Use of Gene Expression Markers To Screen for BRCA-1 Germline Mutations in Triple Negative Breast Cancer
Eric A Swanson, Xinmin Li, Peggy S Sullivan, Neda A Moatamed, Sophia K Apple. University of California, Los Angeles, Los Angeles, CA
Background: Breast tumors from women who harbor germline BRCA1 mutations are commonly triple-negative breast cancers (TNBC). Identifying BRCA1 germline mutations in patients with TNBC has significant clinical implications including the consideration of risk-reducing bilateral salpingo-oophorectomy and bilateral prophylactic mastectomy for the patient, as well as consideration of BRCA1 testing for blood-relatives. The gold standard for assessment of BRCA1 status is costly and involves full-sequencing and analysis of the gene. A faster, more cost effective screening test would be helpful in selecting a subpopulation of TNBC patients that should undergo full-sequencing. We sought to determine whether TNBCs from BRCA-1 positive and negative patients have a unique gene expression profile with the goal of developing a PCR-based screening test for the BRCA1 germline mutation.
Design: TNBC specimens from five confirmed BRCA1-positive and four negative patients were obtained in formalin fixed paraffin embedded blocks. Tumor cells were dissected from the blocks using a dissection microscope. Total RNA was isolated using the Ambion Recover ALL Kit, amplified using the Nu-GEN WT-Ovation® FFPE RNA Amplification System, labeled with the FL-Ovation® cDNA Biotin Module V2, and hybridized to the Affymetrix Gene Chip® Human U133 Plus 2.0 Array. Raw data was analyzed using the Partek® Genomics Suite Version 6.4. Differentially expressed genes were selected at >=1.5 fold and p<0.05.
Results: 119 differentially expressed genes were identified between BRCA1-positive and BRCA1-negative tumors. Of those, 18 are cellular function and maintenance-related genes (p=2.69E-03-4.59E-02), 16 are cell cycle-related genes (p=3.02E-03-4.59E-02) and 12 are cell-cell signaling & interaction-related genes (p=1.45E-03-4.87E-02). The ERK/MAPK signaling pathway was significantly enriched, with MAPKSP and ATF1 over-expressed in the BRCA1-positive tumors, and RAP1A under-expressed. Both ERBB3 and SOS2 were overexpressed in the BRCA1 group, which belong to the Her2 signaling pathway in breast cancer. Using a gene signature profile, we developed a regression index which is predictive for BRCA1 positivity.
Conclusions: This study demonstrates that TNBC from BRCA1-positive patients have a unique gene expression profile compared with tumors from BRCA1-negative patients. BRCA1 positive TNBCs showed increased expression of genes involved in cell growth & proliferation. Our data demonstrate a rapid and cost-effective screening test that can identify TNBC patients with BRCA1 germline mutations.
Monday, March 19, 2012 9:30 AM
Poster Session I Stowell-Orbison/Surgical Pathology/Autopsy Awards Poster Session # 16, Monday Morning