Alley, K. R. | Search bioRxiv

bioRxiv2025

Transcriptome-wide mapping reveals an RNA-dependent mechanism of platinum cancer drugs.

Off-target interactions frequently compromise the clinical utility of anticancer agents by driving dose-limiting toxicity and therapeutic resistance. Although RNA has been predicted to be an off-target for numerous FDA-approved drugs, the extent and functional significance of RNA off-targeting among anticancer small molecules remain poorly understood. Using a systematic drug-binding screen, we identified cisplatin, a frontline chemotherapeutic that acts canonically through DNA adduct formation, as a prominent RNA binder. We employed cisplatin as a model compound to characterize the mechanistic basis and functional impact of RNA-small molecule off-targeting. To map transcriptome-wide cisplatin-RNA interactions, we developed PlatRNA-seq, a click-chemistry-enabled RNA-binding profiling platform. Genomic and functional analyses reveal that cisplatin preferentially accumulates at RNA G-quadruplex (rG4) structures near 5' transcript ends, inducing R-loop formation. Critically, we demonstrate that cisplatin cytotoxicity is partially mediated through RNA binding, revealing a noncanonical mechanism of action. Collectively, these findings illustrate the functional consequences of RNA-small-molecule off-targeting and provide a generalizable framework for investigating small-molecule-RNA interactions, opening new avenues for therapeutic innovation.

molecular biology↗

bioRxiv2024

The Unique Pt(II)-Induced Nucleolar Stress Response and its Deviation from DNA Damage Response Pathways

The mechanisms of action for the platinum compounds cisplatin and oxaliplatin have yet to be fully elucidated, despite the worldwide use of these drugs. Recent studies suggest that the two compounds may be working through different mechanisms, with cisplatin inducing cell death via the DNA damage response (DDR) and oxaliplatin utilizing a nucleolar stress-based cell death pathway. While cisplatin- induced DDR has been subject to much research, the mechanisms for oxaliplatins influence on the nucleolus are not well understood. Prior work has outlined structural parameters for Pt(II) derivatives capable of nucleolar stress induction. In this work, we gain insight into the nucleolar stress response induced by these Pt(II) derivatives by investigating potential correlations between this unique pathway and DDR. Key findings from this study indicate that Pt(II)-induced nucleolar stress occurs when DDR is inhibited and works independently of the ATM/ATR-dependent DDR pathway. We also determine that Pt(II)-induced stress may be linked to the G1 cell cycle phase, as cisplatin can induce nucleolar stress when cell cycle inhibition occurs at the G1/S checkpoint. Finally, we compare Pt(II)-induced nucleolar stress with other small-molecule nucleolar stress-inducing compounds Actinomycin D, BMH-21, and CX-5461, and find that only Pt(II) compounds cause irreversible nucleolar stress. Taken together, these findings contribute to a better understanding of Pt(II)-induced nucleolar stress, its deviation from ATM/ATR- dependent DDR, and the possible influence of cell cycle on the ability of Pt(II) compounds to cause nucleolar stress.

cell biology↗