Lynch, J. T. | Search bioRxiv

bioRxiv2025

PRMT activity promotes global 3' UTR shortening in proliferating cells

Protein methyltransferase (PRMT)-catalysed arginine methylation is a widespread post-translational modification that regulates numerous RNA-binding proteins and frequently becomes dysregulated in cancer. While PRMT inhibitors have shown promise as an anti-cancer strategy, greater understanding of the downstream pathways linking arginine methylation to tumour-promoting phenotypes is needed to improve patient stratification and develop more effective therapeutic approaches. Here, we reveal arginine methylation as a critical regulator of alternative polyadenylation (APA) patterns that are fundamental to tumour progression. 3' RNA-sequencing assays uncover a rapid and global shift toward longer 3' UTR isoforms upon dual (symmetric and asymmetric) methylation (DMAi), impacting a broad range of cellular proliferation and signalling genes. Arginine methylation is required for sustaining proximal poly(A) site usage under high proliferative demand, as DMAi treatment blocks use of such sites in activated T cells, various cancer cell lines and patient-derived lung organoids. DMAi also counteracts the 3' UTR shortening caused by reduced CFIM25 expression, which normally promotes oncogenic isoforms. DMAi treatment affects APA in many of the same mRNAs as impaired cleavage and polyadenylation activity, and these mRNAs contain characteristic signatures such as high GC-content and long 3 UTRs. This systematic impact of PRMT activity on APA regulation broadens the potential utility of PRMT inhibitors as therapeutic agents for both cancer and immune-related diseases.

molecular biology↗

bioRxiv2020

Drug mechanism-of-action discovery through the integration of pharmacological and CRISPR screens

Low success rates during drug development are due in part to the difficulty of defining drug mechanism-of-action and molecular markers of therapeutic activity. Here, we integrated 199,219 drug sensitivity measurements for 397 unique anti-cancer drugs and genome-wide CRISPR loss-of-function screens in 484 cell lines to systematically investigate in cellular drug mechanism-of-action. We observed an enrichment for positive associations between drug sensitivity and knockout of their nominal targets, and by leveraging protein-protein networks we identified pathways that mediate drug response. This revealed an unappreciated role of mitochondrial E3 ubiquitin-protein ligase MARCH5 in sensitivity to MCL1 inhibitors. We also estimated drug on-target and off-target activity, informing on specificity, potency and toxicity. Linking drug and gene dependency together with genomic datasets uncovered contexts in which molecular networks when perturbed mediate cancer cell loss-of-fitness, and thereby provide independent and orthogonal evidence of biomarkers for drug development. This study illustrates how integrating cell line drug sensitivity with CRISPR loss-of-function screens can elucidate mechanism-of-action to advance drug development.

systems biology↗