HLA-DPB1 Locus Research Articles

Sequence analysis and identification of a novel HLA-DPB1*02:01:69 allele by third-generation sequencing

To analyze the sequence of a novel HLA-DPB1 allele in an individual. A individual identified from the database of blood donors for matched platelet transfusion at the Blood Center of Zhejiang Province in May 2022 was selected as the study subject. HLA genotype of the individual was determined by next-generation sequencing (NGS) on an Ion Torrent S5 platform. The sequence of the HLA-DPB1 locus was also determined by NGS on an Illumina Miseq platform and third-generation sequencing using Oxford Nanopore MinION. This study was approved by the Blood Center of Zhejiang Province (Ethics No. 2021-001). A novel HLA-DPB1*02 allele was identified in the specimen, for which the closest genotype was HLA-DPB1*02:new,17:01:01G, with the variant located in exon 3. Meanwhile, the NGS also revealed a novel HLA-DPB1*17 allele, with the closest genotype being HLA-DPB1*02:01,17:new. Both the HLA-DPB1*17:01:01:01 and HLA-DPB1*02 alleles were identified by third-generation sequencing. Compared with the HLA-DPB1*02:01:02:01 allele, the novel allele had a G>A variation at position 369 in the exon 3, which however did not result in amino acid change. A novel HLA-DPB1 allele has been identified and validated by both NGS and TGS, which has been named as HLA-DPB1*02:01:69 by the World Health Organization Committee on Nomenclature of Factors of the HLA System.

The HLA region in ANCA-associated vasculitis: characterisation of genetic associations in a Scandinavian patient population

ObjectiveThe antineutrophil cytoplasmic antibody (ANCA)-associated vasculitides (AAV) are inflammatory disorders with ANCA autoantibodies recognising either proteinase 3 (PR3-AAV) or myeloperoxidase (MPO-AAV). PR3-AAV and MPO-AAV have been associated with distinct loci...

Recognition of HLA-DPB1 alleles and their associated HLA haplotypes in 55 randomized unrelated Taiwanese individuals.

Here, we report the distribution of HLA-DPB1 alleles studied in a cohort of 55 randomly collected blood samples from unrelated Taiwanese individuals and the deduced most likely HLA haplotypes associated with the defined DPB1 alleles in the cohort. Our aim is to reveal the unprecedented data on the distribution of HLA-DPB1 alleles in the Taiwanese population and to find out the most probable HLA haplotypes associated with the HLA-DPB1 alleles detected. The material for this study was blood samples, preserved in K2EDTA and/or acid citrate dextrose anticoagulants. The blood donors were voluntary individuals of Tzu Chi Bone Marrow Donor Registry, Tzu Chi Stem Cells Center, Hualien Tzu Chi Hospital. Sequence-based typing of the Sanger's sequencing method was performed for the HLA allelic typing. To discern the HLA-DPB1 alleles, exons 2 and 3 of the HLA-DPB1 locus were sequenced. Target exon sequence amplifications were achieved by polymerase chain reaction, and the resulting amplicons were sequenced by BigDye Terminator Cycle Sequencing Ready Reaction Kit according to the manufacturer's protocols. In the total number of 55 randomized unrelated Taiwanese individuals studied, we detected 11 different HLA-DPB1 alleles. DPB1*05:01 (44.54%) was the allele with the highest frequency observed and the next highest frequency allele found was DPB1*02:01 (17.27%), while DPB1*38:01 (0.90%) and DPB1*700:01N (0.90%) ranked the least observed DPB1 alleles. Our findings in this study may be useful in researches reinforcing the comprehensive understanding on the distribution of DPB1 alleles and their associated HLA haplotypes and their clinical applications in Taiwanese.

HLA Alleles, Genotype and Haplotype Analyzes from Central Anatolia Region of Turkey.

Although human leukocyte antigen (HLA) data for the Turkish population has been reported, there are no statistics on the HLA-DPB1 locus, which has recently received significant attention, particularly in hematopoietic stem cell transplantation. In addition, there is no study that has reported the 2-6 loci HLA haplotype distribution, 8-digit HLA allele frequency, and genotype frequency in the Turkish population. To evaluate the low and high resolution (2-4-8 digits) HLA-A, -B, -C, -DRB1, -DQB1, -DPB1 allele data using the data of 6100 healthy individuals from the Central Anatolian region of Turkey. Retrospective cross-sectional study. All tests were performed using molecular HLA techniques: low-resolution DNA-based sequence-specific oligonucleotides, low/high-resolution DNA-based sequence-specific primer, and high-resolution next generation sequencing. A total of 6100 healthy donors with a minimum of 3 loci (HLA-A, -B, -DRB1) were analyzed for their HLA-A, -B, -C, -DRB1, -DQB1, and -DPB1 data. Pypop and HLA-net GENE[RATE] were used to analyze the data. Among the HLA class I alleles, the following were the most frequently observed alleles: for HLA-A, A*02, A*24, A*03, and A*01; for HLA-B, B*35, B*51, and B*44; and for HLA-C, C*07, C*04, and C*12. Among the HLA class II alleles, the following alelles were the most frequently observed: for HLA-DRB1, DRB1*11, DRB1*04, and DRB1*13; for HLA-DQB1, DQB1*03, DQB1*05, and DQB1*06; and for HLA- DPB1, DPB1*04, DPB1*02, and DPB1*03. The most common alleles among HLA-DPB1 in the 4-digit evaluation were DPB1*04:01, DPB1*02:01, and DPB1*04:02. Among the HLA classes I and II, the following were the most frequently observed 8-digit alleles in HLA-A, -B, -C, -DRB1, -DQB1 and -DPB1 were A*02:01:01:01, B*49:01:01:01, C*04:01:01:06, DRB1*07:01:01:01, DQB1*03:01:01:02, and DPB1*02:01:02:05, respectively. The most common 6 loci haplotype was A*02~B*35~C*04~DRB1*11~DQB1*03~DPB1*04 (2.71%). Our study has included the highest number of healthy individuals from Turkey till date. Furthermore, we have reported the low- and high-resolution HLA-DPB1 allele frequency, 6 loci haplotype frequency, and genotype frequency in the Turkish population for the first time. This new data may be used to map HLA in our country and provide insight for potential future studies.

Analysis of Gene Recombination between HLA-B and -DRB1, HLA-DQB1 and -DPB1 Loci

To investigate the recombinations within the human leukocyte antigen (HLA) region in two families. Genomic DNA was extracted from the peripheral blood specimens of the different family members. HLA-A, -B, -C, -DRB1, -DQB1 and -DPB1 loci were genotyped using polymerase chain reaction-sequence specific oligonucleotide probing technique (PCR-SSO) and next-generation sequencing technique. HLA haplotype was determined by genetic analysis of the pedigree. The haplotypes of HLA-A*11:01~C*03:04~B*13:01~DRB1*12:02~DQB1*03:01~DPB1*05:01:01G and HLA-A*03:01~C*04:01~B*35:03~DRB1*12:01~DQB1*03:01~DPB1*04:01:01G in the family 1 were recombined between HLA-B and HLA-DRB1 loci, which formed the haplotype of HLA-A*11:01~C*03:04~B*13:01~DRB1* 12:01~DQB1*03:01~DPB1*04:01:01G. The haplotypes of HLA-A *02:06~C*03:03~B*35:01~DRB1*08:02~DQB1*04:02~ DPB1*13:01:01G and HLA-A *11:01~C*07:02~B*38:02~DRB1*15:02~DQB1*05:01~DPB1*05:01:01G in the family 2 were recombined between HLA-DQB1 and HLA-DPB1 loci, which formed the haplotype of HLA-A*02:06~C*03:03~B*35:01~ DRB1*08:02~DQB1*04:02~DPB1*05:01:01G. The gene recombination events between HLA-B and -DRB1, HLA-DQB1 and -DPB1 loci were found respectively in two Chinese Han families.

Association Between HLA-DPB1 and Antineutrophil Cytoplasmic Antibody-Associated Vasculitis in Children.

Antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV) is a rare, life-threatening inflammation of blood vessels that can affect both adults and children. Compared to adult-onset disease, AAV is especially rare in children, with an annual prevalence of 0.5-6.4 cases per million children. The etiology of AAV remains largely unknown, and both environmental and genetic factors are likely involved. The present study was undertaken to explore the genetic susceptibility factors recently identified in adult patients, including HLA-DP and HLA-DQ, in pediatric patients. We performed a genome-wide association study of pediatric AAV in patients of European ancestry (n=63 AAV cases, n=315 population-matched controls). We identified a significant genetic association between pediatric AAV and the HLA-DPB1*04:01 allele (P=1.5 × 10-8 , odds ratio [OR] 3.5), with a stronger association observed in children with proteinase 3-ANCA positivity than in children with myeloperoxidase-ANCA positivity. Among the HLA alleles, the HLA-DPB1*04:01 allele was the most highly associated with AAV, although not significantly, in a follow-up adult AAV cohort (P=2.6 × 10-4 , OR 0.4). T cell receptor and interferon signaling pathways were also shown to be enriched in the pediatric AAV cohort. The HLA-DPB1 locus showed an association with pediatric AAV, as similarly shown previously in adult AAV. Despite the difference in the age of onset, these findings suggest that childhood- and adult-onset vasculitis share a common genetic predisposition. The identification of genetic variants contributing to AAV is an important step to improved classification tools and treatment strategies.

Molecular disparity of HLA-DPB1 is associated with the development of subsequent solid cancer after allogeneic hematopoietic stem cell transplantation.

An increased incidence of subsequent solid cancers (SSCs) has been reported in long-term survivors of allogeneic hematopoietic stem cell transplantation (allo-HSCT), and SSC is associated with inferior mortality and morbidity. Previous studies showed that the incidence of SSC is significantly higher in those who underwent allo-HSCT from HLA-mismatched donors, suggesting that persistent alloimmunity may predispose patients to SSCs. It was recently reported that, in a cohort of patients who received allo-HSCT from an unrelated donor matched at HLA-A, -B, -C, -DRB1/3/4/5, and -DQB1 loci, HLA-DPB1 alloimmunity determined by high mismatched eplets (MEs) and Predicted Indirectly Recognizable HLA Epitopes (PIRCHE) score (PS), was associated with relapse protection and increased risk of acute graft-versus-host disease (GVHD). In the present study, the impact of HLA-DPB1 alloimmunity assessed by molecular mismatch algorithms on the development of SSCs in a cohort of 1514 patients who underwent allo-HSCT for hematologic malignancies was further investigated. ME load at the HLA-DPB1 locus was measured using the HLAMatchmaker module incorporated in HLA Fusion software, and the PS for mismatched HLA-DPB1 was calculated using the HSCT module from the PIRCHE online matching service. In multivariable analysis after adjusting for baseline risk factors, higher ME, PS-I, and PS-II in the GVH direction, but not in the HVG direction, were associated with an increased risk of SSCs (ME: subdistribution hazard ratio [SHR] 1.58, p= .01; PS-I: SHR 1.59, p= .009; PS-II: SHR 1.71, p= .003). In contrast, nonpermissive HLA-DPB1 mismatches defined by the conventional T-cell epitope algorithm were not predictive of the risk of SSCs. Moreover, posttransplant cyclophosphamide-based GVHD prophylaxis was associated with a reduced risk of subsequent solid cancer (SHR 0.34, p= .021). These results indicate for the first time that increased GVH alloreactivity could contribute to the development of SSCs in allo-HSCT survivors.

Predicting HLA-DPB1 permissive probabilities through a DPB1 prediction service towards the optimization of HCT donor selection

Despite its demonstrated importance in hematopoietic cell transplantation, the HLA-DPB1 locus is only typed in one in five unrelated donors in the United States. Addressing this issue, we developed a DPB1 Prediction Service that leverages seven-locus haplotype frequencies (HLA-A ∼ C ∼ B ∼ DRB3/4/5 ∼ DRB1 ∼ DQB1 ∼ DPB1) to extend the imputation of six-locus HLA typing (HLA-A ∼ C ∼ B ∼ DRB3/4/5 ∼ DRB1 ∼ DQB1) to the HLA-DPB1 locus, including the novel prediction of HLA-DPB1 TCE groups to calculate donor-recipient TCE permissive match probabilities. Simulations of current-day patient searches reveal the service can fill in missing gaps for another four in five donors that appears on lists. To validate its performance, samples of 206,328 registered donors and 5,218 donor-recipient pairs with known high-resolution HLA-DPB1 typing were used for predicted-versus-observed comparisons. These comparisons demonstrated that the predictions were correct for 11.9–19.7% of HLA-DPB1 genotypes, 64.9–70.0% of TCE groups, and 61.0% of permissive match categories. Although HLA-DPB1 match predictions must be confirmed by additional typing, knowledge of TCE match probabilities facilitates rapid and improved identification of best donor options, especially for populations of color. Thus, we developed the TCE Prediction Tool user interface for a pilot program with several transplant centers to preview the accuracy and utility of this prediction framework, which provides valuable upfront optimization of donor selection.

Use of DPB1 T-cell epitope algorithm among italian transplant centers: A survey on behalf of Associazione Italiana di Immunogenetica e Biologia dei Trapianti.

The HLA-DPB1 locus has been demonstrated to have a significant role on patients' outcome after allogeneic HSCT, and the so-called T-cell epitope (TCE) algorithm has been incorporated in international guidelines for the selection of unrelated donors. The purpose of the present study is to measure, through a national survey conducted on behalf of the Associazione Italiana di Immunogenetica e Biologia dei Trapianti (AIBT), the extent of awareness and use of HLA-DPB1 TCE-based algorithms during the donor search. 89% of the HLA laboratories answered to a short questionnaire and the results showed a progressive increase of the laboratories typing DPB1 in patients and their potential donors during the search (from 44% to 79% during the 2010-2019 period) as well as the application of a TCE-based algorithm for the donor choice whenever possible (from 24% to 65% during the same period). The DP-permissiveness status is detailed in the official HLA typing report by 12%, 32% and 50% of laboratories in 2010, 2015 and 2019, respectively. The present data indicate an encouraging raise in the awareness of the HLA-DPB1 role in unrelated donor selection; noteworthy, mentioning the TCE-based permissiveness status in the HLA typing report of each potential unrelated donor represents a notable mean to raise awareness among transplant physicians and to support them in their task of choosing the best donor. Nonetheless, despite the compelling evidence of the predictive ability of TCE-based algorithms, further efforts are still needed to extend its application to all transplant centers in Italy.

Revisit of Optimal Donor Number Estimation in the Hong Kong Bone Marrow Donor Registry.

High resolution typing of the HLA-DPB1 locus for patient who requested for hematopoietic stem cell transplantation (HSCT) workup has recently become mandatory by the National Marrow Donor Program (NMDP) in order to facilitate matching between donors and recipients for better outcomes. The likelihood of identifying HLA matched donors in Hong Kong, on top of the existing HLA-A, -B, -C, and -DRB1 loci, is revisited in this study. HLA-A, -B, -C, -DRB1 and -DPB1 genotypes of 5,266 volunteer unrelated Chinese donors from the Hong Kong Bone Marrow Donor Registry (HKBMDR), were included in this study. Matching models were employed to determine the matching probabilities for 10/10(DPB1) and 9/10(DPB1) HLA match. The matching probabilities are 20% at 10/10(DPB1) HLA match and 55% at 9/10(DPB1) match, based on the existing 130,000 donors in the HKBMDR. The likelihoods of match become 27% and 65% respectively, by increasing the registry to 250,000. However, if DPB T-cell-epitope (TCE) model is considered in the matching, the probability will increase to 46% at 10/10 DPB1 permissive mismatching. Our findings provide vital information about the future planning on the targeted recruitment size, HLA typing and search strategies of the donor registry and arose the transplant physicians’ acceptability to 9/10(DBP1) or 10/10(DBP1) HLA match. Nevertheless, the marrow donor registry has planned for increasing the registry size and bringing down the age of recruited donors which will ultimately enhance patient outcome.

HLA-DPB1 and HLA-C alleles are associated with leprosy in a Brazilian population

Despite intense efforts, the number of new cases of leprosy has remained significantly high over the past 20 years. Host genetic background is strongly linked to the pathogenesis of this disease, which is caused by Mycobacterium leprae (M. leprae), and there is a consensus that the most significant genetic association with leprosy is attributed to the major histocompatibility complex (MHC). Here, we investigated the association of human leukocyte antigen (HLA) class I and II genes with leprosy in a Brazilian population encompassing 826 individuals from a hyperendemic area of Brazil; HLA typing of class I (-A, -B, -C) and class II (-DRB1, -DQA1, -DQB1, -DPA1, and -DPB1) loci was conducted. Initially, the associations were tested using the chi-square test, with p-values adjusted using the false discovery rate (FDR) method. Next, statistically significant signals of the associations were submitted to logistic regression analyses to adjust for sex and molecular ancestry data. The results showed that HLA-C*08, -DPB1*04, and -DPB1*18 were associated with protective effects, while HLA-C*12 and -DPB1*105 were associated with susceptibility to leprosy. Thus, our findings reveal new associations between leprosy and the HLA-DPB1 locus and confirm previous associations between the HLA-C locus and leprosy.

IFNL4 and donor selection for matched unrelated donor haematopoietic stem-cell transplantation

IFNL4 and donor selection for matched unrelated donor haematopoietic stem-cell transplantation

IMPACT OF HLA-DPB1 MATCHING ON CLINICAL OUTCOMES AFTER HAPLOIDENTICAL-RELATED HEMATOPOIETIC STEM CELL TRANSPLANTATION.

The impact of HLA-DPB1 compatibility and its role as a transplantation antigen in haploidentical-related hematopoietic stem cell transplant (haplo-R-HSCT) have not been established, and a negative effect on survival has been suggested. The objective of the determine was to study the frequency and clinical effects of incompatibility at the HLA-DPB1 locus in the haplo-R-HSCT setting. Clinical records and electronic files of 91 patients with a hematological disease who underwent haplo-HSCT from January 2009 to October 2017 in a university medical center were scrutinized. Overall survival (OS) was estimated by the Kaplan-Meier method; the cumulative incidence of transplant-related mortality (TRM) and relapse rates was determined. Acute graft-versus-host disease was assessed by binary logistic regression. Cox regression model with a 95% confidence interval was used to examine the association between the different variables and their effect on OS. Of the 91 donor-recipient pairs, 24 (26.37%) shared complete DPB1 identity, 60 (65.93%) had a mismatch at one allele, and 7 (7.70%) were mismatched at two alleles. Twenty-four different HLA-DPB1 alleles were found; the most frequent were DPB1*04:01 (34.1%) and DPB1*04:02 (27.5%). Two-year OS, the cumulative incidence of TRM and relapse was 51.3 ± 6.8%, 28 ± 6% and 60 ± 7.8% for all haplo-related transplants, respectively, with no statistical difference between HLA-DPB1 matched and partially matched patients. In Cox regression analysis, no risk factors associated with OS, TRM, or relapses were identified. HLA-DPB1 mismatching in the haplo-R-HSCT setting did not influence transplant outcomes and was clinically tolerable. A high degree of homozygosity was found.

Protective effect of HLA-DPB1 mismatch remains valid in reduced-intensity conditioning unrelated donor hematopoietic cell transplantation.

SummaryA mismatch at HLA-DPB1 locus is associated with higher acute GVHD and lower relapse rate after myeloablative (MAC) allogeneic hematopoietic cell transplantation (alloHCT). Also, in MAC setting, mismatch permissiveness and expression level impact alloHCT outcomes. However, in reduced intensity (RIC), DP mismatch effect on transplant outcomes is unknown. We retrospectively evaluated DP mismatch influence (number, permissiveness, and expression) on HCT outcomes in 310 patients with high-resolution typing (HLA-A, -B, -C, -DRB1, -DQB1 and -DPB1), who underwent RIC-HCT. By multivariable analysis, 11/12 had better overall survival (OS) and relapse vs. 12/12 (HR=1.61 and 2.02; p=0.04 and 0.01, respectively) and better OS vs. 10/12 (HR=1.68; p=0.02). Within the 11/12, non-permissive mismatch (NoPR) was associated with higher risk of grade II-IV acute GVHD (HR=1.97; p=0.005) and non-relapse mortality (HR=2.13; p=0.02) vs. permissive (PR). Grouping 11/12 based on the DP expression conferred higher mortality (HR=3.78; p= 0.003) when low expressers received a graft from high expressers (AG) vs. low expressers (AA). Better OS was achieved in PR 11/12, when expression was low in patient and donor (AA) vs. all other combinations. Therefore, in RIC HCT, a single DP mismatch has a protective role, especially in permissive setting, when donor and recipient are low expressers.

Impact of HLA-DPB1 Matching on Outcome of Unrelated Transplant for Hematologic Malignant Diseases: A Systematic Review and Meta-analysis

ObjectiveHuman leukocyte antigen match is the most important donor factor affecting transplant outcome. The HLA-DPB1 mismatch on the clinical outcome of hematopoietic stem cell transplant (HSCT) is less clear. This study is the first meta-analysis to investigate the impact of HLA-DPB1 loci mismatch on clinical outcome after unrelated donor HSCT for hematologic malignant disease. MethodsWe electronically searched the PubMed, EMBASE, Cochrane Central Register of Controlled Trials, and a related database (January 1995-December 2018) for all relevant articles. Comparative studies were carried out to investigate the impact of HLA-DPB1 loci mismatch on clinical outcome after unrelated donor HSCT, that is, the disease-free survival, engraftment, graft-vs-host disease, relapse, and transplant-related mortality (TRM). We performed a meta-analysis using Review Manager 5.3.5 software and adopted funnel plot regression to assess the publication bias. ResultsA total of 1570 articles were retrieved; 21 studies including 27,852 patients were assessed. Pooled comparisons of studies found that the HLA-DPB1–mismatched group had a lower rate of disease-free survival than the DPB1-matched group and lower overall survival in non–T cell–depleted transplant than the DPB1-matched group. The DPB1-mismatched group has higher incidence of acute graft-vs-host disease (aGVHD) and severe (≥ III degree) aGVHD, lower relapse rate, and higher TRM. Moreover, compared with 1-antigen mismatch, 2-antigen mismatch in DPB1 had a higher risk of TRM and a lower relapse rate, and the nonpermissive DPB1 mismatch had significantly higher rate of severe aGvHD and lower rate of disease relapse. ConclusionsThis analysis confirmed that HLA-DPB1 has important influence on survival and transplant-related complications during unrelated donor HSCT, and HLA-DPB1 donor selection strategies have been proposed based on personalized algorithm.

P002 Standard duo typing of 1196 specimens revealed a strategy to use next generation sequencing as a standalone HLA typing method in clinical laboratory

Aim Next generation sequencing (NGS) permits sequencing of the entire HLA genes and generate unambiguous phased-resolved HLA typing. NGS is increasingly used in clinical HLA laboratories for both stem cells and solid organ transplantation. Herein, we investigated if NGS can be used as a standalone HLA typing method in clinical laboratory. Methods 1196 samples were typed in parallel using NGS (Omixon) and high-definition rSSO (One Lambda) methods. In addition, SSP (Olerup) was used to type HLA-DRB4 alleles. The frequency of allelic dropout by NGS was evaluated for all nine HLA loci (A, B, C, DRB1, DRB3/4/5, DQA1, DQB1, DPA1, and DPB1). Results No allelic dropout was observed at HLA-A, - B , - C , -DRB1, -DRB5, -DQA1, -DQB1, and -DPA1 loci. However, 4.6% of the samples (55/1,196) showed allelic dropouts at one of the other three loci: HLA-DRB3, -DRB4, and -DPB1. Frequent allelic dropouts were observed at HLA-DRB4 (3.7%; 44/1,196 samples) and HLA-DPB1 (0.8%; 10/1,196 samples) loci. HLA-DRB3 allele dropout was noted in a single sample (0.1%). The table below lists the specific dropped out alleles and their associated haplotypes or other alleles. Conclusions Our results suggest that the NGS can be used as a standalone method for HLA-A, - B , - C , -DRB1, -DRB5, -DQA1, -DQB1, and -DPA1 typing. However, additional typing assays are required to confirm the homozygosity of HLA-DRB3, -DRB4, and -DPB1 loci. DRB1-DRB3/4/5 linkage can be used to identify the allelic dropouts in HLA-DRB3/4 loci for certain cases. Concurrent typing of HLA-DRB3/4 and -DPB1 by rSSO would improve the NGS workflow and turnaround time.

Identification of Functional and Expression Polymorphisms Associated With Risk for Antineutrophil Cytoplasmic Autoantibody-Associated Vasculitis.

ObjectiveTo identify risk alleles relevant to the causal and biologic mechanisms of antineutrophil cytoplasmic antibody (ANCA)–associated vasculitis (AAV).MethodsA genome‐wide association study and subsequent replication study were conducted in a total cohort of 1,986 cases of AAV (patients with granulomatosis with polyangiitis [Wegener's] [GPA] or microscopic polyangiitis [MPA]) and 4,723 healthy controls. Meta‐analysis of these data sets and functional annotation of identified risk loci were performed, and candidate disease variants with unknown functional effects were investigated for their impact on gene expression and/or protein function.ResultsAmong the genome‐wide significant associations identified, the largest effect on risk of AAV came from the single‐nucleotide polymorphism variants rs141530233 and rs1042169 at the HLA–DPB1 locus (odds ratio [OR] 2.99 and OR 2.82, respectively) which, together with a third variant, rs386699872, constitute a triallelic risk haplotype associated with reduced expression of the HLA–DPB1 gene and HLA–DP protein in B cells and monocytes and with increased frequency of complementary proteinase 3 (PR3)–reactive T cells relative to that in carriers of the protective haplotype. Significant associations were also observed at the SERPINA1 and PTPN22 loci, the peak signals arising from functionally relevant missense variants, and at PRTN3, in which the top‐scoring variant correlated with increased PRTN3 expression in neutrophils. Effects of individual loci on AAV risk differed between patients with GPA and those with MPA or between patients with PR3‐ANCAs and those with myeloperoxidase‐ANCAs, but the collective population attributable fraction for these variants was substantive, at 77%.ConclusionThis study reveals the association of susceptibility to GPA and MPA with functional gene variants that explain much of the genetic etiology of AAV, could influence and possibly be predictors of the clinical presentation, and appear to alter immune cell proteins and responses likely to be key factors in the pathogenesis of AAV.

Clinical implications of HLA locus mismatching in unrelated donor hematopoietic cell transplantation: a meta-analysis.

It remains controversial that the impacts of individual HLA locus mismatches on clinical outcomes of patients receiving unrelated-donor hematopoietic cell transplantation (HCT), as compared to HLA allele matched controls. We conducted a meta-analysis to address these issues. Four databases (PubMed, Embase, Web of Science and the Cochrane Library) were searched to select eligible studies. All donor-recipient pairs were high-resolution typing for HLA-A, -B, -C, -DRB1, DQB1 and DPB1 loci. Multivariate-adjusted hazard ratios (HRs) were extracted and pooled using a random-effects model. A total of 36 studies were included, with 100,072 patients receiving HCT. Surprisingly, we found that HLA-DQB1 locus mismatches had no significantly increased risk of multiple outcomes including acute and chronic graft-versus-host disease (GVHD), overall mortality and disease relapse (HR, 1.07; P = .153; HR, 1.07; P = .271; HR, 1.09; P = .230; HR, 1.07; P = .142 and HR, 1.02; P = .806, respectively). Mismatched HLA-DPB1 was significantly associated with a reduced risk of disease relapse (HR, 0.74; P < .001) but not with increased risks of transplant-related mortality (TRM) and overall mortality (HR, 1.09; P = .591; I2 = 74.2% and HR, 1.03; P = .460, respectively). In conclusion, HLA-DQB1 locus mismatches is a permissive mismatching. HLA-DPB1 locus mismatches significantly protect against leukemia relapse. Refining effects of individual HLA locus mismatches contributes to predicting prognosis of patients receiving unrelated donor HCT.

MHC Class II Risk Alleles and Amino Acid Residues in Idiopathic Membranous Nephropathy.

Epitopes of phospholipase A2 receptor (PLA2R), the target antigen in idiopathic membranous nephropathy (iMN), must be presented by the HLA-encoded MHC class II molecules to stimulate autoantibody production. A genome-wide association study identified risk alleles at HLA and PLA2R loci, with the top variant rs2187668 within HLA-DQA1 showing a risk effect greater than that of the top variant rs4664308 within PLA2R1. How the HLA risk alleles affect epitope presentation by MHC class II molecules in iMN is unknown. Here, we genotyped 261 patients with iMN and 599 healthy controls at the HLA-DRB1, HLA-DQA1, HLA-DQB1, and HLA-DPB1 loci with four-digit resolution and extracted the encoded amino acid sequences from the IMGT/HLA database. We predicted T cell epitopes of PLA2R and constructed MHC-DR molecule-PLA2R peptide-T cell receptor structures using Modeler. We identified DRB1*1501 (odds ratio, 4.65; 95% confidence interval [95% CI], 3.39 to 6.41; P<0.001) and DRB1*0301 (odds ratio, 3.96; 95% CI, 2.61 to 6.05; P<0.001) as independent risk alleles for iMN and associated with circulating anti-PLA2R antibodies. Strong gene-gene interaction was noted between rs4664308(AA) and HLA-DRB1*1501/DRB1*0301. Amino acid positions 13 (P<0.001) and 71 (P<0.001) in the MHC-DRβ1 chain independently associated with iMN. Structural models showed that arginine13 and alanine71, encoded by DRB1*1501, and lysine71, encoded by DRB1*0301, facilitate interactions with T cell epitopes of PLA2R. In conclusion, we identified two risk alleles of HLA class II genes and three amino acid residues on positions 13 and 71 of the MHC-DRβ1 chain that may confer susceptibility to iMN by presenting T cell epitopes on PLA2R.

Host Genetic Variants in HLA Loci Influence Risk for Hepatitis B Virus Infection in Children.

BackgroundHepatitis B virus (HBV) infection is a serious public health problem in China and worldwide. Mother-to-child transmission is one of HBV’s main transmission routes in highly endemic regions. Genome-wide association studies (GWAS) identify single nucleotide polymorphisms (SNPs) at HLA loci as associated with HBV infection. However, the mechanisms of HBV perinatal transmission and breakthrough in children have not yet been clearly defined.ObjectivesWe aimed to explore the association between SNPs at HLA loci and HBV infection and breakthrough in children.MethodsA total of 274 HBV-infected children and 353 controls were selected among children aged between 6 months and 12 years in China. Seven SNPs at HLA-DP and HLA-DQ loci were genotyped to analyze their association with HBV infection in children.ResultsAlleles G in both HLA-DPA1 rs3077 and HLA-DPB1 rs9277535 were found to be significantly associated with HBV infection in children with odds ratios (OR) of 1.309 (95% CI 1.046 to 1.639) and 1.411 (95% CI 1.125 to 1.771), respectively. In addition, overdominant analysis found that the rs2281388 (HLA-DPB1) GA genotype and the rs9366816 (HLA-DPB2) TC genotype were related to HBV infection (rs2281388, OR = 1.422, 95% CI: 1.032-1.961; rs9366816, OR = 1.444, 95% CI: 1.045-1.994). Furthermore, this study highlighted that rs9277535 was also significantly associated with HBV breakthrough infection in children whose mothers were positive for hepatitis B surface antigen (HBsAg).ConclusionsOur study confirmed that genetic variants in HLA-DPA1 and HLA-DPB1 loci have significant associations with HBV infection, especially with HBV breakthrough in children. This study provides insight into HBV infection in children and is valuable for the targeted management of, and control strategies for, this disease.