PRMT5 抑制的多组学表征识别出 MTAP 缺失癌症中联合治疗的脆弱性

Homozygous deletion of CDKN2A on chromosome 9p21 is the most frequent genomic loss in cancer and often extends into the adjacent MTAP gene. This co-deletion occurs in ~10% of tumors (>200,000 cases annually in the U.S) and is particularly enriched in aggressive malignancies such as glioblastoma (GBM), malignant peripheral nerve sheath tumors (MPNST), pancreatic ductal adenocarcinoma (PDAC), and non-small cell lung cancer (NSCLC). In these tumors, MTAP loss leads to intracellular accumulation of its substrate methylthioadenosine (MTA), which partially inhibits protein arginine methyltransferase 5 (PRMT5) by competing with its methyl donor S-adenosyl-methionine (SAM) at the active site, reducing its ability to symmetrically dimethylate arginine residues (SDMA). This creates a synthetic-lethal dependence on residual PRMT5 activity and has driven the development of MTA-cooperative PRMT5 inhibitors, which show encouraging preclinical activity and single-agent response rates of 21-29% in early clinical trials in the advanced, refractory setting. We therefore hypothesized that defining the molecular consequences of PRMT5 inhibition could guide patient stratification and inform rational combination strategies capable of enhancing therapeutic efficacy and preventing resistance. To test this, we performed multi-omics profiling, including short- and long-read transcriptomics and whole-cell proteome mass spectrometry, across MTAP-deleted NSCLC, GBM, and PDAC models, integrating these data with in-house and publicly available datasets to define PRMT5-dependent methyl events and their downstream molecular consequences. Transcriptomic and proteomic analyses revealed strong and consistent pathway-level alterations across models following PRMT5 inhibition, including activation of MAPK signaling, a compensatory program validated to synergize with PRMT5 inhibitors in vitro and in vivo. Across eight distinct PRMT5 methyl-enrichment mass spectrometry studies, we identified 180 PRMT5 substrates enriched mainly for proteins involved in RNA metabolism and pre-mRNA splicing, including multiple snRNP-associated components of the spliceosome. We therefore examined the splicing consequences of PRMT5 inhibition and observed widespread increases in intron retention and reductions in exon skipping, with enrichment of splicing alterations in transcripts involved in DNA damage repair across models. Overall, this study provides a comprehensive substrate map of PRMT5 and characterizes the transcriptional, proteomic, and splicing programs activated upon its inhibition across MTAP-deleted GBM, NSCLC, and PDAC models. These findings highlight pathway and splicing-associated vulnerabilities as targets for rational combination strategies and establish a mechanistic framework to guide biomarker development and future therapeutic exploration.