Glioblastoma Embryonic-like Stem Cells Exhibit Immune-Evasive Phenotype

SIMPLE SUMMARY: Most glioblastoma (GBM) patients relapse after an initial response to treatment. These aggressive traits are often associated with the presence of glioma stem cells (GSCs) within the tumor bulk, which are thought to participate in GBM therapy resistance. Given GBM cellular heterogeneity, we hypothesized that GSCs might also display cellular hierarchies associated with different degrees of stemness. Based on single-cell RNAseq data from GBM patients, we identified a subpopulation of GSCs, named core-GSCs (c-GSCs), with a similar profile to embryonic stem cells and downregulation of immune-associated pathways. In addition, we developed an in vitro induced c-GSC (ic-GSC) model resembling their tumor counterpart. The characterization of immune-privileged c-GSCs provides a valuable resource to study immune evasion mechanisms in GBM and to identify potential unexplored targets to improve immunotherapy treatments. ABSTRACT: Background: Glioma stem cells (GSCs) have self-renewal and tumor-initiating capacities involved in drug resistance and immune evasion mechanisms in glioblastoma (GBM). Methods: Core-GSCs (c-GSCs) were identified by selecting cells co-expressing high levels of embryonic stem cell (ESC) markers from a single-cell RNA-seq patient-derived GBM dataset (n = 28). Induced c-GSCs (ic-GSCs) were generated by reprogramming GBM-derived cells (GBM-DCs) using induced pluripotent stem cell (iPSC) technology. The characterization of ic-GSCs and GBM-DCs was conducted by immunostaining, transcriptomic, and DNA methylation (DNAm) analysis. Results: We identified a GSC population (4.22% ± 0.59) exhibiting concurrent high expression of ESC markers and downregulation of immune-associated pathways, named c-GSCs. In vitro ic-GSCs presented high expression of ESC markers and downregulation of antigen presentation HLA proteins. Transcriptomic analysis revealed a strong agreement of enriched biological pathways between tumor c-GSCs and in vitro ic-GSCs (κ = 0.71). Integration of our epigenomic profiling with 833 functional ENCODE epigenetic maps identifies increased DNA methylation on HLA genes’ regulatory regions associated with polycomb repressive marks in a stem-like phenotype. Conclusions: This study unravels glioblastoma immune-evasive mechanisms involving a c-GSC population. In addition, it provides a cellular model with paired gene expression, and DNA methylation maps to explore potential therapeutic complements for GBM immunotherapy.