METHODS AND COMPOSITIONS FOR IDENTIFYING BIOMARKERS USEFUL IN DIAGNOSIS AND/OR TREATMENT OF BIOLOGICAL STATES

• US 20070092891A1
• Filed: 09/05/2006
• Published: 04/26/2007
• Est. Priority Date: 09/02/2005
• Status: Abandoned Application

• Current Assignee: University of Toledo
• Original Assignee: University of Toledo
• Inventors: Crawford, Erin, Willey, James, Mullins, D'Anna
• Application Number:
  US11/470,159
• Publication Number:
  US 20070092891A1
• Time in Patent Office: Days
• US Class Current: 435/6.12
• 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 2600/106 Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
• CPC Class Codes: C12Q 2600/112 Disease subtyping, staging or classification
• CPC Class Codes: C12Q 2600/16 Primer sets for multiplex assays
• CPC Class Codes: G01N 33/6842 Proteomic analysis of subsets of protein mixtures with reduced complexity, e.g. membrane proteins, phosphoproteins, organelle proteins
• 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

The present invention relates to methods and compositions for identifying biomarkers that indicate a biological state, in particular transcription factor biomarkers and genes that can be regulated by such transcription factor biomarkers. The invention also relates to identifying polymorphisms in such transcription factors and regulated genes indicative of the biological state. The biomarkers and polymorphisms identified find use in diagnostic and treatment approaches, e.g., some embodiments the invention provide methods and kits for detecting bronchogenic carcinoma and risks thereof.

Claims

1. A method of identifying a transcription factor biomarker that indicates a biological state, comprising:

assaying in a plurality of control samples expression levels of a transcription factor and of a first gene, said first gene being associated with said biological state;

assaying in a plurality of case samples expression levels of said transcription factor and of said first gene; and

deducing whether said expression levels of said transcription factor are correlated with said expression levels of said first gene in said control samples but not correlated in said case samples, thereby identifying a transcription factor biomarker for said biological state.

2. The method as recited in claim 1, wherein said first gene is regulated by said transcription factor in said control samples.

3. The method as recited in claim 1, further comprising assaying expression levels of one or more additional genes associated with said biological state.

4. The method as recited in claim 3, wherein said first gene and said one or more additional genes are regulated by said transcription factor in said control samples.

5. The method as recited in claim 1, wherein at least one of said expression levels is assayed by assaying abundance of an mRNA transcript.

6. The method as recited in claim 5, wherein assaying said mRNA transcript abundance comprises:

measuring a nucleic acid corresponding to said transcription factor in relation to a competitive template for said transcription factor;

co-measuring a nucleic acid corresponding to said first gene in relation to a competitive template for said first gene; and

obtaining a relation comparing the value for said transcription factor to the value for said first gene.

7. The method as recited in claim 6, wherein said competitive templates are provided in a standardized mixture.

8. The method as recited in claim 6, wherein assaying said mRNA transcript abundance comprises:

amplifying a nucleic acid corresponding to said transcription factor with a competitive template for said transcription factor;

co-amplifying a nucleic acid corresponding to said first gene with a competitive template for said first gene; and

obtaining a relation by comparing amplified products obtained from said co-amplifications.

9. The method as recited in claim 1, wherein at least one of said expression levels is assayed by assaying abundance of a protein.

10. The method as recited in claim 1, wherein about 10 case samples and about 10 control samples are used.

11. The method as recited in claim 1, wherein about 30 case samples and about 30 control samples are used.

12. The method as recited in claim 1, wherein about 50 case samples and about 50 control samples are used.

13. The method as recited in claim 1, wherein about 100 case samples and about 100 control samples are used.

14. The method as recited in claim 1, wherein said biological state is bronchogenic carcinoma or a risk thereof and said transcription factor is CEBPG.

15. The method as recited in claims 14, wherein said first gene is XRCC1, ERCC1, ERCC2, ERCC5, CAT, GSTZ1, mGST1, GSTP1, SOD1 or GPX1.

16. The method as recited in claim 1, wherein said biological state is bronchogenic carcinoma or risk thereof and said transcription factor is E2F1.

17. The method as recited in claims 16, wherein said first gene is ERCC5, GSTP1 or SOD1.

18. The method as recited in claim 1, wherein said biological state is COPD or risk thereof and said transcription factor is CEBPG.

19. The method as recited in claims 18, wherein said first gene is XRCC1, CAT, ERCC1, ERCC2, GSTZ1, mGST1, ERCC5, GSTP1, SOD1 or GPX1.

20. The method as recited in claim 1, wherein said biological state is COPD or risk thereof and said transcription factor is E2F1.

21. The method as recited in claims 20, wherein said first gene is ERCC5, GSTP1 or SOD1.

22. The method as recited in claim 1, further comprising making a diagnostic decision based on identifying said transcription factor biomarker.

23. The method as recited in claim 1, further comprising administering a therapeutic based on identifying said transcription factor biomarker.

44. The method as recited in claims 19 wherein said gene is ERCC5, GSTP1 or SOD1.

24. A method of identifying a biomarker that indicates a biological state, comprising:

assaying in a plurality of control samples expression levels of a gene and of a first transcription factor, said first transcription factor being associated with said biological state;

assaying in a plurality of case samples expression levels of said gene and of said first transcription factor; and

deducing whether said expression levels of said gene are correlated with said expression levels of said first transcription factor in said control samples but not correlated in said case samples, thereby identifying a biomarker for said biological state.

25. The method as recited in claim 24, wherein said gene is regulated by said first transcription factor in said control samples.

26. The method as recited in claim 24, further comprising assaying expression levels of one or more additional transcription factors associated with said biological state.

27. The method as recited in claim 26, wherein said gene is regulated by said first transcription factor and by said one or more additional transcription factors in said control samples.

28. The method as recited in claim 24, wherein at least one of said expression levels is assayed by assaying abundance of an mRNA transcript.

29. The method as recited in claim 28, wherein assaying said mRNA transcript abundance comprises:

mixing a nucleic acid corresponding to said gene with a competitive template for said gene;

measuring a nucleic acid corresponding to said first transcription factor in relation to a competitive template for said first transcription factor; and

obtaining a relation comparing said transcription factor to said competitive template.

30. The method as recited in claim 29, wherein said competitive templates are provided in a standardized mixture.

31. The method as recited in claim 29, wherein assaying said mRNA transcript abundance comprises:

co-amplifying a nucleic acid corresponding to said gene with a competitive template for said gene;

co-amplifying a nucleic acid corresponding to said first transcription factor with a competitive template for said first transcription factor; and

obtaining a relation comparing amplified products obtained from said co-amplifications.

32. The method as recited in claim 24, wherein at least one of said expression levels is assayed by assaying abundance of a protein.

33. The method as recited in claim 24, wherein about 10 case samples and about 10 control samples are used.

34. The method as recited in claim 24, wherein about 30 case samples and about 30 control samples are used.

35. The method as recited in claim 24, wherein about 50 case samples and about 50 control samples are used.

36. The method as recited in claim 24, wherein about 100 case samples and about 100 control samples are used.

37. The method as recited in claim 24, wherein said biological state is bronchogenic carcinoma or risk thereof and said first transcription factor is CEBPG.

38. The method as recited in claims 36, wherein said gene is XRCC1, CAT, ERRC1, ERCC2, ERCC5, GSTZ1, mGST1, GSTP1, SOD1 or GPX1.

39. The method as recited in claim 24, wherein said biological state is bronchogenic carcinoma or risk thereof and said first transcription factor is E2F1.

40. The method as recited in claim 38, wherein said gene is ERCC5, GSTP1 or SOD1.

41. The method as recited in claim 24, wherein said biological state is COPD or risk thereof and said first transcription factor is CEBPG.

42. The method as recited in claims 40, wherein said gene is XRCC1, ERCC1, ERCC2, CAT, ERCC5, GSTZ1, mGST1, GSTP1, SOD1 or GPX1.

43. The method as recited in claim 24, wherein said biological state is COPD or risk thereof and said first transcription factor is E2F1.

45. The method as recited in claim 24, further comprising making a diagnostic decision based on identifying said biomarker.

46. The method as recited in claim 24, further comprising administering a therapeutic based on identifying said biomarker.

47. A method of identifying a polymorphism that indicates a biological state, comprising:

obtaining a plurality of control samples wherein expression levels of a transcription factor are correlated with expression levels of a gene;

obtaining a plurality of case samples wherein expression levels of said transcription factor are not correlated with expression levels of said gene; and

identifying a nucleotide variation in said transcription factor and/or in said gene in one or more of said case samples compared with one or more of said control samples, thereby identifying a polymorphism that indicates said biological state.

48. The method as recited in claim 47, wherein said gene is known to be associated with said biological state.

49. The method as recited in claim 47, wherein said transcription factor is known to be associated with said biological state.

50. The method as recited in claim 47, wherein said transcription factor regulates said gene in said control samples.

51. The method as recited in claim 47, wherein at least one of said expression levels is assayed by assaying abundance of an mRNA transcript.

52. The method as recited in claim 51, wherein assaying said mRNA transcript abundance comprises:

co-amplifying a nucleic acid corresponding to said transcription factor with a competitive template for said transcription factor;

co-amplifying a nucleic acid corresponding to said gene with a competitive template for said gene; and

obtaining a relation comparing amplified products obtained from said co-amplifications.

53. The method as recited in claim 52, wherein said competitive templates are provided in a standardized mixture.

54. The method as recited in claim 47, wherein at least one of said expression levels is assayed by assaying abundance of a protein.

55. The method as recited in claim 47, wherein about 10 case samples and about 10 control samples are used.

56. The method as recited in claim 47, wherein about 30 case samples and about 30 control samples are used.

57. The method as recited in claim 47, wherein about 50 case samples and about 50 control samples are used.

58. The method as recited in claim 47, wherein about 100 case samples and about 100 control samples are used.

59. The method as recited in claim 47, wherein said biological state is bronchogenic carcinoma or risk thereof and said transcription factor is CEBPG.

60. The method as recited in claims 59, wherein said gene is XRCC1, ERCC1, ERRC2, ERCC5, GSTP1, SOD1, GSTZ1, mGST1, CAT or GPX1.

61. The method as recited in claim 47, wherein said polymorphism is in a YY1 transcription factor recognition site in ERCC5.

62. The method as recited in claim 47, wherein said polymorphism is at base -222 and/or base -228 within the ERCC5 gene.

63. The method as recited in claim 47, wherein said polymorphism is in an Sp1 transcription factor recognition site in XRCC1.

64. The method as recited in claim 47, wherein said polymorphism is at base -77 within the XRCC1 gene.

65. The method as recited in claim 47, wherein said polymorphism is in a YY1 transcription factor recognition site in XRCC1.

66. The method as recited in claim 47, wherein said biological state is bronchogenic carcinoma or risk thereof and said transcription factor is E2F1.

67. The method as recited in claims 66, wherein said gene is ERCC5, GSTP1 or SOD1.

68. The method as recited in claim 47, wherein said biological state is COPD or risk thereof and said transcription factor is CEBPG.

69. The method as recited in claims 68, wherein said gene is XRCC1, ERCC1, ERCC2, ERCC5, GSTP1, GSTZ1, mGST1, SOD1 or GPX1.

70. The method as recited in claim 47, wherein said biological state is COPD or risk thereof and said transcription factor is E2F1.

71. The method as recited in claims 70, wherein said gene is ERCC5, GSTP1 or SOD1.

72. The method as recited in claim 47, further comprising:

obtaining a first relation comparing expression levels of said gene to expression levels of said transcription factor in said control samples;

obtaining a second relation comparing an expression level of said gene to an expression level of said transcription factor in one of said case samples;

comparing said first and second relations; and

analyzing a region of said transcription factor and/or said gene based on said comparison in order to identify said nucleotide variation.

73. The method as recited in claim 72, wherein said first relation is a regression line obtained from plotting expression levels of said transcription factor versus expression levels of said gene.

74. The method as recited in claim 73, wherein said second relation is a coordinate point of said expression level of said transcription factor versus said expression level of said gene.

75. The method as recited in claim 74, wherein said comparison involves determining whether said coordinate point falls on, above, or below said regression line.

76. The method as recited in claim 75, wherein said coordinate point falls above said regression line and said region is a 5′

regulatory region of said transcription factor.

77. The method as recited in claim 76, wherein said biological state is BC or risk thereof and said transcription factor is CEBPG.

78. The method as recited in claim 75, wherein said coordinate point falls above said regression line and said region is a 3′

untranslated region of said transcription factor.

79. The method as recited in claim 78, wherein said biological state is BC or risk thereof and said transcription factor CEBPG.

80. The method as recited in claim 75, wherein said coordinate point falls below said regression line and said region is a coding region of said transcription factor.

81. The method as recited in claim 80, wherein said biological state is BC or risk thereof and said transcription factor is CEBPG.

82. The method as recited in claim 80, wherein said biological state is BC or risk thereof and said coding region is bZip of CEBPG.

83. The method as recited in claim 80, wherein said biological state is BC or risk thereof and said transcription factor is CEBPA, CEBPB, or FOS.

84. The method as recited in claim 75, wherein said coordinate point falls below said regression line and said region is a transcription factor recognition site of said gene.

85. The method as recited in claim 84, wherein said biological state is BC or risk thereof and said region is a CEBPG recognition site of said gene.

86. The method as recited in claim 85, wherein said gene is XRCC1, ERCC1, ERCC2, ERCC5, SOD1, GSTZ1, mGST1, CAT, GSTP1, or GPX1.

87. The method as recited in claim 47, further comprising making a diagnostic decision based on identifying said polymorphism.

88. The method as recited in claim 47, further comprising administering a therapeutic based on identifying said polymorphism.