US20180104331A1 - Autoimmune antibodies for use in inhibiting cancer cell growth - Google Patents

Autoimmune antibodies for use in inhibiting cancer cell growth Download PDF

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US20180104331A1
US20180104331A1 US15/573,323 US201615573323A US2018104331A1 US 20180104331 A1 US20180104331 A1 US 20180104331A1 US 201615573323 A US201615573323 A US 201615573323A US 2018104331 A1 US2018104331 A1 US 2018104331A1
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cancer
cancer cell
antibody
cell
autoimmune
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Andrew J. Ewald
Veena Padmanaban
Livia Casciola-Rosen
Antony Rosen
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Johns Hopkins University
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Johns Hopkins University
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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
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/395—Antibodies; Immunoglobulins; Immune serum, e.g. antilymphocytic serum
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/06—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies from serum
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C07K16/2863—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against receptors for growth factors, growth regulators
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C07K16/30—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants from tumour cells
    • 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
    • G01N33/5005—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells
    • G01N33/5008—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics
    • G01N33/5011—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics for testing antineoplastic activity
    • 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
    • G01N33/5005—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells
    • G01N33/5008—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics
    • G01N33/502—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics for testing non-proliferative effects
    • G01N33/5029—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics for testing non-proliferative effects on cell motility
    • 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
    • G01N33/564—Immunoassay; Biospecific binding assay; Materials therefor for pre-existing immune complex or autoimmune disease, i.e. systemic lupus erythematosus, rheumatoid arthritis, multiple sclerosis, rheumatoid factors or complement components C1-C9
    • 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
    • G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/505—Medicinal preparations containing antigens or antibodies comprising antibodies
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/40—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against enzymes

Definitions

  • the present disclosure is based, at least in part, on the discovery that autoimmune antibodies inhibit cancer cell invasion. That is, the disclosure provides the results of experiments showing that antibodies from patients with autoimmune diseases specifically recognize antigens expressed in human breast tumors. These results indicate that autoantibodies may play a role in controlling tumor progression by targeting gene products (e.g., mutant gene products) associated with aberrant proliferation or cell invasion. Accordingly, the disclosure provides, among other things, a variety of compositions and methods useful for diagnostic, screening, and therapeutic applications relevant to cancer.
  • the disclosure provides a method for inhibiting a cancer cell.
  • the method comprises contacting the cancer cell with an autoimmune antibody in an amount effective to inhibit the cancer cell.
  • the autoimmune antibody inhibits the growth of the cancer cell.
  • the autoimmune antibody inhibits the viability of the cancer cell.
  • the autoimmune antibody inhibits the mobility of the cancer cell.
  • the contacting occurs in vitro. In some embodiments, the contacting occurs in vivo.
  • the cancer cell can be, e.g., a lung cancer cell, breast cancer cell, colon cancer cell, pancreatic cancer cell, renal cancer cell, stomach cancer cell, liver cancer cell, bone cancer cell, hematological cancer cell, neural tissue cancer cell, melanoma, thyroid cancer cell, ovarian cancer cell, testicular cancer cell, prostate cancer cell, cervical cancer cell, vaginal cancer cell, or bladder cancer cell.
  • the cancer cell is contacted with more than one autoimmune antibody.
  • the cancer cell is contacted with blood or a blood fraction comprising one or more autoimmune antibodies.
  • Blood fractions include, e.g., plasma and serum.
  • the blood or blood fraction was obtained from a subject afflicted with lupus.
  • the blood or blood fraction was obtained from a subject afflicted with a dermatomyositis, scleroderma, rheumatoid arthritis, or multiple sclerosis.
  • the cancer cell is of the same histological type as one or more of the cells of the organ affected in the organ-specific autoimmune disease.
  • autoimmune antibodies to the skin or skin components may be useful for treating melanomas or other skin cancers.
  • autoantibodies reactive with normal lung may be used for treating lung cancers or inhibiting the growth of lung cancer cells.
  • the autoantibody is from a subject having dermatomyositis and the cancer is a breast cancer (or the cancer cell is a breast cancer cell).
  • the autoimmune antibody is a monoclonal antibody. In some embodiments of any of the methods described herein, the antibody is an isolated and/or recombinant antibody. In some embodiments of any of the methods described herein, e.g., where blood or blood fraction products are used, a plurality of autoantibodies can be contacted to the cell, each antibody of different specificity (e.g., a polyclonal preparation).
  • the disclosure features a method for treating a subject afflicted with a cancer.
  • the method comprises administering to the subject an autoimmune antibody in an amount effective to treat the cancer.
  • the subject is a human.
  • the cancer is, e.g., a lung cancer, breast cancer, colon cancer, pancreatic cancer, renal cancer, stomach cancer, liver cancer, bone cancer, hematological cancer, neural tissue cancer, melanoma, thyroid cancer, ovarian cancer, testicular cancer, prostate cancer, cervical cancer, vaginal cancer, or bladder cancer.
  • more than one autoimmune antibody is administered to the subject.
  • a blood or a blood fraction comprising one or more autoimmune antibodies is administered to the subject.
  • the blood or blood fraction was obtained from a subject afflicted with lupus or any other autoimmune disease described herein or known in the art.
  • the subject can have dermatomyositis, scleroderma, rheumatoid arthritis, or multiple sclerosis.
  • the subject with autoimmune disease does not have a cancer. In some embodiments, the subject with autoimmune disease does have a cancer or had a cancer.
  • the autoantibody binds to a cell surface protein. In some embodiments of any of the methods described herein, the autoantibody binds to an intracellular antigen.
  • the disclosure features a method for identifying a compound (e.g., a small molecule, a nucleic acid, or an antibody) that inhibits a cancer cell.
  • the method comprises: assaying in vitro the growth, viability, or mobility of a cancer cell in the presence of an antibody from a B cell obtained from a subject afflicted with an autoimmune disease, wherein a reduction in the growth, viability, or mobility of the cancer cell in the presence of the antibody, as compared to the growth, viability or mobility of the cancer cell in the absence of the antibody, identifies the antibody as an inhibitor of the cancer cell.
  • the assaying step is run in the absence of a stromal cell population.
  • the assaying step is run in the presence of a stromal cell population.
  • the stromal cell population may be selected from the group consisting of fibroblasts, T-cells, B-cells, dendritic cells, and eosinophils.
  • the cancer cell is a group of cancer cells.
  • the disclosure features a screening method for identifying one or more antibodies that inhibit a cancer cell.
  • the method comprises: assaying in vitro the growth, viability, or mobility of a cancer cell in the presence of each antibody of a plurality of antibodies from a subject afflicted with an autoimmune disease, wherein a reduction in the growth, viability, or mobility of the cancer cell in the presence of at least one of the antibodies, as compared to the growth, viability or mobility of the cancer cell in the absence of the antibody, identifies the antibody as an inhibitor of the cancer cell.
  • the assaying step is run in the absence of a stromal cell population.
  • the assaying step is run in the presence of a stromal cell population.
  • the stromal cell population may be selected from the group consisting of fibroblasts, T-cells, B-cells, dendritic cells, and eosinophils.
  • the cancer cell is a group of cancer cells.
  • the disclosure features a method for identifying an autoimmune antibody that binds to a cancer cell or preparation of the cancer cell, the method comprising detecting the presence or absence of an interaction between an antibody and a cancer cell, wherein the antibody is from a subject afflicted with an autoimmune disease, wherein the presence of an interaction between the antibody and the cancer cell identifies the antibody as binding to the cancer cell.
  • the assaying or identification involves an organoid assay, such as one described and exemplified herein.
  • any of the methods described herein further comprise determining that the antibody binds selectively to the cancer cell as compared to the binding of the antibody to a normal cell of the same histological type as the cancer cell.
  • Suitable techniques include fluorescence assisted cell sorting (FACS) or immunoassay techniques, such as ELISA, Western blotting, or dot blotting.
  • any of the methods described herein can include determining whether the antibody inhibits the growth, viability, or mobility of the cancer cell. Suitable methods for detecting inhibition of cell growth are described and exemplified herein. Cancer growth inhibition assays, migration assays, and apoptosis assays are also well known in the art.
  • any of the methods described herein can further comprise determining whether the antibody selectively inhibits the growth, viability, or mobility of the cancer cell, as compared to the growth, viability, or mobility of a normal cell of the same histological type as the cancer cell.
  • the antibody can be assayed for any inhibitory or toxic effects on normal cells or in animals (e.g., non-human mammals or clinical studies in humans).
  • any of the methods described herein can further comprise determining the antigen (e.g., the epitope or all or part of the protein, nucleic acid, or hapten) to which the antibody binds.
  • the antigen e.g., the epitope or all or part of the protein, nucleic acid, or hapten
  • any of the methods described herein further comprise isolating the antibody or a nucleic acid encoding the antibody from a B cell from the subject. In some embodiments, any of the methods described herein further comprise isolating the B cell from the subject.
  • any of the methods described herein can further include producing the antibody in a non-human host cell comprising a nucleic acid encoding the antibody.
  • the host cell can be a mammalian cell, such as a primate cell or a rodent cell (e.g., Chinese Hamster Ovary or NS0).
  • the disclosure features an antibody identified by any of the methods described herein, which antibody may be used in any of the methods described herein.
  • the disclosure provides a blood product (comprising one or more autoimmune antibodies) for use in treating a cancer or inhibiting the growth, viability, or mobility of a cancer cell.
  • the antibody is a whole antibody. In some embodiments of any of the methods described herein, the antibody is an antigen-binding fragment of an antibody, such as an scFv, an Fd, a Fab, or a F(ab′) 2 . In some embodiments of any of the methods described herein, the autoantibody is from a human with autoimmune disease. In some embodiments, the antibody can be from a non-human mammal with an autoimmune disease, and, in such embodiments, the antibody can be humanized, chimerized, or de-immunized, prior to administration to a human.
  • the disclosure features a method for isolating cancer organoids, which comprises isolating a tumor from a host, generating organoids from the tumor, and embedding the organoids in collagen I (e.g., a 3-D fibrillar collagen I matrix).
  • the disclosure provides a screening method for identifying a compound, such as an autoantibody, using the collagen embedded organoids.
  • the embedded organoids can be contacted with one or more (e.g., a plurality) of candidate compounds to determine whether such one or more compounds modulate (e.g., inhibit) the growth or invasion of the organoids.
  • FIG. 1 includes 7 panels, A-G, and depicts (Panel A) Workflow for isolation of tumor organoids from fresh patient samples.
  • Panel B Workflow of human tumor organoid generation with pictures taken during the experiment.
  • Panel C Primary human tumor organoids were scored for invasive morphology into four categories.
  • Panel E Left panel: DIC image of a collectively invading strand of a tumor organoid into Collagen I. Right panel: Confocal image displaying the K14 expression in leader cells at the invasive front.
  • Panel F Strong positive correlation between the level of invasion and K14 expression in the organoids.
  • Patent G Strong positive correlation between the level of invasion and K14 conversion.
  • FIG. 2 includes three panels, A-C.
  • Panel A Schematic for immunofluorescence staining.
  • Control 1 Staining with control antisera from normal patients
  • Control 2 Staining normal mammary organoids with all antisera.
  • Panel B Distribution of the total number of autoantibodies among the various disease types, and fraction of positive staining with normal breast and tumor organoids.
  • Panel C List of all antisera, disease type, known antibodies for each, and positivity of staining in the cytoplasm and nucleus against tumor and normal organoids. Positivity of staining was scored as ⁇ , + or ++.
  • FIG. 3 includes two panels, A and B.
  • Panel A Representative images of staining results for two control antisera (C19, LCR) and eighteen patient antisera used to stain patient breast tumor organoids. Images are arranged in decreasing order of intensity.
  • Panel B Representative images of staining results for two control antisera (C19, LCR) and eighteen patient antisera used to stain normal breast organoids. Images are order matched to the panel above.
  • FIG. 4 depicts representative images of normal mammary organoids stained with control autoantibodies (LCR, C19, C3, C17 and C34). Staining procedures were completed with one of two secondary antibodies—goat anti-human IgG (H+L) or goat anti-human Fc-gamma specific IgG.
  • FIG. 5 depicts representative images of tumor organoids generated from three human breast tumors stained with patient derived autoantibodies (12106, 13040, 13142, 13200, S£1269, and FW1366).
  • FIG. 6 depicts representative images of tumor organoids generated from three human breast tumors stained with patient derived autoantibodies.
  • 10095 and 9070 are autoantibodies directed against TIF1 gamma purified from the serum of patients without or with cancer respectively.
  • anti-NXP2 autoantibodies 9109 and 7107 were purified from the serum of patients without or with cancer respectively.
  • FIG. 7 includes five panels, A-E.
  • Panel A Effect of autoantibodies on tumor invasion in 3D organotypic culture. Representative DIC images depicting the invasion profile of tumor organoids collected on d0, or d6 without any autoantibody, or d6 with one of the following autoantibodies—SLE1269, FW1366, 13200, 12106, C33 or C34 (control autoantibodies).
  • Panel B Bar graph comparing the cytotoxicity of each autoantibody.
  • Panel D Bar graph comparing the effect of each autoantibody on collective invasion of tumor organoids derived from 2 tumors.
  • Panel E Dose-dependency of autoantibodies 13200 and 12106 in reducing tumor invasion.
  • FIG. 8 includes four panels, A-D, and depicts the effect of patient cancer-status on autoantibody-mediated decrease in tumor invasion.
  • Panel A Representative DIC images depicting the invasion profile of tumor organoids collected on d0, or d6 without any autoantibody, or d6 with one of the following autoantibodies—7107, 9070, 9109, 10015 or C34 (control autoantibody).
  • Panel C Bar graph comparing the effect of each autoantibody on invasion.
  • Panel D Bar graph comparing the cytotoxicity of each autoantibody.
  • FIG. 9 depicts a working model: autoantibodies derived from patients with autoimmune diseases (AutoAbs) block tumor invasion in 3D organotypic cultures.
  • compositions e.g., autoantibodies
  • applications such as therapeutic and diagnostic methods, in which the agents are useful, as well as screening methods for identifying autoantibodies useful in the applications.
  • exemplary compositions e.g., pharmaceutical compositions and formulations
  • methods for preparing and using these compositions are elaborated on below.
  • the disclosure features, e.g., methods for inhibiting the growth of a cancer cell, and/or treating a subject having a cancer, using one or more autoimmune antibodies.
  • the term “antibody” refers to whole antibodies including antibodies of different isotypes, such as IgM, IgG, IgA, IgD, and IgE antibodies.
  • the term “antibody” includes a polyclonal antibody, a monoclonal antibody, a chimerized or chimeric antibody, a humanized antibody, a primatized antibody, a deimmunized antibody, and a fully human antibody.
  • the antibody can be made in or derived from any of a variety of species, e.g., mammals such as humans, non-human primates (e.g., orangutan, baboons, or chimpanzees), horses, cattle, pigs, sheep, goats, dogs, cats, rabbits, guinea pigs, gerbils, hamsters, rats, and mice.
  • mammals such as humans, non-human primates (e.g., orangutan, baboons, or chimpanzees), horses, cattle, pigs, sheep, goats, dogs, cats, rabbits, guinea pigs, gerbils, hamsters, rats, and mice.
  • the antibody can be a purified or a recombinant antibody.
  • antibody fragment refers to a fragment of an antibody that retains the ability to bind to an target antigen.
  • fragments include, e.g., a single chain antibody, a single chain Fv fragment (scFv), an Fd fragment, an Fab fragment, an Fab′ fragment, or an F(ab′) 2 fragment.
  • scFv fragment is a single polypeptide chain that includes both the heavy and light chain variable regions of the antibody from which the scFv is derived.
  • intrabodies, minibodies, triabodies, and diabodies are also included in the definition of antibody and are compatible for use in the methods described herein.
  • Bispecific antibodies are monoclonal, preferably human or humanized, antibodies that have binding specificities for at least two different antigens.
  • the term “antibody” also includes, e.g., single domain antibodies such as camelized single domain antibodies. See, e.g., Muyldermans et al. (2001) Trends Biochem Sci 26:230-235; Nuttall et al. (2000) Curr Pharm Biotech 1:253-263; Reichmann et al. (1999) J Immunol Meth 231:25-38; PCT application publication nos. WO 94/04678 and WO 94/25591; and U.S. Pat. No. 6,005,079, all of which are incorporated herein by reference in their entireties.
  • the disclosure provides single domain antibodies comprising two VH domains with modifications such that single domain antibodies are formed.
  • an autoimmune antibody refers to an antibody produced by the immune system that is directed against one or more of a host's own antigens, such as an epitope of a protein, a peptide, or a non-protein epitope. Such autoantibodies can be associated with autoimmune disease.
  • an autoimmune antibody is obtained from a subject (or the therapeutic antibody used (e.g., affinity matured antibody) is derived from an autoantibody from a subject) with an autoimmune disease.
  • the term “autoimmune disease” means a disease resulting from an immune response against a self-tissue or tissue component, including both self-antibody responses and cell-mediated responses.
  • autoimmune disease encompasses organ-specific autoimmune diseases, in which an autoimmune response is directed against a single tissue, such as type I diabetes mellitus (T1D), Crohn's disease, ulcerative colitis, myasthenia gravis, vitiligo, Graves' disease, Hashimoto's disease, Addison's disease and autoimmune gastritis and autoimmune hepatitis.
  • organ-specific autoimmune diseases in which an autoimmune response is directed against a single tissue, such as type I diabetes mellitus (T1D), Crohn's disease, ulcerative colitis, myasthenia gravis, vitiligo, Graves' disease, Hashimoto's disease, Addison's disease and autoimmune gastritis and autoimmune hepatitis.
  • non-organ specific autoimmune diseases in which an autoimmune response is directed against a component present in several or many organs throughout the body.
  • Such autoimmune diseases include, for example, rheumatoid diseases, systemic lupus erythematosus, progressive systemic sclerosis and variants, polymyositis and dermatomyositis. Additional autoimmune diseases include pernicious anemia including some of autoimmune gastritis, primary biliary cirrhosis, autoimmune thrombocytopenia, Sjogren's syndrome, multiple sclerosis and psoriasis. Exemplary autoimmune diseases are elaborated on below.
  • Inflammatory myositis which refers to the inflammation of muscle, is used to describe dermatomyositis, polymyositis, necrotizing myopathy, and inclusion-body myositis. Dermatomyositis affects 5 in every 100,000 persons in the United States (Furst et al., 2012). Common symptoms include a characteristic rash and muscle weakness which developed within a few weeks. The pathology of the disease includes binding of immune complexes to endothelial cells, activation of the complement system and subsequent lysis, leading to a decreased number of capillaries in the muscle (Mammen, 2010). Autoantibodies preferentially associated with dermatomyositis include those recognizing Mi-2, MDA5, TIF1 ⁇ , and NXP-2—each associated with a distinct phenotype (Shah et al., 2015).
  • Scleroderma is a systemic autoimmune disease best characterized by the hardening of the skin due to the increased synthesis of collagen leading to abnormal connective tissue (Fleming and Schwartz, 2008).
  • the overall incidence rate of scleroderma in the adult population of the United States is approximately 20 per million per year (Mayes et al., 2003).
  • Most patients affected by the disease present with Raynaud's phenomenon—reduced blood flow resulting in discoloration of fingers and toes.
  • the most common scleroderma-specific autoantibodies include anticentromere, anti-topoisomerase, and anti-RNA polymerase (Shah et al., 2015).
  • SLE Systemic lupus erythematosus
  • SLE Systemic lupus erythematosus
  • the disease is characterized by a multisystem inflammation with the generation of autoantibodies including antinuclear, anti-ds DNA, anti-ribonucleoprotein, anti-Ro, and anti-La (Ippolito et al., 2011).
  • the incidence of lupus is about 5-7 per 100,000 persons (Somers et al., 2014). Symptoms for the disease may vary between individuals, but usually include chest pain, fatigue, hair loss, mouth sores, fever with no cause, and/or a butterfly rash.
  • B cell cells e.g., B cells from a patient with an autoimmune disease
  • the methods can involve obtaining a biological sample from a subject.
  • a biological sample can be a biological fluid such as urine, whole blood or a fraction thereof (e.g., plasma or serum), saliva, semen, sputum, cerebrospinal fluid, tears, or mucus.
  • a biological sample can be further fractionated, if desired, to a fraction containing particular analytes (e.g., proteins) of interest.
  • a whole blood sample can be fractionated into serum or into fractions containing particular types of proteins or cells.
  • a biological sample can be a combination of different biological samples from a subject such as a combination of two different fluids.
  • Biological samples suitable for the invention may be fresh or frozen samples collected from a subject, or archival samples with known diagnosis, treatment and/or outcome history.
  • the biological samples can be obtained from a subject, e.g., a subject having, suspected of having, or at risk of developing, an autoimmune disorder. Any suitable methods for obtaining the biological samples can be employed, although exemplary methods include, e.g., phlebotomy, swab (e.g., buccal swab), lavage, or fine needle aspirate biopsy procedure.
  • Biological samples can also be obtained from bone marrow or spleen.
  • a biological sample can be further contacted with one or more additional agents such as appropriate buffers and/or inhibitors, including protease inhibitors, the agents meant to preserve or minimize changes (e.g., changes in osmolarity or pH) in protein structure.
  • additional agents such as appropriate buffers and/or inhibitors, including protease inhibitors, the agents meant to preserve or minimize changes (e.g., changes in osmolarity or pH) in protein structure.
  • additional agents such as appropriate buffers and/or inhibitors, including protease inhibitors, the agents meant to preserve or minimize changes (e.g., changes in osmolarity or pH) in protein structure.
  • additional agents such as appropriate buffers and/or inhibitors, including protease inhibitors, the agents meant to preserve or minimize changes (e.g., changes in osmolarity or pH) in protein structure.
  • inhibitors include, for example, chelators such as ethylenediamine tetraacetic acid (EDTA), ethylene glycol
  • a sample also can be processed to eliminate or minimize the presence of interfering substances.
  • a biological sample can be fractionated or purified to remove one or more materials (e.g., cells) that are not of interest.
  • Methods of fractionating or purifying a biological sample include, but are not limited to, flow cytometry, fluorescence activated cell sorting, and sedimentation.
  • the antibody is present in a preparation made from blood from a subject.
  • the antibody is a recombinant antibody. Techniques for the preparation of recombinant antibody molecules are described in, e.g.: WO97/08320; U.S. Pat. No. 5,427,908; U.S. Pat. No. 5,508,717; Smith (1985) Science 225:1315-1317; Parmley and Smith (1988) Gene 73:305-318; De La Cruz et al. (1988) J Biol Chem 263:4318-4322; U.S. Pat. No. 5,403,484; U.S. Pat. No.
  • the cell culture supernatants are screened for the desired antibodies, e.g., by immunofluorescent staining of target antigen-expressing cells, by immunoblotting, by an enzyme immunoassay, e.g. a sandwich assay or a dot-assay, or a radioimmunoassay.
  • an enzyme immunoassay e.g. a sandwich assay or a dot-assay, or a radioimmunoassay.
  • the immunoglobulins in the culture supernatants may be concentrated, e.g., by precipitation with ammonium sulfate, dialysis against hygroscopic material such as polyethylene glycol, filtration through selective membranes, or the like.
  • the antibodies are purified by the customary chromatography methods, for example gel filtration, ion-exchange chromatography, chromatography over DEAE-cellulose and/or (immuno-) affinity chromatography, e.g. affinity chromatography with one or more surface polypeptides derived from a target antigen-expressing cell line, or with Protein-A or -G.
  • Another embodiment provides a process for the preparation of a bacterial cell line secreting antibodies directed against a target antigen in a suitable mammal.
  • a rabbit is immunized with pooled samples from target antigen-expressing tissue or cells or the target antigen itself (or fragments thereof).
  • a phage display library produced from the immunized rabbit is constructed and panned for the desired antibodies in accordance with methods well known in the art (such as, e.g., the methods disclosed in the various references incorporated herein by reference).
  • a “subject,” as used herein, can be any mammal.
  • a subject can be a human, a non-human primate (e.g., monkey, baboon, or chimpanzee), a horse, a cow, a pig, a sheep, a goat, a dog, a cat, a rabbit, a guinea pig, a gerbil, a hamster, a rat, or a mouse.
  • the subject is an infant (e.g., a human infant).
  • the subject can have cancer, an autoimmune disease, or both a cancer and an autoimmune disease.
  • compositions described herein can be formulated as a pharmaceutical solution, e.g., for administration to a subject treating a cancer.
  • the pharmaceutical compositions will generally include a pharmaceutically acceptable carrier.
  • a “pharmaceutically acceptable carrier” refers to, and includes, any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like that are physiologically compatible.
  • the compositions can include a pharmaceutically acceptable salt, e.g., an acid addition salt or a base addition salt (see e.g., Berge et al. (1977) J Pharm Sci 66:1-19).
  • compositions can be formulated according to standard methods.
  • Pharmaceutical formulation is a well-established art, and is further described in, e.g., Gennaro (2000) “Remington: The Science and Practice of Pharmacy,” 20 th Edition, Lippincott, Williams & Wilkins (ISBN: 0683306472); Ansel et al. (1999) “Pharmaceutical Dosage Forms and Drug Delivery Systems,” 7 th Edition, Lippincott Williams & Wilkins Publishers (ISBN: 0683305727); and Kibbe (2000) “Handbook of Pharmaceutical Excipients American Pharmaceutical Association,” 3 rd Edition (ISBN: 091733096X).
  • a composition can be formulated, for example, as a buffered solution at a suitable concentration and suitable for storage at 2-8° C. (e.g., 4° C.).
  • a composition can be formulated for storage at a temperature below 0° C. (e.g., ⁇ 20° C. or ⁇ 80° C.).
  • the composition can be formulated for storage for up to 2 years (e.g., one month, two months, three months, four months, five months, six months, seven months, eight months, nine months, 10 months, 11 months, 1 year, 11 ⁇ 2 years, or 2 years) at 2-8° C. (e.g., 4° C.).
  • the compositions described herein are stable in storage for at least 1 year at 2-8° C. (e.g., 4° C.).
  • compositions can be in a variety of forms. These forms include, e.g., liquid, semi-solid and solid dosage forms, such as liquid solutions (e.g., injectable and infusible solutions), dispersions or suspensions, tablets, pills, powders, liposomes and suppositories.
  • liquid solutions e.g., injectable and infusible solutions
  • dispersions or suspensions tablets, pills, powders, liposomes and suppositories.
  • the preferred form depends, in part, on the intended mode of administration and therapeutic application.
  • compositions containing a composition intended for systemic or local delivery can be in the form of injectable or infusible solutions.
  • the compositions can be formulated for administration by a parenteral mode (e.g., intravenous, subcutaneous, intraperitoneal, or intramuscular injection).
  • Parenteral administration refers to modes of administration other than enteral and topical administration, usually by injection, and include, without limitation, intravenous, intranasal, intraocular, pulmonary, intramuscular, intraarterial, intrathecal, intracapsular, intraorbital, intracardiac, intradermal, intrapulmonary, intraperitoneal, transtracheal, subcutaneous, subcuticular, intraarticular, subcapsular, subarachnoid, intraspinal, epidural, intracerebral, intracranial, intracarotid and intrasternal injection and infusion (see below).
  • compositions can be formulated as a solution, microemulsion, dispersion, liposome, or other ordered structure suitable for stable storage at high concentration.
  • Sterile injectable solutions can be prepared by incorporating a composition described herein in the required amount in an appropriate solvent with one or a combination of ingredients enumerated above, as required, followed by filtered sterilization.
  • dispersions are prepared by incorporating a composition described herein into a sterile vehicle that contains a basic dispersion medium and the required other ingredients from those enumerated above.
  • sterile powders for the preparation of sterile injectable solutions methods for preparation include vacuum drying and freeze-drying that yield a powder of a composition described herein plus any additional desired ingredient (see below) from a previously sterile-filtered solution thereof.
  • the proper fluidity of a solution can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants.
  • Prolonged absorption of injectable compositions can be brought about by including in the composition a reagent that delays absorption, for example, monostearate salts, and gelatin.
  • compositions described herein can also be formulated in immunoliposome compositions.
  • Such formulations can be prepared by methods known in the art such as, e.g., the methods described in Epstein et al. (1985) Proc Natl Acad Sci USA 82:3688; Hwang et al. (1980) Proc Natl Acad Sci USA 77:4030; and U.S. Pat. Nos. 4,485,045 and 4,544,545.
  • Liposomes with enhanced circulation time are disclosed in, e.g., U.S. Pat. No. 5,013,556.
  • compositions can be formulated with a carrier that will protect the compound against rapid release, such as a controlled release formulation, including implants and microencapsulated delivery systems.
  • a carrier that will protect the compound against rapid release
  • a controlled release formulation including implants and microencapsulated delivery systems.
  • Biodegradable, biocompatible polymers can be used, such as ethylene vinyl acetate, polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and polylactic acid. Many methods for the preparation of such formulations are known in the art. See, e.g., J. R. Robinson (1978) “Sustained and Controlled Release Drug Delivery Systems,” Marcel Dekker, Inc., New York.
  • compositions described herein are administered in an aqueous solution by parenteral injection.
  • the disclosure features pharmaceutical compositions comprising an effective amount of the agent (or more than one agent) and optionally include pharmaceutically acceptable diluents, preservatives, solubilizers, emulsifiers, adjuvants and/or carriers.
  • compositions include sterile water, buffered saline (e.g., Tris HCl, acetate, phosphate), pH and ionic strength; and optionally, additives such as detergents and solubilizing agents (e.g., TWEEN® 20, TWEEN 80, Polysorbate 80), anti-oxidants (e.g., ascorbic acid, sodium metabisulfite), and preservatives (e.g., thimersol, benzyl alcohol) and bulking substances (e.g., lactose, mannitol).
  • the formulations may be sterilized, e.g., using filtration, incorporating sterilizing agents into the compositions, by irradiating the compositions, or by heating the compositions.
  • compositions can be formulated at a concentration of the active agent of between about 10 mg/mL to 100 mg/mL (e.g., between about 9 mg/mL and 90 mg/mL; between about 9 mg/mL and 50 mg/mL; between about 10 mg/mL and 50 mg/mL; between about 15 mg/mL and 50 mg/mL; between about 15 mg/mL and 110 mg/mL; between about 15 mg/mL and 100 mg/mL; between about 20 mg/mL and 100 mg/mL; between about 20 mg/mL and 80 mg/mL; between about 25 mg/mL and 100 mg/mL; between about 25 mg/mL and 85 mg/mL; between about 20 mg/mL and 50 mg/mL; between about 25 mg/mL and 50 mg/mL; between about 30 mg/mL and 100 mg/mL; between about 30 mg/mL and 50 mg/mL; between about 40 mg/mL and
  • compositions can be formulated at a concentration of greater than 5 mg/mL and less than 50 mg/mL.
  • Methods for formulating a protein in an aqueous solution are known in the art and are described in, e.g., U.S. Pat. No. 7,390,786; McNally and Hastedt (2007), “Protein Formulation and Delivery,” Second Edition, Drugs and the Pharmaceutical Sciences , Volume 175, CRC Press; and Banga (1995), “Therapeutic peptides and proteins: formulation, processing, and delivery systems,” CRC Press.
  • the aqueous solution has a neutral pH, e.g., a pH between, e.g., 6.5 and 8 (e.g., between and inclusive of 7 and 8). In some embodiments, the aqueous solution has a pH of about 6.6, 6.7, 6.8, 6.9, 7, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, or 8.0.
  • the aqueous solution has a pH of greater than (or equal to) 6 (e.g., greater than or equal to 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, or 7.9), but less than pH 8.
  • Nucleic acids encoding a therapeutic polypeptide can be incorporated into a gene construct to be used as a part of a gene therapy protocol to deliver nucleic acids that can be used to express and produce agents within cells.
  • Expression constructs of such components may be administered in any therapeutically effective carrier, e.g. any formulation or composition capable of effectively delivering the component gene to cells in vivo.
  • Approaches include insertion of the subject gene in viral vectors including recombinant retroviruses, adenovirus, adeno-associated virus, lentivirus, and herpes simplex virus-1 (HSV-1), or recombinant bacterial or eukaryotic plasmids.
  • Viral vectors can transfect cells directly; plasmid DNA can be delivered with the help of, for example, cationic liposomes (lipofectin) or derivatized, polylysine conjugates, gramicidin S, artificial viral envelopes or other such intracellular carriers, as well as direct injection of the gene construct or CaPO 4 precipitation (see, e.g., WO04/060407) carried out in vivo.
  • suitable retroviruses include pLJ, pZIP, pWE and pEM which are known to those skilled in the art (see, e.g., Eglitis et al.
  • adenoviral vectors derived from the adenovirus strain Ad type 5 d1324 or other strains of adenovirus (e.g., Ad2, Ad3, Ad7, etc.) are known to those skilled in the art.
  • Ad2, Ad3, Ad7, etc. adeno-associated virus
  • AAV adeno-associated virus
  • compositions When compositions are to be used in combination with a second active agent, the compositions can be coformulated with the second agent or the compositions can be formulated separately from the second agent formulation.
  • the respective pharmaceutical compositions can be mixed, e.g., just prior to administration, and administered together or can be administered separately, e.g., at the same or different times (see below).
  • compositions described herein can be administered to a subject, e.g., a human subject, using a variety of methods that depend, in part, on the route of administration.
  • the route can be, e.g., intravenous injection or infusion (IV), subcutaneous injection (SC), intraperitoneal (IP) injection, or intramuscular injection (IM).
  • Administration can be achieved by, e.g., local infusion, injection, or by means of an implant.
  • the implant can be of a porous, non-porous, or gelatinous material, including membranes, such as sialastic membranes, or fibers.
  • the implant can be configured for sustained or periodic release of the composition to the subject. See, e.g., U.S. Patent Application Publication No. 20080241223; U.S. Pat. Nos. 5,501,856; 4,863,457; and 3,710,795; EP488401; and EP 430539, the disclosures of each of which are incorporated herein by reference in their entirety.
  • composition can be delivered to the subject by way of an implantable device based on, e.g., diffusive, erodible, or convective systems, e.g., osmotic pumps, biodegradable implants, electrodiffusion systems, electroosmosis systems, vapor pressure pumps, electrolytic pumps, effervescent pumps, piezoelectric pumps, erosion-based systems, or electromechanical systems.
  • an implantable device based on, e.g., diffusive, erodible, or convective systems, e.g., osmotic pumps, biodegradable implants, electrodiffusion systems, electroosmosis systems, vapor pressure pumps, electrolytic pumps, effervescent pumps, piezoelectric pumps, erosion-based systems, or electromechanical systems.
  • the term “effective amount” or “therapeutically effective amount”, in an in vivo setting, means a dosage sufficient to treat, inhibit, or alleviate one or more symptoms of the disorder being treated or to otherwise provide a desired pharmacologic and/or physiologic effect.
  • the precise dosage will vary according to a variety of factors such as subject-dependent variables (e.g., age, immune system health, etc.), the disease, and the treatment being effected.
  • Suitable human doses of any of the antibodies or fragments thereof described herein can further be evaluated in, e.g., Phase I dose escalation studies. See, e.g., van Gurp et al. (2008) Am J Transplantation 8(8):1711-1718; Hanouska et al. (2007) Clin Cancer Res 13(2, part 1):523-531; and Hetherington et al. (2006) Antimicrobial Agents and Chemotherapy 50(10): 3499-3500.
  • Toxicity and therapeutic efficacy of such compositions can be determined by known pharmaceutical procedures in cell cultures or experimental animals (e.g., animal models of cancer). These procedures can be used, e.g., for determining the LD 50 (the dose lethal to 50% of the population) and the ED 50 (the dose therapeutically effective in 50% of the population).
  • the dose ratio between toxic and therapeutic effects is the therapeutic index and it can be expressed as the ratio LD 50 /ED 50 .
  • Agents that exhibits a high therapeutic index are preferred. While compositions that exhibit toxic side effects may be used, care should be taken to design a delivery system that targets such compounds to the site of affected tissue and to minimize potential damage to normal cells and, thereby, reduce side effects.
  • the data obtained from the cell culture assays and animal studies can be used in formulating a range of dosage for use in humans.
  • the dosage of such antibodies or antigen-binding fragments thereof lies generally within a range of circulating concentrations of the antibodies or fragments that include the ED 50 with little or no toxicity.
  • the dosage may vary within this range depending upon the dosage form employed and the route of administration utilized.
  • a therapeutically effective dose can be estimated initially from cell culture assays.
  • a dose can be formulated in animal models to achieve a circulating plasma concentration range that includes the IC 50 (i.e., the concentration of the antibody which achieves a half-maximal inhibition of symptoms) as determined in cell culture. Such information can be used to more accurately determine useful doses in humans. Levels in plasma may be measured, for example, by high performance liquid chromatography.
  • cell culture or animal modeling can be used to determine a dose required to achieve a therapeutically effective concentration within the local site.
  • an agent can be administered to a mammal in conjunction with one or more additional therapeutic agents (e.g., therapeutic agents for treating a cancer).
  • additional therapeutic agents e.g., therapeutic agents for treating a cancer.
  • additional anti-cancer therapies include, e.g., chemotherapeutic agents, ionizing radiation, immunotherapy agents, or hyperthermotherapy.
  • Chemotherapeutic agents include, but are not limited to, aminoglutethimide, amsacrine, anastrozole, asparaginase, bcg, bicalutamide, bleomycin, buserelin, busulfan, camptothecin, capecitabine, carboplatin, carmustine, chlorambucil, cisplatin, cladribine, clodronate, colchicine, cyclophosphamide, cyproterone, cytarabine, dacarbazine, dactinomycin, daunorubicin, dienestrol, diethylstilbestrol, docetaxel, doxorubicin, epirubicin, estradiol, estramustine, etoposide, exemestane, filgrastim, fludarabine, fludrocortisone, fluorouracil, fluoxymesterone, flutamide, gemcitabine, genistein, gosereli
  • chemotherapeutic anti-tumor compounds may be categorized by their mechanism of action into groups, including, for example, the following: anti-metabolites/anti-cancer agents, such as pyrimidine analogs (5-fluorouracil, floxuridine, capecitabine, gemcitabine and cytarabine) and purine analogs, folate antagonists and related inhibitors (mercaptopurine, thioguanine, pentostatin and 2-chlorodeoxyadenosine (cladribine)); antiproliferative/antimitotic agents including natural products such as vinca alkaloids (vinblastine, vincristine, and vinorelbine), microtubule disruptors such as taxane (paclitaxel, docetaxel), vincristine, vinblastine, nocodazole, epothilones and navelbine, epidipodophyllotoxins (etoposide, teniposide), DNA damaging agents (actinomycin, amsacrine, an
  • immunotherapeutic agent can include any molecule, peptide, antibody or other agent which can stimulate a host immune system to generate an immune response to a tumor or cancer in the subject.
  • Various immunotherapeutic agents are useful in the compositions are known in the art and include, e.g., PD-1 and/or PD-1L inhibitors, CD200 inhibitors, CTLA4 inhibitors, and the like.
  • Exemplary PD-1/PD-L1 inhibitors e.g., anti-PD-1 and/or anti-PD-L1 antibodies
  • International Patent Application Publication Nos. WO 2010036959 and WO 2013/079174 as well as U.S. Pat. Nos.
  • Exemplary CD200 inhibitors are also known in the art and described in, e.g., International Patent Application Publication No. WO 2007084321.
  • Suitable anti-CTLA4 antagonist agents are described in International Patent Application Publication Nos. WO 2001/014424 and WO 2004/035607; U.S. Patent Application Publication No. 2005/0201994; and European Patent No. EP 1212422.
  • Additional CTLA-4 antibodies are described in U.S. Pat. Nos. 5,811,097, 5,855,887, 6,051,227, and 6,984,720.
  • the immunomodulatory agents can also be used in conjunction with a compound described herein for the treatment of an infection, such a viral, bacterial, or fungal infection, or any other condition in which an enhanced immune response to an antigen of interest would be therapeutically beneficial.
  • zebra spin desalting columns (89882; Life Technologies) were used to perform buffer exchange into sodium phosphate for the subsequent steps.
  • the flow through was collected from running the sample through Melon gel IgG spin purification kits (45206; Life technologies).
  • the IgG concentrations of the sample was then estimated by coomassie staining of samples that were electrophoresed on SDS-PAGE gels.
  • rabbit IgG samples of 5, 10, 20, 40 and 80 ⁇ g were run on each of these gels. Purified IgGs were then stored at ⁇ 80° C.
  • tumor organoids Using mechanical disruption, enzyme digestion, and centrifugation we purified fragments of primary mammary tumors called tumor organoids.
  • Human tumors arrive from the Cooperative Human Tissue Network (CHTN) in DMEM. The media washed out, tumors are then treated very briefly with 5 mL of fungizone solution: 10 ml Pen-Strep (P4333; Sigma), 10 ml Fungizone (15290-018; Life Technologies), and 500 ml DPBS (D8662; Sigma).
  • DMEM collagenase solution: (DMEM (10565-018; Gibco) with 2 mg/ml collagenase (C2139; Sigma-Aldrich), 5% FBS (F0926; Sigma-Aldrich), 5 ⁇ g/ml insulin (19278; Sigma-Aldrich), GlutaMAX (35050-079; Gibco) and Penicilin-Streptamycin (15140-122; Gibco)).
  • the suspension was centrifuged at 1500 rpm to remove adipocytes, and the pellet was treated with 2U/ ⁇ L DNase (D4263; Sigma-Aldrich) to separate out organoids. Single cells were removed using four quick spins at 1500 rpm, and the solution was enriched for organoids.
  • Organoids were embedded in collagen I gels at a density of 1-2 organoids/ ⁇ l and plated as 100- ⁇ l suspensions in 24-well (662892; Greiner Bio-One) or 8-well (154534; Lab Tek) coverslip-bottomed plates over a 37° C. heating block. Gels were allowed to polymerize for 30 min at 37° C.
  • Tumor organoids isolated from primary human breast tumors were embedded in collagen solution prepared from rat tail collagen I (354236; Corning) using the following recipe. Combine 375 ⁇ L of 10 ⁇ DMEM (D2429; Sigma) and 100 ⁇ L of NaOH (S2770; Sigma) and mix well until the solution turns to a dark pink color. Add 3.5 mL of collagen I and mix well until the color remains stable. As the pH changes from acidic to neutral to basic, the solution changes color from yellow to light pink/orange to dark pink. Titrate with small volumes of NaOH until the desired color of light pink or salmon is attained. All steps were performed on ice. Allow this solution to polymerize on ice for 1-2 hours until the solution turns cloudy.
  • Tumor organoids collected on day 0 (day of plating them in culture) were fixed in 4% paraformaldehyde solution for 15 minutes. The remaining organoids were allowed to grow in culture medium with or without 10% of a specific autoantibody* (225 ⁇ L of culture medium plus 25 ⁇ L of autoantibody) for 6 days, or until the organoids were invasive into the surrounding collagen I gels. These gels were then fixed in 4% paraformaldehyde solution for 15 minutes and analyzed for their levels of invasion. (*—variations of this experiment were also performed at 4% culture volume, and at a constant autoantibody concentration of 150 ug/mL or 1 uM.)
  • Tumors organoids in collagen I gels were harvested at day 6 of culture and fixed for 15 minutes in 4% paraformaldehyde. They were then embedded in Tissue Tek® Optimal Cutting Temperature compound (O.C.T., Sakura) and frozen at ⁇ 80° C. overnight. O.C.T blocks were sectioned at 50 micron thickness using a Leica cryostat (Leica Biosystems, Germany) set to ⁇ 27° C. For antibody staining, the O.C.T was removed by rinsing with PBS for 45 minutes.
  • Samples were blocked for 2 hours with 10% FBS/1% BSA/PBS solution, incubated with the serum autoantibodies (50 ug/ml) diluted in a 1% FBS/1% BSA/PBS solution overnight at 4° C. Samples were rinsed with PBS for 30 minutes. Slides were incubated with goat anti-human 488 secondary antibody (A-11013; Life Technologies) diluted at a 1:200 ratio in a 1% FBS/1% BSA/PBS solution for three hours. Samples were rinsed with PBS for 30 minutes, mounted with Fluoromount (F4680; Sigma), and sealed with coverslips.
  • DIC Differential interference contrast
  • Score b The organoid cannot be evaluated or not an organoid.
  • Score d The organoid contains only cells that are rounded up. If there are small clusters, the organoid is not dead.
  • Score 0 Organoid has rounded borders.
  • Score 1 Organoid has at least one protrusive cell or a wide front with no clear leaders or has an invasive strand but the tip is out of focus.
  • Score 2 Organoid has two or fewer invasive strands (defined as containing at least 4 cells in the strand, even if the tip of the strand is blunt).
  • Score 3 Organoid has three or more large invasive strands.
  • K14 intensity scoring Score 0: Organoid is negative for K14. Score 1: Organoid has a weak diffuse staining or less than 5% focal K14 positive cells. Score 2: Organoid has bright diffused staining or greater than 50% of its surface that is K14 positive. Score 3: Organoid has greater than 75% surface with K14 positive cells where individual cells are clearly identified.
  • IgGs Purified IgGs from the sera of patients with lupus erythematosus, myositis, and scleroderma were obtained. Organoids generated from human breast tumors were fixed on day 6 of culture, and stained with eighteen autoantibodies. As a control, tumor tissue was stained with antisera collected from two normal patients ( FIG. 2 , Panel A).
  • FIG. 2 Panel C
  • 10015 and 9070 contained anti-TIF1 gamma antibodies, the former had no cancer, while the latter developed cancer. Similarly, 9109 and 7107 were anti-NXP2 antibody sera from individuals who had no cancer and cancer respectively.
  • the effect of serum autoantibodies on tumor invasion was also assessed.
  • the tumor organoids generated from two primary breast tumors (both ER+/PR+/HER2 ⁇ ) were not invasive on day 0 (or the day of plating organoids in culture), but became invasive at day 6 of culture ( FIG. 7 , Panel A).
  • the baseline level of invasion of the two tumors in the absence of autoantibodies was 33.3% (9/27 of the organoids analyzed) and 8.3% (2/24 of the organoids analyzed), respectively ( FIG. 7 , Panel C).
  • invasion of organoids increased to 56.3% and 41.2% respectively for tumor #1 and 30% and 25% respectively for tumor #2 ( FIG. 7 , Panels A and C).
  • the patient-derived autoantibodies FW1366 increased tumor invasion to 57.1% for tumor #1 and 31.6% for tumor #2 ( FIG. 7 , Panels A, C, and D).
  • Autoantibodies 13200 and 12106 decreased invasion in both tumors to 12.5% and 26.1% respectively for tumor #1 and 8.7% and 7.8% respectively for tumor #2 ( FIG. 7 , Panels A, C, and D).
  • 13200 decreased tumor invasion by 77.8% (tumor #1) and 70.1% (tumor #2).
  • 12106 decreased invasion by 53.6% and 60.8% in tumors #1 and #2 respectively.
  • both 13200 and 12106 were the autoantibodies that stained tumor organoids better than normal organoids.
  • Purified IgG SLE1269 increased baseline invasion of tumor
  • the tumor (#3) used for this set of experiments was a ER+/PR+/HER2 ⁇ breast tumor whose organoids were 20% invasive in the absence of any autoantibodies ( FIG. 8 , Panel B).
  • the invasion levels remained almost unchanged at 20.5% ( FIG. 8 , Panels B and C).
  • patient derived autoantibodies added at the same concentration altered tumor invasion in 3D culture.
  • autoantibodies isolated from patients with no cancer are more effective in reducing tumor invasion than those isolated from cancer patients.

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EP3294334A1 (fr) 2018-03-21
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