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

Abstract

SummaryTumor-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 uncover that CD11B+ myeloid cells in human IDHmutgliomas 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 microglial responses to environmental stimuli. Prolonged exposure of human primary microglia to D-2-hydroxyglutarate (D-2HG) inhibited 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 an IDH mutant inhibitor was associated with enhanced microglial responses, as assessed by snRNA-seq. Our findings provide a mechanistic rationale for the hyporesponsive state of microglia in IDHmutgliomas and support the concept that oncometabolites may disrupt the function of immune cells residing in the tumor microenvironment.