Regulation of non‐canonical proteins from diverse origins through the nonsense‐mediated mRNA decay pathway

Abstract Immunotherapy harnesses neoantigens encoded within the human genome, but their therapeutic potential is hampered by low expression, which may be controlled by the nonsense‐mediated mRNA decay (NMD) pathway. This study investigates the impact of UPF1 ‐knockdown on the expression of non‐canonical/mutant proteins, employing proteogenomic to explore UPF1 role within the NMD pathway. Additionally, we conducted a comprehensive pan‐cancer analysis of UPF1 expression and evaluated UPF1 expression in Triple‐Negative Breast Cancer (TNBC) tissue in ‐ vivo . Our findings reveal that UPF1 ‐knockdown leads to increased translation of non‐canonical/mutant proteins, particularly those originating from retained‐introns, pseudogenes, long non‐coding RNAs, and unannotated transcript biotypes. Moreover, our analysis demonstrates elevated UPF1 expression in various cancer types, with notably heightened protein levels in patient‐derived TNBC tumors compared to adjacent tissues. This study elucidates UPF1 role in mitigating transcriptional noise by degrading transcripts encoding non‐canonical/mutant proteins. Targeting this mechanism may reveal a new spectrum of neoantigens accessible to the antigen presentation pathway. Our novel findings provide a strong foundation for the development of therapeutic strategies aimed at targeting UPF1 or modulating the NMD pathway.