Expression-driven genetic dependency reveals targets for precision oncology

BACKGROUND: Cancer cells are heterogeneous, each harboring distinct molecular aberrations and being dependent on different genes for their survival and proliferation. While targeted therapies based on driver DNA mutations have shown success, many tumors lack druggable mutations, limiting treatment options. We hypothesize that new precision oncology targets may be identified through "expression-driven dependency," where cancer cells with high expression of specific genes are more vulnerable to the knockout of those same genes. RESULTS: We developed BEACON, a Bayesian approach to identify expression-driven dependency targets by analyzing global transcriptomic and proteomic profiles alongside genetic dependency data from cancer cell lines across 17 tissue lineages. BEACON successfully identified known druggable genes, including BCL2, ERBB2, EGFR, ESR1, and MYC, while revealing novel targets confirmed by both mRNA- and protein-expression-driven dependency. The identified genes showed a 3.8-fold enrichment for approved drug targets and a 7- to 10-fold enrichment for druggable oncology targets. Experimental validation demonstrated that depletion of GRHL2, TP63, and PAX5 effectively reduced tumor cell growth and survival in their dependent cells. CONCLUSIONS: Our approach provides a systematic method to identify precision oncology targets based on expression-driven dependency patterns. By integrating multi-omics data with genetic dependency screens, we have created a comprehensive catalog of potential therapeutic targets that may expand treatment options for cancer patients lacking druggable mutations. This resource offers new opportunities for precision oncology target discovery beyond mutation-based approaches.