No significant impact of IFN-γ pathway gene variants on tuberculosis susceptibility in a West African population

Mycobacterium tuberculosis and host interactions in the manifestation of tuberculosis

The final step of epigenetic processes is changing the gene expression in a new microenvironment in the body, such as neuroendocrine changes, active infections, oncogenes, or chemical agents. The case of tuberculosis (TB) is an outcome of Mycobacterium tuberculosis (M.tb) and host interaction in the manifestation of active and latent TB or clearance. This comprehensive review explains and interprets the epigenetics findings regarding gene expressions on the host-pathogen interactions in the development and progression of tuberculosis. This review introduces novel insights into the complicated host-pathogen interactions, discusses the challengeable results, and shows the gaps in the clear understanding of M.tb behavior. Focusing on the biological phenomena of host-pathogen interactions, the epigenetic changes, and their outcomes provides a promising future for developing effective TB immunotherapies when converting gene expression toward appropriate host immune responses gradually becomes attainable. Overall, this review may shed light on the dark sides of TB pathogenesis as a life-threatening disease. Therefore, it may support effective planning and implementation of epigenetics approaches for introducing proper therapies or effective vaccines.

Discovering the link between IL12RB1 gene polymorphisms and tuberculosis susceptibility: a comprehensive meta-analysis

Introduction

Numerous studies suggest that the risk of tuberculosis (TB) is linked to gene polymorphisms of the interleukin-12 receptor b subunit 1 (IL12RB1), but the association between IL12RB1 polymorphisms and TB susceptibility has not been thoroughly investigated.

Methods

A meta-analysis was conducted based on eight case-control studies with 10,112 individuals to further explore this topic. A systematic search of PubMed, Web of Science, Excerpt Medica Database, and Google Scholar up until April 6th, 2023 was performed. ORs and 95% CIs were pooled using the random-effect model. The epidemiological credibility of all significant associations was assessed using the Venice criteria and false-positive report probability (FPRP) analyses.

Results

The IL12RB1 rs11575934 and rs401502 showed solid evidence of no significant association with TB susceptibility. However, a weak association was observed between the IL12RB1 rs375947 biomarker and pulmonary tuberculosis (PTB) susceptibility (OR = 1.64, 95% CI: 1.22, 2.21).

Discussion

These findings should be confirmed through larger, better-designed studies to clarify the relationship between biomarkers in IL12RB1 gene and different types of TB susceptibility.

Single nucleotide polymorphism rs2234711 of interferon gamma receptor 1 is associated with pulmonary tuberculosis in the population of North India

Interferon-gamma (IFN-γ) is a pro-inflammatory cytokine playing essential role in immunity against tuberculosis (TB). IFN-γ performs function by binding to its receptor complex, consisting of two polypeptide chains viz. IFN-γ receptor 1 (IFN-γR1) and IFN-γ receptor 2 (IFN-γR2). Structural and functional deficiencies in IFN-γR1 can make individual vulnerable to even weak mycobacterial infections. Studies from different populations of the world have reported the association of single nucleotide polymorphisms (SNPs) present in IFNGR1 gene with TB, however, there are no such studies from India. Thus, the present study was designed to analyse the association of rs2234711 (C/T), rs7749390 (C/T) and rs1327475 (C/T) SNPs of IFNGR1 with TB in the population of North India. For the present study, 263 TB patients (at zero day of anti-tuberculosis therapy) and 256 healthy controls (HCs) were recruited. The genotyping of selected SNPs was done by high-resolution melting (HRM) curve analysis. The mRNA and surface expression data of IFNGR1 was extracted from our previous study and was grouped according to the genotypes of studied SNPs. The genotype 'TT' and 'T' allele of SNP rs2234711 (C/T) were found to be associated with TB in studied population ['T' vs 'C': OR (CI) = 1.79 (1.39-2.29); p-value < 0.0001]. The haplotypes 'C-C-C' of rs2234711-rs7749390-rs1327475 confers protection, while haplotype 'T-C-C' is a risk factor for TB in studied population. It was also found that 'TT' genotype of rs2234711 in HCs is associated with lower surface expression of IFNGR1 (p-value = 0.0078). In conclusion, 'TT' genotype is associated with lower surface expression of IFNGR1 and is increasing the susceptibility to TB in North Indian population.

Association between IFNGR1 gene polymorphisms and tuberculosis susceptibility: A meta-analysis

The association of IFN-γ receptor 1 (IFNGR1) gene polymorphisms with tuberculosis (TB) susceptibility has not been systematically studied. We therefore conducted a meta-analysis to assess their association. Literature search was conducted in PubMed, EMBASE, Web of Science, and the Cochrane Library. Odds ratio (OR) and 95% confidence interval (CI) was pooled by the random-effect model. Statistical analyses were performed using STATA 12.0 software. Fourteen studies involved 7,699 TB cases and 8,289 controls were included in this meta-analysis. A significant association was found between the IFNGR1 rs2234711 polymorphism and TB susceptibility among Africans in dominant model (OR = 1.24, 95%CI:1.01-1.52), and among Asians in allele model (OR = 0.89, 95%CI: 0.79-0.99), homozygote model (OR = 0.82, 95%CI: 0.70-0.98) and additive model (OR = 0.90, 95%CI: 0.83-0.97). In addition, a significant association was observed between the IFNGR1 rs7749390 polymorphism and TB susceptibility among Africans in allele model (OR = 0.89, 95%CI: 0.82-0.98). No significant association was found between the IFNGR1 rs1327474 polymorphism and TB susceptibility. In summary, IFNGR1 rs2234711 polymorphism was associated with increased TB susceptibility in Africans and decreased TB susceptibility in Asians, while IFNGR1 rs7749390 polymorphism was associated with decreased TB susceptibility in Africans.

Genetic Polymorphism of Tumor Necrosis Factor-Alpha, Interferon-Gamma and Interleukin-10 and Association With Risk of Mycobacterium Tuberculosis Infection

BACKGROUND

Mycobacterium tuberculosis has become the leading cause of morbidity and death in humans worldwide. Thus, genetic variability of the host plays a major role in human susceptibility to the pathogen, among others. Therefore, the objective of this finding was to assess the association of genetic polymorphisms of cytokines with tuberculosis infection.

METHOD

A cross-sectional study was conducted between January and May 2018. Five ml of whole blood was collected and extracted the genomic DNA through simple salting out method. The patterns of genetic polymorphism were determined by amplification refractory method PCR using specific primers. Finally, the PCR run on electrophoresis of agarose gel and the band was visualized under UV light. A logistical regression model has been adapted to assess the association of genetic polymorphisms with tubercular infection. In order to determine the association between the explanatory and outcome variable, the odds ratio with 95% CI was calculated. P < 0.05 is a statistically significant value.

RESULT

In present study, the frequency of TNF-α -308 G allele and GG genotype OR (95% CI)= 0.20 (0.11-0.37), and OR (95% CI)= 0.29 (0.18-0.46)), respectively) and IFN-γ +874 A allele and AA genotype OR (95% CI)= 3.80 (2.11-6.86) and (OR (95% CI)= 1.61(1.13-2.28), respectively) were significantly associated with tuberculosis incidence. In contrast, there is no significant correlation between IL-10 -1082 A and AA of allele and genotype, respectively in tuberculosis patients (p > 0.05) was evident.

CONCLUSION

From our finding, the genetic variability of TNF-α -308 A and IFN-γ +874 alleles are the potent host genetic risk factors associated with tuberculosis infection.

A Novel Genetic Variation in NCF2, the Core Component of NADPH Oxidase, Contributes to the Susceptibility of Tuberculosis in Western Chinese Han Population

Mycobacterium tuberculosis (Mtb) is the causative agent of the disease tuberculosis (TB). Macrophages eliminate the Mtb, delivering it to the degradative, phagolysosomal compartment for degradation, in which reactive oxygen species generated by nicotinamide adenine dinucleotide phosphate oxidase (NADPHO) plays an important role. In our study, we aimed at investigating the association of polymorphisms in neutrophil cytosolic factor 2 (NCF2) gene, the core component of NADPHO, with susceptibility of TB in the Western Chinese Han population. We conducted a case-control study of 900 cases and 1534 controls and genotyped four single-nucleotide polymorphisms within the NCF2 gene. We found that the rs10911362 variants were associated with a decreased TB risk in this population (odds ratio [OR_G] = 0.83 [0.72-0.95], OR_add = 0.83 [0.72-0.95], OR_dom = 0.78 [0.66-0.93], p < 0.05). rs10911362 might fall in a transcriptional factor binding site associated with ZNF410 and may be the expression quantitative trait loci (eQTL) for the SMG7 gene according to the Ensembl data. Our study demonstrated for the first time that the G allele of NCF2 rs10911362 provided a protective role against TB risk in the Western Chinese Han population.

Influence of Genetic Polymorphism Towards Pulmonary Tuberculosis Susceptibility

Tuberculosis (TB) is still remains the major threat for human health worldwide. Several case-control, candidate-gene, family studies and genome-wide association studies (GWAS) suggested the association of host genetic factors to TB susceptibility or resistance in various ethnic populations. Moreover, these factors modulate the host immune responses to tuberculosis. Studies have reported genetic markers to predict TB development in human leukocyte antigen (HLA) and non-HLA genes like killer immunoglobulin-like receptor (KIR), toll-like receptors (TLRs), cytokine/chemokines and their receptors, vitamin D receptor (VDR) and SLC11A1 etc. Highly polymorphic HLA loci may influence antigen presentation specificities by modifying peptide binding motifs. The recent meta-analysis studies revealed the association of several HLA alleles in particular class II HLA-DRB1 with TB susceptibility and valuable marker for disease development especially in Asian populations. Case-control studies have found the association of HLA-DR2 in some populations, but not in other populations, this could be due to an ethnic specific association of gene variants. Recently, GWAS conducted in case-control and family based studies in Russia, Chinese Han, Morocco, Uganda and Tanzania revealed the association of genes such as ASAP1, Alkylglycerol monooxygenase (AGMO), Forkhead BoxP1 (FOXP1), C-terminal domain phosphatase 1 (UBLCP1) and intergenic SNP rs932347C/T with TB. Whereas, SNP rs10956514A/G were not associated with TB in western Chinese Han and Tibetan population. In this review, we summarize the recent findings of genetic variants with susceptibility/resistance to TB.

Comprehensive analysis of three TYK2 gene variants in the susceptibility to Chagas disease infection and cardiomyopathy

Tyrosine kinase 2 (TYK2) is a member of the Janus kinases family implicated in the signal transduction of type I interferons and several interleukins. It has been described that genetic mutations within TYK2 lead to multiple deleterious effects in the immune response. In this work, we have analyzed three functional independent variants from the frequency spectrum on the TYK2 gene (common and low-frequency variants) suggested to reduce the function of the gene in mediating cytokine signaling and the susceptibility to infections by Trypanosoma cruzi and/or the development of Chagas cardiomyopathy in the Colombian population. A total of 1,323 individuals from a Colombian endemic region for Chagas disease were enrolled in the study. They were classified as seronegative (n = 445), seropositive asymptomatic (n = 336), and chronic Chagas Cardiomyopathy subjects (n = 542). DNA samples were genotyped using TaqMan probes. Our results showed no statistically significant differences between the allelic frequencies of the three analyzed variants when seropositive and seronegative individuals were compared, therefore these variants were not associated with susceptibility to Chagas disease. Moreover, when Chagas cardiomyopathy patients were compared to asymptomatic patients, no significant associations were found. Previous reports highlighted the association of this gene in immune-related disorders under an autoimmunity context, but not predisposing patients to infectious diseases, which is consistent with our findings. Therefore, according to our results, TYK2 gene variants do not seem to play an important role in Chagas disease susceptibility and/or chronic Chagas cardiomyopathy.

Human genetic factors in tuberculosis: an update

Tuberculosis (TB) is a major threat to human health, especially in many developing countries. Human genetic variability has been recognised to be of great relevance in host responses to Mycobacterium tuberculosis infection and in regulating both the establishment and the progression of the disease. An increasing number of candidate gene and genome-wide association studies (GWAS) have focused on human genetic factors contributing to susceptibility or resistance to TB. To update previous reviews on human genetic factors in TB we searched the MEDLINE database and PubMed for articles from 1 January 2014 through 31 March 2017 and reviewed the role of human genetic variability in TB. Search terms applied in various combinations were 'tuberculosis', 'human genetics', 'candidate gene studies', 'genome-wide association studies' and 'Mycobacterium tuberculosis'. Articles in English retrieved and relevant references cited in these articles were reviewed. Abstracts and reports from meetings were also included. This review provides a recent summary of associations of polymorphisms of human genes with susceptibility/resistance to TB.

The Role of Host Genetics (and Genomics) in Tuberculosis

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.