Background The rising burden of metabolic dysfunction-associated steatotic liver disease (MASLD)-associated hepatocellular carcinoma (HCC) underscores the need for innovative therapeutic strategies.

Methods We integrated RNA-seq fusion detection, immunopeptidomics, and proteogenomics to systematically prioritize tumor-specific neoantigen candidates arising from gene fusions in MASLD-HCC.

Results We elucidated a landscape of private, clonally expressed fusions, and identified a previously unrecognized class of predicted phosphorylated fusion-neoepitopes. Cross-tumor proteomic analysis revealed that these phospho-motifs are present across malignancies, providing a broader context for their biological relevance. Importantly, fusion-positive tumors display immunosuppressive microenvironments, highlighting the need for future therapeutic strategies that combine fusion-targeted immunotherapy with approaches that overcome T-cell dysfunction.

Conclusions This study establishes a discovery pipeline and publicly available resource for fusion-derived phospho-neoepitopes in MASLD-HCC. The identified candidates provide a prioritized framework to guide and accelerate rigorous functional immunogenicity testing for future clinical validation.

Highlights

• The landscape of MASLD-HCC fusions is dominated by predominantly private, with rare recurrent candidate genetic events

• Proteogenomic data supports high-confidence fusion-derived candidate neoepitopes

• Novel phosphorylated fusion-derived candidate neoepitopes are identified in MASLD-HCC

• Immunotherapy-treated HCC patients inform personalized fusion-derived candidate neoepitope discovery