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Zheng X, Jing J, Yuan M, Liu N, Song Y. Contribution of gene polymorphisms on 3p25 to salivary gland carcinoma, ameloblastoma, and odontogenic keratocyst in the Chinese Han population. Oral Surg Oral Med Oral Pathol Oral Radiol 2023; 136:220-230. [PMID: 37495273 DOI: 10.1016/j.oooo.2023.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 04/30/2023] [Accepted: 05/10/2023] [Indexed: 07/28/2023]
Abstract
OBJECTIVE This study aimed to investigate the contribution of gene polymorphisms in 3p25 to salivary gland carcinoma (SGC), ameloblastoma (AM), and odontogenic keratocyst (OKC) in the Chinese Han population. STUDY DESIGN Sixteen tag-single nucleotide polymorphisms (SNPs) within 5 genes (SYN2, TIMP4, PPARG, RAF1, and IQSEC1) in 3p25 were genotyped in 411 individuals with or without SGC, AM, and OKC. Genotype, clinical phenotype, and bioinformatics analyses were performed to evaluate the function of candidate SNPs. RESULTS SYN2-rs3773364, TIMP4-rs3755724, PPARG-rs10865710, and PPARG-rs1175544 were related to decreased SGC susceptibility, whereas IQSEC1-rs2600322 and IQSEC1-rs2686742 decreased and increased AM risk, respectively. Stratification analysis revealed that the significance of the identified SNPs was stronger in females or individuals younger than 46 years in SGC. PPARG-rs10865710 and PPARG-rs1175544 were associated with lower lymph node metastasis. SYN2-rs3773364 and PPARG-rs1175544 were associated with favorable SGC patient survival. Functional assessments linked PPARG-rs1175544 to PPARG expression regulation. Linkage disequilibrium analysis revealed a haplotype (SYN2-rs3773364-A, TIMP4-rs3817004-A, and TIMP4-rs3755724-C) associated with decreased susceptibility to SGC. Generalized multifactor dimensionality reduction analysis indicated the gene-gene interactions among IQSEC1, TIMP4, and PPARG in SGC, AM, and OKC progression. CONCLUSIONS These variants play important roles in the progression of SGC, AM, and OKC in the Chinese Han population and may be considered biomarkers for early diagnosis and prognosis prediction.
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Affiliation(s)
- Xueqing Zheng
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei_MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Jiaojiao Jing
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei_MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China; Department of Pediatric Dentistry, Peking University Shenzhen Hospital, Shenzhen 518036, Guangdong, China
| | - Minyan Yuan
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei_MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Nianke Liu
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei_MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Yaling Song
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei_MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China.
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Association between SNPs in Leptin Pathway Genes and Anthropometric, Biochemical, and Dietary Markers Related to Obesity. Genes (Basel) 2022; 13:genes13060945. [PMID: 35741707 PMCID: PMC9222344 DOI: 10.3390/genes13060945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/16/2022] [Accepted: 05/19/2022] [Indexed: 02/04/2023] Open
Abstract
Obesity is one of the main public health problems in Mexico and the world and one from which a large number of pathologies derive. Single nucleotide polymorphisms (SNPs) of various genes have been studied and proven to contribute to the development of multiple diseases. SNPs of the leptin pathway have been associated with the control of hunger and energy expenditure as well as with obesity and type 2 diabetes mellitus. Therefore, the present work focused on determining the association between anthropometric markers and biochemical and dietary factors related to obesity and SNPs of leptin pathway genes, such as the leptin gene (LEP), the leptin receptor (LEPR), proopiomelanocortin (POMC), prohormone convertase 1 (PCSK1), and the melanocortin 4 receptor (MC4R). A population of 574 young Mexican adults of both sexes, aged 19 years old on average and without metabolic disorders previously diagnosed, underwent a complete medical and nutritional evaluation, biochemical determination, and DNA extraction from the blood; DNA samples were subsequently genotyped. Association analyses between anthropometric, biochemical, and dietary variables with SNPs were performed using binary logistic regressions (p-value = 0.05). Although the sampled population did not have previously diagnosed diseases, the evaluation results showed that 33% were overweight or obese according to BMI and 64% had non-clinically elevated levels of body fat. From the 74 SNP markers analyzed from the five previously mentioned genes, 62 showed polymorphisms within the sampled population, and only 35 of these had significant associations with clinical variables. The risk associations (OR > 1) occurred between clinical markers with elevated values for waist circumference, waist−height index, BMI, body fat percentage, glucose levels, insulin levels, HOMA-IR, triglyceride levels, cholesterol levels, LDL-c, low HDL-c, carbohydrate intake, and protein intake and SNPs of the LEP, LEPR, PCSK1, and MC4R genes. On the other hand, the protective associations (OR < 1) were associated with markers including elevated values for insulin, HOMA-IR, cholesterol, c-LDL, energy intake > 2440 Kcal/day, and lipid intake and SNPs of the LEP and LEPR genes and POMC. The present study describes associations between SNPs in leptin pathway genes, revealing positive and negative interactions between reported SNPs and the clinical markers related to obesity in a sampled Mexican population. Hence, our results open the door for the further study of new genetic variants and their influence on obesity.
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Marcos-Pasero H, Aguilar-Aguilar E, Colmenarejo G, Ramírez de Molina A, Reglero G, Loria-Kohen V. The Q223R Polymorphism of the Leptin Receptor Gene as a Predictor of Weight Gain in Childhood Obesity and the Identification of Possible Factors Involved. Genes (Basel) 2020; 11:genes11050560. [PMID: 32429577 PMCID: PMC7288327 DOI: 10.3390/genes11050560] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/11/2020] [Accepted: 05/15/2020] [Indexed: 12/13/2022] Open
Abstract
(1) Background: Childhood rapid weight gain during development has been postulated as a predictor of obesity. The objective of this study was to investigate the effect of single nucleotide polymorphisms (SNPs) on the annual weight gain and height growth, as well as identifying possible lifestyle factors involved. (2) Methods: As part of the GENYAL study, 221 children (6–8 years old) of Madrid (Spain) were enrolled. A total of 11 SNPs associated with high childhood body mass indexes (BMIs) were assessed. Anthropometric measurements, dietary and physical activity data, were collected in 2017 and 2018. Bonferroni-corrected linear models were used to fit the data. (3) Results: A significant association between the Q223R LEPR and the weight growth was found, showing a different behavior between GA and GG genotypes (p = 0.001). Regarding lifestyle factors, an interaction between Q223R genotypes and total active weekly hours/week to predict the weight growth (kg/year) was observed (p = 0.023). In all the genotypes, a beneficial effect against rapid weight growth was observed, but the effect size of the interaction was much more significant in homozygous (GG) minor homozygous (β = −0.61 (−0.95, −0.26) versus heterozygous (AG) and wild-type homozygous (AA) genotypes (β = −0.07 (−0.24, 0.09) and β = −0.12 (−0.32, 0.08), respectively). (4) Conclusions: These results may contribute to more personalized recommendations to prevent childhood obesity.
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Affiliation(s)
- Helena Marcos-Pasero
- Nutrition and Clinical Trials Unit, GENYAL Platform IMDEA-Food Institute, CEI UAM+CSIC, 28049 Madrid, Spain; (H.M.-P.); (E.A.-A.)
| | - Elena Aguilar-Aguilar
- Nutrition and Clinical Trials Unit, GENYAL Platform IMDEA-Food Institute, CEI UAM+CSIC, 28049 Madrid, Spain; (H.M.-P.); (E.A.-A.)
| | - Gonzalo Colmenarejo
- Biostatistics and Bioinformatics Unit, IMDEA Food Institute, CEI UAM+CSIC, Ctra. De Canto Blanco 8, 28049 Madrid, Spain;
| | - Ana Ramírez de Molina
- Molecular Oncology and Nutritional Genomics of Cancer, IMDEA-Food Institute, CEI UAM+CSIC, 28049 Madrid, Spain;
| | - Guillermo Reglero
- Production and Development of Foods for Health, IMDEA-Food Institute, CEI UAM+CSIC, 28049 Madrid, Spain;
- Production and Characterization of Novel Foods, CIAL, CEI UAM+CSIC, 28049 Madrid, Spain
| | - Viviana Loria-Kohen
- Nutrition and Clinical Trials Unit, GENYAL Platform IMDEA-Food Institute, CEI UAM+CSIC, 28049 Madrid, Spain; (H.M.-P.); (E.A.-A.)
- Correspondence: ; Tel.: +34-912-796-957
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Duggan C, Baumgartner RN, Baumgartner KB, Bernstein L, George S, Ballard R, Neuhouser ML, McTiernan A. Genetic variation in TNFα, PPARγ, and IRS-1 genes, and their association with breast-cancer survival in the HEAL cohort. Breast Cancer Res Treat 2017; 168:567-576. [PMID: 29256014 DOI: 10.1007/s10549-017-4621-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 12/08/2017] [Indexed: 12/20/2022]
Abstract
PURPOSE Tumor necrosis factor-α (TNF-α), peroxisome proliferator-activated receptor-γ (PPARγ), and insulin receptor substrate-1 (IRS-1) are associated with obesity, insulin resistance, and inflammation. Few data exist on associations between polymorphisms in these genes and mortality in breast cancer survivors. METHODS We investigated associations between TNF-α -308G > A (rs1800629); PPARγ Pro12Ala (rs1801282); and IRS-1 Gly972Arg (rs1801278) polymorphisms and anthropometric variables, circulating levels of previously measured biomarkers, and tumor characteristics in 553 women enrolled in the Health, Eating, Activity, and Lifestyle Study, a multiethnic, prospective cohort study of women diagnosed with stage I-IIIA breast cancer between 1995 and 1999 (median follow-up 14.7 years). Using Cox proportional hazards models adjusted for possible confounders, we evaluated associations between these polymorphisms and mortality. RESULTS Carriers of the PPARγ variant allele had statistically significantly lower rates of type 2 diabetes (P = 0.04), lower BMI (P = 0.01), and HOMA scores [P = 0.004; non-Hispanic White (NHWs) only]; carriers of the TNF-α variant A allele had higher serum glucose (P = 0.004, NHW only); and the IRS-1 variant was associated with higher leptin levels (P = 0.003, Hispanics only). There were no associations between any of the polymorphisms and tumor characteristics. Among 141 deaths, 62 were due to breast cancer. Carriers of the TNF-α-variant A allele had a decreased risk of breast-cancer-specific mortality [hazard ratio (HR) 0.30; 95% confidence interval (CI) 0.10-0.83] and all-cause mortality (HR 0.51; 95% CI 0.28-0.91). CONCLUSIONS Neither the PPARγ nor the IRS-1 polymorphism was associated with mortality outcome. The TNF-α -308 G > A polymorphism was associated with reduced breast-cancer-specific and all-cause mortality.
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Affiliation(s)
- Catherine Duggan
- Epidemiology Program, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
| | - Richard N Baumgartner
- Department of Epidemiology & Population Health, University of Louisville, Louisville, KY, USA
| | - Kathy B Baumgartner
- Department of Epidemiology & Population Health, University of Louisville, Louisville, KY, USA
| | - Leslie Bernstein
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Stephanie George
- Office of Disease Prevention, National Institutes of Health, Rockville, MD, USA
| | - Rachel Ballard
- Office of Disease Prevention, National Institutes of Health, Rockville, MD, USA
| | - Marian L Neuhouser
- Epidemiology Program, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Anne McTiernan
- Epidemiology Program, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA
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Olza J, Rupérez AI, Gil-Campos M, Leis R, Cañete R, Tojo R, Gil Á, Aguilera CM. Leptin Receptor Gene Variant rs11804091 Is Associated with BMI and Insulin Resistance in Spanish Female Obese Children: A Case-Control Study. Int J Mol Sci 2017; 18:ijms18081690. [PMID: 28771179 PMCID: PMC5578080 DOI: 10.3390/ijms18081690] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 07/27/2017] [Accepted: 07/28/2017] [Indexed: 12/28/2022] Open
Abstract
Leptin is an endocrine hormone that has a critical role in body weight homoeostasis and mediates its effects via the leptin receptor (LEPR). Common polymorphisms in the genes coding leptin receptors have been associated with metabolic abnormalities. We assessed the association of 28 LEPR polymorphisms with body mass index (BMI) and their relationship with obesity-related phenotypes, inflammation and cardiovascular disease risk biomarkers. A multicentre case-control study was conducted in 522 children (286 with obesity and 236 with normal-BMI). All anthropometric, metabolic factors and biomarkers were higher in children with obesity except apolipoprotein (Apo)-AI, cholesterol, high-density lipoprotein cholesterol (HDL-c), and adiponectin, which were lower in the obesity group; and glucose, low-density lipoprotein cholesterol (LDL-c), and matrix metalloproteinase-9 that did not differ between groups. We identified the associations between rs11208659, rs11804091, rs10157275, rs9436303 and rs1627238, and BMI in the whole population, as well as the association of rs11804091, rs10157275, and rs1327118 with BMI in the female group, although only the rs11804091 remained associated after Bonferroni correction (p = 0.038). This single nucleotide polymorphisms (SNP) was also associated with insulin (p = 0.004), homeostasis model assessment for insulin resistance (HOMA-IR) (p = 0.006), quantitative insulin sensitivity check index (QUICKI) (p = 0.005) and adiponectin (p = 0.046) after adjusting for age, Tanner stage and BMI. Our results show a sex-specific association between the rs11804091 and obesity suggesting an influence of this SNP on insulin resistance.
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Affiliation(s)
- Josune Olza
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, Institute of Nutrition and Food Technology, University of Granada, Av. Del Conocimiento s/n., 18016 Granada, Spain.
- CIBER Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, 28029 Madrid, Spain.
- Instituto de Investigación Biosanitaria ibs.GRANADA, 18012 Granada, Spain.
| | - Azahara I Rupérez
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, Institute of Nutrition and Food Technology, University of Granada, Av. Del Conocimiento s/n., 18016 Granada, Spain.
| | - Mercedes Gil-Campos
- CIBER Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, 28029 Madrid, Spain.
- Paediatric Research and Metabolism Unit, Reina Sofía University Hospital, Maimonides Institute for Biomedical Research (IMIBIC), Av. Menendez Pidal s/n., 14010 Córdoba, Spain.
| | - Rosaura Leis
- CIBER Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, 28029 Madrid, Spain.
- Unit of Investigation in Nutrition, Growth and Human Development of Galicia, Paediatric Department, Clinic University Hospital of Santiago, University of Santiago de Compostela, Travesia de Choupana, 15706 Galicia, Spain .
| | - Ramón Cañete
- CIBER Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, 28029 Madrid, Spain.
- Paediatric Research and Metabolism Unit, Reina Sofía University Hospital, Maimonides Institute for Biomedical Research (IMIBIC), Av. Menendez Pidal s/n., 14010 Córdoba, Spain.
| | - Rafael Tojo
- Unit of Investigation in Nutrition, Growth and Human Development of Galicia, Paediatric Department, Clinic University Hospital of Santiago, University of Santiago de Compostela, Travesia de Choupana, 15706 Galicia, Spain .
| | - Ángel Gil
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, Institute of Nutrition and Food Technology, University of Granada, Av. Del Conocimiento s/n., 18016 Granada, Spain.
- CIBER Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, 28029 Madrid, Spain.
- Instituto de Investigación Biosanitaria ibs.GRANADA, 18012 Granada, Spain.
| | - Concepción M Aguilera
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, Institute of Nutrition and Food Technology, University of Granada, Av. Del Conocimiento s/n., 18016 Granada, Spain.
- CIBER Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, 28029 Madrid, Spain.
- Instituto de Investigación Biosanitaria ibs.GRANADA, 18012 Granada, Spain.
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Pacilli A, Prudente S, Copetti M, Fontana A, Mercuri L, Bacci S, Marucci A, Alberico F, Viti R, Palena A, Lamacchia O, Cignarelli M, De Cosmo S, Trischitta V. The PPARγ2 P12A polymorphism is not associated with all-cause mortality in patients with type 2 diabetes mellitus. Endocrine 2016; 54:38-46. [PMID: 26956846 DOI: 10.1007/s12020-016-0906-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Accepted: 02/19/2016] [Indexed: 11/26/2022]
Abstract
The high mortality risk of patients with type 2 diabetes mellitus may well be explained by the several comorbidities and/or complications. Also the intrinsic genetic component predisposing to diabetes might have a role in shaping the risk of diabetes-related mortality. Among type 2 diabetes mellitus SNPs, rs1801282 is of particular interest because (i) it is harbored by peroxisome proliferator-activated receptor-γ2 (PPARγ2), which is the target for thiazolidinediones which are used as antidiabetic drugs, decreasing all-cause mortality in type 2 diabetes mellitus, and (ii) it is associated with insulin resistance and related traits, risk factors for overall mortality in type 2 diabetes mellitus. We investigated the role of PPARγ2 P12A, according to a dominant model (PA + AA vs. PP individuals) on incident all-cause mortality in three cohorts of type 2 diabetes mellitus, comprising a total of 1672 patients (462 deaths) and then performed a meta-analysis of ours and all available published data. In the three cohorts pooled and analyzed together, no association between PPARγ2 P12A and all-cause mortality was observed (HR 1.02, 95 % CI 0.79-1.33). Similar results were observed after adjusting for age, sex, smoking habits, and BMI (HR 1.09, 95 % CI 0.83-1.43). In a meta-analysis of ours and all studies previously published (n = 3241 individuals; 666 events), no association was observed between PPARγ2 P12A and all-cause mortality (HR 1.07, 95 % CI 0.85-1.33). Results from our individual samples as well as from our meta-analysis suggest that the PPARγ2 P12A does not significantly affect all-cause mortality in patients with type 2 diabetes mellitus.
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Affiliation(s)
- Antonio Pacilli
- Department of Medical Sciences, Scientific Institute "Casa Sollievo della Sofferenza", San Giovanni Rotondo, FG, Italy
| | - Sabrina Prudente
- Mendel-Laboratory, Scientific Institute "Casa Sollievo della Sofferenza", San Giovanni Rotondo, FG, Italy
| | - Massimiliano Copetti
- Unit of Biostatistics, Scientific Institute "Casa Sollievo della Sofferenza", San Giovanni Rotondo, FG, Italy
| | - Andrea Fontana
- Unit of Biostatistics, Scientific Institute "Casa Sollievo della Sofferenza", San Giovanni Rotondo, FG, Italy
| | - Luana Mercuri
- Mendel-Laboratory, Scientific Institute "Casa Sollievo della Sofferenza", San Giovanni Rotondo, FG, Italy
| | - Simonetta Bacci
- Department of Medical Sciences, Scientific Institute "Casa Sollievo della Sofferenza", San Giovanni Rotondo, FG, Italy
| | - Antonella Marucci
- Research Unit of Diabetes and Endocrine Diseases, Scientific Institute "Casa Sollievo della Sofferenza", Viale Padre Pio, 71013, San Giovanni Rotondo, FG, Italy
| | - Federica Alberico
- Mendel-Laboratory, Scientific Institute "Casa Sollievo della Sofferenza", San Giovanni Rotondo, FG, Italy
| | - Raffaella Viti
- Department of Medical Sciences, Scientific Institute "Casa Sollievo della Sofferenza", San Giovanni Rotondo, FG, Italy
| | - Antonio Palena
- Department of Medical Sciences, Scientific Institute "Casa Sollievo della Sofferenza", San Giovanni Rotondo, FG, Italy
| | - Olga Lamacchia
- Unit of Endocrinology and Metabolic Diseases, Department of Surgical and Medical Sciences, University of Foggia, Foggia, Italy
| | - Mauro Cignarelli
- Unit of Endocrinology and Metabolic Diseases, Department of Surgical and Medical Sciences, University of Foggia, Foggia, Italy
| | - Salvatore De Cosmo
- Department of Medical Sciences, Scientific Institute "Casa Sollievo della Sofferenza", San Giovanni Rotondo, FG, Italy
| | - Vincenzo Trischitta
- Mendel-Laboratory, Scientific Institute "Casa Sollievo della Sofferenza", San Giovanni Rotondo, FG, Italy.
- Research Unit of Diabetes and Endocrine Diseases, Scientific Institute "Casa Sollievo della Sofferenza", Viale Padre Pio, 71013, San Giovanni Rotondo, FG, Italy.
- Department of Experimental Medicine, "Sapienza" University of Rome, Rome, Italy.
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Piñero J, Queralt-Rosinach N, Bravo À, Deu-Pons J, Bauer-Mehren A, Baron M, Sanz F, Furlong LI. DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015; 2015:bav028. [PMID: 25877637 PMCID: PMC4397996 DOI: 10.1093/database/bav028] [Citation(s) in RCA: 589] [Impact Index Per Article: 65.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 03/09/2015] [Indexed: 11/25/2022]
Abstract
DisGeNET is a comprehensive discovery platform designed to address a variety of questions concerning the genetic underpinning of human diseases. DisGeNET contains over 380 000 associations between >16 000 genes and 13 000 diseases, which makes it one of the largest repositories currently available of its kind. DisGeNET integrates expert-curated databases with text-mined data, covers information on Mendelian and complex diseases, and includes data from animal disease models. It features a score based on the supporting evidence to prioritize gene-disease associations. It is an open access resource available through a web interface, a Cytoscape plugin and as a Semantic Web resource. The web interface supports user-friendly data exploration and navigation. DisGeNET data can also be analysed via the DisGeNET Cytoscape plugin, and enriched with the annotations of other plugins of this popular network analysis software suite. Finally, the information contained in DisGeNET can be expanded and complemented using Semantic Web technologies and linked to a variety of resources already present in the Linked Data cloud. Hence, DisGeNET offers one of the most comprehensive collections of human gene-disease associations and a valuable set of tools for investigating the molecular mechanisms underlying diseases of genetic origin, designed to fulfill the needs of different user profiles, including bioinformaticians, biologists and health-care practitioners. Database URL: http://www.disgenet.org/
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Affiliation(s)
- Janet Piñero
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, C/Dr Aiguader 88, E-08003 Barcelona, Spain, Roche Pharma Research and Early Development, pRED Informatics, Roche Innovation Center Penzberg, Roche Diagnostics GmbH, Nonnenwald 2, 82377 Penzberg, Germany and Scientific & Business Information Services, Roche Diagnostics GmbH, Nonnenwald 2, 82377 Penzberg, Germany
| | - Núria Queralt-Rosinach
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, C/Dr Aiguader 88, E-08003 Barcelona, Spain, Roche Pharma Research and Early Development, pRED Informatics, Roche Innovation Center Penzberg, Roche Diagnostics GmbH, Nonnenwald 2, 82377 Penzberg, Germany and Scientific & Business Information Services, Roche Diagnostics GmbH, Nonnenwald 2, 82377 Penzberg, Germany
| | - Àlex Bravo
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, C/Dr Aiguader 88, E-08003 Barcelona, Spain, Roche Pharma Research and Early Development, pRED Informatics, Roche Innovation Center Penzberg, Roche Diagnostics GmbH, Nonnenwald 2, 82377 Penzberg, Germany and Scientific & Business Information Services, Roche Diagnostics GmbH, Nonnenwald 2, 82377 Penzberg, Germany
| | - Jordi Deu-Pons
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, C/Dr Aiguader 88, E-08003 Barcelona, Spain, Roche Pharma Research and Early Development, pRED Informatics, Roche Innovation Center Penzberg, Roche Diagnostics GmbH, Nonnenwald 2, 82377 Penzberg, Germany and Scientific & Business Information Services, Roche Diagnostics GmbH, Nonnenwald 2, 82377 Penzberg, Germany
| | - Anna Bauer-Mehren
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, C/Dr Aiguader 88, E-08003 Barcelona, Spain, Roche Pharma Research and Early Development, pRED Informatics, Roche Innovation Center Penzberg, Roche Diagnostics GmbH, Nonnenwald 2, 82377 Penzberg, Germany and Scientific & Business Information Services, Roche Diagnostics GmbH, Nonnenwald 2, 82377 Penzberg, Germany
| | - Martin Baron
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, C/Dr Aiguader 88, E-08003 Barcelona, Spain, Roche Pharma Research and Early Development, pRED Informatics, Roche Innovation Center Penzberg, Roche Diagnostics GmbH, Nonnenwald 2, 82377 Penzberg, Germany and Scientific & Business Information Services, Roche Diagnostics GmbH, Nonnenwald 2, 82377 Penzberg, Germany
| | - Ferran Sanz
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, C/Dr Aiguader 88, E-08003 Barcelona, Spain, Roche Pharma Research and Early Development, pRED Informatics, Roche Innovation Center Penzberg, Roche Diagnostics GmbH, Nonnenwald 2, 82377 Penzberg, Germany and Scientific & Business Information Services, Roche Diagnostics GmbH, Nonnenwald 2, 82377 Penzberg, Germany
| | - Laura I Furlong
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, C/Dr Aiguader 88, E-08003 Barcelona, Spain, Roche Pharma Research and Early Development, pRED Informatics, Roche Innovation Center Penzberg, Roche Diagnostics GmbH, Nonnenwald 2, 82377 Penzberg, Germany and Scientific & Business Information Services, Roche Diagnostics GmbH, Nonnenwald 2, 82377 Penzberg, Germany
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Poveda A, Ibáñez ME, Rebato E. Common variants in BDNF, FAIM2, FTO, MC4R, NEGR1, and SH2B1 show association with obesity-related variables in Spanish Roma population. Am J Hum Biol 2014; 26:660-9. [PMID: 24948161 DOI: 10.1002/ajhb.22576] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 04/29/2014] [Accepted: 05/28/2014] [Indexed: 12/30/2022] Open
Abstract
OBJECTIVES The objective of this study is to investigate the association between previously GWAS identified genetic variants predisposing to obesity in Europeans and obesity-related phenotypes in Roma population. METHODS A total of 24 representative single nucleotide polymorphisms (SNPs) were genotyped in 372 individuals belonging to 50 extended families of Roma population. SNPs were tested for association with seven quantitative obesity-related phenotypes in the PLINK program. RESULTS Risk variants in NEGR1, FAIM2, FTO, and SH2B1 genes were associated with increased adiposity accumulation in Roma population with effect sizes between 0.21 and 0.34 Z-scores for each copy of the BMI increasing allele. Additionally, variants in BDNF and MC4R were significantly associated with adiposity distribution but not with overall fatness. No significant association was detected between obesity-related phenotypes and variants in the first intron of the FTO gene (e.g., rs9939609). CONCLUSIONS The results of this study suggest that SNPs in or near six genes (BDNF, FAIM2, FTO, MC4R, NEGR1, and SH2B1) are significantly associated with body fat accumulation and distribution in Roma people. However, the association observed among variants in the first intron of FTO and obesity in European derived populations is not evident in the analyzed Roma sample.
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Affiliation(s)
- Alaitz Poveda
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48080, Bilbao, Spain
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Oliveira RD, Cerda A, Genvigir FDV, Sampaio MF, Armaganijan D, Bernik MMS, Dorea EL, Hirata MH, Hinuy HM, Hirata RDC. Leptin receptor gene polymorphisms are associated with adiposity and metabolic alterations in Brazilian individuals. ACTA ACUST UNITED AC 2014; 57:677-84. [PMID: 24402012 DOI: 10.1590/s0004-27302013000900002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Accepted: 08/07/2013] [Indexed: 12/31/2022]
Abstract
OBJECTIVE The aim of the study was to investigate whether adiposity and metabolic markers, such as leptin, glucose, and lipids, are influenced by leptin (LEP) and leptin receptor (LEPR) gene polymorphisms in a sample of our population. SUBJECTS AND METHODS A group of 326 individuals of Caucasian-European descent, aged 30 to 80 years, 87 men and 239 women, 148 obese and 178 non-obese, was randomly selected at two clinical hospitals in the city of Sao Paulo, Brazil. All individuals declared their ethnic group as white during the initial interview. Anthropometric measurements, body mass index (BMI), and fat mass were evaluated. Blood samples were drawn for DNA extraction and measurements of leptin, soluble leptin receptor, glucose, and lipids. LEP -2548G>A and LEPR Lys109Arg (c.326A>G), Gln233Arg (c.668A>G) and Lys656Asn (c.1968G>C) polymorphisms were detected by PCR-RFLP. RESULTS Increased leptin and serum lipids, and LEPR Arg223Arg (GG genotype) were associated with higher risk for obesity (p < 0.05), while reduced risk was found in LEPR Arg109Arg (GG genotype) carriers (OR: 0.38, 95%CI: 0.19-0.77, p = 0.007). Multiple linear regression analysis showed a relationship between LEPR 223Arg, increased waist circumference, and leptinemia (p < 0.05), while LEPR 109Arg was associated with high total cholesterol and triglycerides (p < 0.05). LEPR haplotype 3 (AGG: 109Lys/233Arg/656Lys) carriers have increased risk for obesity (OR: 2.56, 95% CI: 1.19-5.49, p = 0.017). Moreover, this haplotype was associated with increased BMI, waist circumference, and leptinemia (p < 0.05). CONCLUSIONS LEPR polymorphisms are associated with obesity, hyperleptinemia, and atherogenic lipid profile, suggesting their potential role for leptin resistance and cardiovascular risk. Moreover, LEPR haplotype 3 confers susceptibility to adiposity and hyperleptinemia in our population.
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Leptin and leptin-related gene polymorphisms, obesity, and influenza A/H1N1 vaccine-induced immune responses in older individuals. Vaccine 2013; 32:881-7. [PMID: 24360890 DOI: 10.1016/j.vaccine.2013.12.009] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 11/15/2013] [Accepted: 12/01/2013] [Indexed: 02/08/2023]
Abstract
Obesity is a risk factor for complicated influenza A/H1N1 disease and poor vaccine immunogenicity. Leptin, an adipocyte-derived hormone/cytokine, has many immune regulatory functions and therefore could explain susceptibility to infections and poor vaccine outcomes. We recruited 159 healthy adults (50-74 years old) who were immunized with inactivated TIV influenza vaccine that contained A/California/7/2009/H1N1 virus. We found a strong correlation between leptin concentration and BMI (r=0.55, p<0.0001), but no association with hemagglutination antibody inhibition (HAI), B-cell, or granzyme B responses. We found a slight correlation between leptin concentration and an immunosenescence marker (TREC: T-cell receptor excision circles) level (r=0.23, p=0.01). We found eight SNPs in the LEP/LEPR/GHRL genes that were associated with leptin levels and four SNPs in the PTPN1/LEPR/STAT3 genes associated with peripheral blood TREC levels (p<0.05). Heterozygosity of the synonymous variant rs2230604 in the PTPN1 gene was associated with a significantly lower (531 vs. 259, p=0.005) TREC level, as compared to the homozygous major variant. We also found eight SNPs in the LEP/PPARG/CRP genes associated with variations in influenza-specific HAI and B-cell responses (p<0.05). Our results suggest that specific allelic variations in the leptin-related genes may influence adaptive immune responses to influenza vaccine.
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Li L, Lee KJ, Choi BC, Baek KH. Relationship between leptin receptor and polycystic ovary syndrome. Gene 2013; 527:71-4. [PMID: 23769971 DOI: 10.1016/j.gene.2013.05.074] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 05/10/2013] [Accepted: 05/24/2013] [Indexed: 10/26/2022]
Abstract
Polycystic ovary syndrome (PCOS) is one of the most common endocrine disorders, which is involved in the multi-system disease, and its etiology is still not clearly understood. It is currently considered that not only the genetic factors but also the environment factors play a crucial role in the pathogenesis of PCOS. Obesity plays an important role through the insulin, leptin and endocannabinoid system in the pathological process of PCOS, leading to more severe clinical manifestations. The aim of our present study is to investigate whether there is association between single nucleotide polymorphisms (SNPs) of Gln223Arg and Pro1019Pro in the leptin receptor gene (LEPR) and PCOS in a Korean population. Interestingly, a significant association was found between the Pro1019Pro in LEPR gene and PCOS, and a highly significant association was found between the Gln223Arg in LEPR gene and PCOS (P=0.033, OR=1.523, 95% confidence interval and P<0.0001, OR=0.446, 95% confidence interval). Moreover, genotype combination and haplotype analyses indicate that Gln223Arg and Pro1019Pro polymorphisms of LEPR are significantly associated with the risk of PCOS.
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Affiliation(s)
- Lan Li
- Department of Biomedical Science, CHA University, Bundang CHA Hospital, 502 Yatap-Dong, Bundang-Gu, Seongnam-Si, Gyeonggi-Do 463-840, Republic of Korea
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Goldfield GS, Dowler LM, Walker M, Cameron JD, Ferraro ZM, Doucet E, Adamo KB. Are dopamine-related genotypes risk factors for excessive gestational weight gain? Int J Womens Health 2013; 5:253-9. [PMID: 23723720 PMCID: PMC3665497 DOI: 10.2147/ijwh.s43935] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Background Excessive gestational weight gain is associated with postpartum weight retention and downstream child obesity. Dopamine plays a critical role in the regulation of energy intake and body weight. The purpose of this study was to examine the relationship between excessive gestational weight gain and dopamine pathway-related polymorphisms, namely the variable nucleotide tandem repeat in the 3′untranslated region (UTR) region of the SLC6A3 (DAT-1) dopamine transporter gene and the 30-base pair variable nucleotide tandem repeat polymorphism of the 5′UTR of the monoamine oxidase-A (MAO-A) gene. Methods Ninety-three women of mean age 31.7 ± 4.2 years were recruited from the Ottawa and Kingston birth cohort and assessed at 12–20 weeks’ gestation. Mean body mass index was 22.7 ± 2.5 kg/m2. Excessive gestational weight gain was defined according to the 2009 Institute of Medicine guidelines based on body mass index. Genotype analyses were performed using polymerase chain reaction and agarose gel electrophoresis. Results There was no relationship between the prevalence or magnitude of excessive gestational weight gain among women with the 3′ UTR single nucleotide polymorphism of the DAT-1 gene. However, 70% (19 of 27) of women carrying the MAO-A 4/4 (high activity) allele exceeded recommendations for gestational weight gain compared with 48% (32 of 60) of those with the pooled 3/3, 3/4, and 3/3.5 (low activity) alleles (P < 0.05). Similarly, those with the MAO-A 4/4 allele had significantly greater gestational weight gain than those with the 3/3, 3/4, or 3/3.5 pooled genotypes (19.3 ± 4.1 versus 17.0 ± 5.0 kg, P = 0.03). Conclusion Carriers of the 4/4 variants of the MAO-A gene may be at increased risk for excessive gestational weight gain.
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Affiliation(s)
- Gary S Goldfield
- Healthy Active Living and Obesity Research Group, Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada ; Department of Paediatrics, University of Ottawa, Ottawa, ON, Canada ; School of Human Kinetics, University of Ottawa, Ottawa, ON, Canada ; School of Psychology, University of Ottawa, Ottawa, ON, Canada ; Department of Psychology, Carleton University, Ottawa, ON, Canada
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Nguyen KDH, Pihur V, Ganesh SK, Rakha A, Cooper RS, Hunt SC, Freedman BI, Coresh J, Kao WHL, Morrison AC, Boerwinkle E, Ehret GB, Chakravarti A. Effects of rare and common blood pressure gene variants on essential hypertension: results from the Family Blood Pressure Program, CLUE, and Atherosclerosis Risk in Communities studies. Circ Res 2013; 112:318-26. [PMID: 23149595 PMCID: PMC3548950 DOI: 10.1161/circresaha.112.276725] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 11/12/2012] [Indexed: 12/16/2022]
Abstract
RATIONALE Hypertension affects ≈30% of adults in industrialized countries and is the major risk factor for cardiovascular disease. OBJECTIVE We sought to study the genetic effect of coding and conserved noncoding variants in syndromic hypertension genes on systolic blood pressure (BP) and diastolic BP to assess their overall impact on essential hypertension. METHODS AND RESULTS We resequenced 11 genes (AGT, CYP11B1, CYP17A1, HSD11B2, NR3C1, NR3C2, SCNN1A, SCNN1B, SCNN1G, WNK1, and WNK4) in 560 European American (EA) and African American ancestry GenNet participants with extreme systolic BP. We investigated genetic associations of 2535 variants with BP in 19997 EAs and in 6069 African Americans in 3 types of analyses. First, we studied the combined effects of all variants in GenNet. Second, we studied 1000 Genomes imputed polymorphic variants in 9747 EA and 3207 African American Atherosclerosis Risk in Communities subjects. Finally, we genotyped 37 missense and common noncoding variants in 6591 EAs and in 6521 individuals (3659 EA/2862 African American) from the CLUE and Family Blood Pressure Program studies, respectively. None of the variants individually reached significant false-discovery rates ≤0.05 for systolic BP and diastolic BP. However, on pooling all coding and noncoding variants, we identified at least 5 loci (AGT, CYP11B1, NR3C2, SCNN1G, and WNK1) with higher association at evolutionary conserved sites. CONCLUSIONS Both rare and common variants at these genes affect BP in the general population with modest effects sizes (<0.05 standard deviation units), and much larger sample sizes are required to assess the impact of individual genes. Collectively, conserved noncoding variants affect BP to a greater extent than missense mutations.
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Affiliation(s)
- Khanh-Dung H. Nguyen
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Pre-doctoral Training Program in Human Genetics and Molecular Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Vasyl Pihur
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Santhi K. Ganesh
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Ankit Rakha
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Richard S. Cooper
- Department of Community Medicine, Loyola University School of Medicine, Maywood, IL, USA
| | - Steven C. Hunt
- Cardiovascular Genetics Division, Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
| | - Barry I. Freedman
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Joe Coresh
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Wen H. L. Kao
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Alanna C. Morrison
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Eric Boerwinkle
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Georg B. Ehret
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Cardiology, Department of Specialties of Internal Medicine, Geneva University Hospital, Geneva, Switzerland
| | - Aravinda Chakravarti
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Gene-gene interaction between PPARδ and PPARγ is associated with abdominal obesity in a Chinese population. J Genet Genomics 2012; 39:625-31. [PMID: 23273766 DOI: 10.1016/j.jgg.2012.08.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Revised: 07/31/2012] [Accepted: 08/16/2012] [Indexed: 10/27/2022]
Abstract
The peroxisome proliferator-activated receptors (PPARs) -α, -δ/β and -γ are the ligand-activated transcription factors that function as the master regulators of glucose, fatty acid and lipoprotein metabolism, energy balance, cell proliferation and differentiation, inflammation, and atherosclerosis. The objective of the current study was to examine the main and interactive effect of seven single nucleotide polymorphisms (SNPs) of PPARδ/γ in contribution to abdominal obesity. A total of 820 subjects were randomly selected and no individuals were related. The selected SNPs in PPARδ (rs2016520 and rs9794) and PPARγ (rs10865710, rs1805192, rs709158, rs3856806, and rs4684847) were genotyped. Mean difference and 95% confident interval were calculated. Interactions were explored by the method of generalized multifactor dimensionality reduction. After adjustment for gender, age, and smoking status, it was found that the carriers of the C allele (TC + CC) of rs2016520 were associated with a decreased risk of abdominal obesity compared to the carriers of the TT genotype (mean difference = -2.63, 95% CI = -3.61--1.64, P < 0.0001). A significant two-locus model (P = 0.0107) involving rs2016520 and rs10865710 and a significant three-locus model (P = 0.0107) involving rs2016520, rs9794, and rs1805192 were observed. Overall, the three-locus model had the highest level of testing accuracy (59.85%) and showed a better cross-validation consistency (9/10) than two-locus model. Therefore, for abdominal obesity defined by waist circumference, we chose the three-locus model as the best interaction model. In conclusion, the C allele in rs2016520 was significantly associated with a lower abdominal obesity. Moreover, an interaction among rs2016520, rs1805192, and rs9794 on incident abdominal obesity could be demonstrated.
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Ruczinski I, Jorgensen TJ, Shugart YY, Schaad YB, Kessing B, Hoffman-Bolton J, Helzlsouer KJ, Kao W, Wheless L, Francis L, Alani RM, Strickland PT, Smith MW, Alberg AJ. A population-based study of DNA repair gene variants in relation to non-melanoma skin cancer as a marker of a cancer-prone phenotype. Carcinogenesis 2012; 33:1692-8. [PMID: 22581838 PMCID: PMC3514896 DOI: 10.1093/carcin/bgs170] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Revised: 05/02/2012] [Accepted: 05/08/2012] [Indexed: 11/13/2022] Open
Abstract
For unknown reasons, non-melanoma skin cancer (NMSC) is associated with increased risk of other malignancies. Focusing solely on DNA repair or DNA repair-related genes, this study tested the hypothesis that DNA repair gene variants contribute to the increased cancer risk associated with a personal history of NMSC. From the parent CLUE II cohort study, established in 1989 in Washington County, MD, the study consisted of a cancer-free control group (n 5 2296) compared with three mutually exclusive groups of cancer cases ascertained through 2007: (i) Other (non-NMSC) cancer only (n 5 2349); (ii) NMSC only (n 5 694) and (iii) NMSC plus other cancer (n 5 577). The frequency of minor alleles in 759 DNA repair gene single nucleotide polymorphisms (SNPs) was compared in these four groups. Comparing those with both NMSC and other cancer versus those with no cancer, 10 SNPs had allelic trend P-values <0.01. The two top-ranked SNPs were both within the thymine DNA glycosylase gene (TDG). One was a non-synonymous coding SNP (rs2888805) [per allele odds ratio (OR) 1.40, 95% confidence interval (CI) 1.16-1.70; P-value 5 0.0006] and the other was an intronic SNP in high linkage disequilibrium with rs2888805 (rs4135150). None of the associations had a P-value <6.6310(-5), the threshold for statistical significance after correcting for multiple comparisons. The results pinpoint DNA repair genes most likely to contribute to the NMSC cancer-prone phenotype. A promising lead is genetic variants in TDG, important not only in base excision repair but also in regulating the epigenome and gene expression, which may contribute to the NMSC-associated increase in overall cancer risk.
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Affiliation(s)
- Ingo Ruczinski
- Department of Biostatistics, The Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
- These authors contributed equally to this work
| | - Timothy J. Jorgensen
- Department of Radiation Medicine, Georgetown University School of MedicineWashington, DC, USA,
- These authors contributed equally to this work
| | - Yin Yao Shugart
- Division of Intramural Research Program, National Institute of Mental HealthBethesda, MD, USA
| | - Yvette Berthier Schaad
- Department of Epidemiology, The Johns Hopkins University Bloomberg School of Public HealthBaltimore, MD, USA
- Laboratory of Genomic Diversity, SAIC-Frederick, NCI-FrederickFrederick, MD
| | - Bailey Kessing
- Laboratory of Genomic Diversity, SAIC-Frederick, NCI-FrederickFrederick, MD
| | - Judith Hoffman-Bolton
- Department of Epidemiology, The Johns Hopkins University Bloomberg School of Public HealthBaltimore, MD, USA
- George W. Comstock Center for Public Health Research and PreventionWashington County, MD, USA,
| | | | - W.H.Linda Kao
- Department of Epidemiology, The Johns Hopkins University Bloomberg School of Public HealthBaltimore, MD, USA
| | - Lee Wheless
- Hollings Cancer Center and Division of Epidemiology and Biostatistics, Department of Medicine, Medical University of South CarolinaCharleston, SC, USA,
| | - Lesley Francis
- Hollings Cancer Center and Division of Epidemiology and Biostatistics, Department of Medicine, Medical University of South CarolinaCharleston, SC, USA,
| | - Rhoda M. Alani
- Department of Dermatology, Boston University School of MedicineBoston, MA, USA
| | - Paul T. Strickland
- Department of Epidemiology, The Johns Hopkins University Bloomberg School of Public HealthBaltimore, MD, USA
- Department of Environmental Health Sciences, The Johns Hopkins University Bloomberg School of Public HealthBaltimore, MD, USA
| | - Michael W. Smith
- Genetics and Genomics Group, Advanced Technology Program, SAIC-Frederick, Inc., NCI-FrederickFrederick, MD, USA
| | - Anthony J. Alberg
- Hollings Cancer Center and Division of Epidemiology and Biostatistics, Department of Medicine, Medical University of South CarolinaCharleston, SC, USA,
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Jorgensen TJ, Ruczinski I, Yao Shugart Y, Wheless L, Berthier Schaad Y, Kessing B, Hoffman-Bolton J, Helzlsouer KJ, Kao WHL, Francis L, Alani RM, Strickland PT, Smith MW, Alberg AJ. A population-based study of hedgehog pathway gene variants in relation to the dual risk of basal cell carcinoma plus another cancer. Cancer Epidemiol 2012; 36:e288-93. [PMID: 22677152 DOI: 10.1016/j.canep.2012.05.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2012] [Revised: 05/01/2012] [Accepted: 05/03/2012] [Indexed: 11/28/2022]
Abstract
INTRODUCTION A personal history of basal cell carcinoma (BCC) is associated with increased risk of other malignancies, but the reason is unknown. The hedgehog pathway is critical to the etiology of BCC, and is also believed to contribute to susceptibility to other cancers. This study tested the hypothesis that hedgehog pathway and pathway-related gene variants contribute to the increased risk of subsequent cancers among those with a history of BCC. METHODS The study was nested within the ongoing CLUE II cohort study, established in 1989 in Washington County, Maryland, USA. The study consisted of a cancer-free control group (n=2296) compared to three different groups of cancer cases ascertained through 2007, those diagnosed with: (1) Other (non-BCC) cancer only (n=2349); (2) BCC only (n=534); and (3) BCC plus other cancer (n=446). The frequencies of variant alleles were compared among these four groups for 20 single nucleotide polymorphisms (SNPs) in 6 hedgehog pathway genes (SHH, IHH, PTCH2, SMO, GLI1, SUFU), and also 22 SNPs in VDR and 8 SNPs in FAS, which have cross-talk with the hedgehog pathway. RESULTS Comparing those with both BCC and other cancer versus those with no cancer, no significant associations were observed for any of the hedgehog pathway SNPs, or for the FAS SNPs. One VDR SNP was nominally significantly associated with the BCC cancer-prone phenotype, rs11574085 [per minor allele odds ratio (OR) 1.38, 95% confidence interval (CI) 1.05-1.82; p-value=0.02]. CONCLUSION The hedgehog pathway gene SNPs studied, along with the VDR and FAS SNPs studied, are not strongly associated with the BCC cancer-prone phenotype.
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Affiliation(s)
- Timothy J Jorgensen
- Department of Radiation Medicine, Georgetown University School of Medicine, Washington, DC, USA
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Enns JE, Taylor CG, Zahradka P. Variations in Adipokine Genes AdipoQ, Lep, and LepR are Associated with Risk for Obesity-Related Metabolic Disease: The Modulatory Role of Gene-Nutrient Interactions. J Obes 2011; 2011:168659. [PMID: 21773001 PMCID: PMC3136149 DOI: 10.1155/2011/168659] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2011] [Accepted: 03/10/2011] [Indexed: 02/08/2023] Open
Abstract
Obesity rates are rapidly increasing worldwide and facilitate the development of many related disease states, such as cardiovascular disease, the metabolic syndrome, type 2 diabetes mellitus, and various types of cancer. Variation in metabolically important genes can have a great impact on a population's susceptibility to becoming obese and/or developing related complications. The adipokines adiponectin and leptin, as well as the leptin receptor, are major players in the regulation of body energy homeostasis and fat storage. This paper summarizes the findings of single nucleotide polymorphisms in these three genes and their effect on obesity and metabolic disease risk. Additionally, studies of gene-nutrient interactions involving adiponectin, leptin, and the leptin receptor are highlighted to emphasize the critical role of diet in susceptible populations.
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Affiliation(s)
- Jennifer Emily Enns
- Department of Physiology, University of Manitoba and Canadian Centre for Agri-Food Research in Health and Medicine, St. Boniface Hospital Research Centre, 351 Tache Ave, Winnipeg, Manitoba, Canada R2H 2A6
| | - Carla G. Taylor
- Departments of Human Nutritional Sciences and Physiology, University of Manitoba, 351 Tache Ave, Winnipeg, Manitoba, Canada R2H 2A6
| | - Peter Zahradka
- Departments of Physiology and Human Nutritional Sciences, University of Manitoba and Canadian Centre for Agri-Food Research in Health and Medicine, St. Boniface Hospital Research Centre, 351 Tache Ave, Winnipeg, Manitoba, Canada R2H 2A6
- *Peter Zahradka:
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