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Liu Z, Deligen B, Han Z, Gerile C, Da A. Integrated sequence-based genomic, transcriptomic, and methylation characterization of the susceptibility to tuberculosis in monozygous twins. Heliyon 2024; 10:e31712. [PMID: 38845983 PMCID: PMC11153169 DOI: 10.1016/j.heliyon.2024.e31712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 05/08/2024] [Accepted: 05/21/2024] [Indexed: 06/09/2024] Open
Abstract
Background Tuberculosis (TB) is a complex disease with a spectrum of outcomes for more than six decades; however, the genomic and epigenetic mechanisms underlying the highly heritable susceptibility to TB remain unclear. Methods Integrated sequence-based genomic, transcriptomic, and methylation analyses were conducted to identity the genetic factors associated with susceptibility to TB in two pairs of Mongolian monozygous twins. In this study, whole-genome sequencing was employed to analyze single nucleotide polymorphisms (SNPs), insertions and deletions (InDels), and copy number variations (CNVs). Gene expression was assessed through RNA sequencing, and methylation patterns were examined using the Illumina Infinium Methylation EPIC BeadChip. The gene-gene interaction network was analyzed using differentially expressed genes. Results Our study revealed no significant difference in SNP and InDel profiles between participants with and without TB. Genes with CNVs were involved in human immunity (human leukocyte antigen [HLA] family and interferon [IFN] pathway) and the inflammatory response. Different DNA methylation patterns and mRNA expression profiles were observed in genes participating in immunity (HLA family) and inflammatory responses (IFNA, interleukin 10 receptor [IL-10R], IL-12B, Toll-like receptor, and IL-1B). Conclusions The results of this study suggested that susceptibility to TB is associated with transcriptional and epigenetic alternations of genes involved in immune and inflammatory responses. The genes in the HLA family (HLA-A, HLA-B, and HLA-DRB1) and IFN pathway (IFN-α and IFN-γ) may play major roles in susceptibility to TB.
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Affiliation(s)
- Zhi Liu
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Inner Mongolia Minzu University, Tongliao, 028007, Inner Mongolia, China
| | - Batu Deligen
- Institute of Mongolian Medicine Pharmacology, Affiliated Hospital of Inner Mongolia Minzu University, Tongliao, 028007, Inner Mongolia, China
| | - Zhiqiang Han
- Institute of Mongolian Medicine Pharmacology, Affiliated Hospital of Inner Mongolia Minzu University, Tongliao, 028007, Inner Mongolia, China
| | - Chaolumen Gerile
- Department of Internal Medicine, Xilinguole Meng Mongolian General Hospital, Xilinhaote, 026000, Inner Mongolia, China
| | - An Da
- Institute of Mongolian Medicine Pharmacology, Affiliated Hospital of Inner Mongolia Minzu University, Tongliao, 028007, Inner Mongolia, China
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Badamasi IM, Muhammad M, Umar AA, Madugu UAM, Gadanya MA, Aliyu IA, Kabir IM, Umar IA, Johnson O, Stanslas J. Role of the IL8 rs4073 polymorphism in central nervous system toxicity in patients receiving multidrug-resistant tuberculosis treatment. J Bras Pneumol 2024; 50:e20230338. [PMID: 38359298 PMCID: PMC11095930 DOI: 10.36416/1806-3756/e20230338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 11/01/2023] [Indexed: 02/17/2024] Open
Abstract
OBJECTIVE To determine the role of the IL8 rs4073 polymorphism in predicting the risk of central nervous system (CNS) toxicity in patients receiving standard pharmacological treatment for multidrug-resistant tuberculosis (MDR-TB). METHODS A cohort of 85 consenting MDR-TB patients receiving treatment with second-line antituberculosis drugs had their blood samples amplified for the IL8 (rs4073) gene and genotyped. All patients were clinically screened for evidence of treatment toxicity and categorized accordingly. Crude and adjusted associations were assessed. RESULTS The chief complaints fell into the following categories: CNS toxicity; gastrointestinal toxicity; skin toxicity; and eye and ear toxicities. Symptoms of gastrointestinal toxicity were reported by 59% of the patients, and symptoms of CNS toxicity were reported by 42.7%. With regard to the genotypes of IL8 (rs4073), the following were identified: AA, in 64 of the study participants; AT, in 7; and TT, in 11. A significant association was found between the dominant model of inheritance and CNS toxicity for the crude model (p = 0.024; OR = 3.57; 95% CI, 1.18-10.76) and the adjusted model (p = 0.031; OR = 3.92; 95% CI, 1.13-13.58). The AT+TT genotype of IL8 (rs4073) showed a 3.92 times increased risk of CNS toxicity when compared with the AA genotype. CONCLUSIONS The AT+TT genotype has a tendency to be associated with an increased risk of adverse clinical features during MDR-TB treatment.
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Affiliation(s)
- Ibrahim Mohammed Badamasi
- . Pharmacogenomic Unit, Department of Human Anatomy, Faculty of Basic Medical Sciences - FBMS - College of Medicine, Bayero University, Kano, Kano, Nigeria
| | - Muktar Muhammad
- . Pharmacogenomic Unit, Department of Human Anatomy, Faculty of Basic Medical Sciences - FBMS - College of Medicine, Bayero University, Kano, Kano, Nigeria
| | - Aishat Ahmad Umar
- . Pharmacogenomic Unit, Department of Human Anatomy, Faculty of Basic Medical Sciences - FBMS - College of Medicine, Bayero University, Kano, Kano, Nigeria
| | - Umm-ayman Misbahu Madugu
- . Pharmacogenomic Unit, Department of Human Anatomy, Faculty of Basic Medical Sciences - FBMS - College of Medicine, Bayero University, Kano, Kano, Nigeria
| | - Muktar Ahmed Gadanya
- . Department of Community Medicine, Faculty of Clinical Sciences, Bayero University, Kano, Kano, Nigeria
| | - Isa Abubakar Aliyu
- . Department of Medical Laboratory Science, Faculty of Allied Health Sciences - FAHS - Bayero University, Kano, Kano, Nigeria
| | - Imam Malik Kabir
- . Department of Medical Laboratory Science, Faculty of Allied Health Sciences - FAHS - Bayero University, Kano, Kano, Nigeria
| | - Ibrahim Aliyu Umar
- . Kano State TB and Leprosy Control Program, Kano State Ministry of Health, Kano, Nigeria
| | - Ochigbo Johnson
- . Kano State Infectious Disease Hospital, Kano State Ministry of Health, Kano, Nigeria
| | - Johnson Stanslas
- . Pharmacotherapeutics Lab, Department of Medicine, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
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Khan N, Das A. Can the personalized medicine approach contribute in controlling tuberculosis in general and India in particular? PRECISION CLINICAL MEDICINE 2020; 3:240-243. [PMID: 35694414 PMCID: PMC8982531 DOI: 10.1093/pcmedi/pbaa021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 06/01/2020] [Indexed: 11/13/2022] Open
Abstract
Poor drug compliance and drug-resistant Mycobacterium tuberculosis are the two principal obstacles in controlling tuberculosis (TB) in endemic regions including India, which has contributed the most to global TB burden. We argue here that a personalized medicine approach, to start with the N-acetyl transferase-2–isoniazid (NAT2–INH) model, could be a step forward in dealing with both these limitations in controlling TB in India.
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Affiliation(s)
- Nikhat Khan
- ICMR-National Institute of Research in Tribal Health, NIRTH Campus, Jabalpur, Madhya Pradesh 482 003, India
| | - Aparup Das
- ICMR-National Institute of Research in Tribal Health, NIRTH Campus, Jabalpur, Madhya Pradesh 482 003, India
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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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The proprotein convertase subtilisin/kexin furinA regulates zebrafish host response against Mycobacterium marinum. Infect Immun 2015; 83:1431-42. [PMID: 25624351 DOI: 10.1128/iai.03135-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Tuberculosis is a chronic bacterial disease with a complex pathogenesis. An effective immunity against Mycobacterium tuberculosis requires both the innate and adaptive immune responses, including proper T helper (Th) type 1 cell function. FURIN is a proprotein convertase subtilisin/kexin (PCSK) enzyme, which is highly expressed in Th1 type cells. FURIN expression in T cells is essential for maintaining peripheral immune tolerance, but its role in the innate immunity and infections has remained elusive. Here, we utilized Mycobacterium marinum infection models in zebrafish (Danio rerio) to investigate how furin regulates host responses against mycobacteria. In steady-state furinAtd204e/+ fish reduced furinA mRNA levels associated with low granulocyte counts and elevated Th cell transcription factor expressions. Silencing furin genes reduced the survival of M. marinum-infected zebrafish embryos. A mycobacterial infection upregulated furinA in adult zebrafish, and infected furinAtd204e/+ mutants exhibited a proinflammatory phenotype characterized by elevated tumor necrosis factor a (tnfa), lymphotoxin alpha (lta) and interleukin 17a/f3 (il17a/f3) expression levels. The enhanced innate immune response in the furinAtd204e/+ mutants correlated with a significantly decreased bacterial burden in a chronic M. marinum infection model. Our data show that upregulated furinA expression can serve as a marker for mycobacterial disease, since it inhibits early host responses and consequently promotes bacterial growth in a chronic infection.
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Castro-Martínez XH, Leal-Cortés C, Flores-Martínez SE, García-Zapién AG, Sánchez-Corona J, Portilla-de Buen E, Gómez-Espinel I, Zamora-Ginez I, Pérez-Fuentes R, Islas-Andrade S, Revilla-Monsalve C, Guerrero-Romero F, Rodríguez-Morán M, Mendoza-Carrera F. Tumor necrosis factor haplotype diversity in Mestizo and native populations of Mexico. ACTA ACUST UNITED AC 2014; 83:247-59. [PMID: 24517517 DOI: 10.1111/tan.12300] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 12/06/2013] [Accepted: 01/06/2014] [Indexed: 11/30/2022]
Abstract
The so-called tumor necrosis factor (TNF) block includes the TNFA, lymphotoxin alpha and beta (LTA and LTB) genes with single-nucleotide polymorphisms (SNP) and microsatellites with an allele frequency that exhibits interpopulation variability. To date, no reports have included both SNPs and microsatellites at the TNF block to study Mestizo or Amerindian populations from Mexico. In this study, samples of five Mexican Mestizo populations (Durango, Guadalajara, Monterrey, Puebla, and Tierra Blanca) and four native-Mexican populations (North Lacandonians, South Lacandonians, Tepehuanos, and Yaquis) were genotyped for two SNPs (LTA+252A>G and TNFA-308G>A) and four microsatellites (TNFa, d, e, and f), to analyze the genetic substructure of the Mexican population. Allele and haplotype frequencies, linkage disequilibrium (LD), and interpopulation genetic relationships were calculated. There was significant LD along almost all of the TNF block but the lowest D' values were observed for the TNFf-TNFd pair. Mestizos showed higher allele and haplotype diversity than did natives. The genetic differentiation level was reduced among Mestizos; however, a slightly, but significant genetic substructure was observed between northern and southern Mexican Mestizos. Among the Amerindian populations, the genetic differentiation level was significantly elevated, particularly in both North and South Lacandonians. Furthermore, among Southern Lacandonians, inhabitants of Lacanja town were the most differentiated from all the Mexicans analyzed. The data presented here will serve as a reference for further population and epidemiological studies including these TNF polymorphisms in the Mexican population.
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Affiliation(s)
- X H Castro-Martínez
- Molecular Medicine Division, Centro de Investigación Biomédica de Occidente (CIBO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara, Mexico; Doctorate Program in Human Genetics, Universidad de Guadalajara, Guadalajara, Mexico
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García-Elorriaga G, Vera-Ramírez L, del Rey-Pineda G, González-Bonilla C. -592 and -1082 interleukin-10 polymorphisms in pulmonary tuberculosis with type 2 diabetes. ASIAN PAC J TROP MED 2013; 6:505-9. [PMID: 23768819 DOI: 10.1016/s1995-7645(13)60086-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 11/15/2012] [Accepted: 12/15/2012] [Indexed: 01/09/2023] Open
Abstract
OBJECTIVE To determine the polymorphisms of Interleukin-10 (IL-10) (-592, -1082) in pulmonary tuberculosis (PTB) with and without type 2 diabetes (T2D). METHODS We studied a Mexican mestizo population of 37 patients with TB in remission (TBr) and 40 with active pulmonary TB (PTB), 21 patients with TB + T2D, 47 blood donors accepted, and 13 healthy health-care workers with tuberculin skin test positive. Determination of IL-10 polymorphisms was performed by real-time Polymerase chain reaction. RESULTS IL-10-592C/A presented in a greater proportion in healthy individuals than in patients with type 2 diabetes and TB in a not quite significant statistically manner. IL-10-1082A/A presented more frequently in the group of patients with both diseases, not being statistically significant in comparison with the group of healthy subjects. CONCLUSIONS This study describes two important new findings. First, it reveals that the IL-10 (-592 A/A and -592 C/C) polymorphisms were found in a greater proportion in a group of patients with T2D and TB than in healthy subjects. Second, the study provides evidence that the (-1082 G/G) polymorphism presented with greater frequency in healthy individuals than in patients with both of these diseases.
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Affiliation(s)
- Guadalupe García-Elorriaga
- Unidad de Investigación Médica en Inmunología e Infectología, Hospital de Infectología, Centro Médico Nacional La Raza (CMNR), Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico.
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Wan QQ, Li JL, Ye QF, Zhou JD. Genetic Association of Tumor Necrosis Factor-β, Interleukin-10, and Interleukin-1 Gene Cluster Polymorphism With Susceptibility to Pneumonia in Kidney Transplant Recipients. Transplant Proc 2013; 45:2211-4. [DOI: 10.1016/j.transproceed.2013.02.122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 01/15/2013] [Accepted: 02/05/2013] [Indexed: 01/22/2023]
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Shmarina G, Pukhalsky A, Petrova N, Zakharova E, Avakian L, Kapranov N, Alioshkin V. TNF gene polymorphisms in cystic fibrosis patients: contribution to the disease progression. J Transl Med 2013; 11:19. [PMID: 23343370 PMCID: PMC3565881 DOI: 10.1186/1479-5876-11-19] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 01/18/2013] [Indexed: 02/06/2023] Open
Abstract
Background It is well known that the disease progression in cystic fibrosis (CF) patients may be diverse in subjects with identical mutation in CFTR gene. It is quite possible that such heterogeneity is associated with TNF-α and/or LT-α gene polymorphisms since their products play a key role in inflammation. The aim of the study was to investigate the possible roles of TNF gene polymorphisms in CF disease phenotype and progression. Methods 198 CF patients and 130 control subjects were genotyped for both TNF-α–308GA and LT-α + 252AG polymorphisms. Results The carriers of the TNF-α–308A allele more frequently had asthma as compared to patients homozygous for the TNF-α–308 G allele. In 9 of 108 (8.3%) of LTα + 252AA carriers, tuberculosis infection has been documented, whereas there was no case of tuberculosis among patients, either homozygous or heterozygous for LTα +252 G alleles (p = 0.01). We never observed virus hepatitis among LTα + 252GA carriers. The genotypes TNF-α–308GG – LT-α + 252AA and TNF-α–308GA – LT-α + 252AG were unfavorable with regard to liver disease development (both p < 0.05). It was also shown that neutrophil elastase activity was higher in sputum specimens from high TNF producers with genotypes TNF-α–308GA or LT-α + 252GG. In addition the carriers of such genotypes demonstrated a higher risk of osteoporosis development (p values were 0.011 and 0.017, respectively). Conclusions The carriers of genotypes, which are associated with higher TNF-α production, demonstrated increased frequency of asthma, higher levels of neutrophil elastase, and decrease of bone density. On the contrary, the carriers of genotypes associated with low TNF-α production showed a higher frequency of tuberculosis infection.
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Affiliation(s)
- Galina Shmarina
- Department of Cystic Fibrosis, Research Centre for Medical Genetics, 1 Moskvorechie Street, Moscow 115478, Russia
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Abstract
Mycobacterial diseases are a group of illnesses that cause a considerable number of deaths throughout the world, regardless of years of public health control efforts. Personalized medicine is a new but rapidly advancing field of healthcare. Personalized medicine in the field of mycobacteriology may be applied in the different levels of management such as prevention, diagnosis, treatment and prognosis. A genetic predisposition and a protein dysfunction study are recommended to tailor an individual approach in mycobacterial diseases.
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Affiliation(s)
- Mehdi Mirsaeidi
- Division of Pulmonary and Critical Care, University of Illinois at Chicago, Chicago, IL, USA
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Cruz-Olivo F, García-Elorriaga G, González-Bonilla C, del Rey-Pineda G, Mancilla-Ramírez J. Tumor Necrosis Factor −308 and Lymphotoxin +252 Polymorphisms in Mexican Children with Kawasaki Disease and Coronary Aneurysms. Arch Med Res 2011; 42:602-7. [DOI: 10.1016/j.arcmed.2011.11.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Accepted: 10/26/2011] [Indexed: 01/22/2023]
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