Proteogenomic discovery of novel open reading frames with HLA immune presentation on human beta cells

Ribosome profiling (Ribo-seq) provides a comprehensive view of translational regulation, crucial for understanding cellular processes. Here, we applied Ribo-seq to map the translatome of human stem cell-derived beta cells (sBCs). Our analysis revealed close to 1000 novel open reading frames (nuORFs) in sBCs, with a majority showing protein-level support, suggesting functional relevance. Furthermore, we detected an immunogenic peptide, INS-DRiP, originating from an alternative start site in INS mRNA. Comparison with primary human islets highlighted beta cell specificity of the identified nuORFs. Notably, we identified a regulatory upstream ORF within TYK2, a gene implicated in type 1 diabetes (T1D) and crucial for beta cell function and interferon response. Our findings underscore the importance translational regulation in beta cell function and its implications in T1D. Overall design: FLAG-RPL22 IP ribosome profiling samples from hPSC cells, DE cells and stem cell derived beta-cells all differentiated from hPSC cells and RNA-seq samples from INS promoter driven GFP sorted stem cell derived beta cells.