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

Malignant gliomas are primary brain cancers with a poor prognosis marked by rapid progression. Pro-tumorigenic Glioma associated macrophages (GAM) within the tumor microenvironment have been implicated in disease progression however identification and isolation of human pathogenic functional subsets has been elusive. Macrophages are highly plastic innate immune cells, and their functional specification is driven by transcription factor-associated gene regulatory networks; however the core regulatory transcription factors that govern GAM functions remain unclear. Here we apply parallel single cell RNA and ATAC sequencing and gene regulatory network inference to derive the imprint of the glioma tumor microenvironment on transcriptional program specification in GAMs; we identify cell surface markers to prospectively isolate a functionally distinct subpopulation in human patient samples and demonstrate a pathogenic gene regulatory network linked to the transcription factor FOSL2, present in transformed high grade tumors irrespective of IDH mutation status. This subset of GAMs, termed malignancy associated GAMs (mGAMs) are spatially localized within tumor hypoxic niches with a distinct metabolomic profile; possess pro-tumorigenic functions such as increased proliferation of glioma cells, extracellular matrix protein production, invasion, angiogenesis, phagocytosis, and can induce regulatory T-cell expansion. Using mitochondrial lineage tracing we also show that mGAMs share somatic mutations with matched autologous monocytes, suggesting a common bone marrow origin. mGAMs therefore represent a functional subset of GAMs in humans and thus a potential target for therapy in malignant adult diffuse gliomas.