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Palittapongarnpim P, Tantivitayakul P, Aiewsakun P, Mahasirimongkol S, Jaemsai B. Genomic Interactions Between Mycobacterium tuberculosis and Humans. Annu Rev Genomics Hum Genet 2024; 25:183-209. [PMID: 38640230 DOI: 10.1146/annurev-genom-021623-101844] [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] [Indexed: 04/21/2024]
Abstract
Mycobacterium tuberculosis is considered by many to be the deadliest microbe, with the estimated annual cases numbering more than 10 million. The bacteria, including Mycobacterium africanum, are classified into nine major lineages and hundreds of sublineages, each with different geographical distributions and levels of virulence. The phylogeographic patterns can be a result of recent and early human migrations as well as coevolution between the bacteria and various human populations, which may explain why many studies on human genetic factors contributing to tuberculosis have not been replicable in different areas. Moreover, several studies have revealed the significance of interactions between human genetic variations and bacterial genotypes in determining the development of tuberculosis, suggesting coadaptation. The increased availability of whole-genome sequence data from both humans and bacteria has enabled a better understanding of these interactions, which can inform the development of vaccines and other control measures.
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Affiliation(s)
- Prasit Palittapongarnpim
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand; , ,
| | - Pornpen Tantivitayakul
- Department of Oral Microbiology, Faculty of Dentistry, Mahidol University, Bangkok, Thailand;
| | - Pakorn Aiewsakun
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand; , ,
| | - Surakameth Mahasirimongkol
- Medical Life Sciences Institute, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
- Information and Communication Technology Center, Office of Permanent Secretary, Ministry of Public Health, Nonthaburi, Thailand;
| | - Bharkbhoom Jaemsai
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand; , ,
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2
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Meade RK, Smith CM. Immunological roads diverged: mapping tuberculosis outcomes in mice. Trends Microbiol 2024:S0966-842X(24)00170-7. [PMID: 39034171 DOI: 10.1016/j.tim.2024.06.007] [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: 05/06/2024] [Revised: 06/24/2024] [Accepted: 06/25/2024] [Indexed: 07/23/2024]
Abstract
The journey from phenotypic observation to causal genetic mechanism is a long and challenging road. For pathogens like Mycobacterium tuberculosis (Mtb), which causes tuberculosis (TB), host-pathogen coevolution has spanned millennia, costing millions of human lives. Mammalian models can systematically recapitulate host genetic variation, producing a spectrum of disease outcomes. Leveraging genome sequences and deep phenotyping data from infected mouse genetic reference populations (GRPs), quantitative trait locus (QTL) mapping approaches have successfully identified host genomic regions associated with TB phenotypes. Here, we review the ongoing optimization of QTL mapping study design alongside advances in mouse GRPs. These next-generation resources and approaches have enabled identification of novel host-pathogen interactions governing one of the most prevalent infectious diseases in the world today.
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Affiliation(s)
- Rachel K Meade
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA; University Program in Genetics and Genomics, Duke University, Durham, NC, USA
| | - Clare M Smith
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA; University Program in Genetics and Genomics, Duke University, Durham, NC, USA.
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3
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Kurtz SL, Baker RE, Boehm FJ, Lehman CC, Mittereder LR, Khan H, Rossi AP, Gatti DM, Beamer G, Sassetti CM, Elkins KL. Multiple genetic loci influence vaccine-induced protection against Mycobacterium tuberculosis in genetically diverse mice. PLoS Pathog 2024; 20:e1012069. [PMID: 38452145 PMCID: PMC10950258 DOI: 10.1371/journal.ppat.1012069] [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: 10/16/2023] [Revised: 03/19/2024] [Accepted: 02/26/2024] [Indexed: 03/09/2024] Open
Abstract
Mycobacterium tuberculosis (M.tb.) infection leads to over 1.5 million deaths annually, despite widespread vaccination with BCG at birth. Causes for the ongoing tuberculosis endemic are complex and include the failure of BCG to protect many against progressive pulmonary disease. Host genetics is one of the known factors implicated in susceptibility to primary tuberculosis, but less is known about the role that host genetics plays in controlling host responses to vaccination against M.tb. Here, we addressed this gap by utilizing Diversity Outbred (DO) mice as a small animal model to query genetic drivers of vaccine-induced protection against M.tb. DO mice are a highly genetically and phenotypically diverse outbred population that is well suited for fine genetic mapping. Similar to outcomes in people, our previous studies demonstrated that DO mice have a wide range of disease outcomes following BCG vaccination and M.tb. challenge. In the current study, we used a large population of BCG-vaccinated/M.tb.-challenged mice to perform quantitative trait loci mapping of complex infection traits; these included lung and spleen M.tb. burdens, as well as lung cytokines measured at necropsy. We found sixteen chromosomal loci associated with complex infection traits and cytokine production. QTL associated with bacterial burdens included a region encoding major histocompatibility antigens that are known to affect susceptibility to tuberculosis, supporting validity of the approach. Most of the other QTL represent novel associations with immune responses to M.tb. and novel pathways of cytokine regulation. Most importantly, we discovered that protection induced by BCG is a multigenic trait, in which genetic loci harboring functionally-distinct candidate genes influence different aspects of immune responses that are crucial collectively for successful protection. These data provide exciting new avenues to explore and exploit in developing new vaccines against M.tb.
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Affiliation(s)
- Sherry L. Kurtz
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Richard E. Baker
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, Massachusetts, United States of America
| | - Frederick J. Boehm
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Chelsea C. Lehman
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Lara R. Mittereder
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Hamda Khan
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Amy P. Rossi
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
- College of Medicine, University of Cincinatti, Cincinatti, Ohio, United States of America
| | - Daniel M. Gatti
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Gillian Beamer
- Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Christopher M. Sassetti
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, Massachusetts, United States of America
| | - Karen L. Elkins
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
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4
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Ogishi M, Yang R, Rodriguez R, Golec DP, Martin E, Philippot Q, Bohlen J, Pelham SJ, Arias AA, Khan T, Ata M, Al Ali F, Rozenberg F, Kong XF, Chrabieh M, Laine C, Lei WT, Han JE, Seeleuthner Y, Kaul Z, Jouanguy E, Béziat V, Youssefian L, Vahidnezhad H, Rao VK, Neven B, Fieschi C, Mansouri D, Shahrooei M, Pekcan S, Alkan G, Emiroğlu M, Tokgöz H, Uitto J, Hauck F, Bustamante J, Abel L, Keles S, Parvaneh N, Marr N, Schwartzberg PL, Latour S, Casanova JL, Boisson-Dupuis S. Inherited human ITK deficiency impairs IFN-γ immunity and underlies tuberculosis. J Exp Med 2023; 220:213662. [PMID: 36326697 PMCID: PMC9641312 DOI: 10.1084/jem.20220484] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 09/14/2022] [Accepted: 10/04/2022] [Indexed: 11/06/2022] Open
Abstract
Inborn errors of IFN-γ immunity can underlie tuberculosis (TB). We report three patients from two kindreds without EBV viremia or disease but with severe TB and inherited complete ITK deficiency, a condition associated with severe EBV disease that renders immunological studies challenging. They have CD4+ αβ T lymphocytopenia with a concomitant expansion of CD4-CD8- double-negative (DN) αβ and Vδ2- γδ T lymphocytes, both displaying a unique CD38+CD45RA+T-bet+EOMES- phenotype. Itk-deficient mice recapitulated an expansion of the γδ T and DN αβ T lymphocyte populations in the thymus and spleen, respectively. Moreover, the patients' T lymphocytes secrete small amounts of IFN-γ in response to TCR crosslinking, mitogens, or forced synapse formation with autologous B lymphocytes. Finally, the patients' total lymphocytes secrete small amounts of IFN-γ, and CD4+, CD8+, DN αβ T, Vδ2+ γδ T, and MAIT cells display impaired IFN-γ production in response to BCG. Inherited ITK deficiency undermines the development and function of various IFN-γ-producing T cell subsets, thereby underlying TB.
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Affiliation(s)
- Masato Ogishi
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY.,The David Rockefeller Graduate Program, Rockefeller University, New York, NY
| | - Rui Yang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY
| | - Rémy Rodriguez
- Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, INSERM UMR1163, Paris, France.,Imagine Institute, University of Paris Cité, Paris, France
| | - Dominic P Golec
- Cell Signaling and Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Emmanuel Martin
- Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, INSERM UMR1163, Paris, France.,Imagine Institute, University of Paris Cité, Paris, France
| | - Quentin Philippot
- Imagine Institute, University of Paris Cité, Paris, France.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
| | - Jonathan Bohlen
- Imagine Institute, University of Paris Cité, Paris, France.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
| | - Simon J Pelham
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY
| | - Andrés Augusto Arias
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY.,Primary Immunodeficiencies Group, University of Antioquia UdeA, Medellin, Colombia.,School of Microbiology, University of Antioquia UdeA, Medellin, Colombia
| | - Taushif Khan
- Department of Immunology, Research Branch, Sidra Medicine, Doha, Qatar
| | - Manar Ata
- Department of Immunology, Research Branch, Sidra Medicine, Doha, Qatar
| | - Fatima Al Ali
- Department of Immunology, Research Branch, Sidra Medicine, Doha, Qatar
| | - Flore Rozenberg
- Department of Virology, Cochin Hospital, University of Paris, Paris, France
| | - Xiao-Fei Kong
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY
| | - Maya Chrabieh
- Imagine Institute, University of Paris Cité, Paris, France.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
| | - Candice Laine
- Imagine Institute, University of Paris Cité, Paris, France.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
| | - Wei-Te Lei
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY
| | - Ji Eun Han
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY
| | - Yoann Seeleuthner
- Imagine Institute, University of Paris Cité, Paris, France.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
| | - Zenia Kaul
- Cell Signaling and Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Emmanuelle Jouanguy
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY.,Imagine Institute, University of Paris Cité, Paris, France.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
| | - Vivien Béziat
- Imagine Institute, University of Paris Cité, Paris, France.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
| | - Leila Youssefian
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Philadelphia, PA.,Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA
| | - Hassan Vahidnezhad
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Philadelphia, PA.,Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA
| | - V Koneti Rao
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Bénédicte Neven
- Pediatric Immunology and Hematology Department, Necker Hospital for Sick Children Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Claire Fieschi
- Clinical Immunology Department, Saint Louis Hospital, AP-HP Université de Paris, Paris, France.,INSERM UMR1126, Institut de Recherche Saint-Louis, Université de Paris, Paris, France
| | - Davood Mansouri
- Clinical Tuberculosis and Epidemiology Research Center, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Shahrooei
- Department of Microbiology and Immunology, Laboratory of Clinical Bacteriology and Mycology, KU Leuven, Leuven, Belgium
| | - Sevgi Pekcan
- Department of Pediatric Pulmonology, Necmettin Erbakan University, Meram Medical Faculty, Konya, Turkey
| | - Gulsum Alkan
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Selcuk University Faculty of Medicine, Konya, Turkey
| | - Melike Emiroğlu
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Selcuk University Faculty of Medicine, Konya, Turkey
| | - Hüseyin Tokgöz
- Department of Pediatric Hematology, Meram School of Medicine, Necmettin Erbakan University, Konya, Turkey
| | - Jouni Uitto
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Philadelphia, PA.,Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA
| | - Fabian Hauck
- Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, INSERM UMR1163, Paris, France.,Imagine Institute, University of Paris Cité, Paris, France.,Division of Pediatric Immunology and Rheumatology, Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jacinta Bustamante
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY.,Imagine Institute, University of Paris Cité, Paris, France.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.,Center for the Study of Primary Immunodeficiencies, Necker Hospital for Sick Children Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY.,Imagine Institute, University of Paris Cité, Paris, France.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
| | - Sevgi Keles
- Division of Pediatric Allergy and Immunology, Necmettin Erbakan University, Meram Medical Faculty, Konya, Turkey
| | - Nima Parvaneh
- Division of Allergy and Clinical Immunology, Department of Pediatrics, Tehran University of Medical Sciences, Tehran, Iran.,Research Center for Immunodeficiencies, Tehran University of Medical Sciences, Tehran, Iran
| | - Nico Marr
- Department of Immunology, Research Branch, Sidra Medicine, Doha, Qatar.,College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Pamela L Schwartzberg
- Cell Signaling and Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Sylvain Latour
- Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, INSERM UMR1163, Paris, France.,Imagine Institute, University of Paris Cité, Paris, France
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY.,Imagine Institute, University of Paris Cité, Paris, France.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.,Department of Pediatrics, Necker Hospital for Sick Children, Paris, France.,Howard Hughes Medical Institute, New York, NY
| | - Stéphanie Boisson-Dupuis
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY.,Imagine Institute, University of Paris Cité, Paris, France.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
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5
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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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6
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Saadat M. Prevalence and mortality of COVID-19 are associated with the L55M functional polymorphism of Paraoxonase 1. PROCEEDINGS OF SINGAPORE HEALTHCARE 2021. [PMCID: PMC9198663 DOI: 10.1177/20101058211040582] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Introduction Accumulating evidence recommends that infectious diseases including coronavirus disease 2019 (COVID-19) are often associated with oxidative stress and inflammation. Paraoxonase 1 (PON1, OMIM: 168,820), a member of the paraoxonase gene family, has antioxidant properties. Enzyme activity of paraoxonase depends on a variety of influencing factors such as polymorphisms of PON1, ethnicity, gender, age, and a number of environmental variables. The PON1 has two common functional polymorphisms, namely, Q192R (rs662) and L55M (rs854560). The R192 and M55 alleles are associated with increase and decrease in enzyme activity, respectively. Objective The present study was conducted to investigate the possible association of rs662 and rs854560 polymorphisms with morbidity and mortality of COVID-19. Methods Data for the prevalence, mortality, and amount of accomplished diagnostic test (per 106 people) on 25 November 2020 from 48 countries were included in the present study. The Human Development Index (HDI) was used as a potential confounding variable. Results The frequency of M55 was positively correlated with the prevalence (partial r = 0.487, df = 36, p = 0.002) and mortality of COVID-19 (partial r = 0.551, df = 36, p < 0.001), after adjustments for HDI and amount of the accomplished diagnostic test as possible confounders. Conclusions This means that countries with higher M55 frequency have higher prevalence and mortality of COVID-19.
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Affiliation(s)
- Mostafa Saadat
- Department of Biology, College of Sciences, Shiraz University, Shiraz, Iran
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7
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Cui Z, Liu J, Chang Y, Lin D, Luo D, Ou J, Huang L. Interaction analysis of Mycobacterium tuberculosis between the host environment and highly mutated genes from population genetic structure comparison. Medicine (Baltimore) 2021; 100:e27125. [PMID: 34477155 PMCID: PMC8415957 DOI: 10.1097/md.0000000000027125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 08/18/2021] [Indexed: 01/05/2023] Open
Abstract
We aimed to investigate the genetic and demographic differences and interactions between areas where observed genomic variations in Mycobacterium tuberculosis (M. tb) were distributed uniformly in cold and hot spots.The cold and hot spot areas were identified using the reported incidence of TB over the previous 5 years. Whole genome sequencing was performed on 291 M. tb isolates between January and June 2018. Analysis of molecular variance and a multifactor dimensionality reduction (MDR) model was applied to test gene-gene-environment interactions. Adjusted odds ratios (OR) and 95% confidence intervals (CI) were computed to test the extent to which genetic mutation affects the TB epidemic using a multivariate logistic regression model.The percentage of the Beijing family strain in hot spots was significantly higher than that in cold spots (64.63% vs 50.69%, P = .022), among the elderly, people with a low BMI, and those having a history of contact with a TB patient (all P < .05). Individuals from cold spot areas had a higher frequency of out-of-town traveling (P < .05). The mutation of Rv1186c, Rv3900c, Rv1508c, Rv0210, and an Intergenic Region (SNP site: 3847237) showed a significant difference between cold and hot spots. (P < .001). The MDR model displayed a clear negative interaction effect of age groups with BMI (interaction entropy: -3.55%) and mutation of Rv0210 (interaction entropy: -2.39%). Through the mutations of Rv0210 and BMI had a low independent effect (interaction entropy: -1.46%).Our data suggests a statistically significant role of age, BMI and the polymorphisms of Rv0210 genes in the transmission and development of M. tb. The results provide clues for the study of susceptibility genes of M. tb in different populations. The characteristic strains showed a local epidemic. Strengthening genotype monitoring of strains in various regions can be used as an early warning signal of epidemic spillover.
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Affiliation(s)
- Zhezhe Cui
- Department of Tuberculosis Control, Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning, Guangxi, China
| | - Jun Liu
- Department of Neurosurgery, Liuzhou People's Hospital, Liuzhou, Guangxi, China
| | - Yue Chang
- School of Medicine and Health Management, Guizhou Medical University, Guiyang, Guizhou, China
| | - Dingwen Lin
- Department of Tuberculosis Control, Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning, Guangxi, China
| | - Dan Luo
- Department of Biostatistics, Public Health and Management, Guangxi University of Chinese Medicine, Nanning, China
| | - Jing Ou
- Department of Tuberculosis Control, Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning, Guangxi, China
| | - Liwen Huang
- Department of Tuberculosis Control, Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning, Guangxi, China
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8
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Miller JE, Carter KW, de Klerk N, Burgner DP. The familial risk of infection-related hospitalization in children: A population-based sibling study. PLoS One 2021; 16:e0250181. [PMID: 33909680 PMCID: PMC8081236 DOI: 10.1371/journal.pone.0250181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 04/01/2021] [Indexed: 11/19/2022] Open
Abstract
Objective To assess the risk of severe childhood infections within families, we conducted a sibling analysis in a population-based cohort study with genealogical linkage. We investigated the sibling risk of hospitalization with common infections, a marker of severity. We hypothesized that having siblings hospitalized for infection would increase the proband’s risk of admission with infection. Study design We used population data on Western Australian live-born singletons and their siblings between 1980 and 2014. Measures of infection were infection-related hospitalizations from discharge diagnostic codes. Exposure was having a sibling who had an infection-related hospitalization. Outcomes were infection-related hospitalizations in the child/proband. Probands were followed until an infection-related hospitalization admission (up to the first three), death, 18th birthday, or end of 2014, whichever occurred first. Infection risks were estimated by adjusted Cox proportional hazard models for multiple events. Results Of 512,279 probands, 142,915 (27.9%) had infection-related hospitalizations; 133,322 (26.0%) had a sibling with a previous infection-related hospitalization (i.e. exposed). Median interval between sibling and proband infection-related hospitalizations was 1.4 years (inter-quartile range 0.5–3.7). Probands had a dose-dependent increase in risk if sibling/s had 1, 2, or 3+ infection-related hospitalizations (adjusted hazard ratio, aHR 1.41, 95% CI 1.39–1.43; aHR 1.65, 1.61–1.69; aHR 1.83, 1.77–1.90, respectively). Among siblings with the same clinical infection type, highest sibling risks were for genitourinary (aHR 2.06, 1.68–2.53), gastrointestinal (aHR 2.07, 1.94–2.19), and skin/soft tissue infections (aHR 2.34, 2.15–2.54). Overall risk of infection-related hospitalization was higher in children with more siblings and with older siblings. Conclusion In this population-based study, we observed an increased risk of infection-related hospitalization in children whose siblings were previously hospitalized for infection. Public health interventions may be particularly relevant in families of children hospitalized with infection.
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Affiliation(s)
- Jessica E. Miller
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
- * E-mail:
| | - Kim W. Carter
- Telethon Kids Institute, University of Western Australia, Perth, Western Australia, Australia
| | - Nicholas de Klerk
- Telethon Kids Institute, University of Western Australia, Perth, Western Australia, Australia
| | - David P. Burgner
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
- Department of Paediatrics, Monash University, Clayton, Victoria, Australia
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9
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Host genetics and infectious disease: new tools, insights and translational opportunities. Nat Rev Genet 2020; 22:137-153. [PMID: 33277640 PMCID: PMC7716795 DOI: 10.1038/s41576-020-00297-6] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/14/2020] [Indexed: 12/22/2022]
Abstract
Understanding how human genetics influence infectious disease susceptibility offers the opportunity for new insights into pathogenesis, potential drug targets, risk stratification, response to therapy and vaccination. As new infectious diseases continue to emerge, together with growing levels of antimicrobial resistance and an increasing awareness of substantial differences between populations in genetic associations, the need for such work is expanding. In this Review, we illustrate how our understanding of the host–pathogen relationship is advancing through holistic approaches, describing current strategies to investigate the role of host genetic variation in established and emerging infections, including COVID-19, the need for wider application to diverse global populations mirroring the burden of disease, the impact of pathogen and vector genetic diversity and a broad array of immune and inflammation phenotypes that can be mapped as traits in health and disease. Insights from study of inborn errors of immunity and multi-omics profiling together with developments in analytical methods are further advancing our knowledge of this important area. Infectious diseases are an ever-present global threat. In this Review, Kwok, Mentzer and Knight discuss our latest understanding of how human genetics influence susceptibility to disease. Furthermore, they discuss emerging progress in the interplay between host and pathogen genetics, molecular responses to infection and vaccination, and opportunities to bring these aspects together for rapid responses to emerging diseases such as COVID-19.
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10
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Xu M, Li J, Xiao Z, Lou J, Pan X, Ma Y. Integrative genomics analysis identifies promising SNPs and genes implicated in tuberculosis risk based on multiple omics datasets. Aging (Albany NY) 2020; 12:19173-19220. [PMID: 33051402 PMCID: PMC7732298 DOI: 10.18632/aging.103744] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 07/07/2020] [Indexed: 02/07/2023]
Abstract
More than 10 GWASs have reported numerous genetic loci associated with tuberculosis (TB). However, the functional effects of genetic variants on TB remains largely unknown. In the present study, by combining a reported GWAS summary dataset (N = 452,264) with 3 independent eQTL datasets (N = 2,242) and other omics datasets downloaded from public databases, we conducted an integrative genomics analysis to highlight SNPs and genes implicated in TB risk. Based on independent biological and technical validations, we prioritized 26 candidate genes with eSNPs significantly associated with gene expression and TB susceptibility simultaneously; such as, CDC16 (rs7987202, rs9590408, and rs948182) and RCN3 (rs2946863, rs2878342, and rs3810194). Based on the network-based enrichment analysis, we found these 26 highlighted genes were jointly connected to exert effects on TB susceptibility. The co-expression patterns among these 26 genes were remarkably changed according to Mycobacterium tuberculosis (MTB) infection status. Based on 4 independent gene expression datasets, 21 of 26 genes (80.77%) showed significantly differential expressions between TB group and control group in mesenchymal stem cells, mice blood and lung tissues, as well as human alveolar macrophages. Together, we provide robust evidence to support 26 highlighted genes as important candidates for TB.
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Affiliation(s)
- Mengqiu Xu
- Department of Infectious Diseases, Shengzhou People’s Hospital, The First Affiliated Hospital of Zhejiang University Shengzhou Branch, Shengshou 312400, Zhejiang, China
| | - Jingjing Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University School of Medicine, Hangzhou 310003, Zhejiang, China
| | - Zhaoying Xiao
- Department of Infectious Diseases, Shengzhou People’s Hospital, The First Affiliated Hospital of Zhejiang University Shengzhou Branch, Shengshou 312400, Zhejiang, China
| | - Jiongpo Lou
- Department of Infectious Diseases, Shengzhou People’s Hospital, The First Affiliated Hospital of Zhejiang University Shengzhou Branch, Shengshou 312400, Zhejiang, China
| | - Xinrong Pan
- Department of Infectious Diseases, Shengzhou People’s Hospital, The First Affiliated Hospital of Zhejiang University Shengzhou Branch, Shengshou 312400, Zhejiang, China
| | - Yunlong Ma
- Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou 325027, Zhejiang, China,School of Biomedical Engineering, School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
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11
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Sokołowska A, Świerzko AS, Szala-Poździej A, Augustynowicz-Kopeć E, Kozińska M, Niemiec T, Błachnio M, Borkowska-Tatar D, Jensenius JC, Thiel S, Dziadek J, Cedzyński M. Selected factors of the innate immunity in Polish patients suffering from pulmonary tuberculosis. Immunobiology 2020; 225:151905. [PMID: 32007302 DOI: 10.1016/j.imbio.2020.151905] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/20/2020] [Accepted: 01/21/2020] [Indexed: 02/01/2023]
Abstract
We conducted a prospective study of 453 Polish patients suffering from pulmonary tuberculosis and 267 healthy controls. Selected polymorphisms of the genes encoding for collectins, ficolins and MBL-associated serine protease 2 were investigated as were serum concentrations of mannose-binding lectin, surfactant protein D, ficolin-1 and ficolin-3. The number of MBL2 gene exon 1 variant allele carriers was significantly higher in patients, compared with controls. The homozygosity for SFTPA2 +26 C > A SNP variant allele occurred less commonly within TB, while homozygosity for the FCN1 -542 G > A major allele was less frequent within the control group. Two patients were found MASP-2-deficient. Serum concentrations of MBL, SP-D and ficolin-1 were higher amongst patients while the converse was found for ficolin-3. Ficolin-1 had high specificity to differentiate between individuals with tuberculosis and healthy persons and therefore may be considered potential disease marker.
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Affiliation(s)
- Anna Sokołowska
- Laboratory of Immunobiology of Infections, Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232, Łódź, Poland
| | - Anna S Świerzko
- Laboratory of Immunobiology of Infections, Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232, Łódź, Poland
| | - Agnieszka Szala-Poździej
- Laboratory of Immunobiology of Infections, Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232, Łódź, Poland
| | | | - Monika Kozińska
- Institute of Tuberculosis and Lung Diseases, Plocka 26, 01-138, Warsaw, Poland
| | - Tomasz Niemiec
- The Voivodeship Hospital of Lung Diseases in Jaroszowiec, Kolejowa 1a, 32-312, Jaroszowiec, Poland
| | - Maria Błachnio
- Masovian Center of Lung Diseases and Tuberculosis Treatment, Narutowicza 80, 05-400, Otwock, Poland
| | | | - Jens C Jensenius
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, 8000, Aarhus, Denmark
| | - Steffen Thiel
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, 8000, Aarhus, Denmark
| | - Jarosław Dziadek
- Laboratory of Mycobacterium Genetics and Physiology, Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232, Łódź, Poland
| | - Maciej Cedzyński
- Laboratory of Immunobiology of Infections, Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232, Łódź, Poland.
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12
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Allelic-Specific Regulation of xCT Expression Increases Susceptibility to Tuberculosis by Modulating microRNA-mRNA Interactions. mSphere 2020; 5:5/2/e00263-20. [PMID: 32321821 PMCID: PMC7178550 DOI: 10.1128/msphere.00263-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Tuberculosis (TB) is the leading cause of death from a single infectious agent globally, and the development of multidrug resistance represents a serious health concern, particularly in the developing world. Novel effective treatments are urgently required. xCT expression is known to increase susceptibility to TB, and certain polymorphisms in the gene encoding this protein interrupt the binding of microRNA and prevent its suppression. Taking advantage of the FDA approval for the use of sulfasalazine (SASP), which inhibits xCT-mediated cystine transport in humans, we demonstrate how host genotype-specific therapies tailored to the xCT genotype can improve TB outcomes. xCT forms part of the xc− cysteine-glutamate antiporter which inhibits antimicrobial inflammatory immune functions and thus increases susceptibility to tuberculosis (TB). However, the associations between xCT gene polymorphisms and susceptibility to TB, as well as whether these modulate xCT expression or affect treatment with the xCT inhibitor sulfasalazine (SASP), are unclear. In the present study, we genotyped xCT polymorphisms in a large Chinese cohort and found that the single-nucleotide polymorphism (SNP) rs13120371 was associated with susceptibility to TB. The rs13120371 AA genotype was strongly associated with an increased risk of TB and increased xCT mRNA expression levels compared to those with the GG or AG genotype. rs13120371 is located on the 3′ untranslated (UTR) region of the xCT gene, in the putative binding site for miR-142-3p, and the results of luciferase reporter assays indicated that the rs13120371 AA genotype inhibited the binding of miR-42-3p to xCT. Bacterial burden was also significantly higher in cells with the AA genotype than in those with the GG genotype. Furthermore, pretreatment with SASP alleviated this burden in cells with the AA genotype but conferred no benefit in cells with the GG phenotype. In summary, we identified a functional SNP (rs13120371) in the xCT 3′ UTR region that increases susceptibility to TB through interacting with miR-142-3p. IMPORTANCE Tuberculosis (TB) is the leading cause of death from a single infectious agent globally, and the development of multidrug resistance represents a serious health concern, particularly in the developing world. Novel effective treatments are urgently required. xCT expression is known to increase susceptibility to TB, and certain polymorphisms in the gene encoding this protein interrupt the binding of microRNA and prevent its suppression. Taking advantage of the FDA approval for the use of sulfasalazine (SASP), which inhibits xCT-mediated cystine transport in humans, we demonstrate how host genotype-specific therapies tailored to the xCT genotype can improve TB outcomes.
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13
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Luo Y, Suliman S, Asgari S, Amariuta T, Baglaenko Y, Martínez-Bonet M, Ishigaki K, Gutierrez-Arcelus M, Calderon R, Lecca L, León SR, Jimenez J, Yataco R, Contreras C, Galea JT, Becerra M, Nejentsev S, Nigrovic PA, Moody DB, Murray MB, Raychaudhuri S. Early progression to active tuberculosis is a highly heritable trait driven by 3q23 in Peruvians. Nat Commun 2019; 10:3765. [PMID: 31434886 PMCID: PMC6704092 DOI: 10.1038/s41467-019-11664-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 07/24/2019] [Indexed: 12/13/2022] Open
Abstract
Of the 1.8 billion people worldwide infected with Mycobacterium tuberculosis, 5-15% will develop active tuberculosis (TB). Approximately half will progress to active TB within the first 18 months after infection, presumably because they fail to mount an effective initial immune response. Here, in a genome-wide genetic study of early TB progression, we genotype 4002 active TB cases and their household contacts in Peru. We quantify genetic heritability ([Formula: see text]) of early TB progression to be 21.2% (standard error 0.08). This suggests TB progression has a strong genetic basis, and is comparable to traits with well-established genetic bases. We identify a novel association between early TB progression and variants located in a putative enhancer region on chromosome 3q23 (rs73226617, OR = 1.18; P = 3.93 × 10-8). With in silico and in vitro analyses we identify rs73226617 or rs148722713 as the likely functional variant and ATP1B3 as a potential causal target gene with monocyte specific function.
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Affiliation(s)
- Yang Luo
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sara Suliman
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Samira Asgari
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Tiffany Amariuta
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Graduate School of Arts and Sciences, Harvard University, Cambridge, MA, 02138, USA
| | - Yuriy Baglaenko
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Marta Martínez-Bonet
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kazuyoshi Ishigaki
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Maria Gutierrez-Arcelus
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | | | | | | | | | - Jerome T Galea
- School of Social Work, University of South Florida, Tampa, FL, USA
| | - Mercedes Becerra
- Department of Global Health and Social Medicine, and Division of Global Health Equity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sergey Nejentsev
- Department of Medicine, University of Cambridge, Cambridge, UK
- Department of Molecular Cell Biology and Immunology, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Peter A Nigrovic
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Immunology, Boston Children's Hospital, Boston, MA, USA
| | - D Branch Moody
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Megan B Murray
- Department of Global Health and Social Medicine, and Division of Global Health Equity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Soumya Raychaudhuri
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Arthritis Research UK Centre for Genetics and Genomics, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK.
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14
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Ma J, Lv Z, Wang J, Lu J. Relationship Between IL-10 Gene Polymorphism and Spinal Tuberculosis. Med Sci Monit 2019; 25:4901-4906. [PMID: 31264664 PMCID: PMC6618335 DOI: 10.12659/msm.914039] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Background To investigate the relation between interleukin-10 (IL-10) gene rs1800871 (A/G) polymorphism and spinal tuberculosis. Material/Methods A total of 129 patients with spinal tuberculosis (spinal tuberculosis group) and 106 healthy subjects receiving physical examination (control group) were enrolled in this study. The general data of these subjects were collected, and the C-reactive protein, erythrocyte sedimentation rate (ESR) and baseline hematologic function were examined. The rs1800871 (A/G) polymorphism in IL-10 gene was detected by TaqMan-MGB probe method. Results The C-reactive protein, ESR, white blood cell count, absolute neutrophil count and relative neutrophil count in spinal tuberculosis group were higher than those in control group, while the absolute lymphocyte count and relative lymphocyte count were lower than those in control group (p<0.05). Compared with AA genotype, GG and AG+GG genotypes showed statistically significant difference in distribution frequency (p<0.05), but no significant difference was detected between AG genotype and AA genotype (p>0.05). In spinal tuberculosis group, the frequency of G allele was higher than that of A allele (p<0.01). The C-reactive protein, ESR, white blood cell count and relative neutrophil count in GG genotype were increased compared with those in AG+GG genotype (p<0.05). Conclusions The rs1800871 (A/G) polymorphism in IL-10 gene is related to the susceptibility to spinal tuberculosis. Moreover, carrying G allele increases the risk of spinal tuberculosis.
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Affiliation(s)
- Jinming Ma
- Department of Orthopedics, Affiliated Zhongshan Hospital of Dalian University, Dalian, Liaoning, China (mainland)
| | - Zhongzhe Lv
- Department of Orthopedics, Affiliated Zhongshan Hospital of Dalian University, Dalian, Liaoning, China (mainland)
| | - Jianchuan Wang
- Department of Orthopedics, Affiliated Zhongshan Hospital of Dalian University, Dalian, Liaoning, China (mainland)
| | - Jianmin Lu
- Department of Orthopedics, Affiliated Zhongshan Hospital of Dalian University, Dalian, Liaoning, China (mainland)
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15
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Association between CD53 genetic polymorphisms and tuberculosis cases. Genes Genomics 2018; 41:389-395. [DOI: 10.1007/s13258-018-0764-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 11/07/2018] [Indexed: 01/23/2023]
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16
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Zheng R, Li Z, He F, Liu H, Chen J, Chen J, Xie X, Zhou J, Chen H, Wu X, Wu J, Chen B, Liu Y, Cui H, Fan L, Sha W, Liu Y, Wang J, Huang X, Zhang L, Xu F, Wang J, Feng Y, Qin L, Yang H, Liu Z, Cui Z, Liu F, Chen X, Gao S, Sun S, Shi Y, Ge B. Genome-wide association study identifies two risk loci for tuberculosis in Han Chinese. Nat Commun 2018; 9:4072. [PMID: 30287856 PMCID: PMC6172286 DOI: 10.1038/s41467-018-06539-w] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 09/05/2018] [Indexed: 12/04/2022] Open
Abstract
Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis (Mtb), and remains a leading public health problem. Previous studies have identified host genetic factors that contribute to Mtb infection outcomes. However, much of the heritability in TB remains unaccounted for and additional susceptibility loci most likely exist. We perform a multistage genome-wide association study on 2949 pulmonary TB patients and 5090 healthy controls (833 cases and 1220 controls were genome-wide genotyped) from Han Chinese population. We discover two risk loci: 14q24.3 (rs12437118, Pcombined = 1.72 × 10−11, OR = 1.277, ESRRB) and 20p13 (rs6114027, Pcombined = 2.37 × 10−11, OR = 1.339, TGM6). Moreover, we determine that the rs6114027 risk allele is related to decreased TGM6 transcripts in PBMCs from pulmonary TB patients and severer pulmonary TB disease. Furthermore, we find that tgm6-deficient mice are more susceptible to Mtb infection. Our results provide new insights into the genetic etiology of TB. Genetic risk loci for tuberculosis (TB) have so far been identified in African and Russian populations. Here, the authors perform a three-stage GWAS for TB in Han Chinese populations and find two risk loci near ESRRB and TGM6 and further demonstrate that tgm6 protects mice from Mtb infection.
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Affiliation(s)
- Ruijuan Zheng
- Shanghai Key Lab of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200043, China
| | - Zhiqiang Li
- The Affiliated Hospital of Qingdao University &The Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, 266003, China.,Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education) and the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Fusheng He
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Haipeng Liu
- Shanghai Key Lab of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200043, China.
| | - Jianhua Chen
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education) and the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Jiayu Chen
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Xuefeng Xie
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Juan Zhou
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education) and the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Hao Chen
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, 200092, China
| | - Xiangyang Wu
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, 200092, China
| | - Juehui Wu
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, 200092, China
| | - Boyu Chen
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education) and the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Yahui Liu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education) and the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Haiyan Cui
- Tuberculosis Center for Diagnosis and Treatment, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200043, China
| | - Lin Fan
- Tuberculosis Center for Diagnosis and Treatment, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200043, China
| | - Wei Sha
- Tuberculosis Center for Diagnosis and Treatment, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200043, China
| | - Yin Liu
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200043, China
| | - Jiqiang Wang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education) and the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Xiaochen Huang
- Shanghai Key Lab of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200043, China
| | - Linfeng Zhang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Feifan Xu
- Clinical Laboratory, The Sixth People's Hospital of Nantong, Jiangsu, 226011, China
| | - Jie Wang
- Shanghai Key Lab of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200043, China
| | - Yonghong Feng
- Shanghai Key Lab of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200043, China
| | - Lianhua Qin
- Shanghai Key Lab of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200043, China
| | - Hua Yang
- Shanghai Key Lab of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200043, China
| | - Zhonghua Liu
- Shanghai Key Lab of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200043, China
| | - Zhenglin Cui
- Shanghai Key Lab of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200043, China
| | - Feng Liu
- Shanghai Key Lab of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200043, China
| | - Xinchun Chen
- Shenzhen University School of Medicine, Shenzhen, 518060, China
| | - Shaorong Gao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Silong Sun
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.
| | - Yongyong Shi
- The Affiliated Hospital of Qingdao University &The Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, 266003, China. .,Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education) and the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, China. .,Department of Psychiatry, First Teaching Hospital of Xinjiang Medical University, Urumqi, 830054, China.
| | - Baoxue Ge
- Shanghai Key Lab of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200043, China. .,Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, 200092, China.
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17
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Hsieh MH, Ou CY, Hsieh WY, Kao HF, Lee SW, Wang JY, Wu LSH. Functional Analysis of Genetic Variations in Surfactant Protein D in Mycobacterial Infection and Their Association With Tuberculosis. Front Immunol 2018; 9:1543. [PMID: 30013576 PMCID: PMC6036787 DOI: 10.3389/fimmu.2018.01543] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 06/21/2018] [Indexed: 01/02/2023] Open
Abstract
Surfactant proteins (SPs)-A and -D are C-type lectins of the collectin family and function in the clearance of infectious particles in the lungs. Some polymorphisms of SPs that give rise to amino acid changes have been found to affect their function. Several SP-A gene polymorphisms have been reported to be associated with respiratory infection diseases, such as tuberculosis (TB). However, the relationship between surfactant proteins D (SP-D) polymorphisms and TB is still unclear. To study the associations between SP-D polymorphisms and TB, the correlations of SP-D polymorphisms with TB were examined in a case-control study, which included 364 patients with TB and 177 control subjects. In addition, we cloned two major SP-D exonic polymorphism C92T (rs721917) and A538G (rs2243639) constructs and used these for in vitro assays. The effects of SP-D polymorphisms on agglutination and other interactions with Mycobacterium bovis bacillus Calmette-Guérin (M. bovis BCG) were evaluated. In comparison with SP-D 92C (amino acid residue 16, Threonine), our results showed that SP-D 92T (amino acid residue 16, Methionine) had a lower binding ability to M. bovis BCG, a lower capacity to inhibit phagocytosis, lesser aggregation, poorer survival of bacillus Calmette-Guérin (BCG)-infected MH-S cells, and less inhibition of intracellular growth of M. bovis BCG. The case-control association study showed that the 92T homozygous genotype was a risk factor for TB. However, a lesser effect was seen for polymorphism A538G. In conclusion, the results of functional and genetic analyses of SP-D variants consistently showed that the SP-D 92T variant increased susceptibility to TB, which further confirmed the role of SP-D in pulmonary innate immunity against mycobacterial infection.
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Affiliation(s)
- Miao-Hsi Hsieh
- Institute of Basic Medical Science, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chih-Ying Ou
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Wen-Yu Hsieh
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Hui-Fang Kao
- Allergy and Clinical Immunology Research (ACIR) Center, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Shih-Wei Lee
- Chest Medicine, General Taoyuan Hospital, Taoyuan, Taiwan
| | - Jiu-Yao Wang
- Institute of Basic Medical Science, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Institute of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Institute of Respiratory Research, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Lawrence S H Wu
- Allergy and Clinical Immunology Research (ACIR) Center, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
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Jin HS, Lee SI, Park S. Association between ITGB2Genetic Polymorphisms and Tuberculosis. KOREAN JOURNAL OF CLINICAL LABORATORY SCIENCE 2018. [DOI: 10.15324/kjcls.2018.50.2.118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Hyun-Seok Jin
- Department of Biomedical Laboratory Science, College of Life and Health Sciences, Hoseo University, Asan, Korea
| | - Sang-In Lee
- Department of Biomedical Laboratory Science, College of Life and Health Sciences, Hoseo University, Asan, Korea
| | - Sangjung Park
- Department of Biomedical Laboratory Science, College of Life and Health Sciences, Hoseo University, Asan, Korea
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Correlation between MBL2/CD14/TNF-α gene polymorphisms and susceptibility to spinal tuberculosis in Chinese population. Biosci Rep 2018; 38:BSR20171140. [PMID: 29298876 PMCID: PMC5794501 DOI: 10.1042/bsr20171140] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 12/09/2017] [Accepted: 12/12/2017] [Indexed: 02/04/2023] Open
Abstract
Objective: The present study investigated the clinical significance of mannose-binding lectin 2 (MBL2), cluster of differentiation 14 (CD14) and tumour necrosis factor-α (TNF-α) gene polymorphisms in patients with spinal tuberculosis (TB) in Chinese population. Methods: A total of 240 patients with spinal TB were enrolled in the present study from May 2013 to August 2016 at Hangzhou Red Cross Hospital. A total of 150 age- and sex-matched healthy subjects were enrolled as controls. The genomic DNA was extracted from the peripheral blood of all subjects, and the MBL2, CD14 and TNF-α gene polymorphisms were detected by direct DNA sequencing. Results: (1) Compared with controls, patients with spinal TB exhibited a significantly higher frequency of the XY genotype at the −221G>C polymorphism as well as the Q allele and PQ genotype or an association with the QQ genotype at the +4C>T polymorphism in the MBL2 gene. (2) Compared with controls, patients with spinal TB exhibited a significantly higher frequency of the T allele and TT genotype or an association with the CT genotype at the −159C>T polymorphism in the CD14 gene. (3) Compared with controls, patients with spinal TB exhibited a significantly higher frequency of the T allele and the CT genotype or an association with the TT genotype at the TNF-857 polymorphism in the TNF-α gene. Conclusion: The −221G>C polymorphism of MBL2, the −159C>T polymorphism of CD14 and the TNF-857 polymorphism of TNF-α are risk factors for spinal TB and may be involved in the development of spinal TB in the Chinese population. These factors are indicators of susceptibility to spinal TB and require clinical attention.
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Areeshi MY, Mandal RK, Dar SA, Jawed A, Wahid M, Lohani M, Panda AK, Mishra BN, Akhter N, Haque S. MIF -173 G > C (rs755622) Gene Polymorphism Modulates Tuberculosis Risk: Evidence from a Meta-analysis and Trial Sequential Analysis. Sci Rep 2017; 7:17003. [PMID: 29208960 PMCID: PMC5717251 DOI: 10.1038/s41598-017-17308-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 11/22/2017] [Indexed: 01/07/2023] Open
Abstract
The macrophage migration inhibitory factor (MIF) is a cytokine that plays an important role in inhibiting the growth of pathogenic Mycobacterium tuberculosis (M.tb) and regulates immune responses against M.tb pathogen. MIF -173 G > C gene polymorphism may affect immunity in an individual and leads to susceptibility to tuberculosis (TB). A large number of studies have investigated the relevance of this polymorphism with TB risk, but their results were inconclusive. To obtain a precise conclusion, a meta-analysis was performed by retrieving six eligible studies from Google Scholar, PubMed (Medline), and EMBASE online databases. Overall combined analysis suggested increased TB risk between MIF -173 G > C polymorphism and overall risk in four genetic models, i.e., allelic (C vs. G: p = 0.001; OR = 1.517, 95% CI = 1.312 to 1.753), homozygous (CC vs. GG: p = 0.026; OR = 1.874, 95% CI = 1.079 to 3.257), heterozygous (GC vs. GG: p = 0.001; OR = 1.542, 95% CI = 1.273 to 1.868) and dominant model (CC + GC vs. GG: p = 0.001; OR = 1.631, 95% CI = 1.362 to 1.955). Similarly, increased TB risk was observed in subgroup analysis of Asian ethnicity. No publication bias was observed. These results suggested that MIF -173 G > C variant is a significant risk factor for TB in overall and in Asian populations, and can be used as prognostic marker for TB susceptibility.
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Affiliation(s)
- Mohammed Y Areeshi
- Research and Scientific Studies Unit, College of Nursing & Allied Health Sciences, Jazan University, Jazan, 45142, Saudi Arabia
| | - Raju K Mandal
- Research and Scientific Studies Unit, College of Nursing & Allied Health Sciences, Jazan University, Jazan, 45142, Saudi Arabia
| | - Sajad A Dar
- Research and Scientific Studies Unit, College of Nursing & Allied Health Sciences, Jazan University, Jazan, 45142, Saudi Arabia.,University College of Medical Sciences & GTB Hospital (University of Delhi), Delhi, 110095, India
| | - Arshad Jawed
- Research and Scientific Studies Unit, College of Nursing & Allied Health Sciences, Jazan University, Jazan, 45142, Saudi Arabia
| | - Mohd Wahid
- Research and Scientific Studies Unit, College of Nursing & Allied Health Sciences, Jazan University, Jazan, 45142, Saudi Arabia
| | - Mohtashim Lohani
- Research and Scientific Studies Unit, College of Nursing & Allied Health Sciences, Jazan University, Jazan, 45142, Saudi Arabia
| | - Aditya K Panda
- Centre for Life Sciences, Central University of Jharkhand, Ranchi, 835205, Jharkhand, India
| | - B N Mishra
- Department of Biotechnology, Institute of Engineering & Technology, Lucknow, 226021, Uttar Pradesh, India
| | - Naseem Akhter
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Albaha University, Albaha, 65431, Saudi Arabia
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing & Allied Health Sciences, Jazan University, Jazan, 45142, Saudi Arabia.
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Kinnear C, Hoal EG, Schurz H, van Helden PD, Möller M. The role of human host genetics in tuberculosis resistance. Expert Rev Respir Med 2017; 11:721-737. [PMID: 28703045 DOI: 10.1080/17476348.2017.1354700] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Tuberculosis (TB) remains a public health problem: the latest estimate of new incident cases per year is a staggering 10.4 million. Despite this overwhelming number, the majority of the immunocompetent population can control infection with Mycobacterium tuberculosis. The human genome underlies the immune response and contributes to the outcome of TB infection. Areas covered: Investigations of TB resistance in the general population have closely mirrored those of other infectious diseases and initially involved epidemiological observations. Linkage and association studies, including studies of VDR, SLC11A1 and HLA-DRB1 followed. Genome-wide association studies of common variants, not necessarily sufficient for disease, became possible after technological advancements. Other approaches involved the identification of those individuals with rare disease-causing mutations that strongly predispose to TB, epistasis and the role of ethnicity in disease. Despite these efforts, infection outcome, on an individual basis, cannot yet be predicted. Expert commentary: The early identification of future disease progressors is necessary to stem the TB epidemic. Human genetics may contribute to this endeavour and could in future suggest pathways to target for disease prevention. This will however require concerted efforts to establish large, well-phenotyped cohorts from different ethnicities, improved genomic resources and a better understanding of the human genome architecture.
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Affiliation(s)
- Craig Kinnear
- a SAMRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical TB Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences , Stellenbosch University , Cape Town , South Africa
| | - Eileen G Hoal
- a SAMRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical TB Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences , Stellenbosch University , Cape Town , South Africa
| | - Haiko Schurz
- a SAMRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical TB Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences , Stellenbosch University , Cape Town , South Africa
| | - Paul D van Helden
- a SAMRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical TB Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences , Stellenbosch University , Cape Town , South Africa
| | - Marlo Möller
- a SAMRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical TB Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences , Stellenbosch University , Cape Town , South Africa
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Lu Y, Zhu Y, Wang X, Wang F, Peng J, Hou H, Sun Z. FOXO3 rs12212067: T > G Association with Active Tuberculosis in Han Chinese Population. Inflammation 2016. [PMID: 26223437 DOI: 10.1007/s10753-015-0217-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
It is well known that the human innate immune and adaptive immune response play important role in tuberculosis (TB) infection and progress. Emerging evidence shows that FOXO3 plays an important role in the human immune system. Recent research has shown that the FOXO3 genetic variants are associated malaria infection. In this study, 268 confirmed TB patients, 321 patients with latent tuberculosis infection (LTBI), and 475 TB-free controls were recruited; the single-nucleotide polymorphism (SNP) rs12212067: T > G in FOXO3 was genotyped using predesigned TaqMan® allelic discrimination assays. The results showed that the G allele of rs12212067 in FOXO3 was more common in health control and the latent TB group compared with the active TB group (p = 0.048, odds ratio (OR) 95 % confidence intervals (CI) = 1.37 (1.00-1.89); p = 0.042, OR 95 % CI = 1.42 (1.01-1.99), respectively); furthermore, within active TB patients, the G allele of rs12212067 in FOXO3 was more frequent in extra-pulmonary tuberculosis (EPTB) group compared to pulmonary tuberculosis (PTB) group (p = 0.035, OR 95 % CI = 0.57 (0.33-0.97). In conclusion, this study found that rs12212067 in FOXO3 was associated with increased risk of active TB. The minor G allele might be a protection factor which was found more common in latent TB patients and healthy controls than active TB patients.
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Affiliation(s)
- Yanjun Lu
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095# Jiefangdadao, Wuhan, 430030, China
| | - Yaowu Zhu
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095# Jiefangdadao, Wuhan, 430030, China
| | - Xiong Wang
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095# Jiefangdadao, Wuhan, 430030, China
| | - Feng Wang
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095# Jiefangdadao, Wuhan, 430030, China
| | - Jing Peng
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095# Jiefangdadao, Wuhan, 430030, China
| | - Hongyan Hou
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095# Jiefangdadao, Wuhan, 430030, China
| | - Ziyong Sun
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095# Jiefangdadao, Wuhan, 430030, China.
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WILBUR RACHELE, CORBETT STEVENM, DRISKO JEANNEA. Tuberculosis morbidity at Haskell Institute, a Native American Youth Boarding School 1910-1940: ∧. ANNALS OF ANTHROPOLOGICAL PRACTICE 2016. [DOI: 10.1111/napa.12092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Abstract
ABSTRACT
Familial risk of tuberculosis (TB) has been recognized for centuries. Largely through studies of mono- and dizygotic twin concordance rates, studies of families with Mendelian susceptibility to mycobacterial disease, and candidate gene studies performed in the 20th century, it was recognized that susceptibility to TB disease has a substantial host genetic component. Limitations in candidate gene studies and early linkage studies made the robust identification of specific loci associated with disease challenging, and few loci have been convincingly associated across multiple populations. Genome-wide and transcriptome-wide association studies, based on microarray (commonly known as genechip) technologies, conducted in the past decade have helped shed some light on pathogenesis but only a handful of new pathways have been identified. This apparent paradox, of high heritability but few replicable associations, has spurred a new wave of collaborative global studies. This review aims to comprehensively review the heritability of TB, critically review the host genetic and transcriptomic correlates of disease, and highlight current studies and future prospects in the study of host genomics in TB. An implicit goal of elucidating host genetic correlates of susceptibility to
Mycobacterium tuberculosis
infection or TB disease is to identify pathophysiological features amenable to translation to new preventive, diagnostic, or therapeutic interventions. The translation of genomic insights into new clinical tools is therefore also discussed.
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Nakauchi A, Wong JH, Mahasirimongkol S, Yanai H, Yuliwulandari R, Mabuchi A, Liu X, Mushiroda T, Wattanapokayakit S, Miyagawa T, Keicho N, Tokunaga K. Identification of ITPA on chromosome 20 as a susceptibility gene for young-onset tuberculosis. Hum Genome Var 2016; 3:15067. [PMID: 27081565 PMCID: PMC4760120 DOI: 10.1038/hgv.2015.67] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 10/30/2015] [Accepted: 11/04/2015] [Indexed: 01/31/2023] Open
Abstract
Tuberculosis (TB) is a complex disease, and both genetic and environmental factors contribute to disease progression. A previous genome-wide linkage study in Thailand determined that chromosome 20p13-12.3 may contain risk factors for young-onset disease. The present study aimed to identify novel susceptibility genes for young-onset TB within a 1-Mbp target region adjacent to the top-ranking risk marker in Chr.20p13-12.3. We performed next-generation sequencing (NGS) of the region in 13 young patients from multi-case families in Thailand. We then selected the functionally interesting single-nucleotide polymorphisms as candidates for subsequent analyses. The detected candidates rs13830 and rs1127354 in ITPA showed an association with young (<45 years old) TB patients. However, there was no association in old (⩾45 years old) patients. These findings confirm that stratifying patients based on age of TB onset can be important for identifying genetic risk factors for TB susceptibility. In addition, in silico expression quantitative trait loci analyses indicated that ITPA expression was associated with rs13830 genotype. This is the first study to use NGS resequencing to gain insight into host genetic factors associated with TB and to report a significant association for ITPA with host susceptibility in young-onset TB. The study also demonstrated the effectiveness of NGS in identifying susceptibility genes in common diseases.
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Affiliation(s)
- Ayaka Nakauchi
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo , Tokyo, Japan
| | - Jing Hao Wong
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo , Tokyo, Japan
| | - Surakameth Mahasirimongkol
- Medical Genetics Center, Medical Life Sciences Institute, Department of Medical Sciences, Ministry of Public Health , Nonthaburi, Thailand
| | - Hideki Yanai
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Fukujuji Hospital, Japan Anti-Tuberculosis Association (JATA), Tokyo, Japan
| | - Rika Yuliwulandari
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Genomic Medicine Research Group, YARSI Research Institute, YARSI University, Jakarta, Indonesia
| | - Akihiko Mabuchi
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo , Tokyo, Japan
| | - Xiaoxi Liu
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; RIKEN Brain Science Institute, Saitama, Japan
| | - Taisei Mushiroda
- Research Group for Pharmacogenomics, RIKEN Center for Integrative Medical Sciences , Kanagawa, Japan
| | - Sukanya Wattanapokayakit
- Medical Genetics Center, Medical Life Sciences Institute, Department of Medical Sciences, Ministry of Public Health , Nonthaburi, Thailand
| | - Taku Miyagawa
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo , Tokyo, Japan
| | - Naoto Keicho
- Department of Pathophysiology and Host Defense, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association (JATA) , Tokyo, Japan
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo , Tokyo, Japan
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Pitchappan RM. Not all the infected develop the disease - A "Lotus and Cactus" model. INFECTION GENETICS AND EVOLUTION 2015; 40:303-309. [PMID: 26611827 DOI: 10.1016/j.meegid.2015.11.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 11/07/2015] [Accepted: 11/09/2015] [Indexed: 10/22/2022]
Abstract
The immunogenetic dictum "not all the infected develop the disease" can best be explained by a "Lotus and Cactus" model. Lotuses grow in ponds and cacti in deserts: analogously, we can say that tubercle patient's lung (genetic makeup) functions as an ideal 'broth' for Mycobacterium tuberculosis (M.tb) germs to grow, but not the lungs of an endemic control. HLA association studies from Europe to Asia since 1983 till date, have shown a persistent HLA DR2 (15) association. Further, HLA DR2 and non-DR2 endemic controls showed disparate patterns of immune responses and gene expressions. The host and pathogen MHC diversities, Th1-Th2 paradigm and cytokine circuits all may play a crucial role in TB susceptibility. It is possible to decipher the protective immunity by controlling the known confounders - epidemiological, demographic, socio-biological and also host and pathogen diversities. This has become significant with our understanding on the 'out of Africa' migration and neolithic co-dispersal of M.tb with modern human. Divergence and expansion of various MHCs (eg HLA-DRB1*15, HLA-B*57) and non-MHC alleles in various continents might be responsible for the skewed transmission and distribution of the infectious diseases around the globe. The 'Lotus and Cactus' model proposed here exemplifies this. A holistic genetic epidemiology approach employing modern tools is the need of the hour to better understand infectious disease susceptibility.
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Affiliation(s)
- Ramasamy M Pitchappan
- Chettinad Academy of Research & Education, OMR Road, Kelambakkam, (Chennai), Tamil Nadu 603103, India
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Campo M, Randhawa AK, Dunstan S, Farrar J, Caws M, Bang ND, Lan NN, Hong Chau TT, Horne DJ, Thuong NT, Thwaites GE, Hawn TR. Common polymorphisms in the CD43 gene region are associated with tuberculosis disease and mortality. Am J Respir Cell Mol Biol 2015; 52:342-8. [PMID: 25078322 DOI: 10.1165/rcmb.2014-0114oc] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
CD43, a surface glycoprotein, regulates Mycobacterium tuberculosis macrophage binding, replication, and proinflammatory cytokine induction in a murine model. We hypothesized that single-nucleotide polymorphisms (SNPs) in the CD43 gene region are associated with human tuberculosis (TB) susceptibility. We performed a case-population study in discovery (352 TB cases and 382 control subjects) and validation cohorts (339 TB cases and 376 control subjects). We examined whether 11 haplotype-tagging SNPs in the CD43 gene region were associated with tuberculous meningitis (TBM) and pulmonary TB (PTB) in Vietnam. Three SNPs from the CD43 gene region were associated with TB susceptibility with a genotypic model. The association fit a recessive genetic model and was greater for TBM than for PTB (for TBM: rs4788172, odds ratio [OR], 1.64; 95% confidence interval [CI], 1.04-2.59, rs17842268 [OR, 2.20; 95% CI, 1.29-3.76, and rs12596308 [OR, 2.38; 95% CI, 1.47-3.89]). Among TBM cases, rs17842268 was associated with decreased survival (hazard ratio, 2.7; 95% CI, 1.1-6.5; P = 0.011). In addition, rs12596308 and rs17842268 were associated with focal neurologic deficit at TBM presentation. Our data suggest that CD43 polymorphisms are associated with TB susceptibility, disease manifestations, and worse outcomes. To our knowledge, this is the first report that links CD43 genetic variants with susceptibility and outcome from a disease.
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Epstein-Barr virus-induced gene 3 (EBI3) polymorphisms and expression are associated with susceptibility to pulmonary tuberculosis. Tuberculosis (Edinb) 2015; 95:497-504. [PMID: 25937126 DOI: 10.1016/j.tube.2015.03.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 03/21/2015] [Indexed: 11/23/2022]
Abstract
Tuberculosis (TB) remains a major global health problem and host genetic factors play a critical role in susceptibility and resistance to TB. The aim of this study was to identify novel candidate genes associated with TB susceptibility. We performed a population-based case-control study to genotype 13 tag SNPs spanning Epstein-Barr virus-induced gene 3 (EBI3), colony stimulating factor 2 (CSF2), IL-4, interferon beta 1 (IFNB1), chemokine (C-X-C motif) ligand 14 (CXCL14) and myeloid differentiation primary response gene 88 (Myd88) genes in 435 pulmonary TB patients and 375 health donors from China. We observed that EBI3 gene rs4740 polymorphism was associated with susceptibility to pulmonary tuberculosis (PTB) and the allele G was associated with a protective effect against PTB. Furthermore, EBI3 deficiency led to reduced bacterial burden and histopathological impairment in the lung of mice infected with Mycobacterium bovis BCG. Meanwhile, higher abundance of EBI3 was observed in the granuloma of PTB patients and in the lung tissue of BCG-infected mice. Of note, the expression of EBI3 in macrophages was remarkably induced by mycobacteria infection at both mRNA and protein level. In conclusion, EBI3 gene rs4740 polymorphism is closely associated with susceptibility to PTB and the elevation and enrichment of EBI3 in the lung which at least partially derived from macrophages may contribute to the exacerbation of mycobacterial infection.
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Balcells ME, García P, Meza P, Peña C, Cifuentes M, Couvin D, Rastogi N. A first insight on the population structure of Mycobacterium tuberculosis complex as studied by spoligotyping and MIRU-VNTRs in Santiago, Chile. PLoS One 2015; 10:e0118007. [PMID: 25671320 PMCID: PMC4324903 DOI: 10.1371/journal.pone.0118007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 01/05/2015] [Indexed: 02/04/2023] Open
Abstract
Tuberculosis (TB) remains a significant public health problem worldwide, but the ecology of the prevalent mycobacterial strains, and their transmission, can vary depending on country and region. Chile is a country with low incidence of TB, that has a geographically isolated location in relation to the rest of South American countries due to the Andes Mountains, but recent migration from neighboring countries has changed this situation. We aimed to assess the genotypic diversity of Mycobacterium tuberculosis complex (MTBC) strains in Santiago, Chile, and compare with reports from other Latin-American countries. We analyzed MTBC isolates from pulmonary tuberculosis cases collected between years 2008 and 2013 in Central Santiago, using two genotyping methods: spoligotyping and 12-loci mycobacterial interspersed repetitive unit-variable number of tandem repeats (MIRU-VNTRs). Data obtained were analyzed and compared to the SITVIT2 database. Mean age of the patients was 47.5 years and 61% were male; 11.6% were migrants. Of 103 strains (1 isolate/patient) included, there were 56 distinct spoligotype patterns. Of these, 16 strains (15.5%) corresponded to orphan strains in the SITVIT2 database, not previously reported. Latin American and Mediterranean (LAM) (34%) and T (33%) lineages were the most prevalent strains, followed by Haarlem lineage (16.5%). Beijing family was scarcely represented with only two cases (1.9%), one of them isolated from a Peruvian migrant. The most frequent clustered spoligotypes were SIT33/LAM3 (10.7%), SIT53/T1 (8.7%), SIT50/H3 (7.8%), and SIT37/T3 (6.8%). We conclude that LAM and T genotypes are the most prevalent genotypes of MTBC in Santiago, Chile, and together correspond to almost two thirds of analyzed strains, which is similar to strain distribution reported from other countries of Latin America. Nevertheless, the high proportion of SIT37/T3, which was rarely found in other Latin American countries, may underline a specific history or demographics of Chile related to probable human migrations and evolutions.
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Affiliation(s)
- María Elvira Balcells
- Infectious Diseases Department, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Patricia García
- Microbiology Laboratory, Clinical Laboratory Department, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Paulina Meza
- Microbiology Laboratory, Clinical Laboratory Department, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Carlos Peña
- Respiratory Division and Microbiology Laboratory, Hospital San Borja Arriarán, Santiago, Chile
| | - Marcela Cifuentes
- Respiratory Division and Microbiology Laboratory, Hospital San Borja Arriarán, Santiago, Chile
| | - David Couvin
- WHO Supranational TB Reference Laboratory, Institut Pasteur de la Guadeloupe, Abymes, Guadeloupe, France
| | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory, Institut Pasteur de la Guadeloupe, Abymes, Guadeloupe, France
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Polymorphisms of SP110 are associated with both pulmonary and extra-pulmonary tuberculosis among the Vietnamese. PLoS One 2014; 9:e99496. [PMID: 25006821 PMCID: PMC4090157 DOI: 10.1371/journal.pone.0099496] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Accepted: 05/15/2014] [Indexed: 11/20/2022] Open
Abstract
Background Tuberculosis (TB) is an infectious disease that remains a major cause of morbidity and mortality worldwide, yet the reasons why only 10% of people infected with Mycobacterium tuberculosis go on to develop clinical disease are poorly understood. Genetically determined variation in the host immune response is one factor influencing the response to M. tuberculosis. SP110 is an interferon-responsive nuclear body protein with critical roles in cell cycling, apoptosis and immunity to infection. However association studies of the gene with clinical TB in different populations have produced conflicting results. Methods To examine the importance of the SP110 gene in immunity to TB in the Vietnamese we conducted a case-control genetic association study of 24 SP110 variants, in 663 patients with microbiologically proven TB and 566 unaffected control subjects from three tertiary hospitals in northern Vietnam. Results Five SNPs within SP110 were associated with all forms of TB, including four SNPs at the C terminus (rs10208770, rs10498244, rs16826860, rs11678451) under a dominant model and one SNP under a recessive model, rs7601176. Two of these SNPs were associated with pulmonary TB (rs10208770 and rs16826860) and one with extra-pulmonary TB (rs10498244). Conclusion SP110 variants were associated with increased susceptibility to both pulmonary and extra-pulmonary TB in the Vietnamese. Genetic variants in SP110 may influence macrophage signaling responses and apoptosis during M. tuberculosis infection, however further research is required to establish the mechanism by which SP110 influences immunity to tuberculosis infection.
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Jiang Y, Wan L, Zhang Z, Liu H, Pang H, Zhang W, Zhao X, Wang H, Li G, Chen C, Kan B, Wan K. Conserved alanine rich protein Rv3878 in Mycobacterium tuberculosis contains sequence polymorphisms. Tuberculosis (Edinb) 2014; 94:245-51. [PMID: 24674998 DOI: 10.1016/j.tube.2014.02.002] [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: 09/16/2013] [Revised: 02/03/2014] [Accepted: 02/04/2014] [Indexed: 11/28/2022]
Abstract
Host immune pressure and associated parasite immune evasion are key features of host-pathogen co-evolution. A previous study showed that human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved and thus it was deduced that M. tuberculosis lacks antigenic variation and immune evasion. Here, we selected 162 clinical M. tuberculosis complex (MTBC) isolates from China, amplified gene encoding Rv3878 and compared the sequences. The results showed that Rv3878, a conserved hypothetical alanine rich protein, is not conserved in M. tuberculosis strains and there are polymorphisms existing in the protein. The large number of amino acid changes in its T cell epitopes may reflect ongoing immune evasion.
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Affiliation(s)
- Yi Jiang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Beijing 102206, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China.
| | - Li Wan
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Beijing 102206, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
| | - Zhijian Zhang
- Respiratory Diseases Department of Nanlou, Chinese People's Liberation Army General Hospital, 28# Fuxing Road, Haidian District, Beijing 100853, China
| | - Haican Liu
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Beijing 102206, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
| | - Hui Pang
- Immunology Department, Changzhi Medical College, Shanxi, China
| | - Wen Zhang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Beijing 102206, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
| | - Xiuqin Zhao
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Beijing 102206, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
| | - Haiyin Wang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Beijing 102206, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
| | - Guilian Li
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Beijing 102206, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
| | - Chen Chen
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Beijing 102206, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
| | - Biao Kan
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Beijing 102206, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China.
| | - Kanglin Wan
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Beijing 102206, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China.
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Macrophage migration inhibitory factor (MIF) is a critical mediator of the innate immune response to Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 2013; 110:E2997-3006. [PMID: 23882081 DOI: 10.1073/pnas.1301128110] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Macrophage migration inhibitory factor (MIF), an innate cytokine encoded in a functionally polymorphic genetic locus, contributes to detrimental inflammation but may be crucial for controlling infection. We explored the role of variant MIF alleles in tuberculosis. In a Ugandan cohort, genetic low expressers of MIF were 2.4-times more frequently identified among patients with Mycobacterium tuberculosis (TB) bacteremia than those without. We also found mycobacteria-stimulated transcription of MIF and serum MIF levels to be correlated with MIF genotype in human macrophages and in a separate cohort of US TB patients, respectively. To determine mechanisms for MIF's protective role, we studied both aerosolized and i.v. models of mycobacterial infection and observed MIF-deficient mice to succumb more quickly with higher organism burden, increased lung pathology, and decreased innate cytokine production (TNF-α, IL-12, IL-10). MIF-deficient animals showed increased pulmonary neutrophil accumulation but preserved adaptive immune response. MIF-deficient macrophages demonstrated decreased cytokine and reactive oxygen production and impaired mycobacterial killing. Transcriptional investigation of MIF-deficient macrophages revealed reduced expression of the pattern recognition receptor dectin-1; restoration of dectin-1 expression recovered innate cytokine production and mycobacterial killing. Our data place MIF in a crucial upstream position in the innate immune response to mycobacteria and suggest that commonly occurring low expression MIF alleles confer an increased risk of TB disease in some populations.
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Grant AV, El Baghdadi J, Sabri A, El Azbaoui S, Alaoui-Tahiri K, Abderrahmani Rhorfi I, Gharbaoui Y, Abid A, Benkirane M, Raharimanga V, Richard V, Orlova M, Boland A, Migaud M, Okada S, Nolan DK, Bustamante J, Barreiro LB, Schurr E, Boisson-Dupuis S, Rasolofo V, Casanova JL, Abel L. Age-dependent association between pulmonary tuberculosis and common TOX variants in the 8q12-13 linkage region. Am J Hum Genet 2013; 92:407-14. [PMID: 23415668 DOI: 10.1016/j.ajhg.2013.01.013] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 10/12/2012] [Accepted: 01/22/2013] [Indexed: 11/19/2022] Open
Abstract
Only a small fraction of individuals infected with Mycobacterium tuberculosis develop clinical tuberculosis (TB) in their lifetime. Genetic epidemiological evidence suggests a genetic determinism of pulmonary TB (PTB), but the molecular basis of genetic predisposition to PTB remains largely unknown. We used a positional-cloning approach to carry out ultrafine linkage-disequilibrium mapping of a previously identified susceptibility locus in chromosomal region 8q12-13 by genotyping 3,216 SNPs in a family-based Moroccan sample including 286 offspring with PTB. We observed 44 PTB-associated SNPs (p < 0.01), which were genotyped in an independent set of 317 cases and 650 controls from Morocco. A single signal, consisting of two correlated SNPs close to TOX, rs1568952 and rs2726600 (combined p = 1.1 × 10(-5) and 9.2 × 10(-5), respectively), was replicated. Stronger evidence of association was found in individuals who developed PTB before the age of 25 years (combined p for rs1568952 = 4.4 × 10(-8); odds ratio of PTB for AA versus AG/GG = 3.09 [1.99-4.78]). The association with rs2726600 (p = 0.04) was subsequently replicated in PTB-affected subjects under 25 years in a study of 243 nuclear families from Madagascar. Stronger evidence of replication in Madagascar was obtained for additional SNPs in strong linkage disequilibrium with the two initial SNPs (p = 0.003 for rs2726597), further confirming the signal. We thus identified around rs1568952 and rs2726600 a cluster of SNPs strongly associated with early-onset PTB in Morocco and Madagascar. SNP rs2726600 is located in a transcription-factor binding site in the 3' region of TOX, and further functional explorations will focus on CD4 T lymphocytes.
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Affiliation(s)
- Audrey V Grant
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale U980, Paris, France
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Abstract
Tuberculosis (TB) is a leading cause worldwide of human mortality attributable to a single infectious agent. Recent studies targeting candidate genes and "case-control" association have revealed numerous polymorphisms implicated in host susceptibility to TB. Here, we review current progress in the understanding of causative polymorphisms in host innate immune genes associated with TB pathogenesis. We discuss genes encoding several types of proteins: macrophage receptors, such as the mannose receptor (MR, CD206), dendritic cell-specific ICAM-3-grabbing nonintegrin (DC-SIGN, CD209), Dectin-1, Toll-like receptors (TLRs), complement receptor 3 (CR3, CD11b/CD18), nucleotide oligomerization domain 1 (NOD1) and NOD2, CD14, P2X7, and the vitamin D nuclear receptor (VDR); soluble C-type lectins, such as surfactant protein-A (SP-A), SP-D, and mannose-binding lectin (MBL); phagocyte cytokines, such as tumor necrosis factor (TNF), interleukin-1β (IL-1β), IL-6, IL-10, IL-12, and IL-18; chemokines, such as IL-8, monocyte chemoattractant protein 1 (MCP-1), RANTES, and CXCL10; and other important innate immune molecules, such as inducible nitric oxide synthase (iNOS) and solute carrier protein 11A1 (SLC11A1). Polymorphisms in these genes have been variably associated with susceptibility to TB among different populations. This apparent variability is probably accounted for by evolutionary selection pressure as a result of long-term host-pathogen interactions in certain regions or populations and, in part, by lack of proper study design and limited knowledge of molecular and functional effects of the implicated genetic variants. Finally, we discuss genomic technologies that hold promise for resolving questions regarding the evolutionary paths of the human genome, functional effects of polymorphisms, and corollary impacts of adaptation on human health, ultimately leading to novel approaches to controlling TB.
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Affiliation(s)
- Abul K. Azad
- Department of Microbial Infection and Immunity, Center for Microbial Interface Biology
| | - Wolfgang Sadee
- Department of Pharmacology, Program in Pharmacogenomics, The Ohio State University, Columbus, Ohio, USA
| | - Larry S. Schlesinger
- Department of Microbial Infection and Immunity, Center for Microbial Interface Biology
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Tagging single nucleotide polymorphisms in the IRF1 and IRF8 genes and tuberculosis susceptibility. PLoS One 2012; 7:e42104. [PMID: 22879909 PMCID: PMC3412841 DOI: 10.1371/journal.pone.0042104] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Accepted: 07/02/2012] [Indexed: 11/19/2022] Open
Abstract
Genes encoding IRF1 and IRF8 protein have been proposed as candidate tuberculosis susceptibility genes. In order to elucidate whether the IRF1 and IRF8 variants were associated with tuberculosis susceptibility, we conducted a case-control study consisting of 495 controls and 452 ethnically matched cases with tuberculosis in a Chinese population. Seven haplotype tagging single-nucleotide polymorphisms (tagSNPs) (rs2057656; rs2706381; rs2070724; rs2070721; rs2549008; rs2549007; rs2706386) from HapMap database were analyzed, which provided an almost complete coverage of the genetic variations in the IRF1 gene. Fifteen tagSNPs (rs12924316; rs182511; rs305080; rs2292980; rs925994; rs424971; rs16939967; rs11117415; rs4843860; rs9926411; rs8064189; rs12929551; rs10514611; rs1044873; rs6638) were observed in the IRF8 gene. All these tagSNPs were genotyped by SNPstream genotyping and SNaPshot typing. None of the seven tagSNPs was individually associated with tuberculosis in the IRF1 gene. In the IRF8 gene, interestingly, we found that three tagSNPs (rs925994 and rs11117415 located in the intron region; rs10514611 located in the 3′UTR) were associated with risk of tuberculosis after Bonferroni correction. Per allele OR was 1.75 (95% CI 1.35∼2.27, P = 0.002), 4.75 (95% CI 2.16∼10.43, P = 0.002) and 3.39 (95% CI 1.60∼7.20, P = 0.015) respectively. Luciferase reporter gene assay showed that the construct that contained the non-risk allele C of rs10514611 showed significantly higher luciferase activity than did the risk T allele (P<0.01), which implied rs10514611 was a potential functional SNP site. Our results indicated that the IRF8 gene might participate in genetic susceptibility to tuberculosis in a Chinese population.
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Higa GM, Hicks J, Isabella C. Adjudication of the alleged role of vitamin d in the antimicrobial pathway. SCIENTIFICA 2012; 2012:129516. [PMID: 24278668 PMCID: PMC3820478 DOI: 10.6064/2012/129516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 06/13/2012] [Indexed: 06/02/2023]
Abstract
Dynamic interactions between microorganism and host have evolved in such a way that while microbial pathogens are the cause of many human infections, a symbiotic relationship is also known to exist. Another important anomaly is that exposure to pathogenic organisms does not necessarily result in development of clinical disease. The latter conclusion infers that susceptibility to infectious disease can be modified by host-related factors. Arguably the two most prominent factors are genetic variability and immunologic status of the exposed individual. Because of the Human Genome and the HapMap projects, developments in genotyping technology have brought the possibility of identifying associations between specific genetic alterations and common diseases closer to reality. In addition, a growing body of evidence suggests vitamin D has an important contributory role in the antimicrobial pathway.
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Affiliation(s)
- Gerald M. Higa
- Schools of Pharmacy and Medicine and the Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, WV 26506, USA
| | - Jason Hicks
- School of Pharmacy, West Virginia University, Morgantown, WV 26506, USA
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38
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Kobayashi K, Yuliwulandari R, Yanai H, Lien LT, Hang NTL, Hijikata M, Keicho N, Tokunaga K. Association of CD209 polymorphisms with tuberculosis in an Indonesian population. Hum Immunol 2011; 72:741-5. [DOI: 10.1016/j.humimm.2011.04.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Revised: 04/09/2011] [Accepted: 04/18/2011] [Indexed: 10/18/2022]
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Randhawa AK, Shey MS, Keyser A, Peixoto B, Wells RD, de Kock M, Lerumo L, Hughes J, Hussey G, Hawkridge A, Kaplan G, Hanekom WA, Hawn TR. Association of human TLR1 and TLR6 deficiency with altered immune responses to BCG vaccination in South African infants. PLoS Pathog 2011; 7:e1002174. [PMID: 21852947 PMCID: PMC3154845 DOI: 10.1371/journal.ppat.1002174] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Accepted: 06/06/2011] [Indexed: 12/19/2022] Open
Abstract
The development of effective immunoprophylaxis against tuberculosis (TB) remains a global priority, but is hampered by a partially protective Bacillus Calmette-Guérin (BCG) vaccine and an incomplete understanding of the mechanisms of immunity to Mycobacterium tuberculosis. Although host genetic factors may be a primary reason for BCG's variable and inadequate efficacy, this possibility has not been intensively examined. We hypothesized that Toll-like receptor (TLR) variation is associated with altered in vivo immune responses to BCG. We examined whether functionally defined TLR pathway polymorphisms were associated with T cell cytokine responses in whole blood stimulated ex vivo with BCG 10 weeks after newborn BCG vaccination of South African infants. In the primary analysis, polymorphism TLR6_C745T (P249S) was associated with increased BCG-induced IFN-γ in both discovery (n = 240) and validation (n = 240) cohorts. In secondary analyses of the combined cohort, TLR1_T1805G (I602S) and TLR6_G1083C (synonymous) were associated with increased IFN-γ, TLR6_G1083C and TLR6_C745T were associated with increased IL-2, and TLR1_A1188T was associated with increased IFN-γ and IL-2. For each of these polymorphisms, the hypo-responsive allele, as defined by innate immunity signaling assays, was associated with increased production of TH1-type T cell cytokines (IFN-γ or IL-2). After stimulation with TLR1/6 lipopeptide ligands, PBMCs from TLR1/6-deficient individuals (stratified by TLR1_T1805G and TLR6_C745T hyporesponsive genotypes) secreted lower amounts of IL-6 and IL-10 compared to those with responsive TLR1/6 genotypes. In contrast, no IL-12p70 was secreted by PBMCs or monocytes. These data support a mechanism where TLR1/6 polymorphisms modulate TH1 T-cell polarization through genetic regulation of monocyte IL-10 secretion in the absence of IL-12. These studies provide evidence that functionally defined innate immune gene variants are associated with the development of adaptive immune responses after in vivo vaccination against a bacterial pathogen in humans. These findings could potentially guide novel adjuvant vaccine strategies as well as have implications for IFN-γ-based diagnostic testing for TB. Tuberculosis (TB) is one of the leading infectious causes of death worldwide. The current vaccine for TB, BCG, is widely used but it is not highly effective in preventing disease. We investigated the role of host genetics in the immune response to BCG vaccination. We found that variants of innate immunity genes (TLR1 and TLR6) were associated with BCG-induced immune responses after vaccination. These findings may guide new strategies for vaccine development as well as diagnosis of TB.
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Affiliation(s)
- April Kaur Randhawa
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Muki S. Shey
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Diseases and Molecular Medicine and School of Child and Adolescent Health, University of Cape Town, South Africa
| | - Alana Keyser
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Diseases and Molecular Medicine and School of Child and Adolescent Health, University of Cape Town, South Africa
| | - Blas Peixoto
- Public Health Research Institute, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, United States of America
| | - Richard D. Wells
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Marwou de Kock
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Diseases and Molecular Medicine and School of Child and Adolescent Health, University of Cape Town, South Africa
| | - Lesedi Lerumo
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Diseases and Molecular Medicine and School of Child and Adolescent Health, University of Cape Town, South Africa
| | - Jane Hughes
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Diseases and Molecular Medicine and School of Child and Adolescent Health, University of Cape Town, South Africa
| | - Gregory Hussey
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Diseases and Molecular Medicine and School of Child and Adolescent Health, University of Cape Town, South Africa
| | - Anthony Hawkridge
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Diseases and Molecular Medicine and School of Child and Adolescent Health, University of Cape Town, South Africa
| | - Gilla Kaplan
- Public Health Research Institute, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, United States of America
| | - Willem A. Hanekom
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Diseases and Molecular Medicine and School of Child and Adolescent Health, University of Cape Town, South Africa
| | - Thomas R. Hawn
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
- * E-mail:
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Hussain R, Talat N, Ansari A, Shahid F, Hasan Z, Dawood G. Endogenously activated interleukin-4 differentiates disease progressors and non-progressors in tuberculosis susceptible families: a 2-year biomarkers follow-up study. J Clin Immunol 2011; 31:913-23. [PMID: 21755390 DOI: 10.1007/s10875-011-9566-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Accepted: 06/29/2011] [Indexed: 01/09/2023]
Abstract
OBJECTIVE Dynamic cytokine profiles from endogenously activated T cells in transit from lymph node to the infected sites via the blood compartment after recent exposure to Mycobacterium tuberculosis may differentiate disease progressors from non-disease progressors in a BCG-vaccinated population. METHODS Household contacts (N = 107) from families with (six families) or without (14 families) secondary cases were assessed for Types 1 and 2 cytokines serially in plasma of whole blood cultures without exogenous stimulation. "ARMS" PCR was carried out for detection of single nucleotide polymorphism T/A in IFN-γ +874. RESULTS In the absence of IFN-γ expansion, raised IL-4 at 6 months was associated with disease progression in TB-susceptible families. Resistant families on the other hand showed overrepresentation of IFN-γ +874 A allele and expansion of IFN-γ secreting cells at 6 months followed by contraction at 12 months. CONCLUSION Six months may be an important checkpoint for biomarker assessment in high-risk individuals post-exposure.
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Affiliation(s)
- Rabia Hussain
- Department of Pathology and Microbiology, Aga Khan University, Stadium Road, P.O. Box 3500, Karachi, 74800, Pakistan.
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Abstract
Tuberculosis (TB) is a serious health issue in the developing world. Lack of knowledge on the etiological mechanisms of TB hinders the development of effective strategies for the treatment or prevention of TB disease. Human genetic study is an indispensable approach to understand the molecular basis of common diseases. Numerous efforts were made to screen the human genome for TB susceptibility by linkage mapping. A large number of candidate-based association studies of TB were conducted to examine the association of predicted functional DNA variations in candidate genes. Recently, the first genome-wide association study (GWAS) on TB was reported. The GWAS is a proof-of-principle evidence that justifies the genetic approach to understand TB. Further hypothesis-free efforts on TB research may renovate the traditional idea of TB genetic susceptibility as none of the candidate genes with important roles in containing Mycobacterium tuberculosis (MTB) infection was identified of association with active TB, whereas the TB-associated loci in the GWAS harbors no gene with function in MTB infection.
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Ridruechai C, Mahasirimongkol S, Phromjai J, Yanai H, Nishida N, Matsushita I, Ohashi J, Yamada N, Moolphate S, Summanapan S, Chuchottaworn C, Manosuthi W, Kantipong P, Kanitvittaya S, Sawanpanyalert P, Keicho N, Khusmith S, Tokunaga K. Association analysis of susceptibility candidate region on chromosome 5q31 for tuberculosis. Genes Immun 2010; 11:416-22. [PMID: 20485362 DOI: 10.1038/gene.2010.26] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Chromosome 5q31 spans the T helper (Th) 2-related cytokine gene cluster, which is potentially important in Th1/Th2 immune responses. The chromosome 5q23.2-31.3 has been recently identified as a region with suggestive evidence of linkage to tuberculosis in the Asian population. With the aim of fine-mapping a putative tuberculosis susceptibility locus, we investigated a family-based association test between the dense single nucleotide polymorphism (SNP) markers within chromosome 5q31 and tuberculosis in 205 Thai trio families. Of these, 75 SNPs located within candidate genes covering SLC22A4, SLC22A5, IRF1, IL5, RAD50, IL13, IL4, KIF3A and SEPT8 were genotyped using the DigiTag2 assay. Association analysis revealed the most significant association with tuberculosis in haplotypes comprising SNPs rs274559, rs274554 and rs274553 of SLC22A5 gene (P(Global)=2.02 x 10(-6)), which remained significant after multiple testing correction. In addition, two haplotypes within the SLC22A4 and KIF3A region were associated with tuberculosis. Haplotypes of SLC22A5 were significantly associated with the expression levels of RAD50 and IL13. The results show that the variants carried by the haplotypes of SLC22A4, SLC22A5 and KIF3A region potentially contribute to tuberculosis susceptibility among the Thai population.
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Affiliation(s)
- C Ridruechai
- Department of Microbiology and Immunology, Mahidol University, Bangkok, Thailand
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Obel N, Christensen K, Petersen I, Sørensen TIA, Skytthe A. Genetic and environmental influences on risk of death due to infections assessed in Danish twins, 1943-2001. Am J Epidemiol 2010; 171:1007-13. [PMID: 20375195 DOI: 10.1093/aje/kwq037] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Genetic differences have been proposed to play a strong role in risk of death from infectious diseases. The study base of 44,005 included all same-sex twin pairs born in 1870-2001, with both twins alive on January 1, 1943, or those born thereafter. Cause of death was obtained from the Danish Cause of Death Register and was available for 18,359 deaths. The authors classified death due to infections by 3 definitions (narrow, broader, and broadest) and calculated concordance rates for same-sex monozygotic and dizygotic twin pairs. Heritability was estimated by using structural equation models. When the 3 definitions were applied, 211 (1.1%), 1,089 (5.9%), and 2,907 (15.8%) deaths, respectively, were due to infections. The probandwise concordance rates for monozygotic twin pairs were consistently higher than for dizygotic twin pairs regardless of the definition (9% vs. 0% (P = 0.04), 10% vs. 3% (P < 0.01), and 19% vs. 15% (P = 0.07), respectively). For the broader and broadest definitions, heritability was 40% (95% confidence interval: 12, 50) and 19% (95% confidence interval: 3, 35), respectively. The concordance rates were generally low, and, although a genetic influence on the risk of death from infectious diseases could be demonstrated, the absolute effect of the genetic component on mortality was small.
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Affiliation(s)
- Niels Obel
- Department of Infectious Diseases, Rigshospitalet, Copenhagen University, Blegdamsvej 9, 2100 Copenhagen, Denmark.
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Zhang HQ, Deng A, Guo CF, Wang YX, Chen LQ, Wang YF, Wu JH, Liu JY. Association between FokI polymorphism in vitamin D receptor gene and susceptibility to spinal tuberculosis in Chinese Han population. Arch Med Res 2010; 41:46-9. [PMID: 20430254 DOI: 10.1016/j.arcmed.2009.12.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2009] [Accepted: 11/12/2009] [Indexed: 11/20/2022]
Abstract
BACKGROUND AND AIMS Studies have shown that the vitamin D receptor (VDR) gene polymorphisms may be associated with pulmonary tuberculosis (TB) and play important roles in the regulation of calcium in a variety of tissues including bone. To our knowledge, however, whether FokI polymorphism in VDR gene is associated with susceptibility to spinal TB is still unknown. We undertook this study to investigate the association between FokI polymorphism in VDR gene and susceptibility to spinal TB in Chinese Han population. METHODS This study included 110 patients with spinal TB and 102 volunteers as controls. FokI polymorphism in VDR gene was analyzed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) in the spinal TB group and the control group. The frequencies of VDR-FokI genotypes in the two groups were compared using chi(2) test. RESULTS There was a significant difference between groups in regard to the frequencies of the VDR-FokI genotypes (p <0.05). In the spinal TB group, the frequency of the ff genotype was 46.36%, which was significantly higher than the corresponding value for the control group (28.43%). Furthermore, the odds ratio (OR) was 2.176 (p <0.05), and the 95% confidence interval (CI) ranged from 1.236-3.832. CONCLUSIONS FokI polymorphism in VDR gene may be associated with the susceptibility to spinal TB in Chinese Han population. Furthermore, the ff genotype may be the susceptible genotype of spinal TB.
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Affiliation(s)
- Hong-Qi Zhang
- Department of Spine Surgery, Xiangya Hospital of Central South University, ChangSha, China.
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45
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Möller M, Hoal EG. Current findings, challenges and novel approaches in human genetic susceptibility to tuberculosis. Tuberculosis (Edinb) 2010; 90:71-83. [PMID: 20206579 DOI: 10.1016/j.tube.2010.02.002] [Citation(s) in RCA: 174] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Accepted: 02/03/2010] [Indexed: 12/22/2022]
Abstract
The evidence for a human genetic component in susceptibility to tuberculosis (TB) is incontrovertible. Quite apart from studies of rare disease events illustrating the importance of key genes in humans and animals, TB at the population level is also influenced by the genetics of the host. Heritability of disease concordance and immune responses to mycobacterial antigens has been clearly shown, and ranges up to 71%. Linkage studies, designed to identify major susceptibility genes in a disease, have produced a number of candidate loci but few, except for regions on chromosome 5p15, 20p and 20q, have been replicated. The region on 5p15 regulates the intensity of the response to the tuberculin skin test, and another locus on 11p14 appears to control resistance to the bacterium. In addition, numerous genes and pathways have been implicated in candidate gene association studies, with validation of polymorphisms in IFNG, NRAMP1, and NOS2A and equivocal results for IL10, CCL2, DC-SIGN, P2RX7, VDR, TLR2, TLR9 and SP110. Other more recently researched candidate genes such as TNFRSF1B remain to be validated, preferably in meta-analyses. New approaches have provided early evidence for the importance of gene-gene interactions in regulating resistance to disease, and also the prospect that applying host genetics in the field of vaccinomics could lead to a more targeted approach in designing interventions to aid the human immune system in combating mycobacteria. Genome-wide association studies and admixture mapping are approaches that remain to be applied to TB, and it is not clear, as is the case with other complex diseases, how much of the heritability of the TB susceptibility phenotype will be determined by multiple genes of small effect versus rare variants with disproportionately large effects.
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Affiliation(s)
- Marlo Möller
- Molecular Biology and Human Genetics, MRC Centre for Molecular and Cellular Biology and the DST/NRF Centre of Excellence for Biomedical TB Research, Faculty of Health Sciences, P.O. Box 19063, Stellenbosch University, Tygerberg 7505, South Africa
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Taype CA, Shamsuzzaman S, Accinelli RA, Espinoza JR, Shaw MA. Genetic susceptibility to different clinical forms of tuberculosis in the Peruvian population. INFECTION GENETICS AND EVOLUTION 2010; 10:495-504. [PMID: 20188863 DOI: 10.1016/j.meegid.2010.02.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2009] [Revised: 02/18/2010] [Accepted: 02/18/2010] [Indexed: 10/19/2022]
Abstract
Racial variation, twin studies, segregation analyses, linkage and association studies all suggest that genetic factors play an important role in predisposition to tuberculosis. Many previous studies have been performed with pulmonary TB patients, as the most prevalent form of clinical TB (nearly 95%), and very few of them have considered extrapulmonary TB. The present study evaluates the effects of variation in eight candidate genes (LTA, TNF, IL1B, IL1RN, IL10, TGFB1, TIRAP and P2X7) with pulmonary, pleural, miliary and other extrapulmonary forms of TB in a Peruvian population from the North of Lima. 626 TB cases and 513 healthy controls were enrolled in this study. LTA(+368) and IL10(-592) were associated with different clinical forms of TB (P<0.05). LTA(+368) genotype A/A was protective for pleural TB, LTA(+368) G/A was correlated with susceptibility to miliary TB. Genotypes A/A and G/A were associated with protection and susceptibility respectively when considering all extrapulmonary TB forms versus either healthy controls or pulmonary TB patients. Carriers of IL10(-592)*C were under-represented among those with pulmonary TB and all TB forms (P<0.001). IL10(-1082)-IL10(-592) haplotypes showed different distributions among patients with pulmonary TB and all TB forms (P<0.01) when compared to healthy controls. In addition, IL10(-1082)-IL10(-592) haplotypes showed differences between pleural, miliary and all forms of extrapulmonary TB when compared with pulmonary TB (P<0.05). All findings are consistent with an under-representation of the IL10(-1082)*A-IL10(-592)*A haplotype in pulmonary TB patients. These results suggest that the polymorphisms LTA(+368) and IL10(-592), or variants in strong linkage disequilibrium, variably affect susceptibility to the differing clinical forms of TB in Peruvians.
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Affiliation(s)
- C A Taype
- Institute of Integrative and Comparative Biology, Faculty of Biological Sciences, University of Leeds, UK.
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Möller M, de Wit E, Hoal EG. Past, present and future directions in human genetic susceptibility to tuberculosis. ACTA ACUST UNITED AC 2009; 58:3-26. [PMID: 19780822 DOI: 10.1111/j.1574-695x.2009.00600.x] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The historical impression that tuberculosis was an inherited disorder has come full circle and substantial evidence now exists of the human genetic contribution to susceptibility to tuberculosis. This evidence has come from several whole-genome linkage scans, and numerous case-control association studies where the candidate genes were derived from the genome screens, animal models and hypotheses pertaining to the disease pathways. Although many of the associated genes have not been validated in all studies, the list of those that have been is growing, and includes NRAMP1, IFNG, NOS2A, MBL, VDR and some TLR. Certain of these genes have consistently been associated with tuberculosis in diverse populations. The future investigation of susceptibility to tuberculosis is almost certain to include genome-wide association studies, admixture mapping and the search for rare variants and epigenetic mechanisms. The genetic identification of more vulnerable individuals is expected to inform personalized treatment and perhaps vaccination strategies.
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Affiliation(s)
- Marlo Möller
- Molecular Biology and Human Genetics, MRC Centre for Molecular and Cellular Biology and the DST/NRF Centre for Biomedical TB Research, Faculty of Health Sciences, Stellenbosch University, Tygerberg, South Africa
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Affiliation(s)
- Wing Wai Yew
- Tuberculosis and Chest Unit, Grantham Hospital, Hong Kong, China.
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Rieder HL. Of contagion and inherited susceptibility: an epidemiologic tribute to George W. Comstock. Am J Respir Crit Care Med 2007; 176:1176-7. [PMID: 18057423 DOI: 10.1164/rccm.200708-1275ed] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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