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Klussmeier A, Massalski C, Putke K, Schäfer G, Sauter J, Schefzyk D, Pruschke J, Hofmann J, Fürst D, Carapito R, Bahram S, Schmidt AH, Lange V. High-Throughput MICA/B Genotyping of Over Two Million Samples: Workflow and Allele Frequencies. Front Immunol 2020; 11:314. [PMID: 32153595 PMCID: PMC7047279 DOI: 10.3389/fimmu.2020.00314] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 02/07/2020] [Indexed: 01/23/2023] Open
Abstract
MICA and MICB are ligands of the NKG2D receptor and thereby influence NK and T cell activity. MICA/B gene polymorphisms, expression levels and the amount of soluble MICA/B in the serum have been linked to autoimmune diseases, infections, and cancer. In hematopoietic stem cell transplantation, MICA matching between donor and patient has been correlated with reduced acute and chronic graft-vs.-host disease and improved survival. Hence, we developed an extremely cost-efficient high-throughput workflow for genotyping MICA/B for newly registered potential stem cell donors. Since mid-2017, we have genotyped over two million samples using NGS amplicon sequencing for MICA/B exons 2–5. In donors of German origin, MICA*008 is the most common MICA allele with a frequency of 42.3%. It is followed by MICA*002 (11.7%) and MICA*009 (8.8%). The three most common MICB alleles are MICB*005 (43.9%), MICB*004 (21.7%), and MICB*002 (18.9%). In general, MICB is less diverse than MICA and only 6 alleles, instead of 15, account for a cumulative allele frequency of 99.5%. In 0.5% of the samples we observed at least one allele of MICA or MICB which has so far not been reported to the IPD/IMGT-HLA database. By providing MICA/B typed voluntary donors, clinicians become empowered to include MICA/B into their donor selection process to further improve unrelated hematopoietic stem cell transplantation.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Daniel Fürst
- Institute of Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service, Baden Wuerttemberg - Hessen, and University Hospital Ulm, Ulm, Germany.,Institute of Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Raphael Carapito
- Laboratoire d'ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR_S 1109, LabEx TRANSPLANTEX, Université de Strasbourg, Strasbourg, France
| | - Seiamak Bahram
- Laboratoire d'ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR_S 1109, LabEx TRANSPLANTEX, Université de Strasbourg, Strasbourg, France
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Liu X, Chen X, Wei X, Meng Y, Liu L, Dai S. Genetic polymorphism analysis of MICB gene in Jing ethnic minority of Southern China. HLA 2018; 92:224-230. [PMID: 29934983 DOI: 10.1111/tan.13325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 06/08/2018] [Accepted: 06/17/2018] [Indexed: 12/01/2022]
Abstract
In the present study, the polymorphism in the 5'-upstream regulation region (5'-URR), coding region (exons 2-4), and the 3'-untranslated region (3'-UTR) of MICB gene were investigated for 150 healthy unrelated Jing individuals in Guangxi Zhuang Autonomous Region, by using PCR-SBT method. A total of 14 variation sites in the 5'-URR, 9 in coding region, and 6 in the 3'-UTR were detected in the Jing population. The MICB gene seems to present two different lineages showing functional variations mainly in nucleotides of the promoter region. Nineteen different MICB extended haplotypes (EHs) encompassing the 5'-URR, exons 2-4, and 3'-UTR were found in this population, and the most frequent was EH2 (20.33%). The findings here are of importance for future studies on the potential role of regulation region of MICB gene in disease association, transplantation, viral infection, and tumor progression among Jing population.
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Affiliation(s)
- Xuexiang Liu
- Medical Science Laboratory, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, Guangxi, 545005, China
| | - Xiang Chen
- Medical Science Laboratory, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, Guangxi, 545005, China
| | - Xiaomou Wei
- Medical Science Laboratory, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, Guangxi, 545005, China
| | - Yuming Meng
- Medical Science Laboratory, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, Guangxi, 545005, China
| | - Limin Liu
- Medical Science Laboratory, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, Guangxi, 545005, China
| | - Shengming Dai
- Medical Science Laboratory, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, Guangxi, 545005, China
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3
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MICB gene diversity and balancing selection on its promoter region in Yao population in southern China. Hum Immunol 2016; 77:1187-1193. [DOI: 10.1016/j.humimm.2016.08.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 08/09/2016] [Accepted: 08/30/2016] [Indexed: 11/19/2022]
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4
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Wang WY, Tian W, Zhu F, Liu XX, Li LX, Wang F. MICA,MICBPolymorphisms and Linkage Disequilibrium withHLA-Bin a Chinese Mongolian Population. Scand J Immunol 2016; 83:456-62. [DOI: 10.1111/sji.12437] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 03/22/2016] [Indexed: 11/30/2022]
Affiliation(s)
- W. Y. Wang
- Immunogenetics Research Group; Department of Immunology; College of Basic Medical Sciences; Central South University; Changsha China
| | - W. Tian
- Immunogenetics Research Group; Department of Immunology; College of Basic Medical Sciences; Central South University; Changsha China
- Laboratory of Cellular and Molecular Biology; College of Basic Medical Sciences; Central South University; Changsha China
| | - F.M. Zhu
- HLA typing laboratory; Blood Center of Zhejiang Province; Hangzhou Zhejiang China
- Key Laboratory of Blood Safety Research; Ministry of Health; Hangzhou China
| | - X. X. Liu
- Immunogenetics Research Group; Department of Immunology; College of Basic Medical Sciences; Central South University; Changsha China
| | - L. X. Li
- Immunogenetics Research Group; Department of Immunology; College of Basic Medical Sciences; Central South University; Changsha China
- Laboratory of Cellular and Molecular Biology; College of Basic Medical Sciences; Central South University; Changsha China
| | - F. Wang
- Immunogenetics Research Group; Department of Immunology; College of Basic Medical Sciences; Central South University; Changsha China
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5
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Abstract
Human and mouse NKG2D ligands (NKG2DLs) are absent or only poorly expressed by most normal cells but are upregulated by cell stress, hence, alerting the immune system in case of malignancy or infection. Although these ligands are numerous and highly variable (at genetic, genomic, structural, and biochemical levels), they all belong to the major histocompatibility complex class I gene superfamily and bind to a single, invariant, receptor: NKG2D. NKG2D (CD314) is an activating receptor expressed on NK cells and subsets of T cells that have a key role in the recognition and lysis of infected and tumor cells. Here, we review the molecular diversity of NKG2DLs, discuss the increasing appreciation of their roles in a variety of medical conditions, and propose several explanations for the evolutionary force(s) that seem to drive the multiplicity and diversity of NKG2DLs while maintaining their interaction with a single invariant receptor.
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Affiliation(s)
- Raphael Carapito
- ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx TRANSPLANTEX, Centre de Recherche d'Immunologie et d'Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France.,Laboratoire International Associé (LIA) INSERM, Strasbourg (France) - Nagano (Japan), Strasbourg, France.,Fédération Hospitalo-Universitaire (FHU) OMICARE, Strasbourg, France
| | - Seiamak Bahram
- ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx TRANSPLANTEX, Centre de Recherche d'Immunologie et d'Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France.,Laboratoire International Associé (LIA) INSERM, Strasbourg (France) - Nagano (Japan), Strasbourg, France.,Fédération Hospitalo-Universitaire (FHU) OMICARE, Strasbourg, France.,Laboratoire Central d'Immunologie, Pôle de Biologie, Nouvel Hôpital Civil, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
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Baek IC, Jang JP, Choi EJ, Kim TG. MICB Allele Genotyping on Microarrays by Improving the Specificity of Extension Primers. PLoS One 2015; 10:e0142467. [PMID: 26569110 PMCID: PMC4646348 DOI: 10.1371/journal.pone.0142467] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 10/22/2015] [Indexed: 11/25/2022] Open
Abstract
Major histocompatibility complex (MHC) class I chain-related gene B (MICB) encodes a ligand for activating NKG2D that expressed in natural killer cells, γδ T cells, and αβ CD8+ T cells, which is associated with autoimmune diseases, cancer, and infectious diseases. Here, we have established a system for genotyping MICB alleles using allele-specific primer extension (ASPE) on microarrays. Thirty-six high quality, allele-specific extension primers were evaluated using strict and reliable cut-off values using mean fluorescence intensity (MFI), whereby an MFI >30,000 represented a positive signal and an MFI <10,000 represented a negative signal. Eight allele-specific extension primers were found to be false positives, five of which were improved by adjusting their length, and three of which were optimized by refractory modification. The MICB alleles (*002:01, *003, *005:02/*010, *005:03, *008, *009N, *018, and *024) present in the quality control panel could be exactly defined by 22 allele-specific extension primers. MICB genotypes that were identified by ASPE on microarrays were in full concordance with those identified by PCR-sequence-based typing. In conclusion, we have developed a method for genotyping MICB alleles using ASPE on microarrays; which can be applicable for large-scale single nucleotide polymorphism typing studies of population and disease associations.
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Affiliation(s)
- In-Cheol Baek
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jung-Pil Jang
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Eun-Jeong Choi
- Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Tai-Gyu Kim
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, Korea
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Chen NY, He JJ, He J, Zhu FM, Lv HJ. Two novel alleles,HLA-A*02:07:06andHLA-A*02:426, were identified in Chinese individuals. ACTA ACUST UNITED AC 2015; 85:499-501. [DOI: 10.1111/tan.12548] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 01/29/2015] [Accepted: 02/16/2015] [Indexed: 11/26/2022]
Affiliation(s)
- N.-Y. Chen
- HLA Typing Laboratory; Blood Center of Zhejiang Province; Hangzhou China
- Key Laboratory of Blood Safety Research; Ministry of Health; Hangzhou China
| | - J.-J. He
- HLA Typing Laboratory; Blood Center of Zhejiang Province; Hangzhou China
- Key Laboratory of Blood Safety Research; Ministry of Health; Hangzhou China
| | - J. He
- HLA Typing Laboratory; Blood Center of Zhejiang Province; Hangzhou China
- Key Laboratory of Blood Safety Research; Ministry of Health; Hangzhou China
| | - F.-M. Zhu
- HLA Typing Laboratory; Blood Center of Zhejiang Province; Hangzhou China
- Key Laboratory of Blood Safety Research; Ministry of Health; Hangzhou China
| | - H.-J. Lv
- HLA Typing Laboratory; Blood Center of Zhejiang Province; Hangzhou China
- Key Laboratory of Blood Safety Research; Ministry of Health; Hangzhou China
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Lin L, Yang W, Chen E, Gong Z, Luo QZ, Wei XB, Yu P. MIC gene polymorphism and haplotype diversity in Li nationality of Southern China. ACTA ACUST UNITED AC 2014; 85:45-9. [DOI: 10.1111/tan.12449] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Revised: 08/08/2014] [Accepted: 09/05/2014] [Indexed: 12/15/2022]
Affiliation(s)
- L. Lin
- Department of Immunology, College of Basic Medical Sciences; Central South University; Changsha 410078 China
| | - W. Yang
- Department of Immunology, College of Basic Medical Sciences; Central South University; Changsha 410078 China
| | - E. Chen
- Department of Immunology, College of Basic Medical Sciences; Central South University; Changsha 410078 China
| | - Z. Gong
- Department of Immunology, College of Basic Medical Sciences; Central South University; Changsha 410078 China
| | - Q. Z. Luo
- Department of Immunology, College of Basic Medical Sciences; Central South University; Changsha 410078 China
| | - X. B. Wei
- Department of Immunology, College of Basic Medical Sciences; Central South University; Changsha 410078 China
| | - P. Yu
- Department of Immunology, College of Basic Medical Sciences; Central South University; Changsha 410078 China
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Cox ST, Madrigal JA, Saudemont A. Diversity and characterization of polymorphic 5' promoter haplotypes of MICA and MICB genes. ACTA ACUST UNITED AC 2014; 84:293-303. [PMID: 24962621 DOI: 10.1111/tan.12400] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 04/25/2014] [Accepted: 05/26/2014] [Indexed: 01/07/2023]
Abstract
The major histocompatibility complex (MHC) class I-related chain A (MICA) and B (MICB) are ligands for the natural killer group 2, member D (NKG2D) activating receptor expressed on natural killer (NK) cells, natural killer T (NKT) cells, CD8+ T cells and γδ T cells. Natural killer group 2, member D (NKG2D) ligand expression is stress-related and upregulated by infected or oncogenic cells leading to cytolysis. MICA and MICB genes display considerable polymorphism among individuals and studies have investigated allelic association with disease and relevance of MICA in transplantation, with variable success. It is now known that promoters of MICA and MICB are polymorphic with some polymorphisms associating with reduced expression. We sequenced International Histocompatibility Workshop (IHW) cell line DNA to determine promoter types and alleles encoded by exons 2-6. We found 8 of 12 known MICA promoter polymorphisms and although promoter P7 dominated, other promoters associated with the same allele. For example, MICA*002:01 had promoters P3, P4 or P7 and the common MICA*008:01/04 type had P1, P6 or P7. Similarly, we sequenced 8 of 12 known MICB promoter haplotypes. Some coding region defined MICB alleles had a single promoter, for example, MICB*002:01 and promoter P9, whereas the promiscuous MICB*005 allele had promoters P1, P2, P5, P6, P10 or P12. The results indicate potential for variation in expression of MICA and MICB ligands between individuals with the same allelic types. If differential expression by polymorphic MICA and MICB promoters is confirmed by functional studies, involvement of these genes in disease susceptibility or adverse transplantation outcomes may require knowledge of both promoter and allelic types to make meaningful conclusions.
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Affiliation(s)
- S T Cox
- Anthony Nolan Research Institute, The Royal Free Hospital, London, UK
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Pan F, Li L, Luo J, Liu X, Tian W. The 5′ promoter region of MHC class I chain-related gene B. ACTA ACUST UNITED AC 2014; 83:337-43. [DOI: 10.1111/tan.12348] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 02/05/2014] [Accepted: 03/04/2014] [Indexed: 01/07/2023]
Affiliation(s)
- F. Pan
- Immunogenetics Research Group, Department of Immunology, College of Basic Medical Sciences; Central South University; Changsha China
| | - L. Li
- Immunogenetics Research Group, Department of Immunology, College of Basic Medical Sciences; Central South University; Changsha China
| | - J. Luo
- Immunogenetics Research Group, Department of Immunology, College of Basic Medical Sciences; Central South University; Changsha China
| | - X. Liu
- Immunogenetics Research Group, Department of Immunology, College of Basic Medical Sciences; Central South University; Changsha China
| | - W. Tian
- Immunogenetics Research Group, Department of Immunology, College of Basic Medical Sciences; Central South University; Changsha China
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Marsh SG. Nomenclature for factors of the HLA system, update July 2013. Hum Immunol 2013. [DOI: 10.1016/j.humimm.2013.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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12
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Marsh SGE. Nomenclature for factors of the HLA system, update July 2013. ACTA ACUST UNITED AC 2013; 82:447-51. [DOI: 10.1111/tan.12235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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13
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Nomenclature for factors of the HLA system, update July 2013. Int J Immunogenet 2013. [DOI: 10.1111/iji.12100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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