Transcriptome-wide mapping reveals an RNA-dependent mechanism of platinum cancer drugs [Plat-RNAseq A549]

Clinically used small molecules has been predicted to off-target to RNAs. However, the extend of this interaction is small molecule cancer therapeutics has not been characterized. Here, we screened for anticancer smalll molecules for their RNA interactions and uncovered widespread RNA off-targeting. Cisplatin was found to be one among the RNA binders. We used it as a model agent to identify the specific transcripts it interact with. To accomplish this, we developed Plat-RNAseq, a click-chemistry-mediated transcriptome-wide assay. Our results revealed that cisplatin binding was enriched at guanine-rich regions capable of forming RNA G-quadruplexes (rG4s) .We found that the recruitment of cisplatin to rG4s partially contributed to its cytotoxicity, revealing a noncanonical mechanism of action for this widely used chemotherapeutic agent. Overall design: Cells were treated with Cisplatin (10 µM) or DMF for 6 hours followed by 1,3-platin (30 µM). The cells were harvested 18 hours after 1,3-platin treatment and proecessed according to the Plat-RNAseq protocol described below. The goal of the experiment is to identify RNAs bound specifically by the chemotherapeutic drug cisplatin in A549 cells.