Gene expression markers for response to EGFR inhibitor drugs

• US 20050164218A1
• Filed: 05/28/2004
• Published: 07/28/2005
• Est. Priority Date: 05/30/2003
• Status: Abandoned Application

• Current Assignee: Cedars-Sinai Medical Center (Cedars Sinai Health System), Genomic Health Incorporated (Exact Sciences Corporation)
• Original Assignee: Genomic Health Incorporated (Exact Sciences Corporation)
• Inventors: Natale, Ron, Shak, Steven, Baker, Joffre B., Agus, David
• Application Number:
  US10/857,715
• Publication Number:
  US 20050164218A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: A61P 43/00 Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
• 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 2600/158 Expression markers

Abstract

The present invention concerns prognostic markers associated with cancer. In particular, the invention concerns prognostic methods based on the molecular characterization of gene expression in paraffin-embedded, fixed samples of cancer tissue, which allow a physician to predict whether a patient is likely to respond well to treatment with an EGFR inhibitor.

Claims

1. A method for predicting the likelihood that a subject will respond to treatment with an EGFR inhibitor, comprising

determining the expression level of one or more prognostic RNA transcripts or their expression products in a biological sample comprising cancer cells obtained from said patient, wherein the prognostic transcript is the transcript of one or more genes selected from the group consisting of:

hCRA a;

LAMC2;

B2M;

STAT5B;

LMYC;

CKAP4;

TAGLN;

Furin;

DHFR;

CCND3;

TITF1;

FUS;

FLT1;

TIMP2;

RASSF1;

WISP1;

VEGFC;

GPX2;

CTSH;

AKAP12;

APC;

RPL19;

IGFBP6;

Bak;

CyclinG1;

Hepsin1;

MMP2;

XIAP;

MUC1;

STMY3;

PDGFRb;

GSTp;

p53R2;

DPYD;

IGFBP3;

MMP9;

RRM;

KRT17;

PDGFRa;

EPHX1;

E2F1;

HNF3A;

mGST1;

STAT3;

IGF1R;

EGFR;

cdc25A;

RPLPO;

YB-1;

CKAP4;

Kitlng;

HER2;

Surfact A;

BTC;

PGK1;

MTA1;

FOLR1;

Claudin 4;

EMP1 wherein

(a) for every unit of increased expression of one or more of hCRA a;

LAMC2;

STAT5B;

CKAP4;

TAGLN;

Furin;

FUS;

FLT1;

TIMP2;

RASSF1;

WISP1;

VEGFC;

GPX2;

AKAP12;

RPL19;

IGFBP6;

MMP2;

STMY3;

PDGFRb;

GSTp;

IGFBP3;

MMP9;

KRT17;

PDGFRa;

IGF1R;

cdc25A;

RPLPO;

YB-1;

CKAP4, EMP1 or the corresponding expression product, said subject is expected to have a decreased likelihood of response to treatment with an EGFR inhibitor, and

(b) for every unit of increased expression of one or more of B2M;

LMYC;

DHFR;

CCND3;

TITF1;

CTSH;

APC;

Bak;

CyclinG1;

Hepsin1;

XIAP;

MUC1;

p53R2;

DPYD;

RRM;

EPHX1;

E2F1;

HNF3A;

mGST1;

STAT3;

EGFR;

Kitlng;

HER2;

Surfact A;

BTC;

PGK1;

MTA1;

FOLR1;

Claudin 4, or the corresponding expression product, said subject is expected to have an increased likelihood of response to treatment with an EGFR inhibitor.

2. The method of claim 1 wherein said subject is a human patient.

3. The method of claim 2 comprising determining the expression level of at least two of said prognostic transcripts or their expression products.

4. The method of claim 2 comprising determining the expression level of at least 5 of said prognostic transcripts or their expression products.

5. The method of claim 2 comprising determining the expression level of all of said prognostic transcripts or their expression products.

6. The method of claim 2 wherein said cancer is selected from the group consisting of ovarian cancer, colon cancer, pancreatic cancer, non-small cell lung cancer, breast cancer, and head and neck cancer.

7. The method of claim 2 wherein said biological sample is a tissue sample comprising cancer cells.

8. The method of claim 7 where the tissue is fixed, paraffin-embedded, or fresh, or frozen.

9. The method of claim 7 where the tissue is from fine needle, core, or other types of biopsy.

10. The method of claim 7 wherein the tissue sample is obtained by fine needle aspiration, bronchial lavage, or transbronchial biopsy.

11. The method of claim 1 wherein the expression level of said prognostic RNA transcript or transcripts is determined by RT-PCR.

12. The method of claim 1 wherein the expression level of said expression product or products is determined by immunohistochemistry.

13. The method of claim 1 wherein the expression level of said expression product or products is determined by proteomics technology.

14. The method of claim 1 wherein the assay for measurement of the prognostic RNA transcripts or their expression products is provided in the form of a kit or kits.

15. The method of claim 1 wherein the EGFR inhibitor is an antibody or an antibody fragment.

16. The method of claim 1 wherein the EGFR inhibitor is a small molecule.

17. An array comprising polynucleotides hybridizing to one of more of the following genes:

hCRA a;

LAMC2;

B2M;

STAT5B;

LMYC;

CKAP4;

TAGLN;

Furin;

DHFR;

CCND3;

TITF1;

FUS;

FLT1;

TIMP2;

RASSF1;

WISP1;

VEGFC;

GPX2;

CTSH;

AKAP12;

APC;

RPL19;

IGFBP6;

Bak;

CyclinG1;

Hepsin1;

MMP2;

XIAP;

MUC1;

STMY3;

PDGFRb;

GSTp;

p53R2;

DPYD;

IGFBP3;

MMP9;

RRM;

KRT17;

PDGFRa;

EPHX1;

E2F1;

HNF3A;

mGST1;

STAT3;

IGF1R;

EGFR;

cdc25A;

RPLPO;

YB-1;

CKAP4;

Kitlng;

HER2;

Surfact A;

BTC;

PGK1;

MTA1;

FOLR1;

Claudin 4;

EMP1, immobilized on a solid surface.

18. The array of claim 17 comprising polynucleotides hybridizing to a plurality of said genes.

19. The array of claim 18 comprising polynucleotides hybridizing to at least 5 of sad genes.

20. The array of claim 18 comprising polynucleotides hybridizing to at least 10 of said genes.

21. The array of claim 18 comprising polynucleotides hybridizing to at least 15 of said genes.

22. The array of claim 18 comprising polynucleotides hybridizing to all of said genes.

23. The array of claim 18 comprising more than one polynucleotide hybridizing to the same gene.

24. The array of claim 18, wherein at least one of said polynucleotides comprises an intron-based sequence, the expression of which correlates with the expression of a corresponding exon sequence.

25. The array of claim 17 wherein said polynucleotides are cDNAs.

26. The array of claim 25 wherein said cDNAs are about 500 to 5000 bases long.

27. The array of claim 17 wherein said polynucleotides are oligonucleotides.

28. The array of claim 27 wherein said oligonucleotides are about 20 to 80 bases long.

29. The array of claim 28 which comprises about 330,000 oligonucleotides.

30. The array of claim 17 wherein said solid surface is glass.

31. A method of preparing a personalized genomics profile for a patient, comprising the steps of:

(a) subjecting RNA extracted from cancer cells obtained from the patient to gene expression analysis;

(b) determining the expression level in the tissue of one or more genes selected from the group consisting of hCRA a;

LAMC2;

B2M;

STAT5B;

LMYC;

CKAP4;

TAGLN;

Furin;

DHFR;

CCND3;

TITF1;

FUS;

FLT1;

TIMP2;

RASSF1;

WISP1;

VEGFC;

GPX2;

CTSH;

AKAP12;

APC;

RPL19;

IGFBP6;

Bak;

CyclinG1;

Hepsin1;

MMP2;

XIAP;

MUC1;

STMY3;

PDGFRb;

GSTp;

p53R2;

DPYD;

IGFBP3;

MMP9;

RRM;

KRT17;

PDGFRa;

EPHX1;

E2F1;

HNF3A;

mGST1;

STAT3;

IGF1R;

EGFR;

cdc25A;

RPLPO;

YB-1;

CKAP4;

Kitlng;

HER2;

Surfact A;

BTC;

PGK1;

MTA1;

FOLR1, EMP1 wherein the expression level is normalized against a control gene or genes and optionally is compared to the amount found in a corresponding cancer reference tissue set; and

(c) creating a report summarizing the data obtained by said gene expression analysis.

32. The method of claim 31 wherein said cancer cells are obtained from a solid tumor.

33. The method of claim 32 wherein said solid tumor is selected from the group consisting of breast cancer, ovarian cancer, gastric cancer, colorectal cancer, pancreatic cancer, and lung cancer.

34. The method of claim 31 wherein said cancer cells are obtained from a fixed, paraffin-embedded biopsy sample.

35. The method of claim 34 wherein said RNA is fragmented.

36. The method of claim 31 wherein said report includes prediction of the likelihood that the patient will respond to treatment with an EGFR inhibitor.

37. The method of claim 36 wherein said report includes recommendation for a treatment modality of said patient.

38. The method of claim 31 wherein if increased expression of one or more of B2M;

LMYC;

DHFR;

CCND3;

TITF1;

CTSH;

APC;

Bak;

CyclinG1;

Hepsin1;

XIAP;

MUC1;

p53R2;

DPYD;

RRM;

EPHX1;

E2F1;

HNF3A;

mGST1;

STAT3;

EGFR;

Kitlng;

HER2;

Surfact A;

BTC;

PGK1;

MTA1;

FOLR1;

Claudin 4, or the corresponding expression product, is determined, said report includes a prediction that said subject has an increased likelihood of response to treatment with an EGFR inhibitor.

39. The method of claim 38 further comprising the step of treating said patient with an EGFR inhibitor.

40. A method for amplification of a gene selected from the group consisting of hCRA a;

LAMC2;

B2M;

STAT5B;

LMYC;

CKAP4;

TAGLN;

Furin;

DHFR;

CCND3;

TITF1;

FUS;

FLT1;

TIMP2;

RASSF1;

WISP1;

VEGFC;

GPX2;

CTSH;

AKAP12;

APC;

RPL19;

IGFBP6;

Bak;

CyclinG1;

Hepsin1;

MMP2;

XIAP;

MUC1;

STMY3;

PDGFRb;

GSTp;

p53R2;

DPYD;

IGFBP3;

MMP9;

RRM;

KRT17;

PDGFRa;

EPHX1;

E2F1;

HNF3A;

mGST1;

STAT3;

IGF1R;

EGFR;

cdc25A;

RPLPO;

YB-1;

CKAP4;

Kitlng;

HER2;

Surfact A;

BTC;

PGK1;

MTA1;

FOLR1;

Claudin 4;

EMP1 by polymerase chain reaction (PCR), comprising performing said PCR by using a corresponding amplicon listed in Table 3, and a corresponding primer-probe set listed in Table 4.

41. A PCR primer-probe set listed in Table 4.

42. A PCR amplicon listed in Table 3.