Tumor-type specific methylation patterns of MTAP in human samples and cell lines

Loss of methylthioadenosine phosphorylase creates a therapeutically dependency on PRMT5, yet current strategies select patients based only on MTAP genomic deletion. We performed an integrated analysis of DNA methylation and gene expression using TCGA, TARGET and ENCODE data to identify alternative mechanisms of MTAP inactivation. A promoter-proximal CpG site (cg25162921) showed a frequent hypermethylation and strong inverse correlation with MTAP mRNA expression across multiple tumor types and cell lines, including lung squamous cell carcinoma and glioblastoma. These findings identify promoter hypermethylation as a copy-number-independent mechanism of MTAP silencing and support epigenetic profiling evaluation in tumor samples into MTAP-based precision oncology.