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

## TL;DR

This study shows that methylation of TUBB2A and TM4SF1 genes can help predict survival outcomes in adult diffuse glioma patients, improving risk classification beyond current markers.

## Contribution

The study identifies TUBB2A and TM4SF1 methylation as novel prognostic biomarkers in adult-type diffuse gliomas.

## Key findings

- Higher methylation of TUBB2A and TM4SF1 promoters is linked to better overall survival in glioma patients.
- These methylation patterns remain significant even after adjusting for age, tumor grade, IDH status, and 1p/19q codeletion.
- The findings reveal molecular heterogeneity within IDH-defined G-CIMP gliomas.

## Abstract

Adult-type diffuse gliomas are brain tumors that often look similar under the microscope but behave very differently in patients. Current markers, such as IDH mutation and MGMT promoter methylation, do not fully explain why some patients live much longer than others. In this study, we analyzed DNA methylation and gene expression data from two large The Cancer Genome Atlas cohorts of glioblastoma and lower-grade gliomas. We focused on two genes, TUBB2A and TM4SF1, whose activity can be switched off by methylation in their promoter regions. We found that higher promoter methylation of these genes, which corresponds to lower gene expression, was consistently linked to better overall survival, even after accounting for age, tumor grade, IDH status, and 1p/19q codeletion. Our results show that TUBB2A and TM4SF1 methylation can define clinically meaningful prognostic subgroups and may help refine risk stratification and treatment planning for patients with 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.