DNA methylation in glioblastoma: insights from single-cell epigenomics

Isocitrate dehydrogenase (IDH)-wildtype glioblastoma is an aggressive brain tumor characterized by limited therapeutic options and poor survival outcomes. Beyond well-established genomic alterations, epigenetic mechanisms such as DNA methylation have gained attention for their roles in glioblastoma pathogenesis. Tumor suppressor genes are frequently silenced through promoter hypermethylation, whereas global hypomethylation of repetitive elements contributes to genomic instability and oncogenic progression. Clinically, O⁶-methylguanine-DNA methyltransferase (MGMT) promoter methylation remains an important biomarker for predicting patient response to alkylating chemotherapies. Advances in single-cell epigenomic sequencing have characterized the remarkable heterogeneity of DNA methylation within glioblastoma. Techniques including single-cell bisulfite sequencing (scBS-seq) and single-cell reduced representation bisulfite sequencing (scRRBS) provide high-resolution insights into the methylation landscapes of individual tumor cells. These analyses reveal that epigenetic diversity underlies subclonal expansion, therapy resistance, and tumor recurrence. Moreover, integrating single-cell methylation data with other modalities such as transcriptomics and proteomics offers a multidimensional view of tumor evolution and microenvironmental dynamics. Despite ongoing challenges in cost, data interpretation, and large-scale integration, single-cell epigenomics has potential applications in refining glioblastoma classification and guiding personalized therapeutic strategies in the future. This review explores emerging roles of DNA methylation in glioblastoma alongside cutting-edge single-cell techniques and translational prospects.