Diverse Gene Fusions Confer Resistance to EGFR-Targeted Therapy via Differential Modulation of BRAF Activity.

Fusion genes can be oncogenic drivers in a variety of cancer types and represent potential targets for targeted therapy. The gene is frequently involved in oncogenic gene fusions, with fusion frequencies of 0.2%-3% throughout different cancers. However, fusions rarely occur in the same gene configuration, potentially challenging personalized therapy design. In particular, the impact of the wide variety of fusion partners on the oncogenic role of during tumor growth and drug response is unknown. Here, we used patient-derived colorectal cancer organoids to functionally characterize and cross-compare fusions containing various partner genes (, and ) with respect to cellular behavior, downstream signaling activation, and response to targeted therapies. We demonstrate that 5' fusion partners mainly promote canonical oncogenic activity by replacing the auto-inhibitory N-terminal region. In addition, the 5' partner of BRAF fusions influences their subcellular localization and intracellular signaling capacity, revealing distinct subsets of affected signaling pathways and altered gene expression. Presence of the different BRAF fusions resulted in varying sensitivities to combinatorial inhibition of MEK and the EGF receptor family. However, all fusions conveyed resistance to targeted monotherapy against the EGF receptor family, suggesting that fusions should be screened alongside other MAPK pathway alterations to identify patients with metastatic colorectal cancer to exclude from anti-EGFR-targeted treatment. IMPLICATIONS: Although intracellular signaling and sensitivity to targeted therapies of fusion genes are influenced by their 5' fusion partner, we show that all investigated fusions confer resistance to clinically relevant EGFR inhibition.