B*2707 differs in peptide specificity from B*2705 and B*2704 as much as from HLA-B27 subtypes not associated to spondyloarthritis

Polymorphisms in the F Pocket of HLA-B27 Subtypes Strongly Affect Assembly, Chaperone Interactions, and Heavy-Chain Misfolding

OBJECTIVE

HLA-B27 is associated with the inflammatory spondyloarthritides (SpA), although subtypes HLA-B*27:06 and HLA-B*27:09 are not. These subtypes differ from the HLA-B*27:05 disease-associated allele primarily at residues 114 and 116 of the heavy chain, part of the F pocket of the antigen-binding groove. Dimerization of HLA-B27 during assembly has been implicated in disease onset. The purpose of this study was to investigate the factors that influence differences in dimerization between disease-associated and non-disease-associated HLA-B27 alleles.

METHODS

HLA-B*27:05 and mutants resembling the HLA-B*27:06 and 09 subtypes were expressed in the rat C58 T cell line, the human CEM T cell line and its calnexin-deficient variant CEM.NKR. Immunoprecipitation, pulse-chase experiments, flow cytometry, and immunoblotting were performed to study the assembly kinetics, heavy-chain dimerization, and chaperone associations.

RESULTS

By expressing HLA-B*27:05, 06-like, and 09 alleles on a restrictive rat transporter associated with antigen processing background, we demonstrate that a tyrosine expressed at p116, either alone or together with an aspartic acid residue at p114, inhibited HLA-B27 dimerization and increased the assembly rate. F-pocket residues altered the associations with chaperones of the early major histocompatibility complex class I folding pathway. Calnexin was demonstrated to participate in endoplasmic reticulum (ER) stress-mediated degradation of dimers, whereas the oxidoreductase ERp57 does not appear to influence dimerization.

CONCLUSION

Residues within the F pocket of the peptide-binding groove, which differ between disease-associated and non-disease-associated HLA-B27 subtypes, can influence the assembly process and heavy-chain dimerization, events which have been linked to the initiation of disease pathogenesis.

Human Leukocyte Antigen (HLA) B27 Allotype-Specific Binding and Candidate Arthritogenic Peptides Revealed through Heuristic Clustering of Data-independent Acquisition Mass Spectrometry (DIA-MS) Data

Expression of HLA-B27 is strongly associated with ankylosing spondylitis (AS) and other spondyloarthropathies. While this is true for the majority of HLA-B27 allotypes, HLA-B*27:06 and HLA-B*27:09 are not associated with AS. These two subtypes contain polymorphisms that are ideally positioned to influence the bound peptide repertoire. The existence of disease-inducing peptides (so-called arthritogenic peptides) has therefore been proposed that are exclusively presented by disease-associated HLA-B27 allotypes. However, we have recently demonstrated that this segregation of allotype-bound peptides is not the case and that many peptides that display sequence features predicted to favor binding to disease-associated subtypes are also capable of being presented naturally by protective alleles. To further probe more subtle quantitative changes in peptide presentation, we have used a combination of data-independent acquisition (DIA) and multiple reaction monitoring (MRM) mass spectrometry to quantify the abundance of 1646 HLA-B27 restricted peptides across the eight most frequent HLA-B27 allotypes (HLA-B*27:02-HLA-B*27:09). We utilized K means cluster analysis to group peptides with similar allelic binding preferences across the eight HLA-B27 allotypes, which enabled us to identify the most-stringent binding characteristics for each HLA-B27 allotype and further refined their existing consensus-binding motifs. Moreover, a thorough analysis of this quantitative dataset led to the identification of 26 peptides, which are presented in lower abundance by HLA-B*27:06 and HLA-B*27:09 compared with disease-associated HLA-B27 subtypes. Although these differences were observed to be very subtle, these 26 peptides might encompass the sought-after arthritogenic peptide(s).

Revisiting the arthritogenic peptide theory: quantitative not qualitative changes in the peptide repertoire of HLA-B27 allotypes

OBJECTIVE

The association of HLA-B27 with spondyloarthropathy is one of the strongest documented for any autoimmune disease. A common hypothesis for this association is the arthritogenic peptide concept. This dictates that differences in the peptide binding preferences of disease-associated and non-disease-associated HLA-B27 allotypes underlie the presentation of bacterial and self-peptides, leading to cross-reactive T cell immunity and subsequent autoimmune attack of affected tissues. The aim of this study was to analyze and compare self-peptides from 8 HLA-B27 allotypes, to increase existing data sets of HLA-B27 ligands, to refine and compare their consensus-binding motifs, and to reveal similarities and differences in the peptide repertoire of the HLA-B27 subtypes.

METHODS

Qualitative differences in the peptides bound to the 8 most frequent HLA-B27 subtypes were determined by tandem mass spectrometry, and quantitative changes in allelic binding specificities were determined by highly sensitive and targeted multiple reaction monitoring mass spectrometry.

RESULTS

We identified >7,500 major histocompatibility complex class I peptides derived from the 8 most common HLA-B27 allotypes (HLA-B*27:02 to HLA-B*27:09). We describe individual binding motifs for these alleles for the 9-12-mer ligands. The peptide repertoires of these closely related alleles showed significant overlap. Allelic polymorphisms resulting in changes in the amino acid composition of the antigen-binding cleft manifested largely as quantitative changes in the peptide cargo of these molecules.

CONCLUSION

Absolute binding preferences of HLA-B27 allotypes do not explain disease association. The arthritogenic peptide theory needs to be reassessed in terms of quantitative changes in self-peptide presentation, T cell selection, and altered conformation of bound peptides.

Peptide handling by HLA-B27 subtypes influences their biological behavior, association with ankylosing spondylitis and susceptibility to endoplasmic reticulum aminopeptidase 1 (ERAP1)

HLA-B27 is strongly associated with ankylosing spondylitis (AS). We analyzed the relationship between structure, peptide specificity, folding, and stability of the seven major HLA-B27 subtypes to determine the role of their constitutive peptidomes in the pathogenicity of this molecule. Identification of large numbers of ligands allowed us to define the differences among subtype-bound peptidomes and to elucidate the peptide features associated with AS and molecular stability. The peptides identified only in AS-associated or high thermostability subtypes with identical A and B pockets were longer and had bulkier and more diverse C-terminal residues than those found only among non-AS-associated/lower-thermostability subtypes. Peptides sequenced from all AS-associated subtypes and not from non-AS-associated ones, thus strictly correlating with disease, were very rare. Residue 116 was critical in determining peptide binding, thermodynamic properties, and folding, thus emerging as a key feature that unified HLA-B27 biology. HLA-B27 ligands were better suited to TAP transport than their N-terminal precursors, and AS-associated subtype ligands were better than those from non-AS-associated subtypes, suggesting a particular capacity of AS-associated subtypes to bind epitopes directly produced in the cytosol. Peptides identified only from AS-associated/high-thermostability subtypes showed a higher frequency of ERAP1-resistant N-terminal residues than ligands found only in non-AS-associated/low-thermostability subtypes, reflecting a more pronounced effect of ERAP1 on the former group. Our results reveal the basis for the relationship between peptide specificity and other features of HLA-B27, provide a unified view of HLA-B27 biology and pathogenicity, and suggest a larger influence of ERAP1 polymorphism on AS-associated than non-AS-associated subtypes.

HLA and pharmacogenetics of drug hypersensitivity

Immunologically mediated drug reactions have been traditionally classified as unpredictable based on the fact that they cannot be predicted strictly on the pharmacological action of the drug. Such adverse drug reactions are associated with considerable morbidity and include severe cutaneous adverse reactions such as Stevens-Johnson syndrome/toxic epidermal necrolysis and the drug hypersensitivity syndromes (drug reaction with eosinophilia and systemic symptoms/drug-induced hypersensitivity syndrome). Over the last decade there have been many associations between these syndromes and Class I and II HLA alleles of the MHC, which have enriched and driven our knowledge of their immunopathogenesis. Significant translation has also occurred in the case of HLA-B*5701 screening being used to exclude at risk patients from abacavir and prevent abacavir hypersensitivity. The ultimate translation of the knowledge of how drugs interact with HLA would be applicable to preclinical drug screening programs to improve the safety and cost-effectiveness of drug design and development.

Functional interaction of the ankylosing spondylitis-associated endoplasmic reticulum aminopeptidase 1 polymorphism and HLA-B27 in vivo

The association of ERAP1 with ankylosing spondylitis (AS)1 among HLA-B27-positive individuals suggests that ERAP1 polymorphism may affect pathogenesis by altering peptide-dependent features of the HLA-B27 molecule. Comparisons of HLA-B*27:04-bound peptidomes from cells expressing different natural variants of ERAP1 revealed significant differences in the size, length, and amount of many ligands, as well as in HLA-B27 stability. Peptide analyses suggested that the mechanism of ERAP1/HLA-B27 interaction is a variant-dependent alteration in the balance between epitope generation and destruction determined by the susceptibility of N-terminal flanking and P1 residues to trimming. ERAP1 polymorphism associated with AS susceptibility ensured efficient peptide trimming and high HLA-B27 stability. Protective polymorphism resulted in diminished ERAP1 activity, less efficient trimming, suboptimal HLA-B27 peptidomes, and decreased molecular stability. This study demonstrates that natural ERAP1 polymorphism affects HLA-B27 antigen presentation and stability in vivo and proposes a mechanism for the interaction between these molecules in AS.

The Genetic Basis of Spondyloarthritis: SPARTAN/IGAS 2009

A joint meeting was held in July 2009 in Houston, Texas, of members of the Spondyloarthritis Research and Therapy Network (SPARTAN), founded in 2003 to promote research, education, and treatment of ankylosing spondylitis (AS) and related forms of spondyloarthritis (SpA), and members of International Genetics of AS (IGAS), founded in 2003 to encourage and coordinate studies internationally in the genetics of AS. The general topic was the genetic basis of SpA, with presentations on the future of human genetic studies; microbes, SpA, and innate immunity; susceptibility of AS to the major histocompatibility complex (MHC) and non-MHC; and individual discussions of the genetics of psoriasis and psoriatic arthritis, uveitis, inflammatory bowel disease, and enteropathic arthritis. Summaries of those discussions are presented.

Mutational analysis reveals a complex interplay of peptide binding and multiple biological features of HLA-B27

Molecular polymorphism influences the strong association of HLA-B27 with ankylosing spondylitis through an unknown mechanism. Natural subtypes and site-directed mutants were used to analyze the effect of altering the peptide-binding site of this molecule on its stability, interaction with tapasin, folding, and export. The disease-associated subtypes B*2705, B*2702, and B*2704 showed higher thermostability at 50 °C than all other subtypes and mutants, except some mimicking B*2702 polymorphism. The lowest values were found among pocket B mutants, most of which interacted strongly with tapasin, but otherwise there was no correlation between thermostability and tapasin interaction. Mutants resulting in increased hydrophobicity frequently acquired their maximal thermostability faster than those with increased polarity, suggesting that this process is largely driven by the thermodynamics of peptide binding. Folding, export, and tendency to misfold were influenced by polymorphism all along the peptide-binding site and were not specifically dependent on any particular region or structural feature. Frequent uncoupling of thermostability, folding/misfolding, and export can be explained by the distinct effect of mutations on the acquisition of a folded conformation, the optimization rate of B27-peptide complexes, and their quality control in the endoplasmic reticulum, all of which largely depend on the ways in which mutations alter peptide binding, without excluding additional effects on interactions with tapasin or other proteins involved in folding and export. The similarity of the generally disease-associated B*2707 to nondisease-associated subtypes in all the features analyzed suggests that molecular properties other than antigen presentation may not currently explain the relationship between HLA-B27 polymorphism and ankylosing spondylitis.

HLA-B27-bound peptide repertoires: their nature, origin and pathogenetic relevance

Peptide binding is a central biological property of HLA-B27. The availability of HLA-B27 subtypes differentially associated to ankylosing spondylitis provides a unique tool to explore the relationship between peptide specificity and pathogenetic potential. Many studies have focused on defining the nature of subtype-bound repertoires, aiming to identify peptide features that may correlate with association to disease and to find constitutive self-ligands with sequence homology to microbial epitopes. These studies were pursued on the assumption that molecular mimicry between self and foreign ligands of HLA-B27 might trigger autoimmunity. A second level of involvement ofpeptide repertoires in the biology and immunopathology of HLA-B27 is through their critical influence on folding, maturation and cell surface expression and stability. Recent studies have emphasized the mechanisms ofpeptide loading and optimization, the interactions ofHLA-B27 with other components of the peptide-loading complex and the contribution of these interactions to shaping HLA-B27-bound peptide repertoires. A novel, more comprehensive and integrative, view is emerging in which the peptide binding specificity is a critical determinant of the whole HLA-B27 biology. A proper understanding of the relationships between peptide specificity and other molecular and functional features of HLA-B27 should provide the key to unveiling its pathogenetic role in spondyloarthritis.

Subtypes of HLA-B27: history and implications in the pathogenesis of ankylosing spondylitis

HLA-B27 represents a family of 38 closely related cell surface proteins (encoded by the alleles HLA-B*2701-39) called subtypes of HLA-B27, most of which have evolved from the ubiquitous HLA-B*2705 (specifically the B*27052 allele). HLA-B27 subtypes are largely characterized by nucleotide substitutions (mostly nonsynonymous) in exons 2 and 3 which encode alpha1 and alpha2 domains ofthe peptide binding groove respectively. Table 1 shows the description of sequences of HLA-B27 allele sequences. The subtypes could have arisen from B*2705 by point mutation (B*2703, B*2709, B*2704), gene conversion (B*2701, B*2702, B*2708) and reciprocal recombination (B*2707) B*2706 could have arisen by interlocus gene conversion. Studies from different parts of the world reveal differences in the population distribution.

Peptides: the cornerstone of HLA-B27 biology and pathogenetic role in spondyloarthritis

The association of human leukocyte antigen (HLA)-B27 to ankylosing spondylitis is one of the strongest between a major histocompatibility complex molecule and a disease. Yet, the basis for this association remains unknown. Several hypotheses, each based on a particular feature of HLA-B27, guide much of the current research on the pathogenesis of this disease, but none has yet satisfactorily explained its mechanism and the differential association of B27 subtypes to it. In this review, the pathogenetic role of HLA-B27 will be analyzed from a global perspective of its biology, emphasizing the interdependency of multiple molecular features and the likely influence of disease-modifying gene products. From this perspective, peptide binding emerges as the cornerstone of all other biological properties.

Human leukocyte antigen class I-restricted activation of CD8+ T cells provides the immunogenetic basis of a systemic drug hypersensitivity

The basis for strong immunogenetic associations between particular human leukocyte antigen (HLA) class I allotypes and inflammatory conditions like Behçet's disease (HLA-B51) and ankylosing spondylitis (HLA-B27) remain mysterious. Recently, however, even stronger HLA associations are reported in drug hypersensitivities to the reverse-transcriptase inhibitor abacavir (HLA-B57), the gout prophylactic allopurinol (HLA-B58), and the antiepileptic carbamazepine (HLA-B*1502), providing a defined disease trigger and suggesting a general mechanism for these associations. We show that systemic reactions to abacavir were driven by drug-specific activation of cytokine-producing, cytotoxic CD8+ T cells. Recognition of abacavir required the transporter associated with antigen presentation and tapasin, was fixation sensitive, and was uniquely restricted by HLA-B*5701 and not closely related HLA allotypes with polymorphisms in the antigen-binding cleft. Hence, the strong association of HLA-B*5701 with abacavir hypersensitivity reflects specificity through creation of a unique ligand as well as HLA-restricted antigen presentation, suggesting a basis for the strong HLA class I-association with certain inflammatory disorders.

Th1/Th17 cytokine profiles in patients with reactive arthritis/undifferentiated spondyloarthropathy

OBJECTIVE

Data on synovial fluid (SF) cytokine concentrations in patients with reactive arthritis (ReA) or undifferentiated spondyloarthropathy (uSpA) are limited and contradictory. We measured levels of several proinflammatory and immunoregulatory cytokines in SF and sera from patients with ReA/uSpA.

METHODS

Interleukin 17 (IL-17), IL-6, interferon-g (IFN-g), and IL-12p40, and immunoregulatory cytokines IL-10 and transforming growth factor-beta (TGF-beta) were assayed using ELISA in SF specimens from 51 patients with ReA/uSpA (ReA 21, uSpA 30), 40 patients with rheumatoid arthritis (RA), and 11 patients with osteoarthritis (OA). IL-17, IL-6, IFN-g, and IL-10 levels were also measured in paired sera samples from patients with ReA/uSpA.

RESULTS

SF concentrations of IL-17, IL-6, TGF-beta, and IFN-g were significantly higher in patients with ReA/uSpA as compared to RA patients (for IL-17 median 46 pg/ml, range < 7.8-220 vs median < 7.8 pg/ml, range < 7.8-136, p < 0.05; for TGF-beta median 4.2 ng/ml, range 1.32-12 vs median 3.01 ng/ml, range 0.6-9.6, p < 0.01; for IL-6 median 58 ng/ml, range 2-540 vs median 34.5 ng/ml, range < 0.009-220, p < 0.05; for IFN-g median 290 pg/ml, range < 9.4-1600 vs median 100 pg/ml, range < 9.4-490, p < 0.05). SF levels of IL-10 were comparable but the ratio of IFN-g/IL-10 was significantly higher in ReA/uSpA patients than RA patients (median 3.18, range 0.06-200 for ReA/uSpA vs median 1.0, range 0.03-26.9 for RA; p < 0.05). IL-17, IL-6, IL-10, and IFN-g SF levels were significantly higher than paired serum levels in ReA/uSpA patients (p < 0.01 for IL-17, p < 0.0001 for IL-6, p < 0.0001 for IL-10, and p < 0.001 for IFN-g).

CONCLUSION

Increased IL-17, IL-6, TGF-beta, and IFN-g concentrations in ReA/uSpA than in RA suggest that Th1 and Th17 cells could be the major agents in inflammation in ReA/uSpA.

Identification of endogenously presented peptides from Chlamydia trachomatis with high homology to human proteins and to a natural self-ligand of HLA-B27

A strategy for the stable expression of proteins, or large protein fragments, from Chlamydia trachomatis into human cells was designed to identify bacterial epitopes endogenously processed and presented by HLA-B27. Fusion protein constructs in which the green fluorescent protein gene was placed at the 5'-end of the bacterial DNA primase gene or some of its fragments were transfected into B*2705-C1R cells. One of these constructs, including residues 90-450 of the bacterial protein, was stably and efficiently expressed. Mass spectrometry-based comparative analysis of HLA-B27-bound peptide pools led to identification of three HLA-B27 ligands differentially presented in the transfectant cells. Sequencing of these peptides confirmed that they were derived from the bacterial DNA primase. One of them, spanning residues 211-221, showed 55% sequence identity with a known self-ligand of HLA-B27 derived from its own molecule. The other two bacterial ligands, P-(112-121) and P-(112-122), were derived from the same region and differed in length by one residue at the C terminus. Both peptides showed >50% identity with multiple human protein sequences that possessed the optimal peptide motifs for HLA-B27 binding. Thus, expression of proteins from arthritogenic bacteria in HLA-B27-positive human cells allows identifying bacterial peptides that are endogenously processed and presented by HLA-B27 and show molecular mimicry with known self-ligands of this molecule and human proteins.

Identification of previously unrecognized predisposing factors for ankylosing spondylitis from analysis of HLA-B27 extended haplotypes in Sardinia

OBJECTIVE

To define the contribution of HLA genes other than HLA-B27 in conferring susceptibility to ankylosing spondylitis (AS), through analysis of HLA-B27 haplotypes in Sardinian subjects.

METHODS

Ninety-eight patients with AS, 133 HLA-B27-positive controls (of whom 33 were positive for HLA-B*2709), and 190 randomly selected controls were genotyped for microsatellites and single-nucleotide polymorphisms (SNPs) spanning the HLA region.

RESULTS

Haplotypes carrying either the B*2705 or the B*2709 allele were found to share a conserved region downstream of the HLA-B gene and a functional polymorphism in the HLA-E gene (R128G), while differing in all other markers. Notably, the presence of an A at SNP rs1264457, encoding for Arg-128, was significantly increased in the cohort of patients (P = 6 x 10(-6), corrected P = 3 x 10(-5)) but not in B*2705- or B*2709-positive controls. Comparing the alleles co-occurring at each HLA marker, we identified a region differentiating patients with AS and B*2705-matched controls. In particular, there was a markedly increased prevalence of heterozygosity at rs1264457 among B27-positive controls (74%, versus 47% in patients and 54% in random controls), suggesting a protective role of G128 in AS. Moreover, other markers around the HLA-B gene were also differentially represented.

CONCLUSION

These results demonstrate a significant difference in the frequency of some HLA markers between AS patients and B*2705-positive controls, which could be attributed to the opposite chromosome. In particular, the differential distribution of a functional polymorphism in the HLA-E gene suggests a possible role of natural killer function in AS pathogenesis.

Proteasome-independent HLA-B27 ligands arise mainly from small basic proteins

Many of the constitutive peptide ligands of HLA-B27, a molecule strongly associated with spondyloarthritis, are proteasome-independent. Stable isotope tagging, mass spectrometry, and epoxomicin-mediated inhibition were used to determine their percentage, structural features, and parental proteins. Of 104 molecular species examined, 29.8% were proteasome-independent, paralleling the level of HLA-B27 re-expression in the presence of epoxomicin after acid stripping. Proteasome-dependent and -independent ligands differed little in peptide motifs, flanking sequences, and cellular localization of the parental proteins. In contrast, whereas the former set arose from proteins whose size and isoelectric point distribution largely reflected those in the human proteome, proteasome-independent ligands, other than a few matching signal sequences, were almost totally derived from small (about 6-16.5 kDa) and basic proteins, which account for only 6.6% of the human proteome. Thus, a non-proteasomal proteolytic pathway with strong preference for small proteins is responsible for a significant fraction of the HLA-B27-bound peptide repertoire.

HLA-B27 and the pathogenesis of spondyloarthropathies

The association of HLA-B27 with ankylosing spondylitis, a chronic inflammatory disease of the axial skeleton, and other spondyloarthropathies, is among the strongest of an MHC antigen and any disease. Yet, the basis for this association remains unknown. In this review the main current hypotheses concerning the pathogenetic role of HLA-B27 will be discussed. They focus on three molecular properties of the molecule: (1) its peptide-presenting specificity, (2) its slow folding and tendency to misfold, and (3) its capacity to form covalent heavy chain homodimers amenable to recognition by leukocyte receptors. On the basis of the peptide specificity spondyloarthropathies would be triggered through T-cell autoimmunity against a self-ligand of HLA-B27 elicited by a cross-reactive foreign antigen. HLA-B27 misfolding would trigger disease through activation of inflammatory pathways following induction of endoplasmic reticulum stress, thus independently of antigen presentation. Recognition of heavy chain homodimers by leukocyte receptors might be involved in disease through immunomodulation of both innate and adaptive responses to arthritogenic pathogens. None of these hypotheses can yet satisfactorily account for the pathogenesis of spondyloarthritides. It is proposed that the pathogenetic role of HLA-B27 will eventually be explained through a global understanding of its biology, in which the various features of this molecule are envisaged as inter-dependent in their contribution to disease.