We and others have shown that IDH-mutant astrocytomas and oligodendrogliomas share a common lineage hierarchy and a common cell of origin. However, IDH-mutant astrocytomas are infiltrated with immunosuppressive myeloid cells from the periphery to a degree not observed in IDH-mutant oligodendrogliomas. The abundance of blood-derived myeloid cells is prognostic in IDH-mutant glioma, and myeloid-derived suppressive cells are a barrier to emerging immunotherapies. Nonetheless, the cause of the differences observed between IDH-mutant subtypes is unknown. We performed single-cell RNA sequencing (scRNA-seq) and/or single-cell assay for transposon-accessible chromatin sequencing (scATAC-seq) on a cohort of 30 human primary IDH-mutant gliomas, including both astrocytomas and oligodendrogliomas. We integrated these single-cell multi-omics data to elucidate receptor-ligand interactions between tumor cells and myeloid cells, as well as the cis-regulatory grammars and associated transcription factors regulating these interactions. We validated these interactions in situ using imaging mass-cytometry on human specimens. We identified macrophage colony-stimulating factor (CSF1) and other genes responsible for myeloid cell chemotaxis, interlukin 10 (IL10), transforming growth factor beta (TGFB1) and genes responsible for promoting aberrant myeloid activation, as differentially expressed and showing differential chromatin accessibility between astrocytomas and oligodendrogliomas. The promoters of these genes were enriched for STAT3, SOX2, and SOX17/OCT4 recognition motifs, which were also differentially enriched between astrocytomas and oligodendrogliomas in our scATAC-seq data and differentially expressed in our scRNA-seq data. Since the scATAC-seq peaks in these genes correlated with known binding sites of the chromatin-modifying enzyme ATRX, and since ATRX possesses loss-of-function mutations in over %80 of IDH-mutant astrocytomas but almost never in oligodendrogliomas, we hypothesize that the observed differences in myeloid abundance are driven by a loss of ATRX binding in key chemotactic and immunosuppressive cytokines and their upstream transcription factors. To test this hypothesis, we knocked out ATRX in a a syngeneic, immunocompetent glioma mouse model using CRISPR and profiled the resulting tumors via a battery of genomics and protein-level assays. We conclude that the differences in immune composition between IDH-mutant glioma subtypes are due to genetics. In particular, ATRX loss of function in IDH-mutant astrocytoma leads to chromatin changes in STAT3 and downstream effector cytokines, resulting in a greater influx of immunosuppressive myeloid cells.
Citation Format: Lin Wang, Husam Babikir, Karin Shamardani, Francisca Catalan, Aaron Diaz. The differences in immune composition observed between astrocytomas and oligodendrogliomas are due to genetics [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5096.