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Qian J, Chen Y, Yang X, Wang Q, Zhao J, Deng X, Ding Y, Li S, Liu Y, Tian Z, Shen J, Liao Q, Wang Y, Zuo X, Zhang X, Li M, Cui Y, Yu X, Zeng X. Association Study Identified HLA-DQA1 as a Novel Genetic Risk of Systemic Lupus Erythematosus-Associated Pulmonary Arterial Hypertension. Arthritis Rheumatol 2023; 75:2207-2215. [PMID: 37382296 DOI: 10.1002/art.42641] [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: 01/09/2023] [Revised: 05/19/2023] [Accepted: 06/27/2023] [Indexed: 06/30/2023]
Abstract
OBJECTIVE Pulmonary arterial hypertension (PAH) is a severe complication of systemic lupus erythematosus (SLE). However, the genetic signatures of SLE-associated PAH have not been well studied. We aimed to identify genetic variants implicated in SLE-associated PAH susceptibility within the major histocompatibility complex (MHC) region and assess the contribution to clinical outcomes. METHODS A total of 172 patients with SLE-associated PAH confirmed by right heart catheterization, 1,303 patients with SLE without PAH, and 9,906 healthy controls were included. Deep sequencing of the MHC region was performed to identify alleles, single-nucleotide polymorphisms, and amino acids. We compared patients with SLE-associated PAH with patients with SLE without PAH and healthy controls. Clinical association study was conducted to explore the contribution to phenotypes. RESULTS A total of 19,881 genetic variants were identified within the MHC region. HLA-DQA1*03:02 was identified as a novel genetic variant associated with SLE-associated PAH in the discovery cohort (P = 5.68 × 10-12 ) and authenticated in an independent replication cohort (P = 1.30 × 10-9 ). The strongest associated amino acid position was mapped to HLA-DQα1 in the region affecting MHC/peptide-CD4+ T cell receptor affinity and antigen binding. Clinical association study demonstrated that patients with SLE-associated PAH with HLA-DQA1*03:02 had significantly lower rates of target role achievement (P = 0.005) and survival (P = 0.04). CONCLUSION This study, based on the largest cohort of SLE-associated PAH, is the first to investigate how MHC region genetic variants contribute to SLE-associated PAH susceptibility. HLA-DQA1*03:02 is a novel genetic risk factor and a prognostic factor in SLE-associated PAH. Patients with SLE with this allele require regular monitoring and careful follow-up for early diagnosis and interventions for potential PAH.
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Affiliation(s)
- Junyan Qian
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases, Ministry of Science and Technology, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education and State Key Laboratory of Complex Severe and Rare Diseases, Ministry of Science and Technology, Beijing, China
| | | | - Xinzhuang Yang
- Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qian Wang
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases, Ministry of Science and Technology, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education and State Key Laboratory of Complex Severe and Rare Diseases, Ministry of Science and Technology, Beijing, China
| | - Jiuliang Zhao
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases, Ministry of Science and Technology, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education and State Key Laboratory of Complex Severe and Rare Diseases, Ministry of Science and Technology, Beijing, China
| | - Xiaoyue Deng
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases, Ministry of Science and Technology, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education and State Key Laboratory of Complex Severe and Rare Diseases, Ministry of Science and Technology, Beijing, China
| | - Yufang Ding
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases, Ministry of Science and Technology, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education and State Key Laboratory of Complex Severe and Rare Diseases, Ministry of Science and Technology, Beijing, China
| | - Shengjie Li
- Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yongtai Liu
- Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - Zhuang Tian
- Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | | | | | - Yanhong Wang
- Department of Epidemiology and Bio-Statistics, Institute of Basic Medical Sciences, China Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xianbo Zuo
- Department of Dermatology, China-Japan Friendship Hospital, Beijing, China
| | - Xuejun Zhang
- Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China
| | - Mengtao Li
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases, Ministry of Science and Technology, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education and State Key Laboratory of Complex Severe and Rare Diseases, Ministry of Science and Technology, Beijing, China
| | - Yong Cui
- Department of Dermatology, China-Japan Friendship Hospital, Beijing, China
| | - Xueqing Yu
- Division of Nephrology, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Xiaofeng Zeng
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases, Ministry of Science and Technology, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education and State Key Laboratory of Complex Severe and Rare Diseases, Ministry of Science and Technology, Beijing, China
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Lee YH, Hyun YS, Jo HA, Baek IC, Kim SM, Sohn HJ, Kim TG. Comprehensive analysis of mycobacterium tuberculosis antigen-specific CD4+ T cell responses restricted by single HLA class II allotype in an individual. Front Immunol 2022; 13:897781. [PMID: 35967347 PMCID: PMC9366214 DOI: 10.3389/fimmu.2022.897781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/28/2022] [Indexed: 11/13/2022] Open
Abstract
Mycobacterium tuberculosis infection is generally asymptomatic as latent tuberculosis, but it is still known as the world’s leading bacterial cause of death. The diagnosis of latent tuberculosis infection relies on the evidence of cellular immunity to mycobacterial antigens. Since the association between HLA class II and tuberculosis infection has been reported in several population groups, a detailed study on the CD4+ T cell response to major tuberculosis antigens is needed. To elucidate which HLA class II allotypes in an individual are preferentially used in tuberculosis, CD4+ T cells specific to TB10.4, Ag85b, ESAT-6, and CFP-10 of Mycobacterium tuberculosis antigens were analyzed comprehensively. A total of 33 healthy donors were analyzed by ex vivo and cultured ELISPOT using panels of artificial antigen-presenting cells expressing a single HLA class II allotype. The CD4+ T cell responses were increased by an average of 39-fold in cultured ELISPOT compared with ex vivo ELISPOT. In ex vivo and cultured ELISPOT, CD4+ T cell responses showed significantly higher by HLA-DR than those of HLA-DQ and HLA-DP locus. In cultured ELISPOT, 9 HLA-DR allotypes, 4 HLA-DQ allotypes, and 3 HLA-DP allotypes showed positive CD4+ T cell responses. Among ten donors with positive CD4+ T cell responses when tested for mixed Mycobacterium tuberculosis antigens, seven donors were positive for only a single allotype, and three were positive for two allotypes in an individual. However, only one allotype was used for a single antigen-specific response when a single tuberculosis antigen was used individually. These results on the distribution of HLA class II allotypes showing high CD4+ T-cell responses to Mycobacterium tuberculosis antigens and the intra-individual allotype dominance will provide valuable information for understanding the immunobiology and immunogenetics of tuberculosis, which can contribute to the development of more effective vaccines.
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Affiliation(s)
- Yong-Hun Lee
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, South Korea
- Department of Biomedicine and Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - You-Seok Hyun
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, South Korea
- Department of Biomedicine and Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Hyeong-A Jo
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, South Korea
- Department of Biomedicine and Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - In-Cheol Baek
- Catholic Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Sun-Mi Kim
- Catholic Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Hyun-Jung Sohn
- Catholic Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Tai-Gyu Kim
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, South Korea
- Department of Biomedicine and Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, South Korea
- Catholic Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, South Korea
- *Correspondence: Tai-Gyu Kim,
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Tshabalala M, Mellet J, Vather K, Nelson D, Mohamed F, Christoffels A, Pepper MS. High Resolution HLA ∼A, ∼B, ∼C, ∼DRB1, ∼DQA1, and ∼DQB1 Diversity in South African Populations. Front Genet 2022; 13:711944. [PMID: 35309124 PMCID: PMC8931603 DOI: 10.3389/fgene.2022.711944] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 01/17/2022] [Indexed: 01/10/2023] Open
Abstract
Background: Lack of HLA data in southern African populations hampers disease association studies and our understanding of genetic diversity in these populations. We aimed to determine HLA diversity in South African populations using high resolution HLA ∼A, ∼B, ∼C, ∼DRB1, ∼DQA1 and ∼DQB1 data, from 3005 previously typed individuals. Methods: We determined allele and haplotype frequencies, deviations from Hardy-Weinberg equilibrium (HWE), linkage disequilibrium (LD) and neutrality test. South African HLA class I data was additionally compared to other global populations using non-metrical multidimensional scaling (NMDS), genetic distances and principal component analysis (PCA). Results: All loci strongly (p < 0.0001) deviated from HWE, coupled with excessive heterozygosity in most loci. Two of the three most frequent alleles, HLA ∼DQA1*05:02 (0.2584) and HLA ∼C*17:01 (0.1488) were previously reported in South African populations at lower frequencies. NMDS showed genetic distinctness of South African populations. Phylogenetic analysis and PCA clustered our current dataset with previous South African studies. Additionally, South Africans seem to be related to other sub-Saharan populations using HLA class I allele frequencies. Discussion and Conclusion: Despite the retrospective nature of the study, data missingness, the imbalance of sample sizes for each locus and haplotype pairs, and induced methodological difficulties, this study provides a unique and large HLA dataset of South Africans, which might be a useful resource to support anthropological studies, disease association studies, population based vaccine development and donor recruitment programs. We additionally provide simulated high resolution HLA class I data to augment the mixed resolution typing results generated from this study.
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Affiliation(s)
- Mqondisi Tshabalala
- Department of Immunology, Institute for Cellular and Molecular Medicine, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
- South African Medical Research Council (SAMRC) Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Juanita Mellet
- Department of Immunology, Institute for Cellular and Molecular Medicine, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
- South African Medical Research Council (SAMRC) Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Kuben Vather
- South African National Blood Service (SANBS), Roodepoort, South Africa
| | - Derrick Nelson
- South African National Blood Service (SANBS), Roodepoort, South Africa
| | - Fathima Mohamed
- South African National Blood Service (SANBS), Roodepoort, South Africa
| | - Alan Christoffels
- SAMRC Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
| | - Michael S. Pepper
- Department of Immunology, Institute for Cellular and Molecular Medicine, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
- South African Medical Research Council (SAMRC) Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
- *Correspondence: Michael S. Pepper,
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Chhibber A, Huang L, Zhang H, Xu J, Cristescu R, Liu X, Mehrotra DV, Shen J, Shaw PM, Hellmann MD, Snyder A. Germline HLA landscape does not predict efficacy of pembrolizumab monotherapy across solid tumor types. Immunity 2022; 55:56-64.e4. [PMID: 34986342 DOI: 10.1016/j.immuni.2021.12.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 10/21/2021] [Accepted: 12/08/2021] [Indexed: 12/14/2022]
Abstract
We evaluated the impact of class I and class II human leukocyte antigen (HLA) genotypes, heterozygosity, and diversity on the efficacy of pembrolizumab. Seventeen pembrolizumab clinical trials across eight tumor types and one basket trial in patients with advanced solid tumors were included (n > 3,500 analyzed). Germline DNA was genotyped using a custom genotyping array. HLA diversity (measured by heterozygosity and evolutionary divergence) across class I loci was not associated with improved response to pembrolizumab, either within each tumor type evaluated or across all patients. Similarly, HLA heterozygosity at each class I and class II gene was not associated with response to pembrolizumab after accounting for the number of tests conducted. No conclusive association between HLA genotype and response to pembrolizumab was identified in this dataset. Germline HLA genotype or diversity alone is not an important independent determinant of response to pembrolizumab and should not be used for clinical decision-making in patients treated with pembrolizumab.
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Affiliation(s)
- Aparna Chhibber
- Department of Biomarker and Genome Sciences, Merck & Co., Kenilworth, NJ 07033, USA
| | - Lingkang Huang
- Department of Biostatistics and Research Decision Sciences, Merck & Co., Kenilworth, NJ 07033, USA
| | - Hong Zhang
- Department of Biostatistics and Research Decision Sciences, Merck & Co., Kenilworth, NJ 07033, USA
| | - Jialin Xu
- Department of Biostatistics and Research Decision Sciences, Merck & Co., Kenilworth, NJ 07033, USA
| | - Razvan Cristescu
- Department of Biomarker and Genome Sciences, Merck & Co., Kenilworth, NJ 07033, USA
| | - Xiaoqiao Liu
- Department of Biomarker and Genome Sciences, Merck & Co., Kenilworth, NJ 07033, USA
| | - Devan V Mehrotra
- Department of Biostatistics and Research Decision Sciences, Merck & Co., Kenilworth, NJ 07033, USA
| | - Judong Shen
- Department of Biostatistics and Research Decision Sciences, Merck & Co., Kenilworth, NJ 07033, USA
| | - Peter M Shaw
- Department of Biomarker and Genome Sciences, Merck & Co., Kenilworth, NJ 07033, USA.
| | - Matthew D Hellmann
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA.
| | - Alexandra Snyder
- Department of Medical Oncology, Merck & Co., Kenilworth, NJ 07033, USA.
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5
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The Role of HLA in the Association between IgA Deficiency and Celiac Disease. DISEASE MARKERS 2021; 2021:8632861. [PMID: 35186163 PMCID: PMC8856801 DOI: 10.1155/2021/8632861] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 10/17/2021] [Accepted: 11/10/2021] [Indexed: 01/18/2023]
Abstract
Selective IgA deficiency (SIgAD) is the most frequent primary immune defect. Since SIgAD is not characterized by relevant infectious issues in most cases, it is often diagnosed during the diagnostic work up of several and different autoimmune disorders, which are associated with this primary immune defect. The genetic background of SIgAD is complex and three HLA haplotypes resulted to be more frequently associated with it; in detail, two of them include HLA-DQB1∗02 allelic variants, which are essential predisposing factors to develop Celiac Disease (CD). Here, we discuss the evidence regarding the role of HLA in the etiopathogenesis of SIgAD and its association with CD. Actually, the HLA region seems to play a modest role in the genetic predisposition to SIgAD and we may speculate that the association with the HLA-DQB1∗02 alleles (or haplotypes including them) could derive from its link with CD. Indeed, SIgAD and some related immunological alterations are likely to predispose to several autoimmune diseases (with and despite different HLA backgrounds), including CD, which is relatively common and directly associated with the HLA-DQB1∗02 allelic variants coding the DQ2 heterodimer. Further and specific studies are needed to make final conclusions in this regard.
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Motozono C, Toyoda M, Zahradnik J, Saito A, Nasser H, Tan TS, Ngare I, Kimura I, Uriu K, Kosugi Y, Yue Y, Shimizu R, Ito J, Torii S, Yonekawa A, Shimono N, Nagasaki Y, Minami R, Toya T, Sekiya N, Fukuhara T, Matsuura Y, Schreiber G, Ikeda T, Nakagawa S, Ueno T, Sato K. SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Cell Host Microbe 2021; 29:1124-1136.e11. [PMID: 34171266 PMCID: PMC8205251 DOI: 10.1016/j.chom.2021.06.006] [Citation(s) in RCA: 331] [Impact Index Per Article: 110.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/22/2021] [Accepted: 06/09/2021] [Indexed: 01/15/2023]
Abstract
Many SARS-CoV-2 variants with naturally acquired mutations have emerged. These mutations can affect viral properties such as infectivity and immune resistance. Although the sensitivity of naturally occurring SARS-CoV-2 variants to humoral immunity has been investigated, sensitivity to human leukocyte antigen (HLA)-restricted cellular immunity remains largely unexplored. Here, we demonstrate that two recently emerging mutations in the receptor-binding domain of the SARS-CoV-2 spike protein, L452R (in B.1.427/429 and B.1.617) and Y453F (in B.1.1.298), confer escape from HLA-A24-restricted cellular immunity. These mutations reinforce affinity toward the host entry receptor ACE2. Notably, the L452R mutation increases spike stability, viral infectivity, viral fusogenicity, and thereby promotes viral replication. These data suggest that HLA-restricted cellular immunity potentially affects the evolution of viral phenotypes and that a further threat of the SARS-CoV-2 pandemic is escape from cellular immunity.
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Affiliation(s)
- Chihiro Motozono
- Division of Infection and Immunity, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan
| | - Mako Toyoda
- Division of Infection and Immunity, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan
| | - Jiri Zahradnik
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Akatsuki Saito
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki 8892192, Japan; Center for Animal Disease Control, University of Miyazaki, Miyazaki 8892192, Japan; Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki 8892192, Japan
| | - Hesham Nasser
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan; Department of Clinical Pathology, Faculty of Medicine, Suez Canal University, Ismailia 41511, Egypt
| | - Toong Seng Tan
- Division of Infection and Immunity, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan
| | - Isaac Ngare
- Division of Infection and Immunity, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan
| | - Izumi Kimura
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
| | - Keiya Uriu
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
| | - Yusuke Kosugi
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
| | - Yuan Yue
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan
| | - Ryo Shimizu
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan
| | - Jumpei Ito
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
| | - Shiho Torii
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka 5650871, Japan; Division of Microbiology and Immunology, Center for Infectious Diseases Education and Research, Osaka University, Osaka 5650871, Japan; Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Osaka 5650871, Japan
| | - Akiko Yonekawa
- Department of Medicine and Biosystemic Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 8128582, Japan
| | - Nobuyuki Shimono
- Department of Medicine and Biosystemic Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 8128582, Japan
| | - Yoji Nagasaki
- Division of Infectious Diseases, Clinical Research Institute, National Hospitalization Organization, Kyushu Medical Center, Fukuoka 8108563, Japan
| | - Rumi Minami
- Internal Medicine, Clinical Research Institute, National Hospital Organization, Kyushu Medical Center, Fukuoka 8108563, Japan
| | - Takashi Toya
- Hematology Division, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo 1138677, Japan
| | - Noritaka Sekiya
- Department of Infection Prevention and Control, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo 1138677, Japan; Department of Clinical Laboratory, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo 1138677, Japan
| | - Takasuke Fukuhara
- Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Hokkaido 0608638, Japan
| | - Yoshiharu Matsuura
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka 5650871, Japan; Division of Microbiology and Immunology, Center for Infectious Diseases Education and Research, Osaka University, Osaka 5650871, Japan; Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Osaka 5650871, Japan
| | - Gideon Schreiber
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | - Terumasa Ikeda
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan.
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa 2591193, Japan; CREST, Japan Science and Technology Agency, Saitama 3220012, Japan.
| | - Takamasa Ueno
- Division of Infection and Immunity, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan.
| | - Kei Sato
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan; CREST, Japan Science and Technology Agency, Saitama 3220012, Japan.
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7
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Hyun YS, Jo HA, Lee YH, Kim SM, Baek IC, Sohn HJ, Cho HI, Kim TG. Comprehensive Analysis of CD4 + T Cell Responses to CMV pp65 Antigen Restricted by Single HLA-DR, -DQ, and -DP Allotype Within an Individual. Front Immunol 2021; 11:602014. [PMID: 33658991 PMCID: PMC7917246 DOI: 10.3389/fimmu.2020.602014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 12/15/2020] [Indexed: 01/18/2023] Open
Abstract
Within an individual, six different HLA class II heterodimers are expressed co-dominantly by two alleles of HLA-DR, -DQ, and -DP loci. However, it remained unclear which HLA allotypes were used in T cell responses to a given antigen. For the measurement of the CD4+ T cell responses restricted by a single HLA allotype, we established a panel of artificial antigen-presenting cells (aAPCs) expressing each single HLA allele of 20 HLA-DRB1, 16 HLA-DQ, and 13 HLA-DP alleles. CD4+ T cell responses to cytomegalovirus (CMV) pp65 restricted by single HLA class II allotype defined in 45 healthy donors. The average magnitude of CD4+ T cell responses by HLA-DR allotypes was higher than HLA-DQ and HLA-DP allotypes. CD4+ T cell responses by DRA*01:01/DRB1*04:06, DQA1*01:02/DQB1*06:02, DPA1*02:02/DPB1*05:01 were higher among the other alleles in each HLA-DR, -DQ, and -DP locus. Interestingly, the frequencies of HLA-DR alleles and the positivity of specific allotypes showed an inverse correlation. One allotype within individuals is dominantly used in CD4+ T cell response in 49% of donors, and two allotypes showed that in 7% of donors, and any positive response was detected in 44% of donors. Even if one individual had several dominant alleles, CD4+ T cell responses tended to be restricted by only one of them. Furthermore, CD8+ and CD4+ T cell responses by HLA class I and class II were correlated. Our results demonstrate that the CD4+ T cell preferentially use a few dominant HLA class II allotypes within individuals, similar to CD8+ T cell response to CMV pp65.
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Affiliation(s)
- You-Seok Hyun
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, South Korea.,Department of Biomedicine and Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Hyeong-A Jo
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, South Korea.,Department of Biomedicine and Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Yong-Hun Lee
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, South Korea.,Department of Biomedicine and Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Sun-Mi Kim
- Catholic Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - In-Cheol Baek
- Catholic Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Hyun-Jung Sohn
- Translational and Clinical Division, ViGenCell Inc., Seoul, South Korea
| | - Hyun-Il Cho
- Translational and Clinical Division, ViGenCell Inc., Seoul, South Korea
| | - Tai-Gyu Kim
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, South Korea.,Department of Biomedicine and Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, South Korea.,Catholic Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, South Korea
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8
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Poddighe D, Turganbekova A, Baymukasheva D, Saduakas Z, Zhanzakova Z, Abdrakhmanova S. Genetic predisposition to celiac disease in Kazakhstan: Potential impact on the clinical practice in Central Asia. PLoS One 2020; 15:e0226546. [PMID: 31895924 PMCID: PMC6939901 DOI: 10.1371/journal.pone.0226546] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 11/24/2019] [Indexed: 02/08/2023] Open
Abstract
Background Celiac disease (CD) is a systemic immune-mediated disorder developing in HLA genetically predisposed individuals carrying HLA-DQ2 and/or HLA-DQ8 molecules. Recent evidences supported a predominant importance of HLA-DQB1 locus and, in particular, HLA-DQB1*02 alleles. This diagnosis is poorly considered in Kazakhstan, because of the assumption that CD is not prevalent in this population. Objective To demonstrate that the genetic predisposition to CD in Kazakhstan is not negligible and is actually comparable to Western populations. Methods Through the analysis of HLA-DQ genotypes of healthy bone marrow donors from Kazakhstan’s national registry, we estimated the HLA-related genetic predisposition to CD in the country. Results We demonstrated that the frequency of CD-related HLA-DQB1 alleles and, as a consequence, of predisposed individuals to CD in Kazakhstan is significant and comparable to countries with the highest disease prevalence. Conclusion Considering the dietary style in Kazakhstan, including wheat as a staple food, these results provided a preliminary background of knowledge to expect a significant CD prevalence in Kazakhstan and Central Asia by implementing appropriate and cost-effective diagnostic strategies.
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Affiliation(s)
- Dimitri Poddighe
- Department of Medicine, Nazarbayev University School of Medicine, Nur-Sultan City, Kazakhstan
- * E-mail:
| | - Aida Turganbekova
- RSE on REM «Research and Production Center of Transfusion», Ministry of Health of the Republic of Kazakhstan, Nur-Sultan City, Kazakhstan
| | - Dana Baymukasheva
- RSE on REM «Research and Production Center of Transfusion», Ministry of Health of the Republic of Kazakhstan, Nur-Sultan City, Kazakhstan
| | - Zhazira Saduakas
- RSE on REM «Research and Production Center of Transfusion», Ministry of Health of the Republic of Kazakhstan, Nur-Sultan City, Kazakhstan
| | - Zhuldyz Zhanzakova
- RSE on REM «Research and Production Center of Transfusion», Ministry of Health of the Republic of Kazakhstan, Nur-Sultan City, Kazakhstan
| | - Saniya Abdrakhmanova
- RSE on REM «Research and Production Center of Transfusion», Ministry of Health of the Republic of Kazakhstan, Nur-Sultan City, Kazakhstan
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Next-generation sequencing reveals new information about HLA allele and haplotype diversity in a large European American population. Hum Immunol 2019; 80:807-822. [PMID: 31345698 DOI: 10.1016/j.humimm.2019.07.275] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 06/21/2019] [Accepted: 07/06/2019] [Indexed: 12/11/2022]
Abstract
The human leukocyte antigen (HLA) genes are extremely polymorphic and are useful molecular markers to make inferences about human population history. However, the accuracy of the estimation of genetic diversity at HLA loci very much depends on the technology used to characterize HLA alleles; high-resolution genotyping of long-range HLA gene products improves the assessment of HLA population diversity as well as other population parameters compared to lower resolution typing methods. In this study we examined allelic and haplotype HLA diversity in a large healthy European American population sourced from the UCSF-DNA bank. A high-resolution next-generation sequencing method was applied to define non-ambiguous 3- and 4-field alleles at the HLA-A, HLA-C, HLA-B, HLA-DRB1, HLA-DRB3/4/5, HLA-DQA1, HLA-DQB1, HLA-DPA1, and HLA-DPB1 loci in samples provided by 2248 unrelated individuals. A number of population parameters were examined including balancing selection and various measurements of linkage disequilibrium were calculated. There were no detectable deviations from Hardy-Weinberg proportions at HLA-A, HLA-DRB1, HLA-DQA1 and HLA-DQB1. For the remaining loci moderate and significant deviations were detected at HLA-C, HLA-B, HLA-DRB3/4/5, HLA-DPA1 and HLA-DPB1 loci mostly from population substructures. Unique 4-field associations were observed among alleles at 2 loci and haplotypes extending large intervals that were not apparent in results obtained using testing methodologies with limited sequence coverage and phasing. The high diversity at HLA-DPA1 results from detection of intron variants of otherwise well conserved protein sequences. It may be speculated that divergence in exon sequences may be negatively selected. Our data provides a valuable reference source for future population studies that may allow for precise fine mapping of coding and non-coding sequences determining disease susceptibility and allo-immunogenicity.
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