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

Abstract Glioblastoma is the most aggressive and lethal adult brain tumour. The cellular heterogeneity within the tumour microenvironment plays a crucial role in the complexity of treatment and poor survival. Glioblastoma is typically classified into three molecular subtypes (classical, mesenchymal and proneural) associated with EGFR, NF1 and PDGFRA genetic drivers, respectively. Yet, the role of these driver mutations in the glioblastoma tumour microenvironment is not fully understood. Here, we used single-cell RNA sequencing of genetically engineered mouse glioblastoma models incorporating human-relevant EGFRvIII, PDGFB and NF1 driver mutations to characterize the genotype–immunophenotype relationship of the three glioblastoma subtypes systematically. Murine genetic glioblastoma models at the single-cell level effectively mimic the inter- and intra-tumour heterogeneity found in human counterparts. Our analysis revealed that PDGFB-driven tumours were more proliferative and enriched for Wnt signalling interactions, whereas EGFRvIII-driven tumours showed an elevated interferon signalling response. Moreover, Nf1-silenced tumours displayed higher myeloid abundance, myeloid immunosuppressive interactions involving Spp1, regulatory T-cell 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 glioblastoma.