ERAP2 increases the abundance of a peptide submotif highly selective for the Birdshot Uveitis-associated HLA-A29

Abstract

Birdshot Uveitis (BU) is a blinding inflammatory eye condition that only affects HLA-A29-positive individuals. Genetic association studies linked ERAP2 with BU, an aminopeptidase which trims peptides before their presentation by HLA class I at the cell surface, which suggests that ERAP2-dependent peptide presentation by HLA-A29 drives the pathogenesis of BU. However, it remains poorly understood whether the effects of ERAP2 on the HLA-A29 peptidome are distinct from its effect on other HLA allotypes. To address this, we focused on the effects of ERAP2 on the immunopeptidome in patient-derived antigen presenting cells. Using complementary HLA-A29-based and pan-class I immunopurifications, isotope-labelled naturally processed and presented HLA-bound peptides were sequenced by mass spectrometry. We show that the effects of ERAP2 on the N-terminus of ligands of HLA-A29 are shared across endogenous HLA allotypes, but discover and replicate that one peptide motif generated in the presence of ERAP2 is specifically bound by HLA-A29. This motif can be found in the amino acid sequence of putative autoantigens. We further show evidence for internal sequence specificity for ERAP2 imprinted in the immunopeptidome. These results reveal that ERAP2 can generate an HLA-A29-specific antigen repertoire, which supports that antigen presentation is a key disease pathway in BU.

HLA-A29 and Birdshot Uveitis: Further Down the Rabbit Hole

“…(B) The effect of amino acid substitutions for position 62 and 63 on predicted binding affinity for HLA-A29-presented peptides. The average binding scores of 9-mers (n = 948) detected by mass-spectrometry analysis of HLA-A29 reported by Venema et al ( 43 ). Replacement of position 62 and 63 with the most commonly occurring amino acids at that position encoded by HLA-A alleles was done in netMHCpan 4.1 server ( 44 ).…”

“…Other studies from the López de Castro group also demonstrated these ERAP2 effects on the immunopeptidome of risk HLA allotypes of other types of uveitis, such as HLA-B27 ( 94 ). In a recent study, we demonstrated that the effect of ERAP2 on P1 is actually a common feature of ERAP2 observable in the immunopeptidomes of all HLA class I alleles expressed by the cell ( 43 ). Intriguingly, Abelin and coworkers showed that peptides presented by HLA class I allotypes show a depletion for K, R and A residues at P1, which we believe can be attributed to the fact that their studied cell line expresses ERAP2 ( 60 ).…”

“…This includes peptides that are detected in the binding groove of more than one HLA-A allotype (demonstrated by mass-spectrometry studies of single-HLA-expressing cell lines), a phenomenon termed peptide ‘promiscuity’ ( 59 ). We and others have studied the complete set of antigenic peptides (termed the ‘immunopeptidome’) bound by HLA-A29 and used multidimensional scaling (a visual representation of the immunopeptidome where all peptides are positioned in a graph based on their relative similarity or difference in amino acid sequence) to cluster the peptides into subdominant binding motifs (or “submotifs”) ( 43 , 45 , 60 ). This approach facilitates the identification of clusters of antigenic peptides (submotifs) that are shared with other HLA class allotypes or that are unique to HLA-A29.…”

“…As discussed, a fraction of peptides presented by HLA-A29 is also found in the binding groove of other HLA-A alleles and consequently some submotifs of HLA-A29 were also detected in immunopeptidome data of other HLA allotypes. This helped to narrow down a submotif that is specific to HLA-A29 ( 43 ), which is characterized by the amino acids F or Y at P2 in conjunction with the HLA-A29-characteristic C-terminal (PC) Y (F/Y-P2 + Y-PC motif). This motif makes up ~15% of the HLA-A29 immunopeptidome ( Figure 1C ).…”

“…Large aromatic amino acids F and Y are poor substrates for ERAP2. Because ERAP2 destroys competing peptides that harbor optimal residues (K, R, or A at P1) for ERAP2, peptides that contain F or Y at P1 consequently make up a relatively larger proportion of the available antigen peptides to bind HLA-A29 and become “over-represented” in the presence of ERAP2 ( 43 , 92 ). Other studies from the López de Castro group also demonstrated these ERAP2 effects on the immunopeptidome of risk HLA allotypes of other types of uveitis, such as HLA-B27 ( 94 ).…”