Insights on the HLA-Binding Peptidome in Cancer

The intracellular compartments for proteolytic antigen processing in tumor cells produce peptides that are presented by MHC molecules to T cells. But first, the ubiquitin ligase system tags defective, misfolded, aged, and unstable proteins for degradation through the proteasome. Ubiqitinated proteins are unfolded and fed into the barrel-shaped core of the proteasome where a collection of multiple different proteases cleave proteins into oligopeptides. After exiting the proteasome, these oligopeptides are either completely degraded into amino acids or trimmed at the N- and C-termini so that they bind to transporter associated with antigen processing (TAP). TAP translocates oligopeptides into the ER where they are further trimmed and may bind to MHC molecules. Resulting peptide-MHC complexes then travel to the cell surface for T cell recognition. Many defects or anomalies in the proteolytic processing of tumor-derived proteins may suppress the expression of peptide-MHC complexes, which plays a role in escape of tumors from the immune system. However, due to the general dysregulated intracellular machinery of tumors, many proteins are translated from unconventional RNA transcripts including noncoding RNA, exon-intron retentions, and alternative splicing. These products of translation can serve as novel peptides for T cells as they recognize and kill tumors.