SMARCA4-loss increases RNA Polymerase II pausing and elevates R-loops to inhibit BRCA1-mediated repair in ovarian cancer
Small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) is a rare and aggressive cancer mainly affecting young women. It is driven by inactivating mutations in SMARCA4 (BRG1), a key SWI/SNF chromatin remodeling gene. To reveal its druggable vulnerabilities, we perform a compound screen and find that SCCOHT cells and tumors are sensitive to PARP inhibitors. Paradoxically, SCCOHT displays BRCA-deficient traits while retaining wild-type BRCA1 expression. This is caused by elevated R-loop accumulation in SCCOHT cells and tumors, which sequesters BRCA1 limiting its availability for DNA damage repair. Through proximity-dependent biotin identification approach using pathogenic SMARCA4 variants that retain protein expression, we uncover that SMARCA4 promotes RNA polymerase II (Pol II) elongation by mediating the assembly of the polymerase-associated factor 1 (PAF1) complex and its association with Pol II.  Thus, SMARCA4 loss increases Pol II pausing, resulting in elevated R-loops and BRCA1 redistribution. This leads to the sensitivity of SCCOHT cells and tumors to PARP inhibitors, which is further enhanced by addition of a CDK9 inhibitor targeting Pol II elongation. Our findings reveal a link between SMARCA4 loss and perturbed Pol II elongation causing hampered BRCA1 repair, which can be exploited therapeutically to target SCCOHT. (These studies were supported by Canadian Institute of Health Research (CIHR) grants PJT-156233 and PJT-438303). Overall design: FT190 cells expressing shRNA against SMARCA4 or PLKO control were collected. CUT&RUN for BRCA1 and DRIP (DNA:RNA Immunoprecipitation)-seq for Rloop was performed in indiucated cells.