Association between STAT4 gene polymorphism and susceptibility to pulmonary tuberculosis in the Moldavian population

Signal transducer and activator of transcription 4 (STAT4) plays a crucial role in the host immune response against Mycobacterium tuberculosis. This study investigates the association between STAT4 gene polymorphisms and pulmonary tuberculosis (TB) risk in the Moldavian population. A total of 272 TB patients and 251 community-matched controls underwent screening for functional single-nucleotide polymorphisms (SNPs) rs897200 and rs7574865 in the STAT4 gene. The minor T allele and the TT/CT genotype of rs897200 demonstrated a significant association with reduced pulmonary TB risk (allelic model: adjusted OR = .74, p = .025; log-additive model: adjusted OR = .72, p = .02; and dominant model: adjusted OR = .65, p = .023), indicating a protective effect. Similar associations, characterized by an even more pronounced reduction in risk, were observed among females and late-onset TB patients (>44 years). No significant associations were found for rs7574865. In addition, a combined genotype analysis incorporating 43 SNPs from our previous studies revealed potential associations, such as STAT4 rs897200 CT with IFNG rs2430561 AA (adjusted OR = .36, p = .0025) and STAT4 rs897200 CT with TNFA rs1800629 GA (adjusted OR = .33, p = .0012). This study emphasizes the significant association of STAT4 rs897200 with pulmonary TB risk in the Moldavian population, underscoring its role in the disease development.

Modeling and cleaning RNA-seq data significantly improve detection of differentially expressed genes

Background

RNA-seq has become a standard technology to quantify mRNA. The measured values usually vary by several orders of magnitude, and while the detection of differences at high values is statistically well grounded, the significance of the differences for rare mRNAs can be weakened by the presence of biological and technical noise.

Results

We have developed a method for cleaning RNA-seq data, which improves the detection of differentially expressed genes and specifically genes with low to moderate transcription. Using a data modeling approach, parameters of randomly distributed mRNA counts are identified and reads, most probably originating from technical noise, are removed. We demonstrate that the removal of this random component leads to the significant increase in the number of detected differentially expressed genes, more significant pvalues and no bias towards low-count genes.

Conclusion

Application of RNAdeNoise to our RNA-seq data on polysome profiling and several published RNA-seq datasets reveals its suitability for different organisms and sequencing technologies such as Illumina and BGI, shows improved detection of differentially expressed genes, and excludes the subjective setting of thresholds for minimal RNA counts. The program, RNA-seq data, resulted gene lists and examples of use are in the supplementary data and at https://github.com/Deyneko/RNAdeNoise.

Candidate genes and sequence variants for susceptibility to mycobacterial infection identified by whole-exome sequencing

Inborn errors of immunity are known to influence susceptibility to mycobacterial infections. The aim of this study was to characterize the genetic profile of nine patients with mycobacterial infections (eight with BCGitis and one with disseminated tuberculosis) from the Republic of Moldova using whole-exome sequencing. In total, 12 variants in eight genes known to be associated with Mendelian Susceptibility to Mycobacterial Disease (MSMD) were detected in six out of nine patients examined. In particular, a novel splice site mutation c.373–2A>C in STAT1 gene was found and functionally confirmed in a patient with disseminated tuberculosis. Trio analysis was possible for seven out of nine patients, and resulted in 23 candidate variants in 15 novel genes. Four of these genes - GBP2, HEATR3, PPP1R9B and KDM6A were further prioritized, considering their elevated expression in immune-related tissues. Compound heterozygosity was found in GBP2 in a single patient, comprising a maternally inherited missense variant c.412G>A/p.(Ala138Thr) predicted to be deleterious and a paternally inherited intronic mutation c.1149+14T>C. Functional studies demonstrated that the intronic mutation affects splicing and the level of transcript. Finally, we analyzed pathogenicity of variant combinations in gene pairs and identified five patients with putative oligogenic inheritance. In summary, our study expands the spectrum of genetic variation contributing to susceptibility to mycobacterial infections in children and provides insight into the complex/oligogenic disease-causing mode.

Synergistic effect of genetic polymorphisms in TLR6 and TLR10 genes on the risk of pulmonary tuberculosis in a Moldavian population

Polymorphisms in genes that control immune function and regulation may influence susceptibility to pulmonary tuberculosis (TB). In this study, 14 polymorphisms in 12 key genes involved in the immune response (VDR, MR1, TLR1, TLR2, TLR10, SLC11A1, IL1B, IL10, IFNG, TNF, IRAK1, and FOXP3) were tested for their association with pulmonary TB in 271 patients with TB and 251 community-matched controls from the Republic of Moldova. In addition, gene-gene interactions involved in TB susceptibility were analyzed for a total of 43 genetic loci. Single nucleotide polymorphism (SNP) analysis revealed a nominal association between TNF rs1800629 and pulmonary TB (Fisher exact test P = 0.01843). In the pairwise interaction analysis, the combination of the genotypes TLR6 rs5743810 GA and TLR10 rs11096957 GT was significantly associated with an increased genetic risk of pulmonary TB (OR = 2.48, 95% CI = 1.62-3.85; Fisher exact test P value = 1.5 × 10^-5, significant after Bonferroni correction). In conclusion, the TLR6 rs5743810 and TLR10 rs11096957 two-locus interaction confers a significantly higher risk for pulmonary TB; due to its high frequency in the population, this SNP combination may serve as a novel biomarker for predicting TB susceptibility.

Staged Combined Endovascular and Open Surgical Approach in a Patient with Takayasu's Arteritis

Takayasu's arteritis (TA) is a systemic large vessel vasculitis that affects the aorta and its branches. Most patients with TA respond to medical therapy with a minority of patients requiring surgical intervention. In our report, we describe the case of a 59-year-old Caucasian female with TA who underwent revascularization due to cerebrovascular symptoms refractory to medical therapy. She initially presented with amaurosis fugax and developed episodes of syncope and slurred speech during corticosteroid tapering. Vascular studies showed right common carotid artery (RCCA), left internal carotid artery (LICA), and left subclavian artery (LSA) occlusion with the right vertebral artery (RVA) ostium stenosis, and retrograde flow through the left vertebral artery (LVA). The sole source of cerebral perfusion flowed through her stenosed RVA, so it was decided to first stent the RVA to restore adequate posterior cerebral circulation before creating a right subclavian artery to RCCA bypass to restore anterior circulation. This case represents the successful management of TA utilizing a two-staged combined endovascular and surgical approach.

Polymorphisms of glutathione S-transferase and methylenetetrahydrofolate reductase genes in Moldavian patients with ulcerative colitis: Genotype-phenotype correlation

Background

Glutathione S-transferases (GSTM1, GSTT1, and GSTP1) and methylenetetrahydrofolate reductase (MTHFR) are important enzymes for protection against oxidative stress. In addition, MTHFR has an essential role in DNA synthesis, repair, and methylation. Their polymorphisms have been implicated in the pathogenesis of ulcerative colitis (UC). The aim of the present study was to investigate the role of selected polymorphisms in these genes in the development of UC in the Moldavian population.

Methods

In a case-control study including 128 UC patients and 136 healthy individuals, GSTM1 and GSTT1 genotypes (polymorphic deletions) were determined using multiplex polymerase chain reaction (PCR). The GSTP1 rs1695 (Ile105Val), MTHFR rs1801133 (C677T), and MTHFR rs1801131 (A1298C) polymorphisms were studied with restriction fragment length polymorphism (RFLP) analysis. Genotype–phenotype correlations were examined using logistic regression analysis.

Results

None of the genotypes, either alone or in combination, showed a strong association with UC. The case-only sub-phenotypic association analysis showed an association of the MTHFR rs1801133 polymorphism with the extent of UC under co-dominant (p corrected = 0.040) and recessive (p corrected = 0.020; OR = 0.15; CI = 0.04–0.63) genetic models. Also, an association between the MTHFR rs1801131 polymorphism and the severity of UC was reported for the over-dominant model (p corrected = 0.023; coefficient = 0.32; 95% CI = 0.10–0.54).

Conclusion

The GST and MTHFR genotypes do not seem to be a relevant risk factor for UC in our sample. There was, however, evidence that variants in MTHFR may influence the clinical features in UC patients. Additional larger studies investigating the relationship between GST and MTHFR polymorphisms and UC are required.

Analysis of polymorphisms in RIG-I-like receptor genes in German multiple sclerosis patients

Variation in genes encoding retinoid acid-inducible gene I (RIG-I)-like receptors (RLRs) has been implicated in the pathogenesis of autoimmune disorders. We investigated if polymorphisms in the IFIH1, RIG-I, LGP2 and VISA genes influence the risk for multiple sclerosis (MS) in a German case-control cohort comprising 716 patients and 706 controls. Evaluation of 18 single nucleotide polymorphisms (SNPs) in the four genes did not reveal significant single-SNP associations with MS risk, but two VISA polymorphisms were modestly associated with age of onset. Further, we provide initial evidence for combinatorial effects of polymorphic variants in the RIG-I, LGP2 and IFIH1 genes on MS risk.

Searching for the origin of Gagauzes: inferences from Y-chromosome analysis

The Gagauzes are a small Turkish-speaking ethnic group living mostly in southern Moldova and northeastern Bulgaria. The origin of the Gagauzes is obscure. They may be descendants of the Turkic nomadic tribes from the Eurasian steppes, as suggested by the "Steppe" hypothesis, or have a complex Anatolian-steppe origin, as postulated by the "Seljuk" or "Anatolian" hypothesis. To distinguish these hypotheses, a sample of 89 Y-chromosomes representing two Gagauz populations from the Republic of Moldova was analyzed for 28 binary and seven STR polymorphisms. In the gene pool of the Gagauzes a total of 15 Y-haplogroups were identified, the most common being I-P37 (20.2%), R-M17 (19.1%), G-M201 (13.5%), R-M269 (12.4%), and E-M78 (11.1%). The present Gagauz populations were compared with other Balkan, Anatolian, and Central Asian populations by means of genetic distances, nonmetric multidimentional scaling and analyses of molecular variance. The analyses showed that Gagauzes belong to the Balkan populations, suggesting that the Gagauz language represents a case of language replacement in southeastern Europe. Interestingly, the detailed study of microsatellite haplotypes revealed some sharing between the Gagauz and Turkish lineages, providing some support of the hypothesis of the "Seljuk origin" of the Gagauzes. The faster evolving microsatellite loci showed that the two Gagauz samples investigated do not represent a homogeneous group. This finding matches the cultural and linguistic heterogeneity of the Gagauzes well, suggesting a crucial role of social factors in shaping the Gagauz Y-chromosome pool and possibly also of effects of genetic drift.

Population history of the Dniester-Carpathians: evidence from Alu markers

The area between the Dniester and the eastern Carpathian mountain range is at a geographical crossroads between eastern Europe and the Balkans. Little is known about the genetics of the population of this region. We performed an analysis of 12 binary autosomal markers in samples from six Dniester-Carpathian populations: two Moldavian, one Romanian, one Ukrainian and two Gagauz populations. The results were compared with gene frequency data from culturally and linguistically related populations from Southeast Europe and Central Asia. Small genetic differences were found among southeastern European populations (in particular those of the Dniester-Carpathian region). The observed homogeneity suggests either a very recent common ancestry of all southeastern European populations or strong gene flow between them. Despite this low level of differentiation, tree reconstruction and principle component analyses allowed a distinction between Balkan-Carpathian (Macedonians, Romanians, Moldavians, Ukrainians and Gagauzes) and eastern Mediterranean (Turks, Greeks and Albanians) population groups. The genetic affinities among Dniester-Carpathian and southeastern European populations do not reflect their linguistic relationships. The results indicate that the ethnic and genetic differentiations occurred in these regions to a considerable extent independently of each other. In particular, Gagauzes, a Turkic-speaking population, show closer affinities to their geographical neighbors than to other Turkic populations.