Using an intersection of RiboSeq and RNAseq data from 3 DLBCL cell lines to generate sample-specific reference libraries for immunopeptidome and peptidome analysis, Cuevas, Hardy, Holly et. al. identified a large group of MHC-I-associated peptides (MAPs) derived from encoded non-canonical proteins representing over 15% of translated proteins. These MAPs derived mostly from regions that were previously considered untranslated, or from frame-shifted reads of canonical genes (cryptic proteins) and were mostly <100 AAs in length. Per AA, cryptic proteins were about 5-fold more abundantly presented, potentially due to a more disordered structure.
Contributed by Ed Fritsch
ABSTRACT: Combining RNA sequencing, ribosome profiling, and mass spectrometry, we elucidate the contribution of non-canonical translation to the proteome and major histocompatibility complex (MHC) class I immunopeptidome. Remarkably, of 14,498 proteins identified in three human B cell lymphomas, 2,503 are non-canonical proteins. Of these, 28% are novel isoforms and 72% are cryptic proteins encoded by ostensibly non-coding regions (60%) or frameshifted canonical genes (12%). Cryptic proteins are translated as efficiently as canonical proteins, have more predicted disordered residues and lower stability, and critically generate MHC-I peptides 5-fold more efficiently per translation event. Translating 5' "untranslated" regions hinders downstream translation of genes involved in transcription, translation, and antiviral responses. Novel protein isoforms show strong enrichment for signaling pathways deregulated in cancer. Only a small fraction of cryptic proteins detected in the proteome contribute to the MHC-I immunopeptidome, demonstrating the high preferential access of cryptic defective ribosomal products to the class I pathway.