A single cell atlas of human glioma

Although tumor-propagating cells can be derived from glioblastomas (GBMs)of theproneural and mesenchymal subtypes,a gliomastem-like cell (GSC) of the classical subtype has not been identified. It is unclear if mesenchymal GSCs (mGSCs) and/orproneural GSCs (pGSCs) alone are sufficient to generate the heterogeneity observed in GBM.We performed single-cell/nuclei RNA-sequencing of 28 gliomas, and single-cell ATAC-sequencing for8 cases. We find that GBM GSCs reside ona single axis of variation, rangingfrom proneural to mesenchymal. In silico lineage tracing using both transcriptomics and genetics supports mGSCs as the progenitors of pGSCs.Dual inhibition of pGSC-enrichedand mGSC-enrichedgrowth and survival pathways provides a more complete treatment thancombinations targetingone GSC phenotype alone.This study sheds light on a long-standing debate regarding lineage relationships among GSCs and presents a paradigm by which personalized combination therapies can be derived from single-cell RNA signatures, to overcome intra-tumor heterogeneity. We performed single-cell RNA sequencing (scRNA-seq), single-nuclei RNA sequencing (snRNA-seq), single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq), and whole-exome DNA sequencing (exome-seq) of specimens from untreated human gliomas.Via in-silico transcriptomic and genetic lineage tracing of these data we defined the lineage relationships between glioma cell types.Integrating this with meta-analysis of sequencing data from The Cancer Genome Atlas (TCGA) (https://cancergenome.nih.gov/) and spatial data from The Ivy Foundation Glioblastoma Atlas Project (Ivy GAP)(http://glioblastoma.alleninstitute.org/), we mapped glioma cells to analogous cell types in the developing brain and to specific tumor-anatomical structures. From the scATAC-seq we elucidated cell-type specific cis-regulatory grammarsand associated transcription factors. Using immunohistochemistry (IHC) and automated image analysisof human GBM microarray we validated learned phenotypes at the protein level. Lastly, we performed an in vitro screen of drug combinations that target genes identified from our single-cell analysisof GSCs. Raw data not available due to privacy concerns Please note that processed data files for the GSM4119521-GSM4119530 samples have been updated on Feb 16, 2021.