TUBB2A and TM4SF1 Methylation Define Prognostic Subgroups in Adult-Type Diffuse Glioma

Background/Objectives: Gliomas arise from distinct subgroups driven by different genetic alterations. Gain-of-function mutations in isocitrate dehydrogenase 1/2 (IDH1/2) are frequent in a subset of gliomas and are associated with improved survival compared with wild-type tumors. IDH-mutant gliomas can be classified as having the CpG island methylator phenotype (G-CIMP), which is characterized by widespread epigenetic changes associated with IDH1 mutations. G-CIMP-based stratification provides an added improvement in glioma classification when considered alongside grade and histology. Despite the success of G-CIMP-based stratification in predicting outcome in some patients, it does not fully account for non-responders, largely due to heterogeneity within G-CIMP gliomas. Methods: Using a The Cancer Genome Atlas (TCGA) glioblastoma, IDH-wildtype discovery cohort, we identified gene-level DNA methylation and expression patterns associated with clinical outcomes, including epigenetically regulated genes such as TUBB2A and TM4SF1. Results: In an independent TCGA diffuse glioma validation cohort enriched for IDH-mutant tumors, canonical IDH-defined G-CIMP classification was applied, and promoter methylation of TUBB2A and TM4SF1 showed significant associations with overall survival. Conclusions: These findings highlight molecular heterogeneity within IDH-defined G-CIMP gliomas and demonstrate that gene-specific methylation events can refine prognostic stratification beyond IDH status alone.