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-labeled 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.

Retina-arrestin is not a CD8+ T-cell autoantigen in HLA-A29-positive birdshot chorioretinitis

“…The immunopeptidome analysis of HLA-A29 was performed as described previously 21 . Briefly, LCL1-SAG+ cells were cultured in a medium supplemented with stable isotope labelled amino acids and combined with unlabelled CRISPR-edited cells for SILAC-labelled immuno peptidomics as described in detail in Venema et al .…”

“…Briefly, LCL1-SAG+ cells were cultured in a medium supplemented with stable isotope labelled amino acids and combined with unlabelled CRISPR-edited cells for SILAC-labelled immuno peptidomics as described in detail in Venema et al . 21 . LCL2-SAG+ cells were cultured in unlabelled conditions.…”

“…Mass spectrometry was performed using on-line C18 nanoHPLC MS/MS with a system consisting of an Easy nLC 1200 gradient HPLC system (Thermo, Bremen, Germany), and a (for LCL1) LUMOS mass spectrometer (Thermo) or (for LCL2) a Q Exactive Plus Hybrid Quadrupole-Orbitrap as described in detail in Venema et al . 21 .…”

ERAP2 Inhibition Induces Cell-Surface Presentation by MOLT-4 Leukemia Cancer Cells of Many Novel and Potentially Antigenic Peptides

“…Both ERAP2 and its homologous ERAP1 have been shown to regulate the cellular immunopeptidome [9]. In particular, ERAP2 has been shown to underlie changes in peptidomes of particular HLA alleles related to predisposition to inflammatory autoimmunity, [10][11][12][13], although its role on regulating the global immunopeptidome has not been thoroughly studied. Accordingly, high ERAP2 expression levels have been associated with predisposition to inflammatory autoimmunity [14], suggesting that antigen processing by ERAP2 could be a key regulator of cellular antigenicity in human disease [15].…”

EnRAPtured: Is Endoplasmic Reticulum Aminopeptidase a New Clue to the Pathogenesis and ThERAPy of Uveitis?

“…Although it is certainly possible that HLA class I, ERAP, or both affect the likelihood of disease by a mechanism other than antigen presentation, the epistatic effect between the 2 genes strongly suggests that antigen presentation is the key function. 21 An additional possibility is that antigen presentation is the critical function, but perhaps the antigen presentation is at the thymic epithelium, where ERAP is known to be active. 22 The thymic epithelium is responsible for deleting clones of autoreactive T cells.…”