ASSESSMENT OF HUMAN PAPILLOMA VIRUS-RELATED DISEASE

• US 20110097708A1
• Filed: 12/22/2010
• Published: 04/28/2011
• Est. Priority Date: 12/12/1997
• Status: Abandoned Application

• Current Assignee: QIAGEN Gaithersburg, Inc. (Qiagen NV)
• Original Assignee: QIAGEN Gaithersburg, Inc. (Qiagen NV)
• Inventors: LORINCZ, Attila T., Lazar, James G.
• Application Number:
  US12/976,428
• Publication Number:
  US 20110097708A1
• Time in Patent Office: Days
• US Class Current: 435/5
• CPC Class Codes: A01N 1/021 Preservation or perfusion media, liquids, solids or gases used in the preservation of cells, tissue, organs or bodily fluids
• CPC Class Codes: C12Q 1/6806 Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 1/708 for papilloma
• CPC Class Codes: C12Q 2523/101 Crosslinking agents, e.g. psoralen
• CPC Class Codes: C12Q 2543/10 the purpose being "in situ" analysis
• CPC Class Codes: C12Q 2545/114 involving a quantitation step
• CPC Class Codes: C12Q 2600/112 Disease subtyping, staging or classification
• CPC Class Codes: C12Q 2600/118 Prognosis of disease development

Abstract

This invention provides novel methods for assessing HPV infection. Gene expression levels are used to assess the progression of HPV infection from benign to malignant growth. Also provided are kits for carrying out the methods of this invention.

Claims

1. A method of determining the medical character of an HPV-based disease comprising measuring the expression level of an HPV gene selected from the group consisting of E6, E7, E2, and L1 and correlating the expression level of the gene to the medical character of the HPV-based disease.

2. The method of claim 1 wherein low expression of E6 and/or E7 indicates a benign HPV infection.

3. The method of claim 1 wherein low to medium expression of E6 and/or E7 indicates a benign HPV infection characterized as CIN I.

4. The method of claim 1 wherein high expression of E6 and/or E7 indicates a neoplastic HPV infection.

5. The method of claim 1 wherein medium to high expression of E6 and/or E7 indicates a neoplastic HPV infection.

6. The method of claim 1 wherein high expression of E2 and/or L1 indicates a benign HPV infection.

7. The method of claim 1 wherein low to high expression of E2 indicates a benign HPV infection.

8. The method of claim 1 wherein medium to high expression of L1 indicates a benign HPV infection characterized as CIN I.

9. The method of claim 1 wherein low to undetectable expression of E2 indicates a neoplastic HPV infection.

10. The method of claim 1 wherein low to medium expression of E6 and/or E7 and medium to high expression of L1 indicates a benign HPV infection characterized as CIN I.

11. The method of claim 1 wherein low to medium expression of E6 and/or E7 and low to high expression of E2 indicates a benign HPV infection characterized as CIN I.

12. The method of claim 1 wherein medium to high expression of E6 and/or E7 and low to undetectable expression of E2 and/or L1 indicates a neoplastic HPV infection characterized as CIN II/III or cancer.

13. A method of determining progression of an HPV-based disease comprising measuring the expression level of an HPV gene selected from the group consisting of E6, E7, E2, and L1 at a first time point and a second later time point, and correlating the change in expression level to the medical character of the HPV-based disease.

14. The method of claim 13 wherein an increase in E6 and/or E7 gene expression from the first time point to the second time point indicates progression of the HPV-based disease.

15. The method of claim 13 wherein a decrease in E6 and/or E7 gene expression from the first time point to the second time point indicates regression of the HPV-based disease.

16. The method of claim 13 wherein a change in E6 and/or E7 gene expression from low at the first time point to high at the second time point to indicates progression from a benign to a neoplastic HPV infection.

17. The method of claim 13 wherein a change in E6 and/or E7 gene expression from high at the first time point to low at the second time point indicates regression from a neoplastic to a benign HPV infection.

18. The method of claim 13 wherein a change in E6 and/or E7 gene expression from low at the first time point to a range of medium to high at the second time point indicates progression from a benign to a neoplastic HPV infection.

19. The method of claim 13 wherein a change in E6 and/or E7 gene expression from a range of medium to high at the first time point to low at the second time point indicates regression from a neoplastic to a benign HPV infection.

20. The method of claim 13 wherein a change in E6 and/or E7 gene expression from a range of low to medium at the first time point to a range of medium to high at the second time point indicates progression from a benign to a neoplastic HPV infection.

21. The method of claim 13 wherein a change in E6 and/or E7 gene expression from a range of medium to high at the first time point to a range of low to medium at the second time point indicates regression from a neoplastic to a benign HPV infection.

22. The method of claim 13 wherein a decrease in E2 and/or L1 gene expression from the first time point to the second time point indicates progression of the HPV-based disease.

23. The method of claim 13 wherein an increase in E2 and/or L1 gene expression from the first time point to the second time point indicates regression of the HPV-based disease.

24. The method of claim 13 wherein a change in E2 gene expression from a range of low to high at the first time point to a range of low to undetectable at the second time point indicates progression from a benign to a neoplastic HPV infection.

25. The method of claim 13 wherein a change in E2 gene expression from a range of low to undetectable at the first time point to a range of low to high at the second time point indicates regression from a neoplastic to a benign HPV infection.

26. The method of claim 13 wherein a change in E2 gene expression from high at the first time point to undetectable at the second time point indicates progression from a benign to a neoplastic HPV infection.

27. The method of claim 13 wherein a change in E2 gene expression from undetectable at the first time point to high at the second time point indicates regression from a neoplastic to a benign HPV infection.

28. The method of claim 13 wherein a change in L1 gene expression from a range of medium to high at the first time point to a range of low to undetectable at the second time point indicates progression from a benign to a neoplastic HPV infection.

29. The method of claim 13 wherein a change in L1 gene expression from a range of low to undetectable at the first time point to a range of medium to high at the second time point indicates regression from a neoplastic to a benign HPV infection.

30. The method of claim 13 wherein progression of the HPV-based disease is indicated by:

(a) an increase in E6 and/or E7 gene expression from the first time point to the second time point; and

(b) a decrease in E2 and/or L1 gene expression from the first time point to the second time point.

31. The method of claim 13 wherein regression of the HPV-based disease is indicated by:

(a) a decrease in E6 and/or E7 gene expression from the first time point to the second time point;

(b) an increase in E2 and/or L1 gene expression from the first time point to the second time point.

32. The method of claim 13 wherein progression from a benign to a neoplastic HPV infection is indicated by:

(a) an increase in E6 and/or E7 gene expression from low at the first time point to high at the second time point; and

(b) a decrease in E2 gene expression from high at the first time point to undetectable at the second time point.

33. The method of claim 13 wherein progression from a benign to a neoplastic HPV infection is indicated by:

(a) an increase in E6 and/or E7 gene expression from low at the first time point to high at the second time point; and

(b) a decrease in L1 gene expression from a range of medium to high at the first time point to a range of low to undetectable at the second time point.

34. The method of claim 13 wherein progression from a benign to a neoplastic HPV infection is indicated by:

(a) an increase in E6 and/or E7 gene expression from low at the first time point to high at the second time point;

(b) a decrease in E2 gene expression from high at the first time point to undetectable at the second time point; and

(c) a decrease in L1 gene expression from a range of medium to high at the first time point to a range of low to undetectable at the second time point.

35. The method of claim 13 wherein regression from a neoplastic to a benign HPV infection is indicated by:

(a) a decrease in E6 and/or E7 gene expression from high at the first time point to low at the second time point; and

(b) an increase in E2 gene expression from undetectable at the first time point to high at the second time point.

36. The method of claim 13 wherein regression from a neoplastic to a benign HPV infection is indicated by:

(a) a decrease in E6 and/or E7 gene expression from high at the first time point to low at the second time point; and

(b) an increase in L1 gene expression from a range of low to undetectable at the first time point to a range of medium to high at the second time point.

37. The method of claim 13 wherein regression from a neoplastic to a benign HPV infection is indicated by:

(a) a decrease in E6 and/or E7 gene expression from high at the first time point to low at the second time point;

(b) an increase in E2 gene expression from undetectable at the first time point to high at the second time point; and

(c) an increase in L1 gene expression from a range of low to undetectable at the first time point to a range of medium to high at the second time point.

38. The method of claim 13 wherein progression from a benign to a neoplastic HPV infection is indicated by:

(a) an increase in E6 and/or E7 gene expression from low at the first time point to a range of medium to high at the second time point; and

(b) a decrease in E2 gene expression from a range of low to high at the first time point to a range of low to undetectable at the second time point.

39. The method of claim 13 wherein progression from a benign to a neoplastic HPV infection is indicated by:

(a) an increase in E6 and/or E7 gene expression from low at the first time point to a range of medium to high at the second time point; and

(b) a decrease in L1 gene expression from a range of medium to high at the first time point to a range of low to undetectable at the second time point.

40. The method of claim 13 wherein progression from a benign to a neoplastic HPV infection is indicated by:

(a) an increase in E6 and/or E7 gene expression from low at the first time point to a range of medium to high at the second time point;

(b) a decrease in E2 gene expression from a range of low to high at the first time point to a range of low to undetectable at the second time point; and

(c) a decrease in L1 gene expression from a range of medium to high at the first time point to a range of low to undetectable at the second time point.

41. The method of claim 13 wherein regression from a neoplastic to a benign HPV infection is indicated by:

(a) a decrease in E6 and/or E7 gene expression from a range of medium to high at the first time point to low at the second time point; and

(b) an increase in E2 gene expression from a range of low to undetectable at the first time point to a range of low to high at the second time point.

42. The method of claim 13 wherein regression from a neoplastic to a benign HPV infection is indicated by:

(a) a decrease in E6 and/or E7 gene expression from a range of medium to high at the first time point to low at the second time point; and

(b) an increase in L1 gene expression from a range of low to undetectable at the first time point to a range of medium to high at the second time point.

43. The method of claim 13 wherein regression from a neoplastic to a benign HPV infection is indicated by:

(a) a decrease in E6 and/or E7 gene expression from a range of medium to high at the first time point to low at the second time point;

(b) an increase in E2 gene expression from a range of low to undetectable at the first time point to a range of low to high at the second time point; and

(c) an increase in L1 gene expression from a range of low to undetectable at the first time point to a range of medium to high at the second time point.

44. The method of claim 13 wherein progression from a benign to a neoplastic HPV infection is indicate by:

(a) an increase in E6 and/or E7 gene expression from a range of low to medium at the first time point to a range of medium to high at the second time point; and

(b) a decrease in E2 gene expression from a range of low to high at the first time point to a range of low to undetectable at the second time point.

45. The method of claim 13 wherein progression from a benign to a neoplastic HPV infection is indicate by:

(a) an increase in E6 and/or E7 gene expression from a range of low to medium at the first time point to a range of medium to high at the second time point; and

(b) a decrease in L1 gene expression from a range of medium to high at the first time point to a range of low to undetectable at the second time point.

46. The method of claim 13 wherein progression from a benign to a neoplastic HPV infection is indicate by:

(a) an increase in E6 and/or E7 gene expression from a range of low to medium at the first time point to a range of medium to high at the second time point;

(b) a decrease in E2 gene expression from a range of low to high at the first time point to a range of low to undetectable at the second time point; and

(c) a decrease in L1 gene expression from a range of medium to high at the first time point to a range of low to undetectable at the second time point.

47. The method of claim 13 wherein regression from a neoplastic to a benign HPV infection is indicated by:

(a) a decrease in E6 and/or E7 gene expression from a range of medium to high at the first time point to a range of low to medium at the second time point; and

(b) an increase in E2 gene expression from a range of low to undetectable at the first time point to a range of low to high at the second time point.

48. The method of claim 13 wherein regression from a neoplastic to a benign HPV infection is indicated by:

(a) a decrease in E6 and/or E7 gene expression from a range of medium to high at the first time point to a range of low to medium at the second time point; and

(b) an increase in L1 gene expression from a range of low to undetectable at the first time point to a range of medium to high at the second time point.

49. The method of claim 13 wherein regression from a neoplastic to a benign HPV infection is indicated by:

(a) a decrease in E6 and/or E7 gene expression from a range of medium to high at the first time point to a range of low to medium at the second time point;

(b) an increase in E2 gene expression from a range of low to undetectable at the first time point to a range of low to high at the second time point; and

(c) an increase in L1 gene expression from a range of low to undetectable at the first time point to a range of medium to high at the second time point.

50. The method of claim 13 wherein progression from HPV-infected normal tissue to CIN-I is indicated by:

(a) an increase in L1 gene expression from a range of low to undetectable at the first time point to a range of medium to high at the second time point; and

(b) low to medium E6 and/or E7 gene expression at the second time point.

51. The method of claim 13 wherein progression from CIN-I to CIN II/II or cancer is indicated by:

(a) a decrease in L1 gene expression from a range of medium to high at the first time point to a range of low to undetectable at the second time point; and

(b) a medium to high level of E6 and/or E7 gene expression at the second time point.