Woods, K., et al. The diversity of the immunogenic components of the melanoma immunopeptidome. 10.1101/623223

Antigen-recognition by CD8+ T cells is governed largely by the pool of peptide antigens presented on the cell surface in the context of MHC class I complexes. Recent studies have shown not only a high degree of plasticity in the immunopeptidome, but also that a considerable fraction of all presented peptides are generated through proteasome-mediated splicing of non-contiguous regions of proteins to form novel peptide antigens. Here we used high-resolution mass-spectrometry combined with new bioinformatic approaches to characterize the immunopeptidome of melanoma cells in the presence or absence of interferon-γ. In total, we identified 30,120 peptides and demonstrate that interferon-γ induces marked changes in the peptidome (with an overlap of only 49.3% between conditions as revealed by data independent acquisition mass spectrometry). Moreover, around 6% (1,821) of the peptides were identified as cis-spliced peptides with 712 derived from known melanoma-associated antigens. Several of these peptides were shown to be immunogenic in unrelated melanoma patients. These observations highlight the breadth and complexity of the repertoire of immunogenic peptides that may be exploited therapeutically and suggest that spliced peptides may be a major class of tumour antigens.