WO2024055077A1 - Enrichissement de cellules immunitaires modifiées - Google Patents

Enrichissement de cellules immunitaires modifiées Download PDF

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WO2024055077A1
WO2024055077A1 PCT/AU2023/050890 AU2023050890W WO2024055077A1 WO 2024055077 A1 WO2024055077 A1 WO 2024055077A1 AU 2023050890 W AU2023050890 W AU 2023050890W WO 2024055077 A1 WO2024055077 A1 WO 2024055077A1
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receptor
cells
population
polypeptide
dysfunctional
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PCT/AU2023/050890
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English (en)
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Patrick Schlegel
Coralie WERBROUCK
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Biosceptre (Aust) Pty Ltd
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Priority claimed from AU2022902655A external-priority patent/AU2022902655A0/en
Application filed by Biosceptre (Aust) Pty Ltd filed Critical Biosceptre (Aust) Pty Ltd
Publication of WO2024055077A1 publication Critical patent/WO2024055077A1/fr

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    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/531—Production of immunochemical test materials
    • G01N33/532—Production of labelled immunochemicals
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/46—Cellular immunotherapy
    • A61K39/461—Cellular immunotherapy characterised by the cell type used
    • A61K39/4611—T-cells, e.g. tumor infiltrating lymphocytes [TIL], lymphokine-activated killer cells [LAK] or regulatory T cells [Treg]
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/46—Cellular immunotherapy
    • A61K39/463—Cellular immunotherapy characterised by recombinant expression
    • A61K39/4631—Chimeric Antigen Receptors [CAR]
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/46—Cellular immunotherapy
    • A61K39/464—Cellular immunotherapy characterised by the antigen targeted or presented
    • A61K39/4643—Vertebrate antigens
    • A61K39/4644—Cancer antigens
    • A61K39/464402—Receptors, cell surface antigens or cell surface determinants
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K19/00—Hybrid peptides, i.e. peptides covalently bound to nucleic acids, or non-covalently bound protein-protein complexes
    • 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
    • C12N5/00—Undifferentiated human, animal or plant cells, e.g. cell lines; Tissues; Cultivation or maintenance thereof; Culture media therefor
    • C12N5/06—Animal cells or tissues; Human cells or tissues
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/5002—Partitioning blood components
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/531—Production of immunochemical test materials
    • G01N33/532—Production of labelled immunochemicals
    • G01N33/533—Production of labelled immunochemicals with fluorescent label
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/543—Immunoassay; Biospecific binding assay; Materials therefor with an insoluble carrier for immobilising immunochemicals
    • G01N33/54313—Immunoassay; Biospecific binding assay; Materials therefor with an insoluble carrier for immobilising immunochemicals the carrier being characterised by its particulate form
    • G01N33/54326—Magnetic particles
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/30—Non-immunoglobulin-derived peptide or protein having an immunoglobulin constant or Fc region, or a fragment thereof, attached thereto

Definitions

  • the present invention relates to methods for enriching a population of immune cells, and compositions and molecules for performing same.
  • Related applications [0002] This application claims priority from Australian provisional applications AU 2022902655 and AU 2023901949, the entire contents of which are hereby incorporated by reference.
  • Background of the invention [0003] Cell therapy to treat cancer and other disease states is a rapidly growing field. The development of immune effector cells such as T cells expressing chimeric antigen receptors (CARs) has revolutionised adoptive cell therapies.
  • CARs chimeric antigen receptors
  • a key issue with CAR-engineered T cell therapies is the low transduction efficiency of T cells with CAR-expressing constructs.
  • peripheral blood T cells that are often the target of CAR gene therapy typically have transduction efficiencies less than 50%, often 10-20%.
  • production of sufficient cell numbers for therapy requires an increase in the scale of patient cell collection as well as more extensive ex vivo T-cell selection and expansion. This contributes to CAR T cell therapies high manufacturing costs.
  • a fusion protein comprising: (i) a dysfunctional P2X 7 receptor epitope moiety; and (ii) an Fc region of an antibody.
  • the dysfunctional P2X 7 receptor epitope moiety may comprise a peptide that comprises any amino acid sequence which is derived from the dysfunctional P2X 7 receptor although preferably, comprises the sequence of an epitope which is found on dysfunctional P2X 7 receptor but not on functional P2X 7 receptor.
  • the amino acid sequence of the dysfunctional P2X 7 receptor epitope moiety comprises or consists at least of the amino acid sequence as set 1004874325 3 forth in SEQ ID NO: 14.
  • the moiety comprises at least the sequence as set forth in SEQ ID NO: 7 or 9.
  • the dysfunctional P2X 7 receptor epitope moiety comprises an amino acid sequence as set forth in any of SEQ ID NOs: 7 to 69 or 122 or sequences at least 80%, at least 81%, at least 82%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% identical thereto, provided that the sequences comprise at least the sequence set forth in SEQ ID NO: 14 or 7 or 9.
  • the present invention provides a fusion protein comprising: (i) a peptide; and (ii) an Fc region of an antibody, wherein the peptide comprises or consists of the amino acid sequence of SEQ ID NO: 7 (preferably the amino acid sequence of SEQ ID NO: 14).
  • the peptide comprises or consists of the amino acid sequence of any of SEQ ID NOs: 7 to 69 or 122 or sequences at least 80%, at least 81%, at least 82%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% identical thereto, provided that the sequences comprise at least the sequence set forth in SEQ ID NO: 14 or 7 or 9.
  • the Fc region of an antibody is an Fc region of an IgG, IgA, IgD, IgE, or IgM.
  • the Fc region is from an IgG antibody, such as an IgG1, an IgG2, an IgG2b, an IgG3 or an IgG4 antibody.
  • the Fc region of the fusion protein comprises two heavy chain fragments, more preferably the CH2 and CH3 domains of said heavy chain.
  • the Fc region of the fusion protein comprises one or more amino acid substitutions compared to naturally occurring Fc sequences, which prevent or reduce the ability of the Fc region to homodimerise.
  • the amino acid substitutions comprise one or more substitutions of the cysteine residues so as to prevent the formation of disulphide bonds between Fc molecules.
  • the cysteine residues of the Fc 1004874325 4 region may be substituted to any other amino acid residue, optionally to glycine, serine, alanine, lysine and glutamic acid, preferably glycine or serine.
  • the cysteine residues for substitution are preferably one or more of the cysteine residues located in the region of the Fc region which corresponds to the hinge region of an immunoglobulin. Examples of the IgG1 hinge regions, and variations thereof including cysteine to serine substitutions are provided herein in Table 3.
  • the hinge region of an immunoglobulin comprises three cysteine residues (which are number C220, C226 and C229 according to EU numbering. Accordingly, in any embodiment, at least one, at least two, or all three of the cysteine residues in the immunoglobulin hinge region are substituted. Preferably, at least two or all three of the cysteine residues are substituted. More preferably, all cysteine residues in the Fc region, such as the hinge region, are substituted. In particularly preferred embodiments, at least one of C226 and C229 are substituted, preferably wherein both C226 and C229 are substituted.
  • the fusion protein comprises a hinge region for linking the a peptide as described herein (eg a dysfunctional P2X 7 receptor epitope moiety) and Fc region of an antibody, wherein the hinge region comprises an amino acid sequence that corresponds to any of the sequences set forth in SEQ ID NOs: 76 to 113, or 136 to 137 or 141 or 142.
  • the Fc region preferably comprises one or more amino acid substitutions for reducing affinity for the Fc receptor (FcR, including any of Fc ⁇ RI, Fc ⁇ RII and Fc ⁇ RIII) and thereby reducing the ability of the fusion protein to elicit antibody- dependent cell-mediated toxicity (ADCC).
  • the Fc region may also comprise substitutions which abrogate recruitment of complement C1q. Such mutations are also well known in the art and are further described herein. Further still, the Fc region may comprise substitutions to reduce serum half-life (through attenuating or reducing capacity to bind to the FcRN receptor). Relevant amino acid substitutions for altering effector function, serum half-life and aggregation are well known to the skilled person and further described herein, including as exemplified in Table 1.
  • the present invention also provides a heterodimeric asymmetric molecule comprising a fusion protein as described herein (preferably comprising a peptide of SEQ 1004874325 5 ID NO: 7 or 14, or variations thereof as exemplified in any of SEQ ID NOs: 2 to 69) and an Fc region of an antibody, and further comprising an Fc region of an antibody that does not comprise the peptide.
  • asymmetric heterodimeric molecules may be obtained using the knob-in-hole technology, as further described herein, for facilitating dimerisation of non-identical Fc regions.
  • the present invention provides a heterodimeric asymmetric molecule or monomeric fusion protein for use in accordance with any of the methods further described herein, and which have application in methods for enriching immune cells which comprise exogenous cell surface receptors for binding to tumour specific or tumour associated antigens, and comprising an intracellular signalling domain (eg chimeric antigen receptors, including expressed on T cells).
  • exogenous cell surface receptors for binding to tumour specific or tumour associated antigens
  • an intracellular signalling domain eg chimeric antigen receptors, including expressed on T cells.
  • a monomeric fusion protein comprising i) an amino acid sequence that is recognised or capable of being bound by an antigen recognition domain of an exogenous cell surface receptor comprising an intracellular signalling domain (such as a chimeric antigen receptor), and ii) an Fc region of an antibody.
  • an antigen recognition domain of an exogenous cell surface receptor comprising an intracellular signalling domain (such as a chimeric antigen receptor)
  • an Fc region of an antibody ii) an antibody.
  • the amino acid sequence of the Fc region of the antibody is unable to form a homodimer with another Fc region of an antibody.
  • a heterodimeric asymmetric molecule comprising i) an amino acid sequence that is recognised or capable of being bound by an antigen recognition domain of an exogenous cell surface receptor comprising an intracellular signalling domain (eg chimeric antigen receptors, including expressed on T cells), wherein the amino acid sequence is joined to a first Fc region of an antibody; ii) a second Fc region of an antibody capable of forming a heterodimer with the first Fc region.
  • the fusion protein has an affinity for FcR that is less than about 250 nM, preferably less than 500 nM, less than 1000 nM, most preferably less than 2000 nM.
  • the fusion protein may comprise the amino acid sequence of a fusion protein as set forth in any of SEQ ID NOs: 145 to 158, 160 and 161.
  • the fusion protein or the heterodimeric asymmetric molecule consists or consists essentially of the peptide and an Fc region of an antibody, such that the fusion protein or heterodimeric asymmetric molecule does not comprise an antigen binding domain of an antibody (ie such that the fusion protein does not comprise a VH, VL, Fab, Fv, or an scFv derived from an antibody).
  • the fusion protein of the invention may comprise one or more modifications for enabling the capture of the fusion protein, including when the protein is bound to immune cells expressing a receptor comprising an antigen binding domain for binding dysfunctional P2X 7 receptor (such as a chimeric antigen receptor (CAR) or modified TCR).
  • a receptor comprising an antigen binding domain for binding dysfunctional P2X 7 receptor (such as a chimeric antigen receptor (CAR) or modified TCR).
  • CAR chimeric antigen receptor
  • TCR modified TCR
  • the one or more modifications to the fusion protein may be selected from: a biotin moiety, fluorescein (FITC), a peptide tag (such as His, Myc, Flag and related tags) and a magnetic label.
  • FITC fluorescein
  • a peptide tag such as His, Myc, Flag and related tags
  • a magnetic label Preferably the modification is a biotin moiety or a magnetic moiety.
  • the magnetic moiety can be any commercially available magnetic moiety for use in separation or capture of proteins or cells.
  • the magnetic moiety may comprise iron oxide microbeads (up to 50 nm diameter) or macrobeads (1-5 ⁇ m diameter).
  • the magnetic moiety comprises microbeads.
  • the moieties may be conjugated to the fusion protein using any method known to the skilled person.
  • the moieties are conjugated to the fusion protein via one or more lysine residues of the protein and/or at the amino-termini of the protein.
  • nucleic acid sequence encoding the tags can be included in the nucleic acid construct encoding the fusion protein, such that when expressed, the fusion protein is expressed with the tag already linked to the protein.
  • the tag will be located at either the N or C terminus of the fusion protein.
  • the tag will be located on the fusion protein so as not to interfere with the binding of the peptide (eg dysfunctional P2X 7 receptor epitope moiety) by a receptor on an immune cell, comprising an antigen binding domain for binding to the peptide.
  • the present invention also provides a method for obtaining a population of immune cells, which are enriched for cells which express an exogenous cell surface receptor that comprises an antigen binding domain and intracellular signalling domain.
  • the receptor expressed by the immune cells is a chimeric antigen receptor (CAR), or optionally, a modified T cell receptor (TCR).
  • the exogenous cell surface receptor comprises an antigen binding domain for binding to a tumour associated or tumour specific antigen on a cancer cell although it will be appreciated that the exogenous cell surface receptor may be a receptor for use in a “universal CAR” system.
  • a method for obtaining a population of immune cells or for enriching for a population of cells expressing a receptor that comprises an antigen binding domain for binding to a tumour associated or tumour specific antigen on a cancer cell comprising: (i) providing a population of immune cells, preferably immune effector cells, wherein the cells have been subjected to transduction with a nucleic acid encoding a receptor comprising an antigen binding domain for binding to a tumour associated or tumour specific antigen on a cancer cell; (ii) contacting the population of cells with a polypeptide, wherein the polypeptide comprises an epitope which is recognised by the antigen binding domain of the receptor, and wherein the polypeptide comprises a moiety for enabling capture of the polypeptide; to thereby form a complex of the polypeptide and the cells; (iii) isolating the complex from the population of cells, 1004874325 8 thereby obtaining a population of immune cells
  • a method for obtaining a population of immune cells or for enriching for a population of cells expressing a receptor that comprises an antigen binding domain for binding to a tumour associated or tumour specific antigen on a cancer cell comprising: (i) providing a mixed population of immune cells, preferably immune effector cells, wherein a subpopulation of the cells express receptor comprising an antigen binding domain for binding to a tumour associated or tumour specific antigen on a cancer cell; (ii) contacting the mixed population of cells with a polypeptide, wherein the polypeptide comprises an epitope which is recognised by the antigen binding domain of the receptor, and wherein the polypeptide comprises a moiety for enabling capture of the polypeptide; to thereby form a complex of the polypeptide and cells; (iii) isolating the complex from the population of cells, thereby obtaining a population of immune cells expressing a receptor having an antigen binding domain for binding to a tumour associated or tumour specific antigen on a cancer
  • the cells are immune cells which express a chimeric antigen receptor (CAR) for binding to a tumour associated or tumour specific antigen on a cancer cell.
  • a method for obtaining a population of immune cells expressing a chimeric antigen receptor (CAR) for binding to a tumour associated or tumour specific antigen on a cancer cell comprising: (i) providing a population of immune cells, preferably immune effector cells, wherein the population comprises cells which have been transduced with a nucleic acid encoding a chimeric antigen receptor (CAR) for binding to a tumour associated or tumour specific antigen on a cancer cell; or wherein the cells 1004874325 9 express a chimeric antigen receptor (CAR) for binding to a tumour associated or tumour specific antigen on a cancer cell; (ii) contacting the population of cells with a polypeptide, wherein the polypeptide comprises an epitope which is recognised by the CAR, and wherein the polypeptid
  • a method for enriching a population of immune cells expressing a chimeric antigen receptor comprising an antigen binding domain for binding to a tumour associated or tumour specific antigen on a cancer cell comprising: (i) providing a population of immune cells, preferably immune effector cells, wherein the cells have been subjected to transduction with a nucleic acid encoding a chimeric antigen receptor (CAR) for binding to a tumour associated or tumour specific antigen on a cancer cell; (ii) contacting the population of cells with a polypeptide, wherein the polypeptide comprises an epitope which is recognised by the CAR, and wherein the polypeptide comprises a moiety for enabling capture of the polypeptide, to thereby form a complex of the polypeptide and the cells; (iii) isolating the complex of cells from the mixed population, thereby enriching a population of immune cells expressing a chimeric antigen receptor (CAR) for
  • tumour associated or tumour specific antigens which are typically targeted by cellular immunotherapeutics such as CARs, include, but are not limited to: dysfunctional (nf)P2X 7 receptor, mesothelin, EGFR, GPC3, MUC1, HER2, GD2, CEA, 1004874325 10 EpCAM, LeY, PCSA, CD19, CD20, Clec9a, CD276, PD-L1 and PD-L2.
  • CARs include, but are not limited to: dysfunctional (nf)P2X 7 receptor, mesothelin, EGFR, GPC3, MUC1, HER2, GD2, CEA, 1004874325 10 EpCAM, LeY, PCSA, CD19, CD20, Clec9a, CD276, PD-L1 and PD-L2.
  • Other examples of target antigens are further described herein.
  • a polypeptide or nucleic acid encoding the polypeptide as the case may be
  • a CAR or other receptor for binding to a tumour antigen
  • the skilled person will be able to design a fusion protein (preferably a monomeric Fc fusion protein or asymmetric heterodimeric Fc fusion protein as described herein), for binding to the CAR, and for use in the methods.
  • the polypeptide will comprise a similar epitope of the CD19 molecule that is recognised by the receptor, fused to an Fc region of an antibody, and preferably having an Fc region as defined herein in any of SEQ ID NOs: 159 or 162, or an Fc region which is not capable of forming a homodimer.
  • the present invention also provides a use of a fusion protein according to the first aspect, or polypeptide as further described herein, for obtaining a population of immune cells, which are enriched for cells which express a receptor that comprises an antigen binding domain for binding to dysfunctional P2X 7 receptor.
  • the receptor expressed by the immune cells is a chimeric antigen receptor (CAR), or optionally, a modified T cell receptor (TCR).
  • CAR chimeric antigen receptor
  • TCR modified T cell receptor
  • a method for obtaining a population of immune cells or for enriching for a population of cells expressing a receptor that comprises an antigen binding domain for binding to dysfunctional P2X7 receptor comprising: (i) providing a population of immune cells, preferably immune effector cells, wherein the cells have been subjected to transduction with a nucleic acid encoding a receptor comprising an antigen binding domain for binding to dysfunctional P2X 7 receptor; (ii) contacting the population of cells with a polypeptide, wherein the polypeptide comprises an epitope of dysfunctional P2X7 receptor which is recognised by the antigen binding domain of the receptor, and wherein the polypeptide comprises a moiety for enabling capture of the polypeptide; 1004874325 11 to thereby form a complex of the polypeptide
  • a method for obtaining a population of immune cells or for enriching for a population of cells expressing a receptor that comprises an antigen binding domain for binding to dysfunctional P2X7 receptor comprising: (i) providing a mixed population of immune cells, preferably immune effector cells, wherein a subpopulation of the cells express receptor comprising an antigen binding domain for binding to dysfunctional P2X 7 receptor; (ii) contacting the mixed population of cells with a polypeptide, wherein the polypeptide comprises an epitope of dysfunctional P2X7 receptor which is recognised by the antigen binding domain of the receptor, and wherein the polypeptide comprises a moiety for enabling capture of the polypeptide; to thereby form a complex of the polypeptide and cells; (iii) isolating the complex from the population of cells, thereby obtaining a population of immune cells expressing a receptor having an antigen binding domain for binding to dysfunctional P2X 7 receptor.
  • the cells are immune cells which express a chimeric antigen receptor (CAR) for binding to a linear epitope of a P2X7 receptor (such as an epitope of dysfunctional P2X7 receptor) wherein the epitope comprises or consists of the amino acid sequence of SEQ ID NO: 7 (preferably the amino acid sequence of SEQ ID NO: 14), or comprises or consists of the amino acid sequence of any of SEQ ID NOs: 7 to 69 or 122 or sequences at least 80%, at least 81%, at least 82%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% identical thereto, provided that the sequences comprise at least the sequence set forth in SEQ ID NO: 14 or 7 or 9.
  • CAR chimeric antigen receptor
  • a method for obtaining a population of immune cells expressing a chimeric antigen receptor (CAR) for binding to a linear epitope of a P2X7 receptor comprising: (i) providing a population of immune cells, preferably immune effector cells, wherein the population comprises cells which have been transduced with a nucleic acid encoding a chimeric antigen receptor (CAR) for binding to linear epitope of a P2X7 receptor (such as an epitope of dysfunctional P2X 7 receptor); or wherein the cells express a chimeric antigen receptor (CAR) for binding to linear epitope of a P2X7 receptor (such as an epitope of dysfunctional P2X 7 receptor); (ii) contacting the population of cells with a polypeptide, wherein the polypeptide comprises an epitope of linear epitope of a P2X7 receptor (
  • a method for enriching a population of immune cells expressing a chimeric antigen receptor comprising an antigen binding domain for binding to dysfunctional P2X 7 receptor comprising: (i) providing a population of immune cells, preferably immune effector cells, wherein the cells have been subjected to transduction with a nucleic acid encoding a chimeric antigen receptor (CAR) for binding to dysfunctional P2X 7 receptor; (ii) contacting the population of cells with a polypeptide, wherein the polypeptide comprises an epitope of dysfunctional P2X7 receptor which is recognised by the 1004874325 13 CAR, and wherein the polypeptide comprises a moiety for enabling capture of the polypeptide, to thereby form a complex of the polypeptide and the cells; (iii) isolating the complex of cells expressing a chimeric antigen receptor (CAR) for binding to dysfunctional P2X 7 receptor bound to fusion protein,
  • CAR chimeric antigen receptor
  • the present invention also finds application in the methods for enriching for a population of immune cells for use in a universal CAR system. Accordingly, in a further embodiment of the second aspect, there is provided a method for obtaining a population of immune cells or for enriching for a population of cells expressing an exogenous cell surface receptor that comprises an antigen binding domain for binding to a peptide, wherein the peptide comprises or consists of the amino acid sequence of SEQ ID NO: 7 or 14 (or optionally the amino acid sequence of any of SEQ ID NOs: 2 to 69 and 122); the method comprising: (i) providing a population of immune cells, preferably immune effector cells, wherein the cells have been subjected to transduction with a nucleic acid encoding a receptor comprising an antigen binding domain for binding to the peptide; (ii) contacting the population of cells with a polypeptide, wherein the polypeptide comprises the peptide that is recognised by the antigen binding domain of the receptor, and a moiety for
  • a method for obtaining a population of immune cells or for enriching for a population of cells expressing an exogenous cell surface receptor that comprises an antigen binding domain for binding to a peptide wherein the peptide comprises or consists of the amino acid sequence of SEQ ID NO: 7 or 14 (or optionally the amino acid sequence of any of SEQ ID NOs: 2 to 69 and 122); the method comprising: (i) providing a mixed population of immune cells, preferably immune effector cells, wherein a subpopulation of the cells express receptor comprising an antigen binding domain for binding to the peptide; (ii) contacting the mixed population of cells with a polypeptide, wherein the polypeptide comprises the peptide that is recognised by the antigen binding domain of the receptor, and wherein the polypeptide comprises a moiety for enabling capture of the polypeptide; to thereby form a complex of the polypeptide and cells; (iii) isolating the complex from the population
  • the cells are immune cells which express a chimeric antigen receptor (CAR) for binding to the peptide.
  • CAR chimeric antigen receptor
  • a method for obtaining a population of immune cells expressing a chimeric antigen receptor (CAR) for binding to a peptide comprising or consisting of the amino acid sequence of SEQ ID NO: 7 or 14 (or optionally the amino acid sequence of any of SEQ ID NOs: 2 to 69 and 122) comprising: (i) providing a population of immune cells, preferably immune effector cells, wherein the population comprises cells which have been transduced with a nucleic acid encoding a chimeric antigen receptor (CAR) for binding to a peptide comprising or consisting of the amino acid sequence of SEQ ID NO: 7 or 14 (or optionally the amino acid sequence of any of SEQ ID NOs: 2 to 69 and 122); or wherein the cells express a chimeric antigen receptor (CAR) for binding to a 1004874
  • the polypeptide comprises the amino acid sequence of a fusion protein of any embodiment of the first aspect of the invention (such that the polypeptide comprises a peptide as described herein, such as an epitope of dysfunctional P2X7 receptor, joined to an Fc region of an antibody).
  • the polypeptide comprises a first portion comprising a peptide as described herein, such as an epitope of dysfunctional P2X7 receptor, joined to a further amino acid sequence for facilitating the solubility and stability of the first portion.
  • the further amino acid sequence joined to the peptide may comprise any suitable linker or hinge region, such as those exemplified in Tables 1 and 3.
  • linker or hinge regions may comprise amino acid sequences comprised of glycine and serine repeats (so-called “GS” linker sequences, and variations thereof as further defined herein).
  • the hinge region may also comprise sequences derived from the hinge region of an immunoglobulin, such as those defined in Table 3.
  • the linker sequence may comprise a cleavable sequence.
  • the polypeptide may be in the form of a fusion protein comprising a peptide as described herein (such as an epitope of dysfunctional P2X7 receptor) joined to a further amino acid sequence.
  • the further sequence may comprise a serum albumin, transferrin, a carboxy-terminal peptide of chorionic gonadotropin (CG) ⁇ chain, a non-exact repeat peptide sequence, a polypeptide sequence composed of proline-alanine-serine polymer, an elastin-like peptide (ELP) repeat sequence), a homopolymer of glycine residues or a gelatin-like protein.
  • CG chorionic gonadotropin
  • ELP elastin-like peptide
  • the polypeptide may comprise a linker or hinge region, such as described above, for joining the epitope of dysfunctional P2X 7 receptor to the further amino acid sequence.
  • the polypeptide may be in the form of a conjugate comprising a carbohydrate, a lipid, a liposome, a peptide, and an aptamer conjugated to the amino acid sequence comprising the peptide (eg epitope of dysfunctional P2X7 receptor).
  • the fusion protein or polypeptide may comprise of the amino acid sequence as set forth in any one of SEQ ID NOs: 145 to 158 or 160 and 161, or a sequence at least 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical thereto.
  • the moiety for enabling capture of the polypeptide may be any suitable moiety that can be bound by a capture agent or system, such as a biotin label, fluorescein (FITC), a peptide tag (such as His, Myc, Flag and related tags) or a magnetic label.
  • a capture agent or system such as a biotin label, fluorescein (FITC), a peptide tag (such as His, Myc, Flag and related tags) or a magnetic label.
  • FITC fluorescein
  • a peptide tag such as His, Myc, Flag and related tags
  • the modification is a biotin moiety or a magnetic moiety.
  • the magnetic moiety can be any commercially available magnetic moiety for use in separation or capture of proteins or cells.
  • the magnetic moiety may be magnetic micro- or macro- beads.
  • the moieties may be conjugated to the polypeptide using any method known to the skilled person.
  • the moieties are conjugated to the polypeptide via one or more lysine residues of the protein and/or at the amino-termini of the polypeptide.
  • nucleic acid sequence encoding the tags can be included in the nucleic acid construct encoding the polypeptide, such that when expressed, the polypeptide is expressed with the tag already linked to the protein.
  • the tag will be located at either the N or C terminus of the polypeptide.
  • the tag will be located on the polypeptide so as not to interfere with the binding of the dysfunctional P2X 7 receptor epitope moiety by a receptor on an immune cell, comprising an antigen binding domain for binding to the epitope moiety.
  • the method may further comprise the step of contacting the cells (after step ii), with an anti-biotin antigen binding protein, preferably wherein the anti-biotin antigen binding protein comprises one or more moieties for enabling capture of the complex.
  • the one 1004874325 18 or more moieties for enabling capture of the complex comprises iron oxide particles (micro- or macrobeads).
  • the step of isolating may comprise i) applying a magnetic field to the population of cells; ii) removing or discarding the cells that are not attracted to the magnetic field, iii) removal of the magnetic field to thereby provide a population of immune cells expressing a chimeric antigen receptor (CAR) for binding to dysfunctional P2X7 receptor.
  • the method may further comprise the steps of expanding the isolated immune cells.
  • the method may further comprise a step of treating the complex so as to release the cells from being bound by the polypeptide.
  • the fusion protein or polypeptide may comprise a cleavable linker joining the epitope bound by the receptor (eg an epitope of dysfunctional P2X7 receptor) and Fc region and/or further sequence for enabling capture of the fusion protein or polypeptide.
  • Cleavable linkers are well known in the art and are further described herein.
  • the method may further comprise subjecting the polypeptide to treatment with a protease or other agent for cleaving the cleavable linker and thereby releasing the Fc region or further amino acid sequence therefrom.
  • the method further comprises the step of administering the isolated or enriched cells to a subject requiring treatment with the immune cells, such as cancer.
  • the complex of immune cells/polypeptide may be administered directly to the subject.
  • the population of immune cells is a population of effector immune cells, such as T cells, NK cells or NKT cells.
  • the 1004874325 19 T cells are derived from stem cells, optionally wherein the stem cells are induced pluripotent stem cells (iPSCs) or embryonic stem cells.
  • the population of immune cells are derived from a subject requiring treatment for cancer.
  • the immune cells may be obtained from an allogeneic donor who does not require treatment.
  • the exogenous cell surface receptor that comprises an antigen binding domain eg the chimeric antigen receptor.
  • the CAR comprises an antigen binding domain that comprises the CDR amino acid sequences of PEP2-2-1 described in PCT/AU2010/001070 (WO2011020155, or in any one of the corresponding US patents US 9,127,059, US 9,688,771, or US 10,053,508). More preferably, the antigen binding domain of the receptor (eg CAR) comprises or consists of the amino acid sequence of the PEP2-2-1 antigen binding protein as described in PCT/AU2010/001070 (WO2011020155 or in any one of the corresponding US patents US 9,127,059, US 9,688,771, or US 10,053,508), incorporated herein by reference.
  • the present invention also provides a composition
  • a composition comprising a population of immune cells expressing a chimeric antigen receptor (CAR) for binding to dysfunctional P2X7 receptor, wherein the population of cells is obtained by a method described herein.
  • the composition comprises greater than 30%, 40%, 50%, 60%, 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98 or 99% of cells that express a chimeric antigen receptor (CAR) for binding to tumour associated or tumour specific antigen (such as dysfunctional P2X7 receptor).
  • kits for use in a method described herein comprising: - a fusion protein capable of being bound by a CAR for binding to tumour associated or tumour specific antigen (such as dysfunctional P2X 7 receptor); - optionally, one or more reagents for enabling isolation of the fusion protein and complexes thereof.
  • the kit comprises written instructions for use in a method of the second aspect of the invention. 1004874325 20
  • the term "comprise” and variations of the term, such as “comprising”, “comprises” and “comprised” are not intended to exclude further additives, components, integers or steps.
  • Table 1 exemplary sequences of dysfunctional P2X 7 receptor and receptor epitope moieties Peptide/protein Sequence SEQ ID name NO: Full length P2X 7 MPACCSCSDVFQYETNKVTRIQSMNYGTIKWFFHVIIFSYVCFAL 1 receptor VSDKLYQRKEPVISSVHTKVKGIAEVKEEIVENGVKKLVHSVFDT E200 and E300 ADYTFPLQGNSFFVMTNFLKTEGQEQRLCPEYPTRRTLCSSDR shown in bold GCKKGWMDPQSKGIQTGRCVVYEGNQKTCEVSAWCPIEAVEE APRPALLNSAENFTVLIKNNIDFPGHNYTTRNILPGLNITCTFHKT and underline QNPQCPIFRLGDIFRETGDNFSDVAIQGGIMGIEI
  • A. shows the proportion of transduced cells enriched using a biotinylated protein comprising an amino acid sequence of the E200 epitope.
  • B. shows that the cells 48 hours after enrichment retain high levels of purity and that the cells are not negatively impacted by the enrichment procedure. Grey shading indicates pre-enrichment; red shading indicates post- enrichment.
  • Figure 2 Enrichment of primary donor cells (Donor 12) transduced with nucleic acids encoding a CAR for binding dysfunctional P2X 7 receptor. Grey shading indicates pre-enrichment; red shading indicates post-enrichment.
  • Figure 3 Enrichment of primary donor cells (Donor 12) transduced with nucleic acids encoding an alternative CAR for binding dysfunctional P2X 7 receptor. Grey shading indicates pre-enrichment; red shading indicates post-enrichment. Enrichment was using MACS Column (Miltenyi Bioscience).
  • Figure 4 Enrichment of primary donor cells (Donor 12) transduced with nucleic acids encoding an alternative CAR for binding dysfunctional P2X 7 receptor. Grey shading indicates pre-enrichment; red shading indicates post-enrichment. Enrichment was using Magnet Stand, Stem Cell Technologies.
  • Figure 5 EGFR staining for direct staining of CAR expressing cells following enrichment using either monomeric or dimeric Fc attenuated fusion proteins comprising nfP2X 7 receptor epitope moiety for binding by the CAR.
  • A dimeric fusion protein (SEQ ID NO: 149)
  • B monomeric fusion protein (SEQ ID NO: 145);
  • C monomeric fusion protein (SEQ ID NO:146).
  • Figure 6 Viability and purity of CAR expressing cells using monomeric Fc fusion comprising nfP2X 7 receptor epitope moiety.
  • Figure 8 Transduction efficiency (%) on day 2 post MACS sorting using monomeric or dimeric fusion proteins (having the amino acid sequence of SEQ ID NOs: 145 and 149, respectively).
  • D50, D53 and D71 T cells from donors 50, 53 and 71, respectively.
  • Figure 9 Cell count (normalised to maximum expected cell count) following enrichment using monomeric or dimeric fusion proteins (having the amino acid sequence of SEQ ID NOs: 145 and 149, respectively). Cell counts on days 1 and 2 following enrichment are shown for T cells from healthy donors 50 (D50) and 71 (D71). 1004874325 36
  • Figure 10 Viability of enriched CAR T cells 2 days following MACS sorting.
  • the present invention provides fusion proteins, compositions and kits comprising the same, and uses of the same in methods for enriching for a population of immune cells, preferably cells that express an exogenous cell surface receptor that comprises an antigen binding domain and intracellular signalling domain.
  • the fusion proteins comprise (i) a linear peptide epitope moiety derived from P2X 7 receptor (eg comprising an amino acid sequence derived from SEQ ID NO: 7 or 14) and that is recognised or capable of being bound by an antigen recognition 1004874325 37 domain of a receptor expressed on an immune cell, and (ii) a an Fc region of an antibody and optionally iii) a moiety for enabling capture of the fusion protein.
  • the epitope moiety allows for specific binding of the fusion protein to the target immune cells for enrichment and the Fc region (preferably when comprising a moiety for enabling capture), enables capture of a complex of the fusion protein and the immune cells.
  • the inventors have demonstrated utility of both homodimeric and monomeric proteins derived from the fusion proteins described herein, for use in obtaining a population of immune cells or enriching for a population of immune cells.
  • the Fc fusion proteins are designed so as to comprise only a single copy of the linear epitope derived from the P2X 7 receptor.
  • asymmetric heterodimeric molecule eg comprising a E200 peptide-Fc fusion protein and an Fc region that does not comprise an E200 peptide.
  • Such monomeric or asymmetric heterodimeric molecules have the advantage of reducing activation of the target immune cells and preventing unwanted exhaustion of the target immune cells during the enrichment process c(as further described herein in the examples).
  • X and/or Y will be understood to mean either “X and Y” or “X or Y” and shall be taken to provide explicit support for both meanings or for either meaning.
  • 1004874325 38 The articles “a” and “an” are used herein to refer to one or to more than one (i.e. to at least one) of the grammatical object of the article.
  • a dysfunctional P2X 7 receptor epitope moiety means one dysfunctional P2X 7 receptor epitope moiety or more than one dysfunctional P2X 7 receptor epitope moiety.
  • tumor-associated antigen refers to an antigen that is expressed by cancer cells (the term “tumour-antigen” may also be used to refer to same). Tumour antigens are proteins that are produced by tumour cells that elicit an immune response, particularly T-cell mediated immune responses.
  • Tumour antigens are well known in the art and include, for example, a glioma-associated antigen, carcinoembryonic antigen (CEA), ⁇ -human chorionic gonadotropin, alpha fetoprotein (AFP), lectin-reactive AFP, thyroglobulin RAGE-1, MN-CAIX, human telomerase reverse transcriptase, RU1, RU2 (AS), intestinal carboxyl esterase, mut hsp70-2, M-CSF, hK4 prostase, prostate- specific antigen (PSA), PAP, NY-ESO- 1 , LAGE-1a, p53, P501S prostein, PSMA, Her2/neu, survivin and telomerase, prostate-carcinoma tumour antigen- 1 (PCTA-1), MAGE, ELF2M, neutrophil elastase, ephrinB2, CD22, insulin growth factor (IGF)-I, IGF- II, IGF
  • Malignant tumours express a number of proteins that can serve as target antigens for an immune attack. These molecules include but are not limited to tissue-specific antigens such as MART-1, tyrosinase and GP 100 in melanoma and prostatic acid phosphatase (PAP) and prostate-specific antigen (PSA) in prostate cancer. Other target molecules belong to the group of transformation-related molecules such as the oncogene HER-2/Neu/ErbB-2. Yet another group of target antigens are onco-foetal antigens such as carcinoembryonic antigen (CEA). In B-cell lymphoma the tumour-specific idiotype immunoglobulin constitutes a truly tumour-specific immunoglobulin antigen that is unique to the individual tumour.
  • CEA carcinoembryonic antigen
  • B-cell differentiation antigens such as CD 19, CD20 and CD37 are other candidates for target antigens in B- cell lymphoma. Some of these antigens (CEA, HER-2, CD19, CD20, idiotype) have been used as targets for passive immunotherapy with monoclonal antibodies with limited success.
  • the type of tumour antigen referred to in the invention may also be a tumour- 1004874325 39 specific antigen (TSA).
  • TSA is unique to tumour cells and does not occur on other cells in the body.
  • a tumour-associated antigen (TAA) is not unique to a tumour cell and instead is also expressed on a normal cell under conditions that fail to induce a state of immunologic tolerance to the antigen.
  • TAAs may be antigens that are expressed on normal cells during foetal development when the immune system is immature and unable to respond or they may be antigens that are normally present at extremely low levels on normal cells but which are expressed at much higher levels on tumour cells.
  • Those tumour-associated antigens of greatest clinical interest are differentially expressed compared to the corresponding non-tumour tissue and allow for a preferential recognition of tumour cells by specific T-cells or immunoglobulins.
  • TSA or TAA antigens include the following: Differentiation antigens such as MART-1/MelanA (MART-1), gp 100 (Pmel 17), tyrosinase, TRP-1 , TRP-2 and tumour-specific multilineage antigens such as MAGE-1, MAGE-3, BAGE, GAGE- 1 , GAGE-2, p15; overexpressed embryonic antigens such as CEA; overexpressed oncogenes and mutated tumour-suppressor genes such as p53, Ras, HER-2/neu; unique tumour antigens resulting from chromosomal translocations; such as BCR-ABL, E2A-PRL, H4-RET, 1GH-IGK, MYL-RAR; and viral antigens, such as the Epstein Barr virus antigens EBVA and the human papillomavirus (HPV) antigens E6 and E7.
  • Differentiation antigens such as MART-1/MelanA (M
  • tumour antigens in accordance with the present invention include: CD33 (Siglec-3), CD123 (IL3RA), CD135 (FLT-3), CD44 (HCAM), CD44V6, CD47, CD184 (CXCR4), CLEC12A (CLL1), LeY, FRp, MICA/B, CD305 (LAIR-1), CD366 (TIM-3), CD96 (TACTILE), CD133, CD56, CD29 (ITGB1), CD44 (HCAM), CD47 (IAP), CD66 (CEA), CD112 (Nectin2), CD117 (c-Kit), CD133, CD146 (MCAM), CD155 (PVR), CD171 (LI CAM), CD221 (IGF1), CD227 (MUC1), CD243 (MRD1), CD246 (ALK), CD271 (LNGFR), CD19, CD20, GD2, and especially EGFR, 1004874325 40 mesothelin, GPC3, MUC1, HER2, GD2,
  • P2X 7 receptor generally refers to a receptor that uses a purine (such as ATP) as a ligand.
  • ⁇ 2 ⁇ 7 receptor generally refers to a purinergic receptor formed from three protein subunits or monomers, with at least one of the monomers having an amino acid sequence substantially as shown in SEQ ID NO: 1 in Table 1 herein.
  • P2X 7 receptor is formed from three monomers, it is a “trimer” or “trimeric”.
  • ⁇ 2 ⁇ 7 receptor encompasses naturally occurring variants of ⁇ 2 ⁇ 7 receptor, e.g., wherein the ⁇ 2 ⁇ 7 monomers are splice variants, allelic variants, SNPs and isoforms including naturally-occurring truncated or secreted forms of the monomers forming the ⁇ 2 ⁇ 7 receptor (e.g., a form consisting of the extracellular domain sequence or truncated form of it), naturally-occurring variant forms (e.g., alternatively spliced forms) and naturally-occurring allelic variants.
  • the ⁇ 2 ⁇ 7 monomers are splice variants, allelic variants, SNPs and isoforms including naturally-occurring truncated or secreted forms of the monomers forming the ⁇ 2 ⁇ 7 receptor (e.g., a form consisting of the extracellular domain sequence or truncated form of it), naturally-occurring variant forms (e.g., alternatively spliced
  • the native sequence ⁇ 2 ⁇ 7 monomeric polypeptides disclosed herein are mature or full-length native sequence polypeptides comprising the full-length amino acids sequence shown in SEQ ID NO: 1.
  • the ⁇ 2 ⁇ 7 receptor may have an amino acid sequence that is modified, for example various of the amino acids in the sequence shown in SEQ ID NO: 1 may be substituted, deleted, or a residue may be inserted.
  • “Functional ⁇ 2 ⁇ 7 receptor” generally refers to a form of the ⁇ 2 ⁇ 7 receptor having three intact binding sites or clefts for binding to ATP.
  • the functional receptor When bound to ATP, the functional receptor forms a non-selective sodium/calcium channel that converts to a pore-like structure that enables the ingress of calcium ions and molecules of up to 900 Da into the cytosol, one consequence of which may be induction of programmed cell death.
  • expression of functional ⁇ 2 ⁇ 7 receptors is generally limited to cells that undergo programmed cell death such as thymocytes, dendritic cells, lymphocytes, macrophages and monocytes. There may also be some expression of functional P2X 7 receptors on erythrocytes and other cell types.
  • Dysfunctional ⁇ 2 ⁇ 7 receptor (also called “non-functional” or (nf) P2X 7 ) is a P2X 7 receptor that has an impaired response to ATP such that it is unable to form an apoptotic pore under physiological conditions.
  • a dysfunctional P2X 7 receptor or (nfP2X 7 1004874325 41 receptor) generally refers to a form of a ⁇ 2 ⁇ 7 receptor having a conformation, distinct from functional P2X 7 , whereby the receptor is unable to form an apoptotic pore, but which is still able to operate as a non-selective channel through the maintenance of a single functional ATP binding site located between adjacent monomers.
  • one or more of the monomers has a cis isomerisation at Pro210 (according to SEQ ID NO: 1).
  • the isomerisation may arise from any molecular event that leads to misfolding of the monomer, including for example, mutation of monomer primary sequence or abnormal post translational processing.
  • One consequence of the isomerisation is that the receptor is unable to bind to ATP at one, or more particularly two, ATP binding sites on the trimer and as a consequence not be able to extend the opening of the channel. In the circumstances, the receptor cannot form a pore and this limits the extent to which calcium ions may enter the cytosol.
  • Dysfunctional ⁇ 2 ⁇ 7 receptors are expressed on a wide range of epithelial and haematopoietic cancers.
  • the term “dysfunctional ⁇ 2 ⁇ 7 receptors” may be used interchangeably with the term “non-functional ⁇ 2 ⁇ 7 receptors” or “nf ⁇ 2 ⁇ 7 receptors”.
  • “Cancer associated- ⁇ 2 ⁇ 7 receptors” are generally ⁇ 2 ⁇ 7 receptors that are found on cancer cells (including, pre-neoplastic, neoplastic, malignant, benign or metastatic cells), but not on non-cancer or normal cells.
  • E200 epitope generally refers to an epitope having the sequence GHNYTTRNILPGLNITC (SEQ ID NO: 2). Variants thereof are exemplified in Table 1 and include any of SEQ ID NOs: 3, or 7 to 69 and 122.
  • E300 epitope generally refers to an epitope having the sequence KYYKENNVEKRTLIK (SEQ ID NO: 4) or a variant thereof, as defined in SEQ ID NO: 5.
  • a “composite epitope” generally refers to an epitope that is formed from the juxtaposition of the E200 and E300 epitopes or parts of these epitopes.
  • an example of a composite epitope comprising E200 and E300 epitopes is GHNYTTRNILPGAGAKYYKENNVEK (SEQ ID NO: 6).
  • the term “antigen” is intended to include substances that bind to or evoke the production of one or more antibodies and may comprise, but is not limited to, proteins, peptides, polypeptides, oligopeptides, lipids, carbohydrates, and combinations thereof, for example a glycosylated protein or a glycolipid.
  • antigen refers to a molecular entity that may be expressed on a target cell and that can be recognised by means of the adaptive immune system including but not restricted to antibodies or TCRs, or engineered molecules including but not restricted to transgenic TCRs, CARs, scFvs or multimers thereof, Fab-fragments or multimers thereof, antibodies or multimers thereof, single chain antibodies or multimers thereof, or any other molecule that can execute binding to a structure with high affinity.
  • epipe generally refers to that part of an antigen that is bound by the antigen binding site of an antibody.
  • An epitope may be “linear” in the sense that the hypervariable loops of the antibody CDRs that form the antigen binding site bind to a sequence of amino acids as in a primary protein structure.
  • the epitope is a “conformational epitope” i.e. one in which the hypervariable loops of the CDRs bind to residues as they are presented in the tertiary or quaternary protein structure.
  • Binding affinity generally refers to the strength of the sum total of non-covalent interactions between a single binding site of a molecule (e.g., an antibody) and its binding partner (e.g., an antigen). Unless indicated otherwise, as used herein, "binding affinity” refers to intrinsic binding affinity, which reflects a 1 : 1 interaction between members of a binding pair (e.g., antibody and antigen).
  • the affinity of a molecule X for its partner Y can generally be represented by the dissociation constant (Kd).
  • Kd dissociation constant
  • Affinity can be measured by common methods known in the art, including those described herein. Low-affinity antibodies generally bind antigen slowly and tend to dissociate readily, whereas high- affinity antibodies generally bind antigen faster and tend to remain bound longer. A variety of methods of measuring binding affinity are known in the art, any of which can be used for purposes of the present invention.
  • immune cell refers to a cell that may be part of the immune system and executes a particular effector function such as alpha-beta T cells, NK cells, NKT cells, B cells, Breg cells, Treg cells, innate lymphoid cells (ILC), cytokine induced killer (CIK) cells, lymphokine activated killer (LAK) cells, gamma-delta T cells, mesenchymal stem cells or mesenchymal stromal cells (MSC), monocytes or 1004874325 43 macrophages or any hematopoietic progenitor cells such as pluripotent stem cells and early progenitor subsets that may mature or differentiate into somatic cells.
  • a particular effector function such as alpha-beta T cells, NK cells, NKT cells, B cells, Breg cells, Treg cells, innate lymphoid cells (ILC), cytokine induced killer (CIK) cells, lymphokine activated killer (LAK) cells, gamm
  • the cells may be naturally occurring or generated by cytokine exposure, artificial/genetically modified cells (such as iPSCs and other artificial cell types).
  • Preferred immune cells are cells with cytotoxic effector function such as alpha-beta T cells, NK cells, NKT cells, ILC, CIK cells, LAK cells or gamma-delta T cells.
  • cytotoxic effector function such as alpha-beta T cells, NK cells, NKT cells, ILC, CIK cells, LAK cells or gamma-delta T cells.
  • Effective function means a specialised function of a cell, e.g. in a T cell an effector function may be cytolytic activity or helper cell activity including the secretion of cytokines.
  • autologous refers to any material derived from the same subject to whom it is later re-introduced.
  • an "enriched” or “purified” population of cells is an increase in the ratio of particular cells to other cells, for example, in comparison to the cells as found in a subject's body, or in comparison to the ratio prior to exposure to a peptide, nucleic acid or vector of the invention.
  • the particular cells include at least 20%, 30%, 40%, 50%, 60%, 70%, 75%, 80%, 90%, 95% or 99% of the total cell population.
  • a population of cells may be defined by one or more cell surface markers and/or properties.
  • engineered cell and “genetically modified cell” as used herein can be used interchangeably.
  • the terms mean containing and/or expressing a foreign gene or nucleic acid sequence that in turn modifies the genotype or phenotype of the cell or its progeny.
  • the terms refer to the fact that cells, preferentially immune cells, can be manipulated by recombinant methods well known in the art to express stably or transiently peptides or proteins that are not expressed in these cells in the natural state.
  • immune cells are engineered to express an artificial construct such as a chimeric antigen receptor on their cell surface.
  • the CAR sequences may be delivered into cells using an adenoviral, adeno-associated viral (AAV)-based, retroviral or lentiviral vector or any other pseudotyped variations thereof or any other gene delivery mechanism such as electroporation or lipofection with CRISPR/Cas9, transposons (e.g. sleeping-beauty) or variations thereof.
  • the gene delivery may be in the form of mRNA (transient) or DNA (transient or permanent).
  • 1004874325 44 Amino acid structure and single and three letter abbreviations used throughout the specification are defined in Table 2, which lists the twenty proteinogenic naturally occurring amino acids which occur in proteins as L-isomers.
  • non-proteinogenic amino acid refers to an amino acid having a side chain that does not occur in the naturally occurring L- ⁇ -amino acids recited in Table 2.
  • non-proteinogenic amino acids and derivatives include, but are not limited to, norleucine, 4-aminobutyric acid, 4-amino-3-hydroxy-5-phenylpentanoic acid, 6-aminohexanoic acid, t-butylglycine, norvaline, phenylglycine, ornithine, citrulline, sarcosine, 4-amino-3-hydroxy-6-methylheptanoic acid, 2-thienyl alanine and/or D- isomers of natural amino acids [0122]
  • ⁇ -amino acid refers to an amino acid that has a single carbon atom (the ⁇ -carbon atom) separating a carboxyl terminus (C-terminus) and an amino terminus (N-terminus).
  • an ⁇ -amino acid includes naturally occurring and non- naturally occurring L-amino acids and their D-isomers and derivatives thereof such as salts or derivatives where functional groups are protected by suitable protecting groups.
  • amino acid refers to an ⁇ -amino acid.
  • alkyl refers to a straight chain or branched saturated hydrocarbon group having 1 to 6 carbon atoms. Where appropriate, the alkyl group may have a specified number of carbon atoms, for example, C 1-6 alkyl which includes alkyl groups having 1, 2, 3, 4, 5 or 6 carbon atoms in a linear or branched arrangement.
  • alkyl groups include, but are not limited to, methyl, ethyl, n-propyl, i-propyl, n- butyl, i-butyl, t-butyl, n-pentyl, 2-methylbutyl, 3-methylbutyl, 4-methylbutyl, n-hexyl, 2- methylpentyl, 3-methylpentyl, 4-methylpentyl, and 5-methylpentyl.
  • the term "subject” refers to a mammal such as mouse, rat, cow, pig, goat, chicken, dog, monkey or human. Preferentially, the subject is a human.
  • the subject may be a subject suffering from a disorder such as cancer (a patient).
  • a disorder such as cancer
  • the terms “subject” and “individual” may be used interchangeably.
  • Receptor epitope moiety disfunctional P2X7 receptor epitope moiety
  • the present invention relates to methods which utilise polypeptides which comprise an epitope that is recognised by the antigen binding domain of a receptor on an immune cell (such as a CAR or TCR).
  • the receptors are typically for binding to tumour associated or tumour specific antigens on cancer cells, and consequently, the epitope moieties of the polypeptides for use according to the invention, comprise a sequence that 1004874325 46 is derived from the tumour associated or tumour specific antigen that is bound by the receptor.
  • the immune cell comprises a receptor for binding the extracellular domain of CD19 on a target cell.
  • the polypeptide for use in accordance with the second aspect of the invention will comprise the same epitope of the ECD of CD19 that is bound by the receptor.
  • Cellular immunotherapeutics having receptor for targeting CD19 are known to the skilled person, as are the epitopes to which such immunotherapeutics bind.
  • the polypeptide for use in accordance with the second aspect of the invention should comprise an epitope that is bound by scFv FMC683.
  • the polypeptide for use in accordance with the second aspect of the invention should comprise an epitope that is bound by scFv A3B1.
  • the immune cell may comprise a receptor for binding CD20 on a target cell.
  • the polypeptide for use in accordance with the second aspect of the invention will comprise the same epitope of CD20 that is bound by the receptor.
  • the immune cell may comprise a receptor (eg CAR) for binding mesothelin and therefore the polypeptide comprises an epitope of mesothelin.
  • the immune cells may comprise a receptor (eg CAR) for binding EGFR and therefore the polypeptide comprises an epitope of EGFR.
  • the immune cell may comprise a receptor (eg CAR) for binding GPC3 and therefore the polypeptide comprises an epitope of GPC3.
  • the immune cell may comprise a receptor for binding MUC1 and therefore the polypeptide comprises an epitope of the MUC1.
  • the immune cell comprises a receptor for binding HER2 and therefore the polypeptide comprises an epitope of HER2.
  • the immune cell comprises a receptor for binding GD2 and therefore the polypeptide comprises an epitope of GD2.
  • the immune cell comprises a receptor for binding CEA and therefore the polypeptide comprises an epitope of CEA.
  • the immune cell comprises a receptor for binding EpCAM and therefore the polypeptide comprises an epitope of EpCAM.
  • the immune cell comprises a receptor for binding LeY and therefore the polypeptide comprises an epitope of LeY.
  • the immune cell comprises a receptor for binding PSCA and therefore the polypeptide comprises an epitope of PCSA.
  • the immune cell comprises a receptor for binding CD276 and therefore the polypeptide comprises an epitope of CD276.
  • the present invention also provides fusion proteins comprising a dysfunctional P2X 7 receptor epitope moiety.
  • the dysfunctional P2X 7 receptor epitope moiety may be provided in the form of a dysfunctional P2X7 receptor, or a fragment of a dysfunctional P2X 7 receptor, that has at least one of the three ATP binding sites that are formed at the interface between adjacent correctly packed monomers that are unable to bind ATP.
  • the dysfunctional P2X 7 receptor epitope moiety is typically in the form of a peptide fragment of a dysfunctional P2X 7 receptor.
  • the peptide comprises an epitope that is not found or not available for binding on a functional P2X 7 receptor.
  • the peptide comprises the proline at amino acid position 210 of the dysfunctional P2X 7 receptor.
  • the peptide comprises one or more amino acid residues spanning from glycine at amino acid position 200 to cysteine at amino acid position 216, inclusive, of the dysfunctional P2X 7 receptor.
  • a range of peptide fragments of a dysfunctional P2X 7 receptor are known and discussed in PCT/AU2002/000061 (and in corresponding publications WO 2002/057306 and US 7,326,415, US 7,888,473, US 7,531,171, US 8,080,635, US 8,399,617, US 8,709,425, US 9,663,584, or US 10,450,380), PCT/AU2008/001364 (and in corresponding publications WO 2009/033233 and US 8,440,186, US 9,181,320, US 9,944,701 or US 10,597,45) and PCT/AU2009/000869 (and in corresponding publications WO 2010/000041 and US 8,597,643, US 9,328,155 or US 10,238,716) the contents of all of which are incorporated in entirety.
  • the amino acid sequences of any one of SEQ ID NOs: 2 to 69 or 155 may comprise a portion of the epitope moiety that is recognised or capable of being bound by a receptor expressed on an immune cell (also referred to herein as the “recognition sequence” of the epitope moiety).
  • the epitope moiety comprises or consists of an amino acid sequence selected from any of the peptide sequences listed in Table 1 above.
  • the N-terminus of the epitope moiety is a free amine (- NH 2 ). 1004874325 49
  • the C-terminus of the epitope moiety is a free acid (- COOH).
  • the C-terminus is a derivative or analogue of a free acid group, for example an ester (-COOC1-6alkyl) or a primary or secondary amide (-CONHR4 wherein R4 is selected from H and C1-6alkyl).
  • having a C-terminus that is a derivative or analogue of a free acid group may improve the biological stability of the peptide compared to the free acid.
  • the C-terminus is a derivative or analogue of a free acid group that comprises a functional moiety, for example biotin.
  • the epitope of a dysfunctional P2X 7 receptor comprises or consists of an epitope that is only found on dysfunctional P2X 7 receptor but is not found on a functional form of the P2X 7 receptor.
  • the polypeptide comprises or consists of an epitope that is specific to a dysfunctional P2X 7 receptor.
  • the fusion protein comprises an epitope corresponding to the E200, E300 or composite E200/E300 epitopes as herein defined. It will be within the purview of the skilled person to obtain various polypeptides for use in accordance with the invention.
  • additional amino acids N- or C-terminal to the region comprising the epitope bound by the anti-nfP2X 7 receptor CAR.
  • E200 which is typically defined as having an amino acid sequence substantially as defined in SEQ ID NO: 2 or 7 (and having a minimum sequence as defined in SEQ ID NO: 14)
  • additional amino acids derived from the native sequence of P2X 7 receptor can be included in the polypeptide, for example, the residues “DFP” N- terminal to the epitope in the P2X 7 receptor sequence and/or residues “TFHKT” C- terminal to the epitope in the P2X 7 receptor sequence.
  • the polypeptide may comprise at least 1, at least 2, at least 3, at least 4, at least 5 or at least 6 amino acids derived from the P2X 7 receptor sequence, in addition to the sequence of the E200 or E300 or composite epitopes.
  • the sequence of the E200 epitope is further modified to substitute the cysteine residue (residue 17 in SEQ ID NO: 2) to a serine residue (eg to provide the sequence of SEQ ID NO: 7). The skilled person will appreciate that this can be done to reduce likelihood of any disulphide bonding between the polypeptide and another molecule.
  • additional amino acid residues to the E200, E300 or composite epitopes (or extended epitopes as discussed in the paragraph above), such as, for example, by the addition 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 or at least 10 additional amino acid residues to the N- and C-terminal regions of peptides consisting of the amino acid sequence of the relevant epitope.
  • additional amino acids can be derived from linker sequences (such as peptides comprising glycine and serine residues); or be derived from the hinge region of an immunoglobulin.
  • the amino acid sequence of the epitope of a dysfunctional P2X 7 receptor may be fused via its C terminal region to the N terminal region of an Fc region of an antibody, or variant thereof.
  • the amino acid sequence of epitope of a dysfunctional P2X 7 receptor may be fused via its N terminal region to the C terminal region of an Fc region of an antibody, or variant thereof.
  • the Fc region of the fusion protein comprises two heavy chain fragments, more preferably the CH2 and CH3 domains of said heavy chain.
  • the Fc region may comprise one or more amino acid sequence modifications compared to naturally occurring Fc sequences.
  • the Fc region may comprise one or more amino acid substitutions, such as substitution of one or more cysteine residues, so as to prevent dimerisation of the molecule to identical molecules. It will be appreciated that any amino acid substitution which prevents dimerisation of the Fc regions may be employed.
  • the Fc fusion proteins described herein may be monomeric proteins.
  • the Fc region and hinge region derived from an immunoglobulin comprises substitution of at least one, at least two or at least three cysteine residues.
  • the substituted residues are at least C220, C226 and C229.
  • the monomeric protein comprises substitutions at all three of C220, C226 and C229 (numbering according to the EU system). 1004874325 51 [0156]
  • the Fc region of the fusion protein may therefore comprise one or more amino acid substitutions compared to naturally occurring Fc sequences, which prevent or reduce the ability of the Fc region to homodimerise.
  • the amino acid substitutions comprise one or more substitutions of the cysteine residues so as to prevent the formation of disulphide bonds between Fc molecules.
  • the cysteine residues of the Fc region may be substituted to any other amino acid residue, optionally to glycine, serine, alanine, lysine and glutamic acid, preferably glycine or serine.
  • the cysteine residues for substitution are preferably one or more of the cysteine residues located in the region of the Fc region which corresponds to the hinge region of an immunoglobulin. Examples of the IgG1 hinge regions, and variations thereof including cysteine to serine substitutions are provided herein in Table 3.
  • the hinge region of an immunoglobulin (eg of IgG1) comprises three cysteine residues (which are number C220, C226 and C229 according to EU numbering.
  • At least one, at least two, or all three of the cysteine residues in the immunoglobulin hinge region are substituted.
  • at least two or all three of the cysteine residues are substituted.
  • all cysteine residues in the Fc region, such as the hinge region are substituted.
  • at least one of C226 and C229 are substituted, preferably wherein both C226 and C229 are substituted.
  • the fusion protein comprises a hinge region for linking the a dysfunctional P2X 7 receptor epitope moiety and Fc region of an antibody, wherein the hinge region comprises an amino acid sequence that corresponds to any of the sequences set forth in SEQ ID NOs: 76 to 113, or 136 to 137 or 141 or 142.
  • the fusion protein region may comprise an Fc region corresponding to an Fc “hole” or “knob” for use in a “knob-in-hole” heterodimer.
  • Fc sequences are known in the art and provides for an asymmetric heterodimeric molecule comprising a fusion protein with a single copy of the epitope moiety as described herein and Fc region, bound to a further Fc region that does not comprise the epitope moiety.
  • the skilled person will be familiar with technology and Fc sequences for enabling the formation of so-called monomeric fusion proteins, including although not limited to the use of the “knobs-into-holes” IgG1 format (Ridgway et al., (1996), Protein Eng, 9: 617- 621).
  • Such approaches in the context of the present invention enable expression and 1004874325 52 purification of a heterodimeric fusion protein with only one copy of the peptide epitope (eg an epitope moiety derived from the E200 epitope as herein described), per molecule.
  • Examples of the “knob-into-hole” Fc pairing is provided herein in SEQ ID NOs: 157 and 159 (knob and hole, respectively), 158 and 159, respectively, 160 and 162 (hole and knob, respectively) and 161 and 162, respectively.
  • the present invention provides a fusion protein comprising the amino acid sequence of any of SEQ ID NOs: 2 to 69 and 122, linked to an Fc region as defined in SEQ ID NO: 160 or 162, wherein the fusion protein is capable of forming a heterodimer with an Fc region that does not comprise an E200 peptide moiety.
  • a fusion protein of the invention is preferably one that is capable of forming a heterodimeric molecule that comprises a single E200-containing amino acid sequence. (In other words, the Fc portion of the fusion protein may form a heterodimer with an Fc region of an antibody that does not comprise an E200 peptide fused thereto).
  • the Fc region may comprise one or more substitutions for ablating or reducing effector function, such as to reduce binding and activation via the FcR as further described below.
  • the term “Fc region” herein is used to define a C-terminal region of an immunoglobulin heavy chain that contains at least a portion of the constant region. In other words, the Fc region contains two heavy chain fragments comprising the C H 2 and C H 3 domains of an antibody. In the context of the present invention, the Fc region comprises two heavy chain fragments, preferably the CH2 and CH3 domains of said heavy chain. The two heavy chain fragments are held together by two or more disulfide bonds and by hydrophobic interactions of the C H 3 domains.
  • the fusion protein does not exhibit any effector function or any detectable effector function.
  • “Effector functions” or “effector activities” refer to those biological activities attributable to the Fc region of an antibody, which vary with the antibody isotype. Examples of antibody effector functions include: C1q binding and complement dependent cytotoxicity (CDC); Fc receptor binding; antibody dependent cell- mediated cytotoxicity (ADCC); phagocytosis; down regulation of cell surface receptors (e.g. B cell receptor); and B cell activation.
  • Fc receptor (FcR) binding assays can be conducted to ensure that the antibody lacks Fc ⁇ R binding (hence likely lacking ADCC activity), but retains FcRn binding ability.
  • FcR expression on hematopoietic cells is summarized in Table 3 on page 464 of Ravetch and Kinet, Annu. Rev. Immunol.9:457- 492 (1991).
  • Non-limiting examples of in vitro assays to assess ADCC activity of a molecule of interest is described in U.S. Patent No.5,500,362 (see, e.g., Hellstrom, I. et al. Proc. Nat’l Acad. Sci. USA 83:7059-7063 (1986)) and Hellstrom, I et al., Proc. Nat’l Acad. Sci. USA 82:1499-1502 (1985); 5,821,337 (see Bruggemann, M. et al., J. Exp. Med. 166:1351-1361 (1987)).
  • non-radioactive assays methods may be employed (see, for example, ACTITM non-radioactive cytotoxicity assay for flow cytometry (CellTechnology, Inc. Mountain View, CA; and CytoTox 96 ® non-radioactive cytotoxicity assay (Promega, Madison, WI).
  • Useful effector cells for such assays include peripheral blood mononuclear cells (PBMC) and Natural Killer (NK) cells.
  • PBMC peripheral blood mononuclear cells
  • NK Natural Killer
  • ADCC activity of the molecule of interest may be assessed in vivo, e.g., in an animal model such as that disclosed in Clynes et al. Proc. Nat’l Acad. Sci. USA 95:652- 656 (1998).
  • C1q binding assays may also be carried out to confirm that the antibody is unable to bind C1q and hence lacks CDC activity. See, e.g., C1q and C3c binding ELISA in WO 2006/029879 and WO 2005/100402.
  • a CDC assay may be performed (see, for example, Gazzano-Santoro et al., J. Immunol. Methods 202:163 (1996); Cragg, M.S. et al., Blood 101:1045-1052 (2003); and Cragg, M.S. and M.J. Glennie, Blood 103:2738-2743 (2004)).
  • the Fc fusion proteins of the invention comprise Fc regions with reduced effector function.
  • Fc regions with reduced effector function include those with substitution of one or more of Fc region residues 238, 265, 269, 270, 297, 327 and 329 (U.S. Patent No. 6,737,056).
  • Such Fc mutants include Fc mutants with substitutions at two or more of amino acid positions 265, 269, 270, 297 and 327, including the so-called “DANA” Fc mutant with substitution of residues 265 and 297 to alanine (US Patent No.7,332,581).
  • an antibody variant may comprise an Fc region with 1004874325 54 one or more amino acid substitutions which diminish Fc ⁇ R binding, e.g., substitutions at positions 234 and 235 of the Fc region (EU numbering of residues).
  • the substitutions are L234A and L235A (LALA) (See, e.g., WO 2012/130831).
  • modified Fc regions include those comprising the “LALALS” (amino acid substitutions L234A/L235A/M428L/N434S as described in Zalevsky et al., (2010) Nat. Biotechnol.
  • the Fc region of the Fc fusion proteins of the invention may comprise at least the “LALA” mutations (L234A and L235A) for reducing binding to FcR.
  • the fusion protein may in addition or alternatively comprise the mutation G346R for abrogating recruitment of complement C1q.
  • Other Fc modifications for use in the present invention include variants that reduce or ablate binding to Fc ⁇ Rs and/or complement proteins, thereby reducing or ablating Fc-mediated effector functions such as ADCC, ADCP, and CDC.
  • knockout variants Such variants are also referred to herein as “knockout variants” or “KO variants”.
  • Variants that reduce binding to Fc ⁇ Rs and complement are useful for reducing unwanted interactions mediated by the Fc region.
  • Preferred knockout variants are described in US 2008- 0242845 A1, published on Oct.2, 2008, entitled “Fc Variants with Optimized Properties, expressly incorporated by reference herein.
  • Preferred modifications include but are not limited substitutions, insertions, and deletions at positions 234, 235, 236, 237, 267, 269, 325, and 328, wherein numbering is according to the EU index.
  • substitutions include but are not limited to 234G, 235E, 235G, 236R, 237K, 267R, 269R, 325L, and 328R, wherein numbering is according to the EU index.
  • a preferred variant comprises 236R/328R.
  • Variants may be used in the context of any IgG isotype or IgG isotype Fc region, including but not limited to human IgG1, IgG2, IgG3, and/or IgG4.
  • Preferred IgG Fc regions for reducing Fc ⁇ R and complement binding and reducing Fc-mediated effector functions are IgG2 and IgG4 Fc regions.
  • Hybrid isotypes may also be useful, for example hybrid IgG1/IgG2 isotypes as described in U.S. Ser. No.11/256,060.
  • Other modifications for reducing Fc ⁇ R and complement interactions include but are not limited to substitutions 1004874325 55 297A, 297D, 234A, 235A, 237A, 318A, 228P, 236E, ⁇ G236, 265G, 268Q, 297Q, 309L, 330S, 331S, 327Q, 220S, 226S, 229S, 238S, 233P, 234A, and 234V, as well as removal of the glycosylation at position 297 by mutational or enzymatic means or by production in organisms such as bacteria that do not glycosylate proteins.
  • the Fc region of the fusion protein includes mutations to the complement (C1q) and/or to Fc gamma receptor (Fc ⁇ R) binding sites. In some aspects, such mutations can render the fusion protein incapable of antibody directed cytotoxicity (ADCC) and complement directed cytotoxicity (CDC).
  • the Fc region as used in the context of the present invention preferably does not trigger cytotoxicity such as antibody-dependent cellular cytotoxicity (ADCC) or complement dependent cytotoxicity (CDC).
  • the Fc region may comprise one or more substitutions for reducing affinity for the FcRn, and thereby reduce serum or circulating half-life of the fusion protein.
  • substitutions for reducing affinity to FcRn are known in the art and are described for example in Ward et al., (2015), Mol. Immunol., 67: 131-141 and Grevys et al., (2015), 194: 5497-5508. Examples of substitutions include substitutions at one or more of Ile253, His310 and His435, such as I253A and H310A and H435A.
  • the term “Fc region” also includes native sequence Fc regions and variant Fc regions.
  • the Fc region may include the carboxyl-terminus of the heavy chain.
  • Antibodies produced by host cells may undergo post-translational cleavage of one or more, particularly one or two, amino acids from the C-terminus of the heavy chain. Therefore, an antibody produced by a host cell by expression of a specific nucleic acid molecule encoding a full-length heavy chain may include the full-length heavy chain, or it may include a cleaved variant of the full-length heavy chain.
  • numbering of amino acid residues in the Fc region or constant region is according to the EU numbering system, also called the EU index, as described in Kabat et al., Sequences of Proteins of Immunological Interest, 5th Ed.
  • Amino acid sequence variants of the Fc region of an antibody may be contemplated.
  • Amino acid sequence variants of an Fc region of an antibody may be prepared by introducing appropriate modifications into the nucleotide 1004874325 56 sequence encoding the antibody, or by peptide synthesis. Such modifications include, for example, deletions from, and/or insertions into and/or substitutions of residues within the amino acid sequences of the Fc region of the antibody. Any combination of deletion, insertion, and substitution can be made to arrive at the final construct, provided that the final construct possesses the desired characteristics, e.g., inducing or supporting an anti- inflammatory response.
  • the Fc region of the antibody may be an Fc region of any of the classes of antibody, such as IgA, IgD, IgE, IgG, and IgM.
  • the “class” of an antibody refers to the type of constant domain or constant region possessed by its heavy chain. There are five major classes of antibodies: IgA, IgD, IgE, IgG, and IgM, and several of these may be further divided into subclasses (isotypes), e.g., IgG 1 , IgG 2 , IgG 3 , IgG 4 , IgA 1 , and IgA 2 . Accordingly, as used in the context of the present invention, the antibody may be an Fc region of an IgG.
  • the Fc region of the antibody may be an Fc region of an IgG1, an IgG2, an IgG2b, an IgG3 or an IgG4.
  • the fusion protein of the present invention comprises an IgG of an Fc region of an antibody.
  • the Fc region of the antibody is an Fc region of an IgG, preferably IgG1.
  • the dysfunctional P2X7 receptor epitope and Fc region of an antibody may be joined directly or via a linker sequence.
  • the linker sequence may be a spacer sequence as herein defined or as exemplified in Table 1 or 3.
  • the linker sequence may be any amino acid based linker sequence commonly in use in the field.
  • a linker is usually a peptide having a length of up to 20 amino acids although may be up to 50 amino acids in length.
  • the term “linked to” or “fused to” refers to a covalent bond, e.g., a peptide bond, formed between two moieties. Accordingly, in the context of the present invention the linker may have a length of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21 or 22 or more amino acids.
  • the herein provided fusion protein may comprise a linker between the epitope of a dysfunctional P2X 7 receptor and the Fc region of the antibody, such as between the N- 1004874325 57 terminus of the Fc regions and the C-terminus of dysfunctional P2X 7 receptor epitope.
  • the herein provided fusion protein may comprise a linker between the dysfunctional P2X 7 receptor epitope and the Fc region of the antibody, such as between the C-terminus of the Fc regions and the N-terminus of the dysfunctional P2X 7 receptor epitope moiety.
  • the dysfunctional P2X 7 receptor epitope moiety may be fused via a linker at the C-terminus to the N-terminus of the Fc region.
  • linkers have the advantage that they can make it more likely that the different polypeptides of the fusion protein fold independently and behave as expected.
  • the dysfunctional P2X 7 receptor epitope moiety and the Fc region of an antibody may be comprised in a single-chain multi-functional polypeptide.
  • the fusion protein of the present invention or polypeptide for use according to the invention includes a peptide linker.
  • the peptide linker links a dysfunctional P2X 7 receptor epitope moiety with an Fc region of an antibody.
  • the peptide linker can include the amino acid sequence Gly-Gly-Ser (GGS), Gly-Gly-Gly-Ser (GGGS) or Gly-Gly-Gly-Gly-Ser (GGGGS).
  • the peptide linker can include the amino acid sequence GGGGS (a linker of 6 amino acids in length) or even longer.
  • the linker may a series of repeating glycine and serine residues (GS) of different lengths, i.e., (GS)n where n is any number from 1 to 15 or more.
  • the linker may be (GS)3 (i.e., GSGSGS) or longer (GS)11 or longer.
  • n can be any number including 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 or more. Fusion proteins having linkers of such length are included within the scope of the present invention. Preferably n is no more than 3 (ie such that when n equals 3 the linker is GSGSGS).
  • the linker may comprise inclusion of an amino acid that provides rigidity, such as lysine.
  • the linker region may also comprise the sequence GSGK.
  • the peptide linker may consist of a series of repeats of Thr-Pro (TP) comprising one or more additional amino acids N and C terminal to the repeat sequence.
  • the linker may comprise or consist of the sequence GTPTPTPTPTGEF (also known as the TP5 linker).
  • the linker may be a short and/or alpha-helical rigid linker (e.g. A(EAAAK)3A, PAPAP or a dipeptide such as LE or CC). 1004874325 58 [0180]
  • the fusion protein may comprise a dysfunctional P2X 7 receptor epitope moiety, linked to an Fc region of an antibody, via a hinge region.
  • the linking between the dysfunctional P2X 7 receptor epitope moiety and the Fc region may comprise a combination of hinge region and linker regions.
  • suitable hinge regions include hinge regions derived from immunoglobulins.
  • the hinge region may be derived from an IgG1, IgG2, IgG3 or IgG4, and may comprise one or more amino acid substitutions, (for example to prevent or reduce the likelihood of disulphide bridge formation).
  • Alternative hinge sequences may be derived from alternative immunoglobulin domains, CD8A, CD8B, CD4 or CD28, TRAC, TRBC, TRGC, TRDC.
  • Linker sequences may also include any sequence of any length of CL/CH1 domain but not all residues of CL/CH1 domain; for example the first 5-12 amino acid residues of the CL/CH1 domains.
  • Linkers can be derived from immunoglobulin heavy chains of any isotype, including for example C ⁇ 1, C ⁇ 2, C ⁇ 3, C ⁇ 4, C ⁇ 1, C ⁇ 2, C ⁇ , C ⁇ , and C ⁇ .
  • Linkers can be derived from immunoglobulin light chain, for example C ⁇ or C ⁇ .
  • Linker sequences may also be derived from other proteins such as Ig-like proteins (e.g. TCR, FcR, KIR), hinge region-derived sequences, and other natural sequences from other proteins.
  • the dysfunctional P2X 7 receptor epitope moiety may be joined to the Fc regions (or other protein sequence as herein defined) by more than one linker and/or more than one hinge region.
  • the fusion protein may comprise (N to C terminus), the dysfunctional P2X 7 receptor epitope moiety, conjugated directly to the Fc region.
  • the fusion protein may comprise the dysfunctional P2X 7 receptor epitope moiety, followed by a linker region, then the Fc region.
  • the fusion protein may comprise the dysfunctional P2X 7 receptor epitope moiety, followed by a linker region, then a hinge region, and then the Fc region.
  • the fusion protein may comprise the dysfunctional P2X 7 receptor epitope moiety, followed by a linker region, then a hinge region, a further linker region, then the Fc region. 1004874325 59
  • the alternative configuration is possible (ie wherein the dysfunctional P2X 7 receptor epitope moiety is joined to the C terminus of the Fc region, via one or more linker and/or hinge regions.
  • the dysfunctional P2X 7 receptor epitope moiety is directly fused to the Fc region of an antibody (or serum albumin, transferrin, a carboxy- terminal peptide of chorionic gonadotropin (CG) ⁇ chain, a non-exact repeat peptide sequence, a polypeptide sequence composed of proline-alanine-serine polymer, an elastin-like peptide (ELP) repeat sequence), a homopolymer of glycine residues or a gelatin-like protein), such that there is no linker between the two regions of the fusion protein or polypeptide.
  • an antibody or serum albumin, transferrin, a carboxy- terminal peptide of chorionic gonadotropin (CG) ⁇ chain, a non-exact repeat peptide sequence, a polypeptide sequence composed of proline-alanine-serine polymer, an elastin-like peptide (ELP) repeat sequence), a homopolymer of glycine residues
  • the linker joining the dysfunctional P2X 7 receptor epitope moiety and the Fc region of an antibody is a cleavable linker.
  • Cleavable linkers are well known in the art, and include for example, the sequence defined in SEQ ID NO: 144 and which defines a cleavage site for Human Rhinovirus 3C protease. Proteases for sue in cleaving such cleavage sites are also readily available from commercial providers (eg: Pierce HRV 3C Protease. [0189] Other known cleavable linkers and other linker which may be used in accordance with the present invention are disclosed in Chen et al., (2013) Adv. Drug. Deliv. Rev.65: 1357-1369; the contents of which are incorporated herein by reference.
  • the present invention finds application in methods for enriching for subpopulations of immune cells that express receptors comprising antigen binding domains for binding to tumour associated and tumour specific antigens, such dysfunctional P2X 7 receptor.
  • the receptor is preferably a chimeric antigen receptor (CAR) or variant thereof.
  • the receptor may also be a modified TCR.
  • the antigen-recognition domain of the receptor preferably recognises a target antigen expressed on a cancer cell.
  • the immune cell may comprise a receptor with an antigen- recognition domain for binding to any one of: CD33 (Siglec-3), CD123 (IL3RA), CD135 (FLT-3), CD44 (HCAM), CD44V6, CD47, CD184 (CXCR4), CLEC12A (CLL1), FRp, MICA/B, CD305 (LAIR-1), CD366 (TIM-3), CD96 (TACTILE), CD133, CD56, CD29 (ITGB1), CD44 (HCAM), CD47 (IAP), CD66 (CEA), CD112 (Nectin2), CD117 (c-Kit), CD146 (MCAM), CD155 (PVR), CD171 (LI CAM), CD221 (IGF1), CD227 (MUC1), CD243 1004874325 62 (MRD1), CD246 (ALK), CD271 (LNGFR), CD19, CD20, GD2, and especially EGFR, mesothelin, GPC3, MUC1,
  • the immune cell expresses a CAR (or variant thereof) for binding dysfunctional P2X 7 receptor.
  • the extracellular part of the CAR or variant thereof may comprise an nfP2X 7 binding domain that recognises the E200 (or E300 or E200-300 composite) epitope as disclosed herein.
  • a CAR, variant thereof, or TCR may comprise an extracellular domain (extracellular part) comprising the antigen binding domain, a transmembrane domain and an intracellular signaling domain.
  • the extracellular domain may be linked to the transmembrane domain by a linker.
  • the extracellular domain may also comprise a signal peptide.
  • the extracellular part of the CAR, variant thereof, or TCR comprises an nfP2X 7 binding domain that recognises the E200 (or E300 or E200-300 composite) epitope as disclosed herein.
  • the antigen-recognition domain of the CAR or TCR includes a binding polypeptide that includes amino acid sequence homology to one or more complementarity determining regions (CDRs) of an antibody that binds to a dysfunctional P2X 7 receptor.
  • the binding polypeptide includes amino acid sequence homology to the CDR1, 2 and 3 domains of the V H and/or V L chain of an antibody that binds to a dysfunctional P2X 7 receptor.
  • the binding polypeptide of the CAR comprises the amino acid sequence of the CDRs of the V H and/or V L chain of an antibody described in PCT/AU2002/000061 or PCT/AU2002/001204 (or in any one of the corresponding US patents US 7,326,415, US 7,888,473, US 7,531,171, US 8,080,635, US 8,399,617, US 8,709,425, US 9,663,584, or US 10,450,380), PCT/AU2007/001540 (or in corresponding US patent US 8,067,550), PCT/AU2007/001541 (or in corresponding US publication US 2010-0036101), PCT/AU2008/001364
  • the antibody comprises the CDR amino acid sequences of PEP2-2-1 described in PCT/AU2010/001070 (or in any one of the corresponding US patents US 9,127,059, US 9,688,771, or US 10,053,508) or BPM09 described in PCT/AU2007/001541 (or in corresponding US publication US 2010-0036101) and produced by the hybridoma AB253 deposited with the European Collection of Cultures (ECACC) under Accession no.06080101.
  • the binding polypeptide of the CAR comprises the amino acid sequence of the V H and/or V L chains of an antibody described in PCT/AU2002/000061 or PCT/AU2002/001204 (or in any one of the corresponding US patents US 7,326,415, US 7,888,473, US 7,531,171, US 8,080,635, US 8,399,617, US 8,709,425, US 9,663,584, or US 10,450,380), PCT/AU2007/001540 (or in corresponding US patent US 8,067,550), PCT/AU2007/001541 (or in corresponding US publication US 2010-0036101), PCT/AU2008/001364 (or in any one of the corresponding US patents US 8,440,186, US 9,181,320, US 9,944,701 or US 10,597,451), PCT/AU2008/001365 (or in any one of the corresponding US patents US 8,293,491 or US 8,658,385), PCT/AU2009/000
  • the antibody comprises the CDR amino acid sequences of PEP2-2-1 described in PCT/AU2010/001070 (or in any one of the corresponding US patents US 9,127,059, US 9,688,771, or US 10,053,508) or BPM09 described in PCT/AU2007/001541 (or in corresponding US publication US 2010-0036101) and produced by the hybridoma AB253 deposited with the European Collection of Cultures (ECACC) under Accession no.06080101.
  • the binding polypeptide of the CAR comprises the amino acid sequence of an antibody or fragment thereof described in 1004874325 64 PCT/AU2002/000061 or PCT/AU2002/001204 (or in any one of the corresponding US patents US 7,326,415, US 7,888,473, US 7,531,171, US 8,080,635, US 8,399,617, US 8,709,425, US 9,663,584, or US 10,450,380), PCT/AU2007/001540 (or in corresponding US patent US 8,067,550), PCT/AU2007/001541 (or in corresponding US publication US 2010-0036101), PCT/AU2008/001364 (or in any one of the corresponding US patents US 8,440,186, US 9,181,320, US 9,944,701 or US 10,597,451), PCT/AU2008/001365 (or in any one of the corresponding US patents US 8,293,491 or US 8,658,385), PCT/AU2009/000
  • the antibody comprises the CDR amino acid sequences of PEP2-2-1 described in PCT/AU2010/001070 (or in any one of the corresponding US patents US 9,127,059, US 9,688,771, or US 10,053,508) or BPM09 described in PCT/AU2007/001541 (or in corresponding US publication US 2010-0036101) and produced by the hybridoma AB253 deposited with the European Collection of Cultures (ECACC) under Accession no.06080101.
  • the CAR typically also comprises a signal peptide.
  • a "signal peptide” refers to a peptide sequence that directs the transport and localisation of the protein within a cell, e.g.
  • an "antigen binding domain” refers to the region of the CAR that specifically binds to an antigen (and thereby is able to target a cell containing the antigen).
  • a CAR may comprise one or more antigen binding domains.
  • the targeting regions on the CAR are extracellular.
  • the antigen binding domain may comprise an antibody or an antibody binding fragment thereof.
  • the antigen binding domain may comprise, for example, full length heavy chain, Fab fragments, single chain Fv (scFv) fragments, divalent single chain antibodies or diabodies.
  • any molecule that binds specifically to a given antigen such as affibodies or ligand binding domains from naturally occurring receptors may be used as an antigen binding domain.
  • the antigen binding domain is a scFv.
  • a linker may be for example the "(G/S)-linker" and variations thereof but the skilled person will appreciate that various linker sequences and formats may be used.
  • CARs may also comprise a "hinge" region (sometimes called a spacer region or linker region) joining the antigen binding domain to the transmembrane domain. This is typically a hydrophilic region that is between the antigen binding domain and the transmembrane domain.
  • a CAR may comprise an extracellular hinge domain but it is also possible to leave out such a hinge.
  • the hinge region may include for example, Fc fragments of antibodies or fragments thereof, hinge regions of antibodies or fragments thereof, CH2 or CH3 regions of antibodies, accessory proteins, artificial hinge sequences or combinations thereof.
  • One example of a hinge region is the CD8alpha hinge.
  • the transmembrane domain of the CAR may be derived from any desired natural or synthetic source for such a domain.
  • the domain When the source is natural, the domain may be derived from any membrane-bound or transmembrane protein.
  • the transmembrane domain may be derived for example from CD8alpha or CD28.
  • the key signalling and antigen recognition modules domains
  • the CAR may have two (or more) transmembrane domains.
  • the splitting of key signalling and antigen recognition modules enables small molecule- dependent, titratable and reversible control over CAR cell expression (Wu et al, 2015, Science 350: 293-303) due to small molecule-dependent heterodimerising domains in each polypeptide of the CAR.
  • the cytoplasmic domain (or the intracellular signaling domain) of the CAR is responsible for activation of at least one of the normal effector functions of the immune cell in which the CAR is expressed.
  • Effective function means a specialised function of a cell, e.g. in a T cell an effector function may be cytolytic activity or helper cell activity including the secretion of cytokines.
  • the intracellular signalling domain refers to the part of a protein that transduces the effector function signal and directs the cell expressing the CAR to perform a specialised function.
  • the intracellular signalling domain may include any complete, mutated or truncated part of the intracellular signalling domain of a given protein sufficient to transduce a signal that initiates or blocks immune cell effector functions.
  • the function of the intracellular domains may be pro- or anti-inflammatory and/or immunomodulatory, or a combination of such. 1004874325 66
  • Examples of intracellular signalling domains for use in the CARs include the cytoplasmic signaling sequences of the T cell receptor (TCR) and co-receptors that initiate signal transduction following antigen receptor engagement.
  • Primary cytoplasmic signalling sequences that act in a stimulatory manner may contain ITAMs (immunoreceptor tyrosine-based activation motifs) signalling motifs.
  • ITAMs immunoglobulin-based activation motifs
  • Examples of ITAM containing primary cytoplasmic signalling sequences often used in CARs are those derived from TCR zeta (CD3 zeta), FcR gamma, FcR beta, CD3 gamma, CD3 delta, CD3 epsilon, CD5, CD22, CD79a, CD79b and CD66d. Most prominent is the sequence derived from CD3 zeta.
  • the cytoplasmic domain of the CAR may be designed to comprise the CD3-zeta signaling domain by itself or combined with any other desired cytoplasmic domain(s).
  • the cytoplasmic domain of the CAR can comprise a CD3 zeta chain portion and a co- stimulatory signalling region.
  • the co-stimulatory signalling region refers to a part of the CAR comprising the intracellular domain of a co-stimulatory molecule.
  • a co-stimulatory molecule is a cell surface molecule other than an antigen receptor or their ligands that is required for an efficient response of lymphocytes to an antigen.
  • co-stimulatory molecule examples include CD27, CD28, 4-1BB (CD137), OX40, CD30, CD40, PD-1, ICOS, lymphocyte function-associated antigen-1 (LFA-1), CD2, CD7, LIGHT, NKG2C and B7- H3.
  • the activation receptor is the CD3 co-receptor complex or is an Fc receptor.
  • the co-stimulatory receptor is selected from the group consisting of CD27, CD28, CD- 30, CD40, DAP10, OX40, 4-1BB (CD137) and ICOS.
  • the co-stimulatory receptor (from which a portion of signalling domain is derived) is selected from the group consisting of CD28, OX40 or 4- 1BB.
  • the cytoplasmic signalling sequences within the cytoplasmic signalling part of the CAR may be linked to each other with or without a linker in a random or specified 1004874325 67 order.
  • a short oligo-or polypeptide linker which is preferably between 2 and 10 amino acids in length, may form the linkage.
  • a prominent linker is the glycine-serine doublet.
  • the cytoplasmic domain may comprise the signalling domain of CD3-zeta and the signalling domain of CD28.
  • the cytoplasmic domain may comprise the signalling domain of CD3-zeta and the signalling domain of CD27.
  • the cytoplasmic domain may comprise the signalling domain of CD3- zeta, the signalling domain of CD28, and the signalling domain of CD27.
  • either the extracellular part or the transmembrane domain or the cytoplasmic domain of a CAR may also comprise a heterodimerising domain for the aim of splitting key signalling and antigen recognition modules of the CAR.
  • the CAR which binds to a fusion protein of the invention or polypeptide for use according to invention may be designed to comprise any portion or part of the above-mentioned domains as described herein in any order and/or combination resulting in a functional CAR.
  • the affinity at which the dysfunctional P2X 7 receptor binding domain of the CAR binds to the nfP2X 7 recognition site E200 of fusion protein of the invention or polypeptide for use according to the invention can vary, but generally the binding affinity may be in the range of approximately 100 ⁇ , approximately 10 ⁇ M, approximately 1 ⁇ M, approximately 100 nM, approximately 10 nM, or approximately 1 nM, preferably at least about 10 pM or 1 pM. In preferred embodiments, the binding affinity is at least about 1 nM or at least about 10 nM.
  • the receptor (such as a CAR, variant thereof, or TCR, or variant thereof) is typically expressed by an immune cell.
  • the immune cell may be an "engineered cell”, “genetically modified cell”, or “immune effector cell” as described herein. Further, the immune cell may be an immune cell precursor that is capable of differentiating into an immune cell.
  • a cell that is capable of differentiating into an immune cell e.g. T cell that will express the dysfunctional P2X 7 CAR
  • T cell that will express the dysfunctional P2X 7 CAR
  • the immune cell may be a leukocyte, a Peripheral Blood Mononuclear Cell (PBMC), a lymphocyte, a T cell (including a CD4+ T cell or a CD8+ T cell), a natural killer cell, a natural killer T cell, or a ⁇ T cell.
  • PBMC Peripheral Blood Mononuclear Cell
  • the immune cell may be a T cell, wherein optionally said T cell does not express TcR ⁇ , PD1, CD3 or CD96 (e.g. by way of knocking down or knocking out one of these genes on a genetic level or functional level).
  • the immune cell optionally does not express accessory molecules that can be checkpoint, exhaustion or apoptosis-associated signalling receptors as well as ligands such as PD-1, LAG-3, TIGIT, CTLA-4, FAS-L and FAS-R, (e.g. by way of knocking out one of these genes on a genetic level or functional level).
  • the immune cell includes two or more different receptors (e.g., two or more CARs, or variants thereof). The CARs may bind to different epitopes on the same target molecule (e.g., different epitopes on dysfunctional P2X 7 receptor).
  • the CARs may bind different target molecules, such that only one of the CARs binds to dysfunctional P2X 7 receptors.
  • the term “different CARs” or “different chimeric antigen receptors” refers to any two or more CARs that have either non-identical antigen- recognition and/or non-identical signalling domains.
  • “different CARs” includes two CARs with the same antigen-recognition domains (e.g.
  • both CARs may recognise a dysfunctional P2X 7 receptor), but have different signalling domains, such as one CAR having a signalling domain with a portion of an activation receptor and the other CAR having a signalling domain with a portion of an co-stimulatory receptor.
  • at least one of the two or more CARs within this embodiment will have an antigen-recognition domain that recognises the dysfunctional P2X 7 receptor and the other CAR(s) may take any suitable form and may be directed against any suitable antigen.
  • the skilled person will be able to use routine techniques to confirm binding of the polypeptide (or series of 1004874325 69 polypeptides) by the CAR, and thereby determine the suitability of the polypeptide for use in methods of the invention.
  • the methods of the invention can be used to isolate or enrich any population of immune cells that express a receptor (including a CAR), which comprises an antigen binding domain that recognizes the epitope of the dysfunctional P2X 7 receptor contained on the fusion protein.
  • the skilled person can make use of routine laboratory techniques to release the fusion protein/cell complex from the capture agent, and thereby obtain an enriched sample of cells.
  • the use of magnetic micro- or macro- beads for isolating cell and protein populations is well known to the persons skilled in the art.
  • the mean diameter of the beads can range from 10 nm to 10 ⁇ m.
  • Biocompatible magnetic particles are commercially available and consist of, for example, forms of magnetically iron oxide coated by a shell of dextran molecules or silica.
  • the solid support may also be polymers containing magnetic materials. Commercially available forms of such beads are also readily available and known, including MicroBeads (Miltenyi Biotec) for use in conjunction with MACS® columns and Dynabeads magnetic beads (Applied Biosystems). [0228]
  • MicroBeads MicroBeads (Miltenyi Biotec) for use in conjunction with MACS® columns and Dynabeads magnetic beads (Applied Biosystems).
  • the use of microbeads 50 nm diameter
  • macrobeads (1-5 ⁇ m diameter) since these can be injected directly into the patient requiring treatment with the immune cells. Accordingly, in certain embodiments, it is not necessary to isolate the immune cells from the polypeptide/cell complex according to the second aspect of the invention, and the complex can be directly administered.
  • the present invention provides a method of enriching cells expressing a chimeric antigen receptor (CAR) over cells not expressing the CAR in 1004874325 70 a composition, which comprises contacting the cells with a fusion protein as described herein.
  • CAR chimeric antigen receptor
  • the cells expressing the CAR are cells transduced with a nucleic acid molecule encoding the CAR. In some embodiments, the cells expressing the CAR are clones of the cells transduced with a nucleic acid molecule encoding the CAR that express the CAR.
  • Compositions and uses thereof [0231] The present invention also provides a composition comprising, consisting essentially of, or consisting of one or more cells expressing one or more CARs for binding to dysfunctional P2X 7 receptor, that have been enriched according to one or more of the methods of the present invention.
  • compositions “comprising” one or more cells expressing one or more CARs that have been enriched according to one or more of the methods of the present invention may contain other compounds and cells.
  • a composition “consisting essentially of” one or more cells expressing one or more CARs that have been enriched according to one or more of the methods of the present invention may comprise other compounds and cells so long as they do not materially change the activity or function of the cells expressing the one or more CARs in the composition.
  • compositions “consisting of” one or more cells expressing one or more CARs that have been enriched according to one or more of the methods of the present invention means that the composition does not contain other functional cells in addition to the one or more cells expressing one or more CARs.
  • Compositions consisting of one or more cells expressing one or more CARs that have been enriched according to one or more of the methods of the present invention may comprise ingredients other than cells, e.g., compounds, proteins, pharmaceutically acceptable carriers, surfactants, preservatives, etc.
  • compositions consisting of one or more cells expressing one or more CARs that have been enriched according to one or more of the methods of the present invention may contain insignificant amounts of contaminants.
  • the amount of the one or more cells expressing one or more CARs for binding to dysfunctional P2X 7 receptor is at least about 50% of the total cells in the composition. In some embodiments, the amount of the one or more cells 1004874325 71 expressing one or more CARs is at least about 60% of the total cells in the composition. In some embodiments, the amount of the one or more cells expressing one or more CARs is at least about 70% of the total cells in the composition. In some embodiments, the amount of the one or more cells expressing one or more CARs is at least about 80% of the total cells in the composition. In some embodiments, the amount of the one or more cells expressing one or more CARs is at least about 90% of the total cells in the composition.
  • the amount of the one or more cells expressing one or more CARs is at least about 95% of the total cells in the composition.
  • the compositions according to the present invention comprise a therapeutically effective amount of the one or more cells expressing one or more CARs.
  • the compositions or cell populations obtained by the methods of the present invention can be used in the treatment of a disease or condition characterized by the expression of dysfunctional P2X 7 receptor.
  • subjects requiring treatment include those having a benign, pre-cancerous, non-metastatic tumour.
  • the cancer is pre-cancerous or pre-neoplastic.
  • the cancer is a secondary cancer or metastasis.
  • the secondary cancer may be located in any organ or tissue, and particularly those organs or tissues having relatively higher haemodynamic pressures, such as lung, liver, kidney, pancreas, bowel and brain.
  • the secondary cancer may be detected in the ascites fluid and/or lymph nodes.
  • the cancer may be substantially undetectable.
  • Pre-cancerous or “preneoplasia” generally refers to a condition or a growth that typically precedes or develops into a cancer.
  • a "pre-cancerous" growth may have cells that are characterised by abnormal cell cycle regulation, proliferation, or differentiation, which can be determined by markers of cell cycle.
  • the cancer may be a solid or a “liquid” tumour.
  • the cancer may be growth in a tissue (carcinoma, sarcoma, adenomas etc) or it may be a cancer present in bodily fluid such as in blood or bone marrow (e.g., lymphomas and leukaemias). 1004874325 72 [0241]
  • the cancer requiring treatment may be a cancer characterised by low levels of expression of dysfunctional P2X 7 receptor. Examples of such cancers include Burkitt’s lymphoma.
  • immunohistochemical analyses of surface expression of the dysfunctional P2X 7 (nfP2X 7 ) receptor on patient tumour biopsies reveals a range from 1+ to 3+ in IHC score.
  • Samples with low expression may therefore be found in a wide range of tumour types. Examples are found in solid tumours of various types, including but not limited to neuroblastoma, colorectal cancers, lung cancers, kidney cancers, skin cancers, breast cancers, brain cancers and prostate cancer. Such differences in expression level in different tissues may be due to the formation of tumours from cells that are at an earlier state of transformation (the tissues with the highest receptor expression may be those undergoing the highest rate of proliferation).
  • Example 1 enrichment of nfP2X 7 receptor-binding CAR T cells using biotin-labelled fusion protein
  • Jurkat cells and/or primary CD4+ T cells and CD8+ T cells were stably 1004874325 73 transduced by lentivirus (3rd gen LV system) to express an anti-nfP2X 7 chimeric antigen receptor (CAR), wherein the CAR comprised an antigen binding domain for binding to the E200 epitope of the P2X 7 receptor.
  • the Jurkat nfP2X 7 reporter cell line was grown as a single cell clone expressing the nfP2X7-CAR by FACS sorting.
  • the CAR constructs also contained a truncated EGFR (tEGFR) downstream a ribosomal skip site (T2A) as a marker gene, for use in enabling detection of successfully transduced cells after enrichment while the CAR receptor was still occupied by the enrichment reagents (DetR1 or DetR2 as exemplary dimeric or monomeric Fc attenuated fusion proteins and as set forth in Table 1).
  • nfP2X7-CAR-tEGFR expressing cells were mixed with Jurkat nfP2X7-CAR-tEGFR expressing cells at a 1:1 ratio or primary generated nfP2X 7 CAR T cell products were used.
  • One round of positive selection was performed as outlined below.
  • a fusion protein comprising the sequence of SEQ ID NO: 149 was labelled with a biotin label.
  • the Fc fusion protein was conjugated to biotin by EZ-LinkTM NHS-LC-LC- Biotin (ThermoFisher, catalog number 21343) according to manufacturer instructions.
  • the labelled Fc fusion protein was added to the mixture of untransduced and transduced cells at indicated concentrations of 1 or 2 ⁇ g/ml, and the cell/fusion protein mixture was incubated for 10 minutes at room temperature and washed in Magnetic Activated Cell Sorting (MACS) cell separation buffer (Miltenyi Biotec) according to manufacturer instructions.
  • Method 1 Either anti-biotin microbeads (Miltenyi Biotec, 130-090-485) were then added to this mixture, which was incubated for a further 15 minutes at 4 °C.
  • the anti-biotin microbeads are magnetic particles coated with anti-biotin antibody to enable separation of cells bound by the anti-biotin antibody coated microbeads.
  • the probe in the final step is removed from the magnetic field and the magnetically retained material is then eluted.
  • the eluted material comprises those Jurkat cells or primary T cells which were successfully transduced with the lentiviral vector and express the nfP2X 7 -CAR and are therefore capable of being bound by the biotin-labelled fusion protein comprising the E200 epitope of the P2X 7 receptor.
  • Figure 1 shows the results of the enrichment protocol, pre- and post-enrichment, after 0 hr and 48 hr post-enrichment of Jurkat nfP2X 7 CAR T cells, whereby tEGFR was used as the marker gene to identify the CAR expressing cells.
  • FIG. 1 shows the results of the enrichment protocol, pre- and post-enrichment, after 0 hr and 48 hr post-enrichment of “Donor 12” nfP2X 7 CAR T cells whereby tEGFR was used as the marker gene to identify the CAR expressing cells.
  • Figure 3 shows the results of the enrichment protocol, pre- and post-enrichment, after 0 hr and 48 hr post-enrichment of “Donor 12” nfP2X7 CAR T cells (using a CAR with an alternative nfP2X7 receptor-antigen binding domain to the above paragraph, “CAR2”), whereby tEGFR was used as the marker gene to identify the CAR expressing cells.
  • Direct detection of nfP2X 7 CAR positive cells was done by indirect staining using the same LC- LC-biotinylated Fc attenuated fusion protein DetR1 or 2 and a secondary anti-biotin antibody.
  • Figure 4 shows the results of the enrichment protocol, pre- and post-enrichment using the EasySep technology as a comparison to the MACS technology in Figure 3, after 0 hr and 48 hr post-enrichment of “Donor 12” nfP2X 7 CAR T cells, whereby tEGFR was used as the marker gene to identify the CAR expressing cells.
  • FIG. 5 shows the results of the enrichment protocol, pre- and post-enrichment, after 0 hr and 48 hr post-enrichment of “Donor 57” nfP2X7 CAR T cells, whereby tEGFR was used as the marker gene to identify the CAR expressing cells.
  • Direct detection of nfP2X 7 CAR positive cells was done by indirect staining using the same LC-LC- biotinylated Fc attenuated fusion protein DetR1 or 2 and a secondary anti-biotin antibody.
  • the enrichment was done by MACS technology.
  • the data illustrates the enrichment with the dimeric, Fc-attenuated fusion protein DetR1 (SEQ ID NO: 149) compared to the monomeric, Fc-attenuated fusion protein DetR1 (SEQ ID NO: 145) and the monomeric, Fc-attenuated fusion protein DetR2 (SEQ ID NO: 146).
  • the direct detection of the CAR receptor shows still a partially occupied situation of the isolated CAR positive cells.
  • T cells expressing anti-nfP2X 7 CAR were detected by staining of CAR T cells with biotinylated DetR2 (SEQ ID NO: 146) and then with a secondary anti-biotin antibody in Vioblue (130-113-857 Biotin Antibody, VioBlue®, Miltenyi Biotech).
  • SEQ ID NO: 146 biotinylated DetR2
  • a secondary anti-biotin antibody in Vioblue (130-113-857 Biotin Antibody, VioBlue®, Miltenyi Biotech).
  • Example 2 Enrichment using monomeric fusion proteins leads to less activation and exhaustion compared to homodimeric fusion proteins 1004874325 78 [0266] A similar series of enrichment experiments to those described in Example 1 were performed.
  • CAR T cells were enriched using either a monomeric fusion protein or a dimeric fusion protein, each comprising a peptide moiety capable of being bound by the CAR or protein.
  • the fusion proteins used in this experiment comprise the amino acid sequences of SEQ ID NOs: 158 (monomeric) and 149 (which is capable of forming homodimers in vitro).
  • Figure 7 shows the levels of CD25+/CD69+ expression (each measures of T cell activation) and the levels of PD-1 expression (a measure of T cell exhaustion), at 24 hours, 48 hours and 72 hours following enrichment with varying concentrations of the fusion proteins (10 ng/ml to 400 ng/ml).
  • the results show that enrichment using a monomeric fusion protein leads to significantly less T cell activation and significantly less T cell exhaustion, in a concentration dependent manner, compared to when using a dimeric fusion protein.
  • Example 3 Efficiency, viability and yield following CAR T enrichment using Biotin beads and MS columns [0270] Enrichment of CAR T cells using MACS technology was performed according to “method 1” in Example 1. T cells were obtained from three healthy donors (donors 50, 53 and 71, D50, D53 and D71). [0271] Figure 8 shows that enrichment using monomeric or dimeric fusion proteins is approximately equivalent, indicating that there is no significant loss of enrichment potential using a monomeric fusion protein as compared to a dimeric fusion protein. [0272] The results shown are indicative of two repeat experiments using T cells from donors 50 and 71. [0273] Figure 9 shows cell counts on Days 1 and 2 post MACS sorting, normalised to maximal cell count expected.
  • Results shown demonstrate that there is a significantly higher 1004874325 79 cell count obtained when using a monomeric fusion protein for the enrichment process, compared to when using a homodimeric fusion protein.
  • Results shown are for T cells obtained from two health donors (donor 50 and donor 71).
  • Figure 10 shows the viability of cells 2 days following MACS sorting, as measured by the percentage of 7AAD negative cells in the cell population. The results show reduced overall cell viability when enrichment is performed using a dimeric fusion protein when compared to using a monomeric fusion protein. The results shown are indicative of two repeat experiments using T cells from donors 50 and 71.
  • Figure 11 shows CD25+/CD69+ expression and PD-1 expression of the enriched CAR T cells, 2 days following MACS sorting.
  • the results show that cells enriched using a dimeric fusion protein have significantly higher levels of the markers of activation CD25 and CD69, compared to cells that are enriched using a monomeric fusion protein. Further, cells enriched using a dimeric fusion protein have significantly higher levels of the exhaustion marker PD-1 compared to cells enriched using a monomeric fusion protein.

Abstract

L'invention concerne des protéines de fusion et leurs utilisations pour l'obtention et l'isolement de populations enrichies de cellules immunitaires. Des exemples de protéines de fusion comprennent celles comprenant une fraction d'épitope de récepteur P2X7 purinergique dysfonctionnel (P2X7R) et une région Fc d'un anticorps.
PCT/AU2023/050890 2022-09-14 2023-09-14 Enrichissement de cellules immunitaires modifiées WO2024055077A1 (fr)

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