Association between vitamin D receptor gene polymorphisms and pulmonary tuberculosis in a Mexican population

Association between vitamin D receptor gene polymorphisms and susceptibility to tuberculosis: a systematic review and meta-analysis

Objective

Tuberculosis (TB) is the leading cause of mortality worldwide. Previous studies have reported that TB susceptibility can be caused by vitamin D deficiency, which is affected by polymorphisms in the vitamin D receptor (VDR) gene. However, these results have been inconsistent. Therefore, we performed a meta-analysis to investigate the association between VDR polymorphisms and TB susceptibility.

Methods

We systematically searched for relevant literature in PubMed, Embase, and Medline databases through December 31st, 2022. Inclusion and exclusion criteria were made to ensure that HIV-negative population is the targeted subjects. The pooled odds ratio (OR) and 95% confidence interval (CI) were then used to assess the strength of the association, and the quality of the included articles was evaluated using the Newcastle-Ottawa Scale. Potential sources of heterogeneity were evaluated based on subgroup and meta-regression analyses.

Results

In our meta-analysis, we found that the FokI polymorphism in the VDR gene was associated with increased TB susceptibility in the allele and recessive genotype models (OR f vs. F = 1.235, 95%CI: 1.035-1.475; OR ff vs. Ff + FF = 1.317, 95%CI: 1.005-1.727. Further subgroup analysis based on ethnicity demonstrated the association with the risk of TB in all genotype models of the FokI polymorphism for Han population. Meta-regression analysis also indicated that ethnicity could be a potential source of heterogeneity in the FokI and BsmI polymorphisms in the VDR gene. However, publication year was another source of heterogeneity for the TaqI polymorphism.

Conclusion

In summary, the FokI polymorphism in the VDR gene was found to increase the risk of TB in the HIV-negative population, both overall and in Asian populations. The findings presented in this paper could provide clues for preventing TB from the perspective of vitamin D supplementation, which is a controversial topic in the field of medicine and health.

Prevalence of Vitamin D Receptor Genes Polymorphisms in People with Pulmonary Tuberculosis: A Systematic Review and Meta-Analysis

Background

Polymorphisms in the vitamin D receptor (VDR) play an effective role in the susceptibility of pulmonary tuberculosis (TB). Given the importance of this polymorphism and its association with pulmonary TB, this study aimed to investigate the prevalence of VDR polymorphisms in people with pulmonary TB.

Methods

The search process was performed from 2009 to 2023 according to PRISMA (Preferred reporting items for systematic reviews and meta-analyses). The strengthening of the reporting of observational studies in epidemiology (STROBE) checklist was used to qualify the articles. The data was entered into STATA version 14 software, then the fixed effects model and the random effects model, effect size (ES), and Q test (P < 0.10) were used for data analysis at a confidence interval level (CI) of 95%. Two-sided statistical tests were considered with α=0.05.

Results

In this research, 28 articles were analyzed. Polymorphisms showed a significant relationship with susceptibility to pulmonary TB (P = 0.000), and significant heterogeneity (P = 0.000) was seen between polymorphisms. FokI (95% CI: 0.39-0.46, P = 0.000, ES = 43%), ApaI (95% CI: 0.31-0.48, P = 0.000, ES = 39%) and BsmI (95% CI: 0.24-0.50, P = 0.000, ES = 37%) showed the most frequent gene polymorphisms after TaqI (95% CI: 0.34-0.77, P = 0.000, ES = 56%).

Conclusion

ApaI, BsmI, FokI, and TaqI polymorphisms were found in patients suffering from pulmonary TB. Polymorphisms related to the TaqI gene were the most frequent. Controlling and prescribing vitamin D may be needed in these patients.

An Updated Trial Sequential Meta-analysis of Vitamin D Receptor Gene Polymorphism (Fok1, Bsm1, Taq1 and Apa1) and Risk to Tuberculosis

Vitamin D receptor (VDR) is one of the most widely studied genes for the Tuberculosis (TB) susceptibility. Several studies have been conducted to establish some association between them but most of the time they are contradictory and underpowered. So, a trial sequential meta-analysis between VDR gene polymorphisms and TB susceptibility can provide a better understanding of the relationship. A meta-analysis was carried out using a total of 17 case-control studies which includes Fok1 (14 Studies), Bsm1 (8 Studies), Apa1 (8 Studies) and Taq1 (12 Studies) polymorphisms in the VDR gene searched from Pubmed and Google Scholar. Pooled Odds Ratio (OR) and 95% Confidence Interval (CI) were calculated using StatsDirect Version 3, using random effects model. Trial sequential analysis (TSA) was also performed to assess if the statistical significance of the meta-analysis was within monitoring boundaries. It was found that the individuals with BB genotype of Bsm1 polymorphism with OR = 0.713 (95%CI = 0.521, 0.974; p value < 0.05) and FF genotype of Fok1 polymorphism with pooled OR = 0.716 (95%CI = 0.523, 0.979; p value < 0.05) had decreased incidence of TB. Also, the aa genotype of Apa1 gene polymorphism increases susceptibility to TB with pooled OR = 1.997 (95%CI = 1.121, 3.558; p value < 0.05). All these analyses reached the required information size through TSA analysis. No statistically significant result was found for Taq1 polymorphisms and TB susceptibility. VDR polymorphisms in Fok1 and Bsm1 played protective roles against development of TB infection, while Apa1 appeared to have a significant association to TB susceptibility.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12291-022-01091-3.

Differential NRAMP1gene's D543N genotype frequency: Increased risk of contracting tuberculosis among Venezuelan populations

NRAMP1 and VDR gene polymorphisms have been variably associated with susceptibility to tuberculosis (TB) amongst populations having different genetic background. NRAMP1 and VDR gene variants' association with susceptibility to active infection by Mycobacterium tuberculosis (Mtb) was analyzed in the Warao Amerindian population, an ethnic population from Venezuela's Orinoco delta region. Genomic DNA was extracted from individuals with and without TB to evaluate genetic polymorphism by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Four NRAMP1 gene polymorphisms were analyzed: D543N (rs17235409), 3' UTR (rs17235416), INT4 (rs3731865), and 274C/T (rs2276631), and one VDR gene polymorphism: FokI (rs2228570). The results showed that the genotypes D543N-A/A, 3'UTR-TGTG+/+, INT4-C/C, and 274C/T-T/T of known polymorphism in the NRAMP1 gene, as well as the genotypes FokI-F/f and FokI-f/f in the VDR gene were most often found in indigenous Warao with active TB. Binomial logistic regression was used for evaluating associations between polymorphisms and risk of contracting TB, an association between NRAMP1-D543N-A/A genotype distribution and TB susceptibility was found in Warao Amerindians. Regarding Venezuelan populations having different genetic backgrounds; statistically significant TB associations concerning NRAMP1-D543N-A/A, INT4-C/C and 3'UTR-TGTG+/+ variant genotype distributions in Warao Amerindians (indigenous) compared to Creole (admixed non-indigenous population) individuals were found. In conclusion, the results thus indicated that the association between NRAMP1-D543N-A/A genotype and TB in Warao Amerindians could support such allele's role in host susceptibility to Mtb infection.

Plasma 25-Hydroxyvitamin D Level and VDR Gene Single Nucleotide Polymorphism rs2228570 Influence on COVID-19 Susceptibility among the Kazakh Ethnic Group-A Pilot Study

Low plasma levels of the vitamin D metabolite 25-hydroxyvitamin D [25(OH)D] and the vitamin D receptor (VDR) gene single nucleotide polymorphisms (SNPs) have been associated with the body's susceptibility to infectious diseases, including COVID-19. In this pilot retrospective study, representatives of the Kazakh population (central Kazakhstan) were divided into groups based on the test for IgM and IgG for coronavirus infection. We compared the 25(OH)D plasma levels and concluded that the COVID-19-positive group values (25.17 ng/mL ± 16.65) were statistically lower (p = 0.0114) compared to the COVID-19-negative ones (35.58 ng/mL ± 20.67). There was no association between age, gender and 25(OH)D concentration within the groups (p > 0.05). The genotyping of rs2228570 was performed using a TaqMan Real-Time PCR assay. Allele C predominated among the COVID-19-negative participants and significantly reduced the likelihood of coronavirus infection (p < 0.0001; OR = 0.0804; 95% CI 0.02357-0.2798). There were no statistically significant differences in the frequencies of the A, G and T alleles in the studied groups (p > 0.05). The GG genotype of rs2228570 was associated with a 4.131-fold increased likelihood of COVID-19 infection (p = 0.0288; χ2 = 5.364; OR = 4.131; 95% CI 1.223-13.71). Comprehensive studies are required to determine whether low 25(OH)D plasma concentrations and genetic background represent a risk factor for COVID-19 infection.

Correlation between polymorphism of vitamin D receptor TaqI and susceptibility to tuberculosis: An update meta-analysis

BACKGROUND

To investigate the association between TaqI polymorphism of the vitamin D receptor gene and tuberculosis (TB).

METHODS

A systematic search was performed in PubMed, Embase, Web of Science, Elsevier Science Direct, Cochrane Library, Chinese National Knowledge Infrastructure, Wanfang, and Chongqing VIP databases for case-control study on TaqI gene polymorphism and TB susceptivity. Quality assessment of studies was performed using the Newcastle-Ottawa Scale for the methodological assessment of case-control studies, and R 4.0.5 software was used for the meta-analysis.

RESULTS

Among the 243 selected articles, 27 in the meta-analysis. The meta-analysis showed that the TaqI gene polymorphism allene gene model (t vs T, odds ratio [OR]: 1.12, 95% confidence interval [CI]: 0.99-1.27); dominant model (tt + tT vs TT, OR: 1.12, 95% CI: 0.98-1.29); recessive model (tt vs tT + TT, OR: 1.25, 95% CI: 1.03-1.51); codominant A (tt vs TT, OR: 1.37, 95% CI: 1.00-1.87); codominant B (tT vs TT, OR: 1.09, 95% CI: 0.99-1.19). And subgroup dominant model (tt + tT vs TT, OR: 1.27, 95% CI: 1.03-1.55) in Indianas, recessive model (tt vs tT + TT, OR: 1.49, 95% CI: 1.05-2.11) in Iranians, co-dominant B (tT vs TT, OR: 1.28, 95% CI: 1.03-1.59; OR: 1.42, 95% CI: 1.05-1.93) in Indianas and Iranians.

CONCLUSION

This meta-analysis suggests a significant association between TB and the risk of TaqI in Iranians and Indians, but the vitamin D receptor polymorphism TaqI was not associated with Chinese. Thus, validation studies will be required to confirm these findings.

Comprehensive analyses of potential key genes in active tuberculosis: A systematic review

BACKGROUND

Tuberculosis (TB) is a global health problem that brings us numerous difficulties. Diverse genetic factors play a significant role in the progress of TB disease. However, still no key genes for TB susceptibility have been reported. This study aimed to identify the key genes of TB through comprehensive bioinformatics analysis.

METHODS

The series microarray datasets from the gene expression omnibus (GEO) database were analyzed. We used the online tool GEO2R to filtrate differentially expressed genes (DEGs) between TB and health control. Database for annotation can complete gene ontology function analysis as well as Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. Protein-protein interaction (PPI) networks of DEGs were established by STRING online tool and visualized by Cytoscape software. Molecular Complex Detection can complete the analysis of modules in the PPI networks. Finally, the significant hub genes were confirmed by plug-in Genemania of Cytoscape, and verified by the verification cohort and protein test.

RESULTS

There are a total of 143 genes were confirmed as DEGs, containing 48 up-regulated genes and 50 down-regulated genes. The gene ontology and Kyoto Encyclopedia of Genes and Genomes analysis show that upregulated DEGs were associated with cancer and phylogenetic, whereas downregulated DEGs mainly concentrate on inflammatory immunity. PPI networks show that signal transducer and activator of transcription 1 (STAT1), guanylate binding protein 5 (GBP5), 2'-5'-oligoadenylate synthetase 1 (OAS1), catenin beta 1 (CTNNB1), and guanylate binding protein 1 (GBP1) were identified as significantly different hub genes.

CONCLUSION

We conclude that these genes, including TAT1, GBP5, OAS1, CTNNB1, GBP1 are a candidate as potential core genes in TB and treatment of TB in the future.

Vitamin D Receptor Gene Polymorphisms in Childhood Brucellosis in Turkish Children

Objective The vitamin D receptor gene (VDR) polymorphisms and the risk of various infections have been studied. An association with brucellosis and vitamin D levels has been investigated but not yet with VDR gene polymorphisms. We aimed to examine the association between VDR gene polymorphisms and susceptibility to childhood brucellosis.

Methods This case–control study included patients with brucellosis and healthy controls. After extracting genomic DNA using a Qiagen blood DNA isolation kit, five VDR single nucleotide polymorphisms (SNPs), including Cdx-2, FokI, BsmI, ApaI, and TaqI gene, were amplified. Genetic distribution of these SNPs of VDR gene in patient and control groups were compared.

Results A total of 38 patients with brucellosis and 89 healthy controls were evaluated. The genotype distribution of Cdx2, FokI, BsmI, and ApaI polymorphisms were similar between patients and healthy controls. However, the CC homozygous genotype for VDR gene TaqI was significantly overexpressed in patients compared with controls (23.7 vs. 7.9%; p = 0.042). The frequency of the C allele of the TaqI genotype was significantly different between patients and controls (p = 0.018). On the other hand, presence of the A allele in the BsmI was associated considerably with an increased risk of brucellosis (p = 0.037). VDR polymorphism distribution was similar according to age, presence of complicated disease, and presence of bacteremia. The heterozygote TaqI polymorphism was more common in patients presented as subacute and chronic symptoms (p = 0.036).

Conclusion Our results indicated the possible role in TaqI polymorphism of the VDR gene for the risk of brucellosis at the time of exposure to infection.

Association of vitamin D pathway genes polymorphisms with pulmonary tuberculosis susceptibility in a Chinese population

OBJECTIVE

This study aimed to evaluate the association of single nucleotide polymorphisms (SNPs) of vitamin D metabolic pathway genes with susceptibility to pulmonary tuberculosis (PTB).

METHODS

Nine hundred seventy-nine patients (490 PTB cases and 489 healthy controls) were included in this study. Seventeen SNPs of vitamin D metabolic pathway genes, including CYP24A1, CYP27A1, CYP27B1, CYP2R1, GC, and DHCR7, were genotyped with improved multiple ligase detection reaction (iMLDR).

RESULTS

The GC rs3733359 GA, rs16847024 CT genotypes were significantly associated with the reduced risk of PTB, and the rs3733359 A, rs16847024 T alleles were also associated with the decreased PTB susceptibility. The GT genotype of GC rs4588 variant was significantly higher in patients with PTB when compared to controls. Moreover, the increased risk of rs3733359 and rs16847024 variants, and a decreased risk of rs4588, were found under the dominant mode among the PTB patients. However, there was no significant relationship of CYP24A1, CYP27A1, CYP27B1, CYP2R1, and DHCR7 polymorphisms with the risk of PTB. In CYP27A1, the rs17470271 T and rs933994 T alleles were significantly associated with leukopenia, drug resistance in the PTB patients, respectively. In GC gene, the rs7041 and rs3733359 variants were found to be associated with pulmonary infection, fever in the PTB patients, respectively. The increased frequency of rs16847024 TT genotype was found in the PTB patients with fever and drug-induced liver damage. DHCR7 rs12785878 TT genotype, and T allele frequencies were both significantly associated with pulmonary infection in the PTB patients. The haplotype analysis showed that CYP24A1 TACT, CYP2R1 GGCT, GGAT, GC AATG haplotypes were related to PTB susceptibility.

CONCLUSION

Our study suggested that GC SNPs were associated with the genetic background of PTB. CYP27A1, GC, and DHCR7 genetic variations might contribute to several clinical phenotypes of PTB in Chinese.

CLEC4E (Mincle) genetic variation associates with pulmonary tuberculosis in Guinea-Bissau (West Africa)

Tuberculosis (TB) is the leading cause of death from a single infectious agent. According to the WHO, 85% of cases in 2018 were pulmonary tuberculosis (PTB), making it the most prevalent form of the disease. Although the bacillus responsible for disease, Mycobacterium tuberculosis (MTB), is estimated to infect 1.7 billion people worldwide, only a small portion of those infected (5-10%) will transition into active TB. Because such a small fraction of infected people develop active disease, we hypothesized that underlying host genetic variation associates with developing active pulmonary disease. Variation in CLEC4E has been of interest in previous association studies showing either no effect or protection from PTB. For our study we assessed 60 SNPs in 11 immune genes, including CLEC4E, using a case-control study from Guinea-Bissau. The 289 cases and 322 controls differed in age, sex, and ethnicity all of which were included in adjusted models. Initial association analysis with unadjusted logistic regression revealed putative association with seven SNPs (p < 0.05). All SNPs were then assessed in an adjusted model. Of the six SNPs that remained significant, three of them were assigned to the CLEC4E gene (rs12302046, rs10841847, and rs11046143). Of these, only rs10841847 passed FDR adjustment for multiple testing. Adjusted regression analyses showed that the minor allele at rs10841847 associated with higher risk of developing PTB (OR = 1.55, CI = 1.22-1.96, p-value = 0.00036). Based on these initial association tests, CLEC4E seemed to be the predictor of interest for PTB risk in this population. Haplotype analysis (2-SNP and 3-SNP windows) showed that minor alleles in segments including rs10841847 were the only ones to pass the threshold of global significance, compared to other haplotypes (p-value < 0.05). Linkage disequilibrium patterns showed that rs12302046 is in high LD with rs10841847 (r2 = 0.67), and all other SNPs lost significance when adjusted for rs10841847 effects. These findings indicate that rs10841847 in CLEC4E is the single best predictor of pulmonary tuberculosis risk in our study population. These results provide evidence for the hypothesis that genetic variation of CLEC4E influences risk to TB in Guinea-Bissau.

Abdominal tuberculosis in a tertiary care centre in Saudi Arabia

OBJECTIVES

Abdominal tuberculosis (ATB) is the second most common type of extra-pulmonary tuberculosis. Though it does not usually pose a significant risk of infectivity, ATB can go unidentified and progress to disseminated infection. The aim of this study is to highlight the incidence and outcome of this infection in a tertiary care centre in the Kingdom of Saudi Arabia (KSA).

METHODS

In this retrospective study, we included all ATB patients admitted to our centre between January 1 ^st, 2010 and December 31, 2018. A total of 42 patients with a median age of 49 (range 18-83 years, 78.6% males) were identified.

RESULTS

The most common presentation was abdominal pain, weight loss, and abdominal distension. All the patients were HIV negative; however, 50% had a comorbid condition, mainly diabetes mellitus, chronic renal failure, and liver cirrhosis. Tuberculous peritonitis was the predominant type of ATB. Suspicious and potentially malignant abdominal masses appeared on the abdominal CT scans of six patients. This suggest that TB should be excluded in patients from endemic area presenting with abdominal masses. All patients received standard anti-tuberculous medication for an average duration of 7.4 months. The outcome was excellent with 88%% achieving complete response. Adjunctive corticosteroids were not used, and none of the patients had a surgical complication.

CONCLUSION

The diagnosis of ATB is challenging. It can mimic inflammatory bowel disease in young populations and malignancy in middle-aged and elderly population. For this reason, a high index of suspicion with prompt treatment is required to improve the prognosis and prevent complications.

Investigation of genetic susceptibility to Mycobacterium tuberculosis (VDR and IL10 genes) in a population with a high level of substructure in the Brazilian Amazon region

OBJECTIVES

Tuberculosis (TB) is an infectious and contagious disease that has been very influential in human history and presents high rates of mortality. The objective of this study was to investigate the association of VDR, IL10, and SLC11A1 gene polymorphisms with susceptibility to the presence of Mycobacterium tuberculosis infection.

METHODS

A total of 135 patients with confirmed TB and 141 healthy individuals were included in the analysis. Blood samples were collected for DNA extraction. Genotyping of the polymorphisms in the VDR and IL10 genes was performed by real-time PCR, and genotyping of the polymorphisms in the SLC11A1 gene by conventional PCR, followed by visualization in polyacrylamide gel. The genomic ancestry was obtained using an autosomal panel with 48 insertion/deletion ancestry-informative markers.

RESULTS

Polymorphisms TaqI (TT, p=0.004), FokI (CC and CC+CT, p=0.012 and p=0.003, respectively), and BsmI (GG, p=0.008) in the VDR gene, as well as A-592C (GC+AG, p=0.001) in the IL10 gene, were significantly associated with susceptibility to TB In addition, high production of VDR combined with low production of IL10 showed protection for the TB group (p=0.035).

CONCLUSIONS

The VDR polymorphisms may confer an increased risk and the IL10 haplotype may be a protection factor for the presence of M. tuberculosis infection in the Brazilian population.

Association of genetic variations in the vitamin D pathway with susceptibility to tuberculosis in Kazakhstan

Tuberculosis (TB) poses an important health challenge and a significant economic burden for Kazakhstan and in Central Asia. Recent findings show a number of immunological related processes and host Mycobacterium tuberculosis defense are impacted by a variety of genes of the human host including those that play a part in the vitamin D metabolism. We investigated the genetic variation of genes in the vitamin D metabolic pathway of a cohort 50 TB cases in Kazakhstan and compared them to 34 controls living in the same household with someone infected with TB. We specifically analyzed 11 SNPs belonging to the following genes: DHCR7, CYP2R1, GC-1, CYP24A1, CYP27A1, CYP27B1, VDR and TNFα. These genes play a number of different roles including synthesis, activation, delivery and binding of the activated vitamin D. Our preliminary results indicate significant association of VDR (vitamin D receptor) SNPs (rs1544410, BsmI, with OR = 0.425, CI 0.221-0.816, p = 0.009 and rs731236, TaqI with OR = 0.443, CI 0.228-0.859, p = 0.015) and CYP24A1 (rs6013897 with OR = 0.436, CI 0.191-0.996, p = 0.045) with TB. Interaction of genetic variation of VDR and CYP24A1 may impact susceptibility to TB. The findings provided initial clues to understand individual genetic differences in relation to susceptibility and protection to TB.