Endoplasmic Reticulum Aminopeptidase 1 (ERAP1) Polymorphism Relevant to Inflammatory Disease Shapes the Peptidome of the Birdshot Chorioretinopathy-Associated HLA-A*29:02 Antigen

Birdshot chorioretinopathy is a rare ocular inflammation whose genetic association with HLA-A*29:02 is the highest between a disease and a major histocompatibility complex (MHC) molecule. It belongs to a group of MHC-I-associated inflammatory disorders, also including ankylosing spondylitis, psoriasis, and Behçet''s disease, for which endoplasmic reticulum aminopeptidases (ERAP) 1 and/or 2 have been identified as genetic risk factors. Since both enzymes are involved in the processing of MHC-I ligands, it seems reasonable that common peptide-mediated mechanisms may underlie the pathogenesis of these diseases. In this study, comparative immunopeptidomics was used to characterize >5000 A*29:02 ligands and quantify the effects of ERAP1 polymorphism and expression on the A*29:02 peptidome in human cells. The peptides predominant in an active ERAP1 context showed a higher frequency of nonamers and bulkier amino acid side chains at multiple positions, compared with the peptides predominant in a less active ERAP1 background. Thus, ERAP1 polymorphism has a large influence, shaping the A*29:02 peptidome through length-dependent and length-independent effects. These changes resulted in increased affinity and hydrophobicity of A*29:02 ligands in an active ERAP1 context. The results reveal the nature of the functional interaction between A*29:02 and ERAP1 and suggest that this enzyme may affect the susceptibility to birdshot chorioretinopathy by altering the A*29:02 peptidome. The complexity of these alterations is such that not only peptide presentation but also other potentially pathogenic features could be affected.Several major histocompatibility complex class I (MHC-I)¹ alleles are strongly associated with polygenic inflammatory diseases, including birdshot chorioretinopathy (BSCR: A*29:02), ankylosing spondylitis (AS: HLA-B*27), psoriasis (C*06:02), and Behçet''s disease (HLA-B*51). In the three latter disorders, ERAP1, an aminopeptidase of the endoplasmic reticulum performing the final trimming of MHC-I ligands (1, 2), is also a risk factor and is in epistasis with the predisposing MHC-I allele (3–5). These studies suggest common pathogenetic mechanisms involving the MHC-I bound peptidome. ERAP2, a related enzyme that acts in concert with ERAP1 (6, 7), influences the susceptibility to BSCR (8), AS (although not necessarily in epistasis with HLA-B*27) (9), Crohn′s disease (10), and preeclampsia (11–13).BSCR is a rare and severe form of bilateral posterior uveitis, showing a progressive inflammation of the choroid and retina, whose association with HLA-A*29 is the strongest for any disease and MHC. The frequency of this allele is about 7% in healthy individuals but >95% in BSCR patients (14, 15). This association specifically concerns A*29:02 and not the closely related allotype A*29:01 (8).Genetic studies on BSCR also showed a highly significant association within the LNPEP gene (rs7705093) in the 5q15 region, which includes the ERAP1 and ERAP2 genes. One single nucleotide polymorphism (SNP) in this region (rs10044354) correlated with ERAP2 expression. This was confirmed at the protein level, leading to the conclusion that ERAP2 expression predisposes to BSCR. Yet, an involvement of functional ERAP1 polymorphisms, not determining protein expression, was not excluded. These polymorphisms have a large influence on the HLA-B*27 peptidome (16, 17). In contrast, the effects of ERAP2 on MHC-I peptidomes are poorly understood and are probably dependent on the particular ERAP1 context since ERAP2 cooperates with ERAP1 in peptide processing. Thus, the present study was conducted to characterize A*29:02-bound peptidomes in various ERAP1 backgrounds and to determine the influence of ERAP1 polymorphism on the amounts and features of A*29:02 ligands in human cells.