PAF1c depletion confers chemoresistance to topoisomerase inhibitors

The human RNA polymerase II-associated factor 1 complex (PAF1c) functions in transcriptional elongation and mRNA maturation. PAF1c is composed of several subunits: PAF1, CDC73, LEO1, CTR9, RTF1, and SKIC8. Besides its role in transcription, PAF1c subunits have been reported to be associated with tumorigenesis through maintaining cancer genome stability. In this study, we show that depletion of PAF1c leads to a pronounced accumulation of R-loops, which in turn results in an increase in DNA damage. Moreover, we confirmed that PAF1c deficiency increases the cytotoxicity of several DNA-damaging agents, including hydroxyurea (HU), cisplatin (CDDP), methyl methanesulfonate (MMS), and bleomycin (BLM). Unexpectedly, PAF1c depletion confers tolerance specifically to topoisomerase inhibitors, such as camptothecin (CPT), etoposide (ETOP), and doxorubicin (DOX). Further investigation revealed that the resistance to topoisomerase inhibitors induced by PAF1c depletion occurred specifically in G1-but not S-phase cells. Mechanistically, PAF1c depletion paradoxically decreases CPT-induced accumulation of R-loops by impeding mRNA elongation in G1-phase cells, thereby reducing CPT-induced cell death. Collectively, our findings demonstrate that loss of PAF1c subunits not only promotes genomic instability through R-loop accumulation but also alters cellular responses to DNA-damaging agents, conferring resistance particularly to topoisomerase inhibitors. This study underscores the critical role of PAF1c in maintaining genome stability and provides a rationale for developing new therapeutic strategies in cancer treatment.