Single-cell dissection of the genotype-immunophenotype relationship in glioblastoma

Abstract Glioblastoma (GBM) is the most aggressive and lethal adult brain tumor. The cellular heterogeneity within the tumor microenvironment (TME) plays a critical role in the complexity of treatment and poor survival. GBM is typically classified into 3 molecular subtypes—Classical, Mesenchymal, and Proneural—associated with EGFR, NF1, and PDGFRA genetic drivers, respectively. Yet, the role of these driver mutations on the GBM TME is not fully understood. Here, we utilized single-cell RNA-sequencing of genetically engineered mouse GBM models incorporating human-relevant EGFRvIII, PDGFB, and NF1 driver mutations to systematically characterize the genotype-immunophenotype relationship of the three GBM subtypes. Murine genetic GBM models at the single-cell level effectively mimic the inter- and intra-tumor heterogeneity found in human counterparts. Our analysis revealed that PDGFB-driven tumors were more proliferative and enriched for Wnt signaling interactions, while EGFRvIII-driven tumors showed an elevated interferon signaling response. Moreover, Nf1-silenced tumors displayed higher myeloid abundance, myeloid immunosuppressive interactions involving Osteopontin, Treg infiltration, and expression of immune checkpoint molecule Ctla4. Overall, we established a human-mouse analytical platform for genotype-aware target discovery and validation, which offers promising new avenues for more effective, personalized treatments in GBM.