A functional subpopulation of human glioma associated macrophages linked to malignant glioma progression

Malignant gliomas are progressive brain cancers with poor prognosis. Pro-tumorigenic glioma associated macrophages (GAM) have been implicated in disease progression however identification of pathogenic functional subsets is lacking. Macrophage functional specification is driven by transcription factor-associated gene regulatory networks, yet the core regulatory transcription factors that govern GAM functions remain unclear. Here we apply single cell RNA/ATAC sequencing to derive the imprint of the glioma tumor microenvironment on GAM transcriptional program specification and identify cell surface markers to prospectively isolate a functionally distinct subpopulation of GAMs in human samples present high grade tumors irrespective of IDH mutation status. This subset of GAMs, termed malignancy associated GAMs (mGAMs) spatially localize to hypoxic metabolic niches and possess a multitude of pro-tumorigenic functions. mGAMs also share somatic mutations with monocytes, suggesting a common bone marrow origin. mGAMs therefore represent a functional subset of GAMs in humans and a potential therapeutic target. Overall design: Glioma-associated macrophages are thawed and stained for mGAM markers for Fluorescence-activated Cell Sorting (FACS). Sorted cells are then crosslinked in PBS with 1% formaldehyde for 10 min at room temperature, quenched with 0.125M glycine for 5 min and washed in PBS with protease inhibitors (Millipore Sigma, USA) three times before being snap frozen in cryotubes.