Chromatin Blueprint Of Glioblastoma Stem Cells Reveals Common Drug Candidates For Distinct Subtypes

Glioblastoma (GBM) is a form of brain cancer with extremely poor prognosis, and for which the standard treatment, surgery, radiotherapy and temozolomide, provides minimal response in only a small subset of patients. This can be partly imputed to the high level of heterogeneity observed between and within patient tumors, and despite extensive characterisation and stratification of the bulk primary tumors, no patient-specific therapies have been successfully developed. GBM tumors contain a subpopulation of cells, termed glioblastoma stem cells (GSCs), which functionally closely resemble neural precursor cells, have high self-renewal, tumor-initiating capacity, and have been shown to drive disease progression in vivo. We have previously shown that while GSCs derived from different patient tumors share numerous common features in their chromatin accessibility landscape, striking differences do exist between groups of GSCs that exhibit different functional properties, such as differentiation capacity. Here we performed an integrated analysis of chromatin accessibility (ATAC-seq), DNA methylation (EPIC arrays), and gene expression (RNA-seq) on a cohort of GSCs and identified three distinct GSC subtypes. Each of these subtypes is regulated by a specific set of essential transcription factors. Through a single-cell clonal analysis, we show that multiple GSC subtypes are present in each GBM primary tumor. Finally, using an extensive drug screen followed by in vitro validation, we identified subtype-specific candidate drugs as well as a compound that reduces proliferation and self-renewal across all GSC subtypes: perphenazine, a dopamine/serotonin receptor ligand.