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Vică ML, Dobreanu M, Curocichin G, Matei HV, Bâlici Ș, Vușcan ME, Chiorean AD, Nicula GZ, Pavel Mironescu DC, Leucuța DC, Teodoru CA, Siserman CV. The Influence of HLA Polymorphisms on the Severity of COVID-19 in the Romanian Population. Int J Mol Sci 2024; 25:1326. [PMID: 38279325 PMCID: PMC10816224 DOI: 10.3390/ijms25021326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/16/2024] [Accepted: 01/20/2024] [Indexed: 01/28/2024] Open
Abstract
In this study, we aimed to investigate whether specific HLA alleles found in patients from Romania and the Republic of Moldova were associated with the severity of COVID-19 infection and its associated mortality. We analyzed the HLA alleles at the -A, -B, -C, -DRB1, and -DQB1 loci in a cohort of 130 individuals with severe and extremely severe forms of COVID-19, including 44 individuals who died. We compared these findings to a control group consisting of individuals who had either not been diagnosed with COVID-19 or had experienced mild forms of the disease. Using multivariate logistic regression models, we discovered that the B*27 and B*50 alleles were associated with an increased susceptibility to developing a severe form of COVID-19. The A*33 and C*15 alleles showed potential for offering protection against the disease. Furthermore, we identified two protective alleles (A*03 and DQB1*02) against the development of extremely severe forms of COVID-19. By utilizing score statistics, we established a statistically significant association between haplotypes and disease severity (p = 0.021). In summary, this study provides evidence that HLA genotype plays a role in influencing the clinical outcome of COVID-19 infection.
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Affiliation(s)
- Mihaela Laura Vică
- Department of Cell and Molecular Biology, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania; (M.L.V.); (Ș.B.); (M.E.V.); (A.D.C.); (G.Z.N.); (D.C.P.M.)
- Legal Medicine Institute, 400006 Cluj-Napoca, Romania;
| | - Minodora Dobreanu
- Emergency Clinical County Hospital, 540136 Târgu Mureș, Romania;
- Department of Laboratory Medicine, “George Emil Palade” University of Medicine, Pharmacy, Science and Technology, 540142 Târgu Mureș, Romania
- Center for Advanced Medical and Pharmaceutical Research, “George Emil Palade” University of Medicine, Pharmacy, Science and Technology, 540142 Târgu Mureș, Romania
| | - Ghenadie Curocichin
- Department of Family Medicine, “Nicolae Testemițanu” State University of Medicine and Pharmacy, MD-2004 Chișinău, Moldova;
| | - Horea Vladi Matei
- Department of Cell and Molecular Biology, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania; (M.L.V.); (Ș.B.); (M.E.V.); (A.D.C.); (G.Z.N.); (D.C.P.M.)
- Legal Medicine Institute, 400006 Cluj-Napoca, Romania;
| | - Ștefana Bâlici
- Department of Cell and Molecular Biology, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania; (M.L.V.); (Ș.B.); (M.E.V.); (A.D.C.); (G.Z.N.); (D.C.P.M.)
| | - Mihaela Elvira Vușcan
- Department of Cell and Molecular Biology, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania; (M.L.V.); (Ș.B.); (M.E.V.); (A.D.C.); (G.Z.N.); (D.C.P.M.)
- Legal Medicine Institute, 400006 Cluj-Napoca, Romania;
| | - Alin Dan Chiorean
- Department of Cell and Molecular Biology, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania; (M.L.V.); (Ș.B.); (M.E.V.); (A.D.C.); (G.Z.N.); (D.C.P.M.)
- Emergency Clinical Hospital for Children, 400370 Cluj-Napoca, Romania
| | - Gheorghe Zsolt Nicula
- Department of Cell and Molecular Biology, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania; (M.L.V.); (Ș.B.); (M.E.V.); (A.D.C.); (G.Z.N.); (D.C.P.M.)
| | - Daniela Cristina Pavel Mironescu
- Department of Cell and Molecular Biology, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania; (M.L.V.); (Ș.B.); (M.E.V.); (A.D.C.); (G.Z.N.); (D.C.P.M.)
- Legal Medicine Institute, 400006 Cluj-Napoca, Romania;
| | - Daniel Corneliu Leucuța
- Department of Medical Informatics and Biostatistics, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania;
| | - Cosmin Adrian Teodoru
- Clinical Surgical Department, Faculty of Medicine, “Lucian Blaga” University of Sibiu, 550169 Sibiu, Romania;
| | - Costel Vasile Siserman
- Legal Medicine Institute, 400006 Cluj-Napoca, Romania;
- Department of Legal Medicine, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400006 Cluj-Napoca, Romania
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Montero-Martin G, Kichula KM, Misra MK, Vargas LB, Marin WM, Hollenbach JA, Fernández-Viña MA, Elfishawi S, Norman PJ. Exceptional diversity of KIR and HLA class I in Egypt. HLA 2024; 103:e15177. [PMID: 37528739 PMCID: PMC11068459 DOI: 10.1111/tan.15177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 05/25/2023] [Accepted: 07/14/2023] [Indexed: 08/03/2023]
Abstract
Genetically determined variation of killer cell immunoglobulin like receptors (KIR) and their HLA class I ligands affects multiple aspects of human health. Their extreme diversity is generated through complex interplay of natural selection for pathogen resistance and reproductive health, combined with demographic structure and dispersal. Despite significant importance to multiple health conditions of differential effect across populations, the nature and extent of immunogenetic diversity is under-studied for many geographic regions. Here, we describe the first high-resolution analysis of KIR and HLA class I combinatorial diversity in Northern Africa. Analysis of 125 healthy unrelated individuals from Cairo in Egypt yielded 186 KIR alleles arranged in 146 distinct centromeric and 79 distinct telomeric haplotypes. The most frequent haplotypes observed were KIR-A, encoding two inhibitory receptors specific for HLA-C, two that are specific for HLA-A and -B, and no activating receptors. Together with 141 alleles of HLA class I, 75 of which encode a KIR ligand, we identified a mean of six distinct interacting pairs of inhibitory KIR and HLA allotypes per individual. We additionally characterize 16 KIR alleles newly identified in the study population. Our findings place Egyptians as one of the most highly diverse populations worldwide, with important implications for transplant matching and studies of immune-mediated diseases.
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Affiliation(s)
| | - Katherine M. Kichula
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Maneesh K. Misra
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of Chicago Medicine, Chicago, IL, USA
| | - Luciana B. Vargas
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Wesley M. Marin
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Jill A. Hollenbach
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | | | - Sally Elfishawi
- BMT lab unit, Clinical Pathology Dept., National Cancer Institute, Cairo University, Cairo, Egypt
| | - Paul J. Norman
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA
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Prasad N, Yadav B, Prakash S, Yadav D, Singh A, Gautam S, Bhadauria D, Kaul A, Patel MR, Behera MR, Kushwaha RS, Yachha M. Association of Human Leucocyte Antigen Polymorphism with Coronavirus Disease 19 in Renal Transplant Recipients. Vaccines (Basel) 2022; 10:1840. [PMID: 36366349 PMCID: PMC9697220 DOI: 10.3390/vaccines10111840] [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: 08/22/2022] [Revised: 10/28/2022] [Accepted: 10/28/2022] [Indexed: 08/30/2023] Open
Abstract
Human leucocyte antigens (HLAs) are highly polymorphic glycoproteins expressed at the surface of all nucleated cells. It is required for the SARS-CoV-2 peptide antigen presentation to immune cells for their effector response. However, polymorphism in HLA significantly impacts the binding of SARS-CoV-2 antigenic peptide to the HLA pocket and regulates immune activation. In this study, 514 renal transplant recipients (RTRs) were recruited from the outpatient department and categorized either into symptomatic (n = 173) or asymptomatic groups (n = 341) based on Coronavirus disease-19 (COVID-19) symptoms. The anti-SARS-CoV-2 spike protein-specific IgG antibody titer was measured by chemiluminescent microparticle immune-assay methods in 310 RTRs. The HLA details of 514 patients were retrieved from the electronic medical records and analyzed retrospectively. We found that HLA antigen allele A*24 was significantly associated with asymptomatic infection in 22.78%, HLA C*02 in 4.51%, DRB1*12 in 10.85%, and HLA DQA1*02 in 27.74% of RTRs. Whereas HLA A*29 in 3.46%, A*33 in 26.01%, B*13 in 10.40%, DRB1*10 in 4.62%, DRB1*15 in 39.30%, DRB1*30 in 1.15%, and DQA1*60 in 3.57% of RTRs were associated with symptomatic infection. HLA DRB1*13 and DRB1*15 were associated with moderate to severe degrees of COVID-19 disease. The seroconversion rate in asymptomatic patients was 118/137 (86.13%), had a median titer of 647.80 au/ml, compared to symptomatic patients 148/173 (85.54%) with a median titer of 400.00 au/ml, which was not significant between the two groups (P = 0.88 and 0.13). In conclusion, HLA alleles A*24, C*02, DRB1*12, and DQA1*02 were significantly associated with asymptomatic infection, and A*29, A*33, B*13, DRB1*10, DRB*15, and DRB1*30 were significantly associated with symptomatic infection. HLA DRB1*13 and DRB1*15 were associated with moderate to severe degrees of COVID-19 disease.
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Affiliation(s)
- Narayan Prasad
- Department of Nephrology and Renal Transplantation, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow 226014, India
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Tao Y, Han X, Liu N, Shi L, Shi L, Liu S, Yao Y. Association study of TAP and HLA-I gene combination with chronic hepatitis C virus infection in a Han population in China. Int J Immunogenet 2022; 49:169-180. [PMID: 35485366 DOI: 10.1111/iji.12574] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 03/08/2022] [Accepted: 04/03/2022] [Indexed: 11/28/2022]
Abstract
Host immune system genes play key roles in the progression of chronic hepatitis C virus (HCV) infection. Transporters associated with antigen processing (TAP) play an important role in the loading of viral peptides onto MHC class I molecules. This study aimed to investigate the association between TAP gene polymorphisms and chronic HCV in a Chinese Han population. A total of 232 chronic hepatitis C (CHC) patients and 362 healthy individuals were recruited from the Han population in Yunnan province in southwest China, and a TaqMan SNP genotyping assay was used to detect six single nucleotide polymorphisms (SNPs) of TAP1 and three SNPs of TAP2 genes. The association of the TAP gene with CHC was analysed at the allele, genotype, and haplotype levels. There were no significant differences in the allele and genotype frequencies of these SNPs in the TAP gene between CHC patients and controls after Bonferroni correction. A novel TAP1 allele (TAP1*unknown_1: rs41555220-rs41549617-rs1057141-rs1135216-rs1057149-rs41551515: G-G-A-G-G-G) was only present in the CHC group, and this allele significantly increased susceptibility to CHC (p = .005, odds ratio [OR] = 11.105. 95% confidence interval [CI]: 1.362-90.558). Homozygous TAP1*03:01/TAP1*03:01 was observed only in the CHC group that exhibited an obvious risk for CHC (p = .002, OR = 9.637, 95% CI: 1.153-80.574). And the haplotype TAP1*unknown_1-TAP2*01:01 was only present in the CHC group and indicated a significant risk for CHC (p = .002, OR = 9.498, 95% CI: 1.140-79.149). We observed significant interactions among HLA-A, -B,C, TAP1, and TAP2 alleles, and combination analysis revealed that the combination of TAP1*01:01-TAP2*01:01-HLA-B*35:01 was only present in the control group (2.2%) and resulted in significantly increased resistance to CHC (p = .002, OR = 0.096, 95% CI: 0.012-0.759). Whereas, the combination of TAP1*01:01-TAP2*01:01-HLA-C*07:02 and TAP1*03:01-TAP2*01:01-HLA-C*01:02 increased the susceptibility to CHC significantly (p = .001, OR = 2.016, 95% CI: 1.309-3.106 and p = .002, OR = 8.070, 95% CI: 1.018-63.997, respectively). Our results indicated that TAP and HLA-I may exert a combined effect on CHC susceptibility in the Chinese Han population.
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Affiliation(s)
- Yufen Tao
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Disease, Kunming, China
| | - Xue Han
- Department of Immunogenetics, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
| | - Nannan Liu
- Department of Immunogenetics, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
| | - Lei Shi
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Disease, Kunming, China
| | - Li Shi
- Department of Immunogenetics, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
| | - Shuyuan Liu
- Department of Immunogenetics, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
| | - Yufeng Yao
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Disease, Kunming, China
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5
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Yadav B, Prasad N, Yadav D, Singh A, Gautam S, Kushwaha R, Patel M, Bhadauria D, Behera M, Yachha M, Kaul A. Human Leukocyte Antigen Association with anti-SARS-CoV-2 spike protein antibody seroconversion in renal allograft recipients - An observational study. INDIAN JOURNAL OF TRANSPLANTATION 2022. [DOI: 10.4103/ijot.ijot_28_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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6
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Lorente L, Martín MM, Franco A, Barrios Y, Cáceres JJ, Solé-Violán J, Perez A, Marcos Y Ramos JA, Ramos-Gómez L, Ojeda N, Jiménez A. HLA genetic polymorphisms and prognosis of patients with COVID-19. Med Intensiva 2021; 45:96-103. [PMID: 38620408 PMCID: PMC7474921 DOI: 10.1016/j.medin.2020.08.004] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/22/2020] [Accepted: 08/07/2020] [Indexed: 12/22/2022]
Abstract
Objective Different genetic polymorphisms of human leukocyte antigen (HLA) have been associated with the risk and prognosis of autoimmune and infectious diseases. The objectives of this study were to determine whether there is an association between HLA genetic polymorphisms and the susceptibility to and mortality of coronavirus disease 2019 (COVID-19) patients. Design Observational and prospective study. Setting Eight Intensive Care Units (ICU) from 6 hospitals of Canary Islands (Spain). Patients COVID-19 patients admitted in ICU and healthy subjects. Interventions Determination of HLA genetic polymorphisms. Main variable of interest Mortality at 30 days. Results A total of 3886 healthy controls and 72 COVID-19 patients (10 non-survivors and 62 survivor patients at 30 days) were included. We found a trend to a higher rate of the alleles HLA-A*32 (p = 0.004) in healthy controls than in COVID-19 patients, and of the alleles HLA-B*39 (p = 0.02) and HLA-C*16 (p = 0.02) in COVID-19 patients than in healthy controls; however, all these p-values were not significant after correction for multiple comparisons. Logistic regression analysis showed that the presence of certain alleles was associated with higher mortality, such as the allele HLA-A*11 after controlling for SOFA (OR = 7.693; 95% CI = 1.063-55.650; p = 0.04) or APACHE-II (OR = 11.858; 95% CI = 1.524-92.273; p = 0.02), the allele HLA-C*01 after controlling for SOFA (OR = 11.182; 95% CI = 1.053-118.700; p = 0.04) or APACHE-II (OR = 17.604; 95% CI = 1.629-190.211; p = 0.02), and the allele HLA-DQB1*04 after controlling for SOFA (OR = 9.963; 95% CI = 1.235-80.358; p = 0.03). Conclusions The new finding from our preliminary study of small sample size was that HLA genetic polymorphisms could be associated with COVID-19 mortality; however, studies with a larger sample size before definitive conclusions can be drawn.
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Affiliation(s)
- L Lorente
- Intensive Care Unit, Hospital Universitario de Canarias, Ofra, s/n., La Laguna 38320, Santa Cruz de Tenerife, Spain
| | - M M Martín
- Intensive Care Unit, Hospital Universitario Nuestra Señora de Candelaria, Crta del Rosario s/n., Santa Cruz de Tenerife 38010, Spain
| | - A Franco
- Immunology Unit of Laboratory Department, Hospital Universitario de Canarias, Ofra, s/n., La Laguna 38320, Santa Cruz de Tenerife, Spain
| | - Y Barrios
- Immunology Unit of Laboratory Department, Hospital Universitario de Canarias, Ofra, s/n., La Laguna 38320, Santa Cruz de Tenerife, Spain
| | - J J Cáceres
- Intensive Care Unit, Hospital Insular, Plaza Dr. Pasteur s/n., Las Palmas de Gran Canaria 35016, Spain
| | - J Solé-Violán
- Intensive Care Unit, Hospital Universitario Dr. Negrín, Barranco de la Ballena s/n., Las Palmas de Gran Canaria 35010, Spain
| | - A Perez
- Internal Intensive Care Unit, Hospital Universitario de Canarias, Ofra, s/n., La Laguna 38320, Santa Cruz de Tenerife, Spain
| | - J A Marcos Y Ramos
- Intensive Care Unit, Hospital Doctor José Molina Orosa, Ctra. Arrecife-Tinajo, km 1.300, Arrecife, Lanzarote 35550, Spain
| | - L Ramos-Gómez
- Intensive Care Unit, Hospital General La Palma, Buenavista de Arriba s/n, Breña Alta, La Palma 38713, Spain
| | - N Ojeda
- Department of Anesthesiology, Hospital Universitario Dr. Negrín, Barranco de la Ballena s/n., Las Palmas de Gran Canaria 35010, Spain
| | - A Jiménez
- Research Unit, Hospital Universitario de Canarias, Ofra, s/n., La Laguna 38320, Santa Cruz de Tenerife, Spain
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7
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Lorente L, Martín M, Franco A, Barrios Y, Cáceres J, Solé-Violán J, Perez A, Marcos y Ramos J, Ramos-Gómez L, Ojeda N, Jiménez A, Lorente L, Franco A, Barrios Y, Perez A, Jiménez A, Pérez-Cejas A, Pérez-Llombet A, Uribe L, González L, Alvarez R, Martín MM, Alcoba-Flórez J, Estupiñan A, Cáceres JJ, Vega P, Gonzalez L, Solé-Violán J, Ojeda N, López S, Rodríguez-Pérez A, Domínguez C, Marcos y Ramos JA, Zapata MF, Ramos-Gómez L, Ortiz-López R. HLA genetic polymorphisms and prognosis of patients with COVID-19. MEDICINA INTENSIVA (ENGLISH EDITION) 2021. [PMCID: PMC7905376 DOI: 10.1016/j.medine.2020.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Objective Different genetic polymorphisms of human leukocyte antigen (HLA) have been associated with the risk and prognosis of autoimmune and infectious diseases. The objectives of this study were to determine whether there is an association between HLA genetic polymorphisms and the susceptibility to and mortality of coronavirus disease 2019 (COVID-19) patients. Design Observational and prospective study. Setting Eight Intensive Care Units (ICU) from 6 hospitals of Canary Islands (Spain). Patients COVID-19 patients admitted in ICU and healthy subjects. Interventions Determination of HLA genetic polymorphisms. Main variable of interest Mortality at 30 days. Results A total of 3886 healthy controls and 72 COVID-19 patients (10 non-survivors and 62 survivor patients at 30 days) were included. We found a trend to a higher rate of the alleles HLA-A*32 (p = 0.004) in healthy controls than in COVID-19 patients, and of the alleles HLA-B*39 (p = 0.02) and HLA-C*16 (p = 0.02) in COVID-19 patients than in healthy controls; however, all these p-values were not significant after correction for multiple comparisons. Logistic regression analysis showed that the presence of certain alleles was associated with higher mortality, such as the allele HLA-A*11 after controlling for SOFA (OR = 7.693; 95% CI = 1.063–55.650; p = 0.04) or APACHE-II (OR = 11.858; 95% CI = 1.524–92.273; p = 0.02), the allele HLA-C*01 after controlling for SOFA (OR = 11.182; 95% CI = 1.053–118.700; p = 0.04) or APACHE-II (OR = 17.604; 95% CI = 1.629–190.211; p = 0.02), and the allele HLA-DQB1*04 after controlling for SOFA (OR = 9.963; 95% CI = 1.235–80.358; p = 0.03). Conclusions The new finding from our preliminary study of small sample size was that HLA genetic polymorphisms could be associated with COVID-19 mortality; however, studies with a larger sample size before definitive conclusions can be drawn.
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Askar M, Madbouly A, Zhrebker L, Willis A, Kennedy S, Padros K, Rodriguez MB, Bach C, Spriewald B, Ameen R, Shemmari SA, Tarassi K, Tsirogianni A, Hamdy N, Mossallam G, Hönger G, Spinnler R, Fischer G, Fae I, Charlton R, Dunk A, Vayntrub TA, Halagan M, Osoegawa K, Fernández-Viña M. HLA Haplotypes In 250 Families: The Baylor Laboratory Results And A Perspective On A Core NGS Testing Model For The 17 th International HLA And Immunogenetics Workshop. Hum Immunol 2019; 80:897-905. [PMID: 31558329 DOI: 10.1016/j.humimm.2019.07.298] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 07/24/2019] [Accepted: 07/25/2019] [Indexed: 01/05/2023]
Abstract
Since their inception, the International HLA & Immunogenetics Workshops (IHIW) served as a collaborative platform for exchange of specimens, reference materials, experiences and best practices. In this report we present a subset of the results of human leukocyte antigen (HLA) haplotypes in families tested by next generation sequencing (NGS) under the 17th IHIW. We characterized 961 haplotypes in 921 subjects belonging to 250 families from 8 countries (Argentina, Austria, Egypt, Jamaica, Germany, Greece, Kuwait, and Switzerland). These samples were tested in a single core laboratory in a high throughput fashion using 6 different reagents/software platforms. Families tested included patients evaluated clinically as transplant recipients (kidney and hematopoietic cell transplant) and their respective family members. We identified 486 HLA alleles at the following loci HLA-A, -B, -C, -DRB1, -DRB3, -DRB4, -DRB5, -DQA1, -DQB1, -DPA1, -DPB1 (77, 115, 68, 69, 10, 6, 4, 44, 31, 20 and 42 alleles, respectively). We also identified nine novel alleles with polymorphisms in coding regions. This approach of testing samples from multiple laboratories across the world in different stages of technology implementation in a single core laboratory may be useful for future international workshops. Although data presented may not be reflective of allele and haplotype frequencies in the countries to which the families belong, they represent an extensive collection of 3rd and 4th field resolution level 11-locus haplotype associations of 486 alleles identified in families from 8 countries.
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Affiliation(s)
- Medhat Askar
- Baylor University Medical Center, Dallas, TX, USA; Texas A&M Health Science Center College of Medicine, Bryan, TX, USA.
| | - Abeer Madbouly
- Bioinformatics Research, Center for International Blood and Marrow Transplant Research, Minneapolis, MN, USA
| | | | | | | | - Karin Padros
- Primer Centro Argentino de Immunogenetica (PRICAI), Fundacion Favaloro, CABA, Argentina
| | | | - Christian Bach
- Departments of Internal Medicine & Hematology and Oncology, Friedrich-Alexander-University Erlangen-Nürnberg, Germany
| | - Bernd Spriewald
- Departments of Internal Medicine & Hematology and Oncology, Friedrich-Alexander-University Erlangen-Nürnberg, Germany
| | - Reem Ameen
- Health Sciences Center, Kuwait University, Jabriya, Kuwait
| | | | | | | | - Nayera Hamdy
- National Cancer Institute, Cairo University, Cairo, Egypt
| | | | - Gideon Hönger
- Transplantation Immunology, Department of Biomedicine, University Hospital Basel, Basel, Switzerland; HLA-Diagnostics and Immunogenetics, Department of Laboratory Medicine, University Hospital Basel, Basel, Switzerland
| | - Regina Spinnler
- HLA-Diagnostics and Immunogenetics, Department of Laboratory Medicine, University Hospital Basel, Basel, Switzerland
| | | | - Ingrid Fae
- Medical University of Vienna, Vienna, Austria
| | - Ronald Charlton
- Caribbean Bone Marrow Registry, Plantation, FL, USA; Laboratory Consultants of Florida, Jacksonville, FL, USA
| | - Arthur Dunk
- Caribbean Bone Marrow Registry, Plantation, FL, USA
| | | | - Michael Halagan
- Bioinformatics Research, Center for International Blood and Marrow Transplant Research, Minneapolis, MN, USA
| | | | - Marcelo Fernández-Viña
- Stanford Blood Center, Palo Alto, CA, USA; Stanford University School of Medicine, Palo Alto, CA, USA
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Lima THA, Souza AS, Porto IOP, Paz MA, Veiga-Castelli LC, Oliveira MLG, Donadi EA, Meyer D, Sabbagh A, Mendes-Junior CT, Castelli EC. HLA-A promoter, coding, and 3'UTR sequences in a Brazilian cohort, and their evolutionary aspects. HLA 2019; 93:65-79. [PMID: 30666817 DOI: 10.1111/tan.13474] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 01/10/2019] [Accepted: 01/18/2019] [Indexed: 12/17/2022]
Abstract
HLA-A is the second most polymorphic locus of the human leucocyte antigen (HLA) complex encoding a key molecule for antigen presentation and NK cell modulation. Many studies have evaluated HLA-A variability in worldwide populations, focusing mainly on exons, but the regulatory segments have been poorly characterized. HLA-A variability is particularly high in the segment encoding the peptide-binding groove (exons 2 and 3), which is related to the antigen presentation function and the balancing selection in these segments. Here we evaluate the genetic diversity of the HLA-A gene considering a continuous segment encompassing the extended promoter (1.5 kb upstream of the first translated ATG), all exons and introns, and the entire 3' untranslated region, by using massively parallel sequencing. To achieve this goal, we used a freely available bioinformatics workflow that optimizes read mapping for HLA genes and defines complete sequences using either the phase among variable sites directly observed in sequencing data and probabilistic models. The HLA-A variability detected in a highly admixed population sample from Brazil shows that the HLA-A regulatory segments present few, but divergent sequences. The regulatory segments are in close association with the coding alleles. Both exons and introns are highly variable. Moreover, patterns of molecular diversity suggest that the promoter, in addition to the coding region, might be under the same selective pressure, but a different scenario arises when it comes to exon 4 and the 3'UTR segment.
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Affiliation(s)
- Thálitta H A Lima
- Molecular Genetics and Bioinformatics Laboratory - Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil.,São Paulo State University (UNESP), Genetics Program, Institute of Biosciences of Botucatu, Botucatu, Brazil
| | - Andreia S Souza
- Molecular Genetics and Bioinformatics Laboratory - Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil.,São Paulo State University (UNESP), Genetics Program, Institute of Biosciences of Botucatu, Botucatu, Brazil
| | - Iane O P Porto
- Molecular Genetics and Bioinformatics Laboratory - Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil.,Pathology Program, School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
| | - Michelle A Paz
- Molecular Genetics and Bioinformatics Laboratory - Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil.,Pathology Program, School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
| | - Luciana C Veiga-Castelli
- Department of Genetics, School of Medicine of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, Brazil
| | - Maria Luiza G Oliveira
- Department of Genetics, School of Medicine of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, Brazil
| | - Eduardo A Donadi
- Department of Medicine, School of Medicine of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, Brazil
| | - Diogo Meyer
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, Brazil
| | - Audrey Sabbagh
- UMR 216 MERIT, IRD, Université Paris Descartes, Faculté de Pharmacie, Paris, France
| | - Celso T Mendes-Junior
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Erick C Castelli
- Molecular Genetics and Bioinformatics Laboratory - Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil.,São Paulo State University (UNESP), Genetics Program, Institute of Biosciences of Botucatu, Botucatu, Brazil.,Pathology Program, School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
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10
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Luxenburger H, Graß F, Baermann J, Boettler T, Marget M, Emmerich F, Panning M, Thimme R, Nitschke K, Neumann-Haefelin C. Differential virus-specific CD8 + T-cell epitope repertoire in hepatitis C virus genotype 1 versus 4. J Viral Hepat 2018; 25:779-790. [PMID: 29397015 DOI: 10.1111/jvh.12874] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 01/05/2018] [Indexed: 01/06/2023]
Abstract
Virus-specific CD8+ T-cell responses play an important role in the outcome of hepatitis C virus (HCV) infection. To date, most HCV-specific CD8+ T-cell epitopes have been defined in HCV genotype 1 infection. In contrast, the HCV genotype 4-specific CD8+ T-cell response is poorly defined. Here, we analysed whether known HCV-specific CD8+ T-cell epitopes are also recognized in HCV genotype 4-infected patients and set out to identify the first HCV genotype 4-specific CD8+ T-cell epitopes. We studied patients chronically infected with HCV genotype 1 (n = 20) or 4 (n = 21) using 91 well-described HCV-specific epitope peptides. In addition, we analysed 24 genotype 4-infected patients using 40 epitope candidates predicted using an in silico approach. HCV-specific CD8+ T-cell responses targeting previously described epitopes were detectable in the majority of genotype 1-infected patients (11 of 20). In contrast, patients infected with HCV genotype 4 rarely targeted these epitopes (4 of 21; P = .0247). Importantly, we were able to identify eight novel HCV genotype 4-specific CD8+ T-cell epitopes. Only one of these epitopes was shared between genotype 1 and genotype 4. These results indicate that there is little overlap between CD8+ T-cell repertoires targeting HCV genotype 1 and 4. Prophylactic vaccination studies based on HCV genotype 1 are currently underway. However, in countries with the highest prevalence of HCV infection, such as Egypt, most patients are infected with HCV genotype 4. Thus, prophylactic vaccination strategies need to be adapted to HCV genotype 4 before their application to regions where HCV genotype 4 is endemic.
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Affiliation(s)
- Hendrik Luxenburger
- Faculty of Medicine, Department of Medicine II, University Hospital Freiburg, University of Freiburg, Freiburg, Germany
| | - Franziska Graß
- Faculty of Medicine, Department of Medicine II, University Hospital Freiburg, University of Freiburg, Freiburg, Germany
| | - Janina Baermann
- Faculty of Medicine, Department of Medicine II, University Hospital Freiburg, University of Freiburg, Freiburg, Germany
| | - Tobias Boettler
- Faculty of Medicine, Department of Medicine II, University Hospital Freiburg, University of Freiburg, Freiburg, Germany
| | - Matthias Marget
- Institute of Transfusion Medicine, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Florian Emmerich
- Faculty of Medicine, Institute for Cell and Gene Therapy, University Hospital Freiburg, University of Freiburg, Freiburg, Germany
| | - Marcus Panning
- Faculty of Medicine, Institute of Virology, University Hospital Freiburg, University of Freiburg, Freiburg, Germany
| | - Robert Thimme
- Faculty of Medicine, Department of Medicine II, University Hospital Freiburg, University of Freiburg, Freiburg, Germany
| | - Katja Nitschke
- Faculty of Medicine, Department of Medicine II, University Hospital Freiburg, University of Freiburg, Freiburg, Germany
| | - Christoph Neumann-Haefelin
- Faculty of Medicine, Department of Medicine II, University Hospital Freiburg, University of Freiburg, Freiburg, Germany
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11
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Crux NB, Elahi S. Human Leukocyte Antigen (HLA) and Immune Regulation: How Do Classical and Non-Classical HLA Alleles Modulate Immune Response to Human Immunodeficiency Virus and Hepatitis C Virus Infections? Front Immunol 2017; 8:832. [PMID: 28769934 PMCID: PMC5513977 DOI: 10.3389/fimmu.2017.00832] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 06/30/2017] [Indexed: 12/13/2022] Open
Abstract
The genetic factors associated with susceptibility or resistance to viral infections are likely to involve a sophisticated array of immune response. These genetic elements may modulate other biological factors that account for significant influence on the gene expression and/or protein function in the host. Among them, the role of the major histocompatibility complex in viral pathogenesis in particular human immunodeficiency virus (HIV) and hepatitis C virus (HCV), is very well documented. We, recently, added a novel insight into the field by identifying the molecular mechanism associated with the protective role of human leukocyte antigen (HLA)-B27/B57 CD8+ T cells in the context of HIV-1 infection and why these alleles act as a double-edged sword protecting against viral infections but predisposing the host to autoimmune diseases. The focus of this review will be reexamining the role of classical and non-classical HLA alleles, including class Ia (HLA-A, -B, -C), class Ib (HLA-E, -F, -G, -H), and class II (HLA-DR, -DQ, -DM, and -DP) in immune regulation and viral pathogenesis (e.g., HIV and HCV). To our knowledge, this is the very first review of its kind to comprehensively analyze the role of these molecules in immune regulation associated with chronic viral infections.
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Affiliation(s)
- Nicole B Crux
- Faculty of Medicine and Dentistry, Department of Dentistry, University of Alberta, Edmonton, AB, Canada.,Faculty of Medicine and Dentistry, Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada
| | - Shokrollah Elahi
- Faculty of Medicine and Dentistry, Department of Dentistry, University of Alberta, Edmonton, AB, Canada.,Faculty of Medicine and Dentistry, Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada
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12
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Mosaad YM. Clinical Role of Human Leukocyte Antigen in Health and Disease. Scand J Immunol 2015; 82:283-306. [PMID: 26099424 DOI: 10.1111/sji.12329] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 06/02/2015] [Accepted: 06/12/2015] [Indexed: 12/19/2022]
Abstract
Most of the genes in the major histocompatibility complex (MHC) region express high polymorphism that is fundamental for their function. The most important function of human leukocyte antigen (HLA) molecule is in the induction, regulation of immune responses and the selection of the T cell repertoire. A clinician's attention is normally drawn to a system only when it malfunctions. The HLA system is no exception in this regard, but in contrast to other systems, it also arouses interest when it functions well - too well, in fact. Population studies carried out over the last several decades have identified a long list of human diseases that are significantly more common among individuals that carry particular HLA alleles including inflammatory, autoimmune and malignant disorders. HLA-disease association is the name of this phenomenon, and the mechanism underlying is still a subject of hot debate. Social behaviours are affected by HLA genes and preference for HLA disparate mates may provide 'good genes' for an individual's offspring. Also, certain HLA genes may be associated with shorter life and others with longer lifespan, but the effects depend both on the genetic background and on the environmental conditions. The following is a general overview of the important functional aspects of HLA in health and diseases.
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Affiliation(s)
- Y M Mosaad
- Clinical Immunology Unit, Clinical Pathology Department & Mansoura Research Center for Cord Stem Cell (MARC_CSC), Mansoura Faculty of Medicine, Mansoura University, Mansoura, Egypt
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13
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Hussein N, Zekri ARN, Abouelhoda M, Alam El-Din HM, Ghamry AA, Amer MA, Sherif GM, Bahnassy AA. New insight into HCV E1/E2 region of genotype 4a. Virol J 2014; 11:231. [PMID: 25547228 PMCID: PMC4304183 DOI: 10.1186/s12985-014-0231-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 12/17/2014] [Indexed: 01/21/2023] Open
Abstract
Introduction Hepatitis C virus (HCV) genome contains two envelope proteins (E1 and E2) responsible for the virus entry into the cell. There is a substantial lack of sequences covering the full length of E1/E2 region for genotype 4. Our study aims at providing new sequences as well as characterizing the genetic divergence of the E1/E2 region of HCV 4a using our new sequences along with all publicly available datasets. Methods The genomic segments covering the whole E1/E2 region were isolated from Egyptian HCV patients and sequenced. The resulting 36 sequences 36 were analyzed using sequence analysis techniques to study variability within and among hosts in the same time point. Furthermore, previously published HCV E1/E2 sequence datasets for genotype 4a were retrieved and categorized according to the geographical location and date of isolation and were used for further analysis of variability among Egyptian over a period of 15 years, also compared with non-Egyptian sequences to figure out region-specific variability. Results Phylogenetic analysis of the new sequences has shown variability within the host and among different individuals in the same time point. Analysis of the 36 sequences along with the Egyptian sequences (254 sequences in E1 in the period from 1997 to 2010 and 8 E2 sequences in the period from 2006 to 2010) has shown temporal change over time. Analysis of the new HCV sequences with the non-Egyptian sequences (182 sequences in E1 and 155 sequences in the E2) has shown region specific variability. The molecular clock rate of E1 was estimated to be 5E-3 per site per year for Egyptian and 5.38E-3 for non-Egyptian. The clock rate of E2 was estimated to be 8.48E per site per year for Egyptian and 6.3E-3 for non-Egyptian. Conclusion The results of this study support the high rate of evolution of the Egyptian HCV genotype 4a. It has also revealed significant level of genetic variability among sequences from different regions in the world. Electronic supplementary material The online version of this article (doi:10.1186/s12985-014-0231-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nehal Hussein
- Virology and Immunology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Fom El-Khalig, Cairo, 11796, Egypt.
| | - Abdel-Rahman N Zekri
- Virology and Immunology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Fom El-Khalig, Cairo, 11796, Egypt.
| | - Mohamed Abouelhoda
- Faculty of Engineering, Cairo University, Giza, Egypt. .,Center for Informatics Sciences, Nile University, Giza, Egypt.
| | - Hanaa M Alam El-Din
- Virology and Immunology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Fom El-Khalig, Cairo, 11796, Egypt.
| | | | - Mahmoud A Amer
- Faculty of Science, Zoology Department, Cairo University, Giza, Egypt.
| | - Ghada M Sherif
- Biostatistic & Epidemiology Department, National Cancer Institute, Cairo University, Cairo, Egypt.
| | - Abeer A Bahnassy
- Pathology Department, National Cancer Institute, Cairo University, Cairo, Egypt.
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14
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Derbala M, Chandra P, Amer A, John A, Sharma M, Amin A, Thandassery RB, Faris A. Reexamination of the relationship between the prevalence of hepatitis C virus and parenteral antischistosomal therapy among Egyptians resident in Qatar. Clin Exp Gastroenterol 2014; 7:427-33. [PMID: 25395869 PMCID: PMC4224023 DOI: 10.2147/ceg.s65369] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Egypt has the highest prevalence of recorded hepatitis C virus (HCV) worldwide, estimated nationally at 14.7%, which is attributed to extensive iatrogenic transmission during the era of parenteral antischistosomal therapy (PAT) mass-treatment campaigns. The objective of our study was to attempt to highlight to what extent HCV transmission is ongoing and discuss the possible risk factors. We studied the prevalence of HCV among 7.8% of Egyptians resident in Qatar in relation to age, socioeconomic status, and PAT and discuss the possible risk factors. HCV testing was conducted in 2,335 participants, and results were positive for 13.5%, and 8.5% for those aged below 35 years. The prevalence of HCV in the PAT-positive population was 23.7% (123 of 518, 95% confidence interval [CI] 20.2%–27.6%) compared with 11.2% in the PAT-negative group. Significantly higher HCV prevalence occurred in participants who were older than 50 years (23%, 95% CI 19.3%–27.1%) compared to those aged 45–50 years (19.3%, 95% CI 15.2%–23.8%), 35–45 years (11.1%, 95% CI 8.9%–13.7%), and less than 35 years (8.5%, 95% CI 6.8%–10.4%) (P<0.0001). Insignificant higher prevalence occurred in the low socioeconomic group (14.2%, 95% CI 11.3%–17.4%). Logistic regression analysis revealed that increasing age, history of PAT, bilharziasis, and praziquantel were common risk factors, but there was no relation with dental care. Host genetic predisposition seems to be a plausible underlying factor for susceptibility among Egyptians and intense ongoing infection.
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Affiliation(s)
- Moutaz Derbala
- Gastroenterology and Hepatology Department, Hamad Hospital, Doha, Qatar ; Medical Department, Weill Cornell Medical College, Qatar Branch, Doha, Qatar
| | - Prem Chandra
- Medical Research Center, Hamad Medical Corporation, Doha, Qatar
| | - Aliaa Amer
- Laboratory Medicine and Pathology Department, Hamad Hospital, Doha, Qatar
| | - Anil John
- Gastroenterology and Hepatology Department, Hamad Hospital, Doha, Qatar
| | - Manik Sharma
- Gastroenterology and Hepatology Department, Hamad Hospital, Doha, Qatar
| | - Ashraf Amin
- Gastroenterology and Hepatology Department, Hamad Hospital, Doha, Qatar
| | | | - Amr Faris
- Cardiovascular Surgery Department, Hamad Hospital, Doha, Qatar
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15
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Gomaa H, Mahmoud M, Saad N, Saad-Hussein A, Thabet E, Farouk H, Kandil D, Heiba A, Hafez W, Ismail S. Impact of HLA-class I alleles on response to HCV treatment in a cohort of Egyptian patients. J Genet Eng Biotechnol 2014. [DOI: 10.1016/j.jgeb.2014.03.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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16
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Association between human leukocyte antigen class I and II alleles and hepatitis C virus infection in high-risk hemodialysis patients awaiting kidney transplantation. Hum Immunol 2013; 74:1629-32. [PMID: 23974050 DOI: 10.1016/j.humimm.2013.08.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 07/29/2013] [Accepted: 08/10/2013] [Indexed: 02/06/2023]
Abstract
Recent evidences have shown that several host genetic factors influence susceptibility or protection to hepatitis C virus (HCV) infection. There are controversial data regarding the associations of human leukocyte antigens (HLA) and the clearance or progression of HCV. The aim of this study was to investigate whether particular HLA molecules were associated with HCV infection in recipients awaiting kidney transplantation considered at high-risk to infection due to protracted hemodialysis treatment. To this purpose, 301 kidney recipients with HCV infection and 1103 uninfected recipients were examined for HLA class I and II molecules. In our case-control study, HLA-A(*)26 is positively associated with HCV infection while HLA-A(*)29, -B(*)40 and -DRB1(*)01 are negatively associated with HCV infection. Multiple logistic regression analysis demonstrated that age (OR = 1.02; 95% CI = 1.01-1.04; p < 0.00), HLA-A(*)26, -A(*)29, -B(*)40 and -DRB1(*)01 [(OR = 1.54; 95% CI = 1.03-2.30; p = 0.03); (OR = 0.50; 95% CI = 0.26-0.99; p = 0.05); (OR = 0.42; 95% CI = 0.23-0, 7; p = 0.01); (OR = 0.62; 95% CI = 0.41-0, 94; p = 0.03); respectively] are independent predictors of HCV infection. Our results suggest that particular HLA molecules, as host genetic factors, may have a relationship with susceptibility or protection to HCV infection also in recipients awaiting kidney transplantation.
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Urabe Y, Ochi H, Kato N, Kumar V, Takahashi A, Muroyama R, Hosono N, Otsuka M, Tateishi R, Lo PHY, Tanikawa C, Omata M, Koike K, Miki D, Abe H, Kamatani N, Toyota J, Kumada H, Kubo M, Chayama K, Nakamura Y, Matsuda K. A genome-wide association study of HCV-induced liver cirrhosis in the Japanese population identifies novel susceptibility loci at the MHC region. J Hepatol 2013; 58:875-82. [PMID: 23321320 DOI: 10.1016/j.jhep.2012.12.024] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2012] [Revised: 12/15/2012] [Accepted: 12/24/2012] [Indexed: 12/21/2022]
Abstract
BACKGROUND & AIMS We performed a genome-wide association study (GWAS) of hepatitis C virus (HCV)-induced liver cirrhosis (LC) to identify predictive biomarkers for the risk of LC in patients with chronic hepatitis C (CHC). METHODS A total of 682 HCV-induced LC cases and 1045 CHC patients of Japanese origin were genotyped by Illumina Human Hap 610-Quad bead Chip. RESULTS Eight SNPs which showed possible associations (p<1.0 × 10(-5)) at the GWAS stage were further genotyped using 936 LC cases and 3809 CHC patients. We found that two SNPs within the major histocompatibility complex (MHC) region on chromosome 6p21, rs910049 and rs3135363, were significantly associated with the progression from CHC to LC (pcombined=9.15 × 10(-11) and 1.45 × 10(-10), odds ratio (OR)=1.46 and 1.37, respectively). We also found that HLA-DQA1(*)0601 and HLA-DRB1(*)0405 were associated with the progression from CHC to LC (p=4.53 × 10(-4) and 1.54 × 10(-4) with OR=2.80 and 1.45, respectively). Multiple logistic regression analysis revealed that rs3135363, rs910049, and HLA-DQA1(*)0601 were independently associated with the risk of HCV-induced LC. In addition, individuals with four or more risk alleles for these three loci have a 2.83-fold higher risk for LC than those with no risk allele, indicating the cumulative effects of these variations. CONCLUSIONS Our findings elucidated the crucial roles of multiple genetic variations within the MHC region as prognostic/predictive biomarkers for CHC patients.
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Affiliation(s)
- Yuji Urabe
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
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Schmidt J, Thimme R, Neumann-Haefelin C. Host genetics in immune-mediated hepatitis C virus clearance. Biomark Med 2011; 5:155-69. [PMID: 21473719 DOI: 10.2217/bmm.11.19] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Upon infection with hepatitis C virus (HCV), only few patients spontaneously clear the virus, while most patients develop chronic HCV infection. The host innate and adaptive immune response is believed to be the key determinant of viral clearance or persistence. Several host factors have been demonstrated to influence the efficiency of the antiviral immune response, including IL-28B polymorphisms, inhibitory natural killer cell receptors, as well as HLA class I and II alleles presenting viral antigens to CD8(+) and CD4(+) T cells. The understanding of the respective mechanisms is essential for the development of successful vaccination strategies against HCV.
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Affiliation(s)
- Julia Schmidt
- Department of Medicine II, University of Freiburg, Hugstetter Strasse 55, 79106 Freiburg, Germany
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