rs2243268 and rs2243274 of Interleukin-4 (IL-4) gene are associated with reduced risk for extrapulmonary and severe tuberculosis in Chinese Han children

Transcriptional analysis of human peripheral blood mononuclear cells stimulated by Mycobacterium tuberculosis antigen

Background

Mycobacterium tuberculosis antigen (Mtb-Ag) is a polypeptide component with a molecular weight of 10-14 kDa that is obtained from the supernatant of the H37Ra strain after heat treatment. It stimulates the activation and proliferation of γδT cells in the blood to produce an immune response against tuberculosis. Mtb-Ag is therefore crucial for classifying and detecting the central genes and key pathways involved in TB initiation and progression.

Methods

In this study, we performed high-throughput RNA sequencing of peripheral blood mononuclear cells (PBMC) from Mtb-Ag-stimulated and control samples to identify differentially expressed genes and used them for gene ontology (GO) and a Kyoto Encyclopedia of Genomes (KEGG) enrichment analysis. Meanwhile, we used PPI protein interaction network and Cytoscape analysis to identify key genes and qRT-PCR to verify differential gene expression. Single-gene enrichment analysis (GSEA) was used further to elucidate the potential biological functions of key genes. Analysis of immune cell infiltration and correlation of key genes with immune cells after Mtb-Ag-stimulated using R language.

Results

We identified 597 differentially expressed genes in Mtb-Ag stimulated PBMCs. KEGG and GSEA enrichment analyzed the cellular pathways related to immune function, and DEGs were found to be primarily involved in the TNF signaling pathway, the IL-17 signaling pathway, the JAK-STAT signaling pathway, cytokine-cytokine receptor interactions, and the NF-κB signaling pathway. Wayne analysis using GSEA, KEGG, and the protein-protein interaction (PPI) network showed that 34 genes, including PTGS2, IL-1β, IL-6, TNF and IFN-γ et al., were co-expressed in the five pathways and all were up-regulated by Mtb-Ag stimulation. Twenty-four DEGs were identified using qRT-PCR, including fourteen up-regulated genes (SERPINB7, IL20, IFNG, CSF2, PTGS2, TNF-α, IL36G, IL6, IL10, IL1A, CXCL1, CXCL8, IL4, and CXCL3) and ten down-regulated genes (RTN1, CSF1R CD14, C5AR1, CXCL16, PLXNB2, OLIG1, EEPD1, ENG, and CCR1). These findings were consistent with the RNA-Seq results.

Conclusion

The transcriptomic features associated with Mtb-Ag provide the scientific basis for exploring the intracellular immune mechanisms against Mtb. However, more studies on these DEGs in pathways associated with Mtb-Ag stimulation are needed to elucidate the underlying pathologic mechanisms of Mtb-Ag during Mtb infection.

Interleukin 4 gene polymorphisms and the risk of tuberculosis: A meta-analysis

BACKGROUND

Interleukin-4 (IL-4) is implicated in the progression of tuberculosis (TB); however, these results remain controversial.

OBJECTIVES

This meta-analysis examined the relationship between IL and 4 polymorphisms (-589C/T, +4221C > A, and -33C/T) and the risk of TB.

METHODS

A retrospective database analysis was conducted using the CNKI and PubMed databases. Using fixed- and random-effects models, we calculated the combined odds ratios (ORs) and 95% confidence intervals (CIs).

RESULTS

We identified 14 articles related to this topic, and theresultsshowed that the IL-4 -589C/T polymorphism didnotinfluencethe risk of TB. However,in subgroupanalyses we found that the IL-4 -589C/T polymorphism was associated with the risk of TB inCaucasians (recessive modelOR = 2.54, 95% CI = 1.30-4.96). In our study, the IL-4--33C/T polymorphism was not associated with the risk of TB. The IL-4 + 4221C > A polymorphism was associated with the risk of TB (recessive model: OR = 1.40, 95% CI = 1.07-1.83).

CONCLUSION

This meta-analysis showed that the IL-4 -589C/T polymorphism was associated with TB risk in Caucasian populations, and the IL-4 + 4221C > A polymorphism is associated with TB risk.

Deciphering Genetic Susceptibility to Tuberculous Meningitis

Tuberculous meningitis (TBM) is the most severe form of extrapulmonary tuberculosis (TB) that arises when a caseating meningeal granuloma discharges its contents into the subarachnoid space. It accounts for ~1% of all disease caused by Mycobacterium tuberculosis and the age of peak incidence is from 2-4 years. The exact pathogenesis of TBM is still not fully understood and the mechanism(s) by which the bacilli initially invade the blood-brain-barrier are still to be elucidated. This study investigated the involvement of the host genome in TBM susceptibility, by considering common variants (minor allele frequency (MAF) >5%) using microarray genotyping and rare variants (MAF <1%) via exome sequencing. A total of 123 TBM cases, 400 pulmonary TB (pTB) cases and 477 healthy controls were genotyped on the MEGA array. A genome-wide association study (GWAS) comparing 114 TBM cases to 395 healthy controls showed no association with TBM susceptibility. A second analysis comparing 114 TBM cases to 382 pTB cases was conducted to investigate variants associated with different TB phenotypes. No significant associations were found with progression from pTB to TBM. Ten TBM cases and 10 healthy controls were exome sequenced. Gene set association tests SKAT-O and SKAT Common Rare were used to assess the association of rare SNPs and the cumulative effect of both common and rare SNPs with susceptibility to TBM, respectively. Ingenuity Pathway Analysis (IPA) of the top-hits of the SKAT-O analysis showed that NOD2 and CYP4F2 are both important in TBM pathogenesis and highlighted these as targets for future study. For the SKAT Common Rare analysis Centriolar Coiled-Coil Protein 110 (CCP110) was nominally associated (p = 5.89x10^-6) with TBM susceptibility. In addition, several top-hit genes ascribed to the development of the central nervous system (CNS) and innate immune system regulation were identified. Exome sequencing and GWAS of our TBM cohort has identified a single previously undescribed association of CCP110 with TBM susceptibility. These results advance our understanding of TBM in terms of both variants and genes that influence susceptibility. In addition, several candidate genes involved in innate immunity have been identified for further genotypic and functional investigation.

Associations of genetic variants at TAP1 and TAP2 with pulmonary tuberculosis risk among the Chinese population

Tuberculosis (TB) is a common infectious disease, and the present study aims to explore the associations of single nucleotide polymorphisms (SNPs) at rs1135216 and rs1057141 of transporter-associated antigen processing (TAP1) and rs2228396 of TAP2 with pulmonary tuberculosis (PTB) risk. A case-control study including 168 smear-positive PTB cases and 251 controls was conducted. Genotyping of the SNPs at rs1135216, rs1057141 and rs2228396 was performed, and their associations with PTB risk were analysed with SPSS software version 19.0. After conducting stratification for age, a significant association was detected for rs1057141 with increased PTB risk (OR = 0.17, 95% CI 0.04-0.79) among those aged ≥60 years. For those aged <60 years, a marginally significant association was detected between rs1135216 TC/CC and PTB risk (OR = 1.97, 95% CI 0.93-4.19). Haplotype analysis revealed that the haplotype AT at rs1135216 and rs2228396, as well as AAT at rs1057141, rs1135216 and rs2228396, was associated with increased PTB risk, and the ORs were 2.83 (95% CI 1.30-6.14) and 2.89 (95% CI 1.34-6.27), respectively. Rs1057141 is a genetic predictor of reduced PTB risk for those aged ≥60 years, while rs1135216 might be a potential genetic predictor for those aged <60 years. Haplotype AT at rs1135216 and rs2228396, as well as AAT at rs1057141, rs1135216 and rs2228396, is a genetic marker that may predict PTB risk.

Analysis of the association of IL4 polymorphisms with orthodontic mini-implant loss

The aim of this study was to investigate the association of clinical characteristics and IL4 tag single nucleotide polymorphisms (SNPs; rs2227284 and rs2243268) with orthodontic mini-implant (MI) failure. The sample included 135 subjects of both sexes, mean age 48.7±10years (range 20-76years): 104 in the control group (patients without any MI loss) and 31 in the study group (patients presenting ≥1 MI loss). Genotypes were determined by real-time PCR. Bivariate and multivariate analyses were performed (P<0.05). No association was found between the selected tag SNPs and MI loss. The C allele of the IL4 rs2243268 polymorphism in the recessive model was more frequent in patients who had fewer MIs installed (≤2 vs. >2; P=0.043, odds ratio 0.65, 95% confidence interval 0.58-0.74). On multivariate analysis, smoking habit was significantly associated with the group with multiple MIs installed (P=0.036), however the significance of the association with rs2243268 was not maintained. No association was found between the socio-demographic, smoking, or genetic factors studied and MI loss. This study supports the interaction between host and environmental factors and its influence on susceptibility to orthodontic MI failure.

rs1800796 of the IL6 gene is associated with increased risk for anti-tuberculosis drug-induced hepatotoxicity in Chinese Han children

Previous studies have revealed the important contribution of the immune response and oxidative stress to the development of anti-tuberculosis drug-induced hepatotoxicity (ATDH). To investigate whether single-nucleotide polymorphisms (SNPs) of the cytokine gene interleukin-6 (IL6) and oxidative stress genes xanthine dehydrogenase/oxidase (XO) and inducible nitric oxide synthase (NOS2) were associated with susceptibility to ATDH, we performed a case-control study including 41 ATDH cases and 116 ATDH-free controls in Chinese Han children. Significant difference in the allele distribution of rs1800796 in the IL6 gene was observed between the case and control groups, and the G allele of rs1800796 was associated with an increased risk for ATDH (odds ratio: 2.48, 95%CI: 1.40-4.40, P = 0.002). However, no significant difference was observed in the allele and genotype distributions of the other SNPs of the IL6, XO and NOS2 genes between the case and control groups after Bonferroni correction. In addition, no interaction was found between all selected SNPs. These findings indicate that genetic variants of the IL6 gene might contribute to the development of ATDH in the Chinese Han pediatric population.

Discovery of susceptibility loci associated with tuberculosis in Han Chinese

Genome-wide association studies (GWASs) have revealed the worldwide heterogeneity of genetic factors in tuberculosis (TB) susceptibility. Despite having the third highest global TB burden, no TB-related GWAS has been performed in China. Here, we performed the first three-stage GWAS on TB in the Han Chinese population. In the stage 1 (discovery stage), after quality control, 691 388 SNPs present in 972 TB patients and 1537 controls were retained. After replication on an additional 3460 TB patients and 4862 controls (stages 2 and 3), we identified three significant loci associated with TB, the most significant of which was rs4240897 (logistic regression P = 1.41 × 10-11, odds ratio = 0.79). The aforementioned three SNPs were harbored by MFN2, RGS12 and human leukocyte antigen class II beta chain paralogue encoding genes, all of which are candidate immune genes associated with TB. Our findings provide new insight into the genetic background of TB in the Han Chinese population.

Association of IL4, IL6, and IL10 polymorphisms with pulmonary tuberculosis in a Tibetan Chinese population

Background

Pulmonary tuberculosis (PTB) is an infectious disease with a high incidence worldwide. Genes encoding cytokines IL4, IL6, and IL10 are highly polymorphic and can influence the susceptibility to PTB.

Results

We found correlations between one SNP in IL6 (rs2069837 p = 6.63E-11), seven SNPs in IL10 (rs1554286 p = 6.87E-20, rs1518111 p = 6.11E-11, rs3021094 p = 6.75E-29, rs3790622 p = 2.40E-06, rs3024490 p = 6.73E-11, rs1800872 p = 6.18E-11, rs1800871 p = 6.73E-11) and incidences of PTB. The SNPs rs2069837, rs1554286, rs1518111, rs3024490, rs1800872, and rs1800871 increased PTB risk by 1.95-fold, 2.34-fold, 1.84-fold, 1.84-fold, 1.84-fold and 1.84-fold, respectively. The SNPs rs3021094 and rs3790622 decreased PTB risk by 0.33-fold and 0.38-fold, respectively. We also found two linkage disequilibrium blocks in the studied IL SNPs. The IL4 haplotype TCCCGGA (OR = 1.33, p = 0.014) increased PTB risk, the IL10 haplotypes ATGGATA (OR = 0.39, p = 4.84E-06) provided a protective effect and decreased PTB risk.

Materials and Methods

For this study, we recruited 467 subjects with PTB and 503 healthy subjects from a Tibetan population living in Lhasa and nearby, China. Association analyses of sixteen single-nucleotide polymorphisms (SNPs) in IL4, IL6, and IL10 were performed.

Conclusions

Our findings demonstrate an association between polymorphisms in IL6 and IL10 and risk of PTB.

The association of interleukin-10 -1082, -819, -592 polymorphisms and tuberculosis risk

Objectives:

To assess the association between interleukin (IL)-10 -1082, -819, -592 polymorphisms and tuberculosis (TB) risk.

Methods:

This study was conducted between July and October 2014 in West China Hospital, Chengdu, Sichuan, China. We searched and collected data from PUBMED, EMBASE, Web of Science, China National Knowledge Infrastructure, VIP, and WANGFANG up to October 2014.

Results:

A total of 37 studies were enrolled, including 8625 TB cases, and 9928 healthy controls. The IL-10-1082G/A polymorphism was found to be associated with TB susceptibility in Caucasian (GG versus GA+AA, odds ratio [OR] - 1.83, 95% confidence interval [CI] - 1.03-3.24). The IL-10-819C/T polymorphism was related to TB susceptibility among Asians (C versus T, OR - 0.88, 95% CI - 0.81-0.97; CC versus TT: OR - 0.79, 95% CI - 0.64-0.97; CC+CT versus TT: OR - 0.87, 95% CI - 0.77-0.98; CC versus CT+TT: OR - 0.82, 95% CI - 0.68-0.98). The IL-10-592C/A polymorphism was in association with TB susceptibility in Asians (C versus A: OR - 0.74, 95% CI - 0.65-0.85; CC versus AA: OR - 0.55, 95% CI - 0.41-0.75; CA versus AA: OR - 0.73, 95% CI - 0.60-0.89; CC+CA versus AA: OR - 0.69, 95% CI 0.58-0.83; CA versus AA: OR - 0.66, 95% CI 0.51-0.86), Caucasian (C versus A: OR - 1.25, 95% CI - 1.08-1.45; CC versus CA+AA: OR-1.48, 95% CI - 1.16-1.89), and Europeans (C versus A: OR - 1.31, 95% CI - 1.02-1.67; CC versus AA: OR - 1.88, 95% CI - 1.05-3.37).

Conclusion:

This meta-analysis suggests that IL-10-1082G/A, IL-819C/T, and IL-592C/A polymorphisms might be associated with TB susceptibility in certain ethnicities.

Rs1914663 of SFTPA 1 gene is associated with pediatric tuberculosis in Han Chinese population

Surfactant protein A (SP-A), a part of the innate immune system of the lung, performs a vital role in the host defense against Mycobacterium tuberculosis (MTB) infection. In order to investigate the relationship between SFTPA polymorphism variations and Tuberculosis (TB) in a Chinese pediatric group, we conducted a case-control study using single-nucleotide polymorphism (SNP) analysis. Significant difference of the allelic distribution of rs1914663 in SFTPA gene was observed between TB group and control group and, T allele of rs1914663 was associated with increased risk for TB (control vs.

TB, OR

1.42, 95% CI: 1.10-1.81, P=0.005). In addition, the TC+TT genotype of rs1914663 was higher in PTB and non-severe TB than that in controls. The haplotype comprising rs17881720-A and rs17879335-G was a resistance factor while the haplotype comprising rs1914663-T and rs1059225-G was found to be a susceptibility factor to TB. Using a case-control study, we identified a genetic polymorphism in the SFTPA that regulates host susceptibility to pediatric TB in the Han Chinese population.