Predicting outcome with tamoxifen in breast cancer

• US 7,504,214 B2
• Filed: 12/02/2003
• Issued: 03/17/2009
• Est. Priority Date: 09/19/2003
• Status: Active Grant

• Current Assignee: BioTheranostics, Inc. (Hologic Incorporated), The General Hospital Corporation (Mass General Brigham, Inc.)
• Original Assignee: BioTheranostics, Inc. (Hologic Incorporated)
• Inventors: Erlander, Mark G., Ma, Xiao-Jun, Sgroi, Dennis C.
• Primary Examiner(s): Qian; Celine X
• Application Number:
  US10/727,100
• Publication Number:
  US 20050239079A1
• Time in Patent Office: 1,932 Days
• Field of Search: None
• US Class Current: 435/6.14
• 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 2600/154 Methylation markers
• CPC Class Codes: C12Q 2600/158 Expression markers

Abstract

Methods and compositions are provided for the identification of expression signatures in ER+ breast cancer cases, where the signatures correlate with responsiveness, or lack thereof, to tamoxifen treatment. The signature profiles are identified based upon sampling of reference breast tissue samples from independent cases of breast cancer and provide a reliable set of molecular criteria for predicting the efficacy of treating a subject with ER+ breast cancer with tamoxifen. Additional methods and compositions are provided for predicting tamoxifen responsiveness in cases of ER+ breast cancer by use of three biomarkers. Two biomarkers display increased expression correlated with tamoxifen response while the third biomarker displays decreased expression correlated with tamoxifen response.

Claims

1. A method to determine the risk of cancer recurrence in a human subject afflicted with ER+ (estrogen receptor positive) breast cancer, said method comprising

determining an expected cancer recurrence for said subject by assaying a sample of breast cancer cells from said subject for a ratio of HoxB13 and IL17BR RNA expression levels that is higher than the mean (average) ratio of HoxB13 and IL17BR RNA expression levels in ER+ breast cancer cells;

or

determining an expected lack of cancer recurrence for said subject by assaying a sample of breast cancer cells from said subject for a ratio of HoxB13 and IL17BR RNA expression levels that is below the mean (average) ratio of HoxB13 and IL17BR RNA expression levels in ER+ breast cancer cells;

wherein said mean (average) ratio of HoxB13 and IL17BR RNA expression levels is determined from the mean (average) of HoxB13 RNA expression levels, and the mean (average) of IL17BR RNA expression levels, in ER+ breast cancer cell samples from human breast cancer subjects that respond to treatment with tamoxifen and human breast cancer subjects that do not respond to treatment with tamoxifen.

5. The method of claim 1 wherein said assaying comprises determining the expression levels of HoxB13 and IL17BR mRNAs.

6. The method of claim 1 wherein said assaying for the expression levels of HoxB13 and IL17BR RNA comprises mRNA amplification from said sample of breast cancer cells.

7. The method of claim 1 wherein said RNA expression levels are determined by quantitative PCR.

8. The method of claim 1 wherein said assaying comprises RT-PCR (reverse transcription polymerase chain reaction).

9. The method of claim 1 wherein said sample is a formalin fixed paraffin embedded (FFPE), ductal lavage or fine needle aspiration sample.

10. The method of claim 1 wherein said sample is a section of tissue from a subject or comprises cells microdissected from said section.

11. The method of claim 1, wherein said assaying for expression of a HoxB13 sequence comprises assaying for expression of a sequence selected from SEQ ID NOS:

6, 7, 10 or 11-31.

12. The method of claim 1, wherein said assaying for expression of an IL17BR sequence comprises assaying for expression of a sequence selected from SEQ ID NOS:

1, 2, 3, or 8.

38. The method of claim 1 wherein said assaying comprises hybridization to a polynucleotide comprising sequences of at least 24 nucleotides from the 3′

untranslated region, the coding region, or the 5′

untranslated region, of a human HOXB 13 or IL17BR RNA transcript.

2. A method of determining the outcome of a human subject having ER+ (estrogen receptor positive) breast cancer, or of a subject afflicted with ER+ breast cancer, if said subject is treated with tamoxifen, said method comprising:

assaying a breast cancer cell sample from said subject wherein

a ratio of HoxB13 and IL17BR RNA expression levels that is below the mean (average) ratio of HoxB13 and IL17BR expression levels in ER+ breast cancer cells indicates a cancer-free outcome, and

a ratio above the mean (average) ratio of HoxB13 and IL17BR RNA expression levels in ER+ breast cancer cells indicates an outcome comprising cancer recurrence;

wherein said mean (average) ratio of HoxB13 and IL17BR RNA expression levels is determined from the mean (average) of HoxB13 RNA expression levels, and the mean (average) of IL17BR RNA expression levels, in ER+ breast cancer cell samples from human breast cancer subjects that respond to treatment with tamoxifen and human breast cancer subjects that do not respond to treatment with tamoxifen.

13. The method of claim 2 wherein said assaying comprises determining the expression levels of HoxB13 and IL17BR mRNAs.

14. The method of claim 2 wherein said assaying for the expression levels of HoxB13 and IL17BR comprises detection of nucleic acids mRNA amplification from said sample of ER+ breast cancer cells.

15. The method of claim 2 wherein said RNA expression levels are determined by quantitative PCR.

16. The method of claim 2 wherein said assaying comprises RT-PCR (reverse transcription polymerase chain reaction).

17. The method of claim 2 wherein said sample is a formalin fixed paraffin embedded (FFPE), ductal lavage or fine needle aspiration sample.

18. The method of claim 2 wherein said sample is a section of tissue from a subject or comprises cells microdissected from said section.

19. The method of claim 2, wherein said assaying for expression of a HoxB13 sequence comprises assaying for expression of a sequence selected from SEQ ID NOS:

6, 7, 10 or 11-31.

20. The method of claim 2, wherein said assaying for expression of an IL17BR sequence comprises assaying for expression of a sequence selected from SEQ ID NOS:

1, 2, 3, or 8.

39. The method of claim 2 wherein said assaying comprises hybridization to a polynucleotide comprising sequences of at least 24 nucleotides from the 3′

untranslated region, the coding region, or the 5′

untranslated region, of a human HOXB 13 or IL17BR RNA transcript.

42. The method of claim 2 wherein said breast-cancer-free subject has a low risk of cancer tumor recurrence.

43. The method of claim 2 wherein said outcome comprises survival outcome.

3. A method to predict an expected lack of response to tamoxifen treatment in a human ER+ (estrogen receptor positive) breast cancer patient, said method comprising

determining an expected lack of response to tamoxifen treatment for said patient by assaying a sample of breast cancer cells from said patient for a ratio of HoxB13 and IL17BR expression levels that is higher than the mean (average) ratio of HoxB13 and IL17BR expression levels in ER+ breast cancer cells;

wherein said mean (average) ratio of HoxB13 and IL17BR RNA expression levels is determined from the mean (average) of HoxB13 RNA expression levels, and the mean (average) of IL17BR RNA expression levels, in ER+ breast cancer cell samples from human breast cancer subjects that respond to treatment with tamoxifen and human breast cancer subjects that do not respond to treatment with tamoxifen.

21. The method of claim 3 wherein said assaying comprises determining the expression levels of HoxB 13 and IL17BR mRNAs.

22. The method of claim 3 wherein said assaying comprises mRNA amplification from said sample of ER+ breast cancer cells.

23. The method of claim 3 wherein said RNA expression levels are determined by quantitative PCR.

24. The method of claim 3 wherein said assaying comprises RT-PCR (reverse transcription polymerase chain reaction).

25. The method of claim 3 wherein said sample is a formalin fixed paraffin embedded (FFPE), ductal lavage or fine needle aspiration sample.

26. The method of claim 3 wherein said sample is a section of tissue from a subject or comprises cells microdissected from said section.

27. The method of claim 3, wherein said assaying for expression of a HoxB13 sequence comprises assaying for expression of a sequence selected from SEQ ID NOS:

6, 7, 10 or 11-31.

28. The method of claim 3, wherein said assaying for expression of an IL17BR sequence comprises assaying for expression of a sequence selected from SEQ ID NOS:

1, 2, 3, or 8.

40. The method of claim 3 wherein said assaying comprises hybridization to a polynucleotide comprising sequences of at least 24 nucleotides from the 3′

untranslated region, the coding region, or the 5′

untranslated region, of a human HOXB 13 or IL17BR RNA transcript.

4. A method to determine risk of cancer recurrence in a human subject having ER+ (estrogen receptor positive) breast cancer if treated with tamoxifen, said method comprising

assaying a sample of breast cells from said subject for

increased expression of human HOXB 13 sequences, or decreased expression of IL17BR sequences, relative to the mean (average) expression thereof in ER+ breast cancer cell samples from human breast cancer subjects that respond to treatment with tamoxifen and human breast cancer subjects that do not respond to treatment with tamoxifen, as an indicator of tamoxifen non-responsiveness;

or

decreased expression of human HOXB 13 sequences, or increased expression of IL17BR sequences, relative to the mean (average) expression thereof in ER+ breast cancer cell samples from human breast cancer subjects that respond to treatment with tamoxifen and human breast cancer subjects that do not respond to treatment with tamoxifen, as an indicator of tamoxifen responsiveness.

29. The method of claim 4 wherein said assaying comprises determining the expression levels of HoxB13 and IL17BR mRNAs.

30. The method of claim 4 wherein said assaying for the expression levels of HoxB13 and IL17BR comprises mRNA amplification from said sample of ER+ breast cancer cells.

31. The method of claim 4 wherein said RNA expression levels are determined by quantitative PCR.

32. The method of claim 4 wherein said assaying comprises RT-PCR (reverse transcription polymerase chain reaction).

33. The method of claim 4 wherein said sample is a formalin fixed paraffin embedded (FFPE), ductal lavage or fine needle aspiration sample.

34. The method of claim 4 wherein said sample is a section of tissue from a subject or comprises cells microdissected from said section.

35. The method of claim 4 wherein said sample is obtained by solid tissue biopsy or a non-invasive procedure.

36. The method of claim 4, wherein said assaying for expression of a HoxB13 sequence comprises assaying for expression of a sequence selected from SEQ ID NOS:

6, 7, 10 or 11-31.

37. The method of claim 4, wherein said assaying for expression of an IL17BR sequence comprises assaying for expression of a sequence selected from SEQ ID NOS:

1, 2, 3, or 8.

41. The method of claim 4 wherein said assaying comprises hybridization to a polynucleotide comprising sequences of at least 24 nucleotides from the 3′

untranslated region, the coding region, or the 5′

untranslated region, of a human HOXB 13 or IL17BR RNA transcript.