The GF-NEO discovery platform unveils a [KQE][DG] sequence motif within fusion neoantigens in pediatric cancer.

Gene fusions (GFs) are critical events in pediatric oncology, often serving as oncogenic drivers. However, fusion proteins and their derived neoantigens (GF-NEOs) remain underexplored for targeted immunotherapy. We developed ProteoFusioNEO, a computational tool for the in silico translation of transcriptomic data, analyzing 5,190 pediatric patients with cancer and 935 cell lines, yielding 382 and 446 fusion proteins. We highlight that GFs generate multiple translational outcomes, with 97% being in-frame in patients. Fusion junctions exhibit the sequence motif [KQE][DG], which partly reflects the nature of exon-exon junctions, albeit with additional hydrophilicity. Moreover, GF-NEOs' abundance may be shaped by the motif, offering insights into fusion protein biology. Finally, a multipronged validation strategy using in vitro and in vivo systems confirms the GF-NEOs presentation through mass spectrometry-based proteomics and immunopeptidomics. Multiple GF-NEOs encoded by two versions of the ETV6-RUNX1 fusion were validated, paving the way for targeted immunotherapy development.