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Al-Mousa H, Barbouche MR. Genetics of Inborn Errors of Immunity in highly consanguineous Middle Eastern and North African populations. Semin Immunol 2023; 67:101763. [PMID: 37075586 DOI: 10.1016/j.smim.2023.101763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
Consanguineous marriages in Middle Eastern and North African (MENA) countries are deeply-rooted tradition and highly prevalent resulting into increased prevalence of autosomal recessive diseases including Inborn Errors of Immunity (IEIs). Molecular genetic testing is an important diagnostic tool for IEIs since it provides a definite diagnosis, genotype-phenotype correlation, and guide therapy. In this review, we will discuss the current state and challenges of genomic and variome studies in MENA region populations, as well as the importance of funding advanced genome projects. In addition, we will review the MENA underlying molecular genetic defects of over 2457 patients published with the common IEIs, where autosomal recessive mode of inheritance accounts for 76% of cases with increased prevalence of combined immunodeficiency diseases (50%). The efforts made in the last three decades in terms of international collaboration and of in situ capacity building in MENA region countries led to the discovery of more than 150 novel genes involved in IEIs. Expanding sequencing studies within the MENA will undoubtedly be a unique asset for the IEI genetics which can advance research, and support precise genomic diagnostics and therapeutics.
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Affiliation(s)
- Hamoud Al-Mousa
- Section of Allergy and Immunology, Department of Pediatrics, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia; College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.
| | - Mohamed-Ridha Barbouche
- Department of Microbiology, Immunology and Infectious Diseases, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, Bahrain.
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Ghermi M, Reguieg S, Attab K, Mened N, Ghomari N, Guendouz Elghoul FZ, Saichi F, Bossi S, Bouali-Youcef Y, Bey Baba Hamed M, Kallel Sellami M. Interferon-γ (+874 T/A) and interleukin-10 (-1082 G/A) genes polymorphisms are associated with active tuberculosis in the Algerian population of Oran's city. Indian J Tuberc 2021; 68:221-229. [PMID: 33845956 DOI: 10.1016/j.ijtb.2020.08.015] [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: 05/23/2020] [Revised: 07/20/2020] [Accepted: 08/21/2020] [Indexed: 10/23/2022]
Abstract
BACKGROUND AND AIMS Polymorphisms within genes encoding the cytokines involved in anti-tuberculosis immunity have been widely studied and sometimes associated with an increased risk of developing the active form of tuberculosis (TB). This study analyzes for the first time the impact of two polymorphisms, namely IFNG+874 T/A and IL10-1082 G/A, in the Algerian population where tuberculosis is moderately endemic. METHODS This case-control study included 104 healthy controls and 141 active TB patients: 75 extrapulmonary (EPTB) and 66 pulmonary (PTB). They were all genotyped by refractory mutational system-PCR amplification. In order to measure the functional impact of IFNG+874 T/A on the production rate of IFN-γ, 43 patients performed a QuantiFERON®Gold In-tube test. RESULTS The IFNG+874 AA genotype was associated with a higher risk of developing EPTB (OR = 2.52; 95%CI = 1.23-5.18; p = 0.012) while the IFNG+874 TA genotype was associated with a greater protection (OR = 0.34, 95%CI = 0.16-0.74; p = 0.006) which was further characterized by a high production of IFN-γ (p = 0.001). Similarly, the allele A of SNP IL10-1082 G/A, especially in its homozygous form (AA), were overrepresented in PTB patients (p = 0.010 and 0.019, respectively). The combination of both susceptibility genotypes (AA/AA) was strongly associated with risk of development of active TB (OR = 8.58; 95% C.I = 1.95-37.70, p = 0.004). This susceptibility combination was only significant in men regarding PTB (OR = 11.05; 95% C.I = 1.32-92.72, p = 0.027). Additionally, IFNG+874 TA and IL10-1082G∗ genotypes combination was mostly encountered in men controls and conferred the highest protection rate against EPTB (OR = 0.25; 95% C.I = 0.08-0.76, p = 0.015). CONCLUSION These two cytokines genes polymorphisms are associated with active TB susceptibility in the Algerian population. They act synergistically in terms of protection and susceptibility regarding the two forms of the disease. Moreover, these associations were more marked among males suggesting a potential role of gender.
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Affiliation(s)
- Mohamed Ghermi
- Biotechnology Department, University of Oran1 Ahmed Ben Bella, Oran, Algeria; AQUABIOR Laboratory, University of Oran1 Ahmed Ben Bella, Oran, Algeria; Laboratory of Immuno-Rheumatology (LR05 SP01), La Rabta Hospital, Tunis, Tunisia.
| | - Sofiane Reguieg
- Immunology Department, EHU 1(er) Novembre Hospital, Oran, Algeria
| | - Khadidja Attab
- Biotechnology Department, University of Oran1 Ahmed Ben Bella, Oran, Algeria; AQUABIOR Laboratory, University of Oran1 Ahmed Ben Bella, Oran, Algeria
| | - Nedjma Mened
- Tuberculosis and Lung Disease Control Service (UCTMR) of Essenia, Oran, Algeria
| | - Naima Ghomari
- Tuberculosis and Lung Disease Control Service (UCTMR) of Essenia, Oran, Algeria
| | | | - Fatma Saichi
- Tuberculosis and Lung Disease Control Service (UCTMR) of Essenia, Oran, Algeria
| | - Saliha Bossi
- Tuberculosis and Lung Disease Control Service (UCTMR) of Essenia, Oran, Algeria
| | | | - Mohammed Bey Baba Hamed
- AQUABIOR Laboratory, University of Oran1 Ahmed Ben Bella, Oran, Algeria; Higher School of Biological Sciences of Oran (ESSBO), Oran, Algeria
| | - Maryam Kallel Sellami
- Immunology Department, La Rabta Hospital, Tunis, Tunisia; Laboratory of Immuno-Rheumatology (LR05 SP01), La Rabta Hospital, Tunis, Tunisia
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3
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Wu S, Liu X, Wang Y, Zhang M, Wang M, He JQ. Genetic Polymorphisms of IFNG and IFNGR1 with Latent Tuberculosis Infection. DISEASE MARKERS 2019; 2019:8410290. [PMID: 31687049 PMCID: PMC6811791 DOI: 10.1155/2019/8410290] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 08/10/2019] [Accepted: 09/17/2019] [Indexed: 02/05/2023]
Abstract
Previous studies indicated that single-nucleotide polymorphisms (SNPs) of interferon gamma (IFNG) and IFNG receptor 1 (IFNGR1) may be involved in the pathogenesis of pulmonary tuberculosis (PTB) in different populations. In order to further explore the results in a Chinese Han population, this study was designed to investigate potential associations between the polymorphisms in IFNG and IFNGR1 and susceptibility to latent tuberculosis infection (LTBI) and/or PTB in a Chinese Han population. A total of 209 PTB, 173 LTBI, and 183 healthy control subjects (HCS) were enrolled in our study. Genotyping was conducted using an improved multiplex ligase detection reaction (iMLDR). We performed a logistic regression including sex and age as covariates to test the effect of alleles/genotypes on LTBI and/or TB. All six markers studied in IFNG and IFNGR1 conformed to the Hardy-Weinberg equilibrium (HWE). The IFNG rs1861494 was significantly associated with LTBI in recessive model, and the CC+CT genotype decreased risk of LTBI by 50% (P = 0.046, OR = 0.50, 95%CI: 0.25-0.99). The IFNGR1 rs2234711 was significantly associated with LTBI, and allele A increased the risk of LTBI by 55% (P = 0.047, OR = 1.55, 95%CI: 1.00-2.40). In the present study, we found that IFNG and IFNGR1 polymorphisms were associated with LTBI.
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Affiliation(s)
- Shouquan Wu
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xiangmin Liu
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yu Wang
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Miaomiao Zhang
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Minggui Wang
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jian-Qing He
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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The arms race between man and Mycobacterium tuberculosis: Time to regroup. INFECTION GENETICS AND EVOLUTION 2018; 66:361-375. [DOI: 10.1016/j.meegid.2017.08.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/21/2017] [Accepted: 08/22/2017] [Indexed: 12/12/2022]
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Takahashi N, Saitoh T, Gotoh N, Nitta Y, Alkebsi L, Kasamatsu T, Minato Y, Yokohama A, Tsukamoto N, Handa H, Murakami H. The cytokine polymorphisms affecting Th1/Th2 increase the susceptibility to, and severity of, chronic ITP. BMC Immunol 2017; 18:26. [PMID: 28511637 PMCID: PMC5434613 DOI: 10.1186/s12865-017-0210-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 04/21/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND T-helper cell type 1 (Th1) polarization in chronic immune thrombocytopenia (cITP) has been reported at the protein and mRNA levels. We evaluated the impact of Th1/Th2 cytokine and cytokine receptor functional polymorphisms on both susceptibility to, and severity of, cITP. We analysed IFN-γ + 874 T/A, IFN-γR -611G/A, IL-4 -590C/T, and IL-4Rα Q576R polymorphisms in 126 cITP patients (male/female: 34/92; median age: 47.7 years) and 202 healthy control donors. Genotyping was determined by PCR and direct sequencing. The Th1/Th2 ratio was detected in peripheral blood mononuclear cells via flow cytometry. RESULTS cITP patients had a higher frequency of the IL-4Rα 576 non-QQ genotype compared to healthy subjects (P = 0.04). cITP patients with the IFN-γ +874 non-AA genotype (high expression type) showed more severe thrombocytopenia than those with the AA genotype (P < 0.05). cITP patients had a significantly higher Th1/Th2 ratio than control patients (P < 0.01); this ratio was inversely correlated with platelet counts. Furthermore, patients with both IFN-γ +874 non-AA genotype (high expression type) and IFN-γR -611 non-AA genotype (high-function type) had a significantly higher Th1/Th2 ratio (P < 0.05). CONCLUSIONS The cytokine polymorphisms affecting Th1/Th2 increase the susceptibility to, and severity of, chronic ITP.
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MESH Headings
- Adolescent
- Adult
- Aged
- Aged, 80 and over
- Cells, Cultured
- Child
- Child, Preschool
- Chronic Disease
- Female
- Genetic Predisposition to Disease
- Genotype
- Humans
- Interferon-gamma/genetics
- Interferon-gamma/metabolism
- Interleukin-4/genetics
- Interleukin-4/metabolism
- Interleukin-4 Receptor alpha Subunit/genetics
- Interleukin-4 Receptor alpha Subunit/metabolism
- Male
- Middle Aged
- Polymorphism, Single Nucleotide
- Purpura, Thrombocytopenic, Idiopathic/genetics
- Purpura, Thrombocytopenic, Idiopathic/immunology
- Receptors, Interferon/genetics
- Receptors, Interferon/metabolism
- Th1 Cells/immunology
- Th1-Th2 Balance/genetics
- Th2 Cells/immunology
- Young Adult
- Interferon gamma Receptor
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Affiliation(s)
- Noriyuki Takahashi
- Graduate School of Health Sciences, Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma 371-8514 Japan
| | - Takayuki Saitoh
- Graduate School of Health Sciences, Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma 371-8514 Japan
| | - Nanami Gotoh
- Graduate School of Health Sciences, Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma 371-8514 Japan
| | - Yasuhiro Nitta
- Graduate School of Health Sciences, Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma 371-8514 Japan
| | - Lobna Alkebsi
- Graduate School of Health Sciences, Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma 371-8514 Japan
| | - Tetsuhiro Kasamatsu
- Graduate School of Health Sciences, Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma 371-8514 Japan
| | - Yusuke Minato
- Department of Virology and Preventive Medicine, Gunma University, Gunma, Japan
| | - Akihiko Yokohama
- Division of Blood Transfusion Service, Gunma University Hospital, Gunma, Japan
| | | | - Hiroshi Handa
- Department of Medicine and Clinical Science, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Hirokazu Murakami
- Graduate School of Health Sciences, Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma 371-8514 Japan
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Singh DP, Bagam P, Sahoo MK, Batra S. Immune-related gene polymorphisms in pulmonary diseases. Toxicology 2017; 383:24-39. [PMID: 28366820 PMCID: PMC5464945 DOI: 10.1016/j.tox.2017.03.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Revised: 03/12/2017] [Accepted: 03/28/2017] [Indexed: 01/26/2023]
Abstract
Between the DNA sequences of two randomly-selected human genomes, which consist of over 3 billion base pairs and twenty five thousand genes, there exists only 0.1% variation and 99.9% sequence identity. During the last couple of decades, extensive genome-wide studies have investigated the association between single-nucleotide polymorphisms (SNPs), the most common DNA variations, and susceptibility to various diseases. Because the immune system's primary function is to defend against myriad infectious agents and diseases, the large number of people who escape serious infectious diseases underscores the tremendous success of this system at this task. In fact, out of the third of the global human population infected with Mycobacterium tuberculosis during their lifetime, only a few people develop active disease, and a heavy chain smoker may inexplicably escape all symptoms of chronic obstructive pulmonary disease (COPD), lung cancer, and other smoke-associated lung diseases. This may be attributable to the genetic makeup of the individual(s), including their SNPs, which provide some resistance to the disease. Pattern recognition receptors (PRRs), transcription factors, cytokines and chemokines all play critical roles in orchestrating immune responses and their expression/activation is directly linked to human disease tolerance. Moreover, genetic variations present in the immune-response genes of various ethnicities may explain the huge differences in individual outcomes to various diseases and following exposure to infectious agents. The current review focuses on recent advances in our understanding of pulmonary diseases and the relationship of genetic variations in immune response genes to these conditions.
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Affiliation(s)
- Dhirendra P Singh
- Laboratory of Pulmonary Immuno-Toxicology, Department of Environmental Toxicology, Health Research Center, Southern University and A&M College, Baton Rouge, LA, 70813, United States
| | - Prathyusha Bagam
- Laboratory of Pulmonary Immuno-Toxicology, Department of Environmental Toxicology, Health Research Center, Southern University and A&M College, Baton Rouge, LA, 70813, United States
| | - Malaya K Sahoo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94304, United States
| | - Sanjay Batra
- Laboratory of Pulmonary Immuno-Toxicology, Department of Environmental Toxicology, Health Research Center, Southern University and A&M College, Baton Rouge, LA, 70813, United States.
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7
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Wei Z, Wenhao S, Yuanyuan M, Yang L, Daming Z, Jiangchun X, Jijun J. A single nucleotide polymorphism in the interferon-γ gene ( IFNG +874 T/A) is associated with susceptibility to tuberculosis. Oncotarget 2017; 8:50415-50429. [PMID: 28881572 PMCID: PMC5584145 DOI: 10.18632/oncotarget.17304] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Accepted: 03/30/2017] [Indexed: 11/25/2022] Open
Abstract
Interferon-γ (Interferon gamma, IFNG) is an important cytokine involved in providing resistance to mycobacterial diseases. Common variants of IFNG, such as IFNG +874 T/A(rs2430561), may be related to tuberculosis susceptibility, but this association has not been consistently observed. We performed an updated meta-analysis to evaluate the association between the IFNG +874 T/A (rs2430561) polymorphism and tuberculosis susceptibility. PubMed and SinoMed databases were searched up to October 2016, and odds ratios (OR) and 95% confidence intervals (CI) were used to assess the association strength. Based on search criteria for manuscripts reporting tuberculosis susceptibility and its relationship with the IFNG +874 T/A(rs2430561)polymorphism, 42 case-control studies from 39 different articles were retrieved. Significantly positive, decreased, and protective associations were found between the IFNG +874 T/A(rs2430561)polymorphism and tuberculosis risk in five genetic models. Moreover, in the stratified subgroup analysis, a protective relationship was detected in four different ethnicities and sources of the control groups. Furthermore, the IFNG +874 T/A(rs2430561)polymorphism played an important role in protecting individuals from both pulmonary tuberculosis and extra-pulmonary tuberculosis. Our meta-analysis suggests that the IFNG +874 T/A(rs2430561)polymorphism is potentially associated with tuberculosis susceptibility and may be used as a predictive biomarker. Further studies with larger sample sizes and consideration of gene-environment interactions should be conducted to elucidate the role of IFNG +874 T/A(rs2430561) polymorphism in tuberculosis susceptibility.
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Affiliation(s)
- Zhang Wei
- Department of Infectious Disease, Taizhou People's Hospital, Taizhou, China
| | - Shen Wenhao
- Department of Oncology, Taizhou People's Hospital, Taizhou, China
| | - Mi Yuanyuan
- Department of Urology, Third Affiliated Hospital of Nantong University, Wuxi, China
| | - Li Yang
- Department of Infectious Disease, Taizhou People's Hospital, Taizhou, China
| | - Zhou Daming
- Department of Infectious Disease, Taizhou People's Hospital, Taizhou, China
| | - Xian Jiangchun
- Department of Infectious Disease, Taizhou People's Hospital, Taizhou, China
| | - Jiang Jijun
- Department of Infectious Disease, Taizhou People's Hospital, Taizhou, China
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8
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Uren C, Möller M, van Helden PD, Henn BM, Hoal EG. Population structure and infectious disease risk in southern Africa. Mol Genet Genomics 2017; 292:499-509. [PMID: 28229227 DOI: 10.1007/s00438-017-1296-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 02/01/2017] [Indexed: 02/06/2023]
Abstract
The KhoeSan populations are the earliest known indigenous inhabitants of southern Africa. The relatively recent expansion of Bantu-speaking agropastoralists, as well as European colonial settlement along the south-west coast, dramatically changed patterns of genetic diversity in a region which had been largely isolated for thousands of years. Owing to this unique history, population structure in southern Africa reflects both the underlying KhoeSan genetic diversity as well as differential recent admixture. This population structure has a wide range of biomedical and sociocultural implications; such as changes in disease risk profiles. Here, we consolidate information from various population genetic studies that characterize admixture patterns in southern Africa with an aim to better understand differences in adverse disease phenotypes observed among groups. Our review confirms that ancestry has a direct impact on an individual's immune response to infectious diseases. In addition, we emphasize the importance of collaborative research, especially for populations in southern Africa that have a high incidence of potentially fatal infectious diseases such as HIV and tuberculosis.
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Affiliation(s)
- Caitlin Uren
- SA MRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medical and Health Sciences, Stellenbosch University, Tygerberg, Parow, 7500, South Africa
| | - Marlo Möller
- SA MRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medical and Health Sciences, Stellenbosch University, Tygerberg, Parow, 7500, South Africa
| | - Paul D van Helden
- SA MRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medical and Health Sciences, Stellenbosch University, Tygerberg, Parow, 7500, South Africa
| | - Brenna M Henn
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Eileen G Hoal
- SA MRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medical and Health Sciences, Stellenbosch University, Tygerberg, Parow, 7500, South Africa.
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9
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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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10
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Do HLA class II genes protect against pulmonary tuberculosis? A systematic review and meta-analysis. Eur J Clin Microbiol Infect Dis 2016; 35:1567-80. [DOI: 10.1007/s10096-016-2713-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 06/17/2016] [Indexed: 01/25/2023]
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11
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Thada S, Ponnana M, Sivangala R, Joshi L, Alasandagutti M, Ansari MSS, Schumann RR, Valluri V, Gaddam S. Polymorphisms of IFN-γ (+874A/T) and IL-12 (+1188A/C) in tuberculosis patients and their household contacts in Hyderabad, India. Hum Immunol 2016; 77:559-65. [PMID: 27108964 DOI: 10.1016/j.humimm.2016.04.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 04/12/2016] [Accepted: 04/20/2016] [Indexed: 01/27/2023]
Abstract
Several cytokine gene variants have shown to be associated with host susceptibility to infectious diseases including tuberculosis (TB). High rates of transmission were identified within household members of TB patients. In this study, we examined whether single nucleotide polymorphisms of IFN-γ +874A/T and IL-12 +1188A/C affect susceptibility to TB. Genomic DNA from patients with active disease, their household contacts HHC and healthy controls HC was genotyped for IFN-γ +874A/T and IL-12 +1188A/C SNPs by amplification refractory mutation system-polymerase chain reaction (ARMS-PCR). IFN-γ +874 AA and AT genotypes were significantly with different frequencies in patients and total HHC as compared to HC (p<0.0001). In patients IL-12 +1188 AC and CC genotypes were associated with TB (p<0.003, p<0.008). In total HHC AC, CC genotypes and both alleles (A&C) were significantly different as compared to HC (p<0.004, p<0.001, p<0.034) and the same result was obtained when HHC were stratified into related (p<0.02, p<0.001) and unrelated (p<0.009, p<0.017) individuals. Allelic frequencies, however, were significant only in related contacts (p<0.021). Generalized multifactor dimensionality reduction method (GMDR) testing revealed high risk combinations of several genotypes in IFN-γ & IL-12 genes. Our findings suggest an important role of genetic variations of IFN-γ and IL-12 for susceptibility to TB.
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Affiliation(s)
- Shruthi Thada
- Bhagwan Mahavir Medical Research Centre, Hyderabad, Andhra Pradesh, India; Institute for Microbiology and Hygiene, Charite University Medical Center, Berlin, Germany
| | - Meenakshi Ponnana
- Bhagwan Mahavir Medical Research Centre, Hyderabad, Andhra Pradesh, India
| | - Ramya Sivangala
- Bhagwan Mahavir Medical Research Centre, Hyderabad, Andhra Pradesh, India
| | - Lavanya Joshi
- Bhagwan Mahavir Medical Research Centre, Hyderabad, Andhra Pradesh, India
| | | | | | - Ralf R Schumann
- Institute for Microbiology and Hygiene, Charite University Medical Center, Berlin, Germany
| | - Vijayalakshmi Valluri
- Bhagwan Mahavir Medical Research Centre, Hyderabad, Andhra Pradesh, India; LEPRA India - Blue Peter Public Health & Research Centre, Cherlapally, Hyderabad, Andhra Pradesh, India
| | - Sumanlatha Gaddam
- Bhagwan Mahavir Medical Research Centre, Hyderabad, Andhra Pradesh, India; Department of Genetics, Osmania University Hyderabad, Telangana, India.
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12
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Vásquez-Loarte T, Trubnykova M, Guio H. Genetic association meta-analysis: a new classification to assess ethnicity using the association of MCP-1 -2518 polymorphism and tuberculosis susceptibility as a model. BMC Genet 2015; 16:128. [PMID: 26518714 PMCID: PMC4627623 DOI: 10.1186/s12863-015-0280-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Accepted: 10/12/2015] [Indexed: 12/15/2022] Open
Abstract
Background In meta-analyses of genetic association studies, ancestry and ethnicity are not accurately investigated. Ethnicity is usually classified using conventional race/ethnic categories or continental groupings even though they could introduce bias increasing heterogeneity between and within studies; thus decreasing the external validity of the results. In this study, we performed a meta-analysis using a novel ethnic classification system to test the association between MCP-1 -2518 polymorphism and pulmonary tuberculosis. Our new classification considers genetic distance, migration and linguistic origins, which will increase homogeneity within ethnic groups. Methods We included thirteen studies from three continents (Asia, Africa and Latin America) and considered seven ethnic groups (West Africa, South Africa, Saharan Africa, East Asia, South Asia, Persia and Latin America). Results The results were compared to the continental group classification. We found a significant association between MCP-1 -2518 polymorphism and TB susceptibility only in the East Asian and Latin American groups (OR 3.47, P = 0.08; OR 2.73, P = 0.02). This association is not observed in other ethnic groups that are usually considered in the Asian group, such as India and Persia, or in the African group. Conclusions There is an association between MCP-1 -2518 polymorphism and TB susceptibility only in the East Asian and Latin American groups. We suggest the use of our new ethnic classification in future meta-analysis of genetic association studies when ancestry markers are not available. This new classification increases homogeneity for certain ethnic groups compared to the continental classification. We recommend considering previous data about migration, linguistics and genetic distance when classifying ethnicity in further studies.
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Affiliation(s)
- Tania Vásquez-Loarte
- Laboratorio de Biotecnología y Biología Molecular, Instituto Nacional de Salud, Avenida Defensores del, Morro 2268, Lima 9, Peru.
| | - Milana Trubnykova
- Laboratorio de Biotecnología y Biología Molecular, Instituto Nacional de Salud, Avenida Defensores del, Morro 2268, Lima 9, Peru.
| | - Heinner Guio
- Laboratorio de Biotecnología y Biología Molecular, Instituto Nacional de Salud, Avenida Defensores del, Morro 2268, Lima 9, Peru.
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Mabunda N, Alvarado-Arnez LE, Vubil A, Mariamo A, Pacheco AG, Jani IV, Moraes MO. Gene polymorphisms in patients with pulmonary tuberculosis from Mozambique. Mol Biol Rep 2014; 42:71-6. [PMID: 25239251 DOI: 10.1007/s11033-014-3741-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 09/11/2014] [Indexed: 01/09/2023]
Abstract
Several host and environmental factors contribute to tuberculosis outcome, interestingly single nucleotide polymorphisms (SNPs) in candidate genes have been evaluated in populations with different ethnicities and TB infection. In the present study we focused on SNPs in cytokine and inflammatory mediator genes: tumor necrosis factor (TNF) -308G>A (rs1800629), interleukin-10 (IL10) -819C>T (rs1800871), interferon-gamma (IFNG) +874T>A (rs2430561), and leukotriene A4 hydrolase (LTA4H) rs1978331, rs17525495 and rs2660898 in a case-control study involving 102 pulmonary tuberculosis patients and 456 controls from Mozambique. LTA4H, IL10 and IFNG SNPs showed no associations with pulmonary tuberculosis. However, distribution of the TNF -308A allele, genotype and carrier frequencies showed a significant risk association with tuberculosis that was maintained after adjustment for non-genetic variables and Bonferroni correction (AA genotype, OR = 1.9, p Bonf < 0.001; A allele OR = 2.9, p Bonf = 0.005 and GA/AA carrier OR = 2.6, p Bonf = 0.035). Interestingly, this association has not been reported in a sub-Saharan African population before. Our results suggest a role of -308 TNF polymorphism and tuberculosis susceptibility.
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Affiliation(s)
- Nédio Mabunda
- Laboratório de Virologia Molecular, Instituto Nacional de Saúde, PO Box 264, Maputo, Mozambique
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Gong T, Yang M, Qi L, Shen M, Du Y. Association of MCP-1 -2518A/G and -362G/C variants and tuberculosis susceptibility: A meta-analysis. INFECTION GENETICS AND EVOLUTION 2013; 20:1-7. [DOI: 10.1016/j.meegid.2013.08.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 07/17/2013] [Accepted: 08/02/2013] [Indexed: 12/24/2022]
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Yang Y, Li X, Cui W, Guan L, Shen F, Xu J, Zhou F, Li M, Gao C, Jin Q, Liu J, Gao L. Potential association of pulmonary tuberculosis with genetic polymorphisms of toll-like receptor 9 and interferon-gamma in a Chinese population. BMC Infect Dis 2013; 13:511. [PMID: 24176007 PMCID: PMC3819710 DOI: 10.1186/1471-2334-13-511] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Accepted: 10/28/2013] [Indexed: 01/04/2023] Open
Abstract
Background Association studies have been employed to investigate the relationships between host single nucleotide polymorphisms (SNPs) and susceptibility to pulmonary Tuberculosis (PTB). However, such candidate genetic markers have not been widely studied in Chinese population, especially with respect to the disease development from latent M. tuberculosis infection (LTBI). Methods In this case–control study, 44 candidate SNPs were examined in a total of 600 participants (PTB patients, LTBI controls and healthy controls without M. tuberculosis infection) from Zhengzhou, China. The two groups of controls were frequency matched on gender and age with PTB patients. Genotyping was carried out by the Illumina Golden Gate assay. Results When comparing PTB patients with LTBI controls but not healthy controls without M. tuberculosis infection, significant associations with disease development were observed for TLR9 1174 A/G, TLR9 1635 A/G and IFNG 2109G/A. The two loci in TLR9 were in LD in our study population (r2=0.96, D’=1.00). A combined effect of the genotypes associated with increased risk of PTB (i.e. TLR9 1174G/G and IFNG 2109 A/A) was found when comparing PTB patients with LTBI controls (p=0.004) but not with healthy controls without infection (p=0.433). Conclusions Potential associations between TLR9 and IFN-γ genetic polymorphisms and PTB were observed in a Chinese population which supports further study of the roles played by TLR9/IFN-γ pathway during the development of PTB.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Jianmin Liu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
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Zhang Z, Zhu H, Pu X, Meng S, Zhang F, Xun L, Liu Q, Wang Y. Association between tumor necrosis factor alpha-238G/a polymorphism and tuberculosis susceptibility: a meta-analysis study. BMC Infect Dis 2012. [PMID: 23192010 PMCID: PMC3519796 DOI: 10.1186/1471-2334-12-328] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Background Tumor necrosis factor alpha (TNF-α) plays a key role in the containment of tuberculosis. The relationship between the TNF -238G/A polymorphism and tuberculosis susceptibility remains inconclusive. A comprehensive meta-analysis was made to provide a more precise estimate of the relationship between them. Methods Multiple search strategies were used. A fixed effect model was takentook to estimate pooled OR with 95% confidence interval (CI) for the association between the TNF -238G/A polymorphism and tuberculosis susceptibility. The Chi-squared-based Q-test and I-squaredI2 statistic were calculated to examine heterogeneity. Begg’s funnel plot and Egger’s test were used to assess publication bias. Results 9 case-control studies were included in this meta-analysis. No significant heterogeneity was demonstrated, and no obvious publication bias was detected among the included studies. The meta-analysis indicated that there was no significant association between the TNF -238G/A polymorphism and tuberculosis susceptibility (GA+AA versus GG model: OR=1.005, 95% CI: 0.765-1.319; A versus G model: OR=1.000, 95% CI: 0.769-1.300). In the subgroup analyses by ethnicity, types of TB and human immunodeficiency virus (HIV) status, no significant association were identified. Conclusions The meta-analysis involving 2723 subjects did not detect any association between the TNF -238G/A polymorphism and tuberculosis susceptibility.
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Affiliation(s)
- Zhijiao Zhang
- School of Public Health and Health Management, Chongqing Medical University, Chongqing 400016, China
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Chang K, Deng S, Lu W, Wang F, Jia S, Li F, Yu L, Chen M. Association between CD209 -336A/G and -871A/G polymorphisms and susceptibility of tuberculosis: a meta-analysis. PLoS One 2012; 7:e41519. [PMID: 22911807 PMCID: PMC3404017 DOI: 10.1371/journal.pone.0041519] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 06/21/2012] [Indexed: 12/19/2022] Open
Abstract
Background The association between CD209 promoter polymorphisms (-336A/G, -871A/G) and tuberculosis (TB) risk has been widely reported, but results of previous studies remain controversial and ambiguous. To assess the association between CD209 polymorphisms and TB risk, a meta-analysis was performed. Methods Based on comprehensive searches of the PubMed, Embase, Web of Science, Weipu, and CBM databases, we identified outcome data from all articles estimating the association between CD209 polymorphisms and TB risk. The pooled odds ratio (OR) with 95% confidence intervals (CIs) were calculated. Results A total of 14 studies with 3,610 cases and 3,539 controls were identified. There was no significant association between CD209 -336A/G polymorphism and TB risk (OR = 1.04, 95% CI = 0.91–1.19 for G vs. A; OR = 1.13, 95% CI = 0.84–1.53 for GG vs. AA; OR = 1.04, 95% CI = 0.87–1.24 for GG+AG vs. AA; OR = 1.11, 95% CI = 0.88–1.39 for GG vs. AG+AA). However, the significant association was revealed for Asians in GG vs. AA (OR = 2.48, 95% CI = 1.46–4.22, P = 0.0008) and GG vs. AG+AA (OR = 2.10, 95% CI = 1.33–3.32, P = 0.001). For the CD209 -871A/G polymorphism, lack of an association was also found (OR = 0.81, 95% CI = 0.70–0.95 for G vs. A; OR = 1.00, 95% CI = 0.52–1.93 for GG vs. AA; OR = 0.73, 95% CI = 0.60–0.89 for GG+AG vs. AA; OR = 1.09, 95% CI = 0.57–2.10 for GG vs. AG+AA). Conclusion The present meta-analysis suggested that CD209 promoter polymorphisms (-336A/G, -871A/G) were unlikely to substantially contribute to TB susceptibility. However, the GG genotype of CD209 -336A/G polymorphism might be a genetic risk factor that increases TB susceptibility for Asians in GG vs. AA and GG vs. AG+AA.
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Affiliation(s)
- Kai Chang
- Department of Laboratory Medicine, Institute of Surgery Research, Daping Hospital, Third Military Medical University, Chongqing, China
| | - Shaoli Deng
- Department of Laboratory Medicine, Institute of Surgery Research, Daping Hospital, Third Military Medical University, Chongqing, China
| | - Weiping Lu
- Department of Laboratory Medicine, Institute of Surgery Research, Daping Hospital, Third Military Medical University, Chongqing, China
| | - Feng Wang
- Department of Laboratory Medicine, Institute of Surgery Research, Daping Hospital, Third Military Medical University, Chongqing, China
| | - Shuangrong Jia
- Department of Laboratory Medicine, Institute of Surgery Research, Daping Hospital, Third Military Medical University, Chongqing, China
| | - Fake Li
- Department of Laboratory Medicine, Institute of Surgery Research, Daping Hospital, Third Military Medical University, Chongqing, China
| | - Lili Yu
- Department of Obstetrics and Gynecology, Institute of Surgery Research, Daping Hospital, Third Military Medical University, Chongqing, China
- * E-mail: (MC); (LY)
| | - Ming Chen
- Department of Laboratory Medicine, Institute of Surgery Research, Daping Hospital, Third Military Medical University, Chongqing, China
- * E-mail: (MC); (LY)
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