Abstract 1646: Beyond BRCA: Discovery of novel drivers of homologous recombination deficiencies in cancer

Abstract

Abstract Since the discovery of BRCA1 and BRCA2 mutations as cancer risk factors, we have gained much understanding of their role in maintaining genomic stability through homologous recombination (HR) DNA repair. However, mutations in BRCA1/2 and other classical HR proteins such as RAD51 and PALB2 only identify 10-20% of TCGA patients who display HR deficiencies, indicating that we do not understand the vast majority of HR defects. Here, we leveraged the abundance of molecular characterization from TCGA patients for network analysis to fill this knowledge void. We discovered that over half of HR deficiencies originate outside of canonical DNA damage response genes, with particular enrichment for RNA binding proteins (RBPs). Experimental techniques validated over 90% of our predictions in a panel of 50 genes tested by siRNA, as well as 30/31 additional engineered mutations identified in TCGA patients. We further cross-validated these findings in independent patient cohorts, finding that the identified RNA processing mutations again enriched for HR deficient patients to an equal or greater degree than mutations in DNA damage genes. Using a series of experimental approaches, including protein interactome screening, RNA sequencing, and quantitative imaging cytometry, we probed how loss of RBP function induced global DNA damage response rewiring, including changes in RNA splicing, protein-protein interactions, and recruitment of repair factors to DNA damage sites. Clinically, defects in HR are known to promote cancer initiation, but also sensitize cells to targeted therapies such as PARP inhibition. We found that depletion RBPs from PARP-resistant triple-negative breast cancer cells induced sensitivity to multiple PARP inhibitors, indicating that this could identify new cohorts of patients who may benefit from PARP inhibition, beyond the small number of BRCA1/2-mutant patients. Moreover, we find that the identified RBP genes are significantly enriched for genes associated with cancer risk identified through GWAS. In patients, HR deficiencies were not equally distributed across all demographics, so preferential screening of those most at risk could further heighten this benefit. Thus, these novel drivers may show clinical relevance both for treatment stratification and for identifying individuals at high risk for cancer development to improve patient outcomes. Taken together, this exhaustive study greatly expands our repertoire of known drivers of HR deficiencies and mechanisms of damage repair, which may impact research from the most basic biology studies to clinical screening and stratification. Citation Format: Nidhi Sahni, Daniel McGrail, Yongsheng Li, Gordon Mills, Song (Stephen) Yi. Beyond BRCA: Discovery of novel drivers of homologous recombination deficiencies in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1646.