HLA-DR/DQ/DP interactions in rheumatoid arthritis

Independent association of HLA-DPB1*02:01 with rheumatoid arthritis in Japanese populations

Objective

Rheumatoid arthritis (RA) is a chronic autoimmune disease characterized with joint destructions; environmental and genetic factors were thought to be involved in the etiology of RA. The production of anti-citrullinated peptide antibodies (ACPA) is specifically associated with RA. DRB1 is associated with the susceptibility of RA, especially ACPA-positive RA [ACPA(+)RA]. However, a few studies reported on the independent associations of DPB1 alleles with RA susceptibility. Thus, we investigated the independent association of DPB1 alleles with RA in Japanese populations.

Methods

Association analyses of DPB1 were conducted by logistic regression analysis in 1667 RA patients and 413 controls.

Results

In unconditioned analysis, DPB1*04:02 was nominally associated with the susceptibility of ACPA(+)RA (P = 0.0021, corrected P (Pc) = 0.0275, odds ratio [OR] 1.52, 95% confidence interval [CI] 1.16–1.99). A significant association of DPB1*02:01 with the susceptibility of ACPA(+)RA was observed, when conditioned on DRB1 (P_adjusted = 0.0003, Pc_adjusted = 0.0040, OR_adjusted 1.47, 95%CI 1.19–1.81). DPB1*05:01 was tended to be associated with the protection against ACPA(+)RA, when conditioned on DRB1 (P_adjusted = 0.0091, Pc_adjusted = 0.1184, OR_adjusted 0.78, 95%CI 0.65–0.94). When conditioned on DRB1, the association of DPB1*04:02 with ACPA(+)RA was disappeared. No association of DPB1 alleles with ACPA-negative RA was detected.

Conclusion

The independent association of DPB1*02:01 with Japanese ACPA(+)RA was identified.

Association of HLA-DPB1 polymorphisms with rheumatoid arthritis: A systemic review and meta-analysis

BACKGROUND

The current reports on the association between HLA-DPB1 alleles and rheumatoid arthritis (RA) results were controversial. Thus, we conducted a meta-analysis to assess whether DPB1 alleles are associated with increased risk of rheumatoid arthritis.

METHODS

Systematic searches on PubMed, Embase, Elsevier, CNKI (China National Knowledge Infrastructure), Wanfang data and Cochrane Library prior to July 2017 were performed. The pooled odds ratios (ORs) and 95% confidence interval (95% CI) was used to assess the association between frequencies of DPB1 alleles and RA patients.

RESULTS

Eight studies with 592 cases and 935 controls were included in this meta-analysis. Overall, the pooled ORs showed that frequencies of DPB1*0401 and *0601 were higher in the RA group compared with controls (*0401: OR: 1.586, 95%CI: 1.296-1.941, P<0.001; *0601: OR: 1.921, 95%CI: 1.142-3.229, P=0.014). Whereas, the frequencies of DPB1*0101, *0402 and *0501 were lower in the RA control than the controls (*0101: OR: 0.691, 95%CI: 0.481-0.993, P=0.046; *0402: OR: 0.707, 95%CI: 0.555-0.902, P=0.005; *0501: OR: 0.502, 95%CI: 0.329-0.767, P=0.001). No associations were observed for DPB1*0201, *0202, *0301 and *0901 (*0201: OR: 1.129, 95%CI: 0.882-1.446, P = 0.335; *0202: OR: 0.840, 95%CI: 0.940-1.441, P = 0.527; *0301: OR: 0.769, 95%CI: 0.577-1.026, P = 0.074; *0901: OR: 1.221, 95% CI: 0.541-2.755, P = 0.630).

CONCLUSIONS

This meta-analysis demonstrates that high frequency expression of DPB1*0401 and *0601 are significantly associated with susceptibility to RA, it may be a risk factor for occurrence of RA. Low frequency expression of DPB1*0101, *0402 and *0501 may be negatively associated with RA, it may be a protective factor for occurrence of RA.

Genetic polymorphism of rs9277535 in HLA-DP associated with rheumatoid arthritis and anti-CCP production in a Chinese population

HLA-II molecules are critical in triggering human immune response, especially in activating CD4+ T cells. HLA-DP, belonging to HLA-II molecules, draws increasing attention for its role in presentation of viral antigen and autoantigen to T cells. Researches reported single nucleotide polymorphism (SNP) of HLA-DP associated with HBV infection and autoimmune diseases such as SLE. However, little is known about the relationship between HLA-DP and rheumatoid arthritis (RA). Rs9277535 is located in 3' UTR region of HLA-DPB1, a subunit of HLA-DP, and was reported to affect HLA-DP mRNA expression. In the present study, we explored the relationship between gene polymorphism of rs9277535 in HLA-DPB1 and RA susceptibility and progression. Samples from 254 patients with RA and 391 age- and sex-matched healthy controls were collected and genotyped by a polymerase chain reaction-high-resolution melting (PCR-HRM) assay. Serological tests (anti-CCP, rheumatoid factor, C-reactive protein, anti-keratin antibody) were detected by laboratory assays. Strong association was observed between SNP rs9277535 in HLA-DP and RA susceptibility (allele frequency distribution: OR = 1.409, 95%CI = 1.121-1.773, P = 0.004). Further validation was provided by disease model analysis (recessive model: OR = 1.889, 95%CI = 1.194-2.990, P = 0.008; dominant model: OR = 1.464, 95%CI = 1.050-2.041, P = 0.025; additive model: OR = 2.208, 95%CI = 1.335-3.652, P = 0.003). Allele A was correlated to increased risk of RA. Serological test results demonstrated patients carrying allele A of rs9277535 had elevated serum anti-CCP antibody level. The present study provided evidence that HLA-DP gene polymorphism associated with RA susceptibility. Allele A of rs9277535 in HLA-DP correlated to increased risk of RA and elevated serum anti-CCP level.

Effect of swine leukocyte antigen-DQA gene variation on diarrhea in Large White, Landrace, and Duroc piglets

Piglet diarrhea is one of the most common factors that affects the benefits of the swine industry. Although recent studies have shown that exon 2 of SLA-DQA is associated with piglet resistance to diarrhea, contributions of genetic variation in the additional exon coding regions of this gene remain unclear. Here, we investigated variation in exons 1, 3 and 4 of the SLA-DQA gene and evaluated their effects on diarrheal infection in 425 suckling piglets. No variation was identified in exon 1. In exon 3, there were eight alleles detected, generated by 14 single nucleotide polymorphisms (SNPs) and three nucleotide deletions, eight SNPs being newly identified. Four allele sequences and three SNPs were identified in exon 4, only one SNP being newly identified. Statistical analysis showed that the genotypes of exon 3 are significantly associated with piglet diarrhea; indeed, genotypes DQA*wb01/wb02 and wb04/wb05 are clearly associated with resistance to piglet diarrhea, as they have the lowest probabilities of infection (P < 0.05). However, no significant association was found between the genotypes of exon 4 and diarrhea (P > 0.05). These results provide important new information concerning the level of genetic diversity at the SLA-DQA locus and suggest that further genetic association studies of piglet diarrhea resistance should include analyses of both exons 2 and 3 of this locus.

HLA-DPB1-COL11A2 and three additional xMHC loci are independently associated with RA in a UK cohort

The aim of this study was to investigate the complex association pattern of the extended major histocompatibility complex (xMHC) region with rheumatoid arthritis (RA) susceptibility to identify effects independent of HLA-DRB1. A total of 1804 RA cases and 1474 controls were included. High-resolution HLA-DRB1 typing was performed. Subjects were genotyped for 1546 single-nucleotide polymorphisms (SNPs) using Affymetrix GeneChip 500 K (Santa Clara, CA, USA) as part of the Wellcome Trust Case Control Consortium Study. Statistical analysis was carried out using PLINK. To avoid confounding by RA-associated HLA-DRB1 alleles, we analyzed xMHC SNPs using a data set with pairwise matching of cases and controls on DRB1 genotypes. A total of 594 case-control pairs with identical DRB1 genotypes were identified. After this adjustment, 104 SNPs remained significantly associated with RA (P<0.05), suggesting that additional RA loci independent of HLA-DRB1 can be found in the xMHC region. Of these, four loci showed the strongest associations with RA (P<0.005): ZNF391, the olfactory receptor (OR) gene cluster, C6orf26-RDBP and HLA-DPB1-COL11A2. An additional locus mapping to the BTN (butyrophilin) cluster showed independent association with RA in anti-cyclic citrullinated peptide-positive patients exclusively. We have validated the previously described independent association of the HLA-DPB1-COL11A2 locus with RA. In addition, association with three novel independent RA loci in the xMHC region (ZNF391, OR2H1 and C6orf26-RDBP) has been detected.

Characterization of genetic polymorphism of novel MHC B-LB II alleles in Chinese indigenous chickens

Genetic polymorphism of the major histocompatibility complex (MHC) B-LB II gene was studied by amplification of exon 2 using PCR, followed by cloning and DNA sequencing in eight indigenous Chinese chicken populations. To reveal the genetic variation of the B-LB II gene, 37 types of patterns detected by PCR-SSCP were investigated first, which would be used to screen novel B-LB II sequences within the breeds. The types of PCR-SSCP patterns and final sequencing allowed for the identification of 31 novel MHC B-LB II alleles from 30 unrelated individuals of Chinese chickens that were sampled. These are the first designators for the alleles of chicken MHC B-LB II gene based on the rule of assignment for novel mammalian alleles. Sequence alignment of the 31 B-LB II alleles revealed a total of 68 variable sites in the fragment of exon 2, of which 51 parsimony informative and 17 singleton variable sites were observed. Among the polymorphic sites, the nucleotide substitutions in the first and second positions of the codons accounted for 36.76% and 35.29%, respectively. The sequence similarities between the alleles were estimated to be 90.6%-99.5%. The relative frequencies of synonymous and nonsynonymous nucleotide substitutions within the region were 2.92%+/-0.94% and 14.64%+/-2.67%, respectively. These results indicated that the genetic variation within exon 2 appeared to have largely arisen by gene recombination and balancing selection. Alignment of the deduced amino acid sequences of the beta1 domain coded by exon 2 revealed 6 synonymous mutations and 27 nonsynonymous substitutions at the 33 disparate sites. In particular, the nonsynonymous substitutions at the putative peptide-binding sites are considered to be associated with immunological specificity of MHC B-LB II molecule in Chinese native chickens. These results can provide a molecular biological basis for the study of disease resistance in chicken breeding.

Polymorphism of the DQA2 gene in goats

Variation in the caprine DQA2 gene was investigated using PCR-single-strand conformational polymorphism (SSCP) and DNA sequencing. Eleven DQA2 alleles were defined by SSCP patterns from 23 goats. All the caprine alleles shared high sequence homology to ovine DQA2 sequences, and exhibited a pattern of polymorphism similar to DQA2 alleles from sheep and cattle but different from caprine DQA1 sequences. Thirty-eight AA positions in the alpha1 domain of caprine DQA2 molecules were polymorphic, and a high degree of polymorphism was observed in the putative antigen-binding region, with 74% of the positions being polymorphic. Phylogenetic analysis of caprine, ovine, and bovine DQA sequences revealed that the caprine DQA2 sequences identified here grouped with ovine DQA2, bovine DQA2, DQA3, and DQA4 sequences but are separate from the group of caprine DQA1 alleles. Nine of the caprine DQA2 sequences were more similar to ovine DQA2 alleles, whereas the remaining two were more closely related to ovine DQA2-like and bovine DQA3 alleles. This finding suggests that the caprine DQA2 sequences may represent two loci, which probably arose by either gene duplication or gene conversion events. Allelic lineages were evident for both DQA2 and DQA2-like loci, supporting the trans-species mode of evolution of major histocompatibilitly complex genes. The high level of polymorphism and similarity between caprine and ovine DQA2 alleles suggests that the DQA2 gene may play an important role in immune responses to shared pathogens.

HLA and disease

Association of HLA and diseases is well known. Several population studies are available suggesting evidence of association of HLAs in more than 40 diseases. HLA found across various populations vary widely. Some of the reasons attributed for such variation are occurrence of social stratification based on geography, language and religion, consequences of founder effect, racial admixture or selection pressure due to environmental factors. Hence certain HLA alleles that are predominantly associated with disease susceptibility or resistance in one population may or may not show any association in other populations for the same disease. Despite of these limitations, HLA associations are widely studied across the populations worldwide and are found to be important in prediction of disease susceptibility, resistance and of evolutionary maintenance of genetic diversity. This review consolidates the HLA data on some prominent autoimmune and infectious diseases among various ethnic groups and attempts to pinpoint differences in Indian and other population.

Anti-caspase-8 autoantibody response in silicosis patients is associated with HLA-DRB1, DQB1 and DPB1 alleles

We reported previously the autoantibodies directed to caspase-8 among patients with silicosis, systemic sclerosis (SSc) and systemic lupus erythematosus (SLE) , and in healthy individuals. In this study, we analyzed the correlation between anti-caspase-8 autoantibody responses and HLA class II alleles in silicosis patients. The frequencies of HLA-DRB1*0406 were significantly higher in antibody positive patients (16.67%) than in control individuals (3.03%, p=0.0006). The lysine (K) at position 71 as in DRB1*0406 has been reported to be associated with rheumatoid arthritis (RA) and insulin dependent diabetes mellitus (IDDM). The haplotype HLA-DR4; DQB1*0302 was detected in 4 of 12 antibody positive patients. RA, IDDM, or pemphygus vulgaris link to the haplotype. The frequencies of DQB1*0401 were significantly lower in antibody positive patients (0%) than that in controls (13.33%, p=0.0390). The aspartic acid at position 57 in the DQB1 molecule as in DQB1*0401 is reported to play a role in the resistance to IDDM. The frequency of DPB1*0601 in antibody positive patients (5.88%) was significantly higher than that in controls (0.56%, p=0.0003). DPB1*0601 is reported to be a risk factor among RA patients, and glutamate at position 69 of the DPB1 molecule may be involved. Repeated and continuous screening of autoantibodies seems to be necessary among workers in contact with Si-related substances for the detection of immunological disorders in the early stage.

Candidate epitope identification using peptide property models: application to cancer immunotherapy

Peptides derived from pathogens or tumors are selectively presented by the major histocompatibility complex proteins (MHC) to the T lymphocytes. Antigenic peptide-MHC complexes on the cell surface are specifically recognized by T cells and, in conjunction with co-factor interactions, can activate the T cells to initiate the necessary immune response against the target cells. Peptides that are capable of binding to multiple MHC molecules are potential T cell epitopes for diverse human populations that may be useful in vaccine design. Bioinformatical approaches to predict MHC binding peptides can facilitate the resource-consuming effort of T cell epitope identification. We describe a new method for predicting MHC binding based on peptide property models constructed using biophysical parameters of the constituent amino acids and a training set of known binders. The models can be applied to development of anti-tumor vaccines by scanning proteins over-expressed in cancer cells for peptides that bind to a variety of MHC molecules. The complete algorithm is described and illustrated in the context of identifying candidate T cell epitopes for melanomas and breast cancers. We analyzed MART-1, S-100, MBP, and CD63 for melanoma and p53, MUC1, cyclin B1, HER-2/neu, and CEA for breast cancer. In general, proteins over-expressed in cancer cells may be identified using DNA microarray expression profiling. Comparisons of model predictions with available experimental data were assessed. The candidate epitopes identified by such a computational approach must be evaluated experimentally but the approach can provide an efficient and focused strategy for anti-cancer immunotherapy development.

Diversity of the ovine DQA2 gene1

Variation in the ovine DQA2 gene was investigated in approximately 2,000 sheep from six breeds. Fragments of DNA containing the ovine DQA2 exon 2 were amplified using PCR. Single-strand conformational polymorphism analysis and DNA sequence analysis were employed to detect genetic variation. Twenty-three nucleic acid sequences, encoding 22 DQA2 amino acid sequences, were identified. This increases the number of alleles identified from 10 to 23. In some cases, three or four unique sequences were isolated from individual sheep, suggesting that these DQA2 sequences may represent two loci. Phylogenetic tree analysis revealed that 5 of these 23 sequences were more closely related to cattle DQA3 or DQA4 sequences than to other sheep DQA2 sequences. These sequences clustered together and were called DQA2-like to differentiate them from other DQA2 sequences. There was no evidence of DQA5-like sequences in sheep. Information theory-based analysis indicated that some of the DQA2-like sequences had low information content at splice sites, suggesting that these alleles may have low functional activity. Allelic lineages were observed not only at the DQA2 locus, but also at the DQA2-like locus, supporting the trans-species mode of evolution of MHC genes. Comparison of the allelic sequences suggests that polymorphism seems to have arisen largely by point mutation and gene conversion, and a recent gene conversion event seems to have occurred between the DQA2 and DQA2-like loci. The high level of sequence polymorphism detected and varied number of loci demonstrate the extensive diversity of the ovine DQA2 gene.

Allelic polymorphism in the ovine DQA1 gene1

Variation in the ovine DQA1 gene was investigated by amplification of exon 2 using PCR, followed by single-strand conformational polymorphism (SSCP) analysis, cloning, and DNA sequencing. Fourteen novel SSCP patterns, representing 14 different sequences, were identified. Eight of these 14 sequences were identical to published DQA1 sequences from sheep, whereas the remaining six were novel but similar to the published DQA1 sequences from sheep and cattle. These six new sequences exhibited conserved region and variable region patterns similar to the published sheep DQA1 sequences, but were different than the published DQA2 sequences from sheep. All of these 14 putative sheep DQA1 sequences fulfilled the criteria used by the established bovine leukocyte antigens major histocompatibility complex nomenclature committee for assignment as new alleles. Comparison of the available DQA1 sequences from sheep and cattle revealed several clusters of ovine DQA1 sequences, and some sheep alleles were more similar to cattle alleles than other sheep alleles. The occurrence of trans-species polymorphism suggests the action of balancing selection at the DQA1 locus. Twenty-four percent of the nucleotide positions showed variation within exon 2, and this variation seems to have arisen largely by point mutation and gene conversion. The nonsynonymous and synonymous substitution rates were similar in both the putative antigen-binding site codons and the putative nonantigen-binding site codons. The extensive polymorphism reported in this article is consistent with polymorphism reported at the bovine DQA1 locus.

The shared epitope and severity of rheumatoid arthritis

After two decades of research involving thousands of RA patients, it is still not possible to precisely define the relation of HLA-DRB1 SE alleles to RA severity. Improvements in our understanding require more careful consideration of several factors such as ethnicity, gender, and the specific SE allele and genotype inherited. Large studies of heterogeneous groups of patients are required and indicate the need for collaborative efforts among researchers. In the interim, meta-analysis of the existing literature may provide some insight, because it allows utilization of the tremendous amount of research already completed. A preliminary meta-analysis highlighted the significant heterogeneity among the existing literature, and a more ambitious meta-analysis that uses individual patient-level data is currently ongoing. Profound implications exist for determination of the precise relationship between the SE and RA severity. This information could be valuable in identifying patients at greater risk of severe complications or as a stratification variable for clinical trials. Moreover, patients genetically predisposed to severe disease may benefit from early initiation of more aggressive therapy. Ultimately, clarification of the role of the SE may be valuable for the development of specific therapies directed toward DRB1 and related targets.

Do the HLA-DQ and DP genes play a role in rheumatoid arthritis?

Whereas the DRB1 alleles have well-established associations with rheumatoid arthritis (RA), the DQ and DP alleles are of more controversial relevance to RA. Early studies of the DQB1 genes in RA determined the frequencies of the two DQB1*03 subtypes that are in linkage disequilibrium with DR4, DQB1*0301 (DQw7) and *0302 (DQw8). Their results are conflicting and difficult to interpret because molecular biology techniques for determining DR4 specificity polymorphism were not available at the time. None of the more recent studies found compelling evidence that the DQB1 alleles influenced the susceptibility to RA. A few studies suggest that the DQ alleles may influence the clinical or biological expression of the disease, perhaps through a complementary effect of the DRB1 and DQB1 alleles. DR-DQ complementarity has been demonstrated in the DQ8 transgenic mouse model, although this is not necessarily relevant to the human disease. The role of DPB1 remains hypothetical but may involve an influence of some alleles in relatively mild forms of RA. The DQB1 and DPB1 alleles are in strong linkage disequilibrium with the DRB1 alleles, making the elucidation of their independent effects a challenging task. Studies are needed to determine whether these linkage disequilibriums can influence the development of autoimmune diseases.