EP4188959A1 - Anti-variable muc1* antibodies and uses thereof - Google Patents

Anti-variable muc1* antibodies and uses thereof

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Publication number
EP4188959A1
EP4188959A1 EP21850106.2A EP21850106A EP4188959A1 EP 4188959 A1 EP4188959 A1 EP 4188959A1 EP 21850106 A EP21850106 A EP 21850106A EP 4188959 A1 EP4188959 A1 EP 4188959A1
Authority
EP
European Patent Office
Prior art keywords
antibody
cells
consensus sequence
seq
peptide
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Pending
Application number
EP21850106.2A
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German (de)
English (en)
French (fr)
Other versions
EP4188959A4 (en
Inventor
Cynthia Bamdad
Benoit Smagghe
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Minerva Biotechnologies Corp
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Minerva Biotechnologies Corp
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Publication of EP4188959A1 publication Critical patent/EP4188959A1/en
Publication of EP4188959A4 publication Critical patent/EP4188959A4/en
Pending legal-status Critical Current

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    • 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
    • C07K16/30—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants from tumour cells
    • C07K16/3076—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants from tumour cells against structure-related tumour-associated moieties
    • C07K16/3092—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants from tumour cells against structure-related tumour-associated moieties against tumour-associated mucins
    • 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
    • A61K39/464469—Tumor associated carbohydrates
    • A61K39/46447—Mucins, e.g. MUC-1
    • 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
    • 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
    • C12N5/0602—Vertebrate cells
    • C12N5/0634—Cells from the blood or the immune system
    • C12N5/0636—T lymphocytes
    • 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
    • A61K2039/505—Medicinal preparations containing antigens or antibodies comprising antibodies
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K2239/00—Indexing codes associated with cellular immunotherapy of group A61K39/46
    • A61K2239/10—Indexing codes associated with cellular immunotherapy of group A61K39/46 characterized by the structure of the chimeric antigen receptor [CAR]
    • A61K2239/11—Antigen recognition domain
    • A61K2239/13—Antibody-based
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K2239/00—Indexing codes associated with cellular immunotherapy of group A61K39/46
    • A61K2239/10—Indexing codes associated with cellular immunotherapy of group A61K39/46 characterized by the structure of the chimeric antigen receptor [CAR]
    • A61K2239/22—Intracellular domain
    • 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
    • C07K14/70503—Immunoglobulin superfamily
    • C07K14/7051—T-cell receptor (TcR)-CD3 complex
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/30—Immunoglobulins specific features characterized by aspects of specificity or valency
    • C07K2317/34—Identification of a linear epitope shorter than 20 amino acid residues or of a conformational epitope defined by amino acid residues
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/60—Immunoglobulins specific features characterized by non-natural combinations of immunoglobulin fragments
    • C07K2317/62—Immunoglobulins specific features characterized by non-natural combinations of immunoglobulin fragments comprising only variable region components
    • C07K2317/622—Single chain antibody (scFv)
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/70—Immunoglobulins specific features characterized by effect upon binding to a cell or to an antigen
    • C07K2317/73—Inducing cell death, e.g. apoptosis, necrosis or inhibition of cell proliferation
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/01—Fusion polypeptide containing a localisation/targetting motif
    • C07K2319/03—Fusion polypeptide containing a localisation/targetting motif containing a transmembrane segment
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/33—Fusion polypeptide fusions for targeting to specific cell types, e.g. tissue specific targeting, targeting of a bacterial subspecies
    • 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
    • C12N2510/00—Genetically modified cells

Definitions

  • the present application relates to human, humanized and non-human anti-MUC1* antibodies and methods of making and using them.
  • the present application also relates to using an immune cell transfected or transduced with a cleavage enzyme for the treatment of cancer.
  • the present invention also relates to using an immune cell transfected or transduced with a CAR and another protein for the treatment of cancer. [0003] 2.
  • MUC1 cleaved form of the MUC1 (SEQ ID NO:1) transmembrane protein is a growth factor receptor that drives the growth of over 75% of all human cancers.
  • MUC1* pronounced muk 1 star
  • Cleavage and release of the bulk of the extracellular domain of MUC1 unmasks a binding site for activating ligands dimeric NME1, NME6, NME7, NME7 AB , NME7-X1 or NME8.
  • MUC1* is a determinant of trastuzumab (Herceptin) resistance in breast cancer cells,” Breast Cancer Res Treat. 118(1):113-124). After MUC1 cleavage most of its extracellular domain is shed from the cell surface.
  • Antibodies are increasingly used to treat human diseases. Antibodies generated in non-human species have historically been used as therapeutics in humans, such as horse antibodies. More recently, antibodies are engineered or selected so that they contain mostly, or all, human sequences in order to avoid a generalized rejection of the foreign antibody. The process of engineering recognition fragments of a non-human antibody into a human antibody is generally called ‘humanizing’. The amount of non-human sequences that are used to replace the human antibody sequences determines whether they are called chimeric, humanized or fully human. [0006] Alternative technologies exist that enable generation of humanized or fully human antibodies.
  • CAR T chimeric antigen receptor T cell
  • CAR T chimeric antigen receptor T cell
  • a chimeric receptor having an extra cellular domain that recognizes a tumor antigen, a transmembrane domain and cytoplasmic tail comprising T cell signaling and co-stimulatory components
  • Such receptor is composed of a single chain antibody fragment (scFv) that recognizes a tumor antigen, linked to a T cell transmembrane, signaling domain and co-stimulatory domain or domains.
  • T cells are isolated from a patient or donor and transduced with a CAR, expanded and then injected back into the patient. If from a donor, the immune cells may be mutated or engineered such that they do not induce graft versus host disease in the recipient. When the CAR T cells bind to the antigen on a cancer cell, the CAR T cells attack the cancer cells and then expand that population of T cells. [0008] Thus far, CAR T therapies have been very successful in the treatment of blood cancers but as yet have not shown efficacy against solid tumors in humans.
  • the CAR T cells can just eliminate all of the patient’s B cells without causing serious harm to the patient.
  • Most tumor associated antigens are also expressed on normal tissues; they are just expressed at a higher level in cancerous tissues.
  • the challenge is to develop an antibody that recognizes an epitope on a tumor associated antigen that is somehow different in the context of the tumor compared to normal tissue.
  • the antibody should recognize and bind to cancerous tissues at least two-times more than normal tissues. Antibodies that are not so cancer selective may be used therapeutically if they are inducibly expressed at the tumor site.
  • BiTEs Bispecific T cell Engagers
  • the BiTE approach attempts to eliminate the CAR T associated risk of off-tumor/on-target effects.
  • BiTEs are bispecific antibodies that should not pose any greater risk than regular antibody-based therapies.
  • BiTEs are designed to bind to an antigen on the tumor cell and simultaneously bind to an antigen on an immune cell, such as a T cell. In this way, a BiTE recruits the T cell to the tumor.
  • BiTEs are engineered proteins that simultaneously bind to a cancer associated antigen and a T cell surface protein such as CD3-epsilon.
  • BiTEs are antibodies made by genetically linking the scFv’s of an antibody that binds to a T cell antigen, like anti-CD3-epsilon to a scFv of a therapeutic monoclonal antibody that binds to a cancer antigen (Patrick A. Baeuerle, and Carsten Reinhardt (2009) Bispecific T cell engaging antibodies for cancer therapy. Cancer Res. 69(12):4941-4944).
  • a drawback of BiTE technology is that, unlike CAR T cells, they do not expand in the patient, so have limited persistence.
  • ADC antibody drug conjugate
  • a toxin or a precursor to a toxin, is linked to a cancer selective antibody.
  • ADCs carry a toxic payload to the tumor.
  • Drawbacks of ADCs include the potential of delivering the toxic payload to normal cells and that most ADCs require binding to a cell surface molecule which then gets internalized after binding, with an approximate 10,000 surface molecule required for resultant cell death.
  • the present invention is directed to a non-human, human or humanized anti-MUC1* antibody or antibody fragment or antibody-like protein that binds to a region on extracellular domain of MUC1 isoform or cleavage product that is devoid of the tandem repeat domains.
  • the non-human, human or humanized anti-MUC1* antibody or antibody fragment or antibody-like protein may specifically bind to [0012] (i) PSMGFR region of MUC1; [0013] (ii) PSMGFR peptide; [0014] (iii) a peptide having amino acid sequence of QFNQYKTEAASRYNLTISDVSVSDVPFPFSAQSGA (N-10) (SEQ ID NO:3) [0015] (iv) a peptide having amino acid sequence of [0016] ASRYNLTISDVSVSDVPFPFSAQSGA (N-19) (SEQ ID NO:4) [0017] (v) a peptide having amino acid sequence of [0018] NLTISDVSVSDVPFPFSAQSGA (N-23) (SEQ ID NO:5) [0019] (vi) a peptide having amino acid sequence of [0020] ISDVSVSDVPFPFSAQSGA (N-26) (SEQ ID NO:6) [0021] (vii) a
  • the human or humanized antibody fragment or antibody-like protein may be scFv or scFv-Fc.
  • the murine, camelid, human or humanized antibody, antibody fragment or antibody-like protein as in above may comprise a heavy chain variable region and light chain variable region which is derived from mouse monoclonal MNC2, MNE6, 20A10, 3C2B1, 5C6F3, 25E6, 18G12, 28F9, 1E4, B12, B2, B7, B9, 8C7F3, and H11 antibody, and has at least 80%, 90% or 95% or 98% sequence identity to the mouse monoclonal MNC2, MNE6, 20A10, 3C2B1, 5C6F3, 25E6, 18G12, 28F9, 1E4, B12, B2, B7, B9, 8C7F3, and H11 antibody.
  • the heavy chain variable region of CDR1 and CDR2 may have at least 90% or 95% or 98% sequence identity to the particularly indicated antibody heavy chain variable region sequence set forth in the present application in the sequence listing, and the light chain variable region of CDR1 and CDR2 may have at least 90% or 95% or 98% sequence identity to the particularly indicated antibody heavy chain variable region sequence set forth in the present application in the sequence listing section.
  • the heavy chain variable region of CDR3 may have at least 80% or 85% or 90% sequence identity to the particularly indicated antibody heavy chain variable region sequence set forth in the present application in the sequence listing, and the light chain variable region of CDR3 may have at least 80% or 85% or 90% sequence identity to the particularly indicated antibody heavy chain variable region sequence set forth in the present application in the sequence listing section.
  • the murine, camelid, human or humanized antibody, antibody fragment or antibody-like protein according to above may include complementarity determining regions (CDRs) in the heavy chain variable region and light chain variable region having at least 90% or 95% or 98% sequence identity to the particularly indicated antibody heavy chain CDR1, CDR2 or CDR3 region and light chain CDR1, CDR2 or CDR3 region sequences set forth in the present application in the sequence listing section.
  • CDRs complementarity determining regions
  • the present invention is directed to an anti-MUC1* extracellular domain antibody or anti-N-10 antibody, which may be any of the antibodies described above, comprised of sequences represented by humanized IgG2 heavy chain, or humanized IgG1 heavy chain, paired with humanized Kappa light chain, or humanized Lambda light chain.
  • the humanized IgG2 heavy chain may be SEQ ID NOS:55
  • humanized IgG1 heavy chain may be SEQ ID NO:58
  • humanized Kappa light chain may be SEQ ID NO:110
  • humanized Lambda light chain may be SEQ ID NO:114, or a sequence having 90%, 95% or 98% sequence identity thereof.
  • the present invention is directed to an anti-MUC1* extracellular domain antibody or anti-N-10 antibody, which may be any of the antibodies described above, comprised of sequences represented by human IgG2 heavy chain, or human IgG1 heavy chain, paired with human Kappa light chain, or human Lambda light chain.
  • the human IgG2 heavy chain may be SEQ ID NOS:55
  • human IgG1 heavy chain may be SEQ ID NO:58
  • human Kappa light chain may be SEQ ID NO:110
  • human Lambda light chain may be SEQ ID NO:114, or a sequence having 90%, 95% or 98% sequence identity thereof.
  • the invention is directed to an anti-MUC1* extracellular domain antibody or anti-N-10 antibody comprised of sequences of a humanized MNC2 represented by humanized IgG1 heavy chain, humanized IgG2 heavy chain, paired with humanized Lambda light chain, and humanized Kappa light chain.
  • the invention is directed to an anti-MUC1* extracellular domain antibody or anti-N-10 antibody comprised of sequences of a humanized MNC2, MNE6, 20A10, 3C2B1, 5C6F3, 25E6, 18G12, 28F9, 1E4, B12, B2, B7, B9, 8C7F3, or H11 represented by humanized IgG1 heavy chain or humanized IgG2 heavy chain, paired with humanized Lambda light chain, or humanized Kappa light chain.
  • a humanized MNC2, MNE6, 20A10, 3C2B1, 5C6F3, 25E6, 18G12, 28F9, 1E4, B12, B2, B7, B9, 8C7F3, or H11 represented by humanized IgG1 heavy chain or humanized IgG2 heavy chain, paired with humanized Lambda light chain, or humanized Kappa light chain.
  • the invention is directed to an antibody that is “like” MNC2, MNE6, 20A10, 3C2B1, 5C6F3, 25E6, 18G12, 28F9, 1E4, B12, B2, B7, B9, 8C7F3, or H11 in that they have the same or very similar pattern of binding to subsets of peptides derived from the PSMGFR peptide, also do not recognize a linear epitope, competitively inhibit the binding of NME1 or NME7AB to MUC1*, recognize a MUC1 transmembrane cleavage product produced by cleavage by MMP9 or contain CDR sequences that are at least 80% homologous to the MNE6, MNC2, MN18G12, MN20A10, MN25E6, MN28F9, MN5C6F3, MN3C2B1, and MN1E4 CDR consensus sequences.
  • the invention is directed to an antibody that binds to the extra cellular domain of a MUC1 that is devoid of the tandem repeat domain, which may be a cleavage product.
  • the antibody binds to a peptide having the sequence of QFNQYKTEAASRYNLTISDVSVSDVPFPFSAQSGA (N-10).
  • the antibody binds to a peptide having the sequence of ASRYNLTISDVSVSDVPFPFSAQSGA (N-19).
  • the antibody binds to a peptide having the sequence of SVSDVPFPFSAQSGA (N-30).
  • the antibody binds to a peptide having the sequence of FPFSAQSGA (N-36).
  • examples of such antibodies include but are not limited to monoclonal antibodies MNC2, MNE6, 20A10, 3C2B1, 5C6F3, 25E6, 18G12, 28F9, 1E4, B12, B2, B7, B9, 8C7F3, and H11.
  • the heavy chain and light chain complementary determining region sequences for these antibodies are set forth in the present application in the sequence listing section.
  • one or more of these antibodies is administered to a patient diagnosed with or at risk of developing a cancer.
  • the antibody may be human or humanized.
  • the antibody may be murine or camelid.
  • the antibody may be bivalent or monovalent.
  • the antibody may be a fragment, including a single chain fragment, scFv, of one of the antibodies.
  • the antibody or antibody fragment may be administered directly to the patient or incorporated into a multi-specific antibody-like molecule, a bispecific antibody, a bispecific T cell engager , BiTE, or an antibody drug conjugate, ADC.
  • the antibody or antibody fragment may be incorporated into a T cell receptor, TCR.
  • the sequence of the antibody or antibody fragment may be incorporated into a chimeric antigen receptor, a “CAR”, or other similar entity, then introduced into an immune cell, ex vivo, then administered to a patient diagnosed with or at risk of developing a cancer.
  • the immune cell which may be a T cell or natural killer cell, may be derived from a donor or from the patient.
  • the immune cell is derived from a stem cell that has been directed to differentiate to that immune cell type in vitro.
  • the immune cell is derived from a stem cell that has been directed to differentiate to that immune cell type in vitro.
  • a CAR containing sequences of the antibody are expressed in a stem cell, which then may be differentiated into an immune cell.
  • the immune cell is a T cell.
  • the immune cell is an NK cell.
  • the antibody or a CAR containing sequences of the antibody may be expressed off of an inducible promoter.
  • the antibody or the CAR is expressed upon activation of the T cell or other immune cell.
  • the antibody or the CAR of the invention is expressed off of an NFAT response element.
  • CAR recognition of a target tumor cell activates the immune cell, leading to NFAT inducible expression of a cytokine, such as IL-12 or IL-18, or expression of a checkpoint inhibitor such as a PD1 inhibitor or a PDL-1 inhibitor.
  • CAR recognition of a target tumor cell activates the immune cell, leading to NFAT inducible expression of a second CAR that contains sequences of a second antibody.
  • the invention is directed to a murine, camelid, human, humanized anti-MUC1* antibody or antibody fragment or antibody-like protein that binds to the N-10 peptide, according to above, which inhibits the binding of NME protein to MUC1*.
  • the NME may be NME1, NME6, NME7AB, NME7-X1, NME7 or NME8.
  • the invention is directed to a single chain variable fragment (scFv) comprising a heavy and light chain variable regions connected via a linker, further comprising CDRs of antibodies that bind to MUC1* extracellular domain.
  • the CDRs may be derived from MNC2, MNE6, 20A10, 3C2B1, 5C6F3, 25E6, 18G12, 28F9, 1E4, B12, B2, B7, B9, 8C7F3, and H11.
  • the scFv may be one that possesses the SEQ ID NOS:233, 235 or 237 (MNE6); SEQ ID NOS:238-243, 654-655 or 5017-5020 (MNC2); SEQ ID NOS:1574-1581 or 5001-5012 (20A10); SEQ ID NOS:1573 or 1813 (3C2B1); SEQ ID NOS:1385 or 1815 (5C6F3); SEQ ID NOS:1599 or 1601 (25E6).
  • the invention is directed to a chimeric antigen receptor (CAR) comprising a scFv or a humanized variable region that binds to the extracellular domain of a MUC1 that is devoid of tandem repeats, a linker molecule, a transmembrane domain and a cytoplasmic domain.
  • CAR chimeric antigen receptor
  • the single chain antibody fragment may bind to [0042] (i) PSMGFR region of MUC1; [0043] (ii) PSMGFR peptide; [0044] (iii) a peptide having amino acid sequence of QFNQYKTEAASRYNLTISDVSVSDVPFPFSAQSGA (N-10) (SEQ ID NO:3) [0045] (iv) a peptide having amino acid sequence of [0046] ASRYNLTISDVSVSDVPFPFSAQSGA (N-19) (SEQ ID NO:4) [0047] (v) a peptide having amino acid sequence of [0048] NLTISDVSVSDVPFPFSAQSGA (N-23) (SEQ ID NO:5) [0049] (vi) a peptide having amino acid sequence of [0050] ISDVSVSDVPFPFSAQSGA (N-26) (SEQ ID NO:6) [0051] (vii) a peptide having amino acid sequence of [0052] SVSDVPFPFSAQS
  • the CAR also comprises a transmembrane region and a cytoplasmic tail that comprises sequence motifs that signal immune system activation.
  • the extracellular domain may be comprised of murine, camelid, human, non-human, or humanized single chain antibody fragments of an MNC2, MNE6, 20A10, 3C2B1, 5C6F3, 25E6, 18G12, 28F9, 1E4, B12, B2, B7, B9, 8C7F3, and H11.
  • Additional antibodies from which single chain antibody fragments may be made include but are not limited to monoclonal antibodies that are like MNC2, MNE6, 20A10, 3C2B1, 5C6F3, 25E6, 18G12, 28F9, 1E4, B12, B2, B7, B9, 8C7F3, and H11 in that they have the same or very similar pattern of binding to subsets of peptides derived from the PSMGFR peptide, may not recognize a linear epitope or competitively inhibit the binding of NME1 or NME7AB to MUC1*, or recognize a MUC1 transmembrane cleavage product produced by cleavage by MMP9 or contain CDR sequences that are at least 80% homologous to the MNC2, MNE6, 20A10, 3C2B1, 5C6F3, 25E6, 18G12, 28F9, 1E4, B12, B2, B7, B9, 8C7F3, and H11 CDR consensus sequences.
  • the extracellular domain may include a murine, camelid, human, non-human or humanized single chain antibody fragments of an MNE6 scFv set forth as SEQ ID NOS: 233, 235, or 237, MNC2 scFv (SEQ ID NOS:239, 241,243, 655 or 5017-5020), 20A10 scFv as set forth as SEQ ID NOS:1575, 1577, 1579, 1581 or 5001-5012, 3C2B1 scFv as set forth as SEQ ID NOS:1573 or 1813, 5C6F3 scFv as set forth as SEQ ID NOS:1385 or 1815, or 25E6 scFv as set forth as SEQ ID NOS:1599 or 1601.
  • MNE6 scFv set forth as SEQ ID NOS: 233, 235, or 237
  • MNC2 scFv SEQ ID NOS:239, 241,243, 655 or 5017-50
  • CDRs complementarity determining regions
  • framework regions constant regions
  • Various computer programs are available that assign certain sequences to the CDRs, framework regions and constant regions. Depending on the program used, the exact position where one region ends and the next begins may differ by a few amino acids.
  • scFvs humanized single chain constructs, scFvs, contain heavy and light chain CDRs supported by intervening framework regions, wherein the heavy and light chain are connected through a flexible linker.
  • the sequence assigned to framework region IV may extend into the constant region. In some cases, extension of framework region IV may provide more stability to the scFv.
  • framework region IV of the light chain may vary.
  • the C-terminus of Framework region IV ends in the amino acids R, T. In other cases, it ends in R alone. Still in other cases, the terminal R and T are both omitted.
  • the extracellular domain may include a murine, camelid, human, non-human or humanized single chain antibody fragments with framework region IV having variable lengths as set forth as MNE6 scFv (SEQ ID NOS: 5014 or 5016), MNC2 scFv (SEQ ID NOS: 5018 or 5020), or 20A10 scFv (SEQ ID NOS: 5002, 5004, 5006, 5008, 5010 or 5012) or 25E6 scFv (SEQ ID NOS: 5030 or 5032).
  • MNE6 scFv SEQ ID NOS: 5014 or 5016
  • MNC2 scFv SEQ ID NOS: 5018 or 5020
  • 20A10 scFv SEQ ID NOS: 5002, 5004, 5006, 5008, 5010 or 5012
  • 25E6 scFv SEQ ID NOS: 5030 or 5032
  • the cytoplasmic tail may be comprised of one or more of signaling sequence motifs and co-stimulatory domains, including but not limited to CD3-zeta, CD3-zeta-1XX CD27, CD28, 4-1BB, OX40, CD30, CD40, ICAm-1, LFA-1, ICOS, CD2, CD5, or CD7. Additionally, the sequence of the intracellular signaling domain may contain mutations that dampen the signal to improve persistence or to improve killing of low antigen density tumor cells.
  • the cytoplasmic tail may be comprised of one or more of signaling sequence motifs and co-stimulatory sequence motifs CD3-zeta, CD27, CD28, 4- 1BB, OX40, CD30, CD40, ICAm-1, LFA-1, ICOS, CD2, CD5, or CD7.
  • the transmembrane and extracellular hinge region of the CAR may or may not be derived from sequences of the adjacent co-stimulatory domain.
  • a CAR comprising the 4-1BB co-stimulatory domain may have a transmembrane and hinge region derived from CD8 or CD28.
  • a CAR comprising the CD28 co-stimulatory domain may have a transmembrane and hinge region derived from CD28.
  • the cytoplasmic tails may include deletions or mutations that dampen signaling.
  • deletions or mutations in one or more of the three immunoreceptor tyrosine-based activation motifs, also known as ITAMs increase persistence of CAR bearing cells and decrease their differentiation as measured by an increase in the CD62L+ CD45RA- population.
  • ITAMs include but are not limited to Tyrosines that are mutated to inhibit phosphorylation and signaling (Salter et al, 2018).
  • one or two ITAMs are deleted, leaving only one or two ITAMs (Feucht et al 2019).
  • the position of the included ITAM or ITAMs is moved to a position proximal to the co-stimulatory domain.
  • Suitable ITAM configurations for increased persistence of CARs include but are not limited to 1XX, X2X, XX3, 12X and 23X, wherein the numeral 1, 2 or 3 refers to ITAM1, ITAM2, or ITAM3 and X refers to the deletion of that ITAM.
  • ITAM1 is the only functional ITAM included in the CAR construct, also known as 1XX.
  • the ITAMs of CD3-zeta may be deleted or mutated to inhibit or dampen signaling.
  • the CD3 of the cytoplasmic tail may comprise deletions or mutations in or of the ITAMs including those referred to as 1XX (Feucht et al 2019; SEQ ID NO:1796- 1797).
  • the T cell may be engineered to overexpress c- Jun as a method to inhibit T cell exhaustion (Lynn et al 2019).
  • the CAR constructs described above may be expressed in a T cell, an NK cell, a dendritic cell or other immune cell, which may be autologous or allogeneic. Allogeneic cells may be derived from human stem cells.
  • the CAR may include a single chain antibody fragment, scFv comprising a sequence derived from antibody MNE6, including but not limited to (SEQ ID NOS:12-13 and 65-66, 56-57, 107-108, 341-342, 391-394), from antibody MNC2, including but not limited to (SEQ ID NOS:118-119 and 168-169, 144-145 and 194-195, 654-655, 1788-1789), from antibody 20A10, including but not limited to (SEQ ID NOS:988-989 and 1004-1005, 1574-1581, 5001-5012, 1677, 1687), from antibody 3C2B1, including but not limited to (SEQ ID NOS:1820-1823, 1572-1573, 1812-1813), from antibody 5C6F3, including but not limited to (SEQ ID NOS:1816-1819, 1384-1385, 1814- 1815), from antibody 25E6, including but not limited to (SEQ ID NOS:10
  • the sequence may be CAR MNE6 CD28/CD3z (SEQ ID NOS:298); CAR MNE6 4-1BB/CD3z (SEQ ID NOS:301); CAR MNE6 OX40/CD3z (SEQ ID NOS:617); CAR MNE6 CD28/4-1BB/CD3z (SEQ ID NOS:304); CAR MNE6 CD28/OX40/CD3z (SEQ ID NOS:619); CAR MNC2 CD3z (SEQ ID NOS:607); CAR MNC2 CD8 hinge/transmembrane CD28/CD3z SEQ ID NOS:609); CAR MNC2 CD8 hinge/transmembrane 4-1BB/CD3z (SEQ ID NOS:611 and SEQ ID NOS: 719); CAR MNC2 CD8 hinge/transmembrane 4-1BB/1XX (SEQ ID NOS:1619 and SEQ ID NOS: 1621
  • the invention is directed to a composition that includes at least two CARs with different extracellular domain units transfected into the same cell, which may be an immune cell, which may be derived from the patient requiring treatment for a cancer.
  • the expression of the second CAR may be inducible and driven by the recognition of a target by the first CAR.
  • the nucleic acid encoding the second CAR may be linked to an inducible promoter.
  • the expression of the second CAR may be induced by an event that occurs specifically when the immune cell mounts an immune response to a target tumor cell.
  • the antibody fragments of one or both of the CARs may direct the cell to a MUC1* positive tumor.
  • the antibody fragments of the first and second CARs may bind to a MUC1* that is produced when MUC1 is cleaved by two different cleavage enzymes.
  • Expression of the second CAR by the inducible promoter may be induced when the antibody fragment of the first CAR engages or binds to a MUC1 or MUC1* on the tumor.
  • One way to do this is to induce expression of the second CAR when, or shortly after, an NFAT protein is expressed or translocated to the nucleus.
  • a sequence derived from an NFAT promoter region is put upstream of the gene for the second CAR.
  • the NFAT protein may be NFAT1 also known as NFATc2, NFAT2 also known as NFATc or NFATc1, NFAT3 also known as NFATc4, NFAT4 also known as NFATc3, or NFAT5.
  • the NFAT is NFATc1, NFATc3 or NFATc2.
  • the NFAT is NFAT2 also known as NFATc1.
  • SEQ ID NO:646 shows nucleic acid sequence of the upstream transcriptional regulatory region for NFAT2.
  • the recognition unit of the second CAR may be an antibody fragment or a peptide, wherein the recognition units may bind to NME7, PD-1, PDL-1, or a checkpoint inhibitor.
  • the at least two CARs may have one CAR that does not have a tumor antigen targeting recognition unit and the other CAR does have a tumor antigen targeting recognition unit.
  • one of the extracellular domain recognition units may bind to MUC1* extracellular domain.
  • one of the extracellular domain recognition units may be an antibody fragment and the other is a peptide, which may be devoid of transmembrane and signaling motifs; the peptide may be a single chain antibody fragment or antibody.
  • one of the recognition units may bind PD-1 or PDL-1.
  • one extra cellular domain recognition unit is an anti-MUC1* antibody, antibody fragment or scFv chosen from the group consisting of MNC2, MNE6, 20A10, 3C2B1, 5C6F3, 25E6, 18G12, 28F9, 1E4, B12, B2, B7, B9, 8C7F3, and H11.
  • the other recognition unit may be a CAR or may be an anti-NME7 antibody.
  • the invention is directed to a cell comprising a CAR with an extracellular domain that binds to the extra cellular domain of a MUC1 molecule that is devoid of tandem repeats.
  • the invention is directed to a cell comprising a CAR with an extracellular domain that binds to a MUC1* transfected or transduced cell.
  • the cell that includes the CAR may be an immune system cell, preferably a T cell, a natural killer cell (NK), a dendritic cell or mast cell.
  • the invention is directed to an engineered antibody-like protein.
  • the invention is directed to a method for treating a disease in a subject comprising administering an antibody according to any claim above, to a person suffering from the disease, wherein the subject expresses MUC1 aberrantly.
  • the disease may be cancer, such as breast cancer, ovarian cancer, pancreatic cancer, lung cancer, colon cancer, gastric cancer or esophageal cancer.
  • the invention is directed to an antibody, antibody fragment or scFv comprising variable domain fragments derived from an antibody that binds to an extracellular domain of MUC1 isoform or cleavage product that is devoid of the tandem repeat domains.
  • the antibody or antibody fragment binds to the N-10 peptide (SEQ ID NO:3), but does not bind to the C-10 peptide (SEQ ID NO:825).
  • the variable domain fragments may be derived from mouse monoclonal antibody MNE6 (SEQ ID NO:13 and 66) or from the humanized MNE6 (SEQ ID NO: 39 and 94), or from MNE6 scFv (SEQ ID NO: 233, 235 and 237).
  • variable domain fragments may be derived from mouse monoclonal antibody MNC2 (SEQ ID NO: 119 and 169) or from the humanized MNC2 (SEQ ID NO: 145 and 195), or from MNC2 scFv (SEQ ID NO: 239, 241 and 243).
  • the variable domain may be derived from monoclonal antibodies MN18G12, MN20A10, MN25E6, MN28F9, MN5C6F3, MN3C2B1, or MN1E4.
  • the heavy chain and light chain complementary determining region sequences for these antibodies are also set forth in the sequence listing herein.
  • the invention is directed to a method for the treatment of a person diagnosed with, suspected of having or at risk of developing a MUC1 or MUC1* positive cancer involving administering to the person an effective amount of the antibody, antibody fragment or scFv described above, wherein the species may be murine, camelid, human or humanized.
  • the invention is directed to a polypeptide comprising at least two different scFv sequences, wherein one of the scFv sequences is a sequence that binds to extracellular domain of MUC1 isoform or cleavage product that is devoid of the tandem repeat domains.
  • the polypeptide may bind to [0073] (i) PSMGFR region of MUC1; [0074] (ii) PSMGFR peptide; [0075] (iii) a peptide having amino acid sequence of QFNQYKTEAASRYNLTISDVSVSDVPFPFSAQSGA (N-10) (SEQ ID NO:3) [0076] (iv) a peptide having amino acid sequence of [0077] ASRYNLTISDVSVSDVPFPFSAQSGA (N-19) (SEQ ID NO:4) [0078] (v) a peptide having amino acid sequence of [0079] NLTISDVSVSDVPFPFSAQSGA (N-23) (SEQ ID NO:5) [0080] (vi) a peptide having amino acid sequence of [0081] ISDVSVSDVPFPFSAQSGA (N-26) (SEQ ID NO:6) [0082] (vii) a peptide having amino acid sequence of [0083] SVSDVPFPFSAQSGA
  • the cell may be cancer cell.
  • the invention is directed to a method for testing a subject’s cancer for suitability of treatment with a composition comprising antibodies of the invention, which may be murine, camelid, human or humanized, or fragments thereof, or portions of the variable regions of antibodies MNC2, MNE6, 20A10, 3C2B1, 5C6F3, 25E6, 18G12, 28F9, 1E4, B12, B2, B7, B9, 8C7F3, or H11, comprising the steps of contacting a bodily specimen from the patient, in vitro, ex-vivo, or in vivo, with the antibody and determining that the patient exhibits aberrant expression of MUC1* compared to normal tissue or specimen and concluding that the patient’s cancer will beneficially respond to treatment with an agent comprising the antibody or a fragment thereof.
  • the invention is directed to a method of treating a subject suffering from a disease comprising, exposing immune cells, which may be T cells or NK cells from the subject, or from a donor, to MUC1* peptides wherein through various rounds of maturation, the T cells or NK cells develop MUC1* specific receptors, creating adapted T cells or NK cells, and expanding and administering the adapted cells to the donor patient who is diagnosed with, suspected of having, or is at risk of developing a MUC1* positive cancer.
  • immune cells which may be T cells or NK cells from the subject, or from a donor
  • MUC1* peptides wherein through various rounds of maturation, the T cells or NK cells develop MUC1* specific receptors, creating adapted T cells or NK cells, and expanding and administering the adapted cells to the donor patient who is diagnosed with, suspected of having, or is at risk of developing a MUC1* positive cancer.
  • the MUC1* peptide is chosen from among the group: [0093] (i) PSMGFR region of MUC1; [0094] (ii) PSMGFR peptide; [0095] (iii) a peptide having amino acid sequence of QFNQYKTEAASRYNLTISDVSVSDVPFPFSAQSGA (N-10) [0096] (iv) a peptide having amino acid sequence of [0097] ASRYNLTISDVSVSDVPFPFSAQSGA (N-19) [0098] (v) a peptide having amino acid sequence of [0099] NLTISDVSVSDVPFPFSAQSGA (N-23) [00100] (vi) a peptide having amino acid sequence of [00101] ISDVSVSDVPFPFSAQSGA (N-26) [00102] (vii) a peptide having amino acid sequence of [00103] SVSDVPFPFSAQSGA (N-30) [00104] (viii) a peptide having amino acid sequence
  • the antibody can be administered alone, as a monovalent antibody, as an scFv, or a fragment of the antibody can be incorporated into a CAR, a BiTE or an ADC.
  • the antibody that is administered to a patient for the treatment or prevention of a MUC1 or MUC1* positive cancer is selected for its ability to bind to the QFNQYKTEAASRYNLTISDVSVSDVPFPFSAQSGA (N-10) peptide, wherein the presence of the FPFSAQSGA (N-36) sequence is required for binding.
  • the antibody can be administered alone, as a monovalent antibody, as an scFv, or a fragment of the antibody can be incorporated into a CAR, a BiTE or an ADC.
  • the antibody that is administered to a patient for the treatment or prevention of a MUC1 or MUC1* positive cancer is selected for its inability to recognize a linear epitope of MUC1 or MUC1*.
  • the antibody can be administered alone, as a monovalent antibody, as an scFv, or a fragment of the antibody can be incorporated into a CAR, a BiTE or an ADC.
  • the antibody that is administered to a patient for the treatment or prevention of a MUC1 or MUC1* positive cancer is selected for its ability to recognize the MUC1 transmembrane cleavage product after it has been cleaved by MMP9.
  • the antibody can be administered alone, as an antibody, a monovalent antibody, as an scFv, a bispecific antibody, a multi-specific antibody, or a fragment of the antibody can be incorporated into a BiTE, an ADC, or a CAR which can be expressed in an immune cell.
  • the antibody that is administered to a patient for the treatment or prevention of a MUC1 or MUC1* positive cancer is selected for its ability to competitively inhibit the binding of NME7 AB or NME7-X1 to the extra cellular domain of a MUC1 that is devoid of tandem repeats.
  • the antibody can be administered alone, as an antibody, a monovalent antibody, as an scFv, a bispecific antibody, a multi-specific antibody, or a fragment of the antibody can be incorporated into a BiTE, an ADC, or a CAR which can be expressed in an immune cell.
  • the invention is directed to a method of treating cancer in a patient comprising administering to the patient the antibody, antibody fragment, BiTE, ADC or CAR expressed in an immune cell of any of the above, in combination with a checkpoint inhibitor.
  • any of the antibodies, or variable regions thereof, set forth in the following may be used: MNC2, MNE6, 20A10, 3C2B1, 5C6F3, 25E6, 18G12, 28F9, 1E4, B12, B2, B7, B9, 8C7F3, or H11.
  • any of the variable regions set forth in the following may be used: [00118] (i) an anti-MUC1* extracellular domain antibody or anti-N-10 antibody comprised of sequences of a humanized MN-E6 represented by humanized IgG2 heavy chain, or humanized IgG1 heavy chain, paired with humanized Kappa light chain, or humanized Lambda light chain; [00119] (ii) an antibody of (i), wherein the humanized IgG2 heavy chain is SEQ ID NOS:53, humanized IgG1 heavy chain is SEQ ID NO:57, humanized Kappa light chain is SEQ ID NO:108, and humanized Lambda light chain is SEQ ID NO:112, or a sequence having 90%, 95% or 98% sequence identity thereof; [00120] (iii) an anti-MUC1* extracellular domain antibody or anti-N-10 antibody comprised of sequences of a humanized MN-C2 represented by humanized IgG1 heavy chain, humanized I
  • the extracellular domain may be comprised of humanized single chain antibody fragments of an MN-E6 scFv set forth as SEQ ID NOS: 233, 235, or 237), MN-C2 scFv (SEQ ID NOS:239, 241, or 243).
  • the cytoplasmic tail may be comprised of one or more of signaling sequence motifs and co- stimulatory domains, including but not limited to CD3-zeta-1XX, CD27, CD28, 4-1BB, OX40, CD30, CD40, ICAm-1, LFA-1, ICOS, CD2, CD5, or CD7 and CD3-zeta or variants 1XX, X2X, XX3, 12X, or 23X.
  • the sequence of the intracellular signaling domain may contain mutations that dampen the signal to improve persistence or target cell killing.
  • the method above may include two CARs with different extracellular domain units transfected into the same cell.
  • One of the extracellular domain recognition units may bind to MUC1* extracellular domain.
  • One of the extracellular domain recognition units may bind to PD-1.
  • One of the extracellular domain recognition units may be an antibody fragment and the other may be a peptide or an anti-MUC1* antibody fragment.
  • the method may include an immune cell transfected or transduced with a plasmid encoding a CAR and a plasmid encoding a non-CAR species that is expressed from an inducible promoter.
  • the non-CAR species may be expressed from an inducible promoter that is activated by elements of an activated immune cell.
  • the non-CAR species may be expressed from an NFAT inducible promoter.
  • the NFAT may be NFATc1, NFATc3 or NFATc2.
  • the cleavage enzyme may be MMP2, MMP3, MMP9, MMP13, MMP14, MMP16, ADAM10, ADAM17, or ADAM28, or a catalytically active fragment thereof.
  • the non-CAR species may be a cytokine.
  • the cytokine may be IL-7, IL-12, IL-15 or IL-18.
  • the present invention is directed to an antibody, or fragment thereof, for the diagnosis, treatment or prevention of cancers wherein the antibody specifically binds to the PSMGFR peptide (SEQ ID NO:2) or a fragment thereof of the peptide.
  • the antibody binds to the N-10 peptide (SEQ ID NO:3), N-19 peptide (SEQ ID NO:4), N-23 peptide (SEQ ID NO:5), N-26 peptide (SEQ ID NO:6), N-30 peptide (SEQ ID NO:7), N-10/C-5 peptide (SEQ ID NO:8), N-19/C-5 peptide (SEQ ID NO:9), or C-5 peptide (SEQ ID NO:825).
  • the antibody interacts with a peptide comprising conformational epitope SVSDV (SEQ ID NO:1751) and FPFSA (SEQ ID NO:1747) within N-26 sequence ISDVSVSDVPFPFSAQSGA (SEQ ID NO:6), wherein mutation or deletion of FPFS (SEQ ID NO:1747) destroys binding of the antibody or fragment thereof to the N-26 peptide.
  • the antibody interacts with a peptide comprising conformational epitope ASRYNLT (SEQ ID NO:1745), SVSDV (SEQ ID NO:1751), and FPFSA (SEQ ID NO:1747) within the N-19 sequence ASRYNLT ISDVSVSDVPFPFSAQSGA (SEQ ID NO:4), wherein mutation or deletion of ASRYNLT (SEQ ID NO:1745) destroys binding of the antibody or fragment thereof to the N-26 peptide.
  • the antibody does not bind to the C-10 peptide (SEQ ID NO:825).
  • the antibody binds to the N-10 peptide (SEQ ID NO:3), but not to the C-10 peptide (SEQ ID NO:825).
  • the antibody inhibits interaction between NME7AB and MUC1*.
  • the antibody inhibits interaction between NME7 AB and PSMGFR peptide (SEQ ID NO:2).
  • the antibody inhibits interaction between NME7AB and N-10 peptide (SEQ ID NO:3), N- 19 peptide (SEQ ID NO:4), N-23 peptide (SEQ ID NO:5), N-26 peptide (SEQ ID NO:6), N-30 peptide (SEQ ID NO:7), N-10/C-5 peptide (SEQ ID NO:8), N-19/C-5 peptide (SEQ ID NO:9), or C-5 peptide (SEQ ID NO:825).
  • the antibody recognizes a MUC1 transmembrane enzymatic cleavage product.
  • the cleavage enzyme is MMP14 or MMP9 or a catalytically active fragment thereof of the enzyme.
  • the antibody binds to PSMGFR (SEQ ID NO:2) or fragment thereof in which presence of an amino acid sequence within PSMGFR (SEQ ID NO:2) induces binding of the antibody to the PSMGFR.
  • the amino acid sequence of the binding conformationally inducing peptide is present in N-10 peptide (SEQ ID NO:3).
  • the antibody does not bind to a linear form of the binding conformationally inducing peptide sequence wherein the linear form of the peptide is a denatured form.
  • the binding conformationally inducing peptide sequence is in the N-26 peptide sequence ISDVSVSDVPFPFSAQSGA (SEQ ID NO:6), wherein mutation or deletion of FPFS (SEQ ID NO:1747) destroys binding of the antibody or fragment thereof to the N-26 peptide.
  • the binding conformationally inducing peptide sequence is located within the N-19 sequence ASRYNLTISDVSVSDVPFPFSAQSGA (SEQ ID NO:4), wherein mutation or deletion of ASRYNLT (SEQ ID NO:1745) destroys binding of the antibody or fragment thereof to the N-19 peptide.
  • the binding inducing peptide sequence may be located within the N-26 sequence ISDVSVSDVPFPFSAQSGA (SEQ ID NO:6), wherein mutation or deletion within FPFS (SEQ ID NO:1747) destroys binding of the antibody or fragment thereof to PSMGFR.
  • the antibodies may have a consensus sequence.
  • heavy chain CDR1 comprises consensus sequence at least 90% identical to sequence: F or I at position 1, T at position 2, F at position 3, S at position 4, T, G, or R at position 5, Y at position 6, A, G or T at position 7, M at position 8 and S at position 9;
  • heavy Chain CDR2 comprises consensus sequence at least 90% identical to sequence: T at position 1, I or S at position 2, I or S at position 3, G or R at position 5, G or A at position 6, T or I at position 9, Y at position 10, Y at position 11, P or S at position12 and DSVKG for positions 13- 17;
  • heavy chain CDR3 comprises consensus sequence at least 90% identical to sequence:_ G, L, or N at position 2, G or T at position 4, Y at position 7, D or E at position 12, A at position 14, and Y at position 15;
  • light chain CDR1 comprises consensus sequence at least 90% identical to sequence: K or R at position 1, A or S at position 2, S at position 3, K or Q at position 4, S at position 5, L or V at position
  • An antibody binding to a conformational epitope within a peptide having the N-26 sequence ISDVSVSDVPFPFSAQSGA (SEQ ID NO:6), wherein mutation or deletion within FPFS (SEQ ID NO:1747), SVSDV (SEQ ID NO:1751), or ASRYNLT (SEQ ID NO:1745) destroys binding of the antibody or fragment thereof to PSMGFR.
  • heavy chain CDR1 comprises consensus sequence at least 90% identical to sequence: F or I at position 1, T or A at position 2, F at position 3, S at position 4, T, G, or R at position 5, Y or F at position 6, A, G or T at position 7, M at position 8 and S at position 9;
  • heavy Chain CDR2 comprises consensus sequence at least 90% identical to sequence: T or A at position 1, I or S at position 2, I or S at position 3, N, S, T or G at position 4, G or R at position 5, G or A at position 6, G, T, or D at position 7, Y, K, H or S at position 8, T or I at position 9, Y or F at position 10, Y at position 11, P or S at position12 and D at position 13, S or T at position 14, V or L at position 15 and KG for positions 16-17;
  • heavy chain CDR3 comprises consensus sequence at least 90% identical to sequence: G, L, or N at position 2, G, T, or or N at position 2, G, T, or or R at position 5, Y or F at position 6, A, G or T at
  • heavy chain CDR1 comprises consensus sequence FTFSGYAMS; [00160] heavy Chain CDR2 comprises consensus sequence TISSGGTYIYYPDSVKG; [00161] heavy chain CDR3 comprises consensus sequence -LGGDNYYEYFDV--; [00162] light chain CDR1 comprises consensus sequence RASKS--VSTSGYSYMH; [00163] light Chain CDR2 comprises consensus sequence LASNLES; and [00164] light chain CDR3 comprises consensus sequence QHSRELPFT.
  • heavy chain CDR1 comprises consensus sequence FTFSRYGMS
  • heavy Chain CDR2 comprises consensus sequence TISGGGTYIYYPDSVKG
  • heavy chain CDR3 comprises consensus sequence DNYGRNYDYGMDY--
  • light chain CDR1 comprises consensus sequence -------SATSSVSYIH
  • light Chain CDR2 comprises consensus sequence STSNLAS
  • light chain CDR3 comprises consensus sequence QQRSSSPFT.
  • heavy chain CDR1 comprises consensus sequence FAFSTFAMS; [00174] heavy Chain CDR2 comprises consensus sequence AISNGGGYTYYPDTLKG; [00175] heavy chain CDR3 comprises consensus sequence ----RYYDLYFDL--; [00176] light chain CDR1 comprises consensus sequence RSSQNIV-HSNGNTYLE; [00177] light Chain CDR2 comprises consensus sequence KVSNRFS; and [00178] light chain CDR3 comprises consensus sequence FQDSHVPLT.
  • heavy chain CDR1 comprises consensus sequence FTFSRYGMS; [00181] heavy Chain CDR2 comprises consensus sequence TISSGGTYIYYPDSVKG; [00182] heavy chain CDR3 comprises consensus sequence DNYGSSYDYAMDY--; [00183] light chain CDR1 comprises consensus sequence RSSQTIV-HSNGNTYLE; [00184] light Chain CDR2 comprises consensus sequence KVSNRFS; and [00185] light chain CDR3 comprises consensus sequence FQDSHVPLT.
  • heavy chain CDR1 comprises consensus sequence FTFSRYGMS; [00188] heavy Chain CDR2 comprises consensus sequence TISSGGTYIYYPDSVKG; [00189] heavy chain CDR3 comprises consensus sequence DNYGSSYDYAMDY--; [00190] light chain CDR1 comprises consensus sequence -------SASSSVSYMH; [00191] light Chain CDR2 comprises consensus sequence TTSNLAS; and [00192] light chain CDR3 comprises consensus sequence QQRSSYPF-.
  • heavy chain CDR1 comprises consensus sequence FTFSTYAMS; [00195] heavy Chain CDR2 comprises consensus sequence AISNGGGYTYYPDSLKG; [00196] heavy chain CDR3 comprises consensus sequence ----RYYDHYFDY--; [00197] light chain CDR1 comprises consensus sequence --RASESVATYGNNFMQ; [00198] light Chain CDR2 comprises consensus sequence LASTLDS; and [00199] light chain CDR3 comprises consensus sequence QQNNEDPPT.
  • heavy chain CDR1 comprises consensus sequence FAFSTFAMS; [00202] heavy Chain CDR2 comprises consensus sequence AISNGGGYTYYPDTLKG; [00203] heavy chain CDR3 comprises consensus sequence ----RYYDLYFDL--; [00204] light chain CDR1 comprises consensus sequence RSSQNIV-HSNGNTYLE; [00205] light Chain CDR2 comprises consensus sequence KVSNRFS; and [00206] light chain CDR3 comprises consensus sequence FQDSHVPLT.
  • heavy chain CDR1 comprises consensus sequence SYGVH; [00209] heavy Chain CDR2 comprises consensus sequence VIWPGGSTNYNSTLMSRM; [00210] heavy chain CDR3 comprises consensus sequence DRTPRVGAWFAY; and [00211] light chain CDR1 comprises consensus sequence RASESVATYGNNFMQ; [00212] light Chain CDR2 comprises consensus sequence LASTLDS; and [00213] light chain CDR3 comprises consensus sequence QQNNEDPPT.
  • heavy chain CDR1 comprises consensus sequence FTFSTYAMS; [00216] heavy Chain CDR2 comprises consensus sequence -SIGRAGSTYYSDSVKG; [00217] heavy chain CDR3 comprises consensus sequence ---GPIYNDYDEFAY; [00218] light chain CDR1 comprises consensus sequence KSSQSVLYSSNQKNYLA; [00219] light Chain CDR2 comprises consensus sequence WASTRES; and [00220] light chain CDR3 comprises consensus sequence HQYLSSLT.
  • 3C2B1 having [00222] heavy chain CDR1 comprises consensus sequence ITFSTYTMS; [00223] heavy Chain CDR2 comprises consensus sequence TISTGGDKTYYSDSVKG; [00224] heavy chain CDR3 comprises consensus sequence -GTTAMYYYAMDY; [00225] light chain CDR1 comprises consensus sequence RASKS---ISTSDYNYIH ; [00226] light Chain CDR2 comprises consensus sequence LASNLES; and [00227] light chain CDR3 comprises consensus sequence QHSRELPLT.
  • the invention is directed to an antibody, or fragment thereof, for the diagnosis, treatment or prevention of cancers that requires presence of antibody binding conformationally inducing peptide ASRYNLT (SEQ ID NO:1745) of PSMGFR (SEQ ID NO:2).
  • the antibody may be 25E6, having [00229] heavy chain CDR1 comprises consensus sequence FTFSSYGMS; [00230] heavy Chain CDR2 comprises consensus sequence TISNGGRHTFYPDSVKG; [00231] heavy chain CDR3 comprises consensus sequence QTGTEGWFAY; [00232] light chain CDR1 comprises consensus sequence KSSQSLLDSDGKTYLN; [00233] light Chain CDR2 comprises consensus sequence LVSKLDS _; and [00234] light chain CDR3 comprises consensus sequence WQGTHFPQT.
  • the invention is directed to an antibody, or fragment thereof, for the diagnosis, treatment or prevention of cancers that requires presence of antibody binding conformationally inducing peptide SVSDV (SEQ ID NO:1761) of PSMGFR (SEQ ID NO:2).
  • the antibody may be 5C6F3, having [00236] heavy chain CDR1 comprises consensus sequence FTFSTYAMS ; [00237] heavy Chain CDR2 comprises consensus sequence AISNGGGYTYYPDSLKG; [00238] heavy chain CDR3 comprises consensus sequence RYYDHYFDY; [00239] light chain CDR1 comprises consensus sequence RSSQTIVHSNGNTYLE; [00240] light Chain CDR2 comprises consensus sequence KVSNRFS; and [00241] light chain CDR3 comprises consensus sequence FQDSHVPLT. [00242] The antibody or fragment thereof according all of the above may be murine, camelid, human or humanized.
  • the antibody fragment may be scFv or scFv-Fc, which variable regions thereof may be murine, camelid, human or humanized.
  • the invention is directed to a chimeric antigen receptor (CAR) comprising the antibody fragments of above, and may further comprise mutations in the co- stimulatory domain or mutations or deletions of one or two of the ITAMs of the CD3-zeta signaling domain.
  • Tyrosines may be mutated in CD28 or 4-1BB.
  • CD3-zeta may contain a single ITAM such as only ITAM1 also known as 1XX, ITAM2 also known as X2X, or ITAM3 also known as XX3.
  • CD3-zeta may contain two ITAMs, wherein the positions of the ITAMs may be moved to a more proximal position such as 12X or 23X (Feucht et al 2019).
  • tyrosines of one or two ITAMs may be mutated to dampen signaling.
  • the CD3-zeta domain is 1XX.
  • An example of 1XX mutations includes those exemplified in SEQ ID NOS: 1796-1797.
  • the invention is directed to an immune cell comprising the CAR of above. Immune cell may be T cell, NK cell, dendritic cell, or mast cell.
  • the immune cell is derived from a stem cell that has been directed to differentiate to that immune cell type in vitro.
  • a CAR containing sequences of the antibody are expressed in a stem cell, which then may be differentiated into an immune cell.
  • the invention is directed to a cell composition expressed in a cell comprising a CARs of above, and second entity having a biological recognition unit that has a specificity that is different from that of the CAR.
  • the second entity may bind PD-1, PDL-1, or other checkpoint inhibitor, or NME7, or a cytokine such as IL-12 or IL-18, or c- Jun.
  • the invention is directed to an immune cell engineered to express a nucleic encoding a CAR of above and a nucleic acid encoding a second entity as in any of the claims above wherein the second entity expressed from an inducible promoter.
  • the second entity may be expressed from an inducible promoter that is activated by elements of an activated immune cell.
  • the second entity may be expressed from an NFAT inducible promoter.
  • NFAT may be NFATc1, NFATc3 or NFATc2.
  • the second entity may be a cytokine such as IL-7, IL-15, or IL-18.
  • the nucleic acids encoding the second entity may be inserted into a Foxp3 promoter or enhancer region, wherein the cytokine is IL-18.
  • the cytokine may be expressed from an NFAT inducible promoter.
  • the invention is directed to a BiTE construct comprising the antibody fragment of above.
  • the invention is directed to an antibody drug conjugate (ADC) comprising the antibody or antibody fragment of above.
  • ADC antibody drug conjugate
  • the present invention is directed to an antibody or fragment thereof that specifically: [00250] (i) binds to PSMGFR (SEQ ID NO:2) and N-10 (SEQ ID NO:3); and [00251] does not bind to full-length MUC1; [00252] (ii) does not bind to C-10 (SEQ ID NO:825); [00253] (iii) competitively inhibits binding of NME1 or NME7AB to MUC1* extra cellular domain or a PSMGFR peptide; [00254] (iv) recognizes a MUC1* generated by cleavage by a cleavage enzyme; [00255] (v) recognizes a conformational epitope and not a linear epitope; or [00256] (vi) is cancer selective by immunohistochemistry on tissues.
  • the cancer may be breast cancer, pancreatic cancer, ovarian cancer, lung cancer, colon cancer, gastric cancer or esophageal cancer.
  • the present invention is also directed to a method of diagnosing, treating or preventing cancer by administering the antibodies and fragments disclosed herein to a cancer patient in need thereof that has been identified as expressing MUC1 aberrantly and expressing truncated MUC1, such as MUC1*.
  • FIGS 1A-1D show cell growth assay graphs of MUC1* positive cells treated with either bivalent ‘bv’ anti-MUC1* antibody, monovalent ‘mv’ or Fab, NM23-H1 dimers or NME7-AB.
  • Bivalent anti-MUC1* antibodies stimulate growth of cancer cells whereas the monovalent Fab inhibits growth (Fig. 1A-1B).
  • Classic bell-shaped curve indicates ligand induced dimerization stimulates growth.
  • FIG. 1C Dimeric NM23-H1, aka NME1, stimulates growth of MUC1* positive cancer cells but siRNA to suppress MUC1 expression eliminate its effect (Fig.1C). NME7-AB also stimulates the growth of MUC1* positive cells (Fig.1D).
  • Figures 2A-2I show results of ELISA assays. MUC1* peptides PSMGFR, PSMGFR minus 10 amino acids from the N-terminus aka N-10, or PSMGFR minus 10 amino acids from the C-terminus, aka C-10 are immobilized on the plate and the following are assayed for binding: NME7-AB (Fig. 2A), MNC2 monoclonal antibody (Fig. 2B), MNE6 monoclonal antibody (Fig.
  • MUC1* peptides PSMGFR minus 10 amino acids from the N-terminus aka N-10, or PSMGFR minus 10 amino acids from the C-terminus, aka C-10, are immobilized on the plate and the following are assayed for binding: MNC3 (Fig. 2E) and MNC8 (Fig. 2F).
  • Fig. 2G shows the amino acid sequence of the PSMGFR peptide.
  • Fig. 2H shows the amino acid sequence of the N-10 peptide.
  • FIG.2I shows the amino acid sequence of the C-10 peptide.
  • Figures 3A-3C show results of competitive ELISA assays.
  • the PSMGFR MUC1* peptide is immobilized on the plate and dimeric NM23-H1, aka NME1, is added either alone or after the MNE6 antibody has been added (Fig.3A).
  • NM23-H7, NME7-AB is added alone or after MNE6 has been added
  • Results show that MNE6 competitively inhibits the binding of MUC1* activating ligands NME1 and NME7.
  • Fig. 3A shows that MNE6 competitively inhibits the binding of MUC1* activating ligands NME1 and NME7.
  • ZR-75-1 aka 1500, MUC1* positive breast cancer cells were stained with 1:2 or 1:10 dilutions of the 1.5 ug/ml humanized MNC2. After two washes, cells were stained with secondary antibody, Anti-Penta-His antibody conjugated to Alexa 488 (Qiagen) dilutions of 1:200 (Fig. 4A), 1:50 (Fig. 4B), or 1:10 (Fig. 4C) to detect the 6x His tag on the huMNC2 scFv.
  • Fig. 4A shows huMNC2 binding to ZR-75-1 breast cancer cells where secondary antibody is added at a 1:200 dilution.
  • FIG. 4B shows huMNC2 binding to ZR-75-1 breast cancer cells where secondary antibody is added at a 1:50 dilution.
  • Fig. 4C shows huMNC2 binding to ZR-75-1 breast cancer cells where secondary antibody is added at a 1:10 dilution.
  • Flow cytometric analysis revealed a concentration-dependent shift of a subset of cells, indicating specific binding, which is unseen in the absence of the MNC2 scFv (Fig.4A- 4C).
  • Fig. 4D shows anti-MUC1* antibody MNE6 staining of MUC1 negative HCT-116 colon cancer cells transfected with the empty vector, single cell clone #8.
  • FIG.4E shows anti- MUC1* antibody MNE6 staining of HCT-116 colon cancer cells transfected with MUC1* single cell clone #10.
  • Fig. 4F shows anti-MUC1* antibody MNE6 staining of ZR-75-1, aka 1500, MUC1* positive breast cancer cells. As the FACS scans show, both MNC2 and MNE6 only stain MUC1* positive cells and not MUC1 or MUC1* negative cells.
  • Figure 5 shows a graph of an ELISA in which surface is coated with either the MUC1* PSMGFR peptide or a control peptide. Humanized MNC2 scFv is then incubated with the surface, washed and detected according to standard methods.
  • FIGS. 6A-6B show graphs of cancer cell growth inhibition by MUC1* antibody variable region fragment humanized MNC2 scFv.
  • hMNC2 scFv potently inhibited the growth of ZR-75-1, aka 1500, MUC1* positive breast cancer cells (Fig. 6A) and T47D MUC1* positive breast cancer cells (Fig. 6B) with approximately the same EC-50 as the in vitro ELISAs.
  • Figures 7A-7B show graphs of tumor growth in immune compromised mice that have been implanted with human tumors then treated with anti-MUC1* antibody MNE6 Fab or mock treatment.
  • Female nu/nu mice implanted with 90-day estrogen pellets were implanted with 6 million T47D human breast cancer cells that had been mixed 50/50 with Matrigel. Mice bearing tumors that were at least 150 mm 3 and had three successive increases in tumor volume were selected for treatment. Animals were injected sub cutaneously twice per week with 80 mg/kg MNE6 Fab and an equal number of mice fitting the same selection criteria were injected with vehicle alone (Fig. 7A).
  • mice Male NOD/SCID mice were implanted with 6 million DU-145 human prostate cancer cells that had been mixed 50/50 with Matrigel. Mice bearing tumors that were at least 150 mm 3 and had three successive increases in tumor volume were selected for treatment. Animals were injected sub-cutaneously every 48 hours with 160 mg/kg MNE6 Fab and an equal number of mice fitting the same selection criteria were injected with vehicle alone (Fig. 7B). Tumors were measured independently by two researchers twice per week and recorded. Statistics were blindly calculated by independent statistician, giving a P value of 0.0001 for each. Anti-MUC1* Fab inhibited breast cancer growth and prostate cancer growth. Treatment had no effect on weight, bone marrow cell type or number.
  • Figure 8 shows a graph of an ELISA wherein the surface was immobilized with either PSMGFR peptide, PSMGFR minus 10 amino acids from the N-terminus or minus 10 amino acids from the C-terminus.
  • the huMNE6 scFv-Fc bound to the PSMGFR peptide and to the PSMGFR N-10 peptide but not to the PSMGFR C-10 peptide.
  • the parent MNE6 antibody and the humanized MNE6 require the C-terminal 10 amino acids of PSMGFR for binding.
  • Figures 9A-9B show graphs of ELISAs wherein the assay plate surface was immobilized with either PSMGFR peptide, PSMGFR minus 10 amino acids from the N- terminus or minus 10 amino acids from the C-terminus. The MNC3 antibody variants were then assayed for binding to the various MUC1* peptides.
  • Fig. 9A shows purified mouse monoclonal MNC3 antibody; and
  • Figure 9B shows the humanized MNC3 scFv-Fc.
  • ELISAs show binding to the PSMGFR peptide as well as to certain deletion peptides.
  • Figures 10A-10J Figs. 10A10B are photographs of breast cancer tissue arrays. Fig.
  • FIG. 10A was stained with VU4H5 which recognizes MUC1-FL (full length); Fig. 10B was stained with mouse monoclonal antibody MNC2 which recognizes cancerous MUC1*. Following automated staining (Clarient Diagnostics), the tissue staining was scored using Allred scoring method which combines an intensity score and a distribution score.
  • Figs. 10C10F are color coded graphs showing the score calculated for MUC1 full-length staining for each patient’s tissue.
  • Figs. 10G10J are color coded graphs showing the score calculated for MUC1* staining for each patient’s tissue.
  • Figures 11A-11J. Figs. 11A11B are photographs of breast cancer tissue arrays. Fig.
  • Figs. 11A was stained with VU4H5 which recognizes MUC1-FL (full length); Fig. 11B was stained with mouse monoclonal antibody MNC2 which recognizes cancerous MUC1*. Following automated staining (Clarient Diagnostics), the tissue staining was scored using Allred scoring method which combines an intensity score and a distribution score.
  • Figs.11C- 11F are color coded graphs showing the score calculated for MUC1 full-length staining for each patient’s tissue.
  • Figs. 11G-11J are color coded graphs showing the score calculated for MUC1* staining for each patient’s tissue.
  • Figures 12A-12H show photographs of normal breast and breast cancer tissues stained with humanized MNE6-scFv-Fc biotinylated anti-MUC1* antibody at 2.5 ug/mL, then stained with a secondary streptavidin HRP antibody.
  • Fig. 12A is a normal breast tissue.
  • Figs.12B-12D are breast cancer tissues from patients as denoted in the figure.
  • Figs.12E-12H are photographs of the corresponding serial sections that were stained with the secondary antibody alone.
  • Figures 13A-13F show photographs of normal breast and breast cancer tissues stained with humanized MNE6-scFv-Fc biotinylated anti-MUC1* antibody at 2.5 ug/mL, then stained with a secondary streptavidin HRP antibody.
  • Fig. 13A is a normal breast tissue.
  • Figs.13B-13C are breast cancer tissues from patients as denoted in the figure.
  • Figs.13D-13F are photographs of the corresponding serial sections that were stained with the secondary antibody alone.
  • Figures 14A-14H show photographs of breast cancer tissues stained with MNE6 anti-MUC1* antibody at 10 ug/mL, then stained with a rabbit anti mouse secondary HRP antibody.
  • FIGS. 14A-14D are breast cancer tissues from patient #300.
  • Figs. 14E-14H are breast cancer tissues from metastatic patient #291.
  • Figures 15A-15F show photographs of normal lung and lung cancer tissues stained with humanized MNE6-scFv-Fc biotinylated anti-MUC1* antibody at 2.5 ug/mL, then stained with a secondary streptavidin HRP antibody.
  • Fig. 15A is a normal lung tissue.
  • Figs. 15B15C are lung cancer tissues from patients as denoted in the figure.
  • Figs. 15D-15F are photographs of the corresponding serial sections that were stained with the secondary antibody alone.
  • Figures 16A-16F show photographs of normal lung and lung cancer tissues stained with humanized MNE6-scFv-Fc biotinylated anti-MUC1* antibody at 2.5 ug/mL, then stained with a secondary streptavidin HRP antibody.
  • Fig. 16A is a normal lung tissue.
  • Figs. 16B16C are lung cancer tissues from patients as denoted in the figure.
  • Figs. 16D-16F are photographs of the corresponding serial sections that were stained with the secondary antibody alone.
  • Figures 17A-17F show photographs of normal lung and lung cancer tissues stained with humanized MNE6-scFv-Fc biotinylated anti-MUC1* antibody at 25 ug/mL, then stained with a secondary streptavidin HRP antibody.
  • Fig. 17A is a normal lung tissue.
  • Figs. 17B-17C are lung cancer tissues from patients as denoted in the figure.
  • Figs. 17D-17F are photographs of the corresponding serial sections that were stained with the secondary antibody alone.
  • Figures 18A-18F show photographs of normal lung and lung cancer tissues stained with humanized MNE6-scFv-Fc biotinylated anti-MUC1* antibody at 25 ug/mL, then stained with a secondary streptavidin HRP antibody.
  • Fig. 18A is a normal lung tissue.
  • Figs. 18B-18C are lung cancer tissues from patients as denoted in the figure.
  • Figs. 18D-18F are photographs of the corresponding serial sections that were stained with the secondary antibody alone.
  • Figures 19A-19D show photographs of normal small intestine and cancerous small intestine tissues stained with humanized MNE6-scFv-Fc biotinylated anti-MUC1* antibody at 5 ug/mL, then stained with a secondary streptavidin HRP antibody.
  • Fig. 19A is a normal small intestine tissue.
  • Fig.19B is small intestine cancer from patient as denoted in the figure.
  • Figs. 19C-19D are photographs of the corresponding serial sections that were stained with the secondary antibody alone.
  • Figures 20A-20H show photographs of normal small intestine tissues stained with humanized MNE6-scFv-Fc anti-MUC1* antibody at 50 ug/mL, then stained with a secondary goat-anti-human HRP antibody.
  • Figs. 20A-20D are normal small intestine tissue.
  • Figs. 20E- 20H are photographs of the corresponding serial sections that were stained with the secondary antibody alone.
  • Figures 21A-21H show photographs of cancerous small intestine tissues stained with humanized MNE6-scFv-Fc anti-MUC1* antibody at 50 ug/mL, then stained with a secondary goat-anti-human HRP antibody.
  • FIGS. 21A-21D are cancerous small intestine tissue from a patient as denoted in figure.
  • Figs. 21E-21H are photographs of the corresponding serial sections that were stained with the secondary antibody alone.
  • Figures 22A-22H show photographs of cancerous small intestine tissues stained with humanized MNE6-scFv-Fc anti-MUC1* antibody at 50 ug/mL, then stained with a secondary goat-anti-human HRP antibody.
  • Figs. 22A-22D are cancerous small intestine tissue from a patient as denoted in figure.
  • Figs. 22E-22H are photographs of the corresponding serial sections that were stained with the secondary antibody alone.
  • Figures 23A-23H show photographs of normal colon tissues stained with humanized MNE6-scFv-Fc anti-MUC1* antibody at 50 ug/mL, then stained with a secondary goat-anti-human HRP antibody.
  • Figs. 23A-23D are normal colon.
  • Figs. 23E-23H are photographs of the corresponding serial sections that were stained with the secondary antibody alone.
  • Figures 24A-24H show photographs of colon cancer tissues stained with humanized MNE6-scFv-Fc anti-MUC1* antibody at 50 ug/mL, then stained with a secondary goat-anti-human HRP antibody.
  • Figs. 24A-24D are colon cancer tissue from a metastatic patient as denoted in figure.
  • FIGs. 24E-24H are photographs of the corresponding serial sections that were stained with the secondary antibody alone.
  • Figures 25A-25H show photographs of colon cancer tissues stained with humanized MNE6-scFv-Fc anti-MUC1* antibody at 50 ug/mL, then stained with a secondary goat-anti-human HRP antibody.
  • Figs. 25A-25D are colon cancer tissue from a Grade 2 patient as denoted in figure.
  • Figs. 25E-25H are photographs of the corresponding serial sections that were stained with the secondary antibody alone.
  • Figures 26A-26H show photographs of colon cancer tissues stained with humanized MNE6-scFv-Fc anti-MUC1* antibody at 50 ug/mL, then stained with a secondary goat-anti-human HRP antibody.
  • Figs. 26A-26D are colon cancer tissue from a metastatic patient as denoted in figure.
  • Figs. 26E-26H are photographs of the corresponding serial sections that were stained with the secondary antibody alone.
  • Figures 27A-27H show photographs of prostate cancer tissues stained with humanized MNE6-scFv-Fc anti-MUC1* antibody at 50 ug/mL, then stained with a secondary goat-anti-human HRP antibody.
  • FIGS. 27A-27D are prostate cancer tissue from a patient as denoted in figure.
  • FIGs. 27E-27H are photographs of the corresponding serial sections that were stained with the secondary antibody alone.
  • Figures 28A-28H show photographs of prostate cancer tissues stained with humanized MNE6-scFv-Fc anti-MUC1* antibody at 50 ug/mL, then stained with a secondary goat-anti-human HRP antibody.
  • Figs. 28A-28D are prostate cancer tissue from a patient as denoted in figure.
  • Figs. 28E-28H are photographs of the corresponding serial sections that were stained with the secondary antibody alone.
  • Figures 29A-29H show photographs of prostate cancer tissues stained with humanized MNE6-scFv-Fc anti-MUC1* antibody at 50 ug/mL, then stained with a secondary goat-anti-human HRP antibody.
  • Figs. 29A-29D are prostate cancer tissue from a patient as denoted in figure.
  • Figs. 29E-29H are photographs of the corresponding serial sections that were stained with the secondary antibody alone.
  • Figures 30A-30F show photographs of a triple negative breast cancer array stained with anti-MUC1* antibody huMNC2scFv. The first score shown is the Allred score and the second is the tumor grade.
  • FIG. 30A shows the pie chart of score of anti- MUC1* antibody staining.
  • Fig. 30B shows a photograph of the array stained with the antibody.
  • Figs. 30C-30D show magnified photographs of two of the breast cancer specimens from the array.
  • Figs. 30E-30F show more magnified photographs of the portion of the specimen that is marked by a box.
  • Figures 31A-31F show photographs of an ovarian cancer array stained with anti- MUC1* antibody huMNC2scFv. The first score shown is the Allred score and the second is the tumor grade.
  • FIG. 31A shows the pie chart of score of anti-MUC1* antibody staining.
  • Fig. 31B shows a photograph of the array stained with the antibody.
  • Figs. 31C-31D show magnified photographs of two of the breast cancer specimens from the array.
  • Figs.31E- 31F show more magnified photographs of the portion of the specimen that is marked by a box.
  • Figures 32A-32F show photographs of a pancreatic cancer array stained with anti-MUC1* antibody huMNC2scFv. The first score shown is the Allred score and the second is the tumor grade.
  • FIG. 32A shows the pie chart of score of anti-MUC1* antibody staining.
  • Fig. 32B shows a photograph of the array stained with the antibody.
  • Figs. 32C-32D show magnified photographs of two of the breast cancer specimens from the array.
  • Figs. 32E-32F show more magnified photographs of the portion of the specimen that is marked by a box.
  • Figures 33A-33F show photographs of a lung cancer array stained with anti- MUC1* antibody huMNC2scFv. The first score shown is the Allred score and the second is the tumor grade.
  • FIG. 33A shows the pie chart of score of anti-MUC1* antibody staining.
  • Fig. 33B shows a photograph of the array stained with the antibody.
  • Figs. 33C-33D show magnified photographs of two of the breast cancer specimens from the array.
  • Figs.33E- 33F show more magnified photographs of the portion of the specimen that is marked by a box.
  • Figures 34A-34I show photographs of normal tissues stained with anti-MUC1* antibody huMNC2scFv.
  • Figures 35A-35D show FACS scans of cells expressing either no MUC1, MUC1* or full-length MUC1, wherein the cells were probed with either MNC2 or VU4H5.
  • Fig. 35A shows MUC1 negative HCT-116 colon cancer cells probed with antibody MNC2.
  • Fig. 35B shows HCT cells that have been transfected with MUC1* wherein the extra cellular domain is just the sequence of the PSMGFR peptide wherein the cells are probed with antibody MNC2.
  • Fig. 35A shows MUC1 negative HCT-116 colon cancer cells probed with antibody MNC2.
  • Fig. 35B shows HCT cells that have been transfected with MUC1* wherein the extra cellular domain is just the sequence of the PSMGFR peptide wherein the cells are probed with antibody MNC2.
  • HCT-MUC1-18 cells which are a cleavage resistant single cell clone of HCT cells transfected with full-length MUC1, also referred to herein as HCT-MUC1- 41TR, and cells were probed with antibody MNC2.
  • Fig. 35D shows HCT-MUC1-18 cells probed with antibody VU4H5 which is an antibody that recognizes the hundreds of tandem repeats epitopes in full-length MUC1.
  • VU4H5 is an antibody that recognizes the hundreds of tandem repeats epitopes in full-length MUC1.
  • MNC2 recognizes an ectopic epitope that is not accessible in full-length MUC1.
  • Figures 36A-36D show Western blots and corresponding FACs analysis of HCT- 116 cells which are a MUC1 negative colon cancer cell line, that were then stably transfected with either MUC1* or MUC1 full-length.
  • the single cell clones that are shown are HCT- MUC1-41TR, and HCT-MUC1*.
  • Fig.36A shows a Western blot of the parent cell line HCT- 116, HCT-MUC1-41TR and HCT-MUC1* wherein the gel has been probed with a rabbit polyclonal antibody, SDIX, that only recognizes cleaved MUC1.
  • Fig. 36B is a Western blot that was probed with a mouse monoclonal antibody VU4H5 that recognizes the tandem repeats of full-length MUC1. As can be seen, only HCT-MUC1-41TR contains full-length MUC1.
  • FIG. 36C shows FACS scans showing that HCT-MUC1* is 95.7% positive for SDIX which only binds to MUC1* and essentially not at all for MUC1 full-length.
  • Fig. 36D shows FACS scans that show that HCT-MUC1-41TR cells are 95% positive for full-length MUC1 and only about 11% positive for the cleaved form, MUC1*.
  • Figure 37A-37C shows western blots and a bar graph of FACS analysis assessing the ability of MNC2to recognize a full-length MUC1 after it has been cleaved by MMP9. Fig.
  • FIG. 37A shows a Western blot of HCT-MUC1-18 cells, which are a cleavage resistant cell line, to which was added cleavage enzyme MMP9.
  • the cell lysate fraction was run on a gel and probed with a polyclonal anti-PSMGFR antibody.
  • the photo shows that in a dose dependent manner, MMP9 cleaved MUC1 to MUC1*, the ⁇ 25kDa species.
  • Fig.37B shows the Western blot of the conditioned media from the same experiment.
  • the photo shows that the addition of cleavage enzyme MMP9, in a dose dependent manner, increased the release of the tandem repeat domain into the conditioned media.
  • Fig. 37C shows FACS analysis of the experiment.
  • FIG. 38 shows a photograph of a Western blot in which HCT-MUC1-18 cells, labeled here as HCT-18, a cleavage resistant single cell clone of HCT cells transfected with full-length MUC1, are treated with varying amounts of a catalytically active ADAM17 or MMP14.
  • FIG. 39A-39B shows fluorescence activated cell sorting (FACS) measurements of human CD34+ hematopoietic stem cells of human bone marrow stained with anti-MUC1* monoclonal antibodies MNC3, MNC2, MNE6 or an isotype control antibody.
  • FIG. 40A-40G shows the details of FACS analysis of the hematopoietic stem cells probed with either MNC3 or MNE6.
  • Fig.40A shows the FACS scatter plot of total bone marrow cells.
  • FIG. 40B shows the FACS scatter plot of the CD34+ cells.
  • Fig. 40C shows the FACS histogram of the CD34+ cells.
  • Fig. 40D shows the FACS scatter plot of the earliest hematopoietic stem cells, which are CD34+/CD38-, stained with either MNC3 or MNE6.
  • Fig. 40E shows the histogram of the experiment.
  • Fig. 40F shows the histogram overlay of MNC3 binding to CD34+/CD38- cells versus MNE6.
  • Fig. 40G shows the bar graph of that FACS experiment.
  • Figure 41A-42H shows the details of FACS analysis of CD34+/CD38 -/lo hematopoietic stem cells probed with a polyclonal anti-PSMGFR antibody SDIX, MNE6 or MNC2.
  • Fig.41A shows the FACS scatter plot of the CD34+/CD38 -/lo population of cells.
  • Fig. 41E shows a table of the detailed analysis.
  • Fig. 41B shows the FACS scatter plot of the CD34+/CD38 -/lo population of cells probed with the anti-PSMGFR polyclonal antibody SDIX.
  • Fig. 41F shows a table of the detailed analysis.
  • Fig. 41A shows the FACS scatter plot of the CD34+/CD38 -/lo population of cells probed with the anti-PSMGFR polyclonal antibody SDIX.
  • Fig. 41F shows a table of the detailed analysis.
  • Fig. 41A shows the FACS scatter plot of the CD34+/CD38
  • FIG. 41C shows the FACS scatter plot of the CD34+/CD38 -/lo population of cells probed with MNE6.
  • Fig. 41G shows a table of the detailed analysis.
  • Fig. 41D shows the FACS scatter plot of the CD34+/CD38 -/lo population of cells probed with MNC2.
  • Fig.41H shows a table of the detailed analysis.
  • Figure 42A-42H shows photographs of DU145 prostate cancer cells or T47D breast cancer cells that have been treated with either the Fab of anti-MUC1* antibody MNC2, MNE6, MNC3 or MNC8. The images show that cancer specific antibodies MNC2 and MNE6 effectively kill prostate and breast cancer cells while the monoclonal antibodies MNC3 and MNC8 do not.
  • Figure 43 shows a graph of a PCR experiment comparing expression of a wide range of cleavage enzymes expressed in different cells lines, wherein the values have been normalized to those expressed in breast cancer cell line T47D.
  • Cell lines that are compared are prostate cancer cell line DU145, HCT-MUC1-41TR that is a MUC1 negative colon cancer cell line transfected with a MUC1 whose extracellular domain is truncated after 41 tandem repeat units and that is not cleaved to the MUC1* form, T47D breast cancer cell line and CD34+ bone marrow cells.
  • Figure 43 shows a graph of a PCR experiment in which the expression levels of various cleavage enzymes are measured in DU145 prostate cancer cells, HCT116+MUC1FL, also known as HCT-MUC1-18 a cell line expressing full-length MUC1, T47D breast cancer cells, and CD34+ hematopoietic stem cells of the bone marrow. The fold expression is relative to the expression of each cleavage enzyme in T47D breast cancer cells, set as 1.
  • Figure 44 shows the graph of the PCR experiment of Figure 43 but with the Y- axis maximum set to 5.
  • Figures 45A-45P show photographs of a CAR T co-culture assay in which the targeting antibody fragment of the CAR is huMNC2scFv wherein CAR44 has a CD8 transmembrane domain, followed by 41BB-3zeta and CAR50 has a CD4 transmembrane domain, followed by 41BB-3zeta.
  • the target cancer cells are: HCT-FLR which is HCT-116 cells transfected with MUC1*45 and HCT-MUC1-41TR, which is a stable single cell clone HCT-116 cell line that expresses MUC1 with an extracellular domain truncated after 41 tandem repeats and that does not get cleaved to the MUC1* form on its own.
  • HCT- MUC1-41TR cancer cells were also incubated with conditioned media from cells transfected with MMP9 or ADAM17 before co-culture with the CAR T cells.
  • Conditioned media of the MMP9 or ADAM17 expressing cells were also incubated with APMA which is an activator of those cleavage enzymes.
  • Figs. 45A, 45E, 45I, 45M show photographs of cells co-cultured with untransduced human T cells.
  • Figs. 45B, 45F, 45J, 45N show photographs of cells co-cultured with human T cells transduced with anti-MUC1* CAR44 at an MOI of 10.
  • Figs. 45C, 45G, 45K, 45O show photographs of cells co-cultured with human T cells transduced with anti- MUC1* CAR50 at an MOI of 10.
  • Figs. 45A, 45E, 45I, 45M show photographs of cells co-cultured with untransduced human T cells.
  • Figs. 45B, 45F, 45J, 45N show photographs of cells co-cultured with human T cells transduced with anti-MUC1* CAR44 at an MOI of 10.
  • Figs. 45C, 45G, 45K, 45O show photographs of cells co-cultured with human T cells transduced with anti- MUC1* CAR50 at an
  • 45D, 45H, 45L, 45P show photographs of cells co- cultured with human T cells transduced with anti-MUC1* CAR44 at an MOI of 50, which increases transduction efficiency.
  • Figs. 45B, 45C, 45D show that both CAR44 and CAR50 transduced T cells recognized MUC1* expressed in these cancer cells, bound to them, induced clustering and killed many cancer cells.
  • Figs. 45F, 45G, 45H show that neither CAR44 nor CAR50 transduced T cells recognize full-length MUC1 expressed in HCT- MUC1-41TR cancer cells. There is no T cell induced clustering and the number of cancer cells has not decreased.
  • 45J, 45K, 45L show that activated MMP9 has cleaved full- length MUC1 to a MUC1* form that is recognized by both CAR44 and CAR50 transduced T cells. There is clearly visible CAR T cell induced clustering and a decrease in the number of cancer cells as they are killed.
  • Figs. 45N, 45O, 45P show that activated ADAM17 has either not cleaved MUC1 or cleaved it at a position not recognized by MNC2. Neither huMNC2- CAR44 nor huMNC2-CAR50 transduced T cells recognized these cancer cells.
  • FIG. 46A-46T shows photographs of a CAR T co-culture assay in which the targeting antibody fragment of the CAR is MNC2 scFv wherein CAR44 has a CD8 transmembrane domain, followed by 41BB-3zeta and CAR50 has a CD4 transmembrane domain, followed by 41BB-3zeta.
  • the target cancer cells are breast cancer T47D cells that were also incubated with conditioned media from cells transfected with MMP2, MMP9 or ADAM17 before co-culture with the MNC2-CAR T cells. In some cases, the conditioned media of the MMP2 and MMP9 expressing cells were also incubated with APMA, which is an activator of these cleavage enzymes.
  • FIG. 47A-47I show photographs of cancer cells co-cultured with anti-MUC1* CAR T cells, wherein some of the cancer cells were pre-incubated with activated MMP9 prior to co-culture with the CAR T cells.
  • the cancer cells shown in Figs.47A-47C are MUC1 negative colon cancer cell line HCT-116 that have been stably transfected to express MUC1*.
  • 47D-47F are MUC1 positive breast cancer cell line T47Ds that express high levels of both MUC1 full-length and MUC1*.
  • the cancer cells shown in Figs. 47G-47I are MUC1 positive breast cancer cell line T47Ds that were pre-incubated with activated MMP9.
  • the cells shown in Figs. 47A, 47D and 47G were co-cultured with untransduced human T cells and are the controls.
  • the cells shown in Figs. 47B, 47E and 47H were co-cultured with human T cells that were transduced with huMNC2-CAR44 at an MOI of 10, wherein MOI stands for multiplicity of infection and the higher the MOI the more CARs are expressed on the T cells.
  • Figure 48 shows an xCelligence graph of T47D breast cancer cells in co-culture with either untransduced T cells, as a control, or huMNC2-CAR44 T cells over a 45 hour period. After 18 hours of cancer cell growth, a catalytic sub-unit MMP9 was added to some of the cells. At 25 hours, T cells were added. As can be seen, huMNC2-CAR44 T cell killing is greatly improved when the T47D cells are pre-incubated with cleavage enzyme MMP9.
  • target cancer cells which are adherent, are plated onto electrode array plates. Adherent cells insulate the electrode and increase the impedance.
  • Figure 49 shows an xCelligence graph of DU145 prostate cancer cells in co- culture with either untransduced T cells, as a control, or huMNC2-CAR44 T cells over a 45 hour period. After 18 hours of cancer cell growth, a catalytic sub-unit MMP9 was added to some of the cells. At 25 hours, T cells were added. As can be seen, huMNC2-CAR44 T cell killing is not affected by pre-incubation with cleavage enzyme MMP9.
  • FIG. 50 shows a bar graph of a PCR experiment measuring the amount of MUC1 expressed by a panel of cell lines and primary cells, comprised of normal cells as well as cancer cells.
  • Figure 51A-51B shows a bar graph of an ELISA assay measuring the amount of interferon gamma, IFN-g, secreted by huMNC2-CAR44 human T cells after co-culture with the normal cells or the HCT-MUC1* cancer cells for 72 hours.
  • FIG. 51A shows the results of the experiment where the CAR44 T cell to target cell ratio was 1:1.
  • Fig. 51B shows the results of the experiment where the CAR44 T cell to target cell ratio was 0.5:1.
  • Figure 52A-52B shows a bar graph of an ELISA assay measuring the amount of interleukin-2, IL-2, secreted by huMNC2-CAR44 human T cells after co-culture with the normal cells or the HCT-MUC1* cancer cells for 72 hours.
  • Fig. 52A shows the results of the experiment where the CAR44 T cell to target cell ratio was 1:1.
  • Fig.52B shows the results of the experiment where the CAR44 T cell to target cell ratio was 0.5:1.
  • Figure 53A-53J shows bar graphs of FACS analysis of live versus dead markers and photographs of normal cells versus cancer cells after co-culture with huMNC2-CAR44 T cells.
  • Fig. 53A.1 shows the bar graph of FACS analysis of live versus dead cells after HCT- MUC1* cancer cells were co-cultured with huMNC2-CAR44 T cells.
  • Fig. 53A.2 and Fig. 53A.3 show the photographs of the experiment described in Fig.53A.1.
  • Fig.53B.1 shows the bar graph of FACS analysis of live versus dead cells after MCF-12A normal breast cells were co-cultured with huMNC2-CAR44 T cells.
  • FIG. 53B.3 show the photographs of the experiment described in Fig. 53B.1.
  • Fig. 53C.1 shows the bar graph of FACS analysis of live versus dead cells after THLE-3 normal liver cells were co-cultured with huMNC2- CAR44 T cells.
  • Fig. 53C.2 and Fig.53C.3 show the photographs of the experiment described in Fig.53C.1.
  • Fig.53D.1 shows the bar graph of FACS analysis of live versus dead cells after T/G HA-HSMC normal heart cells were co-cultured with huMNC2-CAR44 T cells.
  • Fig. 53D.2 and Fig. 53D.3 show the photographs of the experiment described in Fig. 53D.1.
  • Fig. 53C.1 shows the bar graph of FACS analysis of live versus dead cells after THLE-3 normal liver cells were co-cultured with huMNC2- CAR44 T cells.
  • Fig. 53C.2 and Fig.53C.3 show
  • FIG. 53E.1 shows the bar graph of FACS analysis of live versus dead cells after Hs1.Tes normal testes cells were co-cultured with huMNC2-CAR44 T cells.
  • Fig. 53E.2 and Fig. 53E.3 show the photographs of the experiment described in Fig.53E.1.
  • Fig. 53F.1 shows the bar graph of FACS analysis of live versus dead cells after HEK-293 MUC1 negative cells were co- cultured with huMNC2-CAR44 T cells.
  • Fig. 53F.2 and Fig. 53F.3 show the photographs of the experiment described in Fig. 53F.1.
  • Fig. 53F.1 shows the bar graph of FACS analysis of live versus dead cells after Hs1.Tes normal testes cells were co-cultured with huMNC2-CAR44 T cells.
  • Fig. 53F.1 shows the bar graph of FACS analysis of live versus dead cells after HEK-293 MUC1 negative cells were
  • 53G.1 shows the bar graph of FACS analysis of live versus dead cells after HRCE normal kidney cells were co-cultured with huMNC2- CAR44 T cells.
  • Fig.53G.2 and Fig.53G.3 show the photographs of the experiment described in Fig. 53G.1.
  • Fig. 53H.1 shows the bar graph of FACS analysis of live versus dead cells after CCD-18Lu normal lung cells were co-cultured with huMNC2-CAR44 T cells.
  • Fig. 53H.2 and Fig. 53H.3 show the photographs of the experiment described in Fig. 53H.1.
  • FIG. 53I.1 shows the bar graph of FACS analysis of live versus dead cells after HBEC-5i normal brain cells were co-cultured with huMNC2-CAR44 T cells.
  • Fig. 53I.2 and Fig. 53I.3 show the photographs of the experiment described in Fig. 53I.1.
  • Fig. 53J.1 shows the bar graph of FACS analysis of live versus dead cells after Hs.738.St/Int normal stomach and intestine cells were co-cultured with huMNC2-CAR44 T cells.
  • Fig. 53J.2 and Fig. 53J.3 show the photographs of the experiment described in Fig.53J.1.
  • Figure 54 shows photographs of a breast cancer tissue array in which for each patient there is a specimen from the primary tumor plus a specimen from that patient’s metastasis. As can be seen in the figure, most often the metastasis expresses more MUC1* than the primary tumor.
  • Figures 55A-55H show the cytotoxic effect of huMNC2-CAR44 T cells on MUC1* positive DU145 prostate cancer cells as measured by a variety of assays.
  • Fig.55A is a fluorescent photograph of untransduced T cells co-cultured with the prostate cancer cells, wherein granzyme B is stained with a red fluorophore.
  • Fig.55B shows merging of DAPI and granzyme B.
  • Fig. 55C is a fluorescent photograph of huMNC2-CAR44 T cells co-cultured with the prostate cancer cells, wherein granzyme B is stained with a red fluorophore.
  • Fig. 55D shows merging of DAPI and granzyme B.
  • Fig. 55E is a FACS scan for fluorescently labeled granzyme B for untransduced T cells incubated with the cancer cells.
  • Fig. 55F is a FACS scan showing a positive increase in fluorescently labeled granzyme B for huMNC2- CAR44 T cells incubated with the cancer cells.
  • Fig. 55G is a graph of the mean fluorescent intensity. Fig.
  • FIG. 55H is an xCELLigence scan tracking the real-time killing of DU145 cancer cells by huMNC2-CAR44 T cells (blue trace) but not by untransduced T cells (green).
  • Figures 56A-56H show the cytotoxic effect of huMNC2-CAR44 T cells on MUC1* positive CAPAN-2 pancreatic cancer cells as measured by a variety of assays.
  • Fig. 56A is a fluorescent photograph of untransduced T cells co-cultured with the pancreatic cancer cells, wherein granzyme B is stained with a red fluorophore.
  • Fig. 56B shows merging of DAPI and granzyme B.
  • FIG. 56C is a fluorescent photograph of huMNC2-CAR44 T cells co-cultured with the pancreatic cancer cells, wherein granzyme B is stained with a red fluorophore.
  • Fig. 56D shows merging of DAPI and granzyme B.
  • Fig.56E is a FACS scan for fluorescently labeled granzyme B for untransduced T cells incubated with the cancer cells.
  • Fig. 56F is a FACS scan showing a positive increase in fluorescently labeled granzyme B for huMNC2-CAR44 T cells incubated with the cancer cells.
  • Fig. 56G is a graph of the mean fluorescent intensity. Fig.
  • FIG. 56H is an xCELLigence scan tracking the real-time killing of CAPAN-2 cancer cells by huMNC2-CAR44 T cells (blue trace) but not by untransduced T cells (green).
  • Figures 57A-57C show xCELLigence scans tracking the real-time killing of MUC1* positive cancer cells, but not MUC1* negative cells, by huMNC2-CAR44 T cells.
  • Fig. 57A shows that huMNC2-CAR44 T cells effectively kill HCT colon cancer cells that have been stably transfected with MUC1*.
  • FIG. 57B shows that huMNC2-CAR44 T cells have almost no effect on HCT-MUC1-41TR, which is a MUC1 negative cancer cell that has been stably transfected with a MUC1 full-length. In this cell line only about 10% of the cells have MUC1 cleaved to MUC1*.
  • Fig. 57C shows that huMNC2-CAR44 T cells have no effect on HCT-116 cells, which is a MUC1 negative colon cancer cell line.
  • Figure 58A- 58F shows photographs NOD/SCID/GAMMA mice in an IVIS instrument measuring photon emission from tumor cells after mice were treated with nothing, PBS, untransduced human T cells or huMNC2-CAR44 T cells.
  • Fig. 58A shows the tumor bearing mice that had only been treated with phosphate buffered saline, PBS.
  • Fig.58B shows the tumor bearing mice that had only been treated with untransduced T cells.
  • Fig. 58C shows the tumor bearing mice that had been treated with a single dose of huMNC2-CAR44 T cells.
  • Fig. 58D shows color scale of the images.
  • FIG. 58E shows Kaplan-Meier survival curves of the experiment.
  • Fig. 58F shows a table detailing the molecular makeup of the human T cells that were isolated from the mouse blood after sacrifice.
  • Figure 59A- 59C shows photographs NOD/SCID/GAMMA mice in an IVIS instrument measuring photon emission from tumor cells after mice were treated with nothing, PBS or huMNC2-CAR44 T cells. Mice had been injected sub-cutaneously with T47D-wt breast cancer cells or T47D+more MUC1*, which is a mixed population of cells wherein 95% of the cells were T47D cells that had been stably transfected with even more MUC1*.
  • Fig. 59A shows the tumor bearing mice that had only been treated with phosphate buffered saline, PBS.
  • Fig.59B shows the T47D-wt tumor bearing mice that had been treated with two (2) doses of huMNC2- CAR44 T cells.
  • Fig. T90.1C shows the T47D-MUC1* tumor bearing mice that had been treated with two (2) doses of huMNC2-CAR44 T cells.
  • Figure 60A- 60C shows photographs NOD/SCID/GAMMA mice in an IVIS instrument measuring photon emission from tumor cells after mice were treated with nothing, PBS, untransduced T cells or huMNC2-CAR44 T cells.
  • Mice had been injected sub- cutaneously with a mixed population of 70% T47D-wt breast cancer cells and 30% T47D cells that had been transfected with even more MUC1*. Both cell types had been made Luciferase positive.
  • FIG. 60A shows the tumor bearing mice that had only been treated with phosphate buffered saline, PBS.
  • Fig. 60B shows tumor bearing mice that had only been treated with untransduced T cells.
  • Fig. 60C shows the tumor bearing mice that had been treated with two (2) doses of huMNC2-CAR44 T cells.
  • Figures 61A-61J show fluorescent photographs of mice taken on an IVIS instrument. NSG (NOD/SCID/GAMMA) immune compromised mice that on Day 0 were sub-cutaneously injected into the flank with 500K human BT-20 cells which are a MUC1* positive triple negative breast cancer cell line. The cancer cells had been stably transfected with Luciferase. Tumors were allowed to engraft.
  • mice On Day 6 after IVIS measurement, animals were given a one-time injection of 10 million of either human T cells transduced with huMNC2-scFv-CAR44 or untransduced T cells. 5 million T cells were injected intra-tumor and 5 million were injected into the tail vein. 10 minutes prior to IVIS photographs, mice were IP injected with Luciferin, which fluoresces after cleavage by Luciferase, thus making tumor cells fluoresce. Figs.
  • 61A, 61D, 61G show photographs of mice that were treated with huMNC2-scFv-CAR44 T cells that had been pre-stimulated by co-culturing for 24 hours with 4 ⁇ m beads to which was attached a synthetic MUC1*, PSMGFR peptide 24 hours prior to administration: Protocol 1.
  • Figs. 61B, 61E, 61H show photographs of mice that were treated with huMNC2-scFv-CAR44 T cells that had been pre-stimulated by twice co-culturing for 24 hours with MUC1* positive cancer cells 24 hours prior to administration: Protocol 2.
  • Figs. 61C, 61F, 61I show photographs of mice that were treated with untransduced human T cells.
  • FIG.61J is a color scale relating fluorescence in photons/second to color.
  • Figures 62A-62M show fluorescent photographs of mice taken on an IVIS instrument.
  • NSG NOD/SCID/GAMMA
  • IP intraperitoneal cavity
  • human SKOV-3 cells which are a MUC1* positive ovarian cancer cell line.
  • the cancer cells had been stably transfected with Luciferase. Tumors were allowed to engraft.
  • animals were injected into the intraperitoneal space with 10M either human T cells transduced with huMNC2-scFv-CAR44, untransduced T cells or PBS.
  • mice On Day 11, animals were injected again except that half the cells were injected into the tail vein and the other half was IP injected. Animals were imaged by IVIS on Days 3, 7, 10 and 15. 10 minutes prior to IVIS photographs, mice were IP injected with Luciferin, which fluoresces after cleavage by Luciferase, thus making tumor cells fluoresce.
  • Figs. 62A, 62D, 62G, and 62J show photographs of mice that were treated with huMNC2-scFv-CAR44 T cells that had been pre-stimulated by co-culturing for 24 hours with 1 ⁇ m beads to which was attached a synthetic MUC1*, PSMGFR peptide 24 hours prior to administration. Figs.
  • Figs. 62B, 62E, 62H, and 62K show photographs of mice that were treated with untransduced human T cells.
  • Figs. 62C, 62F, 62I, and 62L show photographs of mice that were treated with PBS.
  • Figs. 62A, 62B and 62C are IVIS images taken Day 3 prior to CAR T, T cell or PBS administration.
  • Figs. 62D, 62E and 62F show IVIS images of animals on Day 7, just four (4) days after treatment.
  • Figs. 62G, 62H, and 62I show IVIS images of animals on Day 10.
  • Figs. 62J, 62K, and 62L show IVIS images of animals on Day 15 Fig.
  • FIG. 62M is the IVIS color scale relating fluorescence in photons/second to color.
  • Figure 63 shows a graph of an ELISA binding assay in which various monoclonal antibodies are tested for their ability to bind to the PSMGFR peptide, the N-10, C-10, N+20/C-27, or the N+9/C-9 peptide, wherein the concentration of the antibody was at 10ug/mL or 1ug/mL.
  • anti-MUC1* monoclonal antibodies C2 and E6 which have been demonstrated to be cancer specific, bind to the PSMGFR peptide, still bind if the 10 N- terminal amino acids are missing, but do not bind if the 10 or 9 C-terminal amino acids are missing.
  • Figure 64A-64B shows a graph of an ELISA binding assay.
  • the antibodies being tested were derived from animals immunized with the PSMGFR peptide. The first selection criteria was to confirm that the antibodies bound to the immunizing PSMGFR peptide.
  • Fig. 64A shows a graph of an ELISA of selected antibodies that were further tested to determine their ability to bind to the PSMGFR peptide, the N-10, the C-10, N+20/C-27, or N+9/C-9 peptide. All the antibodies except 18B4 were able to bind to the N-10 peptide.
  • Fig. 64B shows the sequences of the various peptides. The color of the bars for each antibody in the ELISA graph are color coded to match the deductive cognate sequence, or a portion thereof, of that antibody.
  • Figure 65A-65B shows a graph of an ELISA binding assay in which various monoclonal antibodies are tested for their ability to bind to the PSMGFR peptide, the N-10, the C-10, N+20/C-27, or N+9/C-9 peptide.
  • the antibodies being tested were derived from animals immunized with the N+20/C-27 peptide.
  • the first selection criteria was to confirm that the antibodies bound to the immunizing N+20/C-27 peptide.
  • Fig. 65A shows a graph of ELISA binding assay that tests the ability of each antibody to bind to various peptides.
  • Figure 66A-66B shows a graph of an ELISA binding assay in which various monoclonal antibodies are tested for their ability to bind to the PSMGFR peptide, the N-10, the C-10, N+20/C-27, or N+9/C-9 peptide.
  • the antibodies being tested were derived from animals immunized with the N+9/C-9 peptide.
  • the first selection criteria was to confirm that the antibodies bound to the immunizing N+9/C-9 peptide.
  • Fig. 66A shows a graph of the ELISA assay. All but one, 39H5, were only able to bind to the immunizing peptide, N+9/C-9.
  • FIG. 39H5 showed very weak binding to the PSMGFR and N-10 peptide, consistent with the idea that at least a portion of its cognate epitope must lie within the QFNQYKTE sequence.
  • Fig. 66B shows the sequences of the various peptides. The color of the bars for each antibody in the ELISA graph are color coded to match the deductive cognate sequence, or a portion thereof, of that antibody.
  • Figure 67A-67D shows results of ELISA assays to further define antibody epitopes within the MUC1 or MUC1* extra cellular domain. The antibodies shown in this figure were all generated by immunizing animals with the PSMGFR peptide.
  • Fig. 67A shows the binding of the various antibodies to the various peptides.
  • Fig. 67B shows the sequence of the PSMGFR peptide that has been extended 20 amino acids at the N-terminus.
  • Fig. 67C shows the sequences of the PSMGFR- derived subset peptides.
  • Fig.67D shows the sequences that comprise all or part of the epitope that is essential for antibody recognition.
  • Figure 68A-68D shows results of ELISA assays to further define antibody epitopes within the MUC1 or MUC1* extra cellular domain.
  • the antibodies shown in this figure were all generated by immunizing animals with the N+20/C-27 peptide.
  • Binding assays tested antibodies for their ability to bind to peptides N-19, N-26, N-30, N-10/C-5, N- 19/C-5, PSMGFR, N-10 and C-10, which are all subsets of the PSMGFR peptide and numbering refers back to the PSMGFR peptide.
  • Fig. 68A shows the binding of the various antibodies to the various peptides.
  • FIG. 68B shows the sequence of the PSMGFR peptide that has been extended 20 amino acids at the N-terminus.
  • Fig. 68C shows the sequences of the PSMGFR-derived subset peptides.
  • Fig. 68D shows the sequences that comprise all or part of the epitope that is essential for antibody recognition.
  • Figures 69A-69D show results of ELISA assays to further define antibody epitopes within the MUC1 or MUC1* extra cellular domain. The antibodies shown in this figure were all generated by immunizing animals with the N+9/C-9 peptide.
  • Fig. 69A shows the binding of the various antibodies to the various peptides.
  • Fig. 69B shows the sequence of the PSMGFR peptide that has been extended 20 amino acids at the N-terminus.
  • Fig. 69C shows the sequences of the PSMGFR- derived subset peptides.
  • Fig.69D shows the sequences that comprise all or part of the epitope that is essential for antibody recognition.
  • Figure 70A-70B shows a graph of an ELISA displacement assay.
  • a multi-well plate was coated with the PSMGFR peptide.
  • recombinant NME7 AB was allowed to bind to the surface-immobilized PSMGFR peptide.
  • Various antibodies were added, followed by a wash step.
  • the amount of NME7AB that remained attached to the PSMGFR coated plate, after antibody competition, was measured by detecting a tag on the NME7AB.
  • anti-NME7AB antibodies were also tested for their ability to displace NME7AB from the PSMGFR.
  • Fig. 70B shows that the epitope within the MUC1* extracellular domain to which these antibodies bind is the sequence SVSDVPFPFSAQSGA, wherein binding is destroyed for MNC2, MNE6, 20A10, 3C2B1 if amino acids FPFS are not present or mutated and binding is destroyed for 5C6F3 if amino acids SVSDV are not present or mutated.
  • Figure 71A-71H shows photographs of Western blots in which antibodies are tested for their ability to bind to a linear epitope in full-length MUC1 or MUC1*.
  • Fig. 71A- 71D shows testing of antibodies for ability to bind to a MUC1 negative cell line, HCT-116, or engineered cell lines HCT-MUC1-18, which is a cleavage resistant clone that expresses full- length MUC1, or HCT-MUC1*, which is engineered to express only the PSMGFR sequence in its extra cellular domain.
  • Fig. 71E-71H shows testing of antibodies for ability to bind to breast cancer cell lines T47D or 1500 aka ZR-75-1.
  • Fig. 71A and Fig. 71E show MNC2, a monoclonal antibody raised against PSMGFR peptide that binds to N-10 but not C-10 variants of the PSMGFR peptide.
  • Fig.71B and Fig.71F show MNE6, a monoclonal antibody raised against PSMGFR peptide that binds to N-10 but not C-10 variants of the PSMGFR peptide.
  • Fig. 71C and Fig. 71G show SDIX, a polyclonal antibody raised against PSMGFR peptide and which binds to the PSMGFR peptide.
  • FIG. 71H show VU4H5, a commercially available monoclonal antibody that binds to the tandem repeats of full-length MUC1. As can be seen, neither MNC2 nor MNE6 bind linear epitopes of MUC1 species.
  • Figure 72A-72P shows photographs of Western blots in which antibodies are tested for their ability to bind to a linear epitope in full-length MUC1 or MUC1*. All these antibodies were raised against the PSMGFR peptide and bind to the PSMGFR peptide.
  • 72A-72H shows testing of antibodies for ability to bind to a MUC1 negative cell line, HCT- 116, or engineered cell lines HCT-MUC1-18, which is a cleavage resistant clone that expresses full-length MUC1, or HCT-MUC1*, which is engineered to express only the PSMGFR sequence in its extra cellular domain.
  • Fig. 72I-72P shows testing of antibodies for ability to bind to breast cancer cell lines T47D or 1500 aka ZR-75-1.
  • Fig. 72A and Fig. 72I show 20A10.
  • Fig.72B and Fig. 72J show 25E6.
  • Fig. 72C and Fig.72K show 18B4.
  • Fig.72D and Fig. 72L show 18G12.
  • FIG. 72E and Fig. 72M show 28F9.
  • Fig. 72F and Fig. 72N show 3C2B1.
  • Fig.72G and Fig.72O show 5C6F3.
  • Fig. 72H and Fig.72P show 5C6F3 wherein the blot has been exposed for a longer time period to render more visible the MUC1* specific bands.
  • antibodies 25E6, 18B4 and to a degree 5C6F3 recognize linear epitopes but 20A10, 3C2B1, 18G12 and 28F9 do not.
  • Figure 73A-73J shows photographs of Western blots in which antibodies are tested for their ability to bind to a linear epitope in full-length MUC1 or MUC1*.
  • Fig. 73A-73E shows testing of antibodies for ability to bind to a MUC1 negative cell line, HCT-116, or engineered cell lines HCT-MUC1-18, which is a cleavage resistant clone that expresses full-length MUC1, or HCT-MUC1*, which is engineered to express only the PSMGFR sequence in its extra cellular domain.
  • Fig. 73F-73J shows testing of antibodies for ability to bind to breast cancer cell lines T47D or 1500 aka ZR-75-1.
  • Fig. 73A and Fig. 73F show 1E4.
  • Fig. 73A and Fig. 73F show 1E4.
  • FIG. 73B and Fig. 73G show 45C11.
  • Fig. 73C and Fig. 73H show 31A1.
  • Fig. 73D and Fig. 73I show 32C1.
  • Fig. 73E and Fig. 73J show 29H1.
  • antibodies 31A1 and 32C1 recognize linear epitopes.
  • Figure 74A-74H shows photographs of Western blots in which antibodies are tested for their ability to bind to a linear epitope in full-length MUC1 or MUC1*. All these antibodies were raised against the N+9/C-9 variant of the PSMGFR peptide and bind to the N+9/C-9 peptide.
  • 74A-74D shows testing of antibodies for ability to bind to a MUC1 negative cell line, HCT-116, or engineered cell lines HCT-MUC1-18, which is a cleavage resistant clone that expresses full-length MUC1, or HCT-MUC1*, which is engineered to express only the PSMGFR sequence in its extra cellular domain.
  • Fig. 74E-74H shows testing of antibodies for ability to bind to breast cancer cell lines T47D or 1500 aka ZR-75-1.
  • Fig. 74A and Fig.74E show 8A9.
  • Fig.74B and Fig.74F show 17H6.
  • Fig.74C and Fig.74G show 3C5.
  • Fig.74D and Fig.74H show 39H5.
  • Figure 75A-75P show graphs of FACS analysis.
  • HCT-MUC1-18 cells which express full-length MUC1
  • Each bar graph is labeled with both the name of the antibody used in that assay and its cognate epitope.
  • Fig. 75A shows antibody 1E4.
  • Fig. 75B shows antibody 28F9.
  • Fig. 75C shows antibody 18G12.
  • Fig. 75D shows antibody 25E6.
  • Fig. 75E shows antibody 20A10.
  • Fig. 75F shows antibody 3C5.
  • Fig. 75G shows antibody 29H1.
  • Fig. 75H shows antibody 32C1.
  • Fig. 75I shows antibody 31A1.
  • Fig. 75J shows antibody 18B4.
  • Fig. 75K shows antibody 45C11.
  • Fig. 75L shows antibody 8A9.
  • Fig. 75M shows antibody 17H6.
  • Fig.75N shows antibody 39H5.
  • Fig.75O shows antibody 3C2B1.
  • Figure 76A-76J show graphs of FACS analyses of reference antibodies MNC2, “C2”, and VU4H5 binding to either the MUC1-negative cell line HCT-116, HCTs transfected with MUC1*, “HCT-MUC1*”, a cleavage resistant single cell clone of HCTs transfected with MUC1 full-length, “HCT-MUC1-18”, and MNC2 binding to breast cancer cells line T47D or breast cancer cell line 1500 also known as ZR-75-1.
  • MNC2 binds to an ectopic binding site on the extra cellular domain of MUC1*, within the membrane proximal portion of the PSMGFR sequence.
  • FIG. 76A-76E show percent binding and Fig.76F-76J show Mean Fluorescent Intensity or MFI.
  • Figure 77A-77N show graphs of FACS analyses of reference antibody MNC2, “C2”, binding to a panel of cancer cell lines that are MUC1* positive, with the exception of MDA-MB-231, which expresses MUC1 and MUC1* at a level that is so low that it is often used as a negative control.
  • MNC2 binds to an ectopic binding site on the extra cellular domain of MUC1*, within the membrane proximal portion of the PSMGFR sequence.
  • the MNC2 binding site is only available after cleavage and release of the bulk of the extra cellular domain comprising the tandem repeat domain.
  • Fig. 77A-77G show percent binding and Fig. 77H-77N show Mean Fluorescent Intensity or MFI.
  • Fig. 77A and 77H show the antibodies binding to lung cancer cell line NCI-H292.
  • Fig. 77B and 77I show the antibodies binding to lung cancer cell line NCI-H1975.
  • Fig.77C and 77J show the antibodies binding to ovarian cancer cell line SKOV-3.
  • FIG. 77D and 77K show the antibodies binding to pancreatic cancer cell line HPAF-II.
  • Fig. 77E and 77L show the antibodies binding to pancreatic cancer cell line Capan-1.
  • Fig. 77F and 77M show the antibodies binding to prostate cancer cell line DU145.
  • Fig. 77G and 77N show the antibodies binding to breast cancer cell line MDA-MB-231, which is nearly MUC1 and MUC1* negative.
  • Figure 78A-78C shows a color coded schematic of the basic PSMGFR sequence that has been extended or deleted at both the N- and C-termini.
  • FIG. 78A is an aligned schematic of the various subsets of peptides.
  • Fig. 78B lists the antibodies that bind to each of the color coded sequences.
  • Fig. 78C lists the cancer cell lines that each antibody recognizes.
  • Figure 79A-79I shows color coded graphs that resulted from FACS analyses of each antibody binding to T47D breast cancer cells and their respective cognate sequences within the N-terminally extended PSMGFR sequence. Fig.
  • Fig. 79A-79D are FACS graphs showing the percent cells that were recognized by each antibody.
  • Fig. 79E-79H are FACS graphs showing the Mean Fluorescence Intensity, MFI, of each antibody.
  • Fig. 79A and Fig. 79E show the FACS graph of antibodies that were generated by immunizing with the PSMGFR peptide.
  • Fig. 79B and Fig. 79F show the FACS graph of antibodies that were generated by immunizing with the N+20/C-27 peptide.
  • Fig. 79C and Fig. 79G show the FACS graph of antibodies that were generated by immunizing with the N+9/C-9 peptide.
  • Fig. 79D and Fig.79H also show the FACS graph of antibodies that were generated by immunizing with the PSMGFR peptide.
  • Fig. 79I shows the PSMGFR sequence that is extended at the N-terminus by 20 amino acids.
  • Fig. 79A, Fig.79E show that 20A10 recognizes MUC1* as it exists on T47D breast cancer cells.
  • Fig. 79D, Fig. 79H show that 3C2B1 recognizes MUC1* as it exists on T47D breast cancer cells.
  • Fig.79D, Fig.79H show that 5C6F3 recognizes MUC1* as it exists on T47D breast cancer cells.
  • Figure 80A-80I shows color coded graphs that resulted from FACS analyses of each antibody binding to 1500, also known as ZR-75-1, breast cancer cells and their respective cognate sequences within the N-terminally extended PSMGFR sequence.
  • Fig. 80A-80C are FACS graphs showing the percent cells that were recognized by each antibody.
  • Fig. 80D-80F are FACS graphs showing the Mean Fluorescence Intensity, MFI, of each antibody.
  • Fig.80A, Fig. 80E Fig. 80D and Fig.80H show the FACS graph of antibodies that were generated by immunizing with the PSMGFR peptide.
  • Fig. 80F show the FACS graph of antibodies that were generated by immunizing with the N+20/C-27 peptide.
  • Fig. 80C and Fig. 80G show the FACS graph of antibodies that were generated by immunizing with the N+9/C-9 peptide.
  • Fig. 80I shows the PSMGFR sequence that is extended at the N-terminus by 20 amino acids.
  • Fig. 80A, Fig.80E show that antibody 20A10 recognizes MUC1* as it exists on 1500 aka ZR-75-1 breast cancer cells.
  • Fig. 80D, Fig. 80H show that antibody 3C2B1 recognizes MUC1* as it exists on 1500 aka ZR-75-1 breast cancer cells.
  • Figure 81A-81G shows color coded graphs that resulted from FACS analyses of each antibody binding to NCI-H292 lung cancer cells and their respective cognate sequences within the N-terminally extended PSMGFR sequence.
  • Fig. 81A-81C are FACS graphs showing the percent cells that were recognized by each antibody.
  • Fig. 81D-81F are FACS graphs showing the Mean Fluorescence Intensity, MFI, of each antibody.
  • Fig. 81A and Fig. 81D show the FACS graph of antibodies that were generated by immunizing with the PSMGFR peptide.
  • Fig. 81B and Fig. 81E show the FACS graph of antibodies that were generated by immunizing with the N+20/C-27 peptide.
  • Fig. 81C and Fig. 81F show the FACS graph of antibodies that were generated by immunizing with the N+9/C-9 peptide.
  • Fig. 81G shows the PSMGFR sequence that is extended at the N-terminus by 20 amino acids.
  • Fig. 81A, Fig. 81D show that antibody 20A10 recognizes MUC1* as it exists on H292 lung cancer cells.
  • Figure 82A-82G shows color coded graphs that resulted from FACS analyses of each antibody binding to NCI-H1975 lung cancer cells and their respective cognate sequences within the N-terminally extended PSMGFR sequence.
  • Fig. 82A-82C are FACS graphs showing the percent cells that were recognized by each antibody.
  • Fig. 82D-82F are FACS graphs showing the Mean Fluorescence Intensity, MFI, of each antibody.
  • Fig. 82A and Fig. 82D show the FACS graph of antibodies that were generated by immunizing with the PSMGFR peptide.
  • Fig. 82B and Fig. 82E show the FACS graph of antibodies that were generated by immunizing with the N+20/C-27 peptide.
  • Fig. 82C and Fig. 82F show the FACS graph of antibodies that were generated by immunizing with the N+9/C-9 peptide.
  • Fig. 82G shows the PSMGFR sequence that is extended at the N-terminus by 20 amino acids.
  • Fig. 82A, Fig. 82D show that antibody 20A10 recognizes MUC1* as it exists on H1975 lung cancer cells.
  • Figure 83A-83G shows color coded graphs that resulted from FACS analyses of each antibody binding to SKOV-3 ovarian cancer cells and their respective cognate sequences within the N-terminally extended PSMGFR sequence.
  • Fig. 83A-83C are FACS graphs showing the percent cells that were recognized by each antibody.
  • 83D-83F are FACS graphs showing the Mean Fluorescence Intensity, MFI, of each antibody.
  • Fig. 83A and Fig. 83D show the FACS graph of antibodies that were generated by immunizing with the PSMGFR peptide.
  • Fig. 83B and Fig. 83E show the FACS graph of antibodies that were generated by immunizing with the N+20/C-27 peptide.
  • Fig. 83C and Fig. 83F show the FACS graph of antibodies that were generated by immunizing with the N+9/C-9 peptide.
  • Fig. 83G shows the PSMGFR sequence that is extended at the N-terminus by 20 amino acids.
  • Figure 84A-84G shows color coded graphs that resulted from FACS analyses of each antibody binding to DU145 prostate cancer cells and their respective cognate sequences within the N-terminally extended PSMGFR sequence.
  • Fig. 84A-84C are FACS graphs showing the percent cells that were recognized by each antibody.
  • Fig. 84D-84F are FACS graphs showing the Mean Fluorescence Intensity, MFI, of each antibody.
  • Fig. 84A and Fig. 84D show the FACS graph of antibodies that were generated by immunizing with the PSMGFR peptide.
  • Fig. 84E show the FACS graph of antibodies that were generated by immunizing with the N+20/C-27 peptide.
  • Fig. 84C and Fig. 84F show the FACS graph of antibodies that were generated by immunizing with the N+9/C-9 peptide.
  • Fig. 84G shows the PSMGFR sequence that is extended at the N-terminus by 20 amino acids.
  • Fig. 84A, Fig. 84E show that antibody 20A10 recognizes MUC1* as it exists on DU145 prostate cancer cells.
  • Fig.84D, Fig.84H show that antibody 3C2B1 recognizes MUC1* as it exists on DU145 prostate cancer cells.
  • Figure 85A-85G shows color coded graphs that resulted from FACS analyses of each antibody binding to HPAF-II pancreatic cancer cells and their respective cognate sequences within the N-terminally extended PSMGFR sequence.
  • Fig. 85A-85C are FACS graphs showing the percent cells that were recognized by each antibody.
  • Fig. 85D-85F are FACS graphs showing the Mean Fluorescence Intensity, MFI, of each antibody.
  • Fig. 85A and Fig. 85D show the FACS graph of antibodies that were generated by immunizing with the PSMGFR peptide.
  • FIG. 85E show the FACS graph of antibodies that were generated by immunizing with the N+20/C-27 peptide.
  • Fig. 85C and Fig. 85F show the FACS graph of antibodies that were generated by immunizing with the N+9/C-9 peptide.
  • Fig. 85G shows the PSMGFR sequence that is extended at the N-terminus by 20 amino acids.
  • Fig. 85A, Fig. 85D show that antibody 20A10 recognizes MUC1* as it exists on HPAF II pancreatic cancer cells.
  • Figure 86A-86G shows color coded graphs that resulted from FACS analyses of each antibody binding to Capan-1 pancreatic cancer cells and their respective cognate sequences within the N-terminally extended PSMGFR sequence.
  • 86A-86C are FACS graphs showing the percent cells that were recognized by each antibody.
  • Fig. 86D-86F are FACS graphs showing the Mean Fluorescence Intensity, MFI, of each antibody.
  • Fig. 86A and Fig. 86D show the FACS graph of antibodies that were generated by immunizing with the PSMGFR peptide.
  • Fig. 86B and Fig. 86E show the FACS graph of antibodies that were generated by immunizing with the N+20/C-27 peptide.
  • Fig. 86C and Fig. 86F show the FACS graph of antibodies that were generated by immunizing with the N+9/C-9 peptide.
  • FIG. 86G shows the PSMGFR sequence that is extended at the N-terminus by 20 amino acids.
  • Figure 87A-87G shows color coded graphs that resulted from FACS analyses of each antibody binding to MDA-MB-231 breast cancer cells, which are nearly MUC1 negative, and their respective cognate sequences within the N-terminally extended PSMGFR sequence.
  • Fig. 87A-87C are FACS graphs showing the percent cells that were recognized by each antibody.
  • Fig. 87D-87F are FACS graphs showing the Mean Fluorescence Intensity, MFI, of each antibody.
  • Fig. 87A and Fig.87D show the FACS graph of antibodies that were generated by immunizing with the PSMGFR peptide.
  • FIG. 87B and Fig. 87E show the FACS graph of antibodies that were generated by immunizing with the N+20/C-27 peptide.
  • Fig. 87C and Fig. 87F show the FACS graph of antibodies that were generated by immunizing with the N+9/C-9 peptide.
  • Fig. 87G shows the PSMGFR sequence that is extended at the N- terminus by 20 amino acids.
  • Figure 88A-88L show photographs of normal liver tissue specimens, each from the same donor but stained with a different antibody of the invention.
  • Fig. 88A-88F show the entire tissue core.
  • Fig.88G-88L show the 40X magnification of a particular area of the tissue.
  • the tissues are ordered from right to left with antibodies that bind to the most membrane proximal, that is to say most C-terminal portion of the PSMGFR peptide, on the right and antibodies that bind to the most N-terminal portions of the MUC1 extra cellular domain, even beyond the PSMGFR region, on the left.
  • the most cancer- specific antibodies are those that bind to the more membrane proximal portions of the PSMGFR sequence and antibodies that bind to the most distal, N-terminal portions lose cancer specificity, with those antibodies that bind to epitopes outside of the PSMGFR having lost all cancer specificity.
  • FIG. 89A-89H show photographs of normal heart tissue specimens, stained with different antibodies of the invention.
  • Fig. 89A-89D show the entire tissue core.
  • Fig. 89E-89HL show the 40X magnification of a particular area of the tissue.
  • Fig. 89A and Fig. 89E show staining with MNC2-scFv.
  • Fig. 89B and Fig. 89F show staining with MNE6.
  • Fig. 89G show staining with 20A10.
  • Fig. 89D and Fig. 89H show staining with 3C2B1.
  • These antibodies bind to an epitope that comprises all or part of the sequence FPFS or PFPFSAQSGA. All these antibodies are all able to bind to the PSMGFR peptide, bind to the N-10 peptide but do not bind to the C-10 peptide. In addition, these antibodies disrupt the binding of NME7AB to the MUC1* extra cellular domain as exemplified by the PSMGFR peptide. Further, these antibodies recognize a MUC1 cleavage product when the cleavage enzyme is MMP9. As can be seen in the figure, these antibodies show no binding to normal heart tissue.
  • Figure 90A-90D show photographs of normal heart tissue specimens, stained with different antibodies of the invention.
  • Fig. 90A-90B show the entire tissue core.
  • Fig. 90C-90D show the 40X magnification of a particular area of the tissue.
  • FIG. 90C show staining with MNC3.
  • Fig. 90B and Fig. 90D show staining with 25E6.
  • These antibodies bind to an epitope that comprises all or part of the sequence ASRYNLT.
  • These antibodies are all able to bind to the PSMGFR peptide, bind to the N-10 peptide but also bind to the C-10 peptide. As can be seen, these antibodies are not as cancer-specific and show some binding to normal heart tissue.
  • Figure 91A-91B show photographs of normal heart tissue specimens, stained with an antibody of the invention 1E4.
  • Fig. 91A show the entire tissue core.
  • Fig. 91B show the 40X magnification of a particular area of the tissue.
  • Antibody 1E4 binds to an epitope that comprises all or part of the sequence QFNQYKTEA. Antibody 1E4 can bind to the N-10 peptide but also binds to the C-10 peptide. As can be seen in the figure, 1E4 binds to normal heart tissue. As can be seen, these antibodies are not as cancer-specific and show some binding to normal heart tissue. [00356]
  • Figure 92A-92H show photographs of normal heart tissue specimens, stained with different antibodies of the invention.
  • Fig. 92A-92D show the entire tissue core.
  • Fig. 92E-92HL show the 40X magnification of a particular area of the tissue.
  • Fig. 92A and Fig. 92E show staining with 18B4.
  • FIG. 92B and Fig. 92F show staining with 31A1.
  • Fig. 92C and Fig. 92G show staining with 32C1.
  • Fig. 92D and Fig. 92H show staining with 29H1.
  • These antibodies bind to an epitope that comprises all or part of the sequence GTINVHDVET, which is the most N-terminal part of the PSMGFR peptide. None of these antibodies are able to bind to the N-10 peptide. As can be seen in the figure, all of these antibodies except 18B4 show binding to normal heart tissue.
  • Figure 93A-93D show photographs of normal heart tissue specimens, stained with antibodies of the invention.
  • Fig. 93A-93B show the entire tissue core.
  • 93C-93D show the 40X magnification of a particular area of the tissue.
  • Fig. 93A and Fig. 93C show staining with antibody 8A9.
  • Fig. 93B and Fig 93D show staining with antibody 17H6.
  • Both antibodies bind to an epitope that that is outside of the PSMGFR region and comprises all or part of the sequence VQLTLAFRE. As can be seen in the figure, both antibodies show strong binding to normal heart tissue.
  • Figure 94A-94B show photographs of normal heart tissue specimens, stained with an antibody of the invention 45C11.
  • Fig. 94A show the entire tissue core.
  • Fig. 94B show the 40X magnification of a particular area of the tissue.
  • Antibody 45C11 binds to an epitope that is outside of the PSMGFR region and comprises all or part of the sequence SNIKFRPGSVV. Antibody 45C11 cannot bind to the N-10 peptide. As can be seen in the figure, 45C11 binds strongly to normal heart tissue.
  • Figure 95A-95H show photographs of normal liver tissue specimens, stained with different antibodies of the invention.
  • Fig. 95A-95D show the entire tissue core.
  • Fig. 95E- 95HL show the 40X magnification of a particular area of the tissue.
  • Fig. 95A and Fig. 95E show staining with reference antibody MNC2-scFv.
  • Fig. 95B and Fig. 95F show staining with reference antibody MNE6.
  • Fig. 95C and Fig. 95G show staining with 20A10.
  • Fig. 95D and Fig. 95H show staining with 3C2B1.
  • These antibodies bind to an epitope that comprises all or part of the sequence FPFS or PFPFSAQSGA. All these antibodies are all able to bind to the PSMGFR peptide, bind to the N-10 peptide but do not bind to the C-10 peptide. In addition, these antibodies disrupt the binding of NME7AB to the MUC1* extra cellular domain as exemplified by the PSMGFR peptide. Further, these antibodies recognize a MUC1 cleavage product when the cleavage enzyme is MMP9. As can be seen in the figure, these antibodies show no binding to normal liver tissue.
  • Figure 96A-96D show photographs of normal liver tissue specimens, stained with different antibodies of the invention.
  • Fig. 96A-96B show the entire tissue core.
  • Fig.96C-96D show the 40X magnification of a particular area of the tissue.
  • Fig. 96A and Fig. 96C show staining with MNC3.
  • Fig. 96B and Fig. 96D show staining with 25E6.
  • These antibodies bind to an epitope that comprises all or part of the sequence ASRYNLT.
  • These antibodies are all able to bind to the PSMGFR peptide, bind to the N-10 peptide but also bind to the C-10 peptide.
  • Figure 97A-97B show photographs of normal liver tissue specimens, stained with an antibody of the invention 1E4.
  • Fig. 97A show the entire tissue core.
  • Fig. 97B show the 40X magnification of a particular area of the tissue.
  • Antibody 1E4 binds to an epitope that comprises all or part of the sequence QFNQYKTEA.
  • Antibody 1E4 can bind to the N-10 peptide but also binds to the C-10 peptide.
  • 1E4 binds to normal liver tissue.
  • Figure 98A-98H show photographs of normal liver tissue specimens, stained with different antibodies of the invention.
  • Fig. 98A-98D show the entire tissue core.
  • Fig.98E-98H show the 40X magnification of a particular area of the tissue.
  • Fig. 98A and Fig. 98E show staining with 18B4.
  • Fig. 98B and Fig. 98F show staining with 31A1.
  • Fig. 98C and Fig. 98G show staining with 32C1.
  • Fig. 98D and Fig. 98H show staining with 29H1.
  • These antibodies bind to an epitope that comprises all or part of the sequence GTINVHDVET, which is the most N-terminal part of the PSMGFR peptide. None of these antibodies are able to bind to the N-10 peptide.
  • FIG. 99A-99D show photographs of normal liver tissue specimens, stained with antibodies of the invention.
  • Fig.99A-99B show the entire tissue core.
  • Fig.99C-99D show the 40X magnification of a particular area of the tissue.
  • Fig. 99A and Fig. 99C show staining with antibody 8A9.
  • Fig. 99B and Fig. 99D show staining with antibody 17H6. Both antibodies bind to an epitope that that is outside of the PSMGFR region and comprises all or part of the sequence VQLTLAFRE.
  • FIG. 8A9 shows strong binding to normal liver tissue.17H6 is a weak antibody and it is possible that it was not used at a high enough concentration in this study.
  • Figure 100A-100B show photographs of normal liver tissue specimens, stained with an antibody of the invention 45C11. Fig. 100A show the entire tissue core. Fig. 100B show the 40X magnification of a particular area of the tissue.
  • Antibody 45C11 binds to an epitope that is outside of the PSMGFR region and comprises all or part of the sequence SNIKFRPGSVV. Antibody 45C11 cannot bind to the N-10 peptide. As can be seen in the figure, 45C11 binds strongly to normal liver tissue.
  • Figure 101A-101H show photographs of normal lung tissue specimens, stained with different antibodies of the invention.
  • Fig. 101A-101D show the entire tissue core.
  • Fig. 101E-101H show the 40X magnification of a particular area of the tissue.
  • Fig. 101A and Fig. 101E show staining with MNC2-scFv.
  • Fig. 101B and Fig. 101F show staining with MNE6.
  • Fig. 101C and Fig. 101G show staining with 20A10.
  • Fig.101D and Fig. 101H show staining with 3C2B1.
  • These antibodies bind to an epitope that comprises all or part of the sequence FPFS or PFPFSAQSGA.
  • FIG. 102A-102D show photographs of normal lung tissue specimens, stained with different antibodies of the invention.
  • Fig. 102A-102B show the entire tissue core.
  • Fig. 102C-102D show the 40X magnification of a particular area of the tissue.
  • Fig.102A and Fig. 102C show staining with MNC3.
  • Fig. 102B and Fig. 102D show staining with 25E6.
  • These antibodies bind to an epitope that comprises all or part of the sequence ASRYNLT.
  • These antibodies are all able to bind to the PSMGFR peptide, bind to the N-10 peptide but also bind to the C-10 peptide. As can be seen, these antibodies are not as cancer-specific and show some binding to normal lung tissue.
  • Figure 103A-103B show photographs of normal lung tissue specimens, stained with an antibody of the invention 1E4.
  • Fig.103A show the entire tissue core.
  • Fig.103B show the 40X magnification of a particular area of the tissue.
  • Antibody 1E4 binds to an epitope that comprises all or part of the sequence QFNQYKTEA. Antibody 1E4 can bind to the N-10 peptide but also binds to the C-10 peptide.
  • Figure 104A-104H show photographs of normal lung tissue specimens, stained with different antibodies of the invention.
  • Fig. 104A-104D show the entire tissue core.
  • Fig. 104E-104H show the 40X magnification of a particular area of the tissue.
  • Fig. 104A and Fig. 104E show staining with 18B4.
  • Fig.104B and Fig.104F show staining with 31A1.
  • Fig.104C and Fig. 104G show staining with 32C1.
  • FIG. 104D and Fig. 104H show staining with 29H1. These antibodies bind to an epitope that comprises all or part of the sequence GTINVHDVET, which is the most N-terminal part of the PSMGFR peptide. None of these antibodies are able to bind to the N-10 peptide. As can be seen in the figure, all these antibodies show strong binding to normal lung tissue.
  • Figure 105A-105D show photographs of normal lung tissue specimens, stained with antibodies of the invention.
  • Fig. 105A-105B show the entire tissue core.
  • Fig. 105C- 105D show the 40X magnification of a particular area of the tissue.
  • Fig. 105A and Fig.105C show staining with antibody 8A9. Fig.
  • 105B and Fig. 105D show staining with antibody 17H6. Both antibodies bind to an epitope that that is outside of the PSMGFR region and comprises all or part of the sequence VQLTLAFRE. As can be seen in the figure, 8A9 shows strong binding to normal lung tissue. 17H6 is a weak antibody and it is possible that it was not used at a high enough concentration in this study.
  • Figure 106A-106B show photographs of normal lung tissue specimens, stained with an antibody of the invention 45C11. Fig. 106A show the entire tissue core. Fig. 106B show the 40X magnification of a particular area of the tissue.
  • Antibody 45C11 binds to an epitope that is outside of the PSMGFR region and comprises all or part of the sequence SNIKFRPGSVV. Antibody 45C11 cannot bind to the N-10 peptide. As can be seen in the figure, 45C11 binds to normal lung tissue.
  • Figure 107A-107H show photographs of normal bone marrow tissue specimens, stained with different antibodies of the invention.
  • Fig. 107A-107D show the entire tissue core.
  • Fig. 107E-107H show the 40X magnification of a particular area of the tissue.
  • Fig. 107A and Fig.107E show staining with MNC2-scFv.
  • Fig.107B and Fig. 107F show staining with MNE6.
  • Fig. 107C and Fig. 107G show staining with 20A10.
  • Fig. 107D and Fig. 107H show staining with 3C2B1.
  • These antibodies bind to an epitope that comprises all or part of the sequence FPFS or PFPFSAQSGA. All these antibodies are all able to bind to the PSMGFR peptide, bind to the N-10 peptide but do not bind to the C-10 peptide. In addition, these antibodies disrupt the binding of NME7AB to the MUC1* extra cellular domain as exemplified by the PSMGFR peptide. Further, these antibodies recognize a MUC1 cleavage product when the cleavage enzyme is MMP9.
  • Figure 108A-108D show photographs of normal bone marrow tissue specimens, stained with different antibodies of the invention.
  • Fig. 108A-108B show the entire tissue core.
  • Fig. 108C-108D show the 40X magnification of a particular area of the tissue.
  • Fig. 108A and Fig. 108C show staining with MNC3.
  • Fig. 108B and Fig. 108D show staining with 25E6.
  • These antibodies bind to an epitope that comprises all or part of the sequence ASRYNLT.
  • Figure 109A-109B show photographs of normal bone marrow tissue specimens, stained with an antibody of the invention 1E4.
  • Fig. 109A show the entire tissue core.
  • Fig. 109B show the 40X magnification of a particular area of the tissue.
  • Antibody 1E4 binds to an epitope that comprises all or part of the sequence QFNQYKTEA.
  • Antibody 1E4 can bind to the N-10 peptide but also binds to the C-10 peptide.1E4 binds to normal bone marrow.
  • Figure 110A-110H show photographs of normal bone marrow tissue specimens, stained with different antibodies of the invention.
  • Fig. 110A-110D show the entire tissue core.
  • Fig. 110E-110H show the 40X magnification of a particular area of the tissue.
  • Fig. 110A and Fig. 110E show staining with 18B4.
  • Fig. 110B and Fig. 110F show staining with 31A1.
  • Fig. 110C and Fig. 110G show staining with 32C1.
  • Fig. 110D and Fig. 110H show staining with 29H1.
  • These antibodies bind to an epitope that comprises all or part of the sequence GTINVHDVET, which is the most N-terminal part of the PSMGFR peptide.
  • Figure 111A-111D show photographs of normal bone marrow tissue specimens, stained with antibodies of the invention.
  • Fig. 111A-111B show the entire tissue core.
  • Fig. 111C-111D show the 40X magnification of a particular area of the tissue.
  • Fig. 111A and Fig. 111C show staining with antibody 8A9.
  • Fig. 111B and Fig. 111D show staining with antibody 17H6. Both antibodies bind to an epitope that that is outside of the PSMGFR region and comprises all or part of the sequence VQLTLAFRE.
  • FIG. 8A9 shows strong binding to normal bone marrow tissue.
  • 17H6 is a weak antibody and it is possible that it was not used at a high enough concentration in this study.
  • Figure 112A-112B show photographs of normal bone marrow tissue specimens, stained with an antibody of the invention 45C11.
  • Fig. 112A show the entire tissue core.
  • Fig. 112B show the 40X magnification of a particular area of the tissue.
  • Antibody 45C11 binds to an epitope that is outside of the PSMGFR region and comprises all or part of the sequence SNIKFRPGSVV. Antibody 45C11 cannot bind to the N-10 peptide.
  • FIG. 113A-113C shows photographs, array map and description of FDA normal tissue array MNO1021 stained with the anti-PSMGFR antibody 20A10 at 0.25ug/mL.
  • Fig. 113A shows photographs of the tissue micro array.
  • Fig. 113B shows map of the array with abbreviated tissue descriptors.
  • Fig. 113C detailed description of the tissue micro array with non-identifying donor data.
  • Figure 114A-114X shows photographs of specific tissues from FDA normal tissue array MNO1021 stained with the anti-PSMGFR antibody 20A10 at 0.25ug/mL, magnified to 6X and 20X.
  • Fig. 114A and Fig. 114E are adrenal gland.
  • Fig. 114B and Fig. 114F are breast.
  • Fig. 114C and Fig. 114G are fallopian tube.
  • Fig. 114D and Fig. 114H are kidney.
  • Fig. 114I and Fig. 114M are heart muscle.
  • Fig. 114J and Fig. 114N are liver.
  • Fig. 114K and Fig. 114O are lung.
  • Fig. 114L and Fig. 114P are ureter.
  • Fig. 114Q and Fig. 114U are eye.
  • Fig. 114R and Fig. 114V are cerebral cortex.
  • Fig. 114S and Fig. 114W are bone marrow.
  • FIG.114T and Fig.114X are skeletal muscle.
  • Figure 115A-115C shows photographs, array map and description of breast cancer tissue array BR1141 stained with the anti-PSMGFR antibody 20A10 at 0.25ug/mL.
  • Fig. 115A shows photographs of the tissue micro array.
  • Fig. 115B shows map of the array with abbreviated tissue descriptors.
  • Fig. 115C detailed description of the tissue micro array with non-identifying donor data.
  • Figure 116A-116F shows photographs of specific tissues from breast cancer tissue array BR1141 stained with the anti-PSMGFR antibody 20A10 at 0.25ug/mL, magnified to 6X and 20X.
  • FIG. 116D are photographs of a Grade 2 invasive ductal carcinoma.
  • Fig. 116B and Fig. 116E are photographs of a Grade 2 invasive ductal carcinoma.
  • Fig.116C and Fig.116F are photographs of a Grade 2 invasive ductal carcinoma.
  • Figure 117A-117C shows photographs, array map and description of pancreatic cancer tissue array PA805c stained with the anti-PSMGFR antibody 20A10 at 0.25ug/mL.
  • Fig. 117A shows photographs of the tissue micro array.
  • Fig. 117B shows map of the array with abbreviated tissue descriptors.
  • Fig. 117C detailed description of the tissue micro array with non-identifying donor data.
  • Figure 118A-118F shows photographs of specific tissues from pancreatic cancer tissue array PA805c stained with the anti-PSMGFR antibody 20A10 at 0.25ug/mL, magnified to 6X and 20X.
  • Fig. 118A and Fig. 118D are photographs of a Grade 2 papillary adenocarcinoma.
  • Fig. 118B and Fig. 118E are photographs of a Grade 2-3 ductal carcinoma.
  • Fig.118C and Fig.118F are photographs of a Grade 3 invasive adenocarcinoma.
  • Figure 119A-119C shows photographs, array map and description of esophageal cancer tissue array BC001113 stained with the anti-PSMGFR antibody 20A10 at 0.25ug/mL.
  • Fig. 119A shows photographs of the tissue micro array.
  • Fig. 119B shows map of the array with abbreviated tissue descriptors.
  • Fig. 119C detailed description of the tissue micro array with non-identifying donor data.
  • Figure 120A-120F shows photographs of specific tissues from esophageal cancer tissue array BC001113 stained with the anti-PSMGFR antibody 20A10 at 0.25ug/mL, magnified to 6X and 20X.
  • Fig. 120A and Fig. 120D are photographs of the specimen at position A1.
  • FIG. 120B and Fig. 120E are photographs of the specimen at position A7.
  • Fig. 120C and Fig.120F are photographs of the specimen at position A8.
  • Figure 121A-121C shows photographs, array map and description of FDA normal tissue array MNO1021 stained with the anti-PSMGFR antibody 3C2B1 at 20ug/mL.
  • Fig. 121A shows photographs of the tissue micro array.
  • Fig. 121B shows map of the array with abbreviated tissue descriptors.
  • Fig. 121C detailed description of the tissue micro array with non-identifying donor data.
  • Figure 122A-122X shows photographs of specific tissues from FDA normal tissue array MNO1021 stained with the anti-PSMGFR antibody 3C2B1 at 20ug/mL, magnified to 6X and 20X.
  • Fig. 122A and Fig. 122E are adrenal gland.
  • Fig. 122B and Fig. 122F are breast.
  • Fig. 122C and Fig. 122G are fallopian tube.
  • Fig. 122D and Fig. 122H are kidney.
  • Fig. 122I and Fig. 122M are heart muscle.
  • Fig. 122J and Fig. 122N are liver.
  • Fig. 122K and Fig. 122O are lung.
  • Fig. 122L and Fig. 122P are ureter.
  • FIG. 122Q and Fig. 122U are eye.
  • Fig. 122R and Fig. 122V are cerebral cortex.
  • Fig. 122S and Fig. 122W are bone marrow.
  • Fig.122T and Fig.122X are skeletal muscle.
  • Figure 123A-123C shows photographs, array map and description of pancreatic cancer tissue array PA1003 stained with the anti-PSMGFR antibody 3C2B1 at 20ug/mL.
  • Fig. 123A shows photographs of the tissue micro array.
  • Fig. 123B shows map of the array with abbreviated tissue descriptors.
  • Fig. 123C detailed description of the tissue micro array with non-identifying donor data.
  • Figure 124A-124F shows photographs of specific tissues from pancreatic cancer tissue array PA1003 stained with the anti-PSMGFR antibody 3C2B1 at 20ug/mL, magnified to 6X and 20X.
  • Fig. 124A and Fig.124D are photographs of a Grade 2 adenocarcinoma.
  • Fig. 124B and Fig. 124E are photographs of a Grade 2 adenocarcinoma.
  • Fig. 124C and Fig. 124F are photographs of a Grade 2 adenocarcinoma.
  • Figure 125A-125C shows photographs, array map and description of breast cancer tissue array BR1141 stained with the anti-PSMGFR antibody 3C2B1 at 20ug/mL.
  • Fig. 125A shows photographs of the tissue micro array.
  • Fig. 125B shows map of the array with abbreviated tissue descriptors.
  • Fig. 125C detailed description of the tissue micro array with non-identifying donor data.
  • Figure 126A-126F shows photographs of specific tissues from breast cancer tissue array BR1141 stained with the anti-PSMGFR antibody 3C2B1 at 20ug/mL, magnified to 6X and 20X.
  • Fig. 126A and Fig. 126D are photographs of a Grade 2 invasive ductal carcinoma.
  • Fig. 126B and Fig. 126E are photographs of a Grade 2 invasive ductal carcinoma.
  • Fig.126C and Fig.126F are photographs of a Grade 2 invasive carcinoma.
  • Figure 127A-127C shows photographs, array map and description of FDA normal tissue array MNO1021 stained with the anti-PSMGFR antibody 5C6F3 at 1ug/mL.
  • Fig. 127A shows photographs of the tissue micro array.
  • Fig. 127B shows map of the array with abbreviated tissue descriptors.
  • Fig. 127C detailed description of the tissue micro array with non-identifying donor data.
  • Figure 128A-128X shows photographs of specific tissues from FDA normal tissue array MNO1021 stained with the anti-PSMGFR antibody 5C6F3 at 1ug/mL, magnified to 6X and 20X.
  • Fig. 128A and Fig. 128E are adrenal gland.
  • Fig. 128B and Fig. 128F are breast.
  • Fig. 128C and Fig. 128G are fallopian tube.
  • Fig. 128D and Fig. 128H are kidney.
  • Fig.128I and Fig.128M are heart muscle.
  • Fig.128J and Fig.128N are liver.
  • Fig.128K and Fig. 128O are lung.
  • Fig. 128L and Fig. 128P are ureter.
  • FIG. 128Q and Fig. 128U are eye.
  • Fig.128R and Fig.128V are cerebral cortex.
  • Fig. 128S and Fig.128W are bone marrow.
  • Fig. 128T and Fig.128X are skeletal muscle.
  • Figure 129A-129C shows photographs, array map and description of pancreatic cancer tissue array PA1003 stained with the anti-PSMGFR antibody 5C6F3 at 1-20ug/mL.
  • Fig. 129A shows photographs of the tissue micro array.
  • Fig. 129B shows map of the array with abbreviated tissue descriptors.
  • Fig. 129C detailed description of the tissue micro array with non-identifying donor data.
  • Figure 130A-130F shows photographs of specific tissues from pancreatic cancer tissue array PA1003 stained with the anti-PSMGFR antibody 5C6F3 at 1ug/mL, magnified to 6X and 20X.
  • Fig. 130A and Fig. 130D are photographs of a Grade 2 adenocarcinoma.
  • Fig. 130B and Fig. 130E are photographs of a Grade 2 adenocarcinoma.
  • Fig. 130C and Fig. 130F are photographs of a Grade 2 adenocarcinoma.
  • Figure 131A-131C shows photographs, array map and description of breast cancer tissue array BR1141 stained with the anti-PSMGFR antibody 5C6F3 at 1ug/mL.
  • FIG. 131A shows photographs of the tissue micro array.
  • Fig. 131B shows map of the array with abbreviated tissue descriptors.
  • Fig. 131C detailed description of the tissue micro array with non-identifying donor data.
  • Figure 132A-132F shows photographs of specific tissues from breast cancer tissue array BR1141 stained with the anti-PSMGFR antibody 5C6F3 at 1ug/mL, magnified to 6X and 20X.
  • Fig. 132A and Fig. 132D are photographs of a Grade 2 invasive ductal carcinoma.
  • Fig. 132B and Fig. 132E are photographs of a Grade 2 invasive ductal carcinoma.
  • Fig.132C and Fig.132F are photographs of a Grade 2 invasive carcinoma.
  • Figure 133A-133C shows photographs, array map and description of FDA normal tissue array MNO1021 stained with the anti-PSMGFR antibody 18B4 at 10ug/mL.
  • Fig. 133A shows photographs of the tissue micro array.
  • Fig. 133B shows map of the array with abbreviated tissue descriptors.
  • Fig. 133C detailed description of the tissue micro array with non-identifying donor data.
  • Figure 134A-134X shows photographs of specific tissues from FDA normal tissue array MNO1021 stained with the anti-PSMGFR antibody 18B4 at 10ug/mL, magnified to 6X and 20X.
  • Fig. 134A and Fig. 134E are adrenal gland.
  • Fig. 134B and Fig. 134F are breast.
  • Fig. 134C and Fig. 134G are fallopian tube.
  • Fig. 134D and Fig. 134H are kidney.
  • Fig.134I and Fig.134M are heart muscle.
  • Fig.134J and Fig.134N are liver.
  • Fig.134K and Fig. 134O are lung.
  • Fig. 134L and Fig. 134P are ureter.
  • Fig. 134Q and Fig. 134U are eye.
  • Fig.134R and Fig.134V are cerebral cortex.
  • Fig. 134S and Fig.134W are bone marrow.
  • Fig. 134T and Fig.134X are skeletal muscle.
  • Figure 135A-135C shows photographs, array map and description of breast cancer tissue array BR1141 stained with the anti-PSMGFR antibody 18B4 at 10ug/mL.
  • Fig. 135A shows photographs of the tissue micro array.
  • Fig. 135B shows map of the array with abbreviated tissue descriptors.
  • Fig. 135C detailed description of the tissue micro array with non-identifying donor data.
  • Figure 136A-136F shows photographs of specific tissues from breast cancer tissue array BR1141 stained with the anti-PSMGFR antibody 18B4 at 10ug/mL, magnified to 6X and 20X.
  • Fig. 136A and Fig. 136D are photographs of a Grade 2 invasive ductal carcinoma.
  • Fig. 135A shows photographs of the tissue micro array.
  • Fig. 135B shows map of the array with abbreviated tissue descriptors.
  • Fig. 135C detailed description of the tissue micro array with non-identifying donor data.
  • FIG. 136B and Fig. 136E are photographs of a Grade 2 invasive ductal carcinoma.
  • Fig.136C and Fig.136F are photographs of a Grade 2 invasive ductal carcinoma.
  • Figure 137A-137C shows photographs, array map and description of esophageal cancer tissue array BC001113 stained with the anti-PSMGFR antibody 18B4 at 10ug/mL.
  • Fig. 137A shows photographs of the tissue micro array.
  • Fig. 137B shows map of the array with abbreviated tissue descriptors.
  • Fig. 137C detailed description of the tissue micro array with non-identifying donor data.
  • Figure 138A-138F shows photographs of specific tissues from esophageal cancer tissue array BC001113 stained with the anti-PSMGFR antibody 18B4 at 10ug/mL, magnified to 6X and 20X.
  • Fig. 138A and Fig. 138D are photographs of the specimen at position A1.
  • Fig. 138B and Fig. 138E are photographs of the specimen at position A7.
  • Fig. 138C and Fig. 138F are photographs of the specimen at position A8.
  • Figure 139A-139C shows photographs, array map and description of FDA normal tissue array MNO1021 stained with the anti-PSMGFR antibody 18G12 at 10ug/mL.
  • Fig. 139A shows photographs of the tissue micro array.
  • Fig. 139A shows photographs of the tissue micro array.
  • FIG. 139B shows map of the array with abbreviated tissue descriptors.
  • FIG. 139C detailed description of the tissue micro array with non-identifying donor data.
  • Figure 140A-140X shows photographs of specific tissues from FDA normal tissue array MNO1021 stained with the anti-PSMGFR antibody 18G12 at 10ug/mL, magnified to 6X and 20X.
  • Fig. 140A and Fig. 140E are adrenal gland.
  • Fig. 140B and Fig. 140F are breast.
  • Fig. 140C and Fig. 140G are fallopian tube.
  • Fig. 140D and Fig. 140H are kidney.
  • Fig. 140I and Fig. 140M are heart muscle.
  • Fig. 140J and Fig. 140N are liver.
  • FIG. 140O are lung.
  • Fig. 140L and Fig. 140P are ureter.
  • Fig. 140Q and Fig. 140U are eye.
  • Fig. 140R and Fig. 140V are cerebral cortex.
  • Fig. 140S and Fig. 140W are bone marrow.
  • Fig.140T and Fig.140X are skeletal muscle.
  • Figure 141A-141C shows photographs, array map and description of breast cancer tissue array BR1141 stained with the anti-PSMGFR antibody 18G12 at 15ug/mL.
  • Fig. 141A shows photographs of the tissue micro array.
  • Fig. 141B shows map of the array with abbreviated tissue descriptors.
  • Fig. 141C detailed description of the tissue micro array with non-identifying donor data.
  • Figure 142A-142F shows photographs of specific tissues from breast cancer tissue array BR1141 stained with the anti-PSMGFR antibody 18G12 at 15ug/mL, magnified to 6X and 20X.
  • Fig. 142A and Fig. 142D are photographs of a Grade 2 invasive ductal carcinoma.
  • Fig. 142B and Fig. 142E are photographs of a Grade 2 invasive ductal carcinoma.
  • Fig.142C and Fig.142F are photographs of a Grade 2 invasive ductal carcinoma.
  • Figure 143A-143C shows photographs, array map and description of pancreatic cancer tissue array PA1003 stained with the anti-PSMGFR antibody 18G12 at 15ug/mL.
  • FIG. 143A shows photographs of the tissue micro array.
  • Fig. 143B shows map of the array with abbreviated tissue descriptors.
  • Fig. 143C detailed description of the tissue micro array with non-identifying donor data.
  • Figure 144A-144F shows photographs of specific tissues from pancreatic cancer tissue array PA1003 stained with the anti-PSMGFR antibody 18G12 at 15ug/mL, magnified to 6X and 20X.
  • Fig. 144A and Fig.144D are photographs of a Grade 2 adenocarcinoma.
  • Fig. 144B and Fig. 144E are photographs of a Grade 2 adenocarcinoma.
  • Figure 144F are photographs of a Grade 2-3 adenocarcinoma with lymph node involvement.
  • Figure 145A-145C shows photographs, array map and description of esophageal cancer tissue array BC001113 stained with the anti-PSMGFR antibody 18G12 at 30ug/mL.
  • Fig. 145A shows photographs of the tissue micro array.
  • Fig. 145B shows map of the array with abbreviated tissue descriptors.
  • Fig. 145C detailed description of the tissue micro array with non-identifying donor data.
  • Figure 146A-146F shows photographs of specific tissues from esophageal cancer tissue array BC001113 stained with the anti-PSMGFR antibody 18G12 at 30ug/mL, magnified to 6X and 20X.
  • FIG. 146A and Fig. 146D are photographs of the specimen at position A1.
  • Fig. 146B and Fig. 146E are photographs of the specimen at position A7.
  • Fig. 146C and Fig.146F are photographs of the specimen at position A8.
  • Figure 147A-147C shows photographs, array map and description of FDA normal tissue array MNO1021 stained with the anti-PSMGFR antibody 25E6 at 5.0ug/mL.
  • Fig. 147A shows photographs of the tissue micro array.
  • Fig. 147B shows map of the array with abbreviated tissue descriptors.
  • Fig. 147C detailed description of the tissue micro array with non-identifying donor data.
  • Figure 148A-148X shows photographs of specific tissues from FDA normal tissue array 1021 stained with the anti-PSMGFR antibody 25E6 at 5.0ug/mL, magnified to 6X and 20X.
  • Fig. 148A and Fig. 148E are adrenal gland.
  • Fig. 148B and Fig. 148F are breast.
  • Fig. 148C and Fig.148G are fallopian tube.
  • Fig. 148D and Fig. 148H are kidney.
  • Fig.148I and Fig. 148M are heart muscle.
  • Fig. 148J and Fig. 148N are liver.
  • Fig. 148K and Fig. 148O are lung.
  • Fig. 148L and Fig. 148P are ureter.
  • Fig. 148A and Fig. 148E are adrenal gland.
  • Fig. 148B and Fig. 148F are breast.
  • Fig. 148C and Fig.148G are fallopian tube
  • FIG. 148Q and Fig. 148U are eye.
  • Fig. 148R and Fig. 148V are cerebral cortex.
  • Fig. 148S and Fig. 148W are bone marrow.
  • Fig. 148T and Fig.148X are skeletal muscle.
  • Figure 149A-149C shows photographs, array map and description of breast cancer tissue array BR1141 stained with the anti-PSMGFR antibody 25E6 at 5.0ug/mL.
  • Fig. 149A shows photographs of the tissue micro array.
  • Fig. 149B shows map of the array with abbreviated tissue descriptors.
  • Fig. 149C detailed description of the tissue micro array with non-identifying donor data.
  • Figure 150A-150F shows photographs of specific tissues from breast cancer tissue array BR1141 stained with the anti-PSMGFR antibody 25E6 at 5.0ug/mL, magnified to 6X and 20X.
  • Fig. 150A and Fig. 150D are photographs of a Grade 2 invasive ductal carcinoma.
  • Fig. 150B and Fig. 150E are photographs of a Grade 2 invasive ductal carcinoma.
  • Fig.150C and Fig.150F are photographs of a Grade 2 invasive ductal carcinoma.
  • Figure 151A-151C shows photographs, array map and description of pancreatic cancer tissue array PA1003 stained with the anti-PSMGFR antibody 25E6 at 5.0ug/mL.
  • FIG. 151A shows photographs of the tissue micro array.
  • Fig. 151B shows map of the array with abbreviated tissue descriptors.
  • Fig. 151C detailed description of the tissue micro array with non-identifying donor data.
  • Figure 152A-152F shows photographs of specific tissues from pancreatic cancer tissue array PA1003 stained with the anti-PSMGFR antibody 25E6 at 5.0ug/mL, magnified to 6X and 20X.
  • Fig. 152A and Fig. 152D are photographs of a Grade 2 adenocarcinoma.
  • Fig. 152B and Fig. 152E are photographs of a Grade 1 adenocarcinoma.
  • FIG. 152F are photographs of a Grade 1 adenocarcinoma.
  • Figure 153A-153C shows photographs, array map and description of FDA normal tissue array MNO1021 stained with the anti-PSMGFR antibody 28F9 at 15.0ug/mL.
  • Fig. 153A shows photographs of the tissue micro array.
  • Fig. 153B shows map of the array with abbreviated tissue descriptors.
  • Fig. 153C detailed description of the tissue micro array with non-identifying donor data.
  • Figure 154A-154X shows photographs of specific tissues from FDA normal tissue array MNO1021 stained with the anti-PSMGFR antibody 28F9 at 15.0ug/mL, magnified to 6X and 20X.
  • Fig. 154E are adrenal gland.
  • Fig. 154B and Fig. 154F are breast.
  • Fig. 154C and Fig. 154G are fallopian tube.
  • Fig. 154D and Fig. 154H are kidney.
  • Fig. 154I and Fig. 154M are heart muscle.
  • Fig. 154J and Fig. 154N are liver.
  • Fig. 154K and Fig. 154O are lung.
  • Fig. 154L and Fig. 154P are ureter.
  • Fig. 154Q and Fig. 154U are eye.
  • Fig. 154R and Fig. 154V are cerebral cortex.
  • Fig. 154S and Fig. 154W are bone marrow.
  • FIG.154T and Fig.154X are skeletal muscle.
  • Figure 155A-155C shows photographs, array map and description of breast cancer tissue array BR1141 stained with the anti-PSMGFR antibody 28F9 at 15.0ug/mL.
  • Fig. 155A shows photographs of the tissue micro array.
  • Fig. 155B shows map of the array with abbreviated tissue descriptors.
  • Fig. 155C detailed description of the tissue micro array with non-identifying donor data.
  • Figure 156A-156F shows photographs of specific tissues from breast cancer tissue array BR1141 stained with the anti-PSMGFR antibody 28F9 at 15.0ug/mL, magnified to 6X and 20X.
  • FIG. 156D are photographs of a Grade 2 invasive ductal carcinoma.
  • Fig. 156B and Fig. 156E are photographs of a Grade 2 invasive ductal carcinoma.
  • Fig.156C and Fig.156F are photographs of a Grade 2 invasive ductal carcinoma.
  • Figure 157A-157C shows photographs, array map and description of FDA normal tissue array MNO1021 stained with the N+20/C-27 antibody 1E4 at 7.5ug/mL.
  • Fig. 157A shows photographs of the tissue micro array.
  • Fig. 157B shows map of the array with abbreviated tissue descriptors.
  • Fig. 157C detailed description of the tissue micro array with non-identifying donor data.
  • Figure 158A-158X shows photographs of specific tissues from FDA normal tissue array MNO1021 stained with the N+20/C-27 antibody 1E4 at 7.5ug/mL, magnified to 6X and 20X.
  • Fig. 158A and Fig. 158E are adrenal gland.
  • Fig. 158B and Fig. 158F are breast.
  • Fig.158C and Fig. 158G are fallopian tube.
  • Fig. 158D and Fig. 158H are kidney.
  • Fig.158I and Fig. 158M are heart muscle.
  • Fig. 158J and Fig. 158N are liver.
  • Fig. 158K and Fig. 158O are lung.
  • Fig. 158L and Fig. 158P are ureter.
  • FIG. 158Q and Fig. 158U are eye.
  • Fig. 158R and Fig. 158V are cerebral cortex.
  • Fig. 158S and Fig. 158W are bone marrow.
  • Fig. 158T and Fig.158X are skeletal muscle.
  • Figure 159A-159C shows photographs, array map and description of breast cancer tissue array BR1007 stained with the N+20/C-27 antibody 1E4 at 10.0ug/mL.
  • Fig. 159A shows photographs of the tissue micro array.
  • Fig. 159B shows map of the array with abbreviated tissue descriptors.
  • Fig. 159C detailed description of the tissue micro array with non-identifying donor data.
  • Figure 160A-160F shows photographs of specific tissues from breast cancer tissue array BR1007 stained with the N+20/C-27 antibody 1E4 at 10.0ug/mL, magnified to 6X and 20X.
  • Fig. 160A and Fig. 160D are photographs of a Grade 2 invasive ductal carcinoma with positive lymph nodes.
  • Fig. 160B and Fig. 160E are photographs of a Grade 2 invasive ductal carcinoma.
  • Fig. 160C and Fig. 160F are photographs of a Grade 2 invasive ductal carcinoma.
  • Figure 161A-161C shows photographs, array map and description of FDA normal tissue array MNO1021 stained with the N+20/C-27 antibody 29H1 at 0.5ug/mL.
  • FIG. 161A shows photographs of the tissue micro array.
  • Fig. 161B shows map of the array with abbreviated tissue descriptors.
  • Fig. 161C detailed description of the tissue micro array with non-identifying donor data.
  • Figure 162A-162X shows photographs of specific tissues from FDA normal tissue array MNO1021 stained with the N+20/C-27 antibody 29H1 at 0.5ug/mL, magnified to 6X and 20X.
  • Fig. 162A and Fig. 162E are adrenal gland.
  • Fig. 162B and Fig. 162F are breast.
  • Fig.162C and Fig. 162G are fallopian tube.
  • Fig. 162D and Fig. 162H are kidney.
  • FIG. 162M are heart muscle.
  • Fig. 162J and Fig. 162N are liver.
  • Fig. 162K and Fig. 162O are lung.
  • Fig. 162L and Fig. 162P are ureter.
  • Fig. 162Q and Fig. 162U are eye.
  • Fig. 162R and Fig. 162V are cerebral cortex.
  • Fig. 162S and Fig. 162W are bone marrow.
  • Fig. 162T and Fig.162X are skeletal muscle.
  • Figure 163A-163C shows photographs, array map and description of breast cancer tissue array BR1141 stained with the N+20/C-27 antibody 29H1 at 0.5ug/mL.
  • Fig. 163A shows photographs of the tissue micro array.
  • FIG. 163B shows map of the array with abbreviated tissue descriptors.
  • FIG. 163C detailed description of the tissue micro array with non-identifying donor data.
  • Figure 164A-164F shows photographs of specific tissues from breast cancer tissue array BR1141 stained with the N+20/C-27 antibody 29H1 at 0.5ug/mL, magnified to 6X and 20X.
  • Fig. 164A and Fig. 164D are photographs of a Grade 2 invasive ductal carcinoma.
  • Fig. 164B and Fig. 164E are photographs of a Grade 2 invasive ductal carcinoma.
  • Fig.164C and Fig.164F are photographs of a Grade 2 invasive ductal carcinoma.
  • Figure 165A-165C shows photographs, array map and description of pancreatic cancer tissue array PA1003 stained with the N+20/C-27 antibody 29H1 at 0.5ug/mL.
  • Fig. 165A shows photographs of the tissue micro array.
  • Fig. 165B shows map of the array with abbreviated tissue descriptors.
  • Fig. 165C detailed description of the tissue micro array with non-identifying donor data.
  • Figure 166A-166F shows photographs of specific tissues from pancreatic cancer tissue array PA1003 stained with the N+20/C-27 antibody 29H1 at 0.5ug/mL, magnified to 6X and 20X.
  • FIG. 166D are photographs of a Grade 2 adenocarcinoma.
  • Fig. 166B and Fig. 166E are photographs of a Grade 2 adenocarcinoma.
  • Fig. 166C and Fig. 166F are photographs of a Grade 3 adenocarcinoma.
  • Figure 167A-167C shows photographs, array map and description of FDA normal tissue array MNO1021 stained with the N+20/C-27 antibody 31A1 at 0.5ug/mL.
  • Fig. 167A shows photographs of the tissue micro array.
  • Fig. 167B shows map of the array with abbreviated tissue descriptors.
  • Fig. 167C detailed description of the tissue micro array with non-identifying donor data.
  • Figure 168A-168X shows photographs of specific tissues from FDA normal tissue array MNO1021 stained with the N+20/C-27 antibody 31A1 at 0.5ug/mL, magnified to 6X and 20X.
  • Fig. 168A and Fig. 168E are adrenal gland.
  • Fig. 168B and Fig. 168F are breast.
  • Fig.168C and Fig. 168G are fallopian tube.
  • Fig. 168D and Fig. 168H are kidney.
  • Fig.168I and Fig. 168M are heart muscle.
  • Fig. 168J and Fig. 168N are liver.
  • Fig. 168K and Fig. 168O are lung.
  • Fig. 168L and Fig. 168P are ureter.
  • FIG. 168Q and Fig. 168U are eye.
  • Fig. 168R and Fig. 168V are cerebral cortex.
  • Fig. 168S and Fig. 168W are bone marrow.
  • Fig. 168T and Fig.168X are skeletal muscle.
  • Figure 169A-169C shows photographs, array map and description of breast cancer tissue array BR1141 stained with the N+20/C-27 antibody 31A1 at 0.5ug/mL.
  • Fig. 169A shows photographs of the tissue micro array.
  • Fig. 169B shows map of the array with abbreviated tissue descriptors.
  • Fig. 169C detailed description of the tissue micro array with non-identifying donor data.
  • Figure 170A-170F shows photographs of specific tissues from breast cancer tissue array BR1141 stained with the N+20/C-27 antibody 31A1 at 0.5ug/mL, magnified to 6X and 20X.
  • Fig. 170A and Fig. 170D are photographs of a Grade 2 invasive ductal carcinoma.
  • Fig. 170B and Fig. 170E are photographs of a Grade 2 invasive ductal carcinoma.
  • Fig.170C and Fig.170F are photographs of a Grade 2 invasive ductal carcinoma.
  • Figure 171A-171C shows photographs, array map and description of pancreatic cancer tissue array PA1003 stained with the N+20/C-27 antibody 31A1 at 0.5ug/mL.
  • FIG. 171A shows photographs of the tissue micro array.
  • Fig. 171B shows map of the array with abbreviated tissue descriptors.
  • Fig. 171C detailed description of the tissue micro array with non-identifying donor data.
  • Figure 172A-172F shows photographs of specific tissues from pancreatic cancer tissue array PA1003 stained with the N+20/C-27 antibody 31A1 at 0.5ug/mL, magnified to 6X and 20X.
  • Fig. 172A and Fig. 172D are photographs of a Grade 1 adenocarcinoma.
  • Fig. 172B and Fig. 172E are photographs of a Grade 2 adenocarcinoma.
  • FIG. 173A-173C shows photographs, array map and description of FDA normal tissue array MNO1021 stained with the N+20/C-27 antibody 32C1 at 0.25ug/mL.
  • Fig. 173A shows photographs of the tissue micro array.
  • Fig. 173B shows map of the array with abbreviated tissue descriptors.
  • Fig. 173C detailed description of the tissue micro array with non-identifying donor data.
  • Figure 174A-174X shows photographs of specific tissues from FDA normal tissue array MNO1021 stained with the N+20/C-27 antibody 32C1 at 0.25ug/mL, magnified to 6X and 20X.
  • 174A and Fig. 174E are adrenal gland.
  • Fig. 174B and Fig. 174F are breast.
  • Fig. 174C and Fig. 174G are fallopian tube.
  • Fig. 174D and Fig. 174H are kidney.
  • Fig.174I and Fig.174M are heart muscle.
  • Fig.174J and Fig.174N are liver.
  • Fig.174K and Fig. 174O are lung.
  • Fig. 174L and Fig. 174P are ureter.
  • Fig. 174Q and Fig. 174U are eye.
  • Fig.174R and Fig.174V are cerebral cortex.
  • Fig. 174S and Fig.174W are bone marrow.
  • FIG. 174T and Fig.174X are skeletal muscle.
  • Figure 175A-175C shows photographs, array map and description of breast cancer tissue array BR1141 stained with the N+20/C-27 antibody 32C1 at 5.0ug/mL.
  • Fig. 175A shows photographs of the tissue micro array.
  • Fig. 175B shows map of the array with abbreviated tissue descriptors.
  • Fig. 175C detailed description of the tissue micro array with non-identifying donor data.
  • Figure 176A-176F shows photographs of specific tissues from breast cancer tissue array BR1141 stained with the N+20/C-27 antibody 32C1 at 5.0ug/mL, magnified to 6X and 20X.
  • FIG. 176D are photographs of a Grade 2 invasive ductal carcinoma.
  • Fig. 176B and Fig. 176E are photographs of a Grade 2 invasive ductal carcinoma.
  • Fig.176C and Fig.176F are photographs of a Grade 2 invasive ductal carcinoma.
  • Figure 177A-177C shows photographs, array map and description of esophageal cancer tissue array ES1001 stained with the N+20/C-27 antibody 32C1 at 1.0ug/mL.
  • Fig. 177A shows photographs of the tissue micro array.
  • Fig. 177B shows map of the array with abbreviated tissue descriptors.
  • Fig. 177C detailed description of the tissue micro array with non-identifying donor data.
  • Figure 178A-178F shows photographs of specific tissues from esophageal cancer tissue array BC001113 stained with the N+20/C-27 antibody 32C1 at 1.0ug/mL, magnified to 6X and 20X.
  • Fig. 178A and Fig. 178D are photographs of a squamous cell carcinoma.
  • Fig. 178B and Fig. 178E are photographs of an adenocarcinoma.
  • Fig. 178C and Fig. 178F are photographs of a squamous cell carcinoma.
  • Figure 179A-179C shows photographs, array map and description of FDA normal tissue array MNO1021 stained with the N+20/C-27 antibody 45C11 at 12.5ug/mL.
  • FIG. 179A shows photographs of the tissue micro array.
  • Fig. 179B shows map of the array with abbreviated tissue descriptors.
  • Fig. 179C detailed description of the tissue micro array with non-identifying donor data.
  • Figure 180A-180X shows photographs of specific tissues from FDA normal tissue array MNO1021 stained with the N+20/C-27 antibody 45C11 at 12.5ug/mL, magnified to 6X and 20X.
  • Fig. 180A and Fig. 180E are adrenal gland.
  • Fig. 180B and Fig. 180F are breast.
  • Fig. 180C and Fig. 180G are fallopian tube.
  • Fig. 180D and Fig. 180H are kidney.
  • Fig.180I and Fig.180M are heart muscle.
  • Fig.180J and Fig.180N are liver.
  • Fig.180K and Fig. 180O are lung.
  • Fig. 180L and Fig. 180P are ureter.
  • Fig. 180Q and Fig. 180U are eye.
  • Fig.180R and Fig.180V are cerebral cortex.
  • Fig. 180S and Fig.180W are bone marrow.
  • Fig. 180T and Fig.180X are skeletal muscle.
  • Figure 181A-181C shows photographs, array map and description of breast cancer tissue array BR1007 stained with the N+20/C-27 antibody 45C11 at 10.0ug/mL.
  • Fig. 181A shows photographs of the tissue micro array.
  • Fig. 181A shows photographs of the tissue micro array.
  • FIG. 181B shows map of the array with abbreviated tissue descriptors.
  • FIG. 181C detailed description of the tissue micro array with non-identifying donor data.
  • Figure 182A-182F shows photographs of specific tissues from breast cancer tissue array BR1007 stained with the N+20/C-27 antibody 45C11 at 10.0ug/mL, magnified to 6X and 20X.
  • Fig. 182A and Fig. 182D are photographs of a Grade 2 invasive ductal carcinoma with positive lymph nodes.
  • Fig. 182B and Fig. 182E are photographs of a Grade 2 invasive ductal carcinoma.
  • Fig. 182C and Fig. 182F are photographs of a Grade 2 invasive ductal carcinoma.
  • Figure 183A-183C shows photographs, array map and description of pancreatic cancer tissue array PA805c stained with the N+20/C-27 antibody 45C11 at 12.5ug/mL.
  • Fig. 183A shows photographs of the tissue micro array.
  • Fig. 183B shows map of the array with abbreviated tissue descriptors.
  • Fig. 183C detailed description of the tissue micro array with non-identifying donor data.
  • Figure 184A-184F shows photographs of specific tissues from pancreatic cancer tissue array PA805c stained with the N+20/C-27 antibody 45C11 at 12.5ug/mL, magnified to 6X and 20X.
  • FIG. 184D are photographs of a Grade 2 papillary adenocarcinoma.
  • Fig. 184B and Fig. 184E are photographs of a Grade 2-3 ductal carcinoma.
  • Fig.184C and Fig.184F are photographs of a Grade 3 invasive adenocarcinoma.
  • Figure 185A-185C shows photographs, array map and description of FDA normal tissue array MNO1021 stained with the N+9/C-9 antibody 3C5 at 10.0ug/mL.
  • Fig. 185A shows photographs of the tissue micro array.
  • Fig. 185B shows map of the array with abbreviated tissue descriptors.
  • Fig. 185C detailed description of the tissue micro array with non-identifying donor data.
  • Figure 186A-186X shows photographs of specific tissues from FDA normal tissue array MNO1021 stained with the N+9/C-9 antibody 3C5 at 10.0ug/mL, magnified to 6X and 20X.
  • Fig. 186A and Fig. 186E are adrenal gland.
  • Fig. 186B and Fig. 186F are breast.
  • Fig.186C and Fig. 186G are fallopian tube.
  • Fig. 186D and Fig. 186H are kidney.
  • Fig.186I and Fig. 186M are heart muscle.
  • Fig. 186J and Fig. 186N are liver.
  • Fig. 186K and Fig. 186O are lung.
  • Fig. 186L and Fig. 186P are ureter.
  • FIG. 186Q and Fig. 186U are eye.
  • Fig. 186R and Fig. 186V are cerebral cortex.
  • Fig. 186S and Fig. 186W are bone marrow.
  • Fig. 186T and Fig.186X are skeletal muscle.
  • Figure 187A-187C shows photographs, array map and description of pancreatic cancer tissue array PA1003 stained with the N+9/C-9 antibody 3C5 at 10.0ug/mL.
  • Fig. 187A shows photographs of the tissue micro array.
  • Fig. 187B shows map of the array with abbreviated tissue descriptors.
  • Fig. 187C detailed description of the tissue micro array with non-identifying donor data.
  • Figure 188A-188F shows photographs of specific tissues from pancreatic cancer tissue array PA1003 stained with the N+9/C-9 antibody 3C5 at 10.0ug/mL, magnified to 6X and 20X.
  • Fig. 188A and Fig.188D are photographs of a Grade 2 adenocarcinoma.
  • Fig.188B and Fig. 188E are photographs of a Grade 2 adenocarcinoma.
  • Fig. 188C and Fig. 188F are photographs of a Grade 2-3 adenocarcinoma with lymph node involvement.
  • Figure 189A-189C shows photographs, array map and description of FDA normal tissue array MNO1021 stained with the N+9/C-9 antibody 8A9 at 15.0ug/mL.
  • Fig. 189A shows photographs of the tissue micro array.
  • Fig. 189B shows map of the array with abbreviated tissue descriptors.
  • Fig. 189C detailed description of the tissue micro array with non-identifying donor data.
  • Figure 190A-190X shows photographs of specific tissues from FDA normal tissue array MNO1021 stained with the N+9/C-9 antibody 8A9 at 15.0ug/mL, magnified to 6X and 20X.
  • Fig. 190A and Fig. 190E are adrenal gland.
  • Fig.190F are breast.
  • Fig.190C and Fig. 190G are fallopian tube.
  • Fig. 190D and Fig.190H are kidney.
  • Fig.190I and Fig. 190M are heart muscle.
  • Fig. 190J and Fig. 190N are liver.
  • Fig. 190K and Fig. 190O are lung.
  • Fig. 190L and Fig. 190P are ureter.
  • Fig. 190Q and Fig. 190U are eye.
  • Fig. 190R and Fig. 190V are cerebral cortex.
  • Fig. 190S and Fig. 190W are bone marrow.
  • Fig. 190T and Fig.190X are skeletal muscle.
  • Figure 191A-191C shows photographs, array map and description of pancreatic cancer tissue array PA1003 stained with the N+9/C-9 antibody 8A9 at 15.0ug/mL.
  • Fig. 191A shows photographs of the tissue micro array.
  • Fig. 191B shows map of the array with abbreviated tissue descriptors.
  • Fig. 191C detailed description of the tissue micro array with non-identifying donor data.
  • Figure 192A-192F shows photographs of specific tissues from pancreatic cancer tissue array PA1003 stained with the N+9/C-9 antibody 8A9 at 15.0ug/mL, magnified to 6X and 20X.
  • FIG. 193A-193C shows photographs, array map and description of FDA normal tissue array MNO1021 stained with the N+9/C-9 antibody 17H6 at 30.0ug/mL.
  • Fig. 193A shows photographs of the tissue micro array.
  • Fig. 193B shows map of the array with abbreviated tissue descriptors.
  • Fig. 193C detailed description of the tissue micro array with non-identifying donor data.
  • Figure 194A-194X shows photographs of specific tissues from FDA normal tissue array MNO1021 stained with the N+9/C-9 antibody 17H6 at 30.0ug/mL, magnified to 6X and 20X.
  • Fig. 194A and Fig. 194E are adrenal gland.
  • Fig. 194B and Fig. 194F are breast.
  • Fig.194C and Fig. 194G are fallopian tube.
  • Fig. 194D and Fig. 194H are kidney.
  • Fig.194I and Fig. 194M are heart muscle.
  • Fig. 194J and Fig. 194N are liver.
  • Fig. 194K and Fig. 194O are lung.
  • Fig. 194L and Fig. 194P are ureter.
  • FIG. 194Q and Fig. 194U are eye.
  • Fig. 194R and Fig. 194V are cerebral cortex.
  • Fig. 194S and Fig. 194W are bone marrow.
  • Fig. 194T and Fig.194X are skeletal muscle.
  • Figure 195A-195C shows photographs, array map and description of pancreatic cancer tissue array PA805c stained with the N+9/C-9 antibody 17H6 at 30.0ug/mL.
  • Fig. 195A shows photographs of the tissue micro array.
  • Fig. 195B shows map of the array with abbreviated tissue descriptors.
  • Fig. 195C detailed description of the tissue micro array with non-identifying donor data.
  • Figure 196A-196F shows photographs of specific tissues from pancreatic cancer tissue array PA805c stained with the N+9/C-9 antibody 17H6 at 30.0ug/mL, magnified to 6X and 20X.
  • Fig. 196A and Fig. 196D are photographs of a Grade 2 papillary adenocarcinoma.
  • Fig. 196B and Fig. 196E are photographs of a Grade 2-3 ductal carcinoma with lymph node involvement.
  • Fig. 196C and Fig. 196F are photographs of a Grade 3 invasive adenocarcinoma.
  • Figure 197A-197C shows photographs, array map and description of FDA normal tissue array MNO1021 stained with the N+9/C-9 antibody 39H5 at 5.0ug/mL.
  • Fig. 197A shows photographs of the tissue micro array.
  • Fig. 197B shows map of the array with abbreviated tissue descriptors.
  • Fig. 197C detailed description of the tissue micro array with non-identifying donor data.
  • Figure 198A-198X shows photographs of specific tissues from FDA normal tissue array MNO1021 stained with the N+9/C-9 antibody 39H5 at 5.0ug/mL, magnified to 6X and 20X.
  • Fig. 198A and Fig. 198E are adrenal gland.
  • Fig.198F are breast.
  • Fig.198C and Fig. 198G are fallopian tube.
  • Fig. 198D and Fig.198H are kidney.
  • Fig.198I and Fig. 198M are heart muscle.
  • Fig. 198J and Fig. 198N are liver.
  • Fig. 198K and Fig. 198O are lung.
  • Fig. 198L and Fig. 198P are ureter.
  • Fig. 198Q and Fig. 198U are eye.
  • Fig. 198R and Fig. 198V are cerebral cortex.
  • Fig. 198S and Fig. 198W are bone marrow.
  • Fig. 198T and Fig.198X are skeletal muscle.
  • Figure 199A-199C shows photographs, array map and description of pancreatic cancer tissue array PA1003 stained with the N+9/C-9 antibody 39H5 at 5.0ug/mL.
  • Fig. 199A shows photographs of the tissue micro array.
  • Fig. 199B shows map of the array with abbreviated tissue descriptors.
  • Fig. 199C detailed description of the tissue micro array with non-identifying donor data.
  • Figure 200A-200F shows photographs of specific tissues from pancreatic cancer tissue array PA1003 stained with the N+9/C-9 antibody 39H5 at 5.0ug/mL, magnified to 6X and 20X.
  • Fig. 200A and Fig. 200D are photographs of a Grade 2 adenocarcinoma.
  • FIG. 200B and Fig. 200E are photographs of a Grade 2 adenocarcinoma.
  • Fig. 200C and Fig. 200F are photographs of a Grade 2 adenocarcinoma.
  • Figure 201A-201C show graphs of ELISA assays to determine the binding of another set of antibodies generated by immunizing animals with the PSMGFR peptide.
  • Fig. 201A shows binding to the PSMGFR peptide.
  • Fig. 201B shows binding to the N-10 peptide.
  • Fig.201C shows binding to the C-10 peptide. As can be seen, none of the antibodies bound to the C-10 peptide.
  • FIG. 202A-202C shows photographs of pancreatic cancer tissue array PA1003 that has been stained with monoclonal antibody 1E4, monoclonal antibody 18B4 or the polyclonal anti-PSMGFR antibody SDIX.
  • 18B4 binds to the GTINVHDVET epitope at the most N-terminal portion of the PSMGFR peptide, while the 1E4 antibody binds to the QFNQYKTEA epitope that is immediately adjacent and C-terminal to the 18B4 epitope.
  • Figure 203A-203F shows magnified images of the tissue specimen at position A2 of the pancreatic cancer array PA1003.
  • Fig. 203A and Fig. 203B show the specimen stained with antibody 1E4.
  • Fig. 203C and Fig. 203D show the specimen stained with antibody 18B4.
  • Fig.203E and Fig.203F show the specimen stained with polyclonal antibody SDIX.
  • Figure 204A-204D shows magnified images of the tissue specimen at position D4 of the pancreatic array PA1003.
  • Fig. 204A and Fig. 204B show the specimen stained with antibody 18B4.
  • Fig.204C and Fig. 204D show the specimen stained with polyclonal antibody SDIX.
  • Figure 205A-205D shows magnified images of the tissue specimen at position E1 of the pancreatic cancer array PA1003.
  • Fig. 205A and Fig. 205B show the specimen stained with antibody 18B4.
  • Fig. 205C and Fig. 205D show the specimen stained with polyclonal antibody SDIX.
  • Figure 206A-206D shows magnified images of the tissue specimen at position C3 of the pancreatic cancer array PA1003.
  • Fig. 206A and Fig. 206B show the specimen stained with antibody 1E4.
  • Fig. 206C and Fig. 206D show the specimen stained with polyclonal antibody SDIX.
  • Figure 207A-207D shows magnified images of the tissue specimen at position D1 of the pancreatic cancer array PA1003.
  • Fig. 207A and Fig. 207B show the specimen stained with antibody 1E4.
  • Fig. 207C and Fig. 207D show the specimen stained with polyclonal antibody SDIX.
  • Figure 208A-208C shows photographs of the pancreatic cancer array PA1003.
  • Fig. 208A shows the specimen stained with polyclonal antibody SDIX.
  • Fig. 208B shows the specimen stained with antibody 20A10.
  • Fig. 208C shows the specimen stained with antibody 29H1.
  • Figure 209A-209D shows photographs of the esophageal cancer array ES1001 stained with various antibodies.
  • Fig. 209A shows the array stained with polyclonal antibody SDIX.
  • Fig. 209B shows the array stained with antibody 20A10.
  • Fig. 209C shows the array stained with antibody 29H1.
  • Fig.209D shows the array stained with antibody 31A1.
  • Figure 210A-210C shows photographs of the pancreatic cancer array PA1003 stained with various antibodies.
  • Fig. 210A shows the array stained with polyclonal antibody SDIX.
  • Fig. 210B shows the array stained with antibody 20A10.
  • Fig. 210C shows the array stained with antibody 29H1.
  • Figure 211A- 211C show graphs of an ELISA experiment measuring the amount of IL-18 secreted into the condition media of MUC1* positive cancer cells co-cultured with huMNC2-CAR44 T cells wherein the cells also bear an NFAT inducible IL-18.
  • Fig. 211A shows the graph of IL-18 secreted into the supernatant of T47D breast cancer cells co- cultured with untransduced human T cells.
  • Fig. 211B shows the graph of IL-18 secreted into the supernatant of T47D breast cancer cells co-cultured with huMNC2-CAR44 T cells that also bore an NFAT inducible IL-18 gene inserted into a portion of the Foxp3 enhancer.
  • FIG. 211C shows the graph of IL-18 secreted into the supernatant of T47D breast cancer cells co- cultured with huMNC2-CAR44 T cells that also bore an NFAT inducible IL-18 gene inserted into a portion of the IL-2 enhancer.
  • Figure 212A- 212X shows photographs of T47D breast cancer cells (red) doped with varying percentages of T47D cells engineered to express more MUC1* (green). The target cancer cells have been co-cultured with huMNC2-CAR44 T cells with NFAT inducible IL-18 wherein the IL-18 gene has been inserted into either the Foxp3 enhancer/promoter or the IL-2 enhancer/promoter.
  • 212A-212C, 212I-212K, and 212Q-212S show the cancer cells co-cultured with untranduced T cells.
  • Fig. 212D-212F, 212L-212N, and 212T-212V show the cancer cells co-cultured with hiMNC2-CAR44 T cells with the NFAT inducible IL- 18 gene inserted into the Foxp3 enhancer/promoter.
  • Fig. 212G-212H, 212O-212P, and 212W-212X show the cancer cells co-cultured with hiMNC2-CAR44 T cells with the NFAT inducible IL-18 gene inserted into the IL-2 enhancer/promoter.
  • Figure 213A- 213B shows graphs of ELISA experiments in which levels of IL-18 secreted into the conditioned media are measured for huMNC1-CAR44 T cells with NFAT inducible IL-18 gene, inserted into the Foxp3 enhancer or promoter, co-cultured with either MUC1* positive cancer cells or MUC1 negative non-cancerous cells.
  • Fig. 213A shows IL-18 secretion from huMNC2-CAR44 T cells with NFAT inducible IL-18 in co-culture with T47D breast cancer cells where the population has been doped with 5%, 10% or 30% T47D cells that had been transfected with even more MUC1*.
  • FIG. 213B shows IL-18 secretion from huMNC2-CAR44 T cells with NFAT inducible IL-18 in co-culture with non-cancerous, MUC1 negaive HEK293 cells where the cell population has been doped with 5%, 10% or 30% T47D cells that had been transfected with more MUC1*.
  • Figure 214A-214X shows photographs of T47D breast cancer cells (red) or non- cancerous HEK293 cells (also red), where both cell types have been doped with varying percentages of T47D cells engineered to express more MUC1* (green).
  • Fig.214A-214F shows either T47D cells or HEK293 cells that have not been doped with T47D cells engineered to express high MUC1* density.
  • Fig. 214G-214L shows either T47D cells or HEK293 cells that have been doped with 5% T47D cells engineered to express high MUC1* density.
  • Fig. 214M-214R shows either T47D cells or HEK293 cells that have been doped with 10% T47D cells engineered to express high MUC1* density.
  • 214S-214X shows either T47D cells or HEK293 cells that have been doped with 30% T47D cells engineered to express high MUC1* density.
  • Fig. 214A-B, G-H, M-N, and S-T show T47D breast cancer cells.
  • Fig. 214C-F, I-L, O-R, and U-X show HEK293 cells.
  • the induced secretion of IL-18 resulted in low MUC1* density T47D cells being killed but did not induce non-specific killing of the MUC1* negative HEK293 cells.
  • Figure 215A-215C shows the consensus sequences of the heavy chain CDRs wherein the consensus sequences were generated for each group of antibodies that bound to the same epitope in the PSMGFR and N-terminally extended PSMGFR peptide.
  • Fig. 215A shows consensus sequences for heavy chain CDR1.
  • Fig. 215B shows consensus sequences for heavy chain CDR2.
  • Fig.215C shows consensus sequences for heavy chain CDR3.
  • Figure 216A-216C shows the consensus sequences of the light chain CDRs wherein the consensus sequences were generated for each group of antibodies that bound to the same epitope in the PSMGFR and N-terminally extended PSMGFR peptide.
  • Fig. 216A shows consensus sequences for light chain CDR1.
  • FIG. 216B shows consensus sequences for light chain CDR2.
  • Fig.216C shows consensus sequences for light chain CDR3.
  • Figure 217 shows alternative formats for bispecific antibodies and other bispecific immunotherapeutics subdivided into five major classes: BsIgG, appended IgG, BsAb fragments, bispecific fusion proteins and BsAb conjugates. Heavy chains are shown in dark blue, dark pink and dark green and corresponding light chains are in lighter shades of the same colors. Connecting peptide linkers are shown by thin black lines and engineered disulfide bonds by thin green lines. Approximate molecular weights are shown assuming ⁇ 12.5 kDa per immunoglobulin domain. BsAb formats that have advanced into clinical testing are highlighted (*).
  • Figure 218 shows graphs of tumor volume measured by an IVIS instrument wherein the tumor cells have been genetically modified to express Luciferase.
  • the substrate Luciferin was injected 10 minutes before the photo emissions were measured in the sedated animal.
  • animals were injected sub-cutaneously with 250,000 human breast tumor cells.
  • Tumors were made heterogeneous, comprised of two different tumor cell types.
  • a first tumor cell population was T47D-wt, a breast cancer cell line that expresses both full-length MUC1 and the growth factor receptor form MUC1*, which we engineered to express mCherry fluorescence.
  • the second tumor cell population was the same T47D breast cancer cells, except that they had been stably transduced to express even more MUC1* and GFP fluorescence, referred to here as T47D-MUC1*.
  • animals were implanted with T47D-wt plus T47D-MUC1*, wherein the population of T47D- MUC1* made up 30%, 15% or 7.5% of the tumor population.
  • FIG.219A shows IVIS photographs and graphs of IVIS tumor volume measurement.
  • Fig.219A shows photographs of the mice that had been implanted with tumors in which 30% of the cancer cell population was T47D-MUC1*, referred to here as high antigen expressing cells.
  • FIG. 219B shows a graph of the tumor volume by IVIS measurement by day.
  • animals injected with the huMNC2-CD28-1XX had much smaller tumors than the animals treated huMNC2-4-1BB-3z or huMNC2-CD28-3z, which is the same CAR T except without the 1XX mutations in the CD3-zeta domain.
  • Figure 220A-220T shows the IVIS graphs for 30% tumors treated at a CAR T to Tumor ratio of 10:1.
  • Figure 221A-221B shows IVIS photographs and graphs of IVIS tumor volume measurement.
  • Fig.221A shows photographs of the mice that had been implanted with tumors in which 30% of the cancer cell population was T47D-MUC1*, referred to here as high antigen expressing cells.
  • the various CAR T cells were administered at a CAR T to tumor cell ratio of 1:1 wherein 250,000 tumor cells were implanted and the animals were injected 5 days later with 250,000 CAR T cells.
  • Fig. 221B shows a graph of the tumor volume by IVIS measurement by day.
  • FIG. 222A-222T shows the IVIS graphs for 30% tumors treated at a CAR T to Tumor ratio of 1:1. Here graphs are shown for each individual animal rather than the average of the treatment group.
  • Figure 223A-223B shows IVIS photographs and graphs of IVIS tumor volume measurement.
  • Fig.223A shows photographs of the mice that had been implanted with tumors in which 7.5% of the cancer cell population was T47D-MUC1*, referred to here as high antigen expressing cells.
  • the various CAR T cells were administered at a CAR T to tumor cell ratio of 10:1 wherein 250,000 tumor cells were implanted and the animals were injected 5 days later with 2,500,000 CAR T cells.
  • Fig. 223B shows a graph of the tumor volume by IVIS measurement by day.
  • FIG. 224A-224T shows the IVIS graphs for 7.5% tumors treated at a CAR T to Tumor ratio of 10:1. Here graphs are shown for each individual animal rather than the average of the treatment group.
  • Figure 225A-225B shows IVIS photographs and graphs of IVIS tumor volume measurement.
  • Fig.225A shows photographs of the mice that had been implanted with tumors in which 7.5% of the cancer cell population was T47D-MUC1*, referred to here as high antigen expressing cells.
  • the various CAR T cells were administered at a CAR T to tumor cell ratio of 1:1 wherein 250,000 tumor cells were implanted and the animals were injected 5 days later with 250,000 CAR T cells.
  • Fig. 225B shows a graph of the tumor volume by IVIS measurement by day.
  • FIG. 226A-226T shows the IVIS graphs for 7.5% tumors treated at a CAR T to Tumor ratio of 1:1. Here graphs are shown for each individual animal rather than the average of the treatment group.
  • Figure 227 shows the tabulation of CD3 positive human T cells that were harvested from the spleens of the test animals post sacrifice.
  • cells isolated from mice implanted with tumors comprised of 30% T47D-MUC1* and treated with CAR T cells at a 10:1 ratio.
  • the huMNC2-CD28-1XX treated mice that had smaller tumors, have the greater numbers of CAR T cells and CD8 positive killer T cells.
  • TIM3, LAG3 and PD-1 are molecular markers of T cell exhaustion.
  • FIG. 1 shows that the huMNC2-CD28-1XX CAR T cells harvested from the animals express lower levels of exhaustion markers, consistent with the idea that the 1XX mutations in CD3-zeta increase CAR T cell persistence in vivo.
  • Figure 228 shows the tabulation of CD3 positive human T cells that were harvested from the spleens of the test animals post sacrifice.
  • cells isolated from mice implanted with tumors comprised of 30% T47D-MUC1* and treated with CAR T cells at a 1:1 ratio.
  • the huMNC2-CD28-1XX treated mice, that had smaller tumors have the greater numbers of CAR T cells and CD8 positive killer T cells.
  • TIM3, LAG3 and PD-1 are molecular markers of T cell exhaustion.
  • the table shows that the huMNC2-CD28- 1XX CAR T cells harvested from the animals express lower levels of exhaustion markers, consistent with the idea that the 1XX mutations in CD3-zeta increase CAR T cell persistence in vivo.
  • Figure 229 shows the tabulation of CD3 positive human T cells that were harvested from the blood of the test animals post sacrifice. In this table, cells isolated from mice implanted with tumors comprised of 30% T47D-MUC1* and treated with CAR T cells at a 1:1 ratio.
  • Figure 230 shows the tabulation of CD3 positive human T cells that were harvested from the spleens of the test animals post sacrifice.
  • cells isolated from mice implanted with tumors comprised of 7.5% T47D-MUC1* and treated with CAR T cells at a 10:1 ratio.
  • the huMNC2-CD28-1XX treated mice that had smaller tumors, have the greater numbers of CAR T cells and CD8 positive killer T cells.
  • TIM3, LAG3 and PD-1 are molecular markers of T cell exhaustion.
  • the table shows that the huMNC2-CD28-1XX CAR T cells harvested from the animals express lower levels of exhaustion markers, consistent with the idea that the 1XX mutations in CD3-zeta increase CAR T cell persistence in vivo.
  • Figure 231 shows the tabulation of CD3 positive human T cells that were harvested from the blood of the test animals post sacrifice. In this table, cells isolated from mice implanted with tumors comprised of 7.5% T47D-MUC1* and treated with CAR T cells at a 10:1 ratio.
  • TIM3, LAG3 and PD-1 are molecular markers of T cell exhaustion.
  • the table shows that the huMNC2-CD28-1XX CAR T cells harvested from the animals express lower levels of exhaustion markers, consistent with the idea that the 1XX mutations in CD3-zeta increase CAR T cell persistence in vivo.
  • Figure 232 shows the tabulation of CD3 positive human T cells that were harvested from the spleens of the test animals post sacrifice.
  • mice implanted with tumors comprised of 7.5% T47D-MUC1* and treated with CAR T cells at a 1:1 ratio.
  • the huMNC2-CD28-1XX treated mice that had smaller tumors, have the greater numbers of CAR T cells and CD8 positive killer T cells.
  • TIM3, LAG3 and PD-1 are molecular markers of T cell exhaustion.
  • the table shows that the huMNC2-CD28- 1XX CAR T cells harvested from the animals express lower levels of exhaustion markers, consistent with the idea that the 1XX mutations in CD3-zeta increase CAR T cell persistence in vivo.
  • Figure 233 shows the tabulation of CD3 positive human T cells that were harvested from the blood of the test animals post sacrifice.
  • cells isolated from mice implanted with tumors comprised of 7.5% T47D-MUC1* and treated with CAR T cells at a 1:1 ratio.
  • the huMNC2-CD28-1XX treated mice that had smaller tumors, have the greater numbers of CAR T cells and CD8 positive killer T cells.
  • TIM3, LAG3 and PD-1 are molecular markers of T cell exhaustion.
  • Figure 234A-234U shows photographs of the tumors excised from test animals and shows their weight in grams. Tumors were excised from animals implanted with tumors made up of 30% T47D-MUC1* high antigen density cells and 70% T47D-wt low antigen density cells. Animals were treated with CAR T cells at an effector to target ratio of 10:1.
  • Figure 235A-235N2 shows magnified photographs of dissociated tumors excised from animals implanted with tumors made up of 30% T47D-MUC1* high antigen density cells and 70% T47D-wt low antigen density cells. Animals were treated with CAR T cells at an effector to target ratio of 10:1. Shown are overlays of bright field images and fluorescent images, wherein the red fluorescence, mCherry, shows the low antigen density cells and the green fluorescence, GFP, shows the low antigen density cells.
  • Fig. 235A-235J show tumor cells excised from the control animals treated only with PBS. Fig.
  • 235K-235T show tumor cells excised from the animals treated with huMNC2-41BB-3z CAR T cells.
  • Fig. 235U- 235D2 show tumor cells excised from the animals treated with huMNC2-CD28-1XX CAR T cells.
  • Fig. 235E2-235N2 show tumor cells excised from the animals treated with huMNC2- CD28-3z CAR T cells.
  • Figure 236A-236U shows photographs of the tumors excised from test animals and shows their weight in grams. Tumors were excised from animals implanted with tumors made up of 30% T47D-MUC1* high antigen density cells and 70% T47D-wt low antigen density cells.
  • Fig. 236A-236E show tumors excised from animals mock treated with PBS.
  • Fig. 236F-236J show tumors excised from animals treated with huMNC2-41BB-3z.
  • Fig. 236K-236O show tumors excised from animals treated with huMNC2-CD28-1XX.
  • Fig. 236P-236T show tumors excised from animals treated with huMNC2-CD28-3z.
  • Fig. 236U shows a bar graph of the weights of tumors excised from the test animals.
  • FIG. 237A-237D2 shows magnified photographs of dissociated tumors excised from animals implanted with tumors made up of 30% T47D-MUC1* high antigen density cells and 70% T47D-wt low antigen density cells. Animals were treated with CAR T cells at an effector to target ratio of 1:1. Shown are overlays of bright field images and fluorescent images, wherein the red fluorescence, mCherry, shows the low antigen density cells and the green fluorescence, GFP, shows the low antigen density cells.
  • Fig. 237A-237J show tumor cells excised from the control animals treated only with PBS.
  • Fig. 237K-237T show tumor cells excised from the animals treated with huMNC2-41BB-3z CAR T cells.
  • FIG. 237U- 237D2 show tumor cells excised from the animals treated with huMNC2-CD28-1XX CAR T cells.
  • Fig. 237E2-237N2 show tumor cells excised from the animals treated with huMNC2- CD28-3z CAR T cells.
  • Figure 238A-238T shows photographs of the tumors excised from test animals and shows their weight in grams. Tumors were excised from animals implanted with tumors made up of 7.5% T47D-MUC1* high antigen density cells and 92.5% T47D-wt low antigen density cells. Animals were treated with CAR T cells at an effector to target ratio of 10:1.
  • Figure 239A-239M2 shows magnified photographs of dissociated tumors excised from animals implanted with tumors made up of 7.5% T47D-MUC1* high antigen density cells and 92.5% T47D-wt low antigen density cells. Animals were treated with CAR T cells at an effector to target ratio of 10:1. Shown are overlays of bright field images and fluorescent images, wherein the red fluorescence, mCherry, shows the low antigen density cells and the green fluorescence, GFP, shows the low antigen density cells.
  • Fig. 239A-239J show tumor cells excised from animals mock treated with PBS. Fig.
  • FIG. 239K-239T show tumor cells excised from the animals treated with huMNC2-41BB-3z CAR T cells.
  • Fig. 239U- 239C2 show tumor cells excised from the animals treated with huMNC2-CD28-1XX CAR T cells.
  • Fig. 239D2-239M2 show tumor cells excised from the animals treated with huMNC2- CD28-3z CAR T cells.
  • Figure 240A-240O shows photographs of the tumors excised from test animals and shows their weight in grams. Tumors were excised from animals implanted with tumors made up of 7.5% T47D-MUC1* high antigen density cells and 92.5% T47D-wt low antigen density cells.
  • FIG. 241A-241D2 shows magnified photographs of dissociated tumors excised from animals implanted with tumors made up of 7.5% T47D-MUC1* high antigen density cells and 92.5% T47D-wt low antigen density cells. Animals were treated with CAR T cells at an effector to target ratio of 1:1. Shown are overlays of bright field images and fluorescent images, wherein the red fluorescence, mCherry, shows the low antigen density cells and the green fluorescence, GFP, shows the low antigen density cells.
  • Fig. 241A-241J show tumor cells excised from control animals treated only with PBS. Fig.
  • FIG. 241K-241T show tumor cells excised from the animals treated with huMNC2-41BB-3z CAR T cells.
  • Fig. 241U-241D2 show tumor cells excised from the animals treated with huMNC2-CD28-1XX CAR T cells.
  • Fig. 241E2-241N2 show tumor cells excised from the animals treated with huMNC2-CD28- 3z CAR T cells.
  • Figure 242A-242R shows photographs of live animals, where IVIS measures tumor volume, mCherry detects the low antigen cells within the tumor and GFP detects the high antigen cells within the tumor. Post sacrifice photographs are shown of the excised tumors and a graph of tumor weights.
  • FIG. 243A-243F shows photographs taken at two different timepoints.
  • IVIS photographs measure tumor volume
  • mCherry fluorescent photographs measure low antigen cells
  • GFP fluorescent photographs measure high antigen cells.
  • the animals were implanted with tumors made up of 30% high antigen density cells (GFP+) and 70% low antigen density cells (mCherry+).
  • FIG. 244 shows graphs of IVIS tumor volume measurements over time. Arrows indicate timepoints when fluorescent photographs, mCherry and GFP, of live animals were taken. In this case, the animals were implanted with tumors made up of 30% high antigen density cells (GFP+) and 70% low antigen density cells (mCherry+). Animals had been given a single dose of CAR T cells at a 10:1 or a 1:1 CAR T to tumor cell ratio.
  • GFP+ high antigen density cells
  • mCherry+ 70% low antigen density cells
  • Figure 245 shows graphs of IVIS measurements of tumor volume, mCherry measurements of the growth rate of low antigen cells and GFP measurements of the growth rate of high antigen cells, between two timepoints.
  • GFP high antigen density cells
  • FIG.246A shows photographs of the mice that had been implanted with tumors in which 15% of the cancer cell population was T47D-MUC1*, referred to here as high antigen expressing cells.
  • the various CAR T cells were administered at a CAR T to tumor cell ratio of 10:1 wherein 250,000 tumor cells were implanted and the animals were injected 5 days later with 2,500,000 CAR T cells.
  • Fig. 246B shows a graph of the tumor volume by IVIS measurement by day.
  • animals outlined in red were implanted with 250,000 more 100% high antigen density tumor cells.
  • the animals outlined in green received an additional dose of 2,500,000 CAR T cells.
  • Figure 247A-247T shows graphs of the IVIS measured growth of the tumors in each individual animal.
  • the red arrows indicate injection of more tumor cells and the green arrows indicate injection of 2,500,000 additional CAR T cells.
  • the injection of additional tumor cells does not increase the tumor growth in animals treated with huMNC2-CD28-1XX CAR T cells.
  • FIG. 248A-247D shows a cartoon of the experimental strategy wherein animals were implanted with heterologous tumors comprised of two cell types that carry two different florescent labels.
  • Fig. 248A shows cartoon of animals implanted with tumors in which 30% of the tumors express high levels of MUC1* and those tumor cells fluoresce green.
  • Fig. 248B shows cartoon of animals implanted with tumors in which 15% of the tumors express high levels of MUC1* and those tumor cells fluoresce green.
  • Fig. 248C shows cartoon of animals implanted with tumors in which 7.5% of the tumors express high levels of MUC1* and those tumor cells fluoresce green.
  • FIG.248D lists the variables used in these experiments.
  • Figure 249A-247F shows cartoons of the experimental strategy and data.
  • Fig. 249A shows cartoons of MUC1 full-length as it appears on normal epithelial cells.
  • Fig.249B shows four tissue specimens stained with huMNC2-scFv-Fc.
  • Fig. 249C shows cartoons depicting heterogeneous tumors expressing either high (30%-left) or low (7.5%-right) percentages of high MUC1* expressing tumor cells.
  • Fig. 249D shows flow cytometry verifying the percentages of the heterogeneous tumors before their implantation.
  • FIG. 249E shows bar graphs of bioluminescence measured on an IVIS instrument for animals implanted with 30% high MUC1* cells and treated with the various CAR T cells at an effector to target ratio of 10:1 (top) or 1:1 (bottom).
  • Fig. 249F shows bar graphs of bioluminescence measured on an IVIS instrument for animals implanted with 7.5% high MUC1* cells and treated with the various CAR T cells at an effector to target ratio of 10:1 (top) or 1:1 (bottom).
  • Figure 250A-250F shows bar graphs of bioluminescence of the tumors measured on an IVIS instrument for animals implanted with 30% high MUC1* cells or 7.5% high MUC1* tumors and treated with the various CAR T cells at various effector to target ratios.
  • Fig. 250A shows IVIS graph of animals implanted with tumors in which 30% expressed high levels of MUC1* and where animals were treated with CAR T cells at an effector to target ratio of 10:1.
  • Fig. 250B shows IVIS graph where effector to target ratio was 5:1.
  • Fig. 250C shows IVIS graph where effector to target ratio was 1:1.
  • FIG. 250D shows IVIS graph of animals implanted with tumors in which 7.5% expressed high levels of MUC1* and where animals were treated with CAR T cells at an effector to target ratio of 10:1.
  • Fig. 250E shows IVIS graph where effector to target ratio was 5:1.
  • Fig.250F shows IVIS graph where effector to target ratio was 1:1.
  • Figure 251A-251D shows photographs of bioluminescence of the tumors measured on an IVIS instrument for animals implanted with 30% high MUC1* cells or 7.5% high MUC1* tumors and treated with the various CAR T cells at effector to target ratios of 10:1 or 1:1.
  • 251A shows IVIS photographs for animals implanted with tumors in which 30% expressed high levels of MUC1* and where animals were treated with of CAR T cells at an effector to target ratio of 10:1.
  • Fig.250B shows IVIS photographs where effector to target ratio was 1:1.
  • Fig.251C shows IVIS photographs for animals implanted with tumors in which 7.5% expressed high levels of MUC1* and where animals were treated with of CAR T cells at an effector to target ratio of 10:1.
  • Fig. 250D shows IVIS photographs where effector to target ratio was 1:1.
  • Figure 252A-252D shows magnified fluorescent photographs of dissociated tumors excised from animals implanted with tumors made up of either 30% or 7.5% T47D- MUC1* high antigen density cells and the remainder are low antigen density cells. Animals were treated with various CAR T cells at effector to target ratios of either 10:1 or 1:1. Shown are overlays of bright field images and fluorescent images, wherein the red fluorescence, mCherry, shows the low antigen density cells and the green fluorescence, GFP, shows the low antigen density cells.
  • Fig. 252A shows tumor cells excised from animals implanted with 30% high antigen density tumors and treated with various CAR T cells at effector to target ratio of 10:1.
  • FIG. 252B shows tumor cells excised from animals implanted with 30% high antigen density tumors and treated with various CAR T cells at effector to target ratio of 1:1.
  • Fig. 252C shows tumor cells excised from animals implanted with 7.5% high antigen density tumors and treated with various CAR T cells at effector to target ratio of 10:1.
  • Fig. 252D shows tumor cells excised from animals implanted with 7.5% high antigen density tumors and treated with various CAR T cells at effector to target ratio of 1:1.
  • Figure 253A-253H shows cartoons of the experimental strategy and data.
  • Fig. 253A shows cartoons of MUC1 full-length as it appears on normal epithelial cells.
  • Fig.253B shows four tissue specimens stained with huMNC2-scFv-Fc.
  • Fig. 253C shows cartoons depicting heterogeneous tumors expressing either high or low percentages of high MUC1* expressing tumor cells.
  • Fig. 253D shows flow cytometry verifying 15% percent of the tumor cells expressed high levels of MUC1* before their implantation.
  • Fig. 253E shows bar graphs of bioluminescence measured on an IVIS instrument for animals implanted with 15% high MUC1* cells and treated with the various CAR T cells at an effector to target ratio of 10:1.
  • 253F shows immunofluorescent photographs of the excised tumors for animals implanted with 15% high antigen density tumors and treated with the various CAR Ts at an effector to target ratio of 10:1.
  • Fig. 253G shows bar graphs of bioluminescence measured on an IVIS instrument for animals implanted with 15% high MUC1* cells and treated with the various CAR T cells at an effector to target ratio of 1:1.
  • Fig. 253H shows immunofluorescent photographs of the excised tumors for animals implanted with 15% high antigen density tumors and treated with the various CAR Ts at an effector to target ratio of 1:1.
  • Figure 254A-254B shows bar graphs of bioluminescence measured on an IVIS instrument for animals implanted with 15% high MUC1* cells and treated with the various CAR T cells at an effector to target ratio of 10:1.
  • Fig. 254A shows the graph of animals treated at an effector to target ratio of 10:1.
  • Fig. 254B shows the graph of animals treated at an effector to target ratio of 1:1.
  • Figure 255A-255B shows photographs of bioluminescence of tumors measured on an IVIS instrument for animals implanted with 15% high MUC1* cells and treated with the various CAR T cells at an effector to target ratio of 10:1.
  • Fig. 255A shows the photographs of animals treated at an effector to target ratio of 10:1.
  • Figure 255B shows the photographs of animals treated at an effector to target ratio of 1:1.
  • Figure 256A-256B shows fluorescent photographs of the excised tumors showing the mCherry positive, low antigen density cells in red and the GFP positive, high antigen density cells in green. Animals were all implanted with a mixture of tumor cells that before implantation were 15% high MUC1* expressing cells.
  • Fig. 256A shows the photographs of animals treated at an effector to target ratio of 10:1.
  • Fig. 256B shows the photographs of animals treated at an effector to target ratio of 1:1.
  • Figure 257 shows a table of results of flow cytometry in which cells of the excised tumors were assayed for the presence of human T cells and CAR T cells, which were then enumerated and analyzed for the presence of markers of T cell exhaustion. Shown here is the analysis of tumors excised from animals that had been implanted with tumors that were 30% high antigen expressing cells, wherein animals were treated with various CAR T cells and an effector to target ratio of 10:1. When the number of CAR T cells detected was less than 25, that number is shown in red and the further analysis of those few cells is called into question.
  • Figure 258 shows a table of results of flow cytometry in which cells of the excised tumors were assayed for the presence of human T cells and CAR T cells, which were then enumerated and analyzed for the presence of markers of T cell exhaustion. Shown here is the analysis of tumors excised from animals that had been implanted with tumors that were 15% high antigen expressing cells, wherein animals were treated with various CAR T cells and an effector to target ratio of 10:1. When the number of CAR T cells detected was less than 25, that number is shown in red and the further analysis of those few cells is called into question.
  • Figure 259 shows a table of results of flow cytometry in which cells of the excised tumors were assayed for the presence of human T cells and CAR T cells, which were then enumerated and analyzed for the presence of markers of T cell exhaustion. Shown here is the analysis of tumors excised from animals that had been implanted with tumors that were 7.5% high antigen expressing cells, wherein animals were treated with various CAR T cells and an effector to target ratio of 10:1. When the number of CAR T cells detected was less than 25, that number is shown in red and the further analysis of those few cells is called into question.
  • Figure 260 shows a table of results of flow cytometry in which cells of the excised tumors were assayed for the presence of human T cells and CAR T cells, which were then enumerated and analyzed for the presence of markers of T cell exhaustion. Shown here is the analysis of tumors excised from animals that had been implanted with tumors that were 30% high antigen expressing cells, wherein animals were treated with various CAR T cells and an effector to target ratio of 5:1. When the number of CAR T cells detected was less than 25, that number is shown in red and the further analysis of those few cells is called into question.
  • Figure 261 shows a table of results of flow cytometry in which cells of the excised tumors were assayed for the presence of human T cells and CAR T cells, which were then enumerated and analyzed for the presence of markers of T cell exhaustion. Shown here is the analysis of tumors excised from animals that had been implanted with tumors that were 7.5% high antigen expressing cells, wherein animals were treated with various CAR T cells and an effector to target ratio of 5:1. When the number of CAR T cells detected was less than 25, that number is shown in red and the further analysis of those few cells is called into question.
  • Figure 262 shows a table of results of flow cytometry in which cells of the excised tumors were assayed for the presence of human T cells and CAR T cells, which were then enumerated and analyzed for the presence of markers of T cell exhaustion. Shown here is the analysis of tumors excised from animals that had been implanted with tumors that were 30% high antigen expressing cells, wherein animals were treated with various CAR T cells and an effector to target ratio of 1:1. When the number of CAR T cells detected was less than 25, that number is shown in red and the further analysis of those few cells is called into question.
  • Figure 263 shows a table of results of flow cytometry in which cells of the excised tumors were assayed for the presence of human T cells and CAR T cells, which were then enumerated and analyzed for the presence of markers of T cell exhaustion. Shown here is the analysis of tumors excised from animals that had been implanted with tumors that were 15% high antigen expressing cells, wherein animals were treated with various CAR T cells and an effector to target ratio of 1:1. When the number of CAR T cells detected was less than 25, that number is shown in red and the further analysis of those few cells is called into question.
  • Figure 264 shows a table of results of flow cytometry in which cells of the excised tumors were assayed for the presence of human T cells and CAR T cells, which were then enumerated and analyzed for the presence of markers of T cell exhaustion. Shown here is the analysis of tumors excised from animals that had been implanted with tumors that were 7.5% high antigen expressing cells, wherein animals were treated with various CAR T cells and an effector to target ratio of 1:1. When the number of CAR T cells detected was less than 25, that number is shown in red and the further analysis of those few cells is called into question.
  • Figure 265 shows a table of results of flow cytometry in which cells of the excised spleens of the treated animals were assayed for the presence of human T cells and CAR T cells, which were then enumerated and analyzed for the presence of markers of T cell exhaustion. Shown here is the analysis of tumors excised from animals that had been implanted with tumors that were 30% high antigen expressing cells, wherein animals were treated with various CAR T cells and an effector to target ratio of 10:1. When the number of CAR T cells detected was less than 25, that number is shown in red and the further analysis of those few cells is called into question.
  • Figure 266 shows a table of results of flow cytometry in which cells of the excised spleens of the treated animals were assayed for the presence of human T cells and CAR T cells, which were then enumerated and analyzed for the presence of markers of T cell exhaustion. Shown here is the analysis of tumors excised from animals that had been implanted with tumors that were 15% high antigen expressing cells, wherein animals were treated with various CAR T cells and an effector to target ratio of 10:1. When the number of CAR T cells detected was less than 25, that number is shown in red and the further analysis of those few cells is called into question.
  • Figure 267 shows a table of results of flow cytometry in which cells of the excised spleens of the treated animals were assayed for the presence of human T cells and CAR T cells, which were then enumerated and analyzed for the presence of markers of T cell exhaustion. Shown here is the analysis of tumors excised from animals that had been implanted with tumors that were 7.5% high antigen expressing cells, wherein animals were treated with various CAR T cells and an effector to target ratio of 10:1. When the number of CAR T cells detected was less than 25, that number is shown in red and the further analysis of those few cells is called into question.
  • Figure 268 shows a table of results of flow cytometry in which cells of the excised spleens of the treated animals were assayed for the presence of human T cells and CAR T cells, which were then enumerated and analyzed for the presence of markers of T cell exhaustion. Shown here is the analysis of tumors excised from animals that had been implanted with tumors that were 30% high antigen expressing cells, wherein animals were treated with various CAR T cells and an effector to target ratio of 5:1. When the number of CAR T cells detected was less than 25, that number is shown in red and the further analysis of those few cells is called into question.
  • Figure 269 shows a table of results of flow cytometry in which cells of the excised spleens of the treated animals were assayed for the presence of human T cells and CAR T cells, which were then enumerated and analyzed for the presence of markers of T cell exhaustion. Shown here is the analysis of tumors excised from animals that had been implanted with tumors that were 15% high antigen expressing cells, wherein animals were treated with various CAR T cells and an effector to target ratio of 5:1. When the number of CAR T cells detected was less than 25, that number is shown in red and the further analysis of those few cells is called into question.
  • Figure 270 shows a table of results of flow cytometry in which cells of the excised spleens of the treated animals were assayed for the presence of human T cells and CAR T cells, which were then enumerated and analyzed for the presence of markers of T cell exhaustion. Shown here is the analysis of tumors excised from animals that had been implanted with tumors that were 7.5% high antigen expressing cells, wherein animals were treated with various CAR T cells and an effector to target ratio of 5:1. When the number of CAR T cells detected was less than 25, that number is shown in red and the further analysis of those few cells is called into question.
  • Figure 271 shows a table of results of flow cytometry in which cells of the excised spleens of the treated animals were assayed for the presence of human T cells and CAR T cells, which were then enumerated and analyzed for the presence of markers of T cell exhaustion. Shown here is the analysis of tumors excised from animals that had been implanted with tumors that were 30% high antigen expressing cells, wherein animals were treated with various CAR T cells and an effector to target ratio of 1:1. When the number of CAR T cells detected was less than 25, that number is shown in red and the further analysis of those few cells is called into question.
  • Figure 272 shows a table of results of flow cytometry in which cells of the excised spleens of the treated animals were assayed for the presence of human T cells and CAR T cells, which were then enumerated and analyzed for the presence of markers of T cell exhaustion. Shown here is the analysis of tumors excised from animals that had been implanted with tumors that were 15% high antigen expressing cells, wherein animals were treated with various CAR T cells and an effector to target ratio of 1:1. When the number of CAR T cells detected was less than 25, that number is shown in red and the further analysis of those few cells is called into question.
  • Figure 273 shows a table of results of flow cytometry in which cells of the excised spleens of the treated animals were assayed for the presence of human T cells and CAR T cells, which were then enumerated and analyzed for the presence of markers of T cell exhaustion. Shown here is the analysis of tumors excised from animals that had been implanted with tumors that were 7.5% high antigen expressing cells, wherein animals were treated with various CAR T cells and an effector to target ratio of 1:1. When the number of CAR T cells detected was less than 25, that number is shown in red and the further analysis of those few cells is called into question.
  • Figure 274 shows a table of results of flow cytometry in which blood from the treated animals were assayed for the presence of human T cells and CAR T cells, which were then enumerated and analyzed for the presence of markers of T cell exhaustion. Shown here is the analysis of tumors excised from animals that had been implanted with tumors that were 30% high antigen expressing cells, wherein animals were treated with various CAR T cells and an effector to target ratio of 10:1. When the number of CAR T cells detected was less than 25, that number is shown in red and the further analysis of those few cells is called into question.
  • Figure 275 shows a table of results of flow cytometry in which blood from the treated animals were assayed for the presence of human T cells and CAR T cells, which were then enumerated and analyzed for the presence of markers of T cell exhaustion. Shown here is the analysis of tumors excised from animals that had been implanted with tumors that were 15% high antigen expressing cells, wherein animals were treated with various CAR T cells and an effector to target ratio of 10:1. When the number of CAR T cells detected was less than 25, that number is shown in red and the further analysis of those few cells is called into question.
  • Figure 276 shows a table of results of flow cytometry in which blood from the treated animals were assayed for the presence of human T cells and CAR T cells, which were then enumerated and analyzed for the presence of markers of T cell exhaustion. Shown here is the analysis of tumors excised from animals that had been implanted with tumors that were 7.5% high antigen expressing cells, wherein animals were treated with various CAR T cells and an effector to target ratio of 10:1. When the number of CAR T cells detected was less than 25, that number is shown in red and the further analysis of those few cells is called into question.
  • Figure 277 shows a table of results of flow cytometry in which blood from the treated animals were assayed for the presence of human T cells and CAR T cells, which were then enumerated and analyzed for the presence of markers of T cell exhaustion. Shown here is the analysis of tumors excised from animals that had been implanted with tumors that were 30% high antigen expressing cells, wherein animals were treated with various CAR T cells and an effector to target ratio of 5:1. When the number of CAR T cells detected was less than 25, that number is shown in red and the further analysis of those few cells is called into question.
  • Figure 278 shows a table of results of flow cytometry in which blood from the treated animals were assayed for the presence of human T cells and CAR T cells, which were then enumerated and analyzed for the presence of markers of T cell exhaustion. Shown here is the analysis of tumors excised from animals that had been implanted with tumors that were 15% high antigen expressing cells, wherein animals were treated with various CAR T cells and an effector to target ratio of 5:1. When the number of CAR T cells detected was less than 25, that number is shown in red and the further analysis of those few cells is called into question.
  • Figure 279 shows a table of results of flow cytometry in which blood from the treated animals were assayed for the presence of human T cells and CAR T cells, which were then enumerated and analyzed for the presence of markers of T cell exhaustion. Shown here is the analysis of tumors excised from animals that had been implanted with tumors that were 7.5% high antigen expressing cells, wherein animals were treated with various CAR T cells and an effector to target ratio of 5:1. When the number of CAR T cells detected was less than 25, that number is shown in red and the further analysis of those few cells is called into question.
  • Figure 280 shows a table of results of flow cytometry in which blood from the treated animals were assayed for the presence of human T cells and CAR T cells, which were then enumerated and analyzed for the presence of markers of T cell exhaustion. Shown here is the analysis of tumors excised from animals that had been implanted with tumors that were 30% high antigen expressing cells, wherein animals were treated with various CAR T cells and an effector to target ratio of 1:1. When the number of CAR T cells detected was less than 25, that number is shown in red and the further analysis of those few cells is called into question.
  • Figure 281 shows a table of results of flow cytometry in which blood from the treated animals were assayed for the presence of human T cells and CAR T cells, which were then enumerated and analyzed for the presence of markers of T cell exhaustion. Shown here is the analysis of tumors excised from animals that had been implanted with tumors that were 15% high antigen expressing cells, wherein animals were treated with various CAR T cells and an effector to target ratio of 1:1. When the number of CAR T cells detected was less than 25, that number is shown in red and the further analysis of those few cells is called into question.
  • Figure 282 shows a table of results of flow cytometry in which blood from the treated animals were assayed for the presence of human T cells and CAR T cells, which were then enumerated and analyzed for the presence of markers of T cell exhaustion. Shown here is the analysis of tumors excised from animals that had been implanted with tumors that were 7.5% high antigen expressing cells, wherein animals were treated with various CAR T cells and an effector to target ratio of 1:1. When the number of CAR T cells detected was less than 25, that number is shown in red and the further analysis of those few cells is called into question.
  • FIG. 283A-283L shows photographs of MUC1* positive breast cancer cells, T47D, in culture with human T cells to which have been added various concentrations of bispecific antibody 20A10-OKT3-BiTE.
  • 20A10 is a humanized anti-MUC1* antibody
  • OKT3 is an antibody that binds to CD3 that is present on human T cells.
  • the addition of the bispecific antibody mediates the joining together of T cells and cancer cells, seen here as cell clustering.
  • the concentration of the bispecific antibody is 1,000 ng/mL.
  • Fig. 283B concentration concentration is 333 ng/mL.
  • Fig. 283C concentration is 111 ng/mL.
  • Fig. 283D concentration is 37 ng/mL.
  • Fig. 283E concentration is 12.3 ng/mL.
  • Fig. 283F concentration is 4.1 ng/mL.
  • Fig. 283G concentration is 1.3 ng/mL.
  • Fig. 283H concentration is 0.4 ng/mL.
  • Fig. 283I concentration is 0.15 ng/mL.
  • Fig.283J concentration is 0.05 ng/mL.
  • Fig. 283K is a control well in which both T cells and cancer cells are present, but no bispecific antibody has been added.
  • Fig. 283L is a control well in which bispecific antibody has been added to cancer cells, but no T cells are present.
  • Figure 284A-284L shows photographs of MUC1* positive breast cancer cells, T47D, in culture with human T cells to which have been added various concentrations of bispecific antibody 20A10-12F6-BiTE.
  • 20A10 is a humanized anti-MUC1* antibody
  • 12F6 is an antibody that binds to CD3 that is present on human T cells.
  • the addition of the bispecific antibody mediates the joining together of T cells and cancer cells, seen here as cell clustering.
  • the concentration of the bispecific antibody is 1,000 ng/mL.
  • Fig. 284B concentration concentration is 333 ng/mL.
  • Fig. 284C concentration is 111 ng/mL.
  • Fig. 284D concentration is 37 ng/mL.
  • Fig. 284E concentration is 12.3 ng/mL.
  • Fig. 284F concentration is 4.1 ng/mL.
  • Fig. 284G concentration is 1.3 ng/mL.
  • Fig. 284H concentration is 0.4 ng/mL.
  • Fig. 284I concentration is 0.15 ng/mL.
  • Fig. 284J concentration concentration is 0.05 ng/mL.
  • Fig.284K is a control well in which both T cells and cancer cells are present, but no bispecific antibody has been added.
  • Fig. 284L is a control well in which bispecific antibody has been added to cancer cells, but no T cells are present.
  • Figure 285A-285L shows photographs of HCT-MUC1*-transduced cancer cells in culture with human T cells to which have been added various concentrations of bispecific antibody 20A10-OKT3-BiTE.
  • 20A10 is a humanized anti-MUC1* antibody
  • OKT3 is an antibody that binds to CD3 that is present on human T cells.
  • the addition of the bispecific antibody mediates the joining together of T cells and cancer cells, seen here as cell clustering.
  • the concentration of the bispecific antibody is 1,000 ng/mL.
  • Fig. 285B concentration concentration is 333 ng/mL.
  • Fig. 285C concentration is 111 ng/mL.
  • Fig. 285D concentration is 37 ng/mL.
  • Fig. 285E concentration is 12.3 ng/mL.
  • Fig. 285F concentration is 4.1 ng/mL.
  • Fig. 285G concentration is 1.3 ng/mL.
  • Fig. 285H concentration is 0.4 ng/mL.
  • Fig. 285I concentration is 0.15 ng/mL.
  • Fig. 285J concentration concentration is 0.05 ng/mL.
  • Fig. 285K is a control well in which both T cells and cancer cells are present, but no bispecific antibody has been added.
  • Fig. 285L is a control well in which bispecific antibody has been added to cancer cells, but no T cells are present.
  • Figure 286A-286L shows photographs of HCT-MUC1*-transduced cancer cells in culture with human T cells to which have been added various concentrations of bispecific antibody 20A10-12F6-BiTE.
  • 20A10 is a humanized anti-MUC1* antibody
  • 12F6 is an antibody that binds to CD3 that is present on human T cells.
  • the addition of the bispecific antibody mediates the joining together of T cells and cancer cells, seen here as cell clustering.
  • the concentration of the bispecific antibody is 1,000 ng/mL.
  • Fig. 286B concentration concentration is 333 ng/mL.
  • Fig. 286C concentration is 111 ng/mL.
  • Fig. 286D concentration is 37 ng/mL.
  • Fig. 286E concentration is 12.3 ng/mL.
  • Fig. 286F concentration is 4.1 ng/mL.
  • Fig. 286G concentration is 1.3 ng/mL.
  • Fig. 286H concentration is 0.4 ng/mL.
  • Fig. 286I concentration is 0.15 ng/mL.
  • Fig. 286J concentration concentration is 0.05 ng/mL.
  • Fig. 286K is a control well in which both T cells and cancer cells are present, but no bispecific antibody has been added.
  • Fig. 286L is a control well in which bispecific antibody has been added to cancer cells, but no T cells are present.
  • a polypeptide is indicated as being “transduced or transfected” into a cell. In these occurrences, it is understood that the nucleic acid encoding the polypeptide sequence is transduced or transfected into the cell, as it is an impossibility that a polypeptide could be transduced or transfected into a cell.
  • M refers to millions
  • K refers to thousands.
  • MNC2 which is interchangeable with “C2”, “Min-C2” and “MNC2”
  • MNE6 which is interchangeable with “E6”, “Min-E6” and “MNE6”
  • MNC3 which is interchangeable with “C3”, “Min-C3” and “MNC3”
  • MNC8 which is interchangeable with “C8”, “Min-C8” and “MNC8”.
  • antibody-like means a molecule that may be engineered such that it contains portions of antibodies but is not an antibody that would naturally occur in nature. Examples include but are not limited to CAR (chimeric antigen receptor) T cell technology and the Ylanthia ® technology.
  • CAR chimeric antigen receptor
  • Ylanthia ® Ylanthia
  • the Ylanthia ® technology consists of an “antibody- like” library that is a collection of synthetic human Fabs that are then screened for binding to peptide epitopes from target proteins. The selected Fab regions can then be engineered into a scaffold or framework so that they resemble antibodies.
  • PSMGFR is abbreviation for Primary Sequence of the MUC1 Growth Factor Receptor which is identified by SEQ ID NO:2, and thus is not to be confused with a six amino acid sequence.
  • PSMGFR peptide” or “PSMGFR region” refers to a peptide or region that incorporates the Primary Sequence of the MUC1 Growth Factor Receptor (SEQ ID NO:2).
  • the “MUC1*” extra cellular domain is defined primarily by the PSMGFR sequence (GTINVHDVETQFNQYKTEAASRYNLTISDVSVSDVPFPFSAQSGA (SEQ ID NO:2)). Because the exact site of MUC1 cleavage depends on the enzyme that clips it, and that the cleavage enzyme varies depending on cell type, tissue type or the time in the evolution of the cell, the exact sequence of the MUC1* extra cellular domain may vary at the N-terminus.
  • PSMGFR is an acronym for Primary Sequence of MUC1 Growth Factor Receptor as set forth as GTINVHDVETQFNQYKTEAASRYNLTISDVSVSDVPFPFSAQSGA (SEQ ID NO:2).
  • N-10 PSMGFR or simply “N-10”, “N-15 PSMGFR” or simply “N-15”, or “N-20 PSMGFR” or simply “N-20” refers to the number of amino acid residues that have been deleted at the N-terminal end of PSMGFR.
  • C-number as in “C-10 PSMGFR” or simply “C-10”, “C-15 PSMGFR” or simply “C-15”, or “C-20 PSMGFR” or simply “C-20” refers to the number of amino acid residues that have been deleted at the C-terminal end of PSMGFR. A mixture of deletions and additions is also possible.
  • N+20/C-27 refers to a peptide fragment of wild-type MUC1 in which 20 amino acids are added to the PSMGFR at the N-terminus and 27 amino acids are deleted from the C-terminus.
  • the “extracellular domain of MUC1*” refers to the extracellular portion of a MUC1 protein that is devoid of the tandem repeat domain. In most cases, MUC1* is a cleavage product wherein the MUC1* portion consists of a short extracellular domain devoid of tandem repeats, a transmembrane domain and a cytoplasmic tail.
  • sequence identity means homology in sequence of a particular polypeptide or nucleic acid to a reference sequence of nucleic acid or amino acid such that the function of the homologous peptide is the same as the reference peptide or nucleic acid. Such homology can be so close with the reference peptide such that at times the two sequences may be 90%, 95% or 98% identical yet possess the same function in binding or other biological activities.
  • MUC1 positive cell refers to a cell that expresses a gene for MUC1, MUC1-Y or MUC1-Z or other MUC1 variant.
  • MUC1 negative cell refers to a cell that does not express a gene for MUC1.
  • MUC1* positive cell refers to a cell that expresses a gene for MUC1, wherein that gene’s expressed protein is a transmembrane protein that is devoid of tandem repeats, which may be a consequence of post-translational modification, cleavage, alternative splicing, or transfecting or transducing a cell with a MUC1 protein that is devoid of tandem repeats.
  • MUC1* negative cell refers to a cell that may or may not express a gene for MUC1 but does not express a MUC1 transmembrane protein that is devoid of tandem repeats.
  • MUC1 positive cancer cell refers to a cancer cell that overexpresses the gene for MUC1, expresses MUC1 in an aberrant pattern, wherein its expression is not restricted to the apical border and/or expresses a MUC1 that is devoid of tandem repeats.
  • MUC1 negative cancer cell refers to a cancer cell that may or may not express a gene for MUC1 but does not overexpress MUC1 or does not overexpress a MUC1 transmembrane protein that is devoid of tandem repeats.
  • MUC1* positive cancer cell refers to a cancer cell that overexpresses a MUC1 transmembrane protein that is devoid of tandem repeats.
  • MUC1* negative cancer cell refers to a cancer cell that may or may not express a gene for MUC1 but does not overexpress a MUC1 transmembrane protein that is devoid of tandem repeats.
  • formational epitope refers to a peptide sequence that is required to be present in a specific three-dimensional structure or conformation for an antibody to bind.
  • the antibody binds when the peptide sequence is in the three- dimensional structure or conformation and is not bound when linear.
  • a common technique for determining whether an antibody binds to a linear stretch or a conformational epitope is to use the antibody to probe a denaturing Western blot. Traveling through a denaturing gel linearizes proteins and peptides.
  • Antibodies that do not work in a denaturing Western but do recognize the native target, for example expressed on an intact cell, are determined to recognize a conformational epitope.
  • the antibody may or may not actually bind to the “conformational epitope”, however the presence of the “conformational epitope” sequence is required to render a three dimensional structure so that the MUC1* region on cancer cells is able to be bound by the antibody that is specific for cancer treatment.
  • the conformational epitope is an amino acid sequence that induces the binding of the antibody to the MUC1* region on cancer cells.
  • a term “conformational inducing peptide sequence” may be used, which indicates that a peptide sequence is present within a larger peptide not as a binding site but that induces binding of an antibody to the larger peptide by causing a three- dimensional structure to form that facilitates the binding of the antibody to the larger peptide.
  • MUC1* antibodies anti-PSMGFR
  • a cleaved form of the MUC1 (SEQ ID NO:1) transmembrane protein is a growth factor receptor that drives the growth of over 75% of all human solid tumor cancers.
  • MUC1* The cleaved form of MUC1, which we called MUC1* (pronounced muk 1 star), is a powerful growth factor receptor. Enzymatic cleavage releases the bulk of the MUC1 extracellular domain. It is the remaining portion comprising a truncated extracellular domain, transmembrane domain and cytoplasmic tail that is called MUC1*. Cleavage and release of the bulk of the extracellular domain of MUC1 unmasks a binding site for activating ligands dimeric NME1, NME6, NME8, NME7 AB , NME7-X1 or NME7. Cell growth assays show that it is ligand-induced dimerization of the MUC1* extracellular domain that promotes growth (Fig. 1A-1D).
  • Bivalent anti-MUC1* antibodies stimulate growth of cancer cells whereas the monovalent Fab inhibits growth.
  • Classic bell-shaped curve indicates ligand induced dimerization stimulates growth.
  • Dimeric NM23-H1, aka NME1 stimulates growth of MUC1* positive cancer cells but siRNA to suppress MUC1 expression eliminate its effect (Fig. 1C).
  • NME7-AB also stimulates the growth of MUC1* positive cells (Fig.1D).
  • MUC1* is an excellent target for cancer drugs as it is aberrantly expressed on over 75% of all cancers and is likely overexpressed on an even higher percentage of metastatic cancers. After MUC1 cleavage, most of its extracellular domain is shed from the cell surface. The remaining portion has a truncated extracellular domain that at least comprises the primary growth factor receptor sequence, PSMGFR (SEQ ID NO:2).
  • Antibodies that bind to the PSMGFR sequence and especially those that competitively inhibit the binding of activating ligands such as NME proteins, including NME1, NME6, NME8, NME7AB, NME7- X1 and NME7, are ideal therapeutics and can be used to treat or prevent MUC1 positive or MUC1* positive cancers, as stand-alone antibodies, antibody fragments or variable region fragments thereof incorporated into multi-specific antibody-like molecules, bispecific antibodies, antibody-drug conjugates or chimeric antigen receptors also called CARs, which are then transfected or transduced into immune cells, then administered to a patient.
  • Therapeutic anti-MUC1* antibodies can be monoclonal, polyclonal, antibody mimics, engineered antibody-like molecules, full antibodies or antibody fragments.
  • antibody fragments include but are not limited to Fabs, scFv, and scFv-Fc.
  • Human or humanized antibodies are preferred for use in the treatment or prevention of cancers. In any of these antibody-like molecules, mutations can be introduced to prevent or minimize dimer formation.
  • Anti-MUC1* antibodies that are monovalent or bispecific are preferred because MUC1* function is activated by ligand induced dimerization. Typical binding assays show that NME1 and NME7 AB bind to the PSMGFR peptide portion of MUC1* (Fig. 2A, 2D).
  • these activating growth factors bind to the membrane proximal portion of MUC1*, as they do not bind to the PSMGFR peptide if the 10 C-terminal amino acids are missing.
  • anti-MUC1* antibodies MNC2 and MNE6 bind to the PSMGFR peptide if an only if the 10 C-terminal amino acids are present (Fig. 2B, 2C).
  • Antibodies MNC3 and MNC8 bind to epitopes that are different from MNC2 and MNE6, as they do not depend on the presence of the 10 C-terminal amino acids of the PSMGFR peptide (Fig. 2E, 2F).
  • Antibodies MNC2, MNE6, 20A10, 3C2B1, 5C6F3, 25E6, 18G12, 28F9, 1E4, B12, B2, B7, B9, 8C7F3, and H11 antibody and other antibodies of the invention or fragments derived from them, can be administered to a patient for the treatment or prevention of cancers, as stand-alone antibodies or incorporated into a BiTE, an ADC, a multi-specific antibody-like molecule, bispecific antibodies, with or without an FC region or a portion of an Fc region, a bi-scFv, a di-scFv, a tandem di-scFv, a diabody, triabody, tribody, tetrabody and other antibody-like molecules that are multi-valent and multi-specific.
  • the antibody or antibody fragment may be murine, human, humanized, camelid, rabbit or other non-human species.
  • BiTEs or chimeric antigen receptors also called CARs that have been transduced into immune cells. MNC2, MNE6, 20A10, 3C2B1, 5C6F3, 25E6, 18G12, 28F9, 1E4, B12, B2, B7, B9, 8C7F3, and H11 antibody and other anti-MUC1* antibodies that competitively inhibit the binding of NME1 and NME7AB are preferred.
  • the antibody or antibody fragment may be murine, human, humanized, camelid, rabbit or other non-human species.
  • Therapeutic anti-MUC1* antibodies for use as a stand-alone antibody therapeutic or for integration into a BiTE, a CAR, an ADC, or any of the multi-specific antibody-like molecules can be selected based on specific criteria.
  • the parent antibody can be generated using typical methods for generating monoclonal antibodies in animals. Alternatively, they can be selected by screening antibody or antibody fragment libraries, including but not limited to strategies described in Beckman U.S. Patent No. 9,944,719B2, which is incorporated by reference herein for description of methods of screening antibodies.
  • Antibodies suitable for therapeutic use are chosen based on their ability to bind to a MUC1* peptide, which can be: [00577] (i) PSMGFR region of MUC1; [00578] (ii) PSMGFR peptide; [00579] (iii) a peptide having amino acid sequence of QFNQYKTEAASRYNLTISDVSVSDVPFPFSAQSGA (N-10) [00580] (iv) a peptide having amino acid sequence of [00581] ASRYNLTISDVSVSDVPFPFSAQSGA (N-19) [00582] (v) a peptide having amino acid sequence of [00583] NLTISDVSVSDVPFPFSAQSGA (N-23) [00584] (vi) a peptide having amino acid sequence of [00585] ISDVSVSDVPFPFSAQSGA (N-26) [00586] (vii) a peptide having amino acid sequence of [00587] SV
  • Resultant antibodies or antibody fragments generated or selected in this way can then be further selected by passing additional screens. For example, antibodies or antibody fragments become more preferred based on their ability to bind to MUC1* positive cancer cells or tissues but not to MUC1 negative cancer cells or to normal tissues. Further, anti- MUC1* antibodies or antibody fragments may be de-selected as anti-cancer therapeutics if they bind to stem or progenitor cells. Anti-MUC1* antibodies or antibody fragments become more preferred if they have the ability to competitively inhibit the binding of activating ligands, such as NME7AB or NME7-X1, to MUC1*. Figs.
  • a process for selecting anti-MUC1* antibodies for use in treating a patient diagnosed with a MUC1 positive cancer, at risk of developing a MUC1 positive cancer or suspected of having a MUC1 positive cancer comprises one or more of the following steps of selecting antibodies or antibody fragments that 1) bind to the PSMGFR peptide; 2) bind to the N-10 PSMGFR peptide; 3) selectively bind to cancer cells; 4) do not bind to C-10 PSMGFR peptide; and 5) competitively inhibited the binding of dimeric NME1 or NME7- AB to the PSMGFR peptide.
  • Figs. 3A-3C show that monoclonals MNE6 and MNC2 satisfy all five criteria, while monoclonals MNC3 and MNC8 do not competitively inhibit the binding of activating ligands NME1 and NME7 (Fig. 3C).
  • the MUC1* growth factor receptor is activated by ligand-induced dimerization of its extracellular domain. Therefore, the ideal antibody therapeutic, if used as a straight stand-alone antibody therapeutic, should not dimerize the MUC1* extracellular domain.
  • suitable antibodies in this regard include monovalent antibodies such as those generated in lamas and camels, Fabs, scFv’s, single domain antibodies (sdAb), scFv-Fc as long as the Fc portion is constructed such that it does not homo-dimerize.
  • FACS scans show that anti-MUC1* antibodies MNC2 and MNE6 specifically bind to MUC1* positive solid tumor cancer cells and MUC1* transfected cells but not MUC1* negative or MUC1 negative cells.
  • a humanized MNC2 scFv is shown to bind to ZR-75-1, aka 1500, MUC1* positive breast cancer cells (Fig. 4A-4C).
  • MNE6 was shown to bind to MUC1 negative HCT-116 colon cancer cells if an only if they were transfected with MUC1*. MNE6 also bound to MUC1* positive cancer cells such as ZR-75-1, aka 1500, MUC1* positive breast cancer cells (Fig. 4D-4F). Binding assays such as ELISAs, immunofluorescence, and the like all confirm that MNC2 and MNE6 bind to the PSMGFR peptide and to live MUC1 positive cancer cells. Humanized anti-MUC1* antibodies are selected based on their ability to also bind to the PSMGFR peptide or to MUC1 positive cancer cells.
  • Figure 5 shows that humanized MNC2 scFv binds with high affinity to the MUC1* peptide PSMGFR with an EC-50 of about 333nM.
  • Humanized MNC2 scFv like Fabs, potently inhibits the growth of MUC1* positive cancer cells as is shown in one example in Figs. 6A, 6B.
  • humanized scFv’s show the same binding pattern.
  • huMNE6-scFv binds to the PSMGFR peptide, binds to the N-10 peptide but does not bind to the C-10 peptide (SEQ ID NO:825) (Fig. 8).
  • murine or humanized MNC3-scFv which is less suitable for the treatment of cancers, binds to the, PSMGFR peptide, binds to the N-10 peptide and also binds to the C-10 peptide (Fig.9), which we know is the epitope to which the activating ligand NME7AB binds.
  • the Fabs of MNE6 and MNC2 or the comparable single chain variable regions derived from them potently inhibit the growth of MUC1* positive cancers in vitro and in vivo.
  • the Fabs of Anti-MUC1* antibodies inhibited the growth of human MUC1* positive cancers in vivo.
  • Fig. 7A shows that MNE6 Fab potently inhibited the growth of MUC1* positive breast cancers.
  • Female nu/nu mice implanted with 90-day estrogen pellets were implanted with 6 million T47D human breast cancer cells that had been mixed 50/50 with Matrigel. Mice bearing tumors that were at least 150 mm 3 and had three successive increases in tumor volume were selected for treatment. Animals were injected sub-cutaneously twice per week with 80 mg/kg MNE6 Fab and an equal number of mice fitting the same selection criteria were injected with vehicle alone (Fig.7A).
  • MNE6 was shown to halt the growth of prostate cancer.
  • Fig.7B shows that MNE6 Fab potently inhibited the growth of MUC1* positive prostate cancers.
  • Male NOD/SCID mice were implanted with 6 million DU-145 human prostate cancer cells that had been mixed 50/50 with Matrigel. Mice bearing tumors that were at least 150 mm ⁇ 3 and had three successive increases in tumor volume were selected for treatment. Animals were injected sub-cutaneously every 48 hours with 160 mg/kg MNE6 Fab and an equal number of mice fitting the same selection criteria were injected with vehicle alone (Fig. 7B). Tumors were measured independently by two researchers twice per week and recorded.
  • Anti-MUC1* Fab inhibited breast cancer growth and prostate cancer growth. Treatment had no effect on weight, bone marrow cell type or number. The MNE6 Fab effectively inhibited the growth of the tumors, while the control group’s tumors continued to grow until sacrifice. No adverse effects of treatment were observed or detected. [00599] Recombinant forms of MNE6 and MNC2 were constructed that like the Fab are monomeric. In this case, MNE6 was humanized and MNC2 was humanized. There are a number of methods known to those skilled in the art for humanizing antibodies.
  • scFv humanized MNE6 variable region
  • SEQ ID NO:256 and 257 A single chain of the humanized MNE6 variable region, called an scFv, was genetically engineered such that it was connected to the Fc portion of the antibody (SEQ ID NO:256 and 257). Fc regions impart certain benefits to antibody fragments for use as therapeutics.
  • the Fc portion of an antibody recruits complement, which in general means it can recruit other aspects of the immune system and thus amplify the anti-tumor response beyond just inhibiting the target.
  • the addition of the Fc portion also increases the half-life of the antibody fragment (Czajkowsky DM, Hu J, Shao Z and Pleass RJ.
  • a human or humanized MNE6 antibody or antibody fragment, Fab, MNE6 scFv or hu MNE6 scFv-Fcmut are effective anti-cancer agents that can be administered to a person diagnosed with a MUC1 or MUC1* positive cancer, suspected of having a MUC1 or MUC1* positive cancer or is at risk of developing a MUC1 or MUC1* positive cancer.
  • Humanizing [00603] Humanized antibodies or antibody fragments or fully human antibodies that bind to the extracellular domain of -MUC1* are preferred for therapeutic use. The techniques described herein for humanizing antibodies are but a few of a variety of methods known to those skilled in the art.
  • Humanization is the process of replacing the non-human regions of a therapeutic antibody (usually mouse monoclonal antibody) by human one without changing its binding specificity and affinity.
  • the main goal of humanization is to reduce immunogenicity of the therapeutic monoclonal antibody when administered to human.
  • Three distinct types of humanization are possible.
  • a chimeric antibody is made by replacing the non-human constant region of the antibody by the human constant region.
  • Such antibody will contain the mouse Fab region and will contain about 80-90% of human sequence.
  • a humanized antibody is made by grafting of the mouse CDR regions (responsible of the binding specificity) onto the variable region of a human antibody, replacing the human CDR (CDR- grafting method). Such antibody will contain about 90-95% of human sequence.
  • a full human antibody (100% human sequence) can be created by phage display, where a library of human antibodies, antibody-like molecules or antibody fragments is screened to select antigen specific human antibody or by immunizing transgenic mice expressing human antibody. [00605]
  • a general technique for humanizing an antibody is practiced approximately as follows. Monoclonal antibodies are generated in a host animal, typically in mice. Monoclonal antibodies are then screened for affinity and specificity of binding to the target.
  • a monoclonal antibody that has the desired effect and desired characteristics is identified, it is sequenced.
  • the sequence of the animal-generated antibody is then aligned with the sequences of many human antibodies in order to find human antibodies with sequences that are the most homologous to the animal antibody.
  • Biochemistry techniques are employed to paste together the human antibody sequences and the animal antibody sequences.
  • the non-human CDRs are grafted into the human antibodies that have the highest homology to the non- human antibody. This process can generate many candidate humanized antibodies that need to be tested to identify which antibody or antibodies has the desired affinity and specificity.
  • a human antibody or a humanized antibody can be further modified for use as an Fab fragment, as a full antibody, or as an antibody-like entity such as a single chain molecule containing the variable regions, such as scFv or an scFv-Fc. In some cases it is desirable to have Fc region of the antibody or antibody-like molecule mutated such that it does not dimerize.
  • fully human antibodies can be obtained by a variety of methods known to those skilled in the art, including screening human antibody libraries with a peptide fragment of an antigen.
  • a fully human antibody that functions like MNE6 or MNC2, 20A10 or other antibodies of the invention can be generated by screening a human antibody library or library of antibody fragments with a peptide having the sequence of the PSMGFR N-10 peptide.
  • human antibodies are generated in genetically modified mice. Humanized anti-MUC1* antibodies or antibody fragments were generated based on the sequences of the mouse monoclonal antibodies MNE6, MNC2, 20A10, 3C2B1, 5C6F3 and 25E6.
  • a patient diagnosed with a MUC1* positive cancer is treated with an effective amount of a murine or camelid antibody or antibody fragment comprising sequences from MNC2 (SEQ ID NO:118-119 and 168-169), MNE6 (SEQ ID NOS: 12-13 and 65-66), 20A10 (SEQ ID NOS:988-989 and 1004-1005), 3C2B1 (SEQ ID NOS:1820-1821 and 1822-1823), 5C6F3 (SEQ ID NO:1816-1817 and 1818-1819), 25E6 (SEQ ID NO:1020-1021 and 1036-1037 ), 18G12, 28F9, 1E4, B12, B2, B7, B9, 8C7F3, or H11.
  • MNC2 SEQ ID NO:118-119 and 168-169
  • MNE6 SEQ ID NOS: 12-13 and 65-66
  • 20A10 SEQ ID NOS:988-989 and 1004-1005
  • 3C2B1 SEQ ID NOS:1820
  • a patient diagnosed with a MUC1* positive cancer is treated with an effective amount of human or humanized antibody or antibody fragment comprising sequences from MNE6 (SEQ ID NOS:56-57 and 107-108, or 341-342, or 391- 392, or 393-394) or MNC2 (SEQ ID NO:144-145 and 194-195, or 654-655, or 239-249, or 5017-5020), 20A10 (SEQ ID NOS:1576-1581 or 5001-5012), 3C2B1 (SEQ ID NOS:1820-1823 or 1812-1813), 5C6F3 (SEQ ID NOS:1816-1819, or 1814-1815), 25E6 (SEQ ID NOS:1020- 1021 and 1036-1037, or 1600-1601), 18G12, 28F9, 1E4, B12, B2, B7, B9, 8C7F3, or H11.
  • MNE6 SEQ ID NOS:56-57 and 107-108, or 341-342, or 391-
  • a patient diagnosed with a MUC1* positive cancer is treated with an effective amount of humanized antibody or antibody fragment comprising sequences of MNC2 (SEQ ID NO:654-655), MNE6 (SEQ ID NO:341-342), 20A10 (SEQ ID NO:1580- 1581), 3C2B1 (SEQ ID NO:1812-1813), 5C6F3 (SEQ ID NO:1814-1815), 25E6 (SEQ ID NO:1600-1601).
  • a patient diagnosed with a MUC1* positive cancer is treated with an effective amount of humanized monovalent form of the antibodies such as MNC2 (SEQ ID NOS:239, 241, 243,396 or 5018-5020), MNE6 (SEQ ID NO:), 20A10 (SEQ ID NOS:1574-1581 or SEQ ID NOS:5001-5012) , 3C2B1 (SEQ ID NO:1813), 5C6F3 (SEQ ID NO:1815), 25E6, 18G12, 28F9, 1E4, B12, B2, B7, B9, 8C7F3, or H11, wherein monovalent means the corresponding Fab fragment, the corresponding scFv or the corresponding scFv-Fc fusion.
  • MNC2 SEQ ID NOS:239, 241, 243,396 or 5018-5020
  • MNE6 SEQ ID NO:
  • 20A10 SEQ ID NOS:1574-1581 or SEQ ID NOS:5001-5012
  • a patient diagnosed with a MUC1* positive cancer is treated with an effective amount of a humanized scFv or monomeric humanized scFv-Fc of MNC2, MNE6, 20A10, 3C2B1, 5C6F3, 25E6, 18G12, 28F9, 1E4, B12, B2, B7, B9, 8C7F3, or H11.
  • MUC1* growth factor receptor is activated by ligand induced dimerization of its extracellular domain, and because the Fc portion of an antibody homo-dimerizes, it is preferable that a construct that includes an Fc portion uses a mutated Fc region that prevents or minimizes dimerization.
  • Antibodies that bind to PSMGFR (SEQ ID NO:2) peptide, and more specifically to the N-10 peptide, of the extracellular domain of the MUC1* receptor are potent anti-cancer therapeutics that are effective for the treatment or prevention of MUC1* positive cancers. They have been shown to inhibit the binding of activating ligands dimeric NME1 (SEQ ID NO:1781) and NME7 AB (SEQ ID NOS:827) to the extracellular domain of MUC1*.
  • Anti- MUC1* antibodies that bind to the PSMGFR sequence inhibit the growth of MUC1*-positive cancer cells, specifically if they inhibit ligand-induced receptor dimerization.
  • Antibodies that bind to PSMGFR region of MUC1* or bind to a synthetic PSMGFR peptide are preferred. Especially preferred are antibodies that bind to the N-10 peptide but not to the C-10 peptide. Still more preferred are antibodies that bind to the N-26 peptide wherein mutation or deletion of the PFPFS sequence (SEQ ID NO:1747) destroys binding of the antibody or fragment thereof to the N-26 peptide.
  • mouse monoclonal antibodies that bind to the extracellular domain of MUC1*.
  • MNC2 mouse monoclonal antibodies
  • MNE6 SEQ ID NOS:12-25, 39-59, 65-78, 93-114
  • 20A10 SEQ ID NOS:988-1019, 1574-1597, 1659-1666
  • 3C2B1 SEQ ID NOS:1386-1413, 1572-1573
  • 5C6F3 SEQ ID NOS:1356-1385
  • 25E6 SEQ ID NOS:1020-1051, 1598-1617, 1667-1674
  • 18G12 SEQ ID NOS:956-987
  • 28F9 SEQ ID NOS:1052-1083
  • 1E4 SEQ ID NOS:1116-1227
  • B12 SEQ ID NOS:1414-1431, 1733-1742
  • B2 SEQ ID NOSEQ ID NOS:1116-1227
  • B12 SEQ ID NOS:1414-1431, 1733-1742
  • B2 SEQ ID
  • the CDRs of these antibodies make up the recognition units of the antibodies and are the most important parts of the mouse antibody that should be retained when grafting into a human antibody.
  • the sequences of the CDRs for each mouse monoclonal are as follows, heavy chain sequence followed by light chain: MNE6 CDR1 (SEQ ID NO:16-17 and 69-70) CDR2 (SEQ ID NO:20-21 and 73-74) CDR3 (SEQ ID NO: 24-25 and 77-78), MNC2 CDR1 (SEQ ID NO:122-123 and 172-173) CDR2 (SEQ ID NO:126-127 and 176-177) CDR3 (SEQ ID NO:130-131 and 180-181), 20A10 CDR1 (SEQ ID NO:991-992 and 1008-1009) CDR2 (SEQ ID NO:996-997 and 1012-1013) CDR3 (SEQ ID NO:1000-1001 and 1016-1017), 3C2B1 CDR1 (SEQ ID NO:1388-1389 and 1402-1
  • portions of the framework regions that by modeling are thought to be important for the 3-dimensional structure of the CDRs are also imported from the mouse sequence.
  • Monoclonal antibodies MNE6, MNC2, 20A10, 3C2B1 and 25E6 have greater affinity for MUC1* as it appears on cancer cells.
  • Monoclonal antibodies MNC3 and MNC8 have greater affinity for MUC1* as it appears on stem cells.
  • All seven antibodies have been humanized, which process has resulted in several humanized forms of each antibody. CDRs derived from the variable regions of the mouse antibodies were biochemically grafted into a homologous human antibody variable region sequence.
  • MNE6 Humanized variable regions of MNE6 (SEQ ID NOS: 38-39 and 93-94), MNC2 (SEQ ID NOS: 144-145 and 194-195), 20A10 (SEQ ID NOS:1576-1581 and 5001-5012), 3C2B1 (SEQ ID NOS:1812-1813), 5C6F3 (SEQ ID NOS: 1814-1815), 25E6 (SEQ ID NOS:1600-1601).
  • MNC3 SEQ ID NOS: 439-440 and 486-487
  • MNC8 SEQ ID NOS: 525-526 and 543-544
  • humanized heavy chain variable constructs were then fused into constant regions of either human IgG1 heavy chain constant region (SEQ ID NOS:58-59) or human IgG2 heavy chain constant region (SEQ ID NO:54-55), which are then paired with either humanized light chain variable constructs fused to a human kappa chain (SEQ ID NO: 109-110) or human lambda chain (SEQ ID NO: 113-114) constant region.
  • Other IgG isotypes could be used as constant region including IgG3 or IgG4.
  • IgG constant region which IgG constant region is fused to the humanized variable region depends on the desired effect since each isotype has its own characteristic activity.
  • the isotype of the human constant region is selected on the basis of things such as whether antibody dependent cell cytotoxicity (ADCC) or complement dependent cytotoxicity (CDC) is desired but can also depend on the yield of antibody that is generated in cell-based protein expression systems.
  • ADCC antibody dependent cell cytotoxicity
  • CDC complement dependent cytotoxicity
  • humanized anti-MUC1* antibodies or antibody fragments are administered to a person diagnosed with or at risk of developing a MUC1-positive cancer.
  • One method for testing and selecting the humanized anti-MUC1* antibodies that would be most useful for the treatment of persons with cancer or at risk of developing cancers is to test them for their ability to inhibit the binding of activating ligands to the MUC1* extracellular domain.
  • Dimeric NME1 can bind to and dimerize the MUC1* extracellular domain and in so doing stimulates cancer cell growth.
  • Antibodies and antibody fragments that compete with NME1 for binding to the MUC1* extracellular domain are therefore anti- cancer agents.
  • NME7AB is another activating ligand of MUC1*.
  • antibodies that block the binding of NME7, or an NME7 AB truncation or cleavage product of NME7-X1, to the MUC1* extracellular domain are effective as anti-cancer therapeutics.
  • These antibodies include but are not limited to MNC2, MNE6, 20A10, 3C2B1, 5C6F3, 25E6, 18G12, 28F9, 1E4, B12, B2, B7, B9, 8C7F3, or H11 as well as single chain versions, such as scFv, of these antibodies and humanized version thereof.
  • NME proteins also bind to MUC1 or MUC1* including NME1, NME6 and NME8. Antibodies that compete with these proteins for binding to MUC1* may also be useful as therapeutics.
  • murine, camelid, human or humanized anti-MUC1* antibodies or antibody fragments are administered to a person diagnosed with or at risk of developing a MUC1-positive cancer.
  • single chain antibody fragments, or monomeric scFv-Fc fusions derived from humanized sequences of MNC2, MNE6, 20A10, 3C2B1, 5C6F3, 25E6, 18G12, 28F9, 1E4, B12, B2, B7, B9, 8C7F3, or H11 are administered to a person diagnosed with or at risk of developing a MUC1-positive cancer.
  • Single chain variable fragments, scFv, or other forms that result in a monovalent antibody or antibody-like protein are also useful. In some cases it is desired to prevent dimerization of the MUC1* extracellular domain.
  • Single chain variable fragments, Fabs and other monovalent antibody-like proteins have been shown to be effective in binding to the extracellular domain of MUC1* and blocking MUC1* dimerization. These single chain variable fragments, Fabs and other monovalent antibody-like molecules effectively blocked cancer growth in vitro and in animals xenografted with human MUC1-positive cancer cells. Thus, humanized single chain variable fragments or monovalent anti-MUC1* antibodies or antibody-like molecules would be very effective as an anti-cancer therapeutic. Such humanized single chain antibodies, Fabs and other monovalent antibody-like molecules that bind to the MUC1* extracellular domain or to a PSMGFR peptide are therefore useful as anti-cancer therapeutics.
  • Anti-MUC1* single chain variable fragments are generated by grafting non-human CDRs of antibodies, which bind to extracellular domain of MUC1* or bind to PSMGFR peptide, into a framework of a homologous variable region human antibody.
  • the resultant humanized heavy and light chain variable regions are then connected to each other via a suitable linker, wherein the linker should be flexible and of length that it allows heavy chain binding to light chain but discourages heavy chain of one molecule binding to the light chain of another.
  • a linker of about 10-15 residues.
  • the linker includes [(Glycine)4 (Serine)1]3 (SEQ ID NOS: 401-402), but is not limited to this sequence as other sequences are possible.
  • the humanized variable regions of MNE6 (SEQ ID NOS: 38-39 and 93-94), MNC2 (SEQ ID NOS: 144-145 and 194-195), or other antibodies of the invention are biochemically grafted into a construct that connects heavy and light chains via a linker.
  • Several humanized MNE6 single chain proteins were generated (SEQ ID NOS: 232-237, 397-398).
  • Several humanized MNC2 single chain proteins were generated (SEQ ID NOS: 238-243, 395-396, 654-655, 5017-5018, 5019-5020).
  • humanized anti-MUC1* antibody fragments including variable fragments, scFv antibody fragments derived from MNE6 scFv, MNC2 scFv, 20A10, 3C2B1, 5C6F3, 25E6, 18G12, 28F9, 1E4, B12, B2, B7, B9, 8C7F3, or H11 scFv, which may be incorporated into different therapeutic formats including CARs, Bispecific antibodies, BiTEs, antibody drug conjugates, are administered to a person diagnosed with or at risk of developing a MUC1-positive cancer.
  • One aspect of the invention is a method for treating a patient diagnosed with, suspected of having, or at risk of developing a MUC1 positive or MUC1* positive cancer, wherein the patient is administered an effective amount of an agent containing a monomeric form of MNE6, MNC2, or 20A10, 3C2B1, 5C6F3, 25E6, 18G12, 28F9, 1E4, B12, B2, B7, B9, 8C7F3, or H11, wherein the antibody variable fragment portions are human or have been humanized and wherein the Fc portion of the antibody-like protein, if present, has been mutated such that it resists dimer formation.
  • an agent containing a monomeric form of MNE6, MNC2, or 20A10, 3C2B1, 5C6F3, 25E6, 18G12, 28F9, 1E4, B12, B2, B7, B9, 8C7F3, or H11 wherein the antibody variable fragment portions are human or have been humanized and wherein the Fc portion of the antibody-like protein
  • CAR T and cancer immunotherapy techniques [00618]
  • some or all of the single chain portions of anti- MUC1* antibody fragments are biochemically fused onto immune system molecules, using several different chimeric antigen receptor, ‘CAR’ strategies.
  • the idea is to fuse the recognition portion of an antibody, typically as a single chain variable fragment, to an immune system molecule that has a transmembrane domain and a cytoplasmic tail that is able to transmit signals that activate the immune system for example activating the immune cell to kill the cell that is recognized by the recognition unit.
  • the recognition unit can be an antibody fragment, a single chain variable fragment, scFv, or a peptide.
  • the recognition portion of the extracellular domain of the CAR is comprised of sequences from the human, humanized or non-human variable regions of MNE6 (SEQ ID NOS:12-13 and 65-66, 56-57 and 107-108, 38-39 and 93-94, 341-342, 391-394), MNC2 (SEQ ID NOS:118-119 and 168- 169, or 144-145 and 194-195, 654-655, 239-243, or 5017-5020), 20A10 (SEQ ID NOS:988- 989 and 1004-1005, or 1574-1581, 1677, 1687 or 5001-5012), 3C2B1 (SEQ ID NOS:1386- 1413, or 1820-1823, 1572-1573, or 1812-1813), 5C6F3 (SEQ ID NOS:1816-1819, or 1384- 1385, or 1814-1815), 25E6 (SEQ ID NOS:1020-1021, or 1036-1037, or 1598-1601), 18
  • the recognition unit is comprised of sequences from a single chain variable fragment. Examples of single chain constructs are given.
  • Several humanized MNE6 single chain proteins, scFv were generated (SEQ ID NOS: 232-237).
  • Several humanized MNC2 single chain proteins, scFv were generated (SEQ ID NOS: 238-243, 654-655, or 5017-5020).
  • Several humanized 20A10 single chain proteins, scFv were generated (SEQ ID NOS:1576-1581, 1677, 1687 and 5001-5012).
  • Humanized single chain proteins were also derived from 3C2B1 (SEQ ID NOS:1812-1813), 5C6F3 (SEQ ID NOS:1814-1815) and 25E6 (SEQ ID NOS:1600-1601).
  • the extracellular hinge of the CAR can be derived from a variety of proteins, including CD8 (SEQ ID NOS:345-346), CD4 (SEQ ID NOS:347-348) or CD28 (SEQ ID NOS:349-350).
  • the transmembrane region of the CAR can also be derived from CD3-zeta (SEQ ID NOS:361-362), CD8 (SEQ ID NOS:363- 364), CD4 (SEQ ID NOS:365-366), CD28 (SEQ ID NOS:367-368), 4-1BB (SEQ ID NOS:369-370), OX40 (SEQ ID NOS:371-372), antibody domains or other transmembrane region, including the transmembrane region of the proximal cytoplasmic co-stimulatory domain, such as CD28, 4-1BB or other.
  • the cytoplasmic tail of the CAR can be comprised of one or more motifs that signal immune system activation.
  • a group of cytoplasmic signaling motifs includes but is not limited to CD27, CD28 (SEQ ID NOS:377-378), 4-1BB (SEQ ID NOS:379-380), OX40, CD30, CD40, ICAm-1, LFA-1, ICOS, CD2, CD5, CD7 and Fc receptor gamma domain.
  • the signaling domain can be CD3-zeta (SEQ ID NOS:373-374, or 375-376) or a modified CD3- zeta called 1XX (SEQ ID NOS:1796-1797).
  • a minimal CAR may have the CD3-zeta or an Fc receptor gamma domain then one or two of the above domains in tandem on the cytoplasmic tail.
  • the cytoplasmic tail comprises CD3-zeta, or a mutant thereof such as 1XX, plus a co-stimulatory domain such as CD28, 4-1BB and/or OX40.
  • one or two ITAMs of CD3-zeta are deleted or mutated to slow signaling which increases persistence and decreases differentiation of the immune cell.
  • the extracellular domain recognition unit of a MUC1* targeting CAR can comprise variable regions of any non-human, humanized or human antibody that is able to bind to at least 12 contiguous amino acids of the PSMGFR peptide (SEQ ID NO:2) or more preferably the N-10 peptide (SEQ ID NO:3), still more preferably, is able to bind to the N-10 peptide (SEQ ID NO:3), but is not able to bind to the C-10 peptide (SEQ ID NO:825).
  • the MUC1* targeting portion of the CAR comprises variable regions from non- human, humanized or human MNC2, MNE6, 20A10, 3C2B1, 5C6F3, 25E6, 18G12, 28F9, 1E4, B12, B2, B7, B9, 8C7F3, or H11.
  • the MUC1* targeting portion of the CAR comprises variable regions from non-human, humanized or human MNC2, MNE6, 20A10, 3C2B1, 5C6F3, 25E6.
  • MNE6 SEQ ID NOS:297-298, 300-301, 303-304, 1626-1633 and 5045-5048
  • MNC2 SEQ ID NOS:306- 307, 608-611, 718-719, 1618-1625, 5041-5044, and 1784-1785
  • 20A10 SEQ ID NOS:1582- 1597, 5021-5028, 1798-1799, 1692,1699, and 1706
  • 25E6 SEQ ID NOS:1602-1617, 5033-5040.
  • single chain antibodies derived from 3C2B1 (SEQ ID NOS:1572- 1573 or 1812-1813) or 5C6F3 (SEQ ID NOS:1384-1385 or 1814-1815) can be substituted for the single chain antibody fragment in any of the CARs listed above.
  • the antibody CDRs can be inserted into a number of different framework regions; as a demonstration we generated three versions of a humanized 20A10 which differ only in the framework regions. These have been incorporated into CARs (SEQ ID NOS:1675, 1678, 1685) that when transduced into human T cells are able to recognize target MUC1* expressing cells and kill them.
  • the extracellular domain recognition unit of a CAR is comprised essentially of a humanized MNC2, MNE6, 20A10, 3C2B1, 5C6F3, 25E6, 18G12, 28F9, 1E4, B12, B2, B7, B9, 8C7F3, or H11 single chain variable fragment scFv.
  • the recognition domain which is typically an antibody fragment, can be fused to an extracellular region, often referred to as the hinge.
  • the hinge can be derived from a variety of extracellular regions or peptides, including but not limited to the hinge region of CD8 (SEQ ID NOS:345-346), CD4 (SEQ ID NOS:347-348) or CD28 (SEQ ID NOS:349-350).
  • the transmembrane region of the CAR can be derived from a number of protein transmembrane domains, including but not limited to CD8 (SEQ ID NOS:363-364), or can be the transmembrane domain of CD3-zeta (SEQ ID NOS:361-362), CD4 (SEQ ID NOS:365-366), CD28 (SEQ ID NOS:367-368), 41BB (SEQ ID NOS:369-370), OX40 (SEQ ID NOS:371- 372) or other transmembrane region.
  • CD8 SEQ ID NOS:363-364
  • CD4 SEQ ID NOS:365-366
  • CD28 SEQ ID NOS:367-368
  • 41BB SEQ ID NOS:369-370
  • OX40 SEQ ID NOS:371- 372
  • the cytoplasmic domain of a CAR with antibody fragment targeting MUC1* extracellular domain can be comprised of one or more selected from the group comprising an immune system co-stimulatory cytoplasmic domain and a cytoplasmic signaling domain.
  • the group of immune system co-stimulatory domains includes but is not limited to CD27, CD28, 4-1BB, OX40, CD30, CD40, ICAm-1, LFA-1, ICOS, CD2, CD5, CD7 and Fc receptor gamma domain (SEQ ID NOS:373-382).
  • the group of immune system signaling domains includes but is not limited to CD3-zeta (SEQ ID NOS:373-376) and CD3-zeta-1XX (SEQ ID NOS:1796-1797).
  • the CD3-zeta signaling domain may be wild type or may contain deletions or mutations of one or two of the three ITAMs.
  • the CD3-zeta domain contains only one functional ITAM.
  • ITAM is ITAM1 also known as the 1XX variation of CD3-zeta.
  • a MUC1* targeting CAR is transfected or transduced into a T cell or an NK cell.
  • the immune cell can be autologous or allogeneic.
  • the T cell is a CD3+ T cell, which may be CD8 or CD4 positive.
  • it is a dendritic cell.
  • it is a B cell.
  • it is a mast cell.
  • it is a Natural Killer, NK, cell.
  • the immune cell is derived from a stem cell that has been directed to differentiate to that immune cell type in vitro.
  • a CAR containing sequences of the antibody are expressed in a stem cell, which then may be differentiated into an immune cell.
  • the immune cell is a T cell. In another case, the immune cell is an NK cell.
  • the cell can be from a patient or from a donor. If from a donor, it can be engineered to remove molecules that would trigger rejection.
  • Cells transfected or transduced with a CAR of the invention can be expanded ex vivo or in vitro then administered to a patient. Administrative routes are chosen from a group containing but not limited to bone marrow transplant, intravenous injection, in situ injection or transplant.
  • the MUC1* targeting CAR is administered to a person diagnosed with or at risk of developing a MUC1-positive cancer.
  • CAR constructs that can be transduced into T cells or other immune cells for the treatment or prevention of MUC1* positive cancers.
  • CARs are made up of modules and the identity of some of the modules is relatively unimportant, while the identity of other modules is critically important.
  • intracellular signaling modules such as CD3-zeta (SEQ ID NOS: 373-376), CD28 (SEQ ID NOS: 377-378) and 41BB (SEQ ID NOS: 379-380), alone or in combinations stimulate immune cell expansion, cytokine secretion and immune cell mediated killing of the targeted tumor cells (Pulè MA, Straathof KC, Dotti G, Heslop HE, Rooney CM and Brenner MK (2005) A chimeric T cell antigen receptor that augments cytokine release and supports clonal expansion of primary human T cells. Mol Ther.12(5):933-941; Hombach AA, Heiders J, Foppe M, Chmielewski M and Abken H.
  • CD3-zeta SEQ ID NOS: 373-376
  • CD28 SEQ ID NOS: 377-3708
  • 41BB SEQ ID NOS: 379-380
  • Antibodies of the invention including but not limited to fragments of MNC2, MNE6, 20A10, 3C2B1, 5C6F3, 25E6, 18G12, 28F9, 1E4, B12, B2, B7, B9, 8C7F3, or H11 can also be incorporated into CARs that have mutated cytoplasmic tails, such as mutated or deleted tyrosines of one or more of the ITAMs.
  • the cytoplasmic tails may include mutations or deletions that dampen signaling, which increases persistence and decreases host cell differentiation.
  • Such mutations include but are not limited to Tyrosines that are mutated to inhibit phosphorylation and signaling (Salter et al, 2018; ).
  • the ITAMs of CD3-zeta may be mutated to inhibit or dampen signaling (Feucht et al 2019).
  • the CD3-zeta of the cytoplasmic tail may comprise mutations or deletions in the ITAMs including those referred to as 1XX (SEQ ID NOS:1796-1797).
  • one or two ITAMs are deleted, leaving only one or two ITAMs (Feucht et al 2019).
  • the position of the included ITAM or ITAMs is moved to a position proximal to the co-stimulatory domain.
  • Suitable ITAM configurations for increased persistence of CARs include but are not limited to 1XX, X2X, XX3, 12X and 23X, wherein the numeral 1, 2 or 3 refers to ITAM1, ITAM2, or ITAM3 and X refers to the deletion of that ITAM.
  • ITAM1 is the only functional ITAM included in the CAR construct, also known as 1XX.
  • Examples of antibodies of the invention incorporated into CARs with 1XX mutations in ITAMs of CD3- zeta are given in the following sequences: MNC2 (SEQ ID NOS: 1618-1625, 5041-5044 and 1784-1785), MNE6 (SEQ ID NOS:1626-1633 and 5045-5048 ), 20A10 (SEQ ID NOS:1590- 1597, 5021-5028, and 1798-1799), 25E6 (SEQ ID NOS:1610-1617 and 5037-5040).
  • the transmembrane and extracellular hinge region of the CAR may or may not be derived from sequences of the adjacent co-stimulatory domain.
  • a CAR comprising the 4-1BB co-stimulatory domain may have a transmembrane and hinge region derived from CD8 or CD28.
  • a CAR comprising the CD28 co-stimulatory domain may have a transmembrane and hinge region derived from CD28.
  • Examples of antibodies of the invention incorporated into CARs with 1XX mutations in ITAMs of CD3-zeta, which have a CD28 co-stimulatory domain as well as transmembrane and hinge region derived from CD28, are given in the following sequences: MNC2 (SEQ ID NOS:5041-5044 and 1784-1785) MNE6 (SEQ ID NOS:5045-5048), 20A10 (SEQ ID NOS:5025-5028, 1798-1799, 1692,1699, and 1706); 25E6 (SEQ ID NOS:5037-5040).
  • the cytoplasmic region may be comprised of one or more of signaling sequence motifs and co- stimulatory domains, including but not limited to CD3-zeta, CD3-zeta-1XX, CD27, CD28, 4- 1BB, OX40, CD30, CD40, ICAm-1, LFA-1, ICOS, CD2, CD5, or CD7.
  • the sequence of the intracellular signaling domain may contain mutations, such as CD3-zeta-1XX (SEQ ID NOS:1796-1797) that dampen the signal to improve persistence or target cell killing.
  • Signaling domain CD3-zeta may be wild type or may contain mutations or deletions of one or two ITAMs.
  • ITAMs 2 and 3 are deleted or inactivated, leaving a single ITAM, which is ITAM1 also known as the 1XX construct.
  • the hinge and transmembrane regions of CAR are derived from CD8 (SEQ ID NO: 301, 719, 1675 or 1605).
  • the hinge and transmembrane regions of CAR are derived from CD28 (SEQ ID NO:5048, 5044, 5024 or 5036).
  • the co-stimulatory domain is CD28 (SEQ ID NO: 298, 609, 1589, 1609).
  • the co-stimulatory domain is 4-1BB (SEQ ID NO: 301, 719, 1585 or 1605).
  • the antibody fragment that is the targeting head of the CAR binds to the extracellular domain of a MUC1 that is devoid of the tandem repeat domain.
  • the antibody fragment that is the targeting head of the CAR binds to a region of the MUC1* extracellular domain that contains the 35 most membrane proximal amino acids, also referred to here as N- 10 (SEQ ID NO:3).
  • the antibody fragment that is the targeting head of the CAR binds to N-10 (SEQ ID NO:3) but does not bind to C-10 (SEQ ID NO:825).
  • the antibody fragment that is the targeting head of the CAR binds to N-10 (SEQ ID NO:3), does not bind to C-10 (SEQ ID NO:825) and either does not bind to a linear epitope, that is to say doesn’t work in a standard Western blot, or competes with NME7 AB for binding to the N-10 peptide (SEQ ID NO:3).
  • the extracellular domain may include a murine, camelid, human, non- human or humanized single chain antibody fragment with framework region IV of the light chain having variable lengths as set forth as MNE6 scFv (SEQ ID NOS:5014 or 5016), MNC2 scFv (SEQ ID NOS:5018 or 5020) or 20A10 scFv (SEQ ID NOS 5002, 5004, 5006, 5008, 5010 or 5012), 25E6 scFv (SEQ ID NOS: 5030 or 5032).
  • the Framework region IV of the light chain of the single chain antibody fragment may have the terminal amino acids R and T deleted or just T deleted.
  • the CDRs of antibodies can be inserted into a background of a number of different framework regions.
  • 20A10 CDRs were inserted into three different sets of framework regions (SEQ ID NOS:1692, 1699 and 1706) and all were able to function when transduced into T cells.
  • the T cell may be engineered to overexpress c-Jun as a method to inhibit T cell exhaustion (Lynn et al 2019).
  • a variety of promoters can be used upstream of the genes for CARs and other compositions of the invention, including insertion into a naturally occurring promoter in the cell, such as the TRAC locus, using CRISPR, Sleeping Beauty or similar technology for site directed insertion of a gene.
  • promoters commonly used are the CMV promoter, or a mini CMV (SEQ ID NO: 1634), a minimal IL-2 promoter (SEQ ID NO: 1635), or Minimal Promoter minip (SEQ ID NO: 1636).
  • the MUC1* targeting CARs were then transduced, separately or in combinations, into immune cells.
  • immune cells When challenged with surfaces presenting a MUC1* peptide, an antigen presenting cell transfected with MUC1*, or MUC1* positive cancer cells, the immune cells that were transduced with MUC1* targeting CARs elicited immune responses, including cytokine release, killing of the targeted cells and expansion of the immune cells.
  • the gene encoding the CARs and activated T cell induced genes described herein can be virally transduced into an immune cell using viruses, or inserted into a region downstream of one of the cell’s promoters or enhancers, such as the TRAC (T cell receptor alpha chain) locus.
  • Virus delivery systems and viral vectors including but not limited to retroviruses, including gamma-retroviruses, lentivirus, adenoviruses, adeno-associated viruses, baculoviruses, poxvirus, herpes simplex viruses, oncolytic viruses, HF10, T-Vec and the like can be used.
  • retroviruses including gamma-retroviruses, lentivirus, adenoviruses, adeno-associated viruses, baculoviruses, poxvirus, herpes simplex viruses, oncolytic viruses, HF10, T-Vec and the like
  • CARs and activated T cell induced genes described herein can be directly spliced into the genome of the recipient cell using methods such as CRISPR technology, CRISPR-Cas9 and -CPF1, TALEN, Sleeping Beauty transposon system, and SB 100X.
  • the identity of molecules that make up the non-targeting portions of the CAR are not essential to the function of a MUC1*-targeting CAR.
  • the extracellular domain, transmembrane domain and membrane proximal portion of the cytoplasmic domain can be comprised of portions of CD8, CD4, CD28, or generic antibody domains such as Fc, CH2CH3, or CH3.
  • the non-targeting portions of a CAR can be a composite of portions of one or more of these molecules or other family members.
  • CD3-zeta is critical, as mutations, such as those referred to as 1XX or CD3-zeta-1XX, greatly affect in vivo persistence of CAR T cells.
  • CAR T cells that express CARs whose cytoplasmic tail includes CD3-zeta-1XX have prolonged activity in vivo because they do not get exhausted as quickly as cells containing wild-type CD3-zeta.
  • CARs with the 1XX signaling domain are more effective against cells characterized by low antigen density. Cancer cells with low antigen density may comprise a sub-population of a heterogeneous tumor. Cancer cells with low antigen density may be characteristic of early cancer cells that can lead to cancer recurrence.
  • tumors at the time of treatment may be comprised of cancer cells that express low levels of a particular cancer antigen.
  • patients diagnosed with a cancer or at risk of developing a cancer or a cancer recurrence are treated with immune cells that express a CAR comprising a 1XX signaling domain.
  • the patient is diagnosed with or at risk of developing a MUC1* cancer.
  • the recognition unit of the CAR comprises an antibody fragment that binds to the N-10 peptide (SEQ ID NO:3) but does not bind to the C-10 peptide (SEQ ID NO:825).
  • the antibody fragment is derived from MNC2, MNE6, 20A10, 3C2B1, 5C6F3, or 25E6.
  • a patient diagnosed with a cancer comprised of tumor cells that express low levels of a targeted antigen, or diagnosed with an early cancer, or a patient who has been treated but still has residual tumor cells and is at risk of a cancer recurrence is treated with immune cells that express a CAR comprising a 1XX signaling domain, which enables the CAR T cells to kill both high and low antigen density cancer cells.
  • the patient is diagnosed with or at risk of developing a MUC1* cancer.
  • the recognition unit of the CAR comprises an antibody fragment that binds to the N-10 peptide (SEQ ID NO:3) but does not bind to the C-10 peptide (SEQ ID NO:825).
  • the antibody fragment is derived from MNC2, MNE6, 20A10, 3C2B1, 5C6F3, or 25E6.
  • a patient diagnosed with a cancer or at risk of developing a cancer or a cancer recurrence is treated with an immune cell expressing a CAR with a wild-type CD3-zeta and is also treated with an immune cell expressing a CAR with a mutated CD3-zeta, such as CD3-zeta-1XX.
  • the tumor is attacked by an immune cell expressing a CAR with full CD3-zeta signaling that efficiently kills off the high antigen expressing cells, but which are prematurely exhausted, while the cells expressing a CAR with a mutated CD3-zeta, such as CD3-zeta-1XX, persist longer in the patient and kill of the low antigen expressing cells that likely give rise to tumor recurrence.
  • the patient is diagnosed with or at risk of developing a MUC1* cancer.
  • the recognition unit of the CAR comprises an antibody fragment that binds to the N-10 peptide (SEQ ID NO:3) but does not bind to the C-10 peptide (SEQ ID NO:825).
  • the antibody fragment is derived from MNC2, MNE6, 20A10, 3C2B1, 5C6F3, or 25E6.
  • a patient is treated with a CAR T cell in which the CAR has a wild type CD3-zeta signaling domain, wherein the CAR is chosen from among the group comprising MNC2 CARs (SEQ ID NO:306-307, 608-611, 718-719), MNE6 CARs (SEQ ID NO:297-298, 300-301, 303-304), 20A10 CARs (SEQ ID NO:1582-1589, 5021- 5024), 25E6 CARs (1602-1609, 5033-5036), a CAR comprising an antibody fragment derived from 3C2B1 wherein the signaling domain is wild type CD3-zeta, and a CAR comprising an antibody fragment derived from 5C6F3 wherein the signaling domain is wild type CD3-zeta.
  • a patient is treated with a CAR T cell in which the CAR has a CD3-zeta-1XX signaling domain, wherein the CAR is chosen from among the group comprising MNC2 CARs (SEQ ID NO:1618-1625, 5041-5044, 1784-1785), MNE6 CARs (SEQ ID NO:1626-1633, 5045-5048), 20A10 CARs (SEQ ID NO:1590-1597, 5025-5028, 1798-1799), 25E6 CARs (SEQ ID NOS:1610-1617, 5037-5040), a CAR comprising an antibody fragment derived from 3C2B1 wherein the signaling domain is CD3-zeta-1XX, and a CAR comprising an antibody fragment derived from 5C6F3 wherein the signaling domain is CD3-zeta-1XX.
  • MNC2 CARs SEQ ID NO:1618-1625, 5041-5044, 1784-1785
  • MNE6 CARs SEQ ID NO:
  • a patient is treated with immune cells that express both a CAR having a wild type CD3-zeta signaling domain and a CAR having a 1XX signaling domain.
  • CAR T cells bearing the 1XX mutations in the CD3-zeta are more effective than CAR T cells with wild type CD3-zeta at preventing tumor recurrence.
  • Figure 218 shows graphs of tumor volume measured by an IVIS instrument wherein the tumor cells have been genetically modified to express Luciferase. The substrate Luciferin was injected 10 minutes before the photo emissions were measured in the sedated animal. On Day 1 of the experiment, animals were injected sub-cutaneously with 250,000 human breast tumor cells.
  • Tumors were made heterogeneous, comprised of two different tumor cell types.
  • a first tumor cell population was T47D-wt, a breast cancer cell line that expresses both full- length MUC1 and the growth factor receptor form MUC1*, which we engineered to express mCherry fluorescence.
  • the second tumor cell population was the same T47D breast cancer cells, except that they had been stably transduced to express even more MUC1* and GFP fluorescence, referred to here as T47D-MUC1*.
  • animals were implanted with T47D-wt plus T47D-MUC1*, wherein the population of T47D-MUC1* made up 30%, 15% or 7.5% of the tumor population.
  • mice were then administered a one-time injection of either PBS, huMNC2-41BB-3z CAR T cells (4-1BB), huMNC2-CD28-3z CAR T cells (CD28) or huMNC2-CD28-1XX CAR T cells (CD28-1XX or 1XX).
  • the CAR T cells were injected into the tail vein at an Effector to Target ratio (E:T) of 10:1, 5:1, or 1:1.
  • E:T Effector to Target ratio
  • huMNC2-CD28-1XX out-performs huMNC2-CD28-3z and huMNC2- 41BB-3z and the difference is more pronounced in tumors with low antigen density and when treatment is at a low CAR T cell dose.
  • FIG. 219A-219B shows IVIS photographs and graphs of IVIS tumor volume measurement.
  • Fig. 219A shows photographs of the mice that had been implanted with tumors in which 30% of the cancer cell population was T47D-MUC1*, referred to here as high antigen expressing cells.
  • FIG. 219B shows a graph of the tumor volume by IVIS measurement by day.
  • animals injected with the huMNC2-CD28-1XX had much smaller tumors than the animals treated huMNC2-4-1BB-3z or huMNC2-CD28-3z, which is the same CAR T except without the 1XX mutations in the CD3-zeta domain.
  • Figure 220A-220T shows the IVIS graphs for 30% tumors treated at a CAR T to Tumor ratio of 10:1.
  • FIG. 221A-221B and Figure 222A-222T show essentially the same experiment except that the CAR T cell dose is lower with only 250,000 CAR T cells administered in a single injection.
  • animals injected with the huMNC2-CD28-1XX had much smaller tumors than the animals treated huMNC2-4-1BB-3z or huMNC2-CD28-3z, which is the same CAR T except without the 1XX mutations in the CD3-zeta domain.
  • the lower dose of CAR T cells even tumors in the huMNC2-CD28-1XX treated group begin to grow again, albeit more slowly.
  • the huMNC2-CD28-1XX treated mice that had smaller tumors, have a greater number of live, persisting CAR T cells and CD8 positive killer T cells than the animals treated with the CAR T cells with wild type CD3-zeta. It is also seen that the molecular markers of T cell exhaustion, TIM3, LAG3 and PD-1, are greatly reduced or absent in the cells retrieved from the animals treated with huMNC2-CD28- 1XX CAR T cells. This result is consistent with the idea that the 1XX mutations in CD3-zeta increase CAR T cell persistence in vivo. [00631] After sacrifice, the tumors were excised and analyzed as well. Excised tumors were photographed and weighed (Fig.
  • Fig. 234, Fig. 236, Fig. 238, Fig. 240 weights were recorded. Tumors were then enzymatically dissociated and fluorescent photographs were taken to characterize and quantify the cells that caused the tumor recurrence. Recall that tumors were a heterogeneous population of high antigen expressing cells that were GFP positive and low antigen density cells that were mCherry positive. Red and green fluorescent photographs of the residual tumors show that when tumors have a high percentage of high antigen density cells and a high CAR T cell dose, the all the CAR T cells were able to kill the tumor cells that expressed high levels of the target antigen.
  • Fluorescent photographs taken at two different timepoints showed that for animals implanted with a moderate percentage of high antigen cells and treated with a CAR with wild type CD3-zeta or a CAR with 1XX mutations, the growth rate of low antigen density cells was faster in the animals treated with the CAR with wild type CD3-zeta compared to animals treated with the CAR with the CD3-1XX.
  • the standard CARs showed a faster growth rate o both low and high antigen density tumor cells.
  • a significant problem for the treatment of cancers are the tumor cells that express low levels of tumor-associated antigen, especially with regard to cellular therapies where, to date, the killing of tumor cells has been dependent on the antigen density of the tumor cells.
  • Tumor cells expressing low levels of the target antigen escape CAR T cells as well as engineered CAR NK cells.
  • Essentially all solid tumors are heterogeneous and comprised of cells that express different levels of the target antigen.
  • Fig. 251 shows that in animals that were implanted with 250,000 tumor cells, then treated once with either 2.5M CAR T cells or 250,000 CAR T cells, tumors recur and the timing and degree of recurrence is greater in animals treated with CARs bearing standard CD3z than in animals bearing CD3z with 1XX mutations.
  • the excised tumors were fluorescently photographed at mCherry wavelength and at GFP wavelength.
  • tumor recurrence is minimal for the tumors of animals treated with huMNC2-CD28-1XX.
  • the figure shows that tumor recurrence is dominated by the low antigen expressing cells that are missed by the standard CAR T cells.
  • Fig. 253 and Fig. 256 when tumors expressing low percentage of high antigen expressing cells are coupled with treating with low dose CAR T cells, a combination of CAR T cell exhaustion plus escape of low antigen cells drives tumor resistance.
  • Anti-MUC1* CAR T cells persist longer and stave off T cell exhaustion when the CD3-zeta signaling domain is mutated to slow signaling as in mutating some of the Tyrosines, for example as we have done with the huMNC2-CD28-1XX, see Tables in Fig. 257 – Fig. 282.
  • Excised tumors from the test animals were analyzed by flow cytometry for the presence of human CAR T cells and their expression of exhaustion markers.
  • mice treated with huMNC2-CD28-1XX had an average of 1,516 CAR T cells in the excised tumor, compared to only 196 CAR T cells for the huMNC2-41BB-3z and 395 CAR T cells for the huMNC2-CD28-3z treated mice.
  • the CAR T cells expressed the lowest percentages of exhaustion markers. That means that for tumors with a significant amount of high antigen expressing cells and at high dose of CAR T cells, the mutated CD3z, as in 1XX mutations, gives the CAR T cells an advantage in terms of being able to recognize tumor cells and also being able to stave off exhaustion.
  • Comparison of CAR T cell persistence among CARs, with or without mutated CD3z, is assessed by looking at these same 30% high antigen expressing tumors, but wherein animals were treated with a low dose of CAR T cells: 250,000 CAR T cells and 250,000 tumor cells, i.e.1:1 ratio.
  • the Table of Fig.262 shows that CARs with a standard CD3z signaling domain, administered to animals at low dose have almost no measurable CAR T cells in their tumors after about 70-90 days after CAR T cell injection.
  • CAR T cells with a 1XX mutated CD3z, or similar mutated signaling domain have enhanced ability to recognize and kill tumor cells that express low levels of the target antigen.
  • standard CAR T cells could not recognize nor kill tumors that expressed a low percentage, 7.5%, of high antigen expressing cells when animals were also treated with a low dose of CAR T cells.
  • mice implanted with tumors that were only 7.5% high antigen expressing cells that were treated with low dose CAR T cells (250,000 CAR T cells and 250,000 tumor cells, 1:1 ratio) only the animals treated with huMNC2-CD28-1XX had measurable CAR T cells in their tumors, 841 on average, and those CAR T cells showed almost no signs of exhaustion.
  • CAR T cells Similar results were obtained when cells from the spleens of the animals were analyzed (Fig. 265 – Fig. 273). One striking example is shown in Fig. 273.
  • CAR T cells with the 1XX CD3z domain have enhanced ability to recognize and kill tumor cells that express low levels of the target antigen.
  • CAR T cells bearing 1XX including but not limited to CARs that recognize MUC1*, have improved killing of solid tumor cancers, where tumors are more heterogeneous than blood cancers.
  • CAR T cells bearing 1XX including but not limited to CARs that recognize MUC1*, are far better than standard CAR T cells at preventing tumor recurrence.
  • One aspect of the invention is a method for treating a patient diagnosed with, suspected of having, or at risk of developing a MUC1 positive or MUC1* positive cancer, wherein the patient is administered an effective amount of immune cells that have been transduced with a MUC1* targeting CAR.
  • the immune cells are T cells isolated from a patient, which are then transduced with CARs wherein the targeting head of the CAR binds to MUC1*, and after expansion of transduced T cells, the CAR T cells are administered in an effective amount to the patient.
  • the immune cells are T cells isolated from a patient, which are then transduced with CARs wherein the targeting head of the CAR comprises portions of MNC2, MNE6, 20A10, 3C2B1, 5C6F3, 25E6, 18G12, 28F9, 1E4, B12, B2, B7, B9, 8C7F3, or H11, and after optional expansion of transduced T cells, the CAR T cells are administered in an effective amount to the patient.
  • the antibody fragment of MNC2, MNE6, 20A10, 3C2B1, 5C6F3, or 25E6 is incorporated into a chimeric antigen receptor of a natural killer cell, or NK cell.
  • CARs comprising the MNE6 targeting antibody fragment, and intracellular co-stimulatory domains 41BB and CD3-zeta but having a variety of different extracellular, transmembrane and short cytoplasmic tail all worked in that they specifically killed the targeted cells while stimulating the expansion of the host T cells.
  • the most accurate way of demonstrating antibody specificity is testing the antibody on normal human tissue specimens compared to cancerous tissue specimens. MNC2 and MNE6 were previously shown to specifically bind to MUC1 or MUC1* positive cancer cells.
  • Fig. 10 shows serial sections of breast cancer tissue arrays that were stained with either VU4H5, a commercially available anti- MUC1 antibody that binds to the tandem repeats, or MNC2 that binds to MUC1*.
  • FIGS. 10 and 11 are photographs of breast cancer tissue arrays stained with either VU4H5 which recognizes MUC1-FL (full length) or MNC2 which recognizes cancerous MUC1*. Tissue staining was scored using Allred scoring method which combines an intensity score and a distribution score. Below the photographs of the tissue arrays are color-coded graphs displaying the results. As can be seen, the arrays stained with VU4H5 are very light and many tissues do not stain at all despite the published reports that MUC1 is aberrantly expressed on over 96% of all breast cancers as evidenced by nucleic acid based diagnostics. In contrast, the arrays stained with MNC2 are very dark (red versus yellow or white in graph).
  • Fig. 19 shows photographs of normal small intestine and cancerous small intestine tissues stained with humanized MNE6-scFv-Fc biotinylated anti-MUC1* antibody at 5 ug/mL, then stained with a secondary streptavidin HRP antibody.
  • A) is a normal small intestine tissue.
  • B) is small intestine cancer from patient as denoted in the figure.
  • C,D are photographs of the corresponding serial sections that were stained with the secondary antibody alone. Fig.
  • FIG. 20 shows photographs of normal small intestine tissues stained with humanized MNE6-scFv-Fc anti-MUC1* antibody at 50 ug/mL, then stained with a secondary goat-anti-human HRP antibody.
  • A-D are normal small intestine tissue.
  • E-H are photographs of the corresponding serial sections that were stained with the secondary antibody alone.
  • Fig. 21 shows photographs of cancerous small intestine tissues stained with humanized MNE6-scFv-Fc anti-MUC1* antibody at 50 ug/mL, then stained with a secondary goat-anti-human HRP antibody.
  • A-D are cancerous small intestine tissue from a patient as denoted in figure.
  • E-H are photographs of the corresponding serial sections that were stained with the secondary antibody alone.
  • FIG. 22 shows photographs of cancerous small intestine tissues stained with humanized MNE6-scFv-Fc anti- MUC1* antibody at 50 ug/mL, then stained with a secondary goat-anti-human HRP antibody.
  • A-D are cancerous small intestine tissue from a patient as denoted in figure.
  • E-H are photographs of the corresponding serial sections that were stained with the secondary antibody alone.
  • Fig. 23 shows photographs of normal colon tissues stained with humanized MNE6-scFv-Fc anti-MUC1* antibody at 50 ug/mL, then stained with a secondary goat-anti- human HRP antibody.
  • A-D are normal colon.
  • E-H are photographs of the corresponding serial sections that were stained with the secondary antibody alone.
  • FIG. 24 shows photographs of colon cancer tissues stained with humanized MNE6-scFv-Fc anti-MUC1* antibody at 50 ug/mL, then stained with a secondary goat-anti-human HRP antibody.
  • A-D are colon cancer tissue from a metastatic patient as denoted in figure.
  • E-H are photographs of the corresponding serial sections that were stained with the secondary antibody alone.
  • Fig. 25 shows photographs of colon cancer tissues stained with humanized MNE6-scFv-Fc anti- MUC1* antibody at 50 ug/mL, then stained with a secondary goat-anti-human HRP antibody.
  • A-D are colon cancer tissue from a Grade 2 patient as denoted in figure.
  • E-H are photographs of the corresponding serial sections that were stained with the secondary antibody alone.
  • FIG. 26 shows photographs of colon cancer tissues stained with humanized MNE6-scFv-Fc anti- MUC1* antibody at 50 ug/mL, then stained with a secondary goat-anti-human HRP antibody.
  • A-D are colon cancer tissue from a metastatic patient as denoted in figure.
  • E-H are photographs of the corresponding serial sections that were stained with the secondary antibody alone.
  • Fig. 27 shows photographs of prostate cancer tissues stained with humanized MNE6-scFv-Fc anti-MUC1* antibody at 50 ug/mL, then stained with a secondary goat-anti- human HRP antibody.
  • A-D are prostate cancer tissue from a patient as denoted in figure.
  • E-H are photographs of the corresponding serial sections that were stained with the secondary antibody alone.
  • FIG. 28 shows photographs of prostate cancer tissues stained with humanized MNE6-scFv-Fc anti-MUC1* antibody at 50 ug/mL, then stained with a secondary goat-anti- human HRP antibody.
  • A-D are prostate cancer tissue from a patient as denoted in figure.
  • E-H are photographs of the corresponding serial sections that were stained with the secondary antibody alone.
  • Fig. 29 shows photographs of prostate cancer tissues stained with humanized MNE6-scFv-Fc anti-MUC1* antibody at 50 ug/mL, then stained with a secondary goat-anti- human HRP antibody.
  • A-D are prostate cancer tissue from a patient as denoted in figure.
  • E-H are photographs of the corresponding serial sections that were stained with the secondary antibody alone.
  • One aspect of the invention is a method for treating a patient diagnosed with, suspected of having, or at risk of developing a MUC1 positive or MUC1* positive cancer, wherein a specimen is obtained from the patient’s cancer and is tested for reactivity with an antibody that binds to PSMGFR SEQ ID NO:2, or more specifically to the N-10 peptide (SEQ ID NO:3), or yet more specifically binds to N-10 peptide (SEQ ID NO:3), but does not bind to C-10 peptide (SEQ ID NO:825).
  • the patient is then treated with an scFv, scFv-Fc or CAR T that comprises antibody variable fragments from the antibody that reacted with their cancer specimen or can be chosen from among MNC2, MNE6, 20A10, 3C2B1, 5C6F3, 25E6, 18G12, 28F9, 1E4, B12, B2, B7, B9, 8C7F3, or H11.
  • an scFv, scFv-Fc or CAR T that comprises antibody variable fragments from the antibody that reacted with their cancer specimen or can be chosen from among MNC2, MNE6, 20A10, 3C2B1, 5C6F3, 25E6, 18G12, 28F9, 1E4, B12, B2, B7, B9, 8C7F3, or H11.
  • Another aspect of the invention is a method for treating a patient diagnosed with, suspected of having, or at risk of developing a MUC1 positive or MUC1* positive cancer, wherein a specimen is obtained from the patient’s cancer and is tested for reactivity with MNC2, MNE6, 20A10, 3C2B1, 5C6F3, 25E6, 18G12, 28F9, 1E4, B12, B2, B7, B9, 8C7F3, or H11; the patient is then treated with the antibody, antibody fragment, scFv, scFv-Fc-mut, BiTE or CAR T that comprises portions of the antibody that reacted with their cancer specimen.
  • MUC1* the transmembrane cleavage product, not full-length MUC1
  • the growth factors that activate MUC1* bind to ectopic sites that are only exposed after cleavage and release of the tandem repeat portion of MUC1.
  • Antibodies of the invention like the activating growth factors, cannot bind to full-length MUC1. FACS analysis clearly shows that anti- MUC1* antibody MNC2 is unable to bind to HCT-116, MUC1 negative cells (Fig.
  • MUC1 can be cleaved to MUC1* by more than one cleavage enzyme and that the site of cleavage affects its fold and consequently affects which monoclonal antibody is able to recognize that form of MUC1*.
  • Different cancer cells or cancerous tissues express different cleavage enzymes.
  • cleavage enzyme inhibitors were tested on different cancer cell lines and found that an inhibitor that inhibits cleavage of MUC1 in one cancer cell line did not inhibit its cleavage in another cancer cell line. Similarly, PCR experiments showed that cleavage enzymes are expressed at different levels in different cells or cell lines. For example, hematopoietic stem cells of the bone marrow express a MUC1* that is recognized by monoclonal antibody MNC3 but not MNE6 or MNC2 (Fig. 39).
  • DU145 prostate cancer cells and T47D breast cancer cells are inhibited by the Fabs of MNC2 and MNE6 but not by the Fabs of MNC3 or MNC8, indicating that the cancer cell lines express a MUC1* that is recognized by MNE6 and MNC2 but not by MNC3 or MNC8 (Fig. 42).
  • PCR experiments show that CD34 positive cells of the bone marrow express about 2,500-times more MMP2 and about 350-times more ADAM28 than T47D breast cancer cells, while DU145 prostate cancer cells express about 2,000-times more ADAM TS16, about 400-times more MMP14 and about 100-times more MMP1 than T47D breast cancer cells (Fig. 43 and Fig. 44).
  • T47D breast cancer cells express about 80-times more MMP9 than the bone marrow cells and about twice as much as DU145 prostate cancer cells.
  • Various cleavage enzyme inhibitors were tested for their ability to inhibit cleavage in different kinds of cancer cells.
  • a second factor which may be a cleavage enzyme, an antibody, a cytokine, or a second CAR, and a CAR are transduced into the same T cell.
  • the second factor is on an inducible promoter such that its expression is activated when the CAR engages the targeted cancer cells.
  • the expression of the second factor is controlled by an inducible promoter.
  • expression of the second factor is induced when the immune cell is activated, for example when it recognizes or engages its target.
  • a T cell is transfected or transduced with a second factor whose expression is induced when the T cell recognizes a target cancer cell.
  • One way to do this is to induce expression of the second factor when, or shortly after, an NFAT protein is expressed or translocated to the nucleus.
  • a sequence derived from an NFAT promoter region is put upstream of the gene for the second factor.
  • the NFAT protein may be NFAT1 also known as NFATc2, NFAT2 also known as NFATc or NFATc1, NFAT3 also known as NFATc4, NFAT4 also known as NFATc3, or NFAT5.
  • the NFAT is NFATc1, NFATc3 or NFATc2.
  • the NFAT is NFAT2 also known as NFATc1.
  • SEQ ID NO:646 shows nucleic acid sequence of the upstream transcriptional regulatory region for NFAT2.
  • the promoter sequence for NFAT gene may include the nucleic acid sequence of SEQ ID NO:781-783 or SEQ ID NO:815 as examples, but it can be seen that the optimal sequence or minimal sequence for expression of the second factor may be obtained by making fragments, extensions or mutations of the promoter and testing for the strength of the promoter with respect to expression of the second factor.
  • the transcriptional regulatory region for NFAT2 is engineered upstream of the gene encoding the second factor, which if for cleavage enzyme MMP9 (SEQ ID NO:647) or the catalytic sub-unit of MMP9 (SEQ ID NO:648).
  • the NFAT is NFATc3 and the promoter sequence of NFATc3 includes nucleic acid sequences from SEQ ID NO:816.
  • the transcriptional regulatory region for NFATc3 is engineered upstream of the gene encoding the second factor, here as an example is MMP9.
  • the NFAT is NFATc2.
  • SEQ ID NO:817-818 shows nucleic acid sequence of the upstream transcriptional regulatory region for NFATc2.
  • the transcriptional regulatory region for NFATc2 is engineered upstream of the gene encoding the second factor, which may be cleavage enzyme MMP9 (SEQ ID NO:647) or the catalytic sub-unit of MMP9 (SEQ ID NO:648).
  • MMP9 cleavage enzyme
  • SEQ ID NO:648 the catalytic sub-unit of MMP9
  • Another method for having the expression of the second factor induced when the T cell or CAR T cell is activated is to have the gene for the second factor on an inducible promoter where the NFAT protein itself binds to and induces transcription of the second factor.
  • an NFAT response element NFAT RE
  • the NFAT may bind to its responsive element upstream of the second factor alone or as part of a complex.
  • the NFAT protein may be NFATc1, NFATc2, NFATc3, NFATc4, or NFAT5.
  • the NFAT protein is NFAT2 aka NFATc1, aka NFATc.
  • the gene of the second factor or fragment thereof is cloned downstream of an NFAT-response element (SEQ ID NO:649), which may be repeats of the response element (SEQ ID NO:650) and CMV minimal promoter (mCMV) (SEQ ID NO:651) to induce expression of second factor by NFAT protein.
  • the NFAT response element may include nucleic acid sequence of NFAT consensus sequence (SEQ ID NO:804).
  • the NFAT response element may include the nucleic acid sequence of SEQ ID NOS:805-814 as examples, but it can be seen that the optimal sequence or minimal sequence for expression of the second factor may be obtained by making fragments, extensions or mutations of the responsive element nucleic acid and testing for the strength of the responsive element with respect to expression of the second factor.
  • the enhancer region of Foxp3 also contains NFAT response elements within the 120-bp from 2079 to 2098 (SEQ ID NO:821).
  • the NFAT response element may include nucleic acid NFAT consensus sequence of (5’-cattttttccat-3’) (SEQ ID NO:819) or (5’-tttttcca-3’) (SEQ ID NO:820), which NFATc1 specifically binds to (Xu et al., Closely related T-memory stem cells correlate with in vivo expansion of CAR. CD19-T cells and are preserved by IL-7 and IL-15, Blood 2014 123:3750-3759), or repeats thereof.
  • the NFAT response elements may also be separated by nucleic acid spacer sequences.
  • NFAT responsive elements may exist and may further be discovered, and a skilled artisan in the art when directed to determine NFAT responsive element may do so by carrying out molecular biological assays to obtain it given the guidance of at least the responsive elements as set forth as SEQ ID NOS: 804-814 albeit as only mere examples.
  • the cleavage enzyme that is downstream of the NFAT-response element and CMV minimal promoter is MMP9 (SEQ ID NO:652).
  • the cleavage enzyme is a catalytic sub-unit of MMP9 (SEQ ID NO:653).
  • NFATs 1-4 are regulated by the calcineurin pathway
  • potential toxicities that may arise in a patient can be stopped by treatment with an immunosuppressive agent such as FK506, Cyclosporin, Cyclosporin A, or Tacrolimus that block calcineurin activity and inhibit NFAT translocation to the nucleus.
  • an immunosuppressive agent such as FK506, Cyclosporin, Cyclosporin A, or Tacrolimus that block calcineurin activity and inhibit NFAT translocation to the nucleus.
  • the T cell transduced or transfected with a cleavage enzyme on an inducible promoter may also be transfected or transduced with a CAR that recognizes a protein or molecule on the cancer cell.
  • the cleavage enzyme is one that is able to cleave MUC1 full-length and the CAR bears an antibody fragment that directs it to MUC1* on the surface of cancer cells.
  • FIGs. 36A-36D show Western blots and FACS analysis showing that HCT-MUC1- 41TR is 95% positive for full-length MUC1 and only 5-10% positive for the cleaved form, MUC1*.
  • HCT-MUC1-41TR cells were incubated with MMP9 at varying concentrations and then assayed by immunofluorescence to measure binding of MNC2 monoclonal antibody to the resultant cells. As can be seen in Figs. 37A-37C binding of MNC2 increased as the concentration of MMP9 added to the cells increased.
  • MMP9 cleaves MUC1 to a form that is recognized by MNC2.
  • the human cancer tissue array studies we performed (Fig. 30A-30F, Fig. 31A-31F, Fig. 32A-32F, Fig. 33A-33F) show that MNC2 recognizes the form of cleaved MUC1 that is present on cancerous tissue but not on healthy cells or tissues (Fig. 34A-34I).
  • MNC2 does not recognize the form of cleaved MUC1 that is expressed on healthy hematopoietic stem cells of the bone marrow (Figs. 39- 41).
  • an immune cell is transduced with both a CAR to target the immune cell to the tumor, and a cleavage enzyme.
  • the CAR and the cleavage enzyme can be encoded on the same plasmid or on two different plasmids.
  • the cleavage enzyme is on an inducible promoter.
  • expression of the cleavage enzyme is induced by a protein that is expressed when the immune cell is activated.
  • expression of the cleavage enzyme is induced by an NFAT protein.
  • expression of the cleavage enzyme is induced by NFATc1.
  • the cleavage enzyme is induced when one of the NFAT proteins binds to an NFAT response element that is inserted upstream of the gene for the cleavage enzyme or a catalytically active fragment thereof.
  • the cleavage enzyme is MMP9 or a fragment of MMP9 that is catalytically active.
  • the cleavage enzyme is MMP9 (SEQ ID NO:643).
  • the invention anticipates overcoming this problem by co-expressing the cleavage enzyme with its activator.
  • the cleavage enzyme is MMP9 and the co-activator is MMP3.
  • the cleavage enzyme is expressed in a form that is already active, for example by expressing a fragment of the cleavage enzyme that still has catalytic function.
  • the cleavage enzyme is an MMP9 fragment that is catalytically active.
  • MMP9 catalytic fragment is given as SEQ ID NO:645. [00655] MMP9, which must be activated by MMP3, is overexpressed in a large percentage of solid tumors.
  • MNC2 anti-MUC1* monoclonal antibody recognizes MUC1 after it is cleaved by MMP9.
  • APMA is a biochemical that activates MMPs.
  • the MUC1 and MUC1* expressing cells were stained with a red dye, CMTMR.
  • T47D MUC1 positive tumor cells were incubated with a recombinant catalytic domain of MMP9 (Enzo Life Sciences, Inc., Farmingdale, NY) at either 100ng/mL or 500ng/mL.
  • Fig. 48 shows an xCelligence graph of T47D breast cancer cells in co-culture with either untransduced T cells, as a control, or huMNC2-CAR44 T cells over a 45 hour period. After 18 hours of cancer cell growth, a catalytic sub-unit MMP9 was added to some of the cells. At 25 hours, T cells were added.
  • huMNC2-CAR44 T cell killing is greatly improved when the T47D cells are pre-incubated with cleavage enzyme MMP9.
  • target cancer cells which are adherent, are plated onto electrode array plates.
  • Adherent cells insulate the electrode and increase the impedance.
  • the number of adherent cancer cells is directly proportional to impedance.
  • T cells are not adherent and do not contribute to impedance. Therefore, increasing impedance reflects growth of cancer cells and decreasing impedance reflects killing of cancer cells.
  • Prostate cancer cell line DU145 expresses both MUC1 and MUC1* but at a much lower level of expression than T47D cells.
  • DU145 cells are efficiently killed by anti-MUC1* CAR T cells in the presence or absence of a cleavage enzyme.
  • Fig. 49 shows an xCelligence graph of DU145 prostate cancer cells in co-culture with either untransduced T cells, as a control, or huMNC2-CAR44 T cells over a 45 hour period. After 18 hours of cancer cell growth, a catalytic sub-unit MMP9 was added to some of the cells. At 25 hours, T cells were added. As can be seen, huMNC2-CAR44 T cell killing of low density MUC1/MUC1* positive cancer cells is not affected by pre-incubation with cleavage enzyme MMP9.
  • DU145 cancer cells express a significantly lower amount of MUC1 which includes the full-length form as well as MUC1*.
  • the lower density of full-length MUC1 does not sterically hinder T cell access to the membrane proximal MUC1*.
  • DU145 cells represent an early stage cancer that expresses both full length and cleaved MUC1 but at lower levels so that T cell access is not sterically hindered.
  • T47D cells represent mid-stage cancers that express high levels of both MUC1 and MUC1*, wherein the density of MUC1 full-length sterically hinders access of T cells to the tumor.
  • HCT-MUC1* cells are a MUC1 negative cell line that has been stably transfected with MUC1* 45 , and they represent late stage cancer cells. It is significant that MUC1 cleaved to MUC1* by MMP9 is recognized by the anti-MUC1* antibody MNC2, which is the targeting head of the CAR. Immune cell access to tumor antigens on the cancer cell surface can be sterically hindered by the presence of bulky extra cellular domain proteins or other obstructing elements also known as the tumor micro-environment. The aforementioned serve as an example that can be extended to improve the efficacy of CAR T therapies that target other tumor antigens.
  • an immune cell is transfected or transduced with both a CAR comprising an antibody fragment that targets a tumor antigen and a cleavage enzyme.
  • an immune cell is transfected or transduced with both a CAR comprising an antibody fragment that targets a tumor antigen and a cleavage enzyme that cleaves a tumor antigen to a form recognized by the antibody fragment of the CAR.
  • an immune cell is transfected or transduced with both a CAR comprising an antibody fragment that targets a tumor antigen and a cleavage enzyme that cleaves a tumor antigen to a form recognized by the antibody fragment of the CAR, wherein the antibody fragment of the CAR recognizes MUC1* extra cellular domain and the cleavage enzyme cleaves MUC1 to MUC1*.
  • an immune cell which may be a T cell or an NK cell, is transfected or transduced with a CAR comprising an antibody fragment derived from MNC2, MNE6, MNC3 or MNC8 and a cleavage enzyme chosen from the group comprising MMP1, MMP2, MMP3, MMP7, MMP8, MMP9, MMP11, MMP12, MMP13, MMP14, MMP16, ADAM9, ADAM10, ADAM17, ADAM 19, ADAMTS16, ADAM28 or a catalytically active fragment thereof.
  • the immune cell is derived from a stem cell that has been directed to differentiate into an immune cell type in vitro.
  • a CAR containing sequences of the antibody are expressed in a stem cell, which then may be differentiated into an immune cell.
  • the immune cell is a T cell.
  • the immune cell is an NK cell.
  • a person diagnosed with cancer or at risk of developing cancer is administered a sufficient amount of an immune cell transduced with both a CAR and a cleavage enzyme.
  • a person diagnosed with cancer or at risk of developing cancer is administered a sufficient amount of an immune cell transduced with both a CAR and a cleavage enzyme, wherein the cleavage enzyme is on an inducible promoter that is activated by proteins that are expressed when the immune cell becomes activated.
  • a person diagnosed with cancer or at risk of developing cancer is administered a sufficient amount of an immune cell transduced with both a CAR and a cleavage enzyme, wherein the cleavage enzyme is on an inducible promoter that is activated by one or more NFAT.
  • the NFAT is NFATc1.
  • the NFAT is NFATc3.
  • the NFAT is NFATc2.
  • the extra cellular domain of the CAR comprises a fragment of an anti- MUC1* antibody.
  • the anti-MUC1* antibody is MNC2scFv or a humanized form of MNC2scFv.
  • the anti-MUC1* antibody is MNE6scFv or a humanized form of MNE6scFv.
  • the immune cell can be a T cell, an NK cell, a mast cell, or a dendritic cell.
  • the immune cell is derived from a stem cell that has been directed to differentiate to that immune cell type in vitro.
  • a CAR containing sequences of the antibody are expressed in a stem cell, which then may be differentiated into an immune cell.
  • the immune cell is a T cell.
  • the immune cell is an NK cell.
  • the present invention be limited to one or two specific methods of having expression of a cleavage enzyme induced by an activated T cell.
  • expression of the cleavage enzyme is induced by constructing a plasmid where the cleavage enzyme gene is inserted downstream of an IL-2 promoter sequence or downstream of an IL-2 response element, then inserting the plasmid into an immune cell.
  • expression of the cleavage enzyme is induced by constructing a plasmid where the cleavage enzyme gene is inserted downstream of a Calcineurin promoter sequence or downstream of a Calcineurin response element, then inserting the plasmid into an immune cell and then administering to a patient for the treatment or prevention of cancers.
  • a plasmid where the cleavage enzyme gene is inserted downstream of a Calcineurin promoter sequence or downstream of a Calcineurin response element, then inserting the plasmid into an immune cell and then administering to a patient for the treatment or prevention of cancers.
  • drug-inducible plasmids that can be used to induce expression of the cleavage enzyme or used to stop expression induced by an element of an activated T cell.
  • These drug inducible systems may include tetracycline-inducible systems, Tet-on, Tet-off, tetracycline response elements, doxycycline, tamoxifen inducible systems, ecdysone inducible systems and the like. [00662] It is not intended that the present invention be limited to one or two specific promoters used in the plasmids encoding the CARs or inducible cleavage enzymes.
  • promoters can be interchanged including SV40, PGK1, Ubc, CAG, TRE, UAS, Ac5, polyhedron, CaMKIIa, GAL1, GAL10, TEF1, GDS, ADH1, CaMV35S, Ubi, H1 and U6.
  • Another solution to the problem of steric hindrance of CAR T cell access, caused by bulky cell surface proteins such as MUC1-FL, is to increase the length of the linker region of the CAR that is expressed by the T cell.
  • the length of the extracellular linker region between the transmembrane portion and the antibody fragment is about 45-50 amino acids in length.
  • variable regions of antibodies of the invention, or fragments thereof, can be incorporated into molecular formats wherein one molecule is able to simultaneously bind to at least two different antigens.
  • the stability of these various antibody-like molecules can be increased by the introduction of Cysteines for the formation of disulfide bonds.
  • the stability of antibodies of the invention as well as of various antibody-like molecules, which may be multi-specific can be increased by the introduction of mutations as more fully described in Beckman, US9708388B2, which reference is incorporated by reference herein in its entirety, but in particular with respect to disclosures of making of bispecific antibodies and fragments of antibodies that are bispecific or multispecific.
  • the invention contemplates incorporating variable regions, or fragments thereof, of antibodies of the invention in combination with other antibodies having other binding specificities, or fragments thereof, into a variety of antibody-like formats including but not limited to the following.
  • bispecific antibodies which may or may not include an Fc region.
  • Bispecific antibodies that contain at least one Fc region will have a higher molecular weight and an extended half-life in the body.
  • variable regions, or fragments thereof derived from antibodies with yet other binding specificities are appended to the N- or C-terminus of the IgG scaffold to yield a tetravalent, multi-specificity antibody-like molecule.
  • Combinations of variable regions, or their fragments, of antibodies with diverse binding specificities, which may be incorporated into scFvs, can be appended to an IgG scaffold or other scaffold to yield multi-valent, multi- specificity antibody-like molecules.
  • Antibodies of the invention can be incorporated into mini-antibodies wherein scFvs are fused to the C-terminus of the CH3 portion or hinge region of an antibody Fc region.
  • Divalent (or bivalent) single-chain variable fragments (di-scFvs, bi- scFvs) can be engineered by linking two scFvs. This can be done by producing a single peptide chain with two V H and two V L regions, yielding tandem scFvs.
  • Another possibility is the creation of scFvs with linker peptides that are too short for the two variable regions to fold together (about five amino acids), forcing scFvs to dimerize. This type is known as diabodies.
  • Diabodies have been shown to have dissociation constants up to 40-fold lower than corresponding scFvs, meaning that they have a much higher affinity to their target. Consequently, diabody drugs could be dosed much lower than other therapeutic antibodies and are capable of highly specific targeting of tumors in vivo. Still shorter linkers (one or two amino acids), and optional addition of disulfide bonds, lead to the formation of trimers, so- called triabodies or tribodies. Tetrabodies and higher order multimers have also been produced. They exhibit an even higher affinity to their targets than diabodies. [00666] Other formats of a bispecific antibody-like molecules are bispecific tandem di- scFvs and bispecific T cell engagers, known as BiTEs (BiTE antibody constructs).
  • BiTEs are fusion proteins consisting of two scFvs of different antibodies, on a single peptide chain of about 55 kilodaltons.
  • one of the binding arms binds to a molecule on a T cell, such as the CD3 receptor, and the other binding arm binds to a tumor cell via a tumor specific molecule, such as aberrantly expressed MUC1*.
  • All of these formats can be composed from one or more variable fragments of antibodies of the invention, with specificity for at least two different antigens, to generate multi-valent and multi-specific antibody-like molecules.
  • variable domain fragment derived from a first antibody binds to a first antigen on a first surface and a variable domain fragment derived from a second antibody binds to a second antigen on a second surface, wherein at least one of the surfaces may be the surface of a cell.
  • at least one of the variable domain fragments comprising a multi-valent, multi-specific antibody-like molecule binds to an antigen that is not associated with a surface.
  • the antigen that is not associated with a surface is a cytokine.
  • bispecific antibody As an example of how antibodies of the invention can be incorporated into bispecific antibodies, we constructed a bispecific antibody using a knob-in-hole, also known as KIH (Spiess et al. Molecular Immunology 67, 95-106 (2015)), format.
  • a first arm of the antibody is the humanized anti-MUC1* antibody 20A10, also known as hu20A10, with a 14616 framework region; the second arm of the antibody is either the anti- CD3 antibody OKT3 or 12F6, which both bind to the same epitope on human T cells.
  • the resultant bispecific antibodies are referred to here as 20A10-OKT3-BiTE and 20A10-12F6- BiTE.
  • the bispecific antibodies are added at various concentrations to cells in culture wherein both human T cells and MUC1* positive cancer cells are present.
  • the cancer cells are T47D breast cancer cells and in the other case a MUC1* negative line HCT-116 colon cancer cells have been transduced to express MUC1*, called HCT-MUC1*.
  • a MUC1* negative line HCT-116 colon cancer cells have been transduced to express MUC1*, called HCT-MUC1*.
  • the addition of either bispecific antibody mediated the joining together of the T cells and the MUC1* positive cancer cells as evidenced by a bispecific dose-dependent cell clustering. Two control experiments were performed.
  • bispecific antibody In one control, no bispecific antibody is added, but both T cells and MUC1* cancer cells are present. No clustering is observed. In another control, bispecific antibody is added to MUC1* positive cancer cells, but no T cells are present.
  • the second arm of the bispecific antibody was an antibody that recognizes CD3 on T cells.
  • the invention it is not intended that the invention be limited to bispecific antibodies where one arm binds to MUC1* and the other binds a T cell.
  • a person skilled in the art could readily substitute the second arm of the bispecific antibody with an antibody that binds to an NK cell, or another receptor on a cancer cell for increased affinity.
  • a person diagnosed with a MUC1* positive cancer, or at risk of developing a MUC1* positive cancer is treated with an effective amount of a bispecific antibody that simultaneously binds to a MUC1* positive cancer cell and a human T cell.
  • the bispecific antibody is hu20A10-OKT3-BiTE.
  • the bispecific antibody is hu20A10-12F6-BiTE.
  • the bispecific antibody is huMNC2-OKT3-BiTE. In another aspect of the invention, the bispecific antibody is huMNC2-12F6-BiTE.
  • Another aspect of the invention is a method for treating a patient diagnosed with, suspected of having, or at risk of developing a MUC1 positive or MUC1* positive cancer, wherein the patient is administered an effective amount of one of the multi-valent, multi- specific antibody-like molecules described here wherein at least one of the variable domains, or fragment thereof, is derived from an antibody that binds to PSMGFR (SEQ ID NO:2), or more specifically to N-10 peptide (SEQ ID NO:3), or more specifically to N-19 peptide (SEQ ID NO:4), or N-23 peptide (SEQ ID NO:5), or N-26 peptide (SEQ ID NO:6), or N-30 peptide (SEQ ID NO:7) or still more specifically that binds to a fragment of the PSMGFR
  • the antibody variable fragment that binds to MUC1* comprises portions of MNC2, MNE6, 20A10, 3C2B1, 5C6F3, 25E6, 18G12, 28F9, 1E4, B12, B2, B7, B9, 8C7F3, or H11.
  • At least one of the antibody variable fragments comprising a multi-valent, multi-specific antibody-like molecule that binds to MUC1* comprises portions of MNC2, MNE6, 20A10, 3C2B1, 5C6F3, 25E6, 18G12, 28F9, 1E4, B12, B2, B7, B9, 8C7F3, or H11 and at least one other antibody variable fragment binds to an antigen on an immune cell, which may be a T cell or NK cell.
  • Another aspect of the invention is a method for treating a patient diagnosed with, suspected of having, or at risk of developing a MUC1 positive or MUC1* positive cancer, wherein the patient is administered an effective amount of a BiTE wherein one antibody variable fragment of the BiTE binds to a T cell surface antigen and the other antibody variable fragment of the BiTE binds to PSMGFR (SEQ ID NO:2), or more specifically to N- 10 peptide (SEQ ID NO:3), or more specifically to N-19 peptide (SEQ ID NO:4), or N-23 peptide (SEQ ID NO:5), or N-26 peptide (SEQ ID NO:6), or N-30 peptide (SEQ ID NO:7) or still more specifically that binds to a fragment of the PSMGFR peptide wherein said binding depends on the presence of the amino acids FPFSAQSGA (SEQ ID NO:10).
  • the antibody variable fragment of the BiTE that binds to MUC1* comprises portions of MNC2, MNE6, 20A10, 3C2B1, 5C6F3, 25E6, 18G12, 28F9, 1E4, B12, B2, B7, B9, 8C7F3, or H11.
  • MUC1* peptides including PSMGFR (SEQ ID NO:2), or most or all of N-10 peptide are used in adoptive T cell approaches.
  • a patient’s T cells are exposed to the MUC1* peptides and through various rounds of maturation, the T cells develop MUC1* specific receptors.
  • the adapted T cells are then expanded and administered to the donor patient who is diagnosed with, suspected of having, or is at risk of developing a MUC1* positive cancer.
  • a series of CARs were also made that had MNC2 and humanized MNC2 as the extra cellular, targeting head of the CAR.
  • the constructs for these CARs were inserted into a plasmid that was then inserted into a Lenti viral vector.
  • Human T cells were then transduced with the lenti viral vector carrying the MNC2 CARs and huMNC2 CARs.
  • MNC2-scFv-CARs that were mouse sequence or humanized were generated.
  • the CAR comprised huMNC2-scFv-short hinge region-transmembrane domain derived from CD8-short intracellular piece-4-1BB-3zeta.
  • the transmembrane domain was derived from CD4 transmembrane sequence.
  • the intracellular co- stimulatory domain was CD28-3zeta.
  • the intracellular co-stimulatory domain was CD28-4-1BB-3zeta.
  • FIG. 45-47 show photographs of MUC1* positive T47D breast cancer cells that were either stably transfected with mCherry or dyed with CMTMR, so are red, which were co-cultured with either human T cells without a CAR or human T cells transduced with huMNC2-scFv-CAR44, or with huMNC2-scFv-CAR50.
  • the CAR T cells are clear.
  • T cells recognize and cluster target cells, they overexpress perforin and granzyme B. Together these two molecules activate a cell death pathway in the targeted cell. It is thought that the perforin makes a hole in the target cell into which the T cell injects granzyme B which then activates apoptotic proteases, causing the target cell to lyse.
  • perforin makes a hole in the target cell into which the T cell injects granzyme B which then activates apoptotic proteases, causing the target cell to lyse.
  • IFN-g interferon gamma
  • IL-2 interleukin-2
  • CAR T cells are co-cultured with target cells and after an incubation period, the conditioned media is assayed by ELISA to detect secreted IFN-g and IL-2.
  • the targeting head of the CAR was either huMNC2 or huMNE6
  • these experiments were performed with huMNC2-CAR44 T cells and huMNE6-CAR44 T cells in co-culture with MUC1* positive cancer cells and normal cells.
  • Table 1 details the MUC1 positive normal or primary cells that were tested.
  • Table 1 Normal Cell Lines and Primary Cells
  • Figure 50 is a graph of PCR measurement of the various cell lines tested, wherein mRNA levels of MUC1 are measured.
  • the cancer cell lines that were tested in these assays were HCT-MUC1* and T47D breast cancer cells. These cells were co-cultured with huMNC2-CAR44 human T cells. Co-culture of huMNC2-CAR44 T cells with the cancer cells induced the CAR T cells to secrete large amounts of IFN-g and IL-2 into the surrounding media, yet co-culture with the MUC1 positive normal cells induced no secretion of the cytokines (Fig. 51 and Fig. 52).
  • the normal cells were assayed for signs of cell death, which could have been induced by the CAR T cells if the antibody targeting head were not extremely cancer- specific.
  • the cells were incubated with a cell death marker, then assayed by FACS.
  • huMNC2-CAR44 T cells induced no cell death in the normal cells (Fig.53A-53J).
  • FACS is not the best method for tracking T cell induced cell killing because the T cells lyse the target cell.
  • the xCELLigence instrument uses electrode arrays upon which cancer cells are plated.
  • the adherent cancer cells insulate the electrode and so cause an increase in impedance as they grow.
  • T cells are not adherent and remain in suspension so do not contribute to insulation of the electrode which would increase impedance.
  • the T cells or CAR T cells kill the cancer cells on the electrode plate, the cancer cells ball up and float off as they die, which causes the impedance to decrease.
  • Figs. 55A-55H show the cytotoxic effect of huMNC2-CAR44 T cells on MUC1* positive DU145 prostate cancer cells as measured by a variety of assays.
  • Fig. 55A is a fluorescent photograph of untransduced T cells co-cultured with the prostate cancer cells, wherein granzyme B is stained with a red fluorophore.
  • Fig. 55A is a fluorescent photograph of untransduced T cells co-cultured with the prostate cancer cells, wherein granzyme B is stained with a red fluorophore.
  • Fig. 55C is a fluorescent photograph of huMNC2-CAR44 T cells co-cultured with the prostate cancer cells, wherein granzyme B is stained with a red fluorophore.
  • Fig. 55D is the DAPI and granzyme B merge.
  • Fig. 55E is a FACS scan for fluorescently labeled granzyme B for untransduced T cells incubated with the cancer cells.
  • Fig. 55F is a FACS scan showing a positive increase in fluorescently labeled granzyme B for huMNC2-CAR44 T cells incubated with the cancer cells.
  • Fig. 55G is a graph of the mean fluorescent intensity. Fig.
  • Fig. 55H is an xCELLigence scan tracking the real-time killing of DU145 cancer cells by huMNC2-CAR44 T cells (blue trace) but not by untransduced T cells (green).
  • Figs. 56A-56H show the cytotoxic effect of huMNC2-CAR44 T cells on MUC1* positive CAPAN-2 pancreatic cancer cells as measured by a variety of assays.
  • Fig. 56A is a fluorescent photograph of untransduced T cells co-cultured with the pancreatic cancer cells, wherein granzyme B is stained with a red fluorophore.
  • Fig. 56B is the DAPI and granzyme B merge.
  • FIG. 56C is a fluorescent photograph of huMNC2-CAR44 T cells co-cultured with the pancreatic cancer cells, wherein granzyme B is stained with a red fluorophore.
  • Fig. 56D is the DAPI and granzyme B merge.
  • Fig. 56E is a FACS scan for fluorescently labeled granzyme B for untransduced T cells incubated with the cancer cells.
  • Fig. 56F is a FACS scan showing a positive increase in fluorescently labeled granzyme B for huMNC2-CAR44 T cells incubated with the cancer cells.
  • Fig. 56G is a graph of the mean fluorescent intensity. Fig.
  • Fig. 56H is an xCELLigence scan tracking the real-time killing of CAPAN-2 cancer cells by huMNC2-CAR44 T cells (blue trace) but not by untransduced T cells (green).
  • Figs. 57A-57C show xCELLigence scans tracking the real-time killing of MUC1* positive cancer cells, but not MUC1* negative cells, by huMNC2-CAR44 T cells.
  • Fig. 57A shows that huMNC2-CAR44 T cells effectively kill HCT colon cancer cells that have been stably transfected with MUC1*.
  • huMNC2-CAR44 T cells have almost no effect on HCT-MUC1-41TR, which is a MUC1 negative cancer cell that has been stably transfected with a MUC1 full-length. In this cell line only about 10% of the cell have MUC1 cleaved to MUC1*.
  • Fig. 57C shows that huMNC2-CAR44 T cells have no effect on HCT-116 cells, which is a MUC1 negative colon cancer cell line.
  • huMNC2-scFV-CAR44 transduced into human T cells effectively kill MUC1* positive cancer cells.
  • MNC2-scFV or huMNC2-scFV would have similar efficacy against MUC1 or MUC1* positive tumors.
  • the hinge region that connects the scFv to the transmembrane portion could be any flexible linker.
  • the intracellular co-stimulatory domains could be CD28-3zeta, CD28-4- 1BB-3zeta or any combination of immune cell co-stimulatory domains.
  • Figure 61 shows an experiment in which huMNC2-scFv-CAR44 transduced human T cell that were bead stimulated (Protocol 1) or cancer cell stimulated (Protocol 2) were tested for their ability to inhibit tumor growth in animals.
  • Human cancer cells that had been stably transfected with Luciferase were injected into female NOD/SCID/GAMMA (NSG) mice between 11 and 15 weeks of age.
  • 500,000 BT-20 breast cancer cells were injected sub-cutaneously into a rear flank. Tumor engraftment was verified by injecting the animals with Luciferin and then imaging the fluorescent cancer cells using an IVIS instrument. IVIS images taken Day 5 post implantation showed the presence of tumor cells.
  • mice On Day 6 after IVIS measurement, animals were given a one-time injection of 10 million of either human T cells transduced with huMNC2-scFv-CAR44 or untransduced T cells. 5 million T cells were injected intra-tumor and 5 million were injected into the tail vein. 10 minutes prior to IVIS photographs, mice were IP injected with Luciferin, which fluoresces after cleavage by Luciferase, thus making tumor cells fluoresce. Figs.
  • 61A, 61D, 61G show photographs of mice that were treated with huMNC2-scFv-CAR44 T cells that had been pre- stimulated by co-culturing for 24 hours with 4 ⁇ m beads to which was attached a synthetic MUC1*, PSMGFR peptide 24 hours prior to administration, “Protocol 1”.
  • Figs. 61B, 61E, 61H show photographs of mice that were treated with huMNC2-scFv-CAR44 T cells that had been pre-stimulated by twice co-culturing for 24 hours with MUC1* positive cancer cells 24 hours prior to administration, “Protocol 2”.
  • huMNC2-CAR44 T cells that were peptide-bead stimulated inhibited tumor growth better than cells pre- stimulated by incubation with live cancer cells, which likely contaminated the target cells and increased the tumor volume.
  • huMNC2-scFv-CAR44 transduced human T cell that were bead stimulated (Protocol 1) or cancer cell stimulated (Protocol 2) were also tested for their ability to inhibit tumor growth in animals.
  • Human cancer cells that had been stably transfected with Luciferase were injected into female NOD/SCID/GAMMA (NSG) mice between 11 and 15 weeks of age.
  • 500,000 BT-20 MUC1* positive triple negative breast cancer cells were injected sub-cutaneously into a rear flank. Tumor engraftment was verified by injecting the animals with Luciferin and then imaging the fluorescent cancer cells using an IVIS instrument. IVIS images taken Day 6 post implantation showed the presence of tumor cells. On Day 6, after IVIS imaging, 10M huMNC2-scFv-CAR44 T cells were administered to the animals. 5M of the CAR T cells were administered by intratumor injection and the other 5M were administered by tail vein injection. Control group was injected by same administration routes with the same number of untransduced T cells. IVIS measurements of tumor burden were taken on Days 6, 8, and 12. As can be seen in Figs.
  • mice treated with huMNC2-CAR44 T cells showed a decrease in tumor burden compared to the control group.
  • huMNC2-scFv-CAR44 transduced human T cell that were bead stimulated (Protocol 1) were also tested for their ability to inhibit ovarian cancer growth in animals.
  • Human SKOV-3 MUC1* positive ovarian cancer cells that had been stably transfected with Luciferase were injected into female NOD/SCID/GAMMA (NSG) mice between 11 and 15 weeks of age. In one experiment, 500,000 SKOV-3 cancer cells were injected into the intraperitoneal cavity to mimic metastatic ovarian cancer in humans.
  • Tumor engraftment was verified by injecting the animals with Luciferin and then imaging the fluorescent cancer cells using an IVIS instrument. IVIS images taken Day 3 post implantation showed the presence of tumor cells. On Day 4 and Day 11, post tumor implantation, 10M huMNC2-scFv-CAR44 T cells were IP administered to the animals. On Day 4, CAR T cells were IP injected. On Day 11 half the CAR T cells were injected into the intraperitoneal space and the other half was injected into the tail vein. Control groups were injected by same administration routes with either the same number of untransduced T cells or same volume of PBS. Subsequent IVIS measurements of tumor burden were taken on Day 7, Day 10 and Day 15. As can be seen in Figs.
  • One aspect of the invention is a method for treating a patient diagnosed with, suspected of having, or at risk of developing a MUC1 positive or MUC1* positive cancer, wherein the patient is administered an effective amount of an antibody, antibody fragment which may be incorporated into a BiTE, a bispecific antibody, a multi-specific antibody, an ADC or a CAR expressed in an immune cell wherein the antibody or fragment thereof is derived from an antibody of the invention.
  • the antibody or fragment thereof is derived from MNC2, MNE6, 20A10, 3C2B1, 5C6F3 or 25E6.
  • One aspect of the invention is a method for treating a patient diagnosed with, suspected of having, or at risk of developing a MUC1 positive or MUC1* positive cancer, wherein the patient is administered an effective amount of immune cells that have been transduced with a MUC1* targeting CAR, wherein the CAR is chosen from among the group consisting of MNE6-CD8-CD28-3z (SEQ ID NOS:297-298); MNE6-CD4-CD28-3z (SEQ ID NOS:748-749); MNE6-CD8-41BB-3z (SEQ ID NOS:300-301); MNE6-CD4-41BB-3z (SEQ ID NOS:750-751); MNE6-CD8-CD28-41BB-3z (SEQ ID NOS:303-304); MNE6-CD4- CD28-41BB
  • Another aspect of the invention is a method for treating a patient diagnosed with, suspected of having, or at risk of developing a cancer, wherein the patient is administered an effective amount of immune cells that have been transduced with one of the aforementioned CARs wherein the MNE6 is replaced by a peptide comprising antibody variable domain fragments that are specific for a cancer antigen.
  • the immune cell may be a T cell and may further be isolated from the patient to be treated.
  • the immune cell which may be a T cell is isolated from a donor.
  • the immune cell is derived from a stem cell that has been directed to differentiate to that immune cell type in vitro.
  • a CAR containing sequences of the antibody are expressed in a stem cell, which then may be differentiated into an immune cell.
  • the immune cell is a T cell.
  • the immune cell is an NK cell.
  • Another aspect of the invention is a method for treating a patient diagnosed with, suspected of having, or at risk of developing a MUC1 positive or MUC1* positive cancer, wherein the patient is administered an effective amount of immune cells that have been transduced with a MUC1* targeting CAR.
  • the CAR may include a single chain antibody fragment, scFv, comprising a sequence derived from antibody MNC2, such as MNC2-scFv (SEQ ID NO:239, 241, 243, or 654-655), from antibody 20A10, such as SEQ ID NO:1574-1581 or 5001-5012, from antibody 3C2B1, such as SEQ ID NO:1572- 1573, which may be humanized for example as in SEQ ID NO:1812-1813, or from antibody 5C6F3, such as SEQ ID NO:1384-1385), which may be humanized for example as in SEQ ID NO:1814-1815, or from antibody 25E6 such as SEQ ID NO:1598-1599 or 1600-1601, wherein the hinge and transmembrane sequences may be derived from CD8 (SEQ ID NO:346 and SEQ ID NO:364), or from CD28 (SEQ ID NO:350 and SEQ ID NO:368), further comprising a co-stimulatory domain, which
  • MUC1 is cleaved to the growth factor receptor form, MUC1*, on some healthy cells in addition to cancer cells.
  • MUC1 is cleaved to MUC1* on healthy stem and progenitor cells.
  • a large percentage of bone marrow cells are MUC1* positive.
  • Portions of the intestine are MUC1* positive.
  • MUC1 can be cleaved at different positions that are relatively close to each other but the location of cleavage changes the fold of the remaining portion of the extracellular domain.
  • monoclonal antibodies can be identified that bind to MUC1* cleaved at a first position but do not bind to MUC1* that has been cleaved at a second position.
  • This discovery is disclosed in WO2014/028668, filed August 14, 2013, the contents of which are incorporated by reference herein its entirety.
  • One method used to identify stem specific antibodies is as follows: supernatants from monoclonal hybridomas were separately adsorbed onto 2 multi-well plates. Stem cells, which are non-adherent cells, were put into one plate and cancer cells which are adherent were put into an identical plate. After an incubation period, the plates were rinsed and inverted. If the non-adherent stem cells stuck to the plate, then the monoclonal antibody in that particular well recognizes stem cells and will not recognize cancer cells. Antibodies that did not capture stem cells or antibodies that captured cancer cells were identified as cancer specific antibodies. FACS analysis has confirmed this method works. [00692] Antibodies MNE6 and MNC2 are examples of cancer-specific antibodies.
  • Antibodies MNC3 and MNC8 are examples of stem-specific antibodies. Although both sets of antibodies are able to bind to a peptide having the PSMGFR sequence, FACS analysis shows that the anti-MUC1* polyclonal antibody and MNC3 bind to MUC1* positive bone marrow cells but MNE6 does not.
  • the MUC1* polyclonal antibody was generated by immunizing a rabbit with the PSMGFR peptide.
  • MNC3 binds to stem cells of the intestinal crypts but MNE6 does not.
  • MNE6 antibody binds to cancerous tissue while the stem-specific MNC3 does not.
  • Another method for identifying antibodies that are cancer specific is to immunize with a peptide having the sequence of the PSMGFR peptide minus the 10 N-terminal amino acids or use that peptide to screen for antibodies or antibody fragments that will be cancer specific.
  • Antibodies that bind to a peptide with a sequence of PSMGFR peptide minus the N-terminal 10 amino acids, referred to herein as N-10 peptide, but do not bind to a peptide with a sequence of PSMGFR peptide minus the C-terminal 10 amino acids, C-10 peptide, are cancer specific antibodies for use in the treatment or prevention of cancers.
  • the extracellular domain of MUC1 is also cleaved on stem cells and some progenitor cells, where activation of cleaved MUC1 by ligands NME1 in dimer form or NME7 promotes growth and pluripotency and inhibits differentiation.
  • MUC1* The transmembrane portion of MUC1 that remains after cleavage is called MUC1* and the extracellular domain is comprised essentially of the Primary Sequence of MUC1 Growth Factor Receptor (PSMGFR) sequence.
  • PSMGFR Primary Sequence of MUC1 Growth Factor Receptor
  • Antibodies that recognize different cleavage site conformations may be cancer sub-type specific or patient specific, depending on which cleavage enzyme their tumor expresses.
  • a patient diagnosed with a certain type of cancer is treated with an antibody of the invention that recognizes a cleaved MUC1 wherein the antibody is specific for cleavage by a specific enzyme that is known to be typically expressed by that sub-type of cancer.
  • a patient tumor is analyzed to determine which enzyme his or her tumor expresses and an antibody that recognizes a MUC1 cleaved by that enzyme is then administered to the patient for the treatment of their cancer.
  • the antibody may be in the form of a CAR, a BiTE, an ADC, a bispecific antibody, with or without an FC region or a portion of an Fc region, a bi-scFv, a di-scFv, a tandem di-scFv, a diabody, triabody, tribody, tetrabody and other antibody-like molecules that are multi-valent and multi-specific.
  • MUC1* MUC1 transmembrane cleavage product
  • MUC1* MUC1 transmembrane cleavage product
  • Fig. 1A ligand induced dimerization of its short extra cellular domain
  • Dimerization of the MUC1* extra cellular domain activates the MAP kinase signaling cascade and stimulates growth and survival of cancer cells (Fessler et al 2009).
  • Bivalent antibodies that dimerize the MUC1* extra cellular domain stimulate cancer cell growth while the monovalent Fab of the same antibody, which cannot dimerize, inhibits cancer cell growth.
  • NME1 dimers multimerize and form hexamers, which do not bind to MUC1*, but likely bind to some unknown receptor, as the addition of NME1 hexamers turns off growth.
  • NME1 is an adult form.
  • the embryonic form is NME7AB (Carter et al 2016).
  • Each NME7AB monomer has two binding sites for MUC1* so as a monomer it dimerizes MUC1* (Fig. 1D), stimulates growth and cannot turn itself off.
  • BRD4 turns off NME7 and its co-factor JMJD6 turns on the self- regulating form, NME1.
  • NME7 which should be silenced in adult life, is aberrantly expressed again, where is renders the MUC1* growth factor receptor constitutively active.
  • NME1 SEQ ID NO:4
  • NME7AB SEQ ID NO:827
  • Both growth factors can bind to the PSMGFR peptide (SEQ ID NO:2) even if the 10 N-terminal amino acids are deleted, referred to herein as N-10 (SEQ ID NO:3).
  • N-10 SEQ ID NO:3
  • neither NME1 nor NME7 AB can bind to the PSMGFR peptide if the 10 membrane proximal amino acids are deleted (Fig.
  • NME1 and NME7AB bind to the epitope to which NME1 and NME7AB bind includes all or part of the 10 membrane proximal amino acids: PFPFSAQSGA (SEQ ID NO:1743).
  • PFPFSAQSGA SEQ ID NO:1743
  • MNC2 and MNE6 monoclonal anti- MUC1* antibodies Two other monoclonal antibodies that were generated from immunizing animals with the PSMGFR peptide are MNC3 and MNC8.
  • MNC2, MNE6, MNC3 and MNC8 all bind to the PSMGFR peptide, like NME1 and NME7 AB , MNC2 and MNE6 bind strongly to the N-10 peptide but not to the C-10 peptide (Fig. 2B-2C). In fact, MNC2 and MNE6 competitively inhibit the binding of NME1 and NME7 AB to PSMGFR (Fig. 3A- 3C). Conversely, MNC3 and MNC8 bind to the C-10 peptide, bind less well to the N-10 peptide and do not compete with NME1 nor NME7 AB for binding to MUC1* peptides, including PSMGFR (Fig. 2E-2F).
  • MNC3 and MNC8 are far less cancer specific than MNC2 and MNE6.
  • MNC3 and MNC8 recognize stem and progenitor cells, such as hematopoietic stem cells, whereas MNC2 and MNE6 do not (Fig. 39-41). Because hematopoietic stem cells are the progenitor cells for the blood cells, it would be problematic to have a cancer therapeutic that would also target such an important normal cell type.
  • MUC1* is generated by enzymatic cleavage of MUC1
  • cleavage enzymes cleave MUC1 to a MUC1* and whether or not we could identify antibodies that would recognize a MUC1* generated by a first cleavage enzyme but not MUC1* generated by a second cleavage enzyme.
  • MNC2 and MNE6 recognized a MUC1* generated by cleavage of MUC1 by MMP9 but not by cleavage by other enzymes such as MMP2 (Fig. 37 and Fig. 75).
  • MMP9 is overexpressed in cancers and is a predictor of poor prognosis (vant Veer et al 2002; Dufour et al 2011) and has been implicated in metastasis (Owyong et al, 2019), whereas MMP2 is expressed in bone marrow.
  • One antibody binding to a MUC1* generated by cleavage by a first enzyme but not by cleavage by a second enzyme implies that the antibody recognizes a conformational epitope rather than a linear epitope.
  • MNC2 and MNE6 are cancer specific. [00713] Our experiments show that both MNC2 and MNE6: a) Bind to tumor cells; b) monovalent forms block tumor growth in vitro and in vivo; c) have minimal to no binding of normal tissue while having robust binding to a wide panel of tumor tissues; d) when incorporated into CAR T cells, MNC2 and MNE6 directed CAR T cells do not recognize full-length MUC1 and do not kill cells that only express full-length MUC1; e) MNC2 and MNE6 directed CAR T cells cluster then kill tumor cells expressing MUC1*; and f) MNC2 and MNE6 recognize a MUC1 cleavage product when it is cleaved by MMP9.
  • MNC2 directed CAR T cells do not recognize normal, healthy cells that are MUC1* positive.
  • MNC2 is a highly cancer specific antibody.
  • MNC2 and MNE6 Characterization of MNC2 and MNE6
  • Our gold standard, cancer-specific antibodies MNC2 and MNE6 1) bind to N-10 peptide but not to the C-10 peptide; 2) compete with NME7 AB and dimeric NME1 for the same binding site near the C-terminus of the PSMGFR peptide, which is the membrane proximal portion of MUC1* on cells; 3) do not work in a Western blot assay indicating that they recognize a conformational rather than linear epitope; 4) recognize a MUC1* generated when MUC1 is cleaved by MMP9; 5) do not bind to full-length MUC1 but only to the cleaved form, MUC1*, in model cell lines as well as cancer cell lines; 6) show little to no binding to normal tissues but robustly stain a wide variety of tumor tissues; and 7) share some consensus sequences in their Complementarity Determining Regions, CDRs.
  • Monoclonal antibodies were produced by immunizing animals with peptides derived from a MUC1 that is devoid of tandem repeats. These antibodies included PSMGFR and peptides that were extended at the N-terminus of PSMGFR.
  • Immunizing peptides were: [00719] PSMGFR (SEQ ID NO:2)) [00720] N+9/C-9 (9 amino acids added onto the N-terminus and 9 amino acids deleted from the C-terminus) (SEQ ID NO:824) [00721] N+20/C-27 (20 amino acids added onto the N-terminus and 27 amino acids deleted from the C-terminus) (SEQ ID NO:823) [00722] These monoclonal antibodies were then tested to determine which satisfied the seven (7) characterization criteria cited above, which we reasoned would identify the most cancer specific antibodies.
  • ELISA assays were performed to determine if, in addition to recognizing their immunizing peptide, they recognized PSMGFR, N-10 or C-10. In addition, they were tested for their ability to bind to N+20/C-27, N+9/C-9. We first did the ELISA assay on our set of reference antibodies, MNC2, MNE6, which we know are cancer-specific plus MNC3, which we know recognizes stem cells and progenitor cells (Fig. 63A-63B). None of the reference antibodies bound to the N+20/C-27 peptide.
  • MNC2 and MNE6 cannot bind to PSMGFR peptides with 27, 10 or 9 C-terminal deletions, however, MNC3 binds to C-10 and to N+9/C- 9 peptides.
  • This same ELISA assay was performed on the antibodies of the invention (Fig. 64-66 and Fig. 201). The binding patterns of the antibodies that were generated by immunizing with the PSMGFR peptide are shown in Fig. 64A-64B. Note that only 20A10 exactly matches the binding profile of MNC2 and MNE6.25E6, 28F9 and 18G12 are all able to bind to the N-10 peptide.
  • 18B4 is the only antibody raised against the PSMGFR peptide that requires the 10 most N-terminal amino acids of the peptide.
  • the color of the bars for each antibody in the ELISA graph are color coded to match the deductive cognate sequence, or a portion thereof, of that antibody.
  • another set of antibodies was assayed by ELISA (Fig. 201). Of this set, B12, B2, B7, B9, 8C7F3, and H11 bound to the PSMGFR peptide, bound to the N-10 peptide, but not to the C-10 peptide (Fig. 201).
  • the binding patterns of the antibodies that were generated by immunizing with the N+20/C-27 peptide are shown in Fig. 65A-65B.
  • amino acids ASRYNLT SEQ ID NO:1745
  • amino acids ASRYNLT SEQ ID NO:1745
  • GTINVHDVET SEQ ID NO:1746
  • Amino acids FPFS SEQ ID NO:1747 are important or essential for the binding of 20A10, MNC2 and MNE6.
  • these three antibodies recognize a conformational epitope, not a linear epitope.
  • SNIKFRPGSVVVQLTLAFRE (SEQ ID NO:1748), which is 20 additional amino acids N- terminal to the PSMGFR peptide and outside of the PSMGFR peptide, are important or essential for the binding of antibody 45C11.
  • SNIKFRPGSVVQLTLAFRE (SEQ ID NO:1748), which is 20 additional amino acids N- terminal to the PSMGFR peptide and outside of the PSMGFR peptide, are important or essential for the binding of antibody 45C11.
  • Amino acids QFNQYKTEA (SEQ ID NO:1749), which are still within the sequence of PSMGFR, are important or essential for the binding of antibody 1E4.
  • amino acids GTINVHDVET which comprise the most N-terminal part of the PSMGFR peptide are important or essential for the binding of the 39H5 and 3C5 antibodies.
  • amino acids VQLTLAFRE SEQ ID NO:1750
  • amino acids 17H6 and 8A9 are important or essential for the binding of antibodies 17H6 and 8A9.
  • NME7 AB has two binding sites for MUC1* so that as a monomer it dimerizes MUC1* and mediates cancer cell growth.
  • NME1 and NME7 AB can bind to the MUC1* extra cellular domain.
  • N-10 SEQ ID NO:3
  • C-10 C-10
  • the epitope to which NME1 and NME7 AB bind includes all or part of the 10 membrane proximal amino acids: PFPFSAQSGA (SEQ ID NO:1743).
  • PFPFSAQSGA SEQ ID NO:1743
  • MNC2 and MNE6 monoclonal anti-MUC1* antibodies Two other monoclonal antibodies that were generated from immunizing animals with the PSMGFR peptide are MNC3 and MNC8.
  • MNC2, MNE6, MNC3 and MNC8 all bind to the PSMGFR peptide, like NME1 and NME7 AB , MNC2 and MNE6 bind strongly to the N-10 peptide but not to the C-10 peptide. In fact, MNC2 and MNE6 competitively inhibit the binding of NME1 and NME7 AB to PSMGFR. Conversely, MNC3 and MNC8 are able to bind to the C-10 peptide, bind less well to the N-10 peptide and do not compete with NME1 nor NME7 AB for binding to MUC1* peptides, including PSMGFR (Fig. 70). MNC3 and MNC8 are less cancer specific than MNC2 and MNE6.
  • MNC3 and MNC8 recognize stem and progenitor cells, such as hematopoietic stem cells, whereas MNC2 and MNE6 do not. Because hematopoietic stem cells are the progenitor cells for the blood cells, it would be problematic to have a cancer therapeutic that would also target such an important normal cell type.
  • antibodies of the invention were tested for their ability to displace NME7 AB from binding to the PSMGFR peptide.
  • a multi-well plate was coated with the PSMGFR peptide.
  • Recombinant NME7AB was allowed to bind to the surface-immobilized PSMGFR peptide. Wash steps followed. Various antibodies were added, followed by wash steps.
  • FIG. 70 shows a graph of an ELISA displacement assay. The bar graph is color coded to indicate the cognate epitope to which each antibody binds. As can be seen in the figure, the antibodies that bind to the more C-terminal portions of PSMGFR are the most potent at disrupting the binding of onco-embryonic growth factor NME7AB to the MUC1* extra cellular domain or the PSMGFR peptide.
  • the rank order of potency for disrupting binding of NME7AB to PSMGFR according to their cognate epitope is as follows: FPFS> ASRYNLT> QFNQYKTEA>GTINVHDVET.
  • Antibodies that bind to epitopes outside of the PSMGFR peptide, such as 45C11, 8A9 and 17H6 did not compete with NME7 AB for binding.
  • Western blot assay to determine linear versus conformational cognate epitope [00736] Antibodies were tested to determine whether they recognize a linear or a conformational epitope. Only antibodies that recognize a linear epitope work in Western blots when using denaturing gels.
  • HCT-116 a MUC1 negative cancer cell line
  • HCT-MUC1-18 which is a cleavage resistant clone of HCTs transfected with full-length MUC1
  • HCTs transfected with MUC1* wherein the extra cellular domain comprises only the PSMGFR sequence.
  • the antibodies tested for comparison are MNC2 and MNE6, which were known to only recognize a conformational epitope, SDIX which is a polyclonal antibody raised against PSMGFR and VU4H5, which is a commercially available monoclonal antibody that recognizes the tandem repeats of full-length MUC1 (Fig. 71A-71D).
  • antibodies 25E6 and 18B4 recognize linear epitopes but 20A10 (Fig. 72A; 72I), 3C2B1 (Fig. 72F; 72N), 5C6F3 (Fig. 72G; 72O), 18G12 and 28F9 do not, indicating that they bind to a conformational epitope.
  • Antibodies that were raised against the N+20/C-27 peptide were tested the same way in Western blots (Fig. 73A-73J).
  • antibodies 31A1 and 32C1 recognize linear epitopes.
  • Antibodies 1E4 and 45C11 may recognize a conformational epitope.
  • MNC2 Recognition of a MUC1 cleavage product after cleavage by MMP9 [00739]
  • MMP9 is expressed by tumor tissues and is a predictor of poor prognosis for breast cancers (vant Veer et al 2002; Dufour et al 2011). MMP9 has also been implicated in metastasis (Owyong et al 2019). Recall also that MNC2 competitively inhibits the binding of onco-embryonic growth factor NME7AB to the MUC1* extra cellular domain (Fig. 3).
  • onco- embryonic growth factor which activates growth and survival functions of MUC1*, also recognizes a MUC1* generated by cleavage by MMP9. It then follows that the most cancer specific antibodies are those that recognize a conformational epitope formed when MUC1 is cleaved to MUC1* by MMP9. [00740] Antibodies generated by immunization with PSMGFR, N+20/C-27, or N+9/C-9 were tested for their ability to recognize MUC1 after it is cleaved by MMP9.
  • HCT-116 a MUC1 negative colon cancer cell line, with full-length MUC1 and isolated a single cell clone that is cleavage resistant; this cleavage resistant cell line is called HCT-MUC1-18.
  • HCT-MUC1-18 cells was added either a catalytically active MMP9 or MMP2.
  • the enzymes added over a range of concentrations, were incubated with the cells for 24 hours.
  • the resultant cells were then incubated with the various antibodies and analyzed by FACS to determine which bound to a MUC1 cleavage product produced by cleavage by MMP9 (Fig. 75A-75N).
  • each graph shows that none of the antibodies binds to full-length MUC1 in the absence of cleavage.
  • Each bar graph is labeled with both the name of the antibody used in that assay and its cognate epitope. The order of the graphs from right to left corresponds to the distance from the cell surface of the antibody’s cognate epitope.
  • Antibody 45C11 which binds to the SNIKFRPGSVV epitope, which is outside of the PSMGFR portion of MUC1, does not recognize a MUC1 cleavage product after cleavage by MMP9 or MMP2 (Fig. 75K).
  • antibodies 8A9 and 17H6 bind to the VQLTLAFRE epitope, which is also outside of the PSMGFR sequence, and they do not bind to a MUC1 cleaved by MMP9 or MMP2. This result is consistent with the idea that MMP9 cleaves MUC1 such that the extra cellular domain of the remaining transmembrane cleavage product comprises essentially the amino acids of the PSMGFR peptide.
  • the antibody should recognize a conformational epitope of a MUC1 cleavage product created when MUC1 is cleaved by MMP9.
  • MUC1 cleavage product produced by cleavage by MMP9 and also does not work in a Western blot, indicating it recognizes a conformational epitope, as do MNC2 and MNE6.
  • Cleavage and release of the massive tandem repeat domain of MUC1 unmasks the ectopic binding site on MUC1*; linear epitopes will be unmasked in addition to conformational epitopes.
  • FACS analysis of binding to a panel of cancer cell lines was performed on reference antibodies as well as new antibodies of the invention. FACS analyses of reference antibodies MNC2, “C2”, and VU4H5 binding to either the MUC1-negative cell line HCT-116, HCTs transfected with MUC1*, “HCT-MUC1*”, a cleavage resistant single cell clone of HCTs transfected with MUC1 full-length, “HCT-MUC1-18”, and MNC2 binding to breast cancer cells line T47D or breast cancer cell line 1500 also known as ZR-75-1, was performed (Fig. 76A-76J).
  • MNC2 binds to an ectopic binding site on the extra cellular domain of MUC1*, which is only available after cleavage and release of the bulk of the extra cellular domain comprising the tandem repeat domain.
  • VU4H5 binds to hundreds of repeating epitopes in the tandem repeat domain of full-length MUC1 and does not bind to MUC1*.
  • cancer cell lines express both full-length MUC1 and MUC1*, antibodies against full-length MUC1 have, as yet, been shown to have no therapeutic value.
  • MUC1* and not full-length MUC1
  • MUC1* is a potent growth factor receptor that mediates the growth of cancer cells (Mahanta et al 2008) and their resistance to chemotherapy agents (Fessler et al 2009).
  • Reference antibody MNC2, “C2”, was analyzed by FACS for its ability to bind to a panel of cancer cell lines that are all MUC1* positive, with the exception of MDA-MB-231, which expresses MUC1 and MUC1* at a level that is so low that it is often used as a negative control (Fig. 77A-77N).
  • the panel of cancer cells that was probed with MNC2 included T47D and 1500 breast cancer cells, NCI-H292 and NCI-H1975 lung cancer cells, SKOV-3 ovarian cancer cells, HPAF-II and Capan-1 pancreatic cancer cells, DU145 prostate cancer cells, and MDA-MB-231, breast cancer cells, which are nearly MUC1 and MUC1* negative.
  • FIG. 78A-78C shows a color coded schematic of the PSMGFR sequence that has been extended or deleted at both the N- and C-termini.
  • FIG. 78A is an aligned schematic of the various subsets of peptides.
  • Fig.78B lists the antibodies that bind to each of the color coded sequences.
  • Fig. 78C lists the cancer cell lines that each antibody recognizes.
  • Figures 80-87 show graphs of FACS analyses wherein antibodies of the invention are compared for their ability to specifically recognize different types of cancer cells. Percent cells recognized as well as the Mean Fluorescence Intensity, MFI, was measured.
  • tissue micro array comprises tissues from multiple donors and the cells are in their natural environment, without years of culturing under non-physiologic conditions. Additionally, tissues provide information regarding tumor heterogeneity as well as information regarding normal patterns of expression.
  • Each antibody of the invention was used to probe a normal tissue micro array, FDA Normal Array MNO1021. In addition the antibody was also used to probe a panel of cancerous tissue arrays.
  • Figures 113-200 show photographs of the IHC staining of normal TMAs versus cancerous TMAs for each antibody of the invention.
  • Figure 113-120 show photographs of tissues studies probed with antibody 20A10. Recall that 20A10 binds to the PSMGFR peptide, binds to the N-10 peptide, but does not bind to the C-10 peptide.
  • Refined epitope mapping shows that like MNC2 and MNE6, the binding of 20A10 depends on amino acids FPFS being present in the PSMGFR peptide. 20A10 binds to the most membrane proximal part of the MUC1* extra cellular domain.
  • An overview of FDA Normal Tissue Array MNO1021 is shown in Figure 113.
  • Figure 114A- 114X show that there is little to no cross reactivity of 20A10 for normal tissues.
  • MNC2, MNE6 and 20A10 all react with the MUC1* that is expressed on the luminal edge of the terminal breast ducts, luminal edge of the fallopian tubes, luminal edge of about 10% of the distal collecting ducts of normal kidney, and luminal edge of ureter.
  • MNC2, MNE6 and 20A10 show no staining of critical organs, such as heart, lung and brain.
  • 20A10 like MNC2 and MNE6, robustly binds to cancerous tissues. 20A10 stains nearly all specimens of the BR1141 breast cancer array (Fig. 115-116).
  • the staining is membrane staining, indicating that 20A10 recognizes an extra cellular portion of MUC1*, which is critical for an effective antibody- based anti-cancer therapeutic.
  • 20A10 also showed robust and membranous staining of pancreatic cancer tissues (Fig. 117-118) and esophageal cancer tissues (Fig. 119-120).
  • 20A10 shows great cancer specificity and as an anti-cancer therapeutic offers a large therapeutic window because of the vast difference between staining of normal tissues and cancerous tissues, in terms of the location and intensity of staining.
  • Anti-MUC1* antibody 3C2B1 is an antibody that like MNC2, MNE6 and 20A10, binds to N-10 but not to C-10. More refined epitope mapping shows that like these three other highly cancer-specific antibodies, 3C2B1 requires the FPFS sequence for binding to a MUC1* extra cellular domain peptide.
  • Figure 121 shows the photograph of the FDA normal array MNO1021.
  • Figure 122A-122X shows photographs of specific tissues from FDA normal tissue array MNO1021 stained with the anti-PSMGFR antibody 3C2B1 at 20ug/mL. As can be seen, there is no binding of 3C2B1 to any critical normal organs.
  • Figure 123 shows photograph of pancreatic cancer tissue array PA1003 stained with the anti-PSMGFR antibody 3C2B1 at 1-20ug/mL.
  • Figure 124 shows photographs of specific tissues from pancreatic cancer tissue array PA1003 stained with the anti-PSMGFR antibody 3C2B1 at 20ug/mL.
  • Figure 125 shows photograph of breast cancer tissue array BR1141 stained with the anti-PSMGFR antibody 3C2B1 at 20ug/mL.
  • Figure 126A-126F shows magnified photographs of specific tissues from breast cancer tissue array BR1141 stained with the anti- PSMGFR antibody 3C2B1 at 20ug/mL.
  • 3C2B1 robustly stains breast cancer tissues.
  • Anti-MUC1* antibody 5C6F3 binds to the N-10 peptide, does bind to the C-10 peptide, although binding is reduced somewhat. Its cognate epitope comprises all or some of the sequence SVSDV (SEQ ID NO:1751).
  • Figure 127 shows photograph of FDA normal tissue array MNO1021 stained with the anti-PSMGFR antibody 5C6F3 at 1ug/mL.
  • Figure 128 shows photographs of specific tissues from FDA normal tissue array MNO1021 stained with the anti-PSMGFR antibody 5C6F3 at 1ug/mL.
  • Figure 129 shows photograph of pancreatic cancer tissue array PA1003 stained with the anti-PSMGFR antibody 5C6F3 at 1- 20ug/mL.
  • Figure 130 shows photographs of specific tissues from pancreatic cancer tissue array PA1003 stained with the anti-PSMGFR antibody 5C6F3 at 1ug/mL.
  • Figure 131 shows photograph of breast cancer tissue array BR1141 stained with the anti-PSMGFR antibody 5C6F3 at 1ug/mL.
  • Figure 132 shows photographs of specific tissues from breast cancer tissue array BR1141 stained with the anti-PSMGFR antibody 5C6F3 at 1ug/mL.
  • 5C6F3 is a high affinity antibody that has great cancer-specificity and with the exception of adrenal, which may be an artefact of that tissue, did not show binding to normal tissues.
  • 18B4 In contrast to 20A10, which binds to the most membrane proximal part of the MUC1* extra cellular domain, 18B4 binds within the GTINVHDVET sequence, which is the most distal part of the PSMGFR sequence. Unlike antibodies MNC2, MNE6 or 20A10, 18B4 cannot bind to the N-10 peptide but does bind to the C-10 peptide.
  • Figure 133-134 show the binding of antibody 18B4 to normal tissues. In contrast to 20A10, antibody 18B4 shows strong binding to a wide range of normal tissues (Fig. 134), including lung (Fig. 134K).
  • Figure 135-138 show 18B4 staining of breast cancer tissues and esophageal cancer tissues.
  • Figure 139-144 show the binding of PSMGFR antibody 18G12 to normal tissues, breast cancer tissues and esophageal cancer tissues.
  • 18G12 is able to bind to the N-10 peptide, but is also able to bind to the C-10 peptide.
  • 18G12 binds to the ASRYNLT epitope within the PSMGFR peptide.
  • Antibody 18G12 binds to the luminal edge of many of the collecting ducts of normal kidney (Fig. 140D), binds to normal heart muscle (Fig. 140I) as well as to normal skeletal muscle (Fig. 140X).
  • FIG. 141-146 show 18G12 staining of breast cancer tissues, pancreatic cancer tissues and esophageal cancerous tissues. The contrast between the staining of the normal tissues and the cancer tissues clearly demonstrates cancer specificity.
  • Figure 147-148 show the binding of PSMGFR antibody 25E6 to normal tissues. 25E6 is able to bind to the N-10 peptide, but is also able to bind to the C-10 peptide.
  • 25E6 binds to the ASRYNLT epitope within the PSMGFR peptide.
  • antibody 25E6 binds to the luminal edge of terminal breast ducts, luminal edge of fallopian tubes, to the luminal edge of a subset of the distal collecting ducts of normal kidney and to the luminal edge of ureter.
  • 25E6 binds, albeit very weakly, to normal heart muscle (Fig. 148I) as well as to normal skeletal muscle (Fig. 148X).
  • 25E6 binds much more strongly to cancerous tissues than to the few normal tissues.
  • Figure 149-152 show 25E6 staining of breast cancer tissues and pancreatic cancerous tissues. The contrast between the staining of the normal tissues and the cancer tissues clearly demonstrates cancer specificity.
  • Figure 153-156 show the binding of PSMGFR antibody 28F9 to normal tissues and breast cancer tissues. 28F9 is able to bind to the N-10 peptide, but is also able to bind to the C-10 peptide. 28F9 binds to the ASRYNLT epitope within the PSMGFR peptide.
  • antibody 25E6 binds to the luminal edge of terminal breast ducts, luminal edge of fallopian tubes, to the luminal edge of a subset of the distal collecting ducts of normal kidney and to the luminal edge of ureter.
  • Figure 155-156 show 28F9 staining of breast cancer tissues.
  • Figure 157-158 show the binding of the N+20/C-27 antibody 1E4 to normal tissues. 1E4 is able to bind to the N-10 peptide but also is able to bind to the C-10 peptide. 1E4 binds to the QFNQYKTEA sequence which is within the PSMGFR sequence. Examination of the entire normal tissue micro array (Fig.
  • FIG. 157A shows that antibody 1E4 binds to many normal tissues, including brain, cerebellum, all 3 liver specimens, pancreas, parathyroid, spinal cord and skeletal muscle.
  • Magnified images show that 1E4 stains heart (Fig. 158I) as well.
  • 1E4 staining of a breast cancer array (Fig. 159-160) shows that there is some cancer specificity.
  • Figure 161-162 show the binding of the N+20/C-27 antibody 29H1 to normal tissues. 29H1 binds within the GTINVHDVET sequence, which is the most distal part of the PSMGFR sequence.
  • 29H1 cannot bind to the N- 10 peptide but does bind to the C-10 peptide.
  • Examination of the entire normal tissue micro array shows that even at concentration as low as 0.5 ug/mL, antibody 29H1 strongly stains a wide range of normal tissues, including brain, heart, liver and lung.
  • 29H1 staining of a breast cancer array Fig. 163-164
  • staining of a pancreatic cancer tissue array Fig.165-166 shows that there is no cancer specificity.
  • Antibody 31A1 is similar to 29H1 in that they are both N+20/C-27 antibodies that bind within the GTINVHDVET (SEQ ID NO:1746) sequence, which is the most distal part of the PSMGFR sequence. Unlike antibodies MNC2, MNE6 or 20A10, neither 31A1 nor 29H1 can bind to the N-10 peptide but do bind to the C-10 peptide. Examination of the entire normal tissue micro array and the magnified images (Fig. 167-168) shows that even at concentration as low as 0.5 ug/mL, antibody 31A1 strongly stains a wide range of normal tissues, including brain, heart, lung, spleen, bone marrow, and skeletal muscle.
  • 31A1 was used to stain a breast cancer array, (Fig. 169-170). 31A1 was used over a range of concentrations to stain a pancreatic cancer tissue array (Fig. 171-172). These figure shows that 31A1 has insufficient cancer specificity.
  • Antibody 32C1 is similar to 29H1 and 31A1 in that they are all N+20/C-27 antibodies that bind within the GTINVHDVET sequence, which is the most distal part of the PSMGFR sequence. Unlike antibodies MNC2, MNE6 or 20A10, none of 32C1, 31A1 or 29H1 can bind to the N-10 peptide but all do bind to the C-10 peptide. Examination of the entire normal tissue micro array and the magnified images (Fig.
  • Antibody 45C11 is an N+20/C-27 antibody that binds to epitope SNIKFRPGSVV (SEQ ID NO:1744) that is 20 amino acids outside of the PSMGFR sequence at the N- terminal end.
  • 45C11 does not bind to the N-10 peptide.
  • Normal tissue array FDA MNO1021 was stained with 45C11 at 12.5ug/mL (Fig. 179-180).
  • 45C11 shows strong binding to many normal tissues, including brain, heart, lung, liver, spleen, skeletal muscle and bone marrow.
  • 45C11 was used over a range of concentrations to stain a breast cancer tissue array (Fig. 181-182).
  • 45C11 was also used to stain a pancreatic cancer tissue array (Fig. 183-184). Taken together, these figures show that 45C11 has no cancer specificity.
  • Antibody 3C5 is an N+9/C-9 antibody that binds to epitope GTINVHDVET.
  • Antibody 8A9 is an N+9/C-9 antibody that binds to epitope VQLTLAFRE which is outside of the PSMGFR sequence. Antibody 8A9 cannot bind to the N-10 peptide. Normal tissue array FDA MNO1021 was stained with 8A9 (Fig. 189-190). As can be seen in the figures, like antibody 45C11, which also binds an epitope that is N-terminal beyond the PSMGFR sequence, antibody 8A9 shows strong binding to many normal tissues, including adrenal, brain, heart, lung, liver, spleen, skeletal muscle and bone marrow.
  • a pancreatic cancer array stained with antibody 8A9 showed weak binding to a subset of pancreatic cancer tissues (Fig.191-192). Taken together, these figures show that 8A9 has no cancer specificity.
  • Antibody 17H6 is an N+9/C-9 antibody that binds to epitope VQLTLAFRE, which is outside of the PSMGFR sequence. 17H6 was used to stain normal tissue array MNO1021. Examination of the entire normal tissue micro array and the magnified images (Fig. 193-194) shows that antibody 17H6 stains some normal tissues, including brain, heart, adrenal gland, bone marrow and skeletal muscle. 17H6 was used to probe a pancreatic cancer array and showed weak binding to most pancreatic cancer tissues (Fig. 195-196).
  • Antibody 39H5 is an N+9/C-9 antibody that binds weakly to the intact PSMGFR peptide but not significantly to any of the subset peptides. 39H5 may bind to the GTINVHDVET, which is the most distal part of the PSMGFR sequence. Examination of the entire normal tissue micro array and the magnified images (Fig. 197-198) shows that antibody 39H5 stains some normal tissues, including brain, heart, liver and bone marrow. 39H5 was used to probe a pancreatic cancer array, (Fig. 199-200).
  • MFI Mean Fluorescence Intensity
  • MNC2 binds lung cancer line NCI- H1975 much more strongly than NCI-H292.
  • MNC2 binds pancreatic cell line HPAF-II much better than Capan-1 or prostate cancer line DU145.
  • PCR measurements show that the expression levels of cleavage enzymes varies greatly across a panel of cancer cell lines (Fig. 43 and Fig. 44 ).
  • the fold of the MUC1* extra cellular domain can vary greatly depending on which cleavage enzyme clips it, which likely accounts for differences between cancer cell lines that a single antibody recognizes. This variation in antibody recognition of various cell lines, even within a cancer sub-type is apparent in the figures.
  • IHC analysis of real tissues is more informative than the study of cultured cell lines, as is necessary in FACS analysis.
  • Each antibody was first tested over a range of concentrations to determine optimal concentration.
  • Antibody concentration was increased until the stroma also picked up stain, which indicates non-specific background binding. The optimal concentration for that particular antibody was then deemed to be just below the concentration at which the antibody stained the stroma.
  • An overview of the IHC tissue studies is shown in Figure 88-112. Here, we focused on the binding of antibodies to critical organ tissues, since binding to certain normal tissues would likely eliminate therapeutic use of that antibody. In these figures, the antibodies were grouped according to their cognate epitope.
  • the antibodies with the least binding to normal tissues and the strongest binding to cancerous tissues bind to epitopes within the FPFS or PFPFSAQSGA. Some antibodies that bind to epitopes within the ASRYNLT portion may also be suitable as therapeutics. These antibodies and others that recognize the same epitopes are desirable as anti-cancer therapeutics because they have a large therapeutic window, meaning that because of the low binding to normal tissues, and low side effects, patients can be dosed with antibody levels high enough to effectively kill the tumor cells. More detailed photographs of antibodies of the invention binding, or not binding, to other critical tissues are also shown. Figures 89-94 show magnified photographs of each antibody binding to normal heart tissue, where the antibodies have been categorized according to which epitope they bind.
  • Figures 95-100 show magnified photographs of each antibody binding to normal liver tissue, where the antibodies have been categorized according to which epitope they bind.
  • Figures 101-106 show magnified photographs of each antibody binding to normal lung tissue, where the antibodies have been categorized according to which epitope they bind.
  • Figures 107-112 show magnified photographs of each antibody binding to normal bone marrow, where the antibodies have been categorized according to which epitope they bind.
  • Table 3 Summary of Antibody Cross-Reactivity to Normal Tissues
  • the aim is to identify an antibody that binds much more strongly to tumor tissue than normal tissue and that either binds to non-critical normal tissues or binds to them in a way that would not be physiologically possible in an intact organ.
  • CAR T cells are carried by the blood and the lamina propia is a barrier to their getting to the luminal edge of a duct or gland.
  • the blood brain barrier prevents the passage of large molecules like antibodies from the blood into the brain.
  • the usefulness of an antibody as a therapeutic also depends on the format of the therapeutic.
  • cell based therapies have natural barriers that prevent the CAR T cells from getting to some normal tissues.
  • Antibody Drug Conjugate (ADC) based therapies sometimes depend on a local, cancer-specific molecule to activate the toxin attached to the antibody, minimizing the importance of whether or not a naked antibody binds to some normal tissue.
  • ADC Antibody Drug Conjugate
  • antibodies and antibody-based therapeutics can be administered locally, including intraperitoneally, to maximize the effect on tumor cells while minimizing their effect on normal tissues.
  • an antibody that is not purely cancer-specific can be made more cancer-specific if it is incorporated into a bispecific antibody where a first side of the molecule binds to a first cancer antigen and the second side of the molecule binds to a second antigen that may be a tissue specific antigen, another cancer specific antigen or even an antigen on a cell such as a T cell, which are called BiTES, bispecific T cell engagers.
  • the less cancer-specific antibody can be incorporated into a cell-based therapy where its expression is induced only after the cell recognizes a tumor.
  • a CAR T cell can express a first CAR that recognizes a first antigen which recognition induces expression of a second antibody, or CAR incorporating the second antibody.
  • the cell expresses a CAR directed by an antibody fragment that is cancer-specific and a second antibody or CAR expressing the second antibody is induced to be expressed in an NFAT inducible system.
  • the nucleic acids encoding the second antibody or second CAR are down stream of NFAT response elements.
  • the NFAT inducible gene may be inserted into a Foxp3 enhancer or promoter.
  • the staining pattern of 1E4 is very different from that of 18B4 and the polyclonal antibody SDIX.
  • 18B4 and SDIX antibodies were generated by immunizing animals with the same peptide (PSMGFR), while the 1E4 antibody was generated from immunization with a different peptide (N+20).
  • Figures 203-207 show magnified images of selected tissues from this array to highlight the differences between these antibodies.
  • Figure 208 compares the staining of polyclonal antibody SDIX to monoclonal antibody 20A10, which were both generated from immunization with the PSMGFR peptide. Also shown is the difference in staining pattern for antibody 29H1 which was generated by immunization with an N+20 peptide.
  • FIG. 209 shows that esophageal cancers are better recognized by antibodies that bind to a MUC1* peptide with an extended N-terminus, such as antibody 29H1 and antibody 31A1.
  • Figure 210 shows that prostate cancers are better recognized by antibodies that bind to a MUC1* peptide with an extended N-terminus, such as antibody 29H1.
  • Table 4 shows a summary of the test criteria to determine the cancer- specificity of the various monoclonal antibodies. Table 4: Cancer-Specificity Test Criteria
  • test criteria 1-4 or even 1-5 provide a set of rapid, multiplexed and inexpensive tests that can be performed on hundreds or thousands of impure hybridoma clone supernatants to identify antibodies that are highly selective for cancer-specific forms of MUC1*.
  • Satisfies test criteria [00777] In a preferred embodiment an antibody is chosen for the treatment, prevention or diagnosis of a MUC1* positive cancer based on satisfying four (4) of the seven (7) criteria set out in Table 4.
  • an antibody is chosen for the treatment, prevention or diagnosis of cancer based on satisfying five (5) of the seven (7) criteria set out in Table 4. In a yet more preferred embodiment an antibody is chosen for the treatment, prevention or diagnosis of cancer based on satisfying six (6) of the seven (7) criteria set out in Table 4. In a more preferred embodiment an antibody is chosen for the treatment, prevention or diagnosis of cancer based on satisfying all seven (7) of the criteria set out in Table 4.
  • An antibody selected for suitability as a treatment for MUC1* positive cancers by virtue of satisfying four or more of the criteria set out in Table 4 can be incorporated in part or in whole into several therapeutic formats.
  • the antibody or antibody fragment is incorporated into a CAR that is then expressed in an immune cell, which may be a T cell, then administered to a patient who has been diagnosed with or is at risk of developing a MUC1* positive cancer.
  • an immune cell which may be a T cell
  • a fragment of the antibody which may be an scFv is incorporated into a BiTE, then administered to a patient who has been diagnosed with or is at risk of developing a MUC1* positive cancer.
  • a fragment of the antibody which may be an scFv is incorporated into a bi-specific antibody, then administered to a patient who has been diagnosed with or is at risk of developing a MUC1* positive cancer.
  • the antibody or antibody fragment is conjugated to a toxin or an ADC, antibody drug conjugate, then administered to a patient who has been diagnosed with or is at risk of developing a MUC1* positive cancer.
  • Bind to N-10 [00779] We have demonstrated that a MUC1 transmembrane protein, devoid of tandem repeats and having an extra cellular domain of 45 amino acids of PSMGFR sequence, is sufficient to function as a growth factor receptor and confers oncogenic characteristics to the cell (Mahanta et al 2008).
  • Antibodies that bind to the PSMGFR peptide or portion of a transmembrane MUC1 cleavage product can be cancer specific but may also bind to stem or progenitor cells. Antibodies that bind to the N-10 peptide are more cancer-specific. In a preferred embodiment an antibody is chosen for the treatment, prevention or diagnosis of cancer based on the ability of the antibody to bind to the N-10 peptide. [00780] Do not bind to C-10 [00781] We have demonstrated that the MUC1 extra cellular domain contains an ectopic binding site that is only exposed if the tandem repeat domain is missing, which can occur as a consequence of alternative splice variant or cleavage and release of the extra cellular domain.
  • MNC2 and MNE6 will not bind to full-length MUC1, but do bind to the remaining portion when MUC1 is cleaved and the tandem repeat domain is shed.
  • MNC2 and MNE6 will bind to a MUC1*-like protein if it is devoid of tandem repeats, for example if a MUC1 negative cell is transfected or transduced with an engineered MUC1 that is devoid of tandem repeats, especially if extra cellular domain comprises the PSMGFR.
  • the ectopic site to which MNC2 and MNE6 bind is unmasked when tandem repeat domain is missing or removed.
  • Both MNC2 and MNE6 require the 10 membrane proximal amino acids of a MUC1* extra cellular domain for binding; they do not bind to the C-10 peptide. That means that the ectopic binding site for MNC2 and MNE6 is within or contains all or part of the 10 C-terminal amino acids of the PSMGFR: PFPFSAQSGA.
  • an antibody is chosen for the treatment, prevention or diagnosis of cancer based on the inability of the antibody to bind to the C-10 peptide.
  • an antibody is chosen for the treatment, prevention or diagnosis of cancer based on the ability of the antibody to bind to the N-10 peptide and the inability of the antibody to bind to the C-10 peptide.
  • an antibody is chosen for the treatment, prevention or diagnosis of cancer based on the ability of the antibody to disrupt the binding of NME1, NME7 AB , or NME7-X1 to the PSMGFR peptide, the N-10 peptide, or to the surface of a MUC1* positive cancer cell.
  • Antibodies that are cancer-specific will be chosen based on their ability to bind to a MUC1 that is devoid of tandem repeats and for their inability to bind to full-length MUC1.
  • MUC1* is generated when MUC1 is cleaved by a cleavage enzyme and the tandem repeat domain is released from the cell surface. Cleavage and release of the tandem repeat domain may also unmask portions of MUC1*-like cleavage products that exist on normal tissues.
  • antibodies that recognize a conformation, rather than a linear epitope are more selective. Antibodies that recognize a conformational epitope rather than a linear epitope can be identified by a variety of means. In particular, antibodies that recognize a conformational epitope will not work in a denaturing Western blot assay.
  • an antibody is chosen for the treatment, prevention or diagnosis of cancer based on the ability of the antibody to recognize a conformational epitope.
  • the fold, or conformation, of the MUC1* truncated extra cellular domain differs depending on which enzyme cleaves MUC1.
  • Cleaved MUC1* or MUC1*-like cleavage products can function as growth factor receptors on normal healthy tissues. More than one cleavage enzyme is able to cleave MUC1 to a MUC1*-like form.
  • Cleavage by first enzyme may produce a conformation or a fold that is not the same as that produced by cleavage by a second enzyme. Support for this can be found in this application and is illustrated in Figures 39-41. These figures show that although a polyclonal antibody that binds to PSMGFR recognizes a cleaved MUC1 on hematopoietic stem cells, some monoclonal antibodies that bind to the PSMGFR peptide can bind to this MUC1*-like form on hematopoietic stem cells while others cannot. For example, MNC3 readily recognizes this cleaved form of MUC1 on hematopoietic stem cells, but MNC2 and MNE6 do not.
  • MNC2 and MNE6 recognize a MUC1* that is produced by cleavage by MMP9 but not when it is cleaved by MMP2.
  • MNC2 and MNE6 are cancer-specific while MNC3 is not, as it recognizes stem and progenitor cells.
  • MMP9 is overexpressed in cancers. Bone marrow, where hematopoietic stem cells are made expresses nearly 2,500-times more MMP2 than MMP9 (Fig.65).
  • MMP14 is another enzyme that cleaves MUC1 to a MUC1* growth factor receptor form (Fig. 38).
  • an antibody is chosen for the treatment, prevention or diagnosis of cancer based on the ability of the antibody to recognize a MUC1 cleavage product generated when MUC1 is cleaved by MMP14.
  • an antibody is chosen for the treatment, prevention or diagnosis of cancer based on the ability of the antibody to recognize a MUC1 cleavage product generated when MUC1 is cleaved by MMP9.
  • an antibody is chosen for the treatment, prevention or diagnosis of cancer based on the ability of the antibody to recognize a MUC1 cleavage product generated when MUC1 is cleaved by MMP9 and also recognizes a conformational epitope.
  • a traditional approach to identifying antibodies that are cancer-specific involves testing a panel of antibodies against a panel of different cancer cell lines and determining, by FACS, IF, immunoprecipitation or other method, if the antibody binds to cancer cells. Although this approach is traditional, it is sequential and time-consuming, and thus limits the analysis of large numbers of monoclonal antibody clones, which is required to find an ideal antibody suitable for cancer therapeutic or diagnostic. In addition, there are no real normal cell lines and the selection of normal primary cells is limited. The selection criteria presented above provide a rapid, multiplexed method for identifying monoclonal antibody clones that are specific for MUC1* positive cancers.
  • hybridoma supernatants can be used. This provides a huge advantage over state of the art methods for identifying antibodies that are specific for MUC1* positive cancers.
  • the ability to select antibodies from assay performed using the impure hybridoma supernatants means that much of the selection can be done on hundreds or thousands of clones rapidly and at very little cost. Methods such as FACS analysis ans IHC tissue studies require the use of purified antibodies which limits the number of clones that can be tested to tens, not even hundreds. [00789]
  • selecting an antibody based on its ability to bind to cancer cells, or a cancer cell type or to a cell engineered to express a certain antigen is important for antibody selection.
  • an antibody is chosen for the treatment, prevention or diagnosis of cancer based on the ability of the antibody to bind to MUC1* positive cancer cells.
  • Binds to tumor tissue more than normal tissue [00791] Immunohistochemistry, IHC, tissue studies of cancerous versus normal tissues is a more stringent test of the cancer specificity of antibodies than FACS analysis. Cancer cell lines are a single cell from a single patient that have been expanded in a lab for decades and are not representative of a cross section of the human population. Further, analysis of cell lines is blind to the heterogeneity of actual tumors. Tissue studies require purified antibody, are very expensive, time-consuming and require a skilled pathologist to analyze each stained tissue specimen.
  • an antibody is chosen for the treatment, prevention or diagnosis of cancer based on the ability of the antibody to bind to MUC1* positive tumor tissue at least 2-times more than it binds to normal tissues. In a preferred embodiment an antibody is chosen for the treatment, prevention or diagnosis of cancer based on the ability of the antibody to bind to MUC1* positive tumor tissue at least 5-times more than it binds to normal tissues. In a preferred embodiment an antibody is chosen for the treatment, prevention or diagnosis of cancer based on the ability of the antibody to bind to MUC1* positive tumor tissue at least 10-times more than it binds to normal tissues.
  • an antibody, or fragments thereof, that binds to a peptide comprising the sequence QFNQYKTEAASRYNLTISDVSVSDVPFPFSAQSGA are incorporated into anti-cancer therapeutics or diagnostics for the diagnosis, treatment or prevention of a MUC1* positive cancer.
  • an antibody, or fragments thereof, that binds to a peptide comprising the sequence ASRYNLTISDVSVSDVPFPFSAQSGA are incorporated into anti-cancer therapeutics or diagnostics for the diagnosis, treatment or prevention of a MUC1* positive cancer.
  • an antibody, or fragments thereof, that binds to a peptide comprising the sequence SDVSVSDVPFPFSAQSGA are incorporated into anti- cancer therapeutics or diagnostics for the diagnosis, treatment or prevention of a MUC1* positive cancer.
  • an antibody, or fragments thereof, that binds to a peptide comprising the sequence SVSDV are incorporated into anti-cancer therapeutics or diagnostics for the diagnosis, treatment or prevention of a MUC1* positive cancer.
  • an antibody, or fragments thereof, that binds to a peptide comprising some or all of the sequence PFPFSAQSGA are incorporated into anti-cancer therapeutics or diagnostics for the diagnosis, treatment or prevention of a MUC1* positive cancer.
  • the selected antibodies or fragments thereof are incorporated into a CAR, BiTE, ADC or bi-specific and then administered to a patient diagnosed with or at risk of developing a MUC1* positive cancer.
  • Consensus Sequences [00800] Antibodies of the invention were categorized according to cognate epitope. Sequences of their respective heavy chain CDRs are shown in Table 5.
  • Heavy Chain CDR1 for MNC2 is FTFSGYAMS, with the amino acids numbered from left to right 1 through 9, the consensus of other antibodies that bind to that portion of PSMGFR is: F or I at position 1, T at position 2, F at position 3, S at position 4, T, G, or R at position 5, Y at position 6, A, G or T at position 7, M at position 8 and S at position 9.
  • an antibody is chosen for the treatment, prevention or diagnosis of cancer based on having a heavy chain CDR1 that is at least 90% identical to a CDR1 comprising the following amino acids at the specified positions: F or I at position 1, T at position 2, F at position 3, S at position 4, T, G, or R at position 5, Y at position 6, A, G or T at position 7, M at position 8 and S at position 9.
  • Heavy Chain CDR2 for MNC2 is TISSGGTYIYYPDSVKG, with the amino acids numbered from left to right 1 through 17, the consensus of other antibodies that bind to that portion of PSMGFR is: T at position 1, I or S at position 2, I or S at position 3, G or R at position 5, G or A at position 6, T or I at position 9, Y at position 10, Y at position 11, P or S at position12 and DSVKG for positions 13-17.
  • an antibody is chosen for the treatment, prevention or diagnosis of cancer based on having a heavy chain CDR2 that is at least 90% identical to a CDR2 comprising the following amino acids at the specified positions: T at position 1, I or S at position 2, I or S at position 3, G or R at position 5, G or A at position 6, T or I at position 9, Y at position 10, Y at position 11, P or S at position12 and DSVKG for positions 13-17.
  • Heavy Chain CDR3 for MNC2 is –LGGDNYYEYFDV--, with the amino acids numbered from left to right 1 through 15, the consensus of other antibodies that bind to that portion of PSMGFR is: G, L, or N at position 2, G or T at position 4, Y at position 7, D or E at position 12, A at position 14, and Y at position 15.
  • an antibody is chosen for the treatment, prevention or diagnosis of cancer based on having a heavy chain CDR3 that is at least 90% identical to a CDR3 comprising the following amino acids at the specified positions: G, L, or N at position 2, G or T at position 4, Y at position 7, D or E at position 12, A at position 14, and Y at position 15.
  • Light Chain CDR1 for MNC2 is RASKS--VSTSGYSYMH, with the amino acids numbered from left to right 1 through 17, the consensus of other antibodies that bind to that portion of PSMGFR is: K or R at position 1, A or S at position 2, S at position 3, K or Q at position 4, S at position 5, V at position 6, L at position 7, T or S at position 10, Y at position 15, and I, L or M at position 16.
  • an antibody is chosen for the treatment, prevention or diagnosis of cancer based on having a light chain CDR1 that is at least 90% identical to a CDR1 comprising the following amino acids at the specified positions: K or R at position 1, A or S at position 2, S at position 3, K or Q at position 4, S at position 5, L or V at position 6, L at position 7, T or S at position 10, Y at position 15, and I, L or M at position 16.
  • Light Chain CDR2 for MNC2 is LASNLES, with the amino acids numbered from left to right 1 through 7, the consensus of other antibodies that bind to that portion of PSMGFR is: L or W, or S at position 1, A or T at position 2, S at position 3, N or T at position 4, L or R at position 5, E or A at position 6, and S at position 7.
  • an antibody is chosen for the treatment, prevention or diagnosis of cancer based on having a light chain CDR2 that is at least 90% identical to a CDR2 comprising the following amino acids at the specified positions: L or W, or S at position 1, A or T at position 2, S at position 3, N or T at position 4, L or R at position 5, E or A at position 6, and S at position 7.
  • Light Chain CDR3 for MNC2 is QHSRELPFT, with the amino acids numbered from left to right 1 through 9, the consensus of other antibodies that bind to that portion of PSMGFR is: Q at position 1, H or Q at position 2, S, Q or R at position 3, R, S or Y at position 4, E, L, or S at position 5, L or S at position 6, P or S at position 7, F or L at position 8 and T at position 9.
  • an antibody is chosen for the treatment, prevention or diagnosis of cancer based on having a light chain CDR3 that is at least 90% identical to a CDR3 comprising the following amino acids at the specified positions: Q at position 1, H or Q at position 2, S, Q or R at position 3, R, S or Y at position 4, E, L, or S at position 5, L or S at position 6, P or S at position 7, F or L at position 8 and T at position 9.
  • Another set of antibodies was generated and resultant clones were tested for their ability to bind to PSMGFR, N-10 and C-10 peptides. Antibody clones that bound to PSMGFR and N-10 peptides, but not to the C-10 peptide were selected.
  • Table 7 shows the sequences of the heavy chain CDRs for cancer-specific antibodies MNC2, MNE6, 20A10, 3C2B1, plus new antibodies B2, B7, 8C7F3, H11 and B9.
  • Table 8 shows the sequences of the light chain CDRs for cancer-specific antibodies MNC2, MNE6, 20A10, 3C2B1, plus new antibodies B2, B7, 8C7F3, H11 and B9. Consensus sequences for the heavy and light chain CRDs were generated and are shown in Table 7 and Table 8.
  • antibodies 5C6F3 and 25E6 showed great cancer specificity in IHC tissue studies and they both bound to the PSMGFR and N-10 peptides, but not to the C-10 peptide, epitope mapping showed that they bound to epitopes that were a bit N-terminal to the epitopes to which MNC2, MNE6, 20A10 and 3C2B1 bound. For this reason, consensus sequences were generated for MNC2, MNE6, 20A10, 3C2B1 and the new antibodies plus consensus sequences were generated for all the antibodies that bound to N-10 but not to C-10.
  • Heavy Chain CDR1 for MNC2 is FTFSGYAMS, with the amino acids numbered from left to right 1 through 9, the consensus sequence of MNC2, MNE6, 20A10, 3C2B1 and new antibodies B2, B7, 8C7F3, H11 and B9 is: F or I at position 1, T or A at position 2, F at position 3, S at position 4, T, G, or R at position 5, Y or F at position 6, A, G or T at position 7, M at position 8 and S at position 9.
  • the underlined amino acids at positions 2 and 6 are the only additional variants to the consensus sequence generated for cancer-specific antibodies MNC2, MNE6, 20A10, 3C2B1 alone.
  • an antibody is chosen for the treatment, prevention or diagnosis of cancer based on having a heavy chain CDR1 that is at least 90% identical to a CDR1 comprising the following amino acids at the specified positions: F or I at position 1, T or A at position 2, F at position 3, S at position 4, T, G, or R at position 5, Y or F at position 6, A, G or T at position 7, M at position 8 and S at position 9.
  • Heavy Chain CDR2 for MNC2 is TISSGGTYIYYPDSVKG, with the amino acids numbered from left to right 1 through 17, the consensus sequence of MNC2, MNE6, 20A10, 3C2B1 and new antibodies B2, B7, 8C7F3, H11 and B9 is: [00822] T or A at position 1, I or S at position 2, I or S at position 3, N, S, T or G at position 4, G or R at position 5, G or A at position 6, G, T, or D at position 7, Y, K or S at position 8, T or I at position 9, Y at position 10, Y at position 11, P or S at position12 and D at position 13, S or T at position 14, V or L at position 15 and KG for positions 16-17.
  • the underlined amino acids indicate how this more inclusive consensus sequence differs from the consensus sequence generated for MNC2, MNE6, 20A10 and 3C2B1 alone.
  • the consensus sequence for all nine antibodies differs from the consensus sequence for the original cancer-specific four by only 4 amino acids. Note that 2 of the 4 variants are homologous changes, T for S and L for V, which generally do not significantly impact the structure or specificity of a protein.
  • an antibody is chosen for the treatment, prevention or diagnosis of cancer based on having a heavy chain CDR2 that is at least 90% identical to a CDR2 comprising the following amino acids at the specified positions: T or A at position 1, I or S at position 2, I or S at position 3, N, S, T or G at position 4, G or R at position 5, G or A at position 6, G, T, or D at position 7, Y, K, H or S at position 8, T or I at position 9, Y or F at position 10, Y at position 11, P or S at position12 and D at position 13, S or T at position 14, V or L at position 15 and KG for positions 16-17.
  • Heavy Chain CDR3 for MNC2 is LGGDNYYEYFDV, with the amino acids numbered from left to right 2 through 13, the consensus sequence of MNC2, MNE6, 20A10, 3C2B1 and new antibodies B2, B7, 8C7F3, H11 and B9 is: [00826] G, L, or N at position 2, G, T, or Y at position 3, G or T at position 4, A, D, P, R, or S at position 5, Y, M, I or S at position 6, Y at position 7, D, Y, or N at position 8, E, D, Y, L or H at position 9, Y, A, or G at position 10, M, D or F at position 11, D or E at position 12, V, F, Y or L at position 13, and AY at position 14-15.
  • the underlined amino acids indicate how this more inclusive consensus sequence differs from the consensus sequence generated for MNC2, MNE6, 20A10 and 3C2B1 alone.
  • the consensus sequence for all nine antibodies differs from the consensus sequence for the original cancer-specific four by 7 amino acids, with 3 of the 7 substitutions at position 6. For this reason, we conclude that the amino acid at position 6 can be varied without altering the specificity of the antibody.
  • Analysis of the consensus sequence generated with the inclusion of antibodies 5C6F3 and 25E6 highlighted which amino acids were conserved among all eleven antibodies. For this reason, our preferred consensus sequence for heavy chain CDR3 defines amino acids at positions 2, 3, 4, 7, 10, 11, 12, 14 and 15, where for 11 antibodies, there were 3 or less variants at these positions.
  • an antibody is chosen for the treatment, prevention or diagnosis of cancer based on having a heavy chain CDR3 that is at least 90% identical to a CDR3 comprising the following amino acids at the specified positions: G, L, or N at position 2, G, T, or Y at position 3, G or T at position 4, Y at position 7, Y, A, or G at position 10, M, D or F at position 11, D or E at position 12 and AY at position 14-15.
  • Light Chain CDR1 for MNC2 is RASKS--VSTSGYSYMH, with the amino acids numbered from left to right 1 through 17, the consensus sequence of MNC2, MNE6, 20A10, 3C2B1 and new antibodies B2, B7, 8C7F3, H11 and B9 is: [00830] K or R at position 1, A or S at position 2, S or R at position 3, K, Q or A at position 4, S, N or T at position 5, V, I, E, or K at position 6, L, V or S at position 7, S, Y, I or V at position 8, A, S, or H at position 9, T or S at position 10, N, S, or Y at position 11, G, S, D, or Q at position 12, V, Y, K or N at position 13, N, S, or T at position 14, Y or F at position 15, and I, L or M at position 16, and H, A, E or Q at position 17.
  • the underlined amino acids indicate how this more inclusive consensus sequence differs from the consensus sequence generated for MNC2, MNE6, 20A10 and 3C2B1 alone.
  • the consensus sequence for all nine antibodies differs from the consensus sequence for the original cancer-specific four by 13 amino acids. 4 of the 13 are homologous substitutions, which in general do not significantly alter the structure or specificity of the protein. Of the remaining 9 substitutions, 1 is at position 4, 1 is at position 5, 3 are at position 6, 1 is at position 7, 1 is at position 11, and 2 are at is at position 17.
  • the inclusion of the 5 new antibodies did not alter the amino acids, excluding homologous substitutions, at positions 1, 2, 3, 8, 9, 10, 12, 13, 14, 15 or 16.
  • the conserved consensus sequence for light chain CDR1 that defines a MUC1* cancer-specific antibody comprises the amino acids given above for positions 1, 2, 3, 8, 10, 12, 13, 14, 15 and 16.
  • Analysis of the consensus sequence generated with all the antibodies, including 5C6F3 and 25E6 further altered the consensus sequence for light chain CDR1 with amino acid substitutions as follows: L at position 6; D at position 9; D at position 11 and N at position 17.
  • a conserved consensus sequence for light chain CDR1 that defines at least 90% identity of a cancer-specific antibody comprises amino acids defined above at positions 1, 2, 3, 8, 10, 12, 13, 14, 15 and 16.
  • an antibody is chosen for the treatment, prevention or diagnosis of cancer based on having a light chain CDR1 that is at least 90% identical to a CDR1 comprising K or R at position 1, A or S at position 2, S or R at position 3, S, Y, I or V at position 8, T or S at position 10, G, S, D, or Q at position 12, V, Y, K or N at position 13, N, S, or T at position 14, Y or F at position 15, and I, L or M at position 16.
  • Light Chain CDR2 for MNC2 is LASNLES, with the amino acids numbered from left to right 1 through 7, the consensus sequence of MNC2, MNE6, 20A10, 3C2B1 and new antibodies B2, B7, 8C7F3, H11 and B9 is: L, W, S, T or K at position 1, A, T or V at position 2, S at position 3, N or T at position 4, L or R at position 5, E, A, F or D at position 6, and S at position 7.
  • the underlined amino acids indicate how this more inclusive consensus sequence differs from the consensus sequence generated for MNC2, MNE6, 20A10 and 3C2B1 alone.
  • an antibody is chosen for the treatment, prevention or diagnosis of cancer based on having a light chain CDR2 that is at least 90% identical to a CDR2 comprising the following amino acids at the specified positions: L, W, S, T or K at position 1, A, T or V at position 2, S at position 3, N or T at position 4, L or R at position 5, E, A, F or D at position 6, and S at position 7.
  • L, W, S, T or K at position 1
  • A, T or V at position 2 S at position 3
  • N or T at position 4 L or R at position 5 substitutions of which only 2 were not homologous substitutions.
  • an antibody is chosen for the treatment, prevention or diagnosis of cancer based on having a light chain CDR2 that is at least 90% identical to a CDR2 comprising: A, T or V at position 2, S at position 3, N, T, or K at position 4, L or R at position 5, E, A, F or D at position 6, and S at position 7.
  • Light Chain CDR3 for MNC2 is QHSRELPFT, with the amino acids numbered from left to right 1 through 9, t the consensus sequence of MNC2, MNE6, 20A10, 3C2B1 and new antibodies B2, B7, 8C7F3, H11 and B9 is: Q or F at position 1, H or Q at position 2, S, Q, R, D or N at position 3, R, S, Y or N at position 4, E, L, S or H at position 5, L, S, V, D or Y at position 6, P or S at position 7, F, L or P at position 8 and T at position 9.
  • the underlined amino acids indicate how this more inclusive consensus sequence differs from the consensus sequence generated for MNC2, MNE6, 20A10 and 3C2B1 alone. [00838] Analysis of the consensus sequence generated with all the antibodies, including 5C6F3 and 25E6 further altered the consensus sequence for light chain CDR2 with amino acid substitutions as follows: W at position 1; G at position 3; T at position 4; F at position 5; Q at position 8.
  • an antibody is chosen for the treatment, prevention or diagnosis of cancer based on having a light chain CDR3 that is at least 90% identical to a CDR2 comprising: Q, F or W at position 1, H or Q at position 2, R, S, T, Y or N at position 4, E, L, S or H at position 5, L, S, V, D or Y at position 6, P or S at position 7, and T at position 9.
  • the invention is directed to a composition that includes at least two different plasmids transfected into the same immune cell, wherein the first encodes a CAR comprising an antibody fragment, scFv, or peptide that binds to a tumor antigen and the other encodes a gene that is not a CAR, wherein the gene that is not a CAR is expressed from an inducible promoter that is activated by elements of an activated immune cell.
  • the immune cell is a T cell or an NK cell.
  • the immune cell is derived from a stem cell that has been directed to differentiate to that immune cell type in vitro.
  • a CAR containing sequences of the antibody are expressed in a stem cell, which then may be differentiated into an immune cell.
  • the CAR comprises an antibody fragment, scFv or peptide that binds to the extra cellular domain of MUC1*.
  • the CAR comprises an scFv derived from MNC2, MNE6, 20A10, 3C2B1, 5C6F3, 25E6, 18G12, 28F9, 1E4, B12, B2, B7, B9, 8C7F3, or H11.
  • the non-CAR species is a cleavage enzyme.
  • the cleavage enzyme is MMP2, MMP3, MMP9, MMP13, MMP14, MMP16, ADAM10, ADAM17, ADAM28 or catalytically active fragments thereof.
  • the non-CAR species is a cytokine.
  • the Cytokine is IL-7.
  • the cytokine is IL-15.
  • the cytokine is IL-12.
  • the cytokine is IL-18.
  • the sequence of an activated IL-18 is given (SEQ ID NOS:1637-1638). Two examples of NFAT-inducible IL-18 embedded in the Foxp3 enhancer region are given (SEQ ID NOS:1639-1640).
  • NFAT-inducible IL-18 embedded in the IL-2 enhancer region Two examples of NFAT-inducible IL-18 embedded in the IL-2 enhancer region are given (SEQ ID NOS:1641-1642). In one case, there are three (3) NFAT response elements and in the other acse there are six (6) NFAT response elements. The number of NFAT response elements can be varied in order to get the desired amount of IL-18 expressed upon CAR T cell recognition of the target.
  • Examples of antibodies of the invention incorporated into CARS with inducible IL-18 are shown as: murine or human MNC2 in a CAR with a 4-1BB or CD28 co-stimulatory domain plus inducible IL-18 (SEQ ID NOS:1643-1646), or also with a 1XX mutated CD3-zeta (SEQ ID NOS:1647-1650); murine or human MNE6 in a CAR with a 4-1BB or CD28 co-stimulatory domain plus inducible IL-18 (SEQ ID NOS:1651-1654), or also with a 1XX mutated CD3- zeta (SEQ ID NOS:1655-1658); murine or human 20A10 in a CAR with a 4-1BB or CD28 co-stimulatory domain plus inducible IL-18 (SEQ ID NOS:1659-1662), or also with a 1XX mutated CD3-zeta (SEQ ID NOS:1663-1666); murine or human 25E
  • the cytokine is IL-7 and IL-15.
  • expression of the non-CAR species is induced by elements of an activated immune cell.
  • the element of an activated immune cell is an NFAT.
  • the NFAT is NFATc1, NFATc3 or NFATc2.
  • Cytokines IL-7, IL-15, IL-12 and IL- 18 are known to promote T cell persistence.
  • an immune cell described above is administered to a patient for the treatment or prevention of cancer.
  • the cancer is a MUC1 positive cancer or a MUC1* positive cancer.
  • CAR T cells that also induce expression of a cleavage enzyme
  • CAR T cells that also induce local and transient expression of IL-18.
  • Many of the T cell based inducible systems reported insert the gene to be inducibly expressed into an IL-2 promoter or enhancer.
  • human T cells were transduced with both huMNC2-CAR44 and an NFAT inducible IL-18, wherein the Il-18 gene was either inserted into an IL-2 promoter or the Foxp3 enhancer region.
  • FIG. 211A- 211C show graphs of an ELISA experiment measuring the amount of IL-18 secreted into the condition media of huMNC2-CAR44 T cells, which also bear an NFAT inducible IL-18, co-cultured with MUC1* positive cancer cells.
  • Fig. 211A shows the graph of IL-18 secreted into the supernatant of T47D breast cancer cells co-cultured with untransduced human T cells.
  • 211B shows the graph of IL-18 secreted into the supernatant of T47D breast cancer cells co-cultured with huMNC2-CAR44 T cells that also bore an NFAT inducible IL-18 gene inserted into a portion of the Foxp3 enhancer.
  • Fig. 211C shows the graph of IL-18 secreted into the supernatant of T47D breast cancer cells co-cultured with huMNC2-CAR44 T cells that also bore an NFAT inducible IL-18 gene inserted into a portion of the IL-2 enhancer.
  • the Foxp3 system induces rapid and robust expression of IL-18, which is significantly faster and higher than that of the same construct in an IL-2 promoter.
  • the IL-18 gene is inserted downstream of six (6) NFAT response elements, however one can attenuate the amount of the second factor by using a lesser number of response elements or enhance the amount by increasing the number of NFAT response elements.
  • Figure 212A- 212X shows photographs of T47D breast cancer cells (red) doped with varying percentages of T47D cells engineered to express more MUC1* (green).
  • the target cancer cells have been co-cultured with huMNC2-CAR44 T cells with NFAT inducible IL-18 wherein the IL-18 gene has been inserted into either the Foxp3 enhancer/promoter or the IL-2 enhancer/promoter.
  • Fig. 212A-212C, 212I-212K, and 212Q- 212S show the cancer cells co-cultured with untransduced T cells.
  • 212D-212F, 212L- 212N, and 212T-212V show the cancer cells co-cultured with hiMNC2-CAR44 T cells with the NFAT inducible IL-18 gene inserted into the Foxp3 enhancer/promoter.
  • Fig.212G-212H, 212O-212P, and 212W-212X show the cancer cells co-cultured with hiMNC2-CAR44 T cells with the NFAT inducible IL-18 gene inserted into the IL-2 enhancer/promoter.
  • the low antigen density T47D-wt type cells red are being killed when doped with higher percentages of cells that express more MUC1* and thus secrete more IL- 18.
  • Figure 213A- 213B shows graphs of ELISA experiments in which levels of IL-18 secreted into the conditioned media are measured for huMNC1-CAR44 T cells with NFAT inducible IL-18 gene, inserted into the Foxp3 enhancer or promoter, co-cultured with either MUC1* positive cancer cells or MUC1 negative non-cancerous cells.
  • Fig. 213A shows IL-18 secretion from huMNC2-CAR44 T cells with NFAT inducible IL-18 in co-culture with T47D breast cancer cells where the population has been doped with 5%, 10% or 30% T47D cells that had been transfected with even more MUC1*.
  • 213B shows IL-18 secretion from huMNC2-CAR44 T cells with NFAT inducible IL-18 in co-culture with non-cancerous, MUC1 negative HEK293 cells where the cell population has been doped with 5%, 10% or 30% T47D cells that had been transfected with more MUC1*.
  • the amount of IL-18 secreted into the media can be attributed to the MUC1* positive cells that the population was doped with.
  • Time course fluorescent photographs of the experiment show that even when doped with significant percentages of high antigen density MUC1* positive cells, the MUC1 negative cells are not killed by the MUC1* targeting CAR T cells.
  • Figure 214A-214X shows photographs of T47D breast cancer cells (red) or non-cancerous HEK293 cells (also red), where both cell types have been doped with varying percentages of T47D cells engineered to express more MUC1* (green). These target cancer cells have been co-cultured with huMNC2-CAR44 T cells with NFAT inducible IL-18 wherein the IL-18 gene has been inserted into the Foxp3 enhancer/promoter.
  • Fig. 214A-214F shows either T47D cells or HEK293 cells that have not been doped with T47D cells engineered to express high MUC1* density.
  • Fig.214G-214L shows either T47D cells or HEK293 cells that have been doped with 5% T47D cells engineered to express high MUC1* density.
  • Fig. 214M-214R shows either T47D cells or HEK293 cells that have been doped with 10% T47D cells engineered to express high MUC1* density.
  • Fig. 214S-214X shows either T47D cells or HEK293 cells that have been doped with 30% T47D cells engineered to express high MUC1* density.
  • Fig. 214A-B, G-H, M-N, and S-T show T47D breast cancer cells.
  • Fig.214C-F, I-L, O-R, and U-X show HEK293 cells.
  • the invention is directed to a composition that includes at least two different plasmids transfected into the same immune cell, wherein the first encodes a CAR comprising an antibody fragment, scFv or peptide that binds to the extra cellular domain of an antigen on the surface of a B cell and the other encodes a gene that is not a CAR, wherein the gene that is not a CAR is expressed from an inducible promoter that is activated by elements of an activated immune cell.
  • the immune cell is a T cell or an NK cell.
  • the immune cell is derived from a stem cell that has been directed to differentiate to that immune cell type in vitro.
  • a CAR containing sequences of the antibody are expressed in a stem cell, which then may be differentiated into an immune cell.
  • the CAR comprises an antibody fragment, scFv or peptide that binds to CD19.
  • the antibody fragment, scFv or peptide binds to a surface antigen of a B cell or a B cell precursor, or binds to CD19, CD20, CD22, BCMA, CD30, CD138, CD123, CD33 or LeY antigen.
  • the non-CAR species is a cleavage enzyme.
  • the non-CAR species is a cytokine.
  • the Cytokine is IL-7.
  • the cytokine is IL-15. In another aspect the cytokine is IL-7 and IL-15. In one case expression of the non-CAR species is induced by elements of an activated immune cell. In one aspect the element of an activated immune cell is an NFAT. In one aspect the NFAT is NFATc1, NFATc3 or NFATc2. that is not a CAR, wherein the gene that is not a CAR is expressed from an inducible promoter wherein expression is induced by elements of an activated immune cell. In one aspect the immune cell transfected or transduced with the composition is administered to a patient for the treatment or prevention of cancer. In one case the cancer is a leukemia, lymphoma or blood cancer.
  • the gene or plasmid comprising a sequence encoding a CAR or activated T cell inducible protein or peptide there encoded.
  • the gene encoding the CARs and activated T cell induced genes described herein can be virally transduced into an immune cell using viruses, which may or may not result in the CAR gene being integrated into the genome of the recipient cell.
  • Virus delivery systems and viral vectors include but are not limited to retroviruses, including gamma-retroviruses, lentivirus, adenoviruses, adeno- associated viruses, baculoviruses, poxvirus, herpes simplex viruses, oncolytic viruses, HF10, T-Vec and the like.
  • retroviruses including gamma-retroviruses, lentivirus, adenoviruses, adeno- associated viruses, baculoviruses, poxvirus, herpes simplex viruses, oncolytic viruses, HF10, T-Vec and the like.
  • CARs and activated T cell induced genes decribed herein can be directly spliced into the genome of the recipient cell using methods such as CRISPR technology, CRISPR-Cas9 and -CPF1, TALEN, Sleeping Beauty transposon system, and SB 100X.
  • BiTE Bulky cell surface proteins such as MUC1-FL can also cause a steric hindrance problem for BiTEs.
  • a BiTE is a two-headed bispecific antibody wherein one head binds to a T cell and the other head binds to a tumor-associated antigen. In this way, the BiTE links together the T cell and the tumor cells.
  • the antibody that binds to the T cell should be an antibody that activates the T cell, such as an antibody against CD3 or CD28. To solve the steric hindrance problem, the linker between the T cell specific antibody and the tumor specific antibody is lengthened.
  • an anti-MUC1* single chain molecule is fused to a cleavage enzyme or a catalytically active fragment of a cleavage enzyme.
  • the cleavage enzyme is MMP9 (SEQ ID NO:643).
  • the enzyme is a catalytically active fragment of MMP9 (SEQ ID NO:645).
  • the antibody fragment of the CAR is chosen for its ability to recognize MUC1* when cleaved by that specific cleavage enzyme.
  • the cleavage enzyme is MMP9, MMP3, MMP14, MMP2, ADAM17, ADAM TS16, and/or ADAM28.
  • the antibody or antibody fragment binds to a peptide having the sequence of FSAQSGA.
  • cleavage enzymes MMP9 and MMP3 are transduced into a T cell that is also transduced with a CAR with an antibody fragment that is a fragment of MNC2.
  • the cleavage enzyme expressed only after an immune cell recognizes the tumor-associated target on a solid tumor. In this way, the cleavage enzyme will not freely move throughout the body, cleaving MUC1, MUC16 or other proteins, wherein their cleavage could actually promote cancer.
  • cancers that are physically accessible to direct application of chemotherapy agents, CAR T cells and other anti-cancer agents.
  • CAR T cells have been injected directly into the brain and/or cerebral spinal fluid of glioblastoma patients. Radiation has been directed to the prostate area for the treatment of prostate cancers, including those that have metastasized. Hot chemo therapy agents have been directly injected into the intraperitoneal cavity for the treatment of ovarian cancers.
  • a cleavage enzyme is administered in the presence or absence of another anti-cancer agent, which could be a CAR T cell, an immune cell engineered to recognize a tumor-associated antigen, a BiTE, an ADC, a biological or a standard chemotherapy agent.
  • another anti-cancer agent which could be a CAR T cell, an immune cell engineered to recognize a tumor-associated antigen, a BiTE, an ADC, a biological or a standard chemotherapy agent.
  • ovarian cancer can metastasize to anywhere in the body, it usually stays in the abdomen as it spreads to adjacent organs, such as the intestines, liver and stomach.
  • ovarian cancer an ideal test case for improving the effect of anti-cancer agents by administering a cleavage enzyme in combination with other anti-cancer agents, including a platinum-based drug such as carboplatin (Paraplatin) or cisplatin, and/or a taxane such as paclitaxel (Taxol) or docetaxel (Taxotere).
  • a platinum-based drug such as carboplatin (Paraplatin) or cisplatin
  • a taxane such as paclitaxel (Taxol) or docetaxel (Taxotere).
  • Alkeran (Melphalan), Avastin (Bevacizumab), Carboplatin, Clafen (Cyclophosphamide), and Cytoxan have all been approved for the treatment of ovarian cancer.
  • MMP14 has been shown to efficiently cleave MUC1 to MUC1* (Fig. 38).
  • MMP14 is expressed in an immune cell that is also engineered to express a CAR.
  • the CAR is an anti-MUC1* CAR.
  • it can be an MNC2- CAR44 transduced T cell.
  • the MMP14 is directly administered to the patient either in the location of the tumor or by i.v.
  • the cancer is an ovarian cancer and either MMP9 or MMP14 is directly injected into the abdominal area along with an anti-cancer agent, which can be a chemotherapy agent, a biological, an anti-MUC1* CAR T or an anti- MUC16 CAR T.
  • an anti-cancer agent which can be a chemotherapy agent, a biological, an anti-MUC1* CAR T or an anti- MUC16 CAR T.
  • an immune cell which may be a CAR T cell, which further may be expressed off of an inducible promoter is contemplated.
  • Methods used in carrying out experimentation in relation to the present invention [00855] 1.
  • HEK293 or HEK293T cells were used to produce lentivirus.
  • the day prior transfection plates (6well plate) were coated with poly-D-lysine and cells seeded so that cell density reaches 90-95% at the time of transfection and cultures in a 5% CO2 atmosphere.
  • the next day cells were transfected with Lipofectamine 3000 (life technologies) and Opti- MEM® I Reduced Serum Medium according to the manufacturer instructions (0.75ug of lentiviral expression vector and 2.25ug of pPACKH1 packaging mix was used). After 6h incubation, the media was changed and media containing lentivirus was harvested after 24 and 48 hours.
  • Lentivirus was concentrated with Lenti-X concentrator (Clontech) and titer was calculated using the Lenti-X p@4 Rapid Titer Kit (Clontech). Lentivirus was store at -80C in single-use aliquots.
  • Transduction of immune cells with constructs including CARs [00858] Human T cells, if frozen, were thawed and pre-warmed in 100-200 units IL-2 and TexMACS medium, 20 ml, and pelleted by centrifugation.
  • Cells were resuspended in 10 ml of medium and cultured at 37°C, 5% CO2 at 1x10 6 cells/ml in complete medium with anti- CD3/anti-CD28 beads (TransAct kit). [00859] After 4 days in culture, cells were counted and 450 ul of cell suspension was placed in single well of a 24-well plate at a density of approximately 1x10 6 cells/ml. Cells were allowed to settle. 150 ul was carefully removed from the top of each well.
  • Transduced cells were removed, pelleted by centrifugation, and resuspended in fresh medium, adjusting cell density, not to exceed 1.0 x 10 6 cells/ml.
  • Transduced T cells can be expanded and frozen or used directly. Typically transduced T cells are used or frozen between Day 7 and Day 20 post activation with IL-2 and TransAct media. [00860] 2.
  • Human T cells (ALLCELLS) were transduced with huMNC2-CAR44 or huMNC2-CAR50.
  • CAR44 is huMNC2-scFv-CD8-CD8 (transmembrane-41BB-3z).
  • CAR50 is the same as CAR44 except that CAR50 has a murine MNC2-scFv and a CD4 transmembrane domain.
  • the CAR T cells were incubated for 18 hours with target and non- target cells that have been dyed red using CMTMR. When T cells recognize a target cell, they cluster the target cells and begin to kill them.
  • FIG. 45 shows huMNC2-CAR44 or huMNC2-CAR50 T cells being co-cultured with HCT-116 cells transduced to express MUC1*, “HCT-MUC1*” or with HCT-116 cells transduced with a full-length MUC1, “HCT-MUC1-41TR”.
  • MNC2 recognizes an ectopic epitope that is only revealed after cleavage and release of the MUC1 tandem repeat domain.
  • huMNC2-CAR44 nor huMNC2-CAR50 T cells recognize the cells expressing full-length MUC1 (Fig. 45F-45H).
  • Figure 47 shows the contrast between huMNC2-CAR44 recognition of HCT-MUC1* cells, T47D-wt breast cancer cells, and T47D cells with added MMP9 which presumably cleaves the full-length MUC1 to an MNC2 recognizable MUC1*.
  • Figure 55 shows fluorescent images of the huMNC2-CAR44 T cells secreting Granzyme B when co-cultured with the prostate cancer cells, FACS analysis showing increased expression of Granzyme B by the CAR T cells and an xCELLigence experiment showing that the target prostate cancer cells were in fact killed.
  • [00864] 5 Analysis of CAR T cell induced killing of MUC1* positive cancer cells by FACS analysis [00865]
  • the killing effect of the huMNC2-CAR44 T cells increases as the amount of target MUC1* expressed on the cells increases.
  • IFN- ⁇ secretion in media was measured using a human IFN- ⁇ ELISA kit (Biolegend). Plates were coated with an anti- IFN- ⁇ antibody (capture antibody, 1X in coating buffer). After overnight incubation at 4°C, the plate was washed 4 times with PBS-T and blocking solution was added to block remaining binding site on the well. After 1h at RT (shaking at 500rpm) the plate was washed 4 times with PBS-T and conditioned media (CM) and IFN- ⁇ standard, was added. After 2h at RT with shaking, the plate was washed 4 times with PBS-T and detection antibody (1x), was added.
  • CM conditioned media
  • the xCELLigence instrument uses electrode arrays upon which cancer cells are plated.
  • the adherent cancer cells insulate the electrode and so cause an increase in impedance as they grow.
  • T cells are not adherent and remain in suspension so do not contribute to insulation of the electrode which would increase impedance.
  • the T cells or CAR T cells kill the cancer cells on the electrode plate, the cancer cells ball up and float off as they die, which causes the impedance to decrease.
  • the xCELLigence instrument measures impedance as a function of time, which is correlated to cancer cell killing.
  • the electrode plates also have a viewing window.
  • Fig. 48, Fig. 49, Fig. 55H, Fig. 56H, Figs. 57A-57C all show results of CAR T and cancer cell experiments performed on an xCELLigence instrument.
  • Fig. 48, Fig. 49, Fig. 55H, Fig. 56H, Figs. 57A-57C all show results of CAR T and cancer cell experiments performed on an xCELLigence instrument.
  • Fig. 48, Fig. 49, Fig. 55H, Fig. 56H, Figs. 57A-57C all show results of CAR T and cancer cell experiments performed on an xCELLigence instrument.
  • 7 Anti-MUC1* CAR T cell therapy in mice bearing human tumors [00873] Female NOD/SCID/GAMMA (NSG) mice between 8-12 weeks of age were implanted with 500,000 human cancer cells, wherein the cancer cells had previously been stably transfected with Luciferase. Mice bearing Luciferase positive cells can
  • FIG. 58A-58F show fluorescent photographs of mice taken on an IVIS instrument. 10 minutes prior to IVIS photographs, mice were injected intraperitoneally (IP) with Luciferin, which fluoresces after cleavage by Luciferase, thus making tumor cells fluoresce. NSG (NOD/SCID/GAMMA) immune compromised mice that on Day 0 were subcutaneously implanted on the flank with 500,000 human MUC1* positive cancer cells that had been stably transfected with Luciferase.
  • Figure 58F shows a table summarizing the characteristics of the human T cells that were collected from the test mice upon sacrifice.
  • the starting Car T cell population was 50% CD4 positive helper T cells and 50% CD8 positive killer T cells.
  • the percent of CD8 positive cells has increased in the CAR T treated group, indicating in vivo expansion of that group of cells, which is an indicator of efficacy.
  • the CAR T cells express higher levels of PD1 which is a marker of T cell exhaustion.
  • NSG mice were sub-cutaneously implanted into the flank with 500,000 tumor cells then injected on Day 7 and again on Day 14 with either saline solution, PBS, or 10M huMNC2-CAR44 T cells (Fig. 59A-59C).
  • the amount of MUC1* expressed on the tumor cells was varied.
  • the tumor cells that were implanted were T47D-wildtype (Fig. 59B).
  • the T47D cells were doped with 95% T47D cells that had been transfected to express even more MUC1* (Fig. 59C).
  • the tumors comprised of cells expressing more MUC1* were eliminated more quickly and did not recur.
  • FIG. 60A-60C shows NSG mice implanted with T47D-wt breast cancer cells that have been doped with 30% of T47D cells transfected to express more MUC1*. As can be seen, even a small percentage of cells expressing high levels of MUC1* is sufficient to trigger CAR T cell mediated killing of the entire tumor.
  • Naturally occurring tumors are heterogeneous and are comprised of both high and low antigen expressing cells. This experiment indicates that huMNC2-CAR44 T cells would be effective in eradicating naturally occurring tumors.
  • Figures 61A-61J show fluorescent photographs of mice taken on an IVIS instrument.
  • NSG (NOD/SCID/GAMMA) immune compromised mice that on Day 0 were subcutaneously injected into the flank with 500K human BT-20 cells which are a MUC1* positive triple negative breast cancer cell line. The cancer cells had been stably transfected with Luciferase. Tumors were allowed to engraft. On Day 6 after IVIS measurement, animals were given a one-time injection of 10 million of either human T cells transduced with huMNC2-scFv-CAR44 or untransduced T cells. 5 million T cells were injected intra-tumor and 5 million were injected into the tail vein. 10 minutes prior to IVIS photographs, mice were IP injected with Luciferin.
  • the huMNC2-CAR44 T cells were first incubated with beads to which was attached the PSMGFR peptide to pre-stimulate the T cells and in the figure is marked Protocol 1.
  • Protocol 2 the huMNC2-CAR44 T cells were pre-stimulated with live tumor cells, which likely injected more tumor cells into the animals’ circulation.
  • Figures 62A-62M show fluorescent photographs of mice taken on an IVIS instrument. NSG (NOD/SCID/GAMMA) immune compromised mice that on Day 0 were injected into the intraperitoneal cavity (IP) with 500K human SKOV-3 cells which are a MUC1* positive ovarian cancer cell line. The cancer cells had been stably transfected with Luciferase.
  • the pGL4-14 3xIL2 NFAT and pGL4-14 3xFoxP3 NFAT were digested with XhoI and HindIII restriction enzymes (New England Biolabs).
  • the purified plasmids and the synthesized IL18 sequences were assembled using the Gibson assembly cloning kit (New England Biolab).
  • the resulting constructs contains 3 repeats of NFAT response element (IL2 or FoxP3) followed by a minimum promoter (mCMV: SEQ ID NO:1634) and IL18 (SEQ ID NOS:1752-1753) with CD8 leader sequence.
  • MNC2 CAR sequence was amplified from previously made vector by polymerase chain reaction (PCR) using the following primers: 5’- agggagacccaagctggctagttaagcttggatggccttaccagtgaccgccttgc-3’ (SEQ ID NO:1754) and 5’- taggccagagaaatgttctggcattatcagcgagggggcagggcctgc-3’ (SEQ ID NO:1755).
  • IL18 sequence including NFAT response element was amplify from pGL4-14 3xNFAT-IL18 by polymerase chain reaction (PCR) using the following primers: 5’- tgccagaacatttctctgg-3’ (SEQ ID NO:1756) and 5’- acagtcgaggctgatcagcgggtttaaacttatcagtcctcgttctgcacgg-3’ (SEQ ID NO: 1757).
  • the purified PCR fragments and digested pCDNA 3.1 V5 were assembled using the Gibson assembly cloning kit (New England Biolab) to create the construct pCDNA MNC2CAR-3xIL2NFAT-IL18 and pCDNA MNC2CAR-3xFoxP3NFAT-IL18.
  • MNC2 CAR-NFAT-IL18 sequence was amplified from pCDNA MNC2CAR- 3xIL2NFAT-IL18 and pCDNA MNC2CAR-3xFoxP3NFAT-IL18.by polymerase chain reaction (PCR) using the following primers: 5’- atgcaggccctgcccctcgctgataagtttaaactgccagaacatttctctggcctaac-3’ (SEQ ID NO:1758) and 5’- accggagcgatcgcagatccttcgcggccgcttatcagtcctcgttctgcacggtgaac-3’ (SEQ ID NO:1759).
  • the purified PCR fragments and digested pCDH Dual Hygro (System Biosciences, CA) were assembled using the Gibson assembly cloning kit (New England Biolab) to create the construct pCDH MNC2CAR-3xIL2NFAT-IL18 and pCDH MNC2CAR-3xFoxP3NFAT- IL18.
  • MSCV promoter sequence was amplified from pCDH-MSCV-MCS-EF1a-GFP (System Biosciences).by polymerase chain reaction (PCR) using the following primers: 5’- attgcactagttgaaagaccccacctgtagg-3’ (SED ID NO:1760) and 5’- aatgctctagaatacgggtatccagg- 3’ (SEQ ID NO:1761).
  • MNC2 CAR-IL2NFAT-IL18 sequence was amplified from pCDNA MNC2CAR- 3xIL2NFAT-IL18 by polymerase chain reaction (PCR) using the following primers: 5’ atagcgaattcgtaccgagggccaccatgg-3’ (SEQ ID NO:1762) and 5’- taggcctcccaccgtacacgcctaggtaccacgccttctgtatg-3’ (SEQ ID NO:1763) MNC2 CAR- IL2NFAT-IL18 sequence was amplified from pCDNA MNC2CAR-3xFoxP3NFAT-IL18 by polymerase chain reaction (PCR) using the following primers: 5’ atagcgaattcgtaccgagggccaccatgg -3’ (SEQ ID NO:176
  • 6xNFAT response elements [00891] 6xNFAT (IL2 and FoxP3) response element were synthesized followed by different minimal promoter: mCMV (SEQ ID NO:1634), mIL2P (SEQ ID NO:1635) and miniP (SEQ ID NO:1636).
  • 6xNFAT sequences were amplified by polymerase chain reaction (PCR) using the following primers: 5’-tgccagaacatttctctgg-3’ (SEQ ID NO:1756) and 5’- taaggccatggtggctagc-3’ (SEQ ID NO:1765).
  • the purified PCR fragments and digested (KpnI and XhoI) pCDNA MNC2CAR 3XNFAT IL18 were assembled using the Gibson assembly cloning kit (New England Biolab) to create constructs with 6x NFAT response elements in place of the 3x NFAT response elements.
  • 6xNFAT sequences were amplified, from the pCDNA vector created above, by polymerase chain reaction (PCR) using the following primers: 5’- aataagtttaaactgccagaacatttctctgg-3’ (SEQ ID NO:1766) and 5’- atatagcggccgcttatcagtcctcgttctgcacgg-3’ (SEQ ID NO:1767).

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