Diverse BRAF 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 BRAF gene is frequently involved in oncogenic gene fusions, with fusion frequencies of 0.2-3% throughout different cancers. However, BRAF 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 BRAF during tumor growth and drug response is unknown. Here, we used patient-derived colorectal cancer organoids to functionally characterize and cross-compare BRAF fusions containing various partner genes (AGAP3, DLG1 and TRIM24) with respect to cellular behavior, downstream signaling activation and response to targeted therapies. We demonstrate that 59 fusion partners mainly promote canonical oncogenic BRAF activity by replacing the auto-inhibitory N-terminal region. Additionally, the 59 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 BRAF fusions conveyed resistance to targeted monotherapy against the EGF receptor family, suggesting that BRAF fusions should be screened alongside other MAPK pathway alterations to identify metastatic CRC patients to exclude from anti-EGFR targeted treatment. Implications: Although intracellular signaling and sensitivity to targeted therapies of BRAF fusion genes are influenced by their 59 fusion partner, we show that all investigated BRAF fusions confer resistance to clinically relevant EGFR inhibition.