Functional dyspepsia is associated with GNβ3 C825T and CCK-AR T/C polymorphism

BACKGROUND

A polymorphism (C825T) in G-protein β polypeptide-3 (GNβ3) gene alters intracellular signal transduction, which may cause motor or sensory abnormalities in the gastrointestinal tract. Cholecystokinin-A receptor (CCK-AR) gene T/C polymorphism is associated with a defective splicing of the primary transcript of CCK-AR mRNA, which may modulate satiety signal and delay gastric emptying. Therefore, we evaluated the role of these polymorphisms in patients with functional dyspepsia (FD) as compared with healthy controls (HC).

PATIENTS AND METHODS

A total of 237 consecutive patients with FD (Rome III) and 250 HC were genotyped for GNβ3 C825T and CCK-AR T/C polymorphisms (PCR-RFLP).

RESULTS

Patients with FD [173 (73%) men, age: 38 ± 12 years] were comparable with HC [195 (78%) men, age: 37 ± 12 years] with respect to age and sex. Out of 237 patients, 26 (11%) had epigastric pain syndrome (EPS), 55 (23.2%) had postprandial distress syndrome (PDS), and 156 (65.8%) had EPS-PDS overlap. Among 237 patients with FD, TT genotype (associated with increased intracellular signal transduction) of GNβ3 C825T polymorphism was more common among patients than among HC [26 (11%) vs. 12 (4.8%), P=0.014; odds ratio (OR): 2.47, 95% confidence interval (CI): 1.2-5.1]. CC (variant) genotype of CCK-AR T/C polymorphism was infrequent among patients than among HC [19 (8%) vs. 46 (18.4%), P=0.001; OR: 0.36, 95% CI: 0.19-0.66]. However, these polymorphisms were comparable among patients with different subtypes of FD (P=0.80 and 0.44).

CONCLUSION

TT genotype of GNβ3 C825T is more common among patients with FD than among HC, suggesting that increased signal transduction associated with this genotype may be important in its pathophysiology. However, CCK-AR polymorphism is protective against FD.

Death receptor (DR4) haplotypes are associated with increased susceptibility of gallbladder carcinoma in north Indian population

BACKGROUND AND AIM

Defective apoptosis is a hallmark of cancer development and progression. Death receptors (DR4, FAS) and their ligands (TRAIL, FASL) are thought to mediate the major extrinsic apoptotic pathway in the cell. SNPs in these genes may lead to defective apoptosis. Hence, the present study aimed to investigate the association of functional SNPs of DR4 (rs20575, rs20576 and rs6557634), FAS (rs2234767) and FASL (rs763110) with gallbladder cancer (GBC) risk.

METHODS

This case-control study included 400 GBC and 246 healthy controls (HC). Genotyping was carried out by Taqman genotyping assays. Statistical analysis was performed by using SPSS ver16. Meta-analysis was performed using Comprehensive Meta-analysis software (Version 2.0, BIOSTAT, Englewood, NJ) to systematically summarize the possible association of SNP with cancer risk. Functional prediction of these variants was carried out using Bioinformatics tools (FAST-SNP, F-SNP). False discovery rate (FDR test) was used in multiple comparisons.

RESULTS

The DR4 C rs20575 A rs20576 A rs6557634, G rs20575 A rs20576 G rs6557634 and G rs20575 C rs20576 G rs6557634 haplotypes conferred two-fold increased risk for GBC. Among these, the DR4 C rs20575 A rs20576 A rs6557634 haplotype emerged as main factor influencing GBC susceptibility as the risk was not modulated by gender or gallstone stratification. Our meta-analysis results showed significant association of DR4 rs6557634 with overall cancer risk, GI cancers as well as in Caucasians. We didn't find any association of FAS and FASL SNPs with GBC susceptibility.

CONCLUSIONS

The DR4 haplotype C rs20575 A rs20576 A rs6557634 represents an important factor accounting the patients susceptibility to GBC probably due to decreased apoptosis. However, additional well-designed studies with larger sample size focusing on different ethnicities are required to further validate the results.

Role of cyclooxygenase-2 functional gene polymorphisms in Helicobacter pylori induced gastritis and gastric atrophy

In India, the role of host genetic factors is poorly studied for Helicobacter pylori associated diseases. Therefore, we evaluated the association of functionally relevant COX-2 gene polymorphisms (-765 G>C and +8473 T>C) in gastritis and precancerous lesions susceptibility. After upper GI endoscopy, 130 rapid urease test positive patients with non-ulcer dyspepsia, also showed positivity for H. pylori using modified Geimsa staining and anti-CagA IgG serology were included. All patients and 260 asymptomatic controls were genotyped for COX-2 variations using PCR-RFLP. COX-2 -765 (GC+CC) genotypes, -765 C allele, +8473 CC genotype, +8473 (TC+CC) genotypes, +8473 C allele, and variant haplotypes imparted high risk for gastritis (P = 0.036, OR = 1.82; P = 0.007, 1.92; P = 0.025, OR = 2.13; P = 0.017, OR = 1.80; P = 0.017, OR = 1.45; P = 0.010, OR = 2.40; P = 0.023, OR = 1.50 and P = 0.012, OR = 2.20 folds, respectively). In contrast, COX-2 -765 C allele carriers had low risk for lymphocyte (P = 0.020, OR = 0.35), plasma cell infiltrations (P = 0.016, OR = 0.33), and gastric atrophy (GA) development (P = 0.019, OR = 0.35). In conclusion, COX-2 variant allele/genotype/haplotype carriers may be at high risk for gastritis. However, COX-2 -765 C allele carriers may be at low risk for GA development.

Role of common sarcomeric gene polymorphisms in genetic susceptibility to left ventricular dysfunction

Mutations in sarcomeric genes are common genetic cause of cardiomyopathies. An intronic 25-bp deletion in cardiac myosin binding protein C (MYBPC3) at 3' region is associated with dilated and hypertrophic cardiomyopathies in Southeast Asia. However, the frequency of sarcomeric gene polymorphisms and associated clinical presentation have not been established with left ventricular dysfunction (LVD). Therefore, the aim of the present study was to explore the association of MYBPC3 25-bp deletion, titin (TTN) 18 bp I/D, troponin T type 2 (TNNT2) 5 bp I/D and myospryn K2906N polymorphisms with LVD. This study includes 988 consecutive patients with angiographically confirmed coronary artery disease (CAD) and 300 healthy controls. Among the 988 CAD patients, 253 with reduced left ventricle ejection fraction (LVEF≤45%) were categorized as LVD. MYBPC3 25-bp deletion, TTN 18 bp I/D and TNNT2 5 bp I/D polymorphisms were determined by direct polymerase chain reaction method, while myospryn K2906N polymorphism by TaqMan assay. Our results showed that MYBPC3 25-bp deletion polymorphism was significantly associated with elevated risk of LVD (LVEF <45) (healthy controls versus LVD: OR=3.85, P <0.001; and nonLVD versus LVD: OR=1.65, P = 0.035), while TTN 18 bp I/D, TNNT2 5 bp I/D and myospryn K2906N polymorphisms did not show any significant association with LVD. The results also showed that MYBPC3 25-bp deletion polymorphism was significantly associated with other parameters of LV remodelling, i.e. LV dimensions (LV end diastole dimension, LVEDD: P = 0.037 and LV end systolic dimension, LVESD: P = 0.032). Our data suggests that MYBPC3 25-bp deletion may play significant role in conferring LVD as well as CAD risk in north Indian population.

Lactase persistence/non-persistence genetic variants in irritable bowel syndrome in an endemic area for lactose malabsorption

BACKGROUND AND AIM

Lactase non-persistence is common in India. We evaluated: (i) frequency of lactase gene (C/T-13910 and G/A-22018) polymorphisms in irritable bowel syndrome (IBS) and healthy controls (HC), (ii) association between these polymorphisms and IBS-subtypes and symptoms.

METHODS

A total of 150 IBS patients (Rome-III criteria) and 252 age and gender-matched HC were evaluated for C/T-13910 and G/A-22018 genotypes using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP).

RESULTS

Totals of 79 (52%), 52 (35%) and 19 (13%) patients had diarrhea-predominant IBS (D-IBS), constipation predominant IBS (C-IBS) and alternating diarrhea and constipation IBS (A-IBS), respectively (Rome-III). Frequency of C/T-13910 [genotypes: CC 102 (68%), CT 43 (29%), TT 5 (3%) vs CC 155 (61%), CT 83 (33%), TT 14 (6%), P > 0.05] and G/A-22018 [GG 97 (65%), GA 41 (27%), AA 12 (8%) vs GG 154 (61%), GA 78 (31%), AA 20 (8%), P > 0.05] were similar among IBS and HC. Patients with D-IBS more often had C/T-13910 and G/A-22018 genotypes than C-IBS (CC 71 [90%], CT 6 [8%], TT 2 [2%]) versus (24 [46%], 25 [48%], 3 [6%]), A-IBS (7 [39%], 12 [63%], 0, [0%]) and HC (155 [61%], 83 [33%], 14 [6%]), P < 0.0001 and (GG 69 [87%], GA 6 [8%], AA 4 [5%]) vs (22 [42%], 24 [46%], 6 [12%]) vs (6 [32%], 11 [58%], 2 [10%]), P < 0.0001. IBS with CC and GG genotypes more often had abdominal pain (P = 0.005), distension (P = 0.031) and higher stool frequency (P = 0.003) and reported symptoms following dairy products than non-CC (P < 0.0001).

CONCLUSION

Though C/T-13910 and G/A-22018 polymorphisms were comparable among IBS and HC, these were more common among D-IBS and reported some symptoms like abdominal pain, bloating and exacerbation by dairy products.

DNMT3B -579 G>T promoter polymorphism and risk of gallbladder carcinoma in North Indian population

AIM

Carcinoma of gallbladder (GBC) is a relatively rare but highly fatal disease. The DNA (cytosine-5-)-methyltransferase 3 beta (DNMT3B) -579 G>T promoter polymorphism (rs1569686) influences gene function and has been associated with various malignancies. Present population-based case-control study was undertaken to examine the potential association of DNMT3B -579 G>T variation with GBC in North Indian population.

METHODS

Genotypes and allelic frequencies of the DNMT3B -579 G>T polymorphism were determined for 212 GBC patients and 219 controls using PCR-RFLP. Odds ratio (OR) and 95% confidence interval (95% CI) were calculated for the association of DNMT3B polymorphism with GBC. Analysis of potential transcription factor binding sites was also identified in the region harboring the polymorphism.

RESULTS

The DNMT3B -579 G>T polymorphism was found to be non-significantly associated with an overall increased risk of GBC (OR = 1.10 and 1.56 for T/G and G/G genotypes, respectively, P (trend) = 0.227). The increased risk was predominant in both male and female cohorts and also non-significantly in GBC patients with gallstone status (OR = 1.44; P = 0.280, OR = 1.06; P = 0.804 and OR = 1.45; P = 0.143, respectively).

CONCLUSION

DNMT3B -579 G>T polymorphism may alter susceptibility to GBC although it may not play a major role in the pathoetiology of this disease in North Indian population.

COX-2 gene polymorphisms and risk of chronic periodontitis: a case-control study and meta-analysis

OBJECTIVE

Cyclooxygenase-2 (COX-2) enzyme is a major mediator of inflammation in periodontitis, leading to loss of gingival tissues and alveolar bone supporting the teeth. Previous studies have explored the role of COX-2 polymorphisms with the risk of periodontitis in different ethnic groups; however, findings are inconsistent. So, we aimed to investigate the association of COX-2 polymorphisms (rs20417, rs689466, and rs5275) in susceptibility to chronic periodontitis (CP) in northern Indian population. Meta-analysis was also carried out to precisely estimate the effect of COX-2 polymorphisms in CP.

MATERIALS AND METHODS

Genotyping of COX-2 polymorphisms was carried out through PCR-RFLP in 200 CP cases and 200 controls. For risk estimation, binary logistic regression was applied using SPSS, version 15.0, while meta-analysis was carried using MIX 2.0 software.

RESULTS

None of the COX-2 polymorphisms independently were associated with the risk of CP. Meta-analysis suggested a significant reduced risk of CP with rs5275+8473 C allele and rs20417 in Chinese population.

CONCLUSIONS

No association was observed in any of the studied COX-2 polymorphisms with CP in North India. But, the study should be replicated in larger sample size to arrive at a definitive conclusion. Meta-analysis suggested a role of rs5275 COX-2 polymorphisms in susceptibility to overall CP, and on ethnic basis, rs20417 showed reduced risk of CP in Chinese population.

Significant association of combination of OCT4, NANOG, and SOX2 gene polymorphisms in susceptibility and response to treatment in North Indian breast cancer patients

PURPOSE

Dysregulations of regulatory genes in embryonic stem cells (ESCs) gene polymorphisms may lead to breast cancer cell growth, differentiation, and tumor metastasis.

METHODS

Polymorphisms in OCT4 (rs3130932), NANOG (rs11055786), LIN28 (rs4274112), and SOX2 (rs11915160) genes were evaluated for susceptibility in 297 breast cancer females and 273 healthy controls from north Indian population. Response to neo-adjuvant chemotherapy was followed in 128 locally advanced breast cancer patients along with clinicopathological features. Genotyping was done using TaqMan allelic discrimination assays. Statistical analysis was performed using SPSS and multifactor dimensionality reduction (MDR).

RESULTS

For OCT4 gene polymorphism, protective effect of genotypes AC [P corr = 0.031, OR = 0.63 (0.44-0.91)] and AC+CC [P corr = 0.031, OR = 0.68 (0.48-0.95)] was seen in patients. However, no association of NANOG, LIN28, and SOX2 gene polymorphisms was found with overall breast cancer susceptibility. Further, significant association of AG+GG genotype [P corr = 0.021, OR = 6.08 (1.83-20.15)] and G allele [P corr = 0.021, OR = 3.07 (1.21-7.77)] of rs4274112 polymorphism was seen with positive lymph node. For OCT4, significant association of allele C was seen with patients having negative hormone receptor [P corr = 0.021, OR = 0.51 (0.29-0.90)], but no association of any of the studied polymorphisms individually was found with response to NACT. On MDR analysis, we found combination of SNPs SOX2 rs11915160, OCT4 rs3130932, and NANOG rs11055786 to be the best interaction model for predicting breast cancer risk [p for permutation test <10(-3), OR = 2.04 (1.43-2.910] and response to NACT [p for permutation test = 0.005, OR = 2.09 (1.24-3.52)].

CONCLUSION

Combination of genetic variants of ESCs gene may have a profound effect in breast cancer risk and response to NACT.

Cyclooxygenase-2 gene polymorphisms and risk of cervical cancer in a North Indian population

INTRODUCTION

Single nucleotide polymorphisms in the cyclooxygenase-2 (COX-2) might contribute to differential COX-2 expression and subsequent interindividual variability in susceptibility to cancer. This study sought to evaluate the effects of COX-2 +8473T/C (rs5275) and -765G/C (rs20417) gene polymorphisms on the risk of cervical cancer in women of Northern India.

METHODS

Peripheral blood samples were collected from 200 histopathologically confirmed patients with cervical cancer and 200 unrelated, healthy female controls of similar ethnicity. Questionnaire survey was conducted to comprehend the demographic data, smoking status, and cancer stage of patients. Polymerase chain reaction-based restriction fragment length polymorphism was used to detect the genotypes of the COX-2 gene.

RESULTS

Cyclooxygenase-2 +8473CC genotype was associated with a significantly reduced risk of cervical cancer (P = 0.036; odds ratio, 0.4; 95% confidence interval, 0.1-0.9), whereas COX-2 -765G/C polymorphism demonstrated no association. In addition, no significant association with clinical stages of cervical cancer and modulation of risk due to tobacco usage was observed in our study.

CONCLUSIONS

Cyclooxygenase-2 +8473T/C gene polymorphism demonstrated protective effect in North Indian women. Further studies evaluating the role of COX-2 gene polymorphisms in ethnically diverse populations and a larger cohort may help in understanding the etiopathogenesis of cervical cancer in women worldwide.

Presenilin gene predisposes to late-onset degenerative but not vascular dementia: a comparative study of PS1 and ApoE genes in a North Indian Cohort

BACKGROUND

Variation in the presenilin gene shifts the cleavage site of amyloid precursor protein producing an insoluble peptide Abeta(42) (instead of Abeta(40), which is soluble when produced in restricted amount), which is prone to aggregation in the brain in the form of amyloid plaques not only in Alzheimer's disease (AD) but also in other degenerative dementias. The role of presenilin 1 (PS1) and apolipoprotein E (ApoE) genes has not been explored in degenerative dementias other than AD.

OBJECTIVE

To study the association of PS1 intron 8 and ApoE epsilon4 gene polymorphism in degenerative and vascular dementia patients in the North Indian population.

DESIGN

A hospital-based association study on degenerative and vascular dementia patients proven on the basis of clinical profile and MRI.

PARTICIPANTS

A group of 107 dementia patients and 162 age- and sex-matched controls from a North Indian cohort participated in the study. All patients had Mini Mental State Examination scores less than 24 and met the DSM-IV criteria for dementia.

RESULTS

The frequency of genotype 1/1 and allele 1 in degenerative dementias (73.12 and 83.70%, respectively) was higher than what had been reported so far in AD. A significant association of PS1 intron 8 polymorphism was found with degenerative dementias but not with vascular dementias (OR 2.50, 95% CI 1.27-5.00). On the other hand, ApoE epsilon4 allele was found to significantly increase the risk for both vascular and degenerative dementias (p = 0.0001, OR 3.45, 95% CI 1.74-6.86).

CONCLUSION

While ApoE epsilon4 allele increases the susceptibility to both degenerative and vascular dementia, PS1 allele 1 increases the susceptibility to degenerative dementias only.

Novel corrective equations for complete estimation of human tissue lipids after their partial destruction by perchloric acid pre-treatment: high-resolution (1)H-NMR-based study

Owing to the small quantity of tissue available in human biopsy specimens, aqueous and lipid components often have to be determined in the same tissue sample. Perchloric acid (PCA) used for the extraction of aqueous metabolites has a deleterious effect on lipid components; the severity of the damage is not known. In this study, human muscle tissue was first treated with PCA to extract aqueous metabolites, and the residue was then used for lipid extraction by conventional methods, i.e. the methods of Folch and Bligh & Dyer and a standardised one using methanol/chloroform (1:3, v/v) used in our laboratory. A (1)H-NMR spectrum was obtained for each lipid extract. Lipid was quantified by measuring the integral area of N(+)-(CH(3))(3) signals of phospholipids (PLs). Triacylglycerol (TG) and cholesterol (CHOL) were quantified using the -CH(2)- signals of glycerol and the C18 methyl signal, respectively. This study shows that prior use of PCA caused marked attenuation of TG, PL, and CHOL. This was confirmed by recovery experiments and observation of the direct effect of PCA on the standard lipid components. On the basis of the quantity of lipid lost in each case, three novel equations (with respect to TG, PL, and CHOL) were derived. Application of these equations to lipid quantities estimated in different pathological tissues after PCA pre-treatment produced values equivalent to those estimated without PCA use. This study conclusively shows that PCA pre-treatment damages all three lipid moieties, TG, PL, and CHOL. When PCA is used in a fixed ratio to the tissue, the lipid damage is also proportional and correctable by statistically derived equations. These equations will be useful in human biopsy specimens where aqueous and lipid components have to be studied using the same tissue sample because of the small quantity available.

CYP1A1 Msp1 T/C polymorphism in esophageal cancer: no association and risk modulation

Phase I enzyme CYP1A1 metabolizes environmental carcinogens and a Msp1 T/C functional polymorphism in 3'UTR in its gene has been reported to influence the inducibilty of the enzyme. There are controversies regarding association of the polymorphism with risk of esophageal cancer in Chinese and Caucasian populations. Moreover, no study has been done in Indian populations. The present study was aimed to explore the associations of CYP1A1 3'UTR polymorphism with clinical phenotypes and environmental interaction in esophageal cancer from North Indian population. A total of age- and gender-matched 161 cases and 201 healthy controls were used to genotype the CYP1A1 3'UTR polymorphism by PCR-EFLP methodology. None of the CYP1A1 genotypes and alleles was significantly associated with risk of esophageal cancer, even after adjusting for age and sex. After stratifying the genotypes according to disease characteristics such as tumor histology, location, and lymph nodes, individuals with TT genotype were at high risk for developing tumor in the upper third location (OR: 2.2, 95% CI: 0.81-6.2, p = 0.11). Interaction of tobacco usage (smoking or nonsmoking) and presence of occupational exposure in esophageal cancer patients did not show significant increase in cancer risk with CYP1A1 genotypes. However, in patients with alcohol habits, TT genotype showed a higher risk, which was not significant (OR: 2.5, 95% CI: 0.61-10.6, p = 0.19). In conclusion, CYP1A1 genotype did not influence the susceptibility of developing esophageal cancer. The presence of variant CYP1A1 genotypes together with environmental exposures also did not modulate the cancer risk.

Role of TGF-beta1 (-509C>T) promoter polymorphism in susceptibility to cervical cancer

Transforming growth factor-beta (TGF-beta) family members are multifunctional cytokines that play a key role in cellular growth, proliferation, and differentiation. The aim of study was to evaluate the association of TGF-beta1 -509 C>T gene polymorphism with risk of cervical cancer. The study was carried out in 150 histopathology confirmed patients with cervical cancer and 162 cervical-cytology negative females. Polymorphisms for TGF-beta1 -509C>T gene was genotyped by polymerase chain reaction and restriction enzyme digestion. Frequencies of individuals with -509TT genotype and T allele of TGF-beta1 gene polymorphisms did not differ significantly in patients with cervical cancer and controls (p = 0.328, OR = 1.37 and p = 0.605, OR = 1.09). Cervical cancer patients with -509TT had marginal low risk for stage I (p = 0.04, OR = 0.95, 95% CI = 0.91-0.99) but -509TT genotype of TGF-beta1 was associated with increased risk of stage II of cancer (p = 0.07, OR = 3.13, 95% CI = 0.87-11.14). In gene-environment interaction, carriers of TGF-beta1 -509TT genotype with tobacco usage were at higher risk of cervical cancer (OR = 3.67, 95% CI = 0.38-35.1). In conclusion, our data suggest that TGF-beta1 -509T allele confers marginal protection for early stage 1B but risk for stage II of cervical cancer.

Utility of MLPA in mutation analysis and carrier detection for Duchenne muscular dystrophy

CONTEXT

Multiplex ligation probe amplification (MLPA) is a new technique to identify deletions and duplications and can evaluate all 79 exons in dystrophin gene in patients with Duchenne muscular dystrophy (DMD). Being semi-quantitative, MLPA is also effective in detecting duplications and carrier testing of females; both of which cannot be done using multiplex PCR. It has found applications in diagnostics of many genetic disorders.

AIM

To study the utility of MLPA in diagnosis and carrier detection for DMD.

MATERIALS AND METHODS

Mutation analysis and carrier detection was done by multiplex PCR and MLPA and the results were compared.

RESULTS AND CONCLUSIONS

We present data showing utility of MLPA in identifying mutations in cases with DMD/BMD. In the present study using MLPA, we identified mutations in additional 5.6% cases of DMD in whom multiplex PCR was not able to detect intragenic deletions. In addition, MLPA also correctly confirmed carrier status of two obligate carriers and revealed carrier status in 6 of 8 mothers of sporadic cases.

Association of CYP1A1 Msp1 polymorphism with tobacco-related risk of gallbladder cancer in a north Indian population

Polymorphisms in the gene encoding the metabolic enzyme cytochrome P450 1A1 (CYP1A1) might contribute to the variability in individual susceptibility to gallbladder cancer (GBC). This study comprised 142 consecutive cases of proven GBC and 171 healthy participants of similar ethnicity. CYP1A1 6235 T/C transition was analyzed using polymerase chain reaction-restriction fragment length polymorphism. The CC genotype of CYP1A1 was significantly associated with a risk of GBC [odds ratio (OR) 2.3, 95% confidence interval (CI)=1.1-4.5, P=0.026], and the age- and sex-adjusted OR was 2.0. The CYP1A1 C allele frequency was also higher in GBC patients (OR 1.4, 95% CI=1.0-2.0, P=0.039). After sex stratification, the TC genotype and C allele were significantly higher in men and conferred a risk for GBC (OR 4.2, 95% CI=1.8-9.7, P=0.001; OR 2.2, CI=1.3-3.7, P=0.005). In addition, the TC genotype and C allele frequencies were significantly higher in GBC patients without associated gallstones (OR 2.4, 95% CI=1.2-4.7, P=0.011; OR 1.6, CI=1.0-2.4, P=0.023). The usage of tobacco (smoking or nonsmoking) by GBC patients showed a significant increase in cancer risk with the TC genotype (OR 4.1, 95% CI=1.3-11.9, P=0.012). It seems that the higher risk of the TC genotype in men may be related to tobacco usage.

Microsatellite instability and its correlation with clinicopathological features in a series of thyroid tumors prevalent in iodine deficient areas

Thyroid tumors display diverse spectrum of histopathological groups with geographic variation in its prevalence. Influence of iodine deficiency (a major causative factor) in its etiology, prevalence, or aggressiveness is debatable which reflects the existence of various genetic events in pathogenesis. The present study was undertaken to study the role of Microsatellite instability (MSI) or LOH (loss of heterozygosity), an indicator of defective mismatch repair system as a genetic change and to explore it as a prognostic marker in thyroid tumors. Tumor tissues from total thyroidectomy surgical specimens and blood (matched control) of 36 patients from iodine deficient areas (10 benign; 26 malignant) were obtained after their consent. Urinary iodine analysis was done by alkali ash method for which 10 ml of urine was collected from 18 patients before surgery. Genomic DNA, isolated from tumor tissue and blood was amplified by polymerase chain reaction (PCR) using mono and dinucleotide markers - BAT-26, BAT-40, TGF(RII, IGFIIR, hMSH3, BAX, D2S123, D9S283, D9S851 and D18S58. PCR products were analysed on 8% denaturing polyacrylamide gel followed by autoradiography. Of total, 66.6% of tumors [70% (7/10) benign and 65.4% malignant cases (17/26)] showed MSI/LOH. Strong association of MSI/LOH with low iodine (P = 0.01) and with AMES risk groups i.e. age (P = 0.02), tumor size (P = 0.04) and metastases (P = 0.002) in thyroid tumors was observed. This may help in predicting the biological behaviour and strengthening the hypothesis that iodine deficiency has influence on MSI in thyroid tumors. Our results further substantiate the risk group classification and help in deciding the treatment modality in particular patient.

SMN2-deletion in childhood-onset spinal muscular atrophy

The human genome has two homologous survival motor neuron genes, SMN1 and SMN2. Although deletions of SMN1 are frequently reported in childhood-onset spinal muscular atrophy (SMA), SMN2 have been found to be intact in patients with the disorder. We report on a 5-year-old boy with childhood-onset SMA who has a homozygous deletion of SMN2. He had wasting, weakness, and hyporeflexia, predominantly in the distal muscles. The muscles involved showed chronic neurogenic changes on electromyogram. There was no sensory involvement. A nerve conduction study showed near normal conduction velocity with reduction in the amplitude of the compound muscle action potential. Analysis of polymerase chain reaction-restriction fragment length polymorphism as well as single-strand conformation polymorphism on exons 7 and 8 of the SMN genes revealed the SMN2-deletion. Base sequencing and densitometric analysis of the critical region (exon 7) did not show any microdeletion or duplication of SMN1, but confirmed the deletion of SMN2. We conclude that a deletion of SMN2 may also result in the SMA phenotype.

Targeted Gene Sequencing of Gallbladder Carcinoma Identifies High-impact Somatic and Rare Germline Mutations

BACKGROUND

Gallbladder carcinoma (GBC) is a subtype of biliary tract malignancy with poor prognosis and high fatality rate. The present study was designed to uncover somatic and rare germline mutations in GBC to reveal the disease biology and understand the clinical importance of mutation profile in terms of prognostics and actionability.

MATERIALS AND METHODS

We performed ultra-deep sequencing across 409 cancer-related genes in 11 GBC patients of North-Indian descent. NGS data analysis was performed using Ion Reporter and several other publicly available resources and databases.

RESULTS

We identified 184 nonsynonymous somatic and 60 rare germline mutations in bona-fide cancer drivers such as SMAD family member 4 (SMAD4), lysine methyltransferase 2C (KMT2C), and tumor protein p53 (TP53). All the early-onset cases or hypermutated cases harbored mutation(s) in critical DNA-repair genes. Additionally, we detected 9 novel genes with high-impact somatic mutations in GBC.

CONCLUSION

Our results indicated the significance of inherited rare germline mutations in DNA-repair pathway genes in addition to acquired somatic mutations in GB carcinogenesis.

The impact of VKORC1-1639 G>A polymorphism on the maintenance dose of oral anticoagulants for thromboembolic prophylaxis in North India: A pilot study

BACKGROUND

The dose requirements for oral anticoagulants in thromboembolic events are influenced by promoter polymorphism in the VKORC1 gene. However, limited data are available on the influence of the polymorphism in various Indian populations. The present study aimed at determining the relationship between the VKORC1-1639 G>A genotypes and maintenance doses of oral anticoagulants for therapeutically stable INR values in patients taking Acitrom after valve replacement surgery.

MATERIALS AND METHODS

Fifty patients from the northern Indian region were genotyped for VKORC1-1639 G>A by polymerase chain reaction and restriction fragment length polymorphism. Means of the weight-normalized daily Acitrom dose were calculated for every patient.

RESULTS AND DISCUSSION

The VKORC1 1639G>A minor allele frequency in the study population (n = 50) was found to be 22%. The patients with a wild type genotype required the maximum drug dose as suggested for full functionality of the enzyme. Heterozygous patients were found to have an intermediate drug dose and the patients with a variant homozygous genotype had the minimum maintenance drug dose requirement. These findings are in concurrence with the effect of the promoter polymorphism on vitamin K epoxide reductase activity.1639G>A minor allele frequency in the study population (n = 50) was found to be 22%. The patients with a wild type genotype required the maximum drug dose as suggested for full functionality of the enzyme. Heterozygous patients were found to have an intermediate drug dose and the patients with a variant homozygous genotype had the minimum maintenance drug dose requirement. These findings are in concurrence with the effect of the promoter polymorphism on vitamin K epoxide reductase activity.

CONCLUSION

The VKORC1-1639 G>A status can be indicative of establishing the therapeutic dose of oral anticoagulants in Indian patients.

MTHFR and ACE gene polymorphisms and risk of vascular and degenerative dementias in the elderly

Focal lacunar infarctions due to cerebral small vessel atherosclerosis or single/multiple large cortical infarcts lead to vascular dementia, and different genes and environmental factors have been implicated in causation or aggravation of the disease. Previous reports suggest that some of the risk factors may be common to both vascular as well as degenerative dementia. Among genetic factors, role of angiotensin converting enzyme (ACE) and methylene-tetrahydrofolate reductase (MTHFR) genes as putative risk factors has been examined but the outcome of these studies remain inconclusive. Present study attempted to see the importance of ACE alu insertion/deletion and MTHFR C677T polymorphisms as genetic predisposers to dementia. The study comprised of 80 vascular dementia patients, 90 degenerative dementia patients and 170 age matched controls. All were genotyped for ACE, MTHFR and APOE polymorphisms using PCR-RFLP method. Frequency of ACE D allele was seemingly high in dementia cases (26.7%) when compared to controls (11.2%). However, after adjusting for age and APOE E4*, none of the ACE alleles showed good correlation. MTHFR genotypes or alleles also did not show any correlation. Our study suggests no true correlation of ACE or MTHR genes with dementia in elderly.

Association of apolipoprotein B XbaI gene polymorphism and lipid profile in northern Indian obese

BACKGROUND

Over the last few decades, obesity, diabetes, and hypertension have become main health evils. The health problems of obesity are well-recognized. However, the fact that all obese individuals are not at the same risk of developing a disease is also recognized. The apolipoprotein B (APOB) plays a central role in lipid metabolism. So we compare the association of APOB XbaI gene polymorphism and lipid profile total in obese north Indian population.

MATERIALS AND METHODS

A total of 132 obese (body mass index [BMI] >25 kg/m(2)) and 132 age matched non-obese (BMI ≤ 25 kg/m(2)) subjects were studied after taking detailed clinical profile. Lipid profile in serum/plasma was done using commercial kits. Genetic analysis of APOB XbaI was done using Polymerase Chain Reaction-Restriction Fragment Leanth polymorphism (PCR-RFLP).

STATISTICAL ANALYSIS

Statistical analysis was performed by Statistical Package for the Social Sciences (SPSS) (version 11.5) software (IBM Corporation). All continuous variables were expressed as mean ± SD and tested by analysis of variance test. Comparisons of categorical variables were assessed using χ(2) tests or Fisher's exact test. P < 0.05 was considered as significant.

RESULTS

Analysis showed that obese subjects had significantly higher value of the waist-to-hip ratio, blood pressure (systolic and diastolic), and lipid profile. In APOB XbaI gene polymorphism, we did not find significant differences in genotype or allele frequencies. Moreover, none of the studied metabolic parameters (lipid profile) showed any association with the gene polymorphism.

CONCLUSIONS

Study reveals no considerable association of APOB XbaI gene polymorphism with obesity and lipid profile in north Indians.

A Multiple Interaction Analysis Reveals ADRB3 as a Potential Candidate for Gallbladder Cancer Predisposition via a Complex Interaction with Other Candidate Gene Variations

Gallbladder cancer is the most common and a highly aggressive biliary tract malignancy with a dismal outcome. The pathogenesis of the disease is multifactorial, comprising the combined effect of multiple genetic variations of mild consequence along with numerous dietary and environmental risk factors. Previously, we demonstrated the association of several candidate gene variations with GBC risk. In this study, we aimed to identify the combination of gene variants and their possible interactions contributing towards genetic susceptibility of GBC. Here, we performed Multifactor-Dimensionality Reduction (MDR) and Classification and Regression Tree Analysis (CRT) to investigate the gene-gene interactions and the combined effect of 14 SNPs in nine genes (DR4 (rs20576, rs6557634); FAS (rs2234767); FASL (rs763110); DCC (rs2229080, rs4078288, rs7504990, rs714); PSCA (rs2294008, rs2978974); ADRA2A (rs1801253); ADRB1 (rs1800544); ADRB3 (rs4994); CYP17 (rs2486758)) involved in various signaling pathways. Genotyping was accomplished by PCR-RFLP or Taqman allelic discrimination assays. SPSS software version 16.0 and MDR software version 2.0 were used for all the statistical analysis. Single locus investigation demonstrated significant association of DR4 (rs20576, rs6557634), DCC (rs714, rs2229080, rs4078288) and ADRB3 (rs4994) polymorphisms with GBC risk. MDR analysis revealed ADRB3 (rs4994) to be crucial candidate in GBC susceptibility that may act either alone (p < 0.0001, CVC = 10/10) or in combination with DCC (rs714 and rs2229080, p < 0.0001, CVC = 9/10). Our CRT results are in agreement with the above findings. Further, in-silico results of studied SNPs advocated their role in splicing, transcriptional and/or protein coding regulation. Overall, our result suggested complex interactions amongst the studied SNPs and ADRB3 rs4994 as candidate influencing GBC susceptibility.

Hypoadiponectinemia in obesity: association with insulin resistance

Obesity is risk factor for insulin resistance, diabetes, and other chronic diseases. Adiponectin, an adipose-specific protein with antiatherogenic and antiinflammatory effects, were found to be associated with obesity, type 2 diabetes, and insulin resistance. Our aim to identify possible relationships between circulating adiponectin and obesity as well as obesity related phenotypes. A total of 642, obese and non-obese individuals were included in this cross-sectional study. Hormone and glucose levels were estimated using standard protocols. The adiponectin levels showed a significant decrease with increasing quartiles of insulin resistance index. Subjects in lowest quartile of adiponectin level had a significantly higher risk than those in the highest quartile, with higher body mass index, waist circumference, blood pressure, percentage body fat, fat mass, fasting insulin, insulin resistance index, total cholesterol (p < 0.001), low density lipoprotein-cholesterol (p = 0.001), very low density lipoprotein-cholesterol (p = 0.002), and Triglyceride (p = 0.002). The present study indicates that adiponectin is significantly associated with obesity, insulin resistance and other obesity related phenotypes.

Pre-microRNA Gene Polymorphisms and Risk of Cervical Squamous Cell Carcinoma

INTRODUCTION

MicroRNAs (miRNAs) are short (~22 nucleotides) regulatory RNAs that can modulate gene expression and are aberrantly expressed in many diseases, including cancer. It has been suggested that, the presence of single nucleotide polymorphisms in precursor miRNAs (pre-miRNAs) can alter miRNA processing, expression and binding to target mRNA and represents another type of genetic variability, that can contribute to the susceptibility of human cancers.

AIM

The present study investigated the genetic variants in pre-miRNAs (hsa-miRNA-196a2 rs11614913 C/T, hsa-miRNA-499 rs3746444 T/C and hsa-miRNA-146a rs2910164 G/C) for their role in cervical cancer susceptibility.

MATERIALS AND METHODS

The study comprised 164 controls and 184 patients of cervical cancer. The genotypic frequency of miRNA polymorphisms were determined by using a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay. Logistic regression was used for statistical analysis using SPSS Software version 15.0.

RESULTS

Hsa-miRNA-499 rs3746444 T/C polymorphism showed a statistically significant association with considerable risk for cervical cancer at genotypes (CC, p=0.001, OR=4.801) and variant allele (p<0.001, OR=2.307). MiRNA 146a and miRNA 196a2 polymorphisms showed no association with cervical cancer. However, interaction of miRNA polymorphisms with smoking habit showed higher risk of cervical cancer with miRNA 196a2 polymorphism in patients with smoking but no significant modification in the risk of cervical cancer was seen for other polymorphisms.

CONCLUSION

The results of the present study demonstrate that, miRNA 499 T/C polymorphism is significantly associated with genetic susceptibility to cervical cancer and may have a role in its pathogenesis.

Molecular cystoscopy: Micro-RNAs could be a marker for identifying genotypic changes for transitional cell carcinoma of the urinary bladder

INTRODUCTION

Normal-looking mucosa may harbor genetic changes preceding a visible tumor. This study was aimed at exploring the role of the quantitative expression of micro-RNAs (miRNAs) in bladder cancer tissue in comparison with normal mucosa and healthy controls (HCs) as a molecular marker.

MATERIALS AND METHODS

Between October 2011 to December 2012, tissue from the bladder tumor of 21 patients (cases tumor, CT), normal mucosa (case control, CC) of the same patients (n-21) and normal bladder mucosa from 10 HCs were obtained. miRNAs of angiogenesis, endothelial mesenchymal transition and apoptosis were quantified using stem-loop RT Taq Man polymerase chain reaction. Statistical analysis was performed using the Chi square and independent sample T tests by using SPSS version 16.

RESULTS

The mean age of the patients and controls were 55.41 ± 11.03 and 52.14 ± 13.04 years. miR-21, miR-205, miR-126, miR-10b and miR-200a were highly expressed in CT (P < 0.027, <0.048, <0.025, <0.029 and < 0.005) as compared with HC. Expression of miR-21 and miR-129 were both correlated with grade and stage (P = 0.001 and < 0.009, respectively) and the level of expression was different in the same grade of non-muscle invasive tumors. The fold change of miR129, miR205 and miR200a was significantly higher in the normal-looking mucosa of bladder tumor patients than the HC (P < 0.005).

CONCLUSION

Expression of miR129, miR205 and miR200a in the normal-looking mucosa of bladder cancer patients was significantly higher than the normal mucosa of a HC. This may help in predicting recurrence and formulating the follow-up strategy.