GENETICALLY MODIFIED CELLS, TISSUES, AND ORGANS FOR TREATING

DISEASE

CROSS REFERENCE

[0001] This application claims the benefit of U.S. Provisional Patent Application No. 62/788,044, filed January 3, 2019, which is incorporated herein by reference in its entirety.

BACKGROUND OF THE DISCLOSURE

[0002] There is a shortage of organs, tissues or cells available for transplantation in recipients such as humans. Xenotransplantation or allotransplantation of organs, tissues, or cells into humans has the potential to fulfill this need and help hundreds of thousands of people every year. Non-human animals can be chosen as organ donors based on their anatomical and physiological similarities to humans.

Additionally, xenotransplantation has implications not only in humans, but also in veterinary applications. However, unmodified wild-type non-human animal tissues can be rejected by recipients, such as humans, by the immune system. Rejection is believed to be caused at least in part by antibodies binding to the tissues and cell -mediated immunity leading to graft loss. For example, pig grafts can be rejected by cellular mechanisms mediated by adaptive immune cells.

INCORPORATION BY REFERENCE

[0003] All publications, patents, and patent applications herein are incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference. In the event of a conflict between a term herein and a term in an incorporated reference, the term herein controls.

SUMMARY

[0004] In one aspect provided herein is a genetically modified animal comprising an exogenous nucleic acid molecule comprising a nucleic acid sequence comprising, a first polynucleotide encoding a b chain of a MHC molecule or a fragment thereof, and/or a second polynucleotide encoding an a chain of the MHC molecule or a fragment thereof.

[0005] In some embodiments, the b chain or the fragment thereof and the a chain or the fragment thereof form a peptide binding groove. In some embodiments, the genetically modified animal further comprises a third polynucleotide encoding a peptide derived from the MHC molecule, wherein the peptide is capable of binding the peptide binding groove, to generate a functional MHC -peptide complex. In some embodiments, the (a), (b) or both (a) and (b) lack a functional transmembrane domain. In some embodiments, the nucleic acid sequence comprises from 5’-3’, the third polynucleotide, the first polynucleotide, and the second polynucleotide.

[0006] In some embodiments, the nucleic acid sequence encodes a single chain MHC chimeric peptide comprising covalently linked in a sequence (a) the peptide derived from the MHC molecule, (b) the b chain of the MHC molecule or fragment thereof, and (c) the a chain of the MHC molecule or fragment thereof, wherein the b chain and the a chain form a peptide binding groove, and wherein the peptide derived from the MHC molecule is capable of binding the peptide binding groove, to generate a functional MHC -peptide complex.

[0007] In some embodiments, the genetically modified animal further comprises a regulatory sequence operatively linked to the nucleic acid sequence. In some embodiments, the nucleic acid sequence further comprises in frame a first linker polynucleotide encoding a first linker peptide, wherein the first linker polynucleotide is interposed between the first polynucleotide and the second polynucleotide. In some embodiments, the nucleic acid sequence further comprises in frame a second linker polynucleotide encoding a second linker peptide interposed between the second polynucleotide and the third

polynucleotide. In some embodiments, the first linker peptide is cleavable. In some embodiments, the second linker peptide is cleavable. In some embodiments, the first linker peptide is linked between the C- terminus of a b2 domain of the b chain and the N-terminus of an a1 domain of the a chain.

[0008] In some embodiments, the second linker peptide is linked between the C-terminus of the peptide derived from the MHC molecule and the N-terminus of the b chain of the MHC molecule or fragment thereof. In some embodiments, the exogenous nucleic acid molecule is inserted into an insertion site into the genetically modified animal’s genome. In some embodiments, the insertion site is located in a safe harbor site, a PERV site or a gene encoding a GGTA1, a NOD-like receptor family CARD domain containing 5 (NLRC5), a putative cytidine monophosphatase-N-acetylneuraminic acid hydroxylase-like protein (CMAH), a beta-l,4-N-acetylgalactosaminyltransferase (B4GALNT2), cytidine monophospho-N- acetylneuraminic acid (CMP-N-NeuAc) hydrolase in the genetically modified animal’s genome. In some embodiments, the safe harbor site is in ROSA26 gene. In some embodiments, the genetically modified animal further comprises a disruption in one or more genes, wherein the one or more genes encoding a NOD-like receptor family CARD domain containing 5 (NLRC5), a putative cytidine monophosphatase- N-acetylneuraminic acid hydroxylase -like protein (CMAH), a beta-1, 4-N-acetylgalactosaminyltransferase (B4GALNT2) or a combination thereof.

[0009] In some embodiments, the genetically modified animal further comprises an exogenous polynucleotide, (HLA-E), human leukocyte antigen G (HLA-G), or b-2 -microglobulin (B2M). In some embodiments, the genetically modified animal comprises exogenous polynucleotide encoding HLA-G, wherein the HLA-G is HLA-G 1, HLA-G2, HLA-G3, HLA-G4, HLA-G5, HLA-G6, or HLA-G7. In some embodiments, the HLA-G is HLA-G 1. In some embodiments, the genetically modified animal is a member of the Laurasiatheria superorder. In some embodiments, the genetically modified animal is an ungulate. In some embodiments, the genetically modified animal is a pig. In some embodiments, the genetically modified animal is a non-human primate. In some embodiments, the genetically modified animal is fetus.

[0010] In some embodiments, the first linker peptide comprises a sequence set forth in SEQ ID NO 2. In some embodiments, the second linker peptide comprises a sequence set forth in SEQ ID NO 1. In some embodiments, the MHC molecule is MHC class II molecule selected from the group consisting of HLA- DP, HLA-DQ, and HLA-DR. In some embodiments, the MHC class II molecule is HLA-DR and the b chain is HLA-DR1, HLA-DR2. HLA-DR3, HLA-DR4, or HLA-DR5. In some embodiments, the MHC class II molecule is HLA-DR3 and the b chain is encoded by HLA-DRB1*03 or HLA-DRB1*04 allele.

In some embodiments, the MHC molecule is HLA-DR and the a chain of the MHC class II molecule is encoded by HLA-DRAO 10202 allele.

[0011] In some embodiments, the peptide derived from a MHC class II molecule comprises a sequence from the b chain of the MHC class II molecule. In some embodiments, the peptide derived from a MHC class II molecule comprises a sequence from a hypervariable region of the b chain of the MHC class II molecule. In some embodiments, the peptide derived from a MHC class II molecule is at least 8 to 30 amino acids in length. In some embodiments, the peptide derived from a MHC class II molecule comprises a sequence selected from Table 1. In some embodiments, the nucleic acid sequence is at least 95% identical to SEQ ID NO 3.

[0012] In one aspect provided herein is a population of genetically modified animals comprising two or more animals of any one of aspects above. In some embodiments, at least two or more animals have identical phenotypes. In some embodiments, at least two or more animals have identical genotypes.

[0013] Provided herein is a pancreas or pancreatic islet isolated from said genetically modified animal of any one of aspects above.

[0014] Provided herein is a genetically modified cell, tissue, or organ isolated from said genetically modified animal of any one of aspects above. In some embodiments, the cell is an islet cell, or a kidney cell. In some embodiments, the cell is a stem cell. In some embodiments, the tissue is a solid organ transplant. In some embodiments, the tissue is all or a portion of a liver. In some embodiments, the tissue is all or a portion of a kidney.

[0015] Provided herein is a genetically modified cell, tissue, or organ of any one of aspects above, for use in treating a condition or transplanting to a subject in need thereof to treat a condition in said subject, wherein the subject expresses the MHC molecule, wherein said subject is tolerized to the genetically modified cell, tissue, or organ by use of a vaccine.

[0016] Provided herein is a genetically modified cell comprising an exogenous nucleic acid molecule comprising a nucleic acid sequence comprising, a first polynucleotide encoding a b chain of a MHC molecule or a fragment thereof, and/or a second polynucleotide encoding an a chain of the MHC molecule or a fragment thereof. In some embodiments, the b chain or the fragment thereof and the a chain or the fragment thereof form a peptide binding groove. In some embodiments, the genetically modified cell further comprises a third polynucleotide encoding a peptide derived from the MHC molecule, wherein the peptide is capable of binding the peptide binding groove, to generate a functional MHC- peptide complex. In some embodiments, the nucleic acid sequence comprises from 5’-3’ the third polynucleotide, the first polynucleotide, and the second polynucleotide. In some embodiments, the nucleic acid sequence encodes a single chain chimeric peptide comprising covalently linked in a sequence (a) the peptide derived from the MHC molecule, (b) the b chain of the MHC molecule or fragment thereof, and (c) the a chain of the MHC molecule or fragment thereof, wherein the b chain and the a chain form a peptide binding groove, and wherein the peptide derived from the MHC molecule is capable of binding the peptide binding groove, to generate a functional MHC-peptide complex.

[0017] In some embodiments, the genetically modified cell further comprises a regulatory sequence operatively linked to the nucleic acid sequence. In some embodiments, the nucleic acid sequence further comprises in frame a first linker polynucleotide encoding a first linker peptide interposed between the first polynucleotide and the second polynucleotide. In some embodiments, the nucleic acid sequence further comprises in frame a second linker polynucleotide encoding a second linker peptide interposed between the second polynucleotide and the third polynucleotide. In some embodiments, the first linker peptide is linked between the C-terminus of a b2 domain of the b chain and the N-terminus of an oil domain of the a chain. In some embodiments, the second linker peptide is linked between the C-terminus of the peptide derived from the MHC molecule and the N-terminus of the b chain of the MHC molecule or fragment thereof. In some embodiments, the first linker peptide is cleavable.

[0018] In some embodiments, the second linker peptide is cleavable. In some embodiments, the exogenous nucleic acid molecule is inserted into an insertion site into the genetically modified animal’s genome. In some embodiments, the insertion site is located in a safe harbor site, a PERV site, or a gene encoding a NOD-like receptor family CARD domain containing 5 (NLRC5), a GGTA1, a putative cytidine monophosphatase-N-acetylneuraminic acid hydroxylase-like protein (CMAH), a beta-1, 4-N- acetylgalactosaminyltransferase (B4GALNT2) the genetically modified animal’s genome. In some embodiments, the safe harbor site is in ROSA26 gene.

[0019] In some embodiments, the genetically modified cell further comprises a disruption in one or more genes, wherein the one or more genes encoding a GGTA1, NOD-like receptor family CARD domain containing 5 (NLRC5), a putative cytidine monophosphatase-N-acetylneuraminic acid hydroxylase-like protein (CMAH), a beta-1,4-N-acetylgalactosaminyltransferase (B4GALNT2) or a combination thereof. In some embodiments, the genetically modified cell further comprises an exogenous polynucleotide, (HLA-E), human leukocyte antigen G (HLA-G), or b-2 -microglobulin (B2M). In some embodiments, the genetically modified cell comprising exogenous polynucleotide encoding HLA-G, wherein the HLA-G is HLA-G 1, HLA-G2, HLA-G3, HLA-G4, HLA-G5, HLA-G6, or HLA-G7. In some embodiments, the HLA-G is HLA-G 1.

[0020] In some embodiments, the genetically modified non-human cell is from a member of the

Laurasiatheria superorder. In some embodiments, the member of the Laurasiatheria superorder is an ungulate. In some embodiments, the ungulate is a pig. In some embodiments, the genetically modified cell is a pancreatic, kidney, eye, liver, small bowel, lung, or heart cell. In some embodiments, the genetically modified cell is a pancreatic cell. In some embodiments, the pancreatic cell is a pancreatic b cell. In some embodiments, the genetically modified cell is a spleen, liver, peripheral blood, lymph nodes, thymus, or bone marrow cell. In some embodiments, the genetically modified cell is a porcine cell. In some embodiments, the genetically modified cell is from an embryotic tissue, a non-human fetal animal, perinatal non-human animal, neonatal non-human animal, preweaning non-human animal, young adult non-human animal, or adult non-human animal. In some embodiments, the first linker peptide comprises a sequence set forth in SEQ ID NO: 2. In some embodiments, the second linker peptide comprises a sequence set forth in SEQ ID NO: 1.

[0021] In some embodiments, the MHC molecule is MHC class II molecule selected from the group consisting of HLA-DP, HLA-DQ, and HLA-DR. In some embodiments, the MHC class II molecule is HLA-DR and the b chain is HLA-DR1, HLA-DR2, HLA-DR3, HLA-DR4, or HLA-DR5. In some embodiments, the MHC class II molecule is HLA-DR3 and the b chain is encoded by HLA-DRB1*03 or HLA-DRB1*04 allele. In some embodiments, the MHC molecule is HLA-DR and the a chain of the MHC class II molecule is encoded by HLA-DRAO 10202 allele. In some embodiments, the peptide derived from a MHC class II molecule comprises a sequence from the b chain of the MHC class II molecule.

[0022] In some embodiments, the peptide derived from a MHC class II molecule comprises a sequence from a hypervariable region of the b chain of the MHC class II molecule. In some embodiments, the peptide derived from a MHC class II molecule is at least 8 to 30 amino acids in length. In some embodiments, the peptide derived from a MHC class II molecule comprises a sequence selected from Table 1. In some embodiments, the nucleic acid sequence is at least 95% identical to SEQ ID NO: 3.

[0023] Provided herein is a solid organ transplant comprising the genetically modified cell of any one of aspects above.

[0024] Provided herein is an embryo comprising the genetically modified cell of any one of aspects above.

[0025] Provided herein is a genetically modified cell of any one of aspects above for use in treating a condition or for use in transplantation in a subject, wherein the subject expresses the MHC molecule.

[0026] Provided herein is a tissue or organ comprising said genetically modified cell described above.

[0027] Provided herein is a pancreas or pancreatic islet comprising said genetically modified cell of any one of aspects above.

[0028] Provided herein is a pharmaceutical composition comprising said genetically modified cell of any one of aspects above, and a pharmaceutically acceptable excipient.

[0029] In some embodiments, the pharmaceutical composition is formulated for administration via a subcutaneous, intravenous, intradermal, intraperitoneal, oral, intramuscular, intracerebroventricular, intranasal, intracranial, intracelial, intracerebellar, intrathecal, transdermal, pulmonary, or topical administration route.

[0030] In some embodiments, the pharmaceutical composition is formulated for administration via intravenous administration route. In some embodiments, the pharmaceutical composition is contained in a delivery device selected from the group consisting of a syringe, a blunt tip syringe, a catheter, an inhaler, a nebulizer, a nasal spray pump, a nasal irrigation pump or nasal lavage pump, and an implantable pump. In some embodiments, he pharmaceutical composition has a shelf life of at least 2 days, 2 weeks, 1 month to 2 years at room temperature. In some embodiments, the pharmaceutical composition has a shelf life of at least 2 days, 2 weeks, 1 month to 2 years at 4°C.

[0031] In one aspect provided herein is a tolerizing regimen for transplantation comprising an effective amount of a composition comprising the genetically modified cell described above. In some

embodiments, said genetically modified cell is an apoptotic cell. In some embodiments, said genetically modified cell is a fixed cell. In some embodiments, the tolerizing regimen of any one of aspects above, further comprises a non-fixed cell. In some embodiments, said fixed cell and said non-fixed cell are genetically identical. In some embodiments, said fixed cell is fixed by a chemical and/or said fixed cell induces anergy of immune cells in said subject. In some embodiments, said genetically modified cell is an 1 -Ethyl-3 -(3 -dimethylaminopropyljcarbodiimide (ECDI)-fixed cell .

[0032] In one aspect provided herein is as method for treating a condition in a subject in need thereof comprising (a) transplanting to the subject, said genetically modified cell described above, or said cell, tissue or organ described above; and/or (b) administering a tolerizing regimen of aspects above to said subject.

[0033] Provided herein is a method for treating a condition in a subject in need thereof comprising, (a) administering a tolerizing regimen of any one of aspects above to said subject, and (b) transplanting a genetically modified cell, tissue, or organ comprising a genetically modified cell of any one of aspects above to said subject. In some embodiments, the subject expresses the MHC molecule. In some embodiments, the method further comprises administering to said subject an effective amount of one or more immunomodulatory molecules. In some embodiments, the one or more immunomodulatory molecules inhibit T cell activation, B cell activation, and/or dendritic cell activation in the subject.

[0034] In some embodiments, the one or more immunomodulatory molecules is an anti-CD40 agent, anti-CD40L agent, a B-cell depleting or modulating agent, an mTOR inhibitor, a TNF-alpha inhibitor, a IL-6 inhibitor, a nitrogen mustard alkylating agent, a complement C3 or C5 inhibitor, IFNg, an NFKB inhibitor, vitamin D3, cobalt protoporphyrin, insulin B9-23, a cluster of differentiation protein, alpha 1anti -trypsin inhibitor, dehydroxymethylepoxyquinomycin (DHMEQ), or any combination thereof. In some embodiments, the NF-kB inhibitor is curcumin, triptolide, Bay-117085, or a combination thereof. In some embodiments, the anti-CD40 agent is CD40 siRNA. In some embodiments, the anti-CD40 agent is a CD40 binding peptide inhibitor, anti-CD40 monoclonal antibody, a Fab’ anti-CD40 monoclonal antibody fragment, FcR-engineered, Fc silent anti-CD40 monoclonal domain antibody.

[0035] In some embodiments, the anti CD40F agent is an anti-CD40 F monoclonal antibody, a Fab’ anti- CD40F monoclonal antibody fragment CDP7657, a FcR-engineered, Fc silent anti-CD40F monoclonal domain antibody, a Fab’ anti-CD40F antibody, CD-40 binding peptides or an Fc-engineered anti-CD40F antibody. In some embodiments, said tolerizing regimen comprises from or from about 0.001 to 1.0 endotoxin unit per kg bodyweight of said subject. In some embodiments, said tolerizing regimen comprises from or from about 1 to 10 aggregates per ml. In some embodiments, the tolerizing regimen is provided prior to, concurrently with, or after the transplanting. In some embodiments, said tolerizing regimen is administered 7 days before said transplantation and 1 day after said transplantation. In some embodiments, said tolerizing regimen is provided intravenously. In some embodiments, said transplanted cell, tissue, or organ survives for at least 7 days after the transplanting. In some embodiments, said transplanting is xenotransplanting.

[0036] In some embodiments, a first dose of the one or more immunomodulatory molecule is administered about 8 days before said transplantation. In some embodiments, said subject is a human subject. In some embodiments, said subject is a non -human animal. In some embodiments, is type 1 diabetes, type 2 diabetes, surgical diabetes, cystic fibrosis-related diabetes, and/or mitochondrial diabetes.

[0037] Provided herein is a method for tolerizing a recipient to a graft comprising providing to said recipient said tolerizing regimen of any one of aspects above.

[0038] In one aspect provided herein is an isolated nucleic acid molecule comprising a nucleic acid sequence comprising, a first polynucleotide encoding a b chain of a MHC molecule or a fragment thereof, and/or

[0039] a second polynucleotide encoding an a chain of the MHC molecule or a fragment thereof. In some embodiments, the b chain or the fragment thereof and the a chain or the fragment thereof form a peptide binding groove. In some embodiments, the isolated nucleic acid molecule further comprises a third polynucleotide encoding a peptide derived from the MHC molecule, wherein the peptide is capable of binding the peptide binding groove, to generate a functional MHC-peptide complex. In some embodiments, the (a), (b) or both (a) and (b) lack a functional transmembrane domain. In some embodiments, the nucleic acid sequence comprises from 5’-3’, the third polynucleotide, the first polynucleotide, and the second polynucleotide.

[0040] In some embodiments, the nucleic acid sequence encodes a single chain chimeric peptide comprising covalently linked in a sequence (a) the peptide derived from the MHC molecule, (b) the b chain of the MHC molecule or fragment thereof, and (c) the a chain of the MHC molecule or fragment thereof, wherein the b chain and the a chain form a peptide binding groove, and wherein the peptide derived from the MHC molecule is capable of binding the peptide binding groove, to generate a functional MHC-peptide complex. In some embodiments, the isolated nucleic acid molecule further comprises a regulatory sequence operatively linked to the nucleic acid sequence.

[0041] In some embodiments, the nucleic acid sequence further comprises in frame a first linker polynucleotide encoding a first linker peptide, wherein the first linker polynucleotide is interposed between the first polynucleotide and the second polynucleotide. In some embodiments, the nucleic acid sequence further comprises in frame a second linker polynucleotide encoding a second linker peptide interposed between the second polynucleotide and the third polynucleotide. In some embodiments, the first linker peptide is cleavable. In some embodiments, the second linker peptide is cleavable. In some embodiments, the first linker peptide is linked between the C-terminus of a b2 domain of the b chain and the N-terminus of an a1 domain of the a chain. In some embodiments, the second linker peptide is linked between the C-terminus of the peptide derived from the MHC molecule and the N-terminus of the b chain of the MHC molecule or fragment thereof.

[0042] In some embodiments, the first linker peptide comprises a sequence set forth in SEQ ID NO: 2.

In some embodiments, the second linker peptide comprises a sequence set forth in SEQ ID NO: 1. In some embodiments, the MHC molecule is MHC class II molecule selected from the group consisting of HLA-DP, HLA-DQ, and HLA-DR. In some embodiments, the MHC class II molecule is HLA-DR and the b chain is HLA-DR 1, HLA-DR2, HLA-DR3, HLA-DR4, or HLA-DR5.

[0043] In some embodiments, the MHC class II molecule is HLA-DR3 and the b chain is encoded by HLA-DRB1*03 or HLA-DRB1*04 allele. In some embodiments, the MHC molecule is HLA-DR and the a chain of the MHC class II molecule is encoded by HLA-DRA010202 allele. In some embodiments, the peptide derived from a MHC class II molecule comprises a sequence from the b chain of the MHC class II molecule. In some embodiments, the peptide derived from a MHC class II molecule comprises a sequence from a hypervariable region of the b chain of the MHC class II molecule. In some

embodiments, the peptide derived from a MHC class II molecule is at least 8 to 30 amino acids in length.

[0044] In some embodiments, the peptide derived from a MHC class II molecule comprises a sequence selected from Table 1. In some embodiments, the nucleic acid sequence is at least 95% identical to SEQ ID NO: 3. In some embodiments, the nucleic acid sequence is at least 95% identical to SEQ ID NO: 4. In some embodiments, the isolated nucleic acid molecule further comprises: a first flanking sequence homologous to a first genome sequence upstream of an insertion site, said first flanking sequence located upstream of the nucleic acid sequence; and a second flanking sequence homologous to a second genome sequence downstream of the insertion site, said second flanking sequence located downstream of the nucleic acid sequence.

[0045] In some embodiments, said first flanking sequence, said second flanking sequence, or both comprise at least 50 nucleotides.

[0046] In some embodiments, said first flanking sequence, said second flanking sequence, or both comprise at least 100 nucleotides. In some embodiments, said first flanking sequence, said second flanking sequence, or both comprise at least 500 nucleotides. In some embodiments, the insertion site is in ROSA26 genomic locus. In some embodiments, the insertion site is in gene encoding for a glycoprotein galactosyltransferase alpha 1,3 (GGTA1), a putative cytidine monophosphate-N-acetylneuraminic acid hydroxylase -like protein (CMAH), a b 1,4 N-acetylgalactosaminyltransferase (B4GALNT2), a C-X-C motif chemokine 10 (CXCL10), a MHC class I polypeptide-related sequence A (MICA), a MHC class I polypeptide-related sequence B (MICB), a transporter associated with antigen processing 1 (TAPI), a NOD -like receptor family CARD domain containing 5 (NLRC5). In some embodiments, he first flanking sequence comprises a nucleic acid sequence that is at least 95% identical to SEQ ID NO: 3. In some embodiments, the second flanking sequence comprises a nucleic acid sequence that is at least 95% identical to SEQ ID NO: 4. [0047] Provided herein is a vector comprising the isolated nucleic acid molecule of any one of aspects above.

[0048] Provided herein is a host cell comprising the isolated nucleic acid described above; or the vector above.

[0049] Provided herein is a kit comprising a first container comprising the isolated nucleic acid molecule of any one of aspects above. In some embodiments, the isolated nucleic acid molecule is in a lyophilized form or a solution form. In some embodiments, the kit further comprises a second container comprising a cell for generating a genetically modified cell. In some embodiments, the kit further comprises, a reconstitution solution, diluent, a culture medium, or a combination thereof. In some embodiments, the kit further comprises instructions of introducing the nucleic acid in the genome of the cell to generate the genetically modified cell.

[0050] Provided herein is a kit for transplantation comprising, (a) the genetically modified cell of any one of aspects above, (b) the tolerizing regimen of any one of aspects above, or (c) the cell, tissue or organ of any one of aspects above. In some embodiments, the kit further comprises one or more immunomodulatory agent.

[0051] Provided herein is a method for making a genetically modified animal of any one of aspects above, comprising: (a) obtaining a fetal fibroblast cell from an animal comprising, (i) the isolated nucleic acid molecule described above or (ii) a disruption in one or more gene encoding GGTA1, NLRC5, CMAH, or B4GALNT2, b) genetically modifying said fetal fibroblast using CRISPR/Cas by (i) disrupting one or more gene encoding GGTA1, NLRC5, CMAH, or B4GALNT2 in the fetal fibroblast cell comprising the isolated nucleic acid molecule disclosed above, or (ii) inserting the isolated nucleic acid molecule of any one of aspects above in the fetal fibroblast cell comprising the disruption in the gene encoding GGTA1, NLRC5, CMAH, or B4GALNT2, c) transferring a nucleus of the fetal fibroblast cell to an enucleated oocyte of the animal to generate an embryo, and d) transferring the embryo into a surrogate animal of the same species and growing the embryo to the genetically modified animal in the surrogate animal. In some embodiments, the fetal fibroblast cell further comprises an exogenous nucleotide sequence encoding a human b2-microglobulin polypeptide, an exogenous nucleotide sequences encoding a human leukocyte antigen E (HLA-E) polypeptide, or a combination thereof.

[0052] Provided herein is a method for making a genetically modified cell, the method comprising genetically modifying a cell to express an exogenous single chain MHC chimeric peptide using

CRISPR/Cas. In some embodiments, the genetically modifying comprises inserting the isolated nucleic acid molecule of aspects above in an insertion site into the genome of the cell. In some embodiments, the insertion site is in a safe harbor site. In some embodiments, the safe harbor site is ROSA 26 gene. In some embodiments, the insertion site is a PERV site. In some embodiments, the insertion site is in a gene encoding a glycoprotein galactosyltransferase alpha 1,3 (GGTA1), a putative cytidine monophosphate-N- acetylneuraminic acid hydroxylase-like protein (CMAH), a b1,4 N-acetylgalactosaminyltransferase (B4GALNT2), a C-X-C motif chemokine 10 (CXCL10), a MHC class I polypeptide-related sequence A (MICA), a MHC class I polypeptide-related sequence B (MICB), a transporter associated with antigen processing 1 (TAPI), or a NOD-like receptor family CARD domain containing 5 (NLRC5). In some embodiments, the inserting reduces expression of the gene.

[0053] Provided herein is a method for making a genetically modified animal comprising the steps of: (a) inducing a fusion of a genetically modified cell with one or more oocyte, under conditions suitable for forming a reconstructed embryo, wherein the one or more oocytes are zona pellucida free, and enucleated, (b) activating the reconstructed embryo, (c) culturing the activated reconstructed embryo of step (b), until greater than 2-cell developmental stage, and (d) implanting the cultured embryo into a surrogate and growing the embryo to the genetically modified animal in the surrogate. In some embodiments, the method further comprises forming an aggregate of at least two activated reconstructed embryo prior to step (c), wherein the at least two activated reconstructed embryos are genetically identical. In some embodiments, the culturing of step (c) is done until formation of a blastocyst. In some embodiments, the zona pellucida is removed by physical manipulation, chemical treatment and enzymatic digestion. In some embodiments, the enucleation is by physical removal or chemical expulsion.

[0054] In some embodiments, the physical removal is by bisection. In some embodiments, the fusion is by chemical fusion, electrofusion or biofusion. In some embodiments, the electrofusion is induced by application of an electrical pulse. In some embodiments, the electrofusion is by chamber fusion or electrode fusion. In some embodiments, the electrofusion comprises the step of delivering one or more electrical pulses to the genetically engineered donor cell together with the one or more oocyte. In some embodiments, the chemical fusion or biofusion is accomplished by exposing the genetically engineered donor cell together with the one or more oocyte to a fusion agent. In some embodiments, the fusion agents are selected from the group consisting of polyethylene glycol (PEG), trypsin, dimethylsulfoxide (DMSO), lectins, agglutinin, viruses, and Sendai virus.

[0055] In some embodiments, the activating is by treating with an effective amount of an activating agent. In some embodiments, the activating agent is Thimerosal, dithiothreitol, or a combination thereof. In some embodiments, the genetically modified donor cell is a somatic cell selected from epithelial cells, neural cells, epidermal cells, keratinocytes, hematopoietic cells, melanocytes, chondrocytes, lymphocytes (B and T lymphocytes), erythrocytes, macrophages, monocytes, mononuclear cells, fibroblasts, cardiac muscle cells, and other muscle cells. In some embodiments, the genetically modified cell is a fibroblast cell. In some embodiments, the genetically modified cell is a fetal fibroblast cell. In some embodiments, the genetically modified cell has been modified by insertion, deletion or modification of one or more desired gene.

[0056] Provided herein is a method for making a genetically modified animal comprising, (a) inducing a fusion of a genetically modified cell of aspects above with one or more oocyte, under conditions suitable for forming a reconstructed embryo, wherein the one or more oocytes are zona pellucida free, and enucleated and wherein the genetically engineered porcine fetal fibroblast comprises an exogenous nucleic acid molecule expressing MHC molecule, (b) activating the reconstructed embryo, (c) culturing the activated reconstructed embryo of step (b), until greater than 2-cell developmental stage, and (d) implanting the cultured embryo into a surrogate and growing the embryo to the genetically modified animal in the surrogate.

[0057] In some embodiments, the method further comprises forming an aggregate of at least two activated reconstructed embryo prior to step (c), wherein the at least two activated reconstructed embryos are genetically identical.

[0058] Provided herein is a method for generating a genetically modified embryonic stem cell comprising, (a) inducing a fusion of a genetically modified donor cell with one or more oocyte, under conditions suitable for forming a reconstructed embryo, wherein the one or more oocytes are zona pellucida free, and enucleated, (b) activating the reconstructed embryo, (c) culturing the activated reconstructed embryo of step (b), until formation of a blastocyst, (d) isolating an inner cell mass of the blastocyst, and (e) culturing the inner cell mass to generate the genetically modified embryonic stem cell.

[0059] In some embodiments, the method of aspects above, further comprising forming an aggregate of at least two activated reconstructed embryo prior to step (c), wherein the at least two activated reconstructed embryos are genetically identical.

[0060] Provided herein is a genetically modified cell comprising an (a) an exogenous nucleic acid sequence encoding a b chain of a MHC molecule; and/or (b) an exogenous nucleic acid sequence encoding an a chain of the MHC molecule. In some embodiments, the b chain, and the a chain form a functional MHC complex, wherein the functional MHC complex comprises a peptide binding groove.

[0061] In some embodiments, the genetically modified cell further comprises an exogenous nucleic acid sequence encoding a peptide derived from a MHC molecule, wherein the peptide derived from a MHC molecule is capable of binding the peptide binding groove, thereby forming a functional peptide-MHC complex.

[0062] Provided herein is a genetically modified animal that is a member of the Laurasiatheria superorder or is a non-human primate comprising: (a) an exogenous nucleic acid sequence encoding a b chain of a MHC molecule; and/or (b) an exogenous nucleic acid sequence encoding an a chain of the MHC molecule.

[0063] In some embodiments, the b chain, and the a chain form a functional MHC complex, wherein the functional MHC complex comprises a peptide binding groove.

[0064] In some embodiments, the genetically modified cell further comprises an exogenous nucleic acid sequence encoding a peptide derived from a MHC molecule, wherein the peptide derived from a MHC molecule is capable of binding the peptide binding groove, thereby forming a functional peptide-MHC complex.

[0065] Provided herein is a single chain MHC (scMHC) chimeric peptide comprising, (a) a peptide derived from a MHC molecule, (b) a b chain of the MHC molecule or fragment thereof, and (c) an a chain of the MHC molecule or fragment thereof; wherein the b chain and the a chain form a peptide binding groove, and wherein the peptide derived from the MHC molecule is capable of binding the

-l i peptide binding groove, to generate a functional MHC-peptide complex. In some embodiments, (b), (c) or both (b) and (c) lack a functional transmembrane domain. In some embodiments, the scMHC chimeric peptide further comprises a first linker peptide, wherein the first linker peptide is linked between the C- terminus of a b2 domain of the b chain and the N-terminus of an al domain of the a chain.

[0066] In some embodiments, the scMHC chimeric peptide further comprises a second linker peptide wherein the second linker peptide is linked between the C-terminus of (a) and N-terminus of (b). In some embodiments, the first linker peptide comprises a sequence set forth in SEQ ID NO 2. In some embodiments, the second linker peptide comprises a sequence set forth in SEQ ID NO 1. In some embodiments, the MHC molecule is MHC class II molecule selected from the group consisting of HLA- DP, HLA-DQ, and HLA-DR. In some embodiments, the MHC class II molecule is HLA-DR and the b chain is HLA-DR1, HLA-DR2, HLA-DR3, HLA-DR4, or HLA-DR5. In some embodiments, the MHC class II molecule is HLA-DR3 and the b chain is encoded by HLA-DRB1*03 or HLA-DRB1*04 allele.

[0067] In some embodiments, the MHC molecule is HLA-DR and the a chain of the MHC class II molecule is encoded by HLA-DRAO 10202 allele. In some embodiments, the peptide derived from a MHC class II molecule comprises a sequence from the b chain of the MHC class II molecule. In some embodiments, the peptide derived from a MHC class II molecule comprises a sequence from a hypervariable region of the b chain of the MHC class II molecule. In some embodiments, the peptide derived from a MHC class II molecule is at least 8 to 30 amino acids in length. In some embodiments, the peptide derived from a MHC class II molecule comprises a sequence selected from Table 1. In some embodiments, the scMHC chimeric peptide is recombinant. In some embodiments, the scMHC chimeric peptide is soluble.

[0068] Provided herein is a method of making a genetically modified animal, comprising, (a) obtaining a fetal fibroblast cell from an animal comprising; (i) the isolated nucleic acid molecule of aspects above, b) transferring a nucleus of the fetal fibroblast cell to an enucleated oocyte of the animal to generate an embryo, and c) transferring the embryo into a surrogate animal of the same species and growing the embryo to the genetically modified animal in the surrogate animal.

[0069] Provided herein is a method of making a genetically modified cell, comprising, (a) obtaining a fetal fibroblast cell from an animal, b) genetically modifying said fetal fibroblast using CRISPR/Cas by inserting the isolated nucleic acid molecule of aspects above in the fetal fibroblast cell, c) transferring a nucleus of the fetal fibroblast cell to an enucleated oocyte of the animal to generate an embryo, and d) transferring the embryo into a surrogate animal of the same species and growing the embryo to the genetically modified animal in the surrogate animal.

BRIEF DESCRIPTION OF THE DRAWINGS

[0070] The novel features of the invention are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present invention will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the invention are utilized, and the accompanying drawings of which: [0071] FIG. 1 shows design of a single chain HLA-DR polypeptide (scHLA-DR) with an intact tolerogenic peptide. 4 different peptides that originate from the DR3 molecule derived from the NCBI algorithm for antigneic peptide analysis will be tested. The small MND promoter is chosen and GS linkers have been incorporated. Other promoters such as those from beta actin, EFlalpha can be also be used. Several restriction enzyme sites for future modifications have been included. The flexible linker comprises a sequence of GTGSGSGSGSGSGSGS (SEQ ID NO: 1) or GGGGSGGGG (SEQ ID NO: 2).

[0072] FIGs. 2A-2G shows exemplary HLA-DR molecule comprising an alpha chain and a beta chain which assemble to form a peptide binding region. The present disclosure encompasses the expression of HLA-DR molecule in various forms as illustrated in FIGs. 2A-2G, in a genetically modified cell or genetically modified animal. FIG. 2A shows expression of the native form of the alpha and beta chain assembled to form the HLA-DR molecule comprising a peptide binding region or peptide binding groove. FIG. 2B shows expression of the alpha and beta chain, where both the alpha and beta chain comprise a functional transmembrane region. The beta chain of the HLA-DR molecule has a peptide (tolerogenic peptide) linked to the N terminus via a flexible linker allowing it to assemble in the peptide binding region formed by the alpha and beta chain. FIG. 2C illustrates expression of the alpha and beta chain, where both the alpha and beta chains comprise a transmembrane region. The alpha chain of the HLA-DR molecule has a peptide linked to the N terminus via a flexible linker allowing it to assemble in the peptide binding region. FIG. 2D shows beta chain scHLA-DR molecule. The molecule shows expression of the alpha and beta chain where the alpha chain lacks a transmembrane region and the beta chain comprise a transmembrane region. The C-terminus of alpha chain is linked to the N-terminus of beta chain with a flexible linker, and the alpha and the beta chain assemble to form a peptide binding region. FIG. 2E shows alpha chain scHLA-DR molecule. The molecule shows expression of the alpha chain and the beta chain, where the alpha chain comprise a transmembrane region and the beta chain lacks a transmembrane region. The N-terminus of alpha chain is linked to the C-terminus of the beta chain with a flexible linker, and the alpha and the beta chain assemble to form a peptide binding region. FIG. 2F shows expression of the beta chain scHLA-DR with an N-terminal flexible linker and peptide. The molecule shows expression of the alpha and beta chain where the alpha chain lacks a transmembrane region and the beta chain comprises a transmembrane region. The C-terminus of alpha chain is linked to the N-terminus of beta chain with a flexible linker, and the alpha and the beta chain assemble to form a peptide binding region. The alpha chain of the HLA-DR molecule has a peptide linked to the N terminus via a flexible linker allowing it to assemble in the peptide binding region. FIG. 2G shows expression of the alpha chain scHLA-DR with an N-terminal flexible linker and peptide. The molecule shows expression of the alpha chain and the beta chain, where the alpha chain comprise a transmembrane region and the beta chain lacks a transmembrane region. The N-terminus of alpha chain is linked to the C-terminus of the beta chain with a flexible linker, and the alpha and the beta chain assemble to form a peptide binding region. The beta chain of the HLA-DR molecule has a peptide (tolerogenic peptide) linked to the N terminus via a flexible linker allowing it to assemble in the peptide binding region formed by the alpha and beta chain. The peptides (tolerogenic peptides or cognate peptide) can be derived from MHC class I or the MHC class II DR molecule (i.e. from the polypeptide encoding the beta chain or the alpha chain). The flexible linker can be continuous or have a thrombin or thrombin-like cleavage domain to allow cleavage of the peptide. One or more peptides can be linked each with the aforementioned cleavage domains such that the expression of one or more versions of FIG. 2A, FIG. 2D, or FIG. 2E, along with the co-expression of version illustrated in FIG. 2B, FIG. 2C, FIG. 2F, or FIG. 2G can be done. The various version of HLA- DR molecule can include a single or multiple peptide expression construct where cleavage domains allow the release of peptides individually. The result being the purposeful loading of a unique peptide derived from one expression construct where it is cleaved and released to be bound by a neighboring construct.

[0073] FIG. 3 shows the process of bi-oocyte fusion. The method for embryo generation and development using BOF includes oocyte selection, bi-oocyte fusion cloning, embryo development in culture. Collectively, these steps will enhance the quality of genetically engineered embryos thereby increasing the rate and volume of porcine organ donors produced.

[0074] FIG. 4 shows blastocysts produced by bi-oocyte fusion cultured to day 7.

[0075] FIG. 5 shows immunofluorescence staining of pluripotency markers in embryonic stem cell colonies derived from embryos produced by bi-oocyte fusion: Expressions of pluripotency markers (Tra 1-60, Tra 1-81) are shown in green at passage 5. Nuclei are stained with DAPI (blue). Scale bars =20x [0076] FIGs. 6A-6B shows characterization of ICM derived from bi-oocyte fusion. FIG. 6A shows immunofluorescence staining of stem-like cell markers in ICM colonies derived from bi-oocyte fusion cloned embryos: Expressions of pluripotency markers (Nanog, Oct4) are shown in green at passage 5. Scale bars =20x. FIG. 6B shows real time RT-PCR analysis of stem cell markers Oct4, Sox2 and Nanog gene after 5 culture passages.

[0077] FIG. 7 shows a flow chart summarizing steps involved in bi-oocyte fusion cloning.

[0078] FIGs. 8A-8D shows CRISPR/Cas 9 mediated GGTA1 KO in the PFFs. FIG. 8A shows FACS analysis on CRISPR/Cas9 sgRNA for GGTA1 transfected and wild type non transfected cells. FIG. 8B shows PCR amplification of sorted GGTA1 KO cells (Lane 1) and WT fetal fibroblast cells (Lane 2).

PCR product (586 bp). FIG. 8C shows Sanger sequencing depicts GGTA1 sgRNA cut site and single nucleotide deletion in GGTA1 KO cells for comparison of sequence alignment with WT genomic DNA. FIG. 8D shows TIDE analysis for major induced mutations in the projected editing site frequency in a single cell population of GGTA1 KO fetal fibroblast cells in comparison to WT cells.

[0079] FIGs. 9A-9C shows phenotypic analysis of GGTA1 KO cells. FIG. 9A shows

immunofluorescence analysis of GGTA1 KO in comparison with WT cells. WT Cells and GGTA1 KO cells are stained with DAPI and AF647 conjugated labelling for IB ₄ lectin staining. GGTA1 KO cells. Magnification 20X. FIG. 9B shows Karyotype analysis of wild type fetal cells and FIG. 9C shows Karyotype analysis of GGTA1 KO fetal cells.

[0080] FIGs. 10A-10B shows production of GGTA1 KO blastocysts. Day-7 GGTA1 KO porcine blastocysts produced by BOF cloning are shown in FIG. 4 above. FIG. 10A shows differential staining of GGTA1 KO blastocyst produced by BOF cloning. Blue color (Hoechst 33342) and pink color (propidium iodide) indicate ICM and TE cells, respectively. Magnification 20X. FIG. 10B shows relative gene expression for Klf4, Oct4, Nanog, Igf2, Dnmtl, Bax, Bcl-xl and ASF1 genes in GGTA1 KO blastocysts compared to WT blastocysts. All genes were normalized with the ACTB gene. All values indicate non significant difference within each gene expression, significance calculated at (p<0.05).

[0081] FIG. 11 shows flow cytometry results of genetically modified pig fibroblast cells confirming surface expression of chimeric HLA-DR molecule. The top panel shows threshold and scatter control.

The bottom panel shows genetically modified cells with positive staining with PE anti-human HLA-DR Antibody L243 (1: 100).

[0082] FIGs. 12A-12B shows flow cytometry results of genetically modified pig fibroblast cells confirming surface expression of chimeric HLA-DR molecule. FIG. 12A shows threshold and scatter control in the top panel and genetically modified cells with positive staining with PE anti-human HLA- DR Antibody L243 (1 : 100) in the bottom panel. FIG. 12B shows cytometry sorting of genetically modified porcine fibroblast cells expressing chimeric HLA-DR molecule in a population of porcine fibroblast cells transfected with a plasmid construct expressing HLA-DR transgene.

[0083] FIGs.l3A-13F show immunostaining analysis confirming expression of HLA-DR in HLA-DR transgenic fibroblast cells and absence of expression in non transgenic wild type fetal fibroblast cells using PE anti-human HLA-DR Antibody L243 ( 1 : 100). FIG. 13A shows DAPI staining on HLA-DR transfected cells. FIG. 13B shows fluorescence image showing presence of transgenic HLA-DR3 on transfected fetal cells and stained for PE anti-human HLA-DR Antibody. FIG. 13C shows merged image of DAPI and HLA-DR staining. FIG. 13D shows DAPI staining on non-transfected fetal cells. FIG. 13E shows absence of HLA-DR3 expression when non transfected cells are stained for PE anti -human HLA- DR Antibody. FIG. 13F shows merged image of both DAPI and PE anti -human HLA-DR Antibody staining. Magnification 40x

[0084] FIG. 14 shows a genetically modified pig expressing HLA-DR transgene. Ear clippings and tail skin samples were taken and analyzed to confirm genotype of the pig by sequencing.

[0085] FIGs. 15A-15B show sanger sequencing results of DNA isolated from a genetically modified pig (piglet 114-1) subjected to PCR amplification of the HLA-DR transgene. FIG. 15A shows the forward sequence obtained by sanger sequencing of the amplicon using the forward primer. FIG. 15B shows the reverse sequence obtained by sanger sequencing of the amplicon using the reverse primer.

[0086] FIGs. 16A-16B shows sanger sequencing results of DNA isolated from a genetically modified pig (piglet 114-2) subjected to PCR amplification of the HLA-DR transgene. FIG. 16A shows the forward sequence obtained by sanger sequencing of the amplicon using the forward primer. FIG. 16B shows the reverse sequence obtained by sanger sequencing of the amplicon using the reverse primer.

[0087] FIG. 17 shows alignment of HLA-DR transgene sequences obtained from genetically modified pig (piglet 114-1 and piglet 114-2) with the HLA-DR transgene sequence in the plasmid construct encoding single chain HLA-DR chimeric peptide. DETAILED DESCRIPTION OF THE DISCLOSURE

[0088] The following description and examples illustrate embodiments of the invention in detail. It is to be understood that this invention is not limited to the particular embodiments described herein and as such can vary. Those of skill in the art will recognize that there are numerous variations and

modifications of this invention, which are encompassed within its scope.

[0089] Graft rejection can be prevented by methods tempering the immune response, including those described herein. For example, one method described herein to prevent transplantation rejection or prolong the time to transplantation rejection without or with minimal immunosuppressive drug use, an animal, e.g., a donor non-human animal, could be altered, e.g., genetically. Subsequently, the cells, organs, and/or tissues of the altered animal, e.g., a donor non-human animal, can be harvested and used in allografts or xenografts. Alternatively, cells can be extracted from an animal, e.g., a human or non human animal (including but not limited to primary cells) or cells can be previously extracted animal cells, e.g., cell lines. These cells can be used to create a genetically altered cell.

[0090] Transplant rejection (e.g., T cells-mediated transplant rejection) can be prevented by chronic immunosuppression. However, immunosuppression is costly and associated with the risk of serious side effects. To circumvent the need for chronic immunosuppression, a multifaceted, T cell-targeted rejection prophylaxis was developed (FIG. 1) that

i) utilizes genetically modified grafts lacking functional expression of MHC class I, thereby interfering with activation of CD8 ⁺ T cells with direct specificity and precluding cytolytic effector functions of these CD8 ⁺ T cells,

ii) interferes with B cell (and other APC)-mediated priming and memory generation of anti-donor T cells using induction immunotherapy comprising antagonistic anti-CD40 mAbs (and depleting anti-CD20 mAbs and a mTOR inhibitor), and/or

iii) depletes anti-donor T cells with indirect specificity via peritransplant infusions of apoptotic donor cell vaccines.

[0091] Described herein are genetically modified non-human animals (such as non-human primates or a genetically modified animal that is member of the Laurasiatheria superorder, e.g., ungulates) and organs, tissues, or cells isolated therefrom, tolerizing vaccines, and methods for treating or preventing a disease in a recipient in need thereof by transplantation of an organ, tissue, or cell isolated from a non-human animal. An organ, tissue, or cell isolated from a non-human animal (such as non-human primates or a genetically modified animal that is member of the Laurasiatheria superorder, e.g., ungulates) can be transplanted into a recipient in need thereof from the same species (an allotransplant) or a different species (a xenotransplant). A recipient can be tolerized with a tolerizing vaccine and/or one or more immunomodulatory agents (e.g., an antibody). In embodiments involving xenotransplantation the recipient can be a human. Suitable diseases that can be treated are any in which an organ, tissue, or cell of a recipient is defective or injured, (e.g., a heart, lung, liver, vein, skin, or pancreatic islet cell) and a recipient can be treated by transplantation of an organ, tissue, or cell isolated from a non-human animal. [0092] In one aspect, disclosed herein are genetically modified non-human animals and cells comprising an exogenous nucleic acid sequence encoding for a MHC molecule. In some embodiments, the MHC molecule is a MHC class I molecule. In some embodiments, the MHC molecule is a MHC class II molecule. In some embodiments, the MHC molecule is HLA-DR. For example, the genetically modified cells, or genetically modified non-human animal, and the cells, tissues and organs derived therefrom comprises a transgene comprising a nucleic acid sequence encoding a MHC molecule (e.g., single chain chimeric MHC molecule), a a chain of a MHC molecule or a fragment thereof, or a b chain of a MHC molecule or a fragment thereof, or a peptide derived from a MHC molecule. In some embodiments, the transgene can further comprise a polynucleotide encoding a peptide derived from a MHC molecule capable of binding the peptide binding groove for presentation to a T cell. In some embodiments, the genetically modified non-human animals and cells can further comprise one or more additional genetic modifications, such as any of the genetic modifications (e.g., knock-ins, knock-outs, gene disruptions, etc.) disclosed herein. For example, in some embodiments, the genetically modified cells, or genetically modified non-human animal, and the cells, tissues and organs derived therefrom can further comprise one or more transgenes encoding ICP47, CD46, CD55, CD59, HLA-E, HLA-G (e.g., HLA-G1, HLA-G2, HLA-G3, HLA-G4, HLA-G5, HLA-G6, or HLA-G7), B2M, any functional fragments thereof, and/or any combination thereof.

DEFINITIONS

[0093] The term“about” in relation to a reference numerical value and its grammatical equivalents as used herein can include the numerical value itself and a range of values plus or minus 10% from that numerical value. For example, the amount“about 10” includes 10 and any amounts from 9 to 11. For example, the term“about” in relation to a reference numerical value can also include a range of values plus or minus 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, or 1% from that value.

[0094] The term“non-human animal” and its grammatical equivalents as used herein includes all animal species other than humans, including non-human mammals, which can be a native animal or a genetically modified non-human animal. A non-human mammal includes, an ungulate, such as an even-toed ungulate (e.g., pigs, peccaries, hippopotamuses, camels, llamas, chevrotains (mouse deer), deer, giraffes, pronghorn, antelopes, goat-antelopes (which include sheep, goats and others), or cattle) or an odd-toed ungulate (e.g., horse, tapirs, and rhinoceroses), a non-human primate (e.g., a monkey, or a chimpanzee), a Canidae (e.g., a dog) or a cat. A non-human animal can be a member of the Laurasiatheria superorder. The Laurasiatheria superorder can include a group of mammals as described in Waddell et al, Towards Resolving the Interordinal Relationships of Placental Mammals. Systematic Biology 48 (1): 1-5 (1999). Members of the Laurasiatheria superorder can include Eulipotyphla (hedgehogs, shrews, and moles), Perissodactyla (rhinoceroses, horses, and tapirs), Carnivora (carnivores), Cetartiodactyla (artiodactyls and cetaceans), Chiroptera (bats), and Pholidota (pangolins). A member of Laurasiatheria superorder can be an ungulate described herein, e.g., an odd-toed ungulate or even-toed ungulate. An ungulate can be a pig. A member can be a member of Carnivora, such as a cat, or a dog. In some cases, a member of the Laurasiatheria superorder can be a pig.

[0095] The term“pig” and its grammatical equivalents as used herein can refer to an animal in the genus .Sirv within the Suidae family of even-toed ungulates. For example, a pig can be a wild pig, a domestic pig, mini pigs, a Sus scrofa pig, a Sus scrofa domes ticus pig, or inbred pigs.

[0096] The term“transgene” and its grammatical equivalents as used herein can refer to a gene or genetic material that can be transferred into an organism. For example, a transgene can be a stretch or segment of DNA containing a gene that is introduced into an organism. The gene or genetic material can be from a different species. The gene or genetic material can be synthetic. When a transgene is transferred into an organism, the organism can then be referred to as a transgenic organism. A transgene can retain its ability to produce RNA or polypeptides (e.g., proteins) in a transgenic organism. A transgene can comprise a polynucleotide encoding a protein or a fragment (e.g., a functional fragment) thereof. The polynucleotide of a transgene can be an exogenous polynucleotide. A fragment (e.g., a functional fragment) of a protein can comprise at least or at least about 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, or 99% of the amino acid sequence of the protein. A fragment of a protein can be a functional fragment of the protein. A functional fragment of a protein can retain part or all of the function of the protein.

[0097] The term“exogenous nucleic acid sequence” can refer to a gene or genetic material that was transferred into a cell or animal that originated outside of the cell or animal. An exogenous nucleic acid sequence can by synthetically produced. An exogenous nucleic acid sequence can be from a different species, or a different member of the same species. An exogenous nucleic acid sequence can be another copy of an endogenous nucleic acid sequence.

[0098] The term“genetic modification” and its grammatical equivalents as used herein can refer to one or more alterations of a nucleic acid, e.g., the nucleic acid within an organism’s genome. For example, genetic modification can refer to alterations, additions, and/or deletion of genes. A genetically modified cell can also refer to a cell with an added, deleted and/or altered gene. A genetically modified cell can be from a genetically modified non-human animal. A genetically modified cell from a genetically modified non-human animal can be a cell isolated from such genetically modified non-human animal. A genetically modified cell from a genetically modified non-human animal can be a cell originated from such genetically modified non -human animal.

[0099] The term“gene knock-out” or“knock-out” can refer to any genetic modification that reduces the expression of the gene being“knocked out.” Reduced expression can include no expression. The genetic modification can include a genomic disruption.

[00100] The term“islet” or“islet cells” and their grammatical equivalents as used herein can refer to endocrine (e.g., hormone-producing) cells present in the pancreas of an organism. For example, islet cells can comprise different types of cells, including, but not limited to, pancreatic a cells, pancreatic b cells, pancreatic d cells, pancreatic F cells, and/or pancreatic e cells. Islet cells can also refer to a group of cells, cell clusters, or the like.

[00101] The term“condition” condition and its grammatical equivalents as used herein can refer to a disease, event, or change in health status.

[00102] The term“diabetes” and its grammatical equivalents as used herein can refer to is a disease characterized by high blood sugar levels over a prolonged period. For example, the term“diabetes” and its grammatical equivalents as used herein can refer to all or any type of diabetes, including, but not limited to, type 1, type 2, cystic fibrosis-related, surgical, gestational diabetes, and mitochondrial diabetes. In some cases, diabetes can be a form of hereditary diabetes.

[00103] The term“phenotype” and its grammatical equivalents as used herein can refer to a composite of an organism’s observable characteristics or traits, such as its morphology, development, biochemical or physiological properties, phenology, behavior, and products of behavior. Depending on the context, the term“phenotype” can sometimes refer to a composite of a population’s observable characteristics or traits.

[00104] The term“disrupting” and its grammatical equivalents as used herein can refer to a process of altering a gene, e.g., by deletion, insertion, mutation, rearrangement, or any combination thereof. For example, a gene can be disrupted by knockout. Disrupting a gene can be partially reducing or completely suppressing expression (e.g., mR A and/or protein expression) of the gene. Disrupting can also include inhibitory technology, such as shR A, siR A, microRNA, dominant negative, or any other means to inhibit functionality or expression of a gene or protein.

[00105] The term“gene editing” and its grammatical equivalents as used herein can refer to genetic engineering in which one or more nucleotides are inserted, replaced, or removed from a genome. For example, gene editing can be performed using a nuclease (e.g., a natural-existing nuclease or an artificially engineered nuclease).

[00106] The term“transplant rejection” and its grammatical equivalents as used herein can refer to a process or processes by which an immune response of an organ transplant recipient mounts a reaction against the transplanted material (e.g., cells, tissues, and/or organs) sufficient to impair or destroy the function of the transplanted material.

[00107] The term“hyperacute rejection” and its grammatical equivalents as used herein can refer to rejection of a transplanted material or tissue occurring or beginning within the first 24 hours after transplantation. For example, hyperacute rejection can encompass but is not limited to“acute humoral rejection” and“antibody-mediated rejection”.

[00108] The term“negative vaccine”,“tolerizing vaccine” and their grammatical equivalents as used herein, can be used interchangeably. A tolerizing vaccine can tolerize a recipient to a graft or contribute to tolerization of the recipient to the graft if used under the cover of appropriate immunotherapy. This can help to prevent transplantation rejection. [00109] The term“recipient”,“subject” and their grammatical equivalents as used herein, can be used interchangeably. A recipient or a subject can be a human or non-human animal. A recipient or a subject can be a human or non-human animal that will receive, is receiving, or has received a transplant graft, a tolerizing vaccine, and/or other composition disclosed in the application. A recipient or subject can also be in need of a transplant graft, a tolerizing vaccine and/or other composition disclosed in the application. In some cases, a recipient can be a human or non-human animal that will receive, is receiving, or has received a transplant graft.

[00110] The phrases "translationally fused" and "in frame" are interchangeably used herein to refer to polynucleotides which are covalently linked to form a single continuous open reading frame spanning the length of the coding sequences of the linked polynucleotides. Such polynucleotides can be covalently linked directly or preferably indirectly through a spacer or linker region. Thus, according to some embodiments, the nucleic acid sequence further includes an in-frame linker polynucleotide. This linker polynucleotide encodes a linker peptide and is interposed between two polynucleotides to be fused or linked.

[00111] The linker peptide is selected of an amino acid sequence which is inherently flexible, such that the polypeptides encoded by the first and said second polynucleotides independently and natively fold following expression thereof, thus facilitating the formation of a functional MHC complex and or a functional MHC -peptide complex.

[00112] Some numerical values disclosed throughout are referred to as, for example,“X is at least or at least about 100; or 200 [or any numerical number].” This numerical value includes the number itself and all of the following:

i) X is at least 100;

ii) X is at least 200;

iii) X is at least about 100; and

iv) X is at least about 200.

All these different combinations are contemplated by the numerical values disclosed throughout. All disclosed numerical values should be interpreted in this manner, whether it refers to an administration of a therapeutic agent or referring to days, months, years, weight, dosage amounts, etc., unless otherwise specifically indicated to the contrary.

[00113] The ranges disclosed throughout are sometimes referred to as, for example,“X is administered on or on about day 1 to 2; or 2 to 3 [or any numerical range] .” This range includes the numbers themselves (e.g., the endpoints of the range) and all of the following:

i) X being administered on between day 1 and day 2;

ii) X being administered on between day 2 and day 3;

iii) X being administered on between about day 1 and day 2;

iv) X being administered on between about day 2 and day 3;

v) X being administered on between day 1 and about day 2; vi) X being administered on between day 2 and about day 3;

vii) X being administered on between about day 1 and about day 2; and

viii) X being administered on between about day 2 and about day 3.

All these different combinations are contemplated by the ranges disclosed throughout. All disclosed ranges should be interpreted in this manner, whether it refers to an administration of a therapeutic agent or referring to days, months, years, weight, dosage amounts, etc., unless otherwise specifically indicated to the contrary.

[00114] The terms“and/or” and“any combination thereof’ and their grammatical equivalents as used herein, can be used interchangeably. These terms can convey that any combination is specifically contemplated. Solely for illustrative purposes, the following phrases“A, B, and/or C” or“A, B, C, or any combination thereof’ can mean“A individually; B individually; C individually; A and B; B and C; A and C; and A, B, and C.”

[00115] The term“or” can be used conjunctively or disjunctively, unless the context specifically refers to a disjunctive use.

GENETICALLY MODIFIED NON-HUMAN ANIMALS

[00116] Provided herein are genetically modified non-human animals that can be donors of cells, tissues, and/or organs for transplantation. A genetically modified non-human animal can be any desired species. For example, a genetically modified non-human animal described herein can be a genetically modified non-human mammal. A genetically modified non-human mammal can be a genetically modified ungulate, including a genetically modified even-toed ungulate (e.g., pigs, peccaries, hippopotamuses, camels, llamas, chevrotains (mouse deer), deer, giraffes, pronghorn, antelopes, goat-antelopes (which include sheep, goats and others), or cattle) or a genetically modified odd-toed ungulate (e.g., horse, tapirs, and rhinoceroses), a genetically modified non-human primate (e.g., a monkey, or a chimpanzee) or a genetically modified Canidae (e.g., a dog). A genetically modified non-human animal can be a member of the Laurasiatheria superorder. A genetically modified non-human animal can be a non-human primate, e.g., a monkey, or a chimpanzee. If a non-human animal is a pig, the pig can be at least or at least about 1, 5, 50, 100, or 300 pounds, e.g., the pig can be or be about between 5 pounds to 50 pounds; 25 pounds to 100 pounds; or 75 pounds to 300 pounds. In some cases, a non-human animal is a pig that has given birth at least one time.

[00117] A genetically modified non-human animal can be of any age. For example, the genetically modified non-human animal can be a fetus; from or from about 1 day to 1 month; from or from about 1 month to 3 months; from or from about 3 months to 6 months; from or from about 6 months to 9 months; from or from about 9 months to 1 year; from or from about 1 year to 2 years. A genetically modified non human animal can be a non-human fetal animal, perinatal non-human animal, neonatal non-human animal, preweaning non-human animal, young adult non-human animal, or an adult non-human animal.

[00118] A genetically modified non-human animal can survive for at least a period of time after birth.

For example, the genetically modified non-human animal can survive for at least 1 day, 2 days, 3 days, 1 week, 2 weeks, 3 weeks, 1 month, 2 months, 4 months, 8 months, 1 year, 2 years, 5 years, or 10 years after birth. Multiple genetically modified animals (e.g., a pig) can be bom in a litter. A litter of genetically modified animal can have at least 30%, 50%, 60%, 80%, or 90% survival rate, e.g., number of animals in a litter that survive after birth divided by the total number of animals in the litter.

[00119] The genetically modified non-human animal of the instant disclosure comprises an exogenous nucleic acid sequence encoding for a MHC molecule. In some embodiments, the MHC molecule is a MHC class I molecule. In some embodiments, the MHC molecule is a MHC class II molecule. In some embodiments, the MHC molecule is HLA-DR. For example, genetically modified non-human animal comprises a transgene comprising a nucleic acid sequence encoding a MHC molecule (e.g., single chain chimeric MHC molecule), a a chain of a MHC molecule or a fragment thereof, or a b chain of a MHC molecule or a fragment thereof, or a peptide derived from a MHC molecule. In some embodiments, the transgene can further comprise a polynucleotide encoding a peptide derived from a MHC molecule capable of binding the peptide binding groove for presentation to a T cell. In some embodiments, the genetically modified non-human animal further comprises one or more additional genetic modifications, such as any of the genetic modifications (e.g., knock-ins, knock-outs, gene disruptions, etc.) described herein. For example, in some embodiments, the genetically modified non-human animal, can further comprise one or more transgenes encoding ICP47, CD46, CD55, CD59, HLA-E, HLA-G (e.g., HLA-G1, HLA-G2, HLA-G3, HLA-G4, HLA-G5, HLA-G6, or HLA-G7), B2M, any functional fragments thereof, and/or any combination thereof.

[00120] For example, in some embodiments a genetically modified non-human animal can further comprise reduced expression of one or more genes compared to a non-genetically modified counterpart animal. The reduction of expression of a gene can result from mutations on one or more alleles of the gene. For example, a genetically modified animal can comprise a mutation on two or more alleles of a gene. In some cases, such genetically modified animal can be a diploid animal.

[00121] A genetically modified non-human animal can comprise one or more transgenes or one or more exogenous nucleic acid sequences. In some case, a genetically modified non-human animal comprises two or more transgenes. Exemplary transgenes contemplated in the present disclosure are discussed below. A genetically modified non-human animal can comprise reduced expression of one or more genes compared to a non-genetically modified counterpart animal. A genetically modified non-human animal can comprise reduced expression of two or more genes compared to a non-genetically modified counterpart animal. A genetically modified animal can have a genomic disruption in at least one gene selected from a group consisting of a component of an MHC I-specific enhanceosome, a transporter of an MHC I-binding peptide, a natural killer (NK) group 2D ligand, a CXC chemokine receptor (CXCR)3 ligand, MHC II transactivator (CIITA), C3, an endogenous gene not expressed in a human, and any combination thereof.

[00122] In some cases, a genetically modified animal has reduced expression of a gene in comparison to a non-genetically modified counterpart animal. In some cases, a genetically modified animal survives at least 22 days after birth. In other cases, a genetically modified animal can survive at least or at least about 23 to 30, 25 to 35, 35 to 45, 45 to 55, 55 to 65, 65 to 75, 75 to 85, 85 to 95, 95 to 105, 105 to 115, 115 to 225, 225 to 235, 235 to 245, 245 to 255, 255 to 265, 265 to 275, 275 to 285, 285 to 295, 295 to 305, 305 to 315, 315 to 325, 325 to 335, 335 to 345, 345 to 355, 355 to 365, 365 to 375, 375 to 385, 385 to 395, or 395 to 400 days after birth.

[00123] A non-genetically modified counterpart animal can be an animal substantially identical to the genetically modified animal but without genetic modification in the genome. For example, a non- genetically modified counterpart animal can be a wild-type animal of the same species as the genetically modified animal.

[00124] A genetically modified non-human animal can provide cells, tissues or organs for transplanting to a recipient or subject in need thereof. A recipient or subject in need thereof can be a recipient or subject known or suspected of having a condition. The condition can be treated, prevented, reduced, eliminated, or augmented by the methods and compositions disclosed herein. The recipient can exhibit low or no immuno-response to the transplanted cells, tissues or organs. The transplanted cells, tissues or organs can be non-recognizable by CD8+ T cells, NK cells, or CD4+ T cells of the recipient (e.g., a human or another animal). The genes whose expression is reduced can include MHC molecules, regulators of MHC molecule expression, and genes differentially expressed between the donor non human animal and the recipient (e.g., a human or another animal). The reduced expression can be mRNA expression or protein expression of the one or more genes. For example, the reduced expression can be protein expression of the one or more genes. Reduced expression can also include no expression. For example, an animal, cell, tissue or organ with reduced expression of a gene can have no expression (e.g., mRNA and/or protein expression) of the gene. Reduction of expression of a gene can inactivate the function of the gene. In some cases, when expression of a gene is reduced in a genetically modified animal, the expression of the gene is absent in the genetically modified animal.

[00125] A genetically modified non-human animal can comprise reduced expression of one or more MHC molecules compared to a non-genetically modified counterpart animal. For example, the non human animal can be an ungulate, e.g., a pig, with reduced expression of one or more swine leukocyte antigen (SLA) class I and/or SLA class II molecules.

[00126] A genetically modified non-human animal can comprise reduced expression of any genes that regulate major histocompatibility complex (MHC) molecules (e.g., MHC I molecules and/or MHC II molecules) compared to a non-genetically modified counterpart animal. Reducing expression of such genes can result in reduced expression and/or function of MHC molecules (e.g., MHC I molecules and/or MHC II molecules). In some cases, the one or more genes whose expression is reduced in the non-human animal can comprise one or more of the following: components of an MHC I-specific enhanceosome, transporters of a MHC I-binding peptide, natural killer group 2D ligands, CXC chemical receptor (CXCR) 3 ligands, complement component 3 (C3), and major histocompatibility complex II

transactivator (CIITA). In some cases, the component of a MHC I-specific enhanceosome can be NLRC5. In some cases, the component of a MHC I-specific enhanceosome can also comprise regulatory factor X (RFX) (e.g., RFXl), nuclear transcription factor Y (NFY), and cAMP response element-binding protein (CREB). In some instances, the transporter of a MHC I-binding peptide can be Transporter associated with antigen processing 1 (TAPI). In some cases, the natural killer (NK) group 2D ligands can comprise MICA and MICB. For example, the genetically modified non-human animal can comprise reduced expression of one or more of the following genes: NOD-like receptor family CARD domain containing 5 (NLRC5), Transporter associated with antigen processing 1 (TAPI), C-X-C motif chemokine 10 (CXCL10), MHC class I polypeptide-related sequence A (MICA), MHC class I polypeptide-related sequence B (MICB), complement component 3 (C3), and CIITA. A genetically modified animal can comprise reduced expression of one or more of the following genes: a component of an MHC I-specific enhanceosome (e.g., NLRC5), a transporter of an MHC I-binding peptide (TAPI), and C3.

[00127] A genetically modified non-human animal can comprise reduced expression compared to a non- genetically modified counterpart of one or more genes expressed at different levels between the non human animal and a recipient receiving a cell, tissue, or organ from the non-human animal. For example, the one or more genes can be expressed at a lower level in a human than in the non-human animal. In some cases, the one or more genes can be endogenous genes of the non-human animal. The endogenous genes are in some cases genes not expressed in another species. For example, the endogenous genes of the non-human animal can be genes that are not expressed in a human. For example, in some cases, homologs (e.g., orthologs) of the one or more genes do not exist in a human. In another example, homologs (e.g., orthologs) of the one or more genes whose expression can be reduced can exist in a human but are not expressed.

[00128] In some cases, a non-human animal can be a pig, and the recipient can be a human. The one or more genes with reduced gene expression or comprising a disruption can be any genes expressed in a pig but not in a human. For example, the one or more genes with reduced expression can comprise glycoprotein galactosyltransferase alpha 1, 3 (GGTA1), putative cytidine monophosphate -N- acetylneuraminic acid hydroxylase-like protein (CMAH), and b1,4 N-acetylgalactosaminyltransferase (B4GALNT2).

[00129] The genetically modified non-human animal can comprise reduced expression compared to a non-genetically modified counterpart of one or more of any of the genes disclosed herein, including NLRC5, TAPI, CXCL10, MICA, MICB, C3, CIITA, GGTA1, CMAH, and B4GALNT2.

[00130] A genetically modified non-human animal can comprise one or more genes whose expression is reduced, e.g., where genetic expression is reduced. The one or more genes whose expression is reduced include but are not limited to NOD-like receptor family CARD domain containing 5 (NLRC5),

Transporter associated with antigen processing 1 (TAPI), Glycoprotein galactosyltransferase alpha 1,3 (GGTA1), Putative cytidine monophosphate-N-acetylneuraminic acid hydroxylase -like protein (CMAH), C-X-C motif chemokine 10 (CXCL10), MHC class I polypeptide-related sequence A (MICA), MHC class I polypeptide-related sequence B (MICB), class II major histocompatibility complex transactivator (CIITA), Beta-1, 4-N-Acetyl-Galactosaminyl Transferase 2 (B4GALNT2), complemental component 3 (C3), and/or any combination thereof.

[00131] A genetically modified non-human animal can comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,

14, 15, 16, 17, 18, 19, 20 or more genes whose expression is disrupted. Exemplary disrupted genes contemplated in the disclosure are discussed in sections below. For illustrative purposes, and not to limit various combinations a person of skill in the art can envision, a genetically modified non-human animal can have NLRC5 and TAPI individually disrupted. A genetically modified non-human animal can also have both NLRC5 and TAPI disrupted. A genetically modified non-human animal can also have NLRC5 and TAPI, and in addition to one or more of the following GGTA1, CMAH, CXCL10, MICA, MICB, B4GALNT2, or CIITA genes disrupted; for example,“NLRC5, TAPI, and GGTA1” or“NLRC5, TAPI, and CMAH” can be disrupted. A genetically modified non-human animal can also have NLRC5, TAPI, GGTA1, and CMAH disrupted. Alternatively, a genetically modified non-human animal can also have NLRC5, TAPI, GGTA1, B4GALNT2, and CMAH disrupted. In some cases, a genetically modified non human animal can have C3 and GGTA1 disrupted. In some cases, a genetically modified non-human animal can have reduced expression of NLRC5, C3, GGTA1, B4GALNT2, CMAH, and CXCL10. In some cases, a genetically modified non-human animal can have reduced expression of TAPI, C3, GGTA1, B4GALNT2, CMAH, and CXCL10. In some cases, a genetically modified non-human animal can have reduced expression of NLRC5, TAPI, C3, GGTA1, B4GALNT2, CMAH, and CXCL10. A B4GALNT2 gene can be a Gal2-2 or Gal 2-1.

[00132] Lack of MHC class I expression on transplanted human cells can cause the passive activation of natural killer (NK) cells (Ohlen et al, 1989). Lack of MHC class I expression could be due to NLRC5, TAPI, or B2M gene deletion. NK cell cytotoxicity can be overcome by the expression of the human MHC class 1 gene, HLA-E, can stimulate the inhibitory receptor CD94/NKG2A on NK cells to prevent cell killing (Weiss et al, 2009; Lilienfeld et al, 2007; Sasaki et al, 1999). Successful expression of the HLA-E gene can be dependent on co-expression of the human B2M (beta 2 microglobulin) gene and a cognate peptide (Weiss et al, 2009; Lilienfeld et al, 2007; Sasaki et al, 1999; Pascasova et al., 1999). A nuclease mediated break in the stem cell DNA can allow for the insertion of one or multiple genes via homology directed repair. The HLA-E and hB2M genes in series can be integrated in the region of the nuclease mediated DNA break thus preventing expression of the target gene (for example, NLRC5) while inserting the transgenes.

[00133] Expression levels of genes can be reduced to various extents. For example, expression of one or more genes can be reduced by or by about 100%. In some cases, expression of one or more genes can be reduced by or by about 99%, 95%, 90%, 85%, 80%, 75%, 70%, 65%, 60%, 55%, or 50% of normal expression, e.g., compared to the expression of non-modified controls. In some cases, expression of one or more genes can be reduced by at least or to at least about 99% to 90%; 89% to 80%, 79% to 70%; 69% to 60%; 59% to 50% of normal expression, e.g., compared to the expression of non-modified controls. For example, expression of one or more genes can be reduced by at least or at least about 90% or by at least or at least about 90% to 99% of normal expression.

[00134] Expression can be measured by any known method, such as quantitative PCR (qPCR), including but not limited to PCR, real-time PCR (e.g., Sybr-green), and/or hot PCR. In some cases, expression of one or more genes can be measured by detecting the level of transcripts of the genes. For example, expression of one or more genes can be measured by Northern blotting, nuclease protection assays (e.g., RNase protection assays), reverse transcription PCR, quantitative PCR (e.g., real-time PCR such as real time quantitative reverse transcription PCR), in situ hybridization (e.g., fluorescent in situ hybridization (FISH)), dot-blot analysis, differential display, serial analysis of gene expression, subtractive hybridization, microarrays, nanostring, and/or sequencing (e.g., next-generation sequencing). In some cases, expression of one or more genes can be measured by detecting the level of proteins encoded by the genes. For example, expression of one or more genes can be measured by protein immunostaining, protein immunoprecipitation, electrophoresis (e.g., SDS-PAGE), Western blotting, bicinchoninic acid assay, spectrophotometry, mass spectrometry, enzyme assays (e.g., enzyme-linked immunosorbent assays), immunohistochemistry, flow cytometry, and/or immunoctyochemistry. Expression of one or more genes can also be measured by microscopy. The microscopy can be optical, electron, or scanning probe microscopy. Optical microscopy can comprise use of bright field, oblique illumination, cross- polarized light, dispersion staining, dark field, phase contrast, differential interference contrast, interference reflection microscopy, fluorescence (e.g., when particles, e.g., cells, are immunostained), confocal, single plane illumination microscopy, light sheet fluorescence microscopy, deconvolution, or serial time-encoded amplified microscopy. Expression of MHC I molecules can also be detected by any methods for testing expression as described herein.

Exemplary Disrupted Genes

[00135] Genetically modified non-human animal or genetically modified cells, and cells, organs, and/or tissues derived from a genetically modified animal, having different combinations of disrupted genes are contemplated herein. Genetically modified cells, organs, and/or tissues that are less susceptible to rejection when transplanted into a recipient are described herein. For example, disrupting (e.g., reducing expression of) certain genes, such as NLRC5, TAPI, GGTA1, B4GALNT2, CMAH, CXCL10, MICA, MICB, C3, and/or CIITA, cytidine monophospho-N-acetylneuraminic acid (CMP-N-NeuAc) hydrolase, or a PERV region can increase the likelihood of graft survival. In some cases, at least two genes are disrupted. For example, GGTAl-10 and Gal2-2 can be disrupted. In some cases, GGTAl-10, Gal2-2, and NLRC5-6 can be disrupted. In other cases, NLRC5-6 and Gal2-2 can be disrupted.

[00136] In some cases, the disruptions are not limited to solely these genes. It is contemplated that genetic homologues (e.g., any mammalian version of the gene) of the genes within this application are covered. For example, genes that are disrupted can exhibit a certain identity and/or homology to genes disclosed herein, e.g., cytidine monophospho-N-acetylneuraminic acid (CMP-N-NeuAc) hydrolase, NLRC5, TAPI, GGTA1, B4GALNT2, CMAH, CXCL10, MICA, MICB, C3, and/or CIITA. Therefore, it is contemplated that a gene that exhibits at least or at least about 50%, 55%, 60%, 65%, 70%, 75%,

80%, 85%, 90%, 95%, 99%, or 100% homology (at the nucleic acid or protein level) can be disrupted, e.g., a gene that exhibits at least or at least about from 50% to 60%; 60% to 70%; 70% to 80%; 80% to 90%; or 90% to 99% homology. It is also contemplated that a gene that exhibits at least or at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 99%, or 100% identity (at the nucleic acid or protein level) can be disrupted, e.g., a gene that exhibits at least or at least about from 50% to 60%; 60% to 70%; 70% to 80%; 80% to 90%; or 90% to 99% identity. Some genetic homologues are known in the art, however, in some cases, homologues are unknown. However, homologous genes between mammals can be found by comparing nucleic acid (DNA or RNA) sequences or protein sequences using publicly available databases such as NCBI BLAST.

[00137] Gene suppression can also be done in a number of ways. For example, gene expression can be reduced by knock out, altering a promoter of a gene, and/or by administering interfering RNAs

(knockdown). This can be done at an organism level or at a tissue, organ, and/or cellular level. If one or more genes are knocked down in a non-human animal, cell, tissue, and/or organ, the one or more genes can be reduced by administrating RNA interfering reagents, e.g., siRNA, shRNA, or microRNA. For example, a nucleic acid which can express shRNA can be stably transfected into a cell to knockdown expression. Furthermore, a nucleic acid which can express shRNA can be inserted into the genome of a non-human animal, thus knocking down a gene with in a non-human animal.

[00138] Disruption methods can also comprise overexpressing a dominant negative protein. This method can result in overall decreased function of a functional wild-type gene. Additionally, expressing a dominant negative gene can result in a phenotype that is similar to that of a knockout and/or knockdown.

[00139] In some cases, a stop codon can be inserted or created (e.g., by nucleotide replacement), in one or more genes, which can result in a nonfunctional transcript or protein (sometimes referred to as knockout). For example, if a stop codon is created within the middle of one or more genes, the resulting transcription and/or protein can be truncated, and can be nonfunctional. However, in some cases, truncation can lead to an active (a partially or overly active) protein. In some cases, if a protein is overly active, this can result in a dominant negative protein, e.g., a mutant polypeptide that disrupts the activity of the wild-type protein.

[00140] This dominant negative protein can be expressed in a nucleic acid within the control of any promoter. For example, a promoter can be a ubiquitous promoter. A promoter can also be an inducible promoter, tissue specific promoter, and/or developmental specific promoter.

[00141] The nucleic acid that codes for a dominant negative protein can then be inserted into a cell or non-human animal. Any known method can be used. For example, stable transfection can be used. Additionally, a nucleic acid that codes for a dominant negative protein can be inserted into a genome of a non-human animal.

[00142] One or more genes in a non-human animal can be knocked out using any method known in the art. For example, knocking out one or more genes can comprise deleting one or more genes from a genome of a non-human animal. Knocking out can also comprise removing all or a part of a gene sequence from a non-human animal. It is also contemplated that knocking out can comprise replacing all or a part of a gene in a genome of a non-human animal with one or more nucleotides. Knocking out one or more genes can also comprise inserting a sequence in one or more genes thereby disrupting expression of the one or more genes. For example, inserting a sequence can generate a stop codon in the middle of one or more genes. Inserting a sequence can also shift the open reading frame of one or more genes. In some cases, knock out can be performed in a first exon of a gene. In other cases, knock out can be performed in a second exon of a gene.

[00143] Knockout can be done in any cell, organ, and/or tissue in a non-human animal. For example, knockout can be whole body knockout, e.g., expression of one or more genes is reduced in all cells of a non-human animal. Knockout can also be specific to one or more cells, tissues, and/or organs of a non human animal. This can be achieved by conditional knockout, where expression of one or more genes is selectively reduced in one or more organs, tissues or types of cells. Conditional knockout can be performed by a Cre-lox system, where ere is expressed under the control of a cell, tissue, and/or organ specific promoter. For example, one or more genes can be knocked out (or expression can be reduced) in one or more tissues, or organs, where the one or more tissues or organs can include brain, lung, liver, heart, spleen, pancreas, small intestine, large intestine, skeletal muscle, smooth muscle, skin, bones, adipose tissues, hairs, thyroid, trachea, gall bladder, kidney, ureter, bladder, aorta, vein, esophagus, diaphragm, stomach, rectum, adrenal glands, bronchi, ears, eyes, retina, genitals, hypothalamus, larynx, nose, tongue, spinal cord, or ureters, uterus, ovary, testis, and/or any combination thereof. One or more genes can also be knocked out (or expression can be reduced) in one types of cells, where one or more types of cells include trichocytes, keratinocytes, gonadotropes, corticotropes, thyrotropes, somatotropes, lactotrophs, chromaffin cells, parafollicular cells, glomus cells melanocytes, nevus cells, merkel cells, odontoblasts, cementoblasts comeal keratocytes, retina muller cells, retinal pigment epithelium cells, neurons, glias (e.g., oligodendrocyte astrocytes), ependymocytes, pinealocytes, pneumocytes (e.g., type I pneumocytes, and type II pneumocytes), clara cells, goblet cells, G cells, D cells, Enterochromaffm-like cells, gastric chief cells, parietal cells, foveolar cells, K cells, D cells, I cells, goblet cells, paneth cells, enterocytes, microfold cells, hepatocytes, hepatic stellate cells (e.g., Kupffer cells from mesoderm), cholecystocytes, centroacinar cells, pancreatic stellate cells, pancreatic a cells, pancreatic b cells, pancreatic d cells, pancreatic F cells, pancreatic e cells, thyroid (e.g., follicular cells), parathyroid (e.g., parathyroid chief cells), oxyphil cells, urothelial cells, osteoblasts, osteocytes, chondroblasts, chondrocytes, fibroblasts, fibrocytes, myoblasts, myocytes, myosatellite cells, tendon cells, cardiac muscle cells, lipoblasts, adipocytes, interstitial cells of cajal, angioblasts, endothelial cells, mesangial cells (e.g., intraglomerular mesangial cells and extraglomerular mesangial cells), juxtaglomerular cells, macula densa cells, stromal cells, interstitial cells, telocytes simple epithelial cells, podocytes, kidney proximal tubule brush border cells, sertoli cells, leydig cells, granulosa cells, peg cells, germ cells, spermatozoon ovums, lymphocytes, myeloid cells, endothelial progenitor cells, endothelial stem cells, angioblasts, mesoangioblasts, pericyte mural cells, and/or any combination thereof.

[00144] Conditional knockouts can be inducible, for example, by using tetracycline inducible promoters, development specific promoters. This can allow for eliminating or suppressing expression of a gene/protein at any time or at a specific time. For example, with the case of a tetracycline inducible promoter, tetracycline can be given to a non-human animal any time after birth. If a non-human animal is a being that develops in a womb, then promoter can be induced by giving tetracycline to the mother during pregnancy. If a non-human animal develops in an egg, a promoter can be induced by injecting, or incubating in tetracycline. Once tetracycline is given to a non-human animal, the tetracycline will result in expression of ere, which will then result in excision of a gene of interest.

[00145] A cre/lox system can also be under the control of a developmental specific promoter. For example, some promoters are turned on after birth, or even after the onset of puberty. These promoters can be used to control ere expression, and therefore can be used in developmental specific knockouts.

[00146] It is also contemplated that any combinations of knockout technology can be combined. For example, tissue specific knockout can be combined with inducible technology, creating a tissue specific, inducible knockout. Furthermore, other systems such developmental specific promoter, can be used in combination with tissues specific promoters, and/or inducible knockouts.

[00147] In some cases, gene editing can be useful to design a knockout. For example, gene editing can be performed using a nuclease, including CRISPR associated proteins (Cas proteins, e.g., Cas9), Zinc finger nuclease (ZFN), Transcription Activator-Like Effector Nuclease (TALEN), and maganucleases. Nucleases can be naturally existing nucleases, genetically modified, and/or recombinant. For example, a CRISPR/Cas system can be suitable as a gene editing system.

[00148] It is also contemplated that less than all alleles of one or more genes of a non-human animal can be knocked out. For example, in diploid non-human animals, it is contemplated that one of two alleles are knocked out. This can result in decreased expression and decreased protein levels of genes. Overall decreased expression can be less than or less than about 99%, 95%, 90%, 85%, 80%, 75%, 70%, 65%, 60%, 55%, 50%, 45%, 40%, 35%, 30%, 25%, or 20%; e.g., from or from about 99% to 90%; 90% to 80%; 80% to 70%; 70% to 60%; 60% to 50%; 50% to 40%; 40% to 30%, or 30% to 20%; compared to when both alleles are functioning, for example, not knocked out and/or knocked down. Additionally, overall decrease in protein level can be the same as the decreased in overall expression. Overall decrease in protein level can be about or less than about 99%, 95%, 90%, 80%, 70%, 60%, 50%, 40%, 30%, or 20%, e.g., from or from about 99% to 90%; 90% to 80%; 80% to 70%; 70% to 60%; 60% to 50%; 50% to 40%; 40% to 30%, or 30% to 20%; compared to when both alleles are functioning, for example, not knocked out and/or knocked down. However, it is also contemplated that all alleles of one or more genes in a non-human animal can be knocked out.

[00149] Knockouts of one or more genes can be verified by genotyping. Methods for genotyping can include sequencing, restriction fragment length polymorphism identification (RFLPI), random amplified polymorphic detection (RAPD), amplified fragment length polymorphism detection (AFLPD), PCR (e.g., long range PCR, or stepwise PCR), allele specific oligonucleotide (ASO) probes, and hybridization to DNA microarrays or beads. For example, genotyping can be performed by sequencing. In some cases, sequencing can be high fidelity sequencing. Methods of sequencing can include Maxam -Gilbert sequencing, chain-termination methods (e.g., Sanger sequencing), shotgun sequencing, and bridge PCR.

In some cases, genotyping can be performed by next-generation sequencing. Methods of next-generation sequencing can include massively parallel signature sequencing, colony sequencing, pyrosequencing (e.g., pyrosequencing developed by 454 Life Sciences), single -molecule rea-time sequencing (e.g., by Pacific Biosciences), Ion semiconductor sequencing (e.g., by Ion Torrent semiconductor sequencing), sequencing by synthesis (e.g., by Solexa sequencing by Illumina), sequencing by ligation (e.g., SOLiD sequencing by Applied Biosystems), DNA nanoball sequencing, and hebscope single molecule sequencing. In some cases, genotyping of a non-human animal herein can comprise full genome sequencing analysis. In some cases, knocking out of a gene in an animal can be validated by sequencing (e.g., next-generation sequencing) a part of the gene or the entire gene. For example, knocking out of NLRC5 gene in a pig can be validated by next generation sequencing of the entire NLRC5.

[00150] In some embodiments, the genetically modified animal and the genetically modified cells disclosed herein can comprise a disruption in a PERV site. Methods for disrupting a PERV site are known in the art. For example, see Yang et al. Science 27 Nov 2015: Vol. 350, Issue 6264, pp. 1101-1104, the contents of which are incorporated herein in its entirety.

Transgenes

[00151] Provided herein are genetically modified cells, or genetically modified non-human animal, and the cells, tissues and organs derived therefrom comprising a transgene comprising a nucleic acid sequence encoding a MHC molecule (e.g., single chain chimeric MHC molecule), a a chain of a MHC molecule or a fragment thereof, or a b chain of a MHC molecule or a fragment thereof, or a peptide derived from a MHC molecule. In some embodiments, the transgene can further comprise a polynucleotide encoding a peptide derived from a MHC molecule capable of binding the peptide binding groove for presentation to a T cell. In some embodiments, the genetically modified cells, or genetically modified non-human animal, and the cells, tissues and organs derived therefrom can further comprise one or more transgenes encoding ICP47, CD46, CD55, CD59, HLA-E, HLA-G (e.g, HLA-G1, HLA-G2, HLA-G3, HLA-G4, HLA-G5, HLA-G6, or HLA-G7), B2M, any functional fragments thereof, and/or any combination thereof.

Genetically modified non-human animal or genetically modified cells, and cells, organs, and/or tissues derived from a genetically modified animal, having one or more or different combinations of transgenes are also contemplated herein. Genetically modified cells, organs, and/or tissues that are less susceptible to rejection when transplanted into a recipient are described herein. Transgenes or exogenous nucleic acid sequences, can be useful for overexpressing endogenous genes at higher levels than without the transgenes. Additionally, exogenous nucleic acid sequences can be used to express exogenous genes. Transgenes can also encompass other types of genes, for example, a dominant negative gene. [00152] A transgene of protein X can refer to a transgene comprising an exogenous nucleic acid sequence encoding protein X. As used herein, in some cases, a transgene encoding protein X can be a transgene encoding 100% or about 100% of the amino acid sequence of protein X. In some cases, a transgene encoding protein X can encode the full or partial amino sequence of protein X. For example, the transgene can encode at least or at least about 99%, 95%, 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, or 5%, e.g., from or from about 99% to 90%; 90% to 80%; 80% to 70%; 70% to 60%; or 60% to 50%; of the amino acid sequence of protein X. Expression of a transgene can ultimately result in a functional protein, e.g., a partially or fully functional protein. As discussed above, if a partial sequence is expressed, the ultimate result can be in some cases a nonfunctional protein or a dominant negative protein. A nonfunctional protein or dominant negative protein can also compete with a functional (endogenous or exogenous) protein. A transgene can also encode an RNA (e.g., mRNA, shRNA, siRNA, or microRNA). In some cases, where a transgene encodes for an mRNA, this can in turn be translated into a polypeptide (e.g., a protein). Therefore, it is contemplated that a transgene can encode for protein. A transgene can, in some instances, encode a protein or a portion of a protein. Additionally, a protein can have one or more mutations (e.g., deletion, insertion, amino acid replacement, or rearrangement) compared to a wild-type polypeptide. A protein can be a natural polypeptide or an artificial polypeptide (e.g., a recombinant polypeptide). A transgene can encode a fusion protein formed by two or more polypeptides.

[00153] Where a transgene, or exogenous nucleic acid sequence, encodes for an mRNA based on a naturally occurring mRNA (e.g., an mRNA normally found in another species), the mRNA can comprise one or more modifications in the 5’ or 3’ untranslated regions. The one or more modifications can comprise one or more insertions, on or more deletions, or one or more nucleotide changes, or a combination thereof. The one or more modifications can increase the stability of the mRNA. The one or more modifications can remove a binding site for an miRNA molecule, such as an miRNA molecule that can inhibit translation or stimulate mRNA degradation. For example, an mRNA encoding for a HLA-G and/or HE A -DR protein can be modified to remove a biding site for an miR148 family miRNA. Removal of this binding site can increase mRNA stability.

[00154] Transgenes can be placed into an organism, cell, tissue, or organ, in a manner which produces a product of the transgene. For example, disclosed herein is a non-human animal comprising one or more transgenes. One or more transgenes can be in combination with one or more disruptions as described herein. A transgene can be incorporated into a cell. For example, a transgene can be incorporated into an organism’s germ line. When inserted into a cell, a transgene can be either a complementary DNA (cDNA) segment, which is a copy of messenger RNA (mRNA), or a gene itself residing in its original region of genomic DNA (with or without introns).

[00155] A transgene can comprise a polynucleotide encoding a protein of a species and expressing the protein in an animal of a different species. For example, a transgene can comprise a polynucleotide encoding a human protein. Such a polynucleotide can be used express the human protein (e.g., CD47) in a non-human animal (e.g., a pig). In some cases, the polynucleotide can be synthetic, e.g., different from any native polynucleotide in sequence and/or chemical characteristics.

[00156] The polynucleotide encoding a protein of species X can be optimized to express the protein in an animal of a species Y. There may be codon usage bias (e.g., differences in the frequency of occurrence of synonymous codons in coding DNA). A codon can be a series of nucleotides (e.g., a series of 3 nucleotides) that encodes a specific amino acid residue in a polypeptide chain or for the termination of translation (stop codons). Different species may have different preference in the DNA codons. The optimized polynucleotide can encode a protein of species X, in some cases with codons of a species Y, so that the polynucleotide can express the protein more efficiently in the species Y, compared to the native gene encoding the protein of species X. In some cases, an optimized polynucleotide can express a protein at least 5%, 10%, 20%, 40%, 80%, 90%, 1.5 folds, 2 folds, 5 folds, or 10 folds more efficiently in species Y than a native gene of species X encoding the same protein. Methods for making gene disruption are described, for example, in WO2017218714A1 and WO2016094679A1, the teachings of which are incorporated herein in their entireties. For example, see Tables 4-9, of WO2017218714A1, which describes exemplary sequences for making gRNA constructs targeting genes for disruption and

EXAMPLES 1-9 which describe making the genetic disruption using the gRNA constructs.

Transgene encoding MHC molecule

[00157] Provided herein are methods to generate a genetically modified cell and a genetically modified animal expressing an exogenous functional MHC molecule or MHC complex comprising a peptide binding groove, and in some embodiments, further expressing a peptide capable of binding the peptide binding groove to form a functional MHC -peptide complex. The term“MHC complex” or“MHC molecule” as used herein refers to MHC heterodimer will be understood to include the MHC a chain and MHC b chain associated together to form a peptide binding groove.

[00158] Accordingly, in some embodiments, a genetically modified cell, genetically modified non-human animal or cells, organs or tissues disclosed herein comprise a transgene comprising a polynucleotide encoding a b chain of a MHC molecule or a fragment thereof. In some embodiments, a genetically modified cell, genetically modified non-human animal or cells, organs or tissues disclosed herein comprise a transgene comprising a polynucleotide encoding a a chain of a MHC molecule or a fragment thereof. In some embodiments, a genetically modified cell, genetically modified non-human animal or cells, organs or tissues disclosed herein comprise a transgene comprising a polynucleotide encoding an a chain of a MHC molecule or a fragment thereof, and a polynucleotide encoding a b chain of a MHC molecule or a fragment thereof. In some embodiments, the b chain and the a chain form a functional MHC complex (i.e., a MHC heterodimer or a MHC molecule) wherein the functional MHC complex comprises a peptide binding grove. In some embodiments, the b chain and/or the a chain lacks a functional transmembrane domain. In some embodiments, the genetically modified cells or non-human animals further comprises a transgene comprising a polynucleotide encoding a peptide derived from a MHC molecule. In some embodiments, the peptide derived from a MHC molecule can bind to the peptide binding groove such that it forms a functional MHC-peptide complex. In some embodiments, a polynucleotide encoding the b chain and a polynucleotide a chain are translationally fused.

[00159] In some embodiments, a polynucleotide encoding a b chain or fragment thereof is translationally fused upstream of a polynucleotide encoding a a chain or fragment thereof. In some embodiments, the polynucleotide encoding a peptide derived from a MHC molecule is translationally fused to the polynucleotide encoding the b chain or the polynucleotide encoding the a chain . In some embodiments, the polynucleotide encoding a peptide derived from a MHC molecule is translationally fused upstream to the polynucleotide encoding the b chain . In some embodiments, a transgene comprises translationally fused in a sequence from 5’ -3’, a

polynucleotide encoding a b chain or fragment thereof and a polynucleotide encoding a a chain or fragment thereof. In some embodiments, a transgene comprises translationally fused in a sequence from 5’ -3’, a polynucleotide encoding a peptide derived from a MHC molecule, a polynucleotide encoding a b chain or fragment thereof and a polynucleotide encoding a a chain or fragment thereof. In related embodiments, a transgene encodes a single chain MHC chimeric polypeptide comprising a b chain or fragment thereof and a a chain or fragment thereof, which upon expression folds in a functional MHC molecule. In some embodiments, a single chain MHC chimeric polypeptide further comprises a peptide derived from a MHC molecule covalently linked to a b chain or a a chain , which upon expression folds in a functional MHC- peptide complex. In some embodiments, the single chain MHC chimeric polypeptide further comprises a peptide that can bind in the peptide binding groove of the MHC molecule and can thereby be presented by the MHC molecule, such that it generates a tolerogenic response towards the genetically engineered cell or a cell, tissue or organ isolated from a genetically modified animal upon transplantation. In some embodiments, a transgene encodes a single chain MHC chimeric polypeptide comprising covalently linked in a sequence a peptide derived from a MHC molecule, a b chain of MHC molecule or a fragment thereof, and a a chain of a MHC molecule or a fragment thereof.

[00160] The term "single chain MHC chimeric peptide" or“scMHC chimeric peptide” as used herein means a single polypeptide, the amino acid sequence of which is derived at least in part from two or more different naturally occurring proteins or protein chain sections, in this case at least a a chain of a MHC molecule or a fragment thereof and a b chain of a MHC molecule or a fragment thereof. It is contemplated that upon expression the scMHC chimeric peptide folds to form a functional MHC molecule comprising a peptide binding groove. Accordingly, the term “fragment thereof’ as used herein, with regards to a a chain or b chain part of a peptide chain is meant, a fragment which still exhibits the desired functional characteristics of the full-length peptide it is derived from, i.e., forming a functional MHC molecule forming a peptide binding groove. In some embodiments, the scMHC chimeric peptide further comprises a peptide derived from a MHC molecule. In related embodiments, upon expression the scMHC chimeric peptide folds to form the MHC-peptide complex where the peptide derived from MHC molecule binds the peptide binding groove formed by association of the a chain or a fragment thereof and the b chain or a fragment thereof.

[00161] The phrases "translationally fused" and "in frame" are interchangeably used herein to refer to polynucleotides which are covalently linked to form a single continuous open reading frame spanning the length of the coding sequences of the linked polynucleotides. Such polynucleotides can be covalently linked directly or preferably indirectly through a spacer or linker region. Thus, according to some embodiments a transgene further comprises an in-frame linker polynucleotide. This linker polynucleotide encodes a linker peptide (e.g., a first linker peptide or a second linker peptide). In some embodiments, a transgene comprises a first linker polynucleotide encoding a first linker peptide interposed between the polynucleotide encoding a b chain of MHC molecule or a fragment thereof, and a polynucleotide encoding a a chain of a MHC molecule or a fragment thereof. In some embodiments, a transgene further comprises a second linker polynucleotide encoding a second linker peptide interposed between a

polynucleotide encoding a peptide derived from a MHC molecule and a polynucleotide encoding a b chain or a polynucleotide encoding a a chain . In some embodiments, a linker peptide is cleavable. In some embodiments, a linker peptide is non-cleavable.

[00162] The linker peptide linked between a b chain of MHC molecule or a fragment thereof, and a a chain of a MHC molecule or a fragment thereof is selected of an amino acid sequence which is inherently flexible, such that the polypeptides encoded by the first and said second polynucleotides independently and natively fold following expression thereof, thus facilitating the formation of a functional MHC molecule. The linker peptide linked between a peptide derived from a MHC molecule and a b chain of a MHC molecule or a fragment thereof, or a a chain of a MHC molecule or a fragment thereof is selected of an amino acid sequence which is inherently flexible, such that the peptide derived from MHC molecule independently and natively fold following expression thereof and bind a peptide binding groove, thus facilitating the formation of a functional single chain (sc) human MHC -peptide complex. In some embodiments, a first linker peptide is linked between the C-terminus of a b2 domain of the b chain and the N-terminus of an al domain of the a chain . In some embodiments, a second linker peptide is linked between the C-terminus of a peptide derived from a MHC molecule and a N- terminus of a b chain of the MHC molecule or fragment thereof or N-terminus of a a chain of the MHC molecule or fragment thereof.

[00163] It is to be understood that the disclosure is not limited in its application to the details of construction and the arrangement of the components set forth in the following description or illustrated in the drawings described in the Examples section. The disclosure is capable of other embodiments or of being practiced or carried out in various ways. Also, it is to be understood that the phraseology and terminology employed herein is for the purpose of description and should not be regarded as limiting.

[00164] In some embodiments, a first linker peptide comprises a sequence that is at least about 50%, 60%, 70%, 80%, 90%, 95%, 98%, 99% or 100% identical to a sequence selected from SEQ ID NO 1 or SEQ ID NO: 2. In some embodiments, a second linker peptide comprises a sequence that is at least about 50%, 60%, 70%, 80%, 90%, 95%, 98%, 99% or 100% identical to a sequence selected from SEQ ID NO 1 or SEQ ID NO: 2. In some embodiments, a transgene encoding a single chain MHC chimeric polypeptide comprises a sequence that is at least about 50%, 60%, 70%, 80%, 90%, 95%, 98%, 99% or 100% identical to a sequence selected from SEQ ID NO: 3, or SEQ ID NO: 4.

MHC molecules

[00165] In some embodiments, the MHC molecule is MHC class I. In some embodiments, the MHC molecule is MHC class II. The term“MHC molecule” refers to a molecule comprising Major Histocompatibility Complex (MHC) glycoprotein protein sequences. The term“MHC” as used herein will be understood to refer to the Major Histocompatibility Complex, which is defined as a set of gene loci specifying major histocompatibility complex glycoprotein antigens including the human leukocyte antigen (HLA). The term“HLA” as used herein will be understood to refer to Human Leukocyte Antigens, which is defined as the major

histocompatibility antigens found in humans. As used herein,“HLA” is the human form of “MHC” and therefore can be used interchangeably. Examples of HLA proteins that can be encoded by transgene of instant disclosure and claimed inventive concept(s) include, but are not limited to, an HLA class I a chain , an HLA class II a chain and an HLA class II b chain . Non limiting examples of HLA class II a and/or b proteins that can be encoded by a transgene of the present disclosure and claimed inventive concept(s) include, but are not limited to, those encoded at the following gene loci: HLA-DRA; HLA-DRB 1 ; HLA-DRB3,4,5; HLA-DQA; HLA-DQB; HLA-DPA; and HLA-DPB. In some embodiments, the MHC class II molecule is HLA-DP, HLA-DQ or HLA-DR. In some embodiments, a b chain of a MHC molecule is HLA-DR1, HLA- DR2, HLA-DR3, HLA-DR4, or HLA-DR5. In some embodiments, the MHC molecule is human MHC molecule.

[00166] In general, the major function of MHC molecules is to bind antigenic peptides and display them on the surface of cells. The glycoproteins (MHC molecules) encoded by the MHC have been extensively studied in both the human and murine systems and their nucleic acid and protein sequences are well known in the art. Many of the histocompatibility proteins have been isolated and characterized. For a general review of MHC glycoprotein structure and function, see Fundamental Immunology, 3d Ed., W. E. Paul, ed., (Ravens Press N.Y. 1993).

[00167] In mice, Class I molecules are encoded by the K, D and Qa regions of the MHC. Class II molecules are encoded by the I-A and I-E subregions. The isolated antigens encoded by the murine I-A and I-E subregions have been shown to consist of two noncovalently bonded peptide chains: an a chain of 32-38 kd and a b chain of 26-29 kd. A third, invariant, 31 kd peptide is noncovalently associated with these two peptides, but it is not polymorphic and does not appear to be a component of the antigens on the cell surface. The a and b chains of a number of allelic variants of the I-A region have been cloned and sequenced.

[00168] The human Class I proteins (MHC class I molecules) have also been studied (Bjorkman, P. T, et al , (1987) Nature 329:506-512). These are found to consist of a 44 kd subunit MHC class I heavy chain and a 12 kd b2 -microglobulin subunit which is common to all antigenic specificities. Further work has resulted in a detailed picture of the 3-D structure of HLA-A2, a Class I human antigen.

[00169] Structurally, MHC class I molecules are heterodimers comprised of two noncovalently bound polypeptide chains, a larger“MHC class I heavy chain (a)” and a smaller“light” chain ((b-2-microglobulin). The polymorphic, polygenic heavy chain (45 kDa), is encoded within the MHC on chromosome six. Chromosome 6 has three loci, HLA-A, HLA-B, and HLA-C, the first two of which have a large number of alleles encoding MHC class I heavy chain alloantigens, HLA-A, HLA-B respectively. In some embodiments, a transgene comprises a polynucleotide encoding for a MHC class I heavy chain (a chain) (e.g., HLA-A, HLA-B and HLA-C) or a fragment thereof. MHC class I heavy chain (a chain) (e.g., HLA-A, HLA-B and HLA-C) is subdivided into three extracellular domains (designated al, a2, and a3), one intracellular domain, and one transmembrane domain. The two outermost extracellular domains, al and a2, together form the groove that binds antigenic peptide. Thus, interaction with the TCR occurs at this region of the protein. The 3rd extracellular domain of the molecule contains the recognition site for the CD8 protein on the CTL; this interaction serves to stabilize the contact between the T cell and the APC. In some embodiments, a transgene comprises a polynucleotide encoding for al, a2, a3 domain, intracellular domain, or transmembrane domain. In some embodiments, the transgene encodes a MHC class I heavy chain (a chain ) that lacks a transmembrane domain.

[00170] The invariant light chain (12 kDa), encoded outside the MHC on chromosome 15, consists of a single, extracellular polypeptide. In some embodiments, a transgene encodes a MHC class I light chain (b chain ). The terms“MHC class I light chain”,“b-2-microglobulin”, and“b2ih” may be used interchangeably herein. In some embodiments, the transgene encodes a MHC class I light chain (b chain ) that lacks a transmembrane domain. Association of the class I heavy and light chains is required for expression of MHC class I molecules on cell membranes.

In this picture, the b2 -microglobulin protein and a3 domain of the heavy chain are associated. In some embodiments, a chain or a fragment thereof and the b chain or a fragment thereof, that is encoded by a transgene associate to form a peptide binding groove. Accordingly, the MHC class I molecule as disclosed herein can refer to a MHC class I heterodimer, comprising a MHC class I heavy chain (e.g., HLA-A, HLA-B, or HLA-C), a MHC class I light chain or portions thereof or regions thereof. In some embodiments, the transgene encodes entire MHC class I heavy chain. In some embodiments, the MHC class I molecule can be domains of MHC class I heavy chain (al, a2, or a3). In some embodiments, the MHC class I molecule can comprise sequence from the al, a2, or a3 region of the MHC class I heavy chain. The al and a2 domains of the heavy chain comprise the hypervariable region which forms the antigen-binding sites to which the peptide is bound.

[00171] In some embodiments, a MHC molecule is a MHC class II molecule. MHC class II glycoproteins, HLA-DR, HLA-DQ, and HLA-DP (encoded by alleles at the HLA-DR, DP, and DQ loci) have a domain structure, including antigen binding sites, similar to that of Class I. MHC class II molecules are heterodimers, consist of two nearly homologous subunits; a and b chains, both of which are encoded in the MHC. Accordingly, in some embodiments, the MHC class II molecule refers to a heterodimer of MHC class II a chain and MHC class II b chain (e.g., HLA-DQ, HLA-DR, HLA-DP). In some embodiments, the MHC class II molecule can be a subunit of the heterodimer. In some embodiments, a transgene comprises a polynucleotide encoding a MHC class II a chain (e.g., HLA-DP A, HLA-DQA, or HLA-DRA). In some embodiments, a transgene comprises a polynucleotide encoding a MHC class II b chain (e.g., HLA-DPB, HLA-DQB, or HLA-DRB), or domains thereof. In some embodiments, a transgene comprises a polynucleotide encoding a MHC class II a chain and a polynucleotide encoding a MHC class II b chain . In some embodiments, the b chain is HLA-DRB. [00172] The b chain is encoded by four gene loci in human (HLA-DRB1, HLA-DRB3, HLA- DRB4 and HLA-DRB4), however no more than 3 functional loci are present in a single individual, and no more than two on a single chromosome. In some embodiments, the b chain is encoded by HLA-DRB1, HLA-DRB3, HLA-DRB4 or HLA-DRB4 gene locus. In some embodiments, the b chain is encoded by HLA-DRB1*03 or HLA-DRB1*04. The HLA-DRB1 locus is ubiquitous and encodes a very large number of functionally variable gene products (HLA-DR1 to HLA-DR17). The HLA-DRB3 locus encodes the HLA-DR52 specificity, is moderately variable and is variably associated with certain HLA-DRB1 types. The HLA-DRB4 locus encodes the HLA-DR53. In some embodiments, the b chain is selected from HLA-DR1, HLA-DR2, HLA-DR3, HLA-DR4, or HLA-DR5.

[00173] In some embodiments, a transgene encodes an entire MHC class II b chain and/or MHC class II a chain or large portions thereof. For instance, a transgene can encode an extracellular domain from an MHC class II subunit of about 90-100 residues (e.g., b1 and b2 and/or al and a2 of class II molecules). Each chain in Class II molecules consist of globular domains, referred to as a1, a2, b1, and b2. All except the al domain are stabilized by intrachain disulfide bonds typical of molecules in the immunoglobulin superfamily. Each chain in a class II molecule contains two external domains: the 33-kDa a chain contains al and a2 external domains, while the 28-kDa b chain contains b1 and b2 external domains. The membrane-proximal a2 and b2 domains, like the membrane-proximal 3rd extracellular domain of class I heavy chain molecules, bear sequence homology to the immunoglobulin-fold domain structure. The membrane-distal domain of a class II molecule is composed of the al and b1 domains, which form an antigen binding cleft for processed peptide antigen. Accordingly, in some embodiments, a chain or a fragment thereof and the b chain or a fragment thereof, that is encoded by a transgene associate to form a peptide binding groove. The N-terminal portions of the a and b chain s, the al and b1 domains, contain hypervariable regions which are thought to comprise the majority of the antigen-binding sites (see, Brown et al., Nature 364:33-39 (1993)).

[00174] Polynucleotides encoding a a chain or a fragment thereof and/or a b chain or fragment thereof can be obtained from a variety of sources including polymerase chain reaction (PCR) amplification of publicly available MHC chain sequences. In some embodiments, a transgene encodes a MHC class molecule that is matched to a recipient of a transplant. In some

embodiments, a transgene encodes a MHC molecule that is mismatched to a recipient of a transplant. In some embodiments, the MHC molecule of a recipient is matched with the MHC molecule of a donor of a transplant. Sequences of MHC glycoproteins and genes encoding the glycoproteins are known in the art. In some embodiments, wherein the MHC molecule is matched with a subject (e.g., a recipient or a donor of a transplant or a subject in need of treatment), the MHC molecule can be determined, for example, by conventional methods of HLA-typing or tissue typing known in the arts. Non limiting examples of methods that can be employed for selection of a MHC molecule include serological methods, cellular methods and DNA typing methods. Serology is used to identify the HLA proteins on the surface of cells. A complement dependent cytotoxicity test or microlymphocytotoxicity assay can be used for serological identification of MHC molecules. Peripheral blood lymphocytes (PBLs) express MHC class I antigens and are used for the serologic typing of HLA- A, HLA-B, and HLA-C. MHC class II typing is done with B lymphocytes isolated from PBLs because these cells express class II molecules. HLA typing is performed in multiwell plastic trays with each well containing a serum of known HLA specificity.

[00175] Lymphocytes are plated in the well and incubated, and complement (rabbit serum as a source) is added to mediate the lysis of antibody-bound lymphocytes (See. Terasaki Pi, Nature. 1964). Cellular assays such as the mixed lymphocyte culture (MLC) measure the differences in class II proteins between individuals. This may be accomplished in a number of ways, all of which are known to those skilled in the art, e.g., subtyping may be accomplished by mixed lymphocyte response (MLR) typing and by primed lymphocyte testing (PLT). Both methods are described in Weir and Blackwell, eds., Handbook of Experimental Immunology, which is incorporated herein by reference. It may also be accomplished by analyzing DNA restriction fragment length polymorphism (RFLP) using DNA probes that are specific for the MHC locus being examined. Methods for preparing probes for the MHC loci are known to those skilled in the art. See, e.g., Gregersen et al. (1986), Proc. Natl. Acad. Sci. USA 79:5966, which is incorporated herein by reference. High resolution selection of a MHC molecule can be done by DNA typing methods. Different HLA alleles defined by DNA typing can specify HLA proteins which are indistinguishable using serologic typing. For example, an individual carrying the DRB 1*040101 allele would have the same serologic type (DR4) as an individual carrying the DRB1*0412 allele. Thus, DRB1*040101 and DRB1*0412 are splits of the broad specificity DR4. These splits are identified by DNA typing.

[00176] Sequences of transgene encoding a MHC molecule can be obtained by sequencing of genomic DNA of the locus, or cDNA to mRNA encoded within the locus. The DNA which is sequenced includes the section encoding the hypervariable regions of the MHC encoded polypeptide. Techniques for identifying specifically desired DNA with a probe, for amplification of the desired region are known in the art, and include, for example, the polymerase chain reaction (PCR) technique. Live lymphocytes are not required for DNA typing and DNA is easily extracted from any nucleated cell, although peripheral blood lymphocytes are the usual source. DNA is easily stored, allowing repeat sample testing and amplifying desired MHC sequences when required. The polymerase chain reaction (PCR)-based technology is used for clinical HLA typing. The first method developed uses sequence-specific oligonucleotide probe (SSOP). For HLA class II typing, the variable exon sequences encoding the first amino terminal domains of the DRB1 and DQB1 genes are amplified from genomic DNA. Based on the HLA sequence database, a panel of synthetic oligonucleotide sequences corresponding to variable regions of the gene are designed and used as SSOP in hybridization with the amplified PCR products.

[00177] As an alternative method, polymorphic DNA sequences can be used as amplification primers, and in this case only alleles containing sequences complementary to these primers will anneal to the primers and amplification will proceed. This second strategy of DNA typing is called the sequence-specific primer (SSP) method. Actual DNA sequencing of amplified products of multiple HLA loci is increasingly used as clinical HLA typing. HLA alleles are designated by the locus followed by an asterisk (*), a two-digit number corresponding to the antigen specificity, and the assigned allele number. For example, HLA-A*0210 represents the tenth HLA-A2 allele within the serologically defined HLA-A2 antigen family. Methods for HLA typing and identification of MHC molecules expressed in a donor of transplant and a potential recipient at the protein or DNA level are described for example, in Altaf et al World J

Transplant. 2017, Erlich H. A. et al. Immunity, Vol. 14, 347-356, April, 2001, Dunckley H, Methods Mol Biol. 2012. US20090069190A1, US20110117553 AL One of skill in the art can determine the protein product once the gene sequence of MHC molecule is determined by DNA typing methods. In some embodiments, the amplified DNA sequences can be easily be translationally fused to generate a transgene encoding a single chain MHC chimeric MHC molecule using standard molecular biology techniques such as PCR.

Peptides derived from MHC molecule

[00178] In some embodiments, the transgene comprises a polynucleotide encoding a peptide derived from a MHC molecule.

[00179] As such, the sequences of amino acid residues in the peptide will be identical to or substantially identical to a polypeptide sequence in the MHC molecule. Thus,“a peptide derived from a MHC molecule” refers to a peptide that has a sequence "from a region in an MHC molecule" (e.g., the hypervariable region), and is a peptide that has a sequence either identical to or substantially identical to the naturally occurring MHC amino acid sequence of the region. In some embodiments, the MHC molecule is MHC class II molecule. Thus,“a peptide derived from a MHC class II molecule” refers to a peptide that has a sequence "from a region in an MHC class II molecule" (e.g., the hypervariable region), and is a peptide that has a sequence either identical to or substantially identical to the naturally occurring MHC amino acid sequence of the region. Accordingly,“a peptide derived from a MHC class II molecule of a recipient” refers to a peptide that has a sequence "from a region in an MHC class II molecule of a recipient" (e.g., the hypervariable region), and is a peptide that has a sequence either identical to or substantially identical to the naturally occurring MHC amino acid sequence of the region in the recipient. It is understood that MHC class II molecule of a recipient refers to the MHC class II molecule that is expressed in the recipient.

[00180] In some embodiments, the MHC molecule is MHC class I molecule. Thus,“a peptide derived from a MHC class I molecule” refers to a peptide that has a sequence "from a region in an MHC class I molecule" (e.g., the hypervariable region), and is a peptide that has a sequence either identical to or substantially identical to the naturally occurring MHC amino acid sequence of the region. Accordingly,“a peptide derived from a MHC class I molecule of a recipient” refers to a peptide that has a sequence "from a region in an MHC class I molecule of a recipient" (e.g., the hypervariable region), and is a peptide that has a sequence either identical to or substantially identical to the naturally occurring MHC amino acid sequence of the region in the recipient. It is understood that MHC class I molecule of a recipient refers to the MHC class I molecule that is expressed in the recipient.

[00181] Accordingly,“a peptide derived from a MHC class I molecule of a donor” refers to a peptide that has a sequence "from a region in an MHC class I molecule of a donor" (e.g., the hypervariable region), and is a peptide that has a sequence either identical to or substantially identical to the naturally occurring MHC amino acid sequence of the region in the donor. In some embodiments, the peptide derived from a MHC class I molecule can comprise a sequence from the hypervariable region of the MHC class I molecule. It is understood that MHC class I molecule of a donor refers to the MHC class I molecule that is expressed in the donor. In some embodiments, the MHC class I molecule of the donor is mismatched with the MHC class I molecule of the recipient of the transplant. In some embodiments, the peptide derived from a MHC class I molecule will comprise a sequence from the hypervariable region of the MHC class I molecule.

[00182] As used herein a "hypervariable region" of an MHC molecule is a region of the molecule in which polypeptides encoded by different alleles at the same locus have high sequence variability or polymorphism. The polymorphism is typically concentrated in the al and a2 domains of in Class I molecules and in the al and b1 domains of Class II molecules. The number of alleles and degree of polymorphism among alleles may vary at different loci. For instance, in HLA-DR molecules all the polymorphism is attributed to the b chain and the a chain is relatively invariant. For HLA-DQ, both the a and b chain s are polymorphic. In some embodiments, a peptide derived from a MHC molecule comprises a sequence that is at least about 50%, 60%, 70%, 80%, 90%, 95%, 99%, or 100% identical to a sequence selected from Table 1

Peptides derived from MHC-Class I molecule

[00183] In some embodiments, the peptide derived from a MHC molecule is derived from a MHC class I molecule. The human Class I proteins (MHC class I molecules) have also been studied (Bjorkman, P. T, et al., (1987) Nature 329:506-512). These are found to consist of a 44 kd subunit MHC class I heavy chain and a 12 kd b2 -microglobulin subunit which is common to all antigenic specificities. Further work has resulted in a detailed picture of the 3-D structure of HLA-A2, a Class I human antigen.

[00184] Structurally, MHC class I molecules are heterodimers comprised of two noncovalently bound polypeptide chains, a larger“MHC class I heavy chain (a)” and a smaller“light” chain ((b-2-microglobulin). The polymorphic, polygenic heavy chain (45 kDa), is encoded within the MHC on chromosome six. Chromosome 6 has three loci, HLA-A, HLA-B, and HLA-C, the first two of which have a large number of alleles encoding MHC class I heavy chain alloantigens, HLA-A, HLA-B respectively. MHC class I heavy chain (a) (e g., HLA-A, HLA-B and HLA-C) is subdivided into three extracellular domains (designated al, a2, and a3), one intracellular domain, and one transmembrane domain. The two outermost extracellular domains, al and a2, together form the groove that binds antigenic peptide. Thus, interaction with the TCR occurs at this region of the protein. The 3rd extracellular domain of the molecule contains the recognition site for the CD8 protein on the CTL; this interaction serves to stabilize the contact between the T cell and the APC.

[00185] The invariant light chain (12 kDa), encoded outside the MHC on chromosome 15, consists of a single, extracellular polypeptide. The terms“MHC class I light chain”,“b-2- microglobulin”, and“b2hi” may be used interchangeably herein. Association of the class I heavy and light chains is required for expression of MHC class I molecules on cell membranes. In this picture, the b2 -microglobulin protein and a3 domain of the heavy chain are associated.

Accordingly, the MHC class I molecule as disclosed herein can refer to a MHC class I heterodimer, a MHC class I heavy chain (e.g., HLA-A, HLA-B, or HLA-C), a MHC class I light chain or portions thereof or regions thereof. In some embodiments, the peptide can be derived from a MHC class I heavy chain e.g., HLA-A, or HLA-B. In some embodiments, the peptide can comprise sequence from the al, a2, or a3 region of the MHC class I heavy chain. The al and a2 domains of the heavy chain comprise the hypervariable region which forms the antigen binding sites to which the peptide is bound. In some embodiments, a peptide can be derived from a al or a2 domains of the MHC class I heavy chain. In some embodiments, the peptide derived from a MHC class I molecule can comprise sequence from a hypervariable region of a MHC class I molecule.

Peptide derived from MHC-Class II molecule

[00186] In some embodiments, the peptide derived from a MHC molecule is derived from a MHC class II molecule. MHC class II glycoproteins, HLA-DR, HLA-DQ, and HLA-DP

(encoded by alleles at the HLA-DR, DP, and DQ loci) have a domain structure, including antigen binding sites, similar to that of Class I. MHC class II molecules are heterodimers, consist of two nearly homologous subunits; a and b chain s, both of which are encoded in the MHC. Accordingly, in some embodiments, the peptide derived from MHC class II molecule is derived from a MHC class II a chain (e g., HLA-DP A, HLA-DQA, or HLA-DRA), or MHC class II b chain (e g., HLA-DPB, HLA-DQB, or HLA-DRB), or domains thereof. In some embodiments, the peptide derived from MHC class II molecule is derived from HLA-DRB.

[00187] The HLA-DRB is encoded by four gene loci in human (HLA-DRBl, HLA-DRB3, HLA-DRB4 and HLA-DRB4), however no more than 3 functional loci are present in a single individual, and no more than two on a single chromosome. In some embodiments, the HLA- DRB is encoded by HLA-DRBl, HLA-DRB3, HLA-DRB4 or HLA-DRB4 gene locus. In some embodiments, the HLA-DRB is encoded by HLA-DRB 1*03 or HLA-DRB 1*04. The HLA- DRBl locus is ubiquitous and encodes a very large number of functionally variable gene products (HLA-DRl to HLA-DR17). The HLA-DRB3 locus encodes the HLA-DR52 specificity, is moderately variable and is variably associated with certain HLA-DRBl types. The HLA- DRB4 locus encodes the HLA-DR53. In some embodiments, the peptide derived from a MHC class II molecule is derived from HLA-DRl, HLA-DR2, HLA-DR3, HLA-DR4, or HLA-DR5.

In some embodiments, the peptide derived from HLA-DR3 can comprise a sequence that is at least about 50%, 60%, 70%, 80%, 90%, 95%, 99%, or 100% identical to a sequence selected from Table 1

[00188] In some embodiments, the peptide derived from a MHC class II molecule can be derived from a globular domain e.g., al, a2, b1, or b2. The peptides derived from MHC class II molecule can comprise the entire subunit (a or b chain ) or large portions thereof. For instance, the peptides can comprise an extracellular domain from an MHC class II subunit of about 90-100 residues (e.g., b1 and b2 or al and a2 of class II molecules). The N-terminal portions of the a and b chains, the al and b1 domains, contain hypervariable regions which are thought to comprise the majority of the antigen-binding sites (see, Brown et al., Nature 364:33-39 (1993)). Accordingly, the peptides derived from MHC class II molecule can comprise a sequence from hypervariable region of the MHC class II molecule (e.g., the al and b1 domains of the a and b chain s subunits respectively).

[00189] In some embodiments the peptides are derived from hypervariable regions of the a or b chain of an MHC Class II molecule associated with the deleterious immune response. In this way, the ability of antigen presenting cells (APC) to present the target antigen (e.g., autoantigen or allergen) is inhibited.

[00190] The methods for obtaining sequences of MHC molecule are disclosed above. The amino acid sequences of peptides capable of binding MHC complex are currently known, and others can be determined through routine experimentation well known to those skilled in the art (see, e.g., Rammensee et al., (1995) Immunogenetics 41 : 178-228). For example, if the peptide antigen has been isolated it is possible to identify its sequence by techniques such as Edman degradation (Nelson et al., (1992) Proc. Natl. Acad. Sci. USA 89: 7380-7383) and mass spectrometric methods (see, e.g., Cox et al., (1994) Science 264: 716-719). In addition, whether a given peptide of interest is capable of binding a peptide bindiong groove of a MHC molecule can be determined by scanning the sequence of a peptide of interest with the respective consensus-motif of the restricting MHC-complex (see, e.g., W096/27387). In general, consensus-motifs of MHC -ligands are allele-specific (i.e., the motif of peptides bound, for example, to HLA-A2.1 is different from the motif of peptides which bind to HLA-B2701). Such motifs summarize invariant features contained within such peptides including, for example, length and position of the invariant amino acid positions. Consensus motifs have been identified for the ligands of MHC class I complex and MHC class II complex and methods for the identification of such motifs have been described. These include, for example, pool sequencing (Falk et al., (1991) Nature 351 : 290-296; Falk et al., 0 94) Immunogenetics 39: 230-242) as well as the use of phage display libraries (e.g., Hammer et al., (1992) J. Exp. Med. 179: 1007- 1013); selected motifs are specifically disclosed by Rammensee et al., (1995) Immunogenetics 41 : 178- 228. Methods for the prediction of the binding affinity of a given peptide to MHC complex are known in the art (see for example, WO1998059244A1). In some embodiments, the peptides predicted to bind MHC class II complex of the recipient of a transplant with a high affinity are preferred in the methods disclosed herein. For instance, once the sequence of an polypeptide of a MHC molecule is obtained, for example from a publically available sequences (e.g., IPD-MHC (http://www.ebi.ac.uk/ipd/mhc/) or IPD-IMGT/HLA (https://www.ebi.ac.uk/ipd/imgt/hla/)) by PCR amplification from the genomic DNA of a subject, the peptides that are capable of binding the MHC molecule can be determined, for example, by a in silico prediction tool. A variety of MHC class II complex binding prediction tools are publicly available and will be known to those skilled in the art. Non limiting examples include; ARB, PROPRED, SVMHC, SYFPEITHI, RANKPEP, SMM-align, SVRMHC, MHC2PRED and MHCPRED; see WANG P et al, PLoS Comput Biol. 2008. In some embodiments, the MHC class II binding peptides (e.g., peptides derived from MHC class II or peptides derived from MHC class I molecule can be predicted using the publicly available The Immune Epitope Database and Analysis Resource (IEDB). Cells comprising a variety of MHC genes are readily available, for instance, they may be obtained from the American Type Culture Collection ("Catalogue of Cell Lines and Hybridomas," 6th edition (1988) Rockville, Md., U.S.A. Standard techniques can be used to screen cDNA libraries to identify sequences encoding the desired sequences (see, Sambrook et al., Molecular Cloning— A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., 1989, which is incorporated herein by reference).

[00191] The biochemical approach, involves the fractionation of the MHC complex bound peptides by chromatography, assaying the fractions for immunological activity and sequencing the individual peptides in the active fractions can also be used, e.g, W01994004171A1. The peptides predicted to bind MHC molecule can be tested in an HLA-Binding assay, e.g.,

Prolmmune REVEAL® MHC Class II, Creative Biolabs SIAT®, see Salvat R. et al. J Vis Exp. 2014.

[00192] In some embodiments, the peptide derived from MHC molecule comprises at least 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 or more amino acid residues.

Binding to MHC molecule

[00193] In aspects of the present disclosure, the peptide derived from a MHC molecule are capable of binding the peptide binding groove of the MHC molecule to generate a MHC -peptide complex. As used herein, the term " capable of binding the peptide binding groove " means a peptide is capable of selectively binding within the cleft formed by the a and b chain s of a specified MHC molecule to form an MHC -peptide antigen complex. For MHC class II complexes, the peptides are typically 10-25 amino acids in length, and more typically 13-18 residues in length, although longer and shorter ones may bind effectively. As used herein, the term "selectively binding" means capable of binding in the electro- and stereospecific manner of an antibody to antigen or ligand to receptor. With respect to a peptide capable of binding a peptide binding groove, selective binding entails the non-covalent binding of specific side chains of the peptide within the binding pockets present in the MHC binding cleft in order to form an MHC- peptide complex (see, e.g., Brown et al., (1993) Nature 364:33-39; Stem et al., (1994) Nature 368:215-221; Stern and Wiley (1992) CeU 68: 465-477).

Nucleic acid construct

[00194] The disclosure also pertains to an isolated nucleic acid molecule (RNA, mRNA, cDNA or genomic DNA) comprising a transgene disclosed herein. In some embodiments, the nucleic acid construct further includes a first cis acting regulatory sequence. The cis acting regulatory sequence can include a promoter sequence and additional transcriptional or a translational enhancer sequences all of which serve for facilitating the expression of the nucleic acid sequence when introduced into a host cell. In some cases, the nucleic acid construct is inserted into a DNA vector (i.e., DNA expression vector) capable of expressing the MHC complex in a desired cell, typically a eukaryotic or prokaryotic cell. The nucleic acid molecule can include or be fused to operably linked control elements such as a promoter, leader and/or optional enhancer sequences, to augment expression of the MHC complex in the cell. Alternatively, the nucleic acid segment can be optimized for use in a cell-free translation system if desired. In some embodiments, the nucleic acid molecule is for CRISPR/Cas mediated integration into a specific genomic locus. Homologous recombination can permit site-specific integration of a transgene. Accordingly, in some embodiments, the nucleic acid molecule comprises a first flanking sequence homologous to a genome sequence upstream of a select insertion site, said first flanking sequence located upstream of a transgene. In some embodiments, the nucleic acid molecule comprises a second flanking sequence homologous to a genome sequence downstream of a select insertion site, said second flanking sequence located downstream of a transgene. Vector comprising the isolated nucleic acid construct are also contemplated in the present disclosure. In some embodiments, the first flanking sequence comprises a sequence that is at least about 50%, 60%, 70%, 80%, 90%, 95%, 98%, 99% or 100% identical to sequence set forth in SEQ ID NO: 5. In some

embodiments, the first flanking sequence comprises a sequence that is at least about 50%, 60%, 70%, 80%, 90%, 95%, 98%, 99% or 100% identical to sequence set forth in SEQ ID NO: 6.

[00195] In some embodiments, an isolated nucleic acid molecule comprises a sequence that is at least about 50%, 60%, 70%, 80%, 90%, 95%, 98%, 99% or 100% identical to a sequence selected from SEQ ID NO: 3, or SEQ ID NO: 4.

[00196] The genetically modified non-human animals and cells can also comprise one or more additional genetic modifications, such as any of the genetic modifications (e.g., knock-ins, knock-outs, gene disruptions, etc.) disclosed herein. For example, the genetically modified cells, or genetically modified non-human animal, and the cells, tissues and organs derived therefrom can further comprise one or more additional transgenes encoding ICP47, CD46, CD55, CD59, HLA-E, HLA-G (e g., HLA-G1, HLA-G2, HLA-G3, HLA-G4, HLA-G5, HLA-G6, or HLA- G7), B2M, any functional fragments thereof, and/or any combination thereof. The disclosure is not limited to the exemplified modification and contemplates various combinations of the transgenes and gene disruptions disclosed herein.

Human Leukocyte Antigen G (HLA-G)

[00197] In some embodiments, the genetically modified cells, or genetically modified non-human animal, and the cells, tissues and organs derived therefrom can further comprise a transgene encoding HLA-G. The HLA-G can be a potent immuno -inhibitory and tolerogenic molecule. HLA-G expression in a human fetus can enable the human fetus to elude the maternal immune response. Neither stimulatory functions nor responses to allogeneic HLA-G have been reported to date. HLA-G can be a non-classical HLA class I molecule. It can differ from classical MHC class I molecules by its genetic diversity, expression, structure, and function. HLA-G can be characterized by a low allelic polymorphism.

Expression of HLA-G can be restricted to trophoblast cells, adult thymic medulla , and stem cells . However, HLA-G neo-expression may be induced in pathological conditions such as cancers, multiple sclerosis, inflammatory diseases, or viral infections.

[00198] Seven isoforms of HLA-G have been identified. The different isoforms can be products of alternative splicing. Four of these can be membrane bound (HLA-G1 to -G4), and 3 can be soluble isoforms (HLA-G5 to -G7). HLA-G1 and HLA-G5 isoforms present the typical structure of the classical HLA class I molecules formed by a 3 globular domain (a1-a3) heavy-chain, noncovalently associated to b-2 -microglobulin (B2M) and a nonapeptide. The truncated isoforms lack 1 or 2 domains, although they all contain the al domain, and they are all B2M-free iso forms.

[00199] HLA-G can exert an immuno-inhibitory function through direct binding to inhibitory receptors, e g., ILT2/CD 85j /LILRB 1 , ILT4/CD85d/LILRB2, or KIR2DL4/CD158d.

[00200] ILT2 can be expressed by B cells, some T cells, some NK cells, and monocytes/dendritic cells. ILT4 can be myeloid-specific and its expression can be restricted to monocytes/dendritic cells. KIR2DL4 can be a specific receptor for HLA-G. It can be expressed by the CD56 ^bright subset of NK cells. ILT2 and ILT4 receptors can bind a wide range of classical HLA molecules through the a3 domain and B2M. However, HLA-G can be their ligand of highest affinity.

[00201] ILT2 -HLA-G interaction can mediate the inhibition of, for example: i) NK and antigen-specific CD8+ T cell cytolytic function, ii) alloproliferative response of CD4+T cells, and iii) maturation and function of dendritic cells. ILT2 -HLA-G interaction can impede both naive and memory B cell function in vitro and in vivo. HLA-G can inhibit B cell proliferation, differentiation, and Ig secretion in both T cell-dependent and -independent models of B cell activation. HLA-G can act as a negative B cell regulator in modulating B cell Ab secretion. HLA-G can also induce the differentiation of regulatory T cells, which can then inhibit allogeneic responses themselves may participate in the tolerance of allografts. The expression of HLA-G by tumor cells can enable the escape of immunosurveillance mediated by host T lymphocytes and NK cells. Thus, the expression of HLA-G by malignant cells may prevent tumor immune eradication by inhibiting the activity of tumor-infiltrating NK cells, cytotoxic T lymphocytes (CTLs), and antigen presenting cells (APCs). The HLA-G structure variation, particularly its monomeric/multimeric status and its association with B2M, can play a role in the biological function of HLA-G, its regulation and its interactions with the inhibitory receptors ILT2 and ILT4.

[00202] ILT2 and ILT4 inhibitory receptors may have a higher affinity for HLA-G multimers than monomeric structures. HLA-G1 and HLA-G5 (HLA-G1/5) can form dimers through disulphide bonds between unique cysteine residues at positions 42 (Cys42-Cys42), within the a1 domain. Dimers of B2M- associated HLA-G 1 may bind ILT2 and ILT4 with higher affinity than monomers. This increased affinity of dimers may be due to an oblique orientation that exposes the ILT2- and ILT4-binding sites of the a3 domain, making it more accessible to the receptors. Both ILT2 and ILT4 can bind the HLA-G a3 domain at the level of F195 and Y197 residues.

[00203] ILT2 and ILT4 bind differently to their HLA-G isoforms. ILT2 may recognize only B2M- associated HLA-G structures, whereas ILT4 may recognize both B2M-associated and B2M-free HLA-G heavy chains. B2M-free heavy chains have been detected at the cell surface and in culture supernatants of HLA-G-expressing cells. Furthermore, B2M-free HLA-G heavy chains may be the main structure produced by human villous trophoblast cells. The presence of (B2M-free) al - a3 structures (HLA-G2 and G-6 isoforms) was shown in the circulation of human heart transplant recipients and may be associated with better allograft acceptance. The al - a3 structure may bind only to ILT4 but not ILT2. However, al - a3 dimers (with dimerization of al - a3 monomers achieved through disulfide bonds between two free cysteines in position 42) may be tolerogenic in vivo in an allogeneic murine skin transplantation model. An (al - a3)x2 synthetic molecule may inhibit the proliferation of tumor cell lines that did not express ILT4. This may indicate the existence of yet unknown receptors for HLA-G.

[00204] Accordingly, in some embodiments, genetically modified non-human animals and cells comprises an exogenous nucleic acid sequence encoding for an HLA-G protein.

[00205] In some embodiments, a genetically modified non-human animal, cells, tissues or organs can further comprise one or more transgenes comprising one or more polynucleotide inserts. The

polynucleotide inserts can encode one or more proteins or functional fragments thereof. For example, a non-human genetically modified animal can comprise one or more exogenous nucleic acid sequences encoding one or more proteins or functional fragments thereof. In some cases, a non-human animal can comprise one or more transgenes comprising one or more polynucleotide inserts encoding proteins that can reduce expression and/or function of MHC molecules (e.g., MHC I molecules and/or MHC II molecules). The one or more transgenes can comprise one or more polynucleotide inserts encoding MHC I formation suppressors, regulators of complement activations, inhibitory ligands for NK cells, B7 family members, CD47, serine protease inhibitors, galectins, and/or any fragments thereof. In some cases, the MHC I formation suppressors can be infected cell protein 47 (ICP47). In some cases, regulators of complement activation can comprise cluster of differentiation 46 (CD46), cluster of differentiation 55 (CD55), and cluster of differentiation 59 (CD59). In some cases, inhibitory ligands for NK cells can comprise leukocyte antigen E (HLA-E), human leukocyte antigen G (HLA-G), and b-2 -microglobulin (B2M). An inhibitory ligand for NK cells can be an isoform of HLA-G, e.g., HLA-G 1, HLA-G2, HLA- G3, HLA-G4, HLA-G5, HLA-G6, or HLA-G7. For example, inhibitory ligand for NK cells can be HLA- Gl . A transgene of HLA-G (e.g., HLA-G 1, HLA-G2, HLA-G3, HLA-G4, HLA-G5, HLA-G6, or HLA- G7) can refer to a transgene comprising a nucleotide sequence encoding HLA-G (e.g., HLA-G1, HLA- G2, HLA-G3, HLA-G4, HLA-G5, HLA-G6, or HLA-G7). As used herein, in some cases, a transgene encoding HLA-G (e.g, HLA-G 1, HLA-G2, HLA-G3, HLA-G4, HLA-G5, HLA-G6, or HLA-G7) can be a transgene encoding 100% or about 100% of the amino acid sequence of HLA-G (e.g., HLA-G1, HLA- G2, HLA-G3, HLA-G4, HLA-G5, HLA-G6, or HLA-G7). In other cases, a transgene encoding HLA-G (e.g, HLA-G 1, HLA-G2, HLA-G3, HLA-G4, HLA-G5, HLA-G6, or HLA-G7) can be a transgene encoding the full or partial sequence of HLA-G (e.g., HLA-G1, HLA-G2, HLA-G3, HLA-G4, HLA-G5, HLA-G6, or HLA-G7). For example, the transgene can encode at least or at least about 99%, 95%, 90%, 80%, 70%, 60%, or 50% of the amino acid sequence of HLA-G (e.g., HLA-G1, HLA-G2, HLA-G3, HLA-G4, HLA-G5, HLA-G6, or HLA-G7). For example, the transgene can encode 90% of the HLA-G amino acid sequence. A transgene can comprise polynucleotides encoding a functional (e.g., a partially or fully functional) HLA-G (e.g, HLA-G 1, HLA-G2, HLA-G3, HLA-G4, HLA-G5, HLA-G6, or HLA- G7). In some cases, the one or more transgenes can comprise one or more polynucleotide inserts encoding one or more of ICP47, CD46, CD55, CD59, HLA-E, HLA-G (e.g, HLA-G 1, HLA-G2, HLA- G3, HLA-G4, HLA-G5, HLA-G6, or HLA-G7), and B2M. The HLA-G genomic DNA sequence can have 8 exons by which alternative splicing results in 7 isoforms. The HLA-G 1 isoform can exclude exon 7. The HLA-G2 isoform can exclude exon 3 and 7. Translation of intron 2 or intron 4 can result secreted isoforms due to the loss of the transmembrane domain expression. In some cases, B7 family members can comprise CD80, CD86, programed death-ligand 1 (PD-L1), programed death-ligand 2 (PD-L2), CD275, CD276, V-set domain containing T cell activation inhibitor 1 (VTCN1), platelet receptor Gi24, natural cytotoxicity triggering receptor 3 ligand 1 (NR3L1), and HERV-H LTR-associating 2 (HHLA2). For example, a B7 family member can be PD-L1 or PD-L2. In some cases, a serine protease inhibitor can be serine protease inhibitor 9 (Spi9). In some cases, galectins can comprise galectin-1, galectin-2, galectin-3, galectin-4, galectin-5, galectin-6, galectin-7, galectin-8, galectin-9, galectin-10, galectin-11, galectin-12, galectin-13, galectin-14, and galectin-15. For example, a galectin can be galectin-9.

[00206] In some embodiments, a genetically modified non-human animal or cells, tissues and organs derived therefrom or a genetically modified cell of the present disclosure can further comprise reduced expression of one or more genes and one or more transgenes disclosed herein. In some cases, a genetically modified non-human animal can comprise reduced expression of one or more of NLRC5, TAPI, CXCL10, MICA, MICB, C3, CIITA, GGTA1, CMAH, and B4GALNT2, and one or more transgenes comprising one or more polynucleotide inserts encoding one or more of ICP47, CD46, CD55, CD59, HLA-E, HLA-G (e.g, HLA-G 1, HLA-G2, HLA-G3, HLA-G4, HLA-G5, HLA-G6, or HLA-G7), B2M, PD-L1, PD-L2, CD47, Spi9, and galectin-9. In some cases, a genetically modified non-human animal can comprise reduced expression GGTA1, CMAH, and B4GALNT2, and exogenous polynucleotides encoding HLA-G (e.g., HLA-G1, HLA-G2, HLA-G3, HLA-G4, HLA-G5, HLA-G6, or HLA-G7), CD47 (e.g., human CD47), PD-L1 (e.g., human PD-L1), and PD-L2 (e.g., human PD-L2). In some cases, a genetically modified non-human animal can comprise reduced expression GGTA1, CMAH, and B4GALNT2, and exogenous polynucleotides encoding HLA-E, CD47 (e.g., human CD47), PD-L1 (e.g., human PD-L1), and PD-L2 (e.g., human PD-L2). In some cases, a genetically modified non-human animal can comprise reduced expression NLRC5, C3, CXC10, GGTA1, CMAH, and B4GALNT2, and exogenous polynucleotides encoding HLA-G (e.g., HLA-G1, HLA-G2, HLA-G3, HLA-G4, HLA-G5, HLA-G6, or HLA-G7), CD47 (e.g, human CD47), PD-L1 (e.g., human PD-L1), and PD-L2 (e.g., human PD-L2). In some cases, a genetically modified non-human animal can comprise reduced expression TAPI, C3, CXC10GGTA1, CMAH, and B4GALNT2, and exogenous polynucleotides encoding HLA-G (e.g., HLA-G 1, HLA-G2, HLA-G3, HLA-G4, HLA-G5, HLA-G6, or HLA-G7), CD47 (e.g., human CD47), PD-L1 (e.g., human PD-L1), and PD-L2 (e.g., human PD-L2). In some cases, a genetically modified non-human animal can comprise reduced expression NLRC5, C3, CXC10, GGTA1, CMAH, and B4GALNT2, and exogenous polynucleotides encoding HLA-E, CD47 (e.g., human CD47), PD-L1 (e.g., human PD-L1), and PD-L2 (e.g., human PD-L2). In some cases, a genetically modified non-human animal can comprise reduced expression TAPI, C3, CXC10, GGTA1, CMAH, and B4GALNT2, and exogenous polynucleotides encoding HLA-E. In some cases, a genetically modified non-human animal can comprise reduced expression of GGTA 1 and a transgene comprising one or more polynucleotide inserts encoding HLA-E. In some cases, a genetically modified non-human animal can comprise reduced expression of GGTA1 and a transgene comprising one or more polynucleotide inserts encoding HLA-G (e.g., HLA-G 1, HLA-G2, HLA-G3, HLA-G4, HLA-G5, HLA-G6, or HLA-G7). In some cases, a genetically modified non-human animal can comprise a transgene comprising one or more polynucleotide inserts encoding HLA-G (e.g., HLA-G 1, HLA-G2, HLA-G3, HLA-G4, HLA-G5, HLA-G6, or HLA-G7) inserted adjacent to a Rosa26 promoter, e.g., a porcine Rosa26 promoter. In some cases, a genetically modified non-human animal can comprise reduced expression of NLRC5, C3, GGTA1, CMAH, and B4GALNT2, and transgenes comprising polynucleotides encoding proteins or functional fragments thereof, where the proteins comprise HLA-G1, Spi9, PD-L1, PD-L2, CD47, and galectin-9. In some cases, a genetically modified non-human animal can comprise reduced expression of TAPI, C3, GGTA1, CMAH, and B4GALNT2, and transgenes comprising polynucleotides encoding proteins or functional fragments thereof, where the proteins comprise HLA-G 1, Spi9, PD-L1, PD-L2, CD47, and galectin-9. In some cases, a genetically modified non-human animal can comprise reduced expression of NLRC5, TAPI, C3, GGTA1, CMAH, and B4GALNT2, and transgenes comprising polynucleotides encoding proteins or functional fragments thereof, where the proteins comprise HLA-G 1, Spi9, PD-L1, PD-L2, CD47, and galectin-9. In some cases, a genetically modified non-human animal can comprise reduced protein expression ofNLRC5, C3, GGTA1, and CXCL10, and transgenes comprising polynucleotides encoding proteins or functional fragments thereof, where the protein comprise HLA-G 1 or HLA-E. In some cases, a genetically modified non-human animal can comprise reduced protein expression of TAPI, C3, GGTA1, and CXCL10, and transgenes comprising polynucleotides encoding proteins or functional fragments thereof, where the protein comprise HLA-G1 or HLA-E. In some cases, a genetically modified non-human animal can comprise reduced protein expression of NLRC5, TAPI, C3, GGTA1, and CXCL10, and transgenes comprising polynucleotides encoding proteins or functional fragments thereof, where the protein comprise HLA-G1 or HLA-E. In some cases, CD47, PD-L1, and PD-L2 encoded by the transgenes herein can be human CD47, human PD-L1 and human PD-L2.

[00207] A genetically modified non-human animal and a genetically modified cell can comprise a transgene inserted in a locus in the genome of the animal. In some cases, the transgene is inserted in a safe harbor site, e,g. ROSA26. In some cases, a transgene can be inserted adjacent to the promoter of or inside a targeted gene. In some cases, insertion of the transgene can reduce the expression of the targeted gene. The targeted gene can be a gene whose expression is reduced disclosed herein. For example, a transgene can be inserted adjacent to the promoter of or inside one or more of NLRC5, TAPI, CXCL10, MICA, MICB, C3, CIITA, GGTA1, CMAH, and B4GALNT2. In some cases, a transgene can be inserted adjacent to the promoter of or inside GGTA1. In some cases, a transgene (e.g., a CD47 transgene) can be inserted adjacent to a promoter that allows the transgene to selectively expression in certain types of cells. For example, a CD47 transgene can be inserted adjacent to promoter that allows the CD47 transgene to selectively express in blood cells and splenocytes. One of such promoters can be GGTA1 promoters.

[00208] A non-human animal can comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more transgenes. For example, in addition to a transgene encoding a MHC molecule, a non-human animal and a cell can comprise one or more transgene comprising ICP47, CD46, CD55, CD59, HLA-E, HLA-G (e.g., HLA-G1, HLA-G2, HLA-G3, HLA-G4, HLA-G5, HLA-G6, or HLA-G7), B2M, Spi9, PD- Ll, PD-L2, CD47, galectin-9, any functional fragments thereof, or any combination thereof.

[00209] A combination of transgenes and gene disruptions can be used. A non-human animal can comprise one or more reduced genes and one or more transgenes. For example, one or more genes whose expression is reduced can comprise any one of NLRC5, TAPI, GGTA1, B4GALNT2, CMAH, CXCL10, MICA, MICB, C3, CIITA, and/or any combination thereof, and one or more transgene can comprise ICP47, CD46, CD55, CD 59, any functional fragments thereof, and/or any combination thereof. For example, solely to illustrate various combinations, one or more genes whose expression is disrupted can comprise NLRC5 and one or more transgenes comprise a nucleic acid sequence encoding a MHC molecule (e.g., single chain chimeric MHC molecule), a a chain or a fragment thereof, or a b chain or a fragment thereof, or a peptide derived from a MHC molecule. One or more genes whose expression is disrupted can also comprise TAPI, and one or more transgenes comprise a nucleic acid sequence encoding a MHC molecule (e.g., single chain chimeric MHC molecule), a a chain or a fragment thereof, or a b chain or a fragment thereof, or a peptide derived from a MHC molecule. One or more genes whose expression is disrupted can also comprise NLRC5 and TAPI, and one or more transgenes comprise a nucleic acid sequence encoding a MHC molecule (e.g., single chain chimeric MHC molecule), a a chain or a fragment thereof, or a b chain or a fragment thereof, or a peptide derived from a MHC molecule.

One or more genes whose expression is disrupted can also comprise NLRC5, TAPI, and GGTA1, and one or more transgenes comprise a nucleic acid sequence encoding a MHC molecule (e.g., single chain chimeric MHC molecule), a a chain or a fragment thereof, or a b chain or a fragment thereof, or a peptide derived from a MHC molecule. One or more genes whose expression is disrupted can also comprise NLRC5, TAPI, B4GALNT2, and CMAH, and one or more transgenes comprise a nucleic acid sequence encoding a MHC molecule (e.g., single chain chimeric MHC molecule), a a chain or a fragment thereof, or a b chain or a fragment thereof, or a peptide derived from a MHC molecule. One or more genes whose expression is disrupted can also comprise NLRC5, TAPI, GGTA1, B4GALNT2, and CMAH, and one or more transgenes comprise a nucleic acid sequence encoding a MHC molecule (e.g., single chain chimeric MHC molecule), a a chain or a fragment thereof, or a b chain or a fragment thereof, or a peptide derived from a MHC molecule.

[00210] In some cases, a first exon of a gene is genetically modified. For example, one or more first exons of a gene that can be genetically modified can be a gene selected from a group consisting of NLRC5, TAPI, GGTA1, B4GALNT2, CMAH, CXCL10, MICA, MICB, C3, CIITA, cytidine monophospho-N-acetylneuraminic acid (CMP-N-NeuAc) hydrolase, or a PERV site and any combination thereof. In other cases, a second exon of a gene is targeted. Transgenes that can be used and are specifically contemplated can include those genes that exhibit a certain identity and/or homology to genes disclosed herein, for example, a nucleic acid sequence encoding a MHC molecule (e.g., single chain chimeric MHC molecule), a a chain of a MHC molecule or a fragment thereof, or a b chain of a MHC molecule or a fragment thereof, or a peptide derived from a MHC molecule, ICP47, CD46, CD55, CD59, HLA-E, HLA-G (e.g., HLA-G1, HLA-G2, HLA-G3, HLA-G4, HLA-G5, HLA-G6, or HLA-G7), B2M, Spi9, PD-L1, PD-L2, CD47, galectin-9, any functional fragments thereof, and/or any combination thereof. Therefore, it is contemplated that if gene that exhibits at least or at least about 60%, 70%, 80%, 90%, 95%, 98%, or 99% homology, e.g., at least or at least about 99% to 90%; 90% to 80%; 80% to 70%; 70% to 60% homology; (at the nucleic acid or protein level), it can be used as a transgene. It is also contemplated that a gene that exhibits at least or at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99%, identity e.g., at least or at least about 99% to 90%; 90% to 80%; 80% to 70%; 70% to 60% identity; (at the nucleic acid or protein level) can be used as a transgene.

[00211] A non-human animal can also comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more dominant negative transgenes. Expression of a dominant negative transgenes can suppress expression and/or function of a wild type counterpart of the dominant negative transgene. Thus, for example, a non-human animal comprising a dominant negative transgene X, can have similar phenotypes compared to a different non-human animal comprising an X gene whose expression is reduced. One or more dominant negative transgenes can be dominant negative NLRC5, dominant negative TAPI, dominant negative GGTA1, dominant negative CMAH, dominant negative B4GALNT2, dominant negative CXCL10, dominant negative MICA, dominant negative MICB, dominant negative CIITA, dominant negative C3, or any combination thereof.

[00212] Also provided is a non-human animal comprising one or more transgenes that encodes one or more nucleic acids that can suppress genetic expression, e.g., can knockdown a gene. RNAs that suppress genetic expression can comprise, but are not limited to, shRNA, siRNA, RNAi, and microRNA. For example, siRNA, RNAi, and/or microRNA can be given to a non-human animal to suppress genetic expression. Further, a non-human animal can comprise one or more transgene encoding shRNAs.

shRNA can be specific to a particular gene. For example, a shRNA can be specific to any gene described in the application, including but not limited to, NLRC5, TAPI, GGTA1, B4GALNT2, CMAH, CXCL10, MICA, MICB, B4GALNT2, CIITA, C3, and/or any combination thereof.

[00213] When transplanted to a subject, cells, tissues, or organs from the genetically modified non human animal can trigger lower immune responses (e.g., transplant rejection) in the subject compared to cells, tissues, or organs from a non-genetically modified counterpart. In some cases, the immune responses can include the activation, proliferation and cytotoxicity of T cells (e.g., CD8+ T cells and/or CD4+ T cells) and NK cells. Thus, phenotypes of genetically modified cells disclosed herein can be measured by co-culturing the cells with NK cells, T cells (e.g., CD8+ T cells or CD4+ T cells), and testing the activation, proliferation and cytotoxicity of the NK cells or T cells. In some cases, the T cells or NK cells activation, proliferation and cytotoxicity induced by the genetically modified cells can be lower than that induced by non-genetically modified cells. In some cases, phenotypes of genetically modified cells herein can be measured by Enzyme-Linked ImmunoSpot (ELISPOT) assays.

[00214] One or more transgenes can be from different species. For example, one or more transgenes can comprise a human gene, a mouse gene, a rat gene, a pig gene, a bovine gene, a dog gene, a cat gene, a monkey gene, a chimpanzee gene, or any combination thereof. For example, a transgene can be from a human, having a human genetic sequence. One or more transgenes can comprise human genes. In some cases, one or more transgenes are not adenoviral genes.

[00215] A transgene can be inserted into a genome of a non-human animal in a random or site-specific manner. For example, a transgene can be inserted to a random locus in a genome of a non-human animal. These transgenes can be fully functional if inserted anywhere in a genome. For instance, a transgene can encode its own promoter or can be inserted into a position where it is under the control of an endogenous promoter. Alternatively, a transgene can be inserted into a gene, such as an intron of a gene or an exon of a gene, a promoter, or a non-coding region. A transgene can be integrated into a first exon of a gene.

[00216] Sometimes, more than one copy of a transgene can be inserted into more than a random locus in a genome. For example, multiple copies can be inserted into a random locus in a genome. This can lead to increased overall expression than if a transgene was randomly inserted once. Alternatively, a copy of a transgene can be inserted into a gene, and another copy of a transgene can be inserted into a different gene. A transgene can be targeted so that it could be inserted to a specific locus in a genome of a non human animal. [00217] Expression of a transgene can be controlled by one or more promoters. A promoter can be a ubiquitous, tissue-specific promoter or an inducible promoter. Expression of a transgene that is inserted adjacent to a promoter can be regulated. For example, if a transgene is inserted near or next to a ubiquitous promoter, the transgene will be expressed in all cells of a non-human animal. Some ubiquitous promoters can be a CAGGS promoter, an hCMV promoter, a PGK promoter, an SV40 promoter, or a Rosa26 promoter.

[00218] A promoter can be endogenous or exogenous. For example, one or more transgenes can be inserted adjacent to an endogenous or exogenous Rosa26 promoter. Further, a promoter can be specific to a non-human animal. For example, one or more transgenes can be inserted adjacent to a porcine Rosa26 promoter.

[00219] Tissue specific promoter (which can be synonymous with cell-specific promoters) can be used to control the location of expression. For example, one or more transgenes can be inserted adjacent to a tissue-specific promoter. Tissue-specific promoters can be a FABP promoter, a Fck promoter, a CamKII promoter, a CD 19 promoter, a Keratin promoter, an Albumin promoter, an aP2 promoter, an insulin promoter, an MCK promoter, an MyHC promoter, a WAP promoter, or a Col2A promoter. For example, a promoter can be a pancreas-specific promoter, e.g., an insulin promoter.

[00220] Inducible promoters can be used as well. These inducible promoters can be turned on and off when desired, by adding or removing an inducing agent. It is contemplated that an inducible promoter can be a Fac, tac, trc, trp, araBAD, phoA, recA, proU, cst-1, tetA, cadA, nar, PF, cspA, T7, VHB, Mx, and/or Trex.

[00221] A non-human animal or cells as described herein can comprise a transgene encoding insulin. A transgene encoding insulin can be a human gene, a mouse gene, a rat gene, a pig gene, a cattle gene, a dog gene, a cat gene, a monkey gene, a chimpanzee gene, or any other mammalian gene. For example, a transgene encoding insulin can be a human gene. A transgene encoding insulin can also be a chimeric gene, for example, a partially human gene.

[00222] Expression of transgenes can be measured by detecting the level of transcripts of the transgenes. For example, expression of transgenes can be measured by Northern blotting, nuclease protection assays (e.g., RNase protection assays), reverse transcription PCR, quantitative PCR (e.g., real-time PCR such as real-time quantitative reverse transcription PCR), in situ hybridization (e.g., fluorescent in situ hybridization (FISH)), dot-blot analysis, differential display, Serial analysis of gene expression, subtractive hybridization, microarrays, nanostring, and/or sequencing (e.g., next-generation sequencing). In some cases, expression of transgenes can be measured by detecting proteins encoded by the genes. For example, expression of one or more genes can be measured by protein immunostaining, protein immunoprecipitation, electrophoresis (e.g., SDS-PAGE), Western blotting, bicinchoninic acid assay, spectrophotometry, mass spectrometry, enzyme assays (e.g., enzyme-linked immunosorbent assays), immunohistochemistry, flow cytometry, and/or immunocytochemistry. In some cases, expression of transgenes can be measured by microscopy. The microscopy can be optical, electron, or scanning probe microscopy. In some cases, optical microscopy comprises use of bright field, oblique illumination, cross- polarized light, dispersion staining, dark field, phase contrast, differential interference contrast, interference reflection microscopy, fluorescence (e.g., when particles, e.g., cells, are immunostained), confocal, single plane illumination microscopy, light sheet fluorescence microscopy, deconvolution, or serial time-encoded amplified microscopy.

[00223] Insertion of transgenes can be validated by genotyping. Methods for genotyping can include sequencing, restriction fragment length polymorphism identification (RFLPI), random amplified polymorphic detection (RAPD), amplified fragment length polymorphism detection (AFLPD), PCR (e.g., long range PCR, or stepwise PCR), allele specific oligonucleotide (ASO) probes, and hybridization to DNA microarrays or beads. In some cases, genotyping can be performed by sequencing. In some cases, sequencing can be high fidelity sequencing. Methods of sequencing can include Maxam -Gilbert sequencing, chain-termination methods (e.g., Sanger sequencing), shotgun sequencing, and bridge PCR.

In some cases, genotyping can be performed by next-generation sequencing. Methods of next-generation sequencing can include massively parallel signature sequencing, colony sequencing, pyrosequencing (e.g., pyrosequencing developed by 454 Life Sciences), single -molecule rea-time sequencing (e.g., by Pacific Biosciences), Ion semiconductor sequencing (e.g., by Ion Torrent semiconductor sequencing), sequencing by synthesis (e.g., by Solexa sequencing by Illumina), sequencing by ligation (e.g., SOLiD sequencing by Applied Biosystems), DNA nanoball sequencing, and heliscope single molecule sequencing. In some cases, genotyping of a non-human animal herein can comprise full genome sequencing analysis.

[00224] In some cases, insertion of a transgene in an animal can be validated by sequencing (e.g., next- generation sequencing) a part of the transgene or the entire transgene. For example, insertion of a transgene adjacent to a Rosa26 promoter in a pig can be validated by next generation sequencing of Rosa exons 1 to 4

Populations of Non-Human Animals

[00225] Provided herein is a single non-human animal and also a population of non-human animals. A population of non-human animals can be genetically identical. A population of non-human animals can also be phenotypical identical. A population of non-human animals can be both phenotypical and genetically identical.

[00226] Further provided herein is a population of non-human animals, which can be genetically modified. For example, a population can comprise at least or at least about 2, 5, 10, 50, 100, or 200, non human animals as disclosed herein. The non-human animals of a population can have identical phenotypes. For example, the non-human animals of a population can be clones. A population of non human animal can have identical physical characteristics. The non-human animals of a population having identical phenotypes can comprise a same transgene(s). The non -human animals of a population having identical phenotypes can also comprise a same gene(s) whose expression is reduced. The non-human animals of a population having identical phenotypes can also comprise a same gene(s) whose expression is reduced and comprise a same transgene(s). A population of non-human animals can comprise at least or at least about 2, 5, 10, 50, 100, or 200, non-human animals having identical phenotypes. For example, the phenotypes of any particular litter can have the identical phenotype (e.g., in one example, anywhere from 1 to about 20 non-human animals). The non-human animals of a population can be pigs having identical phenotypes.

[00227] The non-human animals of a population can have identical genotypes. For example, all nucleic acid sequences in the chromosomes of non-human animals in a population can be identical. The non human animals of a population having identical genotypes can comprise a same transgene(s). The non human animals of a population having identical genotypes can also comprise a same gene(s) whose expression is reduced. The non-human animals of a population having identical genotypes can also comprise a same gene(s) whose expression is reduced and comprise a same transgene(s). A population of non-human animals can comprise at least or at least about 2, 5, 50, 100, or 200 non-human animals having identical genotypes. The non-human animals of a population can be pigs having identical genotypes.

[00228] Cells from two or more non-human animals with identical genotypes and/or phenotypes can be used in a tolerizing vaccine or a tolerizing regimen. In some cases, a tolerizing vaccine or tolerizing regimen disclosed herein can comprise a plurality of the cells (e.g., genetically modified cells) from two or more non-human animals (e.g., pigs) with identical genotypes and/or phenotypes. A method for immunotolerizing a recipient to a graft can comprise administering to the recipient a tolerizing vaccine or tolerizing regimen comprising a plurality of cells (e.g., genetically modified cells) from two or more non human animals with identical genotypes or phenotypes.

[00229] Cells from two or more non-human animals with identical genotypes and/or phenotypes can be used in transplantation. In some cases, a graft (e.g., xenograft or allograft) can comprise a plurality of cells from two or more non-human animals with identical genotypes and/or phenotypes. In embodiments of the methods described herein, e.g., a method for treating a disease in a subject in need thereof, can comprise transplanting a plurality of cells (e.g., genetically modified cells) from two or more non-human animals with identical genotypes and/or phenotypes.

[00230] Populations of non-human animals can be generated using any method known in the art. In some cases, populations of non-human animals can be generated by breeding. For example, inbreeding can be used to generate a phenotypically or genetically identical non-human animal or population of non human animals. Inbreeding, for example, sibling to sibling or parent to child, or grandchild to grandparent, or great grandchild to great grandparent, can be used. Successive rounds of inbreeding can eventually produce a phenotypically or genetically identical non-human animal. For example, at least or at least about 2, 3, 4, 5, 10, 20, 30, 40, or 50 generations of inbreeding can produce a phenotypically and/or a genetically identical non-human animal. It is thought that after 10-20 generations of inbreeding, the genetic make-up of a non-human animal is at least 99% pure. Continuous inbreeding can lead to a non-human animal that is essentially isogenic, or close to isogenic as a non-human animal can be without being an identical twin.

[00231] Breeding can be performed using non-human animals that have the same genotype. For example, the non-human animals have the same gene(s) whose expression is reduced and/or carry the same transgene(s). Breeding can also be performed using non-human animals having different genotypes. Breeding can be performed using a genetically modified non-human animal and non-genetically modified non-human animal, for example, a genetically modified female pig and a wild-type male pig, or a genetically modified male pig and a wild-type female pig. All these combinations of breeding can be used to produce a non-human animal of desire.

[00232] Populations of genetically modified non-human animals can also be generated by cloning. For example, the populations of genetically modified non-human animal cells can be asexually producing similar populations of genetically or phenotypically identical individual non-human animals. Cloning can be performed by various methods, such as twinning (e.g., splitting off one or more cells from an embryo and grow them into new embryos), somatic cell nuclear transfer, or artificial insemination. More details of the methods are provided throughout the disclosure.

GENETICALLY MODIFIED CELLS

[00233] Disclosed herein are one or more genetically modified cells that can be used to treat or prevent disease. These genetically modified cells can be from genetically modified non-human animals. For example, genetically modified non-human animals as disclosed above can be processed so that one or more cells are isolated to produce isolated genetically modified cells. These isolated cells can also in some cases be further genetically modified cells. However, a cell can be modified ex vivo, e.g., outside an animal using modified or non-modified human or non-human animal cells. For example, cells (including human and non-human animal cells) can be modified in culture. It is also contemplated that a genetically modified cell can be used to generate a genetically modified non-human animal described herein. In some cases, the genetically modified cell can be isolated from a genetically modified animal.

In some cases, the genetically modified cell can be derived from a cell from a non-genetically modified animal. Isolation of cells can be performed by methods known in the art, including methods of primary cell isolation and culturing. It is specifically contemplated that a genetically modified cell is not extracted from a human.

[00234] Therefore, anything that can apply to the genetically modified non-human animals including the various methods of making as described throughout can also apply herein. For example, all the genes that are disrupted and the transgenes that are overexpressed are applicable in making genetically modified cells used herein. Further, any methods for testing the genotype and expression of genes in the genetically modified non-human animals described throughout can be used to test the genetic

modification of the cells.

[00235] A genetically modified cell can be from a member of the Laurasiatheria superorder or a non human primate. Such genetically modified cell can be isolated from a member of the Laurasiatheria superorder or a non-human primate. Alternatively, such genetically modified cell can be originated from a member of the Laurasiatheria superorder or a non-human primate. For example, the genetically modified cell can be made from a cell isolated from a member of the Laurasiatheria superorder or a non human primate, e.g., using cell culturing or genetic modification methods.

[00236] Genetically modified cells, e.g., cells from a genetically modified animal or cells made ex vivo, can be analyzed and sorted. In some cases, genetically modified cells can be analyzed and sorted by flow cytometry, e.g., fluorescence-activated cell sorting. For example, genetically modified cells expressing a transgene can be detected and purified from other cells using flow cytometry based on a label (e.g., a fluorescent label) recognizing the polypeptide encoded by the transgene.

[00237] In some cases, genetically modified cells can reduce, inhibit, or eliminate an immune response. For example, a genetic modification can decrease cellular effector function, decrease proliferation, decrease, persistence, and/or reduce expression of cytolytic effector molecules such as Granzyme B and CD107alpha in an immune cell. An immune cell can be a monocyte and/or macrophage. In some cases, T cell-derived cytokines, such as IFN-g, can activate macrophages via secretion of IFN -gamma. In some cases, T cell activation is inhibited and may cause a macrophage to also be inhibited.

[00238] Stem cells, including, non-human animal and human stem cells can be used. Stem cells do not have the capability to generating a viable human being. For example, stem cells can be irreversibly differentiated so that they are unable to generate a viable human being. Stem cells can be pluripotent, with the caveat that the stem cells cannot generate a viable human. As discussed above, the genetically modified cells comprise a transgene comprising a nucleic acid sequence encoding a MHC molecule (e.g., single chain chimeric MHC molecule), a a chain of a MHC molecule or a fragment thereof, or a b chain of a MHC molecule or a fragment thereof, or a peptide derived from a MHC molecule. In some embodiments, the transgene can further comprise a polynucleotide encoding a peptide derived from a MHC molecule capable of binding the peptide binding groove for presentation to a T cell. In some embodiments, the genetically modified cells, can further comprise one or more transgenes encoding ICP47, CD46, CD55, CD59, HLA-E, HLA-G (e.g, HLA-G1, HLA-G2, HLA-G3, HLA-G4, HLA-G5, HLA-G6, or HLA-G7), B2M, any functional fragments thereof, and/or any combination thereof.

[00239] As discussed above in the section regarding the genetically modified non-human animals, in some embodiments, the genetically modified cells can further comprise one or more genes whose expression is reduced. The same genes as disclosed above for the genetically modified non-human animals can be disrupted. For example, a genetically modified cell comprising one or more genes whose expression is disrupted, e.g., reduced, where the one or more genes comprise NLRC5, TAPI, GGTA1, B4GALNT2, CMAH, CXCL10, MICA, MICB, C3, CIITA and/or any combination thereof. Further, the genetically modified cell can comprise one or more transgenes comprising one or more polynucleotide inserts. The genetically modified cell can comprise an exogenous nucleic acid sequence encoding a b chain of a MHC molecule; and/or an exogenous nucleic acid sequence encoding an a chain of the MHC molecule. In some embodiments, the b chain and the a chain form a functional MHC complex comprising a peptide binding groove. The genetically modified cell can further comprise an exogenous nucleic acid sequence encoding for a peptide derived from a MHC molecule capable of binding the peptide binding groove for presentation to a T cell. For example, a genetically modified cell can comprise one or more transgenes comprising one or more polynucleotide inserts of ICP47, CD46, CD55, CD 59, HLA-E, HLA- G (e.g., HLA-G1, HLA-G2, HLA-G3, HLA-G4, HLA-G5, HLA-G6, or HLA-G7), B2M, Spi9, PD-L1, PD-L2, CD47, galectin-9, any functional fragments thereof, or any combination thereof. A genetically modified cell can comprise one or more reduced genes and one or more transgenes. For example, one or more genes whose expression is reduced can comprise any one of NLRC5, TAPI, GGTA1, B4GALNT2, CMAH, CXCL10, MICA, MICB, CIITA, cytidine monophospho-N-acetylneuraminic acid (CMP-N- NeuAc) hydrolase, and/or any combination thereof, and one or more transgene can comprise ICP47, CD46, CD55, CD 59, HLA-E, HLA-G (e.g, HLA-G1, HLA-G2, HLA-G3, HLA-G4, HLA-G5, HLA-G6, or HLA-G7), B2M, Spi9, PD-L1, PD-L2, CD47, galectin-9, any functional fragments thereof, and/or any combination thereof. In some cases, a genetically modified cell can comprise reduced expression of NLRC5, C3, GGTA1, CMAH, and B4GALNT2, and transgenes comprising polynucleotides encoding proteins or functional fragments thereof, where the proteins comprise HLA-G 1, Spi9, PD-L1, PD-L2, CD47, and galectin-9. In some cases, a genetically modified cell can comprise reduced expression of TAPI, C3, GGTA1, CMAH, and B4GALNT2, and transgenes comprising a nucleic acid sequence encoding a MHC molecule (e.g., single chain chimeric MHC molecule), a a chain of a MHC molecule or a fragment thereof, or a b chain of a MHC molecule or a fragment thereof, or a peptide derived from a MHC molecule. In some embodiments, the transgene can further comprise a polynucleotide encoding a peptide derived from a MHC molecule capable of binding the peptide binding groove for presentation to a T cell. In some cases, a genetically modified cell can comprise reduced expression of NLRC5, TAPI,

C3, GGTA1, CMAH, and B4GALNT2, and transgenes comprising a nucleic acid sequence encoding a MHC molecule (e.g., single chain chimeric MHC molecule), a a chain of a MHC molecule or a fragment thereof, or a b chain of a MHC molecule or a fragment thereof, or a peptide derived from a MHC molecule. In some embodiments, the transgene can further comprise a polynucleotide encoding a peptide derived from a MHC molecule capable of binding the peptide binding groove for presentation to a T cell.

[00240] As discussed above in the section regarding the genetically modified non-human animals, the genetically modified cell can comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more disrupted genes. A genetically modified cell can also comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,

13, 14, 15, 16, 17, 18, 19, 20, or more transgenes.

[00241] As discussed in detail above, a genetically modified cell, e.g., porcine cell, can also comprise dominant negative transgenes and/or transgenes expressing one or more knockdown genes. Also as discussed above, expression of a transgene can be controlled by one or more promoters.

[00242] A genetically modified cell can be one or more cells from tissues or organs, the tissues or organs including brain, lung, liver, heart, spleen, pancreas, small intestine, large intestine, skeletal muscle, smooth muscle, skin, bones, adipose tissues, hairs, thyroid, trachea, gall bladder, kidney, ureter, bladder, aorta, vein, esophagus, diaphragm, stomach, rectum, adrenal glands, bronchi, ears, eyes, retina, genitals, hypothalamus, larynx, nose, tongue, spinal cord, or ureters, uterus, ovary and testis. For example, a genetically modified cell, e.g., porcine cell, can be from brain, heart, liver, skin, intestine, lung, kidney, eye, small bowel, or pancreas. In some cases, a genetically modified cell can be from a pancreas. More specifically, pancreas cells can be islet cells. Further, one or more cells can be pancreatic a cells, pancreatic b cells, pancreatic d cells, pancreatic F cells (e.g., PP cells), or pancreatic e cells. For example, a genetically modified cell can be pancreatic b cells. Tissues or organs disclosed herein can comprise one or more genetically modified cells. The tissues or organs can be from one or more genetically modified animals described in the application, e.g., pancreatic tissues such as pancreatic islets from one or more genetically modified pigs.

[00243] A genetically modified cell, e.g., porcine cell, can comprise one or more types of cells, where the one or more types of cells include Trichocytes, keratinocytes, gonadotropes, corticotropes, thyrotropes, somatotropes, lactotrophs, chromaffin cells, parafollicular cells, glomus cells melanocytes, nevus cells, Merkel cells, odontoblasts, cementoblasts comeal keratocytes,, retina Muller cells, retinal pigment epithelium cells, neurons, glias (e.g., oligodendrocyte astrocytes), ependymocytes, pinealocytes, pneumocytes (e.g., type I pneumocytes, and type II pneumocytes), clara cells, goblet cells, G cells, D cells, ECL cells, gastric chief cells, parietal cells, foveolar cells, K cells, D cells, I cells, goblet cells, paneth cells, enterocytes, microfold cells, hepatocytes, hepatic stellate cells (e.g., Kupffer cells from mesoderm), cholecystocytes, centroacinar cells, pancreatic stellate cells, pancreatic a cells, pancreatic b cells, pancreatic d cells, pancreatic F cells (e.g., PP cells), pancreatic e cells, thyroid (e.g., follicular cells), parathyroid (e.g., parathyroid chief cells), oxyphil cells, urothelial cells, osteoblasts, osteocytes, chondroblasts, chondrocytes, fibroblasts, fibrocytes, myoblasts, myocytes, myosatellite cells, tendon cells, cardiac muscle cells, lipoblasts, adipocytes, interstitial cells of cajal, angioblasts, endothelial cells, mesangial cells (e.g., intraglomerular mesangial cells and extraglomerular mesangial cells),

juxtaglomerular cells, macula densa cells, stromal cells, interstitial cells, telocytes simple epithelial cells, podocytes, kidney proximal tubule brush border cells, sertoli cells, leydig cells, granulosa cells, peg cells, germ cells, spermatozoon ovums, lymphocytes, myeloid cells, endothelial progenitor cells, endothelial stem cells, angioblasts, mesoangioblasts, and pericyte mural cells. A genetically modified cell can potentially be any cells used in cell therapy. For example, cell therapy can be pancreatic b cells supplement or replacement to a disease such as diabetes.

[00244] A genetically modified cell, e.g., porcine cell, can be from (e.g., extracted from) a non-human animal. One or more cells can be from a mature adult non-human animal. However, one or more cells can be from a fetal or neonatal tissue.

[00245] Depending on the disease, one or more cells can be from a transgenic non-human animal that has grown to a sufficient size to be useful as an adult donor, e.g., an islet cell donor. In some cases, non human animals can be past weaning age. For example, non-human animals can be at least or at least about six months old. In some cases, non-human animals can be at least or at least about 18 months old. A non-human animal in some cases, survive to reach breeding age. For example, islets for xenotransplantation can be from neonatal (e.g., age 3-7 days) or pre-weaning (e.g., age 14 to 21 days) donor pigs. One or more genetically modified cells, e.g., porcine cells, can be cultured cells. For example, cultured cells can be from wild-type cells or from genetically modified cells (as described herein). Furthermore, cultured cells can be primary cells. Primary cells can be extracted and frozen, e.g., in liquid nitrogen or at -20°C to -80°C. Cultured cells can also be immortalized by known methods, and can be frozen and stored, e.g., in liquid nitrogen or at -20°C to -80°C.

[00246] Genetically modified cells, e.g., porcine cells, as described herein can have a lower risk of rejection, when compared to when a wild-type non-genetically modified cell is transplanted.

[00247] Disclosed herein is a nucleic acid construct comprising a nucleic acid sequence encoding a b chain of a MHC molecule; and/or a nucleic acid sequence encoding an a chain of the MHC molecule. In some embodiments, the b chain and the a chain form a functional MHC complex comprising a peptide binding groove. In some embodiments, the b chain, the a chain or both lack a functional transmembrane domain. In some embodiments, the nucleic acid construct can further comprise a nucleic acid sequence encoding for a peptide derived from a MHC molecule capable of binding the peptide binding groove for presentation to a T cell. Disclosed herein is a vector comprising a polynucleotide sequence of ICP47, CD46, CD55, CD59, HLA-E, HLA-G (e.g., HLA-G1, HLA-G2, HLA-G3, HLA-G4, HLA-G5, HLA-G6, or HLA-G7), B2M, Spi9, PD-L1, PD-L2, CD47, galectin-9, any functional fragments thereof, or any combination thereof. These vectors can be inserted into a genome of a cell (by transfection,

transformation, viral delivery, or any other known method). These vectors can encode ICP47, CD46, CD55, CD59, HLA-E, HLA-G (e.g., HLA-G 1, HLA-G2, HLA-G3, HLA-G4, HLA-G5, HLA-G6, or HLA-G7), B2M Spi9, PD-L1, PD-L2, CD47, and/or galectin-9 proteins or functional fragments thereof.

[00248] Vectors contemplated include, but not limited to, plasmid vectors, artificial/mini-chromosomes, transposons, and viral vectors.

[00249] Guide RNA sequences can be used in targeting one or more genes in a genome of a non-human animal. For example, guide RNA sequence can target a single gene in a genome of non-human animal.

In some cases, guide RNA sequences can target one or more target sites of each of one or more genes in a genome of a non-human animal.

[00250] Genetically modified cells can also be leukocytes, lymphocytes, B lymphocytes, or any other cell such as islet cells, islet beta cells, or hepatocytes. These cells can be fixed or made apopototic by any method disclosed herein, e.g., by ECDI fixation.

[00251] A genetically modified cells can be derived (e.g., retrieved) from a non-human fetal animal, perinatal non-human animal, neonatal non-human animal, preweaning non-human animal, young adult non-human animal, adult non-human animal, or any combination thereof. In some cases, a genetically modified non-human animal cell can be derived from an embryonic tissue, e.g., an embryonic pancreatic tissue. For example, a genetically modified cell can be derived (e.g., retrieved) from an embryonic pig pancreatic tissue from embryonic day 42 (E42). [00252] The term“fetal animal” and its grammatical equivalents can refer to any unborn offspring of an animal. The term“perinatal animal” and its grammatical equivalents can refer to an animal immediately before or after birth. For example, a perinatal period can start from 20th to 28th week of gestation and ends 1 to 4 weeks after birth. The term“neonatal animal” and its grammatical equivalents can refer to any new bom animals. For example, a neonatal animal can be an animal bom within a month. The term “preweaning non-human animal” and its grammatical equivalents can refer to any animal before being withdrawn from the mother’s milk.

[00253] Genetically modified non-human animal cells and cells, tissues or organs derived from a genetically modified non-human animal can be formulated into a pharmaceutical composition. For example, the genetically modified non-human animal cells can be combined with a pharmaceutically acceptable excipient. An excipient that can be used is saline. The pharmaceutical composition can be used to treat patients in need of transplantation.

[00254] A genetically modified cell can comprise reduced expression of any genes, and/or any transgenes disclosed herein. Genetic modification of the cells can be done by using any of the same method as described herein for making the genetically modified animals. In some cases, a method of making a genetically modified cell originated from a non-human animal can comprise reducing expression of one or more genes and/or inserting one or more transgenes. The reduction of gene expression and/or transgene insertion can be performed using any methods described in the application, e.g., gene editing.

Genetically modified cells derived from stem cells

[00255] Genetically modified cells can be a stem cell. The genetically modified stem cell cells, and the cells, tissues and organs derived upon their differentiation comprises a transgene comprising a nucleic acid sequence encoding a MHC molecule (e.g., single chain chimeric MHC molecule), a a chain of a MHC molecule or a fragment thereof, or a b chain of a MHC molecule or a fragment thereof, or a peptide derived from a MHC molecule. In some embodiments, the transgene can further comprise a

polynucleotide encoding a peptide derived from a MHC molecule capable of binding the peptide binding groove for presentation to a T cell. In some embodiments, the genetically modified stem cells and the cells, tissues and organs derived upon their differentiation can further comprise one or more transgenes encoding ICP47, CD46, CD55, CD59, HLA-E, HLA-G (e.g, HLA-G1, HLA-G2, HLA-G3, HLA-G4, HLA-G5, HLA-G6, or HLA-G7), B2M, any functional fragments thereof, and/or any combination thereof. These genetically modified stem cells can be used to make a potentially unlimited supply of cells that can be subsequently processed into fixed or apoptotic cells by the methods disclosed herein. As discussed above, stem cells are not capable of generating a viable human being.

[00256] The production of hundreds of millions of insulin-producing, glucose-responsive pancreatic beta cells from human phiripotent stem cells provides an unprecedented cell source for cell transplantation therapy in diabetes. Other human stem cell- (embryonic, pluripotent, placental, induced pluripotent, etc.) derived cell sources for cell transplantation therapy in diabetes and in other diseases are being developed. [00257] These stem cell-derived cellular grafts are subject to rejection. The rejection can be mediated by CD8+ T cells. In Type 1 diabetic recipients, human stem cell-derived functional beta cells are subject to rejection and autoimmune recurrence. Both are thought to be mediated by CD8+ T cells.

[00258] To interfere with activation and effector function of these allo-reactive and auto-reactive CD8+

T cells, established molecular methods of gene modification, including CRISPR/Cas9 gene targeting, can be used to mutate the NLRC5, TAPI, and/or B2M genes in human stem cells for the purpose of preventing cell surface expression of functional MHC class I in the stem cell-derived, partially or fully differentiated cellular graft. Thus, transplanting human stem cell-derived cellular grafts lacking functional expression of MHC class I can minimize the requirements of immunosuppression otherwise required to prevent rejection and autoimmune recurrence.

[00259] However, lack of MHC class I expression on transplanted human cells will likely cause the passive activation of natural killer (NK) cells (Ohlen et al, 1989). NK cell cytotoxicity can be overcome by the expression of the human MHC class 1 gene, HLA-E, which stimulates the inhibitory receptor CD94/NKG2A on NK cells to prevent cell killing (Weiss et al, 2009; Lilienfeld et al. , 2007; Sasaki et al. , 1999). Successful expression of the HLA-E gene was dependent on co-expression of the human B2M (beta 2 microglobulin) gene and a cognate peptide (Weiss et al. , 2009; Lilienfeld et al. , 2007; Sasaki et al, 1999; Pascasova et al, 1999). A nuclease mediated break in the stem cell DNA allows for the insertion of one or multiple genes via homology directed repair. The HLA-E and hB2M genes in series can be integrated in the region of the nuclease mediated DNA break thus preventing expression of the target gene (for example, NLRC5) while inserting the transgenes.

[00260] To further minimize, if not eliminate, the need for maintenance immunosuppression in recipients of stem cell derived cellular grafts lacking functional expression of MHC class I, recipients of these grafts can also be treated with tolerizing apoptotic donor cells disclosed herein.

[00261] The methods for the production of insulin-producing pancreatic beta cells (Pagliuca et al , 2014) can potentially be applied to non-human (e.g., pig) primary isolated pluripotent, embryonic stem cells or stem-like cells (Goncalves et al, 2014; Hall et al. V. 2008). However, the recipient of these insulin- producing pancreatic beta cells likely has an active immune response that threatens the success of the graft. To overcome antibody-mediated and CD8+ T cell immune attack, the donor animal can be genetically modified before isolation of primary non-human pluripotent, embryonic stem cells or stem like cells to prevent the expression of the GGTA1, CMAH, B4GalNT2, or MHC class I-related genes as disclosed throughout the application. The pluripotent, embryonic stem cells or stem-like cells isolated from genetically modified animals could then be differentiated into millions of insulin-producing pancreatic beta cells.

[00262] Xenogeneic stem cell-derived cell transplants can be desirable in some cases. Lor example, the use of human embryonic stem cells may be ethically objectionable to the recipient. Therefore, human recipients may feel more comfortable receiving a cellular graft derived from non-human sources of embryonic stem cells. [00263] Non-human stem cells may include pig stem cells. These stem cells can be derived from wild- type pigs or from genetically engineered pigs. If derived from wild-type pigs, genetic engineering using established molecular methods of gene modification, including CRISP/Cas9 gene targeting, may best be performed at the stem cell stage. Genetic engineering may be targeted to disrupt expression of NLRC5, TAPI, and/or B2M genes to prevent functional expression of MHC class I. Disrupting genes such as NLRC5, TAPI, and B2M in the grafts can cause lack of functional expression of MHC class I on graft cells including on islet beta cells, thereby interfering with the post-transplant activation of autoreactive CD8+ T cells. Thus, this can protect the transplant, e.g., transplanted islet beta cells, from the cytolytic effector functions of autoreactive CD8+ T cells.

[00264] However, as genetic engineering of stem cells may alter their potential for differentiation, an approach can be to generate stem cell lines from genetically engineered pigs, including those pigs, in whom the expression of NLRC5, TAPI, and/or B2M genes has been disrupted.

[00265] Generation of stem cells from pigs genetically modified to prevent the expression also of the GGTA1, CMAH, B4GalNT2 genes or modified to express transgenes that encode for MHC molecule, and in some embodiments, further encode complement regulatory proteins CD46, CD55, or CD59, as disclosed throughout the application, could further improve the therapeutic use of the insulin-producing pancreatic beta cells or other cellular therapy products. Likewise, the same strategy as described herein can be used in other methods and compositions described throughout.

[00266] Like in recipients of human stem cell -derived cellular grafts lacking functional expression of MHC class I, the need for maintenance immunosuppression in recipients of pig stem cell-derived grafts can be further minimized by peritransplant treatments with tolerizing apoptotic donor cells.

TOLERING REGIMEN (TOLERIZING VACCINES)

[00267] Traditionally, vaccines are used to confer immunity to a host. For example, injecting an inactivated virus with adjuvant under the skin can lead to temporary or permanent immunity to the active and/or virulent version of the virus. This can be referred to as a positive vaccine. However, inactivated cells (e.g., cells from a donor or an animal genetically different from the donor) that are injected intravenously can result in tolerance of donor cells or cells with similar cellular markers. This can be referred to as a tolerizing vaccine (also referred to as a negative vaccine). The inactive cells can be injected without an adjuvant. Alternatively, the inactive cells can be injected with an adjuvant. These tolerizing vaccines can be advantageous in transplantation, for example, in xenotransplantation, by tolerizing a recipient and preventing rejection. Tolerization can be conferred to a recipient without the use of immunosuppressive therapies. However, in some cases, other immunosuppressive therapies in combination with tolerizing vaccines can decrease transplantation rejection.

[00268] A donor can provide xenografts for transplantation (e.g., islets), as well as cells (e.g., splenocytes) as a tolerizing vaccine. The tolerizing vaccine cells can be apoptotic cells (e.g., by ECDI fixation) and administered to the recipient before (e.g., the first vaccine, on day 7 before the

transplantation) and after the transplantation (e.g., the booster vaccine, on day 1 after the transplantation). The tolerizing vaccine can provide transient immunosuppression that extends the time of survival of the transplanted grafts (e.g., islets).

[00269] Tolerizing vaccines can comprise the genetically modified cell disclosed herein. This can minimize or eliminate cell-mediated immunity and cell-dependent antibody-mediated immunity to organ, tissue, cell, and cell line grafts (e.g., xenografts) from animals that are genotypically identical with the apoptotic cell vaccine donor animal, or from animals that have undergone additional genetic

modifications (e.g., suppression of NLRC5, TAPI, MICA, MICB, CXCL10, C3, CIITA genes or expression of transgenes comprising two or more polynucleotide inserts of a MHC molecule with or without tolerogenic peptide, ICP47, CD46, CD55, HLA-E, HLA-G (e.g., HLA-G1, HLA-G2, HLA-G3, HLA-G4, HLA-G5, HLA-G6, or HLA-G7), B2M, CD59, or any functional fragments thereof), but are genotypically similar to the donor animal from which the apoptotic cell vaccine is derived; ii) apoptotic stem cell (e.g., embryonic, pluripotent, placental, induced pluripotent, etc.)-derived donor cells (e.g., leukocytes, lymphocytes, T lymphocytes, B lymphocytes, red blood cells, graft cells, or any other donor cell) for minimizing or eliminating cell-mediated immunity and cell -dependent antibody-mediated immunity to organ, tissue, cell, and cell line grafts (e.g, xenografts) from animals that are genotypically identical with the apoptotic cell vaccine donor animal or from animals that have undergone additional genetic modifications (e.g., suppression of GGTA1, NLRC5, TAPI, MICA, MICB, CXCL10, C3, CIITA, cytidine monophospho-N-acetylneuraminic acid (CMP-N-NeuAc) hydrolase genes or expression of transgenes comprising a nucleic acid sequence encoding a MHC molecule (e.g., single chain chimeric MHC molecule), a a chain or a fragment thereof, or a b chain or a fragment thereof, or a peptide derived from a MHC molecule. In some embodiments, the b chain and the a chain form a functional MHC complex comprising a peptide binding groove. In some embodiments, the b chain, the a chain or both lack a functional transmembrane domain. In some embodiments, the transgene can further comprise a nucleic acid sequence encoding for a peptide derived from a MHC molecule capable of binding the peptide binding groove for presentation to a T cell. The cells further comprising one or more additional transgene inserts of ICP47, CD46, CD55, HLA-E, HLA-G (e.g, HLA-G 1, HLA-G2, HLA-G3, HLA-G4, HLA-G5, HLA-G6, or HLA-G7), B2M, CD59, or any functional fragments thereof), but are

genotypically similar to the donor animal from which the apoptotic stem cell-derived cell vaccine is derived; iii) apoptotic stem cell (e.g., embryonic, pluripotent, placental, induced pluripotent, etc.)-derived donor cells (leukocytes, lymphocytes, T lymphocytes, B lymphocytes, red blood cells, graft cells such as functional islet beta cells, or any other donor cell) for minimizing or eliminating cell-mediated immunity and cell-dependent antibody-mediated immunity to organ, tissue, cell, and cell grafts (e.g., allografts) that are genotypically identical with the human stem cell line or to grafts (e.g., allografts) derived from the same stem cell line that have undergone genetic modifications (e.g., suppression of GGTA1, NLRC5, TAPI, MICA, MICB, CXCL10, C3, CIITA, cytidine monophospho-N-acetylneuraminic acid (CMP-N- NeuAc) hydrolase genes) but are otherwise genotypically similar to the apoptotic human stem cell- derived donor cell vaccine; iv) apoptotic donor cells, where the cells are made apoptotic by UV irradiation, gamma-irradiation, or other methods not involving incubation in the presence of ECDI. In some cases, tolerizing vaccine cells can be adminstered, e.g., infused (in some cases repeatedly infused) to a subject in need thereof. Tolerizing vaccines can be produced by disrupting (e.g., reducing expression) one or more genes from a cell. For example, genetically modified cells as described throughout the application can be used to make a tolerizing vaccine. For example, the genetically modified cells comprising a transgene comprising a nucleic acid sequence encoding a MHC molecule (e.g., single chain chimeric MHC molecule), a a chain of a MHC molecule or a fragment thereof, or a b chain of a MHC molecule or a fragment thereof, or a peptide derived from a MHC molecule can be used to make a tolerizing regimen or tolerizing vaccine. In some embodiments, the transgene can further comprise a polynucleotide encoding a peptide derived from a MHC molecule capable of binding the peptide binding groove for presentation to a T cell. In some embodiments, the genetically modified cells of the tolerizing regimen can further comprise one or more transgenes encoding ICP47, CD46, CD55, CD59, HLA-E, HLA-G (e.g., HLA-G1, HLA-G2, HLA-G3, HLA-G4, HLA-G5, HLA-G6, or HLA-G7), B2M, any functional fragments thereof, and/or any combination thereof. For example, in some embodiments, cells used for tolerizing regimen can have one or more genes that can be disrupted (e.g., reduced expression) including glycoprotein galactosyltransferase alpha 1, 3 (GGTA1), putative cytidine monophosphate-N- acetylneuraminic acid hydroxylase-like protein (CMAH), B4GALNT2, and/or any combination thereof. For example, a cell can have disrupted GGTA1 only, or disrupted CMAH only, or disrupted B4GALNT2 only. A cell can also have disrupted GGTA1 and CMAH, disrupted GGTA1 and B4GALNT2, or disrupted CMAH and B4GALNT2. A cell can have disrupted GGTA1, CMAH, and B4GALNT2. In some cases, the disrupted gene does not include GGTA1. A cell can also express NFRC5 (endogenously or exogenously), while GGTA1 and/or CMAH are disrupted. A cell can also have disrupted C3. A cell can also have a disrupted PERV site.

[00270] In some cases, tolerization may comprise administration of a genetically modified graft. A graft can be a cell, tissue, organ, or a combination. In some cases, immunosuppression is combined with a vaccine or tolerizing graft. In some cases, expression of HLA-G1 on a graft and an MHC or HLA class I deficiency of a graft may have tolerogenic activity independent from administration of a vaccine.

[00271] When administered in a subject, a cell of a tolerizing vaccine can have a circulation half-life. A cell of a tolerizing vaccine can have a circulation half-life of at least or at least about 0.1, 0.5, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 18, 24, 36, 48, 60, or 72 hours. For example, the circulation half-life of the tolerizing vaccine can be from or from about 0.1 to 0.5; 0.5 to 1.0; 1.0 to 2.0; 1.0 to 3.0; 1.0 to 4.0; 1.0 to 5.0; 5 to 10; 10 to 15; 15 to 24; 24 to 36; 36 to 48; 48 to 60; or 60 to 72 hours. A cell in a tolerizing vaccine can be treated to enhance its circulation half-life. Such treatment can include coating the cell with a protein, e.g., CD47. A cell treated to enhance its circulation half-life can be a non-apoptotic cell. A cell treated to enhance its circulation half-life can be an apoptotic cell. Alternatively, a cell in a tolerizing vaccine can be genetically modified (e.g., insertion of a transgene such as CD47 in its genome) to enhance its circulation half-life. A cell genetically modified to enhance its circulation half-life can be a non-apoptotic cell. A cell genetically modified to enhance its circulation half-life can be an apoptotic cell.

[00272] A tolerizing vaccine can have both one or more disrupted genes (e.g., reduced expression) and one or more transgenes. Any genes and/or transgenes as described herein can be used.

[00273] A cell that comprises one or more disrupted genes (e.g., reduced expression) can be used as, or be a part of, a tolerizing vaccine. In other words, a cell that comprises one or more disrupted genes can be or can be made into a tolerizing vaccine.

[00274] A tolerizing vaccine can have the same genotype and/or phenotype as cells, organs, and/or tissues used in transplantation. Sometimes, the genotype and/or phenotype of a tolerizing vaccine and a transplant are different. A tolerizing vaccine used for a transplant recipient can comprise cells from the transplant graft donor. A tolerizing vaccine used for a transplant recipient can comprise cells that are genetically and/or phenotypically different from the transplant graft. In some cases, a tolerizing vaccine used for a transplant recipient can comprise cells from the transplant graft donor and cells that are genetically and/or phenotypically different from the transplant graft. The cells that are genetically and/or phenotypically different from the transplant graft can be from an animal of the same species of the transplant graft donor.

[00275] A source of cells for a tolerizing vaccine can be from a human or non -human animal.

[00276] Cells as disclosed throughout the application can be made into a tolerizing vaccine. For example, a tolerizing vaccine can be made of one or more transplanted cells disclosed herein.

Alternatively, a tolerizing vaccine can be made of one or more cells that are different from any of the transplanted cells. For example, the cells made into a tolerizing vaccine can be genotypically and/or phenotypically different from any of the transplanted cells. However in some cases, the tolerizing vaccine will express NLRC5 (endogenously or exogenously). A tolerizing vaccine can promote survival of cells, organs, and/or tissues in transplantation. A tolerizing vaccine can be derived from non-human animals that are genotypically identical or similar to donor cells, organs, and/or tissues. For example, a tolerizing vaccine can be cells derived from pigs (e.g., apoptotic pig cells) that are genotypically identical or similar to donor pig cells, organs, and/or tissues. Subsequently, donor cells, organs, and/or tissues can be used in allografts or xenografts.

[00277] A tolerizing vaccine can comprise non-human animal cells (e.g., non-human mammalian cells). For example, non-human animal cells can be from a pig, a cat, a cow, a deer, a dog, a ferret, a gaur, a goat, a horse, a mouse, a mouflon, a mule, a rabbit, a rat, a sheep, or a primate. Specifically, non-human animal cells can be porcine cells. A tolerizing vaccine can also comprise genetically modified non human animal cells. For example, genetically modified non-human animal cells can be dead cells (e.g., apoptotic cells). A tolerizing vaccine can also comprise any genetically modified cells disclosed herein. Treatment of cells to make a tolerizing vaccine

[00278] A tolerizing vaccine can comprise cells treated with a chemical. In some cases, the treatment can induce apoptosis of the cells. Without being bound by theory, the apoptotic cells can be picked up by host antigen presenting cells (e.g., in the spleen) and presented to host immune cells (e.g., T cells) in a non-immunogenic fashion that leads to induction of anergy in the immune cells (e.g., T cells).

[00279] Tolerizing vaccines can comprise apoptotic cells and non-apoptotic cells. An apoptotic cell in a tolerizing vaccine can be genetically identical to a non-apoptotic cell in the tolerizing vaccine.

Alternatively, an apoptotic cell in a tolerizing vaccine can be genetically different from a non-apoptotic cell in the tolerizing vaccine. Tolerizing vaccines can comprise fixed cells and non-fixed cells. A fixed cell in a tolerizing vaccine can be genetically identifical to a non-fixed cell in the tolerizing vaccine. Alternatively, a fixed cell in a tolerizing vaccine can be genetically different from a non-fixed cell in the tolerizing vaccine. In some cases, the fixed cell can be a l-ethyl-3-(3-dimethylaminopropyl)- carbodiimide (ECDI)-fixed cell.

[00280] Cells in a tolerizing vaccine can be fixed using a chemical, e.g., ECDI. The fixation can make the cells apoptotic. A tolerizing vaccine, cells, kits and methods disclosed herein can comprise ECDI and/or ECDI treatment. For example, a tolerizing vaccine can be cells, e.g., the genetically modified cell as disclosed herein, that are treated with l-ethyl-3-(3-dimethylaminopropyl)-carbodiimide (ECDI). In other words, the genetically modified cells as described throughout can be treated with ECDI to create a tolerizing vaccine. A tolerizing vaccine can then be used in transplantation to promote survival of cells, organs, and/or tissues that are transplanted. It is also contemplated that ECDI derivatives, functionalized ECDI, and/or substituted ECDI can also be used to treat the cells for a tolerizing vaccine. In some cases, cells for a tolerizing vaccine can be treated with any suitable carbodiimide derivatives, e.g., ECDI, N, N'- diisopropylcarbodiimide (DIC), N,N'-dicyclohexylcarbodiimide (DCC), and other carbodiimide derivatives understood by those in the art.

[00281] Cells for tolerizing vaccines can also be made apoptotic methods not involving incubation in the presence of ECDI, e.g., other chemicals or irradiation such as UV irradiation or gamma-irradiation.

[00282] ECDI can chemically cross-link free amine and carboxyl groups, and can effectively induce apoptosis in cells, organs, and/or tissues, e.g., from animal that gave rise to both a tolerizing vaccine and a donor non-human animal. In other words, the same genetically modified animal can give rise to a tolerizing vaccine and cells, tissues and/or organs that are used in transplantation. For example, the genetically modified cells as disclosed herein can be treated with ECDI. This ECDI fixation can lead to the creation of a tolerizing vaccine.

[00283] Genetically modified cells that can be used to make a tolerizing vaccine can be derived from: a spleen (including splenic B cells), liver, peripheral blood (including peripheral blood B cells), lymph nodes, thymus, bone marrow, or any combination thereof. For example, cells can be spleen cells, e.g., porcine spleen cells. In some cases, cells can be expanded ex-vivo. In some cases, cells can be derived from fetal, perinatal, neonatal, preweaning, and/or young adult, non-human animals. In some cases, cells can be derived from an embryo of a non-human animal.

[00284] Cells in a tolerizing vaccine can also be derived from one or more donor non-human animals. In some cases, cells can be derived from the same donor non-human animal. Cells can be derived from one or more recipient non-human animals. In some cases, cells can be derived from two or more non-human animals (e.g., pig).

[00285] A tolerizing vaccine can comprise from or from about 0.001 and about 5.0, e.g., from or from about 0.001 and 1.0, endotoxin unit per kg bodyweight of a prospective recipient. For example, a tolerizing vaccine can comprise from or from about 0.01 to 5.0; 0.01 to 4.5; 0.01 to 4.0, 0.01 to 3.5; 0.01 to 3.0; 0.01 to 2.5; 0.01 to 2.0; 0.01 to 1.5; 0.01 to 1.0; 0.01 to 0.9; 0.01 to 0.8; 0.01 to 0.7; 0.01 to 0.6; 0.01 to 0.5; 0.01 to 0.4; 0.01 to 0.3; 0.01 to 0.2; or 0.01 to 0.1 endotoxin unit per kg bodyweight of a prospective recipient.

[00286] A tolerizing vaccine can comprise from or from about 1 to 100 aggregates, per pi. For example, a tolerizing vaccine can comprise from or from about 1 to 5; 1 to 10, or 1 to 20 aggregate per ml. A tolerizing vaccine can comprise at least or at least about 1, 5, 10, 20, 50, or 100 aggregates.

[00287] A tolerizing vaccine can trigger a release from or from about 0.001 pg/ml to 10.0 pg/ml, e.g., from or from about 0.001 pg/ml to 1.0 pg/ml, IL-1 beta when about 50,000 frozen to thawed human peripheral blood mononuclear cells are incubated with about 160,000 cells of the tolerizing vaccine (e.g., pig cells). For example, atolerizing vaccine triggers a release of from or from about 0.001 to 10.0; 0.001 to 5.0; 0.001 to 1.0; 0.001 to 0.8; 0.001 to 0.2; or 0.001 to 0.1 pg/ml IL-1 beta when about 50,000 frozen to thawed human peripheral blood mononuclear cells are incubated with about 160,000 cell of the tolerizing vaccine (e.g., pig cells). A tolerizing vaccine can trigger a release of from or from about 0.001 to 2.0 pg/ml, e.g., from or from about 0.001 to 0.2 pg/ml, IL-6 when about 50,000 frozen to thawed human peripheral blood mononuclear cells are incubated with about 160,000 cells of the tolerizing vaccine (e.g., pig cells). For example, a tolerizing vaccine can trigger a release of from or from about 0.001 to 2.0; 0.001 to 1.0; 0.001 to 0.5; or 0.001 to 0.1 pg/ml IL-6 when about 50,000 frozen to thawed human peripheral blood mononuclear cells are incubated with about 160,000 cells of the tolerizing vaccine (e.g., pig cells).

[00288] A tolerizing vaccine can comprise more than or more than about 60%, e.g., more than or more than about 85%, Annexin V positive, apoptotic cells after a 4 hour or after about 4 hours post-release incubation at 37°C. For example, a tolerizing vaccine comprises more than 60%, 70%, 80%, 90%, or 99% Annexin V positive, apoptotic cells after about a 4 hour post-release incubation at 37°C.

[00289] A tolerizing vaccine can include from or from about 0.01% to 10%, e.g., from or from about 0.01% to 2%, necrotic cells. For example, a tolerizing vaccine includes from or from about 0.01% to 10%; 0.01% to 7.5%, 0.01% to 5%; 0.01% to 2.5%; or 0.01% to 1% necrotic cells.

[00290] Administering a tolerizing vaccine comprising ECDI-treated cells, organs, and/or tissues before, during, and/or after administration of donor cells can induce tolerance for cells, organs, and/or tissues in a recipient (e.g., a human or a non-human animal). ECDI-treated cells can be administered by intravenous infusion. [00291] Tolerance induced by infusion of a tolerizing vaccine comprising ECDI-treated splenocytes is likely dependent on synergistic effects between an intact programmed death 1 receptor - programmed death ligand 1 signaling pathway and CD4 ⁺ CD25 ⁺ Foxp3 ⁺ regulatory T cells.

[00292] Cells in a telorizing vaccine can be made into apoptotic cells (e.g., tolerizing vaccines) not only by ECDI fixation, but also through other methods. For example, any of the genetically modified cells as disclosed throughout, e.g., non-human cells animal cells or human cells (including stem cells), can be made apopototic by exposing the genetically modified cells to UV irradiation. The genetically modified cells can also be made apopototic by exposing it to gamma-irradiation. Other methods, not involving ECDI are also comtemplated, for example, by EtOH fixation.

[00293] Cells in a tolerizing vaccine, e.g., ECDI-treated cells, antigen-coupled cells, and/or epitope - coupled cells can comprise donor cells (e.g., cells from the donor of transplant grafts). Cells in a tolerizing vaccine, e.g., ECDI-treated cells, antigen-coupled cells, and/or epitope -coupled cells can comprise recipient cells (e.g., cells from the recipient of transplant grafts). Cells in a tolerizing vaccine, e.g., ECDI-treated cells, antigen-coupled cells, and/or epitope-coupled cells can comprise third party (e.g., neither donor nor recipient) cells. In some cases, third party cells are from a non-human animal of the same species as a recipient and/or donor. In other cases, third party cells are from a non-human animal of a different species as a recipient and/or donor.

[00294] ECDI-treatment of cells can be performed in the presence of one or more antigens and/or epitopes. ECDI-treated cells can comprise donor, recipient and/or third party cells. Likewise, antigens and/or epitopes can comprise donor, recipient and/or third party antigens and/or epitopes. In some cases, donor cells are coupled to recipient antigens and/or epitopes (e.g., ECDI-induced coupling). For example, soluble donor antigen derived from genetically engineered and genotypically identical donor cells (e.g., porcine cells) is coupled to recipient peripheral blood mononuclear cells with ECDI and the ECDI- coupled cells are administered via intravenous infusion.

[00295] In some cases, recipient cells are coupled to donor antigens and/or epitopes (e.g., ECDI-induced coupling). In some cases, recipient cells are coupled to third party antigens and/or epitopes (e.g., ECDI- induced coupling). In some cases, donor cells are coupled to recipient antigens and/or epitopes (e.g., ECDI-induced coupling). In some cases, donor cells are coupled to third party antigens and/or epitopes (e.g., ECDI-induced coupling). In some cases, third party cells are coupled to donor antigens and/or epitopes (e.g., ECDI-induced coupling). In some cases, third party cells are coupled to recipient antigens and/or epitopes (e.g., ECDI-induced coupling). For example, soluble donor antigen derived from genetically engineered and genotypically identical donor cells (e.g., porcine cells) is coupled to polystyrene nanoparticles with ECDI and the ECDI-coupled cells are administered via intravenous infusion.

[00296] Tolerogenic potency of any of these tolerizing cell vaccines can be further optimized by coupling to the surface of cells one or more of the following: IFN-g, NF-kB inhibitors (such as curcumin, triptolide, Bay-117085), vitamin D3, siCD40, cobalt protoporphyrin, insulin B9-23, or other immunomodulatory molecules that modify the function of host antigen-presenting cells and host lymphocytes.

[00297] These apoptotic cell vaccines can also be complemented by donor cells engineered to display on their surface molecules (such as FasL, PD-L1, galectin-9, CD8alpha) that trigger apoptotic death of donor-reactive cells.

[00298] Tolerizing vaccines dislosed herein can increase the duration of survival of a transplant (e.g., a xenograft or an allograft transplant) in a recipient. Tolerizing vaccines disclosed herein can also reduce or eliminate need for immunosupression following transplantation. Xenograft or allograft transplant can be an organ, tissue, cell or cell line. Xenograft transplants and tolerizing vaccines can also be from different species. Alternatively, xenograft transplants and the tolerizing vaccines can be from the same species. For example, a xenograft transplant and a tolerizing vaccine can be from substantially genetically identical individuals (e.g., the same individual).

[00299] In some cases, a tolerizing vaccine or negative vaccine can produce synergistic effects in a subject administered a tolerizing or negative vaccine. In other cases, a tolerizing or negative vaccine can produce antagonistic effects in a subject administered a tolerizing or negative vaccine.

[00300] The ECDI fixed cells can be formulated into a pharmaceutical composition. For example, the ECDI fixed cells can be combined with a pharmaceutically acceptable excipient. An excipient that can be used is saline. An excipient that can be used is phosphate buffered saline (PBS). The pharmaceutical compositions can be then used to treat patients in need of transplantation.

METHOD OF MAKING GENETICALLY MODIFIED NON-HUMAN ANIMALS

[00301] In order to make a genetically modified non-human animal as described above, various techniques can be used. Disclosed herein are a few examples to create genetically modified animals. It is to be understood that the methods disclosed herein are simply examples, and are not meant to limiting in any way.

Gene disruption

[00302] Gene disruption can be performed by any methods described above, for example, by knockout, knockdown, RNA interference, dominant negative, etc. A detailed description of the methods is disclosed above in the section regarding genetically modified non-human animals.

CRISPR/Cas system

[00303] Methods described herein can take advantage of a CRISPR/Cas system. For example, double strand breaks (DSBs) can be generated using a CRISPR/Cas system, e.g., a type II CRISPR/Cas system.

A Cas enzyme used in the methods disclosed herein can be Cas9, which catalyzes DNA cleavage.

Enzymatic action by Cas9 derived from Streptococcus pyogenes or any closely related Cas9 can generate double stranded breaks at target site sequences which hybridize to 20 nucleotides of a guide sequence and that have a proto spacer-adjacent motif (PAM) following the 20 nucleotides of the target sequence.

[00304] A vector can be operably linked to an enzyme-coding sequence encoding a CRISPR enzyme, such as a Cas protein. Cas proteins that can be used herein include class 1 and class 2. Non-limiting examples of Cas proteins include Casl, CaslB, Cas2, Cas3, Cas4, Cas5, Cas5d, Cas5t, Cas5h, Cas5a, Cas6, Cas7, Cas8, Cas9 (also known as Csnl or Csxl2), CaslO, Csyl , Csy2, Csy3, Csy4, Csel, Cse2, Cse3, Cse4, Cse5e, Cscl, Csc2, Csa5, Csnl, Csn2, Csml, Csm2, Csm3, Csm4, Csm5, Csm6, Cmrl, Cmr3, Cmr4, Cmr5, Cmr6, Csbl, Csb2, Csb3, Csxl7, Csxl4, CsxlO, Csxl6, CsaX, Csx3, Csxl, CsxlS, Csfl, Csf2, CsO, Csf4, Csdl, Csd2, Cstl, Cst2, Cshl, Csh2, Csal, Csa2, Csa3, Csa4, Csa5, C2cl, C2c2, C2c3, Cpfl, CARF, DinG, homologues thereof, or modified versions thereof. An unmodified CRISPR enzyme can have DNA cleavage activity, such as Cas9. A CRISPR enzyme can direct cleavage of one or both strands at a target sequence, such as within a target sequence and/or within a complement of a target sequence. For example, a CRISPR enzyme can direct cleavage of one or both strands within about 1, 2,

3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 50, 100, 200, 500, or more base pairs from the first or last nucleotide of a target sequence. A vector that encodes a CRISPR enzyme that is mutated to with respect, to a corresponding wild-type enzyme such that the mutated CRISPR enzyme lacks the ability to cleave one or both strands of a target polynucleotide containing a target sequence can be used.

[00305] Cas9 can refer to a polypeptide with at least or at least about 50%, 60%, 70%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity and/or sequence homology to a wild type exemplary Cas9 polypeptide (e.g. , Cas9 from S. pyogenes). Cas9 can refer to a polypeptide with at most or at most about 50%, 60%, 70%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity and/or sequence homology to a wild type exemplary Cas9 polypeptide (e.g., from S. pyogenes). Cas9 can refer to the wild type or a modified form of the Cas9 protein that can comprise an amino acid change such as a deletion, insertion, substitution, variant, mutation, fusion, chimera, or any combination thereof.

[00306] S. pyogenes Cas9 (SpCas9) can be used as a CRISPR endonuclease for genome engineering. However, others can be used. In some cases, a different endonuclease may be used to target certain genomic targets. In some cases, synthetic SpCas9-derived variants with non-NGG PAM sequences may be used. Additionally, other Cas9 orthologues from various species have been identified and these“non- SpCas9s” can bind a variety of PAM sequences that could also be useful for the present invention. For example, the relatively large size of SpCas9 (approximately 4kb coding sequence) can lead to plasmids carrying the SpCas9 cDNA that may not be efficiently expressed in a cell. Conversely, the coding sequence for Staphylococcus aureus Cas9 (SaCas9) is approximately 1 kilo base shorter than SpCas9, possibly allowing it to be efficiently expressed in a cell. Similar to SpCas9, the SaCas9 endonuclease is capable of modifying target genes in mammalian cells in vitro and in mice in vivo. In some cases, a Cas protein may target a different PAM sequence. In some cases, a target gene, such as NLRC5, may be adjacent to a Cas9 PAM, 5'-NGG, for example. In other cases, other Cas9 orthologs may have different PAM requirements. For example, other PAMs such as those of S. thermophilus (5'-NNAGAA for CRISPR1 and 5'-NGGNG for CRISPR3) and Neisseria meningiditis (5'-NNNNGATT) may also be found adjacent to a target gene, such as NLRC5. A transgene of the present invention may be inserted adjacent to any PAM sequence from any Cas, or Cas derivative, protein. In some cases, a PAM can be found every, or about every, 8 to 12 base pairs in a genome. A PAM can be found every 1 to 15 basepairs in a genome. A PAM can also be found every 5 to 20 basepairs in a genome. In some cases, a PAM can be found every 5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20, or more basepairs in a genome. A PAM can be found at or between every 5-100 base pairs in a genome.

[00307] For example, for a S. pyogenes system, a target gene sequence can precede (i.e., be 5' to) a 5'- NGG PAM, and a 20-nt guide RNA sequence can base pair with an opposite strand to mediate a Cas9 cleavage adjacent to a PAM. In some cases, an adjacent cut may be or may be about 3 base pairs upstream of a PAM. In some cases, an adjacent cut may be or may be about 10 base pairs upstream of a PAM. In some cases, an adjacent cut may be or may be about 0-20 base pairs upstream of a PAM. For example, an adjacent cut can be next to,

1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23, 24,25,26,27,28, 29,or 30 base pairs upstream of a PAM. An adjacent cut can also be downstream of a PAM by 1 to 30 base pairs.

[00308] Alternatives to S. pyogenes Cas9 may include RNA-guided endonucleases from the Cpfl family that display cleavage activity in mammalian cells. Unlike Cas9 nucleases, the result of Cpfl -mediated DNA cleavage is a double-strand break with a short 3' overhang. Cpfl’s staggered cleavage pattern may open up the possibility of directional gene transfer, analogous to traditional restriction enzyme cloning, which may increase the efficiency of gene editing. Like the Cas9 variants and orthologues described above, Cpfl may also expand the number of sites that can be targeted by CRISPRto AT-rich regions or AT-rich genomes that lack the NGG PAM sites favored by SpCas9.

[00309] A vector that encodes a CRISPR enzyme comprising one or more nuclear localization sequences (NLSs) can be used. For example, there can be or be about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 NLSs used. A CRISPR enzyme can comprise the NLSs at or near the ammo-terminus, about or more than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 NLSs at or near the carboxy-terminus, or any combination of these (e.g., one or more NLS at the ammo-terminus and one or more NLS at the carboxy terminus). When more than one NLS is present, each can be selected independently of others, such that a single NLS can be present in more than one copy and/or in combination with one or more other NLSs present in one or more copies.

[00310] CRISPR enzymes used in the methods can comprise at most 6 NLSs. An NLS is considered near the N- or C-terminus when the nearest amino acid to the NLS is within about 50 amino acids along a polypeptide chain from the N- or C-terminus, e.g., within 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 40, or 50 amino acids.

Guide RNA

[00311] As used herein, the term“guide RNA” and its grammatical equivalents can refer to

an RNA which can be specific for a target DNA and can form a complex with Cas protein. An RNA/Cas complex can assist in“guiding” Cas protein to a target DNA.

[00312] A method disclosed herein also can comprise introducing into a cell or embryo at least one guide RNA or nucleic acid, e.g., DNA encoding at least one guide RNA. A guide RNA can interact with a RNA-guided endonuclease to direct the endonuclease to a specific target site, at which site the 5' end of the guide RNA base pairs with a specific protospacer sequence in a chromosomal sequence.

[00313] A guide RNA can comprise two RNAs, e.g., CRISPR RNA (crRNA) and transactivating crRNA (tracrRNA). A guide RNA can sometimes comprise a single-chain RNA, or single guide RNA (sgRNA) formed by fusion of a portion (e.g., a functional portion) of crRNA and tracrRNA. A guide RNA can also be a dualRNA comprising a crRNA and a tracrRNA. Furthermore, a crRNA can hybridize with a target DNA.

[00314] As discussed above, a guide RNA can be an expression product. For example, a DNA that encodes a guide RNA can be a vector comprising a sequence coding for the guide RNA. A

guide RNA can be transferred into a cell or organism by transfecting the cell or organism with an isolated guide RNA or plasmid DNA comprising a sequence coding for the guide RNA and a promoter.

A guide RNA can also be transferred into a cell or organism in other way, such as using virus-mediated gene delivery.

[00315] A guide RNA can be isolated. For example, a guide RNA can be transfected in the form of an isolated RNA into a cell or organism. A guide RNA can be prepared by in vitro transcription using any in vitro transcription system known in the art. A guide RNA can be transferred to a cell in the form of isolated RNA rather than in the form of plasmid comprising encoding sequence for a guide RNA.

[00316] A guide RNA can comprise three regions: a first region at the 5' end that can be complementary to a target site in a chromosomal sequence, a second internal region that can form a stem loop structure, and a third 3' region that can be single-stranded. A first region of each guide RNA can also be different such that each guide RNA guides a fusion protein to a specific target site. Further, second and third regions of each guide RNA can be identical in all guide RNAs.

[00317] A first region of a guide RNA can be complementary to sequence at a target site in a chromosomal sequence such that the first region of the guide RNA can base pair with the target site. In some cases, a first region of a guide RNA can comprise from or from about 10 nucleotides to 25 nucleotides (i.e.. from 10 nts to 25nts; or from about lOnts to about 25 nts; or from 10 nts to about 25nts; or from about 10 nts to 25 nts) or more. For example, a region of base pairing between a first region of a guide RNA and a target site in a chromosomal sequence can be or can be about 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, or more nucleotides in length. Sometimes, a first region of a guide RNA can be or can be about 19, 20, or 21 nucleotides in length.

[00318] A guide RNA can also comprise a second region that forms a secondary structure. For example, a secondary structure formed by a guide RNA can comprise a stem (or hairpin) and a loop. A length of a loop and a stem can vary. For example, a loop can range from or from about 3 to 10 nucleotides in length, and a stem can range from or from about 6 to 20 base pairs in length. A stem can comprise one or more bulges of 1 to 10 or about 10 nucleotides. The overall length of a second region can range from or from about 16 to 60 nucleotides in length. For example, a loop can be or can be about 4 nucleotides in length and a stem can be or can be about 12 base pairs. [00319] A guide RNA can also comprise a third region at the 3' end that can be essentially single- stranded. For example, a third region is sometimes not complementarity to any chromosomal sequence in a cell of interest and is sometimes not complementarity to the rest of a guide RNA. Further, the length of a third region can vary. A third region can be more than or more than about 4 nucleotides in length.

For example, the length of a third region can range from or from about 5 to 60 nucleotides in length.

[00320] A guide RNA can target any exon or intron of a gene target. In some cases, a guide can target exon 1 or 2 of a gene, in other cases; a guide can target exon 3 or 4 of a gene. A composition can comprise multiple guide RNAs that all target the same exon or in some cases, multiple guide RNAs that can target different exons. An exon and an intron of a gene can be targeted.

[00321] A guide RNA can target a nucleic acid sequence of or of about 20 nucleotides. A target nucleic acid can be less than or less than about 20 nucleotides. A target nucleic acid can be at least or at least about 5, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, or anywhere between 1-100 nucleotides in length. A target nucleic acid can be at most or at most about 5, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 40, 50, or anywhere between 1-100 nucleotides in length. A target nucleic acid sequence can be or can be about 20 bases immediately 5’ of the first nucleotide of the PAM. A guide RNA can target a nucleic acid sequence. A target nucleic acid can be at least or at least about 1-10, 1-20, 1-30, 1-40, 1-50, 1-60, 1-70, 1-80, 1-90, or 1-100.

[00322] A guide nucleic acid, for example, a guide RNA, can refer to a nucleic acid that can hybridize to another nucleic acid, for example, the target nucleic acid or protospacer in a genome of a cell. A guide nucleic acid can be RNA. A guide nucleic acid can be DNA. The guide nucleic acid can be programmed or designed to bind to a sequence of nucleic acid site-specifically. A guide nucleic acid can comprise a polynucleotide chain and can be called a single guide nucleic acid. A guide nucleic acid can comprise two polynucleotide chains and can be called a double guide nucleic acid. A guide RNA can be introduced into a cell or embryo as an RNA molecule. For example, a RNA molecule can be transcribed in vitro and/or can be chemically synthesized. An RNA can be transcribed from a synthetic DNA molecule, e.g., a gBlocks ^® gene fragment. A guide RNA can then be introduced into a cell or embryo as an RNA molecule. A guide RNA can also be introduced into a cell or embryo in the form of a non-RNA nucleic acid molecule, e.g., DNA molecule. For example, a DNA encoding a guide RNA can be operably linked to promoter control sequence for expression of the guide RNA in a cell or embryo of interest. A RNA coding sequence can be operably linked to a promoter sequence that is recognized by RNA polymerase III (Pol III). Plasmid vectors that can be used to express guide RNA include, but are not limited to, px330 vectors and px333 vectors. In some cases, a plasmid vector (e.g., px333 vector) can comprise at least two guide RNA-encoding DNA sequences. A px333 vector can be used, for example, to introduce transgene disclosed herein.

[00323] A DNA sequence encoding a guide RNA can also be part of a vector. Further, a vector can comprise additional expression control sequences (e.g., enhancer sequences, Kozak sequences, polyadenylation sequences, transcriptional termination sequences, etc.), selectable marker sequences (e.g., antibiotic resistance genes), origins of replication, and the like. A DNA molecule encoding a guide RNA can also be linear. A DNA molecule encoding a guide RNA can also be circular.

[00324] When DNA sequences encoding an RNA-guided endonuclease and a guide RNA are introduced into a cell, each DNA sequence can be part of a separate molecule (e.g., one vector containing an RNA- guided endonuclease coding sequence and a second vector containing a guide RNA coding sequence) or both can be part of a same molecule (e.g., one vector containing coding (and regulatory) sequence for both an RNA-guided endonuclease and a guide RNA).

[00325] Guide RNA can target a gene in a non-human animal or a cell. In some cases, guide RNA can target a safe harbor gene e.g., ROSA26. In some cases a guide RNA can target a PERV site. In some cases, guide RNA can target a pig NLRC5 gene. In some cases, guide RNA can be designed to target pig NLRC5, GGTA1, cytidine monophospho-N-acetylneuraminic acid (CMP-N-NeuAc) hydrolase or CMAH gene. In some cases, at least two guide RNAs are introduced. At least two guide RNAs can each target two genes. For example, in some cases, a first guide RNA can target GGTA1 and a second guide RNA can target Gal2-2. In some cases, a first guide RNA can target NLRC5 and a second guide RNA can target Gal2-2. In other cases, a first guide RNA can target GGTAl-10 and a second guide RNA can target Gal2-2.

[00326] A guide nucleic acid can comprise one or more modifications to provide a nucleic acid with a new or enhanced feature. A guide nucleic acid can comprise a nucleic acid affinity tag. A guide nucleic acid can comprise synthetic nucleotide, synthetic nucleotide analog, nucleotide derivatives, and/or modified nucleotides.

[00327] In some cases, a gRNA can comprise modifications. A modification can be made at any location of a gRNA. More than one modification can be made to a single gRNA. A gRNA can undergo quality control after a modification. In some cases, quality control may include PAGE, HPLC, MS, or any combination thereof.

[00328] A modification of a gRNA can be a substitution, insertion, deletion, chemical modification, physical modification, stabilization, purification, or any combination thereof.

[00329] A gRNA can also be modified by 5’adenylate, 5’ guanosine-triphosphate cap, 5’N ⁷ - Methylguanosine-triphosphate cap, 5’triphosphate cap, 3’phosphate, 3’thiophosphate, 5’phosphate, 5’thiophosphate, Cis-Syn thymidine dimer, trimers, C12 spacer, C3 spacer, C6 spacer, dSpacer, PC spacer, rSpacer, Spacer 18, Spacer 9,3’-3’ modifications, 5’-5’ modifications, abasic, acridine, azobenzene, biotin, biotin BB, biotin TEG, cholesteryl TEG, desthiobiotin TEG, DNP TEG, DNP-X, DOTA, dT-Biotin, dual biotin, PC biotin, psoralen C2, psoralen C6, TINA, 3’DABCYL, black hole quencher 1, black hole quencer 2, DABCYL SE, dT-DABCYL, IRDye QC-1, QSY-21, QSY-35, QSY-7, QSY-9, carboxyl linker, thiol linkers, 2’deoxyribomicleoside analog purine, 2’deoxyribomicleoside analog pyrimidine, ribonucleoside analog, 2’-0-methyl ribonucleoside analog, sugar modified analogs, wobble/universal bases, fluorescent dye label, 2’fluoro RNA, 2’O-methyl RNA, methylphosphonate, phosphodiester DNA, phosphodiester RNA, phosphothioate DNA, phosphorothioate RNA, UNA, pseudouridine-5’-triphosphate, 5-methylcytidine-5’-triphosphate, or any combination thereof.

[00330] In some cases, a modification is permanent. In other cases, a modification is transient. In some cases, multiple modifications are made to a gRNA. A gRNA modification may alter physio-chemical properties of a nucleotide, such as their conformation, polarity, hydrophobicity, chemical reactivity, base pairing interactions, or any combination thereof.

[00331] A modification can also be a phosphorothioate substitute. In some cases, a natural

phosphodiester bond may be susceptible to rapid degradation by cellular nucleases and; a modification of intemucleotide linkage using phosphorothioate (PS) bond substitutes can be more stable towards hydrolysis by cellular degradation. A modification can increase stability in a gRNA. A modification can also enhance biological activity. In some cases, a phosphorothioate enhanced RNA gRNA can inhibit RNase A, RNase Tl, calf serum nucleases, or any combinations thereof. These properties can allow the use of PS-RNA gRNAs to be used in applications where exposure to nucleases is of high probability in vivo or in vitro. For example, phosphorothioate (PS) bonds can be introduced between the last 3-5 nucleotides at the 5'- or 3 '-end of a gRNA which can inhibit exonuclease degradation. In some cases, phosphorothioate bonds can be added throughout an entire gRNA to reduce attack by endonucleases.

Homologous recombination

[00332] Homologous recombination can also be used for any of the relevant genetic modifications as disclosed herein. Homologous recombination can permit site-specific modifications in endogenous genes and thus novel modifications can be engineered into a genome. For example, the ability of homologous recombination (gene conversion and classical strand breakage/rejoining) to transfer genetic sequence information between DNA molecules can render targeted homologous recombination and can be a powerful method in genetic engineering and gene manipulation.

[00333] Cells that have undergone homologous recombination can be identified by a number of methods. For example, a selection method can detect an absence of an immune response against a cell, for example by a human anti-gal antibody. A selection method can also include assessing a level of clotting in human blood when exposed to a cell or tissue. Selection via antibiotic resistance can be used for screening.

Making transgenic non-human animals

Random insertion

[00334] One or more transgenes of the methods described herein can be inserted randomly to any locus in a genome of a cell. These transgenes can be functional if inserted anywhere in a genome. For instance, a transgene can encode its own promoter or can be inserted into a position where it is under the control of an endogenous promoter. Alternatively, a transgene can be inserted into a gene, such as an intron of a gene or an exon of a gene, a promoter, or a non-coding region. A transgene can be integrated into a first exon of a gene. [00335] A DNA encoding a transgene sequences can be randomly inserted into a chromosome of a cell.

A random integration can result from any method of introducing DNA into a cell known to one of skill in the art. This can include, but is not limited to, electroporation, sonoporation, use of a gene gun, lipotransfection, calcium phosphate transfection, use of dendrimers, microinjection, use of viral vectors including adenoviral, AAV, and retroviral vectors, and/or group II ribozymes.

[00336] A DNA encoding a transgene can also be designed to include a reporter gene so that the presence of the transgene or its expression product can be detected via activation of the reporter gene.

Any reporter gene known in the art can be used, such as those disclosed above. By selecting in cell culture those cells in which a reporter gene has been activated, cells can be selected that contain a transgene.

[00337] A DNA encoding a transgene can be introduced into a cell via electroporation. A DNA can also be introduced into a cell via lipofection, infection, or transformation. Electroporation and/or lipofection can be used to transfect fibroblast cells.

[00338] Expression of a transgene can be verified by an expression assay, for example, qPCR or by measuring levels of RNA. Expression level can be indicative also of copy number. For example, if expression levels are extremely high, this can indicate that more than one copy of a transgene was integrated in a genome. Alternatively, high expression can indicate that a transgene was integrated in a highly transcribed area, for example, near a highly expressed promoter. Expression can also be verified by measuring protein levels, such as through Western blotting.

Site specific insertion

[00339] Inserting one or more transgenes in any of the methods disclosed herein can be site-specific. For example, one or more transgenes can be inserted adjacent to a promoter, for example, adjacent to or near a Rosa26 promoter.

[00340] Modification of a targeted locus of a cell can be produced by introducing DNA into cells, where the DNA has homology to the target locus. DNA can include a marker gene, allowing for selection of cells comprising the integrated construct. Homologous DNA in a target vector can recombine with a chromosomal DNA at a target locus. A marker gene can be flanked on both sides by homologous DNA sequences, a 3' recombination arm, and a 5' recombination arm.

[00341] A variety of enzymes can catalyze insertion of foreign DNA into a host genome. For example, site-specific recombinases can be clustered into two protein families with distinct biochemical properties, namely tyrosine recombinases (in which DNA is covalently attached to a tyrosine residue) and serine recombinases (where covalent attachment occurs at a serine residue). In some cases, recombinases can comprise Cre, fC31 integrase (a serine recombinase derived from Streptomyces phage fC31), or bacteriophage derived site-specific recombinases (including Flp, lambda integrase, bacteriophage HK022 recombinase, bacteriophage R4 integrase and phage TP901-1 integrase).

[00342] Expression control sequences can also be used in constructs. For example, an expression control sequence can comprise a constitutive promoter, which is expressed in a wide variety of cell types. For example, among suitable strong constitutive promoters and/or enhancers are expression control sequences from DNA viruses (e.g., SV40, polyoma virus, adenoviruses, adeno-associated virus, pox viruses, CMV, HSV, etc.) or from retroviral LTRs. Tissue-specific promoters can also be used and can be used to direct expression to specific cell lineages. While experiments discussed in the Examples below will be conducted using a Rosa26 gene promoter, other Rosa26-related promoters capable of directing gene expression can be used to yield similar results, as will be evident to those of skill in the art. Therefore, the description herein is not meant to be limiting, but rather disclose one of many possible examples. In some cases, a shorter Rosa26 5'-upstream sequences, which can nevertheless achieve the same degree of expression, can be used. Also useful are minor DNA sequence variants of a Rosa26 promoter, such as point mutations, partial deletions or chemical modifications.

[00343] A Rosa26 promoter is expressible in mammals. For example, sequences that are similar to the 5' flanking sequence of a pig Rosa26 gene, including, but not limited to, promoters of Rosa26 homologues of other species (such as human, cattle, mouse, sheep, goat, rabbit and rat), can also be used.

A Rosa26 gene can be sufficiently conserved among different mammalian species and other mammalian Rosa26 promoters can also be used.

[00344] The CRISPR/Cas system can be used to perform site specific insertion. For example, a nick on an insertion site in the genome can be made by CRISPR/Cas to facilitate the insertion of a transgene at the insertion site.

[00345] The methods described herein, can utilize techniques which can be used to allow a DNA or RNA construct entry into a host cell include, but are not limited to, calcium phosphate/DNA

coprecipitation, microinjection of DNA into a nucleus, electroporation, bacterial protoplast fusion with intact cells, transfection, lipofection, infection, particle bombardment, sperm mediated gene transfer, or any other technique known by one skilled in the art.

[00346] Certain aspects disclosed herein can utilize vectors. Any plasmids and vectors can be used as long as they are replicable and viable in a selected host. Vectors known in the art and those commercially available (and variants or derivatives thereof) can be engineered to include one or more recombination sites for use in the methods. Vectors that can be used include, but not limited to eukaryotic expression vectors such as pFastBac, pFastBacHT, pFastBacDUAF, pSFV, and pTet-Splice (Invitrogen), pEUK-Cl, pPUR, pMAM, pMAMneo, pBHOl, pBI121, pDR2, pCMVEBNA, and pYACneo (Clontech), pSVK3, pSVF, pMSG, pCHl 10, and pKK232-8 (Pharmacia, Inc.), p3'SS, pXTl, pSG5, pPbac, pMbac, pMClneo, and pOG44 (Stratagene, Inc.), and pYES2, pAC360, pBlueBa-cHis A, B, and C, pVF1392, pBlueBacl 11, pCDM8, pcDNAl, pZeoSV, pcDNA3, pREP4, pCEP4, and pEBVHis (Invitrogen, Corp.), and variants or derivatives thereof.

[00347] These vectors can be used to express a gene, e.g., a transgene, or portion of a gene of interest. A gene of portion or a gene can be inserted by using known methods, such as restriction enzyme -based techniques.

Making a similar genetically modified non-human animal using cell nuclear transfer [00348] An alternative method of making a genetically modified non-human animal can be by cell nuclear transfer. A method of making genetically modified non-human animals can comprise a) producing a cell with reduced expression of one or more genes and/or comprise exogenous

polynucleotides disclosed herein; b) providing a second cell and transferring a nucleus of the resulting cell from a) to the second cell to generate an embryo generating an embryo; c) growing the embryo into the genetically modified non-human animal. A cell in this method can be an enucleated cell. The cell of a) can be made using any methods, e.g., gene disruption and/or insertion described herein or known in the art.

[00349] This method can be used to make a similar genetically modified non-human animal disclosed herein. For example, a method of making a genetically modified non-human animal can comprise: a) producing a cell comprising a transgene encoding a MHC molecule (e.g., single chain chimeric MHC molecule), a a chain or a fragment thereof, or a b chain or a fragment thereof, or a peptide derived from a MHC molecule, in some embodiments, further comprising reduced expression of NLRC5, TAPI and/or C3; b) providing a second cell and transferring a nucleus of the resulting cell from a) to the second cell to generate an embryo; and c) growing the embryo to the genetically modified non-human animal. A cell in this method can be an enucleated cell.

[00350] Cells used in this method can be from any disclosed genetically modified cells as described herein. For example, transgenes are not limited to comprising a transgene encoding a MHC molecule (e.g., single chain chimeric MHC molecule), a a chain or a fragment thereof, or a b chain or a fragment thereof, or a peptide derived from a MHC molecule. Other combinations of gene disruptions and transgenes can be found throughout disclosure herein. For example, a method can comprise providing a first cell from any non-human animal disclosed herein; providing a second cell; transferring a nucleus of the first cell of a) to the second cell of b); generating an embryo from the product of c); and growing the embryo to the genetically modified non-human animal.

[00351] A cell of a) in the methods disclosed herein can be a zygote. The zygote can be formed by joining: i) of a sperm of a wild-type non-human animal and an ovum of a wild-type non-human animal; ii) a sperm of a wild-type non-human animal and an ovum of a genetically modified non-human animal; iii) a sperm of a genetically modified non-human animal and an ovum of a wild-type non-human animal; and/or iv) a sperm of a genetically modified non-human animal and an ovum of a genetically modified non-human animal. A non-human animal can be a pig.

[00352] One or more genes in a cell of a) in the methods disclosed herein can be disrupted by generating breaks at desired locations in the genome. For example, breaks can be double -stranded breaks (DSBs). DSBs can be generated using a nuclease comprising Cas (e.g., Cas9), ZFN, TALEN, and maganuclease. Nuclease can be a naturally-existing or a modified nuclease. A nucleic acid encoding a nuclease can be delivered to a cell, where the nuclease is expressed. Cas9 and guide RNA targeting a gene in a cell can be delivered to the cell. In some cases, mRNA molecules encoding Cas9 and guide RNA can be injected into a cell. In some cases, a plasmid encoding Cas9 and a different plasmid encoding guide RNA can be delivered into a cell (e.g., by infection). In some cases, a plasmid encoding both Cas9 and guide RNA can be delivered into a cell (e.g., by infection).

[00353] As described above, following DSBs, one or more genes can be disrupted by DNA repairing mechanisms, such as homologous recombination (HR) and/or nonhomologous end-joining (NHEJ). A method can comprise inserting one or more transgenes to a genome of the cell. Transgene can comprise a nucleic acid sequence encoding a MHC molecule (e.g., single chain chimeric MHC molecule), a a chain or a fragment thereof, or a b chain or a fragment thereof, or a peptide derived from a MHC molecule. In some embodiments, the transgene can further comprise a polynucleotide encoding a peptide derived from a MHC molecule capable of binding the peptide binding groove for presentation to a T cell. One or more transgenes can comprise ICP47, CD46, CD55, CD59, HLA-E, HLA-G (e.g, HLA-G1, HLA-G2, HLA- G3, HLA-G4, HLA-G5, HLA-G6, or HLA-G7), B2M, any functional fragments thereof, and/or any combination thereof. The methods provided herein can comprise inserting one or more transgenes where the one or more transgenes can be any transgene in any non-human animal or genetically modified cell disclosed herein.

[00354] Also disclosed herein are methods of making a non-human animal using a cell from a genetically modified non-human animal. A cell can be from any genetically modified non-human animal disclosed herein. A method can comprise: a) providing a cell from a genetically identified non-human animal; b) providing a cell; c) transferring a nucleus of the cell of a) to the cell of b); c) generating an embryo from the product of c); and d) growing the embryo to the genetically modified non-human animal. A cell of this method can be an enucleated cell.

[00355] Further, cells of a) in the methods can be any cell from a genetically modified non-human animal. For example, a cell of a) in methods disclosed herein can be a somatic cell, such as a fibroblast cell or a fetal fibroblast cell.

[00356] An enucleated cell in the methods can be any cell from an organism. For example, an enucleated cell is a porcine cell. An enucleated cell can be an ovum, for example, an enucleated unfertilized ovum.

[00357] Genetically modified non-human animal disclosed herein can be made using any suitable techniques known in the art. For example, these techniques include, but are not limited to, microinjection (e.g., of pronuclei), sperm-mediated gene transfer, electroporation of ova or zygotes, and/or nuclear transplantation, or bi-oocyte fusion.

[00358] A method of making similar genetically modified non-human animals can comprise a) disrupting one or more genes in a cell, b) generating an embryo using the resulting cell of a); and c) growing the embryo into the genetically modified non-human animal.

[00359] A cell of a) in the methods disclosed herein can be a somatic cell. There is no limitation on a type or source of a somatic cell. For example, it can be from a pig or from cultured cell lines or any other viable cell. A cell can also be a dermal cell, a nerve cell, a cumulus cell, an oviduct epithelial cell, a fibroblast cell (e.g., a fetal fibroblast cell), or hepatocyte. A cell of a) in the methods disclosed herein can be from a wild-type non-human animal, a genetically modified non-human animal, or a genetically modified cell. Furthermore, a cell of b) can be an enucleated ovum (e.g., an enucleated unfertilized ovum).

[00360] Enucleation can also be performed by known methods. For example, metaphase II oocytes can be placed in either HECM, optionally containing or containing about 7-10 micrograms per milliliter cytochalasin B, for immediate enucleation, or can be placed in a suitable medium (e.g., an embryo culture medium such as CRlaa, plus 10% estrus cow serum), and then enucleated later (e.g., not more than 24 hours later or 16-18 hours later). Enucleation can also be accomplished microsurgically using a micropipette to remove the polar body and the adjacent cytoplasm. Oocytes can then be screened to identify those of which have been successfully enucleated. One way to screen oocytes can be to stain the oocytes with or with about 3-10 microgram per milliliter 33342 Hoechst dye in suitable holding medium, and then view the oocytes under ultraviolet irradiation for less than 10 seconds. Oocytes that have been successfully enucleated can then be placed in a suitable culture medium, for example, CRlaa plus 10% serum. The handling of oocytes can also be optimized for nuclear transfer.

[00361] The embryos generated herein can be transferred to surrogate non-human animals (e.g., pigs) to produce offspring (e.g., piglets). For example, the embryos can be transferred to the oviduct of recipient gilts on the day or 1 day after estrus e.g., following mid-line laparotomy under general anesthesia.

Pregnancy can be diagnosed, e.g., by ultrasound. Pregnancy can be diagnosed after or after about 28 days from the transfer. The pregnancy can then checked at or at about 2-week intervals by ultrasound examination. All of the microinjected offspring (e.g., piglets) can be delivered by natural birth.

Information of the pregnancy and delivery (e.g., time of pregnancy, rates of pregnancy, number of offspring, survival rate, etc.) can be documented. The genotypes and phenotypes of the offspring can be measured using any methods described through the application such as sequencing (e.g., next-generation sequencing). Sequencing can also be Zas 258 sequencing. Sequencing products can also be verified by electrophoresis of the amplification product. Cultured cells can be used immediately for nuclear transfer (e.g., somatic cell nuclear transfer), embryo transfer, and/or inducing pregnancy, allowing embryos derived from stable genetic modifications give rise to offspring (e.g., piglets). Such approach can reduce time and cost, e.g., months of costly cell screening that may result in genetically modified cells fail to produce live and/or healthy piglets.

[00362] Embryo growing and transferring can be performed using standard procedures used in the embryo growing and transfer industry. For example, surrogate mothers can be used. Embryos can also be grown and transferred in culture, for example, by using incubators. In some cases, an embryo can be transferred to an animal, e.g., a surrogate animal, to establish a pregnancy.

[00363] It can be desirable to replicate or generate a plurality of genetically modified non-human animals that have identical genotypes and/or phenotypes disclosed herein. For example, a genetically modified non-human animal can be replicated by breeding (e.g., selective breeding). A genetically modified non human animal can be replicated by nuclear transfer (e.g., somatic cell nuclear transfer) or introduction of DNA into a cell (e.g., oocytes, sperm, zygotes or embryonic stem cells). These methods can be reproduced a plurality of times to replicate or generate a plurality of a genetically modified non-human animal disclosed herein. In some cases, cells can be isolated from the fetuses of a pregnant genetically modified non-human animal. The isolated cells (e.g., fetal cells) can be used for generating a plurality of genetically modified non-human animals similar or identical to the pregnant animal. For example, the isolated fetal cells can provide donor nuclei for generating genetically modified animals by nuclear transfer, (e.g., somatic cell nuclear transfer).

[00364] The method of making a genetically modified non-human animal of the present disclosure can include bi-oocyte fusion. For example, the a method for making a genetically modified animal comprising the steps of: (a) inducing a fusion of a genetically modified cell of the present disclosure with one or more oocyte, under conditions suitable for forming a reconstructed embryo, wherein the one or more oocytes are zona pellucida free, and enucleated, (b) activating the reconstructed embryo, (c) culturing the activated reconstructed embryo, until greater than 2-cell developmental stage; and (d) implanting the cultured embryo into a surrogate and growing the embryo to the genetically modified animal in the surrogate. In some embodiments, the genetically modified cell comprises a transgene comprising a nucleic acid sequence encoding a MHC molecule (e.g., single chain chimeric MHC molecule), a a chain or a fragment thereof, or a b chain or a fragment thereof, or a peptide derived from a MHC molecule. The transgene can further comprise a polynucleotide encoding a peptide derived from a MHC molecule capable of binding the peptide binding groove for presentation to a T cell. In some embodiments, the genetically modified cell can further comprise one or more additional transgenes e.g, ICP47, CD46, CD55, CD59, HLA-E, HLA-G (e.g, HLA-Gl, HLA-G2, HLA- G3, HLA-G4, HLA-G5, HLA-G6, or HLA-G7), B2M, any functional fragments thereof, and/or any combination thereof.

[00365] A“reconstructed embryo” is an embryo made by the fusion of an enucleated oocyte with a genetically modified donor somatic or embryonic stem (ES) or embryonic germ (EG) cell. Methods of bio-oocyte fusion are described in Examples herein. The term“enucleated oocyte” as used herein can refer to an oocyte which has had its nucleus, or its chromosomes removed. Typically, a needle can be placed into an oocyte and the nucleus and/or chromosomes can be aspirated into the needle. The needle can be removed from the oocyte without rupturing the plasma membrane. This enucleation technique is well known to a person of ordinary skill in the art. See, e.g., U.S. Pat. No. 4,994,384; U.S. Pat. No.

5,057,420; and Willadsen, 1986, Nature 320:63-65. The oocyte can be enucleated by means of manual bisection. Oocyte bisection may be carried out by any method known to those skilled in the art. In one preferred embodiment, the bisection is carried out using a microsurgical blade as described in

W098/29532 which is incorporated by reference herein. If the oocyte is obtained in an immature state (e.g. as with current bovine techniques), an enucleated oocyte is prepared from an oocyte that has been matured for greater than 24 hours, preferably matured for greater than 36 hours, more preferably matured for greater than 48 hours, and most preferably matured for about 53 hours. [00366] The term“electrical pulses” as used herein can refer to subjecting a nuclear donor and recipient oocyte to electric current. For nuclear transfer, a nuclear donor and recipient oocyte can be aligned between electrodes and subjected to electrical current. Electrical current can be alternating current or direct current. The term“activation” can refer to any materials and methods useful for stimulating a cell to divide before, during, and after a nuclear transfer step. Examples of components that are useful for non-electrical activation include ethanol; inositol trisphosphate (IP3); divalent ions (e.g., addition of Ca2+and/or Sr2+); microtubule inhibitors (e.g., cytochalasin B); ionophores for divalent ions (e.g., the a3+ionophore ionomycin); protein kinase inhibitors (e.g., 6-dimethylaminopurine (DMAP)); protein synthesis inhibitors (e.g., cyclohexamide); phorbol esters such as phorbol 12-myristate 13-acetate (PMA); and thapsigargin. It is also known that temperature change and mechanical techniques are also useful for non-electrical activation. The invention includes any activation techniques known in the art. See, e.g.,

U.S. Pat. No. 5,496,720, entitled“Parthenogenic Oocyte Activation,” issued on Mar. 5, 1996, Susko- Parrish et ah, and Wakayama et al. (1998) Nature 394: 369-374. The zona pellucida can be removed by any means known in the art such as, without limitation, treatment with acidic Tyrode's solution or pronase or by physical manipulation by means of a micro-needle, laser, or the like he term“fusion agent” as used herein can refer to any compound or biological organism that can increase the probability that portions of plasma membranes from different cells will fuse when a nuclear donor is placed adjacent to a recipient oocyte. In preferred embodiments fusion agents are selected from the group consisting of polyethylene glycol (PEG), trypsin, dimethylsulfoxide (DMSO), lectins, agglutinin, viruses, and Sendai virus. These examples are not meant to be limiting and other fusion agents known in the art are applicable and included herein.

METHODS OF USE

[00367] Cells, organs, and/or tissues can be extracted from a non-human animal as described herein. Cells, organs, and/or tissues can be genetically altered ex vivo and used accordingly. These cells, organs, and/or tissues can be used for cell-based therapies. These cells, organs, and/or tissues can be used to treat or prevent disease in a recipient (e.g., a human or non-human animal). Surprisingly, the genetic modifications as described herein can help prevent rejection. Additionally, cells, organs, and/or tissues can be made into tolerizing vaccines to also help tolerize the immune system to transplantation. Further, tolerizing vaccines can temper the immune system, including, abrogating autoimmune responses.

[00368] Disclosed herein are methods for treating a disease in a subject in need thereof can comprise administering a tolerizing vaccine to the subject; administering a pharmaceutical agent that inhibits T cell activation to the subject; and transplanting a genetically modified cell to the subject. The pharmaceutical agent that inhibits T cell activation can be an antibody. The antibody can be an anti-CD40 antibody disclosed herein. The anti-CD40 antibody can be an antagonistic antibody. The anti-CD40 antibody can be an anti-CD40 antibody that specifically binds to an epitope within the amino acid sequence:

EPPTACREKQYLINSQCCSLCQPGQKLVSDCTEFTETECLPCGESEFLDTWNRETHC HQHKYCDP NLGLRVQQKGTSETDTICTCEEGWHCTSEACESCV. The anti-CD40 antibody can be an anti-CD40 antibody that specifically binds to an epitope within the amino acid sequence:

EKQYLINSQCCSLCQPGQKLVSDCTEFTETECL. The anti-CD40 antibody can be a Fab’ anti-CD40L monoclonal antibody fragment CDP7657. The anti-CD-40 antibody can be a FcR-engineered, Fc silent anti-CD40L monoclonal domain antibody. The cell transplanted to the subject can be any genetically modified cell described throughout the application. The tissue or organ transplanted to the subject can comprise one or more of the genetically modified cells. In some cases, the methods can further comprise administering one or more immunosuppression agent described in the application, such as further comprising providing to the recipient one or more of a B-cell depleting antibody, an mTOR inhibitor, a TNF-alpha inhibitor, a IL-6 inhibitor, a nitrogen mustard alkylating agent (e.g., cyclophosphamide), and a complement C3 or C5 inhibitor.

[00369] Also disclosed herein are methods for treating a disease, comprising transplanting one or more cells to a subject in need thereof. The one or more cells can be any genetically modified cells disclosed herein. In some cases, the methods can comprise transplanting a tissue or organ comprising the one or more cells (e.g., genetically modified cells) to the subject in need thereof.

[00370] Described herein are methods of treating or preventing a disease in a recipient (e.g., a human or non-human animal) comprising transplanting to the recipient (e.g., a human or non-human animal) one or more cells (including organs and/or tissues) derived from a genetically modified non-human animal comprising one or more genes with reduced expression. One or more cells can be derived from a genetically modified non-human animal as described throughout.

[00371] The methods disclosed herein can be used for treating or preventing disease including, but not limited to, diabetes, cardiovascular diseases, lung diseases, liver diseases, skin diseases, or neurological disorders. For example, the methods can be used for treating or preventing Parkinson’s disease or Alzheimer’s disease. The methods can also be used for treating or preventing diabetes, including type 1, type 2, cystic fibrosis related, surgical diabetes, gestational diabetes, mitochondrial diabetes, or combination thereof. In some cases, the methods can be used for treating or preventing hereditary diabetes or a form of hereditary diabetes. Further, the methods can be used for treating or preventing type 1 diabetes. The methods can also be used for treating or preventing type 2 diabetes. The methods can be used for treating or preventing pre-diabetes.

[00372] For example, when treating diabetes, genetically modified splenocytes can be fixed with ECDI and given to a recipient. Further, genetically modified pancreatic islet cells can be grafted into the same recipient to produce insulin. Genetically modified splenocytes and pancreatic islet cells can be genetically identical and can also be derived from the same genetically modified non-human animal.

[00373] Provided herein include i) genetically modified cells, tissues or organs for use in administering to a subject in need thereof to treat a condition in the subject; ii) a tolerizing vaccine for use in immunotolerizing the subject to a graft, where the tolerizing vaccine comprise a genetically modified cell, tissue, or organ; iii) one or more pharmaceutical agents for use in inhibiting T cell activation, B cell activation, dendritic cell activation, or a combination thereof in the subject; or iv) any combination thereof.

[00374] Also provided herein include genetically modified cells, tissues or organs for use in

administering to a subject in need thereof to treat a condition in the subject. The subject can have been or become tolerized to the genetically modified cell, tissue or organ by use of a tolerizing vaccine. Further, the subject can be administered one or more pharmaceutical agents that inhibit T cell activation, B cell activation, dendritic cell activation, or a combination thereof.

Transplantation

[00375] The methods disclosed herein can comprise transplanting. Transplanting can be

autotransplanting, allotransplanting, xenotransplanting, or any other transplanting. For example, transplanting can be xenotransplanting. Transplanting can also be allotransplanting.

[00376]“Xenotransplantation” and its grammatical equivalents as used herein can encompass any procedure that involves transplantation, implantation, or infusion of cells, tissues, or organs into a recipient, where the recipient and donor are different species. Transplantation of the cells, organs, and/or tissues described herein can be used for xenotransplantation in into humans. Xenotransplantation includes but is not limited to vascularized xenotransplant, partially vascularized xenotransplant, unvascularized xenotransplant, xenodressings, xenobandages, and nanostructures.

[00377]“Allotransplantation” and its grammatical equivalents as used herein can encompass any procedure that involves transplantation, implantation, or infusion of cells, tissues, or organs into a recipient, where the recipient and donor are the same species. Transplantation of the cells, organs, and/or tissues described herein can be used for allotransplantation in into humans. Allotransplantation includes but is not limited to vascularized allotransplant, partially vascularized allotransplant, unvascularized allotransplant, allodressings, allobandages, and allostructures.

[00378] After treatment (e.g., any of the treatment as disclosed herein), transplant rejection can be improved as compared to when one or more wild-type cells is transplanted into a recipient. For example, transplant rejection can be hyperacute rejection. Transplant rejection can also be acute rejection. Other types of rejection can include chronic rejection. Transplant rejection can also be cell-mediated rejection or T cell-mediated rejection. Transplant rejection can also be natural killer cell-mediated rejection.

[00379] In some cases, a subject is sensitized to major histocompatibility complex (MHC) or human leukocyte antigen (HLA). For example, a subject may have a positive result on a panel reactive antibody (PRA) screen. In some cases, a subject may have a calculated PRA (cPRA) score from 0.1 to 100%. A cPRA score can be or can be about from 0.1 to 10%, 5% to 30%, 10% to 50%, 20% to 80%, 40% to 90%, 50% to 100%. In some cases, a subject with a positive PRA screen may be transplanted with the genetically modified cells of the invention.

[00380] In some cases, a subject may have a quantification performed of their PRA level by a single antigen bead (SAB) test. An SAB test can identify MHC or HLA for which a subject has antibodies to. [00381]“Improving” and its grammatical equivalents as used herein can mean any improvement recognized by one of skill in the art. For example, improving transplantation can mean lessening hyperacute rejection, which can encompass a decrease, lessening, or diminishing of an undesirable effect or symptom.

[00382] The disclosure describes methods of treatment or preventing diabetes or prediabetes. For example, the methods include but are not limited to, administering one or more pancreatic islet cell(s) from a donor non-human animal described herein to a recipient, or a recipient in need thereof. The methods can be transplantation or, in some cases, xenotransplantation. The donor animal can be a non human animal. A recipient can be a primate, for example, a non-human primate including, but not limited to, a monkey. A recipient can be a human and in some cases, a human with diabetes or pre-diabetes. In some cases, whether a patient with diabetes or pre-diabetes can be treated with transplantation can be determined using an algorithm, e.g., as described in Diabetes Care 2015;38: 1016-1029, which is incorporated herein by reference in its entirety.

[00383] The methods can also include methods of xenotransplantation where the transgenic cells, tissues and/or organs, e.g., pancreatic tissues or cells, provided herein are transplanted into a primate, e.g., a human, and, after transplant, the primate requires less or no immunosuppressive therapy. Less or no immunosuppressive therapy includes, but is not limited to, a reduction (or complete elimination of) in dose of the immunosuppressive drug(s)/agent(s) compared to that required by other methods; a reduction (or complete elimination of) in the number of types of immunosuppressive drug(s)/agent(s) compared to that required by other methods; a reduction (or complete elimination of) in the duration of

immunosuppression treatment compared to that required by other methods; and/or a reduction (or complete elimination of) in maintenance immunosuppression compared to that required by other methods.

[00384] The methods disclosed herein can be used for treating or preventing disease in a recipient (e.g., a human or non-human animal). A recipient can be any non-human animal or a human. For example, a recipient can be a mammal. Other examples of recipient include but are not limited to primates, e.g., a monkey, a chimpanzee, a bamboo, or a human. If a recipient is a human, the recipient can be a human in need thereof. The methods described herein can also be used in non-primate, non-human recipients, for example, a recipient can be a pet animal, including, but not limited to, a dog, a cat, a horse, a wolf, a rabbit, a ferret, a gerbil, a hamster, a chinchilla, a fancy rat, a guinea pig, a canary, a parakeet, or a parrot. If a recipient is a pet animal, the pet animal can be in need thereof. For example, a recipient can be a dog in need thereof or a cat in need thereof.

[00385] Transplanting can be by any transplanting known to the art. Graft can be transplanted to various sites in a recipient. Sites can include, but not limited to, liver subcapsular space, splenic subcapsular space, renal subcapsular space, omentum, bursa omentalis, gastric or intestinal submucosa, vascular segment of small intestine, venous sac, testis, brain, spleen, or cornea. For example, transplanting can be subcapsular transplanting. Transplanting can also be intramuscular transplanting. Transplanting can be intraportal transplanting. [00386] Transplanting can be of one or more cells, tissues, and/or organs from a human or non-human animal. For example, the tissue and/or organs can be, or the one or more cells can be from, a brain, heart, lungs, eye, stomach, pancreas, kidneys, liver, intestines, uterus, bladder, skin, hair, nails, ears, glands, nose, mouth, lips, spleen, gums, teeth, tongue, salivary glands, tonsils, pharynx, esophagus, large intestine, small intestine, rectum, anus, thyroid gland, thymus gland, bones, cartilage, tendons, ligaments, suprarenal capsule, skeletal muscles, smooth muscles, blood vessels, blood, spinal cord, trachea, ureters, urethra, hypothalamus, pituitary, pylorus, adrenal glands, ovaries, oviducts, uterus, vagina, mammary glands, testes, seminal vesicles, penis, lymph, lymph nodes or lymph vessels. The one or more cells can also be from a brain, heart, liver, skin, intestine, lung, kidney, eye, small bowel, or pancreas. The one or more cells are from a pancreas, kidney, eye, liver, small bowel, lung, or heart. The one or more cells can be from a pancreas. The one or more cells can be pancreatic islet cells, for example, pancreatic b cells. Further, the one or more cells can be pancreatic islet cells and/or cell clusters or the like, including, but not limited to pancreatic a cells, pancreatic b cells, pancreatic d cells, pancreatic F cells (e.g., PP cells), or pancreatic e cells. In one instance, the one or more cells can be pancreatic a cells. In another instance, the one or more cells can be pancreatic b cells.

[00387] As discussed above, a genetically modified non-human animal can be used in xenograft (e.g., cells, tissues and/or organ) donation. Solely for illustrative purposes, genetically modified non-human animals, e.g., pigs, can be used as donors of pancreatic tissue, including but not limited to, pancreatic islets and/or islet cells. Pancreatic tissue or cells derived from such tissue can comprise pancreatic islet cells, or islets, or islet-cell clusters. For example, cells can be pancreatic islets which can be transplanted. More specifically, cells can be pancreatic b cells. Cells also can be insulin -producing. Alternatively, cells can be islet-like cells. Islet cell clusters can include any one or more of a, b, d, PP or e cells. A disease to be treated by methods and compositions herein can be diabetes. Transplantable grafts can be pancreatic islets and/or cells from pancreatic islets. A modification to a transgenic animal can be to the pancreatic islets or cells from pancreatic islets. In some cases, pancreatic islets or cells from a pancreatic islet can be porcine. In some cases, cells from a pancreatic islet include pancreatic b cells.

[00388] Donor non-human animals can be at any stage of development including, but not limited to, embryonic, fetal, neonatal, young and adult. For example, donor cells islet cells can be isolated from adult non-human animals. Donor cells, e.g., islet cells, can also be isolated from fetal or neonatal non human animals. Donor non-human animals can be under the age of 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 year(s). For example, islet cells can be isolated from a non-human animal under the age of 6 years. Islet cells can also be isolated from a non-human animal under the age of 3 years. Donors can be non-human animals and can be any age from or from about 0 (including a fetus) to 2; 2 to 4; 4 to 6; 6 to 8; or 8 to 10 years. A non-human animal can be older than or than about 10 years. Donor cells can be from a human as well.

[00389] Islet cells can be isolated from non -human animals of varying ages. For example, islet cells can be isolated from or from about newborn to 2 year old non-human animals. Islets cells can also be isolated from or from about fetal to 2 year old non-human animals. Islets cells can be isolated from or from about 6 months old to 2 year old non-human animals. Islets cells can also be isolated from or from about 7 months old to 1 year old non-human animals. Islets cells can be isolated from or from about 2-3 year old non-human animals. In some cases, non-human animals can be less than 0 years (e.g., a fetus or embryo). In some cases, neonatal islets can be more hearty and consistent post-isolation than adult islets, can be more resistant to oxidative stress, can exhibit significant growth potential (likely from a nascent islet stem cell subpopulation), such that they can have the ability to proliferate post-transplantation and engraftment in a transplantation site.

[00390] With regards to treating diabetes, neonatal islets can have the disadvantage that it can take them up to or up to about 4-6 weeks to mature enough such that they produce significant levels of insulin, but this can be overcome by treatment with exogenous insulin for a period sufficient for the maturation of the neonatal islets. In xenograft transplantation, survival and functional engraftment of neo-natal islets can be determined by measuring donor-specific c-peptide levels, which are easily distinguished from any recipient endogenous c-peptide.

[00391] As discussed above, adult cells can be isolated. For example, adult non-human animal islets, e.g., adult porcine cells, can be isolated. Islets can then be cultured for or for about 1-3 days prior to transplantation in order to deplete the preparation of contaminating exocrine tissue. Prior to treatment, islets can be counted, and viability assessed by double fluorescent calcein-AM and propidium iodide staining. Islet cell viability >75% can be used. However, cell viability greater than or greater than about 40%, 50%, 60%, 70%, 80%, 90%, 95%, 99% can be used. For example, cells that exhibit viability from or from about 40% to 50%; 50% to 60%; 60% to 70%; 70% to 80%; 80% to 90%; 90% to 95%, or 90% to 100% can be used. Additionally, purity can be greater than or greater than about 80% islets/whole tissue. Purity can also be at least or at least about 40%, 50%, 60%, 70%, 80%, 90%, 95%, or 99% islets/whole tissue. For example, purity can be from or can be from about 40% to 50%; 50% to 60%; 60% to 70%; 70% to 80%; 80% to 90%; 90% to 100%; 90% to 95%, or 95% to 100%.

[00392] Functional properties of islets, including glucose-stimulated insulin secretion as assed by dynamic perifusion and viability, can be determined in vitro prior to treatment (Balamurugan, 2006). For example, non-human animal islet cells, e.g., transgenic porcine islet cells can be cultured in vitro to expand, mature, and/or purify them so that they are suitable for grafting.

[00393] Islet cells can also be isolated by standard collagenase digestion of minced pancreas. For example, using aseptic techniques, glands can be distended with tissue dissociating enzymes (a mixture of purified enzymes formulated for rapid dissociation of a pancreas and maximal recovery of healthy, intact, and functional islets of Langerhans, where target substrates for these enzymes are not fully identified, but are presumed to be collagen and non-collagen proteins, which comprise intercellular matrix of pancreatic acinar tissue) (1.5 mg/ml), trimmed of excess fat, blood vessels and connective tissue, minced, and digested at 37 degree C in a shaking water bath for 15 minutes at 120 rpm. Digestion can be achieved using bgnocaine mixed with tissue dissociating enzymes to avoid cell damage during digestion.

Following digestion, the cells can be passed through a sterile 50mm to 1000mm mesh, e.g., 100 mm, 200 mm, 300 mm, 400 mm, 500 mm, 600 mm, 700 mm, 800 mm, 900 mm, or 1000 mm mesh into a sterile beaker. Additionally, a second digestion process can be used for any undigested tissue.

[00394] Islets can also be isolated from the adult pig pancreas (Brandhorst et al, 1999). The pancreas is retrieved from a suitable source pig, peri-pancreatic tissue is removed, the pancreas is divided into the splenic lobe and in the duodenal/connecting lobe, the ducts of each lobes are cannulated, and the lobes are distended with tissue dissociating enzymes. The pancreatic lobes are placed into a Ricordi chamber, the temperature is gradually increased to 28 to 32°C, and the pancreatic lobes are dissociated by means of enzymatic activity and mechanical forces. Liberated islets are separated from acinar and ductal tissue using continuous density gradients. Purified pancreatic islets are cultured for or for about 2 to 7 days, subjected to characterization, and islet products meeting all specifications are released for transplantation (Korbutt et al. , 2009).

[00395] Donor cells, organs, and/or tissues before, after, and/or during transplantation can be functional. For example, transplanted cells, organs, and/or tissues can be functional for at least or at least about 1, 5, 10, 20, 30 days after transplantation. Transplanted cells, organs, and/or tissues can be functional for at least or at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 months after transplantation. Transplanted cells, organs, and/or tissues can be functional for at least or at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15,

20, 25, or 30 years after transplantation. In some cases, transplanted cells, organs, and/or tissues can be functional for up to the lifetime of a recipient. This can indicate that transplantation was successful. This can also indicate that there is no rejection of the transplanted cells, tissues, and/or organs.

[00396] Further, transplanted cells, organs, and/or tissues can function at 100% of its normal intended operation. Transplanted cells, organs, and/or tissues can also function at least or at least about 50, 60, 65, 70, 75, 80, 85, 90, 95, 99, or 100% of its normal intended operation, e.g., from or from about 50 to 60; 60 to 70; 70 to 80; 80 to 90; 90 to 100%. In certain instances, the transplanted cells, organs, and/or tissues can function at greater 100% of its normal intended operation (when compared to a normal functioning non-transplanted cell, organ, or tissue as determined by the American Medical Association). For example, the transplanted cells, organs, and/or tissues can function at or at about 110, 120, 130, 140, 150, 175, 200% or greater of its normal intended operation, e.g., from or from about 100 to 125; 125 to 150; 150 to 175; 175 to 200%.

[00397] In certain instances, transplanted cells can be functional for at least or at least about 1 day. Transplanted cells can also functional for at least or at least about 7 days. Transplanted cells can be functional for at least or at least about 14 days. Transplanted cells can be functional for at least or at least about 21 days. Transplanted cells can be functional for at least or at least about 28 days. Transplanted cells can be functional for at least or at least about 60 days.

[00398] Another indication of successful transplantation can be the days a recipient does not require immunosuppressive therapy. For example, after treatment (e.g., transplantation) provided herein, a recipient can require no immunosuppressive therapy for at least or at least about 1, 5, 10, 100, 365, 500, 800, 1000, 2000, 4000 or more days. This can indicate that transplantation was successful. This can also indicate that there is no rejection of the transplanted cells, tissues, and/or organs.

[00399] In some cases, a recipient can require no immunosuppressive therapy for at least or at least about 1 day. A recipient can also require no immunosuppressive therapy for at least or at least about 7 days. A recipient can require no immunosuppressive therapy for at least or at least about 14 days. A recipient can require no immunosuppressive therapy for at least or at least about 21 days. A recipient can require no immunosuppressive therapy for at least or at least about 28 days. A recipient can require no

immunosuppressive therapy for at least or at least about 60 days. Furthermore, a recipient can require no immunosuppressive therapy for at least or at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 30, 40, or 50 years, e.g., for at least or at least about 1 to 2; 2 to 3; 3 to 4; 4 to 5; 1 to 5; 5 to 10; 10 to 15; 15 to 20; 20 to 25; 25 to 50 years.

[00400] Another indication of successful transplantation can be the days a recipient requires reduced immunosuppressive therapy. For example, after the treatment provided herein, a recipient can require reduced immunosuppressive therapy for at least or at least about 1, 5, 10, 50, 100, 200, 300, 365, 400, 500 days, e.g., for at least or at least about 1 to 30; 30 to 120; 120 to 365; 365 to 500 days. This can indicate that transplantation was successful. This can also indicate that there is no or minimal rejection of the transplanted cells, tissues, and/or organs.

[00401] For example, a recipient can require reduced immunosuppressive therapy for at least or at least about 1 day. A recipient can also require reduced immunosuppressive therapy for at least 7 days. A recipient can require reduced immunosuppressive therapy for at least or at least about 14 days. A recipient can require reduced immunosuppressive therapy for at least or at least about 21 days. A recipient can require reduced immunosuppressive therapy for at least or at least about 28 days. A recipient can require reduced immunosuppressive therapy for at least or at least about 60 days.

Furthermore, a recipient can require reduced immunosuppressive therapy for at least or at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 30, 40, or 50 years, e.g., for at least or at least about 1 to 2; 2 to 3; 3 to 4; 4 to 5; 1 to 5; 5 to 10; 10 to 15; 15 to 20; 20 to 25; 25 to 50 years.

[00402] “Reduced” and its grammatical equivalents as used herein can refer to less immunosuppressive therapy compared to a required immunosuppressive therapy when one or more wild-type cells is transplanted into a recipient.

[00403] A donor (e.g., a donor for a transplant graft and/or a cell in a tolerizing vaccine) can be a mammal. A donor of allografts can be an unmodified human cell, tissue, and/or organ, including but not limited to pluripotent stem cells. A donor of xenografts can be any cell, tissue, and/or organ from a non human animal, such as a mammal. In some cases, the mammal can be a pig.

[00404] The methods herein can further comprise treating a disease by transplanting one or more donor cells to an immunotolerized recipient (e.g., a human or a non -human animal).

Kits [00405] Provided herein are kits comprising the isolated nucleic acid molecule of the present disclosure or a vector comprising the isolated nucleic acid molecule disclosed above. In some embodiments, the isolated nucleic acid is in a lyophilized or a solution form. In some embodiments, the kit further comprises a cell of generating a genetically modified cell using methods disclosed herein. In some embodiments, the kit further comprises instructions for insertion of the isolated nucleic molecule into the genome of a cell. The kit is intended for use in generation of genetically modified cell using methods disclosed herein.

[00406] In another embodiment of the disclosure, an article of manufacture which contains the pharmaceutical composition in a solution form or in a lyophilized form or a kit comprising an article of manufacture is provided. The kit of the instant disclosure can be contemplated for use in transplantation of a transplant in a recipient. In some embodiments, the kit comprises a third container comprising one or more immunomodulatory molecules. In some embodiments, kits of the disclosure include a formulation of nanoparticle compositions disclosed herein or nanoparticle compositions disclosed herein packaged for use in combination with the co-administration of a second compound (such as an anti-inflammatory agent, immunomodulating agent, anti-tumor agent, a natural product, a hormone or antagonist, an anti angiogenesis agent or inhibitor, a apoptosis-inducing agent, a chelator, or anti-CD40 agent) or a pharmaceutical composition thereof. The components of the kit may be pre-complexed or each component may be in a separate distinct container prior to administration to a patient.

[00407] In some embodiments, the kits can comprise a container comprising a diluent, a reconstitution solution, and/or a culture medium. The kit can comprise instructions for diluting the composition or for its reconstitution and/or use. The article of manufacture comprises a container. Suitable containers include, for example, bottles, vials (e.g. dual chamber vials), syringes (such as dual chamber syringes) and test tubes. The container may be formed from a variety of materials such as glass or plastic. The container holds the lyophilized formulation and a label on, or associated with, the container may indicate directions for reconstitution and/or use. The label may further indicate that the formulation is useful transformation of cells or intended for subcutaneous administration. The container holding the formulation may be a multi-use vial. The article of manufacture may further include other materials desirable from a commercial and user standpoint, including other buffers, diluents, fdters, needles, syringes, and package inserts with instructions for use.

[00408] The components of the kits may be provided in one or more liquid solutions, preferably, an aqueous solution, more preferably, a sterile aqueous solution. The components of the kit may also be provided as solids, which may be converted into liquids by addition of suitable solvents, which are preferably provided in another distinct container.

[00409] The containers of a kit may be a vial, test tube, flask, bottle, syringe, or any other means of enclosing a solid or liquid. Usually, when there is more than one component, the kit will contain a second vial or additional container, which allows for separate dosing. The kit may also contain another container for a pharmaceutically acceptable liquid. Preferably, a kit will contain apparatus (e.g., one or more needles, syringes, eye droppers, pipette, etc.), which enables administration of the nanoparticle of the disclosure which are components of the present kit.

In some embodiments, the kit disclosed herein further comprises the transplant. In some embodiment, the transplant is cell, tissue or organ transplant. In some embodiments, the transplant is genetically modified. In some embodiments, the transplant is a is a kidney, liver, heart, lung, pancreas, islet cell, small bowel, bone marrow, hematopoietic stem cell, embryonic or induced pluripotent stem cell-derived islet beta cell, embryonic or induced pluripotent stem cell-derived islet, embryonic or induced pluripotent stem cell- derived hepatocyte or a combination thereof. In some embodiments, the transplant can be autologous, allograft, or a xenograft. In some embodiments, the transplant can be genetically modified.

EXAMPLES

EXAMPLE 1: Construction of a transgene encoding single chain MHC (HLA-DR) chimeric polypeptide

[00410] MHC class II matching between donor and recipient limits the activation of CD4+ T cells with direct and indirect donor specificities and promotes the generation of CD4+ T cells with potent regulatory properties that actively suppress alloreactive CD8+ cytotoxic T cell responses and modulate dendritic cells (DC). Without wishing to be bound by theory, it may be possible that because of the propensity of MHC class II molecules to present themselves as peptides the peri-transplant infusions of ADL (including numerous splenic and/or ex vivo expanded, MHC class II expressing B cells) causes a substantial increase of shared MHC class II molecule complexes presenting their MHC class II peptides on the surface of host antigen presenting cells including spleen marginal zone macrophages and possibly also liver sinusoidal endothelial cells. These complexes, also referred to as“T-Lo” or“Suppress Me” complexes, are involved in the thymic differentiation of thymus-derived tTregs and, after being transferred from antigen presenting cells to activated T cells by trogozytosis, provide strong activation signals to pre-existing tTregs. It is well known that tTregs exported to the periphery exhibit a TCR repertoire skewed toward self-recognition. Activation of tTregs profoundly increases their regulatory potency. Treg cells have been shown to trigger the generation of Trl regulatory cells.

[00411] If one MHC class II allele is matched between porcine donor and human recipient, host tTreg activation may be accomplished by graft expression of T-Lo complexes. Whenever the microenvironment of the accepted xenograft changes from quiescent to inflammatory, MHC class II antigen expression is up regulated, leading to increased expression of T-Lo complexes by the graft. The sustained activation of tTregs is also facilitated by the persistent expression of T-Lo complexes on host APC and their transfer to host Teff that are indirectly primed by mismatched MHC -class II peptides presented by host MHC class II.

[00412] The shared self MHC class II peptide self MHC class II T-Lo complexes can spread tolerance when expressed on peripheral antigen presenting cells through T-Lo-specific tTregs, which could inhibit - via linked suppression - and convert - via infectious tolerance - Teff that recognize mismatched donor antigens on the same APC. Without wishing to be bound by theory, sharing of one HLA class II allele between transgenic porcine donors and human porcine xenograft recipients will promote the presentation of HLA class II peptide HLA class II molecule complexes on host immune cells, leading to activation and expansion of CD4+ Tregs and Trl-like cells, thereby resulting in induction of immune tolerance towards the porcine xenograft.

[00413] Provided below are methods for generating genetically modified cells and genetically modified animals expressing a transgene encoding a single chain MHC chimeric polypeptide (scMHC chimeric peptide) in which a MHC molecule is covalently linked to a peptide derived from the MHC molecule.

The transgene encodes a single chain MHC chimeric polypeptide in which a chain of the MHC molecule, b chain of the MHC molecule and a peptide derived from the MHC molecule are functionally fused in a single chain. The chimeric polypeptide folds such that the a chain of the MHC molecule and the b chain of the MHC molecule form a peptide binding groove in which the peptide derived from the MHC molecule binds to form a functional MHC-peptide complex (FIG 2). The methods below exemplifies generation of a genetically modified cell and animal expressing the single chain MHC chimeric polypeptide. The example illustrates expression of a single chain MHC chimeric polypeptide wherein the a chain and the b chain is from HLA -DR which fold to form a HLA-DR MHC molecule.

[00414] The sequence of a nucleic acid construct for the scMHC peptide (HLA-DR transgene construct) to produce the single chain HLA-DR molecule covalently linked with a cognate peptide was optimized and modified to improve gene expression and delivery (FIG. 1). Linker 1 was added to be a

GT(GS)7 linker to improve successful association of the peptide in the binding grove. Gene expression was under the MND promoter and a synthetic polyA sequence was incorporated (FIG. 1). The construct is synthesized with a restriction enzyme site that allows the inclusion of linker 1 and one of 4 peptides to be covalently linked and presented in the final folded protein or no peptide. A first round of synthesis generated the 5 MND HLA-DR transgene constructs. (Exemplary sequence is provided In Table 9)

[00415] A subsequent round of cloning generated these 5 constructs inserted between the ROSA26 homology arms for knock in into a ROSA26 insertion site of a cell (Exemplary sequence is provided in Table 9). The ROSA26 homology arms were designed for homologous recombination of the transgene in exon 1 of ROSA26. The left flanking homologous arm of the HLA-DR transgene cassette was designed to include a 500 basepair (bp) sequence spanning the promoter and exon 1 and a 500 bp sequence located at the 3’ end to exon 1 was selected for design of the right flanking homologous arm.

[00416] Primers used to amplify the 500 bp fragments by PCR and the resulting amplicon sequenced by NGS.

[00417] The mRNA for HLA-DRA010202 for the alpha chain and mRNA for HLA-DRB010301 for the beta chain was used in the single peptide expression construct with a covalently linked peptide at the 5’ end of the beta chain mRNA. One of 4 potential peptides from the DRB010301 AA sequence was derived from the Immune Epitope Database provided by the NIH (Table 1).

[00418] The natural expression of the alpha and beta chains occurs independently and each have their own transmembrane domain. To express a single chimeric peptide of the alpha and beta chains the transmembrane domain of the alpha chain is removed and replaced by a 30 AA linker sequence that allows the folding of the functional peptide binding domain of the alpha chain with the entirety of the beta chain including one of the cognate peptide candidates. The 4 constructs, differing only by cognate peptide, will be flanked by 500bp arms specific for the ROSA26 site designed and validated by sequence analysis prior to transfection. The final successful chimeric DR/peptide expression construct can also be designed for alternative insertion site. The insertion of chimeric DR/peptide will be evaluated at the ROSA26 site for cell surface expression using the BD Melody cell sorter. Sorted cells will be used for functional analysis.

[00419] Table 1 shows exemplary cognate peptides dervied from a MHC molecule that bind the peptide binding grrove of the MHC molecule. The cognate peptides were derived from the entire HLA-DR3 peptide beta chain excluding the signal sequence. The percentile rank indicates the predicted affintiy of the peptide for the proposed peptide binding groove of the HLA-DR folded molecule.

guide RNA

[00420] The ZiFiT Targeter tool version 4.2 (http://zifit.partners.org/ZiFiT/) was used to design guide RNA (gRNA) specific for exon 1 of the porcine ROSA26 locus. The gRNA sequence

GCCGGGGCCGCCTAGAGAAG targeted a PAM site proximal to the start codon and promoter while maintaining a high efficiency of DNA cleavage. Chemically synthesized gRNAs targeting GGTA1 and ROSA26 were obtained from Synthego and reconstituted in 20 nM concentration nuclease free water, as per instructions provided with the Guide-it sgRNA In Vitro Transcription Kit (#632635, Takara

BioTech).

Cell Culture, Electroporation and Flow Sorting

[00421] Cryopreserved pig fetal fibroblasts (PFF) were allowed to thaw at 37°C, washed twice with complete 10% Dulbecco’s Modified Eagle’s Medium (DMEM) (Life Technologies), and 2 x 106 cells per petri dish were subsequently placed in 10% complete DMEM media. Media was changed every 48 hours to allow for at least 70% confluence. Cells were detached by Tryple Express (Life Technologies) and prepared for transfection, as per the Amaxa™ 4D-Nucleofector™ Protocol. In summary, 5 x 105 cells were suspended in 75 mL transfection buffer prepared by mixing 82 mL NucleofectorTM Solution and 18 mL NucleofectorTM Supplement provided in the kit, as per manufacturer instructions. The remaining 25 mL of transfection buffer was used to mix gRNA, Cas9 endonuclease (Aldevron) and HL-DR transgene template prior to incubation at room temperature for 10 minutes. Following incubation, gRNA:Cas9 complex was mixed with PFF cells and transferred to NucleocuvetteTM cuvettes. Cells were subsequently transfected by electroporation using program CM- 137, according to manufacturer instructions. Following transfection, cuvettes were kept at 37°C for 10 minutes to allow for cell recovery prior to being transferred to petri dishes. Media was changed 48 hours after transfection. After successfully attaining 70% confluence, cells were sorted by FC. Briefly, cells were detached by Tryple Express and stained with 1 mg of IB4-APC (Biolegend), 9 mL of PE anti -human HLA-DR in 100 mL of flow buffer composed of DMEM 1% BSA containing ImM CaC12, prior to incubation for 30 minutes at 4°C in the absence of light. Identical temperature incubation and centrifugation steps were performed with unstained cells. After washing twice with flow buffer in a 15 mL tube, cells were suspended in 300 mL flow buffer and loaded into the BD FACSAria II (BD Biosciences) under aseptic conditions for flow sorting. A 130 pm nozzle was used to sort the porcine fibroblast cells.

DNA Isolation

[00422] In this experiment, DNA obtained from sections of transgenic pig tail were isolated using the QIAmp Fast DNA Tissue Kit (#51404, Qiagen). In addition, DNA obtained from flow sorted cells was isolated using the QIAmp DNA Micro Kit (#56304, Qiagen). Following flow sorting, 1000 sorted cells were removed and suspended in 100 mL IX phosphate buffered saline (PBS), prior to the addition of 10 mL PBA [PBS + 1% BSA? 5% below], 100 mL Buffer AL, and proteinase K, all provided in the kit, as per manufacturer instructions. Following 15 minutes incubation at room temperature, DNA obtained from flow sorted cells was eluted in 20 mL Buffer AE, also provided in the kit, and sorted cells were stored at - 20°C for future use.

EXAMPLE 2: Analysis of the HLA-DR-expressing cell line and DR cognate peptide

[00423] The surface expression of cells post transfection for the expression of the chimeric HLA-DR3 molecule was analyzed by flow cytometry. Cells positive for chimeric HLA-DR3 molecule were reserved for DNA isolation and sanger sequence analysis of the junction site where the insertion region begins and the template ends. Sorted porcine HLA-DR3+ positive cells will be lysed for protein isolation to be further validated by western blot. The physical characteristics of the genetically modified cells will meet the following criteria: (a) Positive anti-DR3+ antibody binding by flow cytometry, (b) Homologous DNA sequence of inserted gene to the original template at the specific insertion site, and (c) correct size and specific protein band identified by immunoblotting.

EXAMPLE 3: Exemplary Sites for Gene Insertion for the transgene

[00424] The ROSA 26 gene site has a constitutively active endogenous promoter and has proven to accept additions of DNA without disruption to cell viability in mice and humans, and pigs. However, to create the best genetics for porcine donor the following additional strategies will be to incorporated in the porcine genome the proposed novel transgenes.

[00425] Target an additional site for gene addition and/or“Stack” genes in one site with the same or multiple promoters. Therefore, reducing the transfection burden on the cells through targeting the GGTA1 gene (or other genes where mutation has a desirable phenotype such as NLRC5, CMAH, or B4GalNT2) with the HLA-DR3 transgene or others will both mutate the target gene and express a new desirable immune-regulatory phenotype. 500bp homology arms specific to the gene are designed thereby knocking out a known antigen while inserting the desired transgene. The insertion of the transgene with disrupt the expression of the gene in which it is inserted. This will also simplify the selection of genetically engineered cells by allowing to select for transgene expression in the first round of cell culture. This method will comprise the following steps: i) Sequencing of the flanking regions of the target gene (e.g., ROSA26 or GGTA1) in select porcine cells.

ii) Generation of the proposed transgene construct (e.g., chimeric MHC polypeptide) targeting one of the genes to be deleted (e.g., GGTA1). Additional target sites will follow the same sequencing strategy. iii) Incorporation of the transgene into unique pig cells at the new GGTA1 targeting site identified by Gal2-2 synthetic guide RNA. iv) The HLA-DR gene insertion can occur in only one allele of a gene (e.g. ROSA26) and if gene expression is sufficient then the second allele of gene (e.g., ROSA26) can be targeted for expression of a second transgene (e.g., HLA-G1).

v) To address proper expression and folding of the chimeric HLA-DR3 while preventing accumulation of improperly folded protein, the spacing around the signal sequence in the construct can be modified, the spacing between elements can be lengthened to enhance folding, and the space linking the peptide to the 5’ end of the beta allele can be changed.

vi) Exemplary cognate peptides in Table 1 were determined using an algorithm designed around the affinity of amino acids in the binding groove for the amino acids that compose the antigenic peptide. Additional peptide can be designed and used in the construct using similar approach. Alternatively, the transgene templates that vary by each peptide can be combined to either add or synergize the effects of individual cognate peptide antigens.

EXAMPLE 4: Exemplary methods to make a genetically modified animal expressing the HLA-DR molecule

[00426] The HLA-DR porcine donor will express a very unique protein on the cell surface that combines by three molecule being expressed as a single chimeric polypeptide. The HLA-DRB (beta chain of MHC molecule) and HLA-DRA (alpha chain of MHC molecule) normally associate in the presence of a cognate peptide to form a cognate peptide-MHC complex. We designed and developed a construct so that these three molecules are expressed together and can be inserted as one transgene into the genome of an animal. The generation of a genetically modified cells and animal expressing a transgene encoding a MHC molecule (such as chimeric HLA-DR molecule covalently linked with its cognate peptide) is summarized in the following steps: [00427] LA-DR3 allele was sequenced from Genbank comprised of the HLA-DRB 1*03:01 up to the transmembrane domain and then directly connected in frame to the HLA-DRA full length sequence with the transmembrane domain intact.

[00428] A dsDNA template that contains the MND promoter, a signal peptide, a cognate peptide liked to the HLA-DRB 1*03:01 / HLA-DRA, a synthetic polyA tail, and flanked at the 5 ' and 3 ' ends by 5 OObp domains homologous to each side of the CRISPR directed Cas9 cut site was designed

[00429] The cells were electroporated to allow the entry of the ROSA26 targeting CRISPR guides and recombinant Cas9 to cut the DNA in the presence of the dsDNA repair template described above.

[00430] Cells positive for an HLA-DR specific antibody are sorted away from non-expressing cells.

[00431] HLA-DR positive cells are then used as nuclear donors for SCNT where they are fused with enucleated oocytes to form embryos. SCNT was performed as described by Whitworth et al. Biology of Reproduction 91(3):78, 1-13, (2014). The SCNT was performed using in vitro matured oocytes (DeSoto Biosciences Inc., St. Seymour, TN). Cumulus cells were removed from the oocytes by pipetting in 0.1% hyaluronidase. Only oocytes with normal morphology and a visible polar body were selected for SCNT. Oocytes were incubated in manipulation media (Ca-free NCSU-23 with 5% FBS) containing 5 mg/mL bisbenzimide and 7.5 mg/mL cytochalasin B for 15 min. Oocytes were enucleated by removing the first polar body plus metaphase II plate. A single cell was injected into each enucleated oocyte, fused, and activated simultaneously by two DC pulses of 180 V for 50 psec (BTX cell electroporator, Harvard Apparatus, Hollison, MA, USA) in 280mM Mannitol, 0.1 mM CaC12, and 0.05 mM MgC12. Activated embryos were placed back in NCSU-23 medium with 0.4% bovine serum albumin (BSA) and cultured at 38.5 °C, 5% C02 in a humidified atmosphere for less than 1 hour, and transferred into the surrogate pigs.

[00432] On day 5-6 of embryo development 20-60 embryos are implanted via minimally invasive surgical embryo transfer in matrix-synchronized "in heat" surrogate sows directly into the uterine horn and with a milking motion evenly distributed throughout. The horn is placed into a natural position to encourage a natural movement of fluid and embryos.

[00433] Approximately 50% of pregnancies are successful by ultrasound at day30 post embryo transfer. Those liters are often comprised of 3-7 piglets bom by cesarean section. Ear notches for identity and tail clips are collected and used to determine the genomic presence of the transgene.

[00434] The ear and tail pieces are macerated and digested in collagenase IV to release fibroblasts from the tissue. Tissue fragments are cultured for several days to 70-80% culture plate confluence. The DNA is isolated from the fibroblasts and PCR primers specific for a region inside the DR3 gene that could only be amplified if the gene was inserted.

EXAMPLE 5: Immunological Characterization

Analysis of the functional implications of a natural human DR3 homolog in porcine donors on mechanisms of tolerance. [00435] Peripheral blood leucocytes (PBL) obtained from 20 different donor pigs will be serotyped with anti-HLA DR3 or anti-HLA DR4 specific antibody to identify donor pigs that express the homolog of human HLA-DR3 or HLA-DR4, the common alleles expressed in >30% of patients with type 1 diabetes. The DR sequence of the HLA-DR3 serotyped donor pigs will be sequenced using Sanger sequencing technology. To determine the effect of DR3 matching in induction of tolerance, we will analyze the proliferation of PBLs from RM with and without a human homolog of DR3. Briefly PBLs from Rhesus Macaque (RM) expressing DR03a or DR04 will be stimulated with donor pigs that express human homolog of HLA-DR3 in a CFSE MLR. Proliferation of CD4+, CD8+ and CD20+ lymphocytes will be analyzed by flow cytometry. To determine whether ECDI fixed B cells from the pigs with human homolog of DR3 can induce the expansion of regulatory T cells that promote long term tolerance we will coculture RM PBL from DR03a+ and DR04+ animals with ECDI fixed donor PBLs for 7 days and analyze the expansion of Trl (CD4+ CD49b+Lag3+) and Treg (CD4+ CD25+CD1271ow).

Analysis of the effects of transgenic expression of HLA-DR3 in porcine donors on mechanisms of tolerance.

[00436] To determine the effect of DR3 matching in induction of tolerance, we will analyze the proliferation of PBLs from patients with type 1 diabetes with and without HLA-DR3. Briefly PBLs from patients with type 1 diabetes expressing DR03a or DR04 will be stimulated with transgenic pig PBLs that express chimeric HLA-DR3 with covalently linked cognate peptide in a CFSE MLR. Proliferation of CD4+, CD8+ and CD20+ lymphocytes will be analyzed by flow cytometry. To determine whether ECDI fixed B cells from the HLA-DR3 transgenic pig PBL can induce the expansion of regulatory T cells that promote long term tolerance we will coculture T1D PBL from DR03a+ and DR04+ individuals with ECDI fixed donor PBLs for 7 days and analyze the expansion of Trl (CD4+ CD49b+Lag3+) and Treg (CD4+ CD25+CD1271ow). The frequency of the individual TCR specific clones will be enumerated before and after exposure to the ECDI-fixed B cells using flurochome labeled HLA-DR3 tetramers loaded with the cognate peptide and HLA-DR3 tetramers loaded with irrelevant peptide will serve as controls. EXAMPLE 6: Exemplary methods for making a genetically engineered porcine organ donor

[00437] Procurement and maturation of oocytes, enucleation and fusion of the oocytes with genetically engineered cells, and culture of embryos before implantation are critical steps in development of genetically modified animal. Exemplary method includes:

i) Validation of oocytes for use in the production of embryos by somatic cell nuclear transfer (SCNT) or Bi-oocyte fusion (BOF).

ii) Embryo production by SCNT or BOF

iii) In vitro embryo development and analysis of embryo for genetically engineered targets and viability at day 0 through day 7.

iv) Utilize qualified embryos for embryo transfer to surrogate to generate pregnancies and grow to genetically modified piglets as donors for genetically modified cell, tissue and organs for xenotransplantion. Oocyte Selection Validation of porcine oocytes for cloning.

[00438] Selecting oocytes that are most likely to develop is crucial for both assisted human reproductive technology and animal embryo technologies involving IVM oocytes. Characterizing ovarian oocytes in a non-invasive and non-perturbing manner for selection of oocytes prior to culture has become of prime importance. A non-limiting exemplary method includes zinc supplementation in in vitro medium to increase the oocyte quality and production efficiency of cloned pigs. Zinc can be supplemented in oocyte maturation media, then test them for oocyte quality and embryo developmental rates.

[00439] Glucose-6-phosphate (G6PDH) enzyme activity can be measured as readout of increased developmental competence and as a simple test for porcine oocyte viability. In mouse model, Brilliant Cresyl Blue dye (BCB) staining can be used as an efficient method for oocyte selection, but the competence of the BCB+ oocytes may vary with oocyte diameter, animal sexual maturity and

gonadotropin stimulation. In this test, staining of immature cumulus-oocyte complexes (COCs) with BCB was selected for further maturation. Oocytes stained blue (BCB+, low G6PDH activity) are characterized by higher developmental competence or superior quality when compared with colorless oocytes of reduced quality (BCB negative / high activity of G6PDH). The BCB test is a very useful tool for the selection of superior quality oocytes in. Validation of oocyte for use in production of embryos will include the following:

i) Screen commercially available oocytes (Desoto Inc.) and in-house isolated oocytes for maturation traits beneficial to cloning.

ii) Selection of Immature oocytes based on Glucose-6-phosphate (G6PDH) enzyme activity by using BCB staining.

iii) Evaluation of the maturation efficiency of BCB+ oocytes using standard nutritive media, highly enriched stem cell media, while testing the impact of follicular fluid on development.

iv) Measurement of the oxygen consumption rate among selected oocytes to determine if the Seahorse technology is beneficial to confirm BCB selection and validate final oocytes

v) Supplementation of zinc in in vitro oocyte maturation media

[00440] Completion of steps described above will select viable oocytes, enhance maturation and assess the utility of validation markers for selection of higher quality oocytes for for use in the production of embryos by somatic cell nuclear transfer (SCNT) or Bi-oocyte fusion (BOF).

Bi-Oocyte Fusion Cloning (BOF)

[00441] Exemplary steps for Bi-Oocyte fusion cloning will include;

i) Micro scalpel excision of oocyte nucleus and / or chemical (demecolcine) expulsion of nuclei combined with

ii) Electro fusion of bisected and enucleated oocytes with wild-type or genetically engineered cells (e.g., porcine fibroblasts cells expressing HLA-DR3 transgene and/or comprising a genetic disruption in one or more gene encoding NLRC5, CMAH, GGTA1) followed by iii) Phenotypic and genomic analysis of fusion products.

[00442] Great improvements have been made in nuclear transfer (NT) techniques, following critical investigations on the use of different donor cell types, cell cycle, stage of passaging cells, variation in maturation stage of the recipient oocytes, epigenetic modifications of oocytes, and variations in fusion and activation protocols. These alterations have also led to a substantial increase in the efficiency of production of cloned embryos. A zona free cloning or“handmade cloning” HMC approach is an alternative to the micromanipulation based SCNT. Electro fusion can be performed either through chamber fusion or microelectrode fusion. The fusion efficiency can be higher with the zona free cloning method. In mammalian SCNT, activation is a crucial step to progress reconstructed embryos into the interphase of mitotic division. Addition ofthimerosal will induce complete activation of porcine oocytes. Activation will induce train of Ca2+ spikes in the oocytes and followed by incubation with dithiothreitol (DTT), it can stimulate pronuclear formation. The combined thimerosal/dithiothreitol (DTT) chemical incubation will induce full activation of oocytes that supports development to the blastocyst.

[00443] Treatment of Vitamin C and Latrunculin A in porcine embryos can enhance epigenetic reprogramming and produce viable embryos for pregnancy. By inducing the somatic cell into a totipotent state, the stem cell is able to give rise to the rest of the cells in the body. The efficiency of zona free BOF cloning is increased by optimizing the electrofusion and activation procedure, to improve the developmental competence of zona free BOF cloning to produce superior quality transferable embryos to create porcine organ donors. The zona free BOF cloning method disclosed here will increase the developmental rate of blastocysts and overall quality of embryos. Embryos will be analyzed and validated and then used for embryo transfer for into surrogates for generation of genetically modified animal production. The data shown in Tables 2-6 will be used as a guide for optimization of BOF to generate genetically modified embryos for use in producing the genetically engineered animal.

Table 2: Rate of embryo development derived from demecolcine assisted enucleation (DAOE), and Random handmade enucleation (RHE).

Values having different superscripts with in same column differ significantly (p < 0.05). Table 3: Effect of DC pulse on fusion and cleavage efficiency of oocyte bisection cloned embryos on 6V AC current applied.

Table 4: Effect of single and double step fusion efficiency on in vitro developmental competence of oocyte bisected cloned pig embryos.

Table 5: Effect of holding time between electrofusion and activation on in vitro developmental competence of oocyte bisection cloned embryos of pigs. Interval refers to the period of time between fusion and activation.

Table 6: Blastocyst development of oocyte bisected cloned sow and gilt embryos

Values are mean ± SEM Data from 4 trials. Values having different superscripts with in same column differ significantly (p < 0.05).

Development of embryo

[00444] The generation of genetically modified embryos can be improved through a novel method of electrofusion and subsequent development to day 1-7 embryos in culture conditions. Genetically engineered embryos produced by BOF method and cultured in culture to day 7 result in development to blastocyst stage (FIG. 4). Additionally, developing genetically engineered embryos in culture contain within them a transient cluster of cells inside the blastocyst called the“inner cell mass” (ICM). The ICM is composed of stem cells that give rise to all terminal cell lines in the developing pig. The ICM was isolated and stem-like cells that proliferate in vitro and express stem like cell markers were cultured (FIG. 5 and 6). The ICM (Dark masses in FIG. 4) were placed on a feeder layer porcine fibroblast where they increase in size and spread out onto the feeder layer). The ICM as an indicator of development and durability and consistency of the genetic engineering process.

Embryo Developmental Efficiency

[00445] Apoptosis is a cellular process that plays a vital role in mammalian reproduction and development. Normal preimplantation embryos undergo spontaneous apoptosis to eliminate cells that are abnormal, detrimental, or superfluous, and to regulate embryo cell numbers. Perhaps apoptosis has a similar role in in vitro produced embryos, which are frequently mosaic. In human embryos, apoptosis removed only genetically damaged cells and concurrently enabled normal developing cells to proliferate. In vitro embryos are frequently mosaic, leading researchers to believe apoptosis plays a similar role in these systems. Use of Trichostatin A (TSA), a histone deacetylase inhibitor, in cloning protocols might enhance cloning efficiency by inducing apoptosis of abnormal cells in cloned embryos. Assessment of TSA utility is conducted through the analysis of the expression of apoptosis and pluripotency-related genes, namely Bcl-xl, Bax, Caspase 3, Oct4, and Nanog. The goal is to improve the blastocyst quality, selection and transfer for successful implantation to make live cloned piglets. Biomarkers tested for non- invasive embryo selection included: cumulus cell-related genome marker COX2, steroidogenic acute regulatory protein STAR, pentraxin 3 PTX3, and sCD146. CD 146 is involved in embryo implantation and is the membrane-bound form of sCD146 and sCD146 is a recently discovered biomarker for in vitro fertilized embryo development in humans. sCD146 is a non-invasive biomarker selection for in vitro porcine cloned embryo development by using anti- sCD146 antibody for immunocytochemical staining, EFISA and western blotting.

Aggregation improves cloning efficiency and embryo quality

[00446] Embryo aggregation can improve the developmental competence and quality of cloned pig embryos. After aggregation, the quality of genetically embryos will be determined as compared to wild type as a sample of the total embryos produced based on the following assays: Blast development efficiency, Measure apoptosis, Measure Karyotype, Embryo development efficiency, Size, Rate, Markers of pluripotency, Methylation pattern, Multi blast culture to enrich development, Soluble CD 146 (sCD146) non-invasive biomarker for embryo selection, Follicular fluid/cumulus free DNA biomolecular marker to measure embryo quality cox2/PTX3/ASFlA/PCKl gene expression quantification.

Release Testing

[00447] Genetically engineered embryos generated by methods outlined above will undergo testing to determine whether specifications for release into next stage for embryo transfer. Assays to be included and specifications will be as follows:

[00448] Minimum 20% blast development rate if measured to day 7, Micrometer size threshold, Phenotypic cell surface markers expressed as the result of Genetic Engineering, Potential presence of soluble CD 146 (sCD146) non-invasive biomarker for embryo selection, Potential DNA biomolecular marker present in culture to measure embryo quality, Verify potential of

cox2/PTX3/BCL2Ll 1/ASF 1A/PCK1 embryo gene expression from representative embryos from individual batch., and Viral testing through VDF or MVS: PERV A, B, and C, CMV, PCV2, PPV, PRRS

Cell, Fetus, and Piglet Release

Genetically engineered cells generated by methods outlined above will undergo testing to determine whether fetal fibroblast cells meet specifications for release into the next step of SCNT or bi-oocyte fusion (BOF), or in the case of genetically modified piglets, release into next step for generation of genetically modified cells, tissue and organs for transplantation. Assays to be included and specifications will be as follows:

i) Positive selection of each batch of transfected cells with a flow sorter using an anti-HLA-DR antibody. The specification is to collect a minimum of 1,000 genetically-engineered cells per batch. ii) One to 4 days after sort, secondary validation by flow cytometry of sorted cells using anti-HLA- DR antibody. The specification is a minimum percentage of HLA -DR-positive cells of 80%.

iii) Two to 4 days after sort, Sanger sequencing of sorted cells. The specifications are i) positive PCR for an HLA-DR amplicon and ii) demonstration of high-fidelity HLA -DR sequence from said amplicon. iv) Additionally, at 0 to 4 days after sort, genomic DNA is isolated for next generation sequencing of the HLA-DR genes at the insertion site. The specification is a high-fidelity copy of the original gene template with no mutations, insertions, or deletions at critical signaling or protein folding domains. This criteria may come after SCNT as high fidelity sequencing may take longer than 2 weeks.

v) Within one week of sort, as few as 100,000 cells solubilized in a gentle non-reducing detergent buffer to assess the presence of HLA-DR by immune -blotting with anti-HLA-DR antibodies. Meeting this specification can be required for validation of the specific homology recombination directed template used for the generation of transfected cells but not for the release of each batch of transfected cells for embryo production. vi) Sanger sequencing with primers specific for the genes targeted for deletion or insertion (e.g., GGTA1, Rosa26, CMAH, NLRC5, B4GalNT2) will be performed.

In summary, transfected porcine cells, sorted cells, fetal cells, or neonatal piglet cells will be qualified if the following specifications for demonstration of HLA-DR3 gene expression, deletion of target genes, and ability to grow in culture are met.

Genetically engineered cells or embryos will be used for embryo transfer. Embryo transfer of validated embryos will test the viability of new gene modifications to establish pregnancy, develop to full term, and to produce porcine donors for cells, tissues or organ transplants (e.g., islet/kidney transplant). Genetically engineered embryos will be obtained by methods outlined above (e.g. FIG. 3).

Exemplary method for production of genetically modified porcine donor of cells, tissues and organs for transplantation will entail the following steps:

i) Deliver 5- 30 embryos in culture for up to 36 embryo transfer provided embryos pass validation by methods described above.

ii) Tissue and blood samples collected at the time of fetus retrieval or birth will be used to evaluate genetics of neonates. DNA samples from each fetus or piglet will be sequenced at the target gene sites for evidence of mutation as compared to founder pig samples. The phenotype of tissue and blood cells will reflect the genetic changes of each piglet tested. Other markers of embryo development as described above will be tested as necessary to monitor developmental success.

iii) Continued observation and maintenance of developing piglets will be done. Depending on the number of piglets per litter(s) a piglet / pig possessing the desired gene mutations will be sacrificed after skin fibroblast testing at birth and test all the organs relevant to transplantation or cells of interest to present studies. Alternatively, blood samples will be taken and peripheral blood mononuclear cells analyzed for gene mutations and their impact on human and NHP immune cells, antibody binding, and complement deposition.

The methods described above will deliver genetically modified piglets as donors for islets, kidneys, and vaccines for transplantation.

Somatic cell nuclear transfer (SCNT)

[00449] SCNT was performed as described by Whitworth et al. Biology of Reproduction 91(3):78, 1-13, (2014). The SCNT was performed using in vitro matured oocytes (DeSoto Biosciences Inc., St. Seymour, TN). Cumulus cells were removed from the oocytes by pipetting in 0.1% hyaluronidase. Only oocytes with normal morphology and a visible polar body were selected for SCNT. Oocytes were incubated in manipulation media (Ca-free NCSU-23 with 5% FBS) containing 5 mg/mF bisbenzimide and 7.5 mg/mF cytochalasin B for 15 min. Oocytes were enucleated by removing the first polar body plus metaphase II plate. A single cell was injected into each enucleated oocyte, fused, and activated simultaneously by two DC pulses of 180 V for 50 psec (BTX cell electroporator, Harvard Apparatus, Hollison, MA, USA) in 280mM Mannitol, 0.1 mM CaCl ₂ . and 0.05 mM MgCl ₂ . Activated embryos were placed back in NCSU- 23 medium with 0.4% bovine serum albumin (BSA) and cultured at 38.5 °C, 5% CO2 in a humidified atmosphere for less than 1 hour, and transferred into the surrogate pigs.

[00450] While some embodiments have been shown and described herein, such embodiments are provided by way of example only. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the invention. It should be understood that various alternatives to the embodiments of the invention described herein will be employed in practicing the invention.

Example 7 Bi-oocyte fusion cloning (BOF)

[00451] Exemplary method for the activation of porcine cytoplast-fibroblast fused constructs developed to a-l,3-galactosyltransferase (GGTA1) knockout (KO) blastocysts by the zona free bi-oocyte fusion (BOF) cloning is provided below. The Examples demonstrate that the bi-oocyte method disclosed herein has successfully used DAOE to produce BOF embryos, and in doing so, concluded that DAOE is superior to mechanical enucleation for pre-implantation development of embryos. For the purpose of

electrofusion, membranes to be fused must be placed parallel to the electrodes. This is generally accomplished by employing both an AC alignment pulse and manual alignment. For effective fusion, parameters such as pulse duration, pulse length, number of pulses, fusion medium constituents and fusion chamber configuration etc. are disclosed. During conventional nuclear transfer, the donor cell is held close to the cytoplast by the zona pellucida. However, in zona-free SCNT, stereomicroscopic control of the floating somatic cell is difficult due to its small and transparent nature. The somatic cell’s orientation with the cytoplast following application of AC current is inefficient, therefore, phytohemagglutinin aided gluing of the surface of the cytoplast is required, creating a bond strong enough to keep the majority of the somatic cell-cytoplast pairs together, even in the fusion medium. The Examples disclosed herein demonstrate that fusion, cleavage and blastocyst development rates were all significantly higher for the single-step method (96%, 90%, and 39%, respectively), than those obtained for the double-step fusion method (84%, 81%, and 25%, respectively). The holding time interval between electrofusion and activation can affect the remodeling and reprogramming of donor nuclei and the subsequent development of nuclear transfer embryos. The Examples herein demonstrate that cleavage rates associated with 0, 1- and 4-hour holding times were similar, however, the overall blastocyst development rate for the 1-hour holding time was significantly higher (42%) than that obtained for 0-hour (25%) and 4-hour (7%) holding times. The observed increase in blastocyst development rate can be attributed to electrofusion conditions and an appropriate holding time following electrofusion used in the methods herein.

[00452] Further the Examples demonstrate that the observed cleavage and blastocyst development rate was significantly higher in sow-derived oocytes (88% and 37%, respectively) than that of gilt-derived oocytes (71% and 23%, respectively). GGTA1 KO pigs were successfully generated using the

CRISPR/Cas9 gene editing system in PFF followed by FACS analysis for selection of the a-Gal negative population and subsequent Bi-oocyte fusion method as disclosed herein. WT cells and GGTA1 KO cells used in bi-oocyte fusion method were compared in terms of cleavage rate and blastocyst developmental rate. WT and GGTA1 KO cells showed similar cleavage (91.95% and 90.28%, respectively) and blastocyst development rates (41.10% and 38%, respectively). Cloned embryos obtained by methods disclosed herein exhibited similar levels of expression of pluripotent genes, Klf4, Oct4 and Nanog, differentiation related marker, Igf2, apoptosis markers, Bcl-xl and Bax, modulator of DNA methylation, Dnmtl, and cellular reprogramming factor, ASF1.

Material and Methods

Animal Care and Chemicals

[00453] Animal experiments in this study were approved according to Institutional Animal Care and Use Committee (IACUC) protocols. Except where otherwise indicated, all chemicals were purchased from Sigma Chemicals Co. (St. Louis, MO).

Preparation of Porcine Fetal Cell Culture

[00454] Porcine fetal fibroblast (PFF) cells used during the duration of these experiments were isolated from Mangalista male fetuses 35 days after insemination. PFFs were cultured in Dulbecco’s modified eagle medium (DMEM; Gibco) supplemented with 15% (vol/vol) fetal bovine serum (FBS; Gibco) and 1% GlutamaxTM-I (Gibco) at 38°C in a 5% C02 incubator.

sgRNA Design

[00455] Targeted synthetic single guide RNAs (sgRNAs) within the porcine GGTA1 gene were purchased from Synthego and designed according to manufacturer protocol. The GGTA1 sgRNA sequence was designed targeting the first translated exon.

GGTA1 sgRNA: 5' GCTGCTTGTCTCAACTGTAA 3’.

Transfection of GGTA1 sgRNA Gene

[00456] Prior to nucleofection, PFF cells were thawed and cultured for 48 hours until reaching 70 to 80% confluency. Approximately 5x 106 cells were subjected to nucleofection using the SE Cell Line 4D- NucleofectorTM X Kit (Lonza, Allendale, NJ, USA) for primary mammalian cell lines according to the manufacturer’s protocols. Briefly, 5x 106 cells were suspended in 100 ml NucleofectorTM SE solution at room temperature. Synthego synthesized GGTA1 sgRNA (150mM) and sNLS-SpCas9-Snls Nuclease (10mg/ml) were mixed in a 3: 1 ratio. Following sgRNA synthesis, ribonucleoproteins (RNPs) were incubated for 10 minutes at room temperature. Nucleofection was performed after 10 minutes on a 4D- NucleofectorTM Transfection System (Lonza) using program CM-137.

Selection of GGTA1 KO Cells

[00457] At day 7 post-transfection, PFFs were sorted for GGTA1 KO by flow cytometry (FC) (FIG.8A). Approximately 5 x 106 cells were incubated with AF-647 conjugated Isolectin GS-IB4 (3 mg/mL cell suspension; isolated from Griffonia simplicifolia, Thermo-Fisher Scientific) for 1 hour on ice. Incubated cells were then washed in 4 ml of phosphate buffered saline (PBS) and cell pellets were made by centrifugation at 1000 rpm for 5 minutes. After centrifugation, cell pellets were resuspended in 0.5 ml of PBS. Sorting of GGTA1 KO cells was accomplished by fluorescence-activated cell sorting (FACS) analysis on a BD FACSMelody Cell Sorter (BD Biosciences) with WT cells as a positive control and an additional unstained control.

Sequencing and TIDE Analysis for GGTA1 KO Cells

[00458] Isolation of DNA was performed using the QIAmp DNA Micro Kit (Qiagen) to detect mutations in GGTA1 KO fetal fibroblasts. PCR fragments around the cut site region were amplified by forward and reverse sequencing (FIG. 8B):

Forward 5’ CCTTAGCGCTCGTTGACTATTC 3’;

[00459] The amplicon, measuring approximately 586 bp, was subsequently sent for Sanger sequencing using the primers shown in Table 8. TIDE analysis was performed as previously described in order to analyze the incidence of major induced mutations in the projected editing site frequency in a single cell population when compared with the WT population.

Table 8. Primer Sequences and PCR Product Sizes

Immunofluorescence Staining

[00460] For Gal epitope staining, GGTA1 KO and WT positive control cells were incubated in 4% paraformaldehyde for 30 minutes at 4°C. After fixation, cells were further incubated in AF-647 conjugated Isolectin GS-IB4 (3 mg/mL cell suspension; isolated from Griffonia simplicifolia, Thermo- Fisher Scientific) for 30 minutes 4°C. Following incubation, cells were washed with PBS a total of four times each.

Differential Staining

[00461] Differential staining was performed. Briefly, on day 7, blastocysts were subjected to anti-Bovine Serum antibody produced in rabbit (Sigma, B3759) at a 1:4 dilution in PZM culture media containing 3 mg/ml of bovine serum albumin (BSA) (PZM-3) for 30 minutes. Blastocysts were washed in PZM-3 and then placed into a 1:9 dilution in PZM-3 of complement sera from guinea pig (Sigma- Aldrich, SI 639) containing 5 mg/mF propidium iodide and 40 mg/mF Hoechst 33342 for 15 minutes. Blastocysts were rinsed in DPBS containing 0.1% BSA and mounted on glass slides. Images were taken using an Olympus FluoView 2000 confocal inverted microscope.

Karyotyping

[00462] Cytogenetic analyses were performed using the Cytogenomics Shared Resource at the

University of Minnesota.

RNA Extraction and Reverse Transcription

[00463] Gene expression analysis was performed for both WT and GGTA1 KO cells. For each group, 20 blastocysts were pooled. Each analysis was repeated three times, where each repetition was done by duplicate. Embryos were washed two times in PBS to eliminate any remaining culture media from the blastocysts. RNA was isolated using the PicoPure™ RNA Isolation Kit (Applied Biosystems, Thermo- Fisher Scientific, Fithuania) according to manufacturer’s instructions. Samples were subjected to DNase treatment using the RNase-Free DNase Set (Qiagen, 79254) for genomic DNA digestion. RNA con centration and purity at the absorbance ratio 260/280 nm were determined on a NanoDrop 2000c Spectrophotometer (Thermo-Fisher Scientific). The range of the extracted RNA was between 30 and 65 ng/ml.

[00464] The QuantiTect® Reverse Transcription Kit (Qiagen) was used for reverse transcription (RT) according to the manufacturer’s instructions. Amplification of complementary DNA (cDNA) was performed in 20 mL final volumes containing 2 ml of genomic DNA (gDNA) wipeout, up to 500 ng of template RNA, and RNase-free water, followed by incubation at 42°C for 2 minutes. Following incubation, samples were placed immediately on ice. To further carry out the RT reaction, 1 ml of reverse transcriptase, 4 ml of 5x Quantiscript RT Buffer, and 1 ml RT Primer Mix were added. RT was carried out in a C1000 TouchTM Thermal Cycler (Bio-Rad) at 42°C for 1 hour. The RT reaction was then inactivated at 95°C for 3 minutes and finally maintained at 4°C.

Gene Expression Analysis

[00465] Real-time PCR was performed in accordance with the minimum information for publication of quantitative real-time PCR experiments (MIQE) guidelines. Quantitative PCR was applied using SYBR- Green with a CFX96 TouchTM Real-Time PCR Detection System (Bio-Rad) according to the manufacturer’s instructions. Messenger RNA (mRNA) levels of Klf4, Oct4, Nanog, Igf2, Bax, Bcl-xl, Dnmtl, and ASF1 were measured and normalized with ACTB. PCR was carried out in a total volume of 20 mL contained 10 ml master mix, 1 ml of each primer (10 mmol/ul), 1 ml cDNA template (500 ng), and 7 ml nuclease free water.

[00466] All PCR reactions were initiated at 95°C for 30 seconds, followed by 39 cycles of 95°C for 15 seconds, 60°C for 20 seconds, and 72°C for 30 seconds. Reactions were terminated at around 10 minutes at 72°C. All tests were conducted in duplicate and the final product’s identity was confirmed by melting curve analysis.

Printer Design

[00467] Primers used for expression analysis were designed using the online PrimerQuest tool

(Integrated DNA Technologies) based on available sequences obtained from the NCBI GenBank database. Primers and products sizes are shown (Table 8).

Oocyte collection and IVM

[00468] Sow cumulus-oocyte complexes (COCs) were obtained from a commercial supplier (DeSoto Biosciences, Inc., Seymour, TN). Gilt ovaries were obtained from a local slaughter house (MRS, Glencoe). Immature oocytes were aspirated from follicles measuring between 2 and 6 mm with an 18- gauge needle attached to a 10-ml syringe. Oocytes with 3 to 4 layers of cumulus cells and evenly dark cytoplasm were selected for maturation. Maturation of oocytes was accomplished according to established protocol with the following modifications. COCs were matured in groups of 50 in 500 pF of Ml 99 supplemented with 5 mg/mF of porcine follicle-stimulating hormone (pFSH) , 40 ng/mF fibroblast growth factor-2 (FGF2), 20 ng/mF leukemia inhibition factor (FIF), 20 ng/mF insulin-like growth factor- 1 (IGF1), 10% (v/v) FBS, 10% (v/v) pig follicular fluid, 0.8 mM sodium pyruvate and 50 mg/mF gentamicin at 38.5oC in a humidified 5% C02 incubator for between 41 and 44 hours.

Enucleation followed by Bi-oocyte Fusion Cloning

[00469] DAOE was performed. After 41 hours maturation in vitro, COCs were further cultured for 45 minutes in the media supplemented with 0.4 mg/mF demecolcine. The following steps for BOF cloning are summarized in a flow chart (FIG. 7). Cumulus cells were removed by pipetting in 1 mg/ml hyaluronidase dissolved in HEPES-buffered tissue culture medium 199 (TCM-199). From this point, all steps were performed on a heated stage adjusted to 39oC, except where otherwise indicated.

[00470] The procedures for BOC and HMC were performed. Zona pellucida of oocytes were partially digested by 3 mg/ml pronase dissolved in 30% BSA in HEPES-buffered TCM-199 Medium (T30) (Thenno-Fisher Scientific). Upon observing the occurrence of partial lyses of zonae pellucidae and slight deformation of oocytes, oocytes were picked up and washed quickly in T20 drops. Oocytes were then lined up in a 35 mm dish containing 20% BSA in HEPES-buffered TCM-199 Medium (T20) (Thermo- Fisher Scientific) supplemented with 2.5 wg/m L cytochalasin B (CB). Using finely drawn, fire-polished glass pipettes, oocytes were rotated to find either a light extrusion cone and/or a strongly attached polar body (PB) on the surface, and oocyte bisection was performed with a micro blade ((Ultra-Sharp Splitting Blades, Bioniche, USA)) under a stereo microscope. Following enucleation, bisected oocytes were rested in T20 in a 5% CO2 incubator at 38.5°C for between 20 and 30 minutes.

Oocyte Bisection Enucleation Without Demecolcine Treatment or Random Enucleation

[00471] All steps performed were similar to procedure described above, with the exception that demecolcine pre-incubation was omitted.

Fusion and activation

[00472] Fusion was attempted according to both the double-step fusion method, and the single-step fusion method. Enucleated demi-cytoplasts were immersed in phytohemagglutinin (0.5 mg/ml in T20) for 3 to 4 seconds and transferred into T20-containing, low-density donor cells. Each demi-cytoplast was then allowed to stick to one rounded, medium sized cell by gently rolling the demi-cytoplast over it. Demi-cytoplast-donor cell pairs were transferred to fusion medium (0.3 M D-mannitol, 0.1 mM MgS04, 0.1 mM CaC12 supplemented with 0.01% (w/v) poly-vinyl alcohol (PVA) for equilibration. The couplets and the remaining demi-cytoplasts were then transferred away from the positive and negative poles, respectively, of the fusion chamber using a Model ECM 2001 BTX MicroslideTM with a 0.5 mm gap (BTX, San Diego, CA). A single-step fusion protocol was subsequently followed, wherein a demi- cytoplast and a couplet were picked using fine-pulled Unopette® capillary pipettes (Becton Dickinson, NJ) with an inner diameter of 100 to 120 pm. Initially, the couplet was expelled and aligned with a 6 V AC pulse using an ECM 2001 Electro Cell Manipulator (BTX), where the somatic cell was facing the negative electrode. Immediately after alignment, the demi-cytoplast was introduced into the fusion chamber closest to the somatic cell. Once the somatic cell was sandwiched between the demi-cytoplasts, a single DC pulse was applied, and triplets were then rested in T20 for 1 to 2 hours at 38.5°C. Following incubation, reconstructs were activated by combined thimerosal/DTT treatment. Oocytes were treated with 200 pM thimerosal (Sigma, T8784) for 10 minutes followed by treatment with 8 mM DTT for 30 minutes. Following activation, embryos were transferred to 700 pi PZM-3 medium supplemented with 3 mg/ml of fatty acid free BSA in a well of the well (WOW) system.

Experimental Design

[00473] All of the experiments conducted in this study were performed keeping all parameters constant except the variable intended to be tested, in order to achieve better understanding of each parameter. Experiment 1

[00474] The efficiency of DAOE and oriented random handmade enucleation (RHE), was tested in three replicates using a total of 147 oocytes. After 41 hours of maturation, oocytes were subjected to demecolcine incubation. Oocyte bisection was performed for selected oocytes where either an extrusion cone and/or a strongly attached PB were detected after partial pronase digestion.

[00475] The efficiency and reliability of enucleation without demecolcine treatment was also investigated in three replicates using a total of 75 oocytes. After 41 hours of in vitro maturation, oocyte bisection was performed in selected matured oocytes where either an extrusion cone and/or a strongly attached PB were detected after partial pronase digestion.

Experiment 2

[00476] For electrofusion of oocyte-fibroblast-oocyte triplets, pulse amplitude and number of pulses given were compared according to the following: Group A (1.2 kV/cm for 20 ms, single pulse), Group B (2.0 kV/cm for 80 ps single pulse), Group C (1.0 kV/cm for 9 ps, single pulse). Cleavage rate was determined at day 2 of culture.

Experiment 3

[00477] Two different fusion methods were compared in this experiment. In the first method, a single donor cell was sandwiched between two demi-cytoplasts, after which electrofusion was carried out in a single-step. The second method was comprised of a two-step protocol where the first step included fusion of a single somatic cell with an enucleated demi-cytoplast after which the pair was fused with another demi-cytoplast in the second step.

Experiment 4

[00478] Fused reconstructs were incubated for 0, 1 and 4 hours at 38.5 °C in a humidified 5% C02 incubator in air after electrofusion in T20 for genomic reprogramming of the donor cell. Developmental competence was compared in terms of blastocyst development rate.

Experiment 5

[00479] Difference in developmental competence between sow- and gilt-derived oocytes were investigated through zona-free oocyte bisection cloning after demecolcine treatment, followed by activation in thimerosal/DTT.

EXAMPLE 8 Effect of Demecolcine-Assisted Oocyte Enucleation on Embryo Development to Blastocyst Stage

[00480] Fusion rates were similar for DAOE and RHE. Overall efficiency, cleavage rate, and blastocyst development rate were significantly higher (p<0.05) in the DAOE group, as compared to the RHE group (Table 2) followed by thimerosal/DTT chemical activation.

EXAMPLE 9 DC Pulse Effect on Fusion and Cleavage Efficiency of Oocyte Bisected Cloned Embryos

[00481] Similar fusion rates were found for groups A, B, and C. The cleavage rate was significantly higher (p<0.05) for group C, compared to group A and group B (Table 3) with a voltage of 6 V. Based on these results, the electrofusion parameter of a single pulse of 1.0 kV/cm for a 9 ps duration was subsequently used for further experiments.

EXAMPLE 10 Single-step Fusion Efficiency on Blastocyst Development Competency [00482] Fusion, cleavage and blastocyst development rates were all significantly higher (p<0.05) for the single-step fusion method when compared to the double-step fusion method (Table 4).

EXAMPLE 11 Effect of Differential Holding Time Interval Between Electro-fusion and Activation on In Vitro Developmental Competence of Cloned Embryos

[00483] Cleavage rates for oocytes subjected to 0, 1- and 4-hour incubation were similar, however, the overall blastocyst development rate was significantly higher (p< 0.05) for oocytes incubated for 1 hour, as compared to 0 and 4-hour holding times (Table 5).

EXAMPLE 12 In Vitro Developmental Competence of Sow- and Gilt- Oocyte Derived Blastocysts

[00484] Cleavage and blastocyst development rates were significantly higher (p<0.05) for sow-derived oocytes subjected to BOF cloning followed by activation in thimerosal/DTT, as compared to gilt-derived oocytes (Table 6).

EXAMPLE 13 Generation of GGTA1 KO Cells

[00485] PFFs were isolated from day 35 fetuses bred from male Mangalista pigs. CRISPR/Cas9 GGTA1 sgRNA transfected into PFFs by nucleofection. After 7 days in culture, sorting was performed on WT and GGTA1 KO cells by AF-647 Isolectin GS-IB4 staining. Specific gene product (586 bp) was isolated by PCR amplification and sequencing confirmed the single nucleotide deletion in GGTA 1 KO compared to WTs. TIDE analysis for major induced mutations in the projected editing site frequency in a single cell population of GGTA1 KO fetal fibroblast cells in comparison to WT cells. Comparison of GGTA1 KO cells to WT cells by FACS showed no a-Gal expression on the cells. Karyotyping analysis was performed on WT and KO cells to rule out any chromosomal abnormality and no aberrant chromosomal rearrangements were detected in either GGTA1 KO or WT cells.

EXAMPLE 14 Production of GGTA1 KO Embryos, Gene Expression Pattern, and Embryo Quality Evaluation

[00486] Comparison of in vitro production efficiency for WT and GGTA 1 KO embryos is shown in Table 7. Blastocyst development rates for GGTA1 KO cells (38 ± 1.76) were comparable to the rate of blastocyst development for WT cells (41.1 ± 0.67). As shown in FIG. 4, GGTA1 KO blastocysts generated at day 7 show a proper developmental appearance. In addition, differential staining of GGTA1 KO blastocyst produced by BOF cloning (FIG. 10A), demonstrated by blue color (Hoechst 33342) and pink color (propidium iodide), are indicative of inner cell mass (ICM) and trophectoderm (TE) cells, respectively.

[00487] Accordingly, in order to compare cellular reprogramming between WT and GGTA1 KO blastocysts, the following parameters were assessed (FIG. 10B): relative expression levels of pluripotency genes Klf4, Oct4 and Nanog, the differentiation related marker, Igf2, two apoptosis markers, Bcl-xl and Bax, a key modulator of DNA methylation, Dnmtl, and cellular reprogramming factor, ASF1. Non-significant mRNA levels were observed for Klf4, Oct4, Nanog, Igf2, Dnmtl, Bax, Bcl-xl and ASF1 genes in GGTA1 KO blastocysts, as compared to WT blastocysts.

[00488] Table 9 lists sequences for the disclosure