METHODS AND SYSTEMS FOR EVALUATING THE SENSITIVITY OR RESISTANCE OF TUMOR SPECIMENS TO CHEMOTHERAPEUTIC AGENTS
The present invention provides methods, systems, and kits for evaluating the sensitivity and/or resistance of tumor specimens to one or a combination of chemotherapeutic agents. Particularly, the invention provides malignant cell gene signatures that are predictive of a tumor's response to candidate chemotherapeutic regimens.
1 . A method for preparing a gene expression profile indicative of drug-sensitivity or drug-resistance, comprising:
extracting RNA from a patient tumor specimen or cells cultured therefrom, and
determining the level of expression for at least 5 genes listed in one or more of Tables 1-8, thereby preparing the gene expression profile.
2 . The method of claim 1 , wherein the tumor is derived from a tissue selected from breast, ovaries, lung, colon, skin, prostate, kidney, endometrium, nasopharynx, pancreas, head and neck, kidney, and brain.
3 . The method of claim 1 , wherein the tumor specimen is a carcinoma.
4 . The method of any one of claims 1 to 3 , wherein the specimen is obtained by surgery or biopsy, or is obtained from blood or ascites.
5 . The method of claim 4 , wherein the tumor specimen is a breast tumor specimen.
6 . The method of any one of claims 1 to 5 , wherein the patient has primary cancer.
7 . The method of any one of claims 1 to 5 , wherein the patient has recurrent cancer.
8 . The method of claim 1 , wherein the patient is a candidate for treatment with a combination selected from: cyclophosphamide, doxorubicin, fluorouracil, and paclitaxel (TFAC); cyclophosphamide and epirubicin (EC); cyclophosphamide and doxorubicin (AC); cyclophosphamide, docetaxel, and doxorubicin (ACT).
9 . The method of any one of claims 1 to 8 , wherein the RNA is extracted from a tumor specimen.
10 . The method of claim 9 , wherein the tumor specimen is formalin-fixed and paraffin-embedded.
11 . The method of any one of claims 1 to 8 , wherein the RNA is extracted from cultured cells derived from the tumor specimen.
12 . The method of claim 11 , wherein the cultured cells are enriched for malignant cells.
13 . The method of claim 12 , wherein the cultured cells are grown in a monolayer culture from a plurality of explants of the tumor specimen.
14 . The method of any one of claims 1 to 13 , wherein the levels of expression are determined by hybridizing nucleic acids to oligonucleotide probes, by RT-PCR, or by direct mRNA capture.
15 . The method of any one of claims 1 to 14 , wherein the RNA is total RNA.
16 . The method of any one of claims 1 to 14 , wherein the RNA is polyA+RNA.
17 . The method of any one of claims 1 to 16 , wherein the RNA is reverse transcribed are/or amplified.
18 . The method of any one of claims 1 to 17 , wherein the gene expression profile comprises the level of expression for at least about 10 genes listed in one or more of Tables 1-8.
19 . The method of claim 18 , wherein the gene expression profile comprises the level of expression for at least about 100 genes listed in one or more of Tables 1-8.
20 . The method of claim 18 , wherein the gene expression profile comprises the level of expression for at least about 200 genes listed in one or more of Tables 1-8.
21 . The method of claim 18 , wherein the at least 10 genes are listed in Tables 1 and 2.
22 . The method of claim 18 , wherein the at least 10 genes are listed in Tables 3 and 4.
23 . The method of claim 18 , wherein the at least 10 genes are listed in Tables 5 and 6.
24 . The method of claim 18 , wherein the at least 10 genes are listed in Tables 7 and 8.
25 . The method of any one of claims 21 to 24 , wherein the at least 10 genes have a fold change magnitude of at least about 1.5 (up) or 0.8 (down) in Table 2, 4, 6, or 8.
26 . A method for evaluating the sensitivity of a tumor to one or a combination of therapeutic agents, comprising:
preparing a gene expression profile for a tumor specimen according to any one of claims 1 to 25 ; and
determining the presence of at least one gene expression signature indicative of drug-sensitivity or drug-resistance, thereby classifying the profile as a drug-sensitive or drug-resistant profile.
27 . The method of claim 26 , wherein the gene expression signature comprises threshold gene expression values indicative of drug sensitivity and/or drug resistance.
28 . The method of claim 26 or 27 , wherein the gene expression signature comprises Mean gene expression levels indicative of drug sensitivity and/or drug resistance.
29 . The method of any one of claims 26 to 28 , wherein the gene expression signature is predictive of efficacy for one or more of treatment with TFAC, EC, AC or ACT.
30 . The method of any one of claims 26 to 29 , wherein the gene expression profile is classified by Principal Components Analysis, Naïve Bayes, Support Vector Machines, Nearest Neighbors, Decision Trees, Logistic, Artificial Neural Networks, and Rule-based schemes.
31 . The method of any one of claims 26 to 30 , wherein the gene expression signature is predictive of survival, pathological complete response (pCR), reduction in tumor size, or duration of progression free interval upon treatment with a chemotherapeutic agent or combination.
32 . The method of any one of claims 26 to 31 , further comprising, conducting an in vitro chemoresponse assay with cultured cells derived from the patient tumor specimen.
33 . A computer system for performing the method of any one of claims 1 - 32 .
34 . A probe array or probe set for performing the method of any one of claims 1 - 33 .