A 2011 genome-wide association study of ankylosing spondylitis (AS) discovered an epistatic interaction in which polymorphisms of ERAP1, the endoplasmic reticulum aminopeptidase that trims peptides before loading onto MHC class I molecules, alter disease risk only in individuals carrying HLA-B27, the major genetic risk factor. This established genetically that HLA-B27 promotes AS through aberrant peptide handling, but left the actual mechanism undefined. The open problem is to determine the molecular pathway by which ERAP1 trimming activity modulates HLA-B27 biology to produce disease — discriminating among the arthritogenic-peptide (CD8 T cell/T cell receptor) hypothesis, the peptide-supply folding/misfolding/unfolded-protein-response hypothesis, and the surface free-heavy-chain/homodimer (NK cell/KIR) hypothesis — quantitatively consistent with the human epistasis genetics. The same finding carries a therapeutic implication noted by the source — that, because ERAP1 loss-of-function variants are protective, inhibition of ERAP1 may be effective at least in HLA-B27-positive disease — which remains untested. Extensive follow-up work has validated and quantified ERAP1's shaping of the HLA-B27 peptidome and produced partially protective ERAP1-knockout rat data, but as of 2026 no definitive mechanism is established, and the first clinical ERAP1-inhibitor trials in axial spondyloarthritis are only now underway.

Background

Ankylosing spondylitis (AS), the prototypical form of axial spondyloarthritis (axSpA), is a common inflammatory arthritis affecting the spine and sacroiliac joints. Since the early 1970s its strongest genetic risk factor has been HLA-B27, a human leukocyte antigen class I molecule. HLA class I (MHC-I) proteins bind short peptides (typically 9-mers) generated by intracellular protein degradation and display them on the cell surface to CD8-positive T cells and to natural killer (NK) cell receptors. Before a peptide can bind an MHC-I molecule, precursor peptides are trimmed at their N-termini in the endoplasmic reticulum by ERAP1 (endoplasmic reticulum aminopeptidase 1), assisted by the related enzyme ERAP2; natural ERAP1 polymorphisms combine into allotypes with differing trimming activity. Epistasis means that the effect of variants at one gene depends on the genotype at another. In 2011, Evans, Spencer, Pointon and colleagues reported a genome-wide association meta-analysis (Nature Genetics 43:761-767) identifying new risk loci (RUNX3, LTBR-TNFRSF1A, IL12B, plus suggestive PTGER4, TBKBP1, ANTXR2, CARD9) and, critically, showing that ERAP1 polymorphisms affect AS risk only in HLA-B27-positive individuals. Their recombinant-enzyme trimming assays indicated that disease-associated ERAP1 variants trim peptides more efficiently. This epistasis is strong genetic evidence that HLA-B27 acts in AS through aberrant processing of antigenic peptides — the 'peptide handling' mechanism named in the paper's title — yet it does not reveal which downstream mechanism is causal. Three main hypotheses, none definitively established, dominate the field. First, the arthritogenic-peptide hypothesis: ERAP1 allotype-dependent trimming creates a distinctive HLA-B27-bound peptide repertoire containing self-peptides that resemble microbial peptides, driving autoreactive CD8 T cells. Second, the misfolding hypothesis: the peptide supply shaped by ERAP1 affects how HLA-B27 folds in the endoplasmic reticulum, and misfolded HLA-B27 heavy chains trigger endoplasmic reticulum stress and the unfolded protein response (UPR), a stress-signaling pathway that can promote inflammatory cytokine production. Third, free-heavy-chain mechanisms: peptide-poor HLA-B27 molecules reach the surface as heavy chains that have lost β2-microglobulin (the invariant light chain of MHC class I molecules), including disulfide-linked homodimers, and these engage innate receptors — notably the killer immunoglobulin-like receptor KIR3DL2 — on NK cells and on Th17 cells, a pro-inflammatory CD4 T-cell subset. Later genetics sharpened the puzzle rather than solving it: a fine-mapping study of over 22,000 AS cases and controls (Cortes et al., Nature Communications 2015) confirmed the HLA-B27 dominance of the MHC signal, found additional independent HLA-B, HLA-A, HLA-DPB1 and HLA-DRB1 effects, and showed that the ERAP1 variant rs30187 also affects risk in carriers of HLA-B*40:01 independently of B27 — so the interaction is with specific peptide-loading backgrounds, not B27 alone. Biochemical work then established the phenomenon solidly: ERAP1 polymorphism demonstrably reshapes the HLA-B27 peptidome (the full set of peptide ligands bound to HLA-B27 molecules) and B27 molecular stability in cells and in HLA-B27-transgenic rats, with the protective low-activity allotypes (carrying K528R — p.Lys528Arg, rs30187, written R528K in some papers — D575N/R725Q or Q730E) generating suboptimal peptidomes (García-Medel et al., Molecular & Cellular Proteomics 2012; Sanz-Bravo et al., Arthritis & Rheumatology 2015 and Molecular & Cellular Proteomics 2018; Barnea et al., Molecular & Cellular Proteomics 2017). ERAP2 contributes independently and additively (Martín-Esteban et al., Journal of Autoimmunity 2017). In HLA-B27-transgenic rats, ERAP1 knockout reduces HLA-B27 misfolding and cuts arthritis prevalence by about two-thirds, but increases surface free-heavy-chain forms and leaves gut inflammation unchanged (Tran et al., Arthritis & Rheumatology 2023) — each hypothesis is partially supported and none is excluded. Because ERAP1 loss-of-function variants are protective in HLA-B27-positive people, ERAP1 inhibition has become a pursued therapeutic strategy (the 'MHC-I-opathy' concept, i.e., that several autoimmune diseases share MHC class I alleles as their major risk factors and ERAP1 as a common genetic modifier), with medicinal-chemistry programs reviewed in 2024 and Mendelian-randomization analyses (a genetic-epidemiology method that uses inherited genetic variants as natural experiments to estimate the causal effect of perturbing a protein on disease) prioritizing ERAP1 as an AS drug target; an oral selective ERAP1 inhibitor (GRWD0715) entered phase I/II testing in axial spondyloarthritis in 2025. Authoritative reviews (Navid, Chen, Bowness and Colbert, Nature Reviews Rheumatology 2025) still conclude that no definitive mechanism explaining HLA-B27's role has been established.

Problem Statement

Determine the molecular mechanism by which ERAP1-mediated peptide handling modulates HLA-B27 biology to confer susceptibility to ankylosing spondylitis. Concretely: identify which of the competing hypotheses — an arthritogenic-peptide mechanism in which ERAP1-allotype-dependent trimming produces an HLA-B27-bound self-peptide repertoire recognized by autoreactive CD8 T cells; a peptide-supply folding mechanism in which ERAP1-determined peptide cargo controls HLA-B27 folding, stability, endoplasmic-reticulum misfolding and unfolded-protein-response signaling; or a surface free-heavy-chain/homodimer mechanism in which peptidome quality governs formation of β2-microglobulin-free HLA-B27 forms that engage NK-cell and other innate receptors — actually drives disease, or establish another pathway by which ERAP1 trimming modulates HLA-B27 biology. A mechanistic account should identify the causal ERAP1 variants/allotypes and their quantitative trimming effects, explain the protective effect of low-activity ERAP1 allotypes, and remain consistent with the human epistasis data, in which ERAP1 risk effects are restricted to HLA-B27-positive individuals (later fine-mapping further showed that the rs30187 effect extends to carriers of HLA-B*40:01 independently of B27). The source also notes a therapeutic implication of the same finding: since ERAP1 loss-of-function variants are protective, inhibition of ERAP1 may be effective at least in HLA-B27-positive disease, a hypothesis now being tested by the GRWD0715 phase I/II programme in axial spondyloarthritis. Whether pharmacological inhibition of ERAP1 is safe and clinically effective in adults with established HLA-B27-positive axial spondyloarthritis is an open clinical question that depends on the mechanistic answer, but it is context for this problem rather than a second target to be delivered alongside it.

References

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