Essentiality-driven prediction of anticancer drug responses in preclinical and clinical contexts

Precision oncology relies on tumor molecular profiles to predict drug responses. Instead of using conventional molecular features directly, we construct predictive signatures based on gene essentiality. Here, we present DrGee, an essentiality-centered platform that infers drug sensitivity solely from gene expression profiles. The built-in DeepEEAA model integrates gene expression, gene essentiality, drug-protein affinity, and drug-gene associations to quantitatively predict IC₅₀ values. DeepEEAA achieved competitive predictive performance on independent cell line datasets (R² = 0.764; MSE = 0.9345), outperforming recent benchmark deep learning methods. DrGee prioritized four candidate drugs for the 95-D lung cancer cell line, among which BI-97C1 and trimetrexate were validated by in vitro assays and mouse xenograft experiments. Robust predictive performance was further confirmed in OVCAR8 ovarian cancer cells. In TCGA cohorts, essentiality-driven predictions stratified patients with significantly different overall survival outcomes (AUC-PR = 0.825), highlighting the translational potential of DrGee.