Methods of diagnosis of cancer, compositions and methods of screening for modulators of cancer

• US 20040219579A1
• Filed: 02/19/2004
• Published: 11/04/2004
• Est. Priority Date: 02/19/2003
• Status: Abandoned Application

• Current Assignee: Protein Design Labs, Inc. (PDL BioPharma, Inc.)
• Original Assignee: Protein Design Labs, Inc. (PDL BioPharma, Inc.)
• Inventors: Wilson, Keith E., Zlotnik, Albert, Gish, Kurt C., Aziz, Natasha
• Application Number:
  US10/783,528
• Publication Number:
  US 20040219579A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2600/106 Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
• CPC Class Codes: C12Q 2600/136 Screening for pharmacological compounds
• CPC Class Codes: G01N 33/574 for cancer
• CPC Class Codes: Y02A 90/10 Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation

Abstract

Described herein are genes whose expression are up-regulated or down-regulated in specific cancers or other diseases, or are otherwise regulated in disease. Related methods and compositions that can be used for diagnosis, prognosis, and treatment of those medical conditions are disclosed. Also described herein are methods that can be used to identify modulators of these selected conditions.

Claims

1. A method for detecting a pathological cell in a patient, said method comprising detecting in a biological sample from said patient a nucleic acid or polypeptide comprising a sequence at least 80% identical to a sequence selected from SEQ ID NOs:

1-116.

2. The method of claim 1, wherein said pathological cell has a pathology selected from those listed Table 1.

3. The method of claim 1, wherein said biological sample is tissue from an organ which is affected by a pathology listed in Table 1.

4. The method of claim 1, wherein said nucleic acids are mRNA.

5. The method of claim 1, further comprising a step of amplifying nucleic acids.

6. The method of claim 1, wherein said nucleic acid comprises a sequence selected from SEQ ID NOs:

1-58.

7. The method of claim 1, wherein said polypeptide comprises a sequence selected from SEQ ID NOs:

59-116.

8. The method of claim 1, wherein said detecting comprises using a biochip comprising a nucleic acid at least 80% identical to SEQ ID NOs:

1-58.

9. The method of claim 1, wherein said patient is undergoing a therapeutic regimen to treat a pathology selected from those listed Table 1.

10. The method of claim 1, wherein said patient is suspected of having a pathology selected from those listed Table 1.

11. An isolated nucleic acid molecule comprising a sequence selected from SEQ ID NOs:

1-58.

12. The nucleic acid molecule of claim 11, wherein the nucleic acid is labeled.

13. An expression vector comprising the nucleic acid of claim 11.

14. A host cell comprising the expression vector of claim 13.

15. An isolated nucleic acid encoding a polypeptide sequence selected from SEQ ID NOs:

59-116.

16. An isolated polypeptide encoded by a sequence selected from SEQ ID NOs:

1-58.

17. An antibody that specifically binds a polypeptide of claim 16.

18. The antibody of claim 17, wherein the antibody is a humanized antibody.

19. The antibody of claim 17, wherein the antibody is an antibody fragment.

20. The antibody of claim 17, wherein the antibody is conjugated to an effector component.

21. The antibody of claim 17, wherein the antibody is conjugated to a detectable label or a cytotoxic chemical.

22. A method for specifically targeting a compound to a pathological cell in a patient, said method comprising administering to said patient an antibody of claim 17, wherein said antibody is conjugated to the compound.

23. A method for detecting a pathological cell in a patient, said method comprising contacting a biological sample with an antibody of claim 17.

24. The method of claim 22, wherein said antibody is conjugated to an effector component or a fluorescent label.

25. The method of claim 22, wherein said said biological sample is a blood, serum, urine, or stool sample.

26. A method for identifying a compound that modulates a pathology-associated polypeptide, said method comprising:

a) contacting said compound with a pathology-associated polypeptide, said polypeptide encoded by a polynucleotide that selectively hybridizes to a sequence at least 80% identical to SEQ ID NOs;

1-58; and

b) determining the effect of said compound upon the function of said polypeptide.

27. A screening assay comprising:

a) administering a test compound to a cell from a mammal exhibiting a pathology selected from those listed in Table 1;

b) administering a test compound to a cell from a mammal not exhibiting said pathology;

c) comparing the expression level of a polynucleotide of the cell comprising a sequence at least 80% identical to SEQ ID NOs;

1-58 with the expression level of said polynucleotide of a control cell;

whereby modulation of the expression level of the polynucleotide of the cell indicates that the test compound is a drug candidate.