Identifying polymorphic cis-regulatory variants as risk markers for lung carcinogenesis and chemotherapy responses in tobacco smokers from eastern India.

Aberrant expression of xenobiotic metabolism and DNA repair genes is critical to lung cancer pathogenesis. This study aims to identify the cis-regulatory variants of the genes modulating lung cancer risk among tobacco smokers and altering their chemotherapy responses. From a list of 2984 SNVs, prioritization and functional annotation revealed 22 cis-eQTLs of 14 genes within the gene expression-correlated DNase I hypersensitive sites using lung tissue-specific ENCODE, GTEx, Roadmap Epigenomics, and TCGA datasets. The 22 cis-regulatory variants predictably alter the binding of 44 transcription factors (TFs) expressed in lung tissue. Interestingly, 6 reported lung cancer-associated variants were found in linkage disequilibrium (LD) with 5 prioritized cis-eQTLs from our study. A case-control study with 3 promoter cis-eQTLs (p < 0.01) on 101 lung cancer patients and 401 healthy controls from eastern India with confirmed smoking history revealed an association of rs3764821 (ALDH3B1) (OR = 2.53, 95% CI = 1.57-4.07, p = 0.00014) and rs3748523 (RAD52) (OR = 1.69, 95% CI = 1.17-2.47, p = 0.006) with lung cancer risk. The effect of different chemotherapy regimens on the overall survival of lung cancer patients to the associated variants showed that the risk alleles of both variants significantly decreased (p < 0.05) patient survival.

Analysis of DNMT1 gene variants in progression of neural tube defects-an in silico to in vitro approach.

Neural tube defects (NTDs) are significant congenital deformities of the central nervous system among which spina bifida is the most common form that occurs due to defect in the neurulation process of embryogenesis. NTDs are among the most common type of birth defects occurring at a range of 0.5-10 in every 1000 live births worldwide and are thought to have multifactorial etiology, including multigenetic and epigenetic notions. Epigenetic regulations control differential gene expression in normal and disease phenotypes. DNA methylation is a significant epigenetic process, guided by DNMT1, one of the most important maintenance methylating agents. However, the relationship between DNMT1 and NTDs had always been inconclusive and poorly understood. In the present study, by utilizing in silico methodologies we tried to figure out potent single nucleotide variants (SNVs) that could play roles in generating functional differences in DNMT1 expression and we also tried to check (by in vitro method) if there is any connection between DNMT1 expression and spina bifida condition. A number of coding and non-coding (both intragenic and intergenic) SNVs of DNMT1 were found (using the in silico methods) that have potentials to alter its expression. From the in vitro experimentations, differential DNMT1 RNA expressions were found between spina bifida affected newborns and their respective mothers when compared with controls. It is the first report of NTD from Eastern India precisely showing inverse correlation between DNMT1 expression and occurrence of NTD. The findings of the present study could be further considered for early prognosis and future experimental designs.

A comprehensive meta-analysis and prioritization study to identify vitiligo associated coding and non-coding SNV candidates using web-based bioinformatics tools.

Vitiligo is a prevalent depigmentation disorder affecting around 1% of the general population. So far, various Genome Wide Association Studies (GWAS) and Candidate Gene Association Studies (CGAS) have identified several single nucleotide variants (SNVs) as a risk factor for vitiligo. Nonetheless, little has been discerned regarding their direct functional significance to the disease pathogenesis. In this study, we did extensive data mining and downstream analysis using several experimentally validated datasets like GTEx Portal and web tools like rSNPBase, RegulomeDB, HaploReg and STRING to prioritize 13 SNVs from a set of 291SNVs that have been previously reported to be associated with vitiligo. We also prioritized their underlying/target genes and tried annotating their functional contribution to vitiligo pathogenesis. Our analysis revealed genes like FGFR10P, SUOX, CDK5RAP1 and RERE that have never been implicated in vitiligo previously to have strong potentials to contribute to the disease pathogenesis. The study is the first of its kind to prioritize and functionally annotate vitiligo-associated GWAS and CGAS SNVs and their underlying/target genes, based on functional data available in the public domain database.

Prioritization of human well-being spectrum related GWAS-SNVs using ENCODE-based web-tools predict interplay between PSMC3, ITIH4, and SERPINC1 genes in modulating well-being.

Several traits related to positive and negative affect show a high genetic as well as phenotypic correlation with well-being in humans, and are therefore collectively termed as "Well-being spectrum". Genome-Wide Association studies (GWA studies) on "well-being measurement" have led to identification of several genomic variants (Single Nucleotide Variants - SNVs), but very little has been explained with respect to their functionality and mode of alteration of well-being. Utilizing a pool of 1258 GWA studies based SNVs on "well-being measurement", we prioritized the SNVs and tried to annotate well-being related functionality through several bioinformatic tools to predict whether a protein sequence variation affects protein function, as well as experimentally validated datasets available in ENCODE based web-tools namely rSNPBase, RegulomeDB, Haploreg, along with GTEx Portal and STRING based protein interaction networks. Prioritization yielded three key SNVs; rs3781627-A, rs13072536-T and 5877-C potentially regulating three genes, PSMC3, ITIH4 and SERPINC1, respectively. Interestingly, the genes showed well clustered protein-protein interaction (maximum combined confidence score >0.4) with other well-being candidate genes, namely TNF and CRP genes suggesting their important role in modulation of well-being. PSMC3 and ITIH4 genes are also involved in driving acute phase responses signifying a probable cross-talk between well-being and psychoneuroimmunological system. To best of our knowledge this study is the first of its kind where the well-being associated GWA studies-SNVs were prioritized and functionally annotated, majorly based on functional data available in public domain, which revealed PSMC3, ITIH4 and SERPINC1 genes as probable candidates in regulation of well-being spectrum.

A meta-analysis and in silico analysis of polymorphic variants conferring breast cancer risk in the Indian subcontinent.

Background: Genetic association studies on breast cancer on the Indian subcontinent have yielded conflicting results, and the precise effect of these variants on breast cancer pathogenesis is not known. Methods: Genomic variants, as obtained from selected studies from the Indian subcontinent, were subjected to random-effects and fixed-effect meta-analysis. Functional annotation of the relevant variants was done through a tried and tested in silico pipeline. Results: We found rs4646903/CYP1A1, rs1799814/CYP1A1, rs61886492/GCPII, del2/GSTM1, rs4680/COMT and rs1801394/MTRR to be associated with breast cancer. The del2/GSTM1 holds the association in premenopausal women. Conclusions: This is the first study of its kind from the Indian subcontinent analysing the extent of association of variants across populations followed by their functional annotation in the disease pathway.

Mapping the TYR gene reveals novel and previously reported variants in Eastern Indian patients highlighting preponderance of the same changes in multiple unrelated ethnicities.

Oculocutaneous albinism (OCA) is a group of congenital autosomal recessive disorders with seven known subtypes (OCA1-OCA7) characterized by loss or absence of pigmentation in the skin, hair, and eyes. OCA1, caused by pathogenic variations in the tyrosinase (TYR) gene, has been documented to be the most prevalent subtype across the world including India. In the present study, we recruited 53 OCA-affected individuals from 45 unrelated families belonging to 20 different marriage groups/ethnicities of 15 different districts of West Bengal. We took a targeted sequencing-based approach to find the causal variations in the TYR gene. We report here identification of two novel potentially pathogenic variations [NM_000372.4:c.614C>T, NP_000363.1:p.(Pro205Leu), and NM_000372.4:c.1036+1=/G>T], one novel synonymous TYR variant [NM_000372.4:c.204=/A>G, NP_000363.1:p.(Gln68=)], two pathogenic variations documented for the first time in Indian OCA cases [NM_000372.4:c.1147G>A, NP_000363.1:p.(Asp383Asn), and NM_000372.4:c.585G>A, NP_000363.1:p.(Trp195*)], along with nine previously reported pathogenic variants in 36 out of 53 (∼68%) patients recruited. We report common haplotype backgrounds for the two most prevalent variations [NM_000372.4:c.124G>A, NM_000372.4:c.832C>T] in cases belonging to different marriage/ethnic groups, suggesting a possible founder effect. To our knowledge, this is the most comprehensive genetic study on OCA1 from India, firmly establishing OCA1 as the commonest form of albinism in this part of the world.

Meta-analysis and prioritization of human skin pigmentation-associated GWAS-SNPs using ENCODE data-based web-tools.

Skin pigmentation in human is a complex trait, which varies widely, both within and between human populations. The exact players governing the trait of skin pigmentation remain elusive till date. Various Genome Wide Association Studies (GWAS) have shown the association of different genomic variants with normal human skin pigmentation, often indicating genes with no direct implications in melanin biosynthesis or distribution. Little has been explained in terms of the functionality of the associated Single-Nucleotide Polymorphisms (SNPs) with respect to modulating the skin pigmentation phenotype. In the present study, which, to our knowledge, is the first of its kind, we tried to analyze and prioritize 519 non-coding SNPs and 24 3'UTR SNPs emerging from 14 different human skin pigmentation-related GWAS, primarily using several ENCODE-based web-tools like rSNPBase, RegulomeDB, HaploReg, etc., most of which incorporate experimentally validated evidences in their predictions. Using this comprehensive, in-silico, analytical approach, we successfully prioritized all the pigmentation-associated GWAS-SNPs and tried to annotate pigmentation-related functionality to them, which would pave the way for deeper understanding of the molecular basis of human skin pigmentation variations.

Influence of Apolipoprotein E polymorphism on susceptibility of Wilson disease.

Wilson disease (WD) is an autosomal-recessive disorder caused by mutations in the ATP7B gene leading to abnormal copper deposition in liver and brain. WD manifests diverse neurological and hepatic phenotypes and different age of onset, even among the siblings, with same mutational background suggesting complex nature of the disease and involvement of other candidate genes. In that context, Apolipoprotein E (APOE) and Prion Protein (PRNP) have been proposed to be potential candidates for modifying the WD phenotype and age of onset. This study aims to identify the contribution of APOE and PRNP polymorphisms on the variable phenotypic expression of Indian WD patients. A total of 171 WD patients and 291 controls from Indian population were included in this study. Two APOE cSNPs (rs429358 and rs7412) resulting in three isoforms and M129V (rs1799990) polymorphism of PRNP were examined for their association with WD and its clinical phenotypes. The APOE ԑ4 allele was found to be significantly overrepresented in WD patients compared to controls. However, the frequency of the APOE ԑ3 allele and ԑ3/ԑ3 genotype was significantly higher in WD patients without cognitive behavior impairment compared to the ones with the impairment. On the contrary, the PRNP allele representing Val129 was found to be present in higher proportion in WD patients with cognitive behavioral decline. Our data suggest that the APOE ԑ4 allele could act as a potential risk for the pathogenesis of WD. Also, APOE and PRNP might contribute toward the cognitive behavioral decline in a section of WD patients.