Inhibition of PRMT5 triggers synthetic lethality in ARID1A-deficient endometrial cancer cells by promoting aberrant R-loop accumulation

Background: Endometrial cancer (EC) is a common malignancy of the female reproductive system. The 5-year survival rate for advanced-stage EC patients is less than 20%, highlighting an urgent need for novel therapeutic strategies. ARID1A, a key subunit of the SWI/SNF chromatin remodeling complex, is one of the most frequently mutated genes in EC, presenting a potential avenue for synthetic lethal targeting of ARID1A-deficient EC. This study aims to identify novel synthetic lethal targets for ARID1A-deficient EC and to elucidate the underlying molecular mechanisms, thereby providing new insights for clinical treatment. Methods: The PRMT5 inhibitor JNJ-64619178 was identified via high-throughput compound screening as effectively inducing synthetic lethality in ARID1A-deficient EC cells. RNA-seq, comet assays, immunofluorescence, and Dot-blot experiments were employed to investigate DNA damage and R-loop accumulation. IP-MS, Co-IP, and proximity ligation (PLA) assays were used to detect interactions within the PRMT5-DHX9-R-loop axis. Chromatin immunoprecipitation‒PCR (ChIP‒PCR) experiments were performed to confirm that ARID1A directly transcriptionally regulates PRMT5. The synthetic lethal effect between PRMT5 inhibition and ARID1A loss was further validated using EC xenograft mouse models and patient-derived organoid models (PDOs). Results: In this study, based on high-throughput drug screening, we identified that the PRMT5 inhibitor JNJ-64619178 exerts a significant synthetic lethal effect on ARID1A-deficient EC. PRMT5 inhibition promoted DNA damage, apoptosis, and R-loop accumulation in ARID1A-deficient EC. This synthetic lethality was confirmed in ARID1A-deficient mouse models and PDOs. Mechanistically, we identified an association between ARID1A, PRMT5, and DHX9. Mechanistically, ARID1A directly binds the PRMT5 promoter and regulates its expression. ARID1A loss downregulates PRMT5, impairing arginine methylation and R-loop recruitment of DHX9—a key factor in R-loop resolution. Consequently, ARID1A-deficient cells become dependent on residual PRMT5 activity to maintain R-loop homeostasis. Inhibition of PRMT5 exacerbates R-loop accumulation and DNA damage, leading to synthetic lethality. Conclusion: This study identifies a novel synthetic lethal strategy for ARID1A-deficient EC, demonstrating that the PRMT5 inhibitor JNJ-64619178 acts by disrupting R-loop homeostasis. Our findings highlight the critical role of the ARID1A-PRMT5-DHX9 axis in tumor progression, thereby providing a novel molecular target and theoretical foundation for the precision treatment of ARID1A-deficient EC.