EP1259812A2 - Antigenes associes au cancer du sein, de la prostate et de l'estomac et leur utilisation - Google Patents

Antigenes associes au cancer du sein, de la prostate et de l'estomac et leur utilisation

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Publication number
EP1259812A2
EP1259812A2 EP00932804A EP00932804A EP1259812A2 EP 1259812 A2 EP1259812 A2 EP 1259812A2 EP 00932804 A EP00932804 A EP 00932804A EP 00932804 A EP00932804 A EP 00932804A EP 1259812 A2 EP1259812 A2 EP 1259812A2
Authority
EP
European Patent Office
Prior art keywords
nucleic acid
group
molecule
cancer associated
acid molecule
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Withdrawn
Application number
EP00932804A
Other languages
German (de)
English (en)
Inventor
Yuichi Obata
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Ludwig Institute for Cancer Research Ltd
Ludwig Cancer Research
Original Assignee
Ludwig Institute for Cancer Research Ltd
Ludwig Cancer Research
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Ludwig Institute for Cancer Research Ltd, Ludwig Cancer Research filed Critical Ludwig Institute for Cancer Research Ltd
Publication of EP1259812A2 publication Critical patent/EP1259812A2/fr
Withdrawn legal-status Critical Current

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Classifications

    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
    • C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
    • C07K14/4701—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals not used
    • C07K14/4748—Tumour specific antigens; Tumour rejection antigen precursors [TRAP], e.g. MAGE
    • 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
    • A61K39/0005—Vertebrate antigens
    • A61K39/0011—Cancer antigens
    • A61K39/001193—Prostate associated antigens e.g. Prostate stem cell antigen [PSCA]; Prostate carcinoma tumor antigen [PCTA]; PAP or PSGR
    • A61K39/001194—Prostate specific antigen [PSA]
    • 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
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P43/00—Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
    • 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
    • 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
    • A61K2039/51—Medicinal preparations containing antigens or antibodies comprising whole cells, viruses or DNA/RNA
    • A61K2039/515—Animal cells
    • A61K2039/5152—Tumor cells
    • 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
    • A61K2039/51—Medicinal preparations containing antigens or antibodies comprising whole cells, viruses or DNA/RNA
    • A61K2039/515—Animal cells
    • A61K2039/5156—Animal cells expressing foreign proteins
    • 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
    • A61K2039/51—Medicinal preparations containing antigens or antibodies comprising whole cells, viruses or DNA/RNA
    • A61K2039/53—DNA (RNA) vaccination
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides

Definitions

  • the invention relates to nucleic acids and encoded polypeptides which are cancer associated antigens expressed in patients afflicted with breast, gastric or prostate cancer.
  • the invention also relates to agents which bind the nucleic acids or polypeptides.
  • the nucleic acid molecules, polypeptides coded for by such molecules and peptides derived therefrom, as well as related antibodies and cytolytic T lymphocytes, are useful, inter alia, in diagnostic and therapeutic contexts.
  • T cells recognize foreign materials has been implicated in cancer.
  • CTL cytolytic T lymphocyte
  • autologous CTLs for identifying tumor antigens requires that the target cells which express the antigens can be cultured in vitro and that stable lines of autologous CTL clones which recognize the antigen-expressing cells can be isolated and propagated. While this approach has worked well for melanoma antigens, other tumor types, such as epithelial cancers including breast and colon cancer, have proved refractory to the approach.
  • the invention provides, inter alia, isolated nucleic acid molecules, expression vectors containing those molecules and host cells transfected with those molecules.
  • the invention also provides isolated proteins and peptides, antibodies to those proteins and peptides and CTLs which recognize the proteins and peptides. Fragments including functional fragments and variants of the foregoing also are provided. Kits containing the foregoing molecules additionally are provided. The foregoing can be used in the diagnosis, monitoring, research, or treatment of conditions characterized by the expression of one or more cancer associated antigens.
  • the invention involves the surprising discovery of several genes, some previously known and some previously unknown, which are expressed in individuals who have cancer. These individuals all have serum antibodies against the proteins (or fragments thereof) encoded by these genes. Thus, abnormally expressed genes are recognized by the host's immune system and therefore can form a basis for diagnosis, monitoring and therapy.
  • the invention involves the use of a single material, a plurality of different materials and even large panels and combinations of materials.
  • a single gene, a single protein encoded by a gene, a single functional fragment thereof, a single antibody thereto, etc. can be used in methods and products of the invention.
  • pairs, groups and even panels of these materials and optionally other cancer associated antigen genes and/or gene products can be used for diagnosis, monitoring and therapy.
  • the pairs, groups or panels can involve 2, 3, 4, 5 or more genes, gene products, fragments thereof or agents that recognize such materials.
  • a plurality of such materials are not only useful in monitoring, typing, characterizing and diagnosing cells abnormally expressing such genes, but a plurality of such materials can be used therapeutically.
  • the invention has in vivo and in vitro uses, including for therapeutic, diagnostic, monitoring and research purposes.
  • One aspect of the invention is the ability to fingerprint a cell expressing a number of the genes identified according to the invention by, for example, quantifying the expression of such gene products. Such fingerprints will be characteristic, for example, of the stage of the cancer, the type of the cancer, or even the effect in animal models of a therapy on a cancer. Cells also can be screened to determine whether such cells abnormally express the genes identified according to the invention.
  • the invention in one aspect, is a method of diagnosing a disorder characterized by expression of a cancer associated antigen precursor coded for by a nucleic acid molecule.
  • the method involves the steps of contacting a biological sample isolated from a subject with an agent that specifically binds to the nucleic acid molecule, an expression product thereof, or a fragment of an expression product thereof complexed with an MHC, preferably an HLA, molecule, wherein the nucleic acid molecule is a NA Group 1 nucleic acid molecule, and determining the interaction between the agent and the nucleic acid molecule, the expression product or fragment of the expression product as a determination of the disorder.
  • the agent is selected from the group consisting of (a) a nucleic acid molecule comprising NA Group 1 nucleic acid molecules or a fragment thereof, (b) a nucleic acid molecule comprising NA Group 3 nucleic acid molecules or a fragment thereof, (c) a nucleic acid molecule comprising NA Group 5 nucleic acid molecules or a fragment thereof, (d) an antibody that binds to an expression product, or a fragment thereof, of NA group 1 nucleic acids, (e) an antibody that binds to an expression product, or a fragment thereof, of NA group 3 nucleic acids, (f) an antibody that binds to an expression product, or a fragment thereof, of NA group 5 nucleic acids, (g) and agent that binds to a complex of an MHC, preferably HLA, molecule and a fragment of an expression product of a NA Group 1 nucleic acid, (h) an agent that binds to a complex of an MHC, preferably HLA, molecule and a fragment of an expression
  • the disorder may be characterized by expression of a plurality of cancer associated antigen precursors.
  • the methods of diagnosis may include use of a plurality of agents, each of which is specific for a different human cancer associated antigen precursor (including at least one of the cancer associated antigen precursors disclosed herein), and wherein said plurality of agents is at least 2, at least 3, at least 4, at least S, at least 6, at least 7, at least 8, at least 9 or at least 10 such agents. Any of the diagnostic methods disclosed herein can be applied sequentially over time to permit determination of the prognosis or progression (or regression) of the disorder.
  • the agent may be specific for a human cancer associated antigen precursor, including the breast, gastric and prostate cancer associated antigen precursors disclosed herein.
  • the invention is a method for determining regression, progression or onset of a condition characterized by expression of abnormal levels of a protein encoded by a nucleic acid molecule that is a NA Group 1 molecule.
  • the method involves the steps of monitoring a sample, from a subject who has or is suspected of having the condition, for a parameter selected from the group consisting of (i) the protein, (ii) a peptide derived from the protein, (iii) an antibody which selectively binds the protein or peptide, and (iv) cytolytic T cells specific for a complex of the peptide derived from the protein and an MHC molecule, as a determination of regression, progression or onset of said condition.
  • the sample is a body fluid, a body effusion or a tissue.
  • the step of monitoring comprises contacting the sample with a detectable agent selected from the group consisting of (a) an antibody which selectively binds the protein of (i), or the peptide of (ii), (b) a protein or peptide which binds the antibody of (iii), and (c) a cell which presents the complex of the peptide and MHC molecule of (iv).
  • a detectable agent selected from the group consisting of (a) an antibody which selectively binds the protein of (i), or the peptide of (ii), (b) a protein or peptide which binds the antibody of (iii), and (c) a cell which presents the complex of the peptide and MHC molecule of (iv).
  • the antibody, the protein, the peptide or the cell is labeled with a radioactive label or an enzyme.
  • the sample in a preferred embodiment is assayed for the peptide.
  • samples are isolated from tissue or bodily fluids of the subject at sequential time points
  • the nucleic acid molecule is one of the following: a NA Group 3 molecule or a NA Group 5 molecule.
  • the protein is a plurality of proteins, the parameter is a plurality of parameters, each of the plurality of parameters being specific for a different one of the plurality of proteins.
  • the invention in another aspect is a pharmaceutical preparation for a human subject.
  • the pharmaceutical preparation includes an agent which when administered to the subject enriches selectively the presence of complexes of an HLA molecule and a human cancer associated antigen, and a pharmaceutically acceptable carrier, wherein the human cancer associated antigen is a fragment of a human cancer associated antigen precursor encoded by a nucleic acid molecule which comprises a NA Group 1 molecule.
  • the nucleic acid molecule is a NA Group 3 nucleic acid molecule.
  • the agent in one embodiment comprises a plurality of agents, each of which enriches selectively in the subject complexes of an HLA molecule and a different human cancer associated antigen.
  • the plurality is at least two, at least three, at least four or at least 5 different such agents.
  • the agent is selected from the group consisting of (1) an isolated polypeptide comprising the human cancer associated antigen, or a functional variant thereof, (2) an isolated nucleic acid operably linked to a promoter for expressing the isolated polypeptide, or functional variant thereof, (3) a host cell expressing the isolated polypeptide, or functional variant thereof, and (4) isolated complexes of the polypeptide, or functional variants thereof, and an HLA molecule.
  • the agent may be a cell expressing an isolated polypeptide.
  • the agent is a cell expressing an isolated polypeptide comprising the human cancer associated antigen or a functional variant thereof.
  • the agent is a cell expressing an isolated polypeptide comprising the human cancer associated antigen or a functional variant thereof, and wherein the cell expresses an HLA molecule that binds the polypeptide.
  • the cell can express one or both of the polypeptide and HLA molecule recombinantly.
  • the cell is nonproliferative.
  • the agent is at least two, at least three, at least four or at least five different polypeptides, each representing a different human cancer associated antigen or functional variant thereof.
  • the agent in one embodiment is a PP Group 2 polypeptide. In other embodiments the agent is a PP Group 3 polypeptide or a PP Group 4 polypeptide.
  • each of the pharmaceutical preparations described herein also includes an adjuvant.
  • a composition which includes an isolated agent that binds selectively a PP Group 1 polypeptide.
  • the agent binds selectively to a polypeptide selected from the following: a PP Group 2 polypeptide, a PP Group 3 polypeptide, a PP Group 4 polypeptide, and a PP Group 5 polypeptide.
  • the agent is a plurality of different agents that bind selectively at least two, at least three, at least four, or at least five different such polypeptides.
  • the agent may be an antibody.
  • the invention is a composition of matter composed of a conjugate of the agent of the above-described compositions of the invention and a therapeutic or diagnostic agent.
  • the conjugate is of the agent and a therapeutic or diagnostic that is an antineoplastic.
  • the invention in another aspect is a pharmaceutical composition which includes an isolated nucleic acid molecule selected from the group consisting of: (1) NA Group 1 molecules, and (2) NA Group 2 molecules, and a pharmaceutically acceptable carrier.
  • the isolated nucleic acid molecule comprises a NA Group 3 or NA Group 4 molecule.
  • the isolated nucleic acid molecule comprises at least two isolated nucleic acid molecules coding for two different polypeptides, each polypeptide comprising a different cancer associated antigen.
  • the pharmaceutical composition also includes an expression vector with a promoter operably linked to the isolated nucleic acid molecule.
  • the pharmaceutical composition also includes a host cell recombinantly expressing the isolated nucleic acid molecule.
  • a pharmaceutical composition includes an isolated polypeptide comprising a PP Group 1 or a PP Group 2 polypeptide, and a pharmaceutically acceptable carrier.
  • the isolated polypeptide comprises a PP Group 3 or a PP Group 4 polypeptide.
  • the isolated polypeptide comprises at least two different polypeptides, each comprising a different cancer associated antigen at least one of which is encoded by a NA group 1 molecule as disclosed herein.
  • the isolated polypeptides are selected from the following: breast cancer polypeptides or HLA binding fragments thereof and gastric cancer polypeptides or HLA binding fragments thereof.
  • each of the pharmaceutical compositions described herein also includes an adjuvant.
  • Another aspect the invention is an isolated nucleic acid molecule comprising a NA Group 3 molecule. Another aspect the invention is an isolated nucleic acid molecule comprising a NA Group 4 molecule.
  • the invention in another aspect is an isolated nucleic acid molecule selected from the group consisting of (a) a fragment of a nucleic acid selected from the group of nucleic acid molecules consisting of SEQ ID Nos: 1-593, of sufficient length to represent a sequence unique within the human genome, and identifying a nucleic acid encoding a human cancer associated antigen precursor, (b) complements of (a), provided that the fragment includes a sequence of contiguous nucleotides which is not identical to any sequence selected from the sequence group consisting of (1) sequences having the GenBank accession numbers of Table 1 and other sequences publicly available as of the filing date of this application, (2) complements of (1), and (3) fragments of (1) and (2).
  • the unique fragments are fragments of a nucleic acid selected from the group of nucleic acid molecules consisting of SEQ ID NOs:12, 15, 34-59, 61, 62, 83-95, 186, 190-205, 297, 327-332, and 335-352.
  • sequence of contiguous nucleotides is selected from the group consisting of: (1) at least two contiguous nucleotides nonidentical to the sequences in Table 1, (2) at least three contiguous nucleotides nonidentical to the sequences in Table 1, (3) at least four contiguous nucleotides nonidentical to the sequences in Table 1, (4) at least five contiguous nucleotides nonidentical to the sequences in Table 1, (5) at least six contiguous nucleotides nonidentical to the sequences in Table 1, or (6) at least seven contiguous nucleotides nonidentical to the sequences in Table 1.
  • the fragment has a size selected from the group consisting of at least: 8 nucleotides, 10 nucleotides, 12 nucleotides, 14 nucleotides, 16 nucleotides, 18 nucleotides, 20, nucleotides, 22 nucleotides, 24 nucleotides, 26 nucleotides, 28 nucleotides, 30 nucleotides, 50 nucleotides, 75 nucleotides, 100 nucleotides, 200 nucleotides, 1000 nucleotides and every integer length therebetween.
  • the molecule encodes a polypeptide which, or a fragment of which, binds a human HLA receptor (e.g., class I or class H) or a human antibody.
  • Another aspect of the invention is an expression vector comprising an isolated nucleic acid molecule of the invention described above operably linked to a promoter.
  • the invention is an expression vector comprising a nucleic acid operably linked to a promoter, wherein the nucleic acid is a NA Group 1 or Group 2 molecule.
  • the invention is an expression vector comprising a NA Group 1 or Group 2 molecule and a nucleic acid encoding an MHC, preferably HLA, molecule.
  • the invention is a host cell transformed or transfected with an expression vector of the invention described above.
  • the invention is a host cell transformed or transfected with an expression vector comprising an isolated nucleic acid molecule of the invention described above operably linked to a promoter, or an expression vector comprising a nucleic acid operably linked to a promoter, wherein the nucleic acid is a NA Group 1 or 2 molecule and further comprising a nucleic acid encoding HLA.
  • an isolated polypeptide encoded by the isolated nucleic acid molecules of the invention, described above, is provided. These include PP Group 1-5 polypeptides.
  • the invention also includes a fragment of the polypeptide which is immunogenic. In one embodiment the fragment, or a portion of the fragment, binds HLA or a human antibody.
  • the invention includes in another aspect an isolated fragment of a human cancer associated antigen precursor which, or a portion of which, binds HLA or a human antibody, wherein the precursor is encoded by a nucleic acid molecule that is a NA Group 1 molecule.
  • the fragment is part of a complex with HLA.
  • the fragment is between 8 and 12 amino acids in length.
  • the invention includes an isolated polypeptide comprising a fragment of the polypeptide of sufficient length to represent a sequence unique within the human genome and identifying a polypeptide that is a human cancer associated antigen precursor.
  • a kit for detecting the presence of the expression of a cancer associated antigen precursor includes a pair of isolated nucleic acid molecules each of which consists essentially of a molecule selected from the group consisting of (a) a 12-32 nucleotide contiguous segment of the nucleotide sequence of any of the NA Group 1 molecules and (b) complements of (a), wherein the contiguous segments are nonoverlapping.
  • the pair of isolated nucleic acid molecules is constructed and arranged to selectively amplify an isolated nucleic acid molecule that is a NA Group 3 molecule.
  • the pair amplifies a human NA Group 3 molecule.
  • a method for treating a subject with a disorder characterized by expression of a human cancer associated antigen precursor includes the step of administering to the subject an amount of an agent, which enriches selectively in the subject the presence of complexes of an HLA molecule and a human cancer associated antigen, effective to ameliorate the disorder, wherein the human cancer associated antigen is a fragment of a human cancer associated antigen precursor encoded by a nucleic acid molecule selected from the group consisting of (a) a nucleic acid molecule comprising NA group 1 nucleic acid molecules, (b) a nucleic acid molecule comprising NA group 3 nucleic acid molecules, (c) a nucleic acid molecule comprising NA group 5 nucleic acid molecules.
  • the disorder is characterized by expression of a plurality of human cancer associated antigen precursors and wherein the agent is a plurality of agents, each of which enriches selectively in the subject the presence of complexes of an HLA molecule and a different human cancer associated antigen.
  • the plurality is at least 2, at least 3, at least 4, or at least 5 such agents.
  • the agent is an isolated polypeptide selected from the group consisting of PP Group 1, PP Group 2, PP Group 3, PP Group 4, and PP group 5 polypeptides.
  • the disorder is cancer.
  • the invention is a method for treating a subject having a condition characterized by expression of a cancer associated antigen precursor in cells of the subject.
  • the method includes the steps of (i) removing an immunoreactive cell containing sample from the subject, (ii) contacting the immunoreactive cell containing sample to the host cell under conditions favoring production of cytolytic T cells against a human cancer associated antigen which is a fragment of the precursor, (iii) introducing the cytolytic T cells to the subject in an amount effective to lyse cells which express the human cancer associated antigen, wherein the host cell is transformed or transfected with an expression vector comprising an isolated nucleic acid molecule operably linked to a promoter, the isolated nucleic acid molecule being selected from the group of nucleic acid molecules consisting of NA Group 1, NA Group 2, NA Group 3, NA Group 4, NA Group 5.
  • the host cell recombinantly expresses an HLA molecule which binds the human cancer associated antigen.
  • the host cell endogenously expresses an HLA molecule which binds the human cancer associated antigen.
  • the invention includes in another aspect a method for treating a subject having a condition characterized by expression of a cancer associated antigen precursor in cells of the subject.
  • the method includes the steps of (i) identifying a nucleic acid molecule expressed by the cells associated with said condition, wherein said nucleic acid molecule is a NA Group 1 molecule (ii) transfecting a host cell with a nucleic acid molecule selected from the group consisting of (a) the nucleic acid molecule identified, (b) a fragment of the nucleic acid molecule identified which includes a segment coding for a cancer associated antigen, (c) deletions, substitutions or additions to (a) or (b), and (d) degenerates of (a), (b), or (c); (iii) culturing said transfected host cells to express the transfected nucleic acid molecule, and; (iv) introducing an amount of said host cells or an extract thereof to the subject effective to increase an immune response against the cells of the subject associated with the condition.
  • the antigen is a human antigen and the subject is a human.
  • the method also includes the step of (a) identifying an MHC molecule which presents a portion of an expression product of the nucleic acid molecule, wherein the host cell expresses the same MHC molecule as identified in (a) and wherein the host cell presents an MHC binding portion of the expression product of the nucleic acid molecule.
  • the method also includes the step of treating the host cells to render them non-proliferative.
  • the immune response comprises a B-cell response or a T cell response.
  • the response is a T-cell response which comprises generation of cytolytic T-cells specific for the host cells presenting the portion of the expression product of the nucleic acid molecule or cells of the subject expressing the human cancer associated antigen.
  • the nucleic acid molecule is a NA Group 3 molecule.
  • Another aspect of the invention is a method for treating or diagnosing or monitoring a subject having a condition characterized by expression of an abnormal amount of a protein encoded by a nucleic acid molecule that is a NA Group 1 molecule. The method includes the step of administering to the subject an antibody which specifically binds to the protein or a peptide derived therefrom, the antibody being coupled to a therapeutically useful agent, in an amount effective to treat the condition.
  • the antibody is a monoclonal antibody.
  • the monoclonal antibody is a chimeric antibody or a humanized antibody.
  • the invention is a method for treating a condition characterized by expression in a subject of abnormal amounts of a protein encoded by a nucleic acid molecule that is a NA Group 1 nucleic acid molecule.
  • the method involves the step of administering to a subject at least one of the pharmaceutical compositions of the invention described above in an amount effective to prevent, delay the onset of, or inhibit the condition in the subject.
  • the condition is cancer.
  • the method includes the step of first identifying that the subject expresses in a tissue abnormal amounts of the protein.
  • the invention in another aspect is a method for treating a subject having a condition characterized by expression of abnormal amounts of a protein encoded by a nucleic acid molecule that is a NA Group 1 nucleic acid molecule.
  • the method includes the steps of (i) identifying cells from the subject which express abnormal amounts of the protein; (ii) isolating a sample of the cells; (iii) cultivating the cells, and (iv) introducing the cells to the subject in an amount effective to provoke an immune response against the cells.
  • the method includes the step of rendering the cells non- proliferative, prior to introducing them to the subject.
  • the invention is a method for treating a pathological cell condition characterized by abnormal expression of a protein encoded by a nucleic acid molecule that is a NA Group 1 nucleic acid molecule.
  • the method includes the step of administering to a subject in need thereof an effective amount of an agent which inhibits the expression or activity of the protein.
  • the agent is an inhibiting antibody which selectively binds to the protein and wherein the antibody is a monoclonal antibody, a chimeric antibody, a humanized antibody or a fragment thereof.
  • the agent is an antisense nucleic acid molecule which selectively binds to the nucleic acid molecule which encodes the protein.
  • the nucleic acid molecule is a NA Group 3 nucleic acid molecule.
  • the invention includes in another aspect a composition of matter useful in stimulating an immune response to a plurality of proteins encoded by nucleic acid molecules that are NA Group 1 molecules.
  • the composition is a plurality of peptides derived from the amino acid sequences of the proteins, wherein the peptides bind to one or more MHC molecules presented on the surface of the cells which express an abnormal amount of the protein.
  • at least a portion of the plurality of peptides bind to MHC molecules and elicit a cytolytic response thereto.
  • the composition of matter includes an adjuvant.
  • the adjuvant is a saponin, GM-CSF, or an interleukin.
  • compositions also includes at least one peptide useful in stimulating an immune response to at least one protein which is not encoded by nucleic acid molecules that are NA Group 1 molecules, wherein the at least one peptide binds to one or more MHC molecules.
  • the invention is an isolated antibody which selectively binds to a complex of: (i) a peptide derived from a protein encoded by a nucleic acid molecule that is a NA Group 1 molecule and (ii) and an MHC molecule to which binds the peptide to form the complex, wherein the isolated antibody does not bind to (i) or (ii) alone.
  • the antibody is a monoclonal antibody, a chimeric antibody, a humanized antibody or a fragment thereof.
  • the invention also involves the use of the genes, gene products, fragments thereof, agents which bind thereto, and so on in the preparation of medicaments.
  • a particular medicament is for treating cancers including, e.g., one or more of cancers of the breast, cervix, ovary, prostate, testis, lung, colon, pancreas, stomach, liver, skin (e.g., melanoma), bladder, head and neck, thyroid, blood cells, bone and kidney. Diagnostics for specific cancers and groups of cancers also are envisioned.
  • the nucleic acid molecules are selected from the group consisting of SEQ ID NOs:l-18, and the polypeptides are encoded by these preferred nucleic acid molecules.
  • antigen precursors and antigens are substantially the full-length protein encoded by the coding region of the isolated DNA and the antigen is a peptide which complexes with MHC, preferably HLA, and which participates in the immune response as part of that complex.
  • antigens are typically 9 amino acids long, although this may vary slightly.
  • a subject is a human, non-human primate, cow, horse, pig, sheep, goat, dog, cat or rodent. In all embodiments human cancer antigens and human subjects are preferred.
  • the present invention in one aspect involves the cloning of cDNAs encoding human cancer associated antigen precursors using autologous antisera of subjects having breast, gastric or prostate cancer.
  • the sequences of the clones representing genes identified according to the methods described herein are presented in the attached Sequence Listing. Of the foregoing, it can be seen that some of the clones are considered completely novel as no coding regions were found in the databases searched. Other clones are novel but have some nucleotide or amino acid homologies to sequences deposited in databases (mainly EST sequences). Nevertheless, the entire gene sequence was not previously known. In some cases no function was suspected and in other cases, even if a function was suspected, it was not known that the gene was associated with cancer, or with a particular cancer.
  • the invention thus involves in one aspect cancer associated antigen polypeptides, genes encoding those polypeptides, functional modifications and variants of the foregoing, useful fragments of the foregoing, as well as diagnostics and therapeutics relating thereto.
  • Nucleic Acid Sequences NA Group 1 (a) nucleic acid molecules which hybridize under stringent conditions to a molecule consisting of a nucleic acid sequence selected from the group consisting of nucleic acid sequences among SEQ ID NOs: 1-593, and which code for a cancer associated antigen precursor,
  • nucleic acid molecules that differ from the nucleic acid molecules of (a) or (b) in codon sequence due to the degeneracy of the genetic code
  • NA Group 2 Fragments of NA Group 1, which code for a polypeptide which, or a portion of which, binds an MHC molecule to form a complex recognized by an autologous antibody or lymphocyte.
  • NA Group 3 The subset of NA Group 1 where the nucleotide sequence is selected from the group consisting of:
  • nucleic acid molecules that differ from the nucleic acid molecules of (a) or (b) in codon sequence due to the degeneracy of the genetic code, and (d) complements of (a), (b) or (c).
  • NA Group 4 Fragments of NA Group 3, which code for a polypeptide which, or a portion of which, binds to an MHC molecule to form a complex recognized by an autologous antibody or lymphocyte.
  • NA Group 5 A subset of NA Group 1, comprising human cancer associated antigens that react with allogeneic cancer antisera.
  • polypeptides are those recognized by allogeneic sera of cancer patients, but not by non-cancer patient control sera.
  • polypeptides encoded by SEQ ID NOs:l-18 are recognized only by antibodies in cancer patients antisera.
  • stringent conditions refers to parameters with which the art is familiar. Nucleic acid hybridization parameters may be found in references which compile such methods, e.g. Molecular Cloning: A Laboratory Manual, J. Sambrook, et al., eds., Second Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 1989, or Current Protocols in Molecular Biology, F.M. Ausubel, et al., eds., John Wiley & Sons, Inc., New York.
  • stringent conditions refers, for example, to hybridization at 65°C in hybridization buffer (3.5 x SSC, 0.02% Ficoll, 0.02% polyvinyl pyrrolidone, 0.02% Bovine Serum Albumin, 2.5 mM NaH 2 PO 4 (pH7), 0.5% SDS, 2 mM EDTA).
  • SSC is 0.15 M sodium chloride/0.15 M sodium citrate, pH7; SDS is sodium dodecyl sulphate; and EDTA is ethylenediaminetetracetic acid.
  • the membrane upon which the DNA is transferred is washed, for example, in 2 x SSC at room temperature and then at 0.1 - 0.5 x SSC/0.1 x SDS at temperatures up to 68°C.
  • the skilled artisan will be familiar with such conditions, and thus they are not given here. It will be understood, however, that the skilled artisan will be able to manipulate the conditions in a manner to permit the clear identification of homologs and alleles of cancer associated antigen nucleic acids of the invention (e.g., by using lower stringency conditions).
  • the skilled artisan also is familiar with the methodology for screening cells and libraries for expression of such molecules which then are routinely isolated, followed by isolation of the pertinent nucleic acid molecule and sequencing.
  • homologs and alleles typically will share at least 80% nucleotide identity and/or at least 90% amino acid identity to the sequences of cancer associated antigen nucleic acid and polypeptides, respectively, in some instances will share at least 90% nucleotide identity and/or at least 95% amino acid identity and in still other instances will share at least 95% nucleotide identity and/or at least 99% amino acid identity.
  • the homology can be calculated using various, publicly available software tools developed by NCBI (Bethesda, Maryland) that can be obtained through the Internet (ftp:/ncbi.nlm.nih.gov/pub/).
  • Exemplary tools include the BLAST system available at http://www.ncbi.nlm.nih.gov, preferably using default settings. Pairwise and ClustalW alignments (BLOSUM30 matrix setting) as well as Kyle-Doolittle hydropathic analysis can be obtained using the Mac Vector sequence analysis software (Oxford Molecular Group). Watson-Crick complements of the foregoing nucleic acids also are embraced by the invention.
  • a Southern blot may be performed using the foregoing conditions, together with a radioactive probe. After washing the membrane to which the DNA is finally transferred, the membrane can be placed against X-ray film to detect the radioactive signal.
  • Northern blot hybridizations using the foregoing conditions can be performed on samples taken from breast, gastric or prostate cancer patients or subjects suspected of having a condition characterized by expression of the cancer associated antigen genes disclosed herein.
  • Amplification protocols such as polymerase chain reaction using primers which hybridize to the sequences presented also can be used for detection of the cancer associated antigen genes or expression thereof.
  • the breast, gastric and prostate cancer associated genes correspond to SEQ ID Nos:l- 593. These sequences represent genes previously known in humans and genes previously unknown in humans (e.g., SEQ ID NOs:12, 15, 34-59, 61, 62, 83-95, 186, 190-205, 297, 327- 332, and 335-352).
  • Preferred breast, gastric and prostate cancer associated antigens for the methods of diagnosis disclosed herein are those which encode polypeptides that react with allogeneic cancer antisera (i.e. NA Group 5). Encoded polypeptides (e.g., proteins), peptides and antisera thereto are also preferred for diagnosis.
  • isolated means: (i) amplified in vitro by, for example, polymerase chain reaction (PCR); (ii) recombinantly produced by cloning; (iii) purified, as by cleavage and gel separation; or (iv) synthesized by, for example, chemical synthesis.
  • An isolated nucleic acid is one which is readily manipulable by recombinant DNA techniques well known in the art.
  • PCR polymerase chain reaction
  • An isolated nucleic acid may be substantially purified, but need not be.
  • a nucleic acid that is isolated within a cloning or expression vector is not pure in that it may comprise only a tiny percentage of the material in the cell in which it resides. Such a nucleic acid is isolated, however, as the term is used herein because it is readily manipulable by standard techniques known to those of ordinary skill in the art.
  • An isolated nucleic acid as used herein is not a naturally occurring chromosome.
  • isolated means separated from its native environment and present in sufficient quantity to permit its identification or use.
  • Isolated when referring to a protein or polypeptide, means, for example: (i) selectively produced by expression cloning or (ii) purified as by chromatography or electrophoresis.
  • Isolated proteins or polypeptides may be, but need not be, substantially pure.
  • the term "substantially pure” means that the proteins or polypeptides are essentially free of other substances with which they may be found in nature or in vivo systems to an extent practical and appropriate for their intended use. Substantially pure polypeptides may be produced by techniques well known in the art. Because an isolated protein may be admixed with a pharmaceutically acceptable carrier in a pharmaceutical preparation, the protein may comprise only a small percentage by weight of the preparation.
  • the protein is nonetheless isolated in that it has been separated from the substances with which it may be associated in living systems, i.e. isolated from other proteins.
  • the invention also includes degenerate nucleic acids which include alternative codons to those present in the native materials. For example, serine residues are encoded by the codons TCA, AGT, TCC, TCG, TCT and AGC. Each of the six codons is equivalent for the purposes of encoding a serine residue.
  • any of the serine-encoding nucleotide triplets may be employed to direct the protein synthesis apparatus, in vitro or in vivo, to incorporate a serine residue into an elongating cancer associated antigen polypeptide.
  • nucleotide sequence triplets which encode other amino acid residues include, but are not limited to: CCA, CCC, CCG and CCT (proline codons); CGA, CGC, CGG, CGT, AGA and AGG (arginine codons); ACA, ACC, ACG and ACT (threonine codons); AAC and AAT (asparagine codons); and ATA, ATC and ATT (isoleucine codons).
  • Other amino acid residues may be encoded similarly by multiple nucleotide sequences.
  • the invention embraces degenerate nucleic acids that differ from the biologically isolated nucleic acids in codon sequence due to the degeneracy of the genetic code.
  • the invention also provides modified nucleic acid molecules which include additions, substitutions and deletions of one or more nucleotides.
  • these modified nucleic acid molecules and/or the polypeptides they encode retain at least one activity or function of the unmodified nucleic acid molecule and/or the polypeptides, such as antigenicity, enzymatic activity, receptor binding, formation of complexes by binding of peptides by MHC class I and class II molecules, etc.
  • the modified nucleic acid molecules encode modified polypeptides, preferably polypeptides having conservative amino acid substitutions as are described elsewhere herein.
  • the modified nucleic acid molecules are structurally related to the unmodified nucleic acid molecules and in preferred embodiments are sufficiently structurally related to the unmodified nucleic acid molecules so that the modified and unmodified nucleic acid molecules hybridize under stringent conditions known to one of skill in the art.
  • modified nucleic acid molecules which encode polypeptides having single amino acid changes can be prepared. Each of these nucleic acid molecules can have one, two or three nucleotide substitutions exclusive of nucleotide changes corresponding to the degeneracy of the genetic code as described herein. Likewise, modified nucleic acid molecules which encode polypeptides having two amino acid changes can be prepared which have, e.g., 2-6 nucleotide changes. Numerous modified nucleic acid molecules like these will be readily envisioned by one of skill in the art, including for example, substitutions of nucleotides in codons encoding amino acids 2 and 3, 2 and 4, 2 and 5, 2 and 6, and so on.
  • each combination of two amino acids is included in the set of modified nucleic acid molecules, as well as all nucleotide substitutions which code for the amino acid substitutions.
  • Additional nucleic acid molecules that encode polypeptides having additional substitutions (i.e., 3 or more), additions or deletions (e.g., by introduction of a stop codon or a splice site(s)) also can be prepared and are embraced by the invention as readily envisioned by one of ordinary skill in the art. Any of the foregoing nucleic acids or polypeptides can be tested by routine experimentation for retention of structural relation or activity to the nucleic acids and/or polypeptides disclosed herein.
  • the invention also provides isolated unique fragments of cancer associated antigen nucleic acid sequences or complements thereof.
  • a unique fragment is one that is a 'signature' for the larger nucleic acid. It, for example, is long enough to assure that its precise sequence is not found in molecules within the human genome outside of the cancer associated antigen nucleic acids defined above (and human alleles). Those of ordinary skill in the art may apply no more than routine procedures to determine if a fragment is unique within the human genome.
  • a fragment which is completely composed of the sequence described in the foregoing GenBank deposits is one which does not include any of the nucleotides unique to the sequences of the invention.
  • a unique fragment must contain a nucleotide sequence other than the exact sequence of those in GenBank or fragments thereof. The difference may be an addition, deletion or substitution with respect to the GenBank sequence or it may be a sequence wholly separate from the GenBank sequence.
  • Unique fragments can be used as probes in Southern and Northern blot assays to identify such nucleic acids, or can be used in amplification assays such as those employing PCR. As known to those skilled in the art, large probes such as 200, 250, 300 or more nucleotides are preferred for certain uses such as Southern and Northern blots, while smaller fragments will be preferred for uses such as PCR. Unique fragments also can be used to produce fusion proteins for generating antibodies or determining binding of the polypeptide fragments, or for generating immunoassay components. Likewise, unique fragments can be employed to produce nonfused fragments of the cancer associated antigen polypeptides, useful, for example, in the preparation of antibodies, and in immunoassays.
  • Unique fragments further can be used as antisense molecules to inhibit the expression of cancer associated antigen nucleic acids and polypeptides, particularly for therapeutic purposes as described in greater detail below.
  • Unique fragments also can be used to create chimeric nucleic acid molecule or polypeptide molecules by, for example, joining all or part of the unique fragment to another nucleic acid or polypeptide molecule (homologous or not).
  • the unique fragment may be similar or identical in large part to a known molecule but may have a portion which is nonidentical to the known molecule; the known molecule and the unique fragment can be used to construct a molecule containing in large part the known molecule with the portion unique to the unique fragment added.
  • Other chimeric molecules will be known to one of ordinary skill in the art and can be prepared using standard molecular biology techniques.
  • the size of the unique fragment will depend upon its conservancy in the genetic code. Thus, some regions of cancer associated antigen sequences and complements thereof will require longer segments to be unique while others will require only short segments, typically between 12 and 32 nucleotides (e.g. 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31 and 32 or more bases long), up to the entire length of the disclosed sequence.
  • this disclosure intends to embrace each and every fragment of each sequence, beginning at the first nucleotide, the second nucleotide and so on, up to 8 nucleotides short of the end, and ending anywhere from nucleotide number 8, 9, 10 and so on for each sequence, up to the very last nucleotide (provided the sequence is unique as described above).
  • any segment of the polypeptide coding region of novel cancer associated antigen nucleic acids, or complements thereof, that is 25 or more nucleotides in length will be unique.
  • Those skilled in the art are well versed in methods for selecting such sequences, typically on the basis of the ability of the unique fragment to selectively distinguish the sequence of interest from other sequences in the human genome of the fragment to those on known databases typically is all that is necessary, although in vitro confirmatory hybridization and sequencing analysis may be performed.
  • Especially preferred include nucleic acids encoding a series of epitopes, known as "polytopes".
  • the epitopes can be arranged in sequential or overlapping fashion (see, e.g., Thomson et al., Proc. Natl. Acad. Sci.
  • the polytope is processed to generate individual epitopes which are recognized by the immune system for generation of immune responses.
  • peptides derived from a polypeptide having an amino acid sequence encoded by one of the nucleic acid disclosed herein, and which are presented by MHC molecules and recognized by CTL or T helper lymphocytes can be combined with peptides from one or more other cancer associated antigens (e.g. by preparation of hybrid nucleic acids or polypeptides) to form "polytopes".
  • the two or more peptides (or nucleic acids encoding the peptides) can be selected from those described herein, or they can include one or more peptides of previously known cancer associated antigens.
  • Exemplary cancer associated peptide antigens that can be administered to induce or enhance an immune response are derived from tumor associated genes and encoded proteins including MAGE-A1, MAGE-A2, MAGE-A3, MAGE-A4, MAGE-A5, MAGE-A6, MAGE-A7, MAGE-A8, MAGE-A9, MAGE-A10, MAGE-A11, MAGE-A12, GAGE-1, GAGE-2, GAGE-3, GAGE-4, GAGE-5, GAGE-6, GAGE-7, GAGE-8, GAGE-9, BAGE-1, RAGE-1, LB33/MUM-1, PRAME, NAG, MAGE-B2, MAGE-B3, MAGE-B4, tyrosinase, brain glycogen phosphorylase, Melan-A, MAGE-C1, MAGE-C2, MAGE-C3, MAGE-C4, MAGE-C5, NY- ESO-1, LAGE-1, SSX-1, SSX-2 (HOM-MEL-40), SSX-4, SSX-5
  • polypeptides comprising one or more peptides and one or more of the foregoing cancer associated peptides, or nucleic acids encoding such polypeptides, according to standard procedures of molecular biology.
  • polytopes are groups of two or more potentially immunogenic or immune response stimulating peptides which can be joined together in various arrangements (e.g. concatenated, overlapping).
  • the polytope (or nucleic acid encoding the polytope) can be administered in a standard immunization protocol, e.g. to animals, to test the effectiveness of the polytope in stimulating, enhancing and/or provoking an immune response.
  • the peptides can be joined together directly or via the use of flanking sequences to form polytopes, and the use of polytopes as vaccines is well known in the art (see, e.g., Thomson et al., Proc. Acad. Natl. Acad. Sci USA 92(13):5845-5849, 1995; Gilbert et al., Nature Biotechnol. 15(12):1280-1284, 1997; Thomson et al., J. Immunol. 157(2): 822-826, 1996; Tarn et al., J. Exp. Med. 171(l):299-306, 1990).
  • Tarn showed that polytopes consisting of both MHC class I and class II binding epitopes successfully generated antibody and protective immunity in a mouse model. Tarn also demonstrated that polytopes comprising "strings" of epitopes are processed to yield individual epitopes which are presented by MHC molecules and recognized by CTLs. Thus polytopes containing various numbers and combinations of epitopes can be prepared and tested for recognition by CTLs and for efficacy in increasing an immune response.
  • tumors express a set of tumor antigens, of which only certain subsets may be expressed in the tumor of any given patient.
  • Polytopes can be prepared which correspond to the different combination of epitopes representing the subset of tumor rejection antigens expressed in a particular patient. Polytopes also can be prepared to reflect a broader spectrum of tumor rejection antigens known to be expressed by a tumor type. Polytopes can be introduced to a patient in need of such treatment as polypeptide structures, or via the use of nucleic acid delivery systems known in the art (see, e.g., Allsopp et al., Eur. J. Immunol. 26(8):1951-1959, 1996).
  • Adenovirus, pox virus, Ty-virus like particles, adeno-associated virus, plasmids, bacteria, etc. can be used in such delivery.
  • the expression vector may also include a nucleic acid sequence coding for the HLA molecule that presents any particular tumor rejection antigen derived from these nucleic acids and polypeptides.
  • the nucleic acid sequence coding for such a HLA molecule can be contained within a separate expression vector.
  • the single vector can be used to transfect a cell which does not normally express either one.
  • the expression vectors can be cotransfected.
  • the cancer associated antigen precursor coding sequence may be used alone, when, e.g. the host cell already expresses a HLA molecule which presents a cancer associated antigen derived from precursor molecules.
  • the host cell already expresses a HLA molecule which presents a cancer associated antigen derived from precursor molecules.
  • the vectors which contain the two coding sequences may be used in any antigen-presenting cells if desired, and the gene for cancer associated antigen precursor can be used in host cells which do not express a HLA molecule which presents a cancer associated antigen.
  • cell-free transcription systems may be used in lieu of cells.
  • the invention embraces antisense oligonucleotides that selectively bind to a nucleic acid molecule encoding a cancer associated antigen polypeptide, to reduce the expression of cancer associated antigens. This is desirable in virtually any medical condition wherein a reduction of expression of cancer associated antigens is desirable, e.g., in the treatment of cancer. This is also useful for in vitro or in vivo testing of the effects of a reduction of expression of one or more cancer associated antigens.
  • antisense oligonucleotide or “antisense” describes an oligonucleotide that is an oligoribonucleotide, oligodeoxyribonucleotide, modified oligoribonucleotide, or modified oligodeoxyribonucleotide which hybridizes under physiological conditions to DNA comprising a particular gene or to an mRNA transcript of that gene and, thereby, inhibits the transcription of that gene and/or the translation of that mRNA.
  • the antisense molecules are designed so as to interfere with transcription or translation of a target gene upon hybridization with the target gene or transcript.
  • the exact length of the antisense oligonucleotide and its degree of complementarity with its target will depend upon the specific target selected, including the sequence of the target and the particular bases which comprise that sequence. It is preferred that the antisense oligonucleotide be constructed and arranged so as to bind selectively with the target under physiological conditions, i.e., to hybridize substantially more to the target sequence than to any other sequence in the target cell under physiological conditions.
  • a "gene walk" comprising a series of oligonucleotides of 15-30 nucleotides spanning the length of a cancer associated antigen can be prepared, followed by testing for inhibition of cancer associated antigen expression.
  • gaps of 5-10 nucleotides can be left between the oligonucleotides to reduce the number of oligonucleotides synthesized and tested.
  • antisense oligonucleotides should comprise at least 10 and, more preferably, at least 15 consecutive bases which are complementary to the target, although in certain cases modified oligonucleotides as short as 7 bases in length have been used successfully as antisense oligonucleotides (Wagner et al., Nature Biotechnol. 14:840-844, 1996). Most preferably, the antisense oligonucleotides comprise a complementary sequence of 20-30 bases.
  • oligonucleotides may be chosen which are antisense to any region of the gene or mRNA transcripts, in preferred embodiments the antisense oligonucleotides correspond to N-terminal or 5' upstream sites such as translation initiation, transcription initiation or promoter sites. In addition, 3'-untranslated regions may be targeted. Targeting to mRNA splicing sites has also been used in the art but may be less preferred if alternative mRNA splicing occurs. In addition, the antisense is targeted, preferably, to sites in which mRNA secondary structure is not expected (see, e.g., Sainio et al., CellMol. Neurobiol.
  • the listed sequences are cDNA sequences, one of ordinary skill in the art may easily derive the genomic DNA corresponding to the cDNA of a cancer associated antigen.
  • the present invention also provides for antisense oligonucleotides which are complementary to the genomic DNA corresponding to nucleic acids encoding cancer associated antigens.
  • antisense to allelic or homologous cDNAs and genomic DNAs are enabled without undue experimentation.
  • the antisense oligonucleotides of the invention may be composed of "natural" deoxyribonucleotides, ribonucleotides, or any combination thereof. That is, the 5' end of one native nucleotide and the 3' end of another native nucleotide may be covalently linked, as in natural systems, via a phosphodiester internucleoside linkage.
  • These oligonucleotides may be prepared by art recognized methods which may be carried out manually or by an automated synthesizer. They also may be produced recombinantly by vectors.
  • the antisense oligonucleotides of the invention also may include "modified" oligonucleotides. That is, the oligonucleotides may be modified in a number of ways which do not prevent them from hybridizing to their target but which enhance their stability or targeting or which otherwise enhance their therapeutic effectiveness.
  • modified oligonucleotide as used herein describes an oligonucleotide in which (1) at least two of its nucleotides are covalently linked via a synthetic internucleoside linkage (i.e., a linkage other than a phosphodiester linkage between the 5' end of one nucleotide and the 3' end of another nucleotide) and/or (2) a chemical group not normally associated with nucleic acids has been covalently attached to the oligonucleotide.
  • a synthetic internucleoside linkage i.e., a linkage other than a phosphodiester linkage between the 5' end of one nucleotide and the 3' end of another nucleotide
  • Preferred synthetic internucleoside linkages are phosphorothioates, alkylphosphonates, phosphorodithioates, phosphate esters, alkylphosphonothioates, phosphoramidates, carbamates, carbonates, phosphate triesters, acetamidates, carboxymethyl esters and peptides.
  • modified oligonucleotide also encompasses oligonucleotides with a covalently modified base and/or sugar.
  • modified oligonucleotides include oligonucleotides having backbone sugars which are covalently attached to low molecular weight organic groups other than a hydroxyl group at the 3' position and other than a phosphate group at the 5 1 position.
  • modified oligonucleotides may include a 2'-O- alkylated ribose group.
  • modified oligonucleotides may include sugars such as arabinose instead of ribose.
  • the present invention contemplates pharmaceutical preparations containing modified antisense molecules that are complementary to and hybridizable with, under physiological conditions, nucleic acids encoding breast, gastric or prostate cancer associated antigen polypeptides, together with pharmaceutically acceptable carriers.
  • Antisense oligonucleotides may be administered as part of a pharmaceutical composition.
  • a pharmaceutical composition may include the antisense oligonucleotides in combination with any standard physiologically and/or pharmaceutically acceptable carriers which are known in the art.
  • the compositions should be sterile and contain a therapeutically effective amount of the antisense oligonucleotides in a unit of weight or volume suitable for administration to a patient.
  • pharmaceutically acceptable means a non-toxic material that does not interfere with the effectiveness of the biological activity of the active ingredients.
  • physiologically acceptable refers to a non-toxic material that is compatible with a biological system such as a cell, cell culture, tissue, or organism. The characteristics of the carrier will depend on the route of administration.
  • Physiologically and pharmaceutically acceptable carriers include diluents, fillers, salts, buffers, stabilizers, solubilizers, and other materials which are well known in the art, as further described below.
  • a "vector" may be any of a number of nucleic acids into which a desired sequence may be inserted by restriction and ligation for transport between different genetic environments or for expression in a host cell. Vectors are typically composed of DNA although RNA vectors are also available. Vectors include, but are not limited to, plasmids, phagemids and virus genomes.
  • a cloning vector is one which is able to replicate autonomously or integrated in the genome in a host cell, and which is further characterized by one or more endonuclease restriction sites at which the vector may be cut in a determinable fashion and into which a desired DNA sequence may be ligated such that the new recombinant vector retains its ability to replicate in the host cell.
  • replication of the desired sequence may occur many times as the plasmid increases in copy number within the host bacterium or just a single time per host before the host reproduces by mitosis.
  • replication may occur actively during a lytic phase or passively during a lysogenic phase.
  • An expression vector is one into which a desired DNA sequence may be inserted by restriction and ligation such that it is operably joined to regulatory sequences and may be expressed as an RNA transcript.
  • Vectors may further contain one or more marker sequences suitable for use in the identification of cells which have or have not been transformed or transfected with the vector.
  • Markers include, for example, genes encoding proteins which increase or decrease either resistance or sensitivity to antibiotics or other compounds, genes which encode enzymes whose activities are detectable by standard assays known in the art (e.g., ⁇ -galactosidase, luciferase or alkaline phosphatase), and genes which visibly affect the phenotype of transformed or transfected cells, hosts, colonies or plaques (e.g., green fluorescent protein).
  • Preferred vectors are those capable of autonomous replication and expression of the structural gene products present in the DNA segments to which they are operably joined.
  • a coding sequence and regulatory sequences are said to be "operably” joined when they are covalently linked in such a way as to place the expression or transcription of the coding sequence under the influence or control of the regulatory sequences. If it is desired that the coding sequences be translated into a functional protein, two DNA sequences are said to be operably joined if induction of a promoter in the 5' regulatory sequences results in the transcription of the coding sequence and if the nature of the linkage between the two DNA sequences does not (1) result in the introduction of a frame- shift mutation, (2) interfere with the ability of the promoter region to direct the transcription of the coding sequences, or (3) interfere with the ability of the corresponding RNA transcript to be translated into a protein.
  • a promoter region would be operably joined to a coding sequence if the promoter region were capable of effecting transcription of that DNA sequence such that the resulting transcript might be translated into the desired protein or polypeptide.
  • the precise nature of the regulatory sequences needed for gene expression may vary between species or cell types, but shall in general include, as necessary, 5' non-transcribed and 5' non-translated sequences involved with the initiation of transcription and translation respectively, such as a TATA box, capping sequence, CAAT sequence, and the like.
  • 5' non-transcribed regulatory sequences will include a promoter region which includes a promoter sequence for transcriptional control of the operably joined gene. Regulatory sequences may also include enhancer sequences or upstream activator sequences as desired.
  • the vectors of the invention may optionally include 5' leader or signal sequences.
  • the choice and design of an appropriate vector is within the ability and discretion of one of ordinary skill in the art.
  • Expression vectors containing all the necessary elements for expression are commercially available and known to those skilled in the art. See, e.g., Sambrook et al., Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press, 1989.
  • Cells are genetically engineered by the introduction into the cells of heterologous DNA (RNA) encoding a cancer associated antigen polypeptide or fragment or variant thereof. That heterologous DNA (RNA) is placed under operable control of transcriptional elements to permit the expression of the heterologous DNA in the host cell.
  • RNA heterologous DNA
  • Preferred systems for mRNA expression in mammalian cells are those such as pRc/CMV (available from Invitrogen, Carlsbad, CA) that contain a selectable marker such as a gene that confers G418 resistance (which facilitates the selection of stably transfected cell lines) and the human cytomegalovirus (CMV) enhancer-promoter sequences.
  • pCEP4 vector Invitrogen
  • EBV Epstein Barr Virus
  • Another expression vector is the pEF- BOS plasmid containing the promoter of polypeptide Elongation Factor l ⁇ , which stimulates efficiently transcription in vitro.
  • the plasmid is described by Mishizuma and Nagata (Nuc. Acids Res. 18:5322, 1990), and its use in transfection experiments is disclosed by, for example, Demoulin (Mol. Cell. Biol. 16:4710-4716, 1996).
  • Still another preferred expression vector is an adeno virus, described by Stratford-Perricaudet, which is defective for El and E3 proteins (J. Clin. Invest. 90:626-630, 1992).
  • adenovirus as an Adeno.Pl A recombinant for the expression of an antigen is disclosed by Warmer et al., in intradermal injection in mice for immunization against PI A (Int. J. Cancer, 67:303-310, 1996). Additional vectors for delivery of nucleic acid are provided below.
  • the invention also embraces so-called expression kits, which allow the artisan to prepare a desired expression vector or vectors.
  • Such expression kits include at least separate portions of a vector and one or more of the previously discussed cancer associated antigen nucleic acid molecules. Other components may be added, as desired, as long as the previously mentioned nucleic acid molecules, which are required, are included.
  • the invention also includes kits for amplification of a cancer associated antigen nucleic acid, including at least one pair of amplification primers which hybridize to a cancer associated antigen nucleic acid.
  • the primers preferably are 12-32 nucleotides in length and are non-overlapping to prevent formation of "primer-dimers".
  • One of the primers will hybridize to one strand of the cancer associated antigen nucleic acid and the second primer will hybridize to the complementary strand of the cancer associated antigen nucleic acid, in an arrangement which permits amplification of the cancer associated antigen nucleic acid.
  • Selection of appropriate primer pairs is standard in the art. For example, the selection can be made with assistance of a computer program designed for such a purpose, optionally followed by testing the primers for amplification specificity and efficiency.
  • the invention also permits the construction of cancer associated antigen gene "knockouts" and transgenic overexpression in cells and in animals, providing materials for studying certain aspects of cancer and immune system responses to cancer.
  • the invention also provides isolated polypeptides (including whole proteins and partial proteins) encoded by the foregoing cancer associated antigen nucleic acids. Such polypeptides are useful, for example, alone or as fusion proteins to generate antibodies, as components of an immunoassay or diagnostic assay or as therapeutics.
  • Cancer associated antigen polypeptides can be isolated from biological samples including tissue or cell homogenates, and can also be expressed recombinantly in a variety of prokaryotic and eukaryotic expression systems by constructing an expression vector appropriate to the expression system, introducing the expression vector into the expression system, and isolating the recombinantly expressed protein.
  • Short polypeptides, including antigenic peptides (such as are presented by MHC molecules on the surface of a cell for immune recognition) also can be synthesized chemically using well-established methods of peptide synthesis.
  • a unique fragment of a cancer associated antigen polypeptide in general, has the features and characteristics of unique fragments as discussed above in connection with nucleic acids. As will be recognized by those skilled in the art, the size of the unique fragment will depend upon factors such as whether the fragment constitutes a portion of a conserved protein domain. Thus, some regions of cancer associated antigens will require longer segments to be unique while others will require only short segments, typically between 5 and 12 amino acids (e.g. 5, 6, 7, 8, 9, 10, 11 or 12 or more amino acids including each integer up to the full length).
  • Unique fragments of a polypeptide preferably are those fragments which retain a distinct functional capability of the polypeptide.
  • Functional capabilities which can be retained in a unique fragment of a polypeptide include interaction with antibodies, interaction with other polypeptides or fragments thereof, selective binding of nucleic acids or proteins, and enzymatic activity.
  • One important activity is the ability to act as a signature for identifying the polypeptide.
  • Another is the ability to complex with HLA and to provoke in a human an immune response.
  • Those skilled in the art are well versed in methods for selecting unique amino acid sequences, typically on the basis of the ability of the unique fragment to selectively distinguish the sequence of interest from non-family members. A comparison of the sequence of the fragment to those on known databases typically is all that is necessary.
  • a "variant" of a cancer associated antigen polypeptide is a polypeptide which contains one or more modifications to the primary amino acid sequence of a cancer associated antigen polypeptide.
  • Modifications which create a cancer associated antigen variant can be made to a cancer associated antigen polypeptide 1) to reduce or eliminate an activity of a cancer associated antigen polypeptide; 2) to enhance a property of a cancer associated antigen polypeptide, such as protein stability in an expression system or the stability of protein-protein binding; 3) to provide a novel activity or property to a cancer associated antigen polypeptide, such as addition of an antigenic epitope or addition of a detectable moiety; or 4) to provide equivalent or better binding to an HLA molecule.
  • Modifications to a cancer associated antigen polypeptide are typically made to the nucleic acid which encodes the cancer associated antigen polypeptide, and can include deletions, point mutations, truncations, amino acid substitutions and additions of amino acids or non-amino acid moieties. Alternatively, modifications can be made directly to the polypeptide, such as by cleavage, addition of a linker molecule, addition of a detectable moiety, such as biotin, addition of a fatty acid, substitution of L-amino acids with D-amino acids, and the like. Modifications also embrace fusion proteins comprising all or part of the cancer associated antigen amino acid sequence.
  • variants include cancer associated antigen polypeptides which are modified specifically to alter a feature of the polypeptide unrelated to its desired physiological activity.
  • cysteine residues can be substituted or deleted to prevent unwanted disulfide linkages.
  • certain amino acids can be changed to enhance expression of a cancer associated antigen polypeptide by eliminating proteolysis by proteases in an expression system (e.g., dibasic amino acid residues in yeast expression systems in which KEX2 protease activity is present).
  • Mutations of a nucleic acid which encode a cancer associated antigen polypeptide preferably preserve the amino acid reading frame of the coding sequence, and preferably do not create regions in the nucleic acid which are likely to hybridize to form secondary structures, such a hairpins or loops, which can be deleterious to expression of the variant polypeptide.
  • Mutations can be made by selecting an amino acid substitution, or by random mutagenesis of a selected site in a nucleic acid which encodes the polypeptide. Variant polypeptides are then expressed and tested for one or more activities to determine which mutation provides a variant polypeptide with the desired properties. Further mutations can be made to variants (or to non-variant cancer associated antigen polypeptides) which are silent as to the amino acid sequence of the polypeptide, but which provide preferred codons for translation in a particular host. The preferred codons for translation of a nucleic acid in, e.g., E. coli, are well known to those of ordinary skill in the art.
  • variants of cancer associated antigen polypeptides can be tested by cloning the gene encoding the variant cancer associated antigen polypeptide into a bacterial or mammalian expression vector, introducing the vector into an appropriate host cell, expressing the variant cancer associated antigen polypeptide, and testing for a functional capability of the cancer associated antigen polypeptides as disclosed herein.
  • the variant cancer associated antigen polypeptide can be tested for reaction with autologous or allogeneic sera as disclosed in the Examples.
  • variants may favor testing of other activities, as will be known to one of ordinary skill in the art.
  • conservative amino acid substitutions may be made in cancer associated antigen polypeptides to provide functionally equivalent variants of the foregoing polypeptides, i.e, the variants retain the functional capabilities of the cancer associated antigen polypeptides.
  • a "conservative amino acid substitution” refers to an amino acid substitution which does not alter the relative charge or size characteristics of the protein in which the amino acid substitution is made.
  • Variants can be prepared according to methods for altering polypeptide sequence known to one of ordinary skill in the art such as are found in references which compile such methods, e.g. Molecular Cloning: A Laboratory Manual, J.
  • Exemplary functionally equivalent variants of the cancer associated antigen polypeptides include conservative amino acid substitutions of in the amino acid sequences of proteins disclosed herein. Conservative substitutions of amino acids include substitutions made amongst amino acids within the following groups: (a) M, I, L, V; (b) F, Y, W; (c) K, R, H; (d) A, G; (e) S, T; (f) Q, N; and (g) E, D.
  • a peptide derived from a cancer associated antigen polypeptide is presented by an MHC molecule and recognized by CTLs, one can make conservative amino acid substitutions to the amino acid sequence of the peptide, particularly at residues which are thought not to be direct contact points with the MHC molecule.
  • conservative amino acid substitutions to the amino acid sequence of the peptide, particularly at residues which are thought not to be direct contact points with the MHC molecule.
  • methods for identifying functional variants of HLA class II binding peptides are provided in a published PCT application of Strominger and Wucherpfennig (PCT/US96/03182).
  • Peptides bearing one or more amino acid substitutions also can be tested for concordance with known HLA MHC motifs prior to synthesis using, e.g.
  • amino acid sequence of cancer associated antigen polypeptides to produce functionally equivalent variants of cancer associated antigen polypeptides typically are made by alteration of a nucleic acid encoding a cancer associated antigen polypeptide.
  • substitutions can be made by a variety of methods known to one of ordinary skill in the art.
  • amino acid substitutions may be made by PCR-directed mutation, site-directed mutagenesis according to the method of Kunkel (Kunkel, Proc. Nat. Acad. Sci. U.S.A. 82: 488-492, 1985), or by chemical synthesis of a gene encoding a cancer associated antigen polypeptide.
  • substitutions are made to a small unique fragment of a cancer associated antigen polypeptide, such as an antigenic epitope recognized by autologous or allogeneic sera or cytolytic T lymphocytes
  • the substitutions can be made by directly synthesizing the peptide.
  • the activity of functionally equivalent fragments of cancer associated antigen polypeptides can be tested by cloning the gene encoding the altered cancer associated antigen polypeptide into a bacterial or mammalian expression vector, introducing the vector into an appropriate host cell, expressing the altered cancer associated antigen polypeptide, and testing for a functional capability of the cancer associated antigen polypeptides as disclosed herein.
  • Peptides which are chemically synthesized can be tested directly for function, e.g., for binding to antisera recognizing associated antigens.
  • the invention permits production and/or isolation of the cancer associated antigen protein molecules.
  • a variety of methodologies well-known to the skilled practitioner can be utilized to obtain isolated cancer associated antigen molecules.
  • the polypeptide may be purified from cells which naturally produce the polypeptide by chromatographic means or immunological recognition.
  • an expression vector may be introduced into cells to cause production of the polypeptide.
  • mRNA transcripts may be microinjected or otherwise introduced into cells to cause production of the encoded polypeptide. Translation of mRNA in cell-free extracts such as the reticulocyte lysate system also may be used to produce polypeptide.
  • cancer associated antigen polypeptides include, but are not limited to, immunochromatography, HPLC, size-exclusion chromatography, ion-exchange chromatography and immune-affinity chromatography.
  • the isolation and identification of cancer associated antigen genes also makes it possible for the artisan to diagnose a disorder characterized by expression of cancer associated antigens.
  • These methods involve determining expression of one or more cancer associated antigen nucleic acids, and/or encoded cancer associated antigen polypeptides and/or peptides derived therefrom. In the former situation, such determinations can be carried out via any standard nucleic acid determination assay, including the polymerase chain reaction, or assaying with labeled hybridization probes. In the latter situation, such determinations can be carried out by screening patient antisera for recognition of the polypeptide.
  • the invention also makes it possible isolate proteins which bind to cancer associated antigens as disclosed herein, including antibodies and cellular binding partners of the cancer associated antigens. Additional uses are described further herein.
  • the invention also provides, in certain embodiments, "dominant negative" polypeptides derived from cancer associated antigen polypeptides.
  • a dominant negative polypeptide is an inactive variant of a protein, which, by interacting with the cellular machinery, displaces an active protein from its interaction with the cellular machinery or competes with the active protein, thereby reducing the effect of the active protein.
  • a dominant negative receptor which binds a ligand but does not transmit a signal in response to binding of the ligand can reduce the biological effect of expression of the ligand.
  • a dominant negative catalytically-inactive kinase which interacts normally with target proteins but does not phosphorylate the target proteins can reduce phosphorylation of the target proteins in response to a cellular signal.
  • a dominant negative transcription factor which binds to a promoter site in the control region of a gene but does not increase gene transcription can reduce the effect of a normal transcription factor by occupying promoter binding sites without increasing transcription.
  • the end result of the expression of a dominant negative polypeptide in a cell is a reduction in function of active proteins.
  • One of ordinary skill in the art can assess the potential for a dominant negative variant of a protein, and using standard mutagenesis techniques to create one or more dominant negative variant polypeptides.
  • one of ordinary skill in the art can modify the sequence of the cancer associated antigens by site- specific mutagenesis, scanning mutagenesis, partial gene deletion or truncation, and the like. See, e.g., U.S. Patent No.
  • binding agents can be used, for example, in screening assays to detect the presence or absence of cancer associated antigen polypeptides and complexes of cancer associated antigen polypeptides and their binding partners and in purification protocols to isolated cancer associated antigen polypeptides and complexes of cancer associated antigen polypeptides and their binding partners.
  • Such agents also can be used to inhibit the native activity of the cancer associated antigen polypeptides, for example, by binding to such polypeptides.
  • the invention therefore, embraces peptide binding agents which, for example, can be antibodies or fragments of antibodies having the ability to selectively bind to cancer associated antigen polypeptides.
  • Antibodies include polyclonal and monoclonal antibodies, prepared according to conventional methodology.
  • an antibody from which the pFc' region has been enzymatically cleaved, or which has been produced without the pFc' region designated an F(ab') 2 fragment
  • an antibody from which the Fc region has been enzymatically cleaved, or which has been produced without the Fc region designated an Fab fragment
  • Fab fragments consist of a covalently bound antibody light chain and a portion of the antibody heavy chain denoted Fd.
  • the Fd fragments are the major determinant of antibody specificity (a single Fd fragment may be associated with up to ten different light chains without altering antibody specificity) and Fd fragments retain epitope-binding ability in isolation.
  • CDRs complementarity determining regions
  • FRs framework regions
  • CDRl through CDR3 complementarity determining regions
  • non-CDR regions of a mammalian antibody may be replaced with similar regions of conspecific or heterospecific antibodies while retaining the epitopic specificity of the original antibody.
  • This is most clearly manifested in the development and use of "humanized" antibodies in which non-human CDRs are covalently joined to human FR and/or Fc/pFc' regions to produce a functional antibody. See, e.g., U.S. patents 4,816,567, 5,225,539, 5,585,089, 5,693,762 and 5,859,205.
  • PCT International Publication Number WO 92/04381 teaches the production and use of humanized murine RSV antibodies in which at least a portion of the murine FR regions have been replaced by FR regions of human origin.
  • Such antibodies including fragments of intact antibodies with antigen-binding ability, are often referred to as "chimeric" antibodies.
  • the present invention also provides for F(ab') 2 , Fab, Fv and Fd fragments; chimeric antibodies in which the Fc and/or FR and/or CDRl and/or CDR2 and/or light chain CDR3 regions have been replaced by homologous human or non-human sequences; chimeric F(ab') 2 fragment antibodies in which the FR and/or CDRl and/or CDR2 and/or light chain CDR3 regions have been replaced by homologous human or non-human sequences; chimeric Fab fragment antibodies in which the FR and/or CDRl and/or CDR2 and/or light chain CDR3 regions have been replaced by homologous human or non-human sequences; and chimeric Fd fragment antibodies in which the FR and or CDRl and/or CDR2 regions have been replaced by homologous human or non-human sequences.
  • the present invention also includes so-called single chain antibodies.
  • polypeptides of numerous size and type that bind specifically to cancer associated antigen polypeptides, and complexes of both cancer associated antigen polypeptides and their binding partners.
  • polypeptide binding agents can be provided by degenerate peptide libraries which can be readily prepared in solution, in immobilized form or as phage display libraries.
  • Combinatorial libraries also can be synthesized of peptides containing one or more amino acids. Libraries further can be synthesized of peptoids and non-peptide synthetic moieties. Phage display can be particularly effective in identifying binding peptides useful according to the invention. Briefly, one prepares a phage library (using e.g.
  • inserts from 4 to about 80 amino acid residues using conventional procedures.
  • the inserts may represent, for example, a completely degenerate or biased array.
  • One then can select phage-bearing inserts which bind to the cancer associated antigen polypeptide. This process can be repeated through several cycles of reselection of phage that bind to the cancer associated antigen polypeptide. Repeated rounds lead to enrichment of phage bearing particular sequences.
  • DNA sequence analysis can be conducted to identify the sequences of the expressed polypeptides. The minimal linear portion of the sequence that binds to the cancer associated antigen polypeptide can be determined.
  • Yeast two-hybrid screening methods also may be used to identify polypeptides that bind to the cancer associated antigen polypeptides.
  • the cancer associated antigen polypeptides of the invention, or a fragment thereof can be used to screen peptide libraries, including phage display libraries, to identify and select peptide binding partners of the cancer associated antigen polypeptides of the invention.
  • Such molecules can be used, as described, for screening assays, for purification protocols, for interfering directly with the functioning of cancer associated antigen and for other purposes that will be apparent to those of ordinary skill in the art.
  • antibodies and other binding molecules may be used for example to identify tissues expressing protein or to purify protein.
  • Antibodies also may be coupled to specific diagnostic labeling agents for imaging of cells and tissues that express cancer associated antigens or to therapeutically useful agents according to standard coupling procedures.
  • Diagnostic agents include, but are not limited to, barium sulfate, iocetamic acid, iopanoic acid, ipodate calcium, diatrizoate sodium, diatrizoate meglumine, metrizamide, tyropanoate sodium and radiodiagnostics including positron emitters such as fluorine- 18 and carbon- 11 , gamma emitters such as iodine- 123, technetium-99m, iodine- 131 and indium- 111, and nuclides for nuclear magnetic resonance such as fluorine and gadolinium.
  • Other diagnostic agents useful in the invention will be apparent to one of ordinary skill in the art.
  • therapeutically useful agents include any therapeutic molecule which desirably is targeted selectively to a cell expressing one of the cancer antigens disclosed herein, including antineoplastic agents, radioiodinated compounds, toxins, other cytostatic or cytolytic drugs, and so forth.
  • Antineoplastic therapeutics include: aminoglutethimide, azathioprine, bleomycin sulfate, busulfan, carmustine, chlorambucil, cisplatin, cyclophosphamide, cyclosporine, cytarabidine, dacarbazine, dactinomycin, daunorubicin, doxorubicin, taxol, etoposide, fluorouracil, interferon- ⁇ , lomustine, mercaptopurine, methotrexate, mitotane, procarbazine HCl, thioguanine, vinblastine sulfate and vincristine sulfate.
  • Additional antineoplastic agents include those disclosed in Chapter 52, Antineoplastic Agents (Paul Calabresi and Bruce A. Chabner), and the introduction thereto, 1202-1263, of Goodman and Gilman's "The Pharmacological Basis of Therapeutics", Eighth Edition, 1990, McGraw-Hill, Inc. (Health Professions Division).
  • Toxins can be proteins such as, for example, pokeweed anti- viral protein, cholera toxin, pertussis toxin, ricin, gelonin, abrin, diphtheria exotoxin, or Pseudomonas exotoxin.
  • Toxin moieties can also be high energy-emitting radionuclides such as cobalt-60.
  • antibodies prepared according to the invention also preferably are specific for the cancer associated antigen/MHC complexes described herein.
  • disorder refers to any pathological condition where the cancer associated antigens are expressed.
  • An example of such a disorder is cancer, including breast, gastric and prostate cancer as particular examples.
  • an immunoreactive cell sample is removed from a subject.
  • immunoreactive cell is meant a cell which can mature into an immune cell (such as a B cell, a helper T cell, or a cytolytic T cell) upon appropriate stimulation.
  • immunoreactive cells include CD34 + hematopoietic stem cells, immature T cells and immature B cells.
  • the immunoreactive cell When it is desired to produce cytolytic T cells which recognize a cancer associated antigen, the immunoreactive cell is contacted with a cell which expresses a cancer associated antigen under conditions favoring production, differentiation and/or selection of cytolytic T cells; the differentiation of the T cell precursor into a cytolytic T cell upon exposure to antigen is similar to clonal selection of the immune system.
  • Some therapeutic approaches based upon the disclosure are premised on a response by a subject's immune system, leading to lysis of antigen presenting cells, such as breast, gastric or prostate cancer cells which present one or more cancer associated antigens.
  • One such approach is the administration of autologous CTLs specific to a cancer associated antigen MHC complex to a subject with abnormal cells of the phenotype at issue. It is within the ability of one of ordinary skill in the art to develop such CTLs in vitro.
  • An example of a method for T cell differentiation is presented in International Application number
  • a sample of cells taken from a subject are contacted with a cell presenting the complex and capable of provoking CTLs to proliferate.
  • the target cell can be a transfectant, such as a COS cell. These transfectants present the desired complex at their surface and, when combined with a CTL of interest, stimulate its proliferation.
  • COS cells are widely available, as are other suitable host cells. Specific production of CTL clones is well known in the art. The clonally expanded autologous CTLs then are administered to the subject.
  • CTL proliferation can be increased by increasing the level of tryptophan in T cell cultures, by inhibiting enzymes which catabolize tryptophan, such as indoleamine 2,3- dioxygenase (IDO), or by adding tryptophan to the culture.
  • Proliferation of T cells is enhanced by increasing the rate of proliferation and/or extending the number of divisions of the T cells in culture.
  • increasing tryptophan in T cell cultures also enhances the lytic activity of the T cells grown in culture.
  • Tetramers are formed by mixing the biotinylated peptide-MHC complex with labeled avidin (e.g. phycoerythrin) at a molar ratio or 4:1. Tetramers are then contacted with a source of CTLs such as peripheral blood or lymph node. The tetramers bind CTLs which recognize the peptide antigen/MHC class I complex. Cells bound by the tetramers can be sorted by fluorescence activated cell sorting to isolate the reactive CTLs. The isolated CTLs then can be expanded in vitro for use as described herein.
  • avidin e.g. phycoerythrin
  • the foregoing therapy assumes that at least some of the subject's abnormal cells present the relevant HLA/cancer associated antigen complex. This can be determined very easily, as the art is very familiar with methods for identifying cells which present a particular HLA molecule, as well as how to identify cells expressing DNA of the pertinent sequences, in this case a cancer associated antigen sequence.
  • Once cells presenting the relevant complex are identified via the foregoing screening methodology, they can be combined with a sample from a patient, where the sample contains CTLs. If the complex presenting cells are lysed by the mixed CTL sample, then it can be assumed that a cancer associated antigen is being presented, and the subject is an appropriate candidate for the therapeutic approaches set forth supra.
  • Adoptive transfer is not the only form of therapy that is available in accordance with the invention.
  • CTLs can also be provoked in vivo, using a number of approaches.
  • One approach is the use of non-proliferative cells expressing the complex.
  • the cells used in this approach may be those that normally express the complex, such as irradiated tumor cells or cells transfected with one or both of the genes necessary for presentation of the complex (i.e. the antigenic peptide and the presenting HLA molecule).
  • Chen et al. Proc. Natl. Acad. Sci. USA 88: 110-114,1991
  • Chen et al. (Proc. Natl. Acad. Sci. USA 88: 110-114,1991) exemplifies this approach, showing the use of transfected cells expressing HPV-E7 peptides in a therapeutic regime.
  • Various cell types may be used.
  • vectors carrying one or both of the genes of interest may be used.
  • Viral or bacterial vectors are especially preferred.
  • nucleic acids which encode a cancer associated antigen polypeptide or peptide may be operably linked to promoter and enhancer sequences which direct expression of the cancer associated antigen polypeptide or peptide in certain tissues or cell types.
  • the nucleic acid may be incorporated into an expression vector.
  • Expression vectors may be unmodified extrachromosomal nucleic acids, plasmids or viral genomes constructed or modified to enable insertion of exogenous nucleic acids, such as those encoding cancer associated antigens, as described elsewhere herein.
  • Nucleic acids encoding one or more cancer associated antigens also may be inserted into a retro viral genome, thereby facilitating integration of the nucleic acid into the genome of the target tissue or cell type.
  • the gene of interest is carried by a microorganism, e.g., a Vaccinia virus, pox virus, herpes simplex virus, retrovirus or adenovirus, and the materials de facto "infect" host cells. The cells which result present the complex of interest, and are recognized by autologous CTLs, which then proliferate.
  • a similar effect can be achieved by combining the cancer associated antigen or a stimulatory fragment thereof with an adjuvant to facilitate incorporation into antigen presenting cells in vivo.
  • the cancer associated antigen polypeptide is processed to yield the peptide partner of the HLA molecule while a cancer associated antigen peptide may be presented without the need for further processing.
  • subjects can receive an intradermal injection of an effective amount of the cancer associated antigen. Initial doses can be followed by booster doses, following immunization protocols standard in the art.
  • Preferred cancer associated antigens include those found to react with allogeneic cancer antisera, shown in the examples below.
  • the invention involves the use of various materials disclosed herein to "immunize" subjects or as "vaccines".
  • immunomunization means increasing or activating an immune response against an antigen. It does not require elimination or eradication of a condition but rather contemplates the clinically favorable enhancement of an immune response toward an antigen.
  • Generally accepted animal models can be used for testing of immunization against cancer using a cancer associated antigen nucleic acid.
  • human cancer cells can be introduced into a mouse to create a tumor, and one or more cancer associated antigen nucleic acids can be delivered by the methods described herein. The effect on the cancer cells (e.g., reduction of tumor size) can be assessed as a measure of the effectiveness of the cancer associated antigen nucleic acid immunization.
  • testing of the foregoing animal model using more conventional methods for immunization can include the administration of one or more cancer associated antigen polypeptides or peptides derived therefrom, optionally combined with one or more adjuvants and/or cytokines to boost the immune response.
  • Methods for immunization including formulation of a vaccine composition and selection of doses, route of administration and the schedule of administration (e.g. primary and one or more booster doses), are well known in the art.
  • the tests also can be performed in humans, where the end point is to test for the presence of enhanced levels of circulating CTLs against cells bearing the antigen, to test for levels of circulating antibodies against the antigen, to test for the presence of cells expressing the antigen and so forth.
  • one or more cancer associated antigens or stimulatory fragments thereof are administered with one or more adjuvants to induce an immune response or to increase an immvine response.
  • An adjuvant is a substance incorporated into or administered with antigen which potentiates the immune response.
  • Adjuvants may enhance the immuno logical response by providing a reservoir of antigen (extracellularly or within macrophages), activating macrophages and stimulating specific sets of lymphocytes.
  • Adjuvants of many kinds are well known in the art.
  • adjuvants include monophosphoryl lipid A (MPL, SmithKline Beecham), a congener obtained after purification and acid hydrolysis of Salmonella minnesota Re 595 lipopolysaccharide; saponins including QS21 (SmithKline Beecham), a pure QA-21 saponin purified from Quillja saponaria extract; DQS21, described in PCT application WO96/33739 (SmithKline Beecham); QS-7, QS-17, QS-18, and QS-L1 (So et al., Mol.
  • MPL monophosphoryl lipid A
  • SPL SmithKline Beecham
  • saponins including QS21 (SmithKline Beecham), a pure QA-21 saponin purified from Quillja saponaria extract
  • DQS21 described in PCT application WO96/33739 (SmithKline Beecham)
  • QS-7, QS-17, QS-18, and QS-L1 So et al., Mol.
  • the peptides are administered mixed with a combination of DQS21/MPL.
  • the ratio of DQS21 to MPL typically will be about 1 :10 to 10:1, preferably about l:5 to 5:l and more preferably about 1:1.
  • DQS21 and MPL will be present in a vaccine formulation in the range of about 1 ⁇ g to about 100 ⁇ g.
  • Other adjuvants are known in the art and can be used in the invention (see, e.g. Goding, Monoclonal Antibodies: Principles and Practice, 2nd Ed., 1986). Methods for the preparation of mixtures or emulsions of peptide and adjuvant are well known to those of skill in the art of vaccination.
  • cytokines are also useful in vaccination protocols as a result of their lymphocyte regulatory properties.
  • cytokines useful for such purposes will be known to one of ordinary skill in the art, including interleukin-12 (IL-12) which has been shown to enhance the protective effects of vaccines (see, e.g., Science 268: 1432-1434, 1995), GM-CSF and IL-18.
  • IL-12 interleukin-12
  • GM-CSF GM-CSF
  • IL-18 interleukin-18
  • cytokines can be administered in conjunction with antigens and adjuvants to increase the immune response to the antigens.
  • immune response potentiating compounds that can be used in vaccination protocols. These include costimulatory molecules provided in either protein or nucleic acid form.
  • costimulatory molecules include the B7-1 and B7-2 (CD80 and CD86 respectively) molecules which are expressed on dendritic cells (DC) and interact with the CD28 molecule expressed on the T cell.
  • DC dendritic cells
  • This interaction provides costimulation (signal 2) to an antigen/MHC/TCR stimulated (signal 1) T cell, increasing T cell proliferation and effector function.
  • B7 also interacts with CTLA4 (CD 152) on T cells and studies involving CTLA4 and B7 ligands indicate that the B7-CTLA4 interaction can enhance antitumor immunity and CTL proliferation (Zheng P., et al. Proc. Natl. Acad. Sci. USA 95 (11):6284-6289 (1998)).
  • B7 typically is not expressed on tumor cells so they are not efficient antigen presenting cells (APCs) for T cells. Induction of B7 expression would enable the tumor cells to stimulate more efficiently CTL proliferation and effector function.
  • a combination of B7/IL-6/IL-12 costimulation has been shown to induce IFN-gamma and a Thl cytokine profile in the T cell population leading to further enhanced T cell activity (Gajewski et al., J. Immunol, 154:5637- 5648 (1995)).
  • Tumor cell transfection with B7 has ben discussed in relation to in vitro CTL expansion for adoptive transfer immunotherapy by Wang et al., (J. Immunol, 19: 1-8 (1986)).
  • B7 molecule delivery mechanisms for the B7 molecule would include nucleic acid (naked DNA) immunization (Kim J., et al. Nat Biotechnol, 15:7:641-646 (1997)) and recombinant viruses such as adeno and pox (Wendtner et al., Gene Ther., 4:7:726-735 (1997)).
  • nucleic acid naked DNA
  • recombinant viruses such as adeno and pox
  • adeno and pox Wang et al., Gene Ther., 4:7:726-735 (1997).
  • These systems are all amenable to the construction and use of expression cassettes for the coexpression of B7 with other molecules of choice such as the antigens or fragment(s) of antigens discussed herein (including polytopes) or cytokines.
  • These delivery systems can be used for induction of the appropriate molecules in vitro and for in vivo vaccination situations.
  • anti- CD28 antibodies to directly stimulate T cells in vitro and in vivo could also be considered.
  • the inducible co-stimulatory molecule ICOS which induces T cell responses to foreign antigen could be modulated, for example, by use of anti-ICOS antibodies (Hutloff et al., Nature 397:263-266, 1999).
  • Lymphocyte function associated antigen-3 (LFA-3) is expressed on APCs and some tumor cells and interacts with CD2 expressed on T cells. This interaction induces T cell IL-2 and IFN-gamma production and can thus complement but not substitute, the B7/CD28 costimulatory interaction (Parra et al., J.
  • Lymphocyte function associated antigen- 1 (LFA-1) is expressed on leukocytes and interacts with ICAM-1 expressed on APCs and some tumor cells. This interaction induces T cell IL-2 and IFN-gamma production and can thus complement but not substitute, the B7/CD28 costimulatory interaction (Fenton et al., J. Immunother., 21:2:95-108 (1998)).
  • LFA- 1 is thus a further example of a costimulatory molecule that could be provided in a vaccination protocol in the various ways discussed above for B7.
  • Th cell help through the interaction between the Th cell CD40L (CD40 ligand) molecule and the CD40 molecule expressed by DCs (Ridge et al., Nature, 393:474 (1998), Bennett et al., Nature, 393:478 (1998), Schoenberger et al., Nature, 393:480 (1998)).
  • This mechanism of this costimulatory signal is likely to involve upregulation of B7 and associated IL-6/IL-12 production by the DC (APC).
  • the CD40-CD40L interaction thus complements the signal 1 (antigen/MHC-TCR) and signal 2 (B7-CD28) interactions.
  • anti-CD40 antibodies to stimulate DC cells directly, would be expected to enhance a response to tumor antigens which are normally encountered outside of a inflammatory context or are presented by non-professional APCs (tumor cells). In these situations Th help and B7 costimulation signals are not provided. This mechanism might be used in the context of antigen pulsed DC based therapies or in situations where Th epitopes have not been defined within known cancer antigen precursors.
  • a cancer associated antigen polypeptide, or a fragment thereof also can be used to isolate their native binding partners. Isolation of such binding partners may be performed according to well-known methods. For example, isolated cancer associated antigen polypeptides can be attached to a substrate (e.g., chromatographic media, such as polystyrene beads, or a filter), and then a solution suspected of containing the binding partner may be applied to the substrate. If a binding partner which can interact with cancer associated antigen polypeptides is present in the solution, then it will bind to the substrate-bound cancer associated antigen polypeptide. The binding partner then may be isolated.
  • a substrate e.g., chromatographic media, such as polystyrene beads, or a filter
  • the invention embraces the use of the cancer associated antigen cDNA sequences in expression vectors, as well as to transfect host cells and cell lines, be these prokaryotic (e.g., E. coli), or eukaryotic (e.g., dendritic cells, B cells, CHO cells, COS cells, yeast expression systems and recombinant baculovirus expression in insect cells).
  • prokaryotic e.g., E. coli
  • eukaryotic e.g., dendritic cells, B cells, CHO cells, COS cells, yeast expression systems and recombinant baculovirus expression in insect cells.
  • mammalian cells such as human, mouse, hamster, pig, goat, primate, etc. They may be of a wide variety of tissue types, and include primary cells and cell lines.
  • keratinocytes include peripheral blood leukocytes, bone marrow stem cells and embryonic stem cells.
  • the expression vectors require that the pertinent sequence, i.e., those nucleic acids described supra, be operably linked to a promoter.
  • the invention also contemplates delivery of nucleic acids, polypeptides or peptides for vaccination. Delivery of polypeptides and peptides can be accomplished according to standard vaccination protocols which are well known in the art. In another embodiment, the delivery of nucleic acid is accomplished by ex vivo methods, i.e. by removing a cell from a subject, genetically engineering the cell to include a cancer associated antigen, and reintroducing the engineered cell into the subject.
  • ex vivo methods i.e. by removing a cell from a subject, genetically engineering the cell to include a cancer associated antigen, and reintroducing the engineered cell into the subject.
  • U.S. Patent 5,399,346 One example of such a procedure is outlined in U.S. Patent 5,399,346 and in exhibits submitted in the file history of that patent, all of which are publicly available documents.
  • a virus vector for delivering a nucleic acid encoding a cancer associated antigen is selected from the group consisting of adenoviruses, adeno- associated viruses, poxviruses including vaccinia viruses and attenuated poxviruses, Semliki Forest virus, Venezuelan equine encephalitis virus, retroviruses, Sindbis virus, and Ty viruslike particle.
  • viruses and virus-like particles which have been used to deliver exogenous nucleic acids include: replication-defective adenoviruses (e.g., Xiang et al., Virology 219:220-227, 1996; Eloit et al., J.
  • the virus vector is an adenovirus.
  • the adeno-associated virus is capable of infecting a wide range of cell types and species and can be engineered to be replication-deficient. It further has advantages, such as heat and lipid solvent stability, high transduction frequencies in cells of diverse lineages, including hematopoietic cells, and lack of superinfection inhibition thus allowing multiple series of transductions.
  • the adeno-associated virus can integrate into human cellular DNA in a site-specific manner, thereby minimizing the possibility of insertional mutagenesis and variability of inserted gene expression.
  • adeno-associated virus infections have been followed in tissue culture for greater than 100 passages in the absence of selective pressure, implying that the adeno-associated virus genomic integration is a relatively stable event.
  • the adeno-associated virus can also function in an extrachromosomal fashion.
  • Non-cytopathic viral vectors are based on non-cytopathic eukaryotic viruses in which non-essential genes have been replaced with the gene of interest.
  • Non-cytopathic viruses include retro viruses, the life cycle of which involves reverse transcription of genomic viral RNA into DNA with subsequent proviral integration into host cellular DNA.
  • Adenoviruses and retroviruses have been approved for human gene therapy trials.
  • the retroviruses are replication-deficient (i.e., capable of directing synthesis of the desired proteins, but incapable of manufacturing an infectious particle).
  • retroviral expression vectors have general utility for the high-efficiency transduction of genes in vivo.
  • nucleic acid delivery vectors (1) contain exogenous genetic material that can be transcribed and translated in a mammalian cell and that can induce an immune response in a host, and (2) contain on a surface a ligand that selectively binds to a receptor on the surface of a target cell, such as a mammalian cell, and thereby gains entry to the target cell.
  • nucleic acids of the invention may be introduced in vitro or in vivo in a host.
  • Such techniques include transfection of nucleic acid-CaPO 4 precipitates, transfection of nucleic acids associated with DEAE, transfection or infection with the foregoing viruses including the nucleic acid of interest, liposome mediated transfection, and the like.
  • a vehicle used for delivering a nucleic acid of the invention into a cell e.g., a retrovirus, or other virus; a liposome
  • a molecule such as an antibody specific for a surface membrane protein on the target cell or a ligand for a receptor on the target cell can be bound to or incorporated within the nucleic acid delivery vehicle.
  • Preferred antibodies include antibodies which selectively bind a cancer associated antigen, alone or as a complex with a MHC molecule.
  • monoclonal antibodies are employed.
  • proteins which bind to a surface membrane protein associated with endocytosis may be incorporated into the liposome formulation for targeting and/or to facilitate uptake.
  • Such proteins include capsid proteins or fragments thereof tropic for a particular cell type, antibodies for proteins which undergo internalization in cycling, proteins that target intracellular localization and enhance intracellular half life, and the like.
  • Polymeric delivery systems also have been used successfully to deliver nucleic acids into cells, as is known by those skilled in the art. Such systems even permit oral delivery of nucleic acids.
  • the therapeutics of the invention can be administered by any conventional route, including injection or by gradual infusion over time.
  • the administration may, for example, be oral, intravenous, intraperitoneal, intramuscular, intracavity, subcutaneous, or transdermal.
  • modes of administration which effectively deliver the cancer associated antigen and adjuvant, such that an immune response to the antigen is increased, can be used.
  • preferred methods include intradermal, intravenous, intramuscular and subcutaneous administration.
  • Standard references in the art provide modes of administration and formulations for delivery of immunogens with adjuvant or in a non-adjuvant carrier.
  • a preferred route of administration is by pulmonary aerosol.
  • Techniques for preparing aerosol delivery systems containing antibodies are well known to those of skill in the art. Generally, such systems should utilize components which will not significantly impair the biological properties of the antibodies, such as the paratope binding capacity (see, for example, Sciarra and Cutie, "Aerosols," in Remington's Pharmaceutical Sciences. 18th edition, 1990, pp 1694-1712; incorporated by reference).
  • Those of skill in the art can readily determine the various parameters and conditions for producing antibody aerosols without resort to undue experimentation. When using antisense preparations of the invention, slow intravenous administration is preferred.
  • compositions of the invention are administered in effective amounts.
  • An "effective amount" is that amount of a cancer associated antigen composition that alone, or together with further doses, produces the desired response, e.g. increases an immune response to the cancer associated antigen.
  • the desired response is inhibiting the progression of the disease. This may involve only slowing the progression of the disease temporarily, although more preferably, it involves halting the progression of the disease permanently. This can be monitored by routine methods or can be monitored according to diagnostic methods of the invention discussed herein.
  • the desired response to treatment of the disease or condition also can be delaying the onset or even preventing the onset of the disease or condition.
  • Such amounts will depend, of course, on the particular condition being treated, the severity of the condition, the individual patient parameters including age, physical condition, size and weight, the duration of the treatment, the nature of concurrent therapy (if any), the specific route of administration and like factors within the knowledge and expertise of the health practitioner. These factors are well known to those of ordinary skill in the art and can be addressed with no more than routine experimentation. It is generally preferred that a maximum dose of the individual components or combinations thereof be used, that is, the highest safe dose according to sound medical judgment. It will be understood by those of ordinary skill in the art, however, that a patient may insist upon a lower dose or tolerable dose for medical reasons, psychological reasons or for virtually any other reasons.
  • compositions used in the foregoing methods preferably are sterile and contain an effective amount of cancer associated antigen or nucleic acid encoding cancer associated antigen for producing the desired response in a unit of weight or volume suitable for administration to a patient.
  • the response can, for example, be measured by determining the immune response following administration of the cancer associated antigen composition via a reporter system by measuring downstream effects such as gene expression, or by measuring the physiological effects of the cancer associated antigen composition, such as regression of a tumor or decrease of disease symptoms.
  • Other assays will be known to one of ordinary skill in the art and can be employed for measuring the level of the response.
  • cancer associated antigen compositions e.g., polypeptide, peptide, antibody, cell or nucleic acid
  • doses of cancer associated antigen compositions can be chosen in accordance with different parameters, in particular in accordance with the mode of administration used and the state of the subject. Other factors include the desired period of treatment. In the event that a response in a subject is insufficient at the initial doses applied, higher doses (or effectively higher doses by a different, more localized delivery route) may be employed to the extent that patient tolerance permits. In general, for treatments for eliciting or increasing an immune response, doses of cancer associated antigen are formulated and administered in doses between 1 ng and 1 mg, and preferably between 10 ng and 100 ⁇ g, according to any standard procedure in the art.
  • cancer associated antigen compositions where nucleic acids encoding cancer associated antigen of variants thereof are employed, doses of between 1 ng and 0.1 mg generally will be formulated and administered according to standard procedures. Other protocols for the administration of cancer associated antigen compositions will be known to one of ordinary skill in the art, in which the dose amount, schedule of injections, sites of injections, mode of administration (e.g., intra-tumoral) and the like vary from the foregoing. Administration of cancer associated antigen compositions to mammals other than humans, e.g. for testing purposes or veterinary therapeutic purposes, is carried out under substantially the same conditions as described above.
  • compositions of the invention When administered, the pharmaceutical compositions of the invention are applied in pharmaceutically-acceptable amounts and in pharmaceutically-acceptable preparations.
  • pharmaceutically acceptable means a non-toxic material that does not interfere with the effectiveness of the biological activity of the active ingredients. Such preparations may routinely contain salts, buffering agents, preservatives, compatible carriers, and optionally other therapeutic agents.
  • the salts When used in medicine, the salts should be pharmaceutically acceptable, but non-pharmaceutically acceptable salts may conveniently be used to prepare pharmaceutically-acceptable salts thereof and are not excluded from the scope of the invention.
  • Such pharmacologically and pharmaceutically-acceptable salts include, but are not limited to, those prepared from the following acids: hydrochloric, hydrobromic, sulfuric, nitric, phosphoric, maleic, acetic, salicylic, citric, formic, malonic, succinic, and the like.
  • pharmaceutically-acceptable salts can be prepared as alkaline metal or alkaline earth salts, such as sodium, potassium or calcium salts.
  • a cancer associated antigen composition may be combined, if desired, with a pharmaceutically-acceptable carrier.
  • pharmaceutically-acceptable carrier as used herein means one or more compatible solid or liquid fillers, diluents or encapsulating substances which are suitable for administration into a human.
  • carrier denotes an organic or inorganic ingredient, natural or synthetic, with which the active ingredient is combined to facilitate the application.
  • the components of the pharmaceutical compositions also are capable of being co-mingled with the molecules of the present invention, and with each other, in a manner such that there is no interaction which would substantially impair the desired pharmaceutical efficacy.
  • the pharmaceutical compositions may contain suitable buffering agents, including: acetic acid in a salt; citric acid in a salt; boric acid in a salt; and phosphoric acid in a salt.
  • suitable buffering agents including: acetic acid in a salt; citric acid in a salt; boric acid in a salt; and phosphoric acid in a salt.
  • compositions also may contain, optionally, suitable preservatives, such as: benzalkonium chloride; chlorobutanol; parabens and thimerosal.
  • suitable preservatives such as: benzalkonium chloride; chlorobutanol; parabens and thimerosal.
  • compositions may conveniently be presented in unit dosage form and may be prepared by any of the methods well-known in the art of pharmacy. All methods include the step of bringing the active agent into association with a carrier which constitutes one or more accessory ingredients. In general, the compositions are prepared by uniformly and intimately bringing the active compound into association with a liquid carrier, a finely divided solid carrier, or both, and then, if necessary, shaping the product.
  • compositions suitable for oral administration may be presented as discrete units, such as capsules, tablets, lozenges, each containing a predetermined amount of the active compound.
  • Other compositions include suspensions in aqueous liquids or non-aqueous liquids such as a syrup, elixir or an emulsion.
  • compositions suitable for parenteral administration conveniently comprise a sterile aqueous or non-aqueous preparation of cancer associated antigen polypeptides or nucleic acids, which is preferably isotonic with the blood of the recipient.
  • This preparation may be formulated according to known methods using suitable dispersing or wetting agents and suspending agents.
  • the sterile injectable preparation also may be a sterile injectable solution or suspension in a non-toxic parenterally-acceptable diluent or solvent, for example, as a solution in 1,3-butane diol.
  • the acceptable vehicles and solvents that may be employed are water, Ringer's solution, and isotonic sodium chloride solution.
  • sterile, fixed oils are conventionally employed as a solvent or suspending medium.
  • any bland fixed oil may be employed including synthetic mono-or di-glycerides.
  • fatty acids such as oleic acid may be used in the preparation of injectables.
  • Carrier formulation suitable for oral, subcutaneous, intravenous, intramuscular, etc. administrations can be found in Remington 's Pharmaceutical Sciences, Mack Publishing Co., Easton, PA.
  • Example 1 SEREX screening of breast gastric and prostate cancer cells
  • mRNA was removed by passing the sample over an oligo-dT cellulose column.
  • the cDNA libraries were then constructed by taking 5 ⁇ g of mRNA, using standard methodologies to reverse transcribe the material.
  • Breast cancer libraries were prepared from two different breast cancer patients, referred to as "MT” and “MK”.
  • Gastric cancer libraries were prepared from a gastric cancer patient, referred to as "YS”.
  • the cDNA was used to construct a lambda phage library, and 500 phages were plated onto XLl-Blue MRF E. coli, and incubated for eight hours at 37°C. A nitrocellulose membrane was then placed on the plate, followed by overnight incubation. The membrane was then washed, four times, with Tris buffered saline (TBS) which contained 0.05% Tween, and was then immersed in TBS containing 5% non-fat dried milk. After one hour, the membrane was incubated with conjugates of peroxidase-goat anti human IgG specific for Fc portions of human antibodies (1 :2000, diluted in TBS with 1% BSA). The incubation was carried out for one hour, at room temperature, and the membrane was then washed three times with TBS. Those clones which produced antibodies were visualized with 0.06%
  • the membranes were then incubated in 1:100 diluted patient serum, overnight, at 4°C.
  • the patient serum had been pretreated. Specifically, 5 ml samples were diluted to 10 ml with TBS containing 1% bovine serum albumin, and 0.02% Na 3 N.
  • the serum had been treated to remove antibodies to bacteriophage, by passing it through a 5 ml Sepharose column, to which a lysate of E. coli Y1090 had been attached, followed by passage over a second column which had E. coli lysate and lysate of E. coli infected with lambda bacteriophage.
  • the screening was carried out five times. The samples were then diluted to 50 ml, and kept at -80°C, until used as described herein.
  • the membrane was washed twice with TBS/0.05% Tween 20, and then once with TBS. A further incubation was carried out, using the protocols discussed supra, for the peroxidase labeled antibodies.
  • clones were then sequenced, using standard techniques. Following comparison of the sequences to information available in data banks, clones were resolved into known and unknown genes. Some clones corresponded to previously identified human proteins and nucleotide sequences, and other clones have not been identified in humans previously, although there were related molecules found in other species. Still other clones represent molecules for which no related sequences were found (most clones contained very short sections (e.g. 25 or fewer nucleotides) that corresponded to portions of unrelated sequences).
  • GenBank accession numbers representative of sequences having homology to the cancer associated antigen nucleotide sequences of the invention are presented in Table 1. All of the homologous sequences are accessible in publicly-available databases by reference to the sequences' accession numbers provided in Table 1.
  • nucleotide sequences of clones derived from breast cancer patients "MT” and “MK” are presented as SEQ ID NOs: 1-205.
  • Polypeptides encoded by open reading frames of the nucleic acid clones are presented as SEQ ID Nos: 594-829; the correspondence between nucleic acid molecules and encoded polypeptides is shown in Table 2.
  • nucleotide sequences of clones derived from gastric cancer patient "YS” are presented as SEQ ID NOs:206-352 (clones beginning with “YS”).
  • Polypeptides encoded by open reading frames of the YS nucleic acid clones are presented as SEQ ID Nos: 830- 1083; the correspondence between nucleic acid molecules and encoded polypeptides is shown in Table 2.
  • nucleotide sequences of clones derived from prostate cancer patient "ZH” are presented as SEQ ID NOs:353-593(clones beginning with "ZH”).
  • Polypeptides encoded by open reading frames of the ZH nucleic acid clones are presented as SEQ ID N ⁇ s.1084-1332; the correspondence between nucleic acid molecules and encoded polypeptides is shown in Table 2.
  • NM_006644.1 AF039695.1, AB003334.1, AB003333.1, D86956.1, D67017.1, D67016.1, Z47807.1, NM_013559.1,
  • NM_005716.1, AF089816.1, AF032120.1 AF089818.1, AF089817.1, AF104358.1 , AF061263.1, AL050318.12 > AC007678.3, AC012099.4, NM_004364.1, AC006019.2, AC007397.21 , AC007535.3, U51244.1, U34070.1, U94788.1, U92845.1, Z69303.1, Z95127.1, Z31375.1, X54156.1, X87248.1, Y11525.1, AP000559.1. M93344.1, AW732338.1,
  • AK001824.1 A 001625.1, AB020657.1 , AK000931.1, AL137640.1, NM_016389.1, AF161553.1, AK001273.1 , NM_006469.1, AJ012449.1, AL031674.1, AC006928.15, AC006581.16, AC007436.1, AL049861.18, AC009303.2, AE003772.1, AC004843.1, AF003141.1, U88180.1, AL034350.2, AP000606.1, AC006068.3, AC006031.2, AC006996.2, AC013417.4, AC005319.1, AC003050.1, AJ009736.1, AC002065.1, Z69383.1, L14324.1 , AP000185.1, AP000283.1, AP000109.1, AI887429.1, Z42725.1, AA486796.1 , AI697765.1, AI300924.1, W31762.1, AA5
  • NM_003263.1 U88540.1, AL161557.2, AL009028.1, D13637.1, AL021635.1, AI734450.1, AW865983.1, AW531012.1, AW405405.1, AW148645.1, AI583168.1, AI290663.1, AA451993.1 , AA302993.1, AA297912.1, AA288614.1 , AA178091.1 , R78273.1, AW816433.1, AW816426.1, AW290918.1, AL133903.1, AV221162.1, AI504039.1, AI403713.1, AI238618.1, H23080.1 , AL356055.1, AC019071.3, AC061993.2, AC06891 1.1, AC025594.3, AC009546.3, AC010537.2, AC010687.2, AC010090.3, AC004229.1, AL354956.1, AL162405.2, AP001098.2,
  • AI640340.1 AA129330, H66266, AA817737, AA841970, E02685, 146903, E02810, A70722.1, A58497.1, A58525.1, A58521.1 , A58526.1, AR009500, A58523.1 , A70697.1, A58522.1, A58498.1, A58524.1 , 136936, AR013983, E12486, A68194.1, 150036, 113539, 150038, E12631, A63583.1, A39440.1 SEQ ID NO:20
  • AI609942.1 AAl 94969, AA009861, AA236889, AI022130, AA782106, T25462, AI084529, AA888853, N92587, R76998, AI221007, AI362557, AI285412, AI274861, AI264779, AI309998, AI636254.1 , AA962495, AI334147, AA706222, AA482724, N75832, AI421045.1, AI349116, AI376079, AI372898, AA587812, AI147618, AI096659, AI176212, AA801413, AA891042, AI029315, AA998967, AI232767, AI484819.1, AAl 16210, N98132, M75842, U38033, AI059570, AI059076, AU060339.1, T44877, E01546, A51764.1, A15353.1, A15354.1, 132307
  • AF028824, AF089816, L38482, AEOOl 104 AL033502, AC005757, U34830, AC004076, Zl 1490, AJ222796, AL022069, Z75543, AC006056.2, AC006508, AA285636, AA711082, W64914, W20880, AA172932, W09810, AA793773, W62886, AV026607.1, W18328, AA734581 , W53794, AA674963, AA175523, AA222652, AA286301, AA067058, AA727901, AA692352, AA608460, AI429553, AA216860, AA163431, W97171 , AI286788, AA450721, AA273318, AA267167, AA203863, W98132, AA733321, W61471 , W10683, AV042841.2, AI
  • AI044039 AI010110, AA751823, AR020909, AR003505, 174786, 116884, A67424.1, 109371, 159642, 155948, 176960, A42329.1, 145974, AR007159, 181226, AR007160, A52294.1, A62731.1, A47886.1, 117291, A12032.1, 108101, 108711, A65971.1, 138533, E12183, 119138, 122241, 173182, 128360, 122254, AR014241, 140899, 196182, A51135.1, AR008154, 140904, A51133.1, 141409, 134189, 108667, A62791.1, 173181, A62929.1, A47885.1, A28928.1, 125678, AR016035, 140908, 193602, 131750, E03829, 107993, 171461, A58884.1, E03350
  • AI617214.1 AA933363, AI616967.1, AA140828, AA660165, T18197, AI616808.1, AA933116, AI616416.1, AU065197.1, H34782, AA202074, AI171924, C28274, 117659, A27635.1, A04374.1, A29286.1, A71440.1, Al 1323.1, 183451, 183450, E12434, AR018093, AR018092, 175052, 105558, AR013726, A37287.1, 124703 SEQ ID NO:82
  • AA418204 HI 1780, AA906203, R13493, AA626308, R21616, AA627829, H67699, N72268, AA483210, AA705542, AA836379, AA399099, T06701, H99959, AA886062, AI498087.1, AI129945, R22315, N78414, AAl 13241, AI124535, H58271, AI643503.1, AA445695, AA673655, AA104978, AV034590.1, AI551985.1, AA142747, AI046551, AI020135, AI603873.1, AV035454.1, AA560196, AV037887.1, AV034119.1, AA522204, AV034487.1, AI594423.1, AI467549, AA615061, AA536264, AA391903, AA536375, AI545190, AI394892
  • NM_006644.1 AB003333.1, AF039695.1, AB003334.1, D86956.1, NM H3559.1, D67017.1, D67016.1, L40406.1,
  • AI341168.1 All 15351.1, C56104.1, C55163.1, C54236.1, C54007.1, D64277.1, T26732.1, D33807.1, AL137142.8, AC008689.4, AC010785.3, AC016715.2, ACOl 1743.3, AF129408.1, AC025243.3, AC027399.2, AC026927.2, AC012569.3, AC005506.6, AC009039.5, AC007337.2, AC008361.7, AC021326.1, AC014468.1, AF176680.1, AP001895.1, AP001563.1, AC055800.2, AC027502.3, AC044830.2, AC034128.2, AC008155.6, AC016926.4, AC027359.2, AC027002.2, AC027057.2, AC026650.3, AC020991.3, AC009925.3, AC018954.4, AC024681.2, AC016306.3, AC016997.4, AC019032.3, AC
  • NMJJ06644.1 AF039695.1, AB003334.1, AB003333.1, D86956.1, D67017.1, D67016.1, NM_013559.1, L40406.1, Z47807.1, AB005282.1, AB005281.1, AC005215.1, AL163279.2, AF193508.1, AC006080.1, AC009223.2, AF016672.2, U22892.1, AL161539.2, Z98981.2, X04465.1, Z92838.1, Z83109.1, AL035258.10, AB042297.1, Z97336.1, L08612.1, X01647.1, AI658961.1, AW571648.1, AW474070.1, AW572452.1, AW608075.1, AW385582.1, AW470142.1, A W316651.1 , AA232636.1 , AAl 66806.1 , AI751852.1 , AW771160.1 , AW
  • NM_004120.2 M55543.1, NM_002053.1, M55542.1, AK001823.1 , NM_010259.1, M63961.1, M55544.1, M80367.1, NM_010260.1, AF109168.1, AF077007.1, AJ007970.1, U44731.1, NM_008620.1, M81128.1, AC0061 12.2, X77129.1 , Z95388.1, Z78546.1, AE003472.1, AC004969.1, AC005053.1, AC005061.2, AF085699.1, AC007980.1, AC005557.1, AL109935.39, AL133283.9, AL008639.15, X921 12.1, ALl 17265.1, AB015429.1, AB020867.1, AF257304.1, AF257303.1, AE003459.1, NM_013134.1, AC007177.1, AC004798.1, AC003111.1,
  • NM_005134.1 AF 11 1106.1 , AC007736.3, AC008168.3, NM_013658.1 , AC005324.1 , X85991.1, AC004539.1 , NM_009134.1 , AC006287.1, AF075627.1 , ALl 22020.3, U58743.1, Y09108.1 , AC009486.3, AE003769.1, AC004888.1 , AC005013.1, AC007463.3, AC008067.3, AF189157.1, AE001980.1 , AC009888.1, AC005549.1, AL008733.10, Z68760.2, L46672.1, X94768.1, AP001278.1, AP000816.1, M2441 1.1, Z99105.1, AB006424.1, AW673704.1, AW371829.1 , AW382321.1, AW371827.1, AI081867.1 ) AW382320.1, AW38
  • NM_014731.1 ABOl 1124.1, AF123659.1, AF123658.1, AF123657.1, AF123656.1 , AF123655.1, AF123653.1, AL133215.16, AE0035O6.1 , NM_003980.1, AJ242502.1, AJ242501.1, AL023284.1, X73882.1, AF130782.1, AF190465.1 , AC006544.19, AC005033.1, AC003065.1, AC006985.2, U84269.1, U84268.1, AC003047.1 , AL031295.1, AE001862.1, U51197.1, AC004231.1, AP000279.1, AB004043.1, AB004042.1 , AB002339.1, AW416906.1, D56085.1, AW263065.1, AJ281091.1, AI911142.1, AI501468.1, W45377.1, AW530214.1, AW140903.1, AA819761.1,
  • AF086824.1 U39904.1, AF039218.1, AF070066.1, AC004811.2, AC002563.1, NM H5239.1, AK00I544.1, AC007023.3, AC007078.3, AC000039.3, AC006480.3, AC005488.2, AC005088.2, AF030453.1, ALl 21823.12, ALl 61571.2,
  • AA918819.1 T58078.1 , T58198.1 , AV349661.1, AV349644.1 , AV350717.1 , AV328677.1 , AW070252.1 , AW775904.1 , AW792828.1, AW274009.1, AW193700.1, AL121308.1, AW023476.1, AI910455.1 , AI765240.1, AI567672.1, AI376609.1, AI351633.1 , AI291783.1, AI291446.1, AA652658.1, AA570928.1, AA496039.1, H93102.1, R86033.1, R77622.1, R68550.1, AW774292.1, AW413948.1, AW155190.1, AW029172.1, AW009281.1 , AU069485.1, AU03001 1.1 , AI182684.1, AI122141.1, AI096187.1, AA839637.1, AA76
  • AE003618.1, AC007504.3 AB007651.1, AE003764.1, AE003738.1, AF165124.1, AL163258.2, AL078581.11, AL031259.1, Z81455.2, Z82900.1, L77246.I, AP001713.1, AP000178.1, AP000033.1, AB025604.1, AP000266.1, AP000102.1, Z99115.1, M15318.1, Z30211.1, AC012082.6, AC004521.2, AC024750.1, AL121716.16, AL10980I .13, AL008723.8, AL021182.1, ABO 18107.1 , AB005246.1 , AI052691.1, AI346408.1 , AW304965.1 , AWl 90867.1 , AI709369.1 , AWl 92823.1 , AI434577.1 , AI818211.1, AW264130.1.
  • AI334964.1 AI669755.1, N95392.1, AW005947.1 , AI982567.1 , AI144435.1, AA171398.1, AA788576.1, AW815621.1, F33435.1, AI631440.1, AA101255.1, AA676341.1, AA669918.1, AW815443.1, AA169326.1, AW391454.1, AW815833.1, AA101351.1, U69195.1, AA908462.1, AW815622.1, AW391447.1, AW815635.1, AW801962.1, AW249892.1, AA126685.1, AA044415.1, AW815508.1, AW815506.1, AW815512.1, AW609613.1, AA678797.1, AW462450.1, AW381515.1, AW474060.1, AW381537.1, AA156824.1, AW379059.1, AW371260.1, AI720
  • AC032001.2 AF252831.1, AF252830.1, AF202031.1, AF189745.1, AC027473.2, AL354869.1, AL160258.3, AC020550.3, AF260011.1, AC008821.4, AC008840.3, AC008511.4, AC009077.5, AC016517.4, AP001561.1, AP000641.1, AL121980.6, AC010746.3, AC018953.5, AC007521.11, AC017670.1, AC023505.8, AC009800.6, AC024321.3, AC053499.2, AC009702.4, AC027301.3, AC007716.2, AC024986.2, AC006440.8, AC013618.3, AC026185.1, AC018811.3, AC018494.3, AC013802.2, AL138997.6, AL158054.5, AL139821.2, AL138683.2, AC068767.2, AC068639.3, AC068036.3, AC044841.2
  • AW32361 1.1, AI653280.1, AI217226.1, AI208802.1, AI028745.1 , AIO 18748.1, AA815401.1, AA412669.1, AA399269.1 , AW742226.1, AA103723.1, AA030780.1, AW743307.1 , AW229796.1 , AA066905.1, AW012459.1, AA575384.1, AW478977.1, AA467514.1, AAl 15569.1, W89322.1, AA027130.1, AA690248.1 , AI891994.1, AI891993.1, AI789433.1, AI303965.1, AA717411.1, AA277873.1, AI509051.1, AI891995.1, AI154739.1, AA675395.1, AI564314.1, AA980640.1, AI608378.1, W78509.1, AA289292.1, AA813227.1, AI12
  • AW469194.1 AW072040.1, AI801767.1, AA129398.1, AA129437.1, N47701.1, AW055203.1 , AA204842.1, AA403256.1, AW162590.1, AW873160.1, N47715.1, AA428207.1, AI802539.1 , AW474265.1, AW517489.1, AA155636.1, AA187844.1 , AI708178.1, AI298177.1, AA084865.1 , AW196881.1, AI802262.1, AA223606.1, AA188417.1, AW182589.1, AW601976.1, AI125376.1, AA983384.1, AI669267.1, AA047175.1, AI369594.1, AA640599.1, AA629829.1 , AA506517.1, AA426576.1, AI034453.1 , AI927125.1, AI198409.1, AA08819
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Abstract

Des antigènes associés au cancer ont été identifiés par le criblage d'anticorps autologues de banques d'acides nucléiques exprimés dans des cellules cancéreuses du sein, de la prostate et de l'estomac, au moyen du sérum immun de patients atteints d'un cancer. L'invention concerne des acides nucléiques et des polypeptides codés qui sont des antigènes associés au cancer exprimés chez des patients atteints d'un cancer. Plus spécialement, l'invention concerne, entre autres, des molécules isolées d'acide nucléique, des vecteurs d'expression renfermant ces molécules et des cellules hôtes dans lesquelles on a transfecté ces molécules. La présente invention concerne également des protéines et des peptides isolés, des anticorps de ces derniers, ainsi que des lymphocytes T cytotoxiques reconnaissant les protéines et les peptides. L'invention concerne en outre des fragments des éléments précités, dont des fragments fonctionnels et des variantes, ainsi que des kits contenant lesdites molécules. Les molécules de la présente invention peuvent être utilisées à des fins de diagnostic, de surveillance, de recherche ou de traitement des conditions caractérisées par l'expression d'un ou plusieurs antigènes associés au cancer.
EP00932804A 1999-05-28 2000-05-26 Antigenes associes au cancer du sein, de la prostate et de l'estomac et leur utilisation Withdrawn EP1259812A2 (fr)

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US13652699P 1999-05-28 1999-05-28
US136526P 1999-05-28
US15345499P 1999-09-10 1999-09-10
US153454P 1999-09-10
PCT/US2000/014749 WO2000073801A2 (fr) 1999-05-28 2000-05-26 Antigenes associes au cancer du sein, de la prostate et de l'estomac et leur utilisation

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