Spliced HLA-bound peptides: a Black Swan event in immunology

Abstract

Peptides that bind to and are presented on the cell surface by human leucocyte antigen (HLA) molecules play a critical role in adaptive immunity. For a long time it was believed that all the HLA-bound peptides were generated through simple proteolysis of linear sequences of cellular proteins, and therefore are templated in the genome and proteome. However, evidence for untemplated peptide ligands of HLA molecules has accumulated during the last two decades, with a recent global analysis of HLA-bound peptides suggesting that a considerable proportion of HLA-bound peptides are potentially generated through splicing/fusion of discontinuous peptide segments from one or two distinct proteins. In this review, we will evaluate recent discoveries and debates on the contribution of spliced peptides to the HLA class I immunopeptidome, consider biochemical rules for splicing and the potential role of these spliced peptides in immune recognition.

Keywords: MHC peptides; immunopeptidomics; peptide splicing.

Fig. 1

The generation of linear, cis‐spliced, reverse‐cis‐spliced (r‐cis‐spliced) and trans‐spliced peptides by proteasome and their subsequent presentation by human leucocyte antigen (HLA)‐I molecules.

Fig. 2

Direct transpeptidation as the leading peptide splicing mechanism. (a) In proteolysis, a nucleophile (Thr1 of the beta subunits in proteasome) attacks the peptide bond and forms a peptidyl‐enzyme or acyl‐enzyme (Acyl‐Ez) intermediate. The Acyl‐Ez is either hydrolysed by a water molecule or is attacked by another peptide fragment to make a spliced peptide. (b) Visualization of how P1 and P1′ side chain bulkiness hinders the splicing to happen. Right and left columns compare the putative efficiency of the second nucleophilic attack between exemplary pairs of amino acids in P1 and P1, respectively. In each pair, the relative size of red arrows conveys the relative arbitrary efficiency. (c) Different factors endorsed by several publications as transpeptidation‐favouring conditions. The higher the relative abundance of splice‐reactants, the greater the chance of transpeptidation will be. Also, smaller nucleophilic peptides have greater chances to attack the Acy‐Ez intermediate. As presented in the previous section, the bulkiness of P1 and P1′ amino acids hinders the second nucleophilic attack and favours hydrolysis. Meanwhile, any factor that increases the half‐life of the Acyl‐Ez intermediate increases the chance of transpeptidation.

Fig. 3

The contribution of linear and spliced peptides in the presentation of cancer‐associated antigens in the leucocyte antigen (HLA)‐I immunopeptidome. A total of 1608 linear and 1214 spliced HLA‐I‐bound peptides derived from cancer‐associated antigens have been reported from melanoma, breast and colon cancer tumours. This figure represents cancer‐associated antigens that had at least 10 reported peptides.