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Akçakaya A, Ünver N, Aydoğan Kiriş T, Güzel M, Akçakaya FB, Çakmakoğlu B, Hasbahçeci M. Association of CDH1 -160 C → A and -347 G→ GA polymorphisms and expression of E-cadherin and gastric cancer: A case-control study. Turk J Surg 2021; 37:41-48. [PMID: 34585093 DOI: 10.47717/turkjsurg.2021.5097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 03/05/2021] [Indexed: 12/15/2022]
Abstract
Objectives The loss of function of the E-cadherin (CDH1) gene with -160 C→A and -347 G→GA polymorphisms is regarded as a critical step for gastric cancer. It was aimed to investigate possible association of these polymorphisms and immunoexpression of E-cadherin with gastric cancer. Material and Methods Gastric adenocarcinoma patients and individuals with benign gastric pathologies were included in this case-control study. Demographic data and pathological findings were recorded. Immunohistochemical staining of E-cadherin expression and analysis of -160 C→A and -347 G→GA polymorphisms were done. Differences between allele frequencies of -160 C→A and -347 G→GA polymorphisms and expression of E-cadherin were the primary outcomes. Results There were 78 gastric cancer patients (Group A) and 113 individuals with benign gastric pathologies (Group B). The number of male patients and mean age were higher in Group A (p <0.001). -160 C→A and 347 G→GA polymorphisms and their allelic distributions showed no difference between the groups (p> 0.05 for all). There was a significant association between -160 C→A polymorphism and grade of E-cadherin expression (p= 0.013). There were no significant differences between survival rates with -160 C→A, 347 G→GA and intensity of E-cadherin expression (p> 0.05 for all). There was no significant association between -160 C→A and -347 G→GA polymorphisms and gastric cancer. Conclusion There was no impact of E-cadherin expression on tumoral features and survival in gastric cancer. -160 C→A polymorphism may influence the expression of E-cadherin in gastric cancer.
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Affiliation(s)
- Adem Akçakaya
- Department of General Surgery, Bezmialem Vakif University, Faculty of Medicine, İstanbul, Turkey
| | - Nurcan Ünver
- Clinic of Pathology, Yedikule Chest Diseases and Thoracic Surgery Training and Research Hospital, İstanbul, Turkey
| | | | - Mehmet Güzel
- Clinic of General Surgery, Patnos State Hospital, Ağrı, Turkey
| | | | - Bedia Çakmakoğlu
- Department of Molecular Medicine, Istanbul University Aziz Sancar Institute of Experimental Medicine, İstanbul, Turkey
| | - Mustafa Hasbahçeci
- Department of General Surgery, Istanbul Istinye University, Faculty of Medicine, İstanbul, Turkey.,A.D.E.M., Center for Academic Support and Education, Istanbul, Turkey
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Graham CAM, Pedlar CR, Hearne G, Lorente-Cebrián S, González-Muniesa P, Mavrommatis Y. The Association of Parental Genetic, Lifestyle, and Social Determinants of Health with Offspring Overweight. Lifestyle Genom 2020; 13:99-106. [PMID: 32069471 DOI: 10.1159/000505749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 01/03/2020] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION In the UK, the number of comorbidities seen in children has increased along with the worsening obesity rate. These comorbidities worsen into adulthood. Genome-wide association studies have highlighted single nucleotide polymorphisms associated with the weight status of adults and offspring individually. To date, in the UK, parental genetic, lifestyle, and social determinants of health have not been investigated alongside one another as influencers of offspring weight status. A comprehensive obesity prevention scheme would commence prior to conception and involve parental intervention including all known risk factors. This current study aims to identify the proportion of overweight that can be explained by known parental risk factors, including genetic, lifestyle, and social determinants of health with offspring weight status in the UK. METHODS A cross-sectional study was carried out on 123 parents. Parental and offspring anthropometric data and parental lifestyle and social determinants of health data were self-reported. Parental genetic data were collected by use of GeneFiX saliva collection vials and genotype were assessed for brain-derived neurotrophic factor (BDNF) gene rs6265, melanocortin 4 receptor (MC4R) gene rs17782313, transmembrane protein 18 (TMEM18) gene rs2867125, and serine/threonine-protein kinase (TNN13K) gene rs1514175. Associations were assessed between parental data and the weight status of offspring. RESULTS Maternal body mass index modestly predicted child weight status (p < 0.015; R2 = 0.15). More mothers of overweight children carried the MC4R rs17782313 risk allele (77.8%; p = 0.007) compared to mothers of normal-weight children. Additionally, fathers who were not Caucasian and parents who slept for <7 h/night had a larger percentage of overweight children when compared to their counterparts (p = 0.039; p = 0.014, respectively). CONCLUSION Associations exist between the weight status of offspring based solely on parental genetic, lifestyle, and social determinants of health data. Further research is required to appropriately address future interventions based on genetic and lifestyle risk groups on a pre-parent cohort.
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Affiliation(s)
- Catherine A M Graham
- Faculty of Health and Life Sciences, Department of Sport, Health and Social Work, Oxford Brookes University, Oxford, United Kingdom,
| | - Charles R Pedlar
- Faculty of Sport Health and Applied Science, Department of Nutrition, St. Mary's University, Twickenham, London, United Kingdom
| | - Gary Hearne
- Faculty of Science and Technology, Department of Design Engineering and Mathematics, Middlesex University, London, United Kingdom
| | - Silvia Lorente-Cebrián
- Centre for Nutrition Research, School of Pharmacy and Nutrition, University of Navarra, Pamplona, Spain.,IdiSNA - Navarra Health Research Institute, Pamplona, Spain.,CIBERobn Physiopathology of Obesity and Nutrition, Centre of Biomedical Research Network, ISCIII, Madrid, Spain
| | - Pedro González-Muniesa
- Department of Nutrition, Food Science and Physiology, School of Pharmacy and Nutrition, Pamplona, University of Navarra, Pamplona, Spain.,Centre for Nutrition Research, School of Pharmacy and Nutrition, University of Navarra, Pamplona, Spain.,IdiSNA - Navarra Health Research Institute, Pamplona, Spain.,CIBERobn Physiopathology of Obesity and Nutrition, Centre of Biomedical Research Network, ISCIII, Madrid, Spain
| | - Yiannis Mavrommatis
- Faculty of Sport Health and Applied Science, Department of Nutrition, St. Mary's University, Twickenham, London, United Kingdom
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Sharma AC, Srivastava RN, Srivastava SR, Parmar D, Singh A, Raj S. Association between Single Nucleotide Polymorphisms of SMAD3 and BMP5 with the Risk of Knee Osteoarthritis. J Clin Diagn Res 2017; 11:GC01-GC04. [PMID: 28764194 DOI: 10.7860/jcdr/2017/22371.10073] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 03/09/2017] [Indexed: 11/24/2022]
Abstract
INTRODUCTION The role of genetic factors influencing osteoarthritis (OA) susceptibility is well documented and several candidate genes have been identified to be associated with it. Among these genes are Bone Morphogenetic Protein 5 (BMP5) and Smad family member 3 (SMAD3), all involved in Transforming Growth Factor (TGF) signaling pathway. The knee is the commonly affected joint, and knee OA has an especially high prevalence in Asian population. AIM To investigate associations between Single Nucleotide Polymorphisms (SNPs) rs12901499 in SMAD3 and rs921126 in the BMP5 gene with knee OA susceptibility in and around Lucknow, Uttar Pradesh, India. MATERIALS AND METHODS SNPs rs12901499 in SMAD3 and rs921126 in BMP5 were genotyped in patients with knee OA and age- sex matched OA-free controls from our population. A total of 450 patients with knee OA and 458 controls were enrolled in the study. Venous blood samples were obtained from all cases as well as controls for PCR-RFLP (Polymerase Chain Reaction- Restriction Fragment Length Polymorphism). Data was collected and entered in excel sheets. Statistical analyses of the data were performed using statistical software package SPSS version 16.0. Chi-square, Student's t-test and logistic regression tests were used to analyse the data. RESULTS GA and GG genotypes of both SNPs (rs12901499 and rs921126), and variant G, were associated with a significantly increased risk of knee OA. A significantly increased risk of knee OA was associated with the genotype GG and GA of rs12901499 (p < 0.03 and p <0.004 respectively) and rs921126 (p< 0.0001 and p<0.001 respectively) compared with the AA genotype. In addition, those bearing at least one G allele (GG + GA) had a significantly increased risk of knee OA compared with those without the G allele (AA) in rs921126 (p< 0.0001). However, in rs12901499, significant association with the risk of knee OA was not found (p<0.4). On age and gender based stratification, the association between the risk of OA and rs921126 GG mutant compared with AA homozygotes was strong in both gender (adjusted OR= 2.93 for male and 2.25 for female) and in those aged >55 years (adjusted OR= 3.4), similarly in rs12901499, GG mutant compared with AA homozygote was strong in female (adjusted OR= 1.5) and in those aged >55 years (adjusted OR= 1.5). CONCLUSION The results showed that both in SMAD3 rs12901499 and BMP5 921126, G allele is significantly associated with knee OA. A to G change and variant G genotype may contribute to knee OA risk in our study population of Lucknow.
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Affiliation(s)
- Amar Chandra Sharma
- PhD Scholar, Department of Orthopaedic Surgery, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Rajeshwar Nath Srivastava
- Professor, Department of Orthopaedic Surgery, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Sudeepti Ratan Srivastava
- PhD Scholar, Department of Orthopaedic Surgery, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Devendra Parmar
- Senior Scientist, Developmental Toxicology Division, Indian Institute of Toxicology Research, Lucknow, Uttar Pradesh, India
| | - Ajai Singh
- Professor, Department of Orthopaedic Surgery, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Saloni Raj
- MBBS Intern, Department of Orthopaedic Surgery, King George's Medical University, Lucknow, Uttar Pradesh, India
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Beck A, Luedtke A, Liu K, Tintle N. A POWERFUL METHOD FOR INCLUDING GENOTYPE UNCERTAINTY IN TESTS OF HARDY-WEINBERG EQUILIBRIUM. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2016; 22:368-379. [PMID: 27896990 DOI: 10.1142/9789813207813_0035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The use of posterior probabilities to summarize genotype uncertainty is pervasive across genotype, sequencing and imputation platforms. Prior work in many contexts has shown the utility of incorporating genotype uncertainty (posterior probabilities) in downstream statistical tests. Typical approaches to incorporating genotype uncertainty when testing Hardy-Weinberg equilibrium tend to lack calibration in the type I error rate, especially as genotype uncertainty increases. We propose a new approach in the spirit of genomic control that properly calibrates the type I error rate, while yielding improved power to detect deviations from Hardy-Weinberg Equilibrium. We demonstrate the improved performance of our method on both simulated and real genotypes.
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Affiliation(s)
- Andrew Beck
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA,
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Chantarangsu S, Sura T, Mongkornkarn S, Donsakul K, Torrungruang K. Vitamin D Receptor Gene Polymorphism and Smoking in the Risk of Chronic Periodontitis. J Periodontol 2016; 87:1343-1351. [DOI: 10.1902/jop.2016.160222] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Feng Y, Wang F, Pan H, Qiu S, Lü J, Wu L, Wang J, Lu C. Obesity-associated gene FTO rs9939609 polymorphism in relation to the risk of tuberculosis. BMC Infect Dis 2014; 14:592. [PMID: 25377722 PMCID: PMC4226896 DOI: 10.1186/s12879-014-0592-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 10/27/2014] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Obesity is known to affect cell-mediated immune responses. Recent studies have revealed that genetic polymorphisms in the fat mass and obesity associated (FTO) gene are related to human obesity. We hypothesize that this gene may also play a role in the risk of immune-related infectious diseases such as tuberculosis. METHODS This case-control study included 1625 pulmonary tuberculosis cases and 1570 unaffected controls recruited from the Jiangsu province in China. Single nucleotide polymorphisms (SNPs), rs9939609 and rs8050136, in the FTO gene were genotyped using TaqMan allelic discrimination assays. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated using the unconditional logistic regression model. RESULTS We observed a significant association between the genetic polymorphism rs9939609 and tuberculosis risk. Compared with the common genotype TT, individuals carrying AA had a significantly increased risk, with an OR of 3.77 (95% CI: 2.26-6.28). After adjusting for potential confounders, the relationship remains significant. An additive model showed that carriers of an allele A had a 26% increased risk of tuberculosis compared with the T allele (OR: 1.26, 95% CI: 1.08-1.48). Compared with the common haplotype rs9939609T-rs8050136C, the haplotype rs9939609A-rs8050136C was related to an increased risk of tuberculosis (OR = 6.09, 95% CI: 3.27-12.34). CONCLUSIONS The FTO polymorphism rs9939609 is associated with a risk of pulmonary tuberculosis in the Chinese population.
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Méplan C, Dragsted LO, Ravn-Haren G, Tjønneland A, Vogel U, Hesketh J. Association between polymorphisms in glutathione peroxidase and selenoprotein P genes, glutathione peroxidase activity, HRT use and breast cancer risk. PLoS One 2013; 8:e73316. [PMID: 24039907 PMCID: PMC3769272 DOI: 10.1371/journal.pone.0073316] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 07/18/2013] [Indexed: 12/29/2022] Open
Abstract
Breast cancer (BC) is one of the most common cancers in women. Evidence suggests that genetic variation in antioxidant enzymes could influence BC risk, but to date the relationship between selenoproteins and BC risk remains unclear. In this report, a study population including 975 Danish cases and 975 controls matched for age and hormone replacement therapy (HRT) use was genotyped for five functional single nucleotide polymorphisms (SNPs) in SEPP1, GPX1, GPX4 and the antioxidant enzyme SOD2 genes. The influence of genetic polymorphisms on breast cancer risk was assessed using conditional logistic regression. Additionally pre-diagnosis erythrocyte GPx (eGPx) activity was measured in a sub-group of the population. A 60% reduction in risk of developing overall BC and ductal BC was observed in women who were homozygous Thr carriers for SEPP1 rs3877899. Additionally, Leu carriers for GPX1 Pro198Leu polymorphism (rs1050450) were at ∼2 fold increased risk of developing a non-ductal BC. Pre-diagnosis eGPx activity was found to depend on genotype for rs713041 (GPX4), rs3877899 (SEPP1), and rs1050450 (GPX1) and on HRT use. Moreover, depending on genotype and HRT use, eGPx activity was significantly lower in women who developed BC later in life compared with controls. Furthermore, GPx1 protein levels increased in human breast adenocarcinoma MCF7 cells exposed to β-estradiol and sodium selenite.In conclusion, our data provide evidence that SNPs in SEPP1 and GPX1 modulate risk of BC and that eGPx activity is modified by SNPs in SEPP1, GPX4 and GPX1 and by estrogens. Our data thus suggest a role of selenoproteins in BC development.
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Affiliation(s)
- Catherine Méplan
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne, United Kingdom
- Human Nutrition Research Centre, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | - Lars Ove Dragsted
- Department of Human Nutrition, University of Copenhagen, Frederiksberg, Denmark
| | - Gitte Ravn-Haren
- Department of Human Nutrition, University of Copenhagen, Frederiksberg, Denmark
- National Food Institute, Technical University of Denmark, Soborg, Denmark
| | | | - Ulla Vogel
- National Research Centre for the Working Environment, Copenhagen, Denmark
- * E-mail: (JH); (UV)
| | - John Hesketh
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne, United Kingdom
- Human Nutrition Research Centre, Newcastle University, Newcastle-upon-Tyne, United Kingdom
- * E-mail: (JH); (UV)
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