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Tammi S, Koskela S, Hyvärinen K, Partanen J, Ritari J. Accurate multi-population imputation of MICA, MICB, HLA-E, HLA-F and HLA-G alleles from genome SNP data. PLoS Comput Biol 2024; 20:e1011718. [PMID: 39283896 PMCID: PMC11426482 DOI: 10.1371/journal.pcbi.1011718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 09/26/2024] [Accepted: 08/31/2024] [Indexed: 09/27/2024] Open
Abstract
In addition to the classical HLA genes, the major histocompatibility complex (MHC) harbors a high number of other polymorphic genes with less established roles in disease associations and transplantation matching. To facilitate studies of the non-classical and non-HLA genes in large patient and biobank cohorts, we trained imputation models for MICA, MICB, HLA-E, HLA-F and HLA-G alleles on genome SNP array data. We show, using both population-specific and multi-population 1000 Genomes references, that the alleles of these genes can be accurately imputed for screening and research purposes. The best imputation model for MICA, MICB, HLA-E, -F and -G achieved a mean accuracy of 99.3% (min, max: 98.6, 99.9). Furthermore, validation of the 1000 Genomes exome short-read sequencing-based allele calling against a clinical-grade reference data showed an average accuracy of 99.8%, testifying for the quality of the 1000 Genomes data as an imputation reference. We also fitted the models for Infinium Global Screening Array (GSA, Illumina, Inc.) and Axiom Precision Medicine Research Array (PMRA, Thermo Fisher Scientific Inc.) SNP content, with mean accuracies of 99.1% (97.2, 100) and 98.9% (97.4, 100), respectively.
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Affiliation(s)
- Silja Tammi
- Finnish Red Cross Blood Service, Research and Development, Helsinki, Finland
| | - Satu Koskela
- Finnish Red Cross Blood Service, Research and Development, Helsinki, Finland
- Finnish Red Cross Blood Service, Blood Service Biobank, Vantaa, Finland
| | | | - Kati Hyvärinen
- 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, Blood Service Biobank, Vantaa, Finland
| | - Jarmo Ritari
- Finnish Red Cross Blood Service, Research and Development, Helsinki, Finland
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Association between MICA rs2596542 Polymorphism with the Risk of Hepatocellular Carcinoma in Chronic Hepatitis C Patients. Pathol Oncol Res 2019; 26:1519-1525. [PMID: 31471884 DOI: 10.1007/s12253-019-00738-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 08/27/2019] [Indexed: 12/30/2022]
Abstract
In this study we investigated the impact of rs2596542A/G single nucleotide polymorphism (SNP) in the major histocompatibility complex class I chain-related sequence A (MICA) gene on HCV-induced hepatocellular carcinoma (HCC) susceptibility in a Brazilian population. In total, 252 HCV-infected patients (98 with HCV-induced HCC and 154 non-malignant HCV-induced liver cirrhosis) were enrolled and 98 healthy control subjects (negative anti-HCV). The MICA rs2596542 SNP genotypes were determined by real-time PCR assay. No differences in MICA genotype frequencies between HCV-induced cirrhosis patients and controls were observed. However, genotype frequencies of rs2596542A/G SNP were statistically different between HCV-induced HCC patients and controls (p = 0.048), and also between HCC and HCV-induced cirrhosis patients (p = 0.039). The highest frequency of the rs2596542AA genotype was observed in HCC patients (31.6%) when compared with HCV-induced cirrhosis patients (18.8%) and healthy controls (19.4%). Also, rs2596542AA genotype carriers have an increased risk for HCC when compared to HCV-induced cirrhosis status [odds ratio (OR) = 1.99; 95% confidence interval (CI) = 1.06-3.74, p = 0.020)] and healthy individuals (OR = 1.92, 95% CI = 1.00-3.70, p = 0.049). Taken together our study suggest that MICA rs2596542 SNP impacts HCV-induced HCC susceptibility suggesting that genetic variants in MICA are of clinical relevance to hepatocarcinogenesis by impacting host immune response in chronic HCV infection.
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A Valine Mismatch at Position 129 of MICA Is an Independent Predictor of Cytomegalovirus Infection and Acute Kidney Rejection in Simultaneous Pancreas⁻Kidney Transplantation Recipients. Int J Mol Sci 2018; 19:ijms19092618. [PMID: 30181474 PMCID: PMC6164160 DOI: 10.3390/ijms19092618] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 08/30/2018] [Accepted: 08/31/2018] [Indexed: 11/16/2022] Open
Abstract
The polymorphic major histocompatibility complex class I chain-related molecule A (MICA) and its soluble form (sMICA) interact with activating receptor natural-killer group 2 member D (NKG2D) on natural-killer (NK) and T cells, thereby modifying immune responses to transplantation and infectious agents (e.g., cytomegalovirus). Two single-nucleotide polymorphisms (SNPs), rs2596538GA in the MICA promoter and rs1051792AG in the coding region (MICA-129Val/Met), influence MICA expression or binding to NKG2D, with MICA-129Met molecules showing higher receptor affinity. To investigate the impact of these SNPs on the occurrence of cytomegalovirus infection or acute rejection (AR) in individuals who underwent simultaneous pancreas⁻kidney transplantation (SPKT), 50 recipient-donor pairs were genotyped, and sMICA levels were measured during the first year post-transplantation. Recipients with a Val-mismatch (recipient Met/Met and donor Val/Met or Val/Val) showed shorter cytomegalovirus infection-free and shorter kidney AR-free survival. Additionally, Val mismatch was an independent predictor of cytomegalovirus infection and kidney AR in the first year post-transplantation. Interestingly, sMICA levels were lower in rs2596538AA and MICA129Met/Met-homozygous recipients. These results provide further evidence that genetic variants of MICA influence sMICA levels, and that Val mismatch at position 129 increases cytomegalovirus infection and kidney AR risk during the first year post-SPKT.
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Zuo J, Mohammed F, Moss P. The Biological Influence and Clinical Relevance of Polymorphism Within the NKG2D Ligands. Front Immunol 2018; 9:1820. [PMID: 30166984 PMCID: PMC6105697 DOI: 10.3389/fimmu.2018.01820] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 07/24/2018] [Indexed: 01/23/2023] Open
Abstract
NKG2D is a major regulator of the activity of cytotoxic cells and interacts with eight different ligands (NKG2DL) from two families of MIC and ULBP proteins. The selective forces that drove evolution of NKG2DL are uncertain, but are likely to have been dominated by infectious disease and cancer. Of interest, NKG2DL are some of the most polymorphic genes outside the MHC locus and the study of these is uncovering a range of novel observations regarding the structure and function of NKG2DL. Polymorphism is present within all NKG2DL members and varies markedly within different populations. Allelic variation influences functional responses through three major mechanisms. First, it may drive differential levels of protein expression, modulate subcellular trafficking, or regulate release of soluble isoforms. In addition, it may alter the affinity of interaction with NKG2D or modulate cytotoxic activity from the target cell. In particular, ligands with high affinity for NKG2D are associated with down regulation of this protein on the effector cell, effectively limiting cytotoxic activity in a negative-feedback circuit. Given these observations, it is not surprising that NKG2DL alleles are associated with relative risk for development of several clinical disorders and the critical role of the NKG2D:NKG2DL interaction is demonstrated in many murine models. Increased understanding of the biophysical and functional consequences of this polymorphism is likely to provide insights into novel immunotherapeutic approaches.
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Affiliation(s)
- Jianmin Zuo
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Fiyaz Mohammed
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Paul Moss
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
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Rohn H, Tomoya Michita R, Schwich E, Dolff S, Gäckler A, Trilling M, Le-Trilling VTK, Wilde B, Korth J, Heinemann FM, Horn PA, Kribben A, Witzke O, Rebmann V. The Donor Major Histocompatibility Complex Class I Chain-Related Molecule A Allele rs2596538 G Predicts Cytomegalovirus Viremia in Kidney Transplant Recipients. Front Immunol 2018; 9:917. [PMID: 29867932 PMCID: PMC5953334 DOI: 10.3389/fimmu.2018.00917] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 04/13/2018] [Indexed: 01/14/2023] Open
Abstract
The interaction of major histocompatibility complex class I chain-related protein A (MICA) and its cognate activating receptor natural killer (NK) group 2 member D (NKG2D) receptor plays a significant role in viral immune control. In the context of kidney transplantation (KTx), cytomegalovirus (CMV) frequently causes severe complications. Hypothesizing that functional polymorphisms of the MICA/NKG2D axis might affect antiviral NK and T cell responses to CMV, we explored the association of the MICA-129 Met/Val single nucleotide polymorphism (SNP) (affecting the binding affinity of MICA with the NKG2D receptor), the MICA rs2596538 G/A SNP (influencing MICA transcription), and the NKG2D rs1049174 G/C SNP (determining the cytotoxic potential of effector cells) with the clinical outcome of CMV during the first year after KTx in a cohort of 181 kidney donor-recipients pairs. Univariate analyses identified the donor MICA rs2596538 G allele status as a protective prognostic determinant for CMV disease. In addition to the well-known prognostic factors CMV high-risk sero-status of patients and the application of lymphocyte-depleting drugs, the donor MICA rs2596538 G allele carrier status was confirmed by multivariate analyses as novel-independent factor predicting the development of CMV infection/disease during the first year after KTx. The results of our study emphasize the clinical importance of the MICA/NKG2D axis in CMV control in KTx and point out that the potential MICA transcription in the donor allograft is of clinically relevant importance for CMV immune control in this allogeneic situation. Furthermore, they provide substantial evidence that the donor MICA rs2596538 G allele carrier status is a promising genetic marker predicting CMV viremia after KTx. Thus, in the kidney transplant setting, donor MICA rs2596538 G may help to allow the future development of personal CMV approaches within a genetically predisposed patient cohort.
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Affiliation(s)
- Hana Rohn
- Department of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Rafael Tomoya Michita
- Institute for Transfusion Medicine, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Esther Schwich
- Institute for Transfusion Medicine, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Sebastian Dolff
- Department of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Anja Gäckler
- Department of Nephrology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Mirko Trilling
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | | | - Benjamin Wilde
- Department of Nephrology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Johannes Korth
- Department of Nephrology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Falko M Heinemann
- Institute for Transfusion Medicine, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Peter A Horn
- Institute for Transfusion Medicine, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Andreas Kribben
- Department of Nephrology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Oliver Witzke
- Department of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Vera Rebmann
- Institute for Transfusion Medicine, University Hospital Essen, University Duisburg-Essen, Essen, Germany
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Luo Q, Guo X, Peng S, Luo W, Tian F, Yu P, Zou Y. The association between MICA/MICB polymorphism and respiratory syncytial virus infection in children. Int J Immunogenet 2017; 44:328-336. [PMID: 28925058 DOI: 10.1111/iji.12338] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 08/10/2017] [Accepted: 08/27/2017] [Indexed: 12/22/2022]
Abstract
MICA/MICB gene polymorphisms are related to several cancers and infectious diseases, but there are no reports on the association between MICA/MICB gene polymorphisms and respiratory syncytial virus (RSV) infection. To clarify the association between MICA/MICB gene polymorphisms and infection of RSV in children, we collected fresh blood samples from paediatric patients with and without pneumonia after RSV infection. The MICA/MICB alleles were characterized by PCR sequence-specific primers (PCR-SSP) and PCR sequence-based genotyping (PCR-SBT), and then, the frequency of the MICA/MICB alleles and haplotypes was calculated. The results showed that the frequencies of MICA*002:01 and MICA-A9 in RSV-infected patients were significantly lower than in controls (9% vs. 20%, pc = 0.04). The allele frequency of MICA*002:01 in pneumonia patients (8%) and nonpneumonia patients (9%) was significantly lower than in controls (20%, pc = 0.02). MICA*002:01-MICB*008(Δrel = 0.616), MICA*009-MICB*016 (Δrel = 0.506), and MICA*045-MICB*014 (Δrel = 0.700) showed linkage disequilibrium in patients infected with RSV. The haplotype frequency of MICA*002:01-MICB*005:02 in RSV-infected patients was significantly lower than in controls (10% vs. 16%, pc = 0.033). In conclusion, allele MICA*002:01/A9 and haplotype MICA*002:01-MICB*005:02 were negatively associated with RSV respiratory tract infections.
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Affiliation(s)
- Q Luo
- Department of Immunology, Xiangya School of Medicine, Central South University, Hunan, China
| | - X Guo
- Department of Immunology, Xiangya School of Medicine, Central South University, Hunan, China.,Medical college of Hebei University of Engineering, Hebei, China
| | - S Peng
- The Second Xiang Ya Hospital of Central South University, Hunan, China
| | - W Luo
- Department of Immunology, Xiangya School of Medicine, Central South University, Hunan, China
| | - F Tian
- Department of Immunology, Xiangya School of Medicine, Central South University, Hunan, China
| | - P Yu
- Department of Immunology, Xiangya School of Medicine, Central South University, Hunan, China
| | - Y Zou
- Department of Immunology, Xiangya School of Medicine, Central South University, Hunan, China
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Martinez-Chamorro A, Moreno A, Gómez-García M, Cabello MJ, Martin J, Lopez-Nevot MÁ. MICA*A4 protects against ulcerative colitis, whereas MICA*A5.1 is associated with abscess formation and age of onset. Clin Exp Immunol 2016; 184:323-31. [PMID: 26940143 DOI: 10.1111/cei.12786] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2016] [Indexed: 12/15/2022] Open
Abstract
Ulcerative colitis (UC) is one of the two major forms of inflammatory bowel disease, the aetiology of which remains unknown. Several studies have demonstrated the genetic basis of disease, identifying more than 130 susceptibility loci. The major histocompatibility complex class I chain-related gene A (MICA) is a useful candidate to be involved in UC pathogenesis, because it could be important in recognizing the integrity of the epithelial cell and its response to stress. The aim of this study was to analyse the relationship between polymorphisms in the transmembrane domain of MICA and susceptibility to develop UC. A total of 340 patients with UC and 636 healthy controls were genotyped for MICA transmembrane polymorphism using a polymerase chain reaction (PCR) combined with fluorescent technology. Different MICA alleles were determined depending on the PCR product size. The allele MICA*A4 was less frequent in patients than in controls (P = 0·003; OR = 0·643), and this protective role is higher when it forms haplotype with B*27 (P = 0·002; OR = 0·294). The haplotype HLA-B*52/MICA*A6 was also associated with UC [P = 0·001; odds ratio (OR) = 2·914]. No other alleles, genotypes or haplotypes were related with UC risk. Moreover, MICA*A5.1 is associated independently with abscesses (P = 0·002; OR = 3·096) and its frequency is lower in patients diagnosed between ages 17 and 40 years (P = 0·007; OR = 0·633), meaning an extreme age on onset. No association with location, extra-intestinal manifestations or need for surgery was found.
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Affiliation(s)
| | - A Moreno
- Section of Immunology, Hospital Virgen de las Nieves
| | | | - M J Cabello
- Digestive Section, Hospital Virgen de las Nieves
| | - J Martin
- Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain
| | - M Á Lopez-Nevot
- Section of Immunology, Hospital Virgen de las Nieves.,University of Granada
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Isernhagen A, Schilling D, Monecke S, Shah P, Elsner L, Walter L, Multhoff G, Dressel R. The MICA-129Met/Val dimorphism affects plasma membrane expression and shedding of the NKG2D ligand MICA. Immunogenetics 2015; 68:109-23. [PMID: 26585323 PMCID: PMC4728179 DOI: 10.1007/s00251-015-0884-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Accepted: 11/09/2015] [Indexed: 12/16/2022]
Abstract
The MHC class I chain-related molecule A (MICA) is a ligand for the activating natural killer (NK) cell receptor NKG2D. A polymorphism causing a valine to methionine exchange at position 129 affects binding to NKG2D, cytotoxicity, interferon-γ release by NK cells and activation of CD8+ T cells. It is known that tumors can escape NKG2D-mediated immune surveillance by proteolytic shedding of MICA. Therefore, we investigated whether this polymorphism affects plasma membrane expression (pmMICA) and shedding of MICA. Expression of pmMICA was higher in a panel of tumor (n = 16, P = 0.0699) and melanoma cell lines (n = 13, P = 0.0429) carrying the MICA-129Val/Val genotype. MICA-129Val homozygous melanoma cell lines released more soluble MICA (sMICA) by shedding (P = 0.0015). MICA-129Met or MICA-129Val isoforms differing only in this amino acid were expressed in the MICA-negative melanoma cell line Malme, and clones with similar pmMICA expression intensity were selected. The MICA-129Met clones released more sMICA (P = 0.0006), and a higher proportion of the MICA-129Met than the MICA-129Val variant was retained in intracellular compartments (P = 0.0199). The MICA-129Met clones also expressed more MICA messenger RNA (P = 0.0047). The latter phenotype was also observed in mouse L cells transfected with the MICA expression constructs (P = 0.0212). In conclusion, the MICA-129Met/Val dimorphism affects the expression density of MICA on the plasma membrane. More of the MICA-129Met variants were retained intracellularly. If expressed at the cell surface, the MICA-129Met isoform was more susceptible to shedding. Both processes appear to limit the cell surface expression of MICA-129Met variants that have a high binding avidity to NKG2D.
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Affiliation(s)
- Antje Isernhagen
- Institute of Cellular and Molecular Immunology, University Medical Center Göttingen, Humboldtallee 34, 37073, Göttingen, Germany
| | - Daniela Schilling
- Department of Radiation Oncology, Klinikum rechts der Isar, Technische Universität München (TUM), Munich, Germany.,Institute of Innovative Radiotherapy (iRT), Radiation Immune Biology, Department of Radiation Sciences (DRS), Helmholtz Zentrum München, Munich, Germany
| | - Sebastian Monecke
- Institute of Cellular and Molecular Immunology, University Medical Center Göttingen, Humboldtallee 34, 37073, Göttingen, Germany.,DZHK (German Center for Cardiovascular Research), Partner site Göttingen, Göttingen, Germany
| | - Pranali Shah
- Institute of Cellular and Molecular Immunology, University Medical Center Göttingen, Humboldtallee 34, 37073, Göttingen, Germany
| | - Leslie Elsner
- Institute of Cellular and Molecular Immunology, University Medical Center Göttingen, Humboldtallee 34, 37073, Göttingen, Germany
| | - Lutz Walter
- Primate Genetics Laboratory, German Primate Center, Göttingen, Germany.,DZHK (German Center for Cardiovascular Research), Partner site Göttingen, Göttingen, Germany
| | - Gabriele Multhoff
- Department of Radiation Oncology, Klinikum rechts der Isar, Technische Universität München (TUM), Munich, Germany.,Institute of Innovative Radiotherapy (iRT), Radiation Immune Biology, Department of Radiation Sciences (DRS), Helmholtz Zentrum München, Munich, Germany
| | - Ralf Dressel
- Institute of Cellular and Molecular Immunology, University Medical Center Göttingen, Humboldtallee 34, 37073, Göttingen, Germany. .,DZHK (German Center for Cardiovascular Research), Partner site Göttingen, Göttingen, Germany.
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MICA gene polymorphism in kidney allografts and possible impact of functionally relevant variants. Transplant Proc 2011; 42:4318-21. [PMID: 21168690 DOI: 10.1016/j.transproceed.2010.09.118] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
It is likely that the polymorphic MICA (MHC class I related chain A) molecules on graft endothelial cells (ECs) may be a target for specific antibodies and T cells directed against solid organ grafts. Although there is evidence for a role of MICA in vascular and transplant biology, genotyping is not performed routinely, and thus there are few correlations between polymorphism and endothelial phenotype. The present study examined the frequency of the various alleles for the nonclassical MHCI MICA gene among a cohort of kidney transplant donors, particularly MICA genetic variants (MICA A5.1 and MICA-129) that may affect MICA expression and function on graft EC. Genotyping was performed on genomic DNA derived from primary cultures of EC established from transplant donors at the time of transplantation. Herein we have reported that among 106 alleles analyzed, 28/69 MICA alleles were distributed among 7 major variants (*00804, *00801, *004, *00201, *00901*, *011, *010), representing 70% of the donors. MICA*008 the most abundant allele (31.1%) was associated with the MICA A5.1 mutation. The majority of donors (52.8%) had at least one MICA A5.l allele, with 13.2% homozygous for this mutation. The MICA-129 val/val genotype, which encodes a low-affinity ligand, was predominant (49%), while the MICA-129 met/met, corresponding to a high-affinity ligand, was observed in 11.3% of the transplants. Our findings highlighted the MICA gene polymorphism that produces functional diversity in transplant recipients with variable interactions between MICA and its receptor NKG2D.
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MICA polymorphism: biology and importance in immunity and disease. Trends Mol Med 2010; 16:97-106. [DOI: 10.1016/j.molmed.2010.01.002] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Revised: 12/17/2009] [Accepted: 01/08/2010] [Indexed: 11/22/2022]
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