Excessive transcription-replication conflicts are a vulnerability of BRCA1-mutant cancers

BRCA1 primarily functions to maintain genomic integrity; therefore, mutations in BRCA1 are associated with increased risk of developing breast (≥70%) and ovarian (≥40%) cancers. Additionally, tumors arising from BRCA1 mutations are typically high grade and recurrent in nature. Thus, there is an urgent need to identify novel optimal therapeutic options for the majority of these patients. Herein, we performed a targeted CRISPR-Cas9 dropout screen and identified Methylphosphate Capping Enzyme, MEPCE, as a potential synthetic lethal interactor of BRCA1. Mechanistically, depletion of MEPCE in a BRCA1-deficient setting results in increased RNA polymerase II redistribution, R-loop accumulation, as well as replication stress, concomitantly contributing to transcription-replication collision events. These factors compromise genomic integrity, thereby resulting in loss of viability of BRCA1-deficient tumor cells. We also identified RNA polymerase II-associated factor I, PAF1, as a synthetic lethal interactor of BRCA1. Similar to MEPCE depletion, loss of PAF1 in a BRCA1-deficient setting results in R-loop accumulation, transcription-replication conflicts, and cell death. Our study highlights the dependence of BRCA1-defective tumors on factors such as MEPCE and PAF1 that suppress transcription-replication conflicts through RNAPII pausing and release regulation to maintain genomic stability. This highlights the untapped potential of factors such as MEPCE as novel therapeutic targets for the treatment of cancers associated with BRCA1 mutations. ChIP-seq of RNA polymerase II and RNA polymerase II phospho-Serine2 in WT and MEPCE depleted MDA MB 436 cells DRIP-seq in WT and MEPCE depleted MDA MB 436 cells