WO2005005647A2 - Compositions, splice variants and methods relating to ovarian specific genes and proteins - Google Patents

Compositions, splice variants and methods relating to ovarian specific genes and proteins Download PDF

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Publication number
WO2005005647A2
WO2005005647A2 PCT/US2004/021227 US2004021227W WO2005005647A2 WO 2005005647 A2 WO2005005647 A2 WO 2005005647A2 US 2004021227 W US2004021227 W US 2004021227W WO 2005005647 A2 WO2005005647 A2 WO 2005005647A2
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WO
WIPO (PCT)
Prior art keywords
nucleic acid
acid molecule
seq
polypeptide
sequence
Prior art date
Application number
PCT/US2004/021227
Other languages
French (fr)
Other versions
WO2005005647A3 (en
Inventor
Steffan F. Vartanian
Roberto A. Macina
Original Assignee
Diadexus, Inc.
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Publication date
Application filed by Diadexus, Inc. filed Critical Diadexus, Inc.
Publication of WO2005005647A2 publication Critical patent/WO2005005647A2/en
Publication of WO2005005647A3 publication Critical patent/WO2005005647A3/en

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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
    • 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
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers

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  • Chemical & Material Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Organic Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Zoology (AREA)
  • Genetics & Genomics (AREA)
  • General Health & Medical Sciences (AREA)
  • Immunology (AREA)
  • Molecular Biology (AREA)
  • Biochemistry (AREA)
  • Biophysics (AREA)
  • Analytical Chemistry (AREA)
  • Engineering & Computer Science (AREA)
  • Toxicology (AREA)
  • Pathology (AREA)
  • Gastroenterology & Hepatology (AREA)
  • Wood Science & Technology (AREA)
  • Medicinal Chemistry (AREA)
  • Microbiology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • Biotechnology (AREA)
  • Physics & Mathematics (AREA)
  • Oncology (AREA)
  • Hospice & Palliative Care (AREA)
  • Peptides Or Proteins (AREA)
  • Medicines That Contain Protein Lipid Enzymes And Other Medicines (AREA)

Abstract

The present invention relates to newly identified nucleic acid molecules and polypeptides present in normal and neoplastic ovarian cells, including fragments, variants and derivatives of the nucleic acids and polypeptides. The present invention also relates to antibodies to the polypeptides of the invention, as well as agonists and antagonists of the polypeptides of the invention. The invention also relates to compositions containing the nucleic acid molecules, polypeptides, antibodies, agonists and antagonists of the invention and methods for the use of these compositions. These uses include identifying, diagnosing, monitoring, staging, imaging and treating ovarian cancer and non-cancerous disease states in ovarian, identifying ovarian tissue, monitoring and identifying and/or designing agonists and antagonists of polypeptides of the invention. The uses also include gene therapy, production of transgenic animals and cells, and production of engineered ovarian tissue for treatment and research.

Claims

We claim:
1. An isolated nucleic acid molecule comprising: (a) a nucleic acid molecule comprising a nucleic acid sequence that encodes an amino acid sequence of SEQ TD NO: 8, 9, 10, 11, 13 or 14; (b) a nucleic acid molecule comprising a nucleic acid sequence of SEQ ID NO: 2, 3, 5 or 6; (c) a nucleic acid molecule that selectively hybridizes to the nucleic acid molecule of (a) or (b); or (d) a nucleic acid molecule having at least 95% sequence identity to the nucleic acid molecule of (a) or (b).
2. The nucleic acid molecule according to claim 1, wherein the nucleic acid molecule is a cDNA.
3. The nucleic acid molecule according to claim 1 , wherein the nucleic acid molecule is genomic DNA.
4. The nucleic acid molecule according to claim 1, wherein the nucleic acid molecule is an RNA.
5. The nucleic acid molecule according to claim 1, wherein the nucleic acid molecule is a mammalian nucleic acid molecule.
6. The nucleic acid molecule according to claim 5, wherein the nucleic acid molecule is a human nucleic acid molecule.
7. A method for determining the presence of a ovarian specific nucleic acid (OSNA) in a sample, comprising the steps of: (a) contacting the sample with the nucleic acid molecule of SEQ ID NO: 2, 3, 5 or 6 under conditions in which the nucleic acid molecule will selectively hybridize to a ovarian specific nucleic acid; and (b) detecting hybridization of the nucleic acid molecule to a OSNA in the sample, wherein the detection of the hybridization indicates the presence of a OSNA in the sample.
8. A vector comprising the nucleic acid molecule of claim 1.
9. A host cell comprising the vector according to claim 8.
10. A method for producing a polypeptide encoded by the nucleic acid molecule according to claim 1, comprising the steps of: (a) providing a host cell comprising the nucleic acid molecule operably linked to one or more expression control sequences, and (b) incubating the host cell under conditions in which the polypeptide is produced.
11. A polypeptide encoded by the nucleic acid molecule according to claim 1.
12. An isolated polypeptide selected from the group consisting of: (a) a polypeptide comprising an amino acid sequence with at least 95% sequence identity to of SEQ ID NO: 8, 9, 10, 11, 13 or 14; or (b) a polypeptide comprising an amino acid sequence encoded by a nucleic acid molecule having at least 95% sequence identity to a nucleic acid molecule comprising a nucleic acid sequence of SEQ ID NO: 2, 3, 5 or 6.
13. An antibody or fragment thereof that specifically binds to : (a) a polypeptide comprising an amino acid sequence with at least 95% sequence identity to of SEQ ID NO: 8, 9, 10, 11, 13 or 14; or (b) a polypeptide comprising an amino acid sequence encoded by a nucleic acid molecule having at least 95% sequence identity to a nucleic acid molecule comprising a nucleic acid sequence of SEQ ID NO: 2, 3, 5 or 6.
14. A method for determining the presence of a ovarian specific protein in a sample, comprising the steps of: (a) contacting the sample with a suitable reagent under conditions in which the reagent will selectively interact with the ovarian specific protein comprising an amino acid sequence with at least 95% sequence identity to of SEQ ID NO: 8, 9, 10, 11, 13 or 14; and (b) detecting the interaction of the reagent with a ovarian specific protein in the sample, wherein the detection of binding indicates the presence of a ovarian specific protein in the sample.
15. A method for diagnosing or monitoring the presence and metastases of ovarian cancer in a patient, comprising the steps of: (a) determining an amount of: (i) a nucleic acid molecule comprising a nucleic acid sequence that encodes an amino acid sequence of SEQ ID NO: 8, 9, 10, 11, 13 or 14; (ii) a nucleic acid molecule comprising a nucleic acid sequence of SEQ ID NO: 2, 3, 5 or 6; (iii) a nucleic acid molecule that selectively hybridizes to the nucleic acid molecule of (i) or (ii); (iv) a nucleic acid molecule having at least 95% sequence identity to the nucleic acid molecule of (i) or (ii); (v) a polypeptide comprising an amino acid sequence with at least 95% sequence identity to of SEQ ID NO: 8, 9, 10, 11, 13 or 14; or (vi) a polypeptide comprising an amino acid sequence encoded by a nucleic acid molecule having at least 95% sequence identity to a nucleic acid molecule comprising a nucleic acid sequence of SEQ ID NO: 2, 3, 5 or 6 and; (b) comparing the amount of the determined nucleic acid molecule or the polypeptide in the sample of the patient to the amount of the ovarian specific marker in a normal control; wherein a difference in the amount of the nucleic acid molecule or the polypeptide in the sample compared to the amount of the nucleic acid molecule or the polypeptide in the normal control is associated with the presence of ovarian cancer.
16. A kit for detecting a risk of cancer or presence of cancer in a patient, said kit comprising a means for determining the presence of: (a) a nucleic acid molecule comprising a nucleic acid sequence that encodes an amino acid sequence of SEQ ID NO: 8, 9, 10, 11, 13 or 14; (b) a nucleic acid molecule comprising a nucleic acid sequence of SEQ ID NO: 2, 3, 5 or 6; (c) a nucleic acid molecule that selectively hybridizes to the nucleic acid molecule of (a) or (b); or (d) a nucleic acid molecule having at least 95% sequence identity to the nucleic acid molecule of (a) or (b); or (e) a polypeptide comprising an amino acid sequence with at least 95% sequence identity to of SEQ TD NO: 8, 9, 10, 11, 13 or 14; or (f) a polypeptide comprising an amino acid sequence encoded by a nucleic acid molecule having at least 95% sequence identity to a nucleic acid molecule comprising a nucleic acid sequence of SEQ ID NO: 2, 3, 5 or 6.
17. A method of treating a patient with ovarian cancer, comprising the step of administering a composition consisting of: (a) a nucleic acid molecule comprising a nucleic acid sequence that encodes an amino acid sequence of SEQ ID NO: 8, 9, 10, 11, 13 or 14; (b) a nucleic acid molecule comprising a nucleic acid sequence of SEQ ID NO: 2, 3, 5 or 6; (c) a nucleic acid molecule that selectively hybridizes to the nucleic acid molecule of (a) or (b); (d) a nucleic acid molecule having at least 95% sequence identity to the nucleic acid molecule of (a) or (b); (e) a polypeptide comprising an amino acid sequence with at least 95% sequence identity to of SEQ ID NO: 8, 9, 10, 11, 13 or 14; or (f) a polypeptide comprising an amino acid sequence encoded by a nucleic acid molecule having at least 95% sequence identity to a nucleic acid molecule comprising a nucleic acid sequence of SEQ ID NO: 2, 3, 5 or 6; to a patient in need thereof, wherein said adminisfration induces an immune response against the ovarian cancer cell expressing the nucleic acid molecule or polypeptide.
18. A vaccine comprising the polypeptide or the nucleic acid encoding the polypeptide of claim 12.
PCT/US2004/021227 2003-06-30 2004-06-30 Compositions, splice variants and methods relating to ovarian specific genes and proteins WO2005005647A2 (en)

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US48444003P 2003-06-30 2003-06-30
US48450003P 2003-06-30 2003-06-30
US60/484,500 2003-06-30
US60/484,440 2003-06-30

Publications (2)

Publication Number Publication Date
WO2005005647A2 true WO2005005647A2 (en) 2005-01-20
WO2005005647A3 WO2005005647A3 (en) 2006-01-26

Family

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Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2004/021227 WO2005005647A2 (en) 2003-06-30 2004-06-30 Compositions, splice variants and methods relating to ovarian specific genes and proteins

Country Status (1)

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Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US8444975B2 (en) 2004-12-13 2013-05-21 Alethia Biotherapeutics Inc. Method for inhibiting bone resorption

Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20020042067A1 (en) * 2000-08-17 2002-04-11 David Mack Novel methods of diagnosing colorectal cancer, compositions, and methods of screening for colorectal cancer modulators

Patent Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20020042067A1 (en) * 2000-08-17 2002-04-11 David Mack Novel methods of diagnosing colorectal cancer, compositions, and methods of screening for colorectal cancer modulators

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US8444975B2 (en) 2004-12-13 2013-05-21 Alethia Biotherapeutics Inc. Method for inhibiting bone resorption

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Publication number Publication date
WO2005005647A3 (en) 2006-01-26

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