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 previously undescribed CBX3::ALK out-of-frame fusion identified in a case of metastatic melanoma, which produces a functional ALK protein via alternative translation initiation. The patient demonstrated a remarkable clinical response to the ALK inhibitor alectinib. Functional studies confirmed that the resulting ALK isoform retained 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 pan-cancer RNA sequencing analysis of 5,725 cases demonstrated 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.