A functional subpopulation of human glioma associated macrophages linked to malignant glioma progression [mtscATAC-seq]

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. Immune cells were first isolated from dissociated glioma samples via CD45+ MACS followed by FACS purification for mGAM and non-mGAM populations. Peripheral blood from the same patient was collected and PBMCs isolated using gradient separation (Ficoll-Paque PLUS, Cytiva, USA) followed by CD14 MACS sorting to obtain monocytes. Purified viable cells were used as input to the mtscATAC-seq protocol.