Expanding the immune self : impact of non-canonical translation on the repertoire of MHC I-associated peptides
On their surface, nucleated cells present major histocompatibility complex class I (MHC I) molecules in complex with short peptides, that we will refer to as MHC I-associated peptides (MAPs). These MAPs derive from the degradation of cytosolic proteins by the proteasome and provide an integrative view of the inner state of cells to CD8+ T cells, which can, in turn, eliminate abnormal cells, e.g., those presenting viral MAPs or tumor-specific antigens (TSAs).  With the growing body of evidence suggesting that translation does occur outside of protein-coding transcripts, we tried to evaluate the impact of non-canonical translation on the repertoire of MAPs. Combining RNA-sequencing and mass spectrometry to analyze the MAP repertoire of B-lymphoblastoid cell lines, we uncovered that ~ 10 % of the MAP repertoire derives from such non-canonical translation events, including (i) the out-of-frame translation of protein-coding transcripts or (ii) the translation of non-coding regions (UTRs, introns, etc.) or transcripts (antisense, pseudogene, etc.). Interestingly, our data suggest that the biogenesis of cryptic and conventional MAPs differs, as cryptic MAPs derive from unstable transcripts generating short proteins that might be degraded in a proteasome-independent fashion.  Because the global DNA hypomethylation observed in cancer cells tend to de-repress non-coding transcripts, we developed another proteogenomic approach to probe the cryptic MAP repertoire of two murine cancer cell lines (EL4 and CT26) and seven humor primary tumor samples (four B-lineage acute lymphoblastic leukemias and three lung tumor biopsies). This second analysis revealed that ~ 90% of TSAs are cryptic TSAs. Interestingly, most of those TSAs derived from cancer-restricted yet non-mutated sequences, such as endogenous retroelements, thereby suggesting that such TSAs could be shared between patients. Lastly, our validation study in mice demonstrated that at least two parameters can influence the in vivo protective effect of TSAs, namely TSA expression in cancer cells and the frequency of TSA-specific T cells. Altogether, our proteogenomic studies on the MAP repertoire of normal and cancer cells demonstrate that cryptic MAPs significantly expand the immune self and, consequently, the scope of CD8+ T cell immunosurveillance.
Major histocompatibility complex class I Non-canonical translation Tumor-specific antigens T lymphocytes Cancer immunotherapy Proteogenomics Mass spectrometry Next-generation sequencing