Fusion-positive rhabdomyosarcoma oncofusions share a common interactome

Fusion-positive rhabdomyosarcoma (FP-RMS) arises from at least seven distinct oncofusions sharing a common PAX3/7 N-terminal DNA-binding domain fused to divergent C-terminal partners. How different oncofusions produce the same cancer was unknown. Here we show they are functionally interchangeable, associate with a shared protein network we term the common interactome, bind overlapping target genes, and drive a similar core transcriptional program. The common interactome contains the C-terminal partners of known oncofusions and a newly identified translocation, suggesting oncofusions arise by PAX3/7 DNA-binding domain fusing to interactome members. As loss of common interactome proteins impaired oncogenic activity we screened the interactome for shared vulnerabilities. This identified thymidylate synthase as preferentially required for FP-RMS growth. Accordingly, the antifolate pralatrexate suppressed growth across all seven oncofusions, in multiple human FP-RMS cell lines, and a patient-derived xenograft. These findings demonstrate that divergent FP-RMS oncofusions are functionally fungible through a shared interactome that defines common vulnerabilities.