RNA exonuclease REXO4 resolves m6A-marked R-loops and suppresses anti-tumor immunity [RNAseq]

Transcription blockage frequently occurs in tumor cells, and aberrant R-loop forming during this process drives genome instability. However, the regulation of R-loop homeostasis and its dysregulation in tumorigenesis are still under investigation. Here, we report that the RNA exonuclease REXO4 preserves genome stability by reducing excessive R-loops. Mechanistically, REXO4 resolves R-loops by 3’-5’ exonucleolytic cleavage of the RNA strand on RNA-DNA hybrids, where an accessible end is created by RNA endonuclease and N6-methyladenosine (m6A) modification on RNA moieties promotes REXO4 localization and R-loop removal. REXO4 ablation-induced DNA damage stimulates interferon response and tumor immune infiltration to suppress squamous cell carcinoma (SCC) growth and metastasis. Importantly, targeting the exonuclease activity of REXO4 via the inhibitor we developed synergizes with PD-1 blockade to inhibit SCC progression by recruiting and activating CD8+ T cells. Thus, our study provides mechanistic insight into how m6A couples with exonuclease in R-loop clearance and genome maintenance, and uncovers a druggable epi-transcriptional machinery that blocks innate immune response and enables SCC immune evasion.