Functional precision genomics identifies transcriptional features of therapeutic response and drug resistance in high-grade gliomas

High-grade gliomas (HGGs) are aggressive tumors with poor outcomes and limited treatment options. To identify actionable vulnerabilities and predictive biomarkers, we employed a functional precision oncology approach that combines genomic and transcriptomic profiling with drug testing in patient-derived three-dimensional culture models to enable systematic evaluation of potential targeted therapeutic strategies. While most single-agent therapies showed limited efficacy, inhibitors targeting PI3K signaling, epigenetic regulators, and survival pathways demonstrated activity in subsets of cases. Genomic alterations and transcriptional programs provided complementary insight into ex vivo drug response. Mesenchymal gliomas were particularly sensitive to BET inhibition, whereas adaptive PI3K signaling was identified as a candidate resistance mechanism. Rational combination strategies targeting complementary pathways significantly improved therapeutic efficacy across glioma subtypes. The data reveal transcriptional context as a key determinant of therapeutic response in HGG and establish a functional genomics platform to identify biomarkers, resistance mechanisms, and personalized treatment strategies.