Common allotypes of ER aminopeptidase 1 have substrate-dependent and highly variable enzymatic properties

Abstract

Polymorphic variation of immune system proteins can drive variability of individual immune responses. Endoplasmic reticulum aminopeptidase 1 (ERAP1) generates antigenic peptides for presentation by major histocompatibility complex class I molecules. Coding SNPs in ERAP1 have been associated with predisposition to inflammatory rheumatic disease and shown to affect functional properties of the enzyme, but the interplay between combinations of these SNPs as they exist in allotypes has not been thoroughly explored. We used phased genotype data to estimate ERAP1 allotype frequency in 2504 individuals across five major human populations, generated highly pure recombinant enzymes corresponding to the ten most common ERAP1 allotypes, and systematically characterized their in vitro enzymatic properties. We find that ERAP1 allotypes possess a wide range of enzymatic activities, up to 60-fold, whose ranking is substrate dependent. Strikingly, allotype 10, previously associated with Behçet’s disease, is consistently a low-activity outlier, suggesting that a significant percentage of individuals carry a subactive ERAP1 gene. Enzymatic analysis revealed that ERAP1 allotypes can differ in both catalytic efficiency and substrate affinity, differences that can change intermediate accumulation in multistep trimming reactions. Alterations in efficacy of an allosteric inhibitor that targets the regulatory site suggest that allotypic variation influences the communication between the regulatory and the active site. Our work defines the wide landscape of ERAP1 activity in human populations and demonstrates how common allotypes can induce substrate-dependent variability in antigen processing, thus contributing, in synergy with major histocompatibility complex haplotypes, to immune response variability and predisposition to chronic inflammatory conditions.

Allotypic variation in antigen processing controls antigenic peptide generation from SARS-CoV-2 S1 Spike Glycoprotein

“…Allotype 10 was slightly less efficient, with 54-62% of peptide signal originating from product peptides. Still, this difference is much less pronounced than observed in previous in vitro experiments using single peptides that suggested that allotype 10 can be as much as 60-fold less active for some peptides 27 . This finding suggests that although allotype 10 may be less active for some substrates, it is still able to operate with good efficiency in complex substrate mixtures.…”

“…Some differences were, however, evident between ERAP1 allotypes. This was most activity as demonstrated before 27 . Still, allotype 10 was able to efficiently trim large peptide clusters suggesting that its lower activity may be sequence specific.…”

“…Our results, however, suggest that ERAP1 allotypic variation could play, in tandem to HLA-alleles, important roles in determining anti-SARS-CoV-2 immune responses and by extension, susceptibility to severe COVID-19. For example, allotype 10 homozygous individuals, which could represent up to 4.8% of the population in Europe 27 , could be defective in producing epitopes from the S1 glycoprotein that are presented from particular HLA alleles. Conversely, our analysis suggests that particular antigenic epitopes may be produced by only specific ERAP1 allotypes.…”

Allotypic variation in antigen processing controls antigenic peptide generation from SARS-CoV-2 S1 spike glycoprotein

“…ERAP1 is also polymorphic, and coding single nucleotide polymorphisms (SNPs) in the ERAP1 gene associate with predisposition to autoimmunity or cancer often in epistasis with HLA alleles 24 and can help shape the cellular immunopeptidome 25 . ERAP1 SNPs are found in the population in limited combinations that define specific allotypes and have functional consequences in peptide trimming 26,27 . The exact interplay of ERAP1 and HLA polymorphic variation in determining antigen presentation is currently a subject of active research 21,[27][28][29] .…”

The ERAP1 active site cannot productively access the N-terminus of antigenic peptide precursors stably bound onto MHC class I

“…ER aminopeptidase 1 (ERAP1) has been demonstrated to be crucial for the generation of many antigenic peptides and to be able to indirectly regulate adaptive immune responses by influencing the repertoire of antigenic peptides presented on the cell-surface, often referred to as the immunopeptidome 3 . ERAP1 is polymorphic and several common allotypes exist in the population affecting its functional properties and predisposition to disease such as cancer and autoimmunity 4 , 5 . Due to its important role in adaptive immune responses, ERAP1 is an emerging target for cancer immunotherapy and inflammatory diseases with autoimmune etiology 6 – 8 .…”