Gene Expression Profiling in Biopsied Tumor Tissues

Abstract

The invention concerns sensitive methods to measure mRNA levels in biopsied tumor tissues, including archived paraffin-embedded biopsy material. The invention also concerns breast cancer gene sets important in the diagnosis and treatment of breast cancer, and methods for assigning the most optimal treatment options to breast cancer patient based upon knowledge derived from gene expression studies.

1 - 31 . (canceled) 
     
     
         32 . A method of predicting the likelihood of long-term survival of a breast cancer patient without the recurrence of breast cancer, following surgical removal of the primary tumor, comprising determining the expression level of an RNA transcript or its product in a breast cancer tissue sample obtained from said patient, normalized against the expression level of all RNA transcripts or their products in said breast cancer tissue sample, or of a reference set of RNA transcripts or their products, wherein the transcript is the transcript of EREG. 
     
     
         33 . The method of  claim 32  further comprising determining the expression level of one or more RNA transcripts or their products, normalized against the expression level of all RNA transcripts or their products in said breast cancer tissue sample, or of a reference set of RNA transcripts or their products, wherein the transcript is the transcript of one or more genes selected from the group consisting of: FOXM1, PRAME, Bcl2, CEGP1, Ki-67, GSTM1, CA9, PR, BBC3, NME1, SURV, GATA3, TFRC, YB-1, DPYD, GSTM3, RPS6 KB1, Src, Chk1, ID1, EstR1, p27, CCNB1, STK15, XIAP, Chk2, CDC25B, IGF1R, AK055699, P13KC2A, TGFB3, BAGI1, CYP3A4, EpCAM, VEGFC, pS2, hENT1, WISP1, HNF3A, NFKBp65, BRCA2, EGFR, TK1, VDR, Contig51037, pENT1, EPHX1, IF1A, DIABLO, CDH1, HIF1α, IGFBP3, CTSB, and Her2, wherein overexpression of one or more of FOXM1, PRAME, Ki-67, CA9, NME1, SURV, TFRC, YB-1, RPS6 KB1, Src, Chk1, CCNB1, STK15Chk2, CDC25B, CYP3A4, EpCAM, VEGFC, hENT1, BRCA2, EGFR, TK1, VDR, EPHX1, IF1A, Contig51037, CDH1, HIF1α, IGFBP3, CTSB, Her2, and pENT1 indicates a decreased likelihood of long-term survival without breast cancer recurrence, and the overexpression of one or more of Bcl2, CEGP1, GSTM1, PR, BBC3, GATA3, DPYD, GSTM3, ID1, EstR1, p27, XIAP, IGF1R, AK055699, P13KC2A, TGFB3, BAGI1, pS2, WISP1, HNF3A, NFKBp65, and DIABLO indicates an increased likelihood of long-term survival without breast cancer recurrence. 
     
     
         34 . The method of  claim 32  wherein the breast cancer is invasive breast carcinoma, further comprising determination of the expression levels of one or more transcripts, or their products wherein the transcript is the transcript of one or more genes selected from the group consisting of: FOXM1, PRAME, Bcl2, STK15, CEGP1, Ki-67, GSTM1, PR, BBC3, NME1, SURV, GATA3, TFRC, YB-1, DPYD, CA9, Contig51037, RPS6K1 and Her2. 
     
     
         35 . The method of  claim 32  wherein said breast cancer is characterized by overexpression of the estrogen receptor (ER). 
     
     
         36 . The method of  claim 35  further comprising determination of the expression levels of the transcripts of one or more transcripts or their products wherein the transcript is the transcript of one or more genes selected from the group consisting of: PRAME, Bcl2, FOXM1, DIABLO, EPHX1, HIF1A, VEGFC, Ki-67, IGF1R, VDR, NME1, GSTM3, Contig51037, CDC25B, CTSB, p27, CDH1, and IGFBP3. 
     
     
         37 . The method of  claim 33  wherein the expression level of 2 or more RNA transcripts is determined. 
     
     
         38 . The method of  claim 32  wherein said RNA is isolated from a fixed, wax-embedded breast cancer tissue specimen of said patient. 
     
     
         39 - 40 . (canceled) 
     
     
         41 . A method of predicting the likelihood of long-term survival of a patient diagnosed with invasive breast cancer, without the recurrence of breast cancer, following surgical removal of the primary tumor, comprising the steps of:
 (1) determining the expression levels of the RNA transcripts or the expression products of genes of a gene set GSTM1, XIAP, PRAME, p27, Contig51037, ErbB3, GSTp, EREG, ID1, PLAUR;   in a breast cancer tissue sample obtained from said patient, normalized against the expression levels of all RNA transcripts or their products in said breast cancer tissue sample, or of a reference set of RNA transcripts or their products;   (2) subjecting the data obtained in step (1) to statistical analysis; and   (3) determining whether the likelihood of said long-term survival has increased or decreased.   
     
     
         42 . (canceled) 
     
     
         43 . The method of  claim 41  wherein said statistical analysis is performed by using the Cox Proportional Hazards model. 
     
     
         44 . (canceled) 
     
     
         45 . (canceled) 
     
     
         46 . The method of  claim 32 , wherein said RNA is fragmented RNA. 
     
     
         47 . The method of  claim 32 , wherein said RNA is isolated from a fine needle biopsy sample. 
     
     
         48 . The method of  claim 32 , further comprising creating a report summarizing the data obtained by the determination of said gene expression levels. 
     
     
         49 . The method of  claim 48 , wherein said report includes prediction of the likelihood of long term survival of said patient without the recurrence of cancer. 
     
     
         50 . The method of  claim 49 , wherein said report includes recommendation for a treatment modality of said patient. 
     
     
         51 . The method of  claim 32  further comprising the step of subjecting the expression level data to multivariate analysis using the Cox Proportional Hazards model. 
     
     
         52 . The method of  claim 32  wherein the expression level is determined using RNA obtained from a formalin-fixed paraffin-embedded tissue sample. 
     
     
         53 . The method of  claim 32  wherein the expression level is determined by reverse transcriptase polymerase chain reaction (RT-PCR).