Longitudinal changes in DNA methylation in IDH-mutant glioma fuel disease progression through altered cell state differentiation [scRNA-seq]

IDH-mutant gliomas are initially slow-growing but invariably progress to fatal disease. Major gaps remain in our understanding of the molecular underpinnings and cellular dynamics that drive IDH-mutant evolution. To address this, we integrated joint-capture multi-omic single-cell profiling of DNA methylation, transcriptome and genotype in a longitudinal cohort of 35 IDH-mutant gliomas. Transcriptional and epigenetic comparisons of cell states during glioma progression revealed increased stem-like states, decreased differentiation and identified potential cell states regulators. Single-cell DNA methylation analysis demonstrated methylation loss in progressed tumors, however global DNA methylation was similar between different malignant cells states within individual tumors. This suggests that lower DNA methylation is not due to a change in cell state composition, but rather that it may alter cell state landscapes. To address whether decreased methylation in progressed tumors affects cellular dynamics, we applied a quantitative framework to directly measure cell state heritability and plasticity based on transcriptional annotation of high-resolution phylogenetic trees in clinical samples. Our analysis suggested that decreased methylation reshapes cellular architecture to increased heritability of stem-like states and decreased differentiation. Our study provides insight into the functional impact of DNA methylation on glioma evolution, integrating transcriptional cancer cell states with epigenetic encoding and cell state transition dynamics during cancer progression.