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

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 employed BG4-RIP-seq to identify the rG4 harboring RNAs in cisplatin-treated A2780 cells. Overall design: Cells were treated with Cisplatin (10 µM) 6 hours followed by 1,3-platin (30 µM). The rG4 enriched RNAs were pull down using BG4 antibody that recogning G-quadruplexes. The goal of the experiment was to catalogue RNAs that harbor rG4 in cisplatin treated A2780 cells.