The oncometabolite D-2-hydroxyglutarate promotes DNA hypermethylation at lineage-specific enhancers controlling microglial activation in IDHmut gliomas

Tumor-associated macrophages and microglia (TAMs) are highly abundant myeloid cells in gliomas, with their phenotype and immune response determined by ontogeny and microenvironment. TAMs display distinctive transcriptional programs according to the IDH mutation status but the underlying regulatory mechanisms remain largely unknown. Herein, we uncovered that CD11B+ myeloid cells in human IDHmut gliomas exhibit DNA hypermethylation predominantly at distal enhancers. This hypermethylation was linked to decreased expression of genes involved in inflammatory responses and glycolytic metabolism, and the inactivation of transcription factors that regulate the microglial response to environmental stimuli. Prolonged exposure of human primary microglia to D-2-hydroxyglutarate (D-2HG) inhibits TET-mediated 5mC oxidation, resulting in a reduced accumulation of global 5hmC levels. We confirmed high 5mC/5hmC ratios at lineage-specific enhancers, by analyzing CpGs at single-base resolution. D-2HG-treated microglia show reduced proinflammatory capacity and enhanced oxidative phosphorylation, consistent with the remodeled enhancer landscape. Conversely, depletion of D-2HG following treatment of a glioma patient with a mutant IDH inhibitor unleashed an activating response in microglia, as assessed by snRNA-seq. Our findings provide a mechanistic rationale for the hyporesponsive state of microglia in IDHmut gliomas and support the concept that oncometabolites may disrupt the function of immune cells residing in the tumor microenvironment.