Transcriptome-wide mapping reveals an RNA-dependent mechanism of platinum cancer drug [Plat-RNAseq cPDS]
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. We developed Plat-RNAseq, a click-chemistry-mediated transcriptome-wide assay to map transcriptome-wide interaction of cisplatin. Our results revealed that cisplatin binding was enriched at guanine-rich regions capable of forming RNA G-quadruplexes (rG4s). We use an rG4 ligand, carboxy-Pyridostatin (cPDS), to block access of platin-drug to rG4. This experiment test whether cPDS blocked platinum drug accumulation on cellular RNAs. Overall design: Cells were treated with cPDS (5 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 test whether rG4 ligands can influence the RNA binding of platinum drugs.