Transcriptome-wide mapping reveals an RNA-dependent mechanism of platinum cancer drugs [ChIP-seq]

Small molecules developed to target proteins and DNA may also bind RNA, but the extent and biological significance of these interactions remain poorly defined. Here, we systematically profiled RNA interactions of clinically approved chemotherapeutics and uncovered widespread RNA off-targeting. Cisplatin, a frontline chemotherapeutic for solid tumors, emerged as a prominent RNA-binding drug. To map these interactions in vivo, we developed Plat-RNAseq, a click-chemistry-mediated transcriptome-wide assay. Cisplatin binding was enriched at guanine-rich regions capable of forming RNA G-quadruplexes (rG4s) and preferentially accumulated at the 5' ends of nascent transcripts that exhibited rG4 enrichment and R-loop formation. Cisplatin stabilized pre-formed rG4s while interfering with their de novo assembly, thereby altering RNA structure and function. The recruitment of cisplatin to rG4s contributed to its cytotoxicity, revealing a noncanonical mechanism of action for this widely used chemotherapeutic agent. Consistent with this mechanism, the expression level of rG4 cisplatin-RNA targets predicted the platinum sensitivity in ovarian cancer patients. Collectively, these findings broaden platinum pharmacology by revealing RNA interactions as a functionally relevant, non-canonical component of cisplatin's mechanism of action. Our study highlights the importance of incorporating RNA interactions into drug design and establishes a framework for considering RNA as a functionally relevant target in small-molecule therapeutics. Overall design: A2780 ovarian cancer cells were treated with cisplatin (12.5 µM) 1 hour. Chromatin Immunoprecipitation was performed to assess the chromatin distribution of RNA Polymerase II in response to cisplatin treatment.