Process for identification of genes encoding proteins having cell proliferation-promoting activity

• US 20020019005A1
• Filed: 08/02/2001
• Published: 02/14/2002
• Est. Priority Date: 02/18/1999
• Status: Abandoned Application

• Current Assignee: Deltagen Proteomics Incorporated
• Original Assignee: Arcaris, Inc. (Deltagen Incorporated)
• Inventors: Kamb, Carl Alexander
• Application Number:
  US09/921,101
• Publication Number:
  US 20020019005A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12N 15/1086 Preparation or screening of expression libraries, e.g. reporter assays
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2565/20 Detection means characterised by being a gene reporter based analysis
• CPC Class Codes: G01N 33/574 for cancer

Abstract

The present invention is directed to selection systems for the identification of cell proliferation genes based on functional analysis. More specifically, the invention is directed to a process for the identification of a cell proliferation promoting activity, the isolation of genes involved in such cell proliferation promoting activity, and the use of the so identified genes for the diagnosis or treatment of a disease associated with excessive cell proliferation. The invention further is directed to the design and development of antibodies, peptides, nucleic acids, and other compounds which specifically interfere with the function of the identified gene and/or its gene product, and pharmaceutical compositions comprising such compounds, for the treatment of diseases associated with inappropriate or unregulated cell proliferation.

Claims

1. A process for identifying a cell proliferation gene comprising the steps of:

(a) selecting a growth proficient revertant cell from a plurality of cultured cells arrested for growth, said growth arrested cells transformed with a library comprising a plurality of nucleic acid sequence inserts, wherein at least one insert from the library encodes a perturbagen within said revertant cell that results in said reversion to growth proficiency; and

(b) identifying one or more genes or gene products in said revertant cell that cause said reversion to growth proficiency.

2. The process of claim 1, wherein the cell proliferation gene is selected from the group consisting of an oncogene, a dominant transforming gene, a tumor suppressor gene and a gene involved in the control of apoptosis.

3. The process of claim 1, wherein growth arrest of the cultured cells is caused by expression of a tumor suppressor gene or a dominant negative oncogene.

4. The process of claim 1, wherein growth arrest of said cultured cells is caused by the expression of a gene inducing apoptosis in said cells.

5. The process of claims 3 or 4, wherein said gene has been introduced on an expression plasmid under the control of a promoter.

6. The process of claim 5, wherein said gene is expressed under the control of an inducible promoter.

7. The process of claim 6, wherein the promoter is an IPTG inducible promoter.

8. The process of claim 3, wherein said gene is a dominant negative oncogene selected from the group consisting of cJUN, EGF-R, GRB2, RAF, A, RAS, SRC, and tyrosine kinase receptor mutants.

9. The process of claim 3, wherein said gene is a tumor suppressor gene selected from the group consisting of P16, P53, RB1, WT1, BRCA1, BRCA2, NF1, NF2, P15, P18, P19, P21, P27, P57 and VHL.

10. The process of claim 9, wherein the tumor suppressor gene is p16.

11. The process of claim 1, wherein the cultured cells are selected from the group consisting of cells derived from primary tumors, cells derived from metastatic tumors, primary cells, cells which have lost contact inhibition, immortalized primary cells, transformed primary cells, cells which may undergo apoptosis, and cell lines derived therefrom.

12. The process of claim 11, wherein the cultured cells express rb.

13. The process of claim 11, wherein the cultured cells are derived from a melanoma cell line.

14. The process of claim 13, wherein the melanoma cell line is HS294T.

15. The process of claim 1, wherein the perturbagen library is introduced into said cells using a retroviral vector.

16. The process of claim 1, further comprising the steps of:

(a) measuring differences in gene expression between said revertant cells and said growth arrested cultured cells to identify differentially expressed genes; and

(b) isolating genes identified in step (a) to identify a differentially expressed cell proliferation gene.

17. The process of claim 1, wherein the perturbagen is DNA encoding an RNA or polypeptide product which upon expression confers growth proficiency on said revertant cells.

18. The process of claim 1, further comprising the steps of isolating the perturbagen present in said revertant cell and identifying the sequence of said perturbagen.

19. The process of claim 1, wherein the perturbagen is DNA encoding a cell proliferation gene, a gene product thereof, or an active fragment of said gene or gene product.

20. The process of claim 1, further comprising the step of identifying at least one cell component affected by said perturbagen.

21. The process of claim 20, wherein said cell component is selected from the group consisting of a cell proliferation gene and a gene product thereof.

22. The process of claim 1, wherein the perturbagen is or encodes a dominantly active peptide sequence that disrupts the action of an endogenous gene in a growth control pathway.

23. The process of claim 22, wherein the endogenous gene is a tumor suppressor gene or a dominant-negative proto-oncogene.

24. The process of claim 22, wherein the perturbagen disrupts the action of a cellular tumor suppressor gene, or one or more downstream targets, said process further comprising:

(a) identifying said tumor suppressor gene; and

(b) isolating said tumor suppressor gene.

25. The process of claim 22, wherein the perturbagen disrupts the action of a cellular proto-oncogene, or one or more downstream targets, said process further comprising:

(a) identifying said cellular oncogene; and

(b) isolating said cellular oncogene.

26. A process for identifying a compound that inhibits cell proliferation comprising the steps of:

(a) incubating a revertant cell obtained by the process of claim 1 with one or more test compounds; and

(b) selecting from said test compounds a candidate compound that inhibits the growth of said revertant cell.

27. The process of claim 26, wherein the inhibition of growth in step (b) is determined by an assay that tests a physiological response selected from the group consisting of inhibition of foci formation, inhibition of cell growth, inhibition of DNA replication and inhibition of tumor formation.

28. A compound obtained by the process of claim 26 or 27.

29. A process for identifying a compound that inhibits cell proliferation comprising the steps of:

(a) exposing a polypeptide encoded by a cell proliferation gene obtained by the process of claim 16, 18, 24 or 25 to one or more test compounds; and

(b) selecting from said test compounds at least one candidate compound that inhibits a cell proliferative effect of said polypeptide.

30. The process of claim 29, wherein the compound that inhibits cell proliferation is selected from the group consisting of an inhibitor of enzymatic activity, inhibitor of binding of a substrate molecule, inhibitor of phosphorylation, inhibitor of protein/protein interactions, inhibitor of protein/DNA interactions, and an inhibitor of protein/RNA interactions.

31. A compound obtained by the process of claim 29 or 30.

32. A pharmaceutical composition comprising a therapeutically effective amount of a compound of claim 28.

33. A pharmaceutical composition comprising a therapeutically effective amount of a compound of claim 31.

34. A method for treating a disease associated with aberrant cell proliferation comprising the step of administering an effective amount of the pharmaceutical composition of claim 32 or 33.

35. The method according to claim 34, wherein the disease is selected from the group consisting of cancer, arteriosclerosis, psoriasis, rheumatoid arthritis and retenosis.

36. A method for identifying the expression in a tissue sample of a cell proliferation gene identified by the process of claim 1, 16, 18, 20, 24 or 25, comprising the steps of:

(a) exposing nucleic acid derived from mRNA of said tissue sample to a labeled oligonucleotide probe comprising a sequence complementary to a fragment of said cell proliferation gene; and

(b) identifying specific hybridization of said oligonucleotide probe with said nucleic acid.

37. An antibody against a cell proliferation gene or gene product obtained by the process of claim 16, 18, 20, 24 or 25.

38. A method for identifying the expression in a tissue sample of a cell proliferation gene identified by the process of claim 1, 16, 18, 20, 24 or 25, comprising the steps of:

(a) contacting a tissue sample from a patient with an antibody against said cell proliferation gene; and

(b) identifying a specific interaction between said antibody and said tissue sample.

39. A method for identifying an individual predisposed to cancer comprising the steps of:

(a) exposing nucleic acid derived from chromosomal DNA from said individual to a labeled oligonucleotide probe comprising a sequence complementary to a fragment of a cell proliferation gene, said cell proliferation gene identified according to the process of claim 1, 16, 18, 20, 24 or 25; and

(b) identifying specific hybridization of said probe with said nucleic acid.

40. A nucleic acid which encodes a cell proliferation gene, said nucleic acid isolated by the process of claim 16, 18, 20, 24 or 25.

41. A recombinant DNA molecule comprising nucleic acid sequences selected from the sequences which comprise the nucleic acid of claim 40.

42. An expression vector comprising nucleic acid sequences selected from the sequences which comprise the nucleic acid of claim 40.

43. A host cell comprising the recombinant DNA molecule of claim 41.

44. A host cell comprising the expression vector of claim 42.

45. A diagnostic kit comprising a nucleic acid which is complementary to the nucleic acid of claim 40.

46. A diagnostic kit comprising an antibody against a cell proliferation gene or gene product according to claim 37.