Abstract C026: Epigenetic silencing of MTAP defines a distinct class of PRMT5-inhibitor-sensitive cancers

Abstract MTAP encodes a key enzyme in methylthioadenosine (MTA) catabolism. MTAP loss, frequent across human cancers, leads to MTA accumulation and inhibition of PRMT5, a critical regulator of cell cycle and DNA repair. This metabolic vulnerability renders MTAP-deficient tumors selectively sensitive to PRMT5 inhibitors such as TNG-462 and TNG-908. Emerging data indicate that MTAP can also be epigenetically silenced via promoter hypermethylation, independent of genomic deletion, thereby evading detection by DNA-based diagnostics and excluding patients from PRMT5-targeted therapies. Here, we integrate MTAP methylation and expression profiles and evaluate PRMT5 inhibitor sensitivity across diverse tumor types. A comprehensive cohort comprising 6,187 samples with matched DNA methylation and gene expression data was assembled from 17 distinct TCGA projects. Data retrieval, raw RNA-seq read counts, and methylation data analysis were performed using the TCGAbiolinks R package, DESeq2 R package and HM450K arrays, respectively. In addition, we incorporated DNA methylation profiles from established human cell lines obtained from the ENCODE project. In vitro, MTAP-wild type cell lines (human: HCC3153 and HS578T and mouse: GL261); MTAP-null cell lines (human: MDA MB-231, RT4, RT112, UM-UC-3) and MTAP-hypermethylated cell lines (human: U87 and HepG2) were used for viability MTT assays after TNG-462 or TNG-908 treatment. Array assays revealed cg25162921 and cg00230302 probes targeting CpG sites associated with the MTAPlocus. The promoter-proximal probe cg25162921 exhibited a strong inverse correlation with MTAP expression in multiple tumor types, including lung squamous cell carcinoma (TCGA-LUSC; r=-0.48), bladder urothelial carcinoma (TCGA-BLCA; r=-0.42), and glioblastoma multiforme (TCGA-GBM; r=-0.45). We next investigated whether the mechanism of MTAP inactivation, genomic deletion and promoter hypermethylation, influenced cellular sensitivity to PRMT5 inhibition by viability MTT assy. MTAP genomic status and methylation levels were stratified at the promoter-proximal CpG site cg25162921 using DNA methylation from ENCODE project. In viability assays, MTAP-null cell lines or MTAP-hypermethylated models were more sensitive to TNG-462 and TNG-908 with a reduced IC50 compared to MTAP-wild type cell lines. We identify promoter hypermethylation as a distinct mechanism of MTAP silencing, broadening the spectrum of MTAP-low tumors beyond genomic loss. These findings support integration of epigenetic biomarkers to refine patient selection and enhance response rates in PRMT5-targeted clinical trials. Citation Format: Luis Álvarez, Dalma Muller, Lucia Paniagua, Verónica Alonso, Manuel Pedregal, Esther Cabañas Morafraile, Bernard Doger, Emiliano Calvo, Irene Moreno, Irene Gutiérrez, Juan A Ardura, Balazs Gyorffy, Victor Moreno, Alberto Ocaña. Epigenetic silencing of MTAP defines a distinct class of PRMT5-inhibitor-sensitive cancers [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2025 Oct 22-26; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2025;24(10 Suppl):Abstract nr C026.