Out-of-frame CBX3::ALK fusion drives ALK activation and therapy response

Kinase gene fusions are critical oncogenic drivers and key targets in precision oncology. Here, we report a CBX3::ALK out-of-frame fusion identified in a case of metastatic melanoma, which produces functional ALK isoforms via alternative translation start sites. The patient demonstrates a remarkable clinical response to the ALK inhibitor alectinib. Functional studies confirm that the CBX3::ALK-derived isoforms retain oncogenic signaling and tumorigenic potential. Our findings reveal limitations in current tertiary analysis strategies for functional gene fusion detection that may overlook clinically relevant out-of-frame fusions. Additional analysis of pan-cancer RNA sequencing data from 5,725 tumors and genomic datasets comprising 6,977 melanomas demonstrates that such events are rare but potentially significant. This study highlights the need to consider alternative translation mechanisms and incorporate additional analytic filters, such as 5'/3' expression imbalance, to better capture actionable out-of-frame fusion events in the era of precision oncology.