Hypoxic stress dysregulates functions of glioma-associated myeloid cells through epigenomic and transcriptional programs

Hypoxia is a key histopathological feature of glioblastoma, associated with tumor aggressiveness and therapy resistance. Glioma-associated microglia and macrophages (GAMs) are key players in the tumor microenvironment of glioblastoma and acquire immunosuppressive properties during tumor progression. We show that hypoxia alters key GAM identity genes, as it upregulates the expression of monocytic marker lectin galactoside-binding doluble 3 (Lgals3) and downregulates the homeostatic microglial markers purinergic receptor P2Y G-protein coupled 12 (P2ry12) and transmembrane protein 119 (Tmem119) in GAMs co-cultured with glioma cells and in glioblastoma patients' samples. We further identify hypoxia-dependent dysregulation of numerous GAM subtypes and functional markers, which is associated with chromatin accessibility changes, as determined using assay for transposase-accessible chromatin with sequencing (ATAC-seq). Hypoxia upregulates lipid storage-related genes and accumulation of lipid droplets, which can be reversed upon restoration of histone H3 lysine 27 acetylation (H3K27ac) with a histone deacetylase inhibitor. We emphasize the importance of hypoxic stress as a strong intratumoral and epigenomic regulator of myeloid cell functions, which adds a new dimension to the characterization of particular GAM subpopulations.