WRN helicase regulates mitophagy by resolving an intricate nexus of G-quadruplexes-R loops-ATG7 pre-mRNA maturation in cancer

Werner syndrome (WS) is a progeroid and cancer-predisposition disorder caused by loss of the Werner RECQ helicase-exonuclease (WRN), a key genome-maintenance enzyme essential for replication-stress signalling and DNA-repair. WS patients also develop metabolic abnormalities, including fatty-liver and diabetes, suggesting a link between WRN-deficiency and mitochondrial-dysfunction. WRN is frequently epigenetically silenced in cancers, yet its precise role in mitochondrial homeostasis in cancer remains unclear. Here, we define a role for WRN in regulating mitophagy and autophagy in cancer. WRN-deficient cells show defective mitochondrial respiration, morphology, and mitophagosome/autophagosome-maturation under basal and cisplatin-induced stress. Mechanistically, WRN-loss causes strong reduction of ATG7-protein, compromising autophagosome-biogenesis. Chromatin immunoprecipitation reveals accumulation of unresolved G-quadruplex structures (G4-DNA) across the ATG7-locus in WRN-deficient cells. Paradoxically, ATG7-mRNA expression is elevated despite reduced ATG7-protein in WRN-deficient cells, indicating a post-transcriptional defect. Further, we show that WRN resolves G4-DNA which prevent R-loops formation and interacts with the mRNA-processing factor U2AF35, without its helicase-exonuclease functions, to promote maturation of nascent ATG7 transcripts. In cancer patients, WRN level also inversely correlated with post-transcriptional defects in ATG7 mRNA. Collectively, our findings suggest pivotal association of WRN-loss in autophagy fidelity, which may further contribute to oncogenic transformation in WRN-deficient tissues and exacerbate cancer susceptibility in WS-patients.