WO2019165421A1 - Diagnostic methods using anti-muc1* antibodies - Google Patents

Diagnostic methods using anti-muc1* antibodies Download PDF

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Publication number
WO2019165421A1
WO2019165421A1 PCT/US2019/019566 US2019019566W WO2019165421A1 WO 2019165421 A1 WO2019165421 A1 WO 2019165421A1 US 2019019566 W US2019019566 W US 2019019566W WO 2019165421 A1 WO2019165421 A1 WO 2019165421A1
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Prior art keywords
antibody
seq
psmgfr
peptide
muc1
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PCT/US2019/019566
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English (en)
French (fr)
Inventor
Cynthia Bamdad
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Minerva Biotechnologies Corp
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Minerva Biotechnologies Corp
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Priority claimed from PCT/US2018/062569 external-priority patent/WO2019104306A1/en
Application filed by Minerva Biotechnologies Corp filed Critical Minerva Biotechnologies Corp
Priority to AU2019225237A priority Critical patent/AU2019225237B2/en
Priority to EP19757027.8A priority patent/EP3759145A4/en
Priority to CA3092247A priority patent/CA3092247A1/en
Priority to CN201980027373.9A priority patent/CN112272677B/zh
Priority to JP2020544813A priority patent/JP7411559B2/ja
Priority to US16/975,625 priority patent/US11976132B2/en
Publication of WO2019165421A1 publication Critical patent/WO2019165421A1/en
Priority to EP20738367.0A priority patent/EP3908603A4/en
Priority to AU2020205735A priority patent/AU2020205735A1/en
Priority to JP2021540477A priority patent/JP2022527144A/ja
Priority to CN202080020073.0A priority patent/CN113853386A/zh
Priority to PCT/US2020/013410 priority patent/WO2020146902A2/en
Priority to CA3126391A priority patent/CA3126391A1/en
Priority to CN202510558379.6A priority patent/CN120484122A/zh
Priority to IL276925A priority patent/IL276925A/en
Anticipated expiration legal-status Critical
Priority to IL284772A priority patent/IL284772A/en
Priority to US17/373,609 priority patent/US12583927B2/en
Priority to JP2023218543A priority patent/JP7705442B2/ja
Priority to US18/612,767 priority patent/US12351646B2/en
Priority to US18/935,308 priority patent/US20250066505A1/en
Priority to JP2025126649A priority patent/JP2025172739A/ja
Priority to AU2026201952A priority patent/AU2026201952A1/en
Ceased legal-status Critical Current

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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A61P35/04—Antineoplastic agents specific for metastasis
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K35/00—Medicinal preparations containing materials or reaction products thereof with undetermined constitution
    • A61K35/12—Materials from mammals; Compositions comprising non-specified tissues or cells; Compositions comprising non-embryonic stem cells; Genetically modified cells
    • A61K35/14—Blood; Artificial blood
    • A61K35/17—Lymphocytes; B-cells; T-cells; Natural killer cells; Interferon-activated or cytokine-activated lymphocytes
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K40/00—Cellular immunotherapy
    • A61K40/10—Cellular immunotherapy characterised by the cell type used
    • A61K40/11—T-cells, e.g. tumour infiltrating lymphocytes [TIL] or regulatory T [Treg] cells; Lymphokine-activated killer [LAK] cells
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K40/00—Cellular immunotherapy
    • A61K40/30—Cellular immunotherapy characterised by the recombinant expression of specific molecules in the cells of the immune system
    • A61K40/31—Chimeric antigen receptors [CAR]
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K40/00—Cellular immunotherapy
    • A61K40/40—Cellular immunotherapy characterised by antigens that are targeted or presented by cells of the immune system
    • A61K40/41—Vertebrate antigens
    • A61K40/42—Cancer antigens
    • A61K40/4256—Tumor associated carbohydrates
    • A61K40/4257—Mucins, e.g. MUC-1
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/50—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates
    • A61K47/51—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent
    • A61K47/68—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an antibody, an immunoglobulin or a fragment thereof, e.g. an Fc-fragment
    • A61K47/6835—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an antibody, an immunoglobulin or a fragment thereof, e.g. an Fc-fragment the modifying agent being an antibody or an immunoglobulin bearing at least one antigen-binding site
    • A61K47/6851—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an antibody, an immunoglobulin or a fragment thereof, e.g. an Fc-fragment the modifying agent being an antibody or an immunoglobulin bearing at least one antigen-binding site the antibody targeting a determinant of a tumour cell
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/28—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C07K16/30—Immunoglobulins [IG], 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 [IG], 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 [IG], 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
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/575—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • G01N33/57515—Immunoassay; Biospecific binding assay; Materials therefor for cancer of the breast
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/575—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • G01N33/57525—Immunoassay; Biospecific binding assay; Materials therefor for cancer of the liver or pancreas
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/575—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • G01N33/57555—Immunoassay; Biospecific binding assay; Materials therefor for cancer of the prostate
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/575—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • G01N33/57557—Immunoassay; Biospecific binding assay; Materials therefor for cancer of other specific parts of the body, e.g. brain
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/575—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • G01N33/5758—Immunoassay; Biospecific binding assay; Materials therefor for cancer involving compounds serving as markers for tumours, cancers or neoplasias, e.g. cellular determinants, receptors, heat shock/stress proteins, A-protein, oligosaccharides or metabolites
    • G01N33/5759—Immunoassay; Biospecific binding assay; Materials therefor for cancer involving compounds serving as markers for tumours, cancers or neoplasias, e.g. cellular determinants, receptors, heat shock/stress proteins, A-protein, oligosaccharides or metabolites involving compounds localised on the membrane of tumour or cancer cells
    • 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)
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2333/00—Assays involving biological materials from specific organisms or of a specific nature
    • G01N2333/435—Assays involving biological materials from specific organisms or of a specific nature from animals; from humans
    • G01N2333/46—Assays involving biological materials from specific organisms or of a specific nature from animals; from humans from vertebrates
    • G01N2333/47—Assays involving proteins of known structure or function as defined in the subgroups
    • G01N2333/4701—Details
    • G01N2333/4725—Mucins, e.g. human intestinal mucin
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2800/00—Detection or diagnosis of diseases
    • G01N2800/52—Predicting or monitoring the response to treatment, e.g. for selection of therapy based on assay results in personalised medicine; Prognosis

Definitions

  • the present invention is directed to a method of diagnosing cancer and determining suitability of treating a patient suffering from cancer or metastasis of cancer characterized by aberrant expression of MUC1, with a MUC1* targeting therapeutic, comprising contacting cells or tissue of a patient diagnosed with or suspected of having cancer, with an antibody that binds to a form of MUC1 that is devoid of the tandem repeat domain, wherein the presence of specific binding of the antibody to the cleaved or truncated form of MUC1, and wherein such binding is in an abnormal pattern, indicates that a MUC1* targeting therapeutic is suitable to be used to treat the patient.
  • MUC1* as a transmembrane cleavage product of MUC1 that functions as a growth factor receptor and is devoid of the tandem repeat sequences.
  • MUC1 can be cleaved by different enzymes, which cleave at different sites. Which cleavage enzyme clips MUC1 may be tissue specific or patient specific. The conformation of the extra cellular domain of MUC1* may change depending on which cleavage enzyme cleaves it.
  • Anti- MUC1* antibodies may bind to the extra cellular domain of the transmembrane receptor that remains after cleavage.
  • the antibody may bind to a peptide of Primary Sequence of MUC1 Growth Factor (PSMGFR), PSMGFR N-10, PSMGFR C-10, or may bind to PSMGFR N-10 but not to PSMGFR C-10, or may bind to PSMGFR C-10 but not to PSMGFR N-10, or may bind to the PSMGFR N+20 peptides such as N+20/C-22, N+20/C-41, or N+20/C-27 peptide, or a N+9/C-9 peptide.
  • PSMGFR Primary Sequence of MUC1 Growth Factor
  • the antibody may bind to a peptide of sequence N+20-PSMGFR or N+9-PSMGFR.
  • diagnostic assays employing anti-MUCl* antibodies or fragments thereof are used to screen patients to determine their potential benefit from a MUC1* targeting therapeutic.
  • the antibody used in the diagnostic and the antibody or fragment thereof that is incorporated into the therapeutic are derived from the same antibody. The species of the diagnostic antibody and the therapeutic antibody do not need to be the same.
  • a suspect cellular or tissue specimen which may be a biopsy, from a patient diagnosed with cancer or suspected of developing cancer is contacted with an anti- MUC1* antibody;
  • a normal cellular or tissue specimen from the patient or from a healthy donor is contacted with the same anti-MUCl* antibody, which may be an archived reference specimen;
  • antibody binding is detected;
  • the extent and pattern of antibody binding to the suspect specimen is compared to that of the normal specimen;
  • a determination that the suspect specimen overexpresses MUC1*, or expresses MUC1* in a uniform pattern as opposed to expression that is restricted to the apical border indicates that the patient is suffering from a MUC1* positive cancer;
  • a therapeutic agent that incorporates an anti-MUCl* antibody, or fragment thereof, is administered to the patient.
  • anti-MUCl* antibodies can be attached to an imaging agent for use in a patient as a whole body diagnostic to determine if the patient has a MUC1* positive tumor or, depending on the specific antibody used, if the patient would benefit from a therapeutic comprising all or a fragment of the antibody that is attached to the imaging agent.
  • the species of the diagnostic antibody and the therapeutic antibody do not need to be the same.
  • Antibodies generated in camelid species are particularly useful for in vivo diagnostic assays because camelids generated small monovalent antibodies that have a short half-life in humans.
  • anti-MUCl* antibodies which may be attached to an imaging agent are used intra-surgically to detect or mark cancerous tissues so they can be excised during the surgery.
  • anti-MUCl* antibodies or fragments thereof that bind to a peptide having some or all of the sequence of the PSMGFR peptide are used for the diagnosis and/or treatment of breast cancers.
  • anti-MUCl* antibodies or fragments thereof that bind to a peptide having some or all of the sequence of the PSMGFR peptide, extended at the N- terminus by as many as 20 amino acids are used for the diagnosis and/or treatment of pancreatic cancers.
  • anti-MUCl* antibodies or fragments thereof that bind to a peptide having some or all of the sequence of the PSMGFR peptide, extended at the N- terminus by as many as 20 amino acids are used for the diagnosis and/or treatment of esophageal cancers.
  • anti-MUCl* antibodies or fragments thereof that bind to a peptide having some or all of the sequence of the PSMGFR peptide, extended at the N- terminus by as many as 20 amino acids are used for the diagnosis and/or treatment of prostate cancers.
  • the MUC1* targeting therapeutic may be a cancer immunotherapy.
  • the MUC1* targeting therapeutic may be a CAR T, a BiTE, an ADC (antibody drug conjugate), a bispecific antibody or an antibody mimic.
  • the MUC1* targeting therapeutic may be an antibody that binds to a cleaved form of MUC1 wherein the cleaved form is the extra cellular domain of the transmembrane receptor that remains after cleavage.
  • the antibody may bind to a peptide known as Primary Sequence of MUC1 Growth Factor (PSMGFR) or to a peptide that is N-terminally extended for up to 20 amino acids beyond the PSMGFR sequence.
  • PSMGFR Primary Sequence of MUC1 Growth Factor
  • the antibody used in the therapeutic may be derived from the antibody used in the diagnostic assay, but need not be generated in the same species animal.
  • the inventive method may be an in vitro assay.
  • the assay may be carried out on a tissue specimen, bodily fluid sample, or a blood sample.
  • the assay may be an in vivo assay.
  • An imaging agent may be attached to the antibody.
  • the invention may comprise a second antibody, and the steps may comprise determining the ratio of the amount of a first antibody to a second antibody.
  • the first antibody may bind to an extra cellular domain of the transmembrane receptor that remains after cleavage and the second antibody may bind to a portion of the MUC1 extra cellular domain that is N-terminal of the cleavage site, such as the tandem repeat sequences.
  • the non-human, human or humanized anti-MUCl* antibody or antibody fragment or antibody-like protein may specifically bind to
  • PSMGFR peptide as set forth in SEQ ID NO:4; [0019] (iii) PSMGFR N+20/C-22, a peptide having amino acid sequence of
  • V QLTLAFREGTIN VHD VETQFN Q Y (SEQ ID NO:7);
  • PSMGFR N+20/C-41 a peptide having amino acid sequence of
  • V QLTLAFREGTIN VHD VETQFN Q YKTE A AS R YNLTIS D VS VS D VP (SEQ ID NO: 10).
  • the antibody that binds to the extra cellular domain of the transmembrane receptor that remains after cleavage may be SDIX SRY polyclonal antibody, MNC2 monoclonal antibody, MNE6 monoclonal antibody, or monoclonal antibodies 1E4, 29H1, 31A1, 32C1, and 45C11 reactive with PSMGFR N+20/C-27; 17H6, 39H5, 3C5, 8A9 reactive with PSMGFR N+9/C-9; 18G12, 20A10, 25E6, 28F9, and 18B4 reactive with PSMGFR, as well as MNC2 and MNE6, which are also reactive with PSMGFR.
  • These antibodies may be human, humanized, mouse, camelid, llama, alpaca, camel, rabbit, goat, hamster or other non-human species.
  • Figure 1A-1D shows photographs of adjacent serial sections of breast cancer tissue arrays and graphical representations of the pathologist scores, according to Allred scoring system.
  • Pathologist score is 0-3, where 0 showed no staining and 3 is the greatest staining.
  • the graphs are also color coded, where a pathologist score zero is black, 1 is yellow, 2 is orange, and 3 is red; tissues that scored zero when probed with an antibody that recognizes full-length MUC1 but positive when probed with an antibody that recognizes MUC1* were colored green; and missing or uninterpretable tissues were scored -1.
  • Figure 1A shows photographs of the breast cancer tissue arrays after they were stained with VU4H5, which is an antibody that binds to the tandem repeat domains of full-length MUC1.
  • Figure IB shows graphs of the pathologist scores for the tissues pictured in Fig. 1A.
  • Figure 1C shows photographs of the breast cancer tissue arrays after they were stained with MNC2, which is an antibody that binds to an epitope within the PSMGFR region of MUC1*.
  • Figure ID shows graphs of the pathologist scores for the tissues pictured in Fig. 1C.
  • Figure 2A-2B shows pie chart graphs of the pathologist scores of the arrays shown in Fig. 1A and Fig. 1C.
  • Fig. 2A shows that the antibody that binds to tandem repeats of full-length MUC1 misses 30% of breast cancers.
  • Fig. 2B shows that the anti-MUCl* antibody MNC2 recognizes 95% of breast cancers.
  • Anti-MUCl -full-length only binds strongly to 10% of the breast tumors, while anti-MUCl* antibody MNC2 binds strongly to about 50% of breast tumors.
  • Figure 3A-3B shows pie chart graphs of the pathologist scores and a photograph of breast cancer array BR1141 after staining with anti-MUCl* antibody huMNC2-scFv-Fc.
  • Figure 4A-4C shows photographs, at two different magnifications, of individual breast cancer specimens from breast cancer array BR1141 after staining with anti-MUCl* antibody huMNC2-scFv-Fc.
  • the position in the array, cancer sub-type, tumor grade, TNM (Tumor stage, Node involvement, and Metastasis) and pathologist score are indicated in figures.
  • Standard immunohistochemistry methods were used.
  • Antibody concentration was titered using the highest concentration at which the antibody showed expected staining of normal tissues without staining stroma.
  • the antibody was conjugated to a biotin through its Fc region, to avoid false positive due to anti-human secondary antibodies staining host antibodies as well as B cell follicules.
  • FIG. 4A shows the specimen at position A7 which was negative for huMNC2 reactive cells.
  • Fig. 4B shows the specimen at position A9 which is a Grade 2 cancer, with lymph node involvement that scored +1 for huMNC2 reactivity.
  • Fig. 4C shows the specimen at position B10 which is a larger Grade 2 tumor, with lymph node involvement that scored +2 for huMNC2 reactivity.
  • Figure 5A-5B shows photographs, at two different magnifications, of individual breast cancer specimens from breast cancer array BR1141 after staining with anti-MUCl* antibody huMNC2-scFv-Fc.
  • Fig. 5A shows the specimen at position D7 which is a Grade 2 cancer, without lymph node involvement that scored +3 for huMNC2 reactivity.
  • Fig. 5B shows the specimen at position F6 which is a Grade 2 tumor, with lymph node involvement that scored +4 for huMNC2 reactivity.
  • Figure 6A-6B shows pie chart graphs of the pathologist scores and a photograph of ovarian cancer array BCl l l5a after staining with anti-MUCl* antibody huMNC2-scFv-Fc.
  • Figure 7A-7C shows magnified photographs of different cancer sub-types after staining with anti-MUCl* antibody huMNC2-scFv-Fc.
  • Fig. 7A shows a photograph of a Grade 2 breast tumor that pathologist scored +4.
  • Fig. 7B shows a photograph of a Grade 2 ovarian tumor that pathologist scored +3.
  • Fig. 7C shows a photograph of a Grade 3 pancreatic tumor that pathologist scored +3.
  • IHC studies of over 1,000 tumor specimens showed that huMNC2-scFv recognized 95% of Breast Cancers (90% triple negative), 83% Ovarian, 78% Pancreatic & 71% Lung Cancers.
  • Figure 8A-8D shows magnified photographs of different cancer sub-types after staining with anti-MUCl* antibody huMNC2-scFv-Fc.
  • Fig. 8A shows a photograph of a Grade 2 breast tumor that pathologist scored +2.
  • Fig. 8B shows a photograph of a Grade 3 ovarian tumor that pathologist scored +3.
  • Fig. 8C shows a photograph of a Grade 3 pancreatic tumor, with lymph node involvement that pathologist scored +3.
  • Fig. 8D shows a photograph of a lung cancer that pathologist scored +3.
  • Figure 9A-9I shows magnified photographs of various normal tissues after staining with anti-MUCl* antibody huMNC2-scFv-Fc. Conditions and concentrations used were identical to those used for studying cancerous tissues.
  • Fig. 9A shows normal adrenal gland tissue.
  • Fig. 9B shows normal brain tissue.
  • Fig. 9C shows normal breast tissue.
  • Fig. 9D shows normal stomach tissue.
  • Fig. 9E shows normal heart tissue.
  • Fig. 9F shows normal kidney tissue.
  • Fig. 9G shows normal testis tissue.
  • Fig. 9H shows normal intestine tissue.
  • Fig. 91 shows normal liver tissue.
  • FIG. 10A-10F shows photographs of normal kidney tissues after staining with anti- MUCl* antibody huMNC2-scFv-Fc. Conditions and concentrations used were identical to those used for studying cancerous tissues.
  • Fig. 10A shows normal kidney tissue with huMNC2 reactivity limited to the apical border, which is normal expression.
  • Fig. 10B is the same tissue at greater magnification.
  • Fig. 10C shows another example of normal kidney tissue with undetectable huMNC2 reactivity.
  • Fig. 10D is the same tissue at greater magnification.
  • Fig. 10E shows another example of normal kidney tissue with huMNC2 reactivity limited to the apical border, which is normal expression.
  • Fig. 10A shows normal kidney tissue with huMNC2 reactivity limited to the apical border, which is normal expression.
  • 10F is the same tissue at greater magnification. Further studies showed that less than 10% of normal kidney tissue showed huMNC2 reactivity at distal collecting tubules wherein such reactivity was strictly limited to the apical border, which is a normal expression pattern.
  • Figure 11A-11B shows pie chart graphs of the pathologist scores and a photograph of esophageal cancer array BC001113 after staining with anti-MUCl* antibody huMNC2-scFv-Fc.
  • Figure 12A-12F shows photographs, at two different magnifications, of individual esophageal cancer specimens from esophageal cancer array BC001113, after staining with anti- MUCl* antibody huMNC2-scFv-Fc.
  • the position in the array, cancer sub-type, tumor grade, and pathologist score are indicated in figures.
  • Fig. 12A shows the specimen at position A4 which was negative for huMNC2 reactive cells.
  • Fig. 12B shows the same specimen at greater magnification.
  • Fig. 12C shows the specimen at position D2 which the pathologist scored as trace reactivity to huMNC2.
  • Fig. 12D shows the same specimen at greater magnification.
  • Fig. 12E shows the specimen at position B8 which the pathologist scored as +1 reactivity to huMNC2.
  • Fig. 12F shows the same specimen at greater magnification.
  • Figure 13A-13D shows photographs, at two different magnifications, of individual esophageal cancer specimens from esophageal cancer array BC001113, after staining with anti- MUCl* antibody huMNC2-scFv-Fc.
  • the position in the array, cancer sub-type, tumor grade, and pathologist score are indicated in figures.
  • Fig. 13A shows the specimen at position D6, a Grade 4 tumor, which the pathologist scored +2.
  • Fig. 13B shows the same specimen at greater magnification.
  • Fig. 13C shows the specimen at position D5, a Grade 3 tumor, which the pathologist scored +3.
  • Fig. 12D shows the same specimen at greater magnification.
  • Figure 14A-14B shows pie chart graphs of the pathologist scores and a photograph of pancreatic cancer array PA805b after staining with anti-MUCl* antibody huMNC2-scFv-Fc.
  • Figure 15A-15D shows photographs, at two different magnifications, of individual pancreatic cancer specimens from pancreatic cancer array PA805b, after staining with anti- MUCl* antibody huMNC2-scFv-Fc.
  • the position in the array, cancer sub-type, tumor grade, and pathologist score are indicated in figures.
  • Fig. 15A shows the specimen at position F3, a Grade 3 tumor, which the pathologist scored +3.
  • Fig. 15B shows the same specimen at greater magnification.
  • Fig. 15C shows the specimen at position Bl, a Grade 1 tumor, which the pathologist scored +2.
  • Fig. 15D shows the same specimen at greater magnification.
  • Figure 16A-16D shows photographs, at two different magnifications, of individual pancreatic cancer specimens from pancreatic cancer array PA805b, after staining with anti- MUCl* antibody huMNC2-scFv-Fc.
  • the position in the array, cancer sub-type, tumor grade, and pathologist score are indicated in figures.
  • Fig. 16A shows the specimen at position A2, a Grade 1 tumor, which the pathologist scored +2.
  • Fig. 16B shows the same specimen at greater magnification.
  • Fig. 16C shows the specimen at position C3, a Grade 2 tumor, which the pathologist scored +2.
  • Fig. 16D shows the same specimen at greater magnification.
  • Figure 17A-17D shows photographs, at two different magnifications, of individual pancreatic cancer specimens from pancreatic cancer array PA805b, after staining with anti- MUCl* antibody huMNC2-scFv-Fc.
  • the position in the array, cancer sub-type, tumor grade, and pathologist score are indicated in figures.
  • Fig. 17A shows the specimen at position C6, a Grade 2 tumor, which the pathologist scored +2.
  • Fig. 17B shows the same specimen at greater magnification.
  • Fig. 17C shows the specimen at position Dl, a larger Grade 3 tumor, with lymph node involvement that the pathologist scored +3.
  • Fig. 17D shows the same specimen at greater magnification.
  • Figure 18A-18D shows photographs, at two different magnifications, of individual pancreatic cancer specimens from pancreatic cancer array PA805b, after staining with anti- MUCl* antibody huMNC2-scFv-Fc.
  • the position in the array, cancer sub-type, tumor grade, and pathologist score are indicated in figures.
  • Fig. 18A shows the specimen at position E2, a Grade 1 tumor, which the pathologist scored +2.
  • Fig. 18B shows the same specimen at greater magnification.
  • Fig. 18C shows the specimen at position E10, a smaller Grade 3 tumor, with lymph node involvement that the pathologist scored +3.
  • Fig. 18D shows the same specimen at greater magnification.
  • Figure 19 shows a photograph of pancreatic cancer array PA805b that was stained with the secondary antibody alone, as a control.
  • FIG. 20A-20B shows photographs of pancreatic cancer array PA805b that were stained with an anti-MUCl* monoclonal antibody or an anti-MUCl* polyclonal antibody.
  • Fig. 20A shows a photograph of the pancreatic cancer array that was stained with anti-MUCl* monoclonal antibody huMNC2-scFv.
  • Fig. 20B shows a photograph of the pancreatic cancer array that was stained with anti-MUCl* polyclonal antibody SDIX. Both polyclonal and monoclonal antibodies were generated by immunizing the animals with the PSMGFR peptide.
  • the circled specimens are indicated because they show different staining when probed with the monoclonal versus the polyclonal antibody.
  • the numbers beneath each specimen indicate the pathologist score, when probed with huMNC2-scFv, followed by a slash mark, then the tumor grade.
  • Figures 21A-21D show photographs of individual tumor tissue specimens from the pancreatic cancer array, comparing the staining intensity and pattern of staining when the patient sample is probed with monoclonal antibody MNC2 or polyclonal antibody SDIX, wherein both antibodies bind to the PSMGFR peptide.
  • MNC2 monoclonal antibody
  • SDIX polyclonal antibody
  • Figures 22A-22D show photographs of individual tumor tissue specimens from the pancreatic cancer array, comparing the staining intensity and pattern of staining when the patient sample is probed with monoclonal antibody MNC2 or polyclonal antibody SDIX, wherein both antibodies bind to the PSMGFR peptide.
  • MNC2 monoclonal antibody
  • SDIX polyclonal antibody
  • Figures 23A-23D show photographs of individual tumor tissue specimens from the pancreatic cancer array, comparing the staining intensity and pattern of staining when the patient sample is probed with monoclonal antibody MNC2 or polyclonal antibody SDIX, wherein both antibodies bind to the PSMGFR peptide.
  • MNC2 monoclonal antibody
  • SDIX polyclonal antibody
  • Figures 24A-24D show photographs of individual tumor tissue specimens from the pancreatic cancer array, comparing the staining intensity and pattern of staining when the patient sample is probed with monoclonal antibody MNC2 or polyclonal antibody SDIX, wherein both antibodies bind to the PSMGFR peptide.
  • MNC2 monoclonal antibody
  • SDIX polyclonal antibody
  • Figures 25A-25D show photographs of individual tumor tissue specimens from the pancreatic cancer array, comparing the staining intensity and pattern of staining when the patient sample is probed with monoclonal antibody MNC2 or polyclonal antibody SDIX, wherein both antibodies bind to the PSMGFR peptide.
  • MNC2 monoclonal antibody
  • SDIX polyclonal antibody
  • Figures 26A-26D show photographs of individual tumor tissue specimens from the pancreatic cancer array, comparing the staining intensity and pattern of staining when the patient sample is probed with monoclonal antibody MNC2 or polyclonal antibody SDIX, wherein both antibodies bind to the PSMGFR peptide.
  • MNC2 monoclonal antibody
  • SDIX polyclonal antibody
  • Figures 27A-27D show photographs of individual tumor tissue specimens from the pancreatic cancer array, comparing the staining intensity and pattern of staining when the patient sample is probed with monoclonal antibody MNC2 or polyclonal antibody SDIX, wherein both antibodies bind to the PSMGFR peptide.
  • MNC2 monoclonal antibody
  • SDIX polyclonal antibody
  • Figures 28A-28D show photographs of individual tumor tissue specimens from the pancreatic cancer array, comparing the staining intensity and pattern of staining when the patient sample is probed with monoclonal antibody MNC2 or polyclonal antibody SDIX, wherein both antibodies bind to the PSMGFR peptide.
  • MNC2 monoclonal antibody
  • SDIX polyclonal antibody
  • Figures 29A-29D show photographs of individual tumor tissue specimens from the pancreatic cancer array, comparing the staining intensity and pattern of staining when the patient sample is probed with monoclonal antibody MNC2 or polyclonal antibody SDIX, wherein both antibodies bind to the PSMGFR peptide.
  • MNC2 monoclonal antibody
  • SDIX polyclonal antibody
  • Figures 30A-30D show photographs of individual tumor tissue specimens from the pancreatic cancer array, comparing the staining intensity and pattern of staining when the patient sample is probed with monoclonal antibody MNC2 or polyclonal antibody SDIX, wherein both antibodies bind to the PSMGFR peptide.
  • MNC2 monoclonal antibody
  • SDIX polyclonal antibody
  • Figures 31A-31D show photographs of individual tumor tissue specimens from the pancreatic cancer array, comparing the staining intensity and pattern of staining when the patient sample is probed with monoclonal antibody MNC2 or polyclonal antibody SDIX, wherein both antibodies bind to the PSMGFR peptide.
  • MNC2 monoclonal antibody
  • SDIX polyclonal antibody
  • Figures 32A-32D show photographs of individual tissue specimens from the pancreatic cancer array, but the specimens that are shown are normal pancreatic tissues.
  • the staining intensity and pattern of staining of monoclonal antibody MNC2 is compared to that of polyclonal antibody SDIX.
  • (A) is stained with MNC2
  • (B) is the same tissue but at greater magnification
  • (C) is stained with SDIX
  • (D) is that same tissue but shown at greater magnification.
  • Figures 33A-33D show photographs of individual tissue specimens from the pancreatic cancer array, but the specimens that are shown are normal pancreatic tissues.
  • the staining intensity and pattern of staining of monoclonal antibody MNC2 is compared to that of polyclonal antibody SDIX.
  • (A) is stained with MNC2
  • (B) is the same tissue but at greater magnification
  • (C) is stained with SDIX
  • (D) is that same tissue but shown at greater magnification.
  • Figures 34A-34D show photographs of individual tissue specimens from the pancreatic cancer array, but the specimens that are shown are normal pancreatic tissues.
  • the staining intensity and pattern of staining of monoclonal antibody MNC2 is compared to that of polyclonal antibody SDIX.
  • (A) is stained with MNC2
  • (B) is the same tissue but at greater magnification
  • (C) is stained with SDIX
  • (D) is that same tissue but shown at greater magnification.
  • Figure 35A-35B shows cartoons of MUC1* expression on cancer cells and on normal hematopoietic stem cells. Fig.
  • 35A depicts MUC1* on a cancer cell being probed by anti- MUCl* monoclonal antibody, MNC2.
  • Fig. 35B depicts MUC1* on normal hematopoietic stem cells being probed by anti-MUCl* monoclonal antibody, MNC3. Both antibodies were generated by immunizing the animal with a PSMGFR peptide. MNC2 does not bind to normal hematopoietic stem cells but MNC3 does.
  • Figure 36A-36B shows FACS analysis of human hematopoietic stem cells stained with anti-PSMGFR antibodies.
  • Fig. 36A shows a graph of FACS results showing that the SDIX polyclonal antibody and the MNC3 monoclonal antibody recognize nearly 100% of the hematopoietic stem cells but MNC2 monoclonal antibody does not bind to them.
  • Fig. 36B shows an overlay of the FACs scans, which shows that MNC2 binding is no different than the control antibody, while MNC3 produces a clear shift in the cell populations. All three antibodies were generated by immunizing with the PSMGFR peptide.
  • Figure 37 shows a graph of FACS analysis of cells that express 90% full-length MUC1 after addition of a catalytic domain of cleavage enzyme MMP9, then probing with anti- full-length MUC1 antibody VU4H5 or anti-MUCl* antibody MNC2.
  • Figure 38A-38C lists new anti-MUCl* monoclonal antibodies that were generated by immunizing animals with one of three different peptides derived from the MUC1* extra cellular domain sequence.
  • Fig. 38 A lists monoclonal antibodies that were generated when animals were immunized with the PSMGFR peptide.
  • Fig. 38B lists monoclonal antibodies that were generated when animals were immunized with the PSMGFR N+20/C-27 peptide.
  • Fig. 38C lists monoclonal antibodies that were generated when animals were immunized with the PSMGFR N+9/C-9 peptide.
  • the -1 or -2 designation refers to sister clones from the same well. Concentrations of stock antibody solutions are given.
  • Figure 39 shows a graph of an ELISA experiment testing the ability of monoclonal antibodies, generated by immunizing with the PSMGFR peptide, to bind to other peptides derived from the sequence of the MUC1* extra cellular domain. All monoclonal antibodies were first selected based on their ability to bind to the immunizing peptide. To further elucidate the epitope within that peptide to which the antibody binds, antibodies were tested for their ability to bind to the PSMGFR peptide, the N-10 peptide or the C-10 peptide.
  • Figure 40A-40B shows graphs of FACS analysis of the new PSMGFR anti-MUCl* monoclonal antibodies binding to T47D breast cancer cells. Fig. 40A shows the Mean Fluorescence Intensity. Fig. 40B shows the percent of cells that stained positive with the respective antibody.
  • Figure 41 shows a graph of an ELISA experiment testing the ability of monoclonal antibodies, generated by immunizing with the PSMGFR N+20/C-27 peptide, to bind to other peptides derived from the sequence of the MUC1* extra cellular domain. All monoclonal antibodies were first selected based on their ability to bind to the immunizing peptide. To further elucidate the epitope within that peptide to which the antibody binds, antibodies were tested for their ability to bind to the PSMGFR peptide, the N-10 peptide or the C-10 peptide.
  • Figure 42A-42B shows graphs of FACS analysis of the new PSMGFR N+20/C-27 anti-MUCl* monoclonal antibodies binding to T47D breast cancer cells.
  • Fig. 42A shows the Mean Fluorescence Intensity.
  • Fig. 42B shows the percent of cells that stained positive with the respective antibody.
  • Figure 43 shows a graph of an ELISA experiment testing the ability of monoclonal antibodies, generated by immunizing with the PSMGFR N+9/C-9 peptide, to bind to other peptides derived from the sequence of the MUC1* extra cellular domain. All monoclonal antibodies were first selected based on their ability to bind to the immunizing peptide. To further elucidate the epitope within that peptide to which the antibody binds, antibodies were tested for their ability to bind to the PSMGFR peptide, the N-10 peptide or the C-10 peptide.
  • Figure 44A-44B shows graphs of FACS analysis of the new PSMGFR N+9/C-9 anti- MUCl* monoclonal antibodies binding to T47D breast cancer cells.
  • Fig. 44A shows the Mean Fluorescence Intensity.
  • Fig. 44B shows the percent of cells that stained positive with the respective antibody.
  • Figure 45A-45C shows photographs of adjacent serial sections from a pancreatic cancer array, which was stained by standard IHC methods with various anti-MUCl* antibodies.
  • Fig. 45A shows the array stained with the SDIX polyclonal anti-MUCl* antibody, wherein the immunogen for the antibody was the PSMGFR peptide.
  • Fig. 45B shows the array stained with the 18B4 monoclonal anti-MUCl* antibody, wherein the immunogen for the antibody was the PSMGFR peptide.
  • Fig. 45C shows the array stained with the 1E4 monoclonal anti-MUCl* antibody, wherein the immunogen for the antibody was the PSMGFR N+20/C-27 peptide.
  • Figure 46A-46F shows photographs of individual specimens from the pancreatic cancer array shown in Fig. 45.
  • Fig. 46A shows a specimen stained with the SDIX polyclonal antibody.
  • Fig. 46B shows the same tissue specimen at a greater magnification.
  • Fig. 46C shows the adjacent tissue section stained with the 18B4 monoclonal antibody.
  • Fig. 46D shows the same tissue specimen at a greater magnification.
  • Fig. 46E shows the adjacent tissue section stained with the 1E4 monoclonal antibody.
  • Fig. 46F shows the same tissue specimen at a greater magnification.
  • Figure 47A-47D shows photographs of individual specimens from the pancreatic cancer array shown in Fig. 45.
  • Fig. 47A shows a specimen stained with the SDIX polyclonal antibody.
  • Fig. 47B shows the same tissue specimen at a greater magnification.
  • Fig. 47C shows the adjacent tissue section stained with the 18B4 monoclonal antibody.
  • Fig. 47D shows the same tissue specimen at a greater magnification.
  • Figure 48A-48D shows photographs of individual specimens from the pancreatic cancer array shown in Fig. 45.
  • Fig. 48A shows a specimen stained with the SDIX polyclonal antibody.
  • Fig. 48B shows the same tissue specimen at a greater magnification.
  • Fig. 48C shows the adjacent tissue section stained with the 18B4 monoclonal antibody.
  • Fig. 48D shows the same tissue specimen at a greater magnification.
  • Figure 49A-49D shows photographs of individual specimens from the pancreatic cancer array shown in Fig. 45.
  • Fig. 49A shows a specimen stained with the SDIX polyclonal antibody.
  • Fig. 49B shows the same tissue specimen at a greater magnification.
  • Fig. 49C shows the adjacent tissue section stained with the 1E4 monoclonal antibody.
  • Fig. 49D shows the same tissue specimen at a greater magnification. Comparing Fig. 49A to Fig.
  • Figure 50A-50D shows photographs of individual specimens from the pancreatic cancer array shown in Fig. 45.
  • Fig. 50A shows a specimen stained with the SDIX polyclonal antibody.
  • Fig. 50B shows the same tissue specimen at a greater magnification.
  • Fig. 50C shows the adjacent tissue section stained with the 1E4 monoclonal antibody.
  • Fig. 50D shows the same tissue specimen at a greater magnification. Comparing Fig. 50A to Fig.
  • Figure 51A-51C shows photographs of adjacent serial sections from a pancreatic cancer array, which was stained by standard IHC methods with various anti-MUCl* antibodies.
  • Fig. 51A shows the array stained with the SDIX polyclonal anti-MUCl* antibody, wherein the immunogen for the antibody was the PSMGFR peptide.
  • Fig. 51B shows the array stained with the 20A10 monoclonal anti-MUCl* antibody, wherein the immunogen for the antibody was the PSMGFR peptide.
  • Fig. 51C shows the array stained with the 29H1 monoclonal anti-MUCl* antibody, wherein the immunogen for the antibody was the PSMGFR N+20/C-27 peptide.
  • Figure 52A-52D shows photographs of adjacent serial sections from a pancreatic cancer array, which was stained by standard IHC methods with various anti-MUCl* antibodies.
  • Fig. 52A shows the array stained with the 17H6 monoclonal anti-MUCl* antibody, wherein the immunogen for the antibody was the PSMGFR N+9/C-9 peptide.
  • Fig. 52B shows the array stained with the 32C1 monoclonal anti-MUCl* antibody, wherein the immunogen for the antibody was the PSMGFR N+20/C-27 peptide.
  • Fig. 52C shows the array stained with the 45C11 monoclonal anti-MUCl* antibody, wherein the immunogen for the antibody was the PSMGFR N+20/C-27 peptide.
  • Fig. 52D shows the array stained with the 31A1 monoclonal anti- MUCl* antibody, wherein the immunogen for the antibody was the PSMGFR N+20/C-27 peptide.
  • FIG. 53A-53F shows photographs and graphical representations of pathologist staining scores of adjacent serial sections from a pancreatic cancer array, which was stained by standard IHC methods with either antibodies that recognize full-length MUC1 or an antibody that only recognizes MUC1*.
  • Fig. 53 A shows the pancreatic cancer array stained with antibody 5E5, which is an antibody that binds to a trapped O-linked glycan in the tandem repeat domain of full-length MUC1.
  • Fig. 53B shows the pathologist's score for each specimen in the array.
  • Fig. 53C shows the pancreatic cancer array stained with anti-MUCl* antibody 29H1, which is an antibody that binds to the PSMGFR N+20/C-27 peptide of MUC1*.
  • Fig. 53 A shows the pancreatic cancer array stained with antibody 5E5, which is an antibody that binds to a trapped O-linked glycan in the tandem repeat domain of full-length MUC1.
  • Fig. 53B shows the pathologist
  • FIG. 53D shows the pathologist's score for each specimen in the array.
  • Fig. 53E shows the pancreatic cancer array stained with antibody VU4H5, which is an antibody that binds to an epitope in the tandem repeat domain of full-length MUC1.
  • Fig. 53F shows the pathologist's score for each specimen in the array.
  • antibody 5E5 recognizes some specimens that VU4H5 does not recognize, however, anti-MUCl* antibody 29H1 recognizes specimens recognized by both antibodies that recognize full-length MUC1 plus other specimens that are not recognized by either anti-MUCl antibody.
  • Figure 54A-54C shows photographs of adjacent serial sections from an esophageal cancer array, which was stained by standard IHC methods with various anti-MUCl* antibodies.
  • Fig. 54A shows the array stained with the SDIX polyclonal anti-MUCl* antibody, wherein the immunogen for the antibody was the PSMGFR peptide.
  • Fig. 54B shows the array stained with the 20A10 monoclonal anti-MUCl* antibody, wherein the immunogen for the antibody was the PSMGFR peptide.
  • Fig. 54C shows the array stained with the 29H1 monoclonal anti-MUCl* antibody, wherein the immunogen for the antibody was the PSMGFR N+20/C-27 peptide.
  • Fig. 54A shows the array stained with the SDIX polyclonal anti-MUCl* antibody, wherein the immunogen for the antibody was the PSMGFR peptide.
  • Fig. 54B shows the array stained with the 20A10 monoclonal anti-MUCl*
  • 54D shows the array stained with the 31A1 monoclonal anti-MUCl* antibody, wherein the immunogen for the antibody was the PSMGFR N+20/C-27 peptide.
  • This figure shows that antibodies SDIX and 20A10 that both bind to the PSMGFR peptide recognize the same tumor tissue specimens, albeit to differing degrees, while antibodies that bind to the PSMGFR N+20/C- 27 peptide bind to more esophageal tumor specimens as well as most of those recognized by the anti-PSMGFR antibodies.
  • Figure 55A-55C shows photographs of adjacent serial sections from an esophageal cancer array, which was stained by standard IHC methods with various anti-MUCl* antibodies.
  • Fig. 55A shows the array stained with the SDIX polyclonal anti-MUCl* antibody, wherein the immunogen for the antibody was the PSMGFR peptide.
  • Fig. 55B shows the array stained with the 17H6 monoclonal anti-MUCl* antibody, wherein the antibody binds to the PSMGFR N+9/C-9 peptide.
  • Fig. 55C shows the array stained with the MNC2 monoclonal anti-MUCl* antibody, wherein the antibody binds to the PSMGFR peptide.
  • Fig. 55D shows the array stained with the 45C11 monoclonal anti-MUCl* antibody, wherein the antibody binds to the PSMGFR N+20/C- 27 peptide.
  • Figure 56A-56F shows photographs and graphical representations of pathologist staining scores of adjacent serial sections from a esophageal cancer array, which was stained by standard IHC methods with either antibodies that recognize full-length MUC1 or an antibody that only recognizes MUC1*.
  • Fig. 56A shows the esophageal cancer array stained with antibody 5E5, which is an antibody that binds to a trapped O-linked glycan in the tandem repeat domain of full-length MUC1.
  • Fig. 56B shows the pathologist's score for each specimen in the array.
  • 56C shows the esophageal cancer array stained with anti-MUCl* antibody 29H1, which is an antibody that binds to the PSMGFR N+20/C-27 peptide of MUC1*.
  • Fig. 56D shows the pathologist's score for each specimen in the array.
  • Fig. 56E shows the esophageal cancer array stained with antibody VU4H5, which is an antibody that binds to an epitope in the tandem repeat domain of full-length MUC1.
  • Fig. 56F shows the pathologist's score for each specimen in the array.
  • anti-MUCl* antibody 29H1 recognizes specimens recognized by both antibodies that recognize full-length MUC1 plus other specimens that are not recognized by either anti-MUCl antibody.
  • Figure 57A-57G shows photographs of the prostate cancer array, which was stained with either antibody 5E5 or VU4H5, which both recognize full-length MUC1 or 29H1 that only recognizes MUC1* and binds to the PSMGFR N+20/C-27 peptide.
  • Fig. 57 A shows the esophageal cancer array stained with antibody 5E5.
  • Fig. 57B shows the esophageal cancer array stained with antibody 29H1.
  • Fig. 57B shows the esophageal cancer array stained with antibody 29H1.
  • Fig. 57C shows the esophageal cancer array stained with antibody VU4H5.
  • Fig. 57D shows the esophageal cancer array stained with the secondary antibody only, as a control.
  • Fig. 57E shows the tissue marked by red box in Fig. 57A at greater magnification, wherein staining was done with 5E5.
  • Fig. 57F shows the tissue marked by red box in Fig. 57B at greater magnification, wherein staining was done with 29H1.
  • Fig. 57G shows the tissue marked by red box in Fig. 57C at greater magnification, wherein staining was done with VU4H5.
  • the dashed red boxes indicate just one patient’s specimen of many esophageal tumor specimens that stain negative for antibodies that recognize full-length MUC1, but highly positive when probed with anti-MUCl* antibodies, and particularly those antibodies that bind to the PSMGFR N+20/C-27 peptide.
  • Figure 58A-58C shows photographs of adjacent serial sections from a prostate cancer array, which was stained by standard IHC methods with various anti-MUCl* antibodies.
  • Fig. 58A shows the array stained with the SDIX polyclonal anti-MUCl* antibody, wherein the immunogen for the antibody was the PSMGFR peptide.
  • Fig. 58B shows the array stained with the 18B4 monoclonal anti-MUCl* antibody, wherein the antibody binds to the PSMGFR peptide.
  • Fig. 58C shows the array stained with the 1E4 monoclonal anti-MUCl* antibody, wherein the antibody binds to the PSMGFR N+20/C-27 peptide.
  • Figure 59A-59E shows photographs of adjacent serial sections from a prostate cancer array, which was stained by standard IHC methods with various anti-MUCl* antibodies.
  • Fig. 59A shows the array stained with the MNC2 monoclonal antibody that binds to the PSMGFR peptide but not the C-10 peptide.
  • Fig. 59B shows the array stained with the 18B4 antibody that binds to the PSMGFR peptide.
  • Fig. 59C shows the array stained with the 32C1 antibody that binds to the PSMGFR N+20/C-27 peptide.
  • Fig. 59D shows the array stained with the SDIX polyclonal anti-MUCl* antibody, wherein the immunogen for the antibody was the PSMGFR peptide.
  • Fig. 59E shows the array stained with the 31A1 monoclonal anti-MUCl* antibody that binds to the PSMGFR N+20/C-27 peptide.
  • Figure 60A-60F shows photographs and graphical representations of pathologist staining scores of adjacent serial sections from a prostate cancer array, which was stained by standard IHC methods with either antibodies that recognize full-length MUC1 or an antibody that only recognizes MUC1*.
  • Fig. 60A shows the prostate cancer array stained with antibody 5E5, which is an antibody that binds to a trapped O-linked glycan in the tandem repeat domain of full-length MUC1.
  • Fig. 60B shows the pathologist's score for each specimen in the array.
  • Fig. 60C shows the prostate cancer array stained with anti-MUCl* antibody 29H1, which is an antibody that binds to the PSMGFR N+20/C-27 peptide of MUC1*.
  • FIG. 60D shows the pathologist's score for each specimen in the array.
  • Fig. 60E shows the prostate cancer array stained with antibody VU4H5, which is an antibody that binds to an epitope in the tandem repeat domain of full-length MUC1.
  • Fig. 60F shows the pathologist's score for each specimen in the array.
  • antibody 5E5 recognizes some specimens that VU4H5 does not recognize, however, anti-MUCl* antibody 29H1 recognizes specimens recognized by both antibodies that recognize full-length MUC1 plus other specimens that are not recognized by either anti-MUCl antibody.
  • Figure 61A-61G shows photographs of the prostate cancer array, which was stained with either antibody 5E5 or VU4H5, which both recognize full-length MUC1 or 29H1 that only recognizes MUC1* and binds to the PSMGFR N+20/C-27 peptide.
  • Fig. 61 A shows the prostate cancer array stained with antibody 5E5.
  • Fig. 61B shows the prostate cancer array stained with antibody 29H1.
  • Fig. 61B shows the prostate cancer array stained with antibody 29H1.
  • Fig. 61C shows the prostate cancer array stained with antibody VU4H5.
  • Fig. 61D shows the prostate cancer array stained with the secondary antibody only, as a control.
  • Fig. 61E shows the tissue marked by red box in Fig.
  • Fig. 61 A at greater magnification, wherein staining was done with 5E5.
  • Fig. 61F shows the tissue marked by red box in Fig. 61B at greater magnification, wherein staining was done with 29H1.
  • Fig. 61G shows the tissue marked by red box in Fig. 61C at greater magnification, wherein staining was done with VU4H5.
  • the dashed red boxes indicate just one patient’s specimen of many prostate tumor specimens that stain negative for antibodies that recognize full-length MUC1, but highly positive when probed with anti-MUCl* antibodies, and particularly those antibodies that bind to the PSMGFR N+20/C-27 peptide.
  • Figure 62A-62B shows photographs of adjacent serial sections of breast cancer array BR1141 that were stained with two different anti-MUCl* monoclonal antibodies.
  • Fig. 62A shows a photograph of the breast cancer array that was stained with anti-MUCl* monoclonal antibody MNC2.
  • Fig. 62B shows a photograph of the breast cancer array that was stained with anti-MUCl* monoclonal antibody 20A10. Both monoclonal antibodies bind to the PSMGFR peptide, the N-10 peptide but not to the C10 peptide.
  • Figure 63A-63B shows photographs of adjacent serial sections of breast cancer array BR1141 that were stained with two different anti-MUCl* monoclonal antibodies.
  • Fig. 63A shows a photograph of the breast cancer array that was stained with anti-MUCl* monoclonal antibody MNC2.
  • Fig. 63B shows a photograph of the breast cancer array that was stained with anti-MUCl* monoclonal antibody 25E6. Both monoclonal antibodies bind to the PSMGFR peptide and to the N-10 peptide. Whereas MNC2 cannot bind to the C-10 peptide, 25E6 shows some low level of binding to the C-10 peptide, indicating that they bind to different epitopes.
  • Figure 64A-64B shows photographs of adjacent serial sections of breast cancer array BR1141 that were stained with two different anti-MUCl* monoclonal antibodies.
  • Fig. 64A shows a photograph of the breast cancer array that was stained with anti-MUCl* monoclonal antibody MNC2.
  • Fig. 64B shows a photograph of the breast cancer array that was stained with anti-MUCl* monoclonal antibody 18B4. Both monoclonal antibodies bind to the PSMGFR peptide.
  • 18B4 cannot bind to the N-10 epitope, indicating that they bind to different epitopes and that 18B4 may require the 10 N-terminal amino acids of the PSMGFR peptide for binding.
  • Figure 65A-65B shows photographs of adjacent serial sections of breast cancer array BR1141 that were stained with two different anti-MUCl* monoclonal antibodies.
  • Fig. 65A shows a photograph of the breast cancer array that was stained with anti-MUCl* monoclonal antibody MNC2.
  • Fig. 65B shows a photograph of the breast cancer array that was stained with anti-MUCl* monoclonal antibody 18G12. Both monoclonal antibodies bind to the PSMGFR peptide. However, unlike MNC2, 18G12 binds to the C-10 epitope to some degree, indicating they bind to different epitope within PSMGFR peptide.
  • Figure 66A-66B shows photographs of adjacent serial sections of breast cancer array BR1141 that were stained with two different anti-MUCl* monoclonal antibodies.
  • Fig. 66A shows a photograph of the breast cancer array that was stained with anti-MUCl* monoclonal antibody MNC2.
  • Fig. 66B shows a photograph of the breast cancer array that was stained with anti-MUCl* monoclonal antibody 8A9.
  • Monoclonal antibody MNC2 binds to the PSMGFR peptide
  • 8A9 binds to the PSMGFR N+9/C-9 peptide. The peptides to which they bind, combined with the very different staining patterns indicates that they bind to different MUC1* epitopes.
  • Figure 67A-67B shows photographs of adjacent serial sections of breast cancer array BR1141 that were stained with two different anti-MUCl* monoclonal antibodies.
  • Fig. 67A shows a photograph of the breast cancer array that was stained with anti-MUCl* monoclonal antibody MNC2.
  • Fig. 67B shows a photograph of the breast cancer array that was stained with anti-MUCl* monoclonal antibody 28F9. Both monoclonal antibodies bind to the PSMGFR peptide.
  • Figure 68A-68B shows photographs of adjacent serial sections of breast cancer array BR1141 that were stained with two different anti-MUCl* monoclonal antibodies.
  • Fig. 68A shows a photograph of the breast cancer array that was stained with anti-MUCl* monoclonal antibody MNC2.
  • Fig. 68B shows a photograph of the breast cancer array that was stained with anti-MUCl* monoclonal antibody 17H6.
  • Monoclonal antibody MNC2 binds to the PSMGFR peptide, whereas 17H6 binds to the PSMGFR N+9/C-9 peptide. The peptides to which they bind, combined with the very different staining patterns indicates that they bind to different MUC1* epitopes.
  • Figure 69A-69B shows photographs of adjacent serial sections of breast cancer array BR1141 that were stained with two different anti-MUCl* monoclonal antibodies.
  • Fig. 69A shows a photograph of the breast cancer array that was stained with anti-MUCl* monoclonal antibody MNC2.
  • Fig. 69B shows a photograph of the breast cancer array that was stained with anti-MUCl* monoclonal antibody 3C5.
  • Monoclonal antibody MNC2 binds to the PSMGFR peptide
  • 3C5 binds to the PSMGFR N+9/C-9 peptide. The peptides to which they bind, combined with the very different staining patterns indicates that they bind to different MUC1* epitopes.
  • Figure 70A-70G shows photographs of adjacent serial sections of breast cancer array BR1007 that were stained with four different anti-MUCl* monoclonal antibodies.
  • Fig. 70A shows a photograph of the breast cancer array that was stained with anti-MUCl* monoclonal antibody 20A10, which binds to the PSMGFR peptide.
  • Fig. 70B shows a photograph of the breast cancer array that was stained with anti-MUCl* monoclonal antibody 29H1, which binds to the PSMGFR N+20/C-27 peptide.
  • Fig. 70C shows a photograph of the breast cancer array that was stained with anti-MUCl* monoclonal antibody 4501, which binds to the PSMGFR N+20/C-27 peptide.
  • Fig. 70D shows a photograph of the breast cancer array that was stained with anti-MUCl* monoclonal antibody 320, which binds to the PSMGFR N+20/C-27 peptide.
  • Fig. 70E shows a photograph of the breast cancer array that was stained with anti-MUCl* monoclonal antibody 18B4, which binds to the PSMGFR peptide.
  • Fig. 70F shows a photograph of the breast cancer array that was stained with anti-MUCl* monoclonal antibody 31A1, which binds to the PSMGFR N+20/C-27 peptide.
  • Fig. 70G shows a photograph of the breast cancer array that was stained with anti-MUCl* monoclonal antibody 17H6, which binds to the PSMGFR N+9/C-9 peptide.
  • Figure 71A-71F shows photographs and graphical representations of pathologist staining scores of adjacent serial sections from a breast cancer array, which was stained by standard IHC methods with either antibodies that recognize full-length MUC1 or an antibody that only recognizes MUC1*.
  • Fig. 71A shows the breast cancer array stained with antibody 5E5, which is an antibody that binds to a trapped O-linked glycan in the tandem repeat domain of full- length MUC1.
  • Fig. 71B shows the pathologist's score for each specimen in the array.
  • Fig. 71C shows the breast cancer array stained with anti-MUCl* antibody 29H1, which is an antibody that binds to the PSMGFR N+20/C-27 peptide of MUC1*.
  • Fig. 71A shows the breast cancer array stained with antibody 5E5, which is an antibody that binds to a trapped O-linked glycan in the tandem repeat domain of full- length MUC1.
  • Fig. 71B shows the pathologist's score
  • Fig. 71D shows the pathologist's score for each specimen in the array.
  • Fig. 71E shows the breast cancer array stained with antibody VU4H5, which is an antibody that binds to an epitope in the tandem repeat domain of full-length MUC1.
  • Fig. 71F shows the pathologist's score for each specimen in the array.
  • antibody 5E5 recognizes some specimens that VU4H5 does not recognize, however, anti-MUCl* antibody 29H1 recognizes specimens recognized by both antibodies that recognize full-length MUC1 plus other specimens that are not recognized by either anti-MUCl antibody.
  • Figure 72A-72F shows photographs of adjacent serial sections of breast cancer tissue array BR1141 that have been stained with various anti-MUCl* monoclonal antibodies, wherein all antibodies bind to the PSMGFR peptide.
  • Fig. 72A shows breast cancer specimens that were stained with MNC2.
  • Fig. 72B shows breast cancer specimens that were stained with 20A10.
  • Fig. 72C shows breast cancer specimens that were stained with 25E6.
  • Fig. 72D shows breast cancer specimens that were stained with 28F9.
  • Fig. 72E shows breast cancer specimens that were stained with 18G12.
  • Fig. 72F shows breast cancer specimens that were stained with 18B4. All these antibodies bind to the PSMGFR peptide and roughly produce the same staining pattern of this breast cancer array.
  • MNC2 and 20A10 bind to the N-10 peptide but not to the C-10 peptide, indicating the 10 membrane proximal amino acids are important for their binding.
  • Antibodies 18B4, 18G12 and 25E6 show some binding to the C-10 peptide and 28F9 shows even more binding to C-10 peptide.
  • 18B4 does not bind to the N-10 peptide, indicating that it binds to an epitope that is more N-terminal within PSMGFR than the others. Red circles indicate specimens of interest for comparison.
  • Figure 73A-73F shows photographs of adjacent serial sections of breast cancer tissue array BR1141 that have been stained with various anti-MUCl* monoclonal antibodies, wherein antibodies that bind to the PSMGFR N+9/C-9 peptide are compared to MNC2 and its humanized single chain form, huMNC2-scFv-Fc, which both bind to PSMGFR, N-10 but not to C-10 peptides.
  • Fig. 73A shows breast cancer specimens that were stained with MNC2.
  • Fig. 73B shows breast cancer specimens that were stained with 8A9.
  • Fig. 73C shows breast cancer specimens that were stained with 17H6.
  • 73D shows breast cancer specimens that were stained with huMNC2-scFv-Fc.
  • Fig. 73E shows breast cancer specimen that was stained with 3C5.
  • Fig. 73F shows breast cancer specimens that were stained with 39H5.
  • “a” and“an” are used to refer to both single and a plurality of objects.
  • polypeptide As used herein, occasionally, in short hand, 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.
  • interchangeable designations for various monoclonal antibodies are used, such as,“MN-C2”, which is interchangeable with“C2”,“Min-C2” and“MNC2”;“MN- E6”, which is interchangeable with “E6”, “Min-E6” and “MNE6”; “MN-C3”, which is interchangeable with“C3”,“Min-C3” and“MNC3”; and“MN-C8”, which is interchangeable with“C8”,“Min-C8” and“MNC8”.
  • the term“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.
  • the CAR technology uses an antibody epitope fused to a portion of a T cell so that the body’s immune system is directed to attack a specific target protein or cell.
  • 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:4, 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:4).
  • PSMGFR is an acronym for Primary Sequence of MUC1 Growth Factor Receptor as set forth as
  • the“N-number” as in“N-10 PSMGFR”,“N-15 PSMGFR”, or“N-20 PSMGFR” refers to the number of amino acid residues that have been deleted at the N-terminal end of PSMGFR
  • “N+10 PSMGFR”,“N+15 PSMGFR”, or“N+20 PSMGFR” refers to the number of amino acid residues that have been added at the N-terminal end of PSMGFR.
  • Fikewise“C- number” as in“C-10 PSMGFR”,“C-15 PSMGFR”, or“C-20 PSMGFR” refers to the number of amino acid residues that have been deleted at the C-terminal end of PSMGFR
  • “C+10 PSMGFR”,“C+15 PSMGFR”, or“C+20 PSMGFR” refers to the number of amino acid residues that have been added at the C-terminal end of PSMGFR.
  • PSMGFR group refers to peptides that have additional 20 amino acids at the N-terminus, without regard to how the C-terminus is modified, whether amino acids have been deleted, or added and so on.
  • the“extracellular domain of MUC1*” refers to the extracellular portion of a MUC1 protein that is devoid of the tandem repeat domain.
  • 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.
  • the precise location of cleavage of MUC1 is not known perhaps because it appears that it can be cleaved by more than one enzyme.
  • the extracellular domain of MUC1* will include most of the PSMGFR sequence but may have an additional 10-20 N-terminal amino acids.
  • the“MUC1*” extra cellular domain is defined primarily by the PSMGFR sequence (GTIN VHD VETQFN Q YKTE A AS RYNLTIS D VS V S D VPFPFS AQS G A (SEQ ID NO:4)). 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.
  • Other clipped amino acid sequences may include S NIKFRPGS V V V QLTLAFREGTIN VHD VETQFN Q YKTE A AS R Y (SEQ ID NO:5); or S V V V QLTLAFREGTIN VHD VETQFN Q YKTE A AS RY (SEQ ID NO:6).
  • 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.
  • the present invention involves, generally, diagnostic assays related to cancers that are characterized by the aberrant expression of a class of cell surface receptors characterized by interchain binding regions or increased cleavage of extra cellular domain in cancerous tissues.
  • One such set of cancers are those characterized by the aberrant expression of mucin family proteins, such as MUC1, MUC2, MUC3, MUC4, up to and including MUC16.
  • MUC1, MUC2, MUC3, MUC4 up to and including MUC16.
  • Much of the description of the invention herein is directed to cells and tissues that aberrantly express MUC1, as an example of the larger class of proteins involved in cancers which have extra cellular domains that are increasingly cleaved in cancers and/or have an inter-chain binding region (IBR).
  • IBR inter-chain binding region
  • transmembrane proteins that function by a similar mechanism.
  • the invention is based on a novel mechanism involving transmembrane proteins that have regions of their extra cellular domain that self-aggregate and/or are increasingly cleaved, exemplified by MUC1, which was elucidated by the inventors.
  • MUC1 comprises several regions termed herein as follows. From the C-terminus inside the cell to the N-terminus outside the cell, the MUC1 protein is comprised of the following domains: 1) cytoplasmic tail; 2) transmembrane section; 3) MGFR; 4) IBR (interchain binding region) 5) UR (unique region); and 6) the tandem repeats.
  • One aspect of our previous invention featured the discovery that a specific region of the MUC1 receptor, i.e., the IBR, binds strongly to identical regions of other MUC1 molecules. That is, the MUC1 receptor has the ability to aggregate (i.e. self-aggregate) with other MUC1 receptors via the IBR of the respective receptors.
  • a gold nanoparticle experiment was performed that showed that the IBR aggregates with itself which can occlude the binding of ligands to MUC1 or its cleavage product MUC1*.
  • the boundary between the IBR and MGFR varies depending on where MUC1 is cleaved, which is determined by which cleavage enzyme cleaves it.
  • This self-aggregation may contribute to MUC1 receptor clustering, observed in healthy cells.
  • the discovery that the IBR portion of the MUC1 receptor self-aggregates is consistent with the following mechanistic model for which the inventors present supporting evidence.
  • receptor clustering is associated with the healthy state because the aggregated IBR portions block access of ligands, such as growth factors, modifying enzymes and the like to the neighboring extracellular portions of the MUC1 receptor that act as the functional receptor; clustering also blocks access of intracellular tails to intracellular modifying enzymes and signaling ligands;
  • the critical force that keeps the receptors clustered is lost and receptors are free to migrate within the cell membrane or interact with modifying enzymes, secreted ligands such as activating ligands or growth factors or other cell surface receptors.
  • Cleavage of MUC1 releases the bulk of the extra cellular domain, including the tandem repeat domain and leaves a transmembrane protein with a truncated extra cellular domain comprising at least the PSMGFR region. Cleavage and release of the bulk of the tandem repeat domain, exposes binding sites of ligands that bind to and dimerize the truncated extra cellular domain, leading to activation of growth and survival pathways.
  • MUC1 cleavage product “MUC1*”.
  • MUC 1 * is a growth factor receptor that is activated by ligand induced dimerization of its truncated extra cellular domain.
  • Bivalent antibodies that bind to PSMGFR peptide which is the 45 amino acid sequence of the membrane proximal portion of MUC1 dimerize MUC1* and stimulate growth.
  • the anti-PSMGFR antibody stimulated growth of T47D MUC1 positive cancer cells in a concentration dependent manner.
  • a concentration of the anti-PSMGFR antibody identified to maximize cancer cell proliferation, was added to a first group of T47D tumor cells, grown as described above.
  • the same amount of the anti-PSMGFR antibody was added to a set of control cells, K293 cells.
  • the addition of the anti-PSMGFR antibody to MUC1 tumor cells (T47D) enhanced proliferation by 180% 24 hours, but had no effect on the control cells.
  • Ligands that dimerize the extra cellular domain of MUC1* induce growth and survival of cells.
  • Ligands of MUC1* that we identified are NME1, NME2, NME6, NME7-AB and alternative splice variant NME7-X1.
  • MUC1* is the growth factor receptor that drives the growth of cancer cells, whereas full-length MUC1 does not. Therefore, detection of an amount of MUC1* that is above normal levels is an indicator of cancer and the higher the amount of MUC1*, the worse the cancer.
  • Cleavage of MUC1 may occur at more than one site, depending on which cleavage enzyme the tumor expresses. Cleavage of MUC1 releases the portion of the extracellular domain that contains the tandem repeats and could, depending on cleavage site, contain portions of the unique region or portions of the IBR.
  • the amount of MUC1 that has been cleaved can be inferred by measuring the amount of full-length MUC1 that remains on cells or tissues.
  • An antibody that binds to the tandem repeat domain is an antibody that is able to bind to a peptide having the sequence PDTRPAPGSTAPPAHGVTSA (SEQ ID NO:235).
  • Commonly used antibodies that bind to the tandem repeat domain include but are not limited to VU4H5 (Santa Cruz Biotechnology, Dallas Texas Cat. No. SC-7313), HMPV, 5E5 (Sorensen et al., Glycobiology, Vol. 16, no. 2, pp. 96-107, 2006), PR81, and LDQ10.
  • MUC1 full-length MUC1 compared to an amount of MUC1* expressed on the same cells or tissues.
  • the ratio of MUCl*:MUCl full- length is an indicator of cancer and cancer aggressiveness, wherein the more MUC1*, the more aggressive the cancer. Detection of an amount of MUC1* or the ratio of MUC1* to MUC1 full- length can also be used to determine the suitability of a cancer treatment where the therapeutic drug targets MUC1* or MUC1.
  • the effectiveness of such a therapy can be evaluated by detecting an amount of MUC1* or the ratio of MUC1* to MUC1 full-length before and after treatment, wherein a reduction in the amount of MUC1* expressed or a shift in the ratio of MUC1* to MUC1 full-length would be an indicator of efficacy.
  • MUC1-Y or MUC1-X may be alternative splice isoforms of MUC1 that do not contain an IBR or tandem repeats.
  • MUC1-Y or MUC1-X may be alternative splice isoforms of MUC1 that do not contain an IBR or tandem repeats.
  • MUC1-Y or MUC1-X may be alternative splice isoforms of MUC1 that do not contain an IBR or tandem repeats.
  • VU4H5 is a monoclonal antibody that only binds to full-length MUC1 because it recognizes an epitope (PDTRPAPGSTAPPAHGVTSA (SEQ ID NO:235) in the tandem repeat domain of full-length MUC1. This epitope is repeated hundreds of times within the tandem repeat domain of full-length MUC1. Therefore, antibody VU4H5 should give a stronger signal that an antibody that binds to a single epitope on the molecule.
  • MNC2 is a monoclonal antibody that we produced by immunizing animals with the PSMGFR peptide (SEQ ID NO:4). Transfection experiments show that MNC2 does not bind to full-length MUC1. MNC2 binds to a cryptic epitope that is exposed after MUC1 is cleaved to a form of MUC1* that comprises at least the first 35 membrane proximal amino acids of the MUC1* extra cellular domain, as it binds to the PSMGFR peptide (45 amino acids), the N-10 peptide (35 amino acids) but not to the C-10 peptide, indicating that its cognate epitope is encompassed at least in part within the 10 membrane proximal amino acids of the MUC1* extra cellular domain. Importantly, MNC2 competitively inhibits the binding of MUC1* activating growth factors NME1 and NME7-AB.
  • Figure 1A-1D shows photographs of adjacent serial sections of breast cancer tissue arrays and graphical representations of the pathologist scores, according to Allred scoring system.
  • Pathologist score is 0-3, where 0 showed no staining and 3 is the greatest staining.
  • the graphs are also color coded, where a pathologist score zero is black, 1 is yellow, 2 is orange, and 3 is red; tissues that scored zero when probed with an antibody that recognizes full-length MUC1 but positive when probed with an antibody that recognizes MUC1* were colored green; and missing or uninterpretable tissues were scored -1.
  • Figure 1A shows photographs of the breast cancer tissue arrays after they were stained with VU4H5, which is an antibody that binds to the tandem repeat domains of full-length MUC1.
  • Figure IB shows graphs of the pathologist scores for the tissues pictured in Fig. 1A.
  • Figure 1C shows photographs of the breast cancer tissue arrays after they were stained with MNC2, which is an antibody that binds to an epitope within the PSMGFR region of MUC1*.
  • Figure ID shows graphs of the pathologist scores for the tissues pictured in Fig. 1C.
  • Figure 2A-2B shows pie chart graphs of the pathologist scores of the arrays shown in Fig. 1A and Fig. 1C.
  • Fig. 2A shows that the antibody that binds to tandem repeats of full-length MUC1 misses 30% of breast cancers.
  • Fig. 2B shows that the anti-MUCl* antibody MNC2 recognizes 95% of breast cancers.
  • Anti-MUCl -full-length only binds strongly to 10% of the breast tumors, while anti-MUCl* antibody MNC2 binds strongly to about 50% of breast tumors.
  • MUC1* not full-length MUC1
  • Anti-MUCl* antibodies would detect or diagnose nearly all breast cancers, whereas antibodies that bind to full-length MUC1 would fail to detect about 30% of breast cancers.
  • MUC1* is a growth factor receptor driving cancer growth
  • the degree of anti-MUCl* staining of a tissue or cellular specimen would be proportional to the degree or stage of cancer, whereas the expression of full-length MUC1 appears to be inversely proportional to the stage of cancer.
  • MNC2 was used to detect MUC1* positive cancers in a wide range of assays, including fluorescence activated cell sorting (FACS), immunofluorescence (IF), immunohistochemistry (IHC).
  • FACS and IF are generally used to study a cell line which is a single immortalized cell that has been propagated in a lab for decades. After decades of propagation in unnatural growth solutions, these cell lines likely show little resemblance to even a single cell within the patient’s original tumor and in no way represent the tumor of a recently diagnosed patient seeking treatment.
  • tumor micro arrays wherein each dot within the array is tumor specimen from a single patient’s biopsy.
  • the biopsies are from recently diagnosed patients, but the accompanying anonymized patient data gives the age of the patient, cancer sub-type and cancer stage or grade.
  • tissue micro arrays wherein the breast cancers were all HER2+, or all ER+/PR+. In other cases.
  • tumor micro arrays that compared the original biopsy specimen to a later metastasis.
  • MNC2 the recognition of tumors by MNC2 was also compared to staining using anti-full-length-MUCl antibody VU4H5 or a new antibody 5E5 that binds to a trapped O-linked glycan in the tandem repeat domain of full-length MUC1.
  • MNC2 and other anti-MUCl* antibodies consistently recognized tumor tissue better than VU4H5 or 5E5.
  • Normal tissues and normal tissue micro arrays were also extensively studied to determine binding of MNC2 or its humanized singly chain form huMNC2-scFv or huMNC2-scFv-Fc to normal tissues.
  • MNC2 reactive MUC1* On normal tissues, expression of MNC2 reactive MUC1* was restricted to the apical border of ducts and glands in a small percentage of only a few tissues. In all cases, MNC2 reactive MUC1* was expressed to a much higher degree in cancerous tissues than in normal tissues and expressed over 50-100% of the cancerous tissues compared to expression of 0.2%- 5% of the normal tissue that did express MNC2 reactive MUC1*.
  • Figure 3 to Figure 19 show that monoclonal anti-MUCl* antibody MNC2 binds to high percentages of breast, ovarian, pancreatic, lung and esophageal tumors, while having very little if any binding to normal tissues.
  • Figure 3A-3B shows pie chart graphs of the pathologist scores and a photograph of breast cancer array BR1141 after staining with anti-MUCl* antibody huMNC2-scFv-Fc.
  • Figure 4A-4C shows photographs, at two different magnifications, of individual breast cancer specimens from breast cancer array BR1141 after staining with anti- MUCl* antibody huMNC2-scFv-Fc.
  • Fig. 4A shows the specimen at position A7 which was negative for huMNC2 reactive cells.
  • Fig. 4B shows the specimen at position A9 which is a Grade 2 cancer, with lymph node involvement that scored +1 for huMNC2 reactivity.
  • Fig. 4C shows the specimen at position B10 which is a larger Grade 2 tumor, with lymph node involvement that scored +2 for huMNC2 reactivity.
  • Figure 5A-5B shows photographs, at two different magnifications, of individual breast cancer specimens from breast cancer array BR1141 after staining with anti-MUCl* antibody huMNC2-scFv-Fc.
  • Fig. 5A shows the specimen at position D7 which is a Grade 2 cancer, without lymph node involvement that scored +3 for huMNC2 reactivity.
  • Fig. 5B shows the specimen at position F6 which is a Grade 2 tumor, with lymph node involvement that scored +4 for huMNC2 reactivity.
  • Figure 6A-6B shows pie chart graphs of the pathologist scores and a photograph of ovarian cancer array BCl l l5a after staining with anti-MUCl* antibody huMNC2-scFv-Fc.
  • Figure 7A-7C shows magnified photographs of different cancer sub-types after staining with anti-MUCl* antibody huMNC2-scFv-Fc.
  • Fig. 7A shows a photograph of a Grade 2 breast tumor that pathologist scored +4.
  • Fig. 7B shows a photograph of a Grade 2 ovarian tumor that pathologist scored +3.
  • Fig. 7C shows a photograph of a Grade 3 pancreatic tumor that pathologist scored +3.
  • FIG. 8A-8D shows magnified photographs of different cancer sub-types after staining with anti-MUCl* antibody huMNC2-scFv-Fc.
  • Fig. 8A shows a photograph of a Grade 2 breast tumor that pathologist scored +2.
  • Fig. 8B shows a photograph of a Grade 3 ovarian tumor that pathologist scored +3.
  • Fig. 8C shows a photograph of a Grade 3 pancreatic tumor, with lymph node involvement that pathologist scored +3.
  • Fig. 8D shows a photograph of a lung cancer that pathologist scored +3.
  • Figure 9A-9I shows magnified photographs of various normal tissues after staining with anti-MUCl* antibody huMNC2-scFv- Fc. Conditions and concentrations used were identical to those used for studying cancerous tissues.
  • Fig. 9A shows normal adrenal gland tissue.
  • Fig. 9B shows normal brain tissue.
  • Fig. 9C shows normal breast tissue.
  • Fig. 9D shows normal stomach tissue.
  • Fig. 9E shows normal heart tissue.
  • Fig. 9F shows normal kidney tissue.
  • Fig. 9G shows normal testis tissue.
  • Fig. 9H shows normal intestine tissue.
  • Fig. 91 shows normal liver tissue.
  • Figure 10A-10F shows photographs of normal kidney tissues after staining with anti-MUCl* antibody huMNC2-scFv-Fc.
  • Fig. 10A shows normal kidney tissue with huMNC2 reactivity limited to the apical border, which is normal expression.
  • Fig. 10B is the same tissue at greater magnification.
  • Fig. 10C shows another example of normal kidney tissue with undetectable huMNC2 reactivity.
  • Fig. 10D is the same tissue at greater magnification.
  • Fig. 10E shows another example of normal kidney tissue with huMNC2 reactivity limited to the apical border, which is normal expression.
  • Fig. 10F is the same tissue at greater magnification.
  • FIG. 11A-11B shows pie chart graphs of the pathologist scores and a photograph of esophageal cancer array BC001113 after staining with anti-MUCl* antibody huMNC2-scFv-Fc.
  • Figure 12A-12F shows photographs, at two different magnifications, of individual esophageal cancer specimens from esophageal cancer array BC001113, after staining with anti-MUCl* antibody huMNC2-scFv-Fc.
  • Fig. 12A shows the specimen at position A4 which was negative for huMNC2 reactive cells.
  • Fig. 12B shows the same specimen at greater magnification.
  • Fig. 12C shows the specimen at position D2 which the pathologist scored as trace reactivity to huMNC2.
  • Fig. 12D shows the same specimen at greater magnification.
  • Fig. 12E shows the specimen at position B8 which the pathologist scored as +1 reactivity to huMNC2.
  • Fig. 12F shows the same specimen at greater magnification.
  • Figure 13A-13D shows photographs, at two different magnifications, of individual esophageal cancer specimens from esophageal cancer array BC001113, after staining with anti-MUCl* antibody huMNC2-scFv-Fc.
  • the position in the array, cancer sub-type, tumor grade, and pathologist score are indicated in figures.
  • Fig. 13A shows the specimen at position D6, a Grade 4 tumor, which the pathologist scored +2.
  • Fig. 13B shows the same specimen at greater magnification.
  • Fig. 13C shows the specimen at position D5, a Grade 3 tumor, which the pathologist scored +3.
  • Fig. 12D shows the same specimen at greater magnification.
  • Figure 14A- 14B shows pie chart graphs of the pathologist scores and a photograph of pancreatic cancer array PA805b after staining with anti-MUCl* antibody huMNC2-scFv-Fc.
  • Figure 15A-15D shows photographs, at two different magnifications, of individual pancreatic cancer specimens from pancreatic cancer array PA805b, after staining with anti-MUCl* antibody huMNC2-scFv-Fc. The position in the array, cancer sub-type, tumor grade, and pathologist score are indicated in figures.
  • Fig. 15A shows the specimen at position F3, a Grade 3 tumor, which the pathologist scored +3.
  • Fig. 15B shows the same specimen at greater magnification.
  • FIG. 15C shows the specimen at position Bl, a Grade 1 tumor, which the pathologist scored +2.
  • Fig. 15D shows the same specimen at greater magnification.
  • Figure 16A-16D shows photographs, at two different magnifications, of individual pancreatic cancer specimens from pancreatic cancer array PA805b, after staining with anti-MUCl* antibody huMNC2-scFv-Fc. The position in the array, cancer sub-type, tumor grade, and pathologist score are indicated in figures.
  • Fig. 16A shows the specimen at position A2, a Grade 1 tumor, which the pathologist scored +2.
  • Fig. 16B shows the same specimen at greater magnification.
  • Fig. 16C shows the specimen at position C3, a Grade 2 tumor, which the pathologist scored +2.
  • FIG. 16D shows the same specimen at greater magnification.
  • Figure 17A-17D shows photographs, at two different magnifications, of individual pancreatic cancer specimens from pancreatic cancer array PA805b, after staining with anti-MUCl* antibody huMNC2-scFv-Fc. The position in the array, cancer sub-type, tumor grade, and pathologist score are indicated in figures.
  • Fig. 17A shows the specimen at position C6, a Grade 2 tumor, which the pathologist scored +2.
  • Fig. 17B shows the same specimen at greater magnification.
  • Fig. 17C shows the specimen at position Dl, a larger Grade 3 tumor, with lymph node involvement that the pathologist scored +3.
  • Fig. 17D shows the same specimen at greater magnification.
  • Figure 18A-18D shows photographs, at two different magnifications, of individual pancreatic cancer specimens from pancreatic cancer array PA805b, after staining with anti-MUCl* antibody huMNC2-scFv-Fc.
  • the position in the array, cancer sub-type, tumor grade, and pathologist score are indicated in figures.
  • Fig. 18A shows the specimen at position E2, a Grade 1 tumor, which the pathologist scored +2.
  • Fig. 18B shows the same specimen at greater magnification.
  • Fig. 18C shows the specimen at position E10, a smaller Grade 3 tumor, with lymph node involvement that the pathologist scored +3.
  • Fig. 18D shows the same specimen at greater magnification.
  • Figure 19 shows a photograph of pancreatic cancer array PA805b that was stained with the secondary antibody alone, as a control.
  • MNC2 recognized about 95% of breast tumors across all breast cancer sub- types, we noticed that some cancer sub-types did not express as much MNC2 reactive MUC1* as breast cancers. In particular, pancreatic, esophageal and prostate cancers expressed lower levels of MNC2 reactive MUC1*. Pancreatic cancer arrays showed that 78% of the tumors were MNC2 reactive but the strength of staining, which is proportional to the tumor’s expression levels, was relative weak. The pie chart of Figure 14A shows that 65% of the pancreatic tumors scored +1 or +2, only 5% scored +3 and none scored +4.
  • the pie chart of Figure 3A shows that more than half of the breast tumors scored +2 to +3, 6% were +4 and only 4% were negative for MNC2 MUC1* reactivity.
  • Both arrays were stained with the same MNC2 anti-MUCl* antibody and scored by the same board-certified pathologist.
  • MNC2 and SDIX were generated by immunizing animals with the PSMGFR peptide, they showed different binding characteristics to tumor tissue. In general, SDIX recognized more pancreatic tissues and stained more robustly than MNC2, although there were cases where MNC2 recognized a tumor that SDIX did not.
  • MUC1* On cancerous tissues, MUC1* is expressed over most of the tissue and is characteristic of cancer, all anatomical barriers have broken down in cancerous tissues. In contrast, on normal tissues, expression of MUC1* is restricted to the apical border of ducts and glands. Expression of MNC2 reactive MUC1* is even further restricted.
  • Figure 6B shows a photograph of an ovarian cancer micro array. However, Column J is made up of normal ovarian tissues. As can be seen, there is no expression of MNC2 reactive MUC1*. Normal kidney does express some MNC2 reactive MUC1*.
  • MNC2 recognizes MUC1* after MUC1 is cleaved by cleavage enzyme MMP9, which is overexpressed in most breast cancers, but not in hematopoietic stem cells.
  • MMP9 cleavage enzyme
  • V QLTLAFREGTIN VHD VETQFN Q YKTE A AS RYNLTIS D VS VS D VP (SEQ ID NO: 10).
  • Antibody clones were isolated and a subset from each immunization was selected, first based on their ability to bind to the immunizing peptide, then secondly for their ability to recognize cancerous tissues above normal tissues.
  • Figure 38A to Figure 38C shows tables of the selected antibodies, organized according to immunizing peptide. In the tables, designation of -1 or -2 indicates that these are sister clones, which after sequencing showed these were in fact the same antibody. Throughout the rest of the disclosure, antibodies are referred to without the -1 or -2 designation.
  • Figures 39 through Figure 44 show the binding characteristics of new anti-MUCl* antibodies. All antibodies were first selected by virtue of the fact that they bound to the immunizing peptide. For comparison to MNC2 and MNC3, new antibodies were tested for their ability to bind to PSMGFR, the N-10 peptide and the C-10 peptide. New anti-MUCl* antibodies were also tested by FACS to determine their ability to bind to the T47D breast cancer cell line. Because analysis of antibody binding to a single cell line that was generated from a patient decades ago, we expanded the analysis of the new antibodies to hundreds of tumor tissues across multiple cancer sub-types. The number of patients represented in each array varied. Normal tissues were also probed with the antibodies.
  • Figures 45 through Figure 52 compares the binding of the new anti-MUCl* antibodies to the SDIX polyclonal to investigate antibodies that bind to regions that are N- terminal to the PSMGFR sequence.
  • MNC2 recognized about 78% of pancreatic cancers, the binding was not so robust and some very nasty tumors were not recognized at all by MNC2 or the SDIX polyclonal.
  • anti-PSMGFR antibodies such as 18B4, appear to recognize the same pancreatic tumor tissues as the polyclonal anti-PSMGFR antibody SDIX (Fig. 45A-45BC).
  • anti-PSMGFR N+20/C-27 antibody 1E4 appears to recognize the same tumors as SDIX and 18B4, however, the magnified view of these tumor specimens shows that antibody 1E4 recognizes a different population of cancer cells within the tumor than the anti-PSMGFR antibodies (Fig. 46A-46F), Some of the tumors were not recognized well by SDIX but were recognized by monoclonal antibody 18B4 (Fig. 47A-48D).
  • pancreatic tumors were recognized better by anti-PSMGFR N+20/C-27 antibody 1E4 (Fig. 49A-49D).
  • anti-PSMGFR N+20/C-27 antibody 29H1 recognizes some pancreatic tumors that are missed by anti-PSMGFR antibodies SDIX and 20A10 (Fig. 51A-51C).
  • the therapeutic agent incorporates some or all of the antibody that is the diagnostic agent or some or all of an antibody that is derived from the antibody that is the diagnostic antibody.
  • Figure 53 demonstrates that these new antibodies that are extended at the N-terminus are recognize more pancreatic tumors than antibodies that bind to full-length MUC1.
  • This figure compares the binding of 29H1 to a standard antibody, VU4H5, that binds to the tandem repeats of full-length MUC1, and to a new antibody, 5E5 that binds to a trapped O-linked glycan that is present on some cancer cells.
  • the new anti-MUCl* antibodies which bind to peptides PSMGFR N+20/C-27 and/or PSMGFR N+9/C-9, showed markedly better recognition of esophageal and prostate tumors when compared to MNC2, SDIX, and full-length MUC1 antibodies 5E5 and VU4H5.
  • Figure 54A-54C shows photographs of adjacent serial sections from an esophageal cancer array, which was stained by standard IHC methods with various anti-MUCl* antibodies.
  • Fig. 54A shows the array stained with the SDIX polyclonal anti-MUCl* antibody, wherein the immunogen for the antibody was the PSMGFR peptide.
  • Fig. 54B shows the array stained with the 20A10 monoclonal anti-MUCl* antibody, wherein the immunogen for the antibody was the PSMGFR peptide.
  • Fig. 54C shows the array stained with the 29H1 monoclonal anti-MUCl* antibody, wherein the immunogen for the antibody was the PSMGFR N+20/C-27 peptide.
  • Fig. 54A shows the array stained with the SDIX polyclonal anti-MUCl* antibody, wherein the immunogen for the antibody was the PSMGFR peptide.
  • Fig. 54B shows the array stained with the 20A10 monoclonal anti-MUCl*
  • 54D shows the array stained with the 31A1 monoclonal anti-MUCl* antibody, wherein the immunogen for the antibody was the PSMGFR N+20/C-27 peptide.
  • This figure shows that antibodies SDIX and 20A10 that both bind to the PSMGFR peptide recognize the same tumor tissue specimens, albeit to differing degrees, while antibodies that bind to the PSMGFR N+20/C- 27 peptide bind to more esophageal tumor specimens as well as most of those recognized by the anti-PSMGFR antibodies.
  • Figure 55A-55C shows photographs of adjacent serial sections from an esophageal cancer array, which was stained by standard IHC methods with various anti-MUCl* antibodies.
  • Fig. 55A shows the array stained with the SDIX polyclonal anti-MUCl* antibody, wherein the immunogen for the antibody was the PSMGFR peptide.
  • Fig. 55B shows the array stained with the 17H6 monoclonal anti-MUCl* antibody, wherein the antibody binds to the PSMGFR N+9/C-9 peptide.
  • Fig. 55C shows the array stained with the MNC2 monoclonal anti-MUCl* antibody, wherein the antibody binds to the PSMGFR peptide.
  • Fig. 55A shows the array stained with the SDIX polyclonal anti-MUCl* antibody, wherein the immunogen for the antibody was the PSMGFR peptide.
  • Fig. 55B shows the array stained with the 17H6 monoclonal anti-MUCl* antibody, where
  • 55D shows the array stained with the 45C11 monoclonal anti-MUCl* antibody, wherein the antibody binds to the PSMGFR N+20/C-27 peptide.
  • Figure 56A-56F shows photographs and graphical representations of pathologist staining scores of adjacent serial sections from a esophageal cancer array, which was stained by standard IHC methods with either antibodies that recognize full-length MUC1 or an antibody that only recognizes MUC1*.
  • Fig. 56A shows the esophageal cancer array stained with antibody 5E5, which is an antibody that binds to a trapped O-linked glycan in the tandem repeat domain of full-length MUC1.
  • Fig. 56B shows the pathologist's score for each specimen in the array.
  • 56C shows the esophageal cancer array stained with anti-MUCl* antibody 29H1, which is an antibody that binds to the PSMGFR N+20/C-27 peptide of MUC1*.
  • Fig. 56D shows the pathologist's score for each specimen in the array.
  • Fig. 56E shows the esophageal cancer array stained with antibody VU4H5, which is an antibody that binds to an epitope in the tandem repeat domain of full-length MUC1.
  • Fig. 56F shows the pathologist's score for each specimen in the array.
  • anti-MUCl* antibody 29H1 recognizes specimens recognized by both antibodies that recognize full-length MUC1 plus other specimens that are not recognized by either anti-MUCl antibody.
  • Figure 57A-57G shows photographs of the prostate cancer array, which was stained with either antibody 5E5 or VU4H5, which both recognize full-length MUC1 or 29H1 that only recognizes MUC1* and binds to the PSMGFR N+20/C-27 peptide.
  • Fig. 57 A shows the esophageal cancer array stained with antibody 5E5.
  • Fig. 57B shows the esophageal cancer array stained with antibody 29H1.
  • Fig. 57B shows the esophageal cancer array stained with antibody 29H1.
  • Fig. 57C shows the esophageal cancer array stained with antibody VU4H5.
  • Fig. 57D shows the esophageal cancer array stained with the secondary antibody only, as a control.
  • Fig. 57E shows the tissue marked by red box in Fig. 57A at greater magnification, wherein staining was done with 5E5.
  • Fig. 57F shows the tissue marked by red box in Fig. 57B at greater magnification, wherein staining was done with 29H1.
  • Fig. 57G shows the tissue marked by red box in Fig. 57C at greater magnification, wherein staining was done with VU4H5.
  • the dashed red boxes indicate just one patient’s specimen of many esophageal tumor specimens that stain negative for antibodies that recognize full-length MUC1, but highly positive when probed with anti-MUCl* antibodies, and particularly those antibodies that bind to the PSMGFR N+20/C-27 peptide.
  • Figure 58A-58C shows photographs of adjacent serial sections from a prostate cancer array, which was stained by standard IHC methods with various anti-MUCl* antibodies.
  • Fig. 58A shows the array stained with the SDIX polyclonal anti-MUCl* antibody, wherein the immunogen for the antibody was the PSMGFR peptide.
  • Fig. 58B shows the array stained with the 18B4 monoclonal anti-MUCl* antibody, wherein the antibody binds to the PSMGFR peptide.
  • Fig. 58C shows the array stained with the 1E4 monoclonal anti-MUCl* antibody, wherein the antibody binds to the PSMGFR N+20/C-27 peptide.
  • Figure 59A-59E shows photographs of adjacent serial sections from a prostate cancer array, which was stained by standard IHC methods with various anti-MUCl* antibodies.
  • Fig. 59A shows the array stained with the MNC2 monoclonal antibody that binds to the PSMGFR peptide but not the C-10 peptide.
  • Fig. 59B shows the array stained with the 18B4 antibody that binds to the PSMGFR peptide.
  • Fig. 59C shows the array stained with the 32C1 antibody that binds to the PSMGFR N+20/C-27 peptide.
  • Fig. 59D shows the array stained with the SDIX polyclonal anti-MUCl* antibody, wherein the immunogen for the antibody was the PSMGFR peptide.
  • Fig. 59E shows the array stained with the 31A1 monoclonal anti-MUCl* antibody that binds to the PSMGFR N+20/C-27 peptide.
  • Figure 60A-60F shows photographs and graphical representations of pathologist staining scores of adjacent serial sections from a prostate cancer array, which was stained by standard IHC methods with either antibodies that recognize full-length MUC1 or an antibody that only recognizes MUC1*.
  • Fig. 60A shows the prostate cancer array stained with antibody 5E5, which is an antibody that binds to a trapped O-linked glycan in the tandem repeat domain of full-length MUC1.
  • Fig. 60B shows the pathologist's score for each specimen in the array.
  • Fig. 60C shows the prostate cancer array stained with anti-MUCl* antibody 29H1, which is an antibody that binds to the PSMGFR N+20/C-27 peptide of MUC1*.
  • FIG. 60D shows the pathologist's score for each specimen in the array.
  • Fig. 60E shows the prostate cancer array stained with antibody VU4H5, which is an antibody that binds to an epitope in the tandem repeat domain of full-length MUC1.
  • Fig. 60F shows the pathologist's score for each specimen in the array.
  • antibody 5E5 recognizes some specimens that VU4H5 does not recognize, however, anti-MUCl* antibody 29H1 recognizes specimens recognized by both antibodies that recognize full-length MUC1 plus other specimens that are not recognized by either anti-MUCl antibody.
  • FIG. 61A-61G shows photographs of the prostate cancer array, which was stained with either antibody 5E5 or VU4H5, which both recognize full-length MUC1 or 29H1 that only recognizes MUC1* and binds to the PSMGFR N+20/C-27 peptide.
  • Fig. 61 A shows the prostate cancer array stained with antibody 5E5.
  • Fig. 61B shows the prostate cancer array stained with antibody 29H1.
  • Fig. 61B shows the prostate cancer array stained with antibody 29H1.
  • Fig. 61C shows the prostate cancer array stained with antibody VU4H5.
  • Fig. 61D shows the prostate cancer array stained with the secondary antibody only, as a control.
  • Fig. 61E shows the tissue marked by red box in Fig.
  • Fig. 61 A at greater magnification, wherein staining was done with 5E5.
  • Fig. 61F shows the tissue marked by red box in Fig. 61B at greater magnification, wherein staining was done with 29H1.
  • Fig. 61G shows the tissue marked by red box in Fig. 61C at greater magnification, wherein staining was done with VU4H5.
  • the dashed red boxes indicate just one patient’s specimen of many prostate tumor specimens that stain negative for antibodies that recognize full-length MUC1, but highly positive when probed with anti-MUCl* antibodies, and particularly those antibodies that bind to the PSMGFR N+20/C-27 peptide.
  • MNC2 recognizes a MUC1* that is present in large percentages of breast cancers.
  • tumor heterogeneity and the potential of tumor escape by proliferating a population of cells in which MUC1*, the growth factor receptor, is cleaved by a different cleavage enzyme, and thereby recognized by a different anti-MUCl* antibody suggests that treatment with more than one anti-MUCl* antibody would be beneficial.
  • FIG. 62A-62B shows the same breast cancer array but MNC2 compared to 25E6, 18B4 and 18G12. Recall that unlike MNC2, this set of new anti- PSMGFR antibodies are able to bind to the C-10 peptide (Fig. 41). As can be seen in the figure, there are differences between the binding of MNC2 and these new anti-PSMGFR antibodies.
  • anti-MUCl* antibody 29H1 recognizes specimens recognized by both antibodies that recognize full-length MUC1 plus other specimens that are not recognized by either anti-MUCl antibody.
  • Antibodies 18B4, 18G12 and 25E6 show some binding to the C-10 peptide and 28F9 shows even more binding to C-10 peptide. Notably, 18B4 does not bind to the N-10 peptide, indicating that it binds to an epitope that is more N-terminal within PSMGFR than the others. Albeit with the previously mentioned exceptions, the recognition of tumors within this array by anti-PSMGFR antibodies was very similar.
  • Fig. 73A-73F antibodies that bind to the PSMGFR N+9/C-9 peptide robustly recognized a subset of tumors that was either not recognized by MNC2 or weakly recognized by MNC2 and other anti-PSMGFR antibodies.
  • the photographs shown are of adjacent serial sections of breast cancer tissue array BR1141 that have been stained with various anti-MUCl* monoclonal antibodies, wherein antibodies that bind to the PSMGFR N+9/C-9 peptide are compared to MNC2 and its humanized single chain form, huMNC2-scFv-Fc, which both bind to PSMGFR, N-10 but not to C-10 peptides.
  • Fig. 73A shows breast cancer specimen that was stained with MNC2.
  • Fig. 73B shows breast cancer specimen that was stained with 8A9.
  • Fig. 73C shows breast cancer specimen that was stained with 17H6.
  • Fig. 73D shows breast cancer specimen that was stained with huMNC2-scFv-Fc.
  • Fig. 73E shows breast cancer specimen that was stained with 3C5.
  • Fig. 73F shows breast cancer specimen that was stained with 39H5.
  • Anti-MUCl* antibodies 8A9, 17H6, 3C5, and 39H5 recognize a unique subset of cancer cells that are either not recognized or recognized to a lesser degree by anti-PSMGFR antibodies such as MNC2, 20A10, 25E6, 28F9, 18G12, or 18B4.
  • Anti-MUCl* antibodies of the invention which can be used for use in the diagnosis of cancers, include antibodies that bind to the PSMGFR peptide, the PSMGFR N+20/C-27 peptide, the PSMGFR N+9/C-9 peptide, or more specifically antibodies that bind to a peptide having at least 15 contiguous amino acids of the sequences below, with up to four amino acids substitutions;
  • V QLTLAFREGTIN VHD VETQFN Q Y (SEQ ID NO:7);
  • V QLTLAFREGTIN VHD VETQFN Q YKTE A AS R YNLTIS D VS VS D VP (SEQ ID NO: 10).
  • anti-PSMGFR antibodies MNC2, MNE6, 18B4, 18G12, 20A10, 25E6, anti- PSMGFR N+20/C-27 antibodies 1E4, 29H1, 31A1, 32C1, 4501, and anti-PSMGFR N+9/C-9 antibodies 3C5, 8A9, 17H6, and 39H5 are antibodies that can be used to diagnose cancers. These antibodies may be human, humanized or non-human. They may be antibody intact antibodies or antibody fragments. Antibodies may be generated by immunizing animals with peptides of sequences (i) - (viii) above. The animal that is immunized with the MUC1* extra cellular domain peptides to produce the antibodies may be human, rabbit, mouse, goat, donkey, camelid, llama, alpaca or other non-human species.
  • An antibody of the invention can be used in a diagnostic assay wherein it may be derivatized with, or attached to an imaging agent, a dye, a fluorescent entity, a color producing reagent or any other entity that renders the antibody optically, visually, electrically or radioactively detectable.
  • Antibodies of the invention can be used in a variety of diagnostic formats.
  • anti-MUCl* antibodies of the invention can be attached to an imaging agent for use in a live patient as a whole body diagnostic to determine if the patient has a MUC1* positive tumor or to determine if the patient would benefit from a therapeutic comprising all, or a fragment of, an anti-MUCl* antibody, which may be derived from or have similar binding characteristics as the antibody used in the diagnostic.
  • the species of the diagnostic antibody and the therapeutic antibody do not need to be the same.
  • Antibodies generated in camelid species are particularly useful for in vivo diagnostic assays because camelids generate small monovalent antibodies that have a short half-life in humans.
  • anti-MUCl* antibodies of the invention may be attached to an imaging agent and used intra- surgically to detect or mark cancerous tissues so they can be excised completely during the surgery.
  • a bodily fluid or tissue specimen from a patient diagnosed with cancer or suspected to be at risk of cancer is contacted with one or more anti- MUCl* antibodies of the invention; analysis of the binding of the antibody to the cells of the specimen indicate a level of binding or a pattern of binding that is indicative of cancer.
  • a therapeutic agent for the treatment of cancer is then administered to the patient.
  • the therapeutic agent comprises all or a fragment of an anti-MUCl* antibody.
  • diagnostic assays employing anti-MUCl* antibodies or fragments thereof are used to screen patients to determine their potential benefit from a MUC1* targeting therapeutic.
  • the anti-MUCl* antibody used in the diagnostic and the antibody or fragment thereof that is incorporated into the therapeutic may be derived from the same antibody.
  • the species of the diagnostic antibody and the therapeutic antibody do not need to be the same.
  • Diagnostic assays may encompass use of one or more anti-MUCl* antibodies.
  • a patient specimen that reacts with one or more anti-MUCl* antibodies indicates that the patient may benefit from administration of therapeutics that contain the one or more reactive antibodies, or fragments thereof.
  • a suspect cellular or tissue specimen which may be a biopsy, from a patient diagnosed with cancer or suspected of developing cancer is contacted with an anti-MUCl* antibody;
  • a normal cellular or tissue specimen from the patient or from a healthy donor is contacted with the same anti-MUCl* antibody, which may be an archived reference specimen;
  • antibody binding is detected;
  • the extent and pattern of antibody binding to the suspect specimen is compared to that of the normal specimen;
  • a therapeutic agent for the treatment of cancer is then administered to the patient, which may be a therapeutic agent that incorporates an anti-MUCl* antibody, or fragment thereof.
  • a bodily fluid or tissue specimen from a patient diagnosed with or suspected of having cancer is contacted with an anti-MUCl* antibody of the invention and a higher than normal level of MUC1* is detected or an abnormal pattern of MUC1* is detected, indicating that the patient has a MUC1* positive cancer and a therapeutic agent is then administered to the patient, which incorporates an anti-MUCl* antibody or antibody fragment.
  • the therapeutic agent into which the antibody or antibody fragment is incorporated is an immuno-oncology agent, such as a CAR T cell, an engineered NK cell or a dendritic cell.
  • the therapeutic agent into which the antibody or antibody fragment is incorporated is a huMNC2-CAR44 T cell.
  • the therapeutic agent into which the antibody or antibody fragment is incorporated is a bispecific antibody.
  • the therapeutic agent into which the antibody or antibody fragment is incorporated is an antibody drug conjugate (ADC).
  • the therapeutic agent into which the antibody or antibody fragment is incorporated is a bispecific T cell engager (BiTE).
  • the diagnostic assay may comprise an anti-MUCl* antibody and a second antibody, and the steps may comprise determining the ratio of the amount of a first antibody to a second antibody.
  • the first antibody may bind to MUC1* extra cellular domain and the second antibody may bind to a portion of the MUC1 extra cellular domain that is N-terminal of the cleavage site, such as the tandem repeat sequences.
  • the higher the ratio of MUC1* to full-length MUC1 the more progressed is the cancer and the more likely it is that the patient would benefit from a MUC1* targeting therapeutic.
  • the invention includes antibodies as well as antibody-like proteins, including but not limited to polyclonal, monoclonal, chimeras, humanized, single chain, antibody fragments and the like.
  • the invention includes the use of protein scaffolds for generating antibody mimics to obtain proteins that can be characterized by binding assays described herein and
  • the invention further includes using methods set forth here to identify antibodies that recognize specific epitopes, within the MUC1* extra cellular domain, that are differentially expressed on cancer cells.
  • the present invention is directed to a human or humanized anti-MUCl* 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 human or humanized anti-MUCl* antibody or antibody fragment or antibody-like protein may specifically bind to
  • V QLTLAFREGTIN VHD VETQFN Q Y (SEQ ID NO:7);
  • PSMGFR N+20/C-41 a peptide having amino acid sequence of
  • V QLTLAFREGTIN VHD VETQFN Q YKTE A AS R YNLTIS D VS VS D VP (SEQ ID NO: 10).
  • the human or humanized antibody may be IgGl, IgG2, IgG3, IgG4 or IgM.
  • the human or humanized antibody fragment or antibody-like protein may be scFv or scFv-Fc.
  • the 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 MN-E6 antibody, and has at least 80%, 90% or 95% or 98% sequence identity to the mouse monoclonal MN-E6 antibody.
  • the 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 CDR1, CDR2 or CDR3 regions of the antibodies 1E4, 29H1, 31A1, 32C1, and 45C11 reactive with PSMGFR N+20/C-27; 17H6, 39H5, 3C5, 8A9 reactive with PSMGFR N+9/C-9; 18G12, 20A10, 25E6, 28F9, 18B4, MNC2, and MNE6 reactive with PSMGFR.
  • CDRs complementarity determining regions
  • the invention is directed to a human or humanized anti-MUCl* antibody or antibody fragment or antibody-like protein according to above, which inhibits the binding of NME protein to MUC1*.
  • the NME may be NME1, NME6, NME7AB, NME7 or NME8.
  • 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
  • PSMGFR peptide as set forth in SEQ ID NO:4; [00201] (iii) PSMGFR N+20/C-22, a peptide having amino acid sequence of
  • V QLTLAFREGTIN VHD VETQFN Q Y (SEQ ID NO:7);
  • PSMGFR N+20/C-41 a peptide having amino acid sequence of
  • V QLTLAFREGTIN VHD VETQFN Q YKTE A AS R YNLTIS D VS VS D VP (SEQ ID NO: 10).
  • a preferred embodiment is huMNC2-CAR44 set forth in SEQ ID NO:236)
  • 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 a cancer specific antibody such as MNC2 or MNE6, or fragment thereof, wherein the antibody may be human, humanized or of a non-human species.
  • a cancer specific antibody such as MNC2 or MNE6, or fragment thereof
  • the MUC1* targeting therapeutic is an immune cell transduced with a chimeric antigen receptor, also known as CAR T, wherein the antibody fragment of the CAR is derived from a MUC1* cancer cell specific antibody.
  • a chimeric antigen receptor also known as CAR T
  • the antibody fragment of the CAR is derived from a MUC1* cancer cell specific antibody.
  • it is derived from MNC2.
  • MNE6 is derived from MNE6.
  • the invention is directed to a diagnostic assay for the identification of persons who might benefit from treatment of a MUC1 or MUC1* positive cancer with a therapeutic that includes an antibody, or fragment thereof, selected from the group of 1E4, 29H1, 31A1, 32C1, 4501, 17H6, 39H5, 3C5, 8A9, 18G12, 20A10, 25E6, 28F9, 18B4, MNC2, and MNE6 antibodies.
  • the anti-MUCl* antibody or a fragment thereof comprises all or part of the therapeutic and may be derived from the antibody or fragment thereof that is used for the diagnostic, wherein the therapeutic and diagnostic need not be the same species.
  • the anti-MUCl* antibody or fragment thereof that comprises all or part of the therapeutic is not derived from the antibody or fragment thereof that is used for the diagnostic, wherein the therapeutic and diagnostic need not be the same species.
  • the therapeutic agent targets MUC1*.
  • the therapeutic that comprises some or all of an anti-MUCl* antibody is a cancer immunotherapy composition, a CAR T, a BiTE, an antibody or an antibody drug conjugate, ADC.
  • the diagnostic is a companion diagnostic to determine eligibility for treatment with the therapeutic.
  • the diagnostic is used to assess efficacy of the therapeutic treatment.
  • the diagnostic together with results of clinical trials of the therapeutic are analyzed such that results of the diagnostic can be used to predict which patients will benefit from the treatment.
  • the cancer cell antibody or fragment thereof is derivatized with an imaging agent, which composition is then administered to the patient to enable visualization of reactive tumors within the patient.
  • the antibody plus imaging agent can be used to diagnose cancer, assess response of a therapeutic treatment or assess response to a therapeutic treatment wherein the therapeutic targets MUC1* and may comprise some or all of the cancer cell antibody used in the diagnostic.
  • the antibody attached to the imaging agent is a camelid antibody, including but not limited to llama, alpaca, and camel.
  • the diagnostic assays described here can be used on samples that may be tissues, biopsy specimens, cells, or bodily fluids taken from the test subject, patient or a normal person as a control.
  • the diagnostic assays can be performed in vitro or in vivo.
  • the diagnostic assays can be used intraoperatively (e.g. tissue at a surgical site can be studied without removal of the tissue from the subject). In this way, the diagnostic assay guides the surgeon to remove all the MUC1* positive tissues that are detectable, whether or not the tissues appear to be part of the tumor.
  • a primary indicator of tumorigenesis or potential for tumorigenesis is the amount of MUC1* at a cell or tissue surface that is accessible to anti-PSMGFR antibodies or cancer cell antibodies.
  • an exposed cancer cell antibody binding epitope means that the PSMGFR region of MUC1* is also accessible to growth factors that bind to and activate growth and survival functions mediated by the MUC1* growth factor receptor.
  • antibodies to the MUC1* region and to the tandem repeats, IBR or UR can be exposed to the sample and a determination made of the ratio of binding of MUC1* to MUC1 full-length.
  • a healthy sample will exhibit little or no antibody binding to the MUC1* region.
  • a sample indicating tumorigenesis will show a non-zero ratio of anti-MUCl* antibody to anti tandem repeat antibody or anti-IBR antibody, wherein as cancer stage/grade increases, the ratio of MUC1* to MUC1 containing tandem repeats, IBR or UR increases.
  • portions of MUC1 that contain tandem repeats, which are shed from the tissues can be detected in bodily fluids such as blood, breast milk or secretions, urine, lung efflux and the like.
  • a level of MUC1 cleavage to transmembrane MUC1* is inferred by measuring an amount of shed MUC1 using antibodies, including but not limited to antibodies that bind to the tandem repeats, unique regions that are N-terminal to an IBR or the IBR itself.
  • Measuring or inferring an amount of MUC1* on cells or tissues, that is greater than normal tissues or a prior sample from the patient, is an indicator of potential for tumor formation, existence of a tumor, or progression of a tumor, and can thereby serve as a diagnostic and/or an evaluator of the efficacy of a treatment for the patient’s cancer.
  • an amount of MUC1* is measured by contacting a tissue specimen with an anti-MUCl* antibody and determining that the amount of MUC1* is greater than the amount expressed on normal tissues or in a healthy person.
  • underlined sequence refers to CDR sequence and double underlined region refers to framework region.
  • KVSAGNGGSS LSYTNPAVAA ASAND (SEQ ID NO : 1 )
  • PSMGFR GTINVHDVETQFNQYKTEAASRYNLTISDVSVSDVPFPFSAQSGA SEQ ID NO : 4
  • SNIKFRPGSVWQLTLAFREGTINVHDVETQFNQYKTEAASRY SEQ ID NO : 5
  • SWVQLTLAFREGTINVHDVETQFNQYKTEAASRY (SEQ ID NO : 6 )
  • VQLTLAFREGTINVHDVETQFNQY (SEQ ID NO : 7 )
  • VQLTLAFREGTINVHDVETQFNQYKTEAASRYNLTI SDVSVSDVP SEQ ID NO : 10
  • Antibody 17H6 Light chain - Signal sequence-FRl-CDRl-FR2-CDR2-FR3- CDR3-FR4
  • Antibody 17H6 Light chain - Signal peptide-FRl-CDRl-FR2-CDR2-FR3-CDR3- FR4 MKLPVRLLVLMFWIPASNSDILMTOTPLSLPVSLGDOASISCRSSQSIVHSSGNTFLEWYLOKPGOSPKL LIYKVSNRFSGVPDRFSGSGSGIDFTLKISRVEAEDLGVYYCFQGSHVPFTFGSGTKLEIK (SEQ ID NO: 14)
  • FIRNKANGYTAEYSASVKG (SEQ ID NO : 18 )
  • AAAGTTTCCAACCGATTTTCT SEQ ID NO:23
  • FQGSHVPFT (SEQ. ID. NO : 26 ) Antibody 39H5 Heavy chain - Signal sequence-FRl-CDRl-FR2-CDR2-FR3- CDR3-FR4
  • Antibody 39H5 Light chain - Signal sequence-FRl-CDRl-FR2-CDR2-FR3- CDR3-FR4
  • Antibody 39H5 Light chain - Signal sequence-FRl-CDRl-FR2-CDR2-FR3- CDR3-FR4
  • AACTATGGAATGAAC SE. ID NO: 31
  • AAAGTTTCCAACCGATTTTCT (SEQ ID NO : 39 )
  • Antibody 3C5 Light chain - Signal sequence-FRl-CDRl-FR2-CDR2-FR3-CDR3- FR4
  • AACTATGGAATGAAC (SEQ ID NO : 47 )
  • Antibody 8A9 Light chain - Signal sequence-FRl-CDRl-FR2-CDR2-FR3-CDR3- FR4
  • Antibody 8A9 Light chain - Signal sequence-FRl-CDRl-FR2-CDR2-FR3-CDR3- FR4
  • RVSNRFS (SEQ ID NO : 72 )
  • FQGSHVPWA (SEQ ID NO : 74 )
  • Antibody 18G12 Light chain - Signal sequence-FRl-CDRl-FR2-CDR2-FR3- CDR3-FR4
  • Antibody 18G12 Light chain - Signal sequence-FRl-CDRl-FR2-CDR2-FR3- CDR3-FR4
  • GGCTACTTTTTGTAC SEQ ID NO : 79
  • GYFLY (SEQ ID NO : 80 )
  • GINPDNGGIDFNEKFRN (SEQ ID NO: 82)
  • Antibody 20A10 Light chain - Signal sequence-FRl-CDRl-FR2-CDR2-FR3- CDR3-FR4
  • Antibody 20A10 Light chain - Signal sequence-FRl-CDRl-FR2-CDR2-FR3- CDR3-FR4
  • Antibody 25E6 Light chain - Signal sequence-FRl-CDRl-FR2-CDR2-FR3- CDR3-FR4
  • Antibody 25E6 Light chain - Signal sequence-FRl-CDRl-FR2-CDR2-FR3- CDR3-FR4
  • Antibody 25E6 Light Chain CDR2 CTGGTGTCTAAACTGGACTCT (SEQ ID NO : 119 )
  • Antibody 28F9 Light chain - Signal sequence-FRl-CDRl-FR2-CDR2-FR3- CDR3-FR4
  • Antibody 28F9 Light chain - Signal sequence-FRl-CDRl-FR2-CDR2-FR3- CDR3-FR4
  • Antibody 28F9 Heavy Chain CDR2 GIHPSNGDTDFNEKFKN (SEQ ID NQ:130)
  • Antibody 18B4 Heavy chain - Signal sequence-FRl-CDRl-FR2-CDR2-FR3- CDR3-FR4
  • Antibody 18B4 Heavy chain - Signal sequence-FRl-CDRl-FR2-CDR2-FR3- CDR3-FR4
  • Antibody 18B4 Light chain - Signal sequence-FRl-CDRl-FR2-CDR2-FR3- CDR3-FR4
  • Antibody 18B4 Heavy chain - Signal sequence-FRl-CDRl-FR2-CDR2-FR3- CDR3-FR4
  • AAAGTTTCCAGCCGATTTTCT SEQ ID NO:151
  • Antibody 1E4 Heavy chain - Signal sequence-FRl-CDRl-FR2-CDR2-FR3-CDR3- FR4
  • Antibody 1E4 Heavy chain - Signal sequence-FRl-CDRl-FR2-CDR2-FR3-CDR3- FR4
  • Antibody 1E4 Light chain - Signal sequence-FRl-CDRl-FR2-CDR2-FR3-CDR3- FR4
  • Antibody 1E4 Light chain - Signal sequence-FRl-CDRl-FR2-CDR2-FR3-CDR3- FR4
  • RSSQSLVHSNGNTYLH (SEQ ID NO : 166 )
  • AAAGTTTCCAACCGATTTTCT SEQ ID NO:167
  • Antibody 29H1 Heavy chain - Signal sequence-FRl-CDRl-FR2-CDR2-FR3- CDR3-FR4
  • Antibody 29H1 Heavy chain - Signal sequence-FRl-CDRl-FR2-CDR2-FR3- CDR3-FR4
  • Antibody 29H1 Light chain - Signal sequence-FRl-CDRl-FR2-CDR2-FR3- CDR3-FR4
  • Antibody 29H1 Light chain - Signal sequence-FRl-CDRl-FR2-CDR2-FR3- CDR3-FR4
  • DAWMD (SEQ ID NO : 176 )
  • AAAGTTTCCAACCGATTTTCT SEQ ID NO:183
  • Antibody 31A1 Heavy chain - Signal sequence-FRl-CDRl-FR2-CDR2-FR3- CDR3-FR4
  • Antibody 31A1 Heavy chain - Signal sequence-FRl-CDRl-FR2-CDR2-FR3- CDR3-FR4
  • Antibody 31A1 Light chain - Signal sequence-FRl-CDRl-FR2-CDR2-FR3- CDR3-FR4
  • Antibody 31A1 Light chain - Signal sequence-FRl-CDRl-FR2-CDR2-FR3- CDR3-FR4
  • AAAGTTTCCAACCGATTTTCT SEQ ID NO:199
  • Antibody 32C1 Light chain - Signal sequence-FRl-CDRl-FR2-CDR2-FR3- CDR3-FR4
  • Antibody 45C11 Light chain - Signal sequence-FRl-CDRl-FR2-CDR2-FR3- CDR3-FR4
  • Antibody 45C11 Light chain - Signal sequence-FRl-CDRl-FR2-CDR2-FR3- CDR3-FR4
  • CAR44 CD8/HUMNC2/CD8/4—1BB/CD3
  • SASSSISYIH (SEQ ID NO : 269 ) DESCRIBES MIN-A2-1 LIGHT CHAIN VARIABLE COMPLEMENTARITY DETERMINING REGION 1 (CDR1) AMINO ACID SEQUENCE.
  • SASSSVSYMH (SEQ ID NO: 270) DESCRIBES MIN-A2-2 LIGHT CHAIN VARIABLE COMPLEMENTARITY DETERMINING REGION 1 (CDR1) AMINO ACID SEQUENCE.
  • SASSSVSYTY SEQ ID NO: 272
  • CDR1 AMINO ACID SEQUENCE.
  • SASSSVSYMH (SEQ ID NO: 274) DESCRIBES MIN-D7-2 LIGHT CHAIN VARIABLE COMPLEMENTARITY DETERMINING REGION 1 (CDR1) AMINO ACID SEQUENCE.
  • SASSSISYIH (SEQ ID NO: 276) DESCRIBES MIN-F2-2 LIGHT CHAIN VARIABLE COMPLEMENTARITY DETERMINING REGION 1 (CDR1) AMINO ACID SEQUENCE.
  • COMPLEMENTARITY DETERMINING REGION 2 (CDR2) AMINO ACID SEQUENCE.
  • STSNLAS SEQ ID NO : 279
  • GTSNLAS SEQ ID NO:283
  • CDR2 COMPLEMENTARITY DETERMINING REGION 2
  • QQRSNYPFT (SEQ ID NO:285) DESCRIBES MIN-A2-1 LIGHT CHAIN VARIABLE COMPLEMENTARITY DETERMINING REGION 3 (CDR3) AMINO ACID SEQUENCE.
  • QQRSSYPST (SEQ ID NO: 286) DESCRIBES MIN-A2-2 LIGHT CHAIN VARIABLE COMPLEMENTARITY DETERMINING REGION 3 (CDR3) AMINO ACID SEQUENCE.
  • QQRSSYPST (SEQ ID NO: 287) DESCRIBES MIN-C9-1 LIGHT CHAIN VARIABLE COMPLEMENTARITY DETERMINING REGION 3 (CDR3) AMINO ACID SEQUENCE.
  • QQRSSYPST (SEQ ID NO: 288) DESCRIBES MIN-C9-2 LIGHT CHAIN VARIABLE COMPLEMENTARITY DETERMINING REGION 3 (CDR3) AMINO ACID SEQUENCE.
  • QQRSSYPST (SEQ ID NO: 289 ) DESCRIBES MIN-D7-1 LIGHT CHAIN VARIABLE COMPLEMENTARITY DETERMINING REGION 3 (CDR3) AMINO ACID SEQUENCE.
  • QQRSSYPST (SEQ ID NO: 290) DESCRIBES MIN-D7-2 LIGHT CHAIN VARIABLE COMPLEMENTARITY DETERMINING REGION 3 (CDR3) AMINO ACID SEQUENCE.
  • QQRSNYPFT (SEQ ID NO: 291) DESCRIBES MIN-F2-1 LIGHT CHAIN VARIABLE COMPLEMENTARITY DETERMINING REGION 3 (CDR3) AMINO ACID SEQUENCE.
  • QQRSNYPFT (SEQ ID NO: 292) DESCRIBES MIN-F2-2 LIGHT CHAIN VARIABLE COMPLEMENTARITY DETERMINING REGION 3 (CDR3) AMINO ACID SEQUENCE.
  • NYGMN (SEQ ID NO: 293) DESCRIBES MIN-A2-1 HEAVY CHAIN VARIABLE COMPLEMENTARITY DETERMINING REGION 1 (CDR1) AMINO ACID SEQUENCE.
  • NYGMN (SEQ ID NO: 294) DESCRIBES MIN-A2-2 HEAVY CHAIN VARIABLE COMPLEMENTARITY DETERMINING REGION 1 (CDR1) AMINO ACID SEQUENCE.
  • NNGMN (SEQ ID NO: 295) DESCRIBES MIN-C9-1 HEAVY CHAIN VARIABLE COMPLEMENTARITY DETERMINING REGION 1 (CDR1) AMINO ACID SEQUENCE.
  • NNGMN (SEQ ID NO: 296) DESCRIBES MIN-C9-2 HEAVY CHAIN VARIABLE COMPLEMENTARITY DETERMINING REGION 1 (CDR1) AMINO ACID SEQUENCE.
  • NYGMN (SEQ ID NO: 297) DESCRIBES MIN-D7-1 HEAVY CHAIN VARIABLE COMPLEMENTARITY DETERMINING REGION 1 (CDR1) AMINO ACID SEQUENCE.
  • NYGMN (SEQ ID NO: 298) DESCRIBES MIN-D7-2 HEAVY CHAIN VARIABLE COMPLEMENTARITY DETERMINING REGION 1 (CDR1) AMINO ACID SEQUENCE.
  • NYGMN (SEQ ID NO: 299) DESCRIBES MIN-F2-1 HEAVY CHAIN VARIABLE COMPLEMENTARITY DETERMINING REGION 1 (CDR1) AMINO ACID SEQUENCE.
  • AIHPGSGGTAYNQKFKG (SEQ ID NO: 310) DESCRIBES MIN-F2-2 HEAVY CHAIN VARIABLE COMPLEMENTARITY DETERMINING REGION 2 (CDR2) AMINO ACID
  • SGDGYWYYA (SEQ ID NO: 313) DESCRIBES MIN-A2-1 HEAVY CHAIN VARIABLE COMPLEMENTARITY DETERMINING REGION 3 (CDR3) AMINO ACID SEQUENCE.
  • SGDGYWYYA (SEQ ID NO: 314) DESCRIBES MIN- A2-2 HEAVY CHAIN VARIABLE COMPLEMENTARITY DETERMINING REGION 3 (CDR3) AMINO ACID SEQUENCE.
  • TGTARAFYA (SEQ ID NO: 315) DESCRIBES MIN-C9-1 HEAVY CHAIN VARIABLE COMPLEMENTARITY DETERMINING REGION 3 (CDR3) AMINO ACID SEQUENCE.
  • TGTARAFYA (SEQ ID NO: 316) DESCRIBES MIN-C9-2 HEAVY CHAIN VARIABLE COMPLEMENTARITY DETERMINING REGION 3 (CDR3) AMINO ACID SEQUENCE.
  • TGTTAILNG (SEQ ID NO: 317) DESCRIBES MIN-D7-1 HEAVY CHAIN VARIABLE COMPLEMENTARITY DETERMINING REGION 3 (CDR3) AMINO ACID SEQUENCE.
  • SGDGYWYYA (SEQ ID NO: 318) DESCRIBES MIN-D7-2 HEAVY CHAIN VARIABLE COMPLEMENTARITY DETERMINING REGION3 (CDR3) AMINO ACID SEQUENCE.
  • TGTTAILNG (SEQ ID NO: 319) DESCRIBES MIN-F2-1 HEAVY CHAIN VARIABLE COMPLEMENTARITY DETERMINING REGION 3 (CDR3 ) AMINO ACID SEQUENCE.
  • YGSFA SEQ ID NO: 320
  • DESCRIBES MIN-F2-2 HEAVY CHAIN VARIABLE COMPLEMENTARITY DETERMINING REGION 3 (CDR3)
  • TGTTAILNG (SEQ ID NO: 321) DESCRIBES MIN-F2-3 HEAVY CHAIN VARIABLE COMPLEMENTARITY DETERMINING REGION 3 (CDR3) AMINO ACID SEQUENCE.
  • TGTTAILNG SEQ ID NO: 322
  • DESCRIBES MIN-F2-4 HEAVY CHAIN VARIABLE COMPLEMENTARITY DETERMINING REGION 3 (CDR3)
  • AMINO ACID SEQUENCE RASQDIGSSLN (SEQ ID NO: 323)
  • AMINO ACID SEQUENCE RASQDIGSSLN
  • RASKSVSTSGYSYMH (SEQ ID NO:326) DESCRIBES MIN- 29 LIGHT CHAIN VARIABLE COMPLEMENTARITY DETERMINING REGION 1 (CDR1) AMINO ACID SEQUENCE.
  • RASKSVSTSGYSYMH (SEQ ID NO: 327)
  • DESCRIBES MIN- 34 LIGHT CHAIN VARIABLE COMPLEMENTARITY DETERMINING REGION 1 (CDR1)
  • CDR1 AMINO ACID SEQUENCE.
  • KASQNVGTNVG (SEQ ID NO: 328) DESCRIBES MIN- 42 LIGHT CHAIN VARIABLE COMPLEMENTARITY DETERMINING REGION 1 (CDR1) AMINO ACID SEQUENCE.
  • RASGNIHNFLA SEQ ID NO:329)
  • CDR1 AMINO ACID SEQUENCE.
  • AATSLAD (SEQ ID NO: 332) DESCRIBES MIN-17-2 LIGHT CHAIN VARIABLE
  • GIGVT SEQ ID NO:339
  • DESCRIBES MIN-17-2 HEAVY CHAIN COMPLEMENTARITY
  • GYFMS (SEQ ID NO: 342) DESCRIBES MIN-45 HEAVY CHAIN COMPLEMENTARITY
  • EINPSNGRTNYNEKFKS SEQ ID NO: 3444
  • DESCRIBES MIN-17-1 HEAVY CHAIN COMPLEMENTARITY DETERMINING REGION 2 (CDR2)
  • CDR2 AMINO ACID SEQUENCE.
  • COMPLEMENTARITY DETERMINING REGION 2 (CDR2) AMINO ACID SEQUENCE.
  • TISSGGTYTYYPDSVKG (SEQ ID NO: 348)
  • DESCRIBES MIN-42 HEAVY CHAIN COMPLEMENTARITY DETERMINING REGION 2 (CDR2)

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PCT/US2019/019566 2018-02-26 2019-02-26 Diagnostic methods using anti-muc1* antibodies Ceased WO2019165421A1 (en)

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AU2019225237A AU2019225237B2 (en) 2018-02-26 2019-02-26 Diagnostic methods using anti-MUC1* antibodies
EP19757027.8A EP3759145A4 (en) 2018-02-26 2019-02-26 DIAGNOSTIC METHODS USING ANTI-MUC1* ANTIBODIES
CA3092247A CA3092247A1 (en) 2018-02-26 2019-02-26 Diagnostic methods using anti-muc1* antibodies
CN201980027373.9A CN112272677B (zh) 2018-02-26 2019-02-26 使用抗muc1＊抗体的诊断方法
JP2020544813A JP7411559B2 (ja) 2018-02-26 2019-02-26 Ａｎｔｉ－ｍｕｃｉ＊抗体を用いた診断法
US16/975,625 US11976132B2 (en) 2018-02-26 2019-02-26 Diagnostic methods using anti-MUC1* antibodies
CN202510558379.6A CN120484122A (zh) 2019-01-11 2020-01-13 抗可变muc1*抗体及其用途
AU2020205735A AU2020205735A1 (en) 2019-01-11 2020-01-13 Anti-variable MUC1* antibodies and uses thereof
CN202080020073.0A CN113853386A (zh) 2019-01-11 2020-01-13 抗可变muc1*抗体及其用途
CA3126391A CA3126391A1 (en) 2019-01-11 2020-01-13 Anti-variable muc1* antibodies and uses thereof
JP2021540477A JP2022527144A (ja) 2019-01-11 2020-01-13 抗可変ｍｕｃ１＊抗体およびその使用
EP20738367.0A EP3908603A4 (en) 2019-01-11 2020-01-13 ANTI-VARIABLE MUC1* ANTIBODIES AND USES THEREOF
PCT/US2020/013410 WO2020146902A2 (en) 2019-01-11 2020-01-13 Anti-variable muc1* antibodies and uses thereof
IL276925A IL276925A (en) 2018-02-26 2020-08-25 Diagnostic methods using anti-MUC1 antibodies
IL284772A IL284772A (en) 2019-01-11 2021-07-11 Anti-variable muc1* antibodies and uses thereof
US17/373,609 US12583927B2 (en) 2019-01-11 2021-07-12 Anti-variable MUC1* antibodies and uses thereof
JP2023218543A JP7705442B2 (ja) 2018-02-26 2023-12-25 Ａｎｔｉ－ｍｕｃｉ＊抗体を用いた診断法
US18/612,767 US12351646B2 (en) 2018-02-26 2024-03-21 Diagnostic methods using anti-MUC1* antibodies
US18/935,308 US20250066505A1 (en) 2018-02-26 2024-11-01 Diagnostic methods using anti-muc1* antibodies
JP2025126649A JP2025172739A (ja) 2019-01-11 2025-07-29 抗可変ｍｕｃ１＊抗体およびその使用
AU2026201952A AU2026201952A1 (en) 2018-02-26 2026-03-16 Diagnostic methods using anti-MUC1* antibodies

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PCT/US2018/062569 WO2019104306A1 (en) 2017-11-27 2018-11-27 Humanized anti-muc1* antibodies and direct use of cleavage enzyme
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US20200407462A1 (en) 2020-12-31
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AU2019225237B2 (en) 2025-12-18
US11976132B2 (en) 2024-05-07
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