Methods and compositions for diagnosis, monitoring and development of therapeutics for treatment of atherosclerotic disease

• US 20070092886A1
• Filed: 03/22/2006
• Published: 04/26/2007
• Est. Priority Date: 03/22/2005
• Status: Abandoned Application

• Current Assignee: Board of Trustees of the Leland Stanford Junior University (Stanford University)
• Original Assignee: Board of Trustees of the Leland Stanford Junior University (Stanford University)
• Inventors: Quertermous, Thomas, Tabibiazar, Raymond
• Application Number:
  US11/387,484
• Publication Number:
  US 20070092886A1
• Time in Patent Office: Days
• US Class Current: 435/6.11
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 2600/112 Disease subtyping, staging or classification
• CPC Class Codes: C12Q 2600/136 Screening for pharmacological compounds
• CPC Class Codes: C12Q 2600/158 Expression markers

Abstract

Polynucleotide sequences are provided that correspond to genes that are differentially expressed in atherosclerotic disease conditions. Methods for using these sequences to detect gene expression and/or for transcriptional profiling in mammals are also provided. The polynucleotide sequences of the invention may be used, for example, to diagnose atherosclerotic disease, to monitor extent of progression or efficacy of treatment or to assess prognosis of atherosclerotic disease, and/or to identify compounds effective to treat an atherosclerotic disease condition.

Claims

1. A system for detecting gene expression, comprising at least two isolated polynucleotide molecules, wherein each of said at least two isolated polynucleotide molecules detects an expressed gene product from a gene that is differentially expressed in atherosclerotic disease in a mammal, wherein said gene is selected from the group of genes corresponding to the polynucleotide sequences depicted in SEQ ID NOs:

1-927.

3. A system for detecting gene expression according to claim 1, wherein at least one of said isolated polynucleotide molecules detects a expressed gene product from a gene selected from the group of genes corresponding to the polynucleotide sequences depicted in SEQ ID NOs:

8, 14, 26, 32, 50, 64, 83, 99, 142, 154, 159, 161, 177, 181, 200, 390, 430, 434, 439, 440, 476, 491, 508, 530, 534, 565, 567, 572, 624, 647, 657, 690, 733, 745, 806, 824, 886, 882, 901, 905, 913, and 927.

4. A system according to claim 1, wherein the isolated polynucleotide molecules are immobilized on an array.

5. A system according to claim 4, wherein the array is selected from the group consisting of a chip array, a plate array, a bead array, a pin array, a membrane array, a solid surface array, a liquid array, an oligonucleotide array, polynucleotide array or a cDNA array, a microtiter plate, a membrane, and a chip.

6. A system according to claim 1, wherein the isolated polynucleotides are selected from the group consisting of synthetic DNA, genomic DNA, cDNA, RNA, or PNA.

7. A kit comprising the system of claim 1.

8. A kit comprising the system of claim 4.

2. A system for detecting gene expression, comprising at least two isolated polynucleotide sequences, wherein each of said at least two isolated polynucleotide molecules detects an expressed gene product from a gene that is differentially expressed in atherosclerotic disease in a mammal, wherein said gene is selected from the group of genes corresponding to the polynucleotide sequences depicted in SEQ ID NOs:

8, 14, 26, 32, 50, 64, 83, 99, 142, 154, 159, 161, 177, 181, 200, 390, 430, 434, 439, 440, 476, 491, 508, 530, 534, 565, 567, 572, 624, 647, 657, 690, 733, 745, 806, 824, 886, 882, 901, 905, 913, and 927.

9. A method of monitoring atherosclerotic disease in an individual, comprising detecting the expression level of at least one gene selected from the group of genes corresponding to the polynucleotide sequences depicted in SEQ ID NOs:

1-927.

10. The method of claim 9, wherein said at least one gene is selected from the group of genes corresponding to the polynucleotide sequences depicted in SEQ ID NOs:

8, 14, 26, 32, 50, 64, 83, 99, 142, 154, 159, 161, 177, 181, 200, 390, 430, 434, 439, 440, 476, 491, 508, 530, 534, 565, 567, 572, 624, 647, 657, 690, 733, 745, 806, 824, 886, 882, 901, 905, 913, and 927.

11. The method of claim 9, comprising detecting the expression level of at least two of said genes.

12. The method of claim 11, wherein at least one of said at least two genes is selected from the group of genes corresponding to the polynucleotide sequences depicted in SEQ ID NOs:

8, 14, 26, 32, 50, 64, 83, 99, 142, 154, 159, 161, 177, 181, 200, 390, 430, 434, 439, 440, 476, 491, 508, 530, 534, 565, 567, 572, 624, 647, 657, 690, 733, 745, 806, 824, 886, 882, 901, 905, 913, and 927.

13. The method of claim 9, comprising detecting the expression level of at least ten of said genes.

14. The method of claim 13, wherein at least one of said at least ten genes is selected from the group of genes corresponding to the polynucleotide sequences depicted in SEQ ID NOs:

8, 14, 26, 32, 50, 64, 83, 99, 142, 154, 159, 161, 177, 181, 200, 390, 430, 434, 439, 440, 476, 491, 508, 530, 534, 565, 567, 572, 624, 647, 657, 690, 733, 745, 806, 824, 886, 882, 901, 905, 913, and 927.

15. The method of claim 9, comprising detecting the expression level of at least one hundred of said genes.

16. The method of claim 15, wherein at least one of said at least one hundred genes is selected from the group of genes corresponding to the polynucleotide sequences depicted in SEQ ID NOs:

8, 14, 26, 32, 50, 64, 83, 99, 142, 154, 159, 161, 177, 181, 200, 390, 430, 434, 439, 440, 476, 491, 508, 530, 534, 565, 567, 572, 624, 647, 657, 690, 733, 745, 806, 824, 886, 882, 901, 905, 913, and 927.

17. The method of claim 9, wherein said atherosclerotic disease comprises coronary artery disease.

18. The method of claim 9, wherein said atherosclerotic disease comprises carotid atherosclerosis.

19. The method of claim 9, wherein said atherosclerotic disease comprises peripheral vascular disease.

20. The method of claim 9, wherein said expression level is detected by measuring the RNA level expressed by said one or more genes.

21. The method of claim 20, comprising isolating RNA from said individual prior to detecting the RNA expression level.

22. The method of claim 20, wherein said detection of said RNA expression level comprises amplifying RNA from said individual.

23. The method of claim 22, wherein amplification of RNA comprises polymerase chain reaction (PCR).

24. The method of claim 20, wherein detection of said RNA expression level comprises hybridization of RNA from said individual to a polynucleotide corresponding to said at least one gene selected from the group of genes corresponding to the polynucleotide sequences depicted in SEQ ID NOs:

1-927.

25. The method of claim 20, wherein said expression level is detected by measuring the protein level expressed by said one or more genes.

26. The method of claim 9, further comprising selecting an appropriate therapy for said atherosclerotic disease.

27. The method of claim 9, comprising detecting the expression of said at least one gene in serum from said individual.

28. The method of claim 20, comprising measuring said RNA level in serum from said individual.

29. The method of claim 25, comprising measuring said protein level in serum from said individual.

30. A method of monitoring atherosclerotic disease in an individual, comprising detecting RNA expressed from at least one gene selected from the group of genes corresponding to at least one polynucleotide sequence depicted in SEQ ID NOs:

1-927.

31. The method of claim 30, wherein said at least one gene is selected from the group of genes corresponding to the polynucleotide sequences depicted in SEQ ID NOs:

8, 14, 26, 32, 50, 64, 83, 99, 142, 154, 159, 161, 177, 181, 200, 390, 430, 434, 439, 440, 476, 491, 508, 530, 534, 565, 567, 572, 624, 647, 657, 690, 733, 745, 806, 824, 886, 882, 901, 905, 913, and 927.

32. The method of claim 30, comprising measuring said RNA in serum from said individual.

33. A method of monitoring atherosclerotic disease in an individual, comprising detecting protein expressed from at least one gene selected from the group of genes corresponding to at least one polynucleotide sequence depicted in SEQ ID NOs:

1-927.

34. The method of claim 33, wherein said at least one gene is selected from the group of genes corresponding to the polynucleotide sequences depicted in SEQ ID NOs:

8, 14, 26, 32, 50, 64, 83, 99, 142, 154, 159, 161, 177, 181, 200, 390, 430, 434, 439, 440, 476, 491, 508, 530, 534, 565, 567, 572, 624, 647, 657, 690, 733, 745, 806, 824, 886, 882, 901, 905, 913, and 927.

35. The method of claim 33, comprising measuring said protein in serum from said individual.