The Human Leukocyte Antigen (HLA)-B27 Peptidome in Vivo, in Spondyloarthritis-susceptible HLA-B27 Transgenic Rats and the Effect of Erap1 Deletion

Abstract

HLA-B27 is a class I major histocompatibility (MHC-I) allele that confers susceptibility to the rheumatic disease ankylosing spondylitis (AS) by an unknown mechanism. ERAP1 is an aminopeptidase that trims peptides in the endoplasmic reticulum for binding to MHC-I molecules. ERAP1 shows genetic epistasis with HLA-B27 in conferring susceptibility to AS. Male HLA-B27 transgenic rats develop arthritis and serve as an animal model of AS, whereas female B27 transgenic rats remain healthy. We used large scale quantitative mass spectrometry to identify over 15,000 unique HLA-B27 peptide ligands, isolated after immunoaffinity purification of the B27 molecules from the spleens of HLA-B27 transgenic rats. Heterozygous deletion of Erap1, which reduced the Erap1 level to less than half, had no qualitative or quantitative effects on the B27 peptidome. Homozygous deletion of Erap1 affected approximately one-third of the B27 peptidome but left most of the B27 peptidome unchanged, suggesting the possibility that some of the HLA-B27 immunopeptidome is not processed in the presence of Erap1. Deletion of Erap1 was permissive for the AS-like phenotype, increased mean peptide length and increased the frequency of C-terminal hydrophobic residues and of N-terminal Ala, Ser, or Lys. The presence of Erap1 increased the frequency of C-terminal Lys and Arg, of Glu and Asp at intermediate residues, and of N-terminal Gly. Several peptides of potential interest in AS pathogenesis, previously identified in human cell lines, were isolated. However, rats susceptible to arthritis had B27 peptidomes similar to those of non-susceptible rats, and no peptides were found to be uniquely associated with arthritis. Whether specific B27-bound peptides are required for AS pathogenesis remains to be determined. Data are available via ProteomeXchange with identifier PXD005502.

The interplay between HLA-B27 and ERAP1/ERAP2 aminopeptidases: from anti-viral protection to spondyloarthritis

“…Interestingly, the knock-out genotype of ERAP1 altered approximately one-third of the B27 peptidome, but was still disease-permissive [97].…”

“…A very recent work analysed the HLA-B27 peptidome from spleen cells of HLA-B27 transgenic rats in conditions of heterozygous or homozygous deletion of ERAP1 [97]. Interestingly, the knock-out genotype of ERAP1 altered approximately one-third of the B27 peptidome, but was still disease-permissive [97].…”

Genetic Variants inERAP1andERAP2Associated With Immune‐Mediated Diseases Influence Protein Expression and the Isoform Profile

“…At ERAP2, the AS‐associated nonsense mutation rs2248374 is an expression quantitative trait locus (eQTL) at which the protective G allele results in complete loss of gene expression due to nonsense‐mediated decay of an alternatively spliced transcript . The presence of ERAP‐2 influences the HLA–B27 peptide pool, decreasing the abundance of peptides with N‐terminal basic residues and increasing the percentage of 9‐mer peptides presented , lowering the affinity of the HLA–B27 peptidome . Given the intricate role of both aminopeptidases in shaping the HLA–B27 peptidome, it is possible that variants increasing aminopeptidase expression may act concordantly to increase AS risk in individuals carrying disease‐associated active variants of ERAP1 and ERAP2 .…”

MHCSeqNet: A deep neural network model for universal MHC binding prediction

“…In addition to removing duplicated entries and entries with ambiguous peptide sequence or MHC allele name as is regularly performed in other studies (Jurtz et al, 2017;O'Donnell et al, 2018), we also examined the impact of conflicting entries (entries with the same peptide sequence and same MHC allele but opposite binding affinity classification) and low-confidence entries (Positive-Intermediate and Positive Low) on the prediction performance. Although conflicting entries constitute less than 5% of the raw dataset, the vast majority of them (15,305 out of 17,914 conflicts) involve the same source, which reported HLA-B*27 ligands identified in transgenic mice (Barnea et al, 2017), and should be entirely excluded or at least carefully scrutinized. The remaining conflicts could be resolved by majority voting which slightly improves the prediction performance.…”