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Jiang X, Yuan X, Li Y, Zhang T, Chen L, Bao X, He J. Use of next-generation sequencing to detect polymorphism of 11 HLA allele loci in the Chinese Han population and variance from other common and well-documented lists. HLA 2023; 101:222-227. [PMID: 36480173 DOI: 10.1111/tan.14932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 11/12/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022]
Abstract
The focus of this study was to analyze polymorphisms in the HLA gene at 11 loci in 4845 Chinese Han populations using next-generation sequencing methods, and to compare common and well-documented (CWD) allelic differences between China and other CWD lists. A total of 44 DPB1 alleles, 13 DPA1 alleles, 20 DQA1 alleles and 19 DRB3/4/5 alleles were detected in this study. About 20%-50% of the CWD alleles in China differ from the American Society for Histocompatibility and Immunogenetics and European Federation for Immunogenetics (EFI) data. The revised list of HLA-CWD alleles in the Han population will provide additional data for the update of the IMGT/HLA database and contribute to a better understanding of hematopoietic stem cell transplantation and organ transplantation.
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Affiliation(s)
- Xue Jiang
- Department of HLA Laboratory, Jiangsu Institute of Hematology, First Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiaoni Yuan
- Department of HLA Laboratory, Jiangsu Institute of Hematology, First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yang Li
- Department of HLA Laboratory, Jiangsu Institute of Hematology, First Affiliated Hospital of Soochow University, Suzhou, China
| | - TengTeng Zhang
- Department of HLA Laboratory, Jiangsu Institute of Hematology, First Affiliated Hospital of Soochow University, Suzhou, China
| | - Luyao Chen
- Department of HLA Laboratory, Jiangsu Institute of Hematology, First Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiaojing Bao
- Department of HLA Laboratory, Jiangsu Institute of Hematology, First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jun He
- Department of HLA Laboratory, Jiangsu Institute of Hematology, First Affiliated Hospital of Soochow University, Suzhou, China.,Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
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2
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Sarri CA, Giannoulis T, Moutou KA, Mamuris Z. HLA class II peptide-binding-region analysis reveals funneling of polymorphism in action. Immunol Lett 2021; 238:75-95. [PMID: 34329645 DOI: 10.1016/j.imlet.2021.07.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 07/05/2021] [Accepted: 07/17/2021] [Indexed: 01/24/2023]
Abstract
BACKGROUND HLA-class II proteins hold important roles in key physiological processes. The purpose of this study was to compile all class II alleles reported in human population and investigate patterns in pocket variants and their combinations, focusing on the peptide-binding region (PBR). METHODS For this purpose, all protein sequences of DPA1, DQA1, DPB1, DQB1 and DRB1 were selected and filtered, in order to have full PBR sequences. Proportional representation was used for pocket variants while population data were also used. RESULTS All pocket variants and PBR sequences were retrieved and analyzed based on the preference of amino acids and their properties in all pocket positions. The observed number of pocket variants combinations was much lower than the possible inferred, suggesting that PBR formation is under strict funneling. Also, although class II proteins are very polymorphic, in the majority of the reported alleles in all populations, a significantly less polymorphic pocket core was found. CONCLUSIONS Pocket variability of five HLA class II proteins was studied revealing favorable properties of each protein. The actual PBR sequences of HLA class II proteins appear to be governed by restrictions that lead to the establishment of only a fraction of the possible combinations and the polymorphism recorded is the result of intense funneling based on function.
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Affiliation(s)
- Constantina A Sarri
- Department of Biochemistry and Biotechnology, Laboratory of Genetics, Comparative and Evolutionary Biology, University of Thessaly, Viopolis, Mezourlo, 41500, Larisa, Greece
| | - Themistoklis Giannoulis
- Department of Biochemistry and Biotechnology, Laboratory of Genetics, Comparative and Evolutionary Biology, University of Thessaly, Viopolis, Mezourlo, 41500, Larisa, Greece; Department of Animal Science, University of Thessaly, Trikallon 224, 43100 Karditsa, Greece
| | - Katerina A Moutou
- Department of Biochemistry and Biotechnology, Laboratory of Genetics, Comparative and Evolutionary Biology, University of Thessaly, Viopolis, Mezourlo, 41500, Larisa, Greece
| | - Zissis Mamuris
- Department of Biochemistry and Biotechnology, Laboratory of Genetics, Comparative and Evolutionary Biology, University of Thessaly, Viopolis, Mezourlo, 41500, Larisa, Greece.
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3
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Gregersen JW, Erikstrup C, Ivarsen P, Glerup R, Krarup E, Keller KK, Hansen IT, Møller BK. PR3-ANCA-associated vasculitis is associated with a specific motif in the peptide-binding cleft of HLA-DP molecules. Rheumatology (Oxford) 2019; 58:1942-1949. [DOI: 10.1093/rheumatology/kez111] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 02/19/2019] [Indexed: 02/07/2023] Open
Abstract
Abstract
Objectives
This study aimed to characterize the association between HLA alleles and ANCA-associated vasculitis (AAV) in a genetically homogeneous population, and to analyse the contribution of specific HLA molecule amino acid sequences to the risk of AAV.
Methods
We included 187 Danish patients with AAV and 1070 healthy controls. All were HLA typed at two-field resolution. The association of HLA alleles to PR3- or MPO-AAV was analysed. The contribution of the dominant molecular motifs of the HLA-DPB1 molecule to the risk of AAV was investigated by association studies that included specific amino acid sequences of the hypervariable regions in exon 2.
Results
Ninety-four percent of patients with PR3-AAV were carriers of HLA-DPB1*04:01 while all patients with PR3-AAV were carriers of an HLA-DPB1*04 allele, and 85% were homozygous. This was significantly more than in the control group (P < 0.0001). The association was even stronger when HLA-DPB1*04:02 and -DPB1*23:01 were included. HLA-DPB1*04:01, -DPB1*04:02 and -DPB1*23:01 share amino acids in positions 8–9, 69, 76 and 84–87 within the hypervariable regions, but only positions 69 and 84–87 contributed significantly to the disease risk. HLA-DRB1*15 was associated with an increased risk of developing PR3-AAV, while HLA-DRB1*04, -DRB1*07 and -DQB1*03 were associated with a reduced risk of kidney involvement in PR3-AAV. MPO-AAV was only weakly associated with HLA class I alleles.
Conclusion
PR3-AAV is strongly associated with the HLA-DPB1 alleles HLA-DPB1*04:01, -DPB1*04:02 and -DPB1*23:01, which share amino acid sequences crucial for the peptide-binding groove.
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Affiliation(s)
| | | | - Per Ivarsen
- Department of Nephrology, Aarhus University Hospital, Aarhus, Denmark
| | - Rie Glerup
- Department of Nephrology, Aalborg University Hospital, Aalborg, Denmark
| | | | | | - Ib Tønder Hansen
- Department of Rheumatology, Aarhus University Hospital, Aarhus, Denmark
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Voorter CEM, Gerritsen KEH, Groeneweg M, Wieten L, Tilanus MGJ. The role of gene polymorphism in HLA class I splicing. Int J Immunogenet 2016; 43:65-78. [PMID: 26920492 DOI: 10.1111/iji.12256] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 01/28/2016] [Accepted: 02/04/2016] [Indexed: 01/15/2023]
Abstract
Among the large number of human leucocyte antigen (HLA) alleles, only a few have been identified with a nucleotide polymorphism impairing correct splicing. Those alleles show aberrant expression levels, due to either a direct effect of the polymorphism on the normal splice site or to the creation of an alternative splice site. Furthermore, in several studies, the presence of alternatively spliced HLA transcripts co-expressed with the mature spliced transcripts was reported. We evaluated the splice site sequences of all known HLA class I alleles and found that, beside the consensus GT and AG sequences at the intron borders, there were some other highly conserved nucleotides for the different class I genes. In this review, we summarize the splicing mechanism and evaluate what is known today about alternative splicing of HLA class I genes.
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Affiliation(s)
- C E M Voorter
- Department of Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - K E H Gerritsen
- Department of Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - M Groeneweg
- Department of Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - L Wieten
- Department of Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - M G J Tilanus
- Department of Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Centre, Maastricht, the Netherlands
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Voorter CE, Groeneweg M, Groeneveld L, Tilanus MG. Uncommon HLA alleles identified by hemizygous ultra-high Sanger sequencing: haplotype associations and reconsideration of their assignment in the Common and Well-Documented catalogue. Hum Immunol 2016; 77:184-90. [DOI: 10.1016/j.humimm.2015.11.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 10/23/2015] [Accepted: 11/19/2015] [Indexed: 01/24/2023]
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6
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Baldwin KM, Ehrenberg PK, Geretz A, Prentice HA, Nitayaphan S, Rerks-Ngarm S, Kaewkungwal J, Pitisuttithum P, O’Connell RJ, Kim JH, Thomas R. HLA class II diversity in HIV-1 uninfected individuals from the placebo arm of the RV144 Thai vaccine efficacy trial. TISSUE ANTIGENS 2015; 85:117-26. [PMID: 25626602 PMCID: PMC4552183 DOI: 10.1111/tan.12507] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 11/11/2014] [Accepted: 12/13/2014] [Indexed: 11/29/2022]
Abstract
The RV144 HIV vaccine trial in Thailand elicited antibody responses to the envelope of HIV-1, which correlated significantly with the risk of HIV-1 acquisition. Human leukocyte antigen (HLA) class II molecules are essential in antigen presentation to CD4 T cells for activation of B cells to produce antibodies. We genotyped the classical HLA-DRB1, DQB1, and DPB1 genes in 450 individuals from the placebo arm of the RV144 study to determine the background allele and haplotype frequencies of these genes in this cohort. High-resolution 4 and 6-digit class II HLA typing data was generated using sequencing-based methods. The observed diversity for the HLA loci was 33 HLA-DRB1, 15 HLA-DQB1, and 26 HLA-DPB1 alleles. Common alleles with frequencies greater than 10% were DRB1*07:01, DRB1*09:01, DRB1*12:02, DRB1*15:02, DQB1*02:01/02, DQB1*03:01, DQB1*03:03, DQB1*05:01, DQB1*05:02, DPB1*04:01:01, DPB1*05:01:01, and DPB1*13:01:01. We identified 28 rare alleles with frequencies of less than 1% in the Thai individuals. Ambiguity for HLA-DPB1*28:01 in exon 2 was resolved to DPB1*296:01 by next-generation sequencing of all exons. Multi-locus haplotypes including HLA class I and II loci were reported in this study. This is the first comprehensive report of allele and haplotype frequencies of all three HLA class II genes from a Thai population. A high-resolution genotyping method such as next-generation sequencing avoids missing rare alleles and resolves ambiguous calls. The HLA class II genotyping data generated in this study will be beneficial not only for future disease association/vaccine efficacy studies related to the RV144 study, but also for similar studies in other diseases in the Thai population, as well as population genetics and transplantation studies.
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Affiliation(s)
- Karen M. Baldwin
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Philip K. Ehrenberg
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Aviva Geretz
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Heather A. Prentice
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Sorachai Nitayaphan
- Department of Retrovirology, US Army Medical Component, AFRIMS, Bangkok, Thailand
| | | | - Jaranit Kaewkungwal
- Center of Excellence for Biomedical and Public Health Informatics BIOPHICS, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Punnee Pitisuttithum
- Vaccine Trials Centre, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Robert J. O’Connell
- Department of Retrovirology, US Army Medical Component, AFRIMS, Bangkok, Thailand
| | - Jerome H. Kim
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Rasmi Thomas
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
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7
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Allorecognition of HLA-DP by CD4+ T cells is affected by polymorphism in its alpha chain. Mol Immunol 2014; 59:19-29. [DOI: 10.1016/j.molimm.2013.12.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 11/18/2013] [Accepted: 12/27/2013] [Indexed: 11/21/2022]
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8
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Cosentini E, Frison S, Longhi E, Luongo V, Ciardiello G, Bruno P, Mantovani M. Description of the novel HLA-DPB1*137:01 allele found in an Italian subject. Int J Immunogenet 2013; 41:92-4. [DOI: 10.1111/iji.12060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Revised: 04/09/2013] [Accepted: 04/09/2013] [Indexed: 11/28/2022]
Affiliation(s)
- E. Cosentini
- Immunohematology and Transfusion Medicine; Federico II University; Naples Italy
| | - S. Frison
- Organ and Tissue Transplantation Immunology; Fondazione IRCCS ‘‘Ca’ Granda’’ Ospedale Maggiore Policlinico; Milan Italy
| | - E. Longhi
- Organ and Tissue Transplantation Immunology; Fondazione IRCCS ‘‘Ca’ Granda’’ Ospedale Maggiore Policlinico; Milan Italy
| | - V. Luongo
- Immunohematology and Transfusion Medicine; Federico II University; Naples Italy
| | - G. Ciardiello
- Immunohematology and Transfusion Medicine; Federico II University; Naples Italy
| | - P. Bruno
- Immunohematology and Transfusion Medicine; Federico II University; Naples Italy
| | - M. Mantovani
- Organ and Tissue Transplantation Immunology; Fondazione IRCCS ‘‘Ca’ Granda’’ Ospedale Maggiore Policlinico; Milan Italy
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9
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Crivello P, Lauterbach N, Zito L, Sizzano F, Toffalori C, Marcon J, Curci L, Mulder A, Wieten L, Zino E, Voorter CEM, Tilanus MGJ, Fleischhauer K. Effects of transmembrane region variability on cell surface expression and allorecognition of HLA-DP3. Hum Immunol 2013; 74:970-7. [PMID: 23619468 DOI: 10.1016/j.humimm.2013.04.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 03/06/2013] [Accepted: 04/12/2013] [Indexed: 12/01/2022]
Abstract
The functional relevance of polymorphisms outside the peptide binding groove of HLA molecules is poorly understood. Here we have addressed this issue by studying HLA-DP3, a common antigen relevant for functional matching algorithms of unrelated hematopoietic stem cell transplantation (HSCT) encoded by two transmembrane (TM) region variants, DPB1(*)03:01 and DPB1(*)104:01. The two HLA-DP3 variants were found at a overall allelic frequency of 10.4% in 201 volunteer stem cell donors, at a ratio of 4.2:1. No significant differences were observed in cell surface expression levels of the two variants on B lymphoblastoid cell lines (BLCL), primary B cells or monocytes. Three different alloreactive T cell lines or clones showed similar levels of activation marker CD107a and/or CD137 upregulation in response to HLA-DP3 encoded by DPB1(*)03:01 and DPB1(*)104:01, either endogenously on BLCL or after lentiveral-vector mediated transfer into the same cellular background. These data provide, for the first time, direct evidence for a limited functional role of a TM region polymorphism on expression and allorecognition of HLA-DP3 and are compatible with the notion that the two variants can be considered as a single functional entity for unrelated stem cell donor selection.
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Affiliation(s)
- Pietro Crivello
- Unit of Molecular and Functional Immunogenetics, San Raffaele Scientific Institute, Milan, Italy
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10
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Affiliation(s)
- Steven G E Marsh
- WHO Nomenclature Committee for Factors of the HLA System, Anthony Nolan Research Institute, Royal Free Hospital, London, UK.
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11
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Nomenclature for factors of the HLA system, update April 2012. Hum Immunol 2012. [DOI: 10.1016/j.humimm.2012.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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12
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Abad ML, Balas A, Schmidt AH, Rodríguez-Calvo MI, Vicario JL, Eiras A. A novel alleleHLA-DPB1*136:01identified in a German hematopoietic stem cell volunteer donor of Turkish descent. ACTA ACUST UNITED AC 2012; 80:471-2. [DOI: 10.1111/j.1399-0039.2012.01953.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Accepted: 07/24/2012] [Indexed: 12/01/2022]
Affiliation(s)
- M. L. Abad
- Unidad de Biología Molecular e Histocompatibilidad; Centro de Transfusión de Galicia; Santiago de Compostela; Spain
| | - A. Balas
- Departamento de Histocompatibilidad; Centro de Transfusión de la Comunidad de Madrid; Madrid; Spain
| | - A. H. Schmidt
- DKMS German Bone Marrow Donor Center; Tübingen; Germany
| | - M. I. Rodríguez-Calvo
- Unidad de Biología Molecular e Histocompatibilidad; Centro de Transfusión de Galicia; Santiago de Compostela; Spain
| | - J. L. Vicario
- Departamento de Histocompatibilidad; Centro de Transfusión de la Comunidad de Madrid; Madrid; Spain
| | - A. Eiras
- Unidad de Biología Molecular e Histocompatibilidad; Centro de Transfusión de Galicia; Santiago de Compostela; Spain
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13
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Marsh SGE. Nomenclature for factors of the HLA system, update April 2012. Int J Immunogenet 2012. [DOI: 10.1111/j.1744-313x.2012.01148.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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Marsh SGE. Nomenclature for factors of the HLA system, update February 2012. Int J Immunogenet 2012. [DOI: 10.1111/j.1744-313x.2012.01127.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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15
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Marsh SG. Nomenclature for factors of the HLA system, update February 2012. Hum Immunol 2012. [DOI: 10.1016/j.humimm.2012.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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