1
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Koskela S, Tammi S, Clancy J, Lucas JAM, Turner TR, Hyvärinen K, Ritari J, Partanen J. MICA and MICB allele assortment in Finland. HLA 2023. [PMID: 36919857 DOI: 10.1111/tan.15023] [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: 12/30/2021] [Revised: 02/01/2023] [Accepted: 03/04/2023] [Indexed: 03/16/2023]
Abstract
Genetic variation in the MICA and MICB genes located within the major histocompatibility complex region has been reported to be associated with transplantation outcome and susceptibility to autoimmune diseases and infections. Only limited data of polymorphism in these genes in different populations are available. We here report allelic variation at 2-field resolution and the haplotypes of the MICA and MICB genes in Finland (n = 1032 individuals), a north European population with historical bottleneck and founder effects. Altogether 24 MICA and 18 MICB alleles were found, forming 70 estimated MICA-MICB haplotypes. As compared to other populations frequency differences were found, for example, MICA*010:01 was found to be at an allele frequency of 0.133 in Finland which is higher than in other European populations (0.021-0.077), but close to Asian populations (0.151-0.220). Three novel alleles with amino acid change are described. The results demonstrate a relatively high level of polymorphism and population differences in MICA and MICB allele distribution.
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Affiliation(s)
- Satu Koskela
- Finnish Red Cross Blood Service, Research and Development, Helsinki, Finland.,Finnish Red Cross Blood Service Biobank, Helsinki, Finland
| | - Silja Tammi
- Finnish Red Cross Blood Service, Research and Development, Helsinki, Finland.,Finnish Red Cross Blood Service Biobank, Helsinki, Finland
| | - Jonna Clancy
- Finnish Red Cross Blood Service, Research and Development, Helsinki, Finland.,Finnish Red Cross Blood Service Biobank, Helsinki, Finland
| | | | - Thomas R Turner
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK.,UCL Cancer Institute, Royal Free Campus, London, UK
| | - Kati Hyvärinen
- Finnish Red Cross Blood Service, Research and Development, Helsinki, Finland
| | - Jarmo Ritari
- Finnish Red Cross Blood Service, Research and Development, Helsinki, Finland
| | - Jukka Partanen
- Finnish Red Cross Blood Service, Research and Development, Helsinki, Finland.,Finnish Red Cross Blood Service Biobank, Helsinki, Finland
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2
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Al Hadra B, Lukanov TI, Ivanova MI. HLA class I chain-related MICA and MICB genes polymorphism in healthy individuals from the Bulgarian population. Hum Immunol 2022; 83:551-555. [PMID: 35525711 DOI: 10.1016/j.humimm.2022.04.006] [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: 01/12/2022] [Revised: 04/01/2022] [Accepted: 04/18/2022] [Indexed: 11/26/2022]
Abstract
Although human leukocyte antigen (HLA) gene polymorphism has been investigated in many populations around the world, the data on MHC class I chain-related (MIC) genes are still limited. The present study is aimed to analyze the allelic polymorphism of MICA and MICB genes and haplotype associations with HLA-B locus in 132 healthy, unrelated individuals from the Bulgarian population by next generation sequencing (NGS). A total of 36 MICA and 16 MICB alleles were observed with the highest frequency detected for MICA*008:01 (17.1%) and MICB*005:02 (32.4%). Further, two and three-loci haplotype frequencies and pairwise linkage disequilibrium were estimated. Highly significant global linkage disequilibrium was found between either HLA-B and MICA and MICB genes. This is the first study on MICA and MICB allelic polymorphism, linkage disequilibrium, and haplotype polymorphism in the Bulgarian population. These results will allow for better characterization of the genetic heterogeneity of the Bulgarian population and could contribute to further analyses on MICA and MICB clinical significance.
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Affiliation(s)
- Bushra Al Hadra
- Department of Clinical Immunology, Medical University, Sofia, Bulgaria; Department of Clinical Immunology and Stem Cell Bank, Alexandrovska University Hospital, Sofia, Bulgaria.
| | - Tsvetelin I Lukanov
- Department of Clinical Immunology, Medical University, Sofia, Bulgaria; Department of Clinical Immunology and Stem Cell Bank, Alexandrovska University Hospital, Sofia, Bulgaria
| | - Milena I Ivanova
- Department of Clinical Immunology, Medical University, Sofia, Bulgaria; Department of Clinical Immunology and Stem Cell Bank, Alexandrovska University Hospital, Sofia, Bulgaria
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3
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Toledo-Stuardo K, Ribeiro CH, Canals A, Morales M, Gárate V, Rodríguez-Siza J, Tello S, Bustamante M, Armisen R, Matthies DJ, Zapata-Torres G, González-Hormazabal P, Molina MC. Major Histocompatibility Complex Class I-Related Chain A (MICA) Allelic Variants Associate With Susceptibility and Prognosis of Gastric Cancer. Front Immunol 2021; 12:645528. [PMID: 33868281 PMCID: PMC8045969 DOI: 10.3389/fimmu.2021.645528] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 02/23/2021] [Indexed: 12/14/2022] Open
Abstract
Gastric cancer (GC) is the fifth most prevalent type of cancer worldwide. Gastric tumor cells express MICA protein, a ligand to NKG2D receptor that triggers natural killer (NK) cells effector functions for early tumor elimination. MICA gene is highly polymorphic, thus originating alleles that encode protein variants with a controversial role in cancer. The main goal of this work was to study MICA gene polymorphisms and their relationship with the susceptibility and prognosis of GC. Fifty patients with GC and 50 healthy volunteers were included in this study. MICA alleles were identified using Sanger sequencing methods. The analysis of MICA gene sequence revealed 13 MICA sequences and 5 MICA-short tandem repeats (STR) alleles in the studied cohorts We identified MICA*002 (*A9) as the most frequent allele in both, patients and controls, followed by MICA*008 allele (*A5.1). MICA*009/049 allele was significantly associated with increased risk of GC (OR: 5.11 [95% CI: 1.39–18.74], p = 0.014). The analysis of MICA-STR alleles revealed a higher frequency of MICA*A5 in healthy individuals than GC patients (OR = 0.34 [95% CI: 0.12–0.98], p = 0.046). Survival analysis after gastrectomy showed that patients with MICA*002/002 or MICA*002/004 alleles had significantly higher survival rates than those patients bearing MICA*002/008 (p = 0.014) or MICA*002/009 (MICA*002/049) alleles (p = 0.040). The presence of threonine in the position MICA-181 (MICA*009/049 allele) was more frequent in GC patients than controls (p = 0.023). Molecular analysis of MICA-181 showed that the presence of threonine provides greater mobility to the protein than arginine in the same position (MICA*004), which could explain, at least in part, some immune evasion mechanisms developed by the tumor. In conclusion, our findings suggest that the study of MICA alleles is crucial to search for new therapeutic approaches and may be useful for the evaluation of risk and prognosis of GC and personalized therapy.
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Affiliation(s)
- Karen Toledo-Stuardo
- Immunology Program, Faculty of Medicine, Institute of Biomedical Sciences (ICBM), University of Chile, Santiago, Chile
| | - Carolina H Ribeiro
- Immunology Program, Faculty of Medicine, Institute of Biomedical Sciences (ICBM), University of Chile, Santiago, Chile
| | - Andrea Canals
- Biostatistics Program, School of Public Health, University of Chile, Santiago, Chile.,Academic Direction, Clínica Santa María, Santiago, Chile
| | - Marcela Morales
- Immunology Program, Faculty of Medicine, Institute of Biomedical Sciences (ICBM), University of Chile, Santiago, Chile
| | - Valentina Gárate
- Immunology Program, Faculty of Medicine, Institute of Biomedical Sciences (ICBM), University of Chile, Santiago, Chile
| | - Jose Rodríguez-Siza
- Immunology Program, Faculty of Medicine, Institute of Biomedical Sciences (ICBM), University of Chile, Santiago, Chile
| | - Samantha Tello
- Immunology Program, Faculty of Medicine, Institute of Biomedical Sciences (ICBM), University of Chile, Santiago, Chile
| | - Marco Bustamante
- Department of Surgery (Oriente), Hospital del Salvador, University of Chile, Santiago, Chile
| | - Ricardo Armisen
- Center of Genetics and Genomics, Faculty of Medicine Clínica Alemana, Institute for Sciences and Innovations in Medicine (ICIM), Universidad del Desarrollo, Santiago, Chile
| | - Douglas J Matthies
- Department of Inorganic and Analytical Chemistry, Faculty of Chemical and Pharmaceutical Sciences, University of Chile, Santiago, Chile
| | - Gerald Zapata-Torres
- Department of Inorganic and Analytical Chemistry, Faculty of Chemical and Pharmaceutical Sciences, University of Chile, Santiago, Chile
| | | | - María Carmen Molina
- Immunology Program, Faculty of Medicine, Institute of Biomedical Sciences (ICBM), University of Chile, Santiago, Chile
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4
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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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5
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Positive association between MIC gene polymorphism and tuberculosis in Chinese population. Immunol Lett 2019; 213:62-69. [PMID: 31400356 DOI: 10.1016/j.imlet.2019.07.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 07/29/2019] [Accepted: 07/30/2019] [Indexed: 11/23/2022]
Abstract
The disease progression and morbidity of tuberculosis (TB) infections are determined by virulence of the micro-organism, host genetic factors and environmental factors. The highly polymorphic MHC class I chain-related gene (MIC) could serve as a potential host genetic candidate. To investigate the association of MIC polymorphism with TB infection, 124 patients and 191 ethnically matched controls from Hunan province, Southern China, were genotyped for the MIC polymorphism using polymerase chain reaction-sequence specific priming and sequencing-based typing. The results showed that allele frequencies of MIC-sequence and MICA-STR were different in TB patients in comparison to normal controls (both P < 0.05). MICA-A4 and MICA*012:01 alleles were positive associated (OR = 2.42, 95% CI: 1.69-3.87; OR = 3.41, 95% CI: 2.19-5.33, respectively, both Pc < 0.05) while MICA -A5 were inversely associated (OR = 0.59, 95%CI: 0.41-0.94, Pc < 0.05) with TB. Homozygote MICA*012:01/012:01 was observed to have significant risk effects on TB (OR = 4.76, 95% CI: 1.94-11.69, Pc0000-0001-5151-1853 < 0.05). Additionally, MICB*008 allele conduct a significant risk effect for TB (OR = 3.17, 95%CI: 1.80-5.61, Pc < 0.05). All the data showed that MIC polymorphism was associated with the variable susceptibility to TB in Chinese population.
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6
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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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7
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Cox ST, Danby R, Hernandez D, Laza-Briviesca R, Pearson H, Madrigal JA, Saudemont A. Functional Characterisation and Analysis of the Soluble NKG2D Ligand Repertoire Detected in Umbilical Cord Blood Plasma. Front Immunol 2018; 9:1282. [PMID: 29963042 PMCID: PMC6013648 DOI: 10.3389/fimmu.2018.01282] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 05/22/2018] [Indexed: 12/19/2022] Open
Abstract
We previously reported that cord blood plasma (CBP) contains significantly more soluble NKG2D ligands (sNKG2DLs), such as sMICB and sULBP1, than healthy adult plasma. Viral infection or malignant transformation upregulates expression of NKG2D ligand on affected cells, leading to NK group 2, member D (NKG2D)-mediated natural killer (NK) cell lysis. Conversely, sNKG2DL engagement of NKG2D decreases NK cell cytotoxicity leading to viral or tumour immune escape. We hypothesised that sNKG2DLs detected in CBP may represent an additional fetal–maternal tolerance mechanism. To further understand the role of sNKG2DL in pregnancy and individual contributions of the various ligand types, we carried out functional analysis using 181 CBP samples. To test the ability of CBP to suppress the function of NK cells in vitro, we measured expression of NKG2D, CD107a, and IFN-γ in NK cells from control donors after exposure to 181 individual CBP samples and characterised the sMICA, sMICB, and sULBP1 content of each one. Furthermore, to detect possible allelic differences between samples that may also affect function, we carried out umbilical cord blood typing for MHC class I-related chain A (MICA) and MHC class I-related chain B (MICB) coding and promoter allelic types. Strongest functional correlations related to increasing concentration of exosomal sULBP1, which was present in all CBP samples tested. In addition, common MICB alleles, such as MICB*005:02, resulted in increased concentration of sMICB. Interestingly, MICB*005:02 uniquely associated with eight different promoter types. Among promoter polymorphisms, P2 resulted in the highest expression of sMICB and P9 the least and was confirmed using luciferase reporter assays. Higher levels of sMICB associated with lower IFN-γ production, indicating that sMICB also suppressed NK cell function. We also examined the MICA functional dimorphism encoding methionine (met) or valine (val) at residue 129 associated with strong or weak NKG2D binding, respectively. Most sMICA associated with val/val, some with met/val but none with met/met and, counter-intuitively, the presence of sMICA in CBP increased NK cell cytotoxicity. We propose a model for fetal–maternal tolerance, whereby NK cell activity is limited by sULBP1 and sMICB in CBP. The release of 129val sMICA with weak NKG2D signalling may reduce the overall net suppressive signal and break tolerance thus allowing fetal NK cells to overcome immunological threats in utero.
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Affiliation(s)
- Steven T Cox
- Anthony Nolan Research Institute, Royal Free Hospital, London, United Kingdom.,Cancer Institute, University College London, London, United Kingdom
| | - Robert Danby
- Anthony Nolan Research Institute, Royal Free Hospital, London, United Kingdom.,Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Diana Hernandez
- Anthony Nolan Research Institute, Royal Free Hospital, London, United Kingdom.,Cancer Institute, University College London, London, United Kingdom
| | | | - Hayley Pearson
- Anthony Nolan Research Institute, Royal Free Hospital, London, United Kingdom
| | - J Alejandro Madrigal
- Anthony Nolan Research Institute, Royal Free Hospital, London, United Kingdom.,Cancer Institute, University College London, London, United Kingdom
| | - Aurore Saudemont
- Anthony Nolan Research Institute, Royal Free Hospital, London, United Kingdom.,Cancer Institute, University College London, London, United Kingdom
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8
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Association of MICA and MICB polymorphisms with the susceptibility of leukemia in Korean patients. Blood Cancer J 2018; 8:58. [PMID: 29895953 PMCID: PMC5997647 DOI: 10.1038/s41408-018-0092-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 04/19/2018] [Accepted: 05/08/2018] [Indexed: 02/05/2023] Open
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9
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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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10
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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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11
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Allele polymorphism and haplotype diversity of MICA/B in Tujia nationality of Zhangjiajie, Hunan Province, China. Hum Immunol 2016; 77:411-7. [DOI: 10.1016/j.humimm.2016.03.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Revised: 06/14/2015] [Accepted: 03/10/2016] [Indexed: 11/23/2022]
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12
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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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13
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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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14
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Chen E, Lin L, Chen CJ, Zhang XY, Luo QZ, Yu P. MIC gene polymorphism and haplotype diversity in Zhuang nationality of Southern China. Hum Immunol 2014; 75:953-9. [PMID: 25167773 DOI: 10.1016/j.humimm.2014.08.203] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 08/18/2014] [Accepted: 08/18/2014] [Indexed: 02/06/2023]
Abstract
Zhuang ethnic minority is the largest minority group in China. Here, we report for the first time the polymorphisms of MICA and MICB in a healthy Zhuang population of 209 unrelated individuals. Using polymerase chain reaction-sequence specific priming (PCR-SSP) and sequencing-based typing (PCR-SBT), 13 MICA-sequence alleles and 5 MICA-STR alleles, as well as 11 MICB alleles were detected, among which MICA(∗)010, MICA(∗)A5 and MICB(∗)005:02 were the most frequent alleles. Linkage disequilibria was investigated and the most common two-locus haplotypes were MICB(∗)005:02-MICA(∗)010 and MICB(∗)014-MICA(∗)045. These results suggest informative genetic markers for investigating origins and evolution of MHC class I region haplotypes in Zhuang population.
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Affiliation(s)
- E Chen
- Department of Immunology, College of Basic Medical Sciences, Central South University, 110 Xiangya Road, Changsha 410078, China
| | - L Lin
- Department of Immunology, College of Basic Medical Sciences, Central South University, 110 Xiangya Road, Changsha 410078, China
| | - C J Chen
- Department of Immunology, College of Basic Medical Sciences, Central South University, 110 Xiangya Road, Changsha 410078, China
| | - X Y Zhang
- Department of Microbiology, Changzhi Medical College, Changzhi 046000, China
| | - Q Z Luo
- Department of Immunology, College of Basic Medical Sciences, Central South University, 110 Xiangya Road, Changsha 410078, China
| | - P Yu
- Department of Immunology, College of Basic Medical Sciences, Central South University, 110 Xiangya Road, Changsha 410078, China.
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15
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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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Distribution of MICB diversity in the Zhejiang Han population: PCR sequence-based typing for exons 2–6 and identification of five novel MICB alleles. Immunogenetics 2013; 65:485-92. [DOI: 10.1007/s00251-013-0699-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 03/19/2013] [Indexed: 11/26/2022]
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17
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MICB polymorphism in a southern Chinese Han population: The identification of two new MICB alleles, MICB∗005:06 and MICB∗026. Hum Immunol 2012; 73:818-23. [DOI: 10.1016/j.humimm.2012.05.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Revised: 04/24/2012] [Accepted: 05/08/2012] [Indexed: 11/18/2022]
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