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Yerezhepov D, Gabdulkayum A, Akhmetova A, Kozhamkulov U, Rakhimova S, Kairov U, Zhunussova G, Kalendar R, Akilzhanova A. Pulmonary tuberculosis epidemiology and genetics in Kazakhstan. Front Public Health 2024; 12:1340673. [PMID: 38706548 PMCID: PMC11066200 DOI: 10.3389/fpubh.2024.1340673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 04/08/2024] [Indexed: 05/07/2024] Open
Abstract
Background Tuberculosis (TB) is a major public health emergency in many countries, including Kazakhstan. Despite the decline in the incidence rate and having one of the highest treatment effectiveness in the world, the incidence rate of TB remains high in Kazakhstan. Social and environmental factors along with host genetics contribute to pulmonary tuberculosis (PTB) incidence. Due to the high incidence rate of TB in Kazakhstan, our research aimed to study the epidemiology and genetics of PTB in Kazakhstan. Materials and methods 1,555 participants were recruited to the case-control study. The epidemiology data was taken during an interview. Polymorphisms of selected genes were determined by real-time PCR using pre-designed TaqMan probes. Results Epidemiological risk factors like diabetes (χ2 = 57.71, p < 0.001), unemployment (χ2 = 81.1, p < 0.001), and underweight-ranged BMI (<18.49, χ2 = 206.39, p < 0.001) were significantly associated with PTB. VDR FokI (rs2228570) and VDR BsmI (rs1544410) polymorphisms were associated with an increased risk of PTB. A/A genotype of the TLR8 gene (rs3764880) showed a significant association with an increased risk of PTB in Asians and Asian males. The G allele of the rs2278589 polymorphism of the MARCO gene increases PTB susceptibility in Asians and Asian females. VDR BsmI (rs1544410) polymorphism was significantly associated with PTB in Asian females. A significant association between VDR ApaI polymorphism and PTB susceptibility in the Caucasian population of Kazakhstan was found. Conclusion This is the first study that evaluated the epidemiology and genetics of PTB in Kazakhstan on a relatively large cohort. Social and environmental risk factors play a crucial role in TB incidence in Kazakhstan. Underweight BMI (<18.49 kg/m2), diabetes, and unemployment showed a statistically significant association with PTB in our study group. FokI (rs2228570) and BsmI (rs1544410) polymorphisms of the VDR gene can be used as possible biomarkers of PTB in Asian males. rs2278589 polymorphism of the MARCO gene may act as a potential biomarker of PTB in Kazakhs. BsmI polymorphism of the VDR gene and rs2278589 polymorphism of the MARCO gene can be used as possible biomarkers of PTB risk in Asian females as well as VDR ApaI polymorphism in Caucasians.
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Affiliation(s)
- Dauren Yerezhepov
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | - Aidana Gabdulkayum
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | - Ainur Akhmetova
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | - Ulan Kozhamkulov
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | - Saule Rakhimova
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | - Ulykbek Kairov
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | | | - Ruslan Kalendar
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | - Ainur Akilzhanova
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
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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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Swart Y, Uren C, van Helden PD, Hoal EG, Möller M. Local Ancestry Adjusted Allelic Association Analysis Robustly Captures Tuberculosis Susceptibility Loci. Front Genet 2021; 12:716558. [PMID: 34721521 PMCID: PMC8554120 DOI: 10.3389/fgene.2021.716558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 10/01/2021] [Indexed: 11/13/2022] Open
Abstract
Pulmonary tuberculosis (TB), caused by Mycobacterium tuberculosis, is a complex disease. The risk of developing active TB is in part determined by host genetic factors. Most genetic studies investigating TB susceptibility fail to replicate association signals particularly across diverse populations. South African populations arose because of multi-wave genetic admixture from the indigenous KhoeSan, Bantu-speaking Africans, Europeans, Southeast Asian-and East Asian populations. This has led to complex genetic admixture with heterogenous patterns of linkage disequilibrium and associated traits. As a result, precise estimation of both global and local ancestry is required to prevent both false positive and false-negative associations. Here, 820 individuals from South Africa were genotyped on the SNP-dense Illumina Multi-Ethnic Genotyping Array (∼1.7M SNPs) followed by local and global ancestry inference using RFMix. Local ancestry adjusted allelic association (LAAA) models were utilized owing to the extensive genetic heterogeneity present in this population. Hence, an interaction term, comprising the identification of the minor allele that corresponds to the ancestry present at the specific locus under investigation, was included as a covariate. One SNP (rs28647531) located on chromosome 4q22 was significantly associated with TB susceptibility and displayed a SNP minor allelic effect (G allele, frequency = 0.204) whilst correcting for local ancestry for Bantu-speaking African ancestry (p-value = 5.518 × 10-7; OR = 3.065; SE = 0.224). Although no other variants passed the significant threshold, clear differences were observed between the lead variants identified for each ancestry. Furthermore, the LAAA model robustly captured the source of association signals in multi-way admixed individuals from South Africa and allowed the identification of ancestry-specific disease risk alleles associated with TB susceptibility that have previously been missed.
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Affiliation(s)
- Yolandi Swart
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Caitlin Uren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, South Africa
| | - Paul D van Helden
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Eileen G Hoal
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Marlo Möller
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, South Africa
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4
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Association of NOS2A gene polymorphisms with susceptibility to bovine tuberculosis in Chinese Holstein cattle. PLoS One 2021; 16:e0253339. [PMID: 34138949 PMCID: PMC8211175 DOI: 10.1371/journal.pone.0253339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 06/02/2021] [Indexed: 11/30/2022] Open
Abstract
Bovine tuberculosis (bTB) is a global zoonotic disease that has detrimental economic impacts worldwide. The NOS2A gene plays a key role in immunological control of many infectious diseases. However, research on the association between NOS2A polymorphisms and bTB infection in Holstein cattle reared on the Yunnan-Guizhou plateau of China is scarce. This study investigated a possible linkage between NOS2A polymorphisms and risk of developing bTB in Chinese Holstein cattle. The NOS2A gene was genotyped in 144 bTB-infected Holstein cows and 139 healthy controls were genotyped through nucleotide sequencing. Ten single-nucleotide polymorphisms (SNPs) were detected, six of which were associated with susceptibility/resistance patterns of bTB. Furthermore, the C/T genotypes of 671 and 2793, and T/T genotype of E22 (+15) were significantly associated with susceptibility risk; the G/A genotype of 2857, T/T genotype of E9 (+65), and C/C genotype of E9 (+114) probably increased resistance to bTB. In addition, the haplotypes of NOS2A-2 and NOS2A-9 were risk factors for bTB susceptibility, while the NOS2A-5 and NOS2A-8 haplotypes were contributing protective variants against tuberculosis. There is a significant association between variation in SNPs of NOS2A and tuberculosis susceptibility/resistance pattern. These findings suggest that substitution of genetic selection would be helpful for eradicating bTB. However, further investigation is required to study the underlying mechanism through which NOS2A polymorphisms affect bTB infection.
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Exploring the Role of C-C Motif Chemokine Ligand-2 Single Nucleotide Polymorphism in Pulmonary Tuberculosis: A Genetic Association Study from North India. J Immunol Res 2021; 2020:1019639. [PMID: 33381602 PMCID: PMC7759415 DOI: 10.1155/2020/1019639] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 10/31/2020] [Accepted: 12/03/2020] [Indexed: 12/24/2022] Open
Abstract
The C-C motif chemokine ligand-2 (CCL2) was evidenced to be associated with tuberculosis susceptibility in some ethnic groups. In the present study, effort was made to find out the association of CCL2-2518 A>G and -362 G>C variants with susceptibility to TB in a population from North India. The genotyping was carried out in 373 participants with pulmonary TB (PTB) and 248 healthy controls (HCs) for CCL2-2518 A>G and -362 G>C polymorphisms by PCR-RFLP and by melting curve analysis using fluorescence-labeled hybridization fluorescent resonance energy transfer (FRET) probes, respectively, followed by DNA sequencing in a few representative samples. Genotype and allele frequencies were compared by the chi-squared test and crude and Mantel-Haenszel (M-H) odds ratio (OR). OR was calculated using STATA/MP16.1 software. Further, CCL2, IL-12p70, IFN-γ, TNF-α, and TGF-β levels were measured in serum samples of these participants using commercially available kits. Our analysis indicated that the homozygous mutant in both -2518 GG (OR = 2.07, p = 0.02) and -362 CC (OR = 1.92, p = 0.03) genotypes was associated with susceptibility to pulmonary TB. Further, heterozygous genotypes -2518AG (OR = 0.60, p = 0.003) and -362GC (OR = 0.64, p = 0.013) provide resistance from PTB disease. Haplotype analysis revealed AC haplotype (p = 0.006) to be a risk factor associated with PTB susceptibility. The serum CCL2 level was significantly elevated among participants with -2518 AA genotype compared to -2518 GG genotype. CCL2 level was observed to be positively correlated with IL12p70, IFN-γ and TNF-α, thus suggesting the immunological regulatory role of CCL2 against pulmonary tuberculosis. CCL2-2518 GG and -362 CC genotypes were found to be associated with susceptibility to pulmonary tuberculosis and CCL2-2518AG and CCL2-362GC with resistance from PTB. AC haplotype was found to be a risk factor for PTB in the present study. It may be hypothesized from the findings that -2518G allele could be responsible for lower production of CCL2 which leads to defective Th1 response and makes a host susceptible for pulmonary tuberculosis.
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Cai L, Li Z, Guan X, Cai K, Wang L, Liu J, Tong Y. The Research Progress of Host Genes and Tuberculosis Susceptibility. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:9273056. [PMID: 31485302 PMCID: PMC6710736 DOI: 10.1155/2019/9273056] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 05/05/2019] [Accepted: 05/29/2019] [Indexed: 02/05/2023]
Abstract
BACKGROUND/AIMS Nucleotide diversity may affect the immune regulation of tuberculosis (TB) patients, leading to the individual susceptibility to TB. In recent years, there are a lot of researches on the association of host genetic factors and TB susceptibility which has attracted increasing attention, and the in-depth study of its mechanism is gradually clear. MATERIALS We made a minireview on the association of many candidate genes with TB based on recent research studies systematically, such as the human leukocyte antigen (HLA) gene, the solute carrier family 11 member 1 (SLC11A1) gene system, the vitamin D receptor (VDR) gene, the mannan-binding lectin (MBL) gene, the nitric oxide synthase 2A (NOS2A) gene, the speckled 110 (SP110) gene, and the P2X7 receptor (P2X7) gene. The discovery of these candidate genes could reveal the pathogenesis of TB comprehensively and is crucial to provide scientific evidence for formulating the related measures of prevention and cure. DISCUSSION The host genes play important roles in the development of TB, and the host genes may become new targets for the prevention and treatment of TB. Effective regulation of host genes may help prevent or even treat TB. CONCLUSION This minireview focuses on the association of host genes with the development of TB, which may supply some clues for future therapies and novel drug targets for TB.
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Affiliation(s)
- Li Cai
- Wuhan Center for Disease Control and Prevention, Wuhan 430015, China
- School of Health Sciences, Wuhan University, Wuhan 430071, China
| | - Zhan Li
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xuhua Guan
- Hubei Center for Disease Control and Prevention, 430079, China
| | - Kun Cai
- Hubei Center for Disease Control and Prevention, 430079, China
| | - Lei Wang
- Hubei Center for Disease Control and Prevention, 430079, China
| | - Jiafa Liu
- School of Health Sciences, Wuhan University, Wuhan 430071, China
- Hubei Center for Disease Control and Prevention, 430079, China
| | - Yeqing Tong
- Hubei Center for Disease Control and Prevention, 430079, China
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Varzari A, Tudor E, Bodrug N, Corloteanu A, Axentii E, Deyneko IV. Age-Specific Association ofCCL5Gene Polymorphism with Pulmonary Tuberculosis: A Case–Control Study. Genet Test Mol Biomarkers 2018; 22:281-287. [DOI: 10.1089/gtmb.2017.0250] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Alexander Varzari
- Laboratory of Human Genetics, Chiril Draganiuc Institute of Phthisiopneumology, Kishinev, Republic of Moldova
- Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
| | - Elena Tudor
- Laboratory of Human Genetics, Chiril Draganiuc Institute of Phthisiopneumology, Kishinev, Republic of Moldova
| | - Nina Bodrug
- Laboratory of Human Genetics, Chiril Draganiuc Institute of Phthisiopneumology, Kishinev, Republic of Moldova
| | - Andrei Corloteanu
- Laboratory of Human Genetics, Chiril Draganiuc Institute of Phthisiopneumology, Kishinev, Republic of Moldova
| | - Ecaterina Axentii
- Laboratory of Human Genetics, Chiril Draganiuc Institute of Phthisiopneumology, Kishinev, Republic of Moldova
| | - Igor V. Deyneko
- Institute of Microbiology and Braunschweig Integrated Center of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
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8
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Bibert S, Bratschi MW, Aboagye SY, Collinet E, Scherr N, Yeboah-Manu D, Beuret C, Pluschke G, Bochud PY. Susceptibility to Mycobacterium ulcerans Disease (Buruli ulcer) Is Associated with IFNG and iNOS Gene Polymorphisms. Front Microbiol 2017; 8:1903. [PMID: 29046669 PMCID: PMC5632961 DOI: 10.3389/fmicb.2017.01903] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 09/19/2017] [Indexed: 01/10/2023] Open
Abstract
Buruli ulcer (BU) is a chronic necrotizing disease of the skin and subcutaneous fat tissue. The causative agent, Mycobacterium ulcerans, produces mycolactone, a macrolide toxin, which causes apoptosis of mammalian cells. Only a small proportion of individuals exposed to M. ulcerans develop clinical disease, as surrounding macrophages may control the infection by bacterial killing at an early stage, while mycolactone concentration is still low. Otherwise, bacterial multiplication leads to in higher concentrations of mycolactone, with formation of necrotizing lesions that are no more accessible to immune cells. By typing a cohort of 96 Ghanaian BU patients and 384 endemic controls without BU, we show an association between BU and single nucleotide polymorphisms (SNPs) in iNOS (rs9282799) and IFNG (rs2069705). Both polymorphisms influence promoter activity in vitro. A previously reported SNP in SLC11A1 (NRAMP, rs17235409) tended to be associated with BU. Altogether, these data reflect the importance of IFNG signaling in early defense against M. ulcerans infection.
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Affiliation(s)
- Stéphanie Bibert
- Infectious Diseases Service, Department of Medicine, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Martin W Bratschi
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Samuel Y Aboagye
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Emilie Collinet
- Infectious Diseases Service, Department of Medicine, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Nicole Scherr
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Dorothy Yeboah-Manu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Christian Beuret
- Spiez Laboratory, Federal Office for Civil Protection, Spiez, Switzerland
| | - Gerd Pluschke
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Pierre-Yves Bochud
- Infectious Diseases Service, Department of Medicine, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
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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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Kassa D, Ran L, Jager WD, van den Broek T, Jacobi R, Mekonen M, Messele T, Haks MC, Ottenhoff THM, van Baarle D. Discriminative expression of whole blood genes in HIV patients with latent and active TB in Ethiopia. Tuberculosis (Edinb) 2016; 100:25-31. [PMID: 27553407 DOI: 10.1016/j.tube.2016.06.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 05/03/2016] [Accepted: 06/07/2016] [Indexed: 11/18/2022]
Abstract
BACKGROUND Transcriptomic host biomarkers could assist in developing effective diagnostics, vaccines and therapeutics for tuberculosis (TB). However, different biomarkers may be discriminatory in different populations depending on the host and bacillary genetics and HIV infection, and need to be addressed. METHODS The expression levels of 45 genes that are known to be involved in or affected by TB pathogenesis were analyzed using dual color Reverse Transcriptase Multiplex Ligation-dependent Probe Amplification (dcRT-MLPA) assay in whole blood of 106 HIV positive individuals including active TB patients (TB(+)HIV(+), n = 29), and non TB patients that are tuberculin skin test positive (TST+) (TST(+)HIV(+), n = 26), or TST negative (TST(-)HIV(+), n = 51). RESULTS Between the two clinical groups (TB(+)HIV(+) vs. TST(-)HIV(+)) 8 genes were differently expressed (CCL19, CD14, CD8A, FPR1, IL7R, CCL22, TNFRSF1A, and FCGR1A); between TB(+)HIV(+) vs. TST(+)HIV(+), 6 genes (CD14, IL7R, TIMP2, CCL22, TNFRSF1A, and FCGR1A) were differently expressed. Since no difference in gene expression was revealed between TST(+)HIV(+) vs. TST(-)HIV(+), we clustered both the TST(+)HIV(+) and TST(-)HIV(+) individuals as one group (TST(+/-)HIV(+)) and compared gene expression with TB(+)HIV(+) patients. Thus, the results revealed that the levels of five genes (CD8A, TIMP2, CCL22, FCGR1A and TNFRSF1A) were the most accurate single gene markers for differentiation between TB(+)HIV(+) and TST(+/-)HIV(+), with AUCs of 0.71, 0.71, 0.79, 0.83 and 0.73, respectively. However, the combination of two genes (CCL22 + FCGR1A) and FCGR1A alone were the most accurate marker for differentiation between the two groups (TB(+)HIV(+) and TST(+/-)HIV(+)) with AUC of 0.85 and 0.83, respectively. CONCLUSIONS We showed that five genes (CD8A, TIMP2, CCL22, FCGR1A and TNFRSF1A), specifically FCGR1A and CCL22 have the potential to discriminate active TB from non-active TB in HIV patients in Ethiopia and could be used to improve diagnostic tools for active TB in HIV patients, and to understand the pathogenesis of TB/HIV coinfection.
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Affiliation(s)
- Desta Kassa
- HIV/AIDS and Tuberculosis Research Directorate, Ethiopian Public Health Institute (EPHI), Addis Ababa, Ethiopia; Department of Internal Medicine and Infectious Diseases, University Medical Center Utrecht, Utrecht, The Netherlands.
| | - Leonie Ran
- Department of Internal Medicine and Infectious Diseases, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Wilco de Jager
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Theo van den Broek
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ronald Jacobi
- Department of Internal Medicine and Infectious Diseases, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Muluberhan Mekonen
- HIV/AIDS and Tuberculosis Research Directorate, Ethiopian Public Health Institute (EPHI), Addis Ababa, Ethiopia; Axum University, Tigray, Ethiopia
| | - Tsehaynesh Messele
- HIV/AIDS and Tuberculosis Research Directorate, Ethiopian Public Health Institute (EPHI), Addis Ababa, Ethiopia
| | - Mariëlle C Haks
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Tom H M Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Debbie van Baarle
- Department of Internal Medicine and Infectious Diseases, University Medical Center Utrecht, Utrecht, The Netherlands
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11
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Network Analysis of Human Genes Influencing Susceptibility to Mycobacterial Infections. PLoS One 2016; 11:e0146585. [PMID: 26751573 PMCID: PMC4713433 DOI: 10.1371/journal.pone.0146585] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 12/18/2015] [Indexed: 02/08/2023] Open
Abstract
Tuberculosis and nontuberculous mycobacterial infections constitute a high burden of pulmonary disease in humans, resulting in over 1.5 million deaths per year. Building on the premise that genetic factors influence the instance, progression, and defense of infectious disease, we undertook a systems biology approach to investigate relationships among genetic factors that may play a role in increased susceptibility or control of mycobacterial infections. We combined literature and database mining with network analysis and pathway enrichment analysis to examine genes, pathways, and networks, involved in the human response to Mycobacterium tuberculosis and nontuberculous mycobacterial infections. This approach allowed us to examine functional relationships among reported genes, and to identify novel genes and enriched pathways that may play a role in mycobacterial susceptibility or control. Our findings suggest that the primary pathways and genes influencing mycobacterial infection control involve an interplay between innate and adaptive immune proteins and pathways. Signaling pathways involved in autoimmune disease were significantly enriched as revealed in our networks. Mycobacterial disease susceptibility networks were also examined within the context of gene-chemical relationships, in order to identify putative drugs and nutrients with potential beneficial immunomodulatory or anti-mycobacterial effects.
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12
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Logunova N, Korotetskaya M, Polshakov V, Apt A. The QTL within the H2 Complex Involved in the Control of Tuberculosis Infection in Mice Is the Classical Class II H2-Ab1 Gene. PLoS Genet 2015; 11:e1005672. [PMID: 26618355 PMCID: PMC4664271 DOI: 10.1371/journal.pgen.1005672] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 10/26/2015] [Indexed: 12/27/2022] Open
Abstract
The level of susceptibility to tuberculosis (TB) infection depends upon allelic variations in numerous interacting genes. In our mouse model system, the whole-genome quantitative trait loci (QTLs) scan revealed three QTLs involved in TB control on chromosomes 3, 9, and in the vicinity of the H2 complex on chromosome 17. For the present study, we have established a panel of new congenic, MHC-recombinant mouse strains bearing differential small segments of chromosome 17 transferred from the TB-susceptible I/St (H2j) strain onto the genetic background of TB-resistant C57BL/6 (B6) mice (H2b). This allowed narrowing the QTL interval to 17Ch: 33, 77–34, 34 Mb, containing 36 protein-encoding genes. Cloning and sequencing of the H2j allelic variants of these genes demonstrated profound polymorphic variations compare to the H2b haplotype. In two recombinant strains, B6.I-249.1.15.100 and B6.I-249.1.15.139, recombination breakpoints occurred in different sites of the H2-Aβ 1 gene (beta-chain of the Class II heterodimer H2-A), providing polymorphic variations in the domain β1 of the Aβ-chain. These variations were sufficient to produce different TB-relevant phenotypes: the more susceptible B6.I-249.1.15.100 strain demonstrated shorter survival time, more rapid body weight loss, higher mycobacterial loads in the lungs and more severe lung histopathology compared to the more resistant B6.I-249.1.15.139 strain. CD4+ T cells recognized mycobacterial antigens exclusively in the context of the H2-A Class II molecule, and the level of IFN-γ-producing CD4+ T cells in the lungs was significantly higher in the resistant strain. Thus, we directly demonstrated for the first time that the classical H2- Ab1 Class II gene is involved in TB control. Molecular modeling of the H2-Aj product predicts that amino acid (AA) substitutions in the Aβ-chain modify the motif of the peptide–MHC binding groove. Moreover, unique AA substitutions in both α- and β-chains of the H2-Aj molecule might affect its interactions with the T-cell receptor (TCR). Many genes of the host regulate interactions with Mycobacterium tuberculosis and determine the level of susceptibility to, and severity of, tuberculosis (TB). Identification of these genes and their alleles is continuing and contributes new knowledge about the host-pathogen interactions. So far, forward genetic approaches (from phenotype to gene) have identified several chromosomal segments involved in genetic control of TB in mice (quantitative trait loci—QTL), but only one particular gene, Ipr1, has been identified. Here, we report the identification of a second TB-controlling gene. On the basis of a pair of mouse inbred strains with polar susceptibility to TB infection (susceptible I/St and more resistant C57BL/6) we established a panel of recombinant strains carrying small segments of Chromosome 17 from I/St on the genetic background of C57BL/6. A combination of genetic mapping, gene sequencing, TB phenotypes assessment and immunological approaches demonstrates that the H2-Ab1 gene encoding the beta-chain of the Class II heterodimer H2-A determines susceptibility to TB infection. The importance of allelic polymorphisms in Class II genes encoding antigen-presenting molecules in susceptibility to infection has been suspected. This is the first prove of this role obtained by the methods of classical forward genetics.
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Affiliation(s)
- Nadezhda Logunova
- Laboratory for Immunogenetics, Central Institute for Tuberculosis, Moscow, Russia
- * E-mail: (NL); (AA)
| | - Maria Korotetskaya
- Laboratory for Immunogenetics, Central Institute for Tuberculosis, Moscow, Russia
| | - Vladimir Polshakov
- Center for Magnetic Tomography & Spectroscopy, School of Fundamental Medicine, M. V. Lomonosov Moscow State University, Moscow, Russia
| | - Alexander Apt
- Laboratory for Immunogenetics, Central Institute for Tuberculosis, Moscow, Russia
- Department of Immunology, School of Biology, M. V. Lomonosov Moscow State University, Moscow, Russia
- * E-mail: (NL); (AA)
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13
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Gold MC, Napier RJ, Lewinsohn DM. MR1-restricted mucosal associated invariant T (MAIT) cells in the immune response to Mycobacterium tuberculosis. Immunol Rev 2015; 264:154-66. [PMID: 25703558 DOI: 10.1111/imr.12271] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The intracellular pathogen Mycobacterium tuberculosis (Mtb) and its human host have long co-evolved. Although the host cellular immune response is critical to the control of the bacterium information on the specific contribution of different immune cell subsets in humans is incomplete. Mucosal associated invariant T (MAIT) cells are a prevalent and unique T-cell population in humans with the capacity to detect intracellular infection with bacteria including Mtb. MAIT cells detect bacterially derived metabolites presented by the evolutionarily conserved major histocompatibility complex-like molecule MR1. Here, we review recent advances in our understanding of this T-cell subset and address the potential roles for MR1-restricted T cells in the control, diagnosis, and therapy of tuberculosis.
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Affiliation(s)
- Marielle C Gold
- Pulmonary and Critical Care Medicine, Oregon Health and Science University, Portland, OR, USA; VA Portland Health Care System (VAPORHCS), Portland, OR, USA; Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR, USA
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14
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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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15
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Cheng Y, Huang C, Tsai HJ. Relationship of bovine NOS2 gene polymorphisms to the risk of bovine tuberculosis in Holstein cattle. J Vet Med Sci 2015; 78:281-6. [PMID: 26468216 PMCID: PMC4785118 DOI: 10.1292/jvms.15-0295] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Many studies suggest significant genetic variation in the resistance of cattle and humans to infection with
Mycobacterium bovis, the causative agent of zoonotic tuberculosis. The inducible nitric
oxide synthase (iNOS which is encoded by the NOS2 gene) plays a key role in the immunological
control of a broad spectrum of infectious agents. This study aimed to investigate the influence of genetic
variations in the promoter of the NOS2 gene on bovine tuberculosis (bTB) susceptibility. In
this study, the NOS2 genes of 74 bTB-infected Holstein cows and 90 healthy controls were
genotyped using PCR followed by nucleotide sequencing. Polymorphisms at rs207692718, rs109279434, rs209895548,
rs385993919, rs433717754, rs383366213, rs466730386, rs715225976, rs525673647, rs720757654 and g.19958101T>G
in the promoter region of the NOS2 gene were detected. The g.19958101T>G SNP produced two
different conformation patterns (TT and TG) and the TG genotype was over-represented in the bTB group (20.27%)
compared with the control group (2.22%). The TG genotype frequency of the g.19958101T>G variant was
significantly higher in bTB cattle than in healthy controls (OR, 11.19; 95% CI, 2.47–50.73;
P=0.0002). The G allele of the g.19958101T>G polymorphism was more frequent in bTB group
when compared to control group (10.14% versus 1.11%). Furthermore, the G allele was a risk factor for bTB
susceptibility (OR, 10.04; 95% CI, 2.26–44.65; P=0.0002). In conclusion, the g.19958101T>G
polymorphism of the NOS2 gene may contribute to the susceptibility of Holstein cattle to
bTB.
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Affiliation(s)
- Yafen Cheng
- School of Veterinary Medicine, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan
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16
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Xu DD, Wang C, Jiang F, Wei LL, Shi LY, Yu XM, Liu CM, Liu XH, Feng XM, Ping ZP, Jiang TT, Chen ZL, Li ZJ, Li JC. Association of the FCN2 Gene Single Nucleotide Polymorphisms with Susceptibility to Pulmonary Tuberculosis. PLoS One 2015; 10:e0138356. [PMID: 26379154 PMCID: PMC4574923 DOI: 10.1371/journal.pone.0138356] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 08/28/2015] [Indexed: 12/27/2022] Open
Abstract
Ficolin-2 (FCN2) is an innate immune pattern recognition molecule that can activate the complement pathway, opsonophagocytosis, and elimination of the pathogens. The present study aimed to investigate the association of the FCN2 gene single nucleotide polymorphisms (SNPs) with susceptibility to pulmonary tuberculosis (TB). A total of seven SNPs in exon 8 (+6359 C>T and +6424 G>T) and in the promoter region (-986 G>A, -602 G>A, -557 A>G, -64 A>C and -4 A>G) of the FCN2 gene were genotyped using the PCR amplification and DNA sequencing methods in the healthy controls group (n = 254) and the pulmonary TB group (n = 282). The correlation between SNPs and pulmonary TB was analyzed using the logistic regression method. The results showed that there were no significant differences in the distribution of allelic frequencies of seven SNPs between the pulmonary TB group and the healthy controls group. However, the frequency of the variant homozygous genotype (P = 0.037, -557 A>G; P = 0.038, -64 A>C; P = 0.024, +6424 G>T) in the TB group was significantly lower than the control group. After adjustment for age and gender, these variant homozygous genotypes were found to be recessive models in association with pulmonary TB. In addition, -64 A>C (P = 0.047) and +6424 G>T (P = 0.03) were found to be codominant models in association with pulmonary TB. There was strong linkage disequilibrium (r2 > 0.80, P < 0.0001) between 7 SNPs except the -602 G>A site. Therefore, -557 A>G, -64 A>C and +6424 G>T SNPs of the FCN2 gene were correlated with pulmonary TB, and may be protective factors for TB. This study provides a novel idea for the prevention and control of TB transmission from a genetics perspective.
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Affiliation(s)
- Dan-Dan Xu
- Institute of Cell Biology, Zhejiang University, Hangzhou 310058, P.R. China
| | - Chong Wang
- Institute of Cell Biology, Zhejiang University, Hangzhou 310058, P.R. China
| | - Feng Jiang
- Dongzhimen Hospital Affiliated to Beijing University of Chinese Medicine, Beijing 100700, P.R. China
| | - Li-Liang Wei
- Department of Respiratory Medicine, The Sixth Hospital of Shaoxing, Shaoxing 312000, P.R. China
| | - Li-Ying Shi
- Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou 310013, P.R. China
| | - Xiao-Mei Yu
- Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou 310013, P.R. China
| | - Chang-Ming Liu
- Institute of Cell Biology, Zhejiang University, Hangzhou 310058, P.R. China
| | - Xue-Hong Liu
- School of Medicine, Shaoxing University, Shaoxing 312000, P.R. China
| | - Xian-Min Feng
- School of Laboratory Medicine, Jilin Medical College, Jilin 132013, P.R. China
| | - Ze-Peng Ping
- Institute of Cell Biology, Zhejiang University, Hangzhou 310058, P.R. China
| | - Ting-Ting Jiang
- Institute of Cell Biology, Zhejiang University, Hangzhou 310058, P.R. China
| | - Zhong-Liang Chen
- Institute of Cell Biology, Zhejiang University, Hangzhou 310058, P.R. China
| | - Zhong-Jie Li
- Institute of Cell Biology, Zhejiang University, Hangzhou 310058, P.R. China
| | - Ji-Cheng Li
- Institute of Cell Biology, Zhejiang University, Hangzhou 310058, P.R. China
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17
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Oliveira J, Debnath M, Etain B, Bennabi M, Hamdani N, Lajnef M, Bengoufa D, Fortier C, Boukouaci W, Bellivier F, Kahn JP, Henry C, Charron D, Krishnamoorthy R, Leboyer M, Tamouza R. Violent suicidal behaviour in bipolar disorder is associated with nitric oxide synthase 3 gene polymorphism. Acta Psychiatr Scand 2015; 132:218-25. [PMID: 25939888 DOI: 10.1111/acps.12433] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/15/2015] [Indexed: 12/16/2022]
Abstract
OBJECTIVE Given the importance of nitric oxide system in oxidative stress, inflammation, neurotransmission and cerebrovascular tone regulation, we postulated its potential dysfunction in bipolar disorder (BD) and suicide. By simultaneously analysing variants of three isoforms of nitric oxide synthase (NOS) genes, we explored interindividual genetic liability to suicidal behaviour in BD. METHOD A total of 536 patients with BD (DSM-IV) and 160 healthy controls were genotyped for functionally relevant NOS1, NOS2 and NOS3 polymorphisms. History of suicidal behaviour and violent suicide attempt was documented for 511 patients with BD. Chi-squared test was used to perform genetic association analyses and logistic regression to test for gene-gene interactions. RESULTS NOS3 rs1799983 T homozygous state was associated with violent suicide attempts (26.4% vs. 10.8%, in patients and controls, P = 0.002, corrected P (Pc) = 0.004, OR: 2.96, 95% CI = 1.33-6.34), and this association was restricted to the early-onset BD subgroup (37.9% vs. 10.8%, in early-onset BD and controls, P = 0.0003, Pc = 0.0006 OR: 5.05, 95% CI: 1.95-12.45), while we found no association with BD per se and no gene-gene interactions. CONCLUSION Our results bring further evidence for the potential involvement of endothelial NOS gene variants in susceptibility to suicidal behaviour. Future exploration of this pathway on larger cohort of suicidal behaviour is warranted.
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Affiliation(s)
- J Oliveira
- INSERM, U1160, Hôpital Saint Louis, Paris, France.,Fondation FondaMental, Créteil, France
| | - M Debnath
- INSERM, U1160, Hôpital Saint Louis, Paris, France.,Fondation FondaMental, Créteil, France
| | - B Etain
- Fondation FondaMental, Créteil, France.,INSERM, U955, Psychopathologie et Génétique des maladies psychiatriques, Créteil, France.,Faculté de Médecine, Université Paris-Est, Créteil, France.,AP-HP, Pôle de Psychiatrie et d'Addictologie des Hôpitaux Universitaires Henri Mondor, Créteil, France
| | - M Bennabi
- INSERM, U1160, Hôpital Saint Louis, Paris, France.,Fondation FondaMental, Créteil, France
| | - N Hamdani
- Fondation FondaMental, Créteil, France.,INSERM, U955, Psychopathologie et Génétique des maladies psychiatriques, Créteil, France.,Faculté de Médecine, Université Paris-Est, Créteil, France.,AP-HP, Pôle de Psychiatrie et d'Addictologie des Hôpitaux Universitaires Henri Mondor, Créteil, France
| | - M Lajnef
- Fondation FondaMental, Créteil, France.,INSERM, U955, Psychopathologie et Génétique des maladies psychiatriques, Créteil, France.,Faculté de Médecine, Université Paris-Est, Créteil, France
| | - D Bengoufa
- Laboratoire Jean Dausset and LabEx Transplantex, Hôpital Saint Louis, Paris, France
| | - C Fortier
- Laboratoire Jean Dausset and LabEx Transplantex, Hôpital Saint Louis, Paris, France
| | - W Boukouaci
- INSERM, U1160, Hôpital Saint Louis, Paris, France
| | - F Bellivier
- Fondation FondaMental, Créteil, France.,INSERM, U955, Psychopathologie et Génétique des maladies psychiatriques, Créteil, France.,Faculté de Médecine, Université Paris-Est, Créteil, France.,AP-HP, Pôle de Psychiatrie et d'Addictologie des Hôpitaux Universitaires Henri Mondor, Créteil, France
| | - J-P Kahn
- Fondation FondaMental, Créteil, France.,Service de Psychiatrie et Psychologie Clinique, CHU de Nancy, Hôpitaux de Brabois, Vandoeuvre Les Nancy, France
| | - C Henry
- Fondation FondaMental, Créteil, France.,INSERM, U955, Psychopathologie et Génétique des maladies psychiatriques, Créteil, France.,Faculté de Médecine, Université Paris-Est, Créteil, France.,AP-HP, Pôle de Psychiatrie et d'Addictologie des Hôpitaux Universitaires Henri Mondor, Créteil, France
| | - D Charron
- INSERM, U1160, Hôpital Saint Louis, Paris, France.,Fondation FondaMental, Créteil, France.,Laboratoire Jean Dausset and LabEx Transplantex, Hôpital Saint Louis, Paris, France.,Sorbonne Paris-Cité, Université Paris Diderot, Paris, France
| | | | - M Leboyer
- Fondation FondaMental, Créteil, France.,INSERM, U955, Psychopathologie et Génétique des maladies psychiatriques, Créteil, France.,Faculté de Médecine, Université Paris-Est, Créteil, France.,AP-HP, Pôle de Psychiatrie et d'Addictologie des Hôpitaux Universitaires Henri Mondor, Créteil, France
| | - R Tamouza
- INSERM, U1160, Hôpital Saint Louis, Paris, France.,Fondation FondaMental, Créteil, France.,Laboratoire Jean Dausset and LabEx Transplantex, Hôpital Saint Louis, Paris, France.,Sorbonne Paris-Cité, Université Paris Diderot, Paris, France
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18
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Rapovy SM, Zhao J, Bricker RL, Schmidt SM, Setchell KDR, Qualls JE. Differential Requirements for L-Citrulline and L-Arginine during Antimycobacterial Macrophage Activity. THE JOURNAL OF IMMUNOLOGY 2015; 195:3293-300. [PMID: 26311904 PMCID: PMC6432794 DOI: 10.4049/jimmunol.1500800] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 07/28/2015] [Indexed: 12/26/2022]
Abstract
Microbicidal NO production is reliant on inducible NO synthase-mediated L-arginine metabolism in macrophages (MΦs). However, L-arginine supply can be restricted by arginase activity, resulting in inefficient NO output and inhibition of antimicrobial MΦ function. MΦs circumvent this by converting L-citrulline to L-arginine, thereby resupplying substrate for NO production. In this article, we define the metabolic signature of mycobacteria-infected murine MΦs supplied L-arginine, L-citrulline, or both amino acids. Using liquid chromatography-tandem mass spectrometry, we determined that L-arginine synthesized from L-citrulline was less effective as a substrate for arginase-mediated L-ornithine production compared with L-arginine directly imported from the extracellular milieu. Following Mycobacterium bovis bacillus Calmette-Guérin infection and costimulation with IFN-γ, we observed that MΦ arginase activity did not inhibit production of NO derived from L-citrulline, contrary to NO inhibition witnessed when MΦs were cultured in L-arginine. Furthermore, we found that arginase-expressing MΦs preferred L-citrulline over L-arginine for the promotion of antimycobacterial activity. We expect that defining the consequences of L-citrulline metabolism in MΦs will provide novel approaches for enhancing immunity, especially in the context of mycobacterial disease.
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Affiliation(s)
- Shannon M Rapovy
- Division of Infectious Diseases, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229; and
| | - Junfang Zhao
- Division of Pathology and Laboratory Medicine, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229
| | - Rebecca L Bricker
- Division of Infectious Diseases, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229; and
| | - Stephanie M Schmidt
- Division of Infectious Diseases, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229; and
| | - Kenneth D R Setchell
- Division of Pathology and Laboratory Medicine, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229
| | - Joseph E Qualls
- Division of Infectious Diseases, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229; and
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19
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Daya M, van der Merwe L, Gignoux CR, van Helden PD, Möller M, Hoal EG. Using multi-way admixture mapping to elucidate TB susceptibility in the South African Coloured population. BMC Genomics 2014; 15:1021. [PMID: 25422094 PMCID: PMC4256931 DOI: 10.1186/1471-2164-15-1021] [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: 07/07/2014] [Accepted: 11/19/2014] [Indexed: 01/07/2023] Open
Abstract
Background The admixed South African Coloured population is ideally suited to the discovery of tuberculosis susceptibility genetic variants and their probable ethnic origins, but previous attempts at finding such variants using genome-wide admixture mapping were hampered by the inaccuracy of local ancestry inference. In this study, we infer local ancestry using the novel algorithm implemented in RFMix, with the emphasis on identifying regions of excess San or Bantu ancestry, which we hypothesize may harbour TB susceptibility genes. Results Using simulated data, we demonstrate reasonable accuracy of local ancestry inference by RFMix, with a tendency towards miss-calling San ancestry as Bantu. Regions with either excess San ancestry or excess African (San or Bantu) ancestry are less likely to be affected by this bias, and we therefore proceeded to identify such regions, found in cases but not in controls (642 cases and 91 controls). A number of promising regions were found (overall p-values of 7.19×10-5 for San ancestry and <2.00×10-16 for African ancestry), including chromosomes 15q15 and 17q22, which are close to genomic regions previously implicated in TB. Promising immune-related susceptibility genes such as the GADD45A, OSM and B7-H5 genes are also harboured in the identified regions. Conclusion Admixture mapping is feasible in the South African Coloured population and a number of novel TB susceptibility genomic regions were uncovered. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1021) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | - Eileen G Hoal
- Molecular Biology and Human Genetics, MRC Centre for TB Research and the DST/NRF Centre of Excellence for Biomedical TB Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa.
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20
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Jena M, Srivastava AK, Singh RK, Sharma PR, Das P, Bamezai RN. NOS2A promoter (CCTTT)n association with TB lacks independent functional correlation amongst Indians. Tuberculosis (Edinb) 2014; 94:81-6. [DOI: 10.1016/j.tube.2013.10.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 10/18/2013] [Accepted: 10/22/2013] [Indexed: 01/23/2023]
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21
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Daya M, van der Merwe L, Galal U, Möller M, Salie M, Chimusa ER, Galanter JM, van Helden PD, Henn BM, Gignoux CR, Hoal E. A panel of ancestry informative markers for the complex five-way admixed South African coloured population. PLoS One 2013; 8:e82224. [PMID: 24376522 PMCID: PMC3869660 DOI: 10.1371/journal.pone.0082224] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 10/21/2013] [Indexed: 01/25/2023] Open
Abstract
Admixture is a well known confounder in genetic association studies. If genome-wide data is not available, as would be the case for candidate gene studies, ancestry informative markers (AIMs) are required in order to adjust for admixture. The predominant population group in the Western Cape, South Africa, is the admixed group known as the South African Coloured (SAC). A small set of AIMs that is optimized to distinguish between the five source populations of this population (African San, African non-San, European, South Asian, and East Asian) will enable researchers to cost-effectively reduce false-positive findings resulting from ignoring admixture in genetic association studies of the population. Using genome-wide data to find SNPs with large allele frequency differences between the source populations of the SAC, as quantified by Rosenberg et. al's -statistic, we developed a panel of AIMs by experimenting with various selection strategies. Subsets of different sizes were evaluated by measuring the correlation between ancestry proportions estimated by each AIM subset with ancestry proportions estimated using genome-wide data. We show that a panel of 96 AIMs can be used to assess ancestry proportions and to adjust for the confounding effect of the complex five-way admixture that occurred in the South African Coloured population.
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Affiliation(s)
- Michelle Daya
- 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 Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Lize van der Merwe
- 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 Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
- Biostatistics Unit, Medical Research Council, Tygerberg, South Africa
- Statistics Department, University of Western Cape, Cape Town, South Africa
| | - Ushma Galal
- Biostatistics Unit, Medical Research Council, Tygerberg, South Africa
| | - 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 Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Muneeb Salie
- 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 Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Emile R. Chimusa
- Computational Biology Group, Department of Clinical Laboratory Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Medical School, Cape Town, South Africa
| | - Joshua M. Galanter
- University of California San Francisco, San Francisco, California, United States of America
| | - Paul D. van Helden
- 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 Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Brenna M. Henn
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, United States of America
| | - Chris R. Gignoux
- University of California San Francisco, San Francisco, California, United States of America
| | - Eileen Hoal
- 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 Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
- * E-mail:
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Khalilullah SA, Harapan H, Hasan NA, Winardi W, Ichsan I, Mulyadi M. Host genome polymorphisms and tuberculosis infection: What we have to say? EGYPTIAN JOURNAL OF CHEST DISEASES AND TUBERCULOSIS 2013; 63:173-185. [PMID: 26966339 DOI: 10.1016/j.ejcdt.2013.12.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Several epidemiology studies suggest that host genetic factors play important roles in susceptibility, protection and progression of tuberculosis infection. Here we have reviewed the implications of some genetic polymorphisms in pathways related to tuberculosis susceptibility, severity and development. Large case-control studies examining single-nucleotide polymorphisms (SNPs) in genes have been performed in tuberculosis patients in some countries. Polymorphisms in natural resistance-associated macrophage protein 1 (NRAMP1), toll-like receptor 2 (TLR2), interleukin-6 (IL-6), tumor necrosis factor alpha (TNF-α), interleukin-1 receptor antagonist (IL-1RA), IL-10, vitamin D receptor (VDR), dendritic cell-specific ICAM-3-grabbing non-integrin (DC-SIGN), monocyte chemoattractant protein-1 (MCP-1), nucleotide oligomerization binding domain 2 (NOD2), interferon-gamma (IFN-γ), inducible nitric oxide synthase (iNOS), mannose-binding lectin (MBL) and surfactant proteins A (SP-A) have been reviewed. These genes have been variably associated with tuberculosis infection and there is strong evidence indicating that host genetic factors play critical roles in tuberculosis susceptibility, severity and development.
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Affiliation(s)
| | - Harapan Harapan
- Medical Research Unit, School of Medicine Syiah Kuala University, Banda Aceh, Indonesia; Tropical Disease Center, School of Medicine Syiah Kuala University, Banda Aceh, Indonesia
| | - Nabeeh A Hasan
- Research Affiliate, Centre for Genes, Environment and Health, National Jewish Health, Denver, CO, USA; Computational Bioscience Program, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Wira Winardi
- Medical Research Unit, School of Medicine Syiah Kuala University, Banda Aceh, Indonesia; Graduate Institute of Medical Science, Taipei Medical University, Taipei, Taiwan
| | - Ichsan Ichsan
- Medical Research Unit, School of Medicine Syiah Kuala University, Banda Aceh, Indonesia; Tropical Disease Center, School of Medicine Syiah Kuala University, Banda Aceh, Indonesia; Institute of Medical Microbiology and National Reference Center for Systemic Mycosis, University Medical Center Goettingen, Goettingen, Germany
| | - Mulyadi Mulyadi
- Pulmonology Department, School of Medicine, Syiah Kuala University, Banda Aceh, Indonesia
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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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Chimusa ER, Zaitlen N, Daya M, Möller M, van Helden PD, Mulder NJ, Price AL, Hoal EG. Genome-wide association study of ancestry-specific TB risk in the South African Coloured population. Hum Mol Genet 2013; 23:796-809. [PMID: 24057671 DOI: 10.1093/hmg/ddt462] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The worldwide burden of tuberculosis (TB) remains an enormous problem, and is particularly severe in the admixed South African Coloured (SAC) population residing in the Western Cape. Despite evidence from twin studies suggesting a strong genetic component to TB resistance, only a few loci have been identified to date. In this work, we conduct a genome-wide association study (GWAS), meta-analysis and trans-ethnic fine mapping to attempt the replication of previously identified TB susceptibility loci. Our GWAS results confirm the WT1 chr11 susceptibility locus (rs2057178: odds ratio = 0.62, P = 2.71e(-06)) previously identified by Thye et al., but fail to replicate previously identified polymorphisms in the TLR8 gene and locus 18q11.2. Our study demonstrates that the genetic contribution to TB risk varies between continental populations, and illustrates the value of including admixed populations in studies of TB risk and other complex phenotypes. Our evaluation of local ancestry based on the real and simulated data demonstrates that case-only admixture mapping is currently impractical in multi-way admixed populations, such as the SAC, due to spurious deviations in average local ancestry generated by current local ancestry inference methods. This study provides insights into identifying disease genes and ancestry-specific disease risk in multi-way admixed populations.
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Affiliation(s)
- Emile R Chimusa
- Department of Clinical Laboratory Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
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Qualls JE, Subramanian C, Rafi W, Smith AM, Balouzian L, DeFreitas AA, Shirey KA, Reutterer B, Kernbauer E, Stockinger S, Decker T, Miyairi I, Vogel SN, Salgame P, Rock CO, Murray PJ. Sustained generation of nitric oxide and control of mycobacterial infection requires argininosuccinate synthase 1. Cell Host Microbe 2013; 12:313-23. [PMID: 22980328 DOI: 10.1016/j.chom.2012.07.012] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Revised: 06/07/2012] [Accepted: 07/13/2012] [Indexed: 12/17/2022]
Abstract
Nitric oxide (NO) defends against intracellular pathogens, but its synthesis must be regulated due to cell and tissue toxicity. During infection, macrophages import extracellular arginine to synthesize NO, generating the byproduct citrulline. Accumulated intracellular citrulline is thought to fuel arginine synthesis catalyzed by argininosuccinate synthase (Ass1) and argininosuccinate lyase (Asl), which would lead to abundant NO production. Instead, we find that citrulline is exported from macrophages during early stages of NO production with <2% retained for recycling via the Ass1-Asl pathway. Later, extracellular arginine is depleted, and Ass1 expression allows macrophages to synthesize arginine from imported citrulline to sustain NO output. Ass1-deficient macrophages fail to salvage citrulline in arginine-scarce conditions, leading to their inability to control mycobacteria infection. Thus, extracellular arginine fuels rapid NO production in activated macrophages, and citrulline recycling via Ass1 and Asl is a fail-safe system that sustains optimum NO production.
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Affiliation(s)
- Joseph E Qualls
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
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Lugo-Villarino G, Hudrisier D, Benard A, Neyrolles O. Emerging trends in the formation and function of tuberculosis granulomas. Front Immunol 2013; 3:405. [PMID: 23308074 PMCID: PMC3538282 DOI: 10.3389/fimmu.2012.00405] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 12/15/2012] [Indexed: 11/13/2022] Open
Abstract
The granuloma is an elaborated aggregate of immune cells found in non-infectious as well as infectious diseases. It is a hallmark of tuberculosis (TB). Predominantly thought as a host-driven strategy to constrain the bacilli and prevent dissemination, recent discoveries indicate the granuloma can also be modulated into an efficient tool to promote microbial pathogenesis. The aim of future studies will certainly focus on better characterization of the mechanisms driving the modulation of the granuloma functions. Here, we provide unique perspectives from both the innate and adaptive immune system in the formation and the role of the TB granuloma. As macrophages (Mϕs) comprise the bulk of granulomas, we highlight the emerging concept of Mϕ polarization and its potential impact in the microbicide response, and other activities, that may ultimately shape the fate of granulomas. Alternatively, we shed light on the ability of B-cells to influence inflammatory status within the granuloma.
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Affiliation(s)
- Geanncarlo Lugo-Villarino
- CNRS, Institut de Pharmacologie et de Biologie Structurale Toulouse, France ; Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, Université Paul Sabatier Toulouse, France
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27
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The rs1024611 regulatory region polymorphism is associated with CCL2 allelic expression imbalance. PLoS One 2012; 7:e49498. [PMID: 23166687 PMCID: PMC3500309 DOI: 10.1371/journal.pone.0049498] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 10/09/2012] [Indexed: 01/16/2023] Open
Abstract
CC chemokine ligand 2 (CCL2) is the most potent monocyte chemoattractant and inter-individual differences in its expression level have been associated with genetic variants mapping to the cis-regulatory regions of the gene. An A to G polymorphism in the CCL2 enhancer region at position -2578 (rs1024611; A>G), was found in most studies to be associated with higher serum CCL2 levels and increased susceptibility to a variety of diseases such as HIV-1 associated neurological disorders, tuberculosis, and atherosclerosis. However, the precise mechanism by which rs1024611influences CCL2 expression is not known. To address this knowledge gap, we tested the hypothesis that rs1024611G polymorphism is associated with allelic expression imbalance (AEI) of CCL2. We used haplotype analysis and identified a transcribed SNP in the 3'UTR (rs13900; C>T) can serve as a proxy for the rs1024611 and demonstrated that the rs1024611G allele displayed a perfect linkage disequilibrium with rs13900T allele. Allele-specific transcript quantification in lipopolysaccharide treated PBMCs obtained from heterozygous donors showed that rs13900T allele were expressed at higher levels when compared to rs13900C allele in all the donors examined suggesting that CCL2 is subjected to AEI and that that the allele containing rs1024611G is preferentially transcribed. We also found that AEI of CCL2 is a stable trait and could be detected in newly synthesized RNA. In contrast to these in vivo findings, in vitro assays with haplotype-specific reporter constructs indicated that the haplotype bearing rs1024611G had a lower or similar transcriptional activity when compared to the haplotype containing rs1024611A. This discordance between the in vivo and in vitro expression studies suggests that the CCL2 regulatory region polymorphisms may be functioning in a complex and context-dependent manner. In summary, our studies provide strong functional evidence and a rational explanation for the phenotypic effects of the CCL2 rs1024611G allele.
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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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29
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The -2518A/G polymorphism in the MCP-1 gene and tuberculosis risk: a meta-analysis. PLoS One 2012; 7:e38918. [PMID: 22859936 PMCID: PMC3408439 DOI: 10.1371/journal.pone.0038918] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Accepted: 05/15/2012] [Indexed: 02/05/2023] Open
Abstract
Background The -2518A/G polymorphism in the monocyte chemoattractant protein-1 (MCP-1) gene has been implicated in the susceptibility to tuberculosis (TB), but the results are not conclusive. The aim of this study is to investigate the association between the -2518A/G polymorphism in the MCP-1 gene and the risk of tuberculosis by meta-analysis. Methods We searched Pubmed, Embase, CNKI and Wanfang databases, covering all studies until April 29th, 2011. Statistical analyses were performed using the Revman4.2 and STATA10.0 software. Results A total of 5341 cases and 6075 controls in 13 case-control studies were included in the meta-analysis. The results indicated that the GG homozygote carriers had a 67% increased risk of TB compared with the A allele carriers (GG vs. GA+AA: OR = 1.67, 95%CI = 1.25–2.23, P = 0.0006). In the subgroup analysis by ethnicity, significant elevated risks were found in Asians and Latinos, but not in Africans (GG vs. GA+AA: OR = 1.79, 95%CI = 1.19–2.70 and P = 0.005 for Asians; OR = 2.15, 95%CI = 1.32–3.51 and P = 0.002 for Latinos; OR = 1.28, 95%CI = 0.45–3.64 and P = 0.65 for Africans). Conclusion This meta-analysis suggested that the -2518A/G polymorphism of MCP-1 gene would be a risk factor for TB in Asians and Latinos, while not in Africans.
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30
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Qidwai T, Jamal F, Khan MY. DNA Sequence Variation and Regulation of Genes Involved in Pathogenesis of Pulmonary Tuberculosis. Scand J Immunol 2012; 75:568-87. [DOI: 10.1111/j.1365-3083.2012.02696.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Axelsson-Robertson R, Magalhaes I, Parida SK, Zumla A, Maeurer M. The Immunological Footprint of Mycobacterium tuberculosis T-cell Epitope Recognition. J Infect Dis 2012; 205 Suppl 2:S301-15. [DOI: 10.1093/infdis/jis198] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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32
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Heparin-binding hemagglutinin induces IFN-γ(+) IL-2(+) IL-17(+) multifunctional CD4(+) T cells during latent but not active tuberculosis disease. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2012; 19:746-51. [PMID: 22461525 DOI: 10.1128/cvi.00047-12] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The mycobacterial heparin-binding hemagglutinin (HBHA) protein induces a potent gamma interferon (IFN-γ) response in latent tuberculosis (TB) infection and is a candidate vaccine and diagnostic antigen. We have assessed HBHA-specific intracellular IFN-γ, interleukin-2 (IL-2), and IL-17 production by CD4(+) T cells in TB cases and household contacts (HHCs) as well as the level of secreted IFN-γ in whole-blood culture supernatant. HHCs were further classified as tuberculin skin test (TST) positive or negative, and the group was also divided as HIV positive or negative. Our study revealed that HBHA induces multifunctional IFN-γ-, IL-2-, and IL-17-coexpressing CD4(+) T cells in HHCs but not in active TB cases; however, IFN-γ levels in culture supernatant did not differ between participant groups. Further studies are needed to completely understand how HBHA induces immune responses in different disease groups.
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Singla N, Gupta D, Joshi A, Batra N, Singh J, Birbian N. Association of mannose-binding lectin gene polymorphism with tuberculosis susceptibility and sputum conversion time. Int J Immunogenet 2011; 39:10-4. [PMID: 22050925 DOI: 10.1111/j.1744-313x.2011.01047.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mannose-binding lectin (MBL) plays an important role in innate immunity. The effect of low MBL levels producing variants of MBL2 gene on tuberculosis (TB) has been controversial with some studies reporting it to confer protection against the disease, whereas others estimating a susceptibility relation. Other than conducting a case-control study to evaluate the role of MBL A/B polymorphism on TB, we conducted a longitudinal study to check whether this MBL variant can influence the host response to Mycobacterium tuberculosis infection. A total of 357 TB patients (286 pulmonary TB, 71 extrapulmonary (EP) TB) and 392 healthy controls belonging to same ethnicity were included in the study. We found the mutant allele 'B' allele confers a protective role against TB in our study population. This effect was absent in EP patients. On stratification on the basis of sex, the protective role of the 'B' allele was found to be limited to females only and males reported no significant difference. No effect of MBL A/B polymorphism on sputum conversion time was reported. We conclude that MBL 'B' allele is associated with protection against TB, but no influence was found on sputum conversion rate.
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Affiliation(s)
- N Singla
- Department of Biotechnology, Panjab University, Chandigarh, India
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CCL2/MCP-I genotype-phenotype relationship in latent tuberculosis infection. PLoS One 2011; 6:e25803. [PMID: 21991356 PMCID: PMC3186769 DOI: 10.1371/journal.pone.0025803] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Accepted: 09/11/2011] [Indexed: 12/22/2022] Open
Abstract
Among the known biomarkers, chemokines, secreted by activated macrophages and T cells, attract groups of immune cells to the site of infection and may determine the clinical outcome. Association studies of CCL-2/MCP-1 -2518 A/G functional SNP linked to high and low phenotypes with tuberculosis disease susceptibility have shown conflicting results in tuberculosis. Some of these differences could be due the variability of latent infection and recent exposure in the control groups. We have therefore carried out a detailed analysis of CCL-2 genotype SNP -2518 (A/G transition) with plasma CCL-2 levels and related these levels to tuberculin skin test positivity in asymptomatic community controls with no known exposure to tuberculosis and in recently exposed household contacts of pulmonary tuberculosis patients. TST positivity was linked to higher concentrations of plasma CCL2 (Mann Whitney U test; p = 0.004) and was more marked when the G allele was present in TST+ asymptomatic controls (A/G; p = 0.01). Recent exposure also had a significant effect on CCL-2 levels and was linked to the G allele (p = 0.007). Therefore association studies for susceptibility or protection from disease should take into consideration the PPD status as well as recent exposure of the controls group used for comparison. Our results also suggest a role for CCL-2 in maintaining the integrity of granuloma in asymptomatic individuals with latent infection in high TB burden settings. Therefore additional studies into the role of CCL-2 in disease reactivation and progression are warranted.
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35
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Warnich L, Drögemöller BI, Pepper MS, Dandara C, Wright GEB. Pharmacogenomic Research in South Africa: Lessons Learned and Future Opportunities in the Rainbow Nation. ACTA ACUST UNITED AC 2011; 9:191-207. [PMID: 22563365 PMCID: PMC3228231 DOI: 10.2174/187569211796957575] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Revised: 05/25/2011] [Accepted: 05/28/2011] [Indexed: 12/11/2022]
Abstract
South Africa, like many other developing countries, stands to benefit from novel diagnostics and drugs developed by pharmacogenomics guidance due to high prevalence of disease burden in the region. This includes both communicable (e.g., HIV/AIDS and tuberculosis) and non-communicable (e.g., diabetes and cardiovascular) diseases. For example, although only 0.7% of the world's population lives in South Africa, the country carries 17% of the global HIV/AIDS burden and 5% of the global tuberculosis burden. Nobel Peace Prize Laureate Archbishop Emeritus Desmond Tutu has coined the term Rainbow Nation, referring to a land of wealth in its many diverse peoples and cultures. It is now timely and necessary to reflect on how best to approach new genomics biotechnologies in a manner that carefully considers the public health needs and extant disease burden in the region. The aim of this paper is to document and review the advances in pharmacogenomics in South Africa and importantly, to evaluate the direction that future research should take. Previous research has shown that the populations in South Africa exhibit unique allele frequencies and novel genetic variation in pharmacogenetically relevant genes, often differing from other African and global populations. The high level of genetic diversity, low linkage disequilibrium and the presence of rare variants in these populations question the feasibility of the use of current commercially available genotyping platforms, and may partially account for genotype-phenotype discordance observed in past studies. However, the employment of high throughput technologies for genomic research, within the context of large clinical trials, combined with interdisciplinary studies and appropriate regulatory guidelines, should aid in acceleration of pharmacogenomic discoveries in high priority therapeutic areas in South Africa. Finally, we suggest that projects such as the H3Africa Initiative, the SAHGP and PGENI should play an integral role in the coordination of genomic research in South Africa, but also other African countries, by providing infrastructure and capital to local researchers, as well as providing aid in addressing the computational and statistical bottlenecks encountered at present.
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Affiliation(s)
- Louise Warnich
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
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Intemann CD, Thye T, Förster B, Owusu-Dabo E, Gyapong J, Horstmann RD, Meyer CG. MCP1 haplotypes associated with protection from pulmonary tuberculosis. BMC Genet 2011; 12:34. [PMID: 21504590 PMCID: PMC3107163 DOI: 10.1186/1471-2156-12-34] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 04/19/2011] [Indexed: 12/24/2022] Open
Abstract
Background The monocyte chemoattractant protein 1 (MCP-1) is involved in the recruitment of lymphocytes and monocytes and their migration to sites of injury and cellular immune reactions. In a Ghanaian tuberculosis (TB) case-control study group, associations of the MCP1 -362C and the MCP1 -2581G alleles with resistance to TB were recently described. The latter association was in contrast to genetic effects previously described in study groups originating from Mexico, Korea, Peru and Zambia. This inconsistency prompted us to further investigate the MCP1 gene in order to determine causal variants or haplotypes genetically and functionally. Results A 14 base-pair deletion in the first MCP1 intron, int1del554-567, was strongly associated with protection against pulmonary TB (OR = 0.84, CI 0.77-0.92, Pcorrected = 0.00098). Compared to the wildtype combination, a haplotype comprising the -2581G and -362C promoter variants and the intronic deletion conferred an even stronger protection than did the -362C variant alone (OR = 0.78, CI 0.69-0.87, Pnominal = 0.00002; adjusted Pglobal = 0.0028). In a luciferase reporter gene assay, a significant reduction of luciferase gene expression was observed in the two constructs carrying the MCP1 mutations -2581 A or G plus the combination -362C and int1del554-567 compared to the wildtype haplotype (P = 0.02 and P = 0.006). The associated variants, in particular the haplotypes composed of these latter variants, result in decreased MCP-1 expression and a decreased risk of pulmonary TB. Conclusions In addition to the results of the previous study of the Ghanaian TB case-control sample, we have now identified the haplotype combination -2581G/-362C/int1del554-567 that mediates considerably stronger protection than does the MCP1 -362C allele alone (OR = 0.78, CI 0.69-0.87 vs OR = 0.83, CI 0.76-0.91). Our findings in both the genetic analysis and the reporter gene study further indicate a largely negligible role of the variant at position -2581 in the Ghanaian population studied.
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Affiliation(s)
- Christopher D Intemann
- Bernhard Nocht Institute for Tropical Medicine, Dept. Molecular Medicine, Hamburg, Germany
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Ben-Selma W, Harizi H, Boukadida J. MCP-1 -2518 A/G functional polymorphism is associated with increased susceptibility to active pulmonary tuberculosis in Tunisian patients. Mol Biol Rep 2011; 38:5413-9. [PMID: 21384169 DOI: 10.1007/s11033-011-0695-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Accepted: 02/26/2011] [Indexed: 11/30/2022]
Abstract
Monocyte chemoattractant protein-1 (MCP-1) plays crucial role in protective immunity against Mycobacterium tuberculosis (MT). In this study, we examined whether single nucleotide polymorphism (SNP) -2518 A/G (rs 1024611) of MCP-1 affect the susceptibility to active tuberculosis (TB) in Tunisian populations. Genomic DNA from patients with active TB (168 cases of pulmonary TB and 55 cases of extrapulmonary TB) and ethnically controls (150 cases) was genotyped for the MCP-1 -2518 A/G SNP by polymerase chain reaction fragment length polymorphism (PCR-RFLP). We observed that -2518 G allele and GG genotype (high MCP-1 producer) frequencies were significantly more elevated in active pulmonary TB group in comparison to control group [34 vs. 22%; P = 0.0007; 15 vs. 5%, P corrected for the number of genotypes (Pc) = 0.015; respectively]. Additionally, they were associated with increased risk development of this clinical form of TB [odds ratio (OR) = 1.83, 95% confidence intervals (CI) = 1.26-2.66; OR = 3.1, 95% CI = 1.28-7.76; respectively]. However, wild type allele -2518 A and AA genotype were over-represented in control group (78 and 62%) and seem to be protective factors against TB. Moreover, -2518 AA genotype was more frequent in control group and was associated with resistance against development of active pulmonary TB (OR = 0.56, 95% CI = 0.35-0.89, Pc = 0.03). Our findings confirm the key role of -2518 A/G SNP of MCP-1 and support its association with resistance/susceptibility to the development of active pulmonary TB in the Tunisian population.
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Affiliation(s)
- Walid Ben-Selma
- Laboratory of Microbiology and Immunology, UR02SP13, Farhat Hached University Hospital, CHU Farhat Hached - Av. Ibn el Jazzar, 4000 Sousse, Tunisia.
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38
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Tag SNP polymorphism of CCL2 and its role in clinical tuberculosis in Han Chinese pediatric population. PLoS One 2011; 6:e14652. [PMID: 21556333 PMCID: PMC3084193 DOI: 10.1371/journal.pone.0014652] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Accepted: 01/14/2011] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Chemokine (C-C motif) ligand 2 CCL2/MCP-1 is among the key signaling molecules of innate immunity; in particular, it is involved in recruitment of mononuclear and other cells in response to infection, including tuberculosis (TB) and is essential for granuloma formation. METHODOLOGY/PRINCIPAL FINDINGS We identified a tag SNP for the CCL2/MCP-1 gene (rs4586 C/T). In order to understand whether this SNP may serve to evaluate the contribution of the CCL2 gene to the expression of TB disease, we further analysed distribution of its alleles and genotypes in 301 TB cases versus 338 non-infected controls (all BCG vaccinated) representing a high-risk pediatric population of North China. In the male TB subgroup, the C allele was identified in a higher rate (P = 0.045), and, acting dominantly, was found to be a risk factor for clinical TB (P = 0.029). Homozygous TT genotype was significantly associated with lower CSF mononuclear leukocyte (ML) counts in patients with tuberculous meningitis (TBM) (P = 0.001). CONCLUSIONS/SIGNIFICANCE The present study found an association of the CCL2 tag SNP rs4586 C allele and pediatric TB disease in males, suggesting that gender may affect the susceptibility to TB even in children. The association of homozygous TT genotype with decreased CSF mononuclear leukocyte (ML) count not only suggests a clinical significance of this SNP, but indicates its potential to assist in the clinical assessment of suspected TBM, where delay is critical and diagnosis is difficult.
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Qidwai T, Jamal F. Inducible nitric oxide synthase (iNOS) gene polymorphism and disease prevalence. Scand J Immunol 2011; 72:375-87. [PMID: 21039732 DOI: 10.1111/j.1365-3083.2010.02458.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Nitric oxide synthase gene is present on chromosome 17 and has been implicated in a wide variety of diseases. The nitric oxide synthase enzyme forms nitric oxide that besides being a signalling molecule plays an important role in host immune response. Inducible nitric oxide synthase expression is regulated at the level of transcription. Single-nucleotide polymorphisms, copy number variation and simple sequence repeat are important variations that have been reported in human genome. The presence of such variations in the regulatory region affects the level of gene product in the cell, while variation in the coding region influences the structure of proteins and its activity. This alteration in the level of gene product and the structure of the protein molecule might be responsible for the final outcome of genetic as well as infectious diseases. In the present manuscript, we review the role of inducible nitric oxide synthase (iNOS) gene polymorphisms in different diseases and populations. The iNOS gene with one pentanucleotide repeat, two single-nucleotide polymorphisms in promoter region and one polymorphism in exon 16 has been implicated in several diseases. We have also predicted several polymorphisms in the promoter region of iNOS computationally, which might affect the transcription factor binding site (TFBS) and hypothesize that these polymorphisms have some putative role in the outcome of disease(s).
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Affiliation(s)
- T Qidwai
- Department of Biochemistry, Dr. R.M.L. Avadh University, Faizabad, India
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Abstract
Several candidate gene studies have provided evidence for a role of host genetics in susceptibility to tuberculosis (TB). However, the results of these studies have been very inconsistent, even within a study population. Here, we review the design of these studies from a genetic epidemiological perspective, illustrating important differences in phenotype definition in both cases and controls, consideration of latent M. tuberculosis infection versus active TB disease, population genetic factors such as population substructure and linkage disequilibrium, polymorphism selection, and potential global differences in M. tuberculosis strain. These considerable differences between studies should be accounted for when examining the current literature. Recommendations are made for future studies to further clarify the host genetics of TB.
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Affiliation(s)
- Catherine M Stein
- Department of Epidemiology and Biostatistics, and Tuberculosis Research Unit, Case Western Reserve University, Cleveland, Ohio, United States of America.
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Genome-wide analysis of the structure of the South African Coloured Population in the Western Cape. Hum Genet 2010; 128:145-53. [DOI: 10.1007/s00439-010-0836-1] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Accepted: 05/10/2010] [Indexed: 12/26/2022]
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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: 147] [Impact Index Per Article: 10.5] [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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Gola S, Manganelli R, García MJ, Vicente M. News from the antituberculosis front at two recent European meetings. World J Microbiol Biotechnol 2009. [DOI: 10.1007/s11274-009-0056-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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