Genetic association of Nuclear factor of activated T cells' 3'UTR and structural polymorphisms with susceptibility to generalized vitiligo in Gujarat population

Generalized vitiligo(GV) is an autoimmune skin depigmenting disease characterized by loss of functional melanocytes. Nuclear factor of activated T cells(NFATs) play a key role in regulatory T cells' (Tregs) activation and function. Our previous studies have highlighted the role of reduced NFATs expression and activity in impaired Tregs suppressive capacity, leading to GV pathogenesis. 3'UTR region and structural single nucleotide polymorphisms(SNPs) could lead to reduced NFAT expression and activity. Therefore, we studied the association of NFATs 3'UTR [NFATC2 rs4811198(T>G) &NFATC4 rs11848279(A>G)] and structural [NFATC1 rs754093(T>G) &NFATC2 rs12479626(T>C)] SNPs in 427 GV patients and 415 controls from Gujarat population by Polymerase chain reaction-restriction fragment length polymorphism(PCR-RFLP). Additionally, we carried out genotype-phenotype correlation and in silico analysis to assess the effect of NFATs SNPs on NFATs expression and structure. NFATC2 rs4811198(T>G) 3' UTR &NFATC2 rs12479626(T>C) structural SNPs were significantly associated with GV(p<0.0001). Interestingly, for NFATC2 rs4811198(T>G) SNP, there was a significant difference in the TT vs GG genotypes' frequencies (p=0.0034; Table 2), and for NFATC2 rs12479626(T>C) SNP there was a significant difference between TT vs TC and CC genotypes' frequencies(p<0.0001 & p=0.0002) between GV patients and controls. Furthermore, Odds ratio suggested that the susceptible alleles for NFATC2 rs4811198(T>G) &NFATC2 rs12479626(T>C) SNPs increased the risk of GV by 1.38 & 3.043 fold. However, the NFAT 3' UTR [NFATC2 rs4811198 (T>G)] and structural [NFATC1 rs754093(T>G)] SNPs were not significantly associated with GV. Interestingly, the genotype-phenotype correlation suggested that the susceptible 'G' allele of NFATC2 rs4811198(T>G) &NFATC4 rs11848279(A>G) 3' UTR SNPs lead to reduced NFATC2 and NFATC4 expression(p<0.0001). Furthermore, in silico analysis suggested that hsa-miR-3183 & hsa-miR-6720-3p miRNAs specifically bound to 'G' allele of NFATC2 rs4811198 SNP and has-miR-4652-3p miRNA specifically bound to 'G' allele of NFATC4 rs11848279 SNP. Overall, our study suggests that NFATC2 rs4811198(T>G) 3' UTR &NFATC2 rs12479626(T>C) structural SNPs may be associated with GV susceptibility in Gujarat population. Moreover, the susceptible alleles for the 3' UTR SNPs could lead to reduced NFATs levels, which may further possibly, affect the Treg suppressive function leading to GV.

Genetic Variations of Ionotropic Glutamate Receptor Pathways on Interferon-α-induced Depression in Patients with Hepatitis C Viral Infection

IMPORTANCE

The most supportive evidence of the inflammation theory of depression is that up to one-third of patients with Hepatitis C virus infection (HCV) develop clinical depressive episodes during interferon-α (IFN-α) therapy. As glutamate-mediated excitotoxicity has been found to be a consequence of excessive inflammation and a pathogenic mechanism of depression, it is plausible to investigate genes on ionotropic glutamate receptor pathways.

OBJECTIVE

To identify the at-risk genetic variations on ionotropic glutamate receptor pathways for interferon-α-induced depression.

METHOD

We assessed 291 patients with chronic HCV undergoing IFN-α therapy and analyzed the single nucleotide polymorphisms (SNPs) in genes related to ionotropic glutamate receptors in this prospective case-control study. Patients who developed IFN-α-induced depression anytime during the treatment were defined as the case group, while those who did not were defined as the control group. Genomic DNA was extracted from peripheral blood and analyzed by Affymetrix TWB array. Allelic and haplotype association tests were conducted using χ2 tests to assess the difference in allele and haplotype frequencies between cases and controls. Additionally, we performed 5000 permutations to control gene-wide family-wise error rates and create empirical p-values. Stratified analyses were then done to control for confounders and adjust odds ratios for our significant SNPs. We also did an additional stratified analysis to re-assess genes with near-significant SNPs (empirical p-value=0.05-0.10), employing Bonferroni correction with the effective number of independent tests to control gene-wide family-wise error rates.

RESULTS

The minor and major allele frequencies of rs7542 (empirical p-value=0.0310) in MAPK3, rs3026685 (empirical p-value=0.0378) in PICK1, rs56005409 (empirical p-value=0.0332) in PRKCA, rs12914792 (empirical p-value=0.0096), rs17245773 (empirical p-value=0.0340) in RASGRF1, and rs78387863 (empirical p-value=0.0086), rs74365480 (empirical p-value=0.0200) in RASGRF2 were found significantly different between cases and controls. Haplotype association tests also revealed one significant haplotype in PRKCA (empirical p-value=0.0200) and one in RASGRF1 (empirical p-value=0.0048). Stratified analyses showed no signs of confounders for most of our significant SNPs, except for rs78387863 in RASGRF2. After a re-assessment of our near-significant genes by stratified analyses, two SNPs in GRIN2B turned significant.

CONCLUSIONS

This study provided supportive evidence of the involvement of the RAS/RAF/mitogen-activated protein kinase (MAPK) signaling pathway and glutamate ionotropic receptor AMPA type subunit 2(GluR2) transportation in the pathogenesis of IFN-α-induced depression.

Polymorphism studies on microRNA targetome of thalassemia

Thalassemia is one of the most prevalent hemoglobin disorders. It is caused by the decreased or absent synthesis of one globin chain that leads to moderate to severe hemolytic anemia in clinical complications. Some genetic factors cause these phenotypic variations by the alteration of gene expression. MicroRNAs (miRNAs) are post-transcriptional regulators in gene expression. Therefore, variations in 3'-untranslated region (3'-UTR) of target genes may affect gene expression. It is of interest to evaluate the impact of noncoding SNPs in thalassemia related genes on miRNA: mRNA interactions in the severity of thalassemia. Polymorphisms that alter miRNA: mRNA interactions were predicted using PolymiRTS and Mirsnpscore tools. Then, the effect of predicted target SNPs on thermodynamic stability, local RNA structure and regulatory elements was investigated using RNAhybrid, RNAsnp and RegulomeDB, respectively. The molecular functions and the Biological process of candidate genes were extracted and interaction network was created. Forty-six SNPs were predicted to affect 188 miRNA interactions. These results suggest that 3'-UTR SNP may affect gene expression and cause phenotypic variation in thalassemia patients.

Identifying the miRNA signature associated with survival time in patients with lung adenocarcinoma using miRNA expression profiles

Lung adenocarcinoma is a multifactorial disease. MicroRNA (miRNA) expression profiles are extensively used for discovering potential theranostic biomarkers of lung cancer. This work proposes an optimized support vector regression (SVR) method called SVR-LUAD to simultaneously identify a set of miRNAs referred to the miRNA signature for estimating the survival time of lung adenocarcinoma patients using their miRNA expression profiles. SVR-LUAD uses an inheritable bi-objective combinatorial genetic algorithm to identify a small set of informative miRNAs cooperating with SVR by maximizing estimation accuracy. SVR-LUAD identified 18 out of 332 miRNAs using 10-fold cross-validation and achieved a correlation coefficient of 0.88 ± 0.01 and mean absolute error of 0.56 ± 0.03 year between real and estimated survival time. SVR-LUAD performs well compared to some well-recognized regression methods. The miRNA signature consists of the 18 miRNAs which strongly correlates with lung adenocarcinoma: hsa-let-7f-1, hsa-miR-16-1, hsa-miR-152, hsa-miR-217, hsa-miR-18a, hsa-miR-193b, hsa-miR-3136, hsa-let-7g, hsa-miR-155, hsa-miR-3199-1, hsa-miR-219-2, hsa-miR-1254, hsa-miR-1291, hsa-miR-192, hsa-miR-3653, hsa-miR-3934, hsa-miR-342, and hsa-miR-141. Gene ontology annotation and pathway analysis of the miRNA signature revealed its biological significance in cancer and cellular pathways. This miRNA signature could aid in the development of novel therapeutic approaches to the treatment of lung adenocarcinoma.

In silico dissection of miRNA targetome polymorphisms and their role in regulating miRNA-mediated gene expression in esophageal cancer

Esophageal cancer is the eighth most common cancer worldwide. Also middle-aged obese adults with higher body mass index during childhood have a greater risk to develop esophageal cancer. The contribution of microRNAs to esophageal cancer has been extensively studied and it became clear that these noncoding RNAs may play crucial roles in pathogenesis, diagnosis and prognosis of the disease. Increasing evidences have suggested that polymorphisms perturbing microRNA targetome (i.e., the compendium of all microRNA target sites) are associated with cancers including esophageal cancer. However, the extent to which such variants contribute to esophageal cancer is still unclear. In this study, we applied an in silico approach to systematically identify polymorphisms perturbing microRNA targetome in esophageal cancer and performed various analyses to predict the functional consequences of the occurrence of these variants. The computational results were integrated to provide a prioritized list of the most potentially disrupting esophageal cancer-implicated microRNA targetome polymorphisms along with the in silico insight into the mechanisms with which such variations may modulate microRNA-mediated regulation. The results of this study will be valuable for future functional experiments aimed at dissecting the roles of microRNA targetome polymorphisms in the onset and progression of esophageal cancer.

Single nucleotide polymorphisms of the NF-κB and STAT3 signaling pathway genes predict lung cancer prognosis in a Chinese Han population

Inflammation contributes to human carcinogenesis and cancer progression. This study selected and analyzed single nucleotide polymorphisms (SNPs) of the NF-κB and STAT3 signaling pathway genes for associations with prognosis in 1,165 lung cancer patients from a Chinese Han population. The data showed that eight SNPs (i.e., rs10836, rs3732131, rs3732133, rs4072391, rs2273650, rs1053023, rs3744483, and rs28372683) can be grouped into low-, medium-, and high-risk genotypes based on survival data. The median overall survival time (MST) of this cohort of patients was 24.6 months, whereas the MST of patients with low-risk genotypes reached 79.7 months; MST of patients with the medium-risk genotypes was 25.5 months, and those with high-risk genotypes was 22.7 months. Overall survival was statistically different for sex (P = 0.004), age (P = 0.010), histological types (P = 0.035), tumor stage (P < 0.001), tumor size (P < 0.001), surgery (P < 0.001), chemoradiotherapy (P = 0.007), and Karnofsky score (P < 0.001). Multivariate analysis and the data from the current study demonstrated that sex, tumor stage and size, surgery, chemoradiotherapy, and the aforementioned eight SNPs were all independent predictors for overall survival of lung cancer patients.