Human breast cancer is an incredibly diverse disease, exhibiting variety among tumor types in morphology, natural history, and therapeutic response. Multiple studies have shown that breast tumors can be segregated into distinct, reproducible subtypes, characterized by similarities in the genes they express. One subtype, called "Basal-like Tumors" (BBT) is of particular interest because it represents 10-20% of breast cancer diagnoses and it is typically associated with poor outcomes, despite being initially responsive to chemotherapy. Our work has shown that BBT occurs with significantly higher frequency in African Americans and women with germline mutations in breast cancer 1 (BRCA1). Further studies with array comparative genomic hybridization (aCGH) have shown a broader association between BBT and BRCA1-dependent DNA damage repair, with possible genomic loss of BRCA1 pathway repair enzymes. BBT clearly poses a significant challenge to the US health care system, as evidenced by the fact that if BBT were to be treated as a unique disease separate from other breast cancers, it would represent the fourth leading cause of cancer deaths among women. The accumulation of DNA damaging events from normal environmental exposure, when coupled with repair gone awry, in some cases gives rise to cancer. Given the link between BRCA1-germline mutations and BBT, our long-term objective is to determine whether the BRCA1-dependent DNA repair pathway is deficient during sporadic BBT formation using genetic, genomic, and cell biological methodologies. We will characterize copy number changes in the BBT genome using a high density aCGH tiling array and look for germline variants associated with BBT susceptibility. We will also disrupt the BRCA repair pathway using shRNA mediated gene knockdown in mammary cell lines and asses for alterations in DNA damage repair.
Our specific aims i n this proposal are: 1) Refine subtype-specific regions of tumor genomic DNA somatic gain/loss in DNA repair pathways in BBT;2) Determine if the loss of genes in BBT regions of deletion alters the BRCA1-dependent DNA repair pathway in normal mammary epithelial cells;and 3) Evaluate the DNA damage response in normal and tumor-derived human mammary cell lines and primary tumor explants. Lay Summary: The research proposed will lead to a greater understanding of how basal-like breast tumors, a leading cancer killer in women, arise. Knowledge gained from this study will aid in improving identification/classification of this tumor. Perhaps most importantly, these experiments aim to highlight potential therapeutic targets, something that has been critically lacking for this subgroup so far.