LRP-associated protein gene (LRPAP1) and susceptibility to degenerative dementia

Difference in genetic makeup of lipid metabolizing proteins may increase susceptibility to dementia. The aim of this study was to investigate variations in two lipid metabolizing genes, low-density lipoprotein receptor-related protein-associated protein gene (LRPAP) and apolipoprotein E (APOE), in vascular and degenerative dementias. This hospital-based association study included 147 patients with dementia and 163 age-matched controls. Genotyping for LRPAP1 intron 5 insertion/deletion and APOEHhaI polymorphism was carried out by polymerase chain reaction (PCR)/PCR-restriction fragment length polymorphism method. The frequency of DD genotype and *D allele of LRPAP gene was high in degenerative dementias compared with controls (76.6% vs. 44.8% and 86.4% vs. 69.3%, respectively) suggesting increased susceptibility [P < 0.0001, odds ratio (OR) =3.76 for DD genotype and P < 0.0001, OR = 2.80 for D allele]. Vascular dementia patients showed statistically insignificant but increasing trend for allele I (40.0% vs. 30.7%). We also observed significant association of APOEepsilon4 allele with degenerative dementias (P < 0.0001, OR =5.35). Our study suggests that LRPAP1-D and APOE E4 alleles significantly increase the susceptibility to degenerative dementias.

Myotilin dynamics in cardiac and skeletal muscle cells

Myotilin cDNA has been cloned for the first time from chicken muscles and sequenced. Ectopically expressed chicken and human YFP-myotilin fusion proteins localized in avian muscle cells in the Z-bodies of premyofibrils and the Z-bands of mature myofibrils. Fluorescence recovery after photobleaching experiments demonstrated that chicken and human myotilin were equally dynamic with 100% mobile fraction in premyofibrils and Z-bands of mature myofibrils. Seven myotilin mutants cDNAs (S55F, S55I, T57I, S60C, S60F, S95I, R405K) with known muscular dystrophy association localized in mature myofibrils in the same way as normal myotilin without affecting the formation and maintenance of myofibrils. N- and C-terminal halves of human myotilin were cloned and expressed as YFP fusions in myotubes and cardiomyocytes. N-terminal myotilin (aa 1-250) localized weakly in Z-bands with a high level of unincorporated protein and no adverse effect on myofibril structure. C-terminal myotilin (aa 251-498) localized in Z-bands and in aggregates. Formation of aggregated C-terminal myotilin was accompanied by the loss of Z-band localization of C-terminal myotilin and partial or complete loss of alpha-actinin from the Z-bands. In regions of myotubes with high concentrations of myotilin aggregates there were no alpha-actinin positive Z-bands or organized F-actin. The dynamics of the C-terminal-myotilin and N-terminal myotilin fragments differed significantly from each other and from full-length myotilin. In contrast, no significant changes in dynamics were detected after expression in myotubes of myotilin mutants with single amino acid changes known to be associated with myopathies.

Association of functionally important polymorphism of microsomal epoxide hydrolase gene (EPHX1) with lung cancer susceptibility

Distribution and gene-environment interaction of EPHX1 polymorphism was evaluated in 175 lung cancer patients and 322 controls from north India. Two novel non-synonymous, Lys117Arg and Leu263Phe, and twelve single nucleotide polymorphisms were identified in the present study. Binary logistic regression analysis showed association of polymorphism Tyr113His with increased risk of lung cancer (OR = 2.2, 95% CI = 1.2-4.0, p < .05). Gene-environment interaction revealed that patients with His113His and smoking habit had significantly greater risk of lung cancer (OR = 4.52, 95% CI = 0.93-43.05, p < .05). Present study provided evidence that EPHX1 polymorphism is associated with lung cancer susceptibility in Indian population.

Complement receptor 1 (A3650G RsaI and intron 27 HindIII) polymorphisms and risk of gallbladder cancer in north Indian population

Decreased expression due to genetic variations in complement receptor 1 (CR1) on erythrocytes might result in reduced clearance of immune complexes, conferring interindividual variation for gallbladder cancer (GBC) susceptibility. We studied role of CR1 (A(3650)G RsaI and Intron 27 HindIII) polymorphisms in gallstone disease and GBC in north Indian population. Study included 185 GBC patients, 185 gallstone patients and 200 controls. Genotyping was done by PCR-RFLP. Result showed GG genotype and G allele of CR1 A(3650)G RsaI were conferring significant risk for GBC [(P = 0.022; OR = 1.94; 95% CI = 1.1-3.4) and (P = 0.035; OR = 1.35; 95% CI = 1.0-3.8) respectively]. Also, comparison of GBC patients with gallstone patients showed increased risk for GBC in presence of GG genotype and G allele GBC (P = 0.048; OR = 1.74; 95% CI = 1.0-3.0) and (P = 0.027; OR = 1.39; 95% CI = 1.0-1.8) respectively. No association of CR1 A(3650)G RsaI polymorphism was observed when gallstone patients were compared with controls. CR1 Intron 27 HindIII polymorphism was not associated with GBC and gallstone susceptibility. Haplotype analysis showed increased risk of GBC in presence of G,L haplotype (P = 0.046; OR = 1.35: 95% CI = 1.0-1.8). Subgroup stratifications on basis of gender and gallstone status showed GG genotype of CR1 A(3650)G RsaI polymorphism imparted high risk for GBC in females (P = 0.043; OR = 1.99: 95% CI = 1.4-3.9). Also there was increased risk for GBC in presence as well as absence of gallstones (OR = 1.85 and 1.76 respectively), but it was not statistically significant. We conclude that CR1 A(3650)G RsaI polymorphism plays an important role in conferring genetic susceptibility to gallbladder cancer GBC in north Indian population.

Genetics of biliary lithiasis from an ethnic perspective

Gallstone disease represents one of the most common gastroenterological disorders worldwide. Gallstones affect over 15% of adults in Europe and 25-30% of Hispanic populations in Central and South America. The heritability of gallstones varies considerably according to ethnicity, with Native Americans and Hispanics with Amerindian admixture being the most susceptible populations. Genetic factors have been shown to account for 25-30% of total gallstone risk in Europe, however, in Hispanic populations, this risk percentage may increase to 45-65%. Recent genome-wide association and candidate gene studies have identified common polymorphisms in enterohepatic transporters (ABCG5/8, SLC10A2) and the Gilbert syndrome UGT1A1 variant as genetic determinants of gallstone formation. Together, these polymorphisms cover a significant proportion of the previously predicted genetic background of gallstones in European populations. New lithogenic genes need to be discovered in future studies in high-risk populations. In this review, we address the latest developments in the genetic analysis of gallstones and discuss the ethnic background of this condition in European, Central and South American and Asian populations.

Multidrug resistance protein-1 expression, function and polymorphisms in patients with rheumatoid arthritis not responding to methotrexate

OBJECTIVE

To study the expression, function and polymorphism of MDR-1 protein on the peripheral blood lymphocytes in patients with RA following treatment with MTX and its relationship with response to therapy.

METHODS

RA patients naïve to MTX/DMARD- and glucocorticoid were enrolled. Expression and function of MDR-1 was carried out by flow cytometry at baseline and after 4 months of therapy. MDR-1 expression was measured by relative fluorescence intensities and percentage of positive cells. MDR-1 function was assessed by Rhodamine efflux in presence or absence of verapamil. Patients with reduction in disease activity score 28 ≥1.2 were defined as responders and <1.2 as non-responders. Three single nucleotide polymorphisms in MDR-1 gene, 3435T, 1236T and 2677T/A were studied.

RESULTS

Fifty-two patients of RA were grouped into responders (n = 41), and non-responders (n = 11) as per the defined criteria. There was no difference between the groups in terms of age, sex ratio or duration of illness, MTX dose and follow-up duration. The expression and function of the MDR-1 protein reduced significantly in the responder group after the treatment with MTX when compared to the baseline evaluation. The decrease was significant when compared to the non-responders at the fourth month. MDR-1 expression and function either increased or remained the same in the non-responder group after treatment with MTX. MTX unresponsiveness was not related to any of the three polymorphisms studied.

CONCLUSION

Persistent expression and function of MDR-1 identifies a subset of RA patients not responding to MTX. Its early recognition may help in appropriately modulating therapy.

Association of cholesteryl ester transfer protein (TaqIB) and apolipoprotein E (HhaI) gene variants with obesity

Background The pathophysiology of obesity is known to be influenced by alterations in lipid levels. We aimed to evaluate association of cholesteryl ester transfer protein (CETP) and apolipoprotein (APO) E gene variants with asymptomatic obesity. Methods A total of 437 subjects, 159 asymptomatic obese (BMI = 29.29 +/- 3.76) and 278 non-obese (BMI = 23.38 +/- 1.71) individuals, were included in this case-control study. Lipid levels were estimated using standard protocols. Analysis of CETP (TaqIB) and APOE (HhaI) gene polymorphisms was done using PCR-RFLP. Results We found significant difference in blood pressure (systolic, P < 0.0001 and diastolic, P < 0.0001), total cholesterol (P < 0.0001), LDL-cholesterol (P < 0.0001), and HDL-cholesterol (P < 0.0001) in obese as compared to non-obese group. Homozygous APO E4E4 genotype was only observed in 5.7% of obese individuals and none in non-obese group. APO E4 allele carriers were also susceptible for obesity (P = 0.016, OR = 1.73; 95% CI = 1.12-2.68) than non-carriers. Higher blood pressure (Systolic, P = 0.001 and Diastolic, P = 0.004) and triglyceride levels (P = 0.029) were observed in obese subjects with APO E4 allele than individuals without APO E4. However, CETP B1 variant allele carriers did not show alteration in blood pressure and lipid profile in asymptomatic obese subjects. Conclusions APO E4 genotype and allele were found to be associated with asymptomatic obesity, whereas CETP Taq1B polymorphism showed no such association in North Indian subjects.

Role of p53 and p73 genes polymorphisms in susceptibility to esophageal cancer: a case control study in a northern Indian population

Genetic variants in p53 and in its homologue p73 may modulate Esophageal Cancer (EC) risk because they are supposed to influence cell cycle progression, apoptosis and DNA repair. Therefore, we aimed to evaluate the association of p53 intron3 16 bp duplication and p73 G4C14-to-A4T14 polymorphisms with susceptibility to EC in a northern Indian population in 255 EC patients and 255 age and sex matched healthy controls. We found that p53 intron3 16 bp duplication polymorphism was not associated with EC and its clinical characteristics. However, p73 G4C14-to-A4T14 polymorphism was associated with significant higher risk of EC (OR = 1.74, 95% CI = 1.16-2.60, P = 0.007) in an allele dose-dependent manner (P(trend) = 0.0047). Stratification of subjects on the basis of clinical characteristics showed that p73 AT genotype carriers were at significant increased risk of developing esophageal squamous cell carcinoma (OR = 1.78, 95% CI = 1.18-2.67, P = 0.006) at middle third tumor location (OR = 1.87, 95% CI = 1.18-2.97, P = 0.007) with lymph node metastasis (OR = 1.77, 95% CI = 1.04-3.02, P = 0.035). No interaction with environmental risk factors was observed with any of the studied polymorphisms. In summary, p73 G4C14-to-A4T14 polymorphism but not the p53 intron3 16 bp duplication polymorphism is associated with EC and its clinical characteristics in northern Indian population.

Association of lipoprotein receptor, receptor-associated protein, and metabolizing enzyme gene polymorphisms with gallstone disease: A case-control study

INTRODUCTION

To identify high risk alleles for gallstone disease, we analyzed association of LDLRAvaII, LRPAP1 insertion/deletion, CETPTaqI B, and LPLHindIII polymorphisms with gallstone disease.

METHODS

In DNA samples of 214 gallstone patients and 322 age and sex matched controls, specific region containing polymorphisms was PCR amplified and digested with restriction enzymes except for LRPAP1 insertion/deletion polymorphism.

RESULTS

LRPAP1 gene insertion/deletion polymorphism was found to be significantly associated with gallstone disease. Genotype II was conferring significant risk for gallstone disease in females only (P=0.019; OR 2.577, 95% CI 1.144-5.806). LDLRAvaII, CETPTaqI B, and LPLHindIII polymorphisms were not found to be associated with gallstone disease either at genotype or allele level.

CONCLUSIONS

LRPAP1, II genotype carrier females may have increased risk for gallstone disease. On the other hand, LDLR AvaII, CETP TaqI B, and LPL HindIII polymorphisms may not be associated with gallstone disease.

Y chromosome micro-deletions in idiopathic infertility from Northern India

Azoospermia factor locus (AZF) is assumed to contain the genes responsible for spermatogenesis. Deletions in these genes are thought to be pathologically involved in some cases of male infertility associated with azoospermia or oligozoospermia. An attempt was made to establish the prevalence of micro-deletions on the Y chromosome in 79 infertile North Indians with azoospermia and oligozoospermia. Detail clinical examinations as well as endocrinological parameters were also done. Polymerase chain reaction (PCR) micro-deletion analysis was done in 79 infertile men. For this, genomic DNA was extracted from the peripheral blood. Seven sets of primers were used encompassing AZFa, AZFb and AZFc regions. Micro-deletions in five of the 79 cases (6.3%) showed deletions of at least one of the STS markers. Deletions were detected with known and unknown aetiology and at least in one of the infertile male with varicocele. AZF micro-deletions seen in idiopathic infertile males suggest the need for molecular screening in non-idiopathic cases.

PLCE1 rs2274223 A>G polymorphism and cancer risk: a meta-analysis

Phospholipase C epsilon 1 gene (PLCE1) encodes a phospholipase enzyme which regulates various physiological processes (cell growth, differentiation, and apoptosis) and is supposed to play a critical role in carcinogenesis. Recently, a single nucleotide polymorphism (rs2274223 A>G) in PLCE1 was reported as a novel susceptibility locus for esophageal and gastric cancers by genome-wide association studies performed in Chinese population. However, individual association studies replicating this finding showed inconclusive results. Therefore, we performed a meta-analysis of eligible studies to derive precise estimation of the association of PLCE1 rs2274223 A>G polymorphism with cancer risk. We performed pooled analysis of 12 case–control studies including 7,622 cases and 9,555 controls. Odds ratios and 95 % confidence interval were calculated to assess strength of association in overall studies and in subgroup analysis stratified by ethnicity, cancer types, and source of controls. All statistical analyses were performed by MIX 2.0 software. We found that PLCE1 rs2274223 A>G polymorphism was significantly associated with increased risk of cancer in log additive/dominant model and at allele level (GG vs. AA: OR = 1.24, 95 % CI = 1.01–1.53, P = 0.039; AG vs. AA: OR = 1.24, 95 % CI = 1.16–1.32, P < 0.001; AG + GG vs. AA: OR = 1.22, 95 % CI = 1.12–1.34, P < 0.001; and G vs. A allele: OR = 1.15, 95 % CI = 1.05–1.25, P = 0.002). Further, stratified analysis showed elevated risk of only gastric and esophageal tumors. Sub-group analysis based on ethnicity suggests PLCE1 polymorphism conferred significant risk among Asian (Chinese) but not in Caucasian. In conclusion, PLCE1 rs2274223 polymorphism may be used as potential biomarker for cancer susceptibility particularly for esophageal/gastric cancer and for the Chinese population.

CYP7A1 (-204 A>C; rs3808607 and -469 T>C; rs3824260) promoter polymorphisms and risk of gallbladder cancer in North Indian population

Cholesterol 7-alpha hydroxylase (CYP7A1), which is a rate-limiting enzyme for cholesterol catabolism and bile acid synthesis, may affect cholesterol homeostasis and result in gallstone formation that is a major risk factor for gallbladder cancer (GBC) pathogenesis. Genetic variations in CYP7A1 may influence its expression and thus may affect the risk of gallstone disease and GBC. We aimed to study the association of 2 promoter polymorphisms of CYP7A1 (-204 A>C [rs3808607] and -469 T>C [rs3824260]) in gallstone and GBC susceptibility in North Indian population. The study included 185 GBC patients, 195 symptomatic gallstone patients, and 200 healthy controls. Genotyping for both polymorphisms was done by polymerase chain reaction-restriction fragment length polymorphism method. Although the CC genotype of CYP7A1 -204 A>C was not significantly associated with gallstone disease (P = .083, odds ratio [OR] = 1.69, 95% confidence interval [CI] = 0.9-3.0), it was conferring higher risk for GBC (P = .018, OR = 2.05, 95% CI = 1.1-3.7). However, CYP7A1 -469 T>C was not associated with gallstone disease and GBC risk in our population. After subgroup stratifications on the basis of sex and gallstone status, CC genotype and variant allele of CYP7A1 -204 A>C imparted higher risk for GBC in women (P = .003, OR = 3.30, 95% CI = 1.5-7.2) and patients without gallstones (P = .045, OR = 1.91, 95% CI = 1.2-3.6). Haplotype analysis of the 2 polymorphisms showed that C,T (P = .045, OR = 1.84, 95% CI = 1.0-3.3) and C,C (P = .0001, OR = 3.10, 95% CI = 1.6-6.0) haplotypes had elevated risk of GBC predisposition. CYP7A1 -469 T>C is not associated with gallstone disease or GBC risk. Although CYP7A1 -204 A>C might play a modest role in gallstone susceptibility, it is an independent risk factor for GBC in North Indian population. Underlying mechanism for GBC susceptibility by CYP7A1 (-204 A>C and -469 T>C) haplotype appears to be independent of gallstone pathway and is believed to involve genotoxicity resulting from subnormal bile acid production.

Association of TP53 intron 3, 16 bp duplication polymorphism with esophageal and gastric cancer susceptibility in Kashmir Valley

TP53 is one of the major tumor suppressor genes, which is essential for the preservation of genome integrity. Different polymorphic variants of the p53 gene have been demonstrated for their association with several human malignancies. Of these, 16 base pair (bp) duplication in intron 3 of the TP53 gene (PIN3 Ins16bp, rs17878362) is the most extensively studied variant. However, no studies have, so far, investigated the association of this polymorphism with esophageal and gastric cancers. Thus, we aimed to investigate the association of PIN3 Ins16bp polymorphism with esophageal cancer (EC) and gastric cancer (GC) in Kashmir Valley, a northern part of India, where incidence of these cancers is very high. In addition, we also tested other covariates such as smoking/tea consumption as potential confounding factors. We analyzed DNA samples from a total of 243 patients (135 EC and 108 GC patients) and 195 healthy controls for PIN3 Ins16bp polymorphisms using PCR. Data were statistically analyzed using chi-square test and logistic regression models. Results showed that carriers for the PIN3 Ins16bp allele (A2) were associated with increased risk for both EC (OR = 2.31, 95% CI = 1.08-4.97, p = 0.03) and GC (OR = 2.91, 95% CI = 1.28-6.63, p = 0.01). Also, in a recessive model, our results showed that PIN3 Ins16bp A2A2 allele was conferring significant high risk for both EC (OR = 2.18, 95% CI = 1.03-4.59, p = 0.04) and GC (OR = 2.87, 95% CI = 1.29-6.42, p = 0.010). Although smoking (Hukka) and high consumption of salted tea are significant risk factors for both EC and GC, interaction of PIN3 Ins16bp genotypes with these factors did not further modulate the risk of EC and GC. Determination of PIN3 A2A2 genotype may provide a useful genetic marker in predicating high-risk individuals for the development of EC and GC and an early diagnosis.

Transforming growth factor-B1 and matrix metalloproteinase-7 promoter variants induce risk for Helicobacter pylori-associated gastric precancerous lesions

The expression of growth factors, proteolytic enzymes, fibrogenic factors, and cytokines is altered in the Helicobacter pylori-infected gastric mucosa. Therefore, we aimed to evaluate the association of functional promoter variants of transforming growth factor (TGF)-B1 and matrix metalloproteinase (MMP)-7 genes with gastritis and gastric precancerous lesions. After upper gastrointestinal endoscopy, a total of 130 rapid urease test-positive patients with nonulcer dyspepsia were examined for H. pylori infection using modified Giemsa stain and IgG anti-CagA ELISA. All patients and 200 asymptomatic controls were genotyped for TGF-B1 (-509 C>T) and MMP-7 (-181 A>G) substitutions using PCR-RFLP. The genotype and allele frequencies of TGF-B1 and MMP-7 polymorphisms did not differ between patients and controls (p > 0.05). However, the CagA-positive patients with TGF-B1 -509 T allele had higher risk for gastric atrophy (p = 0.026, odds ratio [OR] = 2.38) and lymphoid follicle development (p = 0.028, OR = 2.29). In addition, CagA-positive patients carrying MMP-7 -181 G allele had risk for lymphoid follicle formation (p = 0.027, OR = 2.30). Thus, the present study revealed significant association of functional MMP-7 and TGF-B1 gene variants toward susceptibility to H. pylori-induced precancerous gastric lesions.

Evaluation of MC4R [rs17782313, rs17700633], AGRP [rs3412352] and POMC [rs1042571] Polymorphisms with Obesity in Northern India

OBJECTIVE

Genetic variants of the melanocortin-4 receptor gene (MC4R), agouti related protein (AGRP) and proopiomelanocortin (POMC) are reported to be associated with obesity. Therefore, the aim of this study is to examine MC4R rs17782313, MC4R rs17700633, AGRP rs3412352 and POMCrs1042571 for any association with obesity in North Indian subjects.

METHODS

The variants were investigated for association in 300 individuals with BMI ≥30 kg/m(2) and 300 healthy non-obese individuals BMI <30 kg/m(2.) The genotyping were analyzed by Taqman probes. The statistical analysis was performed by the SPSS software, ver.19 and p≤0.05 was considered statistically significant.

RESULTS

The genotypes of MC4R rs17782313 and POMC rs1042571 were significantly associated with obesity (C), (p=0.02; OR=1.7 and p=0.01; OR=1.6, respectively); however, MC4Rrs17700633 (p=0.001; OR=0.55) was associated with low risk. In addition, AGRPrs3412352 (p=0.93; OR=0.96) showed no association with obesity (BMI ≥30 kg/m(2)) in North Indian subjects.

CONCLUSION

This study provides the report about the significant association of MC4R (rs17782313) and POMC (rs1042571) with morbid obesity (BMI ≥30 kg/m(2)), but MC4R (rs17700633) and AGRP (rs34123523) did not show any association with obesity in the studied North Indian population.

Molecular screening of FRAXA and FRAXE in Indian patients with unexplained mental retardation

Fragile-X mental retardation is the commonest form of inherited mental retardation. We have studied 146 Indian patients (174 X chromosomes) with unexplained mental retardation by molecular methods. All study subjects were unrelated. Three of the 118 males were found to have the FMR1 full mutation. None of the patients tested were positive for the FMR2 full mutation. The Fragile X prevalence was 2.5% among males, which is lower than previously reported in Indian mentally retarded patients. Screening for Fragile X among patients with nonspecific mental retardation is important, even if there is no family history of mental retardation or typical behavioral or physical features associated with the Fragile-X phenotype. Identification of positive cases is also very important for the families, because of the high recurrence risk of the disease. Large multicenter screening programs with uniform criteria would be worthwhile to determine the prevalence of Fragile-X mental retardation in the Indian population.

Evaluation of miR-27a, miR-181a, and miR-570 genetic variants with gallbladder cancer susceptibility and treatment outcome in a North Indian population

INTRODUCTION

miR-27a, miR-181a, and miR-570 genetic variants have been found to play an important role in many cancers, but their contribution in gallbladder carcinoma (GBC) has not been explored. Therefore, we investigated the role of these micro RNA (miRNA) genetic variants in terms of GBC susceptibility, therapeutic response, toxicities associated with chemo-radiotherapy and survival outcome.

METHODS

This study included 606 GBC patients and 200 healthy controls. From among the larger study cohort, 219 patients receiving adjuvant or palliative chemo-radiotherapy as per disease status were followed up for toxicity profile. Treatment response was recorded in 159 patients who received palliative chemo-radiotherapy. Genotypes were determined using allelic discrimination assay. Statistical analysis was carried out with SPSS version 16. Generalized multifactor dimensionality reduction (GMDR) analysis was performed for gene-gene interactions. Survival analysis was performed using Kaplan-Meier and Cox regression tests.

RESULTS

In univariate logistic regression analysis, no association with any of the studied polymorphisms was found in overall GBC susceptibility. Furthermore, univariate and multivariate analyses revealed no significant association with response to chemo-radiotherapy. In GMDR analysis, miR-27ars895819, miR-570rs4143815, and miR-181ars12537 combination was found as the best gene-gene interaction model for susceptibility and treatment response. Furthermore, miR-27ars895819miR-181ars12537 was associated with neutropenia toxicity in patients undergoing chemo-radiotherapy. However, miRNA variants had no influence over the survival outcomes of GBC patients (locally advanced, metastatic).

CONCLUSION

In conclusion, the miRNA variants cumulatively influence GBC susceptibility and treatment outcomes.

Association of liver X receptors (LXRs) genetic variants to gallbladder cancer susceptibility

Liver X receptors (LXRs) α and β are ligand-activated transcription factors belonging to the family of nuclear receptors. LXRs play role in control of lipid homeostasis, glucose metabolism, inflammation, and proliferation. LXRs are expressed in gallbladder cholangiocytes and recent studies have shown that LXR-β (-/-) Mice exhibit an estrogen-dependent gallbladder carcinogenesis. However, there are no studies reported in humans. Therefore, using case-control design in the present study, we have evaluated the associations of LXR-α (rs7120118) and LXR-β (rs35463555 and rs2695121) genetic variants with gallbladder cancer (GBC) susceptibility in 400 cases and 200 controls. Genotypes were determined by TaqMan probes. Statistical analysis was done by SPSS and SNPstats. In silico analysis was performed using Bioinformatics tools (F-SNP, FAST-SNP). LXR-β genotypes (rs35463555) [GA + AA] and (rs2695121) [TC + CC] were associated with risk of GBC [OR = 1.46, p = 0.03; OR = 1.52, p = 0.01, respectively] as compared to healthy controls whereas LXR-α (rs7120118) was not associated with GBC risk. LXR-β haplotype [Ars35463555-Crs2695121] showed statistical significant association with GBC [OR = 5.0, p = 0.03]. On stratification based on gender, LXR-β [GA + AA] and [TC + CC] genotypes were found to be significantly associated in females GBC patients [OR = 1.5, p = 0.04; OR = 1.7, p = 0.005, respectively]. The LXR-β [TC + CC] associated with GBC patients with gallstones [OR; 1.8, p = 0.002]. The genetic risk by LXR-β was not modulated by tobacco consumption or age of onset. In silico analysis using FAST-SNP showed "Low-medium risk" by LXR-β (rs2695121) T > C variation. Our results suggest that LXR-β polymorphisms influence gallbladder cancer susceptibility through estrogen and gallstone-dependent pathways.

Potential influence of interleukin-1 haplotype IL-1 beta-511*T-IL-1RN*1 in conferring low risk to middle third location of esophageal cancer: a case-control study

Interleukin (IL)-1 gene polymorphisms affect several inflammatory diseases, including cancer. Therefore, we studied genetic association of biallelic (-511C>T) polymorphism of IL-1 beta and 86-bp VNTR polymorphism of IL-1RN in 159 patients with esophageal cancer (EC) and 194 age- and gender-matched healthy controls. Genetic analysis for IL-1 polymorphisms was performed by polymerase chain reaction-restriction fragment length polymorphism. The frequencies of IL-1 beta (-511C>T) and IL-1RN (variable number tandem repeat) genotypes, alleles, and haplotypes did not differ significantly between patients and controls. However, IL-1 beta -511TT genotype and T1+ haplotype combination illustrated low risk for disease at the middle third location of the tumor (odds ratio [OR] = 0.27; 95% confidence interval [CI] = 0.11-0.62; p = 0.002; OR = 0.462; 95% CI = 0.253-0.845, p = 0.01). In conclusion, subjects with IL-1 beta -511TT genotype or IL-1 beta*T-IL-1RN*1 (T1) haplotype had lower risk for middle third tumor location of EC in a northern Indian population.

Association of APOE-C1 gene cluster polymorphisms with gallstone disease

BACKGROUND

Genetic polymorphisms in apolipoprotein genes may be associated with alteration in lipid profile and susceptibility to gallstone disease.

AIM

To find out the association of APOE HhaI and APOC1 HpaI polymorphisms with gallstone disease.

SUBJECTS

HhaI polymorphism of APOE and HpaI polymorphism of APOC1 were analysed in DNA samples of 214 gallstone patients and 322 age- and sex-matched healthy controls.

METHODS

For genotyping DNA samples of all study subjects were amplified using polymerase chain reaction, followed by restriction digestion. All statistical analyses were done using SPSS v11.5 and ARLEQUIN v2.0 softwares.

RESULT

APOC1 HpaI polymorphism was found to be significantly associated with gallstone disease. Frequency of H2H2 was significantly higher (P = 0.017) in patients than in controls and it was imposing very high risk (OR 9.416, 95% CI 1.125-78.786) for gallstone disease. When data were stratified in male and female, H2H2 was associated (P = 0.011) with disease in females only. Analysis at allele level revealed no association. APOE HhaI polymorphism and APOE-C1 haplotypes showed no association with gallstone disease.

CONCLUSION

APOC1 HpaI polymorphism is associated with gallstone disease and shows gender-specific differences. APOE HhaI polymorphism may not be associated with gallstone disease.

Association of interleukin-6 -174G>C promoter polymorphism with risk of cervical cancer

BACKGROUND

The etiology of cervical cancer is associated with excessive-inflammation-mediated tumorigenesis. Interleukin-6 (IL-6), a multifunctional cytokine, regulates inflammation and various physiological processes. We therefore aimed to evaluate the association of the IL-6 -174G>C polymorphism with predisposition to cervical cancer.

MATERIALS AND METHODS

The present case-control study comprised 160 histopathologically confirmed cases of cervical cancer and 200 healthy controls. Polymorphism for the IL-6 gene was genotyped by amplification refractory mutation system (ARMS) polymerase chain reaction (PCR).

RESULTS

We observed a significant association of the IL-6 -174CC genotype with risk of cervical cancer (OR=3.16; p=0.014). An increased risk of developing stage I tumors was found in individuals with a heterozygous (GC) genotype (OR=3.63, p=0.003). In a case-only analysis, the risk was further increased in patients consuming tobacco products (OR=3.14; p=0.033).

CONCLUSION

The CC genotype in the IL-6 promoter region may confer a high risk of cervical cancer, which is further modulated in patients who are tobacco users.

Role of genetic variants of deleted in colorectal carcinoma (DCC) polymorphisms and esophageal and gastric cancers risk in Kashmir Valley and meta-analysis

Genetic alterations in the deleted in colorectal carcinoma (DCC) gene have been a priori reported to associate with metastasis in variety of human cancers. We investigated the association between potentially functional SNPs in DCC and susceptibility to esophageal (EC) and gastric (GC) cancers in Kashmir Valley. We genotyped two SNPs DCC rs714 (A>G) and DCC rs2229080 (C>G) of DCC in 135 EC patients, 108 GC patients, and 195 controls matched by age and sex in Kashmir Valley by polymerase chain reaction-RFLP method. Risk for developing EC and GC was estimated by binary logistic regression by using SPSS. We also performed a meta-analysis on DCC rs714 (A>G) and evaluated the association between the DCC rs714 (A>G) polymorphisms and cancer risk. A significant difference in DCC rs714 (A>G) genotype distribution between EC and GC cases and corresponding control groups was observed (odds ratio (OR) = 1.92; P = 0.03; P-trend = 0.04; false discovery rate (FDR) Pcorr = 0.03: OR = 2.15; P = 0.02; P-trend = 0.01; FDR Pcorr = 0.03). But no such association was observed in DCC rs2229080 (C>G). Further, DCC rs714 (A>G) AA genotype showed significantly increased risk for both gastric squamous cell carcinoma (OR = 5.63; P = 0.02; FDR Pcorr = 0.01) and gastric adenocarcinoma (OR = 2.15; P = 0.02; FDR Pcorr = 0.01). Smoking and salted tea are independently associated with both EC and GC, but gene-environment interaction did not further modulate the risk. Meta-analysis also suggested both independent and overall association of DCC rs714 (A>G) polymorphism with cancer (P = 0.000). In conclusion, genetic variations in DCC rs714 (A>G) modulate risk of EC and GC in high-risk Kashmir population.

Association of resistin with metabolic syndrome in Indian subjects

BACKGROUND

The role of resistin in insulin sensitivity and metabolic syndrome has been controversial until now. Increased plasma/serum resistin levels are associated with metabolic syndrome and insulin resistance. The aim of this study was to investigate the relationship between serum resistin levels with markers of metabolic syndrome in males.

METHODS

A total of 386 male volunteers were enrolled in a case-control study. All of the enrolled volunteers were analyzed to confirm metabolic syndrome following the guidelines of National Cholesterol Education Program Adult Treatment Panel III (NCEP ATP III) of 2001. Of the 386 volunteers, 192 were categorized as cases of metabolic syndrome, whereas 194 were registered as controls without metabolic syndrome. Volunteers enrolled in the study were analyzed for anthropometrical parameters, lipid profile status, insulin, insulin resistance, and resistin.

RESULTS

Higher levels of resistin were observed in cases when compared to controls (12.49 ± 4.73 ng/mL vs. 6.99 ± 1.98 ng/mL). Resistin was positively and significantly associated with serum triglyceride, cholesterol, and very-low-density lipoprotein, whereas it was negatively and significantly associated with serum high-density lipoprotein (HDL) levels. Multiple regression analysis of the data observed indicated that the triglyceride level was the major determinant for the development of metabolic syndrome in male samples.

CONCLUSION

This study demonstrates a positive correlation between resistin and factors of metabolic syndrome, except for HDL cholesterol (HDL-C), which was found to be negatively correlated in Indian male subjects. The study also found resistin to be a suitable peripheral blood marker.

Association of potentially functional genetic variants of PLCE1 with gallbladder cancer susceptibility in north Indian population

BACKGROUND AND OBJECTIVES

Phospholipase C epsilon 1 (PLCE1) plays crucial roles in carcinogenesis and progression of esophageal and gastric cancers. In the present study, we investigated association of GWAS identified rs2274223 A>G and. rs7922612 T>C polymorphism of PLCE1 with susceptibility to gallbladder cancer (GBC).

METHODS

The study involved genotyping of selected PLCE1 variants in 416 GBC cases and 225 controls. Haplotype analysis was done by SNPStats. In silico analyses were performed using bioinformatic tools.

RESULTS

PLCE1 rs2274223 [AG] and rs7922612 [CC] genotypes were found to be significantly associated with an increased risk of GBC [OR = 1.9, p = 0.002; OR = 2.0, p = 0.04, respectively]. PLCE1 haplotype [Grs2274223-Crs7922612] also showed significant association with GBC [OR = 1.8, p = 0.04]. The association was significant in females and GBC patients with stones and female GBC patients with gallstones [OR = 2.6, p = 0.01; OR = 3.3, p = 0.007], respectively. However, no significant associations with other risk factors such as tobacco usage and age of onset were found. Functional prediction of rs2274223 A>G suggested change in protein coding and splicing regulation.

CONCLUSION

The present study found a significant association of PLCE1 rs2274223 and rs7922612 polymorphisms with susceptibility to GBC probably through gallstone-mediated inflammatory pathway.

A multigenic approach to evaluate genetic variants of PLCE1, LXRs, MMPs, TIMP, and CYP genes in gallbladder cancer predisposition

Gallbladder cancer (GBC) is a violent neoplasm associated with late diagnosis, unsatisfactory treatment, and poor prognosis. The disease shows complex interplay between multiple genetic variants. We analyzed 15 polymorphisms in nine genes involved in various pathways to find out combinations of genetic variants contributing to GBC risk. The genes included in the study were matrix metalloproteinases (MMP-2, MMP-7, and MMP-9), tissue inhibitor of metalloproteinases (TIMP-2), cytochrome P450 (CYP)1A1, CYP1B1, phospholipase C epsilon 1 (PLCE1), liver X receptor (LXR)-alpha, and LXR-beta. Genotypes were determined by PCR-RFLP and TaqMan probes. Statistical analysis was done by SPSS version 16. Multilocus analysis was performed by Classification and Regression Tree (CART) analysis and multifactor dimensionality reduction (MDR) to gene-gene interactions in modifying GBC risk. In silico analysis was done using various bioinformatics tools (F-SNP, FAST-SNP). Single locus analysis showed association of MMP-2 (-735 C > T, -1306 C > T), MMP-7 - 181 A > G, MMP-9 (P574R, R668Q), TIMP-2 - 418 G > C, CYP1A1-MspI, CYP1A1-Ile462Val, PLCE1 (rs2274223 A > G, rs7922612 T > C) and LXR-beta T > C (rs3546355 G > A, rs2695121 T > C) polymorphisms with GBC risk (p < 0.05) whereas CYP1B1 and LXR-α variants were not associated with GBC risk. Multidimensional reduction analysis revealed LXR-β (rs3546355 G > A, rs2695121 T > C), MMP-2 (-1306 C > T), MMP-9 (R668Q), and PLCE1 rs2274223 A > G to be key players in GBC causation (p < 0.001, CVC = 7/10). The results were further supported by independent CART analysis (p < 0.001). In silico analysis of associated variants suggested change in splicing or transcriptional regulation. Interactome and STRING analysis showed network of associated genes. The study found PLCE1 and LXR-β network interactions as important contributory factors for genetic predisposition in gallbladder cancer.