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Zhao X, Ma S, Wang B, Jiang X, Xu S. PGG.MHC: toward understanding the diversity of major histocompatibility complexes in human populations. Nucleic Acids Res 2022; 51:D1102-D1108. [PMID: 36321663 PMCID: PMC9825418 DOI: 10.1093/nar/gkac997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/15/2022] [Accepted: 10/19/2022] [Indexed: 11/07/2022] Open
Abstract
The human leukocyte antigen (HLA) system, or the human version of the major histocompatibility complex (MHC), is known for its extreme polymorphic nature and high heterogeneity. Taking advantage of whole-genome and whole-exome sequencing data, we developed PGG.MHC to provide a platform to explore the diversity of the MHC in Asia as well as in global populations. PGG.MHC currently archives high-resolution HLA alleles of 53 254 samples representing 190 populations spanning 66 countries. PGG.MHC provides: (i) high-quality allele frequencies for eight classical HLA loci (HLA-A, -B, -C, -DQA1, -DQB1, -DRB1, -DPA1 and -DPB1); (ii) visualization of population prevalence of HLA alleles on global, regional, and country-wide levels; (iii) haplotype structure of 134 populations; (iv) two online analysis tools including 'HLA imputation' for inferring HLA alleles from SNP genotyping data and 'HLA association' to perform case/control studies for HLA-related phenotypes and (v) East Asian-specific reference panels for HLA imputation. Equipped with high-quality frequency data and user-friendly computer tools, we expect that the PGG.MHC database can advance the understanding and facilitate applications of MHC genomic diversity in both evolutionary and medical studies. The PGG.MHC database is freely accessible via https://pog.fudan.edu.cn/pggmhc or https://www.pggmhc.org/pggmhc.
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Affiliation(s)
| | | | | | - Xuetong Jiang
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, FudanUniversity, Shanghai 200438, China
| | | | - Shuhua Xu
- To whom correspondence should be addressed. Tel: +86 21 31246617; Fax: +86 21 31246617;
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Hwang MC, Ridley L, Reveille JD. Ankylosing spondylitis risk factors: a systematic literature review. Clin Rheumatol 2021; 40:3079-3093. [PMID: 33754220 DOI: 10.1007/s10067-021-05679-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 02/12/2021] [Accepted: 03/01/2021] [Indexed: 12/16/2022]
Abstract
Radiographic axial spondyloarthritis (also known as ankylosing spondylitis [AS]) is a chronic immune-mediated arthritis characterized by inflammation of the axial skeleton, peripheral joints, and entheses. It is estimated that 1 in every 200 people are affected by AS, making it an important healthcare and socioeconomic issue. In this review, we aim to explore the current understanding of AS risk factors and provide a comprehensive update. Multiple search strings were used to identify articles of interest published in PubMed between January 1, 2013, and February 1, 2021. On the basis of the literature review and analysis, we present up-to-date information on the risk factors of developing AS and our viewpoints on disease onset and progression. Multiple genetic and nongenetic risk factors have been suggested in the onset of AS. HLA-B27 is known to have a strong association with the disease, but other genes have been implicated in disease development. Aside from genetics, other factors are thought to be involved; up to 70% of patients with AS have subclinical intestinal inflammation, suggesting that the origin of the disease may be in the gut. The exact mechanism by which AS onset begins is most likely complex and multifactorial. Key Points • It remains unclear how interactions between genes, microbes, mechanical stress, gender, and other environmental and lifestyle factors predispose patients to the development of ankylosing spondylitis (AS). • The exact mechanisms of AS are complex and multifactorial which will require much future research • Recognizing the risk factors, as well as understanding gene-environment interactions, may offer valuable insights into the etiology of AS and have important implications for diagnosis and treatment strategies.
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Affiliation(s)
- Mark C Hwang
- Department of Internal Medicine, Division of Rheumatology, McGovern Medical School at The University of Texas Health Science Center, 6431 Fannin, MSB 1.150, Houston, TX, 77030, USA
| | - Lauren Ridley
- Department of Internal Medicine, Division of Rheumatology, McGovern Medical School at The University of Texas Health Science Center, 6431 Fannin, MSB 1.150, Houston, TX, 77030, USA
| | - John D Reveille
- Department of Internal Medicine, Division of Rheumatology, McGovern Medical School at The University of Texas Health Science Center, 6431 Fannin, MSB 1.150, Houston, TX, 77030, USA.
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The Genetics of Spondyloarthritis. J Pers Med 2020; 10:jpm10040151. [PMID: 33023259 PMCID: PMC7711559 DOI: 10.3390/jpm10040151] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/17/2020] [Accepted: 09/24/2020] [Indexed: 12/12/2022] Open
Abstract
The term spondyloarthritis (SpA) encompasses a group of chronic inflammatory diseases with common features in terms of clinical presentation and genetic predisposition. SpA is characterized by inflammation of the spine and peripheral joints, and is also be associated with extra-articular inflammatory manifestations such as psoriasis, uveitis, or inflammatory bowel disease (IBD). The etiology of SpA is not completely understood, but it is known to have a strong genetic component dominated by the human leukocyte antigen (HLA)-B27. In the last few years, our understanding of genetic susceptibility to SpA, particularly ankylosing spondylitis (AS), has greatly improved thanks to the findings derived from powered genome-wide association studies (GWAS) based on single nucleotide polymorphism (SNP) arrays. These studies have identified many candidate genes, therefore providing new potential directions in the exploration of disease mechanisms, especially with regard to the key role of the immune system in the pathogenesis of SpA. SpA is a complex disease where genetic variability, environmental factors, and random events interact to trigger pathological pathways. The aim of this review is to summarize current findings on the genetics of SpA, some of which might help to study new treatment approaches.
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Yan FH, Wang M, Yao JF, Jiang EL, Han MZ. Impact of Human Leukocyte Antigen Loci and Haplotypes on Intestinal Acute Graft-versus-host Disease after Human Leukocyte Antigen-matched Sibling Peripheral Blood Stem Cell Transplantation. Chin Med J (Engl) 2017; 130:1290-1295. [PMID: 28524827 PMCID: PMC5455037 DOI: 10.4103/0366-6999.206356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Background: Acute graft-versus-host disease (aGVHD) is a common and severe complication of allogeneic hematopoietic stem cell transplantation (allo-HSCT). Some studies have found that the presence of certain specific human leukocyte antigen (HLA) loci could affect the occurrence of aGVHD. Meanwhile, the impact of HLA haplotypes on aGVHD has been rarely studied. This study aimed to investigate the effects of HLA loci and haplotypes on intestinal aGVHD. Methods: Totally, 345 consecutive patients undergoing first HLA-matched sibling peripheral blood stem cell transplantation (PBSCT) from February 2004 to June 2013 at Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, were enrolled in this study. HLA loci and haplotypes of recipients with frequency over 5% were searched and their effects on intestinal aGVHD were investigated. Other important factors including donor age, recipient age, donor-recipient sex combinations, and conditioning regimens were also evaluated using logistic regression. Pure upper gastrointestinal tract aGVHD without diarrhea was excluded because the histological proof was unavailable. The follow-up end-point was 6 months after HSCT. Results: The cumulative incidence of intestinal aGVHD was 19.4%, with 18.0% of the patients classified as classic aGVHD and 1.4% as persistent, recurrent, or late aGVHD. Multivariate analysis showed that HLA-A31 locus (odds ratio [OR] 2.893, 95% confidence interval [CI] [1.054, 7.935], P = 0.039), HLA B40-DR15 (OR 3.133, 95% CI [1.250, 7.857], P = 0.015), and HLA B46-DR9 haplotypes (OR 2.580, 95% CI [1.070, 6.220], P = 0.035), female donor for male recipient (OR 2.434, 95% CI [1.319, 4.493], P = 0.004) were risk factors for intestinal aGVHD. Conclusion: The presence of certain HLA loci and haplotypes may influence the occurrence of intestinal aGVHD in PBSCT with HLA-identical sibling donors.
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Affiliation(s)
- Fa-Hong Yan
- Hematopoietic Stem Cell Transplantation Center, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020; Department of Hematology, Weifang People's Hospital, Weifang, Shandong 261041, China
| | - Mei Wang
- Hematopoietic Stem Cell Transplantation Center, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Jian-Feng Yao
- Hematopoietic Stem Cell Transplantation Center, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Er-Lie Jiang
- Hematopoietic Stem Cell Transplantation Center, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Ming-Zhe Han
- Hematopoietic Stem Cell Transplantation Center, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
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Liu X, Yang B, Li L, Cai B, Liao Y, Li L, Wu Z, Wang L. Association of HLA-DP/DQ and STAT4 polymorphisms with ankylosing spondylitis in Southwest China. Int Immunopharmacol 2016; 39:10-15. [PMID: 27394003 DOI: 10.1016/j.intimp.2016.06.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 05/27/2016] [Accepted: 06/30/2016] [Indexed: 02/06/2023]
Abstract
Ankylosing spondylitis (AS) is a highly heritable complex inflammatory arthritis disease. Genetic factors are thought to be crucial in the pathogenesis of AS. However, few data are available on the relationship between HLA-DP/DQ and STAT4 polymorphisms and AS susceptibility in the Chinese population. Therefore, we examined HLA-DP/DQ and STAT4 polymorphisms (rs3077, rs9277535, rs7453920 and rs7574865) in a total of 779 subjects, including 400 AS and 379 age- and sex-matched healthy controls in Chinese. No significant difference was observed between AS patients and healthy controls in the allele frequency of rs3077, rs9277535 and rs7574865. However, there was a significant association between the HLA-DQ rs7453920 G/A variant and AS patients, with minor allele A correlated with a reduced risk of AS (allelic frequency, adjusted OR=0.66, 95% CI=0.55-0.78, p=4.0E-06; dominant model, adjusted OR=0.75, 95% CI=0.66-0.85, p=1.1E-05). Moreover, the haplotypes block AAA and GGA in the HLA gene significantly correlated with reduced risk of AS. This is the first study demonstrating the significant associations of SNP rs7453920 and the haplotypes in the HLA gene with the risk of AS in Southwest Chinese population. This research sheds new light on the significant relationship between HLA polymorphisms and AS.
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Affiliation(s)
- Xinle Liu
- Department of Lab Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Bin Yang
- Department of Lab Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Lixin Li
- Department of Lab Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Bei Cai
- Department of Lab Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Yun Liao
- Department of Lab Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Linhui Li
- Department of Lab Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Zhiqiang Wu
- Department of Lab Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Lanlan Wang
- Department of Lab Medicine, West China Hospital, Sichuan University, Chengdu, China.
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First report on HLA-DPA1 gene allelic distribution in the general Lebanese population. Meta Gene 2016; 8:11-3. [PMID: 27014585 PMCID: PMC4792896 DOI: 10.1016/j.mgene.2016.01.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 12/28/2015] [Accepted: 01/13/2016] [Indexed: 01/20/2023] Open
Abstract
Aims HLA-DPA1 is an important marker in bone marrow and organ transplantation and a highly emerging screening parameter in histocompatibility laboratories. Being highly polymorphic, it has another significant value in detecting population origins and migrations. This is the first study to assess DPA1 allele frequencies in an Arab population. Methods The HLA DPA1 alleles were identified using the One-Lambda assays on a Luminex reverse SSO DNA typing system. Our study included 101 individuals coming from different Lebanese geographical areas representing the different communities and religious sects of the country. Results We compared the results of this study to 16 different populations and found very interesting similarities and differences between Lebanese people and individuals of European ancestry. Conclusion This study is the first to describe the different allelic frequencies of HLA-DPA1 in the Lebanese population and will serve as a template that can be later used for disease association studies both at the level of the country and internationally.
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Voorter CEM, Groeneweg M, Joannis MO, Meertens C, Agis F, Tilanus MGJ. Allele and haplotype frequencies of HLA-DPA1 and -DPB1 in the population of Guadeloupe. ACTA ACUST UNITED AC 2014; 83:147-53. [DOI: 10.1111/tan.12271] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 11/15/2013] [Accepted: 11/28/2013] [Indexed: 11/30/2022]
Affiliation(s)
- C. E. M. Voorter
- Transplantation Immunology, Tissue Typing Laboratory; Maastricht University Medical Center; Maastricht the Netherlands
| | - M. Groeneweg
- Transplantation Immunology, Tissue Typing Laboratory; Maastricht University Medical Center; Maastricht the Netherlands
| | - M.-O. Joannis
- Laboratoire d'Hématologie-Immunologie; Centre Hospitalier Universitaire de Point-à-Pitre/Abymes; Point-à-Pitre Guadeloupe
| | - C. Meertens
- Transplantation Immunology, Tissue Typing Laboratory; Maastricht University Medical Center; Maastricht the Netherlands
| | - F. Agis
- Laboratoire d'Hématologie-Immunologie; Centre Hospitalier Universitaire de Point-à-Pitre/Abymes; Point-à-Pitre Guadeloupe
| | - M. G. J. Tilanus
- Transplantation Immunology, Tissue Typing Laboratory; Maastricht University Medical Center; Maastricht the Netherlands
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Pimentel-Santos FM, Matos M, Ligeiro D, Mourão AF, Ribeiro C, Costa J, Santos H, Barcelos A, Pinto P, Cruz M, Sousa E, Santos RA, Fonseca JE, Trindade H, Guedes-Pinto H, Branco JC. HLA alleles and HLA-B27 haplotypes associated with susceptibility and severity of ankylosing spondylitis in a Portuguese population. TISSUE ANTIGENS 2013; 82:374-9. [PMID: 24498993 DOI: 10.1111/tan.12238] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Revised: 09/11/2013] [Accepted: 10/09/2013] [Indexed: 12/19/2022]
Abstract
Human leukocyte antigen (HLA)-B27 is the mostly known major histocompatibility complex (MHC) gene associated with ankylosing spondylitis (AS). Nonetheless, there is substantial evidence that other MHC genes appear to be associated with the disease, although it has not yet been established whether these associations are driven by direct associations or by linkage disequilibrium (LD) mechanisms. We aimed to investigate the contributions of HLA class I and II alleles and B27-haplotypes for AS in a case-control study. A total of 188 HLA-B27 AS cases and 189 HLA-B27 healthy controls were selected and typed for HLA class I and II by the Luminex polymerase chain reaction-sequence specific oligonucleotide probe (PCR-SSOP) method. Allelic and haplotypic distributions were estimated by maximum likelihood method using Arlequin v3.11 and statistical analysis were performed by Stata10.1. No associations were found between non-HLA-B27 loci and AS susceptibility, but several associations were observed for phenotypic features of the disease. DRB1*08 was identified as a risk factor for uveitis and DQB1*04 seems to provide protection for AS severity (functional, metrological and radiological indexes). A*02/B27/C*02/DRB1*01/DQB1*05 [P<0.0001; odds ratio (OR) = 39.06; 95% confidence interval (CI) (2.34-651)] is the only haplotype that seems to confer susceptibility to AS. Moreover, the haplotype A*02/B27/C*01/DRB1*08/DQB1*04 seems to provide protection for disease functional and radiological repercussions. Our findings are compatible with the hypothesis that other genes within the HLA region besides HLA-B27 might play some role in AS susceptibility and severity.
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Affiliation(s)
- F M Pimentel-Santos
- CEDOC, Faculdade de Ciências Médicas da Universidade Nova de Lisboa, Lisbon, Portugal; Centro Hospitalar Lisboa Ocidental (CHLO), Hospital de Egas Moniz, EPE, Lisbon, Portugal
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Howell WM. HLA and disease: guilt by association. Int J Immunogenet 2013; 41:1-12. [DOI: 10.1111/iji.12088] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 08/10/2013] [Indexed: 02/06/2023]
Affiliation(s)
- W. M. Howell
- Department of Histocompatibility and Immunogenetics; NHS Blood and Transplant; Newcastle upon Tyne UK
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