EP3945799A1 - Personalisierte zellen, gewebe und organe zur transplantation von einem humanisierten, spezifischen, von designiertem pathogen freien, (nichthumanen) spender und verfahren und produkte im zusammenhang damit - Google Patents

Personalisierte zellen, gewebe und organe zur transplantation von einem humanisierten, spezifischen, von designiertem pathogen freien, (nichthumanen) spender und verfahren und produkte im zusammenhang damit

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Publication number
EP3945799A1
EP3945799A1 EP20719309.5A EP20719309A EP3945799A1 EP 3945799 A1 EP3945799 A1 EP 3945799A1 EP 20719309 A EP20719309 A EP 20719309A EP 3945799 A1 EP3945799 A1 EP 3945799A1
Authority
EP
European Patent Office
Prior art keywords
human
swine
sla
reprogrammed
wild
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Pending
Application number
EP20719309.5A
Other languages
English (en)
French (fr)
Inventor
Paul W. HOLZER
Jon ADKINS
Rodney L. MON ROY
Elizabeth J. CHANG
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Alexis Bio Inc
Xenotherapeutics Inc
Original Assignee
Xenotherapeutics Corp
Xenotherapeutics Inc
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Priority claimed from PCT/US2019/054833 external-priority patent/WO2020072982A1/en
Application filed by Xenotherapeutics Corp, Xenotherapeutics Inc filed Critical Xenotherapeutics Corp
Publication of EP3945799A1 publication Critical patent/EP3945799A1/de
Pending legal-status Critical Current

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Classifications

    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01K—ANIMAL HUSBANDRY; AVICULTURE; APICULTURE; PISCICULTURE; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
    • A01K67/00—Rearing or breeding animals, not otherwise provided for; New or modified breeds of animals
    • A01K67/027—New or modified breeds of vertebrates
    • A01K67/0271—Chimeric vertebrates, e.g. comprising exogenous cells
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/0004—Oxidoreductases (1.)
    • C12N9/0071—Oxidoreductases (1.) acting on paired donors with incorporation of molecular oxygen (1.14)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/10—Transferases (2.)
    • C12N9/1048—Glycosyltransferases (2.4)
    • C12N9/1051—Hexosyltransferases (2.4.1)
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01K—ANIMAL HUSBANDRY; AVICULTURE; APICULTURE; PISCICULTURE; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
    • A01K2227/00—Animals characterised by species
    • A01K2227/10—Mammal
    • A01K2227/108—Swine
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01K—ANIMAL HUSBANDRY; AVICULTURE; APICULTURE; PISCICULTURE; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
    • A01K2267/00—Animals characterised by purpose
    • A01K2267/02—Animal zootechnically ameliorated
    • A01K2267/025—Animal producing cells or organs for transplantation

Definitions

  • CMV cytomegalovirus
  • tissue transplants include criteria for donor screening and testing for adventitious agents, as well as strict regulations that govern the processing and distribution of tissue grafts.
  • the transmission of viruses has occurred as a result of allotransplantation.
  • Exogenous retroviruses Human T-cell leukemia virus type 1 (HTLV-1), Human T-cell leukemia virus type 2 (HTLV-2), and Human immunodeficiency virus (HIV) have been transmitted by human tissues during organ and cell transplantation, as have viruses such as human cytomegalovirus, and even rabies. Due to technical and timing constraints surrounding organ viability and post-mortem screening, absolute testing is hindered, and this risk cannot be eliminated.
  • immunosuppressants prolong survival of the transplanted graft in acute and chronic rejection schemas.
  • they leave patients vulnerable to infections from even the most routine of pathogens and require continued use for life but expose the patient to an increased risk of infection, even cancer immunosuppressant can blunt the natural immunological processes; unfortunately, these medications are often a lifelong requirement after organ transplantation and increase recipient susceptibility to otherwise routine pathogens.
  • organ transplantation is unquestionably the preferred therapy for most patients with end stage organ failure, in large part due to a lack of viable alternatives.
  • organ transplantation as a successful life-saving therapeutic intervention, juxtaposed against the paucity of organs available to transplant, unfortunately places medical professionals in an ideologically vexing position of having to decide who lives and who dies.
  • alternative and adjunct treatment options that would minimize the severe shortcomings of allotransplant materials while providing the same mechanism of action that makes them so effective would be of enormous benefit to patients worldwide.
  • Xenotransplantation such as the transplantation of a non-human animal organ into a human recipient, has the potential to reduce the shortage of organs available for transplant, potentially helping thousands of people worldwide.
  • Swine have been considered a potential non human source of organs, tissue and/or cells for use in human xenotransplantation given that their size and physiology are compatible with humans.
  • xenotransplantation using standard, unmodified pig tissue into a human or other primate is accompanied by rejection of the transplanted tissue.
  • Wild type swine organs would evoke rejection by the human immune system upon transplantation into a human where natural human antibodies target epitopes on the swine cells, causing rejection and failure of the transplanted organs, cells or tissue.
  • the rejection may be a cellular rejection (lymphocyte mediated) or humoral (antibody mediated) rejection including but not limited to hyperacute rejection, an acute rejection, a chronic rejection, may involve survival limiting thrombocytopenia coagulopathy and an acute humoral xenograft reaction (AHXR).
  • Other roadblocks with respect to swine to human xenotransplantation include risks of cross-species transmission of disease or parasites.
  • alpha-1, 3- galactosyltransferase (“alpha-l,3-GT”) in porcine cells, which causes the synthesis of alpha-1, 3- galactose epitopes.
  • alpha-l,3-GT galactosyltransferase
  • most mammals carry glycoproteins on their cell surfaces that contain galactose alpha 1,3-galactose (see, e.g., Galili et ah,“Man, apes, and old world monkeys differ from other mammals in the expression of a- galactosyl epitopes on nucleated cells,” J Biol. Chem. 263 : 17755-17762 (1988).
  • Antibodies to the a-Gal, Neu5GC, b1,4-N and Sda-like antigens are present in human blood prior to implantation of xeno-tissue, and are involved in the intense and immediate antibody -mediated rejection of implanted tissue.
  • pig cells express Class I and Class II SLAs on endothelial cells.
  • the SLA cross-reacting antibodies contribute to the intense and immediate rejection of the implanted porcine tissue.
  • SLA antigens may also be involved with the recipient's T-cell mediated immune response.
  • Porcine SLAs may include, but are not limited to, antigens encoded by the SLA-1, SLA- 2, SLAG, SLAG, SLAG, SLAG, SLA-9, SLA-11 and SLA-12 loci.
  • Porcine Class II SLAs include antigens encoded by the SLA-DQ and SLA-DR loci.
  • transgenic swine free of PERV and utilizing transgenic bone marrow for therapy
  • eGenesis, Inc. PCT/US2018/028539
  • creating transgenic swine utilizing stem cell scaffolding see, e,g, United Therapeutics/Revivicor [US20190111180A1 ]
  • mixed chimerism and utilizing transgenic bone marrow for therapy to tolerize patient T-cells see, e,g, Columbia University [US20180070564A1].
  • These“downstream” approaches - post recognition by the human immune system - have not succeeded in producing swine that produce products suitable for prolonged use in xenotransplantation or that survive the above-referenced transgenic and other alterations.
  • the present invention achieves a “patient-specific” solution by modifying the genome of donor swine cells to escape detection from the human immune system in the first instance, avoiding the immune cascade that follows when a patient’s T-cells and antibodies are primed to destroy foreign material.
  • This“upstream” approach is achieved through, in one aspect, specific combinations of minimal genetic alterations that render the donor animal’s cells, tissues, and organs tolerogenic when transplanted into a human without sacrificing the animal’s immune function.
  • the present invention therefore addresses long-felt but unmet need for translating the science of xenotransplantation into a clinical reality.
  • This“upstream” approach is achieved through, in one aspect, -specific combinations of minimal genetic alterations that render the donor animal’s cells, tissues, and organs tolerogenic when transplanted into a human without sacrificing the animal’s immune function.
  • the present invention therefore addresses long-felt but unmet need for translating the science of xenotransplantation into a clinical reality.
  • the present disclosure includes a biological system for generating and preserving a repository of personalized, humanized transplantable cells, tissues, and organs for transplantation, wherein the biological system is biologically active and metabolically active, the biological system comprising genetically reprogrammed cells, tissues, and organs in a non-human animal for transplantation into a human recipient.
  • the non-human animal is a genetically reprogrammed swine for xenotransplantation of cells, tissue, and/or an organ isolated from the genetically reprogrammed swine, the genetically reprogrammed swine comprising a nuclear genome that has been reprogrammed to replace a plurality of nucleotides in a plurality of exon regions of a major histocompatibility complex of a wild-type swine with a plurality of synthesized nucleotides from a human captured reference sequence.
  • cells of said genetically reprogrammed swine do not present one or more surface glycan epitopes selected from alpha-Gal, Neu5Gc, and SD a .
  • genes encoding alpha-1,3 galactosyltransferase, cytidine monophosphate-N-acetylneuraminic acid hydroxylase (CMAH), and b1,4-N- acetylgalactosaminyltransferase are altered such that the genetically reprogrammed swine lacks functional expression of surface glycan epitopes encoded by those genes.
  • the reprogrammed genome comprises site-directed mutagenic substitutions of nucleotides at exon regions of: i) at least one of the wild-type swine’s SLA-1, SLA-2, and SLA-3 with nucleotides from an orthologous exon region of HLA-A, HLA-B, and HLA-C, respectively, of the human captured reference sequence; and ii) at least one the wild-type swine’s SLA-6, SLA-7, and SLA-8 with nucleotides from an orthologous exon region of HLA-E, HLA-F, and HLA-G, respectively, of the human captured reference sequence; and iii) at least one of the wild-type swine’s SLA-DR and SLA-DQ with nucleotides from an orthologous exon region of HLA-DR and HLA-DQ, respectively, of the human captured reference sequence.
  • the reprogrammed genome comprises at least one of A-
  • the reprogrammed swine nuclear genome comprises site-directed mutagenic substitutions of nucleotides at exon regions of the wild-type swine’s b2- microglobulin with nucleotides from orthologous exons of a known human p2-microglobulin from the human captured reference sequence;
  • the reprogrammed swine nuclear genome comprises a polynucleotide that encodes a polypeptide that is a humanized beta 2 microglobulin (hB2M) polypeptide sequence that is at least 95% identical to the amino acid sequence of beta 2 microglobulin glycoprotein expressed by the human captured reference genome;
  • hB2M humanized beta 2 microglobulin
  • the reprogrammed swine nuclear genome has been reprogrammed such that, at the swine’s endogenous p2-microglobulin locus, the nuclear genome has been reprogrammed to comprise a nucleotide sequence encoding p2-microglobulin polypeptide of the human recipient.
  • the reprogrammed swine nuclear genome has been reprogrammed such that the genetically reprogrammed swine lacks functional expression of the wild-type swine’s endogenous P2-microglobulin polypeptides. Further, the reprogramming does not introduce any frameshifts or frame disruptions.
  • the present disclosure includes a method of preparing a genetically reprogrammed swine comprising a nuclear genome that lacks functional expression of surface glycan epitopes selected from alpha-Gal, Neu5Gc, and SD a and is genetically reprogrammed to express a humanized phenotype of a human captured reference sequence comprising:
  • a porcine fetal fibroblast cell a porcine zygote, a porcine Induced Pluripotent Stem Cells (IPSC), or a porcine germ-line cell;
  • ISC porcine Induced Pluripotent Stem Cells
  • b genetically altering said cell in a) to lack functional alpha- 1,3 galactosyltransf erase, cytidine monophosphate-N-acetylneuraminic acid hydroxylase (CMAH), and b1,4- N-acetylgalactosaminyltransferase;
  • CMAH cytidine monophosphate-N-acetylneuraminic acid hydroxylase
  • CRISPR clustered regularly interspaced short palindromic repeats
  • CRISPR clustered regularly interspaced short palindromic repeats
  • SLA-1, SLA-2, and SLA-3 with nucleotides from an orthologous exon region of HLA-A, HLA-B, and HLA-C, respectively, of the human captured reference sequence
  • intron regions of the wild-type swine’s genome are not reprogrammed, and wherein the reprogrammed genome comprises at least one of A-C:
  • the reprogrammed swine nuclear genome comprises site-directed mutagenic substitutions of nucleotides at exon regions of the wild-type swine’s b2- microglobulin with nucleotides from orthologous exons of a known human p2-microglobulin from the human captured reference sequence;
  • the reprogrammed swine nuclear genome comprises a polynucleotide that encodes a polypeptide that is a humanized beta 2 microglobulin (hB2M) polypeptide sequence that is at least 95% identical to beta 2 microglobulin expressed by the human captured reference genome;
  • hB2M humanized beta 2 microglobulin
  • the present disclosure includes a method of producing a donor swine tissue or organ for xenotransplantation, wherein cells of said donor swine tissue or organ are genetically reprogrammed to be characterized by a recipient-specific surface phenotype comprising: a. obtaining a biological sample containing DNA from a prospective human transplant recipient;
  • exon regions encoding at least one of SLA-6, SLA-7, and SLA-8;
  • the present disclosure includes a method of screening for off target edits or genome alterations in the genetically reprogrammed swine comprising a nuclear genome of the present disclosure including: a. performing whole genome sequencing on a biological sample containing DNA from a donor swine before performing genetic reprogramming of the donor swine nuclear genome, thereby obtaining a first whole genome sequence;
  • the present disclosure includes a synthetic nucleotide sequence having wild-type swine intron regions from a wild-type swine MHC Class la, and reprogrammed at exon regions encoding the wild-type swine’s SLA-3 with codons of HLA-C from a human capture reference sequence that encode amino acids that are not conserved between the SLA-3 and the HLA-C from the human capture reference sequence.
  • the wild-type swine’s SLA-1 and SLA-2 each comprise a stop codon.
  • the present disclosure includes a synthetic nucleotide sequence having wild-type swine intron regions from a wild-type swine MHC Class lb, and reprogrammed at exon regions encoding the wild-type swine’s SLA-6, SLA-7, and SLA-8 with codons of HLA- E, HLA-F, and HLA-G, respectively, from a human capture reference sequence that encode amino acids that are not conserved between the SLA-6, SLA-7, and SLA-8 and the HLA-E, HLA-F, and HLA-G, respectively, from the human capture reference sequence.
  • the present disclosure includes a synthetic nucleotide sequence having wild-type swine intron regions from a wild-type swine MHC Class II, and reprogrammed at exon regions encoding the wild-type swine’s SLA-DQ with codons of HLA-DQ, respectively, from a human capture reference sequence that encode amino acids that are not conserved between the SLA-DQ and the HLA-DQ, respectively, from the human capture reference sequence, and wherein the wild-type swine’s SLA-DR comprises a stop codon.
  • the present disclosure includes a synthetic nucleotide sequence having wild-type swine intron regions from a wild-type swine beta-2-microglobulin and reprogrammed at exon regions encoding the wild-type swine’s beta-2-microglobulin with codons of beta-2-microglobulin from a human capture reference sequence that encode amino acids that are not conserved between the wild-type swine’s beta-2-microglobulin and the beta-2- microglobulin from the human capture reference sequence, wherein the synthetic nucleotide sequence comprises at least one stop codon in an exon region such that the synthetic nucleotide sequence lacks functional expression of the wild-type swine’s p2-microglobulin polypeptides.
  • the present disclosure includes a synthetic nucleotide sequence having wild-type swine intron regions from a wild-type swine MIC-2, and reprogrammed at exon regions of the wild-type swine’s MIC-2 with codons of MIC-A or MIC-B from a human capture reference sequence that encode amino acids that are not conserved between the MIC-2 and the MIC-A or the MIC-B from the human capture reference sequence.
  • the present disclosure includes a synthetic nucleotide sequence having wild-type swine intron regions from a wild-type swine CTLA-4, and reprogrammed at exon regions encoding the wild-type swine’s CTLA-4 with codons of CTLA-4 from a human capture reference sequence that encode amino acids that are not conserved between the wild-type swine’s CTLA-4 and the CTLA-4 from the human capture reference sequence.
  • the present disclosure includes a synthetic nucleotide sequence having wild-type swine intron regions from a wild-type swine PD-L1 and reprogrammed at exon regions encoding the wild-type swine’s PD-L1 with codons of PD-L1 from a human capture reference sequence that encode amino acids that are not conserved between the wild-type swine’s PD-L1 and the PD-L1 from the human capture reference sequence.
  • the present disclosure includes a synthetic nucleotide sequence having wild-type swine intron regions from a wild-type swine EPCR and reprogrammed at exon regions encoding the wild-type swine’s EPCR with codons of EPCR from a human capture reference sequence that encode amino acids that are not conserved between the wild-type swine’s EPCR and the EPCR from the human capture reference sequence.
  • the present disclosure includes a synthetic nucleotide sequence having wild-type swine intron regions from a wild-type swine TBM and reprogrammed at exon regions encoding the wild-type swine’ s TBM with codons of TBM from a human capture reference sequence that encode amino acids that are not conserved between the wild-type swine’s TBM and the TBM from the human capture reference sequence.
  • the present disclosure includes a synthetic nucleotide sequence having wild-type swine intron regions from a wild-type swine TFPI and reprogrammed at exon regions encoding the wild-type swine’s TFPI with codons of TFPI from a human capture reference sequence that encode amino acids that are not conserved between the wild-type swine’s TFPI and the TFPI from the human capture reference sequence.
  • the present invention achieves a “patient-specific” solution by modifying the genome of donor swine cells to escape detection from the human immune system in the first instance, avoiding the immune cascade that follows when a patient’s T-cells and antibodies are primed to destroy foreign material.
  • This“upstream” approach is achieved through, in one aspect, minimal, modifications to the swine genome involving distinct combinations of disruptions (such as knocking out al,3-galactosyltransferase (aGal), cytidine monophosphate-N-acetylneuraminic acid hydroxylase (CMAH) and/or b1-4 N- acetylgalactosaminyltransferase such that the donor swine cells do not express such on its cell surfaces), regulation of expression of certain genes (for example, CTLA-4 and PD-1), and replacement of specific sections of the swine genome with synthetically engineered sections based upon recipient human capture sequences (for example, in certain SLA sequences to regulate the swine’s expression of, for example, MHC-I and MHC-II).
  • disruptions such as knocking out al,3-galactosyltransferase (aGal), cytidine monophosphate-N-acetylneur
  • the present disclosure centralizes (predicates) the creation of hypoimmunogenic and/or tolerogenic cells, tissues, and organs that does not necessitate the transplant recipients’ prevalent and deleterious use of exogenous immunosuppressive drugs (or prolonged immunosuppressive regimens) following the transplant procedure to prolong the life saving graft.
  • the present disclosure provides genetically modified, non- transgenic swine that are minimally altered.
  • certain distinct sequences appearing on the donor swine SLA comprising native base pairs are removed and replaced with a synthetic sequence comprising the same number of base pairs but reprogrammed based on the recipient’s human capture sequence.
  • This minimal alteration keeps other aspects of the native swine genome in place and does not disturb, for example, introns and other codons naturally existing in the swine genome.
  • the present invention provides swine with such and other modifications, created in a designated pathogen environment in accordance with the processes and methods provided herein.
  • the products derived from such swine for xenotransplantation are minimally manipulated, viable, live cell, and capable of making an organic union with the transplant recipient, including, but not limited to, inducing vascularization and/or collagen generation in the transplant recipient.
  • products derived from such source animals are preserved, including, but not limited to, through cryopreservation, in a manner that maintains viability and live cell characteristics of such products.
  • such products are for homologous use, i.e., the repair, reconstruction, replacement or supplementation of a recipient’s organ, cell and/or tissue with a corresponding organ, cell and/or tissue that performs the same basic function or functions as the donor (e.g., swine skin is used as a transplant for human skin, swine kidney is used as a transplant for human kidney, swine liver is used as a transplant for human liver, swine nerve is used as a transplant for human nerve and so forth).
  • swine skin is used as a transplant for human skin
  • swine kidney is used as a transplant for human kidney
  • swine liver is used as a transplant for human liver
  • swine nerve is used as a transplant for human nerve and so forth.
  • the present invention that the utilization of such products in xenotransplantation be performed with or without the need to use immunosuppressant drugs or therapies which inhibit or interfere with normal immune function.
  • FIG. 1 illustrates an image of human trophoblast and trophoblast cells.
  • FIG. 2 schematically illustrates a T Cell Receptor (TCR) binding MHC Class I and a peptide.
  • FIG. 3 schematically illustrates HLA Class I on the surface of a cell.
  • FIG. 4 schematically illustrates a Cytotoxic T Cell (CD8+) - Target Cell Interaction.
  • FIG. 5 schematically illustrates a Cytotoxic T Cell (CD4+) - Target Cell Interaction.
  • FIG. 6 schematically illustrates codominant expression of HLA genes and the position of HLA genes on human chromosome 6.
  • FIG. 7 is a table listing numbers of serological antigens, proteins, and alleles for human MHC Class I and Class II isotypes.
  • FIG. 8 schematically illustrates HLA Class I and Class II on the surface of a cell.
  • FIG. 9 shows the structure of MHC Class I (A) and Class II proteins (B).
  • the two globular domains furthest from the plasma membrane that form the peptide binding region (PBR) are shaded in blue.
  • the two Ig-like domains, including the p2-microglobulin, are shaded in grey.
  • FIG. 10 shows the HLA genomic loci map.
  • FIG. 11 schematically illustrates Human MHC Class I and Class II isotypes.
  • FIG. 12 shows the schematic molecular organization of the HLA Class I genes.
  • FIG. 13 shows the schematic molecular organization of the HLA Class II genes. Exons are represented by the rectangles and introns by lines.
  • FIG. 14 showing composite genetic alteration design for“humanization” of extracellular porcine cell expression
  • FIG. 15 shows comparative genomic organization of the human and swine major histocompatibility complex (MHC) Class I region.
  • the human leukocyte antigen (HLA) Class I map is adapted from Ref. [17] and the swine leukocyte antigen (SLA) Class I map is based only on one fully sequenced haplotype (Hp-1.1, H01) [4] Note that not all the genes are shown here and the scale is approximate. The number and location of expressed SLA Class I genes may vary between haplotypes.
  • FIG. 16 shows comparative genomic organization of the human and swine major histocompatibility complex (MHC) Class II region.
  • the human leukocyte antigen (HLA) Class II map is adapted from Ref.
  • FIG. 17 shows a physical map of the SLA complex. Black boxes: loci containing MHC-related sequences. White boxes: loci without MHC -related sequences. From the long arm to the short arm of the chromosome, the order of the regions is Class II (II), Class III (III) and Class I (I).
  • FIG. 18 shows the schematic molecular organization of the SLA genes. Exons are represented by the gray ovals and introns by lines. Gene length is approximate to that found for the Hp-1.1 genome sequence.
  • FIG. 19 shows a side-by-side genomic analysis of the peptide sequences.
  • FIGS. 20 shows the location and the length al(exon 2) of SLA-DQA and b1(ecoh 2) of SLA-DQB1.
  • FIG. 21 shows a spreadsheet detailing nucleotide sequences of exons and introns of SLA-DQA and SLA-DQB 1.
  • FIG. 22 shows SLA-DQ betal domain of sus scrofa (wild boar).
  • FIG. 23 illustrates nomenclature of HLA alleles.
  • Each HLA allele name has a unique number corresponding to up to four sets of digits separated by colons. The length of the allele designation is dependent on the sequence of the allele and that of its nearest relative. All alleles receive at least a four digit name, which corresponds to the first two sets of digits, longer names are only assigned when necessary. The digits before the first colon describe the type, which often corresponds to the serological antigen carried by an allotype. The next set of digits are used to list the subtypes, numbers being assigned in the order in which DNA sequences have been determined.
  • Alleles whose numbers differ in the two sets of digits must differ in one or more nucleotide substitutions that change the amino acid sequence of the encoded protein. Alleles that differ only by synonymous nucleotide substitutions (also called silent or non-coding substitutions) within the coding sequence are distinguished by the use of the third set of digits. Alleles that only differ by sequence polymorphisms in the introns, or in the 5' or 3' untranslated regions that flank the exons and introns, are distinguished by the use of the fourth set of digits.
  • FIG. 24 shows the length of exons and introns in HLA-DQA
  • FIG. 25 A shows nucleotide sequence library between recipient specific HLA-DQA and HLA-DQA acquired from database
  • FIG. 25B shows Nucleotide Sequence Library identifying complete divergence between HLA vs SLA(DQ-A, Exon 2)
  • FIG. 25C shows Human Capture Reference Sequence for DQ-A1 for Three Patients
  • FIG. 25D shows Human Capture Reference Sequence for DQ-B1 for Three Patients
  • FIG. 25E shows Human Capture Reference Sequence for DR-A for Three Patients
  • FIG. 25F shows Human Capture Reference Sequence for DQR-B 1 for Three Patients.
  • FIG. 26A shows example of Human Capture Reference Sequence(DQ-Al) for Three Patients
  • FIG. 26B shows example of Human Capture Reference Sequence(DQ-Bl) for Three Patients
  • FIG. 26C shows example of Human Capture Reference Sequence(DR-A) for Three Patients
  • FIG. 26D shows example of Human Capture Reference Sequence(DR-Bl) for Three Patients.
  • FIG. 27 shows the wild-type human beta-2 mieroglobulin protein and schematic molecular organization of the human B2M gene and swine B2M gene.
  • FIG. 28 shows comparison of amino acid sequences of exon 2 of human B2M vs exon 2 of swine B2M
  • FIG. 29 shows Phenotyping analysis of porcine alveolar macrophages (PAM).
  • PAM porcine alveolar macrophages
  • FIG. 30 shows SI values for BrdU ELISA. Proliferation response of three human CD4+ T cells (A) and PBMCs (B) to untreated and IFN-y activated PAM cells (15K) after seven days incubation.
  • FIG. 31 shows a schematic depiction of a humanized porcine cell according to the present disclosure
  • FIG. 32 shows a graph wherein 1 x 105 purified human CD8+ T cells (A) or human PBMC (B) were stimulated with increasing numbers of irradiated (30 Gy) porcine PBMC from four-fold knockout pig 10261 or a wild-type pig. Proliferation was measured after 5 d + 16 h by 3H-thymidine incorporation. Data represent mean cpm ⁇ SEM of triplicate cultures obtained with cells from one human blood donor in a single experiment. Similar response patterns were observed using responder cells from a second blood donor and stimulator cells from four-fold knockout pig 10262. Proliferation of human CD8+ T cells decreased after stimulation with four-fold knockout porcine PBMC. (Fischer, et ah, 2019)
  • FIG. 33 shows schematic depiction of a humanized porcine cell according to the present disclosure.
  • FIG. 34 shows graph of proliferation of human plasma donors run on 3 separate days with WT 128-11 and Gal T-KO B-174 PBMCs
  • FIG. 35 shows NK cytotoxicity of two donors (upper panel: KH; lower panel: MS) against 13 271 cells transfected with HLA-E/A2 (left column) and HLA-E/B7 (right column) compared to the lysis of untransfected 13 271 cells. Results are depicted as percentage of specific lysis and were obtained at four different E:T ratios. Data are representative of three independent experiments. Open triangles represent HLA-E-transfected 13 271 cells, filled diamonds represent un-transfected 13 271 cells. (Forte, et ah, 2005)
  • FIG. 36 shows graph of % cytotoxicity for each concentration (dilution) of plasma, and the results plotted in Prism. Based on the cytotoxicity curve, the required dilution for 50% kill (IC50) was determined.
  • FIG. 37 illustrates a source animal facility and corresponding designated pathogen free facilities, animals, and herds in accordance with the present invention.
  • FIG. 38 illustrates an extracorporeal liver filter and circuit in accordance with the present invention.
  • FIG. 39 illustrates a combination skin product in accordance with the present invention.
  • FIG. 40A depicts POD-15. H&E, H&E, high power image depicts tissue viability with surface and follicular epithelial necrosis.
  • FIG. 40B depicts POD-22 H&E, high power image demonstrating residual autograft (asterisks) with good overall viability. No surface epithelium and some surface necrosis noted, along with extensive fibrosis with infiltration into the autograft (arrows).
  • FIG. 41 depicts longitudinal progression of porcine split-thickness skin graft used as a temporary wound closure in treatment of full-thickness wound defects in a non-human primate recipient.
  • POD-0 xenotransplantation product at Wound Site 2.
  • POD-30 same xenotransplantation product at Wound Site 2.
  • FIG. 42 shows POD-30 histological images for: Top, Center: H&E, Low power image of wound site depicts complete epithelial coverage. Dotted line surrounds the residual xenotransplantation product.
  • FIG. 43 A graphs the total serum IgM ELISA (pg/mL) for all four subjects (2001, 2002, 2101, 2102) during the course of the study.
  • FIG. 43B graphs the total serum IgG ELISA (pg/mL) for all four subjects (2001, 2002, 2101, 2102) during the course of the study.
  • FIG. 44A graphs systemic concentrations of soluble CD40L as measured by Luminex 23-plex at POD-0, POD-7, POD-14, POD-21, and POD-30.
  • FIG. 44B graphs systemic concentrations of TGF-alpha as measured by Luminex 23-plex at POD-0, POD-7, POD-14, POD- 21, and POD-30.
  • FIG. 44C graphs systemic concentrations of IL-12/23 (p40) as measured by Luminex 23-plex at POD-0, POD-7, POD-14, POD-21, and POD-30.
  • FIG. 45 illustrates a method for preparing a skin product in accordance with the present invention.
  • FIG. 46 shows a cryovial used to store a xenotransplantation product.
  • FIG. 47 shows a shipping process of a xenotransplantation product.
  • FIG. 48 shows a secondary closure or container system for storing a xenotransplantation product at temperatures below ambient temperature, including, but not limited to, -150 degrees Celsius and other temperatures.
  • FIG. 49 A depicts porcine split-thickness skin grafts at wound sites 1, 2, 3, and 4, respectively from left to right at POD-12.
  • FIG. 49B depicts porcine split-thickness skin grafts at wound site 4 at POD-12 (left) and POD-14 (right).
  • FIG. 50A graphs MTT reduction assays fresh vs. cryopreserved (7 years) in porcine tissue samples showing no statistical difference.
  • FIG. 50B graphs MTT reduction assays heat deactivated vs. cryopreserved (7 years) in porcine tissue samples showing a statistically significant different in quantity of formazan produced.
  • FIG. 51A-G shows images of a xenotransplantation product of the present disclosure for treatment of severe and extensive partial and full thickness burns in a human patient.
  • FIG. 52 shows a graph of proliferative response of human lymphocytes responder peripheral blood mononuclear cells (PBMC) in the presence of mitomycin C treated porcine stimulator cells.
  • PBMC peripheral blood mononuclear cells
  • FIG. 53 shows anti-xenogeneic IgM (A) and IgG (B) antibody binding data relative to Median Fluorescence Intensities (MFI) for Xeno-001-00-1 patient sample at multiple time points, Pre, Day 7, Day 16, and Day 30. The data is shown for the plasma samples tested at 1 :2 dilutions.
  • MFI Median Fluorescence Intensities
  • “Best alignment” or“optimum alignment” means the alignment for which the identity percentage determined as described below is the highest. Comparisons of sequences between two nucleic acid sequences are traditionally made by comparing these sequences after aligning them optimally, the said comparison being made by segment or by“comparison window” to identify and compare local regions for similar sequences.
  • sequences may be optimally aligned manually, or by using alignment software, e.g., Smith and Waterman local homology algorithm (1981), the Neddleman and Wunsch local homology algorithm (1970), the Pearson and Lipman similarity search method (1988), and computer software using these algorithms (GAP, BESTFIT, BLAST P, BLAST N, FASTA and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wis.).
  • alignment software e.g., Smith and Waterman local homology algorithm (1981), the Neddleman and Wunsch local homology algorithm (1970), the Pearson and Lipman similarity search method (1988), and computer software using these algorithms (GAP, BESTFIT, BLAST P, BLAST N, FASTA and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wis.).
  • the optimum alignment is obtained using the BLAST program with the BLOSUM 62 matrix or software having similar functionality.
  • The“identity percentage” between two sequences of nucleic acids or amino acids is determined by comparing these two optimally aligned sequences, the sequence of nucleic acids or amino acids to be compared possibly including additions or deletions from the reference sequence for optimal alignment between these two sequences.
  • the identity percentage is calculated by determining the number of positions for which the nucleotide or the amino acid residue is identical between the two sequences, by dividing this number of identical positions by the total number of compared positions and multiplying the result obtained by 100 to obtain the identity percentage between these two sequences.
  • Constant and its grammatical equivalents as used herein include a conservative amino acid substitution, including substitution of an amino acid residue by another amino acid residue having a side chain R group with similar chemical properties (e.g., charge or hydrophobicity). Conservative amino acid substitutions may be achieved by modifying a nucleotide sequence so as to introduce a nucleotide change that will encode the conservative substitution. In general, a conservative amino acid substitution will not substantially change the functional properties of interest of a protein, for example, the ability of MHC I to present a peptide of interest.
  • groups of amino acids that have side chains with similar chemical properties include aliphatic side chains such as glycine, alanine, valine, leucine, and isoleucine; aliphatic-hydroxyl side chains such as serine and threonine; amide-containing side chains such as asparagine and glutamine; aromatic side chains such as phenylalanine, tyrosine, and tryptophan; basic side chains such as lysine, arginine, and histidine; acidic side chains such as aspartic acid and glutamic acid; and, sulfur-containing side chains such as cysteine and methionine.
  • aliphatic side chains such as glycine, alanine, valine, leucine, and isoleucine
  • aliphatic-hydroxyl side chains such as serine and threonine
  • amide-containing side chains such as asparagine and glutamine
  • aromatic side chains such as phenylalanine, tyrosine, and trypto
  • Conservative amino acids substitution groups include, for example, valine/leucine/isoleucine, phenylalanine/tyrosine, lysine/arginine, alanine/valine, glutamate/aspartate, and asparagine/glutamine.
  • nucleic acid residues encoding a human or humanized MHC I polypeptide and/or b2 microglobulin described herein due to the degeneracy of the genetic code, other nucleic acid sequences may encode the polypeptide(s) of the invention.
  • a non-human animal in addition to a genetically modified non-human animal that comprises in its genome a nucleotide sequence encoding MHC I and/or b2 microglobulin polypeptide(s) with conservative amino acid substitutions, a non- human animal whose genome comprises a nucleotide sequence(s) that differs from that described herein due to the degeneracy of the genetic code is also provided.
  • “Conserved” and its grammatical equivalents as used herein include nucleotides or amino acid residues of a polynucleotide sequence or amino acid sequence, respectively, that are those that occur unaltered in the same position of two or more related sequences being compared. Nucleotides or amino acids that are relatively conserved are those that are conserved amongst more related sequences than nucleotides or amino acids appearing elsewhere in the sequences.
  • two or more sequences are said to be“completely conserved” if they are 100% identical to one another.
  • two or more sequences are said to be“highly conserved” if they are at least 70% identical, at least 80% identical, at least 90% identical, or at least 95% identical, but less than 100% identical, to one another. In some embodiments, two or more sequences are said to be“conserved” if they are at least 30% identical, at least 40% identical, at least 50% identical, at least 60% identical, at least 70% identical, at least 80% identical, at least 90% identical, or at least 95% identical, but less than 100% identical, to one another.
  • two or more sequences are said to be“conserved” if they are about 30% identical, about 40% identical, about 50% identical, about 60% identical, about 70% identical, about 80% identical, about 90% identical, about 95% identical, about 98% identical, or about 99% identical to one another.
  • Designated pathogen free and its grammatical equivalents as used herein include reference to animals, animal herds, animal products derived therefrom, and/or animal facilities that are free of one or more specified pathogens.
  • such“designated pathogen free” animals, animal herds, animal products derived therefrom, and/or animal facilities are maintained using well-defined routines of testing for such designated pathogens, utilizing proper standard operating procedures (SOPs) and practices of herd husbandry and veterinary care to assure the absence and/or destruction of such designated pathogens, including routines, testing, procedures, husbandry, and veterinary care disclosed and described herein.
  • SOPs standard operating procedures
  • pathogen free and like terms when used in connection with “pathogen free” are meant to indicate that the subject pathogens are not present, not alive, not active, or otherwise not detectable by standard or other testing methods for the subject pathogens.
  • “Alter,”“altering,”“altered” and grammatical equivalents as used herein include any and/or all modifications to a gene including, but not limited to, deleting, inserting, silencing, modifying, reprogramming, disrupting, mutating, rearranging, increasing expression, knocking-in, knocking out, and/or any or all other such modifications or any combination thereof.
  • Endogenous loci and its grammatical equivalents as used herein include the natural genetic loci found in the animal to be transformed into the donor animal.
  • “Functional,” e.g., in reference to a functional polypeptide, and its grammatical equivalents as used herein include a polypeptide that retains at least one biological activity normally associated with the native protein.
  • a replacement at an endogenous locus e.g., replacement at an endogenous non-human MHC I, MHC II, and/or b2 microglobulin locus results in a locus that fails to express a functional endogenous polypeptide.
  • the term“functional” as used herein in reference to functional extracellular domain of a protein can refer to an extracellular domain that retains its functionality, e.g., in the case of MHC I, ability to bind an antigen, ability to bind a T cell co-receptor, etc.
  • a replacement at the endogenous MHC locus results in a locus that fails to express an extracellular domain (e.g., a functional extracellular domain) of an endogenous MHC while expressing an extracellular domain (e.g., a functional extracellular domain) of a human MHC.
  • Genetic or molecular marker and their grammatical equivalents as used herein include polymorphic locus, i.e. a polymorphic nucleotide (a so-called single nucleotide polymorphism or SNP) or a polymorphic DNA sequence at a specific locus.
  • a marker refers to a measurable, genetic characteristic with a fixed position in the genome, which is normally inherited in a Mendelian fashion, and which can be used for mapping of a trait of interest.
  • a genetic marker may be a short DNA sequence, such as a sequence surrounding a single base-pair change, i.e.
  • SNP single nucleotide polymorphism
  • SSRs Simple Sequence Repeats
  • the nature of the marker is dependent on the molecular analysis used and can be detected at the DNA, RNA or protein level. Genetic mapping can be performed using molecular markers such as, but not limited to, RFLP (restriction fragment length polymorphisms; Botstein et al. (1980), Am J Hum Genet. 32:314-331; Tanksley et al. (1989), Bio/Technology 7:257-263), RAPD [random amplified polymorphic DNA; Williams et al.
  • improving transplantation can mean lessening hyperacute rejection, which can encompass a decrease, lessening, or diminishing of an undesirable effect or symptom. In some aspects, a clinically relevant improvement is achieved.
  • “Locus” (loci plural) or“site” and their grammatical equivalents as used herein include a specific place or places on a chromosome where, for example, a gene, a genetic marker or a QTL is found.
  • “Minimally altered” and its grammatical equivalents as used herein include alteration of a donor animal genome including removing and replacing certain distinct sequences of native base pairs appearing on the donor animal’s genome and replacing each such sequence with a synthetic sequence comprising the same number of base pairs, with no net change to the number of base pairs in the donor animal’ s genome, while not disturbing other aspects of the donor animal’s native genome including, for example, introns and other codons naturally existing in the donor animal genome.
  • a minimally altered swine can include specific alterations removing or deactivating certain SLA exons to regulate the donor swine cell’s extracellular expression or non-expression of MHC Class II, la, and/or lb; reprogramming certain native, naturally occurring swine cell SLA exons to regulate the swine cell’s extracellular expression or non-expression of MHC Class II; conserving or otherwise not removing swine introns existing in or in the vicinity of the otherwise engineered sequences; increasing the expression of swine CTLA4 and PD-1; and removing or deactivating alpha- 1,3 galactosyltransf erase, cytidine monophosphate-N-acetylneuraminic acid hydroxylase, and b1,4- N-acetylgalactosaminyltransferase.
  • “Minimally manipulated” and its grammatical equivalents as used herein include treatment of source animals, biological products derived from those source animals, and other biological products with minimal physical alteration of the related cells, organs or tissues such that such animals and products are substantially in their natural state.
  • “Ortholog,” “orthologous,” and their grammatical equivalents as used herein include a polynucleotide from one species that corresponds to a polynucleotide in another species, which has the same function as the gene or protein or QTL, but is (usually) diverged in sequence from the time point on when the species harboring the genes or quantitative trait loci diverged (i.e. the genes or quantitative trait loci evolved from a common ancestor by speciation).
  • QTL Quality of Life
  • QTL mapping involves the creation of a map of the genome using genetic or molecular markers, like AFLP, RAPD, RFLP, SNP, SSR, and the like, visible polymorphisms and allozymes, and determining the degree of association of a specific region on the genome to the inheritance of the trait of interest.
  • QTL mapping results involve the degree of association of a stretch of DNA with a trait rather than pointing directly at the gene responsible for that trait. Different statistical methods are used to ascertain whether the degree of association is significant or not.
  • a molecular marker is said to be“linked” to a gene or locus, if the marker and the gene or locus have a greater association in inheritance than would be expected from independent assortment, i.e. the marker and the locus co-segregate in a segregating population and are located on the same chromosome.“Linkage” refers to the genetic distance of the marker to the locus or gene (or two loci or two markers to each other).
  • Capture sequence or“reference sequence” and their grammatical equivalents as used herein include a nucleic acid or amino acid sequence that has been obtained, sequenced or otherwise become known from a sample, animal (including humans), or population.
  • a capture sequence from a human patient is a“human patient capture sequence.”
  • a capture sequence from a particular human population is a“human population-specific human capture sequence.”
  • a capture sequence from a human allele group is an“allele-group-specific human capture sequence.”
  • Humanized and its grammatical equivalents as used herein include embodiments wherein all or a portion of an endogenous non-human gene or allele is replaced by a corresponding portion of an orthologous human gene or allele.
  • the term “humanized” refers to the complete replacement of the coding region (e.g., the exons) of the endogenous non-human MHC gene or allele or fragment thereof with the corresponding capture sequence of the human MHC gene or allele or fragment thereof, while the endogenous non-coding region(s) (such as, but not limited to, the promoter, the 5' and/or 3' untranslated region(s), enhancer elements, etc.) of the non-human animal is not replaced.
  • the endogenous non-coding region(s) such as, but not limited to, the promoter, the 5' and/or 3' untranslated region(s), enhancer elements, etc.
  • Personalized or “individualized,” and their grammatical equivalents as used herein, include a gene, allele, genome, proteome, cell, cell surface, tissue, or organ from a non human animal which is adapted to the needs or special circumstances of an individual human recipient or a specific human recipient subpopulation.
  • Reprogram refers to the replacement or substitution of endogenous nucleotides in the donor animal with orthologous nucleotides based on a separate reference sequence, wherein frameshift mutations are not introduced by such reprogramming.
  • reprogramming results in no net loss or net gain in the total number of nucleotides in the donor animal genome, or results in a net loss or net gain in the total number of nucleotides in the donor animal genome that is equal to no more than 1%, no more than 2%, no more than 3%, no more than 4%, no more than 5%, no more than 6%, no more than 7%, no more than 8%, no more than 9%, no more than 10%, no more than 12%, no more than 15%, or no more than 20% of the number of nucleotides in the separate reference sequence.
  • an endogenous non-human nucleotide, codon, gene or fragment thereof is replaced with a corresponding synthetic nucleotide, codon, gene or fragment thereof based on a human capture sequence, through which the total number of base pairs in the donor animal sequence is equal to the total number of base pairs of the human capture sequence.
  • “Tolerogenic” and its grammatical equivalents as used herein include characteristics of an organ, cell, tissue, or other biological product that are tolerated by the reduced response by the recipient’s immune system upon transplantation.
  • Transgenic and its grammatical equivalents as used herein, include donor animal genomes that have been modified to introduce non-native genes from a different species into the donor animal’ s genome at a non-orthologous, non-endogenous location such that the homologous, endogenous version of the gene (if any) is retained in whole or in part.“Transgene,”“transgenic,” and grammatical equivalents as used herein do not include reprogrammed genomes, knock-outs or other modifications as described and claimed herein.
  • “transgenic” swine include those having or expressing hCD46 (“human membrane cofactor protein,” or“MCP”), hCD55 (“human decay-accelerating factor,”“DAF”), human B2M (beta-2-microglobulin), and/or other human genes, achieved by insertion of human gene sequences at a non-orthologous, non- endogenous location in the swine genome without the replacement of the endogenous versions of those genes.
  • hCD46 human membrane cofactor protein
  • DAF human decay-accelerating factor
  • B2M beta-2-microglobulin
  • tolerogenic non-human animal cells, tissues and organs for several human Class I and/or Class II MHC molecules are provided.
  • T-cells are the primary effector cells involved in the cellular response.
  • TCRs antibodies have been developed as therapeutics, (TCRs)
  • TCRs the receptors on the surface of the T-cells, which give them their specificity, have unique advantages as a platform for developing therapeutics. While antibodies are limited to recognition of pathogens in the blood and extracellular spaces or to protein targets on the cell surface, TCRs recognize antigens displayed by MHC molecules on the surfaces of cells (including antigens derived from intracellular proteins).
  • TCRs and T-cells harboring TCRs participate in controlling various immune responses.
  • helper T-cells are involved in regulation of the humoral immune response through induction of differentiation of B cells into antibody secreting cells.
  • activated helper T-cells initiate cell-mediated immune responses by cytotoxic T-cells.
  • TCRs specifically recognize targets that are not normally seen by antibodies and also trigger the T-cells that bear them to initiate wide variety of immune responses.
  • T-cell recognizes an antigen presented on the surfaces of cells by means of the TCRs expressed on their cell surface.
  • TCRs are disulfide-linked heterodimers, most consisting of a and b chain glycoproteins. T-cells use recombination mechanisms to generate diversity in their receptor molecules similar to those mechanisms for generating antibody diversity operating in B cells (Janeway and Travers, Immunobiology 1997). Similar to the immunoglobulin genes, TCR genes are composed of segments that rearrange during development of T-cells. TCR polypeptides consist of variable, constant, transmembrane and cytoplasmic regions.
  • variable region While the transmembrane region anchors the protein and the intracellular region participates in signaling when the receptor is occupied, the variable region is responsible for specific recognition of an antigen and the constant region supports the variable region-binding surface.
  • the TCR a chain contains variable regions encoded by variable (V) and joining (J) segments only, while the b chain contains additional diversity (D) segments.
  • MHCI Major histocompatibility complex Class I
  • MHCII Class II
  • FIG. 2 Within the human population, allelic variation among the classical MHCI and II gene products is the basis for differential peptide binding, thymic repertoire bias and allograft rejection.
  • MHC molecules are cell-surface glycoproteins that are central to the process of adaptive immunity, functioning to capture and display peptides on the surface of antigen-presenting cells (APCs).
  • MHC Class I (MHCI) molecules are expressed on most cells, bind endogenously derived peptides with sizes ranging from eight to ten amino acid residues and are recognized by CD8 cytotoxic T- lymphocytes (CTL). See FIG. 3 and FIG. 4.
  • CTL cytotoxic T- lymphocytes
  • MHC Class II MHCII
  • MHCII are present only on specialized APCs, bind exogenously derived peptides with sizes varying from 9 to 22 residues, and are recognized by CD4 helper T-cells. See FIG. 5.
  • MHCI and MHCII molecules engage two distinct arms of the T-cell-mediated immune response, the former targeting invasive pathogens such as viruses for destruction by CD8 CTLs, and the latter inducing cytokine-based inflammatory mediators to stimulate CD4 helper T-cell activities including B-cell activation, maturation and antibody production.
  • the biological product of the present disclosure is not recognized by CD8+ T cells, do not bind anti-HLA antibodies, and are resistant to NK-mediated lysis.
  • HLA human leukocyte antigen
  • MHC major histocompatibility complex
  • the HLA gene complex resides on a 3 Mbp stretch within chromosome 6p21. See FIG. 6. HLA genes are highly polymorphic, which means that they have many different alleles, allowing them to fine-tune the adaptive immune system. See FIG. 7.
  • the proteins encoded by certain genes are also known as antigens, as a result of their historic discovery as factors in organ transplants. Different classes have different functions. See FIG. 8 and FIG. 9.
  • the HLA segment is divided into three regions (from centromere to telomere), Class II, Class III and Class I. See FIG. 10.
  • Classical Class I and Class II HLA genes are contained in the Class I and Class II regions, respectively, whereas the Class III locus bears genes encoding proteins involved in the immune system but not structurally related to MHC molecules.
  • the classical HLA Class I molecules are of three types, HLA- A, HLA-B and HLA-C. Only the a chains of these mature HLA Class I molecules are encoded within the Class I HLA locus by the respective HLA-A, HLA-B and HLA-C genes. See Fig. 11.
  • the beta-2 microglobulin b2 m chain encoded by the b2 m gene is located on chromosome 15.
  • the classical HLA Class II molecules are also of three types (HLA-DP, HLA-DQ and HLA-DR), with both the a and b chains of each encoded by a pair of adjacent loci.
  • the human MHC locus includes a long array of HLA pseudogenes as well as genes encoding non-classical MHCI and MHCII molecules.
  • HLA-pseudogenes are an indication that gene duplication is the main driving force for HLA evolution, whereas non-classical MHCI and MHCII molecules often serve a restricted function within the immune system quite distinct from that of antigen presentation to ab TCRs.
  • HLA genes Aside from the genes encoding the antigen-presenting proteins, there are a large number of other genes, many involved in immune function, located on the HLA complex. Diversity of HLAs in the human population is one aspect of disease defense, and, as a result, the chance of two unrelated individuals with identical HLA molecules on all loci is extremely low. HLA genes have historically been identified as a result of the ability to successfully transplant organs between HLA-similar individuals.
  • Class I MHC molecules are expressed on all nucleated cells, including tumor cells. They are expressed specifically on T and B lymphocytes, macrophages, dendritic cells and neutrophils, among other cells, and function to display peptide fragments (typically 8-10 amino acids in length) on the surface to CD8+ cytotoxic T lymphocytes (CTLs). CTLs are specialized to kill any cell that bears an MHC I-bound peptide recognized by its own membrane-bound TCR. When a cell displays peptides derived from cellular proteins not normally present (e.g., of viral, tumor, or other non-self origin), such peptides are recognized by CTLs, which become activated and kill the cell displaying the peptide.
  • CTLs cytotoxic T lymphocytes
  • MHC Class I protein comprises an extracellular domain (which comprises three domains: ai, 012 and 013), a transmembrane domain, and a cytoplasmic tail.
  • the ai and ⁇ 12 domains form the peptide-binding cleft, while the 013 interacts with b2-h ⁇ op3 ⁇ 41oI>u1 ⁇ h.
  • Class I molecules consist of two chains: a polymorphic a-chain (sometimes referred to as heavy chain) and a smaller chain called b2-ih ⁇ op3 ⁇ 41oI>u1 ⁇ h (also known as light chain), which is generally not polymorphic. These two chains form a non-covalent heterodimer on the cell surface.
  • the a- chain contains three domains (al, a2 and a3). As illustrated in FIG. 12, Exon 1 of the a-chain gene encodes the leader sequence, exons 2 and 3 encode the al and a2 domains, exon 4 encodes the a3 domain, exon 5 encodes the transmembrane domain, and exons 6 and 7 encode the cytoplasmic tail.
  • the a-chain forms a peptide-binding cleft involving the al and a2 domains (which resemble Ig-like domains) followed by the a3 domain, which is similar to P2-microglobulin.
  • b2 microglobulin is a non-glycosylated 12 kDa protein; one of its functions is to stabilize the MHC Class I a-chain. Unlike the a-chain, the b2 microglobulin does not span the membrane.
  • the human b2 microglobulin locus is on chromosome 15 and consists of 4 exons and 3 introns. Circulating forms of b2 microglobulin are present in serum, urine, and other body fluids; non-covalently MHC I-associated b2 microglobulin can be exchanged with circulating b2 microglobulin under physiological conditions.
  • MHC Class II protein comprises an extracellular domain (which comprises three domains: ai, ⁇ xi , b ⁇ , and b ⁇ ), a transmembrane domain, and a cytoplasmic tail.
  • the ai and b ⁇ domains form the peptide-binding cleft, while the ai and b ⁇ interacts with the transmembrane domain.
  • the Class I antigens include other antigens, termed non-classical Class I antigens, in particular the antigens HLA-E, HLA-F and HLA-G; this latter, in particular, is expressed by the extravillous trophoblasts of the normal human placenta in addition to HLA-C.
  • HLA-C HLA Class la molecule
  • HLA-G HLA Class lb Molecules and Immune Cells in Pregnancy and Preeclampsia
  • HLA-C and HLA-F are weakly expressed. See, e.g., Djurisic et al,“HLA Class lb Molecules and Immune Cells in Pregnancy and Preeclampsia,” Frontiers in Immunology , Vol 5, Art.
  • PD-L1 is upregulated in trophoblastic cells in normal pregnancy, particularly in syncytiotrophoblast cells.
  • HLA Class II molecules are not present on trophoblasts, which may facilitate survival and detection of the embryo in the presence of maternal lymphocytes. See , e.g., Veras et al,“PD-L1 Expression in Human Placentas and gestational Trophoblastic Diseases,” Int. J Gynecol. Pathol. 36(2): 146-153 (2017).
  • the present invention provides a method of creating a tolerogenic xenotransplantation swine cell that mimics the extracellular configuration of a human trophoblast.
  • This method includes, but is not limited to, removing or deactivating certain SLA exons to regulate the swine cell’s extracellular expression or non-expression of MHC Class II, la, and/or lb; reprogramming certain native, naturally occurring swine cell SLA exons to regulate the swine cell’s extracellular expression or non-expression of MHC Class II; conserving or otherwise not removing swine introns existing in or in the vicinity of the otherwise engineered sequences; increasing the expression of swine CTLA4 and PD-1; and removing or deactivating alpha- 1,3 galactosyltransf erase, cytidine monophosphate-N-acetylneuraminic acid hydroxylase, and b1,4- N-acetylgalactosaminyltransfer
  • The“downstream” approach accepts the innate and immovable disparity between donor and recipient, and focuses on interventions, gene alterations, and/or concomitant exogenous immunosuppressive medications used as a method of reducing/eliminating/negatively-altering the recipients' naturally resulting immunologic response.
  • This approach applies beyond the field of xenotransplantation including, but not limited to, the fields of genetics, obstetrics, infectious disease, oncology, agriculture, animal husbandry, food industry and other areas.
  • the present disclosure embodies the above modification in creating a non- transgenic genetically reprogrammed swine for xenotransplantation, wherein the MHC surface characterization of the swine mimic that of the recipient’s trophoblast, wherein the immune response from the xenotransplantation is significantly reduced.
  • the human extravillous trophoblast cells express HLA-C, HLA-E, HLA-F, and HLA-G, but not HLA-A, HLA-B, HLA- DQ and HLA-DR.
  • the current embodiment combines the unique MHC surface characterization of human trophoblast with site-directed mutagenic substitutions to minimize or remove the immune response associated with xenotransplantation while minimizing off target effects on the native donor swine’s SLA/MHC gene.
  • T-cells are the primary effector cells involved in the cellular response.
  • TCRs antibodies have been developed as therapeutics, (TCRs)
  • TCRs the receptors on the surface of the T-cells, which give them their specificity, have unique advantages as a platform for developing therapeutics. While antibodies are limited to recognition of pathogens in the blood and extracellular spaces or to protein targets on the cell surface, TCRs recognize antigens displayed by MHC molecules on the surfaces of cells (including antigens derived from intracellular proteins).
  • TCRs and T-cells harboring TCRs participate in controlling various immune responses.
  • helper T-cells are involved in regulation of the humoral immune response through induction of differentiation of B cells into antibody secreting cells.
  • activated helper T-cells initiate cell-mediated immune responses by cytotoxic T-cells.
  • TCRs specifically recognize targets that are not normally seen by antibodies and also trigger the T-cells that bear them to initiate wide variety of immune responses.
  • a T-cell recognizes an antigen presented on the surfaces of cells by means of the TCRs expressed on their cell surface.
  • TCRs are disulfide-linked heterodimers, most consisting of a and b chain glycoproteins. T-cells use recombination mechanisms to generate diversity in their receptor molecules similar to those mechanisms for generating antibody diversity operating in B cells (Janeway and Travers, Immunobiology 1997). Similar to the immunoglobulin genes, TCR genes are composed of segments that rearrange during development of T-cells. TCR polypeptides consist of variable, constant, transmembrane and cytoplasmic regions.
  • the TCR a chain contains variable regions encoded by variable (V) and joining (J) segments only, while the b chain contains additional diversity (D) segments.
  • a TCR recognizes a peptide antigen presented on the surfaces of antigen presenting cells in the context of self- Major Histocompatibility Complex(MHC) molecules.
  • MHC Histocompatibility Complex
  • Two different types of MHC molecules recognized by TCRs are involved in antigen presentation, the Class I MHC and class II MHC molecules.
  • Mature T-cell subsets are defined by the co-receptor molecules they express. These co-receptors act in conjunction with TCRs in the recognition of the MHC- antigen complex and activation of the T-cell.
  • Mature helper T-cells recognize antigen in the context of MHC Class II molecules and are distinguished by having the co-receptor CD4.
  • Cytotoxic T-cells recognize antigen in the context of MHC Class I determinants and are distinguished by having the CD 8 co-receptor.
  • HLA human leukocyte antigens
  • HLA segment is divided into three regions (from centromere to telomere), Class II, Class III and Class I. See FIG. 10.
  • Classical Class I and Class II HLA genes are contained in the Class I and Class II regions, respectively, whereas the Class III locus bears genes encoding proteins involved in the immune system but not structurally related to MHC molecules.
  • the classical HLA Class I molecules are of three types, HLA- A, HLA-B and HLA-C.
  • HLA Class I Only the a chains of these mature HLA Class I molecules are encoded within the Class I HLA locus by the respective HLA-A, HLA-B and HLA-C genes. See FIG. 11.
  • the beta-2 microglobulin b2ih chain encoded by the b2ih gene is located on chromosome 15.
  • the classical HLA Class II molecules are also of three types (HLA-DP, HLA-DQ and HLA-DR), with both the a and b chains of each encoded by a pair of adjacent loci.
  • the human MHC locus includes a long array of HLA pseudogenes as well as genes encoding non-classical MHCI and MHCII molecules.
  • HLA-pseudogenes are an indication that gene duplication is the main driving force for HLA evolution, whereas non-classical MHCI and MHCII molecules often serve a restricted function within the immune system quite distinct from that of antigen presentation to ab TCRs.
  • HLA Human leukocyte antigen
  • HLA-A the classical Class I genes, termed HLA-A, HLA-B and HLA-C, consist of two chains: a polymorphic a-chain (sometimes referred to as heavy chain) and a smaller chain called P2-microglobulin (also known as light chain), which is generally not polymorphic. These two chains form a non-covalent heterodimer on the cell surface. As shown in FIG. 12, the a-chain contains three domains (al, a2 and a3).
  • Exon 1 of the a-chain gene encodes the leader sequence
  • exons 2 and 3 encode the al and a2 domains
  • exon 4 encodes the a3 domain
  • exon 5 encodes the transmembrane domain
  • exons 6 and 7 encode the cytoplasmic tail.
  • the a-chain forms a peptide-binding cleft involving the al and a2 domains (which resemble Ig-like domains) followed by the a3 domain, which is similar to P2-microglobulin.
  • b2 microglobulin is a non-glycosylated 12 kDa protein; one of its functions is to stabilize the MHC Class I a-chain. Unlike the a-chain, the b2 microglobulin does not span the membrane.
  • the human b2 microglobulin locus is on chromosome 15 and consists of 4 exons and 3 introns.
  • b2-ih ⁇ p3 ⁇ 41o1>o1 ⁇ h-1>ow ⁇ protein complexes undertake key roles in various immune system pathways, including the neonatal Fc receptor (FcRn), cluster of differentiation 1 (CD1) protein, non-classical major histocompatibility complex (MHC), and well-known MHC Class I molecules.
  • FcRn neonatal Fc receptor
  • CD1 cluster of differentiation 1
  • MHC non-classical major histocompatibility complex
  • Class I MHC molecules are expressed on all nucleated cells, including tumor cells. They are expressed specifically on T and B lymphocytes, macrophages, dendritic cells and neutrophils, among other cells, and function to display peptide fragments (typically 8-10 amino acids in length) on the surface to CD8+ cytotoxic T lymphocytes (CTLs). CTLs are specialized to kill any cell that bears an MHC I-bound peptide recognized by its own membrane-bound TCR. When a cell displays peptides derived from cellular proteins not normally present (e.g., of viral, tumor, or other non-self origin), such peptides are recognized by CTLs, which become activated and kill the cell displaying the peptide.
  • CTLs cytotoxic T lymphocytes
  • MHC loci exhibit the highest polymorphism in the genome. All Class I and II MHC genes can present peptide fragments, but each gene expresses a protein with different binding characteristics, reflecting polymorphisms and allelic variants. Any given individual has a unique range of peptide fragments that can be presented on the cell surface to B and T cells in the course of an immune response.
  • the Class I antigens include other antigens, termed non-classical Class I antigens, in particular the antigens HLA-E, HLA-F and HLA-G; this latter, in particular, is expressed by the extravillous trophoblasts of the normal human placenta in addition to HLA-C.
  • MHC Class II protein comprises an extracellular domain (which comprises three domains: al, a2 , b ⁇ , and b ⁇ ), a transmembrane domain, and a cytoplasmic tail as shown in FIG. 13.
  • the a2 and b2 domains form the peptide-binding cleft, while the al and b ⁇ interacts with the transmembrane domain.
  • the current disclosure either inactivate, or where necessary to retain the function of the“find and replace” orthologous SLA proteins with HLA analogs that would result in minimal immune recognition.
  • silencing the genes which encode and are responsible for the expression of SLA-1 removes the highly- problematic and polymorphic HLA-A analog.
  • inactivation or complete removal of genes associated with SLA-2 would reduce the burden imposed by mismatched HLA-B proteins. This would, at the cell surface interface, appear to the human recipient’s T cells as a HLA-A and HLA- B negative cell.
  • HLA-C site-directed mutagenesis of genes that encode for SLA-3 using a reference HLA-C sequence would mimic an allo-transplant with such a disparity.
  • this would be further improved by the replacement of SLA-3 with a reference replacement sequence based on the subclass of HLA-C that is naturally prevalent in nature, and also invoking mechanisms that would allow for the minimal but requisite level of expression that would afford functionality and non-interruption of the numerous known and also those unknown MHC-I dependent processes.
  • the current disclosure either inactivate, or where necessary to retain the function of the“find and replace” orthologous SLA proteins with HLA analogs that would result in minimal immune recognition.
  • silencing the genes which encode and are responsible for the expression of SLA-1 removes the highly- problematic and polymorphic HLA-A analog.
  • inactivation or complete removal of genes associated with SLA-2 would reduce the burden imposed by mismatched HLA-B proteins. This would, at the cell surface interface, appear to the human recipient’s T cells as a HLA-A and HLA- B negative cell.
  • HLA-C site-directed mutagenesis of genes that encode for SLA-3 using a reference HLA-C sequence would mimic an allo-transplant with such a disparity.
  • this would be further improved by the replacement of SLA-3 with a reference replacement sequence based on the subclass of HLA-C that is naturally prevalent in nature, and also invoking mechanisms that would allow for the minimal but requisite level of expression that would afford functionality and non-interruption of the numerous known and also those unknown MHC-I dependent processes.
  • 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.
  • HLA-G gene (HLA-6.0 gene) has been described by GERAGHTY et al., (Proc. Natl. Acad. Sci. USA, 1987, 84, 9145-9149): it comprises 4,396 base pairs and exhibits an intron/exon organization which is homologous to that of the HLA- A, HLA-B and HLA-C genes.
  • this gene comprises 8 exons and an untranslated, 3'UT, end, with the following respective correspondence: exon 1 : signal sequence, exon 2: al domain, exon 3 : a2 domain, exon 4: a3 domain, exon 5: transmembrane region, exon 6: cytoplasmic domain I, exon 7: cytoplasmic domain II, exon 8: cytoplasmic domain III and 3' untranslated region (GERAGHTY et al., mentioned above, ELLIS et al., J. Immunol., 1990, 144, 731-735).
  • the HLA-G gene differs from the other Class I genes in that the in-frame translation termination codon is located at the second codon of exon 6; as a result, the cytoplasmic region of the protein encoded by this gene HLA-6.0 is considerably shorter than that of the cytoplasmic regions of the HLA-A, HLA-B and HLA-C proteins.
  • NK cell-mediated immunity comprising cytotoxicity and cytokine secretion, plays a major role in biological resistance to a number of autologous and allogeneic cells.
  • the common mechanism of target cell recognition appears to be the lack or modification of self MHC Class I-peptide complexes on the cell surface, which can lead to the elimination of virally infected cells, tumor cells and major histocompatibility MHC-incompatible grafted cells.
  • KIRs members of the Ig superfamily which are expressed on NK cells, have recently been discovered and cloned. KIR's are specific for polymorphic MHC Class I molecules and generate a negative signal upon ligand binding which leads to target cell protection from NK cell-mediated cytotoxicity in most systems.
  • NK cell autoimmunity i.e., the lysis of normal autologous cells
  • every given NK cell of an individual expresses at least on KIR recognizing at least one of the autologous HLA-A, B, C, or G alleles.
  • each human recipient will have a major histocompatibility complex (MHC) (Class I, Class II and/or Class III) that is unique to that individual and will not match the MHC of the donor swine. Accordingly, when a donor swine graft is introduced to the recipient, the swine MHC molecules themselves act as antigens, provoking an immune response from the recipient, leading to transplant rejection.
  • MHC major histocompatibility complex
  • porcine ligands for SLA-MIC2 is orthologously reprogrammed with human counterparts, MICA.
  • MICA Human Major Histocompatibility Complex Class I Chain-Related gene A
  • MICA protein at normal states has a low level of expression in epithelial tissues but is upregulated in response to various stimuli of cellular stress. MICA is classified as a non-classical MHC Class I gene ,and functions as a ligand recognized by the activating receptor NKG2D that is expressed on the surface of NK cells and CD8+ T cells (atlasgeneticsoncology.org/Genes/MICAID41364ch6p21.html).
  • porcine ligands for PD-L1, CTLA-4, and others are overexpressed and/or otherwise orthologously reprogrammed with human counterparts.
  • PD-L1 is a transmembrane protein that has major role in suppressing the adaptive immune system in pregnancy, allografts, and autoimmune diseases. It is encoded by the CD274 gene in human and is located in chromosome 9.
  • PD-L1 binds to PD-1, a receptor found on activated T cells, B cells, and myeloid cells, to modulate activation or inhibition. Particularly, the binding of PD-L1 to receptor PD-1 on T cells inhibits activation of IL-2 production and T cell proliferation.
  • CTLA4 is a protein receptor that also functions as an immune checkpoint that downregulates immune responses. It is encoded by the CTLA4 gene and is located in chromosome 2 in human. It is constitutively expressed on regulatory T cells but are upregulated in activated T cells. Gene expression for CTLA-4 and PD-L1 is increased, for example, based on reprogramming promoters thereof. There is a relationship between genotype and CTLA-4 or PD-L1 expression.
  • CTLA-4 gene expression is influenced by promoter and exon 1 polymorphisms, Genes Immun. 2001 May;2(3): 145-52, which is incorporated herein by reference in its entirety for all purposes.
  • a similar upregulation can be achieved to overexpress PD-L1 using a PD-L1 promoter reprogramming.
  • EPCR Endothelial protein C receptor
  • TBM Thrombomodulin
  • TFPI Tissue Factor Pathway Inhibitor
  • FIG. 14 Endothelial protein C receptor is endothelial cell-specific transmembrane glycoprotein encoded by PROCR gene that is located in chromosome 20 in human. It enhances activation of Protein C, an anti -coagulant serine protease, and has crucial role in activated protein C mediated cytoprotive signaling.
  • Thrombomodulin is an integral membrane glycoprotein present on surface of endothelial cells.
  • Tissue Factor Pathway Inhibitor is a glycoprotein that functions as natural anticoagulant by inhibiting Factor Xa. It encoded by TFPI gene located in chromosome 2 in human and the protein structure consists of three tandemly linked Kunitz domains. In human, two major isoforms of TFPi exists, TFPIa and TFPip.
  • TFPIa consists of three inhibitory domains (Kl, K2, and K3) and a positively charged C terminus while TFPip consists of two inhibitory domains (Kl and K2) and C terminus. While Kl and K2 domains are known to bind and inhibit Factor VII and Factor Xa, respectively, the inhibitory function of K3 is unknown.
  • the present disclosure centralizes (predicates) the creation of hypoimmunogenic and/or tolerogenic cells, tissues, and organs that does not necessitate the transplant recipients’ prevalent and deleterious use of exogenous immunosuppressive drugs (or prolonged immunosuppressive regimens) following the transplant procedure to prolong the life-saving organ.
  • the table provided in FIG. 14 shows conceptual design that exhibit summation of various edits to create tolerogenic xenotransplantation swine cell that mimics the extracellular configuration of a human trophoblast.
  • SLA-1 a swine gene orthologous to HLA-A
  • SLA-8 a swine gene orthologous to HLA-G
  • HLA-G is humanized through replacement with “human-capture” reference sequence, as HLA-G is expressed in trophoblast and has crucial role in maternal fetal tolerance, given its interaction with NK cells.
  • multiple source animals with an array of biological properties including, but not limited to, genome modification and/or other genetically engineered properties, can be utilized to reduce immunogenicity and/or immunological rejection (e.g., acute, hyperacute, and chronic rejections) in humans resulting from xenotransplantation.
  • the present disclosure can be used to reduce or avoid thrombotic microangiopathy by transplanting the biological product of the present disclosure into a human patient.
  • the present disclosure can be used to reduce or avoid glomerulopathy by transplanting the biological product of the present disclosure into a human patient.
  • source animals set forth herein is not limiting, and the present invention encompasses any other type of source animal with one or more modifications (genetic or otherwise) that serve(s) to reduce immunogenicity and/or immunological rejection, singularly or in combination.
  • the present disclosure includes using highly conserved MHC-loci between these two species, e.g., numerous genes that correspond in function.
  • the MHC Class la, HLA- A, HLA-B, and HLA-C have an analogous partner in the swine (the SLA 1, 2 and 3 respectively).
  • MHC Class II there are also numerous matches to be utilized during immunogenomic reprogramming according to the present disclosure.
  • MHC genes are categorized into three classes; Class I, Class II, and Class III, all of which are encoded on human chromosome 6.
  • the MHC genes are among the most polymorphic genes of the swine and human genomes, MHC polymorphisms are presumed to be important in providing evolutionary advantage; changes in sequence can result in differences in peptide binding that allow for better presentation of pathogens to cytotoxic T cells.
  • the known human HLA/MHC or an individual recipient’s sequenced HLA/MHC sequence(s) may be utilized as a template to reprogram with precise substitution the swine leukocyte antigen (SLA)/MHC sequence to match, e.g., to have 80%, 85%, 90%, 95%, 98%, 99%, or 100% sequence homology to a known human HLA/MHC sequence or the human recipient’s HLA/MHC sequence.
  • SLA swine leukocyte antigen
  • 3 reprogramming may be performed to SLA/MHC sequences in cells of the swine based on desired HLA/MHC sequences. For example, several targeting guide RNA (gRNA) sequences are administered to the swine of the present disclosure to reprogram SLA/MHC sequences in cells of the swine with the template HLA/MHC sequences of the human recipient.
  • gRNA targeting guide RNA
  • MHC I complex or the like, as used herein, includes the complex between the MHC I a chain polypeptide and the p2-microglobulin polypeptide.
  • MHC I polypeptide or the like, as used herein, includes the MHC I a chain polypeptide alone.
  • HLA human immunoglobulin
  • the donor swine’s SLA/MHC gene is used as a reference template in creating the replacement template.
  • the swine’s SLA/MHC gene may be obtained through online archives or database such as Ensembl (http://vega.archive.ensembl.org/index.html).
  • Ensembl http://vega.archive.ensembl.org/index.html.
  • FIG. 19 the exact location of the SLA-DQA and SLA-DQB1 gene, the length of the respective gene (exon and intron), and the exact nucleotide sequences of SLA-DQA and SLA-DQB 1 are mapped.
  • the donor swine’s SLA/MHC gene may be sequenced.
  • the swine’s whole genome may be sequenced.
  • the sequenced SLA/MHC gene of the donor swine that can be used as a reference template include but are not limited to SLA-3, SLA-6, SLA-7, SLA-8, SLA-DQa, SLA- DQb, and beta-2 microglobulin.
  • the sequenced SLA/MHC gene of the donor swine that can be used as a base template include but are not limited exon regions of SLA-3, SLA- 6, SLA-7, SLA-8, SLA-DQa, SLA-DQb, and beta-2 microglobulin.
  • other SLAs are unaltered and intron regions of the reprogrammed SLA regions are unaltered, thereby producing a minimally altered reprogrammed swine genome that provides cells, tissues and organs that are tolerogenic when transplanted into a human.
  • a donor swine is provided with a genome that is biologically engineered to express a specific set of known human HLA molecules.
  • HLA sequences can be obtained, e.g., from the IPD-IMGT/HLA database (available at ebi.ac.uk/ipd/imgt/hla/) and the international ImMunoGeneTics information system® (available at imgt.org). Nomenclature for such genes is illustrated in FIG. 23.
  • HLA-A1, B8, DR17 is the most common HLA haplotype among Caucasians, with a frequency of 5%.
  • the disclosed method can be performed using the known MHC/HLA sequence information in combination with the disclosures provided herein.
  • the HLA sequences are obtainable through online archives or database such as Ensembl (vega.archive.ensembl.org/index.html). As illustrated in FIG. 24, the exact location of the HLA-DQAl gene, the length of the respective gene(exon and intron), and the exact nucleotide sequences of HLA-DQAl could be obtained.
  • the recipient’s human leukocyte antigen (HLA) genes and MHC are identified and mapped.
  • HLA/MHC genes are usually typed with targeted sequencing methods: either long-read sequencing or long-insert short-read sequencing.
  • HLA types have been determined at 2-digit resolution (e.g., A*01), which approximates the serological antigen groupings.
  • sequence specific oligonucleotide probes has been used for HLA typing at 4-digit resolution (e.g., A*01 :01), which can distinguish amino acid differences.
  • SSOP sequence specific oligonucleotide probes
  • targeted DNA sequencing for HLA typing is the most popular approach for HLA typing over other conventional methods. Since the sequence-based approach directly determines both coding and non-coding regions, it can achieve HLA typing at 6-digit (e.g., A*01 :01 :01) and 8- digit (e.g., A*01 :01 :01 :01) resolution, respectively.
  • HLA typing at the highest resolution is desirable to distinguish existing HLA alleles from new alleles or null alleles from clinical perspective.
  • a replacement template is created for site-directed mutagenic substitutions of nucleotides of the donor swine’s SLA/MHC wherein the reprogramming introduces non-transgenic, minimally-required alteration that does not result in any frameshifts or frame disruptions in specific exon regions of the native donor swine’s SLA/MHC.
  • the nucleotide sequence(s) of the replacement template is identified by: a) obtaining a biological sample containing DNA from a transplant recipient, b) sequencing MHC Class I and II genes in the transplant recipient’s sample, c) comparing the nucleotide sequence of the recipient with that of the donor swine at various loci, and d) creating a replacement template for one or more of said loci, wherein said nucleotide sequence of the replacement template are at least 95% identical to the transplant recipient’s nucleotide sequences, as further described below.
  • the spreadsheet in FIG. 25A and FIG. 25B shows human capture reference sequence of exons of DQ-Ai and DQ-Bi, respectively, of three individual recipients.
  • known human HLA/MHC or an individual recipient’s sequenced HLA/MHC sequence(s) may be utilized as a template to reprogram with precise substitution the swine leukocyte antigen (SLA)/MHC sequence to match, e.g., to have 90%, 95%, 98%, 99%, or 100% sequence homology to a known human HLA/MHC sequence or the human recipient’ s HLA/MHC sequence.
  • SLA swine leukocyte antigen
  • FIG. 25C the known human HLA-DQA acquired through online database and individual recipients’ sequenced HLA-DQA, can be compared in a nucleotide Sequence Library.
  • 26D shows comparison of exon 2 region of the swine’s SLA-DQA acquired through online database and the known and sequenced recipient’s HLA-DQAl .
  • Both exon 2 region of SLA-DQA and HLA-DQAl contain 249 nucleotides.
  • FIG. 25D it can be observed that 11% of the aligned 249 nucleotides between exon 2 regions of SLA-DQA1 and HLA-DQAl are completely divergent. Therefore, this disclosure disclose method of identifying the non-conserved nucleotide sequences at a specific exons of human and swine MHC complex.
  • a site-directed mutagenesis can be performed wherein the specific non-conserved nucleotide sequence between the specific exon regions of the SLA gene and the known or recipient’s HLA gene are replaced without causing any frameshift.
  • the site-directed mutagenesis of the SLA-DQA1 and SLA-DQB1 gene is shown in FIG. 26A and FIG. 26B, wherein the nucleotide sequences of the exon 2 region of the recipient specific HLA-DQAl and HLA-DQB l are used to create a human capture replacement sequence. Therefore, the use of synthetic replacement template specific to the exon regions of the MHC gene, leads to a non-transgenic, minimally altered genome that does not result in any frameshifts or frame disruptions in the native donor swine’s SLA/MHC gene.
  • the present invention discloses method of inhibiting expression of MHC proteins without causing frameshift in the MHC gene.
  • the spreadsheet in FIG. 25E and FIG. 25F shows human capture reference sequence of exons of DR-A and DR-Bi, respectively, of three individual recipients.
  • FIG. 26C and FIG.26D by replacing the initial three nucleotide sequences of the leader exon 1 to a STOP codon, the expression of DR molecule can be inhibited without causing frameshift.
  • the initial three sequences of exon 1, ATG is replaced with stop codon, TAA.
  • the invention provides method of inhibiting expression of desired MHC molecule, wherein the non-transgenic, minimally alteration of genome does not result in any frameshifts or frame disruptions in the native donor swine’s SLA/MHC gene.
  • the beta-2-microglobulin protein which comprises the heterodimer structure of each of the MHC -I proteins is species-specific. Based on the pig genome assembly SSC10.2, a segmental duplication of -45.5 kb, encoding the entire B2M protein, was identified in pig chromosome 1, wherein functional duplication of the B2M gene identified with a completely identical coding sequence between two copies in pigs.
  • B2M duplication could be beneficial to the immune system of pigs by increasing the availability of MHC class I light chain protein, B2M, to complex with the proteins encoded by the relatively large number of MHC class I heavy chain genes in pigs.
  • B2M molecule with respect to MHC Class I molecule can be observed.
  • swine has duplication of B2M gene while human has one.
  • the first copy of the swine B2M gene is reprogrammed through site-directed mutagenesis, as previously disclosed. As shown in FIG.
  • the amino acid sequences of exon 2 of the swine B2M is compared with that of the human, wherein the non-conserved regions are identified.
  • the expression of the second copy of the swine B2M gene is inhibited by use of STOP codon, as previously disclosed.
  • STOP codon as previously disclosed.
  • the fist copy of the swine B2M gene is reprogrammed through site-directed mutagenesis and second duplicated B2M gene is not expressed, wherein the reprogramming does not result in frameshift of B2M gene.
  • Primary macrophages and other antigen presenting cells are useful for studying immune response, however, the long term use of primary cells is limited by the cells’ short life span.
  • primary cells can only be genetically engineered and evaluated one time before the cells reach senescence.
  • PAECs porcine aortic endothelial cells
  • An immortalized cell line that has the desired characteristics (expression of MHC Class I and II molecules and CD80/86) of a macrophage or representative APC would be ideal to conduct multiple modifications of the genome and address impact on immunological reactivity using the same genetic background.
  • the ability to generate a viable immortalized pig cell line has been limited to fibroblasts and epithelial cell lines which are not relevant for the study of the immune response in xenotransplantation.
  • An immortalized porcine alveolar macrophage (PAM) line was developed from Landrace strain of pig [Weingartl 2002] and is commercially available through ATCC [ 3D4/21, ATCC CRL-2843] The cell line showed some percentage of non-specific esterase and phagocytosis which was dependent upon conditions of the medium. Cells could be grown as anchorage dependent or in colonies under serum free conditions. Myeloid/monocyte markers (e.g. CD14) were detected. Desired characteristics of an immortalized cell line was MHC Class I and II. MHC Class I was shown to be broadly expressed on all cells, however, MHC Class II, DR and DQ, expression of 3D4/21 cells was initially reported as being low, 18% and 4%.
  • PAEC have been shown to be activated and DR expression could be upregulated with exposure to IFN-gamma.
  • 3D4/21 cells were exposed to IFN-gamma and Class II expression increased DR: 29.68% to 42.27% and DQ: 2.28% to 57.36% after 24 hours of exposure to IFN-gamma.
  • CD80/86 are expressed on the cell surface, these glycoproteins are essential for the second signal of T cell activation and proliferation.
  • PAM cells, 34D/21 have the desired characteristics of a porcine APC in which genetic changes in genes associated with the MHC can be documented using an immortalized cell line and the resulting changes in the phenotype can be assessed using flow cytometry to address expression or lack of expression of the glycoproteins of interest and cellular immune responses, Mixed Lymphocyte Response (MLR).
  • MLR Mixed Lymphocyte Response
  • a one way MLR is set up in which one set of cells is identified as the stimulator cells, these are donor cells or unmodified or modified PAM cells, and the other set of cells is the responder cells, these are cells from the recipient (these could be from recipient’s who share a similar expression of MHC molecules are the modified PAM cells.
  • the stimulator cells are treated with an agent to prevent the cells from proliferating and this could be either radiation or incubation with mitomycin C which covalently crosslinks DNA, inhibiting DNA synthesis and cell proliferation.
  • mitomycin C which covalently crosslinks DNA, inhibiting DNA synthesis and cell proliferation.
  • the stimulator cells do not proliferate in culture however, the responder cells proliferate in response to interaction at the MHC Class I and II and it is this proliferation that is measured in a MLR.
  • a cell culture containing both stimulator and responder cells is prepared and incubated for 5-7 days and proliferation/ activation is measured. Proliferation can be measured by the amount of radioactive thymidine [ 3 HTdr] or BrdU [analog of thymidine] that is incorporated into the DNA upon proliferation at the end of 5 or 7 days.
  • Responders cells can be either PBMC, CD4+ T cells, CD8+ T cells or other subpopulations of T cells.
  • PBMC represent all the immune cells that are present in the recipient and the measured response reflects the ability of the responders to mount an immune response to the stimulator cells, [unmodified or modified PAM cells].
  • the measured proliferation consists of both CD4+ and CD8+ T cells which interact with MHC Class II and I, respectively. Using only CD4+ T cells against the unmodified or modified PAM cells is to measure the response to MHC Class II glycoproteins, DR and DQ.
  • responder CD8+ T cells will be used to assess an immune response to MHC Class I glycoproteins, SLA 1 AND 2. This type of analysis removes the contribution to the immune response from responder APCs as found in PBMC. Comparative data will demonstrate the contribution of these respective glycoproteins to the immune response of the genetically defined responder and reflects on the genetic modifications made to the PAM cells.
  • Flow cytometry phenotypic analysis of the genetically modified PAM cells.
  • the cell phenotype of genetically modified cells e.g., cells from a genetically modified animal or cells made ex vivo, are analyzed to measure the changes in expression of the glycoproteins encoded by the genes that were modified.
  • Cells are incubated with an antibody with a fluorescent label that binds to the glycoprotein of interest and labeled cells are analyzed using flow cytometry.
  • the analysis has been performed on unmodified PAM cells to identify the expression of MHC Class I, Class II (DR and DQ) and CD80/86. Changes in modified PAM cells will be referenced to this database.
  • Flow cytometry will also be used to characterize the expression of glycoproteins encoded by genes for SLA 3, 6, 7, and 8 as the genes in the PAM cells are modified with recipient specific sequences related to HLA C, E, F, and G.
  • this type of analysis is also used to ensure the glycoprotein encoded by a gene that is knock-out is not expressed.
  • This technique can also be used to sort out genetically modified cells from a pool of cells with mixed phenotypes.
  • Complement Dependent Cytotoxicity (CDC) assays may be performed to determine if anti-HLA antibodies recognize the cells from the biological product of the present disclosure.
  • Assay plates prepared by adding a specific human serum containing previously characterized anti-HLA antibodies (or control serum) can be used.
  • IFN-g treated donor cells are resuspended and added to the assay plates, incubated with a source of complement, e.g., rabbit serum. After at least 1 hour of incubation at room temperature, acridine orange/ethidium bromide solution is added.
  • Percent cytotoxicity is determined by counting dead and live cells visualized on a fluorescent microscope, subtracting spontaneous lysis values obtained in the absence of anti- HLA antibodies, and scoring with a scale.
  • NK cell reactivity modulation to decrease cytotoxicity.
  • Potential mechanisms of activation, recognition, and elimination of target cells by NK cells induce the release of the content of their lytic granules (perforin, granzyme, and cytolysin).
  • NK cells recognize the lack of self-major histocompatibility complex (MHC) Class I molecules on target cells by inhibitory NK cell receptors leading to direct NK cytotoxicity. This is the case for xenotransplantation.
  • NK cells are regulated by HLA C that is recognized by inhibitory NK cell inhibitory killer cell immunoglobulin-like receptors (KIRs), KIR2DL2/2DL3,KIR2DL1, and KIR3DL1.
  • KIRs inhibitory NK cell inhibitory killer cell immunoglobulin-like receptors
  • NK cells inhibitory receptor immunoglobulin-like transcript 2 (ILT2) interacts with MHC Class I and CD94-NKG2A recognizing HLA-E.
  • HLA F and G have similar roles on the trophoblast.
  • the cytolytic activity of recipient NK cells to an unmodified PAM cell can be measured in vitro in which human NK cells are added to an adherent monolayer of unmodified PAM cells and cultured for 4 hours. Cell lysis is measured by release of radioactive Cr 51 or a chromophore measured by flow cytometry.
  • PAM cells with modified SLA 3, 6, 7 or 8 to mirror HLA C, HLA E, HLA G or HLA F, respectively, can be assessed using this cytotoxicity assay.
  • the desired sequences are knocked into the cell genome through insertion of genomic material using, e.g., homology-directed repair (HDR).
  • HDR homology-directed repair
  • the cells are incubated in porcine interferon gamma (IFN-g) for 72 hours which stimulates expression. Expression is then measured by flow cytometry using target specific antibodies. Flow cytometry may include anti-HLA-C, HLA-E, HLA-G, or other HLA antibodies, or pan anti-HLA Class I or Class II antibodies. According to the present disclosure, cell surface HLA expression after knock-in is confirmed.
  • Cell count and viability were determined by trypan blue exclusion method. A total of 1 x 105 cells were stained with mouse anti pig SLA Class I, SLA Class II DR, SLA Class II DQ antibodies for 30 min and APC-conjugated CD152(CTLA-4)-mulg fusion protein (binds to porcine CD80/CD86) for 45 min at 4°C. Cells were washed two times using FACS buffer and antibody stained cells resuspended in 100 pL FACS buffer containing anti mouse APC-conjugated polyclonal IgG secondary antibody. Aftered by incubation for 30 min at 4°C. Cells were washed two times using FACS buffer. All cells were resuspended in 200 pL FACS buffer. Samples were acquired in Novacyte flow cytometry and data was analyzed using NovoExpress.
  • Analysis procedure is based on NovoExpress flow cytometry analysis software. Any equivalent software can be used for the data analysis. Depending on the software used analysis presentation maybe slightly different. Gates maybe named differently and % values might be slightly different.
  • PAM cells were treated with porcine IFN-g for 24 hours and stained with primary MAbs and fluorescein conjugated secondary antibody and APC conjugated CD 152 which has a high affinity for co-stimulatory molecules CD80 (B7-1) and CD86 (B7-2).
  • IFN-g the cells displayed increased SLA and CD80/86 costimulatory molecules expression compared to unstimulated PAM cells. While unstimulated cells were 99.98% SLA Class I+, 29.68% DR+ 2.28 DQ+ and 4.81% CD80/86+, IFN-g stimulated cells were 99.99% SLA Class 1+ 42.27% DR+, 57.36% DQ+, 47.38% CD80/86 +.
  • IFN-g containing cells with LPS resulted similar levels of SLA molecules and CD80/86 expression compared to cells only treated with IFN-g.
  • PBMCs Peripheral Blood Mononuclear Cells
  • CD8 and CD4 positive T cells when they are co-cultured with porcine alveolar macrophages (PAM) cells.
  • Human donor PBMCs or their CD4+ T cells were co-cultured with untreated, IFN-y activated and KLH loaded PAM cells for seven days.
  • FIG. 30A and FIG. 30B one-way allogeneic and autologous MLR experiments were performed using the cells isolated from Donor #11, #50, and #57 as positive and negative controls respectively. Background controls were performed for Mitomycin C (X) treated and untreated PAM cells, and each human donor cells.
  • X Mitomycin C
  • Proliferative response is determined utilizing a bromo-deoxy uridine (BrdU) ELISA assay. On Day 6, BrdU addition was completed. On Day 7 media was collected for cytokine (IFN-y and IL-2) analysis and proliferative responses were determined. Cells were observed under the Olympus CK40 microscopy at 200X magnification on Day 7 of co-culturing.
  • BrdU bromo-deoxy uridine
  • the proliferative responses of three different human CD4+ T cells displayed similar xenogeneic responses with PAM cells SI (Stimulation Indexes) values being between 15 and 18.08.
  • the genetic modification can be made utilizing known genome editing techniques, such as zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), adeno-associated virus (AAV)-mediated gene editing, and clustered regular interspaced palindromic repeat Cas9 (CRISPR-Cas9).
  • ZFNs zinc-finger nucleases
  • TALENs transcription activator-like effector nucleases
  • AAV adeno-associated virus
  • CRISPR-Cas9 clustered regular interspaced palindromic repeat Cas9
  • CRISPR-Cas9 may also be used to perform precise modifications of genetic material.
  • the genetic modification via CRISPR-Cas9 can be performed in a manner described in Kelton, W. et. ah,“Reprogramming MHC specificity by CRISPR-Cas9-assisted cassette exchange,” Nature, Scientific Reports, 7:45775 (2017) (“Kelton”), the entire disclosure of which is incorporated herein by reference.
  • the present disclosure includes reprogramming using CRISPR-Cas9 to mediate rapid and scarless exchange of entire alleles, e.g., MHC, HLA, SLA, etc.
  • CRISPR-Cas9 is used to mediate rapid and scarless exchange of entire MHC alleles at specific native locus in swine cells.
  • Multiplex targeting of Cas9 with two gRNAs is used to introduce single or double-stranded breaks flanking the MHC allele, enabling replacement with the template HLA/MHC sequence (provided as a single or double-stranded DNA template).
  • knocking out one or more genes may include deleting one or more genes from a genome of a non-human animal. Knocking out may also include removing all or a part of a gene sequence from a non-human animal. It is also contemplated that knocking out can include 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 include substituting a sequence in one or more genes thereby disrupting expression of the one or more genes.
  • Knocking out one or more genes can also include replacing a sequence in one or more genes thereby disrupting expression of the one or more genes without frameshifts or frame disruptions in the native donor swine’s SLA/MHC gene.
  • replacing a sequence can generate a stop codon in the beginning of one or more genes, which can result in a nonfunctional transcript or protein.
  • a stop codon is created within one or more genes, the resulting transcription and/or protein can be disrupted, silenced and rendered nonfunctional.
  • the present invention utilizes alteration by nucleotide replacement of STOP codon at exon regions of the wild-type swine’s SLA-DR to avoid provocation of natural cellular mediated immune response (CD8+ T Cell) by the recipient, including making cells that lack functional expression of SLA-DR, SLA-1, SLA-2.
  • the present invention utilizes TAA .
  • the invention utilizes TAG.
  • the invention utilizes TGA.
  • the present invention utilizes insertion or creation (by nucleotide replacement) of STOP codon at exons regions of the wild-type swine’s second, identical duplication B2-microglobulin gene to reduce the B2-microglobulin mRNA expression level in pigs.
  • B2-microglobulin is a predominant immunogen, specifically a non- gal xeno-antigen.
  • the recipient’s HLA/MHC gene is sequenced and template HLA/MHC sequences are prepared based on the recipient’s HLA/MHC genes.
  • a known human HLA/MHC genotype from a World Health Organization (WHO) database may be used for genetic reprogramming of swine of the present disclosure.
  • CRISPR-Cas9 plasmids are prepared, e.g., using polymerase chain reaction and the recipient’s HLA/MHC sequences are cloned into the plasmids as templates.
  • CRISPR cleavage sites at the SLA/MHC locus in the swine cells are identified and gRNA sequences targeting the cleavage sites and are cloned into one or more CRISPR-Cas9 plasmids.
  • CRISPR-Cas9 plasmids are then administered into the swine cells and CRIPSR/Cas9 cleavage is performed at the MHC locus of the swine cells.
  • the SLA/MHC locus in the swine cells are precisely replaced with one or more template HLA/MHC sequences matching the known human HLA/MHC sequences or the recipient’s sequenced HLA/MHC genes.
  • Cells of the swine are sequenced after performing the SLA/MHC reprogramming steps in order to determine if the SLA/MHC sequences in the swine cells have been successfully reprogrammed.
  • One or more cells, tissues, and/or organs from the HLA/MHC sequence-reprogrammed swine are transplanted into a human recipient.
  • the modification to the donor SLA/MHC to match recipient HLA/MHC causes expression of specific MHC molecules in the new swine cells that are identical, or virtually identical, to the MHC molecules of a known human genotype or the specific human recipient.
  • the present disclosure involves making modifications limited to only specific portions of specific SLA regions of the swine’s genome to retain an effective immune profile in the swine while biological products are tolerogenic when transplanted into human recipients such that use of immunosuppressants can be reduced or avoided.
  • xenotransplantation studies of the prior art required immunosuppressant use to resist rejection.
  • the swine genome is reprogrammed to disrupt, silence, cause nonfunctional expression of swine genes corresponding to HLA-A, HLA-B, and DR, and to reprogram via substitution of HLA-C, HLA-E, HLA-F, and/or HLA-G.
  • the swine genome is reprogrammed to knock-out swine genes corresponding to HLA-A, HLA-B, HLA-C, HLA-F, DQ, and DR, and to knock-in HLA-C, HLA-E, HLA-G.
  • the swine genome is reprogrammed to knock out swine genes corresponding to HLA-A, HLA-B, HLA-C, HLA-F, DQ, and DR, and to knock- in HLA-C, HLA-E, HLA-G, HLA-F, and DQ.
  • the swine genome is reprogrammed to knock-out SLA-1; SLA-6,7,8; SLA-MIC2; and SLA-DQA; SLA-DQB 1; SLA-DQB2, and to knock-in HLA-C; HLA-E; HLA-G; and HLA-DQ.
  • HLA-C expression is reduced in the reprogrammed swine genome.
  • this reprogramming thereby minimizes or even eliminates an immune response that would have otherwise occurred based on swine MHC molecules otherwise expressed from the donor swine cells.
  • RNA for the target gene.
  • Each guide RNA is composed of two components, a CRISPRRNA (crRNA) and a trans-activating RNA (tracrRNA). These components may be linked to form a continuous molecule called a single guide RNA (sgRNA) or annealed to form a two-piece guide (crtracrRNA)
  • CRISPR components can be delivered to cells in DNA, RNA, or ribonucleoprotein (RNP) complex formats.
  • the DNA format involves cloning gRNA and Cas9 sequences into a plasmid, which is then introduced into cells. If permanent expression of gRNA and/or Cas9 is desired, then the DNA can be inserted into the host cell’s genome using a lentivirus.
  • Guide RNAs can be produced either enzymatically (via in vitro transcription) or synthetically. Synthetic RNAs are typically more pure than IVT-derived RNAs and can be chemically modified to resist degradation.
  • Cas9 can also be delivered as RNA.
  • the ribonucleoproteins (RNP) format consists of gRNA and Cas9 protein. The RNPs are pre-complexed together and then introduced into cells. This format is easy to use and has been shown to be highly effective in many cell types.
  • the CRISPR components are introduced into cells via one of several possible transfection methods, such as lipofection, electroporation, nucleofection, or microinjection.
  • a guide RNA and Cas9 are introduced into a cell culture, they produce a DSB at the target site within some of the cells.
  • the NHEJ pathway then repairs the break, potentially inserting or deleting nucleotides (indels) in the process. Because NHEJ may repair the target site on each chromosome differently, each cell may have a different set of indels or a combination of indels and unedited sequences.
  • the desired sequences are knocked into the cell genome through insertion of genomic material using, e.g., homology-directed repair (HDR).
  • HDR homology-directed repair
  • disruptions and modifications to the genomes of source animals provided herein can be performed by several methods including, but not limited to, through the use of clustered regularly interspaced short palindromic repeats (“CRISPR”), which can be utilized to create animals having specifically tailored genomes.
  • CRISPR clustered regularly interspaced short palindromic repeats
  • Such genome modification can include, but not be limited to, any of the genetic modifications disclosed herein, and/or any other tailored genome modifications designed to reduce the bioburden and immunogenicity of products derived from such source animals to minimize immunological rejection.
  • CRISPR/CRISPR-associated protein originally known as a microbial adaptive immune system, has been adapted for mammalian gene editing recently.
  • the CRISPR/Cas system is based on an adaptive immune mechanism in bacteria and archaea to defend the invasion of foreign genetic elements through DNA or RNA interference.
  • CRISPR/Cas has been adapted for precise DNA/RNA targeting and is highly efficient in mammalian cells and embryos.
  • CRISPR/Cas9 The most commonly used and intensively characterized CRISPR/Cas system for genome editing is the type II CRISPR system from Streptococcus pyogenes; this system uses a combination of Cas9 nuclease and a short guide RNA (gRNA) to target specific DNA sequences for cleavage.
  • gRNA short guide RNA
  • a 20-nucleotide gRNA complementary to the target DNA that lies immediately 5' of a PAM sequence e.g., NGG
  • a PAM sequence e.g., NGG
  • CRISPR/Cas9 can achieve gene targeting in any N20-NGG site.
  • a genetically modified non-human animal whose genome comprises a nucleotide sequence encoding a human or humanized MHC I polypeptide and/or b2 microglobulin polypeptide, wherein the polypeptide(s) comprises conservative amino acid substitutions of the amino acid sequence(s) described herein.
  • nucleic acid residues encoding a human or humanized MHC I polypeptide and/or b2 microglobulin described herein due to the degeneracy of the genetic code, other nucleic acids may encode the polypeptide(s) of the invention. Therefore, in addition to a genetically modified non-human animal that comprises in its genome a nucleotide sequence encoding MHC I and/or b2 microglobulin polypeptide(s) with conservative amino acid substitutions, a non-human animal whose genome comprises a nucleotide sequence(s) that differs from that described herein due to the degeneracy of the genetic code is also provided.
  • the present disclosure includes reprogramming, or leveraging the inhibitory and co-stimulatory effects of the MHC -I (Class B) molecules.
  • the present disclosure includes a process that“finds and replaces” portions of the donor animal genome corresponding to portions of the HLA gene, e.g., to overexpress HLA-G where possible, retaining and overexpressing portions corresponding to HLA- E, and/or“finding and replacing” portions corresponding to HLA-F.
  • the term “find and replace” includes identification of the homologous/analogous/orthologous conserved genetic region and replacement of the section or sections with the corresponding human components through gene editing techniques.
  • Another aspect includes finding and replacing the beta-2 microglobulin protein which is expressed in HLA -A, -B, -C, -E, -F, and -G. Homologous/analogous/orthologous conserved cytokine mediating complement inhibiting or otherwise immunomodulatory cell markers, or surface proteins, that would enhance the overall immune tolerance at donor-recipient cellular interface.
  • the present invention utilizes immunogenomic reprogramming to reduce or eliminate MHC-I (Class A) components to avoid provocation of natural cellular mediated immune response by the recipient.
  • exon regions in the donor animal e.g., swine
  • exon regions in HLA- A and HLA-B are disrupted, silenced or otherwise nonfunctionally expressed on the donor animal.
  • exon regions in the donor animal e.g., swine genome corresponding to exon regions of HLA-A and HLA-B are disrupted, silenced or otherwise nonfunctionally expressed in the genome of the donor animal and exon regions in the donor animal (e.g., swine) genome corresponding to exon regions of HLA-C may be modulated, e.g., reduced.
  • the present disclosure includes silencing, knocking out, or causing the minimal expression of source animal’s orthologous HLA-C (as compared to how such would be expressed without such immunogenomic reprogramming).
  • the beta-2-microglobulin protein which comprises the heterodimer structure of each of the MHC-I proteins is species-specific. Thus, in one embodiment of the present disclosure, it is reprogrammed. In contrast to its counterparts, the genetic instructions encoding for this prevalent, building-block protein is not located in the MHC-gene loci. Thus, in one embodiment of the present disclosure includes a genetic modification in addition to those specific for the respective targets as described herein.
  • FIG. 33 is a schematic depiction of a humanized porcine cell according to the present disclosure. As shown therein, the present disclosure involves reprogramming exons encoding specific polypeptides or glycoproteins, reprogramming and upregulating specific polypeptides or glycoproteins, and reprogramming the nuclear genome to have nonfunctional expression of specific polypeptides or glycoproteins, all of which are described in detail herein.
  • Genetically modified cells e.g., cells from a genetically modified animal or cells made ex vivo, can be analyzed and sorted.
  • genetically modified cells can be analyzed and sorted by flow cytometry, e.g., fluorescence-activated cell sorting.
  • flow cytometry e.g., fluorescence-activated cell sorting.
  • genetically modified cells expressing a gene of interest 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 gene.
  • the surface expression of SLA-1, SLA-2, SLA-3, SLA- 6, SLA-7, SLA-8, SLA-DR and SLA-DQ on unmodified PAM cells is established using labeled antibodies directed to epitopes on those glycoproteins.
  • specific gene knock outs e.g. SLA-1, SLA-2 and SLA-DR
  • flow cytometry is used to demonstrate the lack of expression of these glycoproteins even after incubation of the cells with interferon gamma.
  • Genes for SLA-3, SLA-6, SLA-7, SLA-8, and SLA-DQ will be modified such that glycoproteins expressed on the cell surface will reflect HLA-C, HLA-E, HLA-F, HLA-G and HLA-DQ glycoproteins, respectively.
  • a different set of antibodies specific for the HLA epitopes will be used to detect expression of the glycoproteins encoded by the modified genes and antibodies directed to the SLA related glycoproteins will not bind to the cell surface of the modified PAM cells.
  • the desired sequences are knocked into the cell genome through insertion of genomic material using, e.g., homology-directed repair (HDR).
  • HDR homology-directed repair
  • the cells are incubated in porcine interferon gamma (IFN-g) for up to 72 hours which stimulates expression. Expression is then measured by flow cytometry using target specific antibodies. Flow cytometry may include anti-HLA-C, HLA-E, HLA-G, or other HLA antibodies, or pan anti-HLA Class I or Class II antibodies. According to the present disclosure, cell surface HLA expression after knock-in is confirmed.
  • the immune response of the modified swine cells are evaluated through Mixed Lymphocyte Reaction (MLR) study.
  • Responders cells can be either PBMC, CD4+ T cells, CD8+ T cells or other subpopulations of T cells.
  • PBMC represent all the immune cells that are present in the recipient and the measured response reflects the ability of the responders to mount an immune response to the stimulator cells, for example, a comparison of unmodified PAM cells and modified PAM cells.
  • PAECs or fibroblasts may be used.
  • the measured proliferation consists of both CD4+ and CD8+ T cells which interact with MHC Class II and I, respectively.
  • Using only CD4+ T cells against the unmodified or modified PAM cells measures the response to MHC Class II glycoproteins, DR and DQ.
  • DR MHC Class II glycoproteins
  • DQ MHC Class II glycoproteins
  • Responder CD8+ T cells were used to assess an immune response to MHC Class I glycoproteins, SLA-1 and SLA-2.
  • 1 x 10 5 purified human CD8+ T cells (A) or human PBMC (B) were stimulated with increasing numbers of irradiated (30 Gy) porcine PBMC from four-fold knockout pig 10261 or a wild-type pig. Proliferation was measured after 5 d + 16 h by 3H- thymidine incorporation. Data represent mean cpm ⁇ SEM of triplicate cultures obtained with cells from one human blood donor in a single experiment. Similar response patterns were observed using responder cells from a second blood donor and stimulator cells from four-fold knockout pig 10262.
  • Proliferation of human CD8+ T cells decreased after stimulation with four-fold knockout porcine PBMC.
  • Factors et ah, Viable pigs after simultaneous inactivation of porcine MHC Class I and three xenoreactive antigen genes GGTA1, CMAH and B4GALNT2, Xenotransplantation, 2019.
  • Modified knock out PAM cells not expressing SLA-1 and SLA-2 will not generate a CD8+ T cell response. This is in contrast with a response using PBMC as the responders. See FIG. 34.
  • CDC Complement Dependent Cytotoxicity assays may be performed to determine if anti-HLA antibodies recognize the cells from the biological product of the present disclosure.
  • Assay plates prepared by adding a specific human plasma containing previously characterized anti-HLA antibodies (or control plasma) can be used. Plasma is serially diluted starting at 1 :50 to 1 :36450 in HBSS media with calcium and magnesium, incubated with modified or unmodified PAM cells for 30 minutes at 4°C followed by incubation with freshly reconstituted baby rabbit complement for 1 hour at 37°C. The cells were then stained with Fluorescein Diacetate (FDA) and Propidium Iodide (PI) for 15 minutes and analyzed by flow cytometry. Appropriate compensation controls were run for each assay. Cells were acquired and analyzed on an ACEA NovoCyte Flow Cytometer. PAM cells can also be treated with interferon gamma to increase surface expression of MHC molecules.
  • FDA Fluorescein Diacetate
  • PI Propidium I
  • Dead Cells PI+, FDA- b. Damaged Cells: PI+, FDA+
  • NK cytotoxicity against unmodified and modified PAM cells where genes for SLA 3, SLA 6, SLA 7, and SLA 8 are modified such that glycoproteins expressed on the cell surface will reflect HLA C, HLA E, HLA F, and HLA G glycoproteins, respectively.
  • the cytotoxic activity of freshly isolated and IL-2-activated human NK cells was tested in 4-hr 51Cr release assays in serum-free AIM-V medium. Labeled unmodified and modified PAM cells are cultured in triplicate with serial 2-fold dilutions of NK cells four E:T ratios ranging from 40: 1 to 5: 1.
  • NK cells from a specific genetically matched “recipient” will have reduced killing of modified PAM cells compared to unmodified PAM cells.
  • the protection provided by HLA E in transfected PAEC cells against NK cells is illustrated in Fig. 34.
  • HLA E expression on porcine lymphoblastoid cells inhibits xenogeneic human NK cytotoxicity.
  • IFN-g porcine interferon gamma
  • Expression is then measured by flow cytometry using target specific antibodies.
  • Flow cytometry may include anti-HLA-C, HLA-E, HLA-G, or other HLA antibodies, or pan anti-HLA Class I or Class II antibodies. According to the present disclosure, cell surface HLA expression after knock-in is confirmed.
  • genetic modifications in a porcine cell line to insert the modifications listed in table listed in FIG. 33 are not expressed in order to reduce the hyperacute rejection phenomenon and the deleterious activation of antibody-mediated immune pathways, namely activation of the complement cascade. With this step, creation of an allogeneic-“like” cell with respect to non-MHC cell markers is grossly achieved.
  • Genetically modified cells e.g., cells from a genetically modified animal or cells made ex vivo, are analyzed and sorted.
  • genetically modified cells can be analyzed and sorted by flow cytometry, e.g., fluorescence-activated cell sorting.
  • flow cytometry e.g., fluorescence-activated cell sorting.
  • genetically modified cells expressing a gene of interest 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 gene.
  • the gene of interest may be as small as a few hundred pairs of cDNA bases, or as large as about a hundred thousand pairs of bases of a genic locus comprising the exonic-intron encoding sequence and regulation sequences necessary to obtain an expression controlled in space and time.
  • the size of the recombined DNA segment is between 25 kb and longer than 500 kb. In any case, recombined DNA segments can be smaller than 25 kb and longer than 500 kb.
  • the immune response of the modified swine cells are evaluated through Mixed Lymphocyte Reaction (MLR) study.
  • MLR Mixed Lymphocyte Reaction
  • the impact of the modification or non-expression of MHC la polypeptides on the immune response are measured through the immune response of CD8+ T Cells.
  • the impact of the modification of MHC lb polypeptides on the immune response are measured through the immune response of NK Cells.
  • the impact of the modification or non expression of MHC II polypeptides on the immune response are measured through the immune response of CD4+ T Cells.
  • the MLR study herein, not only measures the efficacy of the site- directed mutagenic substitution, but also evaluates and identifies the impact of individual modifications, individually and as a whole, as measurements are taken iteratively as additional site-directed mutagenic substitutions are made.
  • the desired sequences are knocked into the cell genome through insertion of genomic material using, e.g., homology-directed repair (HDR).
  • HDR homology-directed repair
  • the cells are incubated in porcine interferon gamma (IFN-g) for 72 hours which stimulates expression. Expression is then measured by flow cytometry using target specific antibodies. Flow cytometry may include anti-HLA-C, HLA-E, HLA-G, or other HLA antibodies, or pan anti-HLA Class I or Class II antibodies. According to the present disclosure, cell surface HLA expression after knock-in is confirmed.
  • Complement Dependent Cytotoxicity (CDC) assays may be performed to determine if anti-HLA antibodies recognize the cells from the biological product of the present disclosure.
  • Assay plates prepared by adding a specific human serum containing previously characterized anti-HLA antibodies (or control serum) can be used.
  • IFN-g treated donor cells are resuspended and added to the assay plates, incubated with a source of complement, e.g., rabbit serum. After at least 1 hour of incubation at room temperature, acridine orange/ethidium bromide solution is added.
  • Percent cytotoxicity is determined by counting dead and live cells visualized on a fluorescent microscope, subtracting spontaneous lysis values obtained in the absence of anti- HLA antibodies, and scoring with a scale.
  • the resulting cell line lacks the above sugar moieties as well as SLA Class I expression.
  • Analysis by flow cytometry and molecular gene are performed to demonstrate no surface expression and changes made at the gene level.
  • Cellular reactivity is assessed using a mixed lymphocyte reaction (MLR) with human PBMCs and the irradiated cell line. In comparison to the WT line, there is a reduction in the T cell proliferation, predominantly in the CD8+ T cells.
  • MLR mixed lymphocyte reaction
  • human antigen presenting cells are absent from the culture such that the cellular response is not the result of pig antigens presented by the APCs.
  • porcine fetal fibroblast cells are reprogrammed using gene editing, e.g., by using CRISPR/Cas for precise reprogramming and transferring a nucleus of the genetically modified porcine fetal fibroblast cell to a porcine enucleated oocyte to generate an embryo; and d) transferring the embryo into a surrogate pig and growing the transferred embryo to the genetically modified pig in the surrogate pig.
  • genetically reprogrammed pigs are bred so that several populations of pigs are bred, each population having one of the desirable human cellular modifications determined from the above assays.
  • the pigs’ cellular activity after full growth is studied to determine if the pig expresses the desired traits to avoid rejection of the pigs’ cells and tissues after xenotransplantation.
  • further genetically reprogrammed pigs are bred having more than one of the desirable human cellular modifications to obtain pigs expressing cells and tissues that will not be rejected by the human patient’s body after xenotransplantation.
  • iPSC induced pluripotent stem cell
  • the PAM cells presented in this disclosure are a transformed cell line but the genetic engineering schema can be transferred to porcine iPSC.
  • the specific genetically modified iPSC line would then be used for somatic cell nuclear transfer (SCNT), transferring a nucleus of the genetically modified porcine fetal fibroblast cell to a porcine enucleated oocyte to generate an embryo; and transferring the embryo into a surrogate pig and growing the transferred embryo to the genetically modified pig in the surrogate pig.
  • SCNT somatic cell nuclear transfer
  • This has the advantage in that the transferred nucleus contains the specific genome, hence the piglets do not need to go through breeding to obtain a homozygous offspring.
  • the genotype and phenotype of the piglets are identical to the iPSC.
  • Specific populations of gene modified iPSC can be cryopreserved as a specific cell line and used as required for development of pigs needed for that genetic background. Thawed iPSCs are cultured and nucleus is transferred into enucleated oocytes to generate blastocysts/embryos for implantation into surrogate pig. This creates a viable bank of genetically modified iPSC for generation of pigs required for patient specific tissue, organ, or cell transplantation.
  • a method for making a genetically modified animal described in the application comprising: a) obtaining a cell with reduced expression of one or more of a component of a MHC I-specific enhanceosome, a transporter of a MHC I-binding peptide, and/or C3; b) generating an embryo from the cell; and c) growing the embryo into the genetically modified animal.
  • the cell is a zygote.
  • HLA/MHC sequence-reprogrammed swine are bred for at least one generation, or at least two generations, before their use as a source for live tissues, organs and/or cells used in xenotransplantation.
  • the CRISPR/Cas9 components can also be utilized to inactivate genes responsible for PERV activity, e.g., the pol gene, thereby simultaneously completely eliminating PERV from the swine donors.
  • the present disclosure includes embryogenesis and live birth of SLA-free and HLA-expressing biologically reprogrammed swine. In certain aspects, the present disclosure includes breeding SLA-free and HLA-expressing biologically reprogrammed swine to create SLA-free and HLA-expressing progeny.
  • the CRISPR/Cas9 components are injected into swine zygotes by intracytoplasmic microinjection of porcine zygotes. In certain aspects, the CRISPR/Cas9 components are injected into swine prior to selective breeding of the CRISPR/Cas9 genetically modified swine.
  • the CRISPR/Cas9 components are injected into donor swine prior to harvesting cells, tissues, zygotes, and/or organs from the swine.
  • the CRISPR/Cas9 components include all necessary components for controlled gene editing including self-inactivation utilizing governing gRNA molecules as described in U.S. Pat. No. 9,834,791 (Zhang), which is incorporated herein by reference in its entirety.
  • genetically reprogrammed pigs are bred so that several populations of pigs are bred, each population having one of the desirable human cellular modifications determined from the above assays.
  • the pigs’ cellular activity after full growth is studied to determine if the pig expresses the desired traits to avoid rejection of the pigs’ cells and tissues after xenotransplantation.
  • further genetically reprogrammed pigs are bred having more than one of the desirable human cellular modifications to obtain pigs expressing cells and tissues that will not be rejected by the human patient’s body after xenotransplantation.
  • any of the above protocols or similar variants thereof can be described in various documentation associated with a medical product.
  • This documentation can include, without limitation, protocols, statistical analysis plans, investigator brochures, clinical guidelines, medication guides, risk evaluation and mediation programs, prescribing information and other documentation that may be associated with a pharmaceutical product. It is specifically contemplated that such documentation may be physically packaged with cells, tissues, reagents, devices, and/or genetic material as a kit, as may be beneficial or as set forth by regulatory authorities.
  • a method for making a genetically modified animal described in the application comprising: a) obtaining a cell with reduced expression of one or more of a component of a MHC I-specific enhanceosome, a transporter of a MHC I-binding peptide, and/or C3; b) generating an embryo from the cell; and c) growing the embryo into the genetically modified animal.
  • the cell is a zygote.
  • Muscle and skin tissue samples taken from each of these pigs were dissected and cultured to grow out the fibroblast cells. The cells were then harvested and used for somatic cell nuclear transfer (SCNT) to produce clones. Multiple fetuses (up to 8) were harvested on day 30. Fetuses were separately dissected and plated on 150 mm dishes to grow out the fetal fibroblast cells. Throughout culture, fetus cell lines were kept separate and labeled with the fetus number on each tube or culture vessel. When confluent, cells were harvested and frozen at about 1 million cells/mL in FBS with 10% DMSO for liquid nitrogen cryo-storage.
  • SCNT somatic cell nuclear transfer
  • the CRISPR/Cas9 components are injected into swine oocytes, ova, zygotes, or blastocytes prior to transfer into foster mothers. Creation of, Procurement of Personalized, Tolerogenic Cells, Tissues, and Organs Donor of Cells, Tissues, and Organs for Transplantation from Humanized,“Bespoke”, Designated-
  • a barrier source animal location including, but not limited to, a Source Animal Facility (“SAF”) 100, that can be used for the housing, propagation, maintenance, care and utilization of a closed colony swine, including a closed colony that is designated pathogen free (“DPF”) (“DPF Closed Colony”) 102, is shown.
  • SAF Source Animal Facility
  • DPF pathogen free
  • DPF Closed Colony a closed colony that is designated pathogen free
  • the SAF has positive pressure, biocontainment characteristics is operated under specific isolation-barrier conditions.
  • the DPF Closed Colony 102 is comprised of source animals maintained and propagated for harvesting various biological products for use in human xenotransplantation and other therapies, wherein such products have reduced bioburden and demonstrate reduced immunogenicity resulting from xenotransplantation and other therapeutic procedures.
  • xenotransplantation products of the present disclosure are less immunogenic than a xenotransplantation product made from conventional Gal-T knockout swine, from conventional triple knockout swine, from transgenic swine, from wild-type animals, and/or allograft.
  • biological products made according to the present disclosure provided unexpectedly high clinical benefit when using a single knockout pig as the donor animal in that, despite the presence of Neu5Gc and porcine B4GALNT2, the biological product made according to the present disclosure had less immunogenicity than allograft, vascularized, and was resistant to rejection for the entire duration of the study period.
  • the SAF 100 and each of its accompanying areas can be utilized to house and maintain source animals from which biological products are harvested and/or processed.
  • the SAF 100 and its areas are designed to minimize and eliminate the potential for contamination of the harvested and/or processed biological products and cross-contamination between such products.
  • utilized animal areas are ventilated.
  • animal areas are ventilated with high efficiency particulate air (HEPA)-filtered fresh air from the roof of the building, for example, having at least 10-15 air changes per hour.
  • HEPA high efficiency particulate air
  • one or more laminar flow hoods e.g., Class II Type A2 Laminar Airflow Biosafety Cabinets
  • a xenotransplantation drug processing suite to providing additional ventilation to minimize or eliminate cross contamination.
  • utilized areas are also temperature controlled and monitored.
  • the areas are heated and cooled to maintain temperature within the range specified by, for example, the Guide for the Care and Use of Laboratory Animals.
  • Utilized animal holding rooms are also alarmed and centrally monitored for high or low temperatures, and staff are notified immediately if temperatures are beyond required temperature.
  • the SAF 100 has multiple levels of containment for the source animals.
  • source animals are contained in a primary level of containment consisting of pens and cages which are secured by stainless steel latches.
  • secondary level of containment functionally designated areas (e.g., rooms, suites or other areas) can have latched inner doors, and an ante-room with card-controlled access to a hallway.
  • a tertiary level of containment can include outside perimeter fencing.
  • the entire SAF is located within a single building. Primary entrance is through a single door via programmable identification (ID) card. All other external doors are alarmed, remain locked, and are for emergency use only.
  • ID programmable identification
  • Security is also a consideration to ensure security of the SAF 100 in general, and to control individuals entering the SAF 100 to minimize the risk of outside contaminants entering the SAF 100 and reaching the source animals. Therefore, in one aspect, the primary entrance to the SAF 100 is through a single door 116 via programmable identification (ID) card 118. All other external doors 120 are alarmed, remain locked, and are for emergency use only.
  • ID programmable identification
  • the SAF 100 animal program is licensed and/or accredited and overseen, evaluated and operated by a team of highly experienced, professional staff.
  • the program is registered and/or accredited with the USDA Animal and Plant Health Inspection Service (as a licensed animal research facility), National Institute of Health (NIH) Office of Laboratory Animal Welfare (OLAW) (confirming compliance with Public Health and Safety (PHS) regulations, Association for Assessment and Accreditation of Laboratory Animal Care (AAALAC) (with veterinary care of the source animals housed at the SAF under the direction of an attending veterinarian), and other federal, state and local regulatory authorities.
  • caretakers have extensive training and experience in handling and caring for the source animals being managed in accordance with the present invention. For example, each caretaker undergoes a documented training program covering the standard operating procedures governing handling and care of these source animals, and be skilled in making daily health assessments and insuring prompt care is directed to any animal in need.
  • the caretakers can be trained in scrubbing and gowning procedures prior to entry into the isolation areas (e.g., rooms, suites or other areas) as described herein, and under a medical surveillance program to ensure staff health and the health of the source animals.
  • swine can be utilized as source animals.
  • the terms“swine,”“pig” and“porcine” are generic terms referring to the same type of animal without regard to gender, size, or breed. It will be understood that any number of source animals could be utilized in accordance with the present invention, including, but not limited to, pigs, non-human primates, monkeys, sheep, goats, mice, cattle, deer, horses, dogs, cats, rats, mules, and any other mammals. Source animals could also include any other animals including, but not limited to, birds, fish, reptiles, and amphibians.
  • any animal serving as a source animal hereunder including swine, regardless of how such swine may be configured, engineered, or otherwise altered and/or maintained, may be created, bred, propagated and/or maintained in accordance with the present disclosure to create and maintain animals and resulting biological products to be used in or in preparation or pursuit of clinical xenotransplantation.
  • the present disclosure includes non-human animals, e.g., swine, having certain combinations of specific genetic characteristics, breeding characteristics and pathogen-free profile.
  • animals may include, as described above and herein, immunogenomic reprogrammed swine having a biologically reprogrammed genome such that it does not express one or more extracellular surface glycan epitopes, e.g., genes encoding alpha-1,3 galactosyltransferase, cytidine monophosphate-N-acetylneuraminic acid hydroxylase (CMAH), and pi,4-N-acetylgalactosaminyltransf erase are disrupted such that surface glycan epitopes encoded by said genes are not expressed, as well as other modifications to the swine’s SLA to express MHC-I or MHC-II, and regulation of PD-1 and CTLA4, as described above and herein.
  • Brucella suis is raised and maintained according to a bioburden-reducing procedure, the procedure comprising maintaining the swine in an isolated closed herd, wherein all other animals in the isolated closed herd are confirmed to be free of said zoonotic pathogens; wherein the swine is isolated from contact with any non-human animals and animal housing facilities outside of the isolated closed herd.
  • the swine source animals may have a combination of one or more genetic modifications including“knockout” and/or““knock-in” swine having one or more characteristics of swine disclosed in U.S. Patent No. 7,795,493 (“Phelps”), the entire disclosure of which is incorporated herein by reference.
  • Such swine lack active (and/or have disrupted) a-(l,3) galactosyl epitopes responsible for hyperacute rejection in humans upon transplantation.
  • Phelps Multiple methods of production of knockout/knock-in swine are disclosed in Phelps including: the inactivation of one or both alleles of the alpha-1, 3-GT gene by one or more point mutations (for example by a T-to-G point mutation at the second base of exon 9) and/or genetic targeting events as disclosed at col. 9, line 6 to col. 10, linel3; col. 21, line 53 to col.28, line 47; and col. 31, line 48 to col. 38, line 22 of Phelps, incorporated herein by reference.
  • the swine source animals include“knockout” and “knock-in” swine having one or more characteristics of swine disclosed in U.S. Patent No. 7,547,816 (“Day”), the entire disclosure of which is incorporated herein by reference.
  • Such swine also lack active (and/or have disrupted) a-(l,3) galactosyl epitopes responsible for hyper-acute rejection in humans upon transplantation.
  • knockout/knock-in swine Multiple methods of production of knockout/knock-in swine are disclosed in Day including: enucleating an oocyte, fusing the oocyte with a porcine cell having a non-functional alpha-1, 3-GT gene, followed by implantation into a surrogate mother, as described more fully at col. 4, line 61 to col. 18, line 55 of Day, incorporated herein by reference.
  • the creation of such swine through the described methods, and/or the utilization of such swine and progeny following creation can be employed in the practice of the present invention, including, but not limited to, utilizing organs, tissue and/or cells derived from such swine.
  • the swine source animals include GGTA Null (“knockouts” and“knock-ins”) swine having one or more characteristics of swine disclosed in U.S. Patent No. 7,547,522 (“Hawley”), the entire disclosure of which is incorporated herein by reference. Such swine also lack active (and/or have disrupted) a-(l,3) galactosyl epitopes responsible for hyper-acute rejection in humans upon transplantation.
  • knockout/knock-in swine includes utilizing homologous recombination techniques, and enucleating oocytes followed by fusion with a cell having a non-functional alpha-l,3-GT gene and implantation into a surrogate mother (as disclosed more fully at col. 6, line 1 to col. 14, line 31).
  • the creation of such swine through the described methods, and/or the utilization of such swine and progeny following creation can be employed in the practice of the present invention, including, but not limited to, utilizing organs, tissue and/or cells derived from such swine.
  • the swine source animals include swine and swine that lack active (and/or have disrupted) a-(l,3) galactosyl epitopes having one or more characteristics of swine as described in U.S. Patent No. 9,883,939 (“Yamada”), the entire disclosure of which is incorporated by reference herein.
  • the swine source animals for use or modification in accordance with the present disclosure include the swine having one or more characteristics of swine described in U.S. 2018/0184630 (Tector, III), the disclosure of which is incorporated by reference herein in its entirety.
  • swine source animals include the swine having one or more characteristics of swine disclosed in U.S. Patent Nos. 8, 106,251 (Ayares), 6,469,229 (Sachs), 7,141,716 (Sachs), each of the disclosures of which are incorporated by reference herein.
  • the creation of such swine through the described methods, and/or the utilization of such swine and progeny following creation, can be employed in the practice of the present invention, including, but not limited to, utilizing organs, tissue and/or cells derived from such swine.
  • the swine can originate from one or more highly inbred herds of pigs (whether genetically modified or not (i.e., wild-type)) with a co-efficient of inbreeding of 0.50 or greater.
  • a higher coefficient of inbreeding indicates the products derived from the source animals may have more consistent biological properties for use in pig-to-human xenotransplantation (e.g., a coefficient of inbreeding of 0.80 or greater in one aspect).
  • Coefficients of inbreeding for animals are disclosed in Mezrich et ah,“Histocompatible Miniature Swine: An Inbred Large-Animal Model,” Transplantation , 75(6):904-907 (2003).
  • An example of a highly inbred herd of swine includes miniature swine descendant from the miniature swine disclosed in Sachs, et al.,“Transplantation in Miniature Swine. I. Fixation of the Major Histocompatibility Complex,” Transplantation 22:559 (1976), which is a highly inbred line possessing reasonable size matches particularly for organs eventually utilized for clinical transplantation.
  • the creation of such swine through the described methods, and/or the utilization of such swine and progeny following creation can be employed in the practice of the present invention, including, but not limited to, utilizing organs, tissue and/or cells derived from such swine.
  • Source animals can also include animals swine that lack active (and/or have disrupted) alpha-1,3- galactosyltransferase, Neu5Gc, and pi,4-N-acetylgalactosaminyltransf erase as described in U.S. Patent Publication No. US2017/0311579 (Tector), the entire disclosure of which is incorporated herein by reference.
  • the creation of such swine through the described methods, and/or the utilization of such swine and progeny following creation can be employed in the practice of the present invention, including, but not limited to, utilizing organs, tissue and/or cells derived from such swine.
  • multiple source animals with an array of biological properties including, but not limited to, genome modification and/or other genetically engineered properties, can be utilized to reduce immunogenicity and/or immunological rejection (e.g., acute, hyperacute, and chronic rejections) in humans resulting from xenotransplantation.
  • the present disclosure can be used to reduce or avoid thrombotic microangiopathy by transplanting the biological product of the present disclosure into a human patient.
  • the present disclosure can be used to reduce or avoid glomerulopathy by transplanting the biological product of the present disclosure into a human patient.
  • source animals set forth herein is not limiting, and the present invention encompasses any other type of source animal with one or more modifications (genetic or otherwise) that serve(s) to reduce immunogenicity and/or immunological rejection, singularly or in combination.
  • preterm swine fetuses and neonatal piglets are derived as offspring from DPF Closed Colony, a- 1,3 -galactosyltransferase [Gal-T] knockout pigs, as shown and described herein in accordance with the present invention.
  • Such preterm swine fetuses and neonatal piglets are utilized as a source for cells, tissues and organs for xenotransplantation therapies, including, but not limited to, in regenerative or direct transplantation therapies. It will be understood that such cells, tissues and organs can be utilized as fresh or following cryopreservation in accordance with the present invention (e.g., cryopreservation in the range of -80° C).
  • mesenchymal cells, pluripotent cells, stem cells and/or other cells that have not differentiated are harvested from such preterm swine fetuses and utilized for regenerative therapies and other therapies as described herein, whereas such undifferentiated cells can be found in high proportion in swine fetuses as well as in neonatal piglets. Since these cells are derived from fetuses earlier along the gestation period, they are less differentiated and more pliable which offers greater potential for regenerative therapies.
  • these cells may be derived from DPF Closed Colony, a-l,3-galactosyltransferase [Gal-T] knockout pigs, as shown and described herein, they do not possess aggravating immunogenic, pathogenic and/or other aggravating factors causing rejection by the human immune system, and the cells will persist and differentiate inside a human recipient offering regain of function of growth of model tissue using these genetic and cellular building blocks.
  • such cells may be utilized to generate an array of organs and/or tissues, through regenerative cell-therapy methods known in the art (e.g., through utilization of biological scaffolds), for xenotransplantation including, but not limited to, skin, kidneys, liver, brain, adrenal glands, anus, bladder, blood, blood vessels, bones, brain, brain, cartilage, ears, esophagus, eye, glands, gums, hair, heart, hypothalamus, intestines, large intestine, ligaments, lips, lungs, lymph, lymph nodes and lymph vessels, mammary glands, mouth, nails, nose, ovaries, oviducts, pancreas, penis, pharynx, pituitary, pylorus, rectum, salivary glands, seminal vesicles, skeletal muscles, skin, small intestine, smooth muscles, spinal cord, spleen, stomach, suprarenal capsule, teeth, tendons, testes,
  • animals are secured from the outside to consider as candidates to add to the General Closed Colony 128 that is housed within the SAF 100 to help propagate the DPF Closed Colony 102 also housed within the SAF 100 in a separate isolation area 152.
  • Transportation of the animals secured from the outside to the SAF is controlled to mitigate exposure to potential infectious agents.
  • mitigation techniques include, but are not limited to, using a sterilized HEPA filtered cage during transport using a van cleaned with chlorhexidine and containing no other animals.
  • Candidate animals are initially quarantined to check health status and suitability for intake into the General Closed Colony 128.
  • animals coming from the outside are first housed in a quarantine intake area 130 within the SAF and accompanied by a complete health record (including, but not limited to, date of birth, vaccinations, infections, and antibiotic history), pedigree, and results of genetic tests.
  • a complete health record including, but not limited to, date of birth, vaccinations, infections, and antibiotic history
  • pedigree including, but not limited to, date of birth, vaccinations, infections, and antibiotic history
  • animals with poor health, questionable medical status, or are not able to be treated for such medical issues will not be accepted into the General Closed Colony 128 and/or will otherwise be culled from the quarantine area 130.
  • acceptance criteria include, but are not limited to: (a) source animals are not born with any congenital defect that was unanticipated from the herd and that could have impacted the quality of health of the animal; (b) source animals have received all vaccinations according to age and the vaccinations were killed agents; (c) any infections that occurred in the source animal’ s lifetime have been reviewed as well as the clinical intervention, and it was determined that the infection and any treatment (if applicable) did not impact the quality of the health of the animal; (d) results of the surveillance testing has been reviewed and it has been verified that the source animal has been tested within the last 3 months (with all source animals tested at sacrifice and all tests must be negative); (e) if the animal was injured in any way which required medical attention, a review has been conducted and it has been confirmed that
  • animals that pass this screening process and timetable are moved out of the quarantine intake area 130 and into a general holding area 132 within the SAF 100 to join or create an existing or newly formed General Closed Colony 128.
  • the general holding area 132 is kept under closed colony conditions substantially similar to the conditions applied to the DPF Closed Colony 102 in the DPF Isolation Area 152.
  • pregnant sows 134 are obtained from the outside or from the General Closed Colony 128 to produce piglets to create and/or add to the DPF Closed Colony 102 herd.
  • sows 134 are placed in a sow quarantine area 136 within the SAF until the time to give birth, in this aspect via Cesarean section in order to avoid exposing the piglet to potential pathogens, including Porcine Cytomegalovirus (pCMV). Contraction of pCMV in piglets can occur when the piglets travel through the vagina of the sow during natural birth. The piglets, by virtue of their birthing through Cesarean section as described herein, prevents such contraction and the piglets produced through the methods described herein are pCMV-free.
  • pCMV Porcine Cytomegalovirus
  • an operating room 138 within the SAF 100 prepared according to standard operating room protocols in a sterile environment with 2 sides: Side A 140 for the Cesarean section of the sow, and Side B 142 to receive the piglets 144 that are candidates to either found or add to the DPF Closed Colony.
  • the sow 134 is brought into the operating room 138 for captive bolt euthanasia. Immediately following this, the sow 134 is placed in the left lateral decubitus position and the abdomen and torso are prepped widely with chlorhexidine and draped in a sterile fashion. A flank incision is expeditiously made and the abdominal muscles are split in order to gain access into the peritoneum. The uterus is exteriorized, incised and the piglets 144 are removed after doubly clamping and dividing the umbilical cord. Immediate execution of the surgical procedures following captive bolt euthanasia is critical to the survival of the piglets 144.
  • Infection controls for the piglets 144 are implemented at birth.
  • the piglets 144 are placed in a warmed 1% chi orhexi dine (or other sterilization agent, such as betadine) in sterile saline bath solution and then passed over to piglet handlers to a resuscitation area 148 for resuscitation, rewarming and gavage feeding of the first dose of colostrum.
  • the sow’s 134 carcass is closed by staff with suture and disposed of following appropriate procedures.
  • the piglets 144 are subsequently quarantined in a separate sterile piglet quarantine room 150 then transferred to a designated pathogen free isolation area (“DPF Isolation Area”) 152 to either create or join the DPF Closed Colony 102.
  • DPF Isolation Area 152 can be of any size suitable to manage and maintain the DPF Closed Colony to the extent needed for breeding, rearing, birthing, harvesting, and overall management as described herein.
  • the DPF Isolation Area 152 that supports the DPF Closed Colony is a restricted access, positive-pressure barrier isolation suite, approximately 500ft 2 , with an animal husbandry capacity to support at least 9 animals (up to 20 kg each), inside the larger SAF 100. It will be understood that the DPF Isolation Area 152 can be significantly larger than this, and can include multiple areas (including, but not limited to, multiple rooms and suites), depending on the need of the number of source animals and demand for products, in accordance with the products and methods as described herein.
  • tracking of piglets is performed and piglets are handled under designated pathogen free conditions in the DPF Isolation Area 152.
  • handling of piglets is performed wearing personal protective equipment (“PPE”) in the DPF Isolation Area 152, including face mask, gloves, shoe covers, and hair bonnet.
  • PPE personal protective equipment
  • the animals are handled by clean personnel, personnel who have not entered any animal room or facility where other swine are housed.
  • piglets are ear notched 3 days after birth and ear tagged with hand-labeled plastic ear tags at weaning (usually 3-5 weeks).
  • Precautions are taken to prevent the exposure of any animals within the DPF Closed Colony 102 to contamination (for example, blood, blood products or tissues obtained from animals outside the DPF Closed Colony 102). If any animals within the DPF Closed Colony 102 are inadvertently exposed to blood, blood products, or tissues obtained from animals outside the DPF Closed Colony 102, those animals are removed from the DPF Closed Colony 102 and will never return to the DPF Closed Colony 102. Aseptic techniques and sterile equipment for all parenteral interventions are used, and routine procedures such as vaccinations, treatment with drugs or biologies, phlebotomy, and biopsies are performed.
  • the DPF Isolation Area 152 is restricted by card access only to specially authorized and trained staff.
  • newborn piglets are handled and hand-reared by trained and gowned staff in the DPF Isolation Area 152 to ensure their health and that they are maintained as designated pathogen free.
  • the DPF Closed Colony 102 can be propagated in multiple ways. For example, as described herein, sows 134 may be taken from the outside or General Closed Colony 128, quarantined, and have their piglets 144 delivered via Cesarean section, with the piglets resuscitated, sterilized, quarantined, and placed into the DPF Isolation Area 152. Newborn piglets may be maintained at 26-30°C or 80-85 °F. In some aspects, heat lamps are used to keep animals warm. Newborn piglets are initially housed in sterilized medium crates in the SAF with sterile towels/drapes on the bottom.
  • the DPF Closed Colony 102 may also be propagated in other ways.
  • the DPF Closed Colony 102 is propagated through natural intercourse amongst the animals in the DPF Closed Colony 102 occurring entirely within the DPF Isolation Area 152. It will be understood that pregnancies may also occur in the DPF Closed Colony 102 within the DPF Isolation Area 152 as a result of artificial insemination or other breeding techniques that do not involve natural intercourse.
  • pregnant sows 154 or gilts in the DPF Closed Colony 102 within the DPF Isolation Area 152 carry the entire pregnancy and piglets are delivered through live vaginal birth and Caesarian section is not necessary.
  • the piglets resulting from natural intercourse and live vaginal birth within the DPF Isolation Area 152 are designated pathogen free, including no infection by pCMV.
  • the breeding of swine disclosed herein is typically homozygous to homozygous breeding.
  • Females are given hormones two weeks before gestation then throughout pregnancy.
  • the General Closed Colony 128 may also be propagated through natural intercourse amongst the animals in the General Closed Colony 128, and may also occur as a result of artificial insemination or other assisted reproductive technologies (ARTs) that do not involve natural intercourse.
  • ARTs assisted reproductive technologies
  • embryo transfer technology allows producers to obtain multiple progeny from genetically superior females.
  • fertilized embryos can be recovered from females (also called embryo donors) of superior genetic merit by surgical or nonsurgical techniques.
  • the genetically superior embryos are then transferred to females (also called embryo recipients) of lesser genetic merit.
  • females also called embryo recipients
  • efficient techniques recover fertilized embryos without surgery, but only one or sometimes two embryos are produced during each normal reproductive cycle.
  • swine and sheep embryos must be recovered by surgical techniques.
  • the embryo donor is treated with a hormone regimen to induce multiple ovulations, or superovulation.
  • Immature oocytes female eggs
  • Ovum (egg) pick up is a nonsurgical technique that uses ultrasound and a guided needle to aspirate immature oocytes from the ovaries. Once the immature oocytes have been removed from the ovary, they are matured, fertilized, and cultured in vitro for up to seven days until they develop to a stage that is suitable for transfer or freezing.
  • the technique involves culturing somatic cells from an appropriate tissue (fibroblasts) from the animal to be cloned. Nuclei from the cultured somatic cells are then microinjected into an enucleated oocyte obtained from another individual of the same or a closely related species. Through a process that is not yet understood, the nucleus from the somatic cell is reprogrammed to a pattern of gene expression suitable for directing normal development of the embryo. After further culture and development in vitro, the embryos are transferred to a recipient female and ultimately result in the birth of live offspring.
  • the success rate for propagating animals by nuclear transfer is often less than 10 percent and depends on many factors, including the species, source of the recipient ova, cell type of the donor nuclei, treatment of donor cells prior to nuclear transfer, the techniques used for nuclear transfer, etc.
  • Most commonly used ARTs rely on fertilization as a first step. This joining of egg and sperm is accompanied by the recombination of the genetic material from the sire and dam, and is often referred to as“shuffling the genetic deck.” It will be understood that these breeding techniques can be used either within the DPF Closed Colony, as a breeding step within the DPF Isolation Area 152, or could be used as a breeding step for females in the General Closed Colony and/or from the outside.
  • birthing of piglets from such females can be as described herein, i.e., sows 134 may be taken from the outside or General Closed Colony 128, quarantined, and have their piglets 144 delivered via Cesarean section, with the piglets resuscitated, sterilized, quarantined, and placed into the DPF Isolation Area 152.
  • Designated pathogens may include any number of pathogens, including, but not limited to, viruses, bacteria, fungi, protozoa, parasites, and/or prions (and/or other pathogens associated with transmissible spongiform encephalopathies (TSEs)).
  • Designated pathogens could include, but not be limited to, any and all zoonotic viruses and viruses from the following families: adenoviridae, anelloviridae, astroviridae, calicivirdae, circoviridae, coronaviridae, parvoviridae, picornaviridae, and reoviridae.
  • Designated pathogens could also include, but not be limited to, adenovirus, arbovirus, arterivirus, bovine viral diarrhea virus, calicivirus, cardiovirus, circovirus 2, circovirus 1, coronavirus, encephalomyocarditus virus, eperytherozoon, haemophilus suis, herpes and herpes-related viruses, iridovirus, kobuvirus, leptospirillum, listeria, mycobacterium TB, mycoplasma, orthomyxovirus, papovirus, parainfluenza virus 3, paramyxovirus, parvovirus, pasavirus-1, pestivirus, picobimavirus (PBV), picomavirus, porcine circovirus-like (po-circo-like) virus, porcine astrovirus, porcine bacovirus, porcine bocavirus-2, porcine bocavirus-4, porcine enterovirus-9, porcine epidemic diarrhea virus (PEDV), porcine
  • the present disclosure provides a specific group of pathogens identified by the present inventors that are critical to exclude for safe and effective xenotransplantation, as set forth in the following Table 1.
  • a product of the present disclosure is sourced from animals having antibody titer levels below the level of detection for a plurality of or all of the pathogens discussed in the present disclosure.
  • subjects transplanted with a product of the present disclosure are tested and found to have antibody titer levels below the level of detection for a plurality of or all of the pathogens discussed in the present disclosure.
  • the present disclosure includes a method of testing for a specific group of pathogens consisting of no more than 18-35, e.g., 35, 34, 33, 32, 31, 30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, 19, or 18 pathogens, the specific group of pathogens including each of the pathogens identified in Table 1.
  • the present disclosure includes creating, maintaining and using donor animals that are free of the 18-35, e.g., 35, 34, 33, 32, 31, 30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, 19, or 18 pathogens, the specific group of pathogens including each of the pathogens identified in Table 1.
  • piglets born via live vaginal birth within the DPF Closed Colony 102 are not infected with pCMV, but are nonetheless tested for pCMV on a continuous basis.
  • Testing for Porcine Cytomegalovirus (pCMV) and Porcine Endogenous Retrovirus (PERV) should be routine and continuous for screening and maintenance as described herein, and should occur routinely and continuously for the DPF Closed Colony.
  • the source animals described herein are positive for PERV A and B only, and some are positive for PERV A, B, and C. In other aspects, the source animals are free of PERV A, B and/or C (through utilization of CRISPR and other techniques).
  • PERV With respect to PERV, it is understood that most, if not all, swine are known to be positive for PERV A and B. While PERV is recognized, the risk of transmission of PERV from treatment with swine derived tissue is expected to be rare. To date eight PERV mRNAs are expressed in all porcine tissues and in all breeds of swine and preclinical and clinical xenotransplantation studies of humans exposed to pig cells, tissues, and organs including pancreatic islets have failed to demonstrate transmission of PERV. See , e.g.
  • PERV is susceptible in vitro to nucleoside and non-nucleoside reverse transcriptase inhibitors in common clinical use. See , e.g.
  • the DPF Closed Colony 102 is maintained to ensure that the animals remain designated pathogen free and that appropriate standards of animal care and well-being are applied at all levels of the SAF 100 (i.e., breeding, maintenance, propagation). No animal is permitted into the DPF Closed Colony if it or a parent has tested positive for any of the pathogens in Table 1. For example, continuous testing for pathogens and other biological markers occurs including the numerous pathogens identified herein (including, but not limited to, pCMV and other pathogens). Environmental and blood samples are collected as necessary for genotyping and testing for pathogens.
  • Test result(s) obtained for pathogens or other health concerns are evaluated by the facility veterinarian who may recommend follow-up testing and observations, and quarantine of the facility or areas (e.g., rooms, suites or other areas) within a facility as needed. Careful documentation of any antimicrobial agents used during routine care of the source animals should be maintained, and exclusive use of killed vaccines used. Examples of antimicrobial agents include cefazolin, bacitracin, neomycin, and polymyxin.
  • routine health surveillance and screening for pathogens e.g., adventitious agents
  • pathogens e.g., adventitious agents
  • Samples of serum, nasal swabs, and stool for each animal in the General and DPF Closed Colonies are obtained and provided for analytical tests for detection of such pathogens every 3 months.
  • Source animal samples of serum, nasal swabs, and stool for testing are obtained immediately after euthanasia via captive bolt and evaluated as disclosed herein including one or more of: conducting a sterility assay and confirming that aerobic and anaerobic bacteria do not grow in the sterility assay; conducting a mycoplasma assay and confirming that mycoplasma colonies do not grow in the mycoplasma assay; conducting an endotoxin assay and confirming that the biological product is free of endotoxins in the endotoxin assay, conducting the MTT-reduction assay and confirming that the product has at least 50% cell viability in the MTT-reduction assay; conducting flow cytometry and confirming that the product does not have galactosyl-a-1, 3-galactose epitopes as determined by the flow cytometry; conducting pathogen-detection assays specific for 18 to 35 pathogens and confirming that the product is free of Ascaris species, Cryptosporidium species, Echinococcus, Strong
  • all swine undergo routine health monitoring, which includes documentation of all illnesses, medical care, procedures, drugs administered, vaccinations, physical examinations, any treatments received, and general health assessments and observations each day at time of feeding with a visual health inspection indicating the animal is able to stand, move freely and appears clinically normal, as well as observations relating to the animal’s appearance, activity and appetite, recording on the Animal Husbandry Log any deficiencies.
  • animals are vaccinated against Mycoplasma Hyopneumoniae, Hemophilus Parasuis, Streptococcus Suis, Pasteurella Multocida, Bordatella Bronchiseptica and Erysipelothrix Rhusiopathiae.
  • Influenza and Parvovirus may be performed, e.g., every six months.
  • health monitoring will normally be performed as part of daily husbandry procedures for cleaning and feeding to minimize entry into swine holding areas (e.g., rooms, suites or other areas).
  • swine holding areas e.g., rooms, suites or other areas.
  • PPE personal protective equipment
  • Personnel in contact with any animals not housed in the designated pathogen free facility will change PPE if contaminated.
  • All implements shovel, other necessary tools
  • Solid waste and soiled bedding is removed. Animal holding areas are sanitized with diluted Quat-PV or bleach a minimum of once every two weeks.
  • bedding is replaced daily using irradiated bedding wood shavings.
  • the replacement amount is an approximate equal amount to that which was removed. All bedding is completely replaced on a weekly basis at a minimum. Daily activities including health status checks, cleaning and water levels are documented in the Animal Husbandry log. Appropriately labeled trash and biological waste is picked up by staff daily and incinerated.
  • piglet newborns are handled and cared for by trained and gowned staff in an isolation suite. All supplies, room and crates are sanitized prior to housing of the piglets. Sterile drapes and towels are used to line the bottom of the crates. Room temperature is controlled to 80-85° F. Animals crates are maintained at 85-95 0 F through the use of heat lamps. Piglets are maintained in the crates through the first 2 weeks after which time piglets are housed on the floor with irradiated wood shavings. Crates are cleaned daily and shavings are removed and replenished daily.
  • Piglets are initially fed fresh-made, sterile colostrum (Bovine Colostrum IgG formulated for swine, Sterling Nursemate ASAP or equivalent) using a feeding tube every 1 to 2 hours until piglet is self-feeding from feeder. During the early days, the piglet is weighed twice a day and well-being is checked and recorded twice a day. Starting at day 14, piglets are fed 3 times per day with a Milk Replacer (Ralco Birthright or equivalent) that is further supplemented with irradiated piglet grain (antibiotic free creep feed, Blue Seal 813 or equivalent). The amount each piglet eats at each feeding is recorded.
  • vaccines use killed agents.
  • Piglets are vaccinated against Mycoplasma Hyopneumoniae, Hemophilus Parasuis, Streptococcus Suis, Pasteurella Multocida, Bordatella Bronchiseptica and Erysipelothrix Rhusiopathiae at day 7 after birth, with a booster vaccination at 28 days of age.
  • vaccines are killed agents.
  • the source animals for the xenotransplantation product are maintained in a positive pressure, biocontainment establishment, under specific isolation-barrier conditions governed by standard operation procedures adopted by the managers of the given program, and receive specialized care, under controlled conditions in order to mitigate adventitious agents.
  • the SAF, personnel, and the caretakers of source animals adhere to procedures for animal husbandry, tissue harvesting, and sacrifice of animals.
  • the source animals are housed in a positive pressure, biocontainment establishment, under specific isolation- barrier conditions.
  • food and bedding are delivered to a loading dock, transported, and stored in a specific feed room off of the clean cage wash area accessible only to staff in the inner hallway. All bedding and feed are sterilized by irradiation and double bagged to insure sterility. Feed used for the piglets and more mature animals is defined grain feed by a specific manufacturer. It does not contain any cattle protein. Water supply is provided either by use of the facility sterile system or purchased sterile water which is dispensed into sterile pans. Records for storage and delivery of feed, water, and other consumables are maintained, and include manufacturer, batch numbers, and other pertinent information, per protocol.
  • animal records are maintained to describe the feed provided to source animals for at least two generations before their use as a source for live tissues, organs and/or cells used in xenotransplantation. This includes source, vendor, and the type of feed used (including its contents). Use of feed that has been derived from animals is prohibited. Source animals are not provided feeds containing animal proteins or other cattle materials that are prohibited by the FDA feed ban as expanded in 2008 as source animals (21 CFR 589.2000) or feeds containing significant drug contamination or pesticide or herbicide residues for source animals (21 CFR 589.2001). [000323] In some aspect, purified water is provided in sufficient quality to prevent unnecessary exposure of animals to infectious pathogens, drugs, pesticides, herbicides, and fertilizers. Newborn animals are provided colostrum specifically qualified for herd qualification. In some aspects, Bovine Colostrum IgG formulated for swine, Sterling Nursemate ASAP or equivalent is used to feed newborn animals.
  • biological products for xenotransplantation are derived from source animals produced and maintained in accordance with the present invention, including from the DPF Closed Colony 102 as described herein.
  • biological products include, but are not limited to, liver, kidney, skin, lung, heart, pancreas, intestine, nerve and other organs, cells and/or tissues.
  • the present disclosure provides a continuous manufacturing process for a xenotransplantation product that has reduced immunogenicity, reduced antigenicity, increased viability, increased mitochondrial activity, a specifically required pathogen profile, and unexpectedly long shelf-life in xenotransplantation tissues subject to cryopreservation.
  • the continuous manufacturing process is surprisingly and unexpectedly effective in avoiding hyperacute rejection, delayed xenograft rejection, acute cellular rejection, chronic rejection, cross species transmission of diseases, cross-species transmission of parasites, cross-species transmission of bacteria, cross-species transmission of fungi, and cross-species transmission of viruses.
  • the continuous manufacturing process is surprisingly and unexpectedly effective in creating a closed herd in which the donor animals survive normally without detectable pathological changes.
  • the source animal is scrubbed by operating staff, e.g., for at least 1-10 minutes with antiseptic, e.g., Chlorhexidine, brushes over the entire area of the animal where the operation will occur, periodically pouring Chlorhexidine over the area to ensure coverage.
  • Surgical area(s) of the animal are scrubbed with opened Betadine brushes and sterile water rinse over the entire area of the animal where the operation will occur for, e.g., 1-10 minutes.
  • operators will be dressed in sterile dress in accordance with program and other standards to maintain designated pathogen free conditions. All organs, cells or tissue from the source animal that will be used for xenotransplantation is harvested within 15 hours of the animal being sacrificed.
  • Bio products can also include, but are not limited to, those disclosed herein (e.g., in the specific examples), as well as any and all other tissues, organs, and/or purified or substantially pure cells and cell lines harvested from the source animals.
  • tissues that are utilized for xenotransplantation as described herein include, but are not limited to, areolar, blood, adenoid, bone, brown adipose, cancellous, cartaginous, cartilage, cavernous, chondroid, chromaffin, connective tissue, dartoic, elastic, epithelial, Epithelium, fatty, fibrohyaline, fibrous, Gamgee, Gelatinous, Granulation, gut-associated lymphoid, Haller's vascular, hard hemopoietic, indifferent, interstitial, investing, islet, lymphatic, lymphoid, mesenchymal, mesonephric, mucous connective, multilocular adipose, muscle, my
  • organs that are utilized for xenotransplantation as described herein include, but are not limited to, skin, kidneys, liver, brain, adrenal glands, anus, bladder, blood, blood vessels, bones, cartilage, cornea, ears, esophagus, eye, glands, gums, hair, heart, hypothalamus, intestines, large intestine, ligaments, lips, lungs, lymph, lymph nodes and lymph vessels, mammary glands, mouth, nails, nose, ovaries, oviducts, pancreas, penis, pharynx, pituitary, pylorus, rectum, salivary glands, seminal vesicles, skeletal muscles, skin, small intestine, smooth muscles, spinal cord, spleen, stomach, suprarenal capsule, teeth, tendons, testes, thymus gland, thyroid gland, tongue, tonsils, trachea, ureters, urethra, uterus, and vagina.
  • purified or substantially pure cells and cell lines that are utilized for xenotransplantation as describe herein include, but are not limited to, blood cells, blood precursor cells, cardiac muscle cells, chondrocytes, cumulus cells, endothelial cells, epidermal cells, epithelial cells, fibroblast cells, granulosa cells, hematopoietic cells, Islets of Langerhans cells, keratinocytes, lymphocytes (B and T), macrophages, melanocytes, monocytes, mononuclear cells, neural cells, other muscle cells, pancreatic alpha-1 cells, pancreatic alpha-2 cells, pancreatic beta cells, pancreatic insulin secreting cells, adipocytes, epithelial cells, aortic endothelial cells, aortic smooth muscle cells, astrocytes, basophils, bone cells, bone precursor cells, cardiac myocytes, chondrocytes, eosinophils, ery
  • An organ is a group of related cells that combine together to perform one or more specific functions within the body.
  • Biologically, skin is the body’s largest and fastest-growing organ, and is classified as the primary component of the integumentary system, one of the ten macro-organ systems found in“advanced” animals.
  • Skin fulfills several critical roles including regulating temperature, providing a dynamic barrier to the external world, and serving as a conduit to support an immense network of sensory receptors.
  • the skin performs several functions that are vital to the survival and health of the body.
  • the skin heals to prevent the loss of blood after wounds, regulates body temperature by dissipating heat and as a layer against cold, absorption, secretion, thermal-regulation, sensory detection and orientation, and barrier protection.
  • This global legislation lists skin - and whole segments of the integumentary system - formally as an organ, and more broadly defines an organ as“any part of the human body consisting of a structured arrangement of tissues which, if wholly removed, cannot be regenerated by the body....” Following, the formal medical definition of a transplant is:“the removal of tissue from one part of the body or from one individual and its implantation or insertion in another especially by surgery.” The HOTO defines a transplant as“the transfer of an organ from one person to another during a transplant operation, regardless of permanence.”
  • grafts typically consist of decellularized and/or reconstituted sheets of homogenized dermis that are used to achieve temporary, superficial wound coverage. Such grafts do not retain the original tissue structure nor the metabolically active, otherwise naturally present cells, and thus do not become vascularized; no capillary ingrowth or vessel-to- vessel connections are made. Consequently, immune rejection is not a concern - the skin graft becomes“ejected” rather than rejected by the growth of a complete host epithelium underneath the graft.
  • the primary qualities that differentiate a transplant from a graft are that of heightened complexity, organization, and inclusion of one or more types of tissue.
  • a skin transplant is fundamentally differentiated from grafts known in the prior art.
  • a skin xenotransplant is comprised of live cells that perform the same function as the patient’s original skin before eventually experiencing immune-mediated rejected.
  • a skin xenotransplant according to the present disclosure is an organ transplant rather than a graft.
  • the harvesting comprises euthanizing the swine and aseptically removing the biological product from the swine; processing said biological product comprising sterilization after harvesting using a sterilization process that does not reduce cell viability to less than 50% cell viability in a 3-(4,5- dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)-reduction assay and does not reduce mitochondrial activity to less than 50% mitochondrial activity; and storing the biological product in a sterile container; and the non-human animal is a non-transgenic genetically reprogrammed swine for xenotransplantation of cells, tissue, and/or an organ isolated from the non-transgenic genetically reprogrammed swine, the non-transgenic genetically reprogrammed swine comprising a nuclear genome that has been reprogrammed to replace a plurality of nucle
  • Xenogeneic kidneys are derived from a genetically engineered, reprogrammed and designated pathogen free swine is produced in accordance with the present invention and transplanted into a non-human primate and a human. It is expected that survival of at least fourteen months is observed in each of the non-human primate and the human. In some aspects, it is expected that survival of at least 24 months is observed in each of the non-human primate and the human. In some aspects, it is expected that survival of at least 36 months is observed in each of the non-human primate and the human. In some aspects, it is expected that survival of at least 48 months is observed in each of the non-human primate and the human. In some aspects, it is expected that survival of at least 60 months is observed in each of the non human primate and the human.
  • Xenogeneic lungs are derived from a genetically engineered, reprogrammed and designated pathogen free swine produced in accordance with the present invention and transplanted into a non-human primate and a human. It is expected that survival of at least 30 days is observed in each of the non-human primate and the human. In some aspects, it is expected that survival of at least 3 months is observed in each of the non-human primate and the human. In some aspects, it is expected that survival of at least 6 months is observed in each of the non-human primate and the human. In some aspects, it is expected that survival of at least 12 months is observed in each of the non-human primate and the human.
  • survival of at least 24 months is observed in each of the non-human primate and the human. In some aspects, it is expected that survival of at least 36 months is observed in each of the non-human primate and the human. In some aspects, it is expected that survival of at least 48 months is observed in each of the non-human primate and the human. In some aspects, it is expected that survival of at least 60 months is observed in each of the non-human primate and the human.
  • Xenogeneic hearts are derived from a genetically engineered, reprogrammed and designated pathogen free swine produced in accordance with the present invention and transplanted into a non-human primate and a human. It is expected that survival of at least 20 months is observed in each of the non-human primate and the human. In some aspects, it is expected that survival of at least 24 months is observed in each of the non-human primate and the human. In some aspects, it is expected that survival of at least 36 months is observed in each of the non-human primate and the human. In some aspects, it is expected that survival of at least 48 months is observed in each of the non-human primate and the human. In some aspects, it is expected that survival of at least 60 months is observed in each of the non-human primate and the human.
  • Xenogeneic nerve tissues are derived from a genetically engineered, reprogrammed and designated pathogen free swine produced in accordance with the present invention and transplanted into a non-human primate and a human. It is expected that survival of at least 75 days is observed in each of the non-human primate and the human. In some aspects, it is expected that survival of at least 3 months is observed in each of the non-human primate and the human. In some aspects, it is expected that survival of at least 6 months is observed in each of the non-human primate and the human. In some aspects, it is expected that survival of at least 12 months is observed in each of the non-human primate and the human.
  • survival of at least 24 months is observed in each of the non-human primate and the human. In some aspects, it is expected that survival of at least 36 months is observed in each of the non-human primate and the human. In some aspects, it is expected that survival of at least 48 months is observed in each of the non-human primate and the human. In some aspects, it is expected that survival of at least 60 months is observed in each of the non-human primate and the human zx
  • Xenogeneic livers are derived from a genetically engineered, reprogrammed and designated pathogen free swine produced in accordance with the present invention and transplanted into a non-human primate and a human. It is expected that survival of at least 60 days is observed in each of the non-human primate and the human. In some aspects, it is expected that survival of at least 3 months is observed in each of the non-human primate and the human. In some aspects, it is expected that survival of at least 6 months is observed in each of the non-human primate and the human. In some aspects, it is expected that survival of at least 12 months is observed in each of the non-human primate and the human.
  • survival of at least 24 months is observed in each of the non-human primate and the human. In some aspects, it is expected that survival of at least 36 months is observed in each of the non-human primate and the human. In some aspects, it is expected that survival of at least 48 months is observed in each of the non-human primate and the human. In some aspects, it is expected that survival of at least 60 months is observed in each of the non-human primate and the human.
  • pig livers produced in accordance with the present invention to serve as extracorporeal filters for humans are disclosed.
  • Levy et al., “Liver allotransplantation after extracorporeal hepatic support with transgenic (hCD55/hCD59) porcine livers: Clinical results and lack of pig-to- human transmission of the porcine endogenous retrovirus,” Transplantation , 69(2):272-280 (2000) (“Levy”), the entire contents of which are incorporated herein by reference, whole organ extracorporeal perfusion of a genetically modified transgenic porcine liver was proposed to sustain patients awaiting human liver transplantation for fulminant hepatic failure.
  • the pig livers used were reported to be transgenic for human CD55 (decay-accelerating factor) and human CD59, however, the livers failed to suppress marked increase of [alpha]-gal antibodies.
  • a liver derived from a genetically reprogrammed source animal in accordance with the present invention is utilized for extracorporeal perfusion as a temporary filter for a human patient until a patient receives a human transplant.
  • pigs with additional genetic modifications may also be utilized, including pigs genetically reprogrammed for any number of traits disclosed elsewhere herein.
  • an extracorporeal circuit utilizes an oxygenator (e.g., Minimax Plus® hollow fiber oxygenator), a pump (e.g., Bio-Medicus model 540 Bio- Console® with a BP50 Pediatric Bio Pump® centrifugal pump), and a warmer (Bio-Medicus model 370 BioCalTM Temperature Controller).
  • the circuit also utilizes a roller pump (e.g., Sarns model 7000; Sams, Ann Arbor, MI) to supplement for lack of gravity return to the patient. Bridges and clamps are utilized to isolate both the perfused liver and the patient.
  • a source animal In an operating area within the DPF Isolation Area, a source animal is placed under a general anesthetic (ketamine, xylazine, enflurane) or euthanized by captive bolt. A hepatectomy is then performed on the source animal in designated pathogen free conditions.
  • ketamine, xylazine, enflurane ketamine, xylazine, enflurane
  • livers can be preserved in any number of ways known in the art prior to use as an extracorporeal filter, including, but not limited to, as disclosed in Levy (e.g.,“a 4°C lactated Ringer’ s/albumin solution and cannulated in the portal vein (28F Research Medical, model SPC- 641-28) and the inferior vena cava (36F Research Medical, model SPC-641-36)”).
  • Levy e.g.,“a 4°C lactated Ringer’ s/albumin solution and cannulated in the portal vein (28F Research Medical, model SPC- 641-28) and the inferior vena cava (36F Research Medical, model SPC-641-36)”.
  • the common bile duct can be intubated in any number of ways, including, but not limited to, as set forth in Levy (e.g.,“with an intravenous extension tube (Extension Set 30, Abbott Hospitals, Inc., Chicago, IL) to allow subsequent quantification of bile production.”)
  • Levy e.g.,“with an intravenous extension tube (Extension Set 30, Abbott Hospitals, Inc., Chicago, IL) to allow subsequent quantification of bile production.”
  • liver product derived from the source animal can be packaged and transported to the location of the procedure in accordance with current practice with human donor livers.
  • the procedure to utilize the liver filtration product can be performed, for example, by percutaneously cannulating a patient’s internal jugular vein for venous return with a 12F pediatric arterial cannula (e.g., Medtronic DLP, Grand Rapids, MI) and percutaneously cannulating a patient’s femoral vein for venous outflow with a 19F femoral artery cannula (e.g, Medtronic Bio-Medicus, Eden Prairie, MN).
  • a 12F pediatric arterial cannula e.g., Medtronic DLP, Grand Rapids, MI
  • femoral vein for venous outflow with a 19F femoral artery cannula
  • cannulas are connected to a bypass circuit, having a centrifugal pump (e.g, Bio-Medicus), a heat exchanger (Medtronic Bio-Medicus), an oxygenator (e.g, Medtronic Cardiopulmonary, Anaheim, CA), and a roller pump (e.g, Sarns) incorporated therein.
  • a centrifugal pump e.g, Bio-Medicus
  • a heat exchanger Medtronic Bio-Medicus
  • an oxygenator e.g, Medtronic Cardiopulmonary, Anaheim, CA
  • a roller pump e.g, Sarns
  • This circuit is primed with crystalloids and run for a period of time (e.g, 20 minutes) before the liver obtained from the genetically reprogrammed source animal is incorporated at a stabilized flow rate of 800 ml/min, maintained in a crystalloid bath occasionally supplemented with warm solution.
  • Xenogeneic pancreases are derived from a genetically engineered, reprogrammed and designated pathogen free swine is produced in accordance with the present invention
  • Xenogeneic pancreas derived from a genetically reprogrammed swine produced in accordance with the present invention is transplanted into a non-human primate and a human. It is expected that survival of at least 20 months is observed in each of the non-human primate and the human. In some aspects, it is expected that survival of at least 24 months is observed in each of the non-human primate and the human. In some aspects, it is expected that survival of at least 36 months is observed in each of the non-human primate and the human. In some aspects, it is expected that survival of at least 48 months is observed in each of the non-human primate and the human. In some aspects, it is expected that survival of at least 60 months is observed in each of the non-human primate and the human.
  • Xenogeneic dermal combination product derived from a genetically engineered, reprogrammed and designated pathogen free swine is produced in accordance with the present invention.
  • Some skin transplantation products for the treatment of burns and other ailments utilize cultured epidermal autografts (see, e.g., products produced by Vericel Corporation under the Epicel® brand name). Such epidermal autografts can be utilized for patients with burns (including severe bums) and result in reduced or no rejection in the transplanted epidermal material since the material is derived from the patient’s own skin. [000351] However, such products are limited to the epidermis only, and do not include the dermis portion of the skin. Referring to FIG. 39, it will be understood that the dermis (which typically accounts for 95% of the thickness of the skin) performs significantly different functions than the epidermis (which is the outer portion of the skin that typically accounts for 5% of the thickness of the skin).
  • epidermal autografts alone lack the ability to perform the critical functions of the dermis, such products are used in combination with a viable dermis.
  • the wound bed includes remaining portions of the patient’s own dermis, which is the ideal dermis to utilize in a procedure grafting cultured epidermal autografts onto a patient.
  • the burn is more severe, and the patient’s own dermis no longer exists or is no longer viable. In those instances, a different dermis is required since an epidermal autograft alone will not suffice.
  • a full thickness skin graft wound dressing consisting of dermal tissue derived from designated pathogen free a-l,3-galactosyltransferase [Gal-T] knockout swine in accordance with the present invention is used in conjunction or combination with cultured epidermal autografts.
  • One treatment process utilizing this combination is as follows.
  • a patient with severe bum wounds is taken to an operating room within 48-72 hours of injury.
  • a biopsy is taken as soon as possible after the patient undergoes care, and the epidermis skin cells are isolated and grown separately according to the known procedures for creating cultured epidermal autografts (see, e.g., products produced by Vericel Corporation under the Epicel® brand name).
  • epidermal autografts are taken from healthy areas to treat burned areas and/or to later create an epidermal autograft mesh used in the grafting process.
  • the debridement may include mechanical debridement, chemical debridement, enzymatic debridement, or a combination thereof.
  • Mechanical debridement may include surgical excision, e.g., tangential excision to remove thin layers of dermis until healthy tissue is visualized, or fascial excision to remove the full thickness of dermis down to the underlying fascia. Tangential excision allows less viable tissue to be removed with the necrotic tissue, but typically results in higher blood loss, is a larger physiologic stressor than fascial excision, and is more likely to result in“incomplete” debridement, with some devitalized tissue remaining in place.
  • Debriding agents may include agents capable of cleaning a burn wound by removing foreign material and dead tissue. Many such agents are known.
  • collagenases or other proteolytic enzymes are employed that break down proteins of the extracellular matrix, allowing devitalized tissue to be wiped away without the need for surgery while preferably leaving healthy tissue substantially intact.
  • Enzymatic debridement involves the application of proteolytic and optionally other exogenous enzymes to a wound surface to break down necrotic tissue.
  • Enzymatic debridement may be a relatively slow process, carried out over a period of a number of weeks in combination with other topical preparations, soakings and repeated dressings.
  • rapid enzymatic debridement can be accomplished using multi-enzyme products, for example, those extracted from the stem of the pineapple plant, as disclosed for example in WO 98/053850 and WO 2006/0006167, and as provided in the product marketed under the trade name Debrase®.
  • a procedure for enzymatic debridement generally utilizes an enzyme such as bromelain derivatives, debridase, collagenase, papain derivatives, streptokinase, sutilains, fibrinolysin, deoxyribonuclease, krill derivatives, trypsin or combinations thereof.
  • Autolytic debridement relies on enhancing the natural process of selective liquefaction, separation and digestion of necrotic tissue and eschar from healthy tissue that occurs in wounds due to macrophage and endogenous proteolytic activity. This is achieved by the use of occlusive, semi occlusive or moist interactive dressings.
  • Enzymatic debridement agents include a bromelain enriched enzyme product, other collagenases, or other enzyme products capable of clearing devitalized tissue or wound debris.
  • NexoBridTM MediWound Ltd.
  • Such products and methods are described in U.S. Patent Nos. 8,540,983; 8, 119,124; 7, 128,719; 7,794,709; 8,624,077; and US2009/0010910A1, each of which is incorporated by reference herein.
  • the wound bed may include or be a chronic wound or an acute wound.
  • Chronic wounds include but are not limited to venous leg ulcers, pressure ulcers, and diabetic foot ulcers.
  • Acute wounds include but are not limited to burns, traumatic injuries, amputation wounds, skin graft donor sites, bite wounds, frostbite wounds, dermabrasions, and surgical wounds.
  • the xenotransplantation products described and disclosed herein are temporary, i.e., their use in patients for xenotransplantation is non-permanent, utilized primarily for the treatment of acute ailments and injuries, able to be utilized for longer periods of time as compared to products that are not produced in accordance with the present invention. It will be understood that some of the aspects of the products described and disclosed herein may also be permanent or more permanent, with transplanted organs, tissues and/or cells being accepted by human recipients over much longer periods of time without adverse rejection.
  • the xenotransplantation products described and disclosed herein are viable, live cell (e.g., vital, biologically active) products; distinct from synthetic or other tissue- based products comprised of terminally sterilized, non-viable cells which are incapable of completing the vascularization process.
  • the product of the present disclosure is not devitalized, or“fixed” with glutaraldehydes or radiation treatment.
  • the xenotransplantation products described and disclosed herein are minimally manipulated (e.g., without physical alteration of the related cells, organs or tissues) such that such products are substantially in their natural state.
  • the xenotransplantation products described and disclosed herein are obtained from a non-human animal, e.g., a non-transgenic genetically reprogrammed swine, including cells, tissue, and/or an organ isolated from the non-transgenic genetically reprogrammed swine, the non-transgenic genetically reprogrammed swine comprising a nuclear genome that has been reprogrammed to replace a plurality of nucleotides in a plurality of exon regions of a major histocompatibility complex of a wild-type swine with nucleotides from orthologous exon regions of a known human major histocompatibility complex sequence from a human capture sequence, and wherein cells of said genetically reprogrammed swine do not present one or more surface glycan epitopes, wherein said reprogramming does not introduce any frameshifts or frame disruptions.
  • a non-human animal e.g., a non-transgenic genetic
  • genes encoding alpha-1,3 galactosyltransferase, cytidine monophosphate-N-acetylneuraminic acid hydroxylase (CMAH), and b1,4-N- acetylgalactosaminyltransferase are disrupted such that surface glycan epitopes encoded by said genes are not expressed.
  • the xenotransplantation products described and disclosed herein are capable of making an organic union with the human recipient, including, but not limited to, being compatible with vascularization, collagen growth (e.g., in regard to skin), and/or other interactions from the transplant recipient inducing graft adherence, organic union, or other temporary or permanent acceptance by the recipient.
  • the xenotransplantation products described and disclosed herein are utilized in xenotransplantation without the need to use, or at least reduction of use, of immunosuppressant drugs or other immunosuppressant therapies to achieve desired therapeutic results.
  • some of the xenotransplantation products described and disclosed herein are stored by cryopreservation, stored fresh (without freezing), or stored via other methods to preserve such products consistent with this invention.
  • Storage involves using conditions and processes that preserve cell and tissue viability.
  • storage may involve storing organs, tissues, or cells, in any combination of a sterile isotonic solution (e.g., sterile saline with or without antibiotics), on ice, in a cryopreservation fluid, cryopreserved at a temperature of around -40°C or around -80°C, and other methods known in the field.
  • a sterile isotonic solution e.g., sterile saline with or without antibiotics
  • cryopreservation fluid cryopreserved at a temperature of around -40°C or around -80°C, and other methods known in the field.
  • Such storage can occur in a primary containment system and secondary containment system.
  • the xenotransplantation products described and disclosed herein are for homologous use, i.e., the repair, reconstruction, replacement or supplementation of a recipient’s organ, cell and/or tissue with a corresponding organ, cell and/or tissue that performs the same basic function or functions as the donor (e.g., swine kidney is used as a transplant for human kidney, swine liver is used as a transplant for human liver, swine skin is used as a transplant for human skin, swine nerve is used as a transplant for human nerve and so forth).
  • swine kidney is used as a transplant for human kidney
  • swine liver is used as a transplant for human liver
  • swine skin is used as a transplant for human skin
  • swine nerve is used as a transplant for human nerve and so forth.
  • the xenotransplantation products described and disclosed herein have a low bioburden, minimizing pathogens, antibodies, genetic markers, and other characteristics that may serve to increase the product’s bioburden and the human body’s immunological rejection of the product upon xenotransplantation. This may include the innate immune system, through PRRs TLRs, detecting PAMPs and rejecting the subject xenotransplantation product.
  • DPF Closed Colony there are numerous therapeutic applications for products derived from DPF Closed Colony in accordance with the present invention.
  • such products may be utilized to treat acute and/or chronic disease, disorders, or injuries to organ, cells or tissue, and any and all other ailments that can utilize the products disclosed herein.
  • treatments and/or therapies can include utilizing such products to repair, reconstruct, replace or supplement (in some aspects on a temporary basis and in other aspects a permanent basis), a human recipient’s corresponding organ, cell and/or tissue that performs the same basic function or functions as the donor.
  • Treatment applications include, but are not limited to, lung transplants, liver transplants, kidney transplants, pancreas transplants, heart transplants, nerve transplants and other full or partial transplants.
  • treatment applications also include, but are not limited to, treatment of burn wounds, diabetic ulcerations, venous ulcerations, chronic skin conditions, and other skin ailments, injuries and/or conditions (including, but not limited to, severe and extensive, deep partial and full thickness injuries, ailments and/or conditions) (see, e.g., Example 2 herein); use in adult and pediatric patients who have deep dermal or full thickness burns comprising a total body surface area greater than or equal to 30%, optionally in conjunction with split-thickness autografts, or alone in patients for whom split-thickness autografts may not be an option due to the severity and extent of their wounds/burns; treatment of liver failure, wounds, ailments, injuries and/or conditions with liver products derived in accordance with the present invention; treatment of peripheral nerve damage, and other nerve ailments,
  • Patent No. 7,795,493 (“Phelps”), including cell therapies and/or infusion for certain disorders (as disclosed in col. 30, line 1 to col. 31, line 9) and treatment or certain disorders or pathologies (as disclosed in col. 31, lines 10 to 42), the disclosure of which is incorporated by reference herein.
  • therapies herein in no way limits the types of therapeutic applications for the products disclosed and described herein, which encompass acute and/or chronic disease, disorders, injuries to the following organs, tissues and/or cells: skin, kidneys, liver, brain, adrenal glands, anus, bladder, blood, blood vessels, bones, brain, brain, cartilage, ears, esophagus, eye, glands, gums, hair, heart, hypothalamus, intestines, large intestine, ligaments, lips, lungs, lymph, lymph nodes and lymph vessels, mammary glands, mouth, nails, nose, ovaries, oviducts, pancreas, penis, pharynx, pituitary, pylorus, rectum, salivary glands, seminal vesicles, skeletal muscles, skin, small intestine, smooth muscles, spinal cord, spleen, stomach, suprarenal capsule, teeth, tendons, testes, thymus gland, thyroid
  • skin products derived in accordance with the present invention are used to treat human patients with severe and extensive deep partial and/or full thickness bum wounds.
  • Such products contain terminally-differentiated cell types that are not expanded ex vivo prior to use and do not migrate from the site of application during intended duration of treatment. Therefore, potential for tumorigenicity is negligible.
  • Such products adhere to the wound bed and provides a barrier function in the immediate post-bum period.
  • Such products have non-terminally sterilized, viable cells, allowing for vascularization of the graft tissue with the recipient.
  • the epidermis remains fully intact, and dermal components are maintained without change to structural morphology or organization of the various cells and tissues. This physiologic mechanism supports the prolonged survival of the graft material, and provides at least a temporary barrier function with significant clinical impact on par with, or better than, allograft.
  • the product of the present disclosure is not applied until the clinical signs of the infection are reduced or eliminated for a predetermined period of time, e.g., 1, 2, 3, 4, 5, 6, or 7 days, 1, 2, 3, or 4 weeks, or if the subject has tested negative for the infection.
  • the wound is cleaned, confirmed to be well-vascularized and nonexuding. If a dermal substitute such as cadaver allograft is also being used, the epidermal layer is removed from engrafted allograft prior to the application of the product without removing the engrafted dermis. The epidermal layer may be removed with a dermatome or other instrument according to standard operating procedures of the facility.
  • Grafts conventionally used in clinical practice consist of decellularized and/or reconstituted sheets of homogenized dermis that are used to achieve temporary, superficial wound coverage. Such conventional grafts do not retain the original tissue structure nor the metabolically active, otherwise naturally present cells, and thus do not become vascularized; no capillary ingrowth or vessel-to-vessel connections are made.
  • skin products described herein are fundamentally differentiated from such grafts because the product of the present disclosure includes live cells that perform the same function as the patient’s original skin, i.e., the product acts as an organ transplant. Skin performs additional, critical roles related to homeostasis, temperature regulation, fluid exchange, and infection prevention.
  • porcine xenografts do not vascularize and are primarily only useful for temporary coverage of superficial burns.
  • the xenotransplantation product of the present disclosure contains metabolically active, minimally manipulated cells in identical conformations and unchanged morphologies as the source tissue.
  • the present disclosure includes using xenotransplanted donor skin as a test for prediction of rejection of other organs from the same animal donor.
  • Techniques for performing such predictive tests using human donor skin have previously been described, e.g., in Moraes et al., Transplantation. 1989;48(6):951-2; Starzl, et ah, Clinical and Developmental Immunology, vol. 2013, Article ID 402980, 1-9; Roberto et al., Shackman et al., Lancet. 1975; 2(7934): 521-4, the disclosures of which are incorporated herein by reference in their entireties for all purposes. Moraes reported that the crossmatch procedure was highly accurate in predicting early kidney transplant rejection.
  • the present disclosure includes a method of using a xenotransplanted skin sample in a human patient in order to determine whether there is a risk of rejection of other organs xenotransplanted from the same animal donor in the human patient.
  • the skin grafting methods described herein can be used to treat any injury for which skin grafts are useful, e.g., for coverage of partial thickness and full thickness wounds including but not limited to burns, e.g. partial thickness or excised full thickness burn wounds; avulsed skin e.g. on an extremity; diabetic wounds, e.g., non-healing diabetic foot wounds, venous stasis ulcers.
  • the xenotransplantation product of the present disclosure has pharmacokinetic and pharmacodynamics properties that meet regulatory requirements. Characterization of such properties requires a unique approach with respect to classical meanings of drug absorption, distribution, metabolism, and excretion. “Absorption” of the xenotransplantation product for the purposes of consideration of pharmacokinetics, may be described by the vascularization process the xenotransplantation product experiences.
  • skin xenotransplantation products may present as warm, soft, and pink, whereas wild-type or traditional xenografts appear as non-vascularized“white grafts.”
  • the distribution of the transplant is limited to the site of transplant as confirmed by DNA PCR testing to demonstrate the presence or absence of pig cells in peripheral blood beyond the transplantation site.
  • the cells of the biological products produced in accordance with the present invention do not migrate following xenotransplantation into the recipient, including into the circulation of the recipient. This includes that PERV or PERV-infected porcine cells do not migrate into the recipient.
  • PBMCs peripheral blood mononuclear cells
  • RNA porcine retroviral
  • bioavailability and mechanism of action of the xenotransplantation product is not affected by size.
  • the distribution of the xenotransplantation product is limited to the site of the administration.
  • the debrided wound bed initially created by the trauma or bum injury is the site of administration.
  • the present disclosure includes testing to detect distribution of cells from the xenotransplantation product in the peripheral blood, wound beds, spleen and/or kidney beyond the site of administration. In certain aspects, such testing will demonstrate an absence of cells from the xenotransplantation product in the peripheral blood, wound beds, spleen and/or kidney beyond the site of administration.
  • Such testing may include DNA PCR testing for various cellular markers present in the type of animal from which the product is obtained, e.g., PERV, swine MHC, and other swine DNA sequences.
  • PERV swine MHC
  • swine MHC swine MHC
  • other swine DNA sequences e.g., PERV, swine MHC, and other swine DNA sequences.
  • cells and nucleic acids from the xenotransplantation product remain limited to the site of administration.
  • the metabolism of the xenotransplantation product may be congruent with the aforementioned natural host rejection phenomenon, which occurs in the absence of exogenous immunosuppressive drugs.
  • xenotransplantation products undergo a delayed, immune rejection course similar to allograft comparators for clinically useful durations.
  • the“dosage” of the xenotransplantation product of the present disclosure is expressed as percentage of viable cells in the product per unit area of transplantation.
  • the xenotransplantation product of the present disclosure can be considered as analogous to the active pharmaceutical ingredient in a pharmaceutical drug product.
  • survival of the xenogeneic cells, tissues, or organs of the present disclosure is increased by avoiding: (a) infiltration of immune or inflammatory cells into the xenotransplantation product or alteration of such cells in other relevant compartments, such as the blood and cerebrospinal fluid; (b) fibrotic encapsulation of the xenotransplantation product, e.g., resulting in impaired function or xenotransplantation product loss; (c) xenotransplantation product necrosis; (d) graft versus host disease (GVHD); and (e) in vivo function and durability of encapsulation or barriers intended to diminish rejection or inflammatory responses.
  • GVHD graft versus host disease
  • Safety tests include bacterial and fungal sterility, mycoplasma, and viral agents.
  • the present disclosure includes cry opreserving and archiving for further testing, as needed, samples of all final xenotransplantation products (i.e., cells or tissues or biopsies of organs), whether fresh or from culture ex vivo. In some cases, for example if the xenotransplantation product is a whole intact organ, a relevant surrogate sample (e.g., adjacent tissues or contra-lateral organ) is archived.
  • porcine skin With regard to skin, storage and cryopreservation of porcine skin has not been fully characterized, especially with regards to viability, as most porcine xenografts are intentionally devitalized, or“fixed” with glutaraldehydes or radiation treatment. Such information is necessary to support the use of vital porcine skin grafts - or porcine skin transplants - as a temporary and clinically advantageous option.
  • results of testing of the xenotransplantation product may not be available before its clinical use. In such cases, testing of the source animal, itself, may be all the testing that is possible before the procedure. Testing of samples taken from such xenotransplantation products or appropriate relevant biological surrogates, e.g., adjacent tissues or contra-lateral organs, may be performed according to the present disclosure.
  • Microbiological examination methods may include aspects set forth in the following Table 2:
  • the present disclosure includes using Buffered Sodium Chloride-Peptone Solution pH 7.0 or Phosphate Buffer Solution pH 7.2 to make test suspensions; to suspend A. brasiliensis spores, 0.05% of polysorbate 80 may be added to the buffer.
  • the present disclosure includes using the suspensions within 2 hours, or within 24 hours if stored between 2°C and 8°C.
  • a stable spore suspension is prepared and then an appropriate volume of the spore suspension is used for test inoculation.
  • the stable spore suspension may be maintained at 2° to 8° for a validated period of time.
  • a negative control is performed using the chosen diluent in place of the test preparation. There must be no growth of microorganisms. A negative control is also performed when testing the products as described under Testing of Products. A failed negative control requires an investigation. Microbiological Examination may be performed according to USP 61, USP 63, USP 71, USP 85 EP section 2.6.13 Microbial Examination of Non- sterile Products (Test for Specified Microorganisms), each of which is incorporated herein by reference in its entirety.
  • PCMV porcine cytomegalovirus
  • Each 25uL PCR reaction included target DNA, 800nM primers 200nMTaqMan probe, 20 nM Rox reference and lx Brilliant III Ultra Fast Master Mix.
  • the PCR cycling conditions were as follows: 1 cycle at 95°C for 5 min followed by 50 cycles of denaturation at 95°C for 10 seconds, and annealing-extension at 60°C for 30 seconds with data collection following each extension.
  • Serial dilutions of gel-extracted amplicon cloned into Invitrogen TOPO plasmid served as quantifying standards.
  • Target DNA is detected with a linear dynamic range of 10 to 106 copies.
  • 300 ng of xenograft pig kidney DNA was run in a TaqMan PCR in triplicate.
  • the analytical procedures used to test the xenotransplantation product can also include:
  • TSB Tryptic Soy Broth
  • FTM Fluid Thiogly collate Medium
  • the FTM samples will be spiked with an inoculum of ⁇ 100 CFU’s of 24-hour cultures of Staphyloccocus aureus , Pseudomonas aeruginosa , and Clostridium sporogenes. If growth is not observed, the product is found to be bacteriostatic or fungistatic and fails the USP ⁇ 71> Sterility Test.
  • MTT Assay for Cell Viability The metabolic activity of the drug product is tested relative to control tissue samples using a biochemical assay for [3-4,5 dimethylthiazol-2-yl]-2,5 diphenyltetrazolium bromide (MTT) metabolism.
  • MTT MTT Assay for Cell Viability.
  • Positive and negative control samples of fresh xenotransplantation product tissue (positive control) or heat inactivated discs of xenotransplantation product tissue (negative control) or the test article of Xenotransplantation product are placed in amber microcentrifuge tubes containing MTT solution (0.3 m g/mL in DMEM, 0.5 mL).
  • the discs are treated with MTT formazan and incubated for 180 ⁇ 15 minutes at 37 °C and an atmosphere of 5% CO 2 in air.
  • the reaction is terminated by removal of the discs and the formazan is extracted by incubation at either ambient temperature for ⁇ 24 hours or refrigerated at 4 °C for ⁇ 72 hours. Samples are protected from light during this time. Aliquots are taken after the extraction is complete and the absorbance at 550 nm (with a reference wavelength of 630 nm) is measured and compared to a standard curve.
  • IB4 Assay for Extracellular Glvcan Epitope The absence of the galactosyl-a-1,3- galactose (Alpha-Gal) epitope on cells will be determined using fluorescence activated flow cytometry.
  • White blood cells in whole blood are stained with a fluorochrome labeled isolectin-B4 (FITC-I-B4) and comparisons are made against blood obtained from wild type positive controls and the Gal-T-KO source animal twice. First, all source animals are tested at birth. Second, the same test will be performed from whole blood collected at sacrifice of the source animal and tested for stability of the gene knockout, and the negative phenotype for Alpha-Gal.
  • FITC-I-B4 fluorochrome labeled isolectin-B4
  • the isolectin binds to the epitope on cells from the wild type pig but no binding occurs on the cells from the Gal-T- KO pigs.
  • the assay serves to confirm alpha-gal epitope is not present in the genetically engineered source animal. Spontaneous re-activation of the gene, and re-expression of the Alpha-Gal moiety post sacrifice is highly improbable and unreasonable to expect; its inclusion would only deteriorate the efficacy of the xenotransplantation product causing it to resemble wild-type porcine tissue and hyperacutely reject as previously demonstrated.
  • PERV pol quantitation lOuL of a 1 :625 dilution of the RT reaction was amplified in a 50 cycle PERV polymerase quantitative TaqMan PCR in triplicate using a Stratagene MX300P real-time thermocycler (Agilent Technologies). lOuL of a 1 :25 dilution of the“No RT enzyme” control RT reaction was similarly treated. PCR conditions included PERV pol forward and reverse primers at 800nM final concentration and PERV pol probe at 200nM final concentration.
  • all final xenotransplantation product must meet acceptance criteria for selecting a donor pig for material including (i) reviewing the medical record for a defined pedigree, (ii) reviewing the medical record for the test results for alpha-1, 3-galactose by Flowmetrics, (iii) reviewing the medical record for a history of full vaccinations; (iv) reviewing the medical record for the surveillance tests performed over the lifetime of the pig; (v) adventitious agent screening of source animal; (vi) reviewing the medical record for infections over the lifetime of the pig; and (vi) reviewing the medical record for any skin abnormalities noted in the animal’s history.
  • Table 3 is a list of the assays and results of the battery of tests performed on the xenotransplantation product materials.
  • an adventitious agent control strategy developed based on the source animal, including the species, strain, geographic origin, type of tissue, and proposed indication.
  • Analytical Tests are conducted for adventitious agents, to include bacteria, fungi, mycoplasma, and viral microorganisms, including as follows: j .
  • Bacteriological Free Status The bacteriological screen is conducted to confirm the drug product is free of potential biological agents of concern Humans. Both Aerobic and Anaerobic screens are conducted to ensure sterility. Samples are thawed as described herein and transferred to Tryptic Soy Broth (TSB) or Fluid Thioglycollate Medium (FTM) as appropriate. Vessels will be incubated to allow for potential growth. If no evidence of microbial growth is found, the product will be judged to comply with the test for sterility.
  • TAB Tryptic Soy Broth
  • FTM Fluid Thioglycollate Medium
  • Mycological (Fungal) Free Status The mycological screen is conducted to confirm the Drug Product is free of potential fungal agents of concern. Samples are thawed as described herein. After thawing, samples are transferred to a soybean-casein digest agar. Vessels will be incubated to allow for potential growth. If no evidence of fungal growth is found, the product will be judged to comply with the test for sterility perUSP ⁇ 71>.
  • the mycoplasma screen is conducted to confirm the drug product is free of mycoplasma.
  • Samples are thawed as described herein and added to lOOmL of Mycoplasma broth and incubated at 37°C for up to 21 days.
  • the sample is sub-cultured after 2-4 days, 7-10 days, 14 days, and 21 days.
  • the plates are then incubated at 37°C for up to 14 days and checked for the presence of Mycoplasma colonies. If none are detected, the product is found to be in compliance with USP ⁇ 63> and is mycoplasma free.
  • Endotoxin Free Status The endotoxin free status is conducted to confirm the drug product is free of endotoxins and related agents of concern. Three samples from the same lot will be tested for the Inhibition/Enhancement of the Limulus amoebocyte lysate (LAL) test. Samples will be thawed as described herein and extracted with 40mL of WFI per sample at 37°C for 1 hour. Samples will then be tested in the LAL Kinetic Chromogenic Test with a standard curve ranging from 5-50EU/mL at a validated dilution. Assays will be performed in compliance with USP ⁇ 85>.
  • LAL Limulus amoebocyte lysate
  • the MTT assay is conducted to confirm the biologically active status of cells in the xenotransplantation product.
  • Evidence of viability is provided through surrogate markers of mitochondrial activity as compared to positive (fresh, not cryopreserved) and negative (heat- denatured) controls.
  • the activity of the cells is required for the xenotransplantation product to afford the intended clinical function. This is required as a lot release criteria, and is currently established that tissue viability should not be less than 50% of the metabolic activity demonstrated by the fresh tissue control comparator.
  • H&E Hematoxylin and Eosin
  • the genetically engineered source animals do not contain any foreign, introduced DNA into the genome; the gene modification employed is exclusively a knock-out of a single gene that was responsible for encoding for an enzyme that causes ubiquitous expression of a cell-surface antigen. It will be understood that the xenotransplantation product in one or more aspects do not incorporate transgene technologies, such as CD-46 or CD-55 transgenic constructs.
  • An endotoxin free status is conducted to confirm the drug product is free of endotoxins and related agents of concern. Protocols for the assurance of Endotoxin free status are as follows: Three samples from the same lot are tested for Inhibition/Enhancement of the Limulus amoebocyte lysate (LAL) test. Samples are thawed, extracted, and tested in the LAL Kinetic Chromogenic Test with a standard curve ranging from 5-50EU/mL at a validated dilution in compliance with USP ⁇ 85>.
  • LAL Limulus amoebocyte lysate
  • the MTT assay is conducted to confirm the biologically active status of cells in the product.
  • Evidence of viability is provided through surrogate markers of mitochondrial activity as compared to positive (fresh, not cryopreserved) and negative (heat-denatured) controls.
  • the activity of the cells is required for the product to afford the intended clinical function and the viability parameters for one aspect ranging from 50% to 100% mitochondrial activity.
  • the xenotransplantation product may be further processed to ensure that it remains free of aerobic and anaerobic bacteria, fungi, viruses, and mycoplasma.
  • the xenotransplantation product is sterilized, e.g., using one or more of UV irradiation or an anti- microbial/anti-fungal.
  • the product may be placed into an anti-microbial/anti-fungal bath (“antipathogen bath”).
  • the antipathogen bath may include: one or more anti -bacterial agents, e.g., ampicillin, ceftazidime, neomycin, streptomycin, chloramphenicol, cephalosporin, penicillin, tetracycline, vancomyocin, and the like; one or more anti-fungal agents, e.g., amphotericin-B, azoles, imidazoles, triazoles, thiazoles, candicidin, hamycin, natamycin, nystatin, rimocidin, allylamines, echinocandins, and the like; and/or one or more anti-viral agents.
  • anti -bacterial agents e.g., ampicillin, ceftazidime, neomycin, streptomycin, chloramphenicol, cephalosporin, penicillin, tetracycline, vancomyocin, and the like
  • anti-fungal agents e.g.,
  • the anti-pathogen bath may include a carrier or medium as a diluent, e.g., RPMI-1640 medium.
  • the anti-pathogen bath may include at least 2 anti -bacterial agents.
  • the anti-pathogen bath may include at least 2 anti -bacterial agents and at least one anti-fungal agent.
  • the anti-pathogen bath may include at least four agents.
  • the anti-pathogen bath may include no more than 4, 5, 6, 7, 8, 9, or 10 agents.
  • the anti-pathogen bath may include any combination of the foregoing.
  • the product may be sterilized using UV light sterilization.
  • the product is placed under the UV lamp for a desired period of time, e.g., 0.5, 1, 1,5, 2, 3, 4, 5, 6, minutes or more, then turned over to the other side, and put under the UV lamp for the same or a different period of time on opposite side.
  • the time period for exposing a given sample to the UV may be varied based on the specific biological agents or the types of biological agents to be sterilized, e.g., as shown in the following Table 11 below.
  • the product may be sterilized using a UV lamp having a UV-C intensity of at least 100 uW/cm 2 for at least 2 minutes and up to 15, 12, 10, 8, 6, 5, 4, 3, or 2.5 minutes, and turned over such that its opposite surface is exposed to the UV lamp for at least 2 minutes and up to 15, 12, 10, 8, 6, 5, 4, 3, or 2.5 minutes to obtain a UV-treated product; a UV-C dosage of at least 100,000 uW sec/cm 2 and up to 800,000, 700,000, 600,000, 500,000, 400,000, 300,000 or 200,000 uW sec/cm 2 ; a UV-C dosage of at least 200,000 uW sec/cm 2 and up to 800,000, 700,000, 600,000, 500,000, 400,000, or 300,000 uW sec/cm 2 ; a UV lamp having a UV-C intensity of at least 100 uW/cm 2 for at least 2 minutes and up to 15, 12, 10, 8, 6, 5, 4, 3, or 2.5 minutes.
  • a UV lamp having a UV-
  • Product processing occurs in a single, continuous, and self-contained, segregated manufacturing event that begins with the sacrifice of the source animal through completion of the production of the final product.
  • the animal is euthanized via captive bolt euthanasia, may be moved, if necessary, in a sterile, non-porous bag, to an operating room where the procedure to harvest biological product from the source animal will occur. All members of the operating team should be in full sterile surgical gear, e.g., dressed in sterile dress to maintain designated pathogen free conditions prior to receiving the source animal and in some instanced be double-gloved to minimize contamination, and surgical areas and tools are sterilized.
  • the source animal is removed from the bag and container in an aseptic fashion.
  • the source animal is scrubbed by operating staff, e.g., for at least 1-10 minutes with antiseptic, e.g., Chlorhexidine, brushes over the entire area of the animal where the operation will occur, periodically pouring Chlorhexidine over the area to ensure coverage.
  • Surgical area(s) of the animal are scrubbed with opened Betadine brushes and sterile water rinse over the entire area of the animal where the operation will occur for, e.g., 1-10 minutes.
  • a full thickness skin graft wound dressing consisting of dermal tissue derived from a swine in accordance with the present invention is used in conjunction or combination with cultured epidermal autografts to produce a product according to the present disclosure and that can be used in methods of the present disclosure.
  • Prior to application of the epidermal autografts significant debridement of wound bed is required to ensure an adequate substrate.
  • To confirm a wound bed is ready for an epidermal autograft apply the skin products described herein, e.g., biological skin products derived from animals of the present disclosure to confirm adherence. Once adherence is confirmed, the temporary wound coverage product is removed, and in some aspects, the wound bed is covered with a meshed autograft, and one or more cultured epidermal autograft products are placed on top to close the gaps in the autograft mesh.
  • the debridement may include mechanical debridement, chemical debridement, enzymatic debridement, or a combination thereof.
  • Mechanical debridement may include surgical excision, e.g., tangential excision to remove thin layers of dermis until healthy tissue is visualized, or fascial excision to remove the full thickness of dermis down to the underlying fascia. Tangential excision allows less viable tissue to be removed with the necrotic tissue, but typically results in higher blood loss, is a larger physiologic stressor than fascial excision, and is more likely to result in“incomplete” debridement, with some devitalized tissue remaining in place.
  • Debriding agents may include agents capable of cleaning a burn wound by removing foreign material and dead tissue. Many such agents are known.
  • collagenases or other proteolytic enzymes are employed that break down proteins of the extracellular matrix, allowing devitalized tissue to be wiped away without the need for surgery while preferably leaving healthy tissue substantially intact.
  • Enzymatic debridement involves the application of proteolytic and optionally other exogenous enzymes to a wound surface to break down necrotic tissue.
  • Enzymatic debridement may be a relatively slow process, carried out over a period of a number of weeks in combination with other topical preparations, soakings and repeated dressings.
  • rapid enzymatic debridement can be accomplished using multi-enzyme products, for example, those extracted from the stem of the pineapple plant, as disclosed for example in WO 98/053850 and WO 2006/0006167, and as provided in the product marketed under the trade name Debrase®.
  • a procedure for enzymatic debridement generally utilizes an enzyme such as bromelain derivatives, debridase, collagenase, papain derivatives, streptokinase, sutilains, fibrinolysin, deoxyribonuclease, krill derivatives, trypsin or combinations thereof.
  • Autolytic debridement relies on enhancing the natural process of selective liquefaction, separation and digestion of necrotic tissue and eschar from healthy tissue that occurs in wounds due to macrophage and endogenous proteolytic activity. This is achieved by the use of occlusive, semi occlusive or moist interactive dressings.
  • Enzymatic debridement agents include a bromelain enriched enzyme product, other collagenases, or other enzyme products capable of clearing devitalized tissue or wound debris.
  • NexoBridTM MediWound Ltd.
  • Such products and methods are described in U.S. Patent Nos. 8,540,983; 8, 119,124; 7, 128,719; 7,794,709; 8,624,077; and US2009/0010910A1, each of which is incorporated by reference herein.
  • the wound bed may include or be a chronic wound or an acute wound.
  • Chronic wounds include but are not limited to venous leg ulcers, pressure ulcers, and diabetic foot ulcers.
  • Acute wounds include but are not limited to burns, traumatic injuries, amputation wounds, skin graft donor sites, bite wounds, frostbite wounds, dermabrasions, and surgical wounds.
  • a liver derived in accordance with the present disclosure is utilized for extracorporeal perfusion as a temporary filter for a human patient until a patient receives a human transplant.
  • a source animal In an operating area within the DPF Isolation Area, a source animal is placed under a general anesthetic (ketamine, xylazine, enflurane) or euthanized by captive bolt. A hepatectomy is then performed on the source animal in designated pathogen free conditions.
  • the liver product derived from the source animal can be packaged and transported to the location of the procedure in accordance with current practice with human donor livers.
  • the procedure to utilize the liver filtration product can be performed, for example, by percutaneously cannulating a human patient’ s internal jugular vein for venous return with an arterial cannula and percutaneously cannulating a patient’ s femoral vein for venous outflow with an artery cannula.
  • These cannulas are connected to a bypass circuit, having a centrifugal pump, a heat exchanger, an oxygenator, and a roller pump incorporated therein.
  • This circuit is primed with crystalloids and run for a period of time (e.g ., 10-30 minutes) before the liver from an animal according to the present disclosure is incorporated at a stabilized flow rate, e.g., 600-1000 ml/min, maintained in a crystalloid bath occasionally supplemented with warm solution, e.g., 30-40°C.
  • each human recipient will have a major histocompatibility complex (MHC) (Class I, Class II and/or Class III) that is unique to that individual and will not match the MHC of the donor swine. Accordingly, it will be understood that when a donor swine graft is introduced to the recipient, the swine MHC molecules themselves act as non-gal xeno-antigens, provoking an immune response from the recipient, leading to transplant rejection.
  • MHC major histocompatibility complex
  • HLA Human leukocyte antigen
  • a donor swine is provided with a genome that is biologically engineered to express a specific set of known human HLA molecules.
  • HLA sequences are available, e.g., in the IPD-IMGT/HLA database (available at ebi.ac.uk/ipd/imgt/hla/) and the international ImMunoGeneTics information system® (available at imgt.org).
  • HLA-Al, B8, DR17 is the most common HLA haplotype among Caucasians, with a frequency of 5%.
  • the disclosed method can be performed using the known MHC/HLA sequence information in combination with the disclosures provided herein.
  • the recipient’s human leukocyte antigen (HLA) genes and MHC are identified and mapped.
  • HLA/MHC genes are usually typed with targeted sequencing methods: either long-read sequencing or long-insert short-read sequencing.
  • HLA types have been determined at 2-digit resolution (e.g., A*01), which approximates the serological antigen groupings.
  • sequence specific oligonucleotide probes has been used for HLA typing at 4-digit resolution (e.g., A*01 :01), which can distinguish amino acid differences.
  • SSOP sequence specific oligonucleotide probes
  • targeted DNA sequencing for HLA typing is the most popular approach for HLA typing over other conventional methods. Since the sequence-based approach directly determines both coding and non-coding regions, it can achieve HLA typing at 6-digit (e.g., A*01 :01 :01) and 8- digit (e.g., A*01 :01 :01 :01) resolution, respectively.
  • HLA typing at the highest resolution is desirable to distinguish existing HLA alleles from new alleles or null alleles from clinical perspective.
  • the known human HLA/MHC or an individual recipient’s sequenced HLA/MHC sequence(s) may be utilized as a template to modify the swine leukocyte antigen (SLA)/MHC sequence to match, e.g., to have 80%, 85%, 90%, 95%, 98%, 99%, or 100% sequence homology to a known human HLA/MHC sequence or the human recipient’s HLA/MHC sequence.
  • SLA leukocyte antigen
  • biological reprogramming may be performed to SLA/MHC sequences in cells of the swine based on desired HLA/MHC sequences. For example, several targeting guide RNA (gRNA) sequences are administered to the swine of the present disclosure to reprogram SLA/MHC sequences in cells of the swine with the template HLA/MHC sequences of the human recipient.
  • gRNA targeting guide RNA
  • CRISPR-Cas9 is used to mediate rapid and scarless exchange of entire MHC alleles at specific native locus in swine cells.
  • Multiplex targeting of Cas9 with two gRNAs is used to introduce single or double-stranded breaks flanking the MHC allele, enabling replacement with the template HLA/MHC sequence (provided as a single or double-stranded DNA template).
  • the CRISPR/Cas9 components are injected into swine oocytes, ova, zygotes, or blastocytes prior to transfer into foster mothers.
  • the present disclosure includes embryogenesis and live birth of SLA-free and HLA-expressing biologically reprogrammed swine. In certain aspects, the present disclosure includes breeding SLA-free and HLA-expressing biologically reprogrammed swine to create SLA-free and HLA-expressing progeny.
  • the CRISPR/Cas9 components are injected into swine zygotes by intracytoplasmic microinjection of porcine zygotes. In certain aspects, the CRISPR/Cas9 components are injected into swine prior to selective breeding of the CRISPR/Cas9 genetically modified swine.
  • the CRISPR/Cas9 components are injected into donor swine prior to harvesting cells, tissues, zygotes, and/or organs from the swine.
  • the CRISPR/Cas9 components include all necessary components for controlled gene editing including self-inactivation utilizing governing gRNA molecules as described in U.S. Pat. No. 9,834,791 (Zhang), which is incorporated herein by reference in its entirety.
  • the genetic modification can be made utilizing known genome editing techniques, such as zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), adeno-associated virus (AAV)-mediated gene editing, and clustered regular interspaced palindromic repeat Cas9 (CRISPR-Cas9).
  • ZFNs zinc-finger nucleases
  • TALENs transcription activator-like effector nucleases
  • AAV adeno-associated virus
  • CRISPR-Cas9 clustered regular interspaced palindromic repeat Cas9
  • CRISPR-Cas9 may also be used to remove viral infections in cells.
  • the genetic modification via CRISPR-Cas9 can be performed in a manner described in Kelton, W. et. al., “Reprogramming MHC specificity by CRISPR-Cas9-assisted cassette exchange,” Nature, Scientific Reports, 7:45775 (2017) (“Kelton”), the entire disclosure of which is incorporated herein by reference.
  • the present disclosure includes reprogramming using CRISPR-Cas9 to mediate rapid and scarless exchange of entire alleles, e.g., MHC, HLA, SLA, etc.
  • the recipient’s HLA/MHC gene is sequenced and template HLA/MHC sequences are prepared based on the recipient’s HLA/MHC genes.
  • a known human HLA/MHC genotype from a WHO database may be used for genetic reprogramming of swine of the present disclosure.
  • CRISPR-Cas9 plasmids are prepared, e.g., using polymerase chain reaction and the recipient’s HLA MHC sequences are cloned into the plasmids as templates.
  • CRISPR cleavage sites at the SLA MHC locus in the swine cells are identified and gRNA sequences targeting the cleavage sites and are cloned into one or more CRISPR-Cas9 plasmids.
  • CRISPR-Cas9 plasmids are then administered into the swine cells and CRIPSR/Cas9 cleavage is performed at the MHC locus of the swine cells.
  • the SLA MHC locus in the swine cells are replaced with one or more template HLA MHC sequences matching the known human HLA MHC sequences or the recipient’s sequenced HLA MHC genes.
  • Cells of the swine are sequenced after performing the SLA MHC reprogramming steps in order to determine if the HLA MHC sequences in the swine cells have been successfully reprogrammed.
  • One or more cells, tissues, and/or organs from the HLA MHC sequence-reprogrammed swine are transplanted into a human recipient.
  • HLA MHC sequence-reprogrammed swine are bred for at least one generation, or at least two generations, before their use as a source for live tissues, organs and/or cells used in xenotransplantation.
  • the CRISPR/Cas9 components can also be utilized to inactivate genes responsible for PERV activity, e.g., the pol gene, thereby simultaneously completely eliminating PERV from the swine donors.
  • the modification to the donor SLA/MHC to match recipient HLA/MHC causes expression of specific MHC molecules from the swine cells that are identical, or virtually identical, to the MHC molecules of a known human genotype or the specific human recipient.
  • the present disclosure involves making modifications limited to only specific portions of specific SLA regions of the swine’s genome to retain an effective immune profile in the swine while biological products are hypoimmunogenic when transplanted into human recipients such that use of immunosuppressants can be reduced or avoided.
  • xenotransplantation studies of the prior art required immunosuppressant use to resist rejection.
  • the swine genome is reprogrammed to knock-out swine genes corresponding to HLA- A, HLA-B, HLA-C, and DR, and to knock-in HLA-C, HLA-E, HLA-G.
  • the swine genome is reprogrammed to knock-out swine genes corresponding to HLA-A, HLA-B, HLA-C, HLA-F, DQ, and DR, and to knock-in HLA-C, HLA-E, HLA-G.
  • the swine genome is reprogrammed to knock-out swine genes corresponding to HLA-A, HLA-B, HLA-C, HLA-F, DQ, and DR, and to knock-in HLA-C, HLA-E, HLA-G, HLA-F, and DQ.
  • the swine genome is reprogrammed to knock-out SLA-11; SLA-6,7,8; SLA-MIC2; and SLA- DQA; SLA-DQB1; SLA-DQB2, and to knock-in HLA-C; HLA-E; HLA-G; and HLA-DQ.
  • HLA-C expression is reduced in the reprogrammed swine genome.
  • this reprogramming thereby minimizes or even eliminates an immune response that would have otherwise occurred based on swine MHC molecules otherwise expressed from the donor swine cells.
  • this aspect i.e., reprogramming the SLA/MHC to express specifically selected human MHC alleles
  • swine cells, tissues, and organs for purposes of xenotransplantation will decrease rejection as compared to cells, tissues, and organs derived from a wild-type swine or otherwise genetically modified swine that lacks this reprogramming, e.g., transgenic swine or swine with non-specific or different genetic modifications.
  • Cryopreservation and storage includes preparing biological product according to the present disclosures, placing in a container, adding freeze media to the container and sealing. For example. 15% dimethyl sulfoxide (DMSO) cryoprotective media is combined with fetal porcine serum (FPS) or donor serum (if FPS is unavailable) in a 1 : 1 ratio, filtered (0.45 micron), and chilled to 4°C prior to use. The containers are subsequently frozen in a controlled rate, phase freezer at a rate of 1°C per minute to -40°C, then rapidly cooled to a temperature -80°C. DMSO displaces intracellular fluid during the freezing process.
  • DMSO dimethyl sulfoxide
  • Cryoprotective media e.g., CryoStor is used in an amount of about 40-80%, or 50-70% based on maximum internal volume of the cryovial (10ml) less the volume of the xenotransplantation product.
  • sealed vials were placed in ⁇ 37°C water baths for approximately 0.5 to 2 minutes, at which point the container is opened and the product was removed using sterile technique.
  • products undergo three, 1-minute serial washes, e.g., in saline with gentle agitation, in order to dilute and systematically remove ambient, residual DMSO and prevent loss of cell viability.
  • the product may then be used surgically.
  • the xenotransplantation product may be processed, stored, transported, and/or otherwise handled using materials, containers and processes to ensure preserved sterility and prevent damage thereto.
  • a sterile non-adhesive material may be used to protect the xenotransplantation product, e.g., to support the xenotransplantation product and prevent adhesive of the product to surfaces and/or to prevent self-adhesion of the xenotransplantation product during manipulation, storage, or transport. Unintentional adhesion of the xenotransplantation product may disrupt the integrity of the xenotransplantation product and potentially reduce its therapeutic viability.
  • the sterile non-adhesive material provides protection and/or physical support and prevents adhesion.
  • the sterile non adhesive material is not biologically or chemically active and does not directly impact the metabolic activity or efficacy of the xenotransplantation product itself.
  • Item 1 A biological system for generating and preserving a repository of personalized, humanized transplantable cells, tissues, and organs for transplantation, wherein the biological system is biologically active and metabolically active, the biological system comprising genetically reprogrammed cells, tissues, and organs in a non-human animal for transplantation into a human recipient,
  • non-human animal is a genetically reprogrammed swine for
  • the genetically reprogrammed swine comprising a nuclear genome that has been reprogrammed to replace a plurality of nucleotides in a plurality of exon regions of a major histocompatibility complex of a wild-type swine with a plurality of synthesized nucleotides from a human captured reference sequence, and
  • cells of said genetically reprogrammed swine do not present one or more surface glycan epitopes selected from alpha-Gal, Neu5Gc, and SD a ,
  • genes encoding alpha- 1,3 galactosyltransferase, cytidine monophosphate-N- acetylneuraminic acid hydroxylase (CMAH), and pi,4-N-acetylgalactosaminyltransf erase are altered such that the genetically reprogrammed swine lacks functional expression of surface glycan epitopes encoded by said genes,
  • the reprogrammed genome comprises site-directed mutagenic substitutions of nucleotides at exon regions of: i) at least one of the wild-type swine’s SLA-1, SLA-2, and SLA-3 with nucleotides from an orthologous exon region of HLA-A, HLA-B, and HLA-C, respectively, of the human captured reference sequence; and ii) at least one the wild-type swine’s SLA-6, SLA-7, and SLA-8 with nucleotides from an orthologous exon region of HLA-E, HLA-F, and HLA-G, respectively, of the human captured reference sequence; and iii) at least one of the wild- type swine’s SLA-DR and SLA-DQ with nucleotides from an orthologous exon region of HLA- DR and HLA-DQ, respectively, of the human captured reference sequence,
  • the reprogrammed genome comprises at least one of A-C:
  • the reprogrammed swine nuclear genome comprises site-directed mutagenic substitutions of nucleotides at exon regions of the wild-type swine’s P2-microglobulin with nucleotides from orthologous exons of a known human p2-microglobulin from the human captured reference sequence;
  • the reprogrammed swine nuclear genome comprises a polynucleotide that encodes a polypeptide that is a humanized beta 2 microglobulin (hB2M) polypeptide sequence that is at least 95% identical to the amino acid sequence of beta 2 microglobulin glycoprotein expressed by the human captured reference genome;
  • hB2M humanized beta 2 microglobulin
  • the reprogrammed swine nuclear genome has been reprogrammed such that, at the swine’s endogenous p2-microglobulin locus, the nuclear genome has been reprogrammed to comprise a nucleotide sequence encoding p2-microglobulin polypeptide of the human recipient, wherein the reprogrammed swine nuclear genome has been reprogrammed such that the genetically reprogrammed swine lacks functional expression of the wild-type swine’s endogenous p2-microglobulin polypeptides, and
  • Item 2 The biological system of item 1, wherein the genetically reprogrammed swine is non-transgenic.
  • Item 3 The biological system of item 1 or item 2, wherein intron regions of the wild-type swine’s genome are not reprogrammed.
  • Item 4 The biological system of any one of or combination of items 1-3, wherein said genetically reprogrammed swine is free of at least the following pathogens: Ascaris species, Cryptosporidium species, Echinococcus, Strongyloids sterocolis, Toxoplasma gondii, Brucella suis, Leptospira species, mycoplasma hyopneumoniae, porcine reproductive and respiratory syndrome, pseudorabies, staphylococcus species, Microphyton species, Trichophyton species, porcine influenza, porcine cytomegalovirus, arterivirus, coronavirus, Bordetella hronchiseptica , and Livestock-associated methicillin-resistant Staphylococcus aureus.
  • pathogens Ascaris species, Cryptosporidium species, Echinococcus, Strongyloids sterocolis, Toxoplasma gondii, Brucella suis, Leptospira species, mycoplasma h
  • Item 5 The biological system of any one of or combination of items 1-4, wherein said genetically reprogrammed swine is maintained according to a bioburden-reducing procedure, said procedure comprising maintaining the swine in an isolated closed herd, wherein all other animals in the isolated closed herd are confirmed to be free of said pathogens, and wherein the swine is isolated from contact with any non-human animals and animal housing facilities outside of the isolated closed herd.
  • the wild-type swine genome comprises reprogrammed nucleotides at SLA-MIC-2 gene and at exon regions encoding SLA-3, SLA-6, SLA-7, SLA-8, SLA-DQ, CTLA-4, PD-L1, EPCR, TBM,
  • TFPI beta-2-microglobulin using the human capture reference sequence, wherein the human cell, tissue, or organ lacks functional expression of swine beta-2-microglobulin, SLA-1, SLA-2, and SLA-DR.
  • Item 7 The biological system of any one of or combination of items 1-5, wherein the wild-type swine genome comprises reprogrammed nucleotides at one or more of a CTLA-4 promoter and a PD-L1 promoter, wherein the one or more of the CTLA-4 promoter and the PD- L1 promoter are reprogrammed to increase expression of one or both of reprogrammed CTLA-4 and reprogrammed PD-L1 compared to the wild-type swine’s endogenous expression of CTLA-4 and PD -LI.
  • Item 8 The biological system of any one of or combination of items 1-6, wherein a total number of the synthesized nucleotides is equal to a total number of the replaced nucleotides, such that there is no net loss or net gain in number of nucleotides after reprogramming the genome of the wild-type swine with the synthesized nucleotides.
  • Item 9 The biological system of any one of or combination of items 1-7, wherein the reprogramming with the plurality of synthesized nucleotides do not include replacement of nucleotides in codon regions that encode amino acids that are conserved between the wild-type swine MHC sequence and the human captured reference sequence
  • Item 10 The biological system of any one of or combination of items 1-8, wherein the reprogrammed genome comprises site-directed mutagenic substitutions of nucleotides at the major histocompatibility complex of the wild-type swine with orthologous nucleotides from the human captured reference sequence.
  • Item 11 The biological system of any one of or combination of items 1-9, wherein site- directed mutagenic substitutions are made in germ-line cells used to produce the non-human animal.
  • Item 12 The biological system of any one of or combination of items 1-10, wherein the human captured reference sequence is a human patient capture sequence, a human population- specific human capture sequence, or an allele-group-specific human capture sequence.
  • Item 13 The biological system of any one of or combination of items 1-11, wherein the reprogrammed genome comprises site-directed mutagenic substitutions of nucleotides at exon regions of the wild-type swine’s SLA-1 with nucleotides from an orthologous exon region of a HLA-A captured reference sequence.
  • Item 14 The biological system of any one of or combination of items 1-12, wherein the reprogrammed genome comprises site-directed mutagenic substitutions of nucleotides at exon regions of the wild-type swine’s SLA-2 with nucleotides from an orthologous exon region of a HLA-B captured reference sequence.
  • Item 14 The biological system of any one of or combination of items 1-13, wherein the reprogrammed genome comprises site-directed mutagenic substitutions of nucleotides at exon regions of the wild-type swine’s SLA-3 with nucleotides from an orthologous exon region of a HLA-C captured reference sequence.
  • Item 15 The biological system of any one of or combination of items 1-14, wherein the reprogrammed genome comprises site-directed mutagenic substitutions of nucleotides at exon regions of the wild-type swine’s SLA-6 with nucleotides from an orthologous exon region of a HLA-E captured reference sequence.
  • Item 16 The biological system of any one of or combination of items 1-15, wherein the reprogrammed genome comprises site-directed mutagenic substitutions of nucleotides at exon regions of the wild-type swine’s SLA-7 with nucleotides from an orthologous exon region of a HLA-F captured reference sequence.
  • Item 17 The biological system of any one of or combination of items 1-16, wherein the reprogrammed genome comprises site-directed mutagenic substitutions of nucleotides at exon regions of the wild-type swine’s SLA-8 with nucleotides from an orthologous exon region of a HLA-G captured reference sequence.
  • Item 18 The biological system of any one of or combination of items 1-17, wherein the reprogrammed genome comprises site-directed mutagenic substitutions of nucleotides at exon regions of the wild-type swine’s MHC class I chain-related 2 (MIC -2).
  • Item 19 The biological system of any one of or combination of items 1-18, wherein the reprogrammed genome lacks functional expression of SLA-1, SLA-2, SLA-DR, or a combination thereof.
  • Item 20 The biological system of any one of or combination of items 1-19, wherein the reprogrammed genome comprises site-directed mutagenic substitutions of nucleotides at exon regions of the wild-type swine’s SLA-DQA from an orthologous exon region of a HLA-DQA1 captured reference sequence.
  • Item 21 The biological system of any one of or combination of items 1-20, wherein the reprogrammed genome comprises site-directed mutagenic substitutions of nucleotides at exon regions of the wild-type swine’s SLA-DQB from an orthologous exon region of a HLA-DQB1 captured reference sequence.
  • Item 22 The biological system of any one of or combination of items 1-21, wherein the reprogrammed genome comprises site-directed mutagenic substitutions of nucleotides at exon regions of the wild-type swine’s SLA-DRA and SLA-DRBlwith nucleotides from orthologous exon regions of HLA-DRA1 and HLA-DRBlof the human captured reference sequence, or wherein the reprogrammed genome lacks functional expression of SLA-DRA and SLA-DRBl.
  • Item 23 The biological system of any one of or combination of items 1-22, wherein the reprogrammed genome comprises site-directed mutagenic substitutions of nucleotides at exon regions of the wild-type swine’s SLA-DQA and SLA-DQB 1 with nucleotides from orthologous exon regions of HLA-DQA1 and HLA-DQB1 of the human captured reference sequence.
  • Item 24 The biological system of any one of or combination of items 1-23, wherein the site-directed mutagenic substitutions of nucleotides are at codons that are not conserved between the wild-type swine’s nuclear genome and the known human sequence.
  • Item 25 The biological system of any one of or combination of items 1-24, wherein the reprogrammed genome comprises site-directed mutagenic substitutions of nucleotides at exon regions of the wild-type swine’s B2-microglobulin with nucleotides from orthologous exons of a known human B2-microglobulin.
  • Item 26 The biological system of any one of or combination of items 1-25, wherein the reprogrammed swine nuclear genome comprises a polynucleotide that encodes a polypeptide that is a humanized beta 2 microglobulin (hB2M) polypeptide sequence that is at least 95% identical to the amino acid sequence of beta 2 microglobulin glycoprotein expressed by the human captured reference genome;
  • Item 27 The biological system of any one of or combination of items 1-26, wherein said nuclear genome has been reprogrammed such that the genetically reprogrammed swine lacks functional expression of the wild-type swine’s endogenous P2-microglobulin polypeptides.
  • hB2M humanized beta 2 microglobulin
  • Item 28 The biological system of any one of or combination of items 1-27, wherein said nuclear genome has been reprogrammed such that, at the swine’s endogenous p2-microglobulin locus, the nuclear genome has been reprogrammed to comprise a nucleotide sequence encoding P2-microglobulin polypeptide of the human captured reference sequence.
  • Item 29 The biological system of any one of or combination of items 1-28, wherein the reprogrammed genome comprises site-directed mutagenic substitutions of nucleotides at exon regions of SLA-3, SLA-6, SLA-7, SLA-8, and MIC-2.
  • Item 30 The biological system of any one of or combination of items 1-29, wherein the reprogrammed genome comprises site-directed mutagenic substitutions of nucleotides at exon regions of SLA-DQ and MIC-2.
  • Item 31 The biological system of any one of or combination of items 1-30, wherein the reprogrammed genome comprises site-directed mutagenic substitutions of nucleotides at SLA-3, SLA-6, SLA-7, SLA-8, SLA-DQ, and MIC-2.
  • Item 32 The biological system of any one of or combination of items 1-31, wherein the reprogrammed genome lacks functional expression of SLA-DR, SLA-1, and/or SLA-2.
  • Item 33 The biological system of any one of or combination of items 1-32, wherein the nuclear genome is reprogrammed using scarless exchange of the exon regions, wherein there are no frameshifts, insertion mutations, deletion mutations, missense mutations, and nonsense mutations.
  • Item 34 The biological system of any one of or combination of items 1-33, wherein the nuclear genome is reprogrammed without introduction of any net insertions, deletions, truncations, or other genetic alterations that would cause a disruption of protein expression via frame shift, nonsense, or missense mutations.
  • Item 35 The biological system of any one of or combination of items 1-34, wherein nucleotides in intron regions of the nuclear genome are not altered.
  • Item 36 The biological system of any one of or combination of items 1-35, wherein said nuclear genome is reprogrammed to be homozygous at the reprogrammed exon regions.
  • Item 37 The biological system of any one of or combination of items 1-36, wherein said nuclear genome is reprogrammed such that extracellular, phenotypic surface expression of polypeptide is tolerogenic in a human recipient.
  • Item 38 The biological system of any one of or combination of items 1-37, wherein said nuclear genome is reprogrammed such that expression of cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) is increased by reprogramming a CTLA-4 promoter sequence.
  • CTLA-4 cytotoxic T-lymphocyte-associated protein 4
  • Item 39 The biological system of any one of or combination of items 1-38, wherein the reprogrammed genome comprises site-directed mutagenic substitutions of nucleotides at exon regions of the wild-type CTLA-4 with nucleotides from orthologous exons of a human captured reference sequence CTLA-4.
  • Item 40 The biological system of any one of or combination of items 1-39, wherein the reprogrammed nuclear genome comprises a polynucleotide that encodes a protein that is a humanized CTLA-4 polypeptide sequence that is at least 95% identical to CTLA-4 expressed by the human captured reference genome.
  • Item 41 The biological system of any one of or combination of items 1-40, wherein said nuclear genome is reprogrammed such that expression of Programmed death-ligand l(PD-Ll) is increased by reprogramming a PD-L1 promoter sequence.
  • Item 42 The biological system of any one of or combination of items 1-41, wherein the reprogrammed genome comprises site-directed mutagenic substitutions of nucleotides at exon regions of the wild-type PD-L1 with nucleotides from orthologous exons of a known human PD- Ll.
  • Item 43 The biological system of any one of or combination of items 1-42, wherein the reprogrammed nuclear genome comprises a polynucleotide that encodes a protein that is a humanized PD-L1 polypeptide sequence that is at least 95% identical to PD-L1 expressed by the human captured reference genome.
  • Item 44 A genetically reprogrammed, biologically active and metabolically active non human cell, tissue, or organ obtained from the biological system of any one of or combination of items 1-43.
  • Item 45 The genetically reprogrammed, biologically active and metabolically active non human cell, tissue, or organ of item 44, wherein the genetically reprogrammed, biologically active and metabolically active non-human cell is a stem cell, an embryonic stem cell, a pluripotent stem cell, or a differentiated stem cell.
  • Item 46 The genetically reprogrammed, biologically active and metabolically active non human cell, tissue, or organ of item 45, wherein the stem cell is a hematopoietic stem cell.
  • Item 47 The genetically reprogrammed, biologically active and metabolically active non human cell, tissue, or organ of item 44, wherein the genetically reprogrammed, biologically active and metabolically active non-human tissue is a nerve, cartilage, or skin.
  • Item 48 The genetically reprogrammed, biologically active and metabolically active non human cell, tissue, or organ of item 44, wherein the genetically reprogrammed, biologically active and metabolically active non-human organ is a solid organ.
  • a method of preparing a genetically reprogrammed swine comprising a nuclear genome that lacks functional expression of surface glycan epitopes selected from alpha-Gal, Neu5Gc, and SD a and is genetically reprogrammed to express a humanized phenotype of a human captured reference sequence comprising:
  • a porcine fetal fibroblast cell a porcine zygote, a porcine Induced Pluripotent Stem Cells (IPSC), or a porcine germ-line cell;
  • ISC porcine Induced Pluripotent Stem Cells
  • b genetically altering said cell in a) to lack functional alpha-1,3 galactosyltransferase, cytidine monophosphate-N-acetylneuraminic acid hydroxylase (CMAH), and b1,4-N- acetylgalactosaminyltransferase;
  • CMAH cytidine monophosphate-N-acetylneuraminic acid hydroxylase
  • b1,4-N- acetylgalactosaminyltransferase b1,4-N- acetylgalactosaminyltransferase
  • CRISPR clustered regularly interspaced short palindromic repeats
  • CRISPR clustered regularly interspaced short palindromic repeats
  • the reprogrammed genome comprises at least one of A-C: A) wherein the reprogrammed swine nuclear genome comprises site-directed mutagenic substitutions of nucleotides at exon regions of the wild-type swine’s p2-microglobulin with nucleotides from orthologous exons of a known human p2-microglobulin from the human captured reference sequence;
  • the reprogrammed swine nuclear genome comprises a polynucleotide that encodes a polypeptide that is a humanized beta 2 microglobulin (hB2M) polypeptide sequence that is at least 95% identical to beta 2 microglobulin expressed by the human captured reference genome;
  • hB2M humanized beta 2 microglobulin
  • endogenous p2-microglobulin polypeptides wherein the reprogrammed swine nuclear genome has been reprogrammed such that, at the swine’s endogenous p2-microglobulin locus, the nuclear genome has been reprogrammed to comprise a nucleotide sequence encoding p2-microglobulin polypeptide of the human recipient,
  • step (a) further comprises replacing a plurality of nucleotides in a plurality of exon regions of a major histocompatibility complex of a wild-type swine with nucleotides from orthologous exon regions of a major histocompatibility complex sequence from the human captured reference sequence, wherein said replacing does not introduce any frameshifts or frame disruptions.
  • Item 51 The method of any one of or combination of items 49-50, wherein said replacing comprises performing site-directed mutagenic substitutions of nucleotides at the major histocompatibility complex of the wild-type swine with orthologous nucleotides from the known human major histocompatibility complex sequence.
  • Item 52 The method of any one of or combination of items 49-51, wherein the human captured reference sequence is a human patient capture sequence, a human population-specific human capture sequence, or an allele-group-specific human capture sequence.
  • Item 53 The method of any one of or combination of items 49-52, wherein the orthologous exon regions are at one or more polymorphic glycoproteins of the wild-type swine’s major histocompatibility complex.
  • Item 54 The method of any one of or combination of items 49-53, further comprising: impregnating the surrogate pig with the embryo, gestating the embryo, and delivering a piglet from the surrogate pig through Cesarean section,
  • LA MRSA Livestock-associated methicillin resistant Staphylococcus aureus
  • Microphyton and Trichophyton spp.
  • maintaining the piglet according to a bioburden-reducing procedure, said procedure comprising maintaining the piglet in an isolated closed herd, wherein all other animals in the isolated closed herd are confirmed to be free of said zoonotic pathogens, wherein the piglet is isolated from contact with any non-human animals and animal housing facilities outside of the isolated closed herd.
  • Item 55 The method of any one of or combination of items 49-54, wherein the wild-type swine genome comprises reprogrammed nucleotides at SLA-MIC-2 gene and at exon regions encoding SLA-3, SLA-6, SLA-7, SLA-8, SLA-DQ, CTLA-4, PD-L1, EPCR, TBM, TFPI, and beta-2-microglobulin using the human capture reference sequence, wherein the human cell, tissue, or organ lacks functional expression of swine beta-2-microglobulin, SLA-DR, SLA-1, and SLA-2.
  • Item 56 The method of any one of or combination of items 49-54, wherein the wild-type swine genome comprises reprogrammed nucleotides at SLA-MIC-2 gene and at exon regions encoding SLA-3, SLA-6, SLA-7, SLA-8, SLA-DQ, CTLA-4, PD-L1, EPCR, TBM, TFPI, and beta-2-microglob
  • the wild-type swine genome comprises reprogrammed nucleotides at one or more of a CTLA-4 promoter and a PD-L1 promoter, wherein the one or more of the CTLA-4 promoter and the PD-L1 promoter are reprogrammed to increase expression of one or both of reprogrammed CTLA-4 and
  • Item 57 The method of any one of or combination of items 49-56, wherein a total number of the synthesized nucleotides is equal to a total number of the replaced nucleotides, such that there is no net loss or net gain in number of nucleotides after reprogramming the genome of the wild-type swine with the synthesized nucleotides.
  • Item 58 The method of any one of or combination of items 49-57, wherein the reprogramming with the plurality of synthesized nucleotides do not include replacement of nucleotides in codon regions that encode amino acids that are conserved between the wild-type swine MHC sequence and the human captured reference sequence
  • Item 59 The method of any one of or combination of items 49-58, wherein the reprogrammed genome comprises site-directed mutagenic substitutions of nucleotides at the major
  • histocompatibility complex of the wild-type swine with orthologous nucleotides from the human captured reference sequence is histocompatibility complex of the wild-type swine with orthologous nucleotides from the human captured reference sequence.
  • Item 60 The method of any one of or combination of items 49-59, wherein site-directed mutagenic substitutions are made in germ-line cells used to produce the non-human animal.
  • Item 61 The method of any one of or combination of items 49-60, wherein the human captured reference sequence is a human patient capture sequence, a human population-specific human capture sequence, or an allele-group-specific human capture sequence.
  • Item 62 The method of any one of or combination of items 49-61, wherein the reprogrammed genome comprises site-directed mutagenic substitutions of nucleotides at exon regions of the wild-type swine’s SLA-1 with nucleotides from an orthologous exon region of a HLA-A captured reference sequence.
  • Item 63 The method of any one of or combination of items 49-62, wherein the reprogrammed genome comprises site-directed mutagenic substitutions of nucleotides at exon regions of the wild-type swine’s SLA-2 with nucleotides from an orthologous exon region of a HLA-B captured reference sequence.
  • Item 64 The method of any one of or combination of items 49-63, wherein the reprogrammed genome comprises site-directed mutagenic substitutions of nucleotides at exon regions of the wild-type swine’s SLA-3 with nucleotides from an orthologous exon region of a HLA-C captured reference sequence.
  • Item 65 The method of any one of or combination of items 49-64, wherein the reprogrammed genome comprises site-directed mutagenic substitutions of nucleotides at exon regions of the wild-type swine’s SLA-6 with nucleotides from an orthologous exon region of a HLA-E captured reference sequence.
  • Item 66 The method of any one of or combination of items 49-65, wherein the reprogrammed genome comprises site-directed mutagenic substitutions of nucleotides at exon regions of the wild-type swine’s SLA-7 with nucleotides from an orthologous exon region of a HLA-F captured reference sequence.
  • Item 67 The method of any one of or combination of items 49-66, wherein the reprogrammed genome comprises site-directed mutagenic substitutions of nucleotides at exon regions of the wild-type swine’s SLA-8 with nucleotides from an orthologous exon region of a HLA-G captured reference sequence.
  • Item 68 The method of any one of or combination of items 49-67, wherein the reprogrammed genome comprises site-directed mutagenic substitutions of nucleotides at exon regions of the wild-type swine’s MHC class I chain-related 2 (MIC -2).
  • Item 69 The method of any one of or combination of items 49-68, wherein the reprogrammed genome lacks functional expression of SLA-1, SLA-2, SLA-DR, or a combination thereof.
  • Item 70 The method of any one of or combination of items 49-69, wherein the reprogrammed genome comprises site-directed mutagenic substitutions of nucleotides at exon regions of the wild-type swine’s SLA-DQA from an orthologous exon region of a HLA-DQA1 captured reference sequence.
  • Item 71 The method of any one of or combination of items 49-70, wherein the reprogrammed genome comprises site-directed mutagenic substitutions of nucleotides at exon regions of the wild-type swine’s SLA-DQB from an orthologous exon region of a HLA-DQB1 captured reference sequence.
  • Item 72 The method of any one of or combination of items 49-71, wherein the reprogrammed genome comprises site-directed mutagenic substitutions of nucleotides at exon regions of the wild-type swine’s SLA-DRA and SLA-DRBlwith nucleotides from orthologous exon regions of HLA-DRA1 and HLA-DRBlof the human captured reference sequence.
  • Item 73 The method of any one of or combination of items 49-72, wherein the reprogrammed genome comprises site-directed mutagenic substitutions of nucleotides at exon regions of the wild-type swine’s SLA-DQA and SLA-DQB1 with nucleotides from orthologous exon regions of HLA-DQA1 and HLA-DQB1 of the human captured reference sequence.
  • Item 74 The method of any one of or combination of items 49-73, wherein the site- directed mutagenic substitutions of nucleotides are at codons that are not conserved between the wild-type swine’s nuclear genome and the known human sequence.
  • Item 75 The method of any one of or combination of items 49-74, wherein the reprogrammed genome comprises site-directed mutagenic substitutions of nucleotides at exon regions of the wild-type swine’s B2-microglobulin with nucleotides from orthologous exons of a known human B2-microglobulin.
  • Item 76 The method of any one of or combination of items 49-75, wherein the reprogrammed swine nuclear genome comprises a polynucleotide that encodes a polypeptide that is a humanized beta 2 microglobulin (hB2M) polypeptide sequence that is at least 95% identical to the amino acid sequence of beta 2 microglobulin glycoprotein expressed by the human captured reference genome;
  • hB2M humanized beta 2 microglobulin
  • Item 77 The method of any one of or combination of items 49-76, wherein said nuclear genome has been reprogrammed such that the genetically reprogrammed swine lacks functional expression of the wild-type swine’s endogenous p2-microglobulin polypeptides.
  • Item 78 The method of any one of or combination of items 49-77, wherein said nuclear genome has been reprogrammed such that, at the swine’s endogenous p2-microglobulin locus, the nuclear genome has been reprogrammed to comprise a nucleotide sequence encoding b2- microglobulin polypeptide of the human captured reference sequence.
  • Item 79 The method of any one of or combination of items 49-78, wherein the reprogrammed genome comprises site-directed mutagenic substitutions of nucleotides at exon regions of SLA-3, SLA-6, SLA-7, SLA-8, and MIC-2.
  • Item 80 The method of any one of or combination of items 49-79, wherein the reprogrammed genome comprises site-directed mutagenic substitutions of nucleotides at exon regions of SLA-DQ, and MIC-2.
  • Item 81 The method of any one of or combination of items 49-80, wherein the reprogrammed genome comprises site-directed mutagenic substitutions of nucleotides at SLA-3, SLA-6, SLA-7, SLA-8, SLA-DQ, and MIC-2.
  • Item 82 The method of any one of or combination of items 49-81, wherein the reprogrammed genome lacks functional expression of SLA-DR, SLA-1, and/or SLA-2.
  • Item 83 The method of any one of or combination of items 49-82, wherein the nuclear genome is reprogrammed using scarless exchange of the exon regions, wherein there are no frameshifts, insertion mutations, deletion mutations, missense mutations, and nonsense mutations.
  • Item 84 The method of any one of or combination of items 49-83, wherein the nuclear genome is reprogrammed without introduction of any net insertions, deletions, truncations, or other genetic alterations that would cause a disruption of protein expression via frame shift, nonsense, or missense mutations.
  • Item 85 The method of any one of or combination of items 49-84, wherein nucleotides in intron regions of the nuclear genome are not altered.
  • Item 86 The method of any one of or combination of items 49-85, wherein said nuclear genome is reprogrammed to be homozygous at the reprogrammed exon regions.
  • Item 87 The method of any one of or combination of items 49-86, wherein said nuclear genome is reprogrammed such that extracellular, phenotypic surface expression of polypeptide is tolerogenic in a human recipient.
  • Item 88 The method of any one of or combination of items 49-87, wherein said nuclear genome is reprogrammed such that expression of cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) is increased by reprogramming a CTLA-4 promoter sequence.
  • CTLA-4 cytotoxic T-lymphocyte-associated protein 4
  • Item 89 The method of any one of or combination of items 49-88, wherein the reprogrammed genome comprises site-directed mutagenic substitutions of nucleotides at exon regions of the wild-type CTLA-4 with nucleotides from orthologous exons of a human captured reference sequence CTLA-4.
  • Item 90 The method of any one of or combination of items 49-89, wherein the reprogrammed nuclear genome comprises a polynucleotide that encodes a protein that is a humanized CTLA-4 polypeptide sequence that is at least 95% identical to CTLA-4 expressed by the human captured reference genome.
  • Item 91 The method of any one of or combination of items 49-90, wherein said nuclear genome is reprogrammed such that expression of Programmed death-ligand l(PD-Ll) is increased by reprogramming a PD-Ll promoter sequence.
  • Item 92 The method of any one of or combination of items 49-91, wherein the reprogrammed genome comprises site-directed mutagenic substitutions of nucleotides at exon regions of the wild-type PD-L1 with nucleotides from orthologous exons of a known human PD- Ll.
  • Item 93 The method of any one of or combination of items 49-92, wherein the reprogrammed nuclear genome comprises a polynucleotide that encodes a protein that is a humanized PD-L1 polypeptide sequence that is at least 95% identical to PD-L1 expressed by the human captured reference genome.
  • Item 94 A method of inducing at least partial immunological tolerance in a recipient human to a xenotransplanted cell, tissue, or organ, the method comprising:
  • non-human cell, tissue, or organ obtained from the biological system of any one of or combination of items 1-48, wherein the wild-type swine genome comprises reprogrammed nucleotides at SLA-MIC-2 gene and at exon regions of one or more encoding the wild-type swine’s MHC Class la, MHC class lb, MHC Class II, and beta-2-microglobulin using the human capture reference sequence and wherein the human cell, tissue, or organ lacks functional expression of swine beta-2-microglobulin; and
  • a method of reducing Natural Killer cell-mediated rejection of a xenograft comprising: producing or obtaining non-human cell, tissue, or organ obtained from the biological system of any one of or combination of items 1-48, wherein the wild-type swine genome comprises reprogrammed nucleotides at SLA-MIC-2 gene and at exon regions encoding one or more of the wild-type swine’s MHC Class la, MHC class lb, MHC Class II, and beta-2- microglobulin using the human capture reference sequence and wherein the human cell, tissue, or organ lacks functional expression of swine beta-2-microglobulin, and wherein the wild-type swine genome comprises reprogrammed nucleotides at exon regions encoding one or more of the wild-type swine’s CTLA-4 and PD-L1; and implanting the non-human cell, tissue, or organ into the recipient human.
  • Item 96 A method of reducing Cytotoxic T-cell Lymphocyte cell-mediated rejection of a xenograft comprising:
  • the wild-type swine genome comprises reprogrammed nucleotides at SLA-MIC-2 gene and at exon regions encoding one or more of the wild-type swine’s MHC Class la, MHC class lb, MHC Class II, and beta-2- microglobulin using the human capture reference sequence and wherein the human cell, tissue, or organ lacks functional expression of swine beta-2-microglobulin, and wherein the wild-type swine genome comprises reprogrammed nucleotides at exon regions encoding one or more of the wild-type swine’s CTLA-4 and PD-L1; and
  • Item 97 A method of preventing or reducing coagulation and/or thrombotic ischemia in a recipient human to a xenotransplanted cell, tissue, or organ, the method comprising:
  • the wild-type swine genome comprises reprogrammed nucleotides at SLA-MIC-2 gene and at exon regions encoding one or more of the wild-type swine’s MHC Class la, MHC class lb, MHC Class II, and beta-2-microglobulin using the human capture reference sequence, wherein the human cell, tissue, or organ lacks functional expression of swine beta-2-microglobulin, and wherein the wild-type swine genome comprises reprogrammed nucleotides at exon regions encoding one or more of the wild-type swine’s endothelial protein C receptor (EPCR), thrombomodulin (TBM), and tissue factor pathway inhibitor (TFPI); and
  • EPCR endothelial protein C receptor
  • TBM thrombomodulin
  • TFPI tissue factor pathway inhibitor
  • Item 98 A method of reducing MHC Class la-mediated rejection of a xenograft comprising:
  • non-human cell, tissue, or organ obtained from the biological system of any one of or combination of items 1-48, wherein the wild-type swine genome comprises reprogrammed nucleotides at SLA-MIC-2 gene and at exon regions encoding SLA-3 and one or more of the wild-type swine’s MHC class lb, MHC Class II, and beta-2- microglobulin using the human capture reference sequence, wherein the human cell, tissue, or organ lacks functional expression of swine beta-2-microglobulin, SLA-1, and SLA-2; and implanting the non-human cell, tissue, or organ into the recipient human.
  • the wild-type swine genome comprises reprogrammed nucleotides at SLA-MIC-2 gene and at exon regions encoding SLA-3 and one or more of the wild-type swine’s MHC class lb, MHC Class II, and beta-2- microglobulin using the human capture reference sequence, wherein the human cell, tissue, or organ lack
  • a method of reducing MHC Class Ib-mediated rejection of a xenograft comprising:
  • non-human cell, tissue, or organ obtained from the biological system of any one of or combination of items 1-48, wherein the wild-type swine genome comprises reprogrammed nucleotides at SLA-MIC-2 gene and at exon regions encoding SLA-6, SLA-7, and SLA-8, and one or more of the wild-type swine’s MHC class la, MHC Class II, and beta-2-microglobulin using the human capture reference sequence, wherein the human cell, tissue, or organ lacks functional expression of swine beta-2-microglobulin; and
  • a method of reducing MHC Class II-mediated rejection of a xenograft comprising:
  • non-human cell, tissue, or organ obtained from the biological system of any one of or combination of items 1-48, wherein the wild-type swine genome comprises reprogrammed nucleotides at SLA-MIC-2 gene and at exon regions encoding at least one of SLA-DR and SLA-DQ, and one or more of the wild-type swine’s MHC class la, MHC Class lb, and beta-2-microglobulin using the human capture reference sequence, wherein the human cell, tissue, or organ lacks functional expression of swine beta-2-microglobulin; and implanting the non-human cell, tissue, or organ into the recipient human.
  • the wild-type swine genome comprises reprogrammed nucleotides at SLA-MIC-2 gene and at exon regions encoding at least one of SLA-DR and SLA-DQ, and one or more of the wild-type swine’s MHC class la, MHC Class lb, and beta-2-microglobulin using the human
  • Item 101 A method of inhibiting apoptotic cell-mediated rejection of a xenograft comprising:
  • the wild-type swine genome comprises reprogrammed nucleotides at SLA-MIC-2 gene and at exon regions encoding one or more of the wild-type swine’s MHC Class la, MHC class lb, MHC Class II, and beta-2- microglobulin using the human capture reference sequence and wherein the human cell, tissue, or organ lacks functional expression of swine beta-2-microglobulin, and wherein the wild-type swine genome comprises reprogrammed nucleotides at exon regions encoding one or more of the wild-type swine’s CTLA-4 and PD-L1; and
  • Item 102 A method of producing a donor swine tissue or organ for xenotransplantation, wherein cells of said donor swine tissue or organ are genetically reprogrammed to be
  • LA MRSA Livestock-associated methicillin resistant Staphylococcus aureus
  • Microphyton and Trichophyton spp.
  • Item 104 The method of any one of or combination of items 102-103, further comprising maintaining the genetically reprogrammed swine according to a bioburden-reducing procedure, said procedure comprising maintaining the genetically reprogrammed swine in an isolated closed herd, wherein all other animals in the isolated closed herd are confirmed to be free of said zoonotic pathogens, wherein the genetically reprogrammed swine is isolated from contact with any non-human animals and animal housing facilities outside of the isolated closed herd.
  • Item 105 The method of any one of or combination of items 102-104, further comprising harvesting a biological product from said swine, wherein said harvesting comprises euthanizing the swine and aseptically removing the biological product from the swine.
  • Item 106 The method of any one of or combination of items 102-105, further comprising processing said biological product comprising sterilization after harvesting using a sterilization process that does not reduce cell viability to less than 50% cell viability as determined by a 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)-reduction assay.
  • Item 107 The method of any one of or combination of items 102-106, further comprising storing said biological product in a sterile container under storage conditions that preserve cell viability.
  • Item 108 A method of screening for off target edits or genome alterations in the genetically reprogrammed swine comprising a nuclear genome of any one of or combination of items 1-49, comprising:
  • Item 109 A synthetic nucleotide sequence having wild-type swine intron regions from a wild-type swine MHC Class la, and reprogrammed at exon regions encoding the wild-type swine’s SLA-3 with codons of HLA-C from a human capture reference sequence that encode amino acids that are not conserved between the SLA-3 and the HLA-C from the human capture reference sequence.
  • Item 110 The synthetic nucleotide sequence of item 109, wherein the wild-type swine’s SLA-1 and SLA-2 each comprise a stop codon.
  • Item 111 A synthetic nucleotide sequence having wild-type swine intron regions from a wild-type swine MHC Class lb, and reprogrammed at exon regions encoding the wild-type swine’s SLA-6, SLA-7, and SLA-8 with codons of HLA-E, HLA-F, and HLA-G, respectively, from a human capture reference sequence that encode amino acids that are not conserved between the SLA-6, SLA-7, and SLA-8 and the HLA-E, HLA-F, and HLA-G, respectively, from the human capture reference sequence.
  • Item 113. A synthetic nucleotide sequence having wild-type swine intron regions from a wild-type swine MHC Class II, and reprogrammed at exon regions encoding the wild-type swine’s SLA-DQ with codons of HLA-DQ, respectively, from a human capture reference sequence that encode amino acids that are not conserved between the SLA-DQ and the HLA- DQ, respectively, from the human capture reference sequence, and wherein the wild-type swine’s SLA-DR comprises a stop codon.
  • Item 114 A synthetic nucleotide sequence having the synthetic nucleotide sequences of: both items 109 and 113; both items 110 and 113; or both items 112 and 113.
  • Item 116 A synthetic nucleotide sequence having wild-type swine intron regions from a wild-type swine MIC -2, and reprogrammed at exon regions of the wild-type swine’s MIC -2 with codons of MIC- A or MIC-B from a human capture reference sequence that encode amino acids that are not conserved between the MIC-2 and the MIC-A or the MIC-B from the human capture reference sequence.
  • Item 117 A synthetic nucleotide sequence having wild-type swine intron regions from a wild-type swine CTLA-4, and reprogrammed at exon regions encoding the wild-type swine’s CTLA-4 with codons of CTLA-4 from a human capture reference sequence that encode amino acids that are not conserved between the wild-type swine’s CTLA-4 and the CTLA-4 from the human capture reference sequence.
  • Item 118 A synthetic nucleotide sequence having wild-type swine intron regions from a wild-type swine PD-L1 and reprogrammed at exon regions encoding the wild-type swine’s PD- L1 with codons of PD-L1 from a human capture reference sequence that encode amino acids that are not conserved between the wild-type swine’s PD-L1 and the PD-L1 from the human capture reference sequence.
  • Item 119 A synthetic nucleotide sequence having wild-type swine intron regions from a wild-type swine EPCR and reprogrammed at exon regions encoding the wild-type swine’s EPCR with codons of EPCR from a human capture reference sequence that encode amino acids that are not conserved between the wild-type swine’s EPCR and the EPCR from the human capture reference sequence.
  • Item 120 A synthetic nucleotide sequence having wild-type swine intron regions from a wild-type swine TBM and reprogrammed at exon regions encoding the wild-type swine’s TBM with codons of TBM from a human capture reference sequence that encode amino acids that are not conserved between the wild-type swine’s TBM and the TBM from the human capture reference sequence.
  • the subject invention has been shown in nonclinical studies to perform on par and surprisingly better than its allograft comparators, without the inherent disadvantage of inconsistent quality and unreliable and limited availability. That is, surprisingly, at least Study No. 1 shows skin grafts derived from a DPF Closed Colony, a-l,3-galactosyltransferase [Gal-T] knockout pigs produced in accordance with the present invention performed better than allograft.
  • FIG. 41 shows the longitudinal progression of porcine split-thickness skin graft used as a temporary wound closure in treatment of full-thickness wound defects in a non-human primate recipient.
  • FIG. 42 shows POD-30 histological images for: Top, Center: H&E, Low power image of wound site depicts complete epithelial coverage. Dotted line surrounds the residual xenograft tissue.
  • the dermal component of the xenograft To the right and below the dotted line is the dermal component of the xenograft, with the xenograft dermal matrix indicated by an open arrow. To the left of the dotted line is the host dermis (black arrow) and the host dermal matrix. Mild inflammation is present and interpreted to be in response to the xenograft test article. Bottom, Right: H&E, higher power image of the small inset box. The dotted line roughly demonstrates the junction between the xenograft test article (below dotted line) and new collagen tissue (above dotted line), with intact epithelium at the top of the image. Mild inflammation in response to the xenograft (open arrows) is observed.
  • FIG. 43 A graphs the total serum IgM ELISA (pg/mL) for all four subjects (2001, 2002, 2101, 2102) during the course of the study.
  • FIG. 43B graphs the total serum IgG ELISA (pg/mL) for all four subjects (2001, 2002, 2101, 2102) during the course of the study.
  • subjects transplanted with the product of the present disclosure will have serum IgM and IgG levels of less than 20,000 pg/ml each.
  • subjects transplanted with the product of the present disclosure will have serum IgM and/or IgG levels below or less than 10%, 5%, 3%, or 1% higher than serum IgM and IgG levels measured prior to transplantation.
  • the claimed method may demonstrate an immunoreactivity incidence rate of less than 5%, 3%, or 1% of subjects transplanted with the product of the present disclosure.
  • FIG. 44A graphs systemic concentrations of soluble CD40L as measured by Luminex 23-plex at POD-0, POD-7, POD-14, POD-21, and POD-30.
  • FIG. 44B graphs systemic concentrations of TGF-alpha as measured by Luminex 23-plex at POD-0, POD-7, POD-14, POD- 21, and POD-30.
  • FIG. 44C graphs systemic concentrations of IL-12/23 (p40) as measured by Luminex 23-plex at POD-0, POD-7, POD-14, POD-21, and POD-30.
  • porcine endogenous retroviruses PERV
  • porcine cytomegalovirus PCMV
  • PCR polymerase chain reaction
  • RT-PCR reverse transcriptase PCR
  • pc perivascular cells - number of cells surrounding dermal vessels (venules, capillaries, and arterioles) in deep and superficial dermis; scored on the most involved vessels; pc3 >50 cells/vessel
  • . pa perivascular dermal infiltrate area -percent area occupied by the most involved dermal vessels at 40x magnification;
  • cav chronic allograft vasculopathy - intimal thickening with luminal reduction; scored as percent luminal reduction;
  • the skin xenotransplants were assessed using a systematic pathologic component scoring and Banff classification .
  • the Banff classification is useful in categorizing xenotransplant rejection, and it is complemented by the component score approach, providing a more comprehensive array of clinical thresholds for the diagnosis of rejection.
  • the results of this assessment and Banff Grades for POD-30 are shown in Table 5.
  • the Banff 2007 Working Classification for Composite Tissue Allografts is based on the level of epidermal apoptosis, epidermal infiltrates, and perivascular/dermal infiltrates .
  • the Banff Grades ranged from II (moderate) to IV (necrotizing acute rejection) with most showing Grade III (severe).
  • sCD40L 1900 7900 ⁇ 7700 ⁇ 8600 ⁇ 8500 ⁇
  • J Values include data at the upper level of detection (12,000 pg/mL)
  • cytokines characteristic of initial wound healing processes or those anticipated in an immunological response to xenogeneic cells were measured. Twelve of the 23 cytokines/chemokines assayed were consistently below the level of detection throughout the entire study period: TNF-a, IFN-g, TGF-b, G-CSF, GM-CSF, IL-1- b, IL-4, IL-5, IL-10, IL-13, IL-17, IL-18, and MIP-1-a.
  • VEGF exceeded the level of detection at only three individual timepoints, and levels of MIP-l-beta were discernable only once (data not presented).
  • cytokines/chemokines detected over the period of the study are listed in Table 6. All cytokines/chemokines shown in the table were observed to increase above background at POD-7, the first day of sampling. IL-2, IL-8, MCP-1 and TGF-a peaked at POD-7 and decreased over time. IL-15 and IL-12/23 (p40) peaked at POD- 14, while sCD40L, IL-lra and IL-6 had an elevated peak at POD-21. In general, all of the factors showed a return to normal by POD-30 with the exception of sCD40L, which remained elevated at POD-30. Of interest, levels of IL-12/23 (p40) were nearly absent until conspicuously elevated on POD-14, gradually reducing in concentration over the remainder of the study.
  • PBMC peripheral blood mononuclear cell
  • IgG immunoglobulin G
  • IgM anti-porcine antibodies increased between 1.4 to 4.9 fold and IgG anti-porcine antibodies increased between 28.7 to 70.8 fold.
  • Naive skin xenotransplants were analyzed for PERV copy number and as expected, each cell contained copies of PERV A (32 ⁇ 1), B (9 ⁇ 0.1) and C (16 ⁇ 0.1).
  • Sera from the four recipients were evaluated for the presence of circulating PERV; all samples were found to be negative for PERV pol and below the limit of detection.
  • PBMC samples from each of the four recipients were also tested for PERV and for microchimerism (i.e., the presence of circulating pig cells) and were also found negative, at all time points.
  • Tissues taken at the end of the study (POD- 30) were evaluated for PERV expression and again were found negative. Wound beds from animal 2102 were negative for the presence of PERV and for microchimerism.
  • the following example provides a description of a process of harvesting and processing skin from a genetically reprogrammed swine produced in accordance with the present invention, with the skin to be used as a xenogeneic skin product for human transplantation.
  • the xenotransplantation product consists of split thickness grafts consisting of dermal and epidermal tissue layers containing vital, non-terminally sterilized porcine cells derived from specialized, genetically reprogrammed, Designated Pathogen Free (DPF), source animals.
  • DPF Designated Pathogen Free
  • the genetically reprogrammed source animal is any genetically reprogrammed animal described in the present disclosure.
  • the genetically engineered source animals in this example do not contain any foreign, introduced DNA into the genome; the gene modification includes a knock-out of a single gene that was responsible for encoding for an enzyme that causes ubiquitous expression of a cell-surface antigen.
  • the xenotransplantation product in this example does not incorporate transgene technologies, such as CD-46 or CD-55 transgenic constructs.
  • such one or more closure systems could include, but not be limited to, a first closure system (e.g., utilizing an inert material for initial closure to surround the organ to prevent the organ from coming into contact with or adhering to other materials proximate to the organ) and/or a second closure system (e.g., a sterile and secure outer container that contains the organ and first closure system (if a first closure system is utilized)).
  • a first closure system e.g., utilizing an inert material for initial closure to surround the organ to prevent the organ from coming into contact with or adhering to other materials proximate to the organ
  • a second closure system e.g., a sterile and secure outer container that contains the organ and first closure system (if a first closure system is utilized)
  • Such organs within such closure system(s) are configured to be transported to a clinical site as whole organs, stored, protected and transported in temperatures, sterility, and other conditions to maintain sterility and cell viability for transplantation as described herein
  • Skin product processing occurs in a single, continuous, and self-contained, segregated manufacturing event that begins with the sacrifice of the source animal through completion of the production of the final product.
  • Xenogeneic skin grafts derived from the genetically reprogrammed source animal is received, with the swine being recently euthanized via captive bolt euthanasia in another section of the DPF Isolation Area.
  • the source animal is contained in a sterile, non-porous bag that is contained within a plastic container which is delivered into the DPF Isolation Area and placed in an operating room where the procedure to harvest skin from the source animal will occur. All members of the operating team should be in full sterile surgical gear dressed in sterile dress to maintain designated pathogen free conditions prior to receiving the source animal and in some instanced be double-gloved to minimize contamination.
  • the operating area is prepared with materials required for harvesting skin from the source animal prior to decontamination (e.g., 24 hours prior with chlorine dioxide gas treatment) and prior to the procedure.
  • Dermatome electronic skin harvesting device, e.g., Amalgatome by Exsurco
  • extension cord are sterilized and placed in the operating area prior to the operation. Any materials not in the room during the chlorine dioxide gas treatment (and therefore non-sterile) will be sprayed with 70% ethanol or isopropanol prior to entering the room.
  • the source animal is removed from the bag and container in an aseptic fashion, for example, a human lifting the source animal from the bag and container using sterilized gloves and/or sterilized device to aid lifting and minimize contamination.
  • the source animal is scrubbed by operating staff for at least 2 minutes with Chlorhexidine brushes over the entire area of the animal where the operation will occur, periodically pouring Chlorhexidine over the area to ensure coverage.
  • the source animal is placed on its right lateral flank and dorsum towards the operating table leaving the left lateral flank and dorsum exposed.
  • the exposed surface is scrubbed to the extreme visible surgical borders, and constrained by sterile drapes secured with towel clamps.
  • the source animal is then scrubbed with opened Betadine brushes and sterile water rinse over the entire area of the animal where the operation will occur for approximately 2 minutes.
  • This Chlorhexidine and Betadine mixture will sit on the source animal for approximately 2 minutes, and staff (dressed in sterile dress to maintain designated pathogen free conditions) will then rinse and dry the source animal with sterile water and sterile gauze.
  • the source animal ’s hair is removed so as to not impact the membrane or introduce another element that would degrade the cells. Hair removal is done using sterilized clippers and/or straight razor in the designated pathogen free environment immediately post-mortem with a clean blade utilizing a chlorhexidine lather.
  • Staff will use the clippers and/or straight razor (lubricated in a sterile bath) to remove any remaining hair on the operating site, taking care to not puncture the skin.
  • This procedure will be repeated (scrubbing to shaving) by turning the source animal onto the left lateral flank so as to expose the right side.
  • the source animal will be rinsed with sterile water and dried with sterile towels and sprayed with 70% ethanol.
  • the source animal will be inspected visually by the surgeon to ensure proper coverage of scrubbing. After the sterile scrub and final shaving, the source animal is ready for skin harvest.
  • the thickness of the skin grafts could range from 0.01 mm to 4 mm, depending on the therapeutic needs at issue. It will also be understood that in some aspects a full thickness graft may also be utilized harvested with alternative harvesting and grafting procedures known in the art. Graft sizes can range from 1 cm 2 to 1000 cm 2 (or approximately 1 ft 2 ). It will be understood that larger graft sizes are also possible depending on the application and harvesting technique utilized and size of the source animal. It will be understood that for all aspects, other depths could be utilized as well, depending on the application and needs of the task at hand for therapeutic and/or other purposes.
  • skin harvesting involves surgically removing a skin flap from the animal first, then the skin flap is placed dermis-side down onto a harvest board (e.g., a solid board made of metal, plastic or other appropriate material) set upon on the operating table.
  • a harvest board e.g., a solid board made of metal, plastic or other appropriate material
  • sterile padding material is added beneath the skin flap and on top of the harvest board, to allow appropriate give for proper dermatome device function.
  • the skin flap is then affixed to the harvest board firmly with steel clamps. Curved towel clamps are utilized on the side of the skin flap opposite the clamps until the skin is firm and taut.
  • the surgeon will choose the most appropriate thickness on the dermatome and adjust per harvest conditions.
  • the surgeon will use the dermatome on the secured skin flap, with an assistant maintaining tension along the dermatome progress.
  • a second assistant may also provide assistance with skin flap tension, and may use rat tooth forceps to pull the graft product emerging from the dermatome
  • Grafts are trimmed to desired sizes.
  • sizes can be: 5 cm x 5 cm, with a total surface area of 25 cm 2 and uniform thickness of approximately 0.55 mm; 5 cm x 15 cm, with a total surface area of 75 cm 2 and uniform thickness of approximately 0.55 mm; 8 cm x 7.5 cm, with a total surface area of 60 cm 2 and uniform thickness of approximately 0.55 mm; 8 cm x 15 cm with a total surface area of 120 cm 2 and uniform thickness of approximately 0.55 mm.
  • customizable sizes i.e., width, thickness and length
  • the xenotransplantation product is further processed to be free of aerobic and anaerobic bacteria, fungus, and mycoplasma.
  • the xenotransplantation product is placed into an anti-microbial/anti-fungal bath (“antipathogen bath”).
  • antipathogen bath an anti-microbial/anti-fungal bath
  • the antipathogen bath includes ampicillin, ceftazidime, vancomyocin, amphotericin-B placed in a sterile container and the xenotransplantation products are diluted as outlined in the following Table 5 and added to RPMI-1640 medium as outlined in the following Table 6. In one aspect, about 10 mL of medium is removed from the bottle before adding the above items.
  • the products are made designated pathogen free by a process and system utilizing ultraviolet light.
  • the operator is dressed in sterile dress in accordance with institutional standards to maintain designated pathogen free conditions.
  • the operator wears eye protection safety glasses for ultraviolet light and lasers.
  • An ultraviolet laser lamp is set up in a laminar flow hood.
  • Each of the four corners of the lamp is placed on two container lids that are stacked on top of each other, i.e., four pairs of lids are used to support the lamp, or other supporting items, able to position the lamp in a temporary or fixed position above the working surface of the hood.
  • the distance from the lamp bulbs (2 bulb tubes total) to the floor of the hood is approximately 1.5 inches.
  • the entire interior of the hood is sprayed with alcohol, e.g., ethanol or isopropanol.
  • the lamp is turned on and the operator performs a calculation of time for desired exposure based on lamp specifications, number of bulbs, and distance between the bulbs and the xenotransplantation product.
  • a package of new sterilized cryovials is placed under the hood. Cryovial caps are unscrewed and placed into the chlorhexidine bath. Each cryovial (without cap) is then turned upside down and plunged open ended into the chlorhexidine bath, for one minute each and then set upright to air dry. Thereafter, the exterior of each cryovial is wiped with chlorhexidine and alcohol utilizing sterile gauze. The cryovial caps are removed from the chlorhexidine bath and placed on sterile gauze. The open ends of each vial were plunged into alcohol bath for 1 minute each and then set aside to air dry.
  • Xenotransplantation products recently obtained from the harvest/procurement phase in the surgical room are transferred into the product processing room, via a one-way entrance into the laminar flow hood. Anything entering the sterile field is wiped down with 70% ethanol prior to transfer to the operator. The operator will have access to all required materials in the laminar flow hood: xenotransplantation product (in sterile container), cryovials, lOmL syringes and needles, phase freezer holding rack, and pre-cut nylon mesh. Only one size of the products is processed at a time to ensure proper control to final vials. The operator is seated at the laminar flow hood in compliance with sterile, aseptic techniques.
  • the product When using UV light sterilization, the product is placed under the UV lamp for a desired period of time, e.g., 2 minutes or more, then turned over to the other side, and put under the UV lamp for the same period of time, e.g., 2 minutes or more on opposite side.
  • the time period for exposing a given sample to the UV is varied based on the specific biological agents or the types of biological agents to be sterilized, e.g., as shown in the following Table 7:
  • product yield will typically depend on how many of each such whole organ a given source animal may have (e.g., one liver, two lungs, two kidneys, one heart, one pancreas and so forth).
  • source animals are processed into aseptic xenotransplantation products.
  • Several items are involved in the manufacture of the product relating to the source animals, including, but not limited to:
  • care and husbandry of the source animals including, as described herein, providing certain vaccinations, carefully maintaining and analyzing pedigree records, performing proper animal husbandry, and maintaining the animals in isolation barrier conditions;
  • product manufacturing including, as described herein, processing the source animals into the subject product from euthanizing to harvest

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EP20719309.5A 2019-03-25 2020-03-25 Personalisierte zellen, gewebe und organe zur transplantation von einem humanisierten, spezifischen, von designiertem pathogen freien, (nichthumanen) spender und verfahren und produkte im zusammenhang damit Pending EP3945799A1 (de)

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