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Schurz H, Naranbhai V, Yates TA, Gilchrist JJ, Parks T, Dodd PJ, Möller M, Hoal EG, Morris AP, Hill AVS. Multi-ancestry meta-analysis of host genetic susceptibility to tuberculosis identifies shared genetic architecture. eLife 2024; 13:e84394. [PMID: 38224499 PMCID: PMC10789494 DOI: 10.7554/elife.84394] [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: 10/23/2022] [Accepted: 11/23/2023] [Indexed: 01/17/2024] Open
Abstract
The heritability of susceptibility to tuberculosis (TB) disease has been well recognized. Over 100 genes have been studied as candidates for TB susceptibility, and several variants were identified by genome-wide association studies (GWAS), but few replicate. We established the International Tuberculosis Host Genetics Consortium to perform a multi-ancestry meta-analysis of GWAS, including 14,153 cases and 19,536 controls of African, Asian, and European ancestry. Our analyses demonstrate a substantial degree of heritability (pooled polygenic h2 = 26.3%, 95% CI 23.7-29.0%) for susceptibility to TB that is shared across ancestries, highlighting an important host genetic influence on disease. We identified one global host genetic correlate for TB at genome-wide significance (p<5 × 10-8) in the human leukocyte antigen (HLA)-II region (rs28383206, p-value=5.2 × 10-9) but failed to replicate variants previously associated with TB susceptibility. These data demonstrate the complex shared genetic architecture of susceptibility to TB and the importance of large-scale GWAS analysis across multiple ancestries experiencing different levels of infection pressure.
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Affiliation(s)
- Haiko Schurz
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch UniversityCape TownSouth Africa
| | - Vivek Naranbhai
- Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
- Massachusetts General HospitalBostonUnited States
- Dana-Farber Cancer InstituteBostonUnited States
- Centre for the AIDS Programme of Research in South AfricaDurbanSouth Africa
- Harvard Medical SchoolBostonUnited States
| | - Tom A Yates
- Division of Infection and Immunity, Faculty of Medical Sciences, University College LondonLondonUnited Kingdom
| | - James J Gilchrist
- Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
- Department of Paediatrics, University of OxfordOxfordUnited Kingdom
| | - Tom Parks
- Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
- Department of Infectious Diseases Imperial College LondonLondonUnited Kingdom
| | - Peter J Dodd
- School of Health and Related Research, University of SheffieldSheffieldUnited Kingdom
| | - Marlo Möller
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch UniversityCape TownSouth Africa
| | - Eileen G Hoal
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch UniversityCape TownSouth Africa
| | - Andrew P Morris
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, The University of ManchesterManchesterUnited Kingdom
| | - Adrian VS Hill
- Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
- Jenner Institute, University of OxfordOxfordUnited Kingdom
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Araujo Z, Camargo M, Moreno Pérez DA, Wide A, Pacheco D, Díaz Arévalo D, Celis Giraldo CT, Salas S, de Waard JH, Patarroyo MA. Differential NRAMP1gene's D543N genotype frequency: Increased risk of contracting tuberculosis among Venezuelan populations. Hum Immunol 2023; 84:484-491. [PMID: 37380553 DOI: 10.1016/j.humimm.2023.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 05/15/2023] [Accepted: 06/11/2023] [Indexed: 06/30/2023]
Abstract
NRAMP1 and VDR gene polymorphisms have been variably associated with susceptibility to tuberculosis (TB) amongst populations having different genetic background. NRAMP1 and VDR gene variants' association with susceptibility to active infection by Mycobacterium tuberculosis (Mtb) was analyzed in the Warao Amerindian population, an ethnic population from Venezuela's Orinoco delta region. Genomic DNA was extracted from individuals with and without TB to evaluate genetic polymorphism by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Four NRAMP1 gene polymorphisms were analyzed: D543N (rs17235409), 3' UTR (rs17235416), INT4 (rs3731865), and 274C/T (rs2276631), and one VDR gene polymorphism: FokI (rs2228570). The results showed that the genotypes D543N-A/A, 3'UTR-TGTG+/+, INT4-C/C, and 274C/T-T/T of known polymorphism in the NRAMP1 gene, as well as the genotypes FokI-F/f and FokI-f/f in the VDR gene were most often found in indigenous Warao with active TB. Binomial logistic regression was used for evaluating associations between polymorphisms and risk of contracting TB, an association between NRAMP1-D543N-A/A genotype distribution and TB susceptibility was found in Warao Amerindians. Regarding Venezuelan populations having different genetic backgrounds; statistically significant TB associations concerning NRAMP1-D543N-A/A, INT4-C/C and 3'UTR-TGTG+/+ variant genotype distributions in Warao Amerindians (indigenous) compared to Creole (admixed non-indigenous population) individuals were found. In conclusion, the results thus indicated that the association between NRAMP1-D543N-A/A genotype and TB in Warao Amerindians could support such allele's role in host susceptibility to Mtb infection.
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Affiliation(s)
- Zaida Araujo
- Laboratorio de Inmunología de Enfermedades Infecciosas, Instituto de Biomedicina "Dr. Jacinto Convit", Universidad Central de Venezuela, Apartado 4043, Caracas 1010A, Venezuela.
| | - Milena Camargo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50 No. 26-20, Bogota, Colombia
| | - Darwin A Moreno Pérez
- Animal Science Faculty, Universidad de Ciencias Aplicadas y Ambientales (U.D.C.A), Calle 222 No. 55-37, Bogotá, Colombia
| | - Albina Wide
- Laboratorio de Biotecnología, Instituto de Medicina Tropical, Universidad Central de Venezuela, Caracas, Venezuela
| | - Dailobivxon Pacheco
- Laboratorio de Inmunología de Enfermedades Infecciosas, Instituto de Biomedicina "Dr. Jacinto Convit", Universidad Central de Venezuela, Apartado 4043, Caracas 1010A, Venezuela
| | - Diana Díaz Arévalo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50 No. 26-20, Bogota, Colombia
| | - Carmen T Celis Giraldo
- Animal Science Faculty, Universidad de Ciencias Aplicadas y Ambientales (U.D.C.A), Calle 222 No. 55-37, Bogotá, Colombia
| | - Sandra Salas
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50 No. 26-20, Bogota, Colombia
| | - Jacobus H de Waard
- Laboratorio de Tuberculosis, Instituto de Biomedicina "Dr. Jacinto Convit", Universidad Central de Venezuela, Apartado 4043, Caracas 1010A, Venezuela
| | - Manuel A Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50 No. 26-20, Bogota, Colombia; Faculty of Medicine, Universidad Nacional de Colombia, Carrera 45 No. 26-85, Bogotá, Colombia; Health Sciences Division, Main Campus, Universidad Santo Tomás, Carrera 9 No. 51-11, Bogotá, Colombia.
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Yu J, Liu M, Mijiti X, Liu H, Wang Q, Yin C, Anwaierjiang A, Xu M, Li M, Deng L, Xiao H, Zhao X, Wan K, Li G, Yuan X. Association of Single-Nucleotide Polymorphisms in the VDR Gene with Tuberculosis and Infection of Beijing Genotype Mycobacterium tuberculosis. Infect Drug Resist 2023; 16:3157-3169. [PMID: 37235072 PMCID: PMC10208660 DOI: 10.2147/idr.s407595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 05/03/2023] [Indexed: 05/28/2023] Open
Abstract
Background The aim of the present study was to investigate the association between vitamin D receptor (VDR) gene polymorphism and tuberculosis susceptibility, as well as the potential interaction of host genetic factors with the heterogeneity of Mycobacterium tuberculosis in the population from Xinjiang, China. Methods From January 2019 to January 2020, we enrolled 221 tuberculosis patients as the case group and 363 staff with no clinical symptoms as the control group from four designated tuberculosis hospitals in southern Xinjiang, China. The polymorphisms of Fok I, Taq I, Apa I, Bsm I, rs3847987 and rs739837 in the VDR were detected by sequencing. M. tuberculosis isolates were collected from the case group and identified as Beijing or non-Beijing lineage by multiplex PCR. Propensity score (PS), univariate analysis and multivariable logistic regression models were used to perform the analysis. Results Our results showed that the allele and genotype frequencies of Fok I, Taq I, Apa I, Bsm I, rs3847987 and rs739837 in VDR were not correlated with tuberculosis susceptibility or lineages of M. tuberculosis. Two out of six loci of the VDR gene formed one haplotype block, and none of the haplotypes was found to correlate with tuberculosis susceptibility or lineages of M. tuberculosis infected. Conclusion Polymorphisms in the VDR gene may not indicate susceptibility to tuberculosis. There was also no evidence on the interaction between the VDR gene of host and the lineages of M. tuberculosis in the population from Xinjiang, China. Further studies are nonetheless required to prove our conclusions.
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Affiliation(s)
- Jinjie Yu
- School of Public Health, University of South China, Hengyang, 421001, People’s Republic of China
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Mengwen Liu
- School of Public Health, Xinjiang Medical University, Urumqi, Xinjiang, 830011, People’s Republic of China
| | - Xiaokaiti Mijiti
- The Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, 830049, People’s Republic of China
| | - Haican Liu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Quan Wang
- The Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, 830049, People’s Republic of China
| | - Chunjie Yin
- School of Public Health, Xinjiang Medical University, Urumqi, Xinjiang, 830011, People’s Republic of China
| | | | - Miao Xu
- The Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, 830049, People’s Republic of China
| | - Machao Li
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Lele Deng
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Hui Xiao
- School of Public Health, Xinjiang Medical University, Urumqi, Xinjiang, 830011, People’s Republic of China
| | - Xiuqin Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Kanglin Wan
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Guilian Li
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Xiuqin Yuan
- School of Public Health, University of South China, Hengyang, 421001, People’s Republic of China
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Ndong Sima CAA, Smith D, Petersen DC, Schurz H, Uren C, Möller M. The immunogenetics of tuberculosis (TB) susceptibility. Immunogenetics 2022; 75:215-230. [DOI: 10.1007/s00251-022-01290-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022]
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Liu M, Wang Q, Liu H, Yin C, Mijiti X, Anwaierjiang A, Wan K, Xu M, Li M, Nong S, Li G, Xiao H. Association of Mannose-Binding Lectin 2 Gene Polymorphism with Tuberculosis Based on Mycobacterium tuberculosis Lineages. Infect Drug Resist 2022; 15:1225-1234. [PMID: 35355619 PMCID: PMC8959721 DOI: 10.2147/idr.s344935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 01/25/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose Polymorphisms in MBL2 may contribute to the susceptibility to tuberculosis. The aim of the present study was to determine the associations of the polymorphisms of five loci (rs1800450, rs1800451, rs7096206, rs7095891, and rs11003125) in the MBL2 gene with susceptibility to tuberculosis and specific lineages of Mycobacterium tuberculosis causing tuberculosis in the Uyghur population of Xinjiang, China. Methods From January 2019 to January 2020, we enrolled 170 Uyghur tuberculosis patients as the case group and 147 Uyghur staff with no clinical symptoms as the control group from four designated tuberculosis hospitals in southern Xinjiang, China. The polymorphisms of five loci in MBL2 of human were detected by sequencing. Whole-genome sequencing was applied in 68 M. tuberculosis isolates from the case group and the data were used to perform genealogy analysis. Results The distributions of allele and genotype frequencies of five loci in MBL2 varied little between the case and control groups and varied little among the groups, including those infected with different lineages of M. tuberculosis and the control (except those of rs11003125), the P values were all >0.05. The distribution of alleles of rs11003125 was statistically different between patients infected with lineages 3 and 4 M. tuberculosis (χ2=7.037, P=0.008). The C allele and CC genotype of rs11003125 were found to be protective factors against lineage 4 infection when compared to lineage 3 (ORs were 0.190 and 0.158, respectively; 95% confidence intervals were 0.053~0.690 and 0.025~0.999, respectively). Conclusion Our results suggested that human’s susceptibility to tuberculosis is affected both by the host genetic polymorphisms and the lineage of the M. tuberculosis that people were exposed to. However, due to the limitation of the sample size in the present study, larger sample size and more rigorous design should be guaranteed in future studies.
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Affiliation(s)
- Mengwen Liu
- School of Public Health, Xinjiang Medical University, Urumqi, 830011, People’s Republic of China
| | - Quan Wang
- The Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, 830001, People’s Republic of China
| | - Haican Liu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Chunjie Yin
- School of Public Health, Xinjiang Medical University, Urumqi, 830011, People’s Republic of China
| | - Xiaokaiti Mijiti
- The Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, 830001, People’s Republic of China
| | - Aiketaguli Anwaierjiang
- School of Public Health, Xinjiang Medical University, Urumqi, 830011, People’s Republic of China
| | - Kanglin Wan
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Miao Xu
- The Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, 830001, People’s Republic of China
| | - Machao Li
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Siqin Nong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People’s Republic of China
| | - Guilian Li
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
- Correspondence: Guilian Li; Hui Xiao, Email ;
| | - Hui Xiao
- School of Public Health, Xinjiang Medical University, Urumqi, 830011, People’s Republic of China
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Swart Y, Uren C, van Helden PD, Hoal EG, Möller M. Local Ancestry Adjusted Allelic Association Analysis Robustly Captures Tuberculosis Susceptibility Loci. Front Genet 2021; 12:716558. [PMID: 34721521 PMCID: PMC8554120 DOI: 10.3389/fgene.2021.716558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 10/01/2021] [Indexed: 11/13/2022] Open
Abstract
Pulmonary tuberculosis (TB), caused by Mycobacterium tuberculosis, is a complex disease. The risk of developing active TB is in part determined by host genetic factors. Most genetic studies investigating TB susceptibility fail to replicate association signals particularly across diverse populations. South African populations arose because of multi-wave genetic admixture from the indigenous KhoeSan, Bantu-speaking Africans, Europeans, Southeast Asian-and East Asian populations. This has led to complex genetic admixture with heterogenous patterns of linkage disequilibrium and associated traits. As a result, precise estimation of both global and local ancestry is required to prevent both false positive and false-negative associations. Here, 820 individuals from South Africa were genotyped on the SNP-dense Illumina Multi-Ethnic Genotyping Array (∼1.7M SNPs) followed by local and global ancestry inference using RFMix. Local ancestry adjusted allelic association (LAAA) models were utilized owing to the extensive genetic heterogeneity present in this population. Hence, an interaction term, comprising the identification of the minor allele that corresponds to the ancestry present at the specific locus under investigation, was included as a covariate. One SNP (rs28647531) located on chromosome 4q22 was significantly associated with TB susceptibility and displayed a SNP minor allelic effect (G allele, frequency = 0.204) whilst correcting for local ancestry for Bantu-speaking African ancestry (p-value = 5.518 × 10-7; OR = 3.065; SE = 0.224). Although no other variants passed the significant threshold, clear differences were observed between the lead variants identified for each ancestry. Furthermore, the LAAA model robustly captured the source of association signals in multi-way admixed individuals from South Africa and allowed the identification of ancestry-specific disease risk alleles associated with TB susceptibility that have previously been missed.
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Affiliation(s)
- Yolandi Swart
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Caitlin Uren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, South Africa
| | - Paul D van Helden
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Eileen G Hoal
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Marlo Möller
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, South Africa
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