Harnessing Tumor‐Specific Transcript Diversity Uncovers a Shared Neoantigen Reservoir for Pancreatic Ductal Adenocarcinoma

ABSTRACT Pancreatic ductal adenocarcinoma (PDAC) is refractory to immunotherapy due to its immunologically cold microenvironment and the scarcity of mutation‐derived neoantigens. Here, we introduce NeoAPP, a computational tool designed to systematically decode neoantigens arising from tumor‐specific transcripts (TSTs) generated by transcriptional dysregulation. By integrating multi‐cohort transcriptomic data from 413 PDAC samples, NeoAPP identified a median of 351 neoantigens per sample, originating from 56 neoantigen‐encoding TSTs (neoTSTs), exceeding mutation‐derived neoantigens in both abundance and patient coverage. Mechanistic analyses show that noncanonical splicing junctions and transposable element activation drive neoantigen generation, while alternative promoter usage regulated by FOXA2 constitutes a potential major source of neoTSTs. In addition, a subset of neoTSTs was detectable in plasma‐derived extracellular vesicles and was associated with patient survival, suggesting their potential as minimally invasive biomarkers. Vaccination with neoTSTs induced CD8 + T cell responses in HLA‐A*02:01 and HLA‐A*11:01 transgenic mice and suppressed tumor growth in syngeneic PDAC models. Collectively, this work establishes TST‐derived neoantigens as a dominant and therapeutically actionable antigen reservoir in PDAC, advancing a transcriptome‐guided framework for neoantigen discovery with potential to overcome immune resistance in low‐mutation cancers.