EP4638709A2 - Nk cell activating receptor ligand knockouts for use in cell therapy - Google Patents

Nk cell activating receptor ligand knockouts for use in cell therapy

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Publication number
EP4638709A2
EP4638709A2 EP23838001.8A EP23838001A EP4638709A2 EP 4638709 A2 EP4638709 A2 EP 4638709A2 EP 23838001 A EP23838001 A EP 23838001A EP 4638709 A2 EP4638709 A2 EP 4638709A2
Authority
EP
European Patent Office
Prior art keywords
cell
ulbp
trail
protein
cd1d
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
EP23838001.8A
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German (de)
French (fr)
Inventor
Gunther Roland Dr. GALLER
Shamim Herbert RAHMAN
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.)
Novo Nordisk AS
Original Assignee
Novo Nordisk AS
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
Application filed by Novo Nordisk AS filed Critical Novo Nordisk AS
Publication of EP4638709A2 publication Critical patent/EP4638709A2/en
Pending legal-status Critical Current

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    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N5/00Undifferentiated human, animal or plant cells, e.g. cell lines; Tissues; Cultivation or maintenance thereof; Culture media therefor
    • C12N5/06Animal cells or tissues; Human cells or tissues
    • C12N5/0602Vertebrate cells
    • C12N5/0676Pancreatic cells
    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07KPEPTIDES
    • C07K14/00Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/705Receptors; Cell surface antigens; Cell surface determinants
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2506/00Differentiation of animal cells from one lineage to another; Differentiation of pluripotent cells
    • C12N2506/02Differentiation of animal cells from one lineage to another; Differentiation of pluripotent cells from embryonic cells
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2510/00Genetically modified cells
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N5/00Undifferentiated human, animal or plant cells, e.g. cell lines; Tissues; Cultivation or maintenance thereof; Culture media therefor
    • C12N5/06Animal cells or tissues; Human cells or tissues
    • C12N5/0602Vertebrate cells
    • C12N5/0603Embryonic cells ; Embryoid bodies
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N5/00Undifferentiated human, animal or plant cells, e.g. cell lines; Tissues; Cultivation or maintenance thereof; Culture media therefor
    • C12N5/06Animal cells or tissues; Human cells or tissues
    • C12N5/0602Vertebrate cells
    • C12N5/0676Pancreatic cells
    • C12N5/0678Stem cells; Progenitor cells; Precursor cells

Definitions

  • the technical field of the present invention is cell therapy, more particularly cell replacement therapy.
  • Immune rejection of grafted cells and organs is triggered by the non-self or missingself recognition of the graft by the immune system of a host patient, involving macrophages and NK cells.
  • HLA-I and/or HLA-II proteins have been described and investigated.
  • One is to prevent the expression of HLA-I and/or HLA-II proteins on the cell surface of the cell(s) to be grafted to limit the non-self-recognition thereof by the host immune system.
  • Another approach is to express B2M-HLA-E or B2M-HLA-G transgenes in the cell(s) lacking surface HLA-I expression to be grafted to limit the missing-self-recognition thereof by the host immune system.
  • a purpose of the present invention is to improve the success of cell therapy.
  • Another purpose is to further protect transplanted cells from immune rejection especially in the context of cell replacement therapy.
  • the invention relates to a cell comprising on its cell surface no fully functional form of at least one protein selected from the list consisting of ULBP-2, CD112, CD155, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2.
  • the cells may comprise no gene encoding a fully functional form of at least one of ULBP-2, CD112, CD155, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7- H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2 proteins.
  • the cells may comprise the knock-out of at least one endogenous gene selected from ULBP-2, CD112, CD155, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2 endogenous gene(s).
  • the cells may be a human cell.
  • the cells may be a non-immune cell.
  • the cell may be B2M-/- and CD155-/-, or B2M-/- and B7-H3-/- or B2M-/-, CD155-/- and B7-H3-/- , and may be a stem cell, a pancreatic progenitor cell, an endocrine progenitor cell, an insulin producing cell or a p cell , may further comprise no fully functional form of at least one protein selected from ULBP-2, CD112, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2.
  • the cell may be a beta cell, an endocrine progenitor cell, or a pancreatic endoderm cell and may comprise no fully functional form of at least one protein selected from CD112, ULBP-2, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL- R1 and TRAIL-R2.
  • the cell may be B2M-/-, CIITA-/- and/or comprises a gene encoding a B2M-HLA fusion protein.
  • the cell may be a stem cell, such as an embryonic stem cell, a pluripotent stem cell or an induced pluripotent stem cell (iPSC), or may be derived from a stem cell or is a mammalian cell obtained from a donor or derived from a cell obtained from a donor, or may be a beta cell, an INS+ and NKX6.1+ double positive cell or a C- peptide+/NKX6.1+ double positive cell, an insulin producing cell, an in vitro derived beta-like cell, a pancreatic endocrine cell or an endocrine cell, an endocrine progenitor cell or a NGN3+/NKX2.2+ double positive cell, a neural cell, such as a neuron, an interneuron cell, an oligodendrocyte, an astrocyte, a dopaminergic cell, an exosome cell, such as ESCs or NSCs, or an exosome cell derived from a ESC or NSC, an immune cell, such
  • the cell may further comprise increased expression of at least one of CD47, HLA-G, HLA-E, HLA-F, PD-L1, CD55 proteins.
  • the invention also relates to a composition comprising cells as defined herein in a pharmaceutically acceptable medium.
  • the invention also relates to a cell or a composition comprising cells as defined herein for use in the treatment, the cure, or the prevention of a chronic disease or of an acute disease. Said use may be in cell replacement therapy. Cell replacement therapy may be by allotransplantation of said cell. Cell replacement therapy may be not by xenotransplantation.
  • Fig. 1 shows the flow cytometry results for CD155 (also called PVR) cell surface expression on cells at 4 differentiation stages of differentiation, namely the embryonic stem cell stage, the pancreatic endoderm stage (PE07), the beta cell stage (BC09) and the islet cell stage (Islets).
  • Fig. 2 shows the flow cytometry results for CD112 (also called Nectin2) cell surface expression on cells at 4 differentiation stages of differentiation, namely the embryonic stem cell stage, the pancreatic endoderm stage (PE07), the beta cell stage (BC09) and the islet cell stage (Islets).
  • CD155 also called PVR
  • PE07 pancreatic endoderm stage
  • BC09 beta cell stage
  • Islets islet cell stage
  • Fig. 3 shows flow cytometry results for the cell surface expression of ULBP-2 in beta cell progenitor stage.
  • the histogram in Fig. 3 shows signal in the presence (highest peak, more towards the left) or absence (lowest peak, more towards the right) of Romidepsin, a drug used in this experiment to induce and/or mimic cellular stress.
  • the graph on Fig.3 shows that LILBP2 surface expression is upregulated following 18h treatment with Romidepsin.
  • DNAX accessory protein-1 (DNAM-1 , also called CD226) is a NK cell receptor receiving activation signals through CD155 and CD112 ligation.
  • LILPB2 is a ligand recognized by NKG2D, an activating receptor present on NK cells.
  • B7-H3 for which the receptor is currently unknow, is another ligand involved in regulating NK cell-mediated immune response.
  • CD155, CD112, ULBP-2, and B7-H3 are able to activate NK cells through multiple pathways and are thought to be involved in the NK cell-mediated suppression of tumours and of transplanted cells and whole organs.
  • the present invention relates in essence to cells for use in cell therapy which lack on their cell surface at least one of NK cell activating ligands CD155, ULPB-2, CD112, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2, at least in their NK cell activating form.
  • NK cell activating ligands CD155, ULPB-2, CD112, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2, at least in their NK cell activating form.
  • these listed proteins can be knocked-out or modified in human stem cell lines used for differentiation towards beta cells prior to transplantation thereof, thereby disabling signals mediated through DNAM-1, NKG2D, or other receptors that function in NK cell activation and NK cell-mediated rejection of transplanted cells.
  • Human stem cell lines with modified CD155, ULPB-2, CD112, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and/or TRAIL-R2, or knockout thereof can also be used for the generation of other therapeutic cell products including e.g. cardiomyocytes and dopaminergic neurons, with the aim to minimize their NK cell activation potential.
  • CD155, ULPB-2, CD112, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP- 6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and/or TRAIL- R2 expression to non-functional or selectively functional form thereof, or knock-out thereof can be performed via MAD7-mediated biallelic engineering of the corresponding endogenous gene in human ESC or iPSC lines.
  • Generated stem cell lines and/or cell products can be tested in NK cell killing assays in vitro or in immune rejection models in vivo.
  • Single cells with knock-out or modification of CD155, ULPB-2, CD112, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and/or TRAIL-R2 can be generated, or combined with knock-in of known receptors involved in immune evasion of transplanted cells such as CD47, HLA-G, HLA-E, PD-L1 and/or CD55.
  • knock-out As used herein, the term “knock-out” of a given protein refers to any mean that deprives the cell from a functional version of said protein.
  • the term “knock-out” implies that said mean is not a natural feature of said cell and, instead, is a feature that has been artificially added to the.
  • said knock-out may be achieved by genetic modification of the gene encoding said protein such that said protein is no longer expressed or is expressed in a non-functional form.
  • the knockout is a non-natural knock-out, also called an artificial knock-out.
  • the cell is a non-naturally occurring cell.
  • the knock-out of a given protein comprises the knock-out of the corresponding endogenous gene(s).
  • a cell comprising the knock-out of a given protein is a said cell that does not express said protein.
  • not an immune cell means “not a cell of the immune system having at least one effector function such as cytotoxic cell killing activity, secretion of cytokines, induction of ADCC and/or CDC”.
  • not an immune cell means “not a T cell, not a macrophage, not a dendritic cell, not a monocyte, not a NK cell, not NKT cell, not a lymphocyte, and not a myeloid cell”.
  • cell replacement therapy 1 does not include cellular immunotherapy, also known as adoptive cell therapy.
  • the invention relates to a cell missing on its cell surface at least one of ULBP-2, CD112, CD155, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2 proteins in its fully functional form.
  • the invention relates to a cell comprising on its cell surface no fully functional form of at least one protein selected from the list consisting of ULBP-2, CD112, CD155, B7- H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2.
  • the invention relates to a cell which comprises on its cell surface no ULBP-2, no CD112, no CD155, no B7-H3 protein, no ULBP-3, no ULBP-4, no ULBP-5, no ULBP-6, no B7-H6, no B7-H7, no MICA, no MICB, no CD48, no CD58, no CD70, no CD1d, no CD318, no TRAIL-R1 and/or no TRAIL-R2 protein.
  • the invention relates to a cell, such as a cell for use in cell therapy, which lacks on its cell surface at least one NK cell activating ligand selected from the group consisting of CD155, ULPB-2, CD112, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2, at least in their NK cell activating form.
  • NK cell activating ligand selected from the group consisting of CD155, ULPB-2, CD112, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2, at least in their NK cell activating form.
  • the invention in another aspect, relates to a cell comprising on its cell surface at least one of ULBP-2, CD112, CD155, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2 proteins in a selectively functional form and comprising no fully functional form thereof.
  • selectively functional form as used herein is a form in which the protein of interest is modified such that it is able to activate some of the molecules and/or pathways that the non-modified version of said protein is able to activate, but not all of them.
  • the term “fully functional form” as used herein is a form in which the protein of interest is able to activate all of the molecules and pathways that the wild-type, also called non-modified, version of said protein is able to activate.
  • the selectively functional form of the protein of interest is a form in which said protein is no longer able to bind and activate NK-cell activating receptor(s) and remains able to bind and activate NK-cell inhibiting receptor(s).
  • CD155 is modified such that it does not bind DNAM-1 but keeps binding TIGIT and CD96.
  • CD112 is modified such that it does not bind DNAM-1 but keeps binding TIGIT and PVRIG.
  • ULBP-2 is modified such that it does not bind to NKG2D.
  • the invention in another aspect, relates to a cell comprising on its cell surface at least one of ULBP-2, CD112, CD155, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2 proteins in a nonfunctional form.
  • non-functional form as used herein is a form in which the protein of interest is modified such that it is not able to activate any of the molecules and pathways that the non-modified version of said protein is able to activate.
  • the invention relates to a cell comprising on its cell surface no ULBP-2 protein, or at least no fully functional form thereof. In an embodiment, the invention relates to a cell comprising no gene encoding a ULBP-2 protein or at least no gene encoding a fully functional form thereof.
  • the invention relates to a cell comprising no gene encoding at least one of ULBP-2, CD112, CD155, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2 proteins.
  • the invention relates to a cell comprising no gene encoding a fully functional form of at least one of ULBP-2, CD112, CD155, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2 proteins.
  • the invention relates to a cell comprising a gene encoding a selectively functional form of at least one of ULBP-2, CD112, CD155, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2 proteins.
  • the invention relates to a cell comprising the knock-out of at least one of ULBP- 2, CD112, CD155, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2 proteins.
  • the protein knock-out may be achieved by genetic modification of the endogenous gene in the cell encoding said protein such that said protein is no longer expressed or is expressed in a non-functional form.
  • the invention relates to a cell comprising the knock-out of at least one of ULBP-2, CD112, CD155, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2 endogenous genes.
  • the invention relates to a cell missing on its cell surface at least 1 , at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least
  • the invention in another aspect, relates to a cell comprising on its cell surface a selectively functional form of at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11 , at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18 or at least 19 protein(s) selected from of ULBP-2, CD112, CD155, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2 proteins and comprising no fully functional form thereof.
  • protein(s) selected from of ULBP-2, CD112, CD155, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58,
  • the cell of the invention may comprise the knock-out of at least 1 , at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11 , at least
  • the cell of the invention may comprise the knock-out of CD155 protein and of at least 1 , at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18 protein(s) selected from ULBP-2, CD112, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7- H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2.
  • the cell of the invention may comprise the knock-out of CD155 protein and of at least one protein selected from B7-H3 and CD112.
  • the cell of the invention may comprise the knock-out of CD112 protein and of at least one protein selected from B7-H3 and CD155.
  • the cell of the invention may comprise the knock-out of B7H3 protein and of at least one protein selected from CD155 and CD112.
  • the cell of the invention may comprise the knock-out of CD155 and CD112 proteins.
  • the cell of the invention may comprise the knock-out of CD155 and B7-H3 proteins.
  • the cell of the invention may comprise the knock-out of CD112 and B7-H3 proteins.
  • the cell of the invention may comprise the knock-out of CD155, B7-H3 and CD112 proteins.
  • the cell of the invention may comprise the knock-out of CD155 protein and comprises knockout of none of B7-H3 and CD112 proteins.
  • the cell of the invention may comprise the knock-out of CD112 protein and comprises knockout of none of B7-H3 and CD155 proteins.
  • the cell of the invention may comprise the knock-out of B7-H3 protein and comprises knockout of none of CD155 and CD112 proteins.
  • the cell of the invention may comprise CD155 protein and at least one protein selected from B7-H3 and CD112, said proteins being in non-functional or selectively functional form(s).
  • the cell of the invention may comprise CD112 protein and of at least one protein selected from B7-H3 and CD155, said proteins being in non-functional or selectively functional form(s).
  • the cell of the invention may comprise B7-H3 protein and at least one protein selected from CD155 and CD112, said proteins being in non-functional or selectively functional form(s).
  • the cell of the invention may comprise CD155 and CD112 proteins in non-functional or selectively functional form(s).
  • the cell of the invention may comprise CD155 and B7-H3 proteins in non-functional or selectively functional form(s).
  • the cell of the invention may comprise CD112 and B7-H3 proteins in non-functional or selectively functional form(s).
  • the cell of the invention may comprise CD155, B7-H3 and CD112 proteins in non-functional or selectively functional form(s).
  • the cell of the invention may comprise CD155 protein in non-functional or selectively functional form and comprises B7-H3 and CD112 proteins in fully functional forms.
  • the cell of the invention may comprise CD112 protein in non-functional or selectively functional form and comprises B7-H3 and CD155 proteins in fully functional forms.
  • the cell of the invention may comprise the B7-H3 protein in non-functional or selectively functional form and comprises CD155 and CD112 proteins in fully functional forms.
  • the invention relates to a cell comprising no gene encoding of at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18 or at least 19 protein(s) selected from ULBP-2, CD112, CD155, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL- R1 and TRAIL-R2 proteins.
  • the invention relates to a cell comprising no gene encoding a fully functional form of at least 1 , at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11 , at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18 or at least 19 protein(s) selected from ULBP-2, CD112, CD155, B7-H3,, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2 proteins.
  • the invention relates to a cell comprising a gene encoding a selectively functional form of at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11 , at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18 or at least 19 protein(s) selected from ULBP-2, CD112, CD155, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2 proteins.
  • the invention relates to a cell comprising the knock-out of endogenous gene(s) encoding at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18 or at least 19 proteins selected from CD155, ULBP-2, CD112, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2.
  • the cell of the invention may comprise the knock-out of CD155 encoding endogenous gene and the knock-out of endogenous gene(s) encoding at least 1 , at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11 , at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18 proteins selected from ULBP-2, CD112, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2.
  • the cell of the invention may comprise the knock-out of CD155 encoding endogenous gene and of at least one of B7-H3 and CD112 encoding endogenous genes.
  • the cell of the invention may comprise the knock-out of CD112 encoding endogenous gene and of at least one of B7-H3 and CD155 encoding endogenous genes.
  • the cell of the invention may comprise the knock-out of B7-H3 encoding endogenous gene and of at least one of CD155 and CD112 encoding endogenous genes.
  • the cell of the invention may comprise the knock-out of CD155 and CD112 encoding endogenous genes.
  • the cell of the invention may comprise the knock-out of CD155 and B7-H3 encoding endogenous genes.
  • the cell of the invention may comprise the knock-out of CD112 and B7-H3 encoding endogenous genes.
  • the cell of the invention may comprise the knock-out of CD155, B7-H3 and CD112 encoding endogenous genes.
  • the cell of the invention may comprise the knock-out of CD155 encoding endogenous gene and comprises knock-out of none of B7-H3 and CD112 encoding endogenous genes.
  • the cell of the invention may comprise the knock-out of CD112 encoding endogenous gene and comprises knock-out of none of B7-H3 and CD155 encoding endogenous genes.
  • the cell of the invention may comprise the knock-out of B7-H3 encoding endogenous gene and comprises knock-out of none of CD155 and CD112 encoding endogenous genes.
  • the cell of the invention may comprise gene(s) encoding CD155 protein and at least one protein selected from B7-H3 and CD112, said proteins being in non-functional or selectively functional form(s).
  • the cell of the invention may comprise gene(s) encoding CD112 protein and of at least one protein selected from B7-H3 and CD155, said proteins being in non-functional or selectively functional form(s).
  • the cell of the invention may comprise gene(s) encoding B7-H3 protein and at least one protein selected from CD155 and CD112, said proteins being in non-functional or selectively functional form(s).
  • the cell of the invention may comprise gene(s) encoding CD155 and CD112 proteins in nonfunctional or selectively functional form(s).
  • the cell of the invention may comprise gene(s) encoding CD155 and B7-H3 proteins in nonfunctional or selectively functional form(s).
  • the cell of the invention may comprise gene(s) encoding CD112 and B7-H3 proteins in nonfunctional or selectively functional form(s).
  • the cell of the invention may comprise gene(s) encoding CD155, B7-H3 and CD112 proteins in non-functional or selectively functional form(s).
  • the cell of the invention may comprise gene(s) encoding CD155 protein in non-functional or selectively functional form and comprises gene(s) encoding B7-H3 and CD112 proteins in fully functional forms.
  • the cell of the invention may comprise gene(s) encoding CD112 protein in non-functional or selectively functional form and comprises gene(s) encoding B7-H3 and CD155 proteins in fully functional forms.
  • the cell of the invention may comprise gene(s) encoding B7-H3 protein in non-functional or selectively functional form and comprises gene(s) encoding CD155 and CD112 proteins in fully functional forms.
  • the cell of the invention is a mammalian cell.
  • the cell is a human cell.
  • the cell is not an immune cell.
  • the cell is B2M-/- and CD155-/-, or is B2M-/- and B7-H3-/- or is B2M-/-, CD155-/- and B7- H3-/- , and said cell is a stem cell, a pancreatic progenitor cell, an endocrine progenitor cell, an insulin producing cell or a cell , said cell further comprises no fully functional form of at least one protein selected from ULBP-2, CD112, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2.
  • the cell of the invention is a stem cell.
  • said stem cell is an embryonic stem cell or a pluripotent stem cell.
  • said stem cell is an induced pluripotent stem cell (iPSC).
  • the cell of the invention is derived from a stem cell.
  • the cell of the invention is at a differentiated stage, such as a differentiated cell or mature cell.
  • the cell of the invention is a beta cell, an INS+ and NKX6.1+ double positive cell or a C-peptide+/NKX6.1+ double positive cell, an insulin producing cell, an in vitro derived beta-like cell, a pancreatic endocrine cell or an endocrine cell, an endocrine progenitor cell or a NGN3+/NKX2.2+ double positive cell, a neural cell, such as a neuron, an interneuron cell, an oligodendrocyte, an astrocyte, a dopaminergic cell, an exosome cell, such as ESCs or NSCs, or an exosome cell derived from a ESC or NSC, an immune cell, such as a T cell, a NK cell, a macrophage, a dendritic cell, or a hepatocyte, a stellate cell, a
  • the cell of the invention is obtained from a donor or is derived from a cell obtained from a donor. In an embodiment, the cell of the invention is a differentiated cell obtained from a donor, such as cell of any type.
  • the cell is a mesenchymal stem cell and comprises a knock-out of at least one protein selected from CD112 and CD155.
  • the cell is a mesenchymal stem cell and comprises a knock-out of at least one protein selected from CD155, CD112, ULBP-2, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2.
  • the cell is a mesenchymal stem cell, comprises a knock-out of at least one protein selected from CD112 and CD155, and further comprises a knock-out of at least one protein selected from ULBP2, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7- H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2 proteins.
  • the cell in addition to the absence of a functional NK-cell activating ligand as discussed herein, the cell may further comprise increased expression of at least one of CD47, HLA-G, HLA-E, PD-L1 and CD55 proteins.
  • Said increased protein expression may result from the insertion in said cell of a transgene encoding said protein.
  • the cell of the invention is a beta cell or a pancreatic endoderm cell or an endocrine progenitor cell, and comprises no fully functional form of at least one protein selected from CD112, ULBP-2, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2.
  • the cell of the invention is a beta cell or a pancreatic endoderm cell an endocrine progenitor cell, and comprises no gene encoding a fully functional form of at least one protein selected from CD112, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7- H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2.
  • the cell is a beta cell or a pancreatic endoderm cell or an endocrine progenitor cell, and comprises no fully functional form of CD155, CD112 and B7H3.
  • the cell is a beta cell or a pancreatic endoderm cell or an endocrine progenitor cell and comprises CD155, CD112 and B7-H3 proteins only in selectively functional form and/or non functional form.
  • the cell is a beta cell or a pancreatic endoderm cell or an endocrine progenitor cell and comprises no gene encoding a fully functional form of CD155, CD112 and B7-H3 proteins.
  • the cell is a beta cell or a pancreatic endoderm cell or an endocrine progenitor cell and comprises CD155, CD112 and B7-H3 encoding genes only in selectively functional form(s) and/or in non functional form(s).
  • the cell is a stealth cell.
  • the term “stealth” means that the cell is not subject to rejection by the immune system of a host upon allogeneic transplantation or is at least less subject to such rejection than the same cell without stealth modification.
  • the stealth cell may comprise genetic modifications to improve its stealth property.
  • the stealth cell may comprise a decrease in the H LA-class I and II proteins expression.
  • the cell of the invention is B2M-/-. In a preferred embodiment, the cell of the invention further comprises the knock-out of B2M endogenous gene.
  • the cell of the invention is CIITA-/-. In a preferred embodiment, the cell of the invention further comprises the knock-out of CIITA endogenous gene.
  • the cell of the invention further expresses a B2M-HLA fusion protein, such as B2M-HLA-E and/or B2M-HLA-G genetic fusion protein.
  • Said fusion protein expression may be achieved by insertion in the cell of a transgene encoding a B2M-HLA fusion protein, such as B2M-HLA-E and/or B2M-HLA-G.
  • Said transgene may be inserted into the cell’s genome or may be located on a vector transfected in the cell.
  • the cell of the invention further comprises a nucleic acid sequence encoding a B2M-HLA fusion protein, such as B2M-HLA-E and/or B2M-HLA-G genetic fusion protein.
  • the cell of the invention is B2M-/-, CIITA-/- and further comprises a nucleic acid sequence encoding a B2M-HLA fusion protein, such as B2M-HLA-E and/or B2M-HLA-G genetic fusion protein.
  • the cell of the invention may be further engineered to have reduced or increased expression of additional immune evasive proteins on the cell surface such as, PDL1, complement factors like, CD55, CD46, CD59, and/or other immune evasive ligands known in the art.
  • the cell comprises increased expression of at least one of CD47, HLA-G, HLA- E, HLA-F, PD-L1 , CD55 proteins.
  • the cell comprises a transgene encoding said protein.
  • the cell of the invention is for use in cell replacement therapy.
  • cell replacement therapy is preferably performed by allotransplantation, which excludes xenotransplantation.
  • the cell of the invention is for use in cell replacement therapy by allotransplantation of said cell and not by xenotransplantation.
  • the cell of the invention is not for use in adoptive cell therapy.
  • a cell comprising on its cell surface no fully functional form of at least one protein selected from the list consisting of ULBP-2, CD112, CD155, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2.
  • a cell such as a cell according to embodiment 1 , wherein said cell comprises on its cell surface no ULBP-2, no CD112, no CD155, no B7-H3 protein, no ULBP-3, no ULBP-4, no ULBP-5, no ULBP-6, no B7-H6, no B7-H7, no MICA, no MICB, no CD48, no CD58, no CD70, no CD1d, no CD318, no TRAIL-R1 and/or no TRAIL-R2 protein.
  • a cell such as cell according to embodiment 1 , wherein said cell is missing on its cell surface at least 1 , at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11 , at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18 or at least 19 protein(s) selected from ULBP-2, CD112, CD155, B7-H3 , ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2.
  • a cell such as a cell according to embodiment 1 , wherein said cell lacks on its cell surface at least one NK cell activating ligand selected from the group consisting of CD155, ULPB-2, CD112, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2, at least in their NK cell activating form.
  • NK cell activating ligand selected from the group consisting of CD155, ULPB-2, CD112, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2, at least in their NK cell activating form.
  • a cell according to embodiment 1 or 4 wherein said cell comprises no gene encoding a fully functional form of at least one of ULBP-2, CD112, CD155, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2 proteins.
  • endogenous gene selected from ULBP-2, CD112, CD155, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2 endogenous gene(s).
  • a cell according to any one of previous embodiments with the proviso that if said cell is B2M-/- and CD155-/-, or is B2M-/- and B7-H3-/- or is B2M-/-, CD155-/- and B7-H3- /- , and said cell is a stem cell, a pancreatic progenitor cell, an endocrine progenitor cell, an insulin producing cell or a cell , said cell further comprises no fully functional form of at least one protein selected from ULBP-2, CD112, ULBP-3, ULBP-4, ULBP- 5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL- R1 and TRAIL-R2.
  • the cell is a stem cell, such as an embryonic stem cell, a pluripotent stem cell or an induced pluripotent stem cell (iPSC).
  • iPSC induced pluripotent stem cell
  • composition comprising cells according to any one of previous embodiments in a pharmaceutically acceptable medium.
  • a cell according to embodiment 31 or a composition according to embodiment 31 wherein in cell therapy is cell replacement therapy is cell replacement therapy.
  • Example 1 Surface staining of human cells using antibodies for NK cell ligands
  • the below described treatment is applied to embryonic stem cells, to pancreatic endoderm cells (PE07), to beta cells (BC09) and to pancreatic islets cells (Islets).
  • the islet cells used in the staining are derived from a human donor and not from differentiated cells in vitro.
  • Adherent ES cells are first washed using RT PBS, followed by addition of TrypLE (just enough to cover bottom surface of culture vessel) and incubation for 5-10 min at 37°C. When cells are starting to detach, cells are re-suspended in either complete media or PBS, 1% BSA, and transferred to ice until further processing. Harvested ES cells were filtered (40
  • Dead cells were stained by addition of 1 pL of reconstituted reactive dye (LIVE/DEAD fixable Near-IR Dead Cell Stain Kit, Invitrogen), followed by mixing of the cell suspension and incubation on ice for 30 minutes. Cells are washed in cold PBS, 1% BSA, and resuspended in 4 mL of cold PBS, 1% BSA (250K cells/mL).
  • LIVE/DEAD fixable Near-IR Dead Cell Stain Kit Invitrogen
  • FcR blocking reagent TruStain FcX Fc Blocker, BioLegend
  • antibody cocktails (antibodies to ligands of interest, each linked to a different fluorochrome, such as PE, APC) are directly added at 2x concentration in 50 pL PBS, 1% BSA (1x concentration in 100 pL, final) to the cell suspension with FcR blocking reagent, followed by mixing of the cell suspension and incubation for additional 30 minutes on ice. Finally, cells are washed twice using 1 mL PBS, 1% BSA, and resuspended in 400 pL of PBS, 1% BSA for flow cytometric acquisition.
  • Fig.3 beta cell clusters were made into single cell suspension by incubation in Versene (Versene is an EDTA solution for use as a gentle non- enzymatic cell dissociation reagent.
  • GibcoTM Versene Solution (0.48 mM) is formulated as 0.2 g EDTA(Na 4 ) per liter of Phosphate Buffered Saline (PBS)) for 30 minutes at 37 degrees Celsius. Cells were then resuspended and filtered. Cells were washed once in PBS + 2% FBS followed by FcR blocking (1 :100) for 10 minutes on ice. Cells were then stained with antibodies (1 :50) for 15 minutes on ice followed by 2 times washing in PBS +2% FBS.

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Abstract

The technical field of the present invention is cell therapy, more particularly cell replacement therapy. The invention relates to a cell comprising on its cell surface no fully functional form of at least one protein selected from the list consisting of ULBP-2, CD112, CD155, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2. The invention also relates to cell compositions and uses thereof.

Description

DESCRIPTION
TITLE: NK CELL ACTIVATING RECEPTOR LIGAND KNOCKOUTS FOR USE IN CELL THERAPY
The technical field of the present invention is cell therapy, more particularly cell replacement therapy.
BACKGROUND
Cellular therapy faces several technical challenges, such as immune rejection of allografts, and a tremendous research effort is being invested in the field of biotechnology to overcome these challenges.
Immune rejection of grafted cells and organs is triggered by the non-self or missingself recognition of the graft by the immune system of a host patient, involving macrophages and NK cells.
Several approaches to overcome those challenges have been described and investigated. One is to prevent the expression of HLA-I and/or HLA-II proteins on the cell surface of the cell(s) to be grafted to limit the non-self-recognition thereof by the host immune system. Another approach is to express B2M-HLA-E or B2M-HLA-G transgenes in the cell(s) lacking surface HLA-I expression to be grafted to limit the missing-self-recognition thereof by the host immune system.
However there remains a need to further improve cell replacement therapy. There remains a need to improve the immune safety of grafted cells and organs upon transplantation in a host patient.
A purpose of the present invention is to improve the success of cell therapy.
Another purpose is to further protect transplanted cells from immune rejection especially in the context of cell replacement therapy.
Further purposes and benefits of the present invention might become apparent in the detailed description thereof.
SUMMARY
The invention relates to a cell comprising on its cell surface no fully functional form of at least one protein selected from the list consisting of ULBP-2, CD112, CD155, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2. The cells may comprise no gene encoding a fully functional form of at least one of ULBP-2, CD112, CD155, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7- H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2 proteins. The cells may comprise the knock-out of at least one endogenous gene selected from ULBP-2, CD112, CD155, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2 endogenous gene(s). The cells may be a human cell. The cells may be a non-immune cell. The cell may be B2M-/- and CD155-/-, or B2M-/- and B7-H3-/- or B2M-/-, CD155-/- and B7-H3-/- , and may be a stem cell, a pancreatic progenitor cell, an endocrine progenitor cell, an insulin producing cell or a p cell , may further comprise no fully functional form of at least one protein selected from ULBP-2, CD112, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2. The cell may be a beta cell, an endocrine progenitor cell, or a pancreatic endoderm cell and may comprise no fully functional form of at least one protein selected from CD112, ULBP-2, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL- R1 and TRAIL-R2. The cell may be B2M-/-, CIITA-/- and/or comprises a gene encoding a B2M-HLA fusion protein. The cell may be a stem cell, such as an embryonic stem cell, a pluripotent stem cell or an induced pluripotent stem cell (iPSC), or may be derived from a stem cell or is a mammalian cell obtained from a donor or derived from a cell obtained from a donor, or may be a beta cell, an INS+ and NKX6.1+ double positive cell or a C- peptide+/NKX6.1+ double positive cell, an insulin producing cell, an in vitro derived beta-like cell, a pancreatic endocrine cell or an endocrine cell, an endocrine progenitor cell or a NGN3+/NKX2.2+ double positive cell, a neural cell, such as a neuron, an interneuron cell, an oligodendrocyte, an astrocyte, a dopaminergic cell, an exosome cell, such as ESCs or NSCs, or an exosome cell derived from a ESC or NSC, an immune cell, such as a T cell, a NK cell, a macrophage, a dendritic cell, or a hepatocyte, a stellate cell, a fibroblast, a keratinocyte or a hair cell, an inner ear cell, an intestinal cell or organoid cell, a nephroid cell or another kidney-related cell, a cortical neural progenitor cell, a cardiomyocyte, a retinal cell, a retinal pigment epithelium cell, a mesenchymal stem cell.
The cell may further comprise increased expression of at least one of CD47, HLA-G, HLA-E, HLA-F, PD-L1, CD55 proteins.
The invention also relates to a composition comprising cells as defined herein in a pharmaceutically acceptable medium.
The invention also relates to a cell or a composition comprising cells as defined herein for use in the treatment, the cure, or the prevention of a chronic disease or of an acute disease. Said use may be in cell replacement therapy. Cell replacement therapy may be by allotransplantation of said cell. Cell replacement therapy may be not by xenotransplantation. BRIEF DESCRIPTION OF DRAWINGS
Fig. 1 shows the flow cytometry results for CD155 (also called PVR) cell surface expression on cells at 4 differentiation stages of differentiation, namely the embryonic stem cell stage, the pancreatic endoderm stage (PE07), the beta cell stage (BC09) and the islet cell stage (Islets). Fig. 2 shows the flow cytometry results for CD112 (also called Nectin2) cell surface expression on cells at 4 differentiation stages of differentiation, namely the embryonic stem cell stage, the pancreatic endoderm stage (PE07), the beta cell stage (BC09) and the islet cell stage (Islets).
Fig. 3 shows flow cytometry results for the cell surface expression of ULBP-2 in beta cell progenitor stage. The histogram in Fig. 3 shows signal in the presence (highest peak, more towards the left) or absence (lowest peak, more towards the right) of Romidepsin, a drug used in this experiment to induce and/or mimic cellular stress. The graph on Fig.3 shows that LILBP2 surface expression is upregulated following 18h treatment with Romidepsin.
DESCRIPTION
DNAX accessory protein-1 (DNAM-1 , also called CD226) is a NK cell receptor receiving activation signals through CD155 and CD112 ligation. LILPB2 is a ligand recognized by NKG2D, an activating receptor present on NK cells. B7-H3, for which the receptor is currently unknow, is another ligand involved in regulating NK cell-mediated immune response. CD155, CD112, ULBP-2, and B7-H3 are able to activate NK cells through multiple pathways and are thought to be involved in the NK cell-mediated suppression of tumours and of transplanted cells and whole organs.
During characterization of in vitro differentiated beta cell progenitors using scRNAseq and flow cytometry technics it was surprisingly demonstrated that these cells can express CD155, ULPB-2, B7-H3, CD112, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7- H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2 on both RNA and protein level. It was surprisingly identified that the cell surface expression of said proteins likely represents a mechanism for recognition and killing of transplanted beta cells by host NK cells, resulting in rejection and reduced therapeutic success in diabetic patients.
Therefore, the present invention relates in essence to cells for use in cell therapy which lack on their cell surface at least one of NK cell activating ligands CD155, ULPB-2, CD112, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2, at least in their NK cell activating form. It is herein proposed that these listed proteins can be knocked-out or modified in human stem cell lines used for differentiation towards beta cells prior to transplantation thereof, thereby disabling signals mediated through DNAM-1, NKG2D, or other receptors that function in NK cell activation and NK cell-mediated rejection of transplanted cells.
Human stem cell lines with modified CD155, ULPB-2, CD112, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and/or TRAIL-R2, or knockout thereof can also be used for the generation of other therapeutic cell products including e.g. cardiomyocytes and dopaminergic neurons, with the aim to minimize their NK cell activation potential.
Modification of CD155, ULPB-2, CD112, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP- 6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and/or TRAIL- R2 expression to non-functional or selectively functional form thereof, or knock-out thereof can be performed via MAD7-mediated biallelic engineering of the corresponding endogenous gene in human ESC or iPSC lines.
Generated stem cell lines and/or cell products can be tested in NK cell killing assays in vitro or in immune rejection models in vivo. Single cells with knock-out or modification of CD155, ULPB-2, CD112, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and/or TRAIL-R2 can be generated, or combined with knock-in of known receptors involved in immune evasion of transplanted cells such as CD47, HLA-G, HLA-E, PD-L1 and/or CD55.
Definitions
• “knock-out": As used herein, the term "knock-out" of a given protein refers to any mean that deprives the cell from a functional version of said protein. The term “knock-out” implies that said mean is not a natural feature of said cell and, instead, is a feature that has been artificially added to the. Amongst other means, said knock-out may be achieved by genetic modification of the gene encoding said protein such that said protein is no longer expressed or is expressed in a non-functional form. In an embodiment, the knockout is a non-natural knock-out, also called an artificial knock-out. In an embodiment, the cell is a non-naturally occurring cell. In an embodiment, the knock-out of a given protein comprises the knock-out of the corresponding endogenous gene(s). In an embodiment, a cell comprising the knock-out of a given protein is a said cell that does not express said protein. • “not an immune cell”: As used herein, the term "not an immune cell" means “not a cell of the immune system having at least one effector function such as cytotoxic cell killing activity, secretion of cytokines, induction of ADCC and/or CDC”. For example, the term "not an immune cell" means “not a T cell, not a macrophage, not a dendritic cell, not a monocyte, not a NK cell, not NKT cell, not a lymphocyte, and not a myeloid cell”.
• “cell replacement therapy1'. As used herein, the term “cell replacement therapy” does not include cellular immunotherapy, also known as adoptive cell therapy.
• Unless otherwise indicated in the specification, terms presented in singular form also include the plural situation
Detailed description:
No functional NK cell activating ligands on cell surface:
In an aspect, the invention relates to a cell missing on its cell surface at least one of ULBP-2, CD112, CD155, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2 proteins in its fully functional form.
In other words, the invention relates to a cell comprising on its cell surface no fully functional form of at least one protein selected from the list consisting of ULBP-2, CD112, CD155, B7- H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2.
In another aspect, the invention relates to a cell which comprises on its cell surface no ULBP-2, no CD112, no CD155, no B7-H3 protein, no ULBP-3, no ULBP-4, no ULBP-5, no ULBP-6, no B7-H6, no B7-H7, no MICA, no MICB, no CD48, no CD58, no CD70, no CD1d, no CD318, no TRAIL-R1 and/or no TRAIL-R2 protein.
In other words, the invention relates to a cell, such as a cell for use in cell therapy, which lacks on its cell surface at least one NK cell activating ligand selected from the group consisting of CD155, ULPB-2, CD112, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2, at least in their NK cell activating form.
In another aspect, the invention relates to a cell comprising on its cell surface at least one of ULBP-2, CD112, CD155, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2 proteins in a selectively functional form and comprising no fully functional form thereof. The term “selectively functional form” as used herein is a form in which the protein of interest is modified such that it is able to activate some of the molecules and/or pathways that the non-modified version of said protein is able to activate, but not all of them. The term “fully functional form” as used herein is a form in which the protein of interest is able to activate all of the molecules and pathways that the wild-type, also called non-modified, version of said protein is able to activate.
In a preferred embodiment, the selectively functional form of the protein of interest is a form in which said protein is no longer able to bind and activate NK-cell activating receptor(s) and remains able to bind and activate NK-cell inhibiting receptor(s).
In a preferred embodiment, CD155 is modified such that it does not bind DNAM-1 but keeps binding TIGIT and CD96.
In a preferred embodiment, CD112 is modified such that it does not bind DNAM-1 but keeps binding TIGIT and PVRIG.
In a preferred embodiment, ULBP-2 is modified such that it does not bind to NKG2D.
In another aspect, the invention relates to a cell comprising on its cell surface at least one of ULBP-2, CD112, CD155, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2 proteins in a nonfunctional form. The term “non-functional form” as used herein is a form in which the protein of interest is modified such that it is not able to activate any of the molecules and pathways that the non-modified version of said protein is able to activate.
In an embodiment, the invention relates to a cell comprising on its cell surface no ULBP-2 protein, or at least no fully functional form thereof. In an embodiment, the invention relates to a cell comprising no gene encoding a ULBP-2 protein or at least no gene encoding a fully functional form thereof.
Gene level:
In an aspect, the invention relates to a cell comprising no gene encoding at least one of ULBP-2, CD112, CD155, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2 proteins.
In an aspect, the invention relates to a cell comprising no gene encoding a fully functional form of at least one of ULBP-2, CD112, CD155, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2 proteins.
In an aspect, the invention relates to a cell comprising a gene encoding a selectively functional form of at least one of ULBP-2, CD112, CD155, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2 proteins. In an aspect, the invention relates to a cell comprising the knock-out of at least one of ULBP- 2, CD112, CD155, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2 proteins.
The protein knock-out may be achieved by genetic modification of the endogenous gene in the cell encoding said protein such that said protein is no longer expressed or is expressed in a non-functional form.
In an embodiment, the invention relates to a cell comprising the knock-out of at least one of ULBP-2, CD112, CD155, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2 endogenous genes.
Combinations, protein level:
In an aspect, the invention relates to a cell missing on its cell surface at least 1 , at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least
11 , at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18 or at least 19 protein(s) selected from ULBP-2, CD112, CD155, B7-H3 , ULBP-3, ULBP-4, ULBP-
5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2.
In another aspect, the invention relates to a cell comprising on its cell surface a selectively functional form of at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11 , at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18 or at least 19 protein(s) selected from of ULBP-2, CD112, CD155, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2 proteins and comprising no fully functional form thereof.
The cell of the invention may comprise the knock-out of at least 1 , at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11 , at least
12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18 or at least 19 protein(s) selected from CD155, ULBP-2, CD112, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-
6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL- R2.
The cell of the invention may comprise the knock-out of CD155 protein and of at least 1 , at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18 protein(s) selected from ULBP-2, CD112, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7- H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2. The cell of the invention may comprise the knock-out of CD155 protein and of at least one protein selected from B7-H3 and CD112.
The cell of the invention may comprise the knock-out of CD112 protein and of at least one protein selected from B7-H3 and CD155.
The cell of the invention may comprise the knock-out of B7H3 protein and of at least one protein selected from CD155 and CD112.
The cell of the invention may comprise the knock-out of CD155 and CD112 proteins.
The cell of the invention may comprise the knock-out of CD155 and B7-H3 proteins.
The cell of the invention may comprise the knock-out of CD112 and B7-H3 proteins.
The cell of the invention may comprise the knock-out of CD155, B7-H3 and CD112 proteins.
The cell of the invention may comprise the knock-out of CD155 protein and comprises knockout of none of B7-H3 and CD112 proteins.
The cell of the invention may comprise the knock-out of CD112 protein and comprises knockout of none of B7-H3 and CD155 proteins.
The cell of the invention may comprise the knock-out of B7-H3 protein and comprises knockout of none of CD155 and CD112 proteins.
The cell of the invention may comprise CD155 protein and at least one protein selected from B7-H3 and CD112, said proteins being in non-functional or selectively functional form(s).
The cell of the invention may comprise CD112 protein and of at least one protein selected from B7-H3 and CD155, said proteins being in non-functional or selectively functional form(s).
The cell of the invention may comprise B7-H3 protein and at least one protein selected from CD155 and CD112, said proteins being in non-functional or selectively functional form(s).
The cell of the invention may comprise CD155 and CD112 proteins in non-functional or selectively functional form(s).
The cell of the invention may comprise CD155 and B7-H3 proteins in non-functional or selectively functional form(s).
The cell of the invention may comprise CD112 and B7-H3 proteins in non-functional or selectively functional form(s).
The cell of the invention may comprise CD155, B7-H3 and CD112 proteins in non-functional or selectively functional form(s).
The cell of the invention may comprise CD155 protein in non-functional or selectively functional form and comprises B7-H3 and CD112 proteins in fully functional forms.
The cell of the invention may comprise CD112 protein in non-functional or selectively functional form and comprises B7-H3 and CD155 proteins in fully functional forms. The cell of the invention may comprise the B7-H3 protein in non-functional or selectively functional form and comprises CD155 and CD112 proteins in fully functional forms.
Combinations, gene level:
In an aspect, the invention relates to a cell comprising no gene encoding of at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18 or at least 19 protein(s) selected from ULBP-2, CD112, CD155, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL- R1 and TRAIL-R2 proteins.
In an aspect, the invention relates to a cell comprising no gene encoding a fully functional form of at least 1 , at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11 , at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18 or at least 19 protein(s) selected from ULBP-2, CD112, CD155, B7-H3,, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2 proteins.
In an aspect, the invention relates to a cell comprising a gene encoding a selectively functional form of at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11 , at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18 or at least 19 protein(s) selected from ULBP-2, CD112, CD155, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2 proteins.
In an aspect, the invention relates to a cell comprising the knock-out of endogenous gene(s) encoding at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18 or at least 19 proteins selected from CD155, ULBP-2, CD112, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2.
The cell of the invention may comprise the knock-out of CD155 encoding endogenous gene and the knock-out of endogenous gene(s) encoding at least 1 , at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11 , at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18 proteins selected from ULBP-2, CD112, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2. The cell of the invention may comprise the knock-out of CD155 encoding endogenous gene and of at least one of B7-H3 and CD112 encoding endogenous genes.
The cell of the invention may comprise the knock-out of CD112 encoding endogenous gene and of at least one of B7-H3 and CD155 encoding endogenous genes.
The cell of the invention may comprise the knock-out of B7-H3 encoding endogenous gene and of at least one of CD155 and CD112 encoding endogenous genes.
The cell of the invention may comprise the knock-out of CD155 and CD112 encoding endogenous genes.
The cell of the invention may comprise the knock-out of CD155 and B7-H3 encoding endogenous genes.
The cell of the invention may comprise the knock-out of CD112 and B7-H3 encoding endogenous genes.
The cell of the invention may comprise the knock-out of CD155, B7-H3 and CD112 encoding endogenous genes.
The cell of the invention may comprise the knock-out of CD155 encoding endogenous gene and comprises knock-out of none of B7-H3 and CD112 encoding endogenous genes.
The cell of the invention may comprise the knock-out of CD112 encoding endogenous gene and comprises knock-out of none of B7-H3 and CD155 encoding endogenous genes.
The cell of the invention may comprise the knock-out of B7-H3 encoding endogenous gene and comprises knock-out of none of CD155 and CD112 encoding endogenous genes.
The cell of the invention may comprise gene(s) encoding CD155 protein and at least one protein selected from B7-H3 and CD112, said proteins being in non-functional or selectively functional form(s).
The cell of the invention may comprise gene(s) encoding CD112 protein and of at least one protein selected from B7-H3 and CD155, said proteins being in non-functional or selectively functional form(s).
The cell of the invention may comprise gene(s) encoding B7-H3 protein and at least one protein selected from CD155 and CD112, said proteins being in non-functional or selectively functional form(s).
The cell of the invention may comprise gene(s) encoding CD155 and CD112 proteins in nonfunctional or selectively functional form(s).
The cell of the invention may comprise gene(s) encoding CD155 and B7-H3 proteins in nonfunctional or selectively functional form(s).
The cell of the invention may comprise gene(s) encoding CD112 and B7-H3 proteins in nonfunctional or selectively functional form(s). The cell of the invention may comprise gene(s) encoding CD155, B7-H3 and CD112 proteins in non-functional or selectively functional form(s).
The cell of the invention may comprise gene(s) encoding CD155 protein in non-functional or selectively functional form and comprises gene(s) encoding B7-H3 and CD112 proteins in fully functional forms.
The cell of the invention may comprise gene(s) encoding CD112 protein in non-functional or selectively functional form and comprises gene(s) encoding B7-H3 and CD155 proteins in fully functional forms.
The cell of the invention may comprise gene(s) encoding B7-H3 protein in non-functional or selectively functional form and comprises gene(s) encoding CD155 and CD112 proteins in fully functional forms.
Cells:
In an embodiment, the cell of the invention is a mammalian cell.
In an embodiment, the cell is a human cell.
In an embodiment, the cell is not an immune cell.
If the cell is B2M-/- and CD155-/-, or is B2M-/- and B7-H3-/- or is B2M-/-, CD155-/- and B7- H3-/- , and said cell is a stem cell, a pancreatic progenitor cell, an endocrine progenitor cell, an insulin producing cell or a cell , said cell further comprises no fully functional form of at least one protein selected from ULBP-2, CD112, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2.
In an embodiment, the cell of the invention is a stem cell. In an embodiment, said stem cell is an embryonic stem cell or a pluripotent stem cell. In another embodiment, said stem cell is an induced pluripotent stem cell (iPSC).
In an embodiment, the cell of the invention is derived from a stem cell.
In another embodiment, the cell of the invention is at a differentiated stage, such as a differentiated cell or mature cell. In an embodiment, the cell of the invention is a beta cell, an INS+ and NKX6.1+ double positive cell or a C-peptide+/NKX6.1+ double positive cell, an insulin producing cell, an in vitro derived beta-like cell, a pancreatic endocrine cell or an endocrine cell, an endocrine progenitor cell or a NGN3+/NKX2.2+ double positive cell, a neural cell, such as a neuron, an interneuron cell, an oligodendrocyte, an astrocyte, a dopaminergic cell, an exosome cell, such as ESCs or NSCs, or an exosome cell derived from a ESC or NSC, an immune cell, such as a T cell, a NK cell, a macrophage, a dendritic cell, or a hepatocyte, a stellate cell, a fibroblast, a keratinocyte or a hair cell, an inner ear cell, an intestinal cell or organoid cell, a nephroid cell or another kidney-related cell, a cortical neural progenitor cell, a cardiomyocyte, a retinal cell, a retinal pigment epithelium cell, a mesenchymal stem cell.
In an embodiment, the cell of the invention is obtained from a donor or is derived from a cell obtained from a donor. In an embodiment, the cell of the invention is a differentiated cell obtained from a donor, such as cell of any type.
In an embodiment, the cell is a mesenchymal stem cell and comprises a knock-out of at least one protein selected from CD112 and CD155. In an embodiment, the cell is a mesenchymal stem cell and comprises a knock-out of at least one protein selected from CD155, CD112, ULBP-2, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2.
In an embodiment, the cell is a mesenchymal stem cell, comprises a knock-out of at least one protein selected from CD112 and CD155, and further comprises a knock-out of at least one protein selected from ULBP2, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7- H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2 proteins.
In another aspect, in addition to the absence of a functional NK-cell activating ligand as discussed herein, the cell may further comprise increased expression of at least one of CD47, HLA-G, HLA-E, PD-L1 and CD55 proteins.
Said increased protein expression may result from the insertion in said cell of a transgene encoding said protein.
In another aspect, the cell of the invention is a beta cell or a pancreatic endoderm cell or an endocrine progenitor cell, and comprises no fully functional form of at least one protein selected from CD112, ULBP-2, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2.
In another aspect, the cell of the invention is a beta cell or a pancreatic endoderm cell an endocrine progenitor cell, and comprises no gene encoding a fully functional form of at least one protein selected from CD112, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7- H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2.
In a preferred embodiment, the cell is a beta cell or a pancreatic endoderm cell or an endocrine progenitor cell, and comprises no fully functional form of CD155, CD112 and B7H3. In a preferred embodiment, the cell is a beta cell or a pancreatic endoderm cell or an endocrine progenitor cell and comprises CD155, CD112 and B7-H3 proteins only in selectively functional form and/or non functional form.
In a preferred embodiment, the cell is a beta cell or a pancreatic endoderm cell or an endocrine progenitor cell and comprises no gene encoding a fully functional form of CD155, CD112 and B7-H3 proteins. In a preferred embodiment, the cell is a beta cell or a pancreatic endoderm cell or an endocrine progenitor cell and comprises CD155, CD112 and B7-H3 encoding genes only in selectively functional form(s) and/or in non functional form(s).
In a preferred embodiment, the cell is a stealth cell. The term “stealth” means that the cell is not subject to rejection by the immune system of a host upon allogeneic transplantation or is at least less subject to such rejection than the same cell without stealth modification. The stealth cell may comprise genetic modifications to improve its stealth property. The stealth cell may comprise a decrease in the H LA-class I and II proteins expression.
In an embodiment, the cell of the invention is B2M-/-. In a preferred embodiment, the cell of the invention further comprises the knock-out of B2M endogenous gene.
In an embodiment, the cell of the invention is CIITA-/-. In a preferred embodiment, the cell of the invention further comprises the knock-out of CIITA endogenous gene.
In an embodiment, the cell of the invention further expresses a B2M-HLA fusion protein, such as B2M-HLA-E and/or B2M-HLA-G genetic fusion protein. Said fusion protein expression may be achieved by insertion in the cell of a transgene encoding a B2M-HLA fusion protein, such as B2M-HLA-E and/or B2M-HLA-G. Said transgene may be inserted into the cell’s genome or may be located on a vector transfected in the cell. In a preferred embodiment, the cell of the invention further comprises a nucleic acid sequence encoding a B2M-HLA fusion protein, such as B2M-HLA-E and/or B2M-HLA-G genetic fusion protein.
In a preferred embodiment, the cell of the invention is B2M-/-, CIITA-/- and further comprises a nucleic acid sequence encoding a B2M-HLA fusion protein, such as B2M-HLA-E and/or B2M-HLA-G genetic fusion protein.
The cell of the invention may be further engineered to have reduced or increased expression of additional immune evasive proteins on the cell surface such as, PDL1, complement factors like, CD55, CD46, CD59, and/or other immune evasive ligands known in the art. In an embodiment, the cell comprises increased expression of at least one of CD47, HLA-G, HLA- E, HLA-F, PD-L1 , CD55 proteins. In an embodiment, the cell comprises a transgene encoding said protein.
Uses:
In another aspect, the cell of the invention is for use in cell replacement therapy. As per the present invention, cell replacement therapy is preferably performed by allotransplantation, which excludes xenotransplantation. In a preferred embodiment, the cell of the invention is for use in cell replacement therapy by allotransplantation of said cell and not by xenotransplantation. In a preferred embodiment, the cell of the invention is not for use in adoptive cell therapy.
Embodiments:
1. A cell comprising on its cell surface no fully functional form of at least one protein selected from the list consisting of ULBP-2, CD112, CD155, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2.
2. A cell, such as a cell according to embodiment 1 , wherein said cell comprises on its cell surface no ULBP-2, no CD112, no CD155, no B7-H3 protein, no ULBP-3, no ULBP-4, no ULBP-5, no ULBP-6, no B7-H6, no B7-H7, no MICA, no MICB, no CD48, no CD58, no CD70, no CD1d, no CD318, no TRAIL-R1 and/or no TRAIL-R2 protein.
3. A cell, such as cell according to embodiment 1 , wherein said cell is missing on its cell surface at least 1 , at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11 , at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18 or at least 19 protein(s) selected from ULBP-2, CD112, CD155, B7-H3 , ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2.
4. A cell, such as a cell according to embodiment 1 , wherein said cell lacks on its cell surface at least one NK cell activating ligand selected from the group consisting of CD155, ULPB-2, CD112, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2, at least in their NK cell activating form.
5. A cell according to embodiment 1 or 4, wherein said cell comprises no gene encoding a fully functional form of at least one of ULBP-2, CD112, CD155, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2 proteins.
6. A cell according to any one of embodiments 1 to 5, wherein said cell comprises the knock-out of at least one endogenous gene selected from ULBP-2, CD112, CD155, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2 endogenous gene(s).
7. A cell according to any one of embodiments 1 to 6, wherein said cell comprises no gene encoding at least one of ULBP-2, CD112, CD155, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2 proteins.
8. A cell according to any of embodiments 1 to 7, wherein said cell comprises the knockout of CD155 encoding endogenous gene and the knock-out of endogenous gene(s) encoding at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18 proteins selected from ULBP-2, CD112, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2.
9. A cell according to any of embodiments 1 to 8, wherein said cell comprises the knockout of CD155 and CD112 encoding endogenous genes.
10. A cell according to any of embodiments 1 to 8, wherein said cell comprises the knockout of CD155 and B7-H3 encoding endogenous genes.
11. A cell according to any of embodiments 1 to 7, wherein said cell comprises the knockout of CD112 and B7-H3 encoding endogenous genes.
12. A cell according to any of embodiments 1 to 8, wherein said cell comprises the knockout of CD155, B7-H3 and CD112 encoding endogenous genes.
13. A cell according to any one of previous embodiments, wherein said cell is a human cell.
14. A cell according to anyone of previous embodiments, wherein said cell is not an immune cell.
15. A cell according to any one of previous embodiments, with the proviso that if said cell is B2M-/- and CD155-/-, or is B2M-/- and B7-H3-/- or is B2M-/-, CD155-/- and B7-H3- /- , and said cell is a stem cell, a pancreatic progenitor cell, an endocrine progenitor cell, an insulin producing cell or a cell , said cell further comprises no fully functional form of at least one protein selected from ULBP-2, CD112, ULBP-3, ULBP-4, ULBP- 5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL- R1 and TRAIL-R2.
16. A cell according to any of previous embodiments, wherein said cell is a beta cell, an endocrine progenitor cell or a pancreatic endoderm cell and comprises no fully functional form of at least one protein selected from CD112, ULBP-2, ULBP-3, ULBP- 4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2.
17. A cell according to any of previous embodiments, wherein said cell is B2M-/-, is CIITA-/- and/or comprises a gene encoding a B2M-HLA fusion protein. A cell according to any of previous embodiments, wherein the cell is a stem cell, such as an embryonic stem cell, a pluripotent stem cell or an induced pluripotent stem cell (iPSC). A cell according to any of previous embodiments, wherein said cell is derived from a stem cell or is a mammalian cell obtained from a donor or derived from a cell obtained from a donor. A cell according to any of previous embodiments, wherein the cell is or is a beta cell, an INS+ and NKX6.1+ double positive cell or a C-peptide+/NKX6.1+ double positive cell, an insulin producing cell, an in vitro derived beta-like cell, a pancreatic endocrine cell or an endocrine cell, an endocrine progenitor cell or a NGN3+/NKX2.2+ double positive cell, a neural cell, such as a neuron, an interneuron cell, an oligodendrocyte, an astrocyte, a dopaminergic cell, an exosome cell, such as ESCs or NSCs, or an exosome cell derived from a ESC or NSC, an immune cell, such as a T cell, a NK cell, a macrophage, a dendritic cell, or a hepatocyte, a stellate cell, a fibroblast, a keratinocyte or a hair cell, an inner ear cell, an intestinal cell or organoid cell, a nephroid cell or another kidney-related cell, a cortical neural progenitor cell, a cardiomyocyte, a retinal cell, a retinal pigment epithelium cell, a mesenchymal stem cell. A cell according to any of previous embodiments, wherein the cell further comprises increased expression of at least one of CD47, HLA-G, HLA-E, HLA-F, PD-L1, CD55 proteins. A cell according to anyone of previous embodiments wherein said cell is B2M-/-. A cell according to anyone of previous embodiments wherein said cell is CIITA-/-. A cell according to anyone of previous embodiments wherein said cell comprises a B2M-HLA-E and/or B2M-HLA-G encoding nucleic sequence and/or a B2M-HLA-E and/or B2M-HLA-G protein on its cell surface. A cell according to anyone of previous embodiments wherein said cell comprises a PD-L1 encoding nucleic sequence and/or a PD-L1 protein on its cell surface. A cell according to anyone of previous embodiments wherein said cell comprises a CD55 encoding nucleic sequence and/or a CD55 protein on its cell surface. A cell according to anyone of previous embodiments wherein said cell comprises a PD-L1 and CD55 encoding nucleic sequence and/or a PD-L1 and CD55 protein on its cell surface. 28. A cell according to anyone of previous embodiments wherein said cell is B2M-/-, CIITA-/- and further comprises a B2M-HLA-E and/or B2M-HLA-G encoding nucleic sequence and/or a B2M-HLA-E and/or B2M-HLA-G protein on its cell surface.
29. A cell according to anyone of previous embodiments wherein said cell is B2M-/-, CIITA-/- and further comprises a PD-L1 and/or CD55 encoding nucleic sequence and/or a PD-L1 and/or CD55 protein on its cell surface.
30. A composition comprising cells according to any one of previous embodiments in a pharmaceutically acceptable medium.
31. A cell according to any one of previous embodiments 1 to 30 or a composition according to embodiment 30 for use in cell therapy.
32. A cell according to embodiment 31 or a composition according to embodiment 31 wherein in cell therapy is cell replacement therapy.
33. A cell according to embodiment 32 or a composition according to embodiment 32 wherein said cell replacement therapy is by allotransplantation of said cell, not by xenotransplantation.
34. A cell according to any one of embodiments 1 to 29 and 31 to 33 or a composition according to anyone of embodiment 30 to 33, wherein said cell is not for use in adoptive cell therapy
35. A cell according to any one of embodiments 1 to 29 and 31 to 34 or a composition according to embodiment 30 to 34 for use in the treatment, the cure, or the prevention of a chronic disease or of an acute disease.
Examples
Example 1 : Surface staining of human cells using antibodies for NK cell ligands
The below described treatment is applied to embryonic stem cells, to pancreatic endoderm cells (PE07), to beta cells (BC09) and to pancreatic islets cells (Islets). The islet cells used in the staining are derived from a human donor and not from differentiated cells in vitro.
Cells surface staining method:
Adherent ES cells are first washed using RT PBS, followed by addition of TrypLE (just enough to cover bottom surface of culture vessel) and incubation for 5-10 min at 37°C. When cells are starting to detach, cells are re-suspended in either complete media or PBS, 1% BSA, and transferred to ice until further processing. Harvested ES cells were filtered (40|JM), washed in cold PBS (4°C, 300g), and resuspended in cold PBS at 1 million cells per mL. Dead cells were stained by addition of 1 pL of reconstituted reactive dye (LIVE/DEAD fixable Near-IR Dead Cell Stain Kit, Invitrogen), followed by mixing of the cell suspension and incubation on ice for 30 minutes. Cells are washed in cold PBS, 1% BSA, and resuspended in 4 mL of cold PBS, 1% BSA (250K cells/mL).
Per staining I tube, 1 mL of cell suspension are aliquoted, pelleted by centrifugation, and resuspended in 40 pL of cold PBS, 1% BSA. To each tube, 5 pL of FcR blocking reagent (TruStain FcX Fc Blocker, BioLegend) are added, followed by mixing of the cell suspension and incubation on ice for 5 minutes. Without washing, antibody cocktails (antibodies to ligands of interest, each linked to a different fluorochrome, such as PE, APC) are directly added at 2x concentration in 50 pL PBS, 1% BSA (1x concentration in 100 pL, final) to the cell suspension with FcR blocking reagent, followed by mixing of the cell suspension and incubation for additional 30 minutes on ice. Finally, cells are washed twice using 1 mL PBS, 1% BSA, and resuspended in 400 pL of PBS, 1% BSA for flow cytometric acquisition.
Flow cytometric analysis results are reported in Fig.1 , Fig.2 and Fig.3.
As far as Fig.3 is concerned, beta cell clusters were made into single cell suspension by incubation in Versene (Versene is an EDTA solution for use as a gentle non- enzymatic cell dissociation reagent. Gibco™ Versene Solution (0.48 mM) is formulated as 0.2 g EDTA(Na4) per liter of Phosphate Buffered Saline (PBS)) for 30 minutes at 37 degrees Celsius. Cells were then resuspended and filtered. Cells were washed once in PBS + 2% FBS followed by FcR blocking (1 :100) for 10 minutes on ice. Cells were then stained with antibodies (1 :50) for 15 minutes on ice followed by 2 times washing in PBS +2% FBS.
While certain features of the invention have been illustrated and described herein, many modifications, substitutions, changes, and equivalents will now occur to those of ordinary skill in the art. It is, therefore, to be understood that the appended claims are intended to cover all such modifications and changes as fall within the true spirit of the invention.

Claims

1. A cell comprising on its cell surface no fully functional form of at least one protein selected from the list consisting of CD155, CD112, B7-H3, ULBP-2, ULBP-3, ULBP-4, ULBP-5, ULBP- 6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL- R2.
2. A cell according to claim 1 cell comprising no gene encoding a fully functional form of at least one of CD155, CD112, B7-H3, ULBP-2, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2 proteins.
3. A cell according to claim 1 or 2 comprising the knock-out of at least one endogenous gene selected from ULBP-2, CD112, CD155, B7-H3, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2 endogenous gene(s).
4. A cell according to any one of previous claims, wherein said cell is a human cell
5. A cell according to anyone of previous claims, wherein said cell is not an immune cell.
6. A cell according to any one of previous claims, with the proviso that if said cell is B2M-/- and CD155-/-, or is B2M-/- and B7-H3-/- or is B2M-/-, CD155-/- and B7-H3-/- , and said cell is a stem cell, a pancreatic progenitor cell, an endocrine progenitor cell, an insulin producing cell or a p cell , said cell further comprises no fully functional form of at least one protein selected from ULBP-2, CD112, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2.
7. A cell according to any of previous claims, wherein said cell is a beta cell or an endocrine progenitor cell or a pancreatic endoderm cell and comprises no fully functional form of at least one protein selected from CD112, ULBP-2, ULBP-3, ULBP-4, ULBP-5, ULBP-6, B7-H6, B7-H7, MICA, MICB, CD48, CD58, CD70, CD1d, CD318, TRAIL-R1 and TRAIL-R2.
8. A cell according to any of previous claims, wherein said cell is B2M-/-, is CIITA-/- and/or comprises a gene encoding a B2M-HLA fusion protein.
9. A cell according to any of previous claims, wherein the cell is a stem cell, such as an embryonic stem cell, a pluripotent stem cell or an induced pluripotent stem cell (iPSC).
10. A cell according to any of claims 1 to 8, wherein said cell is derived from a stem cell or is a mammalian cell obtained from a donor or derived from a cell obtained from a donor.
11. A cell according to any of claims 1 to 8 and 10, wherein the cell is a beta cell, an INS+ and NKX6.1+ double positive cell or a C-peptide+/NKX6.1+ double positive cell, an insulin producing cell, an in vitro derived beta-like cell, a pancreatic endocrine cell or an endocrine cell, an endocrine progenitor cell or a NGN3+/NKX2.2+ double positive cell, a neural cell, such as a neuron, an interneuron cell, an oligodendrocyte, an astrocyte, a dopaminergic cell, an exosome cell, such as ESCs or NSCs, or an exosome cell derived from a ESC or NSC, an immune cell, such as a T cell, a NK cell, a macrophage, a dendritic cell, a hepatocyte, a stellate cell, a fibroblast, a keratinocyte or a hair cell, an inner ear cell, an intestinal cell or organoid cell, a nephroid cell or another kidney-related cell, a cortical neural progenitor cell, a cardiomyocyte, a retinal cell, a retinal pigment epithelium cell, a mesenchymal stem cell.
12. A cell according to any of previous claims, wherein the cell further comprises increased expression of at least one of CD47, HLA-G, HLA-E, HLA-F, PD-L1 , CD55 proteins.
13. A composition comprising cells according to any one of claims 1 to 8 and 10 to 12 in a pharmaceutically acceptable medium.
14. A cell according to any one of claims 1 to 12 or a composition according to claim 13 for use in the treatment, the cure, or the prevention of a chronic disease or of an acute disease.
15. A cell according to any one of claims 1 to 12 or a composition according to claim 13 for use in cell replacement therapy, wherein said cell replacement therapy is by allotransplantation of said cell, not by xenotransplantation.
EP23838001.8A 2022-12-22 2023-12-21 Nk cell activating receptor ligand knockouts for use in cell therapy Pending EP4638709A2 (en)

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