Distinct transcriptional and functional modules mediate resistance to targeted therapy in glioblastoma

To dissect mechanisms underlying drug resistance, we combined single cell RNA-sequencing (scRNA-seq) and functional genomic screens following MEK or SHP2 inhibition in preclinical GBM models. ScRNA-seq of mouse intracranial xenografts revealed that although mesenchymal-like GBM subpopulation exhibits heightened sensitivity to both MEK or SHP2 inhibition, each targeted therapy induces distinct transcriptional signatures.

Genome-wide CRISPR interference (CRISPRi) screens identified shared mediators of MEK or SHP2 inhibitor sensitivity enriched for the conserved downstream effector Ras/RAF/MEK pathway. However, genes uniquely mediating SHP2 inhibitor response were enriched for Ras/RAF/MEK-independent signaling modules such as SRC family kinases, GSK3B, and SMAD proteins regulating cell adhesion and differentiation. Perturb-seq of 39 target genes following MEK or SHP2 inhibition identified 10 discrete clusters with distinct effects on Ras signaling and cellular phenotypes.