Background Gliomas are recalcitrant tumors of the central nervous system. The tumor immune microenvironment (TIME) in gliomas is considered immunosuppressive and making it difficult to treat these tumors with conventional immunotherapy approaches, therefore a better characterization of the immune cell repertoire is needed to fully understand the tumor immune contexture. While single-cell RNA-sequencing (scRNA-seq) approaches have revealed the transcriptional heterogeneity, the gene regulatory landscape at the chromatin level is quintessential for a deeper understanding of lineage and signal-dependent transcription factors (TFs) induced in the brain TIME.
Methods We performed single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) on ~90,000 tumor-associated and sorted CD45+ leukocytes from fourteen genomically classified patients comprising IDH-mutant primary (IMP; n=4), IDH-mutant recurrent (IMR; n=3), IDH-wild type primary (IWP; n=3), or IDH-wild type recurrent (IWR; n=4) gliomas (hereafter referred as glioma subtypes) and two non-glioma brains (NGBs) as controls. The resulting data were quality checked and processed using Cell Ranger ATAC-seq pipeline and trajectory analyses were performed using Monocle2.
Results Using scRNA-seq data from matched specimens and gene tagging approaches, we identified twenty-six clusters of myeloid and seventeen clusters of lymphoid populations across and within gliomas. In this study, we exclusively focused on myeloid subpopulations, which were resolved into microglia and non-microglia myeloid cell subsets. Concordant with our scRNA-seq data, we identified all cell types including monocytes, monocyte-derived cells (MDCs), and dendritic cells by using differential gene accessibility (DGE) analyses. Importantly, although MG from all samples clustered differently, NGB and IM subtypes exhibited concordance in DGE and were separate from IWP and IWR subtypes. Reconstruction of the cell trajectories demonstrated that enhancers for TFs related to mesenchymal transition in GBM such as NF-kB and CEBPB were accessible from normal to tumor-associated microglia. On the other hand, tissue-associated macrophages exhibited enhanced calcium-regulated NFAT TF accessibility. Tumor-associated IWP and IWR myeloid cells also showed a gain of DGE of apoptosis and a reduction of proliferation-related genes.
Conclusions Our studies demonstrate that in addition to the previous dogma of myeloid mediated immune suppression that contributes to tumor immune escape, epigenomic reprogramming in the brain TIME leads to unexpected activation of transcriptional pathways that can trigger transdifferentiation and cell death of myeloid cells further promoting tumor progression. In summary, we provide an unparalleled epigenomic landscape of glioma-associated myeloid cells that may have translational implications.
Acknowledgements This study in Krishna Bhat’s laboratory was supported by the generous philanthropic contributions to The University of Texas (UT) MD Anderson Cancer Center (MDACC) Moon Shots Program™, Marnie Rose Foundation, NIH grants: R21 CA222992 and R01CA225963. This study was partly supported by the UT MDACC start-up research fund to Linghua Wang and CPRIT Single-Core grant RP180684 to Nicholas Navin.
Trial Registration NA
Ethics Approval The brain tumor/tissue samples were collected as per MD Anderson internal review board (IRB)-approved protocol numbers LAB03-0687 and, LAB04-0001. One non-tumor brain tissue sample was collected from a patient undergoing neurosurgery for epilepsy as per Baylor College of Medicine IRB-approved protocol number H-13798. All experiments were compliant with the review board of MD Anderson Cancer Center, USA.
Consent Written informed consent was obtained from the patient for publication of this abstract and any accompanying images. A copy of the written consent is available for review by the Editor of this journal
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