Possible Association Between Polymorphisms in ESR1, COL1A2, BGLAP, SPARC, VDR, and MMP2 Genes and Dental Fluorosis in a Population from an Endemic Region of West Bengal.

Dental fluorosis (DF) is the most prevalent form of fluorosis in India affecting millions of people all over the country. As estrogen receptor 1 (ESR1), collagen type 1 alpha 2 (COL1A2), bone γ-carboxyglutamic acid protein (BGLAP), secreted protein acidic and cysteine-rich (SPARC), vitamin D receptor (VDR), and matrix metallopeptidase 2 (MMP2) genes play critical roles in bone metabolism, bone formation, mineral metabolism, and mineralization, variants in these genes could influence susceptibility to DF. The present study was aimed at evaluating the association between 15 single-nucleotide polymorphisms (SNPs) in the six candidate genes (namely, ESR1, COL1A2, BGLAP, SPARC, VDR, and MMP2) and DF among 132 individuals (case = 71 and control = 61) living in a fluoride endemic region of West Bengal, India. No statistically significant association with disease risk was found when the genotypes and allele frequencies of each of the 15 SNPs was analyzed individually using odd's ratio with 95% confidence interval. "CC" and "AG" haplotypes of the COL1A2 gene showed a borderline association with DF. The present study is the first in India to use multifactor dimensionality reduction (MDR) analysis for identifying gene-gene and gene-environment interactions in fluorosis. The biomarker of serum fluoride showed a significant association with the disease state among the 17 attributes (15 SNPs and 2 biomarkers of urine fluoride and serum fluoride) (P value = 0.011). The best model of MDR analysis with maximized testing accuracy involved two SNPs from the ESR1 gene (rs9340799 and rs2077647) and one SNP from BGLAP gene (rs1543294) (P value < 0.0001).

Epigenetic modifications from arsenic exposure: A comprehensive review.

Arsenic is a notorious element with the potential to harm exposed individuals in ways that include cancerous and non-cancerous health complications. Millions of people across the globe (especially in South and Southeast Asian countries including China, Vietnam, India and Bangladesh) are currently being unknowingly exposed to precarious levels of arsenic. Among the diverse effects associated with such arsenic levels of exposure is the propensity to alter the epigenome. Although a large volume of literature exists on arsenic-induced genotoxicity, cytotoxicity, and inter-individual susceptibility due to active research on these subject areas from the last millennial, it is only recently that attention has turned on the ramifications and mechanisms of arsenic-induced epigenetic changes. The present review summarizes the possible mechanisms involved in arsenic induced epigenetic alterations. It focuses on the mechanisms underlying epigenome reprogramming from arsenic exposure that result in improper cell signaling and dysfunction of various epigenetic components. The mechanistic information articulated from the review is used to propose a number of novel therapeutic strategies with a potential for ameliorating the burden of worldwide arsenic poisoning.

Arsenic exposure from drinking water and staple food (rice): A field scale study in rural Bengal for assessment of human health risk.

Arsenic is a well-known carcinogen with emerging reports showing a range of health outcomes even for low to moderate levels of exposure. This study deals with arsenic exposure and associated increased lifetime cancer risk for populations in arsenic-endemic regions of rural Bengal, where arsenic-safe drinking water is being supplied at present. We found a median total exposure of inorganic arsenic to be 2. 9 µg/Kg BW/day (5th and 95th percentiles were 1.1 µg/Kg BW/day and 7.9 µg/Kg BW/day); with major contribution from cooked rice intake (2.4 µg/Kg BW/day). A significant number of households drank arsenic safe water but used arsenic-rich water for rice cooking. As a result, 67% participants had inorganic arsenic intake above the JEFCA threshold value of 3 µg/Kg BW/day for cancer risk from only rice consumption when arsenic contaminated water was used for cooking (median: 3.5 µg/Kg BW/day) compared to 29% participants that relied on arsenic-free cooking water (median: 1.0 µg/kg BW/day). Arsenic in urine samples of study participants ranged from 31.7 to 520 µg/L and was significantly associated with the arsenic intake (r = 0.76); confirming the preponderance of arsenic exposure from cooked rice. The median arsenic attributable cancer risks from drinking water and cooked rice were estimated to be 2.4 × 10-5 and 2.7 × 10-4 respectively, which further emphasized the importance of arsenic exposure from staple diet. Our results show that any mitigation strategy should include both drinking water and local staple foods in order to minimize the potential health risks of arsenic exposure.

Structural diversity, functional aspects and future therapeutic applications of human gut microbiome.

The research on human gut microbiome, regarded as the black box of the human body, is still at the stage of infancy as the functional properties of the complex gut microbiome have not yet been understood. Ongoing metagenomic studies have deciphered that the predominant microbial communities belong to eubacterial phyla Firmicutes, Bacteroidetes, Proteobacteria, Fusobacteria, Cyanobacteria, Verrucomicrobia and archaebacterial phylum Euryarchaeota. The indigenous commensal microbial flora prevents opportunistic pathogenic infection and play undeniable roles in digestion, metabolite and signaling molecule production and controlling host's cellular health, immunity and neuropsychiatric behavior. Besides maintaining intestinal health via short-chain fatty acid (SCFA) production, gut microbes also aid in neuro-immuno-endocrine modulatory molecule production, immune cell differentiation and glucose and lipid metabolism. Interdependence of diet and intestinal microbial diversity suggests the effectiveness of pre- and pro-biotics in maintenance of gut and systemic health. Several companies worldwide have started potentially exploiting the microbial contribution to human health and have translated their use in disease management and therapeutic applications. The present review discusses the vast diversity of microorganisms playing intricate roles in human metabolism. The contribution of the intestinal microbiota to regulate systemic activities including gut-brain-immunity crosstalk has been focused. To the best of our knowledge, this review is the first of its kind to collate and discuss the companies worldwide translating the multi-therapeutic potential of human intestinal microbiota, based on the multi-omics studies, i.e. metagenomics and metabolomics, as ready solutions for several metabolic and systemic disorders.

Evaluating the Association Between Dental Fluorosis and Polymorphisms in Bone Development and Mineralization Genes Among Population from a Fluoride Endemic Region of Eastern India.

Close to 12 million people in India are affected by more than the desirable level of fluoride in drinking water that could lead to dental, skeletal, and non-skeletal fluorosis. Dental fluorosis is a developmental defect that results in hypo-mineralization and pronounced porosity of enamel in the affected individuals. As estrogen receptor 1 (ESR1), collagen type 1 alpha 2 (COL1A2), bone γ-carboxyglutamic acid protein (BGLAP), and secreted protein acidic and cysteine rich (SPARC) genes are involved in bone development and mineralization, polymorphisms in these genes could be determining factors in influencing the risk to fluorosis among the exposed individuals in fluoride endemic areas. A case-control study was carried out among a total of 87 individuals (case = 36, control = 51) to examine the association between selected polymorphisms in the ESR1, COL1A2, BGLAP, and SPARC genes and risk of dental fluorosis from a fluoride endemic region of Eastern India. Altogether, 10 single nucleotide polymorphisms (SNPs) in ESR1 (rs2234693, rs2228480, rs3798577, rs2077647, and rs9340799), COL1A2 (rs42524, rs412777), BGLAP (rs1800247), and SPARC (rs6579885, rs4958278) genes were genotyped through PCR-RFLP in these subjects. The association of the SNPs for disease risk estimation was measured by odds ratio with 95% confidence interval. The risk genotypes of none of the 10 SNPs showed statistically significant association with risk of dental fluorosis. Frequencies of the haplotypes in the intragenic SNPs of the ESR1, COL1A2, and SPARC genes did not reveal any statistically significant difference between the case and control groups. The present study is the first of its kind from India that has attempted to investigate possible involvement of genetic factors in influencing the risk to fluorosis among the population from a fluoride endemic region.

Arsenic in groundwater of West Bengal, India: A review of human health risks and assessment of possible intervention options.

This paper reviews how active research in West Bengal has unmasked the endemic arsenism that has detrimental effects on the health of millions of people and their offspring. It documents how the pathways of exposure to this toxin/poison have been greatly expanded through intensive application of groundwater in agriculture in the region within the Green Revolution framework. A goal of this paper is to compare and contrast the similarities and differences in arsenic occurrence in West Bengal with those of other parts of the world and assess the unique socio-cultural factors that determine the risks of exposure to arsenic in local groundwater. Successful intervention options are also critically reviewed with emphasis on integrative strategies that ensure safe water to the population, proper nutrition, and effective ways to reduce the transfer of arsenic from soil to crops. While no universal model may be suited for the vast areas of the world affected with by natural contamination of groundwater with arsenic, we have emphasized community-specific sustainable options that can be adapted. Disseminating scientifically correct information among the population coupled with increased community level participation and education are recognized as necessary adjuncts for an engineering intervention to be successful and sustainable.

The genetic influence in fluorosis.

Fluorosis, caused by ingestion of excess fluoride, is endemic in at least 25 countries across the globe, China and India being the worst affected among them. Dental, skeletal and non-skeletal are the major types of fluorosis affecting millions of people in these countries. A number of genetic epidemiological studies carried out by investigators have shown the evidence for association between genetic polymorphisms in candidate genes and differences in the susceptibility pattern of different types of fluorosis among individuals living in the same community and having the same environmental exposure. These studies have pointed out that genetic variants in some candidate genes like COL1A2 (Collagen type 1 alpha 2), CTR (Calcitonin receptor gene), ESR (Estrogen receptor), COMT (Catechol-o-methyltransferase), GSTP1 (Glutathione S-transferase pi 1), MMP-2 (Matrix metallopeptidase 2), PRL (Prolactin), VDR (Vitamin D receptor) and MPO (Myeloperoxidase) could increase or decrease the risk of fluorosis among the exposed individuals in endemic areas. So, it is increasingly becoming evident that an individual's genetic background could play a major role in influencing the risk to fluorosis when other factors like specific environmental exposures including dietary patterns of fluoride intake and other nutrients remain the same. The current manuscript presents an up-to-date critical review on fluorosis, focusing mainly on the genetic association studies that have looked at the possible involvement of genetic factors in fluorosis.

Polymorphisms in DNA repair and multidrug resistance genes among Sindhis of Central India.

Polymorphisms in DNA repair and multidrug resistance genes might contribute to interindividual and interethnic differences in DNA repair capacity and drug disposition respectively. In the present study, we determined the allele and genotype frequencies of four single nucleotide polymorphisms (SNPs) located in the DNA repair genes, XRCC1, XRCC3, XPD, OGG1, namely XRCC1 Arg399Gln, XRCC3 Thr241Met, XPD Lys751Gln, and OGG1 Ser326Cys, respectively and two SNPs located in the multidrug resistance gene, ABCB1, namely ABCB1 C3435T and ABCB1 C1236T, in 33-35 healthy and unrelated Sindhi individuals, residing in the Vidarbha region of Central India and compared them with the Maharashtrian population from the same geographical region and some other HapMap populations from the HapMap database. The study findings reveal that the Indian Sindhis are closely related to the Maharashtrians as well as Utah residents with Northern and Western European ancestry and Gujarati Indians in Houston, Texas in the HapMap database.

Frequency and genotype distribution of ABCB1 gene polymorphisms among Maharashtrian population of Central India.

1. Apart from conferring multidrug resistance to cancer cells, P-glycoprotein (P-gp) encoded by the gene ABCB1 (also, known as Multidrug resistance gene, MDR1), plays a major role in drug disposition. Single nucleotide polymorphisms (SNPs) in the ABCB1 gene might contribute to inter-individual and ethnic differences in drug disposition and thereby, could influence the outcome and prognosis of certain diseases. 2. India is one of the most ethnically and genetically diverse regions of the world. This study was undertaken with a view to determine the allele and genotype frequencies of C3435T and C1236T polymorphisms in the ABCB1 gene among the Maharashtrian population, residing in the Vidarbha region of central India and compare them with HapMap and other Indian populations. The common synonymous C3435T polymorphism has been found to be associated with lower P-gp functional expression and drug uptake, alone or in conjunction with a few other linked SNPs like C1236T. 3. The genotypes of C3435T and C1236T SNPs were determined by PCR-RFLP in 222 healthy and unrelated Maharashtrian individuals. 4. According to the findings of this study, the Maharashtrians were found to be not significantly different from the Gujarati Indians in Houston, Texas in the HapMap database.

Genetic variants associated with breast cancer risk for Ashkenazi Jewish women with strong family histories but no identifiable BRCA1/2 mutation.

The ability to establish genetic risk models is critical for early identification and optimal treatment of breast cancer. For such a model to gain clinical utility, more variants must be identified beyond those discovered in previous genome-wide association studies (GWAS). This is especially true for women at high risk because of family history, but without BRCA1/2 mutations. This study incorporates three datasets in a GWAS analysis of women with Ashkenazi Jewish (AJ) homogeneous ancestry. Two independent discovery cohorts comprised 239 and 238 AJ women with invasive breast cancer or preinvasive ductal carcinoma in situ and strong family histories of breast cancer, but lacking the three BRCA1/2 founder mutations, along with 294 and 230 AJ controls, respectively. An independent, third cohort of 203 AJ cases with familial breast cancer history and 263 healthy controls of AJ women was used for validation. A total of 19 SNPs were identified as associated with familial breast cancer risk in AJ women. Among these SNPs, 13 were identified from a panel of 109 discovery SNPs, including an FGFR2 haplotype. In addition, six previously identified breast cancer GWAS SNPs were confirmed in this population. Seven of the 19 markers were significant in a multivariate predictive model of familial breast cancer in AJ women, three novel SNPs [rs17663555(5q13.2), rs566164(6q21), and rs11075884(16q22.2)], the FGFR2 haplotype, and three previously published SNPs [rs13387042(2q35), rs2046210(ESR1), and rs3112612(TOX3)], yielding moderate predictive power with an area under the curve (AUC) of the ROC (receiver-operator characteristic curve) of 0.74. Population-specific genetic variants in addition to variants shared with populations of European ancestry may improve breast cancer risk prediction among AJ women from high-risk families without founder BRCA1/2 mutations.

Segmental duplication as one of the driving forces underlying the diversity of the human immunoglobulin heavy chain variable gene region.

BACKGROUND: Segmental duplication and deletion were implicated for a region containing the human immunoglobulin heavy chain variable (IGHV) gene segments, 1.9III/hv3005 (possible allelic variants of IGHV3-30) and hv3019b9 (a possible allelic variant of IGHV3-33). However, very little is known about the ranges of the duplication and the polymorphic region. This is mainly because of the difficulty associated with distinguishing between allelic and paralogous sequences in the IGHV region containing extensive repetitive sequences. Inability to separate the two parental haploid genomes in the subjects is another serious barrier. To address these issues, unique DNA sequence tags evenly distributed within and flanking the duplicated region implicated by the previous studies were selected. The selected tags in single sperm from six unrelated healthy donors were amplified by multiplex PCR followed by microarray detection. In this way, individual haplotypes of different parental origins in the sperm donors could be analyzed separately and precisely. The identified polymorphic region was further analyzed at the nucleotide sequence level using sequences from the three human genomic sequence assemblies in the database. RESULTS: A large polymorphic region was identified using the selected sequence tags. Four of the 12 haplotypes were shown to contain consecutively undetectable tags spanning in a variable range. Detailed analysis of sequences from the genomic sequence assemblies revealed two large duplicate sequence blocks of 24,696 bp and 24,387 bp, respectively, and an incomplete copy of 961 bp in this region. It contains up to 13 IGHV gene segments depending on haplotypes. A polymorphic region was found to be located within the duplicated blocks. The variants of this polymorphism unusually diverged at the nucleotide sequence level and in IGHV gene segment number, composition and organization, indicating a limited selection pressure in general. However, the divergence level within the gene segments is significantly different from that in the intergenic regions indicating that these regions may have been subject to different selection pressures and that the IGHV gene segments in this region are functionally important. CONCLUSIONS: Non-reciprocal genetic rearrangements associated with large duplicate sequence blocks could substantially contribute to the IGHV region diversity. Since the resulting polymorphisms may affect the number, composition and organization of the gene segments in this region, it may have significant impact on the function of the IGHV gene segment repertoire, antibody diversity, and therefore, the immune system. Because one of the gene segments, 3-30 (1.9III), is associated with autoimmune diseases, it could be of diagnostic significance to learn about the variants in the haplotypes by using the multiplex haplotype analysis system used in the present study with DNA sequence tags specific for the variants of all gene segments in this region.

DNA repair gene polymorphisms at XRCC1, XRCC3, XPD, and OGG1 loci in Maharashtrian population of central India.

Reduction in DNA repair capacity is associated with increased rates of birth defects, cancer, and accelerated ageing. Genetic polymorphisms in DNA repair genes might influence the repair activities of the enzymes predisposing individuals to cancer risk. Owing to the presence of these genetic variants, inter-individual and ethnic differences in DNA repair capacity have been observed in various populations. India harbors enormous genetic, cultural and linguistic diversity. The present study was undertaken to determine the allele and genotype frequencies of four non-synonymous SNPs, XRCC1 Arg399Gln (C>T, rs25487), XRCC3 Thr241Met (G>A, rs861539), XPD Lys751Gln (T>G, rs13181), and OGG1 Ser326Cys (C>G, rs1052133) in the Maharashtrian population, residing in the Vidarbha region of central India and to compare them with HapMap and other Indian populations. The variant alleles of these polymorphisms have been found to be positively associated with different forms of cancer in several genetic epidemiological studies. The basic prevalence of these polymorphisms in the general population must be known to evaluate their significance in risk assessment in cancer and other phenotypes. About 215 healthy and unrelated individuals from the Maharashtrian population were genotyped for each of these four polymorphisms using PCR-RFLP. The allele and genotype frequency distribution at the four DNA repair gene loci among Maharashtrians revealed a characteristic pattern. To the best of our knowledge, this is the first report of these DNA repair gene polymorphisms in a central Indian population.

Genetic polymorphism of CYP2D6∗2 C→T 2850, GSTM1, NQO1 genes and their correlation with biomarkers in manganese miners of Central India.

Manganese (Mn) intoxication is most often regarded as an occupational manifestation and occurs in places such as manganese mines, dry cell battery plants and ceramic industries. In the present study, the influence of genetic polymorphism in cytochrome P450 2D6 (CYP2D6∗2), glutathione S-transferase M1 (GSTM1) and NAD(P)H quinone oxidoreductase 1 (NQO1) genes on blood manganese and plasma prolactin concentrations in manganese miners was investigated. Genotyping of CYP2D6∗2 C→T 2850 and NQO1 C→T 609 was carried out using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) whereas the genotyping of GSTM1 was carried out by multiplex PCR using beta globin as an internal control. Manganese miners with CYP2D6∗2 C→T 2850 variant genotype had relatively low Mn concentration [GM: 21.4±8.9 µg L(-1)] than the subjects with wild (GM: 36.3±8.5 µg L(-1)) and heterozygous (GM: 34.4±6.9 µg L(-1)) genotypes. Miners with CYP2D6∗2 variant genotypes showed low prolactin levels (GM: 13.13±1.6 ng mL(-1)) compared to the wild (GM: 16.4.4±1.5 µg L(-1)) and heterozygous (GM: 18.7±1.6 ng mL(-1)) genotypes. Gene-gene interaction studies also revealed that the subjects with CYP2D6∗2 C→T 2850 variant genotypes had low levels of Mn and prolactin. Our new findings suggest that CYP2D6∗2 C→T 2850 variant genotypes can regulate plasma prolactin levels in manganese miners of Central India and could be involved in the fast metabolism of blood manganese, compared to wild and heterozygous genotypes.

Novel loci interacting epistatically with bone morphogenetic protein receptor 2 cause familial pulmonary arterial hypertension.

BACKGROUND: Familial pulmonary arterial hypertension (FPAH) is a rare, autosomal-dominant, inherited disease with low penetrance. Mutations in the bone morphogenetic protein receptor 2 (BMPR2) have been identified in at least 70% of FPAH patients. However, the lifetime penetrance of these BMPR2 mutations is 10% to 20%, suggesting that genetic and/or environmental modifiers are required for disease expression. Our goal in this study was to identify genetic loci that may influence FPAH expression in BMPR2 mutation carriers. METHODS: We performed a genome-wide linkage scan in 15 FPAH families segregating for BMPR2 mutations. We used a dense single-nucleotide polymorphism (SNP) array and a novel multi-scan linkage procedure that provides increased power and precision for the localization of linked loci. RESULTS: We observed linkage evidence in four regions: 3q22 ([median log of the odds (LOD) = 3.43]), 3p12 (median LOD) = 2.35), 2p22 (median LOD = 2.21), and 13q21 (median LOD = 2.09). When used in conjunction with the non-parametric bootstrap, our approach yields high-resolution to identify candidate gene regions containing putative BMPR2-interacting genes. Imputation of the disease model by LOD-score maximization indicates that the 3q22 locus alone predicts most FPAH cases in BMPR2 mutation carriers, providing strong evidence that BMPR2 and the 3q22 locus interact epistatically. CONCLUSIONS: Our findings suggest that genotypes at loci in the newly identified regions, especially at 3q22, could improve FPAH risk prediction in FPAH families. We also suggest other targets for therapeutic intervention.

Genetic diversity of the human immunoglobulin heavy chain VH region.

The human immunoglobulin heavy chain VH region is one of the most complex regions in the human genome. The high level of diversity of this region has been shown by a number of studies. However, because of the limitations of the conventional experimental methods, it has been difficult to learn the extent of the diversity and the underlying mechanisms. This review describes a number of new genetic approaches developed in the authors' laboratory. By using these approaches, significant progress has been made in assigning different VH sequences to their respective loci, in learning the diversity of gene segment number and composition among the VH haplotypes, and in learning VH gene segment organization in individual haplotypes. Information obtained toward this direction could help in understanding the mechanisms underlying VH region diversity and the biological impact of the VH region diversity.

Direct detection of insertion/deletion polymorphisms in an autosomal region by analyzing high-density markers in individual spermatozoa.

Direct polymerase chain reaction (PCR) detection of insertion/deletion (indel) polymorphisms requires sample homozygosity. For the indel polymorphisms that have the deletion allele with a relatively low frequency in the autosomal regions, direct PCR detection becomes difficult or impossible. The present study is, to our knowledge, the first designed to directly detect indel polymorphisms in a human autosomal region (i.e., the immunoglobulin V(H) region), through use of single haploid sperm cells as subjects. Unique marker sequences (n=32), spaced at approximately 5-kb intervals, were selected near the 3' end of the V(H) region. A two-round multiplex PCR protocol was used to amplify these sequences from single sperm samples from nine unrelated healthy donors. The parental haplotypes of the donors were determined by examining the presence or absence of these markers. Seven clustered markers in 6 of the 18 haplotypes were missing and likely represented a 35-40-kb indel polymorphism. The genotypes of the donors, with respect to this polymorphism, perfectly matched the expectation under Hardy-Weinberg equilibrium. Three V(H) gene segments, of which two are functional, are affected by this polymorphism. According to these results, >10% of individuals in the human population may not have these gene segments in their genome, and approximately 44% may have only one copy of these gene segments. The biological impact of this polymorphism would be very interesting to study. The approach used in the present study could be applied to understand the physical structure and diversity of all other autosomal regions.