognized by intracellular proteases that allow proteolysis at Argl313 and at Argl648. Proteolytic cleavage between Argl648 and Glul649 separates FVIII protein into heavy chain (A1-A2 domains) and light chain (A3-C1-C2 domains), and the protein is secreted as a two- chain molecule associated through a metal ion bridge (Lenting et al. Blood. 1998 Dec l;92(l l):3983-96). The FVIII B domain comprises residues 741-1648 of FVIII. The B domain is reported to be inessential to FVIII physiological function. B domain-deleted FVIII proteins have been described.

[0017] Mutations in the F8 gene can result in production of a dysfunctional version of the Factor VIII protein (qualitative deficiency), and/or in production of Factor VIII in insufficient amounts (quantitative deficiency) causing hemophilia in subjects having the mutations.

[0018] Accordingly, a Factor VIII is indicated as functional when it is produced in a form and an amount allowing a coagulation functionality comparable with the coagulation functionality of the wild type FVIII protein in a healthy subject). A non-functional Factor VIII instead indicates an FVIII protein functioning aberrantly or FVIII proteins present in circulating blood in a reduced or absent amount, leading to the reduction of or absence of the ability to clot in response to injury by the subject. FVIII function is evaluated by routine clinical laboratory methods that are well established in the art and apparent to one of ordinary skill in the art (Barrowcliffe TW, Raut S, Sands D, Hubbard AR: Coagulation and chromogenic assays of factor VIII activity: general aspects, standardization, and recommendations. Semin Thromb Hemost 2002 Jun;28(3):247- 256). [0019] Over 2100 different hemophilia A (HA)-causing mutations have thus far been identified in the F8 loci of unrelated patients which result in the expression of a non-functional and/or deficient FVIII protein. In particular, defects within the F8 affect about one in 5000 newborn males (Jones et al., Identification and removal of promiscuous CD4+ T cell epitope from the CI domain of factor VIII. J. Throm. Haemost. 2005; 3 : 991-1000).

[0020] Mutations of the F8 gene resulting in a non-functional Factor VIII include point mutations, deletions, insertion and inversion as will be understood by a skilled person. For example, of the 2100 unique mutations identified in human F8 gene, over 980 of them being missense mutations, i.e., a point mutation wherein a single nucleotide is changed, resulting in a codon that codes for a different amino acid than its wild-type counterpart (see HAMSTeRS Database: at the http:// web page: hadb.org.uk WebPages/PublicFiles/Mutation Summary.htm). One of the most common mutations resulting in a non-functional and/or deficient FVIII protein includes inversion of intron 22, which leads to a severe type of HA.

[0021] Accordingly, a mutation in an F8 gene of a subject resulting in a non-functional Factor VIII results in an F8 gene comprising at least one Factor VIII functional coding sequence and at least one Factor VIII non-functional coding sequence.

[0022] The term cDNA or complementary DNA indicates double-stranded DNA that can be synthesized from a messenger RNA (mRNA) template in a reaction catalysed by the enzyme reverse transcriptase. Accordingly cDNA can be synthesized from mature (fully spliced) mRNA using the enzyme reverse transcriptase or be synthesized synthetically based on the mRNA sequence as will be understood by a skilled person.

[0023] The terms "polynucleotide", "oligonucleotide" and "nucleic acid," are used interchangeably and refer to an organic polymer composed of two or more monomers including nucleotides, nucleosides or analogs thereof. The term "nucleotide" refers to any of several compounds that consist of a ribose or deoxyribose sugar joined to a purine or pyrimidine base and to a phosphate group and that is the basic structural unit of nucleic acids. The term "nucleoside" refers to a compound (such as guanosine or adenosine) that consists of a purine or pyrimidine base combined with deoxyribose or ribose and is found especially in nucleic acids. The term "nucleotide analog" or "nucleoside analog" refers respectively to a nucleotide or nucleoside in which one or more individual atoms have been replaced with a different atom or a with a different functional group. Exemplary functional groups that can be comprised in an analog include methyl groups and hydroxyl groups and additional groups identifiable by a skilled person. In general, an analogue of a particular nucleotide has the same base-pairing specificity; i.e., an analogue of A will base-pair with T.

[0024] Exemplary monomers of a polynucleotide comprise deoxyribonucleotide, and ribonucleotides. The term "deoxyribonucleotide" refers to the monomer, or single unit, of DNA, or deoxyribonucleic acid. Each deoxyribonucleotide comprises three parts: a nitrogenous base, a deoxyribose sugar, and one or more phosphate groups. The nitrogenous base is typically bonded to the Γ carbon of the deoxyribose, which is distinguished from ribose by the presence of a proton on the 2' carbon rather than an -OH group. The phosphate group is typically bound to the 5' carbon of the sugar. The term "ribonucleotide" refers to the monomer, or single unit, of RNA, or ribonucleic acid. Ribonucleotides have one, two, or three phosphate groups attached to the ribose sugar.

[0025] Accordingly, the term "polynucleotide", "oligonucleotide includes nucleic acids of any length, and in particular DNA, RNA, analogs thereof, and fragments thereof. Polynucleotides can typically be provided in single-stranded form or double-stranded form (herein also duplex form, or duplex).

[0026] A "single-stranded polynucleotide" refers to an individual string of monomers linked together through an alternating sugar phosphate backbone. In particular, the sugar of one nucleotide is bond to the phosphate of the next adjacent nucleotide by a phosphodiester bond. Depending on the sequence of the nucleotides, a single-stranded polynucleotide can have various secondary structures, such as the stem-loop or hairpin structure, through intramolecular self-base-paring. A hairpin loop or stem loop structure occurs when two regions of the same strand, usually complementary in nucleotide sequence when read in opposite directions, base- pairs to form a double helix that ends in an unpaired loop. The resulting lollipop-shaped structure is a key building block of many RNA secondary structures. The term "small hairpin RNA" or "short hairpin RNA" or "shRNA" as used herein indicate a sequence of RNA that makes a tight hairpin turn and can be used to silence gene expression via RNAi. [0027] A "double-stranded polynucleotide", "duplex polynucleotide" refers to two single- stranded polynucleotides bound to each other through complementarily binding. The duplex typically has a helical structure, such as double-stranded DNA (dsDNA) molecule or double stranded RNA, is maintained largely by non-covalent bonding of base pairs between the strands, and by base stacking interactions.

[0028] In embodiments, herein described a cDNA-repair sequence (RS) is a double stranded polynucleotide comprising a repaired version of the entire F8 gene non-functional coding sequence of the subject or of a portion thereof. In particular in methods and compositions herein described the cDNA-RS comprise at least a repaired version the portion of the non-functional sequence of the Factor VIII of the subject comprising the one or more mutations in the Factor VII of the subject. In some embodiments, cDNA-RS described herein further comprises introns and/or exons located upstream and/or downstream to the non-functional coding sequence. In embodiments described herein, the cDNA-RS is designed so that once recombined into the desired region in the F8 genomic locus it remains in-frame with upstream and downstream functional coding sequences.

[0029] Accordingly in methods systems and related cDNA vehicles and compositions herein described a cDNA-RS are designed based on the one or more mutations within the subject's F8 gene targeted for replacement and repair. In an embodiment, the gene mutation targeted for repair is a point mutation, and the cDNA-RS includes a nucleic acid sequence that replaces the point mutation with a functional sequence for Factor VIII that does not include the point mutation, for example, the wild-type F8 sequence. In one embodiment, the gene mutation targeted for repair is a deletion and the cDNA-RS includes a nucleic acid sequence that replaces the deletion with a functional Factor VIII sequence that does not include the deletion, for example, a corresponding F8 sequence of the wild-type F8 sequence.

[0030] In one embodiment, the gene mutation targeted for repair is an inversion, and the cDNA- RS includes a nucleic acid sequence that encodes a truncated FVIII polypeptide that, upon insertion into the F8 genome, repairs the inversion and provides for the production of a functional FVIII protein. In one embodiment, the gene mutation targeted for repair is an inversion of intron 1. [0031] In the methods and compositions described herein, the cDNA-RS can contain sequences that are homologous to a subject's genomic sequences in the region of interest, thereby stimulating homologous recombination to insert a non-identical sequence in the region of interest.

[0032] The term "homologous" and "homology" when referred to protein or polynucleotide sequences is defined in terms of sequence similarities and percent identity between sequences. Accordingly homologous sequences indicate sequences having a percent identify of at least 80% versus sequences with a percentage identify lower than 80%, which are instead indicated as nonhomologous. The terms "percent homology" and "sequence similarity" are often used interchangeably. Sequence regions that are homologous are also called conserved.

[0033] Thus, in certain embodiments, portions of the cDNA-RS that are homologous to sequences in the region of interest exhibit between about 80 to about 99% sequence identity to the subject's genomic sequence that is replaced. In other embodiments, the homology between the cDNA-RS and the subject's genomic sequence is higher than 99%, for example if only 1 nucleotide differs as between the cDNA-RS and the subject's genomic sequences of over 100 contiguous base pairs. In certain cases, a non-homologous portion of the cDNA-RS contains sequences not present in the region of interest, such that new sequences are introduced into the region of interest. In these instances, the non-homologous sequence is generally flanked by sequences of 50-1,000 base pairs, or any number of base pairs greater than 1,000, that are homologous or identical to the subject's sequences in the region of interest. In other embodiments, the cDNA-RS containing non-homologous sequence is inserted into the subject's genome by homologous recombination mechanisms. Accordingly, cDNA-RS herein described can be comprised within a cDNA sequence encoding for a truncated Factor VIII. The term "truncated FVIII polypeptide" refers to a polypeptide that contains less than the full length of FVIII protein. The truncated FVIII polypeptide is encoded in a portion of the full length F8 gene such as a partial F8 cDNA replacement sequence (cDNA-RS). For example, for FVIII polypeptide that is truncated from the corresponding 3' end of the oligonucleotide sequence, a variable amount of the oligonucleotide sequence can be missing from the 3' end of the gene. In one embodiment, the truncated FVIII polypeptide is encoded by exons 1-14.

[0034] In embodiments herein described the cDNA-RS are designed in combination with the selection of DNA scission Enzyme (DNA-SE) and the related target site.

[0035] A DNA scission enzyme is an enzyme that catalyzes the hydrolytic cleavage of phosphodiester linkages in the DNA backbone in a specific target site. DNA scission refers to the breaking of the chemical bonds between adjacent nucleotides on a nucleotide strand or sequence. DNA scission enzymes comprise nucleases and nickases. "Nucleases" or "Deoxyribonucleases" are enzymes capable of hydrolyzing phosphodiester bonds that link nucleotides. A wide variety of deoxyribonucleases are known, which differ in their substrate specificities, chemical mechanisms, and biological functions. DNA-SEs described herein break the genomic DNA at a target site on the F8 gene upstream from a region to be replaced by a repair vehicle comprising a cDNA-RS. The target site is preferentially located about 50-100 base pairs downstream of the desired region to be replaced on the F8 genomic locus so as to optimize recombination by the repair vehicle, donor plasmid, or editing cassette comprising the cDNA- RS. In studies, it was seen that when a target site is located about 50-100 base pairs adjacent to the desired region to be replaced on the F8 genomic locus, optimal recombination was observed by the repair vehicle, donor plasmid, or editing cassette comprising the cDNA-RS. Following recombination of the repair vehicle, donor plasmid, or editing cassette into the target site, expression of the repaired F8 gene segment results in expression of a repaired and functional FVIII protein. DNA-SEs described herein comprise nucleases or nickases coupled to nucleotide sequences that specifically guide the nuclease or nickase to the target site. DNA-SEs described herein include heterodimeric nucleases that bind to specific regions of the F8 gene, nucleases or nickases guided to specific sites of the F8 gene by short RNA sequences or combinations thereof. Exemplary nucleases include transcription activator-like effector nuclease (TALEN), a zinc finger nuclease (ZFN), a CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)- associated (Cas) nuclease, Paired CRISPR, or CRISPR with ZFN. "Nickases" are enzyme that causes nicks (breaks in one strand) of double stranded nucleic acid, allowing it to unwind. An exemplary nickase is Cas9n (the D10A mutant nickase version of Cas9).

[0036] In embodiments described herein, DNA-SEs are designed to comprise multiple elements to efficiently target a specific target site within the F8 gene and function as heterodimers or heterodimeric nucleases. Such heterodimeric nucleases comprise two monomers (a left monomer and a right monomer) that each comprise a nuclear localization signal, a monomer subunit for binding to a specific region of the F8 gene and a Fokl nuclease domain. Further, the monomer subunit for binding of the left monomer binds upstream (5') of the target site, while the monomer subunit of the right monomer binds to a region downstream (3') of the target site. In such embodiments, a double-stranded break in the DNA of the target region is mediated by dimerization of the Fok-1 nucleases. The monomer binding subunits are designed such that off- target binding non-specific DNA breaks are minimized and such that the location of the target site is optimally placed downstream from a region to be replaced by a repair vehicle comprising a cDNA-RS.

[0037] In embodiments described herein, DNA-SEs are designed to efficiently target a specific target site within the F8 gene by using a short RNA to guide a nuclease to the desired target site; such a DNA-SE is referenced in FIG. 1 and 2 as the CRISPR-Associated Gene Editing system. Such DNA-SEs comprise at least a complementary single strand RNA (CRISPR RNA, labeled as CRISPR g-RNA in FIG. 1 , for example) that localizes a Cas9 nuclease to a target site on F8 gene. The CRISPR RNA binds to a region upstream of a desired target site, allowing the Cas9 nuclease to cause a double-strand break. The CRISPR RNA is designed such that off-target binding non-specific DNA breaks are minimized and such that the location of the target site is optimally placed upstream from a region to be replaced by a repair vehicle comprising a cDNA- RS. In embodiments described herein, such a DNA-SE is modified to further minimize off-target DNA scission events by modifying the CRISPR-Associated Gene editing system DNA-SE described above to carry a mutated Cas9 that functions as a nickase (Cas9-nickase). In such embodiments, CRISPR RNA that is longer in length than the CRISPR RNA of the DNA-SE referenced in FIG. 1 is used to guide a first Cas9-nickase to a target site. The Cas9-nickase then makes a single strand break in the DNA at the target site. A second Cas9-nickase is guided to a second target on the complementary DNA strand site by a second CRISPR RNAand the second Cas9-nickase makes a single strand break in the complementary DNA strand. The two nicking target sites can be separated by 0-30 nucleotides.

[0038] In the methods and compositions set forth herein, the DNA-SEs that targets a mutation in F8 for repair are, for example, a transcription activator-like effector nuclease (TALEN), a zinc finger nuclease (ZFN), a CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)- associated (Cas) nuclease, Paired CRISPR, or CRISPR with ZFN, as described in detail below. [0039] In the methods and systems and related compositions set forth herein, the DNA-SEs is selected for the DNA-SE ability to target a mutation in the F8 gene for repair by cleaving the F8 gene sequence for subsequent repair by the cDNA-RS. In particular in methods and systems and related compositions herein described a DNA-SE has the capability of creating a first break in one strand of the F8 gene and a second break in the other strand of the F8 gene, or a single double-stranded DNA break, which defines a target site located in a position of the F8 gene configured to allow replacement of the F8 gene non-functional coding sequence by a cDNA-RS.

[0040] In methods and systems herein described, the DNA-SE has a target site downstream of the F8 gene nonfunctional coding sequence.

[0041] The wording "upstream" as used herein refers to a position in a polynucleotide relative to a 5' end of the reference point in the polynucleotide. Therefore a sequence or series of nucleotide residues that is "upstream" relative to a site, region or sequence indicates a sequence or series of nucleotides before the 5' end site, region or sequence of the polynucleotide in a 5' to 3' direction.

[0042] The wording "downstream" as used herein refers to a position in a polynucleotide relative to a 3' end of the reference point in the polynucleotide. Therefore a sequence or series of nucleotide residues that is "downstream" relative to a site, region or sequence indicates a sequence or series of nucleotides after the 3' end site, region or sequence of the polynucleotide in a 5' to 3' direction.

[0043] In methods and systems herein described, the cDNA-RS is designed to provide a repaired version of the F8 gene nonfunctional coding sequence or a portion thereof encompassing the one or more mutations to be repaired in frame with the F8 gene functional coding sequence upstream and/or downstream of the DNA-SE target site.

[0044] A sequence or series of nucleotide residues that is "in-frame" or "in frame" with a F8 gene functional sequence refers to a sequence or series of nucleotide residues that does not cause a shift in the open reading frame of the F8 functional sequence. An open reading frame (ORF) is the part of a reading frame of a coding sequence that encodes for a protein or peptide according to the standard genetic code, in this case a functional Factor VIII. An ORF is a continuous stretch of DNA beginning with a start codon, usually methionine (ATG), and ending with a stop codon (TAA, TAG or TGA in most genomes) as will be understood by a skilled person. Accordingly, sequence or series of nucleotide residues is "out of frame" or "out-of-frame" with an F8 functional sequence when to the sequence or series of nucleotide residues causes a shift in the open reading frame of the F8 functional sequence thus resulting in a sequence coding for a nonfunctional Factor VIII.

[0045] For example in some embodiments, the cDNA-RS provides a repaired version of the F8 nonfunctional sequence in a same orientation with the wild type F8 gene. In some embodiments, the cDNA-RS provides a repaired version of the F8 nonfunctional sequence in opposite orientation with the wild type F8 gene in frame with the functional sequence of the F8 gene following the inversion.

[0046] In embodiments herein described, selection of a suitable DNA-SE is performed by selecting a target site among candidate target sites on the F8 gene based on the location of the one or more mutations of the F8 gene to be repaired, the features of the cDNA-RS to be used on the repair, and the donor sequence comprising the cDNA-RS flanked by flanking sequence that is homologous to nucleic acid sequences of the F8 gene.

[0047] The wording "flanked" as used herein refers to a position relative to ends of a reference item. More specifically, in referring to a polynucleotide sequences, "flanked" refers to having a sequences upstream and downstream the end of the polynucleotide sequences. In particular, a flanked referenced polynucleotide has a first sequence or series of nucleotide residues positioned adjacent to the 5' end of the referenced polynucleotide and a second sequence or series of nucleotide residues positioned adjacent to the 3' end of the referenced polynucleotide.

[0048] In some embodiments, selection of a suitable DNA-SE uses algorithms or other means directed to minimize off-target effects associated with the DNA-SEs. For example, in some embodiments a program such as PROGNOS can be used to identify the target site. The PROGNOS algorithm locates for example potential TALEN off-target sites by searching through the genome for sequences similar to the intended TALEN design. It ranks these similar sequences according to various features of TALEN-DNA interactions, including RVD base preferences, polarity of TALEN specificity (5' end is more specific), context dependent compensation of strong RVDs (such as NN and HD), and a model of dimeric TALEN interactions. The PROGNOS model has been shown to accurately predict the majority of all known TALEN off-target sites as discussed in Fine et al. Nucleic Acids Research 2014 v42(6) e42, incorporated herein by reference. As another example, an algorithm employed for ranking potential CRISPR off-target sites disclosed in Hsu et al. Nature Biotech 2013 v31 p827-832, incorporate herein by reference, uses a position-weight-matrix (PWM) to determine the importance of different types of mismatches at each position in the target sequence (both the DNA bases targeted by the guide strand as well as the protospacer adjacent motif sequence). This PWM was derived by experimentally observing the drop in nuclease activity at a target site of artificial guide strands (relative to a perfectly matched guide strand) containing different types of mismatches. This PWM is then used to screen potential sites in the genome with homology to the intended target and assign them a score indicating their likelihood of off-target activity.

[0049] In embodiments herein described a target site is selected based on the features of a cDNA-RS used for repair. Factors influencing the location of the target site include the desired length and sequence of cDNA-RS, proximity of the target site to upstream and downstream functional coding sequences, proximity of the target site to upstream and downstream nonfunctional coding sequences, likelihood of off-target or non-specific DNA scission, likelihood of off-target or non-specific homologous recombination of the cDNA-RS, homology to off-target genomic sites and nature of the DNA scission enzyme used.

[0050] In particular in some embodiments the target site is selected to have a location relative to the desired region of replacement on the F8 genomic locus that optimizes the recombination rate of the cDNA-RS. For instance, in some embodiments, the target site is selected to be from 50- 100 nucleotides downstream of the desired region of replacement on the F8 genomic locus so as to optimize the recombination of the cDNA-RS following scission of the genomic DNA. Location of the target site within about 50-100 base pairs adjacent to the desired region to be replaced on the F8 genomic locus results in optimal recombination by the repair vehicle, donor plasmid, or editing cassette comprising the cDNA-RS. Optimal recombination is an important aspect as it results in an increase in the likelihood that the cDNA-RS will be incorporated at the targeted site within an individual cell and/or population of cells following exposure to the cDNA -RS. Also, following recombination of the repair vehicle, donor plasmid, or editing cassette into the target site, expression of the repaired F8 gene segment results in expression of a repaired and functional FVIII protein. Thus, conditions promoting optimal recombination greatly contribute towards achieving optimal expression of a repaired and functional protein for treatment and/or induction of immune tolerance.

[0051] In embodiments herein described a target site is also selected based on the features of the donor DNA comprising the cDNA-RS flanked by an upstream flanking sequence (uFS) and a downstream flanking sequence (dFS).

[0052] In particular, in embodiments herein described, in a donor sequence the cDNA-RS is flanked on each side by regions of nucleic acids which are homologous to the subject's F8 gene that are called flanking sequences. Each of the flanking sequence can include about 20, 50, 75, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000 or more nucleotides homologous to regions within the subject's F8 gene. In particular, the upstream flanking sequence (uFS) is homologous to a nucleic acid sequence upstream of the first break in the one strand of the F8 gene by a selected DNA-SE and the downstream flanking sequence (dFS) homologous to a nucleic acid sequences downstream of the second break in the other strand of the F8 gene by the selected DNA-SE.

[0053] In some embodiments, each of the homologous regions flanking the donor sequence is between about 200 to about 1,200 nucleotides, e.g. between 400 and about 1000, between about 600 and about 900, or between about 800 and about 900 nucleotides. Thus, each donor sequence includes a cDNA-RS replacing an endogenous mutation in the subject's F8 gene, and upstream and downstream flanking sequences which are homologous to the F8 gene. In preferred embodiments the length of the homologous regions flanking the donor sequence are between 700 - 800 nucleotides in length.

[0054] In some embodiments, the cDNA-RS is comprised within an editing cassette together with one or more transcriptional elements and the upstream flanking sequence (uFS) and downstream flanking sequence (dFS) are located adjacent at the 5' end and at 3' end of the editing cassette, respectively.

[0055] The wording "adjacent" as used herein refers to a location and/or position nearest in space or position; immediately adjoining without intervening space. More specifically, when referring to a sequence or series of nucleotide residues that is "adjacent" to a site or sequence, "adjacent" refers to a location and/or position next to or proximate to the reference site or position without intervening nucleotide residues.

[0056] As used throughout, "operably linked" is defined as a functional linkage between two or more elements. In particular, the term "operably linked" or "operably connected" indicates an operating interconnection between two elements finalized to the expression and translation of a sequence. Functional linkages between elements in the sense of the present disclosure are identifiable by a skilled person. For example, an operable linkage between a polynucleotide of interest and a regulatory sequence (i.e., a promoter) comprise a functional link that allows for expression of the polynucleotide of interest. Another example of operable linkage is provided by a control sequence ligated to a coding sequence in such a way that expression of the coding sequence is achieved under conditions compatible with the control sequences. Operably linked elements are contiguous or non-contiguous and comprise polynucleotides in a same or different reading frame. In an embodiment, each of the operably linked polynucleotide is comprised within the editing cassette. The cassette additionally contains at least one additional gene to be co-transformed into the organism (e.g. a selectable marker gene). One or more additional genes can also be provided on multiple expression cassettes that can further comprise a plurality of restriction sites and/or recombination sites for insertion of other polynucleotides.

[0057] In embodiments herein described, editing cassettes refers to a mobile genetic element that contains a gene and a sequence used to repair an F8 non-functional coding sequence. Editing cassettes carry at least a cDNA-repair sequence (RS) flanked by an upstream flanking sequence (uFS) and a downstream flanking sequence (dFS) to form a DNA donor. The cDNA-RS is a repaired version of the F8 non-functional F8 gene sequence. The upstream flanking sequence (uFS) is homologous to a nucleic acid sequence upstream of a target site on the F8 gene and the downstream flanking sequence (dFS) is homologous to a nucleic acid sequences downstream of a target site on the F8 gene. In embodiments described herein, the cDNA-RS of the editing cassette is designed and oriented such that when recombined into the desired region on the F8 gene, it is in-frame with upstream and downstream functional coding sequences. Exemplary editing cassettes include the sequence comprising the upstream flanking sequence (uFS), a promoter or polycistronic mRNA element, cDNA of Exons 1-14 and the downstream flanking sequence (dFS). [0058] In embodiments herein described, following identification of a target site a DNA-SE is configured for binding to the F8 gene at the selected target site. The DNA-SE is modified to target a target site that is preferentially located about 50-100 base pairs downstream of the desired region to be replaced on the F8 genomic locus so as to optimize recombination by the repair vehicle, donor plasmid, editing cassette comprising the cDNA-RS. Location of the target site within about 50-100 base pairs adjacent to the desired region to be replaced on the F8 genomic locus results in optimal recombination by the repair vehicle, donor plasmid, or editing cassette comprising the cDNA-RS. Optimal recombination is an important aspect as it results in an increase in the likelihood that the cDNA-RS will be incorporated at the targeted site within an individual cell and/or population of cells following exposure to the cDNA -RS. Also, following recombination of the repair vehicle, donor plasmid, or editing cassette into the target site, expression of the repaired F8 gene segment results in expression of a repaired and functional FVIII protein. Thus, conditions promoting optimal recombination greatly contribute towards achieving optimal expression of a repaired and functional protein for treatment and/or induction of immune tolerance. DNA-SEs described herein are modified to comprise nucleases or nickases coupled to nucleotide sequences that specifically guide the nuclease or nickase to the target site. DNA-SEs described herein include heterodimeric nucleases that bind to specific regions of the F8 gene, nucleases or nickases guided to specific sites of the F8 gene by short RNA sequences or combinations thereof. A DNA-SE can be designed and assembled using molecular techniques commonly known and available to one of ordinary skill in the art and as described in Ran, F. A. et al. Genome engineering using the CRISPR-Cas9 system. Nat Protoc 8, 2281-2308 (2013).

[0059] In embodiments described herein, polynucleotides and vectors comprising the DNA-SE and the DNA donor are provided for introduction into a cell of a subject having a mutated F8 gene. In particular the DNA-SE comprises nucleases or nickases coupled to nucleotide sequences that specifically guide the nuclease or nickase to the target site. DNA-SEs described herein include heterodimeric nucleases that bind to specific regions of the F8 gene, nucleases or nickases guided to specific sites of the F8 gene by short RNA sequences or combinations thereof. The polynucleotides and vectors comprising the DNA-SE and DNA donor vary in design and function as a function of the type of gene editing system that is utilized. For instance, different polynucleotides and vectors are used for TALENs, CRISPR/Cas9 nuclease, CRISPR/Cas9n nickase, and CRISPR/Cas9 RFN. [0060] In embodiments herein described, a "donor plasmid" refers to a mobile genetic element in the form of a plasmid, vector, sequence or strand that is be used as a means to deliver or donate a polynucleotide sequence to a specific genomic site. The donor plasmid contains DNA and/or cDNA. Embodiments of donor plasmids described herein consist of at least the following elements: a cDNA-RS for repair of a non-functional F8 coding sequence flanked by an upstream flanking sequence (uFS) and a downstream flanking sequence (dFS). The upstream flanking sequence (uFS) is homologous to a nucleic acid sequence located 5' to the break in the one strand of the F8 gene and the downstream flanking sequence (dFS) is homologous to a nucleic acid sequence located 5' to the break in the other strand of the F8 gene. Donor plasmids are designed and configured to optimally integrate by homologous recombination at a target site following DNA scission by a DNA-SE. The cDNA-RS of donor plasmid designed and oriented such that when recombined into the desired region on the F8 gene, it is in-frame with upstream and downstream functional coding sequences.

[0061] In embodiments herein described the DNA donor is comprised within a repair vehicle (RV). The RV can be a sequence of DNA in the form of a circular plasmid. The RV can be a linear sequence of DNA. The RV provides the template, through which by homologous recombination, a targeted DNA sequence can be introduced into the genomic DNA of the subject at the site of a targeted double strand break. In addition to a cDNA-RS, optionally an editing cassette and flanking sequences of the DNA donor, a RV can also contain sequences important for the preparation of the DNA sequence in bacteria, such as an antibiotic resistance gene for ampicillin, an antibiotic resistance gene for kanamycin, and/or other antibiotic resistance genes. The RV can also contain intervening DNA sequences important for the integrity of the plasmid or linear sequence of DNA, such as sequences that are located between antibiotic-resistance gene-encoding sequences and cDNA-RS, and which intervening DNA sequences can contain gene-encoding sequences or alternatively can contain sequences that do not encode for a gene.

[0062] In methods and systems herein described polynucleotides coding for a DNA-SE and one or more repair vehicles are introduced into a cell of a subject having a mutated F8 for a time and under conditions allowing homologous recombination of the upstream flanking sequence (uFS) and the downstream flanking sequence (dFS) of the donor DNA to corresponding sequences of the F8 gene. [0063] In particular, in some embodiments herein described, the targeting and repair of a mutated F8 gene in a subject is achieved by introducing into a subject's cell one or more plasmids encoding a DNA-SE that specifically targets the F8 mutation of the subject. Each subject's mutation for targeting and repair can be determined using techniques known in the art. The identified mutation in the subject is then directly targeted by DNA-SE for correction according e.g. by selecting a DNA-SE target site located 3' to the mutated non-functional F8 gene sequence. Alternatively, the subject's F8 gene mutations can be corrected by targeting a region of the F8 gene downstream (or 3') from the non-functional coding sequence (i.e. where the mutation occurred), and adding back the corresponding upstream coding regions of the F8 gene. For example, sequence located downstream of exon 14, such as is in the 3' end of exon 14, the 5' end of intron 14, the 3' end of intron 14 or the 5' end of exon 15, could be targeted by the DNA-SE. This allows for gene repair of upstream mutations (eg. missense mutations in exon 1 to exon 14) and inversions (such as the intron 1 inversion), due to the replacement of exons 1 to 14 with the cDNA-RS discussed above. In other embodiments, the F8 gene can be targeted at additional regions downstream, in order to capture an increasing proportion of F8 gene mutations. Thus, the DNA-SE can be engineered to specifically target a subject's F8 mutation, or alternatively, can target regions downstream of a subject's F8 mutation, in order to correct the mutation in combination with a donor sequence which provides cDNA-RS, which is a partial F8 gene during homologous recombination that replaces, and thus repairs, the mutated portion of the subject's F8 gene and possibly includes functional coding sequences downstream of the nonfunctional coding sequence of the mutated F8 gene.

[0064] In particular in some embodiments of methods and systems herein described the repair is performed by introducing into a cell of the subject one or more nucleic acids encoding a DNA scission enzyme (DNA-SE) having a DNA-SE target site located downstream from a 3' end of at least one Factor VIII non-functional coding sequence to be repaired. In one example, the DNA- SE target site is located about 50 bp to about 100 bp downstream from a 3' end of the Factor VIII non-functional coding sequence to be repaired; and the repair is performed by introducing into the cell of the subject a cDNA repair editing cassette comprising a cDNA repair sequence (cDNA-RS) coding for a repaired version of the Factor VIII non-functional coding sequence, the cDNA repair sequence in frame with the Factor VIII functional coding sequence. In those embodiments, location of the target site within about 50-100 base pairs downstream of the desired region to be replaced on the F8 genomic locus results in optimal recombination by the repair vehicle, donor plasmid, or editing cassette comprising the cDNA-RS. Optimal recombination is an important aspect as it results in an increase in the likelihood that the cDNA- RS will be incorporated at the targeted site within an individual cell and/or population of cells following exposure to the cDNA -RS. Also, following recombination of the repair vehicle, donor plasmid, or editing cassette into the target site, expression of the repaired F8 gene segment results in expression of a repaired and functional FVIII protein. Thus, conditions promoting optimal recombination greatly contribute towards achieving optimal expression of a repaired and functional protein for treatment and/or induction of immune tolerance.

[0065] Also in those embodiments the cDNA repair editing cassette within a DNA donor where the cDNA repair editing cassette is flanked by an upstream flanking sequence (uFS) homologous to a genomic nucleic acid sequence of at least 200 bp from the DNA-SE target site and a downstream flanking sequence (dFS) homologous to a genomic nucleic acid sequences of at least 200 bp downstream of the DNA-SE target site. In those embodiments introducing one more nucleic acids encoding a DNA scission enzyme (DNA-SE) and introducing a cDNA repair editing cassette is performed to allow homologous recombination of the upstream flanking sequence (uFS) and the downstream flanking sequence (dFS) with corresponding genomic sequences of the Factor VIII gene of the subject. The DNA-SE target site is located upstream of the endogenous functional coding sequence. In some embodiments, the DNA-SE target site is adjacent to a 5' end of the Factor VIII functional coding sequence, and in particular the 5' end of the functional coding sequence can be a 5' end of a Factor VIII exon.

[0066] In some embodiments, the upstream flanking sequence (uFS) is homologous to a genomic nucleic acid sequence of at least about 400 bp from the DNA-SE target site and the downstream flanking sequence (dFS) is homologous to a genomic nucleic acid sequences of at least about 400 bp downstream of the DNA-SE target site.

[0067] In some embodiments, the upstream flanking sequence (uFS) is homologous to a genomic nucleic acid sequence of at least about 400-800 bp from the DNA-SE target site and the downstream flanking sequence (dFS) is homologous to a genomic nucleic acid sequences of at least about 400-800 bp downstream of the DNA-SE target site. [0068] In some embodiments, the uFS is homologous to a genomic nucleic acid sequence of at least about 800-3000 bp from the DNA-SE target site and the dFS is homologous to a genomic nucleic acid sequences of at least about 800-3000 bp downstream of the DNA-SE target site.

[0069] In some embodiments, the cDNA repair sequence (cDNA-RS) encodes for one or more repaired Factor VIII non-functional sequence consisting essentially of the amino acid sequence encoded by exons 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, or an in frame portion or combination thereof.

[0070] In some embodiments, the methods and compositions set forth herein, the DNA-SEs that targets a mutation in F8 for repair are, for example, a transcription activator-like effector nuclease (TALEN), a zinc finger nuclease (ZFN), a CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-associated (Cas) nuclease (CasN), a pair of wild-type CasN each containing its own CRISPR-single-guide-RNA (CRISPR-sgRNA) targeting a deep intronic sequence of a F8 intron flanking the two sides of a large F8 exonic duplication (to repair a HA- causing F8 mutation comprised of a large duplication of one or more F8 exons by introducing a double-stranded DNA (dsDNA) break on each side of large exonic duplication such that intervening genomic DNA sequence comprising the duplication can be deleted, thereby restoring the transcriptional and post-transcriptional functionality to the repair F8 sequence), a pair of missense mutant Cas nickases — each capable of introducing only a single-stranded DNA (ssDNA) break - using paired CRISPR guide RNAs, or CRISPR with RFN, as described in detail below.

[0071] To minimize off-target effects associated with the DNA-SEs, a program such as PROGNOS is used. The PROGNOS algorithm locates for example potential TALEN off-target sites by searching through the genome for sequences similar to the intended TALEN design. It ranks these similar sequences according to various features of TALEN-DNA interactions, including RVD base preferences, polarity of TALEN specificity (5' end is more specific), context dependent compensation of strong RVDs (such as NN and HD), and a model of dimeric TALEN interactions. The PROGNOS model has been shown to accurately predict the majority of all known TALEN off-target sites as discussed in Fine et al. Nucleic Acids Research 2014 v42(6) e42, incorporated herein by reference in its entirety. [0072] The algorithm employed for ranking potential CRISPR off-target sites described in Hsu et al. Nature Biotech 2013 v31 p827-832, incorporate herein by reference, uses a position- weight-matrix (PWM) to determine the importance of different types of mismatches at each position in the target sequence (both the DNA bases targeted by the guide strand as well as the protospacer adjacent motif sequence). This PWM was derived by experimentally observing the drop in nuclease activity at a target site of artificial guide strands (relative to a perfectly matched guide strand) containing different types of mismatches. This PWM is then used to screen potential sites in the genome with homology to the intended target and assign them a score indicating their likelihood of off-target activity.

[0073] In some embodiments the DNA-SE is Transcription Activator-Like Effector Nucleases (TALENs). The C-terminus of the TALEN component carries nuclear localization signals (NLSs), allowing import of the protein to the nucleus. Downstream of the NLSs, an acidic activation domain (AD) is also present, which is probably involved in the recruitment of the host transcriptional machinery. The central region harbors a series of nearly identical 34/35 amino acids modules repeated in tandem. Residues in positions 12 and 13 are highly variable and are referred to as repeat-variable di-residues (RVDs). Studies of TALENs such as AvrBs3 from X. axonopodis pv. vesicatoria and the genomic regions (e.g., promoters) they bind, led two teams to "crack the TALE code" by recognizing that each RVD in a repeat of a particular TALE determines the interaction with a single nucleotide. Most of the variation between TALEs relies on the number (ranging from 5.5 to 33.5) and/or the order of the quasi-identical repeats. Estimates using design criteria derived from the features of naturally occurring TALEs suggest that, on average, a suitable TALEN target site can be found every 35 base pairs in genomic DNA. Compared with ZFNs, the cloning process of TALENs is easier, the specificity of recognized target sequences is higher, and off-target effects are lower. In one study, TALENs designed to target chemokine receptor 5 (CCR5) were shown to have very little activity at the highly homologous chemokine receptor 2 (CCR2) locus, as compared with CCR5-specific ZFNs that had similar activity at the two sites.

[0074] Methods and systems and related cDNA, polynucleotides, vehicles and compositions can be configured to allow selective repair of one or more mutations in the sequence of Factor VIII gene of a subject according to a downstream repair strategy as will be understood by a skilled person. According to downstream repair strategy, one or more DNA scission enzyme (DNA-SE) such as a nuclease or nickase targets a portion of the F8 gene of the subject and creates a first break in one strand of the F8 gene and a second break in the other strand of the F8 gene for subsequent repair by a repair vehicles (RV). The RV is comprised of one or more cDNA-repair sequence (RS) flanked by an upstream flanking sequence (uFS) and a downstream flanking sequence (dFS) to form a DNA donor within the RVs. The upstream flanking sequence (uFS) is homologous to a nucleic acid sequence located 5' to the break in the one strand of the F8 gene and the downstream flanking sequence (dFS) is homologous to a nucleic acid sequence located 5' to the break in the other strand of the F8 gene. Insertion of the cDNA-RS occurs through homologous recombination of the upstream flanking sequence (uFS) and the downstream flanking sequence (dFS) with the subject's F8 gene (sF8) to provide a repaired F8 gene. The repaired F8 gene upon expression forms functional FVIII that induces immune tolerance to FVIII and confers improved coagulation functionality to the FVIII protein encoded by the sF8 without the repair.

[0075] In some downstream (3 ') gene repair strategies, the DNA-SE is used to introduce DNA- breaks at a target site upstream of the F8 gene nonfunctional coding sequence and the RV comprises cDNA-RS comprising wild-type exons corresponding to the F8 exons downstream (3') of the target site. Using those downstream (3') gene repair strategies, mutations in for example exon 22 may be repaired by a DNA-SE targeting an F8 repair site downstream (3') of exon 21 and insertion by homologous recombination of a cDNA-RS comprising wild-type exons 22-26. Also by this approach, mutations in for example exon 2 may be repaired by a DNA-SE targeting an F8 repair site downstream of exon 1 and insertion by homologous recombination of a cDNA-RS comprising wild-type exons 2-26.

[0076] The efficiency of homologous recombination decreases as the length of the insertion increases. In order for efficient homologous recombination to take place, the insertion comprising the cDNA-RS are preferably less than about 2000 bp and more preferably less than or equal to about 1500 bp. Methods for efficient homologous recombination, including design of homology arms, are identifiable by a skilled person and described for example in Byrne et al. Nucleic Acids Res. 2015 Feb 18;43(3):e21.

[0077] Some downstream, or 3', repair strategies will exhibit decreased homologous recombination efficiency as the length of the cDNA-RS and thereby the insertion length increases. The length of the cDNA-RS is determined by the specific location of the given HA- causing mutation to be repaired; the length increases with the inclusion of additional exons. The length of cDNA-RS required for repairing F VIII coding exon sequences are given in Table 1. For example, when using the downstream (3 ') repair strategy, a cDNA-RS comprising E14_BDD+ El 5- 25+E26pcs is a total of 2282 bp in length. The length requirements of cDNA-RS that would repair mutations located within or upstream (5') of exon 13 are 2492 bp or longer as more exons upstream of exon 12 are included. For example, cDNA-RS comprising E13+E14_BDD + E15-25 + E26pcs will comprise a total of 2492 bp, and length increases (and HR efficiency decreases) as more upstream exons are included.

[0078] The effect of this is that in those downstream (3 ') gene repair strategies, the efficiency of homologous recombination for homologous repair vehicles to repair mutations in or upstream of about exons 13 or 14 are likely to be low due to the length of the homologous repair vehicle insertion. This presents a significant problem, as almost 25-30% of all severe HA patients have a causative F8 mutation that is located within or upstream (5') of exon-14, which may be difficult to repair efficiently using the downstream (3 ') gene repair strategy. Exemplary downstram repair strategies are described in international applications PCT-US2015-035399 and WO2014089541 herein incorporated by reference in their entirety.

[0079] The methods and systems and related cDNA, polynucleotides, vehicles and compositions are performed according to the present disclosure according to an upstream (5') F8 gene repair strategy. One or more DNA-SE is used to introduce DNA-breaks at a target site downstream of the F8 gene nonfunctional coding sequence and the RV comprises cDNA-RS comprising wild-type exons corresponding to the F8 exons upstream (5') of the target site. The upstream (5') F8 gene repair strategy has some similarities and differences to the downstream (3 ') strategy. The fundamental strategy is essentially as follows.

[0080] In the upstream (5') F8 gene repair strategy herein described, one or more DNA scission enzyme(s), DNA-SE(s), such as a nuclease or nickase, target a specific portion of the F8 gene in the subject to create either one double stranded-DNA break (ds-DB) in the F8 gene or two appropriately oriented and spaced single stranded-DNA breaks (ss-DBs) in opposite strands of the F8 gene. The F8 gene is subsequently repaired through a homologous recombination (HR)- mediated process repair vehicle (RV). The RV comprises one or more cDNA-repair sequences (RS) flanked by an upstream flanking sequence (uFS) and a downstream flanking sequence (dFS) (also called homology arms) to form a DNA donor within the RV. The upstream flanking sequence (uFS) is homologous to a nucleic acid sequence located 5' to the break in the one strand of the F8 gene and the downstream flanking sequence (dFS) is homologous to a nucleic acid sequence located 5' to the break in the other strand of the F8 gene. Insertion of the cDNA- RS occurs through homologous recombination of the upstream flanking sequence (uFS) and the downstream flanking sequence (dFS) with the subject's F8 gene (sF8) to provide a repaired F8 gene. The repaired F8 gene upon expression produces functional FVIII protein that induces immune tolerance to FVIII in the subject and/or confers improved coagulation functionality to the FVIII protein encoded by the repaired F8 gene relative to the unrepaired F8. The RV can comprise cDNA-RS comprising wild-type exons corresponding to the F8 exons upstream (5') of the DNA-SE target site.

[0081] The main way in which the upstream (5') F8 gene repair strategy differs from downstream (3') F8 gene repair strategies is in that the cDNA-RS comprises exons upstream (5') of the of the DNA-SE target site, whereas the cDNA-RS of the downstream (3') F8 gene repair strategy comprises exons downstream (3') of the of the DNA-SE target site. The upstream (5') F8 gene repair strategy also includes either a promoter sequence or a polycistronic mRNA element, discussed in further detail below.

[0082] In the upstream (5') F8 gene repair strategy, a mutation located for example within or upstream (5') of exon 14 may be repaired by using a DNA-SE to introduce DNA-breaks downstream of the F8 gene non-coding functional sequence that is to be repaired, for example at the 3' end of exon 14, the 5' end of intron 14, the 3' end of intron 14 or the 5' end of exon 15, and the cDNA-RS of the repair vehicle (RV) comprises exons 1-14. In this example the repaired F8 gene transcribes an mRNA comprising the inserted exogenous wild-type exons 1-14 and the endogenous native exons 15-26 to produce normal, functional FVIII protein (Figure 3). The upstream F8 gene repair strategy can be used to repair any mutation in the F8 gene, including for example the Intron 1 Inversion (III), missense or nonsense mutations, small INDELs, large deletions, and 5'- or 3 '-splice-site mutations in intronic regions.

[0083] Efficiency of repairing F8 mutations at the 5'-most exon by downstream (3') F8 gene repair strategy depends on both cDNA-RS length and the length of other required non-coding elements making up total insert length. This may be determined empirically. Generally, efficiency is higher for inserts of shorter length. The insert sequence which determines total insert length of the necessary homologous repair vehicles comprises cDNA-RS and other non- cDNA elements which can include promoter, poly-A and other 3 '-end forming signals, and other elements including those listed in Table 1.

[0084] It is possible to have a different repair vehicle to target different mutations in the F8 gene. For example, by the upstream 5' gene repair strategy a mutation in exon 3 could be repaired by a RV comprising cDNA-RS comprising exons 1-3 (388 bp), while a mutation in exon 7 could be repaired by a RV comprising cDNA-RS comprising exons 1-7 (1009 bp). Because each different therapeutic agent separately undergoes regulatory testing by the FDA, it can be desirable to have a single upstream 5' repair strategy and a single downstream 3' repair strategy, which between them are capable of repairing any mutation in the F8 gene. In one such embodiment, mutations in any of exons 1-14 (or introns 1-14) are repaired by the upstream 5' strategy using a RV comprising cDNA-RS comprising exons 1-14_BDD (2558 bp). In another embodiment, mutations in any of exons 14-26 (or introns 14-25) are repaired by the downstream 3' strategy using a RV comprising cDNA-RS comprising exons 14_BDD-26_PCS (2282 bp). cDNA-RS

[0085] In cDNA-RS used in methods and systems herein described and related cDNA, polynucleotides, vehicles and compositions, the F8 exons comprising the cDNA-RS can be identical to wild-type F8 exons or can be modified for example to reduce vector length. For example, only the protein coding sequence of exon 1 or 26 may be used (referred to herein as EI C_DS and E26_CDS)- Native F8 exon 14 encodes the FVIII B domain which comprises approximately residues 741-1648 of FVIII. The B domain is reported to be inessential to FVIII physiological function. B domain-deleted exon 14 (referred to herein as E14_BDD), in which some or all of the B domain is deleted from exon 14, may be used. The F8 exons may also be modified for example for codon optimization, to reduce immunogenicity, or to increase protein stability by methods well known in the art. Codon optimisation of F8 is described in for example Mcintosh et al. Blood. 2013 Apr 25 vl21(17) p3335-44. [0086] In methods and systems herein described and related cDNA, polynucleotides, vehicles and compositions, the 5' gene repair strategy can make use of the endogenous F8 sequence downstream of the F8 mutation site, including the native F8 gene polyadenylation signal and other cis-elements required for mRNA 3 '-end formation. For this reason, the 5 '-gene repair strategy can function without including an exogenous polyadenylation signal. An exogenous polyadenylation signal may be included after E26_CDS as part of the 3' gene repair strategy to give higher expression than that of when the endogenous F8 polyA sequence is used. In one embodiment the exogenous polyadenylation signal is the bovine growth hormone- polyadenylation signal (bGH-polyA). In another embodiment the exogenous polyadenylation signal is human growth hormone polyadenylation signal (hGH-pA). In another embodiment the exogenous polyadenylation signal is a minimal length efficient poly-A signal, for example TK65 poly-A, which is 65 bp in length and reported to be almost as efficient as bGH-polyA (Wang et al. Gene Ther. 1999 Apr;6(4):667-75). Such minimal length, efficient poly-A signals can reduce insert length and thus increase the efficiency of homologous recombination.

[0087] In methods and systems herein described and related cDNA, polynucleotides, vehicles and compositions, a heterologous promoter sequence can be used in the upstream (5') gene repair approach of the present disclosure. The promotor can be a tissue-specific promoter such as an endothelial-specific promoter, a megakaryocyte-specific promoter or a platelet-specific promoter or a suitable strong ubiquitous promotor such as the human cytomegalovirus (CMV) immediate- early promoter/enhancer. The promoter is preferably a promoter well characterized in human patients and in-vivo animal models. The promoter can be relatively small in size in order to reduce the length of the homologous repair vehicle insertion matrix donor sequence. The promoter is preferably <750bp is length. Endothelial- and/or megakaryocyte-specific promoters are desirable when the patient autologous cell that is the target of gene repair is an endothelial cell or megakaryocyte (either natural cells or cells differentiated from iPSCs). In one embodiment the therapeutic autologous delivery cells are blood outgrowth endothelial cells (BOECs), liver sinusoidal endothelial cell (LSECs), Megakaryocyte progenitors, Hematopoietic Stem Cells, iPSCs or other stem or stem-like cells.

[0088] The promoter selected for F8 expression and the cell type selected for gene repair can affect the secretion, function, clotting activity and other factors. [0089] A mouse model in which full-length human FVIII cDNA is expressed in a liver specific manner under the control of the liver murine albumin enhancer/promoter has been described (Van Helden et al. Blood. 2008 vl 12(11) 3387, Van Helden et al. Blood. 2011 Sep 29 vl 18(13) p3698-707, US20090235369). The mice express human F8 mRNA in the liver and various other organs but do not have FVIII protein in the circulation. The mice are immunologically tolerant to challenge with recombinant human FVIII. Accordingly, F8 gene repair that provides expression in the liver can be useful in inducing immunological tolerance to the repaired FVIII.

[0090] Gene therapy of hemophilia A mice to give platelet-specific expression of FVIII driven by the platelet-specific glycoprotein lib promoter (2bF8) can improve hemostasis (Shi et al. J Clin Invest. 2006 Jul vl l6(7) pl974-82, Shi et al. Blood. 2014 Jan 16 vl23(3) p395-403). No FVIII is observed in the plasma of the mice, but FVIII is stored in platelets and released at the site of platelet activation, restoring clotting function even in the presence of inhibitory antibodies. Accordingly, F8 gene repair that provides expression in platelets or their producer or progenitor cells, including megakaryocytes and megakaryocyte progenitors, can be useful in restoring hemostasis in HA patients even in the presence of inhibitory antibodies.

[0091] In one embodiment of F8 gene repair, a promoter is selected that gives expression in both endothelial cells and platelets. Expression in endothelial cells results in FVIII in the circulation, while expression in platelets results in FVIII being stored in platelets. By utilising these two mechanisms, this strategy can give particularly effective restoration of clotting function, with the further advantage that clotting function can remain even in the presence of inhibitors.

[0092] In methods and systems herein described and related cDNA, polynucleotides, vehicles and compositions, the upstream (5') F8 gene repair strategy inserts cDNA-RS comprising F8 exons upstream of the repair site. For this reason, in order to express the repaired FVIII protein comprising the repaired wild-type exons and the native wild-type exons, the upstream (5') F8 gene repair strategy requires including either a promoter or a polycistronic mRNA element upstream of exon 1 cDNA repair sequence. Promoter elements have been described above.

[0093] An alternative to including a promoter is to use a tool commonly used to enable polycistronic vectors to express multiple proteins from a single mRNA transcript. Examples of such tools are sequence encoding an internal ribosome entry site (IRES) or a 2A self-cleaving peptide. 2A self-cleaving peptides are around 18-22 residues in length, with GSG residues optionally added to the 5' end of the peptide to improve cleavage efficiency. Such a 2A self- cleaving peptide will be about 54-75 nucleotides in length. 2A self-cleaving peptides are likely to be more useful than IRES because they are much shorter in length (IRES being longer than 500 nucleotides) and are reported to have up to 100% cleavage efficiency. 2A self-cleaving peptides are described further in Kim et al. PLoS One. 201 1 ; 6(4): el 8556. Examples of 2A self-cleaving peptide amino acid sequences include P2A (GSGATNF SLLKQ AGDVEE PGP), T2A (GSGEGRGSLLTCGDVEE PGP), E2A (GSGQCTNYALLKLAGDVES PGP), and F2A (GSGVKQTL FDLLKLAGDVES PGP) (Kim et al. PLoS One. 201 1 ; 6(4): el 8556),

[0094] Sequence encoding the polycistronic element is included upstream of the exon-1 cDNA repair sequence. Under control of the native F8 promoter, the native exons upstream of the gene repair site are transcribed, followed by the polycistronic mRNA element, the wild-type exons of the cDNA repair sequence, and the wild-type native F8 exons. Translation yields a nonfunctional truncated FVIII polypeptide comprising the portion of the mutated FVIII protein and a full-length, functional wild-type repaired FVIII protein.

[0095] Figure 3 is a schematic of expected A) genomic DNA, B) spliced mRNA and C) proteins in normal F8 and F8 repaired by the present 5' gene repair strategy. In the example shown, a mutation in any of endogenous exons 1-14 is repaired using a repair vehicle comprising wild- type exons 1-14 and a promoter or a polycistronic mRNA element such as a 2A self-cleaving peptide. The repaired F8 gene expresses F8 mRNA and FVIII protein having exogenous wild- type exons 1-14 in frame with endogenous exons 15-26, giving a functional FVIII protein. In the upper repaired example (promoter) the exogenous promoter drives transcription of the repaired F8 gene, while in the lower repaired example (2A peptide) transcription is driven by the native F8 promoter. Exon 1 of the repair vehicle can be only the protein coding sequence of exon 1 (EI CDS) and exon 14 can be B domain-deleted (E14_BDD)-

[0096] There are several advantages given by using a polycistronic element. The length of the replacement sequence insertion is reduced, increasing the efficiency of homologous recombination in the gene repair. The repaired F8 gene uses the native F8 promoter to give FVIII expression closely mimicking that seen physiologically. Table 1 - length of F8 exons and cDNA-RS required for repairing FVIII coding exon sequences by upstream (5') and downstream (3') F8 gene repair strategies

Table 1 - length of F8 exons and cDNA-RS required for repairing FVIII coding exon sequences by upstream (5') and downstream (3') F8 gene repair strategies

[0097] In methods and systems herein described and related cDNA, polynucleotides, vehicles and compositions, the FVIII polypeptide usually undergoes proteolytic cleavage into heavy chain (A1-A2 domains) and light chain (A3-C1-C2 domains) molecules. FVIII proteins modified such that they are expressed as a single chain protein having the heavy and light chains covalently linked are identifiable by a skilled person .

[0098] Exemplary single chain FVII polypeptide comprises the single-chain, inactivation- resistant FVIII proteins that exhibits inactivation resistance and/or increased secretion while retaining procoagulant activity such as the FVIII protein described in US2002132306, and FVIII derivatives in which most of the B-domain is deleted and heavy chain and light chain are linked by a polypeptide spacer. Some of these single chain FVIII derivatives show similar coagulation activity, similar thrombin activation and higher specific activity compared with full-length FVIII such as the derivative of WO2004067566).

[0099] Exemplary, recombinant single-chain FVIII protein CSL627, which comprises residues 1-764 and 1653-2332 of FVIII, are described in Schulte et al. Thromb Res. 2011; 128 Suppl 1 :S9- ^Schulte, S. Thromb Res. 2013 Mar; 131 Suppl 2:S2-6, Zollner et al. Thromb Res. 2014 Jul; 134(1): 125-31 and WO2013057219. CSL627 is currently the only single-chain FVIII product known to the applicant to be in commercial development. CSL627 is reported to have strong affinity for von Willebrand factor, increased stability and improved plasma half-life.

[00100] Human FVIII-BDD protein modified to disrupt a single PACE/furin protease site by including a R1645H substitution has been reported to show a 2.5-fold increase in the single- chain form of FVIII and a twofold increase in biological activity (Siner et al. Blood. 2013 May 23; 121(21): 4396-44031 It is suggested that the modified FVIII-BDD is likely to be secreted more efficiently than control FVIII-BDD.

[00101] As will be recognised from the above by a skilled person, single chain FVIII molecules can have a number of desirable properties and advantages including increased secretion, specific activity, half-life or stability relative to full-length FVII.

[00102] In one embodiment herein described the F8 gene of a subject is repaired such that it produces a single chain FVIII. The single chain FVIII has increased secretion, specific activity, half-life or stability relative to full-length FVII. In one embodiment, the gene repair is performed such that the cDNA replacement sequence (cDNA-RS) comprises an exon 14 replacement sequence in which the proteolytic cleavage sites found in the full-length F8 exon 14 encoded FVIII regions are disrupted. In one embodiment, the exon 14 replacement sequence is modified to substitute amino acids such that the protease recognition site at residues 1313 and/or 1648 is disrupted. In another embodiment, the exon 14 replacement sequence encodes a C-terminally deleted B-domain in which one or more residues of the protease recognition site at residues 1313 and/or 1648 are deleted or disrupted and the cells secrete a single-chain, B-domain-deleted (BDD) FVIII molecule. Increased FVIII secretion, specific activity, half-life or stability would increase the efficacy of the F8 gene repair in treating HA patients.

[00103] In methods and systems herein described and related cDNA, polynucleotides, vehicles and compositions, the F8 gene can contain other modifications to increase FVIII secretion. For example, including a short B-domain sequence having several N-linked glycosylation consensus sites is reported to increase secretion up to 10-fold compared with BDD-FVIII, possibly by facilitating the interaction between FVIII protein and endoplasmic reticulum (ER) chaperones and ER to Golgi transport through interaction with the mannose-binding lectin LMAN1 (Miao et al. Blood. 2004 May l; 103(9):3412-9). Furthermore, including a Phe309Ser in the FVIII Al- domain is reported to further increase secretion (Miao et al. Blood. 2004 May l; 103(9):3412-9). As with the modifications to FVIII described above, these modifications can be applied to gene repair strategies as well as in recombinant FVIII production and can be used alone or in combination with other FVIII modifications.

[00104] In methods and systems herein described and related cDNA, polynucleotides, vehicles and compositions, the FVIII cDNA can contain other modifications to extend half-life. For example, the FVIII coding sequence can be fused with half-life extending moieties such as the Fc-domain of the IgG molecule or the human albumin protein. Fusions between FVIII and half- life extending moieties are described for example in ASH Education Book December 6, 2013 vol. 2013 no. 1 37-43^61^8 et al. J Thromb Haemost. 2013 Jan; 11(1): 132-141 and WO2009156137. By techniques known to the person skilled in the art, half-life extending moieties can be fused to either the 5' or the 3' end of the F8 cDNA (i.e. fused to either the N- or C-terminal of FVIII) and tested to determine preferred fusions/orientations in which factor VIII activities retains biological activity while half-life is also extended. A FVIII fused at its C- terminal to albumin can be secreted and retains its biological function. Half-life extending moieties can be fused to single chain FVIII or wild-type FVII as for example described in WO2009156137 I.

[00105] In some embodiments, of methods and systems herein described and related cDNA, polynucleotides, vehicles and compositions, the F8 gene repair results in repaired FVIII which has native glycosylation maximally preserved and/or additional engineered glycosylation sites.

[00106] FVIII contains 25 consensus N-linked glycosylation (NLG) sequences, 20 of which are reported to be glycosylated. Four consensus NLG sites are reported to be nonglycosylated while the glycosylation of 1 NLG site is unclear. The B domain contains 19 of the 25 NLG consensus sites (Lenting et al. Blood. 1998 Dec l;92(l l):3983-96). Glycosylation is reported to be important for FVIII biological activity and FVIII-membrane interactions (Kosloski et al. AAPS J. 2009 Sep; 11(3): 424-431).

[00107] An exemplary B-domain deleted FVIII derivative in which the fusion sites between N- terminal sequence of B-domain and the amino acid sequence in the A3 domain contains an additional N-glycosylation sequence is described in WO2004067566.

[00108] The F8 gene is preferably repaired such that the native glycosylation of the FVIII protein is retained. This gives a more native-like FVIII protein and can help retain FVIII specific activity and reduce FVIII antigenicity and/or immunogenicity compared to FVIII protein containing altered and/or non-native glycosylation. If modifications to exon sequences are necessary for efficient gene editing/repair, glycosylation sites are preferably preserved where possible. For example, the engineered junctions of B domain-deleted therapeutic FVIII proteins preferably retains local NLG consensus sites where possible as these synthetic junctional sequences are foreign to all human subjects.

[00109] In some embodiments the F8 is repaired such that the repaired gene includes additional engineered glycosylation sites. Additional glycosylation sites can be useful in reducing the antigenicity of the FVIII protein without substantially affecting its biological activity. Epitope mapping of FVIII inhibitors can be used to identify specific amino acid residues of FVIII that can be useful sites to add a glycosylation site in order to reduce FVIII antigenicity. The C2 domain of FVIII is reported to particularly be involved in the binding of inhibitory antibodies (reviewed in Voorberg and Meems. Blood. 2014 Apr 24; 123(17):2601-2) and so can be particularly relevant in designing FVIII molecules having decreased antigenicity. Epitope mapping methods are identifiable by a skilled person and are detailed in for example Bloem et al. J Biol Chem. 2013 Oct 11; 288(41): 29670-29679 and Scandella et al. Proc Natl Acad Sci U S A. 1988 Aug;85(16):6152-6. In one embodiment a R2159N substitution in FVIII produces an N- linked glycosylation motif that has the effect of reducing FVIII antigenicity.

EXAMPLES

[00110] The methods and system herein disclosed and related cDNA, polynucleotides, vehicles and compositions are further illustrated in the following examples, which are provided by way of illustration and are not intended to be limiting.

[00111] In particular, the following examples illustrate exemplary embodiments in accordance with exemplary procedures in accordance to the present disclosure. A person skilled in the art will appreciate the applicability of the features described in detail for the exemplified embodiments to different methods, different applications and different reaction conditions and reagents in accordance with the present disclosure.

Example 1: Protocol for Factor VIII Gene Repair in Humans

Obtaining a blood sample

[00112] A protocol for gene repair of the F8 gene in blood outgrowth endothelial cells (BOECs) is described in the following example. First, a blood sample is obtained, with 50-100mL of patient blood samples obtained by venipuncture and collection into commercially-available, medical-grade collecting devices that contain anticoagulants reagents, following standard medical guidelines for phlebotomy. Anticoagulant reagents that are used include heparin, sodium citrate, and/or ethylenediaminetetraacetic acid (EDTA). Following blood collection, all steps proceed with standard clinical practices for aseptic technique.

Isolating appropriate cell populations from blood sample

[00113] Procedures for isolating and growing blood outgrowth endothelial cells (BOECs) have been described in detail by Hebbel and colleagues (Lin, Y., Weisdorf, D. J., Solovey, A. & Hebbel, R. P. Origins of circulating endothelial cells and endothelial outgrowth from blood. J Clin Invest 105, 71-77 (2000)). Peripheral blood mononuclear cells (PBMCs) are purified from whole blood samples by differential centrifugation using density media-based separation reagents. Examples of such separation reagents include Histopaque-1077, Ficoll-Paque, Ficoll- Hypaque, and Percoll. From these PBMCs multiple cell populations can be isolated, including BOECs. PBMCs are resuspended in EGM-2 medium without further cell subpopulation enrichment procedures and placed into 1 well of a 6-well plate coated with type I collagen. This mixture is incubated at 37°C in a humidified environment with 5% C02. Culture medium is changed daily. After 24 hours, unattached cells and debris are removed by washing with medium. This procedure leaves about 20 attached endothelial cells plus 100-200 other mononuclear cells. These non-endothelial mononuclear cells die within the first 2-3 weeks of culture.

Cell culture for growing target cell population

[00114] BOECs cells are established in culture for 4 weeks with daily medium changes but with no passaging. The first passaging occurs at 4 weeks, after approximately a 100-fold expansion. In the next step, 0.025% trypsin is used for passaging cells and tissue culture plates coated with collagen-I as substrate. Following this initial 4-week establishment of the cells in culture, the BOECs are passaged again 4 days later (day 32) and 4 days after that (day 36), after which time the cells typically number 1 million cells or more.

In vitro gene repair

[00115] In order to affect gene repair in BOECs, cells are transfected with 0.1-10 micrograms per million cells of each plasmid encoding DNA-SE(s) and 0.1-10 micrograms per million cells of the repair vehicle plasmid. Transfection is done by electroporation, liposome-mediated transfection, polycation-mediated transfection, commercially available proprietary reagents for transfection, or other transfection methods using standard protocols. Following transfection, BOECs are cultured as described above for three days.

Selection of gene-repaired clones

[00116] Using the method of limiting serial dilution, the BOECs are dispensed into clonal subcultures, and grown as described above. Cells are examined daily to determine which subcultures contain single clones. Upon growth of the subcultures to a density of >100 cells per subculture, the cells are trypsinized, re-suspended in medium, and a 1/10 volume of the cells is used for colony PCR. The remaining 9/10 of the cells are returned to culture. Using primers that detect productively repaired F8 genes, each 1/10 volume of colonies are screened by PCR for productive gene repair. Colonies that exhibit productive gene repair are further cultured to increase cell numbers. Using the top 20 predicted potential off-site targets of the DNA-SE(s), each of the colonies selected for further culturing is screened for possible deleterious off-site mutations. The colonies exhibiting the least number of off-site mutations are chosen for further culturing.

Preparation of cells for re-introduction into patients by conditioning and/or outgrowth

[00117] Prior to re-introducing the cells into patients, the BOECs are grown in culture to increase the cell numbers. In addition to continuing cell culture in the manner described above, other methods can be used to condition the cells to increase the likelihood of successful engraftment of the BOECs in the liver sinusoidal bed of the recipient patient. These other methods include: 1) co-culturing the BOECs in direct contact with hepatocytes, wherein the hepatocytes are either autologous patient-derived cells, or cells from another donor; 2) co-culturing the BOECs in conditioned medium taken from separate cultures of hepatocytes, wherein the hepatocytes that yield this conditioned medium are either autologous patient-derived cells, or cells from another donor; or 3) culturing the BOECs as spheroids in the absence of other cell types.

[00118] Co-culturing endothelial cells with hepatocytes is described further in the primary scientific literature {e.g. Kim, Y. & Rajagopalan, P. 3D hepatic cultures simultaneously maintain primary hepatocyte and liver sinusoidal endothelial cell phenotypes. PLoS ONE 5, el 5456 (2010)). Culturing endothelial cells as spheroids is also described in the scientific literature (e.g. Korff, T. & Augustin, H. G. Tensional forces in fibrillar extracellular matrices control directional capillary sprouting. J Cell Sci 112 (Pt 19), 3249-3258 (1999)). Upon growing the colonies of cells to a total cell number of at least 1 billion cells, the number of cells needed for injection (>50 million cells) into the patient are separated from the remainder of the cells and used in the following step for injection into patients. The remainder of the cells are aliquoted and banked using standard cell banking procedures. Injection of ^' gene -repaired BOECs into patients

[00119] BOECs that have been chosen for injection into patients are resuspended in sterile saline at a dose and concentration that is appropriate for the weight and age of the patient. Injection of the cell sample is performed in either the portal vein or other intravenous route of the patient, using standard clinical practices for intravenous injection.

Example 2: Nuclease sites for repair at different exon-intron junctions

[00120] Because mutations causing Hemophilia A occur throughout the FVIII gene, different repair strategies can be employed at different exon-intron junctions in order to allow the use of repair vehicles which correct a wider range of patient mutations. All gene repairs employ the methodology described above and use a DNA-SE to induce a double-strand break downstream of the portion of the F8 gene to be repaired, thereby allowing homologous recombination to incorporate a therapeutic repair vehicle encoding the cDNA for the upstream exons of the gene into the genome in order to be operably linked to the 5' end of that exon. In this example we describe a method using paired CRISPR nickases discussed by Ran FA, Hsu PD et al., in Cell 2013, incorporated herein by reference in order to induce double strand breaks. We also describe paired CRISPRs using a Cas9 fused to the Fokl domain (also known as RNA-guided Fokl nucleases, "RFNs") described by Tsai SQ et al. in Nature Biotechnology 2014, incorporated herein by reference.

[00121] In order to choose CRISPR target sites in exons 2-14, several considerations were taken into account. The -100 bp of the 5' end of each exon (hgl9 human genome build) were searched for CRISPR/Cas9 binding sites using an online algorithm described by Hsu et al. in Nature Biotechnology 2013 v31 p827-832, incorporated herein by reference. Single guide RNAs (sgRNAs) were chosen based on low potential for off-target activity, the proximity of the cleavage site to the 5' end of the exon, and guidelines for increasing the likelihood of high on- target activity (Wang T et al., Science 2014 v343(6166) p80-4). Paired nickases were chosen by adding the additional consideration that they be orientated to create 5' overhangs and be spaced apart within the recommended range for optimal activity (Shen B, et al., Nature Methods 2014 vl l p399-402).

[00122] In order to choose TALEN binding sites in exons, the following considerations can be taken into account. The -100 bp of the 5' end of each exon (hgl9 human genome build) can be searched for TALEN binding sites using the SAPTA algorithm as described by Lin Y, Fine EJ, et al. in Nucleic Acids 2014, incorporated herein by reference. Potential binding sites can then be screened using the TALEN v2.0 algorithm of the PROGNOS tool as described by Fine EJ et al. in Nucleic Acids Research 2013, incorporated herein by reference to ensure that no highly scored potential off-target sites exist in the human genome.

[00123] Sequences listed in Table 2 below contain identified binding sites for CRISPRs within exons 2-14 respectively. If a homologous sequence in the canine genome (canFam3 build) exists that permits the possibility of CRISPR/Cas9 cleavage using the same guide strand as used for the human exon, it is listed with any mismatches in lowercase bold; if no reasonable homology exists, it is listed as "N/A".

[00124]

Table 2 - identified binding sites for CRISPRs within exons 2-14

Table 2 - identified binding sites for CRISPRs within exons 2-14

Table 2 - identified binding sites for CRISPRs within exons 2-14

Table 2 - identified binding sites for CRISPRs within exons 2-14

Table 2 - identified binding sites for CRISPRs within exons 2-14

Table 2 - identified binding sites for CRISPRs within exons 2-14

[00125] Note: When the optimal sg-RNA for CasN-mediated F8 repair at a given exonic 5'- junction is also suitable for use in a paired nickase mediated repair strategy, the DNA sequence encoding that SG/PG-RNA is underlined; the PAM sequence is not underlined as it is not found in the encoded SG-RNA.

Example 3: Homologous Repair Vehicles for repair at different exon-intron junctions

[00126] Repair at different exon-intron junctions throughout the FVIII gene employ methodology similar to examples 1 and 2 described above, the repair vehicles used however are different for each junction. This example describes various repair vehicles. [00127] The repair vehicles contain the same basic components: a left homology arm corresponding to the genomic sequence 5' of the relevant nuclease cut site, a promoter or a polycistronic mRNA element, a cDNA sequence comprising the protein coding sequence of FVIII located upstream of the DNA-SE target site, and a right homology arm corresponding the genomic sequence 3' of the relevant nuclease cut site. The cDNA optionally contains several synonymous SNPs to aid experimental validation that productive repair has occurred. Further, the cDNA in different repair vehicles can contain non-synonymous SNPs in order to be a haplotypic match for different patients.

[00128] For example, a vehicle designed for repair at exon 14 comprises a left homology arm comprising the 3' portion of exon 14 and possibly continuing into the 5' portion of intron 14, a cDNA containing exons 1-14, and a right homology arm comprising a portion of the 3' region of intron 14.

Example 4: Additional Methods and Examples for FVIII Gene Repair in Cells

Purifying CRISPR/Cas9 plasmids and repair plasmids (DNA-RS)

[00129] A protocol for preparing CRISPR/Cas9 plasmids (DNA-SE) and repair plasmids (DNA- RS) using endotoxin-free methods is described in the following example. For this protocol, a Qiagen EndoFree Plasmid Maxi Kit is used. The Qiagen EndoFree Plasmid Maxi Kit and its contents are stored at room temperature. Once RNAse and LyseBlue are added to Buffer PI from the kit, this buffer is stored at 4°C. The kit also requires 100% ethanol and isopropanol (2- propanol).

[00130] According to this protocol, at Day 1, a lmL seed culture of Escherichia coli (E. coli) in Luria Broth (LB) and appropriate antibiotic is prepared and placed on a shaker at 37°C. Whether an antibiotic is appropriate is dependent on the antibiotic resistance gene that is present in the plasmid that is being prepared and purified. For example, such an antibiotic can be ampicillin, kanamycin, or other antibiotics. Approximately 5 hours from when the seed culture is prepared, the seed culture is then used to inoculate a 100 mL LB culture and the suspension is left shaking overnight (or for at least about 8 hours) at 37°C.

[00131] At day 2, the 100 mL culture is transferred into 2x50 mL conical tubes and spun for 10 min at 4000g; the supernatant is dumped out. The resulting cell pellet can be stored at -20 C for an indefinite period of time. During the spin, Buffer P3 is placed on ice. Following the spin and removal of the supernatant, 10 mL of Buffer PI are added to the first 50 mL tube of each prep. This solution is then vortexed to resuspend the pelleted cells. The resuspended mixture is poured a second tube and vortexed to resuspend. Next, 10 mL of Buffer P2 are added and the suspension is inverted 6X to mix (until mixture is homogenously blue). This suspension is incubated for 3 min at room temperature. Next, 10 mL of Buffer P3 is added to each tube, and each tube is inverted ~10X.

[00132] Next, the suspensions are centrifuged for 5 minutes at 4000g. During the spin, a fresh 50 mL tube is labeled for each abovementioned prep. A cap is screwed onto a filter cartridge and placed in the fresh 50 mL tube. After the spin, a pi 000 pipette tip is used to hold back debris while pouring the liquid from the spun suspension into the cartridge. The suspension is then incubated for 10 minutes at room temperature in the cartridge. Next, the cartridge is uncapped and a plunger is used to push the liquid into the 50 mL tube; the cartridge/plunger is trashed following this step. Next, 2.5 mL of Buffer ER is added to each tube, and each tube is inverted 10X until the liquid becomes cloudy. The suspension is incubated on ice for 30 minutes. During the incubation, Qiagen-Tip-500 tubes are labeled and placed in a clamp draining into a 1000 mL beaker. 10 mL of Buffer QBT is added to Qiagen-Tips to equilibrate the system. After the 30 minute incubation, the prep mixture is poured into the respectively labeled Qiagen-tips. Buffer QC is used to wash the tips.

[00133] Next, the Qiagen-Tip-Tubes are placed into 50 mL tubes capable of withstanding spins @ 15000g. 15 mL of Buffer QN is added to the Qiagen-Tip-Tubes and centrifuged at 4°C to allow the DNA to elute from the Qiagen-Tip-Tubes as the buffer QN drains through. The eluted DNA can be stored at 4°C overnight.

[00134] Next, 10.5 mL of Isopropanol is added and the suspension is inverted 10X to mix. The samples are then centrifuged at 15000g for 10 min at 4°C; The DNA will be present as a pellet.

[00135] After the supernatant is dumped out, 5 mL of 70% Ethanol (EtOH) is added to the pelleted DNA. The samples are centrifuged at 15000g for 10 min at 4° C. Then, the supernatant is decanted using a pi 000 pipette. The tube is then left to air-dry for 10 min. Next, 150 uL of Tris EDTA buffer (TE) is added. Isolated plasmid concentration is then determined. Nucleofection Conditions and Methods

[00136] A protocol for nucleofection is described in the following example. The protocol described uses 20uL Nucleovette Strips (Lonza). The number of cells recommended for this technique is 200,000 cells per condition or sample. The maximum mass of DNA used in this technique is -lOOOng. It is recommended that a significantly greater amount of repair plasmid be used compared to the CRISPR/Cas9 plasmid as this minimizes the likelihood of off-target effects while maximizing the likelihood of homologous recombination. Typically a ratio of 4: 1 repair plasmid:CRISPR/Cas9 plasmid is used.

[00137] To facilitate all of the analyses involved with these methods, the following reaction conditions are recommended. First, for the "experimental" condition, 200ng of CRISPR/Cas9 plasmid (DNA-SE), 800ng of repair plasmid (DNA-RS), and 40ng of MaxGFP plasmid are used for transfection. Second, for the "no repair plasmid" control condition (also suitable for T7 Endonuclease (T7E1) analysis), 200ng of CRISPR/Cas9 plasmid (DNA-SE), 800ng of stuffer plasmid (pUC19), and 40ng of MaxGFP plasmid are used for transfection. Third, for the "no CRISPR plasmid" condition, 200ng of stuffer plasmid (pUC19), 800ng of repair plasmid (DNA- RS), and 40ng of MaxGFP plasmid are used for transfection. Fourth, for the "GFP alone" condition, lOOOng of stuffer plasmid (pUC19) and 40ng of MaxGFP plasmid are used for transfection.

[00138] For the method, first, 500ul of media is added to the required number of wells in a 24 well plate. This is pre-warmed in an incubator set to 37°C, 5% C0₂. Next, ^g of total DNA in minimum of 2μ1 is used. Next, the DNA is setup into a new strip tubes.

[00139] Next, the cells are prepared for nucleofection. 200,000 cells per nucleofection reaction are preferred. 1.2X of master mix of cells is prepared to account for cell loss during media aspiration and pipetting errors. Next, the cells are pelleted by centrifugation at 300 xg for 5 minutes. Next, if the Nucleocuvette strip kit is used, a nucleofection solution provided with kit is used. All of the supplement is added to Nucleofector solution; 20μ1 of the combined buffer is required per nucleofection. [00140] Next, during the spin a plate is labeled. The media is then aspirated from the cells and the cells are resuspended in 1.1X Nucleofector buffer (22ul per nucleofection - 352 uL / 16 nucleofections, 374 uL / 17 reactions). Next, 20ul of cell suspension (approx.. 200,000 cells) is aliquoted to DNA solutions. Next, the Nucleocuvette strip is placed in the 4D Nucleofector X- module and the corresponding program is selected. Next, the cuvette is allowed to incubate for 10 minute following shocking of the cells. Next, 50ul of media from 24 well plate is added to the Nucleocuvette. All of the cell/media mix from the cuvette is then added to the 24 well plate and incubated at 37°C for 72 hours.

Protocol for QuickExtract Method for gDNA Extraction

[00141] A protocol for gDNA extraction is described in the following example. This method allows for the extraction of genomic DNA (gDNA) from live cell samples using QuickExtract™ DNA Extraction Solution (Epicentre). First, about 100,000 cells are pelleted by centrifugation. Then 80 μΙ_, of the QuickExtract solution is added to the cells and the suspension is transferred to a thermocycler tube. The suspension is then vortexed. The suspension is then run in a thermocycler for 15 min at 65°C and 8 min at 98°C; The solution can then be stored at -20°C and freeze/thawed for at least 40 times. Next, ~1 iL of this solution is used as the genomic DNA template per 50 μΙ_, of PCR reaction.

Protocol for T7E1 Assay

[00142] A protocol for a T7E1 assay is described in the following example. According to the protocol, 35 cycles of PCR is used on isolated gDNA to amplify a target locus at an exon/intron boundary using T7E1 primers that flank this boundary. The PCR amplicons are then purified using Wizard SV Gel and PCR Clean-up System (Promega) according to manufacturer's instructions.

[00143] Next, 200ng of purified PCR product is placed in lx NEBuffer 2 (New England Biolabs, Buffer 2, a component of the T7 Endonuclease 1 kit that is available from New England Biolabs) in a total volume of 18uL. Next, the suspension is vortexed and centrifuged. Next, the samples are placed in a thermocycler programmed with the following protocol: A) 95 °C for 5 min; B) 95-25 °C in -l°C/s steps; C) hold at 4°C. [00144] 10 units of T7 Endonuclease 1 is are added to the hybridized PCR products in a 2uL volume of lx EBuffer 2 (for a final reaction volume of 20uL). Note that for each sample, a side-by-side negative control (no T7E1 enzyme control) is prepared, wherein 2uL volume of lx NEBuffer is used in the absence of the enzyme. Next, the suspensions are vortexed and centrifuged. The suspensions are then incubated at 37°C for 30 minutes. Following incubation, the samples are placed on ice and stop solution is added to them. The stop solution is prepared by adding 2.45uL 0.5M EDTA to 4.49 uL 6X loading dye for each reaction (6.94uL volume per reaction, resulting in a final concentration of 45mM EDTA and lx loading dye).

[00145] Next, the samples by agarose gel electrophoresis. The gel image can be quantified with ImageJ using the following procedure: 1) the image is inverted; 2) the background is subtracted (set to 30 pixels, check light background box); 3) rectangles are drawn about the middle of a gel lane, avoid the "smiling" on the end of the gel lanes; 4) in the analyze gel lane, "select first lane" option is selected; 5) subsequent lanes are selected; 6) Quantitative analysis is performed (fraction cleaved= area cleaved/ area of all); 7) Calculate % gene modification with the following equation:

1 /7

% gene modification = 100 (1 - (1 - fraction cleaved) ) Protocol for Restriction Fragment Length Polymorphism (RFLP) Assay

[00146] A protocol for a RFLP assay is described in the following example. According to the protocol, 35 cycles of PCR is used on gDNA to amplify a target locus at an exon/intron boundary using RFLP primers that flank this boundary. The PCR amplicons are purified using Wizard SV Gel and PCR Clean-up System (Promega) according to manufacturer's instructions.

[00147] Next, a mixture with 20 μΐ. reaction with 0.5μΙ. (5U) of restriction enzyme, 2uL reaction buffer (provided in the enzyme kit), and then 17.5 μΐ. of the cleaned PCR reaction is prepared.

[00148] This mixture is then incubated at 37°C for 1 hour. Next, the samples are analyzed the samples by agarose gel electrophoresis. The gel image is then quantified with ImageJ using the following procedure: 1) the image is inverted; 2) the background is subtracted (set to 30 pixels, check light background box); 3) rectangles are drawn about the middle of a gel lane, avoid the "smiling" on the end of the gel lanes; 4) in the analyze gel lane, "select first lane" option is selected; 5) subsequent lanes are selected; 6) Quantitative analysis is performed (fraction cleaved= area cleaved/ area of all); 7) Calculation of % homologous recombination with the following equation:

%HR = (cut band) / (cut band + uncut band) Protocol for PCR Amplification at Gene Repair Site

[00149] A protocol for PCR amplification at a gene repair site is described in the following example. According to the protocol, as a first qualitative approach, PCR with RFLP primers is performed to examine the presence of a band distinct from the main band. The primers and procedures in this method are the same as those described above in the section entitled "Protocol for Restriction Fragment Length Polymorphism (RFLP) Assay." The main (uncut) band is larger in size than the cut band.

[00150] In a second qualitative approach according to this protocol, primer that anneals within the gene repair site is paired with a reverse RFLP primer that anneals within an adjacent exon. This PCR will only form a PCR product if there is successful gene correction.

[00151] Following analysis of the results from the PCR analyses described above, clonal colonies are grown out. This is done either through limiting dilution of the cells or by FACS sorting of single cells into a 96-well plate. With either method, initially plate 1 cell into -50 uL of media. Then after 1 week add -150 uL of new media to the wells. After about a second week, or when there are > 10,000 cells, use the QuickExtract protocol to isolate gDNA. Proceed to perform the same two PCRs described above— the 2nd PCR method will demonstrate if there is at least monoallelic gene correction, the first PCR (with the RFLP primers) will demonstrate if there is biallelic correction (because all of the PCR product will be at a different band size) and also serve as a positive control to determine that the QuickExtract for that sample is a viable PCR template.

Protocol for gene repair in FVIII

[00152] A protocol for gene repair in FVIII is described in the following example. According to the protocol, seed cell cultures are prepared 2 days before transfection, with a final target density of 800,000 cells/mL on the day of transfection. Next, CRISPR/Cas9 plasmids (DNA-SE) and repair plasmids (DNA-RS) are prepared as indicated above in the protocol for endotoxin-free plasmid maxiprep. Next, the transfection setup details for nucleofection, such as plasmid concentrations and volumes, cell concentrations and volumes are determined as discussed above in the protocol for nucleofection conditions and methods. Next, nucleofection is performed, followed by culturing the cells for 72 hours as discussed above in the protocol for nucleofection conditions and methods.

[00153] Flow cytometry analysis is used to determine % viability and % GFP+ cells in each sample on one quarter of the cells collected from the nucleofection step.

[00154] In this example, gDNA from one quarter of the cells from the nucleofection event is isolated following the protocol for gDNA extraction described above. The gDNA is then analyzed using the following protocols described above: 1) protocol for T7 El assay; 2) protocol for RFLP assay; and 3) protocol for PCR amplification at gene repair site.

[00155] The results from the T7E1 assay are used to calculate values for percent gene modification by NHEJ (non-homologous end joining).

[00156] Results from the RFLP assay are used to calculate the values for percent gene modification by following CRISPR treatment.

[00157] Next, cells are cloned out either by limiting serial dilution or single-cell FACS. Clones are cultured until the clonal colonies reach cell numbers of >20,000. gDNA from >10,000 cells of each clonal culture is then extracted. PCR is used to amplify across the repair site, using as template each of the extracted gDNA samples from the clonal cultures. Next, Sanger sequencing methods are used to sequence the repair-site PCR amplicons. Next, the DNA sequence immediately upstream (about 25 bases), immediately downstream (about 25 bases), and across the repair is analyzed.

[00158] Clones not displaying the desired or expected integration events are eliminated. Next, it is determined if any DNA sequence modifications have been made at sites in the genome that have been predicted by algorithm to be the top 20 potential off-target sites in the genome. Clonal cultures for which DNA sequence modifications have been made at off-target sites in the genome are eliminated. [00159] Remaining clones are cultured out until clonal colonies reach cell numbers of >lxl0⁶. mRNA is extracted from > 100,000 cells of each clonal culture; mRNA is also extracted from > 100,000 cells of the parent culture (in which no gene repair has been performed).

[00160] Quantitative reverse-transcription PCR (qRT-PCR) primers are designed for the detection of: a) Transcription of the F8 gene, targeting an exonic site 5' of the gene repair site; b) Transcription of the F8 gene, targeting an exonic site 3' of the gene repair site; c) Transcription of the F8 gene, targeting a sequence that is unique to the gene repair site itself, that furthermore overlaps the junction of (i) the gene repair site and (ii) an endogenous, non-repaired exonic site 5' of the gene repair site. This amplified product are only detected in cells that have been correctly repaired; and d) Transcription of house-keeping genes that can be used for normalization of F8 gene transcription, including at least the genes for beta-actin (ACTB), gamma-tubulin (TUBG1), and RNA polymerase II (POLR2A).

[00161] Using qRT-PCR methods, transcription of the F8 gene using the mRNA extracted from each clonal culture and the parent culture is analyzed to yield a quantitative value for each sample analyzed (AC_t value).

[00162] The transcription of the F8 gene across all samples is compared. Clonal cultures that exhibit the highest AC_t values for transcription of F8 when measured using qRT-PCR primers targeting the gene repair site itself are further isolated. These cells are cultured until the clonal colonies reach cell numbers of >5xl0⁷

[00163] Next, >5xl0⁷ cells from each culture are removed and pelleted. Cell lysate from the cell pellets is collected. A modified enzyme-linked immunosorbent assay (mELISA) is then used to detect the presence of FVIII protein in both the culture medium and the whole cell lysates from each culture. This yields a quantitative value for each sample analyzed in units of nanograms of FVIII protein per cell number (ng/5xl0⁷ cells). FVIII protein secretion across all samples is compared. The culture yielding the highest secretion of FVIII protein is chosen to proceed for therapeutic purposes.

[00164] In summary, in some embodiments herein described one or more DNA scission enzyme(s), DNA-SE(s), such as a nuclease or nickase, target a specific portion of the F8 gene in the subject to create either one double stranded-DNA break (ds-DB) in the F8 gene or two appropriately oriented and spaced single stranded-DNA breaks (ss-DBs) in opposite strands of the F8 gene.

[00165] The F8 gene is subsequently repaired through a homologous recombination (HR)- mediated process repair vehicle (RV). The RV comprises one or more cDNA-repair sequences (RS) flanked by an upstream flanking sequence (uFS) and a downstream flanking sequence (dFS) (also called homology arms) to form a DNA donor within the RV. The upstream flanking sequence (uFS) is homologous to a nucleic acid sequence located 5' to the break in the one strand of the F8 gene and the downstream flanking sequence (dFS) is homologous to a nucleic acid sequence located 5' to the break in the other strand of the F8 gene. Insertion of the cDNA- RS occurs through homologous recombination of the upstream flanking sequence (uFS) and the downstream flanking sequence (dFS) with the subject's F8 gene (sF8) to provide a repaired F8 gene.

[00166] The repaired F8 gene upon expression produces functional FVIII protein that induces immune tolerance to FVIII in the subject and/or confers improved coagulation functionality to the FVIII protein encoded by the repaired F8 gene relative to the unrepaired F8. The RV comprises cDNA-RS comprising wild-type exons corresponding to the F8 exons upstream (5') of the DNA-SE target site.

[00167] The examples set forth above are provided to give those of ordinary skill in the art a complete disclosure and description of how to make and use the embodiments of the materials, compositions, systems and methods of the disclosure, and are not intended to limit the scope of what the inventors regard as their disclosure.

[00168] All patents and publications mentioned in the specification are indicative of the levels of skill of those skilled in the art to which the disclosure pertains.

[00169] The entire disclosure of each document cited (including patents, patent applications, journal articles, abstracts, laboratory manuals, books, or other disclosures) in the Background, Summary, Detailed Description, and Examples is hereby incorporated herein by reference. All references cited in this disclosure are incorporated by reference to the same extent as if each reference had been incorporated by reference in its entirety individually. However, if any inconsistency arises between a cited reference and the present disclosure, the present disclosure takes precedence.

[00170] The terms and expressions which have been employed herein are used as terms of description and not of limitation, and there is no intention in the use of such terms and expressions of excluding any equivalents of the features shown and described or portions thereof, but it is recognized that various modifications are possible within the scope of the disclosure claimed. Thus, it should be understood that although the disclosure has been specifically disclosed by embodiments, exemplary embodiments and optional features, modification and variation of the concepts herein disclosed can be resorted to by those skilled in the art, and that such modifications and variations are considered to be within the scope of this disclosure as defined by the appended claims.

[00171] It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to be limiting. As used in this specification and the appended claims, the singular forms "a," "an," and "the" include plural referents unless the content clearly dictates otherwise. The term "plurality" includes two or more referents unless the content clearly dictates otherwise. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which the disclosure pertains.

[00172] When a Markush group or other grouping is used herein, all individual members of the group and all combinations and possible subcombinations of the group are intended to be individually included in the disclosure. Every combination of components or materials described or exemplified herein can be used to practice the disclosure, unless otherwise stated. One of ordinary skill in the art will appreciate that methods, device elements, and materials other than those specifically exemplified can be employed in the practice of the disclosure without resort to undue experimentation. All art-known functional equivalents, of any such methods, device elements, and materials are intended to be included in this disclosure. Whenever a range is given in the specification, for example, a temperature range, a frequency range, a time range, or a composition range, all intermediate ranges and all subranges, as well as, all individual values included in the ranges given are intended to be included in the disclosure. Any one or more individual members of a range or group disclosed herein may be excluded from a claim of this disclosure. The disclosure illustratively described herein suitably can be practiced in the absence of any element or elements, limitation or limitations which is not specifically disclosed herein.

[00173] A number of embodiments of the disclosure have been described. The specific embodiments provided herein are examples of useful embodiments of the invention and it will be apparent to one skilled in the art that the disclosure can be carried out using a large number of variations of the devices, device components, methods steps set forth in the present description. As will be obvious to one of skill in the art, methods and devices useful for the present methods can include a large number of optional composition and processing elements and steps.

[00174] In particular, it will be understood that various modifications can be made without departing from the spirit and scope of the present disclosure. Accordingly, other embodiments are within the scope of the following claims.

Claims

1. A method of repairing a Factor VIII gene (F8 gene) of a subject, the method comprising: introducing into a cell of the subject one or more isolated nucleic acids encoding one or more DNA scission enzyme (DNA-SE) and one or more repair vehicles (RVs) containing at least a cDNA-repair sequence (RS) flanked by an upstream flanking sequence (uFS) and a downstream flanking sequence (dFS) to form a DNA donor within each of the one or more repair vehicles (RVs), wherein the DNA-SE is selected to be capable of targeting a portion of the F8 gene of the subject for subsequent repair by the cDNA-RS, wherein the DNA-SE creates at least one first break in one strand of the F8 gene and at least one second break in the other strand of the F8 gene or at least one double stranded break in the F8 gene; and the cDNA-RS comprises a repaired version of the F8 gene sequence of the subject, the upstream flanking sequence (uFS) is homologous to a nucleic acid sequence located 5' to the break in the one strand of the F8 gene and the downstream flanking sequence (dFS) is homologous to a nucleic acid sequence located 5' to the break in the other strand of the F8 gene; and wherein homologous recombination of the upstream flanking sequence (uFS) and the downstream flanking sequence (dFS) with the F8 gene of the subject (sF8) allows insertion of the cDNA-RS to provide a repaired F8 gene.

2. The method of claim 1, wherein the cDNA-RS comprises F8 exons corresponding to the F8 exons located upstream (5') of the DNA-SE target site.

3. The method of claim 1, wherein the donor sequence further comprises a native F8 5' splice donor site or 3' splice acceptor site operably linked the nucleic acid encoding the cDNA-RS.

4. The method of claim 2, wherein the cDNA-RS comprises a promoter sequence located upstream (5') of the F8 donor sequence.

5. The method of claim 2, wherein the cDNA-RS comprises a polycistronic mRNA element located upstream (5') of the F8 donor sequence.

6. The method of claim 1, wherein the cDNA-RS comprises exon 14 in which all or part of the B domain (residues 741-1648) is deleted.

7. The method of claim 1, wherein the cDNA-RS comprises a Phe309Ser substitution.

8. The method of claim 1, wherein the F8 gene repair results in repaired FVIII that is fused with a half-life extending moiety.

9. The method of claim 8, wherein the half-life extending moiety is the Fc-domain of IgG or the human albumin protein.

10. The method of claim 1, wherein the F8 gene repair results in a single chain FVIII.

11. The method of claim 10, wherein a protease cleavage site motif in FVIII is deleted or otherwise disrupted.

12. The method of claim 10, wherein the protease cleavage site is at FVIII residues 1313 and/or 1648.

13. The method of claim 10, wherein the secretion, specific activity, half-life and/or stability of FVIII produced by a cell is increased relative to full-length FVIII.

14. The method of claim 1, wherein the F8 gene repair results in repaired FVIII that retains native glycosylation and/or comprises additional engineered glycosylation sites.

15. The method of claim 14, wherein FVIII antigenicity and/or immunogenicity is reduced.

16. The method of claim 14, wherein FVIII secretion is increased.

17. The method of claim 1, wherein the cDNA-RS further comprises a half-life extending moiety.

18. The method of claim 17, wherein the half-life extending moiety is albumin or the Fc-domain of the IgG molecule.

19. The method of claim 1 wherein the isolated nucleic acids are administered directly to the subject so that introduction into the subject's cells occurs in vivo.

20. The method of claim 1, wherein the isolated nucleic acids are administered ex vivo to cells that have been isolated from the subject.

21. The method of claim 1, wherein the nuclease is a zinc finger nuclease (ZFN), Transcription Activator-Like Effector Nuclease (TALEN), or a CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-associated (Cas) nuclease.

22. The method of claim 1, wherein the cells are blood outgrowth endothelial cells (BOECs), hepatocytes, liver sinusoidal endothelial cells (LSECs), or stem cells.

23. The method of claim 1, wherein the repaired F8 gene confers an improved coagulation functionality of the encoded FVIII protein of the subject compared to the coagulation

functionality of the FVIII protein encoded by the unrepaired F8 gene of the subject.

24. The method of claim 1, wherein the F8 gene repair induces a tolerogenic immune response to a FVIII protein in the subject.