1
|
Chen XF, Gong C. FTO in Lung Cancer: Its Progression and Therapeutic Potential. Comb Chem High Throughput Screen 2024; 27:2301-2307. [PMID: 38485681 DOI: 10.2174/0113862073281598240227072839] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/18/2024] [Accepted: 01/31/2024] [Indexed: 08/21/2024]
Abstract
One of the most fatal and frequent malignancies on the planet is lung cancer. Its occurrence and development are the results of multifactorial and multigenic interactions. In recent years, RNA N6-methyladenosine transferase (FTO) has gained significant attention in the field of oncology. FTO is the first RNA demethylase to be found to control target mRNA demethylation. The growth, proliferation, and metastasis of tumor cells are greatly influenced by FTO. Recent studies have found that imbalanced m6A methylation regulatory proteins can induce disruption of downstream RNA metabolism, strongly affecting tumor development. This paper provides an overview of the relationship between FTO and lung cancer, discussing the mechanisms by which FTO is involved in lung cancer and its potential clinical applications.
Collapse
Affiliation(s)
- Xue-Fen Chen
- Geriatrics Respiratory Medicine Department, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Chen Gong
- Geriatrics Respiratory Medicine Department, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| |
Collapse
|
2
|
Sprague AC, Niu L, Jandarov R, Zhang X, Zhang G, Chen A, Šarac J, Čoklo M, Missoni S, Rudan P, Langevin SM, Deka R. Stable methylation loci are associated with systolic blood pressure in a Croatian island population. Epigenomics 2022; 14:1343-1354. [PMID: 36453021 PMCID: PMC9816922 DOI: 10.2217/epi-2022-0279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 11/03/2022] [Indexed: 12/03/2022] Open
Abstract
Background: The objective was to identify stable and dynamic DNA methylation loci associated with cardiometabolic traits among an adult population from the Croatian island of Hvar. Materials & methods: An epigenome-wide association study was conducted using peripheral blood longitudinally collected at two time points 10 years apart via Infinium MethylationEPIC beadarray (n = 112). Stable and dynamic loci were identified using linear mixed models. Associations between cardiometabolic traits and loci were assessed using linear models. Results: 22 CpG loci were significantly associated with systolic blood pressure. Twenty were stable and two were dynamic. Conclusion: Multiple genes may be involved in the determination of systolic blood pressure level via stable epigenetic programming, potentially established earlier in life.
Collapse
Affiliation(s)
- Alexander C Sprague
- Division of Epidemiology, Department of Environmental & Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Liang Niu
- Division of Biostatistics & Bioinformatics, Department of Environmental & Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Roman Jandarov
- Division of Biostatistics & Bioinformatics, Department of Environmental & Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Xiang Zhang
- Division of Environmental Genetics & Molecular Toxicology, Department of Environmental & Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Ge Zhang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Aimin Chen
- Department of Biostatistics, Epidemiology & Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jelena Šarac
- Institute for Anthropological Research, Zagreb, Croatia
| | - Miran Čoklo
- Institute for Anthropological Research, Zagreb, Croatia
| | - Sasa Missoni
- Institute for Anthropological Research, Zagreb, Croatia
| | - Pavao Rudan
- Anthropological Center & Scientific Council for Anthropological Research, Croatian Academy of Arts & Sciences, Zagreb, Croatia
| | - Scott M Langevin
- Division of Epidemiology, Department of Environmental & Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
- University of Cincinnati Cancer Center, Cincinnati, OH 45267, USA
| | - Ranjan Deka
- Division of Epidemiology, Department of Environmental & Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| |
Collapse
|
3
|
Wei H, Li Z, Liu F, Wang Y, Ding S, Chen Y, Liu J. The Role of FTO in Tumors and It's Research Progress. Curr Med Chem 2021; 29:924-933. [PMID: 34269659 DOI: 10.2174/0929867328666210714153046] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 05/24/2021] [Accepted: 06/02/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND A malignant tumor is a disease that seriously threatens human health. At present, more and more research results show that the pathogenesis of different tumors is very complicated, and the methods of clinical treatment are also diverse. This review analyzes and summarizes the role of fat mass and obesity-associated (FTO) genes in different tumors and provides a reference value for research and drug treatment methods. METHOD We conducted a comprehensive literature search using the database. According to the article's primary purpose, irrelevant articles were excluded from the research summary and included in the relevant articles. Finally, the relevant information of the article was summarized. RESULT In this article, the relationship between malignant tumors and FTO is introduced by citing many documents. In addition, the inhibitors that act on FTO are listed. CONCLUSION This article has shown that FTO protein is a demethylase that can regulate N6-methyladenosine (m6A) levels in mRNA and plays a crucial role in the progression and resistance of various tumors such as leukemia, breast cancer, and lung cancer.
Collapse
Affiliation(s)
- Hao Wei
- College of Pharmacy of Liaoning University, Shenyang, Liaoning 10036. China
| | - Zhen Li
- College of Pharmacy of Liaoning University, Shenyang, Liaoning 10036. China
| | - Fang Liu
- College of Pharmacy of Liaoning University, Shenyang, Liaoning 10036. China
| | - Yang Wang
- College of Pharmacy of Liaoning University, Shenyang, Liaoning 10036. China
| | - Shi Ding
- College of Pharmacy of Liaoning University, Shenyang, Liaoning 10036. China
| | - Ye Chen
- College of Pharmacy of Liaoning University, Shenyang, Liaoning 10036. China
| | - Ju Liu
- College of Pharmacy of Liaoning University, Shenyang, Liaoning 10036. China
| |
Collapse
|
4
|
Rana S, Sultana A, Bhatti AA. Effect of interaction between obesity-promoting genetic variants and behavioral factors on the risk of obese phenotypes. Mol Genet Genomics 2021; 296:919-938. [PMID: 33966103 DOI: 10.1007/s00438-021-01793-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 04/22/2021] [Indexed: 01/28/2023]
Abstract
The studies investigating gene-gene and gene-environment (or gene-behavior) interactions provide valuable insight into the pathomechanisms underlying obese phenotypes. The Pakistani population due to its unique characteristics offers numerous advantages for conducting such studies. In this view, the current study was undertaken to examine the effects of gene-gene and gene-environment/behavior interactions on the risk of obesity in a sample of Pakistani population. A total of 578 adult participants including 290 overweight/obese cases and 288 normal-weight controls were involved. The five key obesity-associated genetic variants namely MC4R rs17782313, BDNF rs6265, FTO rs1421085, TMEM18 rs7561317, and NEGR1 rs2815752 were genotyped using the TaqMan allelic discrimination assays. The data related to behavioral factors, such as eating pattern, diet consciousness, the tendency toward fat-dense food (TFDF), sleep duration, sleep-wake cycle (SWC), shift work (SW), and physical activity levels were collected via a questionnaire. Gene-gene and gene-behavior interactions were analyzed by multifactor dimensionality reduction and linear regression, respectively. In our study, only TMEM18 rs7561317 was found to be significantly associated with anthropometric traits with no significant effect of gene-gene interactions were observed on obesity-related phenotypes. However, the genetic variants were found to interact with the behavioral factors to significantly influence various obesity-related anthropometric traits including BMI, waist circumference, hip circumference, waist-to-hip ratio, waist-to-height ratio, and percentage of body fat. In conclusion, the interaction between genetic architecture and behavior/environment determines the outcome of obesity-related anthropometric phenotypes. Thus, gene-environment/behavior interaction studies should be promoted to explore the risk of complex and multifactorial disorders, such as obesity.
Collapse
Affiliation(s)
- Sobia Rana
- Molecular Biology and Human Genetics Laboratory, Dr. Panjwani Center for Molecular Medicine and Drug Research (PCMD), International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, 75270, Pakistan.
| | - Ayesha Sultana
- Molecular Biology and Human Genetics Laboratory, Dr. Panjwani Center for Molecular Medicine and Drug Research (PCMD), International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, 75270, Pakistan
| | - Adil Anwar Bhatti
- Molecular Biology and Human Genetics Laboratory, Dr. Panjwani Center for Molecular Medicine and Drug Research (PCMD), International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, 75270, Pakistan
| |
Collapse
|
5
|
Hughes AE, Hayes MG, Egan AM, Patel KA, Scholtens DM, Lowe LP, Lowe WL, Dunne FP, Hattersley AT, Freathy RM. All thresholds of maternal hyperglycaemia from the WHO 2013 criteria for gestational diabetes identify women with a higher genetic risk for type 2 diabetes. Wellcome Open Res 2021; 5:175. [PMID: 33869792 PMCID: PMC8030121 DOI: 10.12688/wellcomeopenres.16097.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2021] [Indexed: 11/20/2022] Open
Abstract
Background: Using genetic scores for fasting plasma glucose (FPG GS) and type 2 diabetes (T2D GS), we investigated whether the fasting, 1-hour and 2-hour glucose thresholds from the WHO 2013 criteria for gestational diabetes (GDM) have different implications for genetic susceptibility to raised fasting glucose and type 2 diabetes in women from the Hyperglycemia and Adverse Pregnancy Outcome (HAPO) and Atlantic Diabetes in Pregnancy (DIP) studies. Methods: Cases were divided into three subgroups: (i) FPG ≥5.1 mmol/L only, n=222; (ii) 1-hour glucose post 75 g oral glucose load ≥10 mmol/L only, n=154 (iii) 2-hour glucose ≥8.5 mmol/L only, n=73; and (iv) both FPG ≥5.1 mmol/L and either of a 1-hour glucose ≥10 mmol/L or 2-hour glucose ≥8.5 mmol/L, n=172. We compared the FPG and T2D GS of these groups with controls (n=3,091) in HAPO and DIP separately. Results: In HAPO and DIP, the mean FPG GS in women with a FPG ≥5.1 mmol/L, either on its own or with 1-hour glucose ≥10 mmol/L or 2-hour glucose ≥8.5 mmol/L, was higher than controls (all P <0.01). Mean T2D GS in women with a raised FPG alone or with either a raised 1-hour or 2-hour glucose was higher than controls (all P <0.05). GDM defined by 1-hour or 2-hour hyperglycaemia only was also associated with a higher T2D GS than controls (all P <0.05). Conclusions: The different diagnostic categories that are part of the WHO 2013 criteria for GDM identify women with a genetic predisposition to type 2 diabetes as well as a risk for adverse pregnancy outcomes.
Collapse
Affiliation(s)
- Alice E Hughes
- Institute of Biomedical and Clinical Science, University of Exeter, Exeter, UK
- Royal Devon and Exeter Hospitals NHS Foundation Trust, Exeter, UK
| | - M Geoffrey Hayes
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Aoife M Egan
- Division of Endocrinology, Diabetes and Metabolism, Mayo Clinic School of Medicine, Rochester, MN, USA
| | - Kashyap A Patel
- Institute of Biomedical and Clinical Science, University of Exeter, Exeter, UK
- Royal Devon and Exeter Hospitals NHS Foundation Trust, Exeter, UK
| | | | - Lynn P Lowe
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - William L Lowe
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Fidelma P Dunne
- Galway Diabetes Research Centre and Saolta Hospital Group, National University of Ireland, Galway, Galway, Ireland
| | - Andrew T Hattersley
- Institute of Biomedical and Clinical Science, University of Exeter, Exeter, UK
- Royal Devon and Exeter Hospitals NHS Foundation Trust, Exeter, UK
- National Institute for Health Research Exeter Clinical Research Facility, Exeter, UK
| | - Rachel M Freathy
- Institute of Biomedical and Clinical Science, University of Exeter, Exeter, UK
| |
Collapse
|
6
|
Hughes AE, Hayes MG, Egan AM, Patel KA, Scholtens DM, Lowe LP, Lowe WL, Dunne FP, Hattersley AT, Freathy RM. All thresholds of maternal hyperglycaemia from the WHO 2013 criteria for gestational diabetes identify women with a higher genetic risk for type 2 diabetes. Wellcome Open Res 2020; 5:175. [PMID: 33869792 PMCID: PMC8030121.2 DOI: 10.12688/wellcomeopenres.16097.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/13/2020] [Indexed: 04/02/2024] Open
Abstract
Background: Using genetic scores for fasting plasma glucose (FPG GS) and type 2 diabetes (T2D GS), we investigated whether the fasting, 1-hour and 2-hour glucose thresholds from the WHO 2013 criteria for gestational diabetes (GDM) have different implications for genetic susceptibility to raised fasting glucose and type 2 diabetes in women from the Hyperglycemia and Adverse Pregnancy Outcome (HAPO) and Atlantic Diabetes in Pregnancy (DIP) studies. Methods: Cases were divided into three subgroups: (i) FPG ≥5.1 mmol/L only, n=222; (ii) 1-hour glucose post 75 g oral glucose load ≥10 mmol/L only, n=154 (iii) 2-hour glucose ≥8.5 mmol/L only, n=73; and (iv) both FPG ≥5.1 mmol/L and either of a 1-hour glucose ≥10 mmol/L or 2-hour glucose ≥8.5 mmol/L, n=172. We compared the FPG and T2D GS of these groups with controls (n=3,091) in HAPO and DIP separately. Results: In HAPO and DIP, the mean FPG GS in women with a FPG ≥5.1 mmol/L, either on its own or with 1-hour glucose ≥10 mmol/L or 2-hour glucose ≥8.5 mmol/L, was higher than controls (all P <0.01). Mean T2D GS in women with a raised FPG alone or with either a raised 1-hour or 2-hour glucose was higher than controls (all P <0.05). GDM defined by 1-hour or 2-hour hyperglycaemia only was also associated with a higher T2D GS than controls (all P <0.05). Conclusions: The different diagnostic categories that are part of the WHO 2013 criteria for GDM identify women with a genetic predisposition to type 2 diabetes as well as a risk for adverse pregnancy outcomes.
Collapse
Affiliation(s)
- Alice E Hughes
- Institute of Biomedical and Clinical Science, University of Exeter, Exeter, UK
- Royal Devon and Exeter Hospitals NHS Foundation Trust, Exeter, UK
| | - M Geoffrey Hayes
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Aoife M Egan
- Division of Endocrinology, Diabetes and Metabolism, Mayo Clinic School of Medicine, Rochester, MN, USA
| | - Kashyap A Patel
- Institute of Biomedical and Clinical Science, University of Exeter, Exeter, UK
- Royal Devon and Exeter Hospitals NHS Foundation Trust, Exeter, UK
| | | | - Lynn P Lowe
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - William L Lowe
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Fidelma P Dunne
- Galway Diabetes Research Centre and Saolta Hospital Group, National University of Ireland, Galway, Galway, Ireland
| | - Andrew T Hattersley
- Institute of Biomedical and Clinical Science, University of Exeter, Exeter, UK
- Royal Devon and Exeter Hospitals NHS Foundation Trust, Exeter, UK
- National Institute for Health Research Exeter Clinical Research Facility, Exeter, UK
| | - Rachel M Freathy
- Institute of Biomedical and Clinical Science, University of Exeter, Exeter, UK
| |
Collapse
|
7
|
Rana S, Bhatti AA. Association and interaction of the FTO rs1421085 with overweight/obesity in a sample of Pakistani individuals. Eat Weight Disord 2020; 25:1321-1332. [PMID: 31468339 DOI: 10.1007/s40519-019-00765-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 08/06/2019] [Indexed: 12/31/2022] Open
Abstract
PURPOSE Genetic variants determine the predisposition of an individual to obesity in a given environment. The present study was conducted to seek an association of the FTO variant rs1421085 with overweight/obesity and related traits in 612 Pakistani subjects in a case-control manner (overweight/obese = 306 and non-obese = 306). Moreover, interaction effects of the rs1421085 and overweight/obesity on multiple metabolic traits were also investigated, which were never explored before in Pakistani as well as in any other population. MATERIALS AND METHODS Anthropometric traits were measured by standard procedures, while metabolic parameters were determined by biochemical assays. Genotyping of the rs1421085 was carried out by TaqMan allelic discrimination assay. The data were analysed using SPSS software version 19. RESULTS The study revealed a significant association of the rs1421085 with overweight/obese phenotype with respect to over-dominant model indicated by h-index. The CT genotype of the rs1421085 was observed to increase the risk of being overweight/obese by 1.583 times (95% CI 1.147-2.185, p = 0.005). The CT genotype was also found to be associated with higher values of all anthropometric variables (except height and waist-to-hip ratio). Moreover, the interaction between the CT genotype of the rs1421085 and overweight/obesity was found to influence several metabolic parameters (raised blood pressure, product of triglyceride and glucose index, triglyceride levels, LDL-C, VLDL-C, coronary risk index, atherogenic index, and triglyceride-to-HDL-C ratio). CONCLUSION In conclusion, the rs1421085 was found to be associated with overweight/obesity and related anthropometric traits independent of age and gender in Pakistani population. Moreover, this variant was found to influence various metabolic traits in the presence of overweight/obesity. LEVEL OF EVIDENCE Level III, case-control analytic study.
Collapse
Affiliation(s)
- Sobia Rana
- Dr. Panjwani Center for Molecular Medicine and Drug Research (PCMD), International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, 75270, Pakistan.
| | - Adil Anwar Bhatti
- Dr. Panjwani Center for Molecular Medicine and Drug Research (PCMD), International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, 75270, Pakistan
| |
Collapse
|
8
|
Hughes AE, Hayes MG, Egan AM, Patel KA, Scholtens DM, Lowe LP, Lowe Jr WL, Dunne FP, Hattersley AT, Freathy RM. All thresholds of maternal hyperglycaemia from the WHO 2013 criteria for gestational diabetes identify women with a higher genetic risk for type 2 diabetes. Wellcome Open Res 2020; 5:175. [PMID: 33869792 PMCID: PMC8030121 DOI: 10.12688/wellcomeopenres.16097.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/09/2020] [Indexed: 04/02/2024] Open
Abstract
Background: Using genetic scores for fasting plasma glucose (FPG GS) and type 2 diabetes (T2D GS), we investigated whether the fasting, 1-hour and 2-hour glucose thresholds from the WHO 2013 criteria for gestational diabetes (GDM) have different implications for genetic susceptibility to raised fasting glucose and type 2 diabetes in women from the Hyperglycemia and Adverse Pregnancy Outcome (HAPO) and Atlantic Diabetes in Pregnancy (DIP) studies. Methods: Cases were divided into three subgroups: (i) FPG ≥5.1 mmol/L only, n=222; (ii) 1-hour glucose post 75 g oral glucose load ≥10 mmol/L only, n=154 (iii) 2-hour glucose ≥8.5 mmol/L only, n=73; and (iv) both FPG ≥5.1 mmol/L and either of a 1-hour glucose ≥10 mmol/L or 2-hour glucose ≥8.5 mmol/L, n=172. We compared the FPG and T2D GS of these groups with controls (n=3,091) in HAPO and DIP separately. Results: In HAPO and DIP, the mean FPG GS in women with a FPG ≥5.1 mmol/L, either on its own or with 1-hour glucose ≥10 mmol/L or 2-hour glucose ≥8.5 mmol/L, was higher than controls (all P <0.01). Mean T2D GS in women with a raised FPG alone or with either a raised 1-hour or 2-hour glucose was higher than controls (all P <0.05). GDM defined by 1-hour or 2-hour hyperglycaemia only was also associated with a higher T2D GS than controls (all P <0.05). Conclusions: The different diagnostic categories that are part of the WHO 2013 criteria for GDM identify women with a genetic predisposition to type 2 diabetes as well as a risk for adverse pregnancy outcomes.
Collapse
Affiliation(s)
- Alice E. Hughes
- Institute of Biomedical and Clinical Science, University of Exeter, Exeter, UK
- Royal Devon and Exeter Hospitals NHS Foundation Trust, Exeter, UK
| | - M. Geoffrey Hayes
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Aoife M. Egan
- Division of Endocrinology, Diabetes and Metabolism, Mayo Clinic School of Medicine, Rochester, MN, USA
| | - Kashyap A. Patel
- Institute of Biomedical and Clinical Science, University of Exeter, Exeter, UK
- Royal Devon and Exeter Hospitals NHS Foundation Trust, Exeter, UK
| | | | - Lynn P. Lowe
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | | | - Fidelma P. Dunne
- Galway Diabetes Research Centre and Saolta Hospital Group, National University of Ireland, Galway, Galway, Ireland
| | - Andrew T. Hattersley
- Institute of Biomedical and Clinical Science, University of Exeter, Exeter, UK
- Royal Devon and Exeter Hospitals NHS Foundation Trust, Exeter, UK
- National Institute for Health Research Exeter Clinical Research Facility, Exeter, UK
| | - Rachel M. Freathy
- Institute of Biomedical and Clinical Science, University of Exeter, Exeter, UK
| |
Collapse
|
9
|
Mehrdad M, Fardaei M, Fararouei M, Eftekhari MH. The association between FTO rs9939609 gene polymorphism and anthropometric indices in adults. J Physiol Anthropol 2020; 39:14. [PMID: 32398148 PMCID: PMC7218491 DOI: 10.1186/s40101-020-00224-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 04/22/2020] [Indexed: 02/06/2023] Open
Abstract
Background Fat mass and obesity-associated gene (FTO) is the most studied obesity-related gene up to date. We aimed to assess anthropometric indices in carriers of FTO rs9939609 polymorphism with overweight across Iranian population (Shiraz) to find out the associations of this polymorphism with obesity indices. Methods This was a cross-sectional study conducted on 198 overweight healthy adults aged 20-45 years old. We assessed the body composition of the participants using bioelectrical impedance analyzer. In addition, we measured the waist circumference (WC) and hip circumference (HC). Waist to hip ratio (WHR) and waist to height ratio (WHtR) were also calculated by equations. The participants’ genotype was determined by ARMS-PCR. Also, data analysis was performed using SPSS software version 20 and R software version 3.6.2. Results The mean values of body mass index (BMI) and age of the participants were 26.93 ± 1.13 kg/m2 and 33.33 ± 6.35 years old, respectively. Homozygous carriers of A-allele had significantly higher values for BMI (0.60 kg/m2, p = 0.026), WHR (0.04 unit, p = 0.003), and WHtR (0.02 unit, p = 0.030) than the homozygous carriers of T-allele. Individuals with AA genotype had greater WC (2.66 cm, p = 0.042, and 4.03 cm, p = 0.002), fat mass (2.24 kg, p = 0.004, and 3.02 kg, p = 0.001), and trunk fat (1.53 kg, p = 0.001, and 2.08 kg, p = 0.001) compared to those with AT and TT genotypes, respectively. Interestingly, after adjustment of the confounders, significant associations were observed among rs9939609 polymorphism and BMI, Wt, WC, trunk fat percentage, WHR, and WHtR. Conclusions A-allele of the FTO rs9939609 polymorphism was indicated to be associated with greater general and central obesity in adult population of Shiraz, Iran.
Collapse
Affiliation(s)
- Mahsa Mehrdad
- Department of Clinical Nutrition, School of Nutrition & Food Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Majid Fardaei
- Department of Medical Genetic, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Fararouei
- HIV/AIDs Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Hassan Eftekhari
- Department of Clinical Nutrition, School of Nutrition & Food Sciences, Shiraz University of Medical Sciences, Shiraz, Iran.
| |
Collapse
|
10
|
Chen A, Jandarov R, Zhou L, Calafat AM, Zhang G, Urbina EM, Sarac J, Augustin DH, Caric T, Bockor L, Petranovic MZ, Novokmet N, Missoni S, Rudan P, Deka R. Association of perfluoroalkyl substances exposure with cardiometabolic traits in an island population of the eastern Adriatic coast of Croatia. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 683:29-36. [PMID: 31129329 PMCID: PMC6581612 DOI: 10.1016/j.scitotenv.2019.05.250] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 05/15/2019] [Accepted: 05/17/2019] [Indexed: 05/31/2023]
Abstract
BACKGROUND Exposure to perfluoroalkyl substances (PFAS), ubiquitous environmental contaminants, may be related to cardiometabolic diseases in adults. Studies in European populations to examine the association of PFAS exposure and comprehensive cardiometabolic traits and metabolic syndrome (MetS) are limited. METHODS In this pilot cross-sectional study of a well-characterized adult population of the island of Hvar, situated off the eastern Adriatic coast of Croatia, we measured PFAS concentrations in plasma samples collected during 2007-2008 and examined their cross-sectional associations with cardiometabolic traits and MetS after adjustment of covariates (n = 122). PFAS investigated in this study included perfluorooctane sulfonic acid (PFOS), perfluorooctanoic acid (PFOA), perfluorohexane sulfonic acid (PFHxS), and perfluorononanoic acid (PFNA). RESULTS The geometric mean (range) was 8.91 (2.36, 33.67) ng/mL for PFOS, 2.87 (1.03, 8.02) ng/mL for PFOA, 0.77 (0.25, 2.40) ng/mL for PFHxS, and 1.29 (0.48, 3.46) ng/mL for PFNA, with frequency of detection at 100%, 100%, 95.9%, and 100%, respectively. PFOS, PFOA, and PFNA concentrations were positively associated with the risk of MetS as defined by the Adult Treatment Panel III (ATP III) criteria, with estimated odds ratios and 95% confidence intervals at 1.89 (0.93, 3.86), 2.19 (0.88, 5.44), and 2.95 (1.12, 7.80), respectively, with only PFNA reaching statistical significance. PFNA concentrations were associated with increased risk of overweight or obesity. CONCLUSIONS Background exposure to PFOS, PFOA, and PFNA was marginally associated with increased risk of MetS in this small study, and these results should be confirmed with a larger sample size and longitudinal follow-up.
Collapse
Affiliation(s)
- Aimin Chen
- Division of Epidemiology, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
| | - Roman Jandarov
- Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Li Zhou
- Division of Epidemiology, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Department of Epidemiology, School of Public Health and Management, Chongqing Medical University, Chongqing, China
| | - Antonia M Calafat
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ge Zhang
- Division of Human Genetics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Elaine M Urbina
- Heart Institute, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Jelena Sarac
- Institute for Anthropological Research, Zagreb, Croatia
| | | | - Tonko Caric
- Institute for Anthropological Research, Zagreb, Croatia
| | - Luka Bockor
- Institute for Anthropological Research, Zagreb, Croatia
| | | | | | - Sasa Missoni
- Institute for Anthropological Research, Zagreb, Croatia; Josip Juraj Strossmayer University of Osijek, Faculty of Medicine, Osijek, Croatia
| | - Pavao Rudan
- Institute for Anthropological Research, Zagreb, Croatia; Croatian Academy of Sciences and Arts, Zagreb, Croatia
| | - Ranjan Deka
- Division of Epidemiology, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
| |
Collapse
|
11
|
Single-Nucleotide-Polymorphism-Panel Population-Genetics Approach Based on the 1000 Genomes Database and Elite Soccer Players. Int J Sports Physiol Perform 2019; 14:711-717. [PMID: 30427247 DOI: 10.1123/ijspp.2018-0715] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Purpose: Soccer is one of the most popular sports worldwide, a physical activity of great physiological demand and complexity. Currently, numerous trials involving physiological responses such as hypertrophy, energy expenditure, vasodilation, cardiac output, VO2max, and recovery have supported the possibility of genomic predictors' affecting performance. In a complementary way to association studies with single nucleotide polymorphisms (SNPs), the objective was to evaluate if the use of population genetics data from human-genomics databases can provide information for a better understanding of the relationship between heritability and sport performance. Methods: The study included 25 healthy male professional soccer players (25.5 [4.3] y, 177.4 [6.4] cm, 76.4 [6.4] kg, body fat 10.5% [4.3%]) from the Brazilian first-division soccer club. Anthropometric measurements and field and isokinetic tests were performed to evaluate performance and physiologic parameters of subjects. Moreover, 10 genetic polymorphisms previously related to performance were genotyped. The genotypes of the same polymorphisms were obtained for 2504 individuals from the populations deposited in the 1000 Genomes database. A principal-component analysis and matrix genetic-distances approach (Fst) were evaluated. Results: As expected, the admixture Brazilian population has numerous genetic similarities with the European and American populations from genomic databases. Although the African component is absolutely recognized in genomes from the Brazilian population, using the specific performance-related SNPs, surprisingly the African population was one of the most genetically distant of the players (P < .00001). Conclusions: The early results suggest a selective pressure on genes of elite soccer players, possibly related simultaneously to physical-performance, environmental, cognitive, and sociocultural aspects.
Collapse
|
12
|
Novel positioning from obesity to cancer: FTO, an m 6A RNA demethylase, regulates tumour progression. J Cancer Res Clin Oncol 2018; 145:19-29. [PMID: 30465076 DOI: 10.1007/s00432-018-2796-0] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 11/13/2018] [Indexed: 12/28/2022]
Abstract
PURPOSE The fat mass- and obesity-associated (FTO) gene on chromosome 16q12.2 shows an intimate association with obesity and body mass index. Recently, research into the FTO gene and its expression product has attracted widespread interest due to the identification of FTO as an N6-methyladenosine (m6A) demethylase. FTO primarily regulates the m6A levels of downstream targets via their 3' untranslated regions. FTO not only plays a critical role in obesity-related diseases but also is involved in the occurrence, development and prognosis of many types of cancer, such as acute myeloid leukaemia, glioblastoma and breast cancer. Currently, studies indicate that FTO is a crucial component of m6A modification, it regulates cancer stem cell function, and promotes the growth, self-renewal and metastasis of cancer cells. In this review, we summarized and analysed the data regarding the structural features and biological functions of FTO as well as its association with different cancers and possible molecular mechanisms. METHODS We systematically reviewed the related literatures regarding FTO and its demethylation activity in many pathologic and physiological processes, especially in cancer-related diseases based on PubMed databases in this article. RESULTS Mounting evidence indicated that FTO plays a critical role in occurrence, progression and treatment of various cancers, even acting as a cancer oncogene in acute myeloid leukaemia, research on which is no longer restricted to metabolic diseases such as obesity and diabetes. CONCLUSION Considering FTO's critical role in many diseases, FTO may become a new promising target for the diagnosis and treatment of various diseases in the near future, especially for specific types of cancers, such as acute myeloid leukaemia, glioblastoma and breast cancer.
Collapse
|
13
|
Abstract
Recently, genome-wide association studies (GWAS) have identified 11 loci associated with adipose-related traits across different populations. However, their functional roles still remain largely unknown. In this study, we aimed to explore the splicing regulation of these GWAS signals in a tissue-specific fashion. For adipose-related GWAS signals, we selected six adipose-related tissues (adipose subcutaneous, artery tibial, blood, heart left ventricle, muscle-skeletal, and thyroid) with the sample size greater than 80 for splicing quantitative trait loci (QTL) analysis using GTEx released datasets. We integrated GWAS summary statistics of nine adipose-related traits (an average of 2.6 million SNPs per GWAS), and splicing QTLs from 6 GTEx tissues with an average of 337,900 splicing QTL SNPs, and 684,859 junctions. Our filtering process generated an average of 86,549 SNPs and 162,841 exon-exon links (junctions) for each tissue. A total of seven exon-exon junctions in four genes (AKTIP, DTNBP1, FTO and UBE2E1) were found to be significantly associated with four SNPs that showed genome-wide significance with body fat distribution (rs17817288, rs7206790, rs11710420 and rs2237199). These splicing events might contribute to the causal effect on the regulation of ectopic-fat, which warrants further experimental validation.
Collapse
|
14
|
Girard H, Potvin O, Nugent S, Dallaire-Théroux C, Cunnane S, Duchesne S. Faster progression from MCI to probable AD for carriers of a single-nucleotide polymorphism associated with type 2 diabetes. Neurobiol Aging 2017; 64:157.e11-157.e17. [PMID: 29338921 DOI: 10.1016/j.neurobiolaging.2017.11.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 11/10/2017] [Accepted: 11/29/2017] [Indexed: 11/27/2022]
Abstract
Sporadic Alzheimer's disease (AD), as opposed to its autosomal dominant form, is likely caused by a complex interaction of genetic, environmental, and health lifestyle factors. Twin studies indicate that sporadic AD heritability could be between 58% and 79%, around half of which is explained by the ε4 allele of the apolipoprotein E (APOE4). We hypothesized that genes associated with known risk factors for AD, namely hypertension, hypercholesterolemia, obesity, diabetes, and cardiovascular disease, would contribute significantly to the remaining heritability. We analyzed 22 AD-associated single-nucleotide polymorphisms (SNPs), associated with these risk factors, that were included in the sequencing data of the Alzheimer's Disease Neuroimaging Initiative 1 data set, which included 355 participants with mild cognitive impairment (MCI). We built survival models with the selected SNPs to predict progression of MCI to probable AD over the 10-year follow-up of the study. The rs391300 SNP, located on the serine racemase (SRR) gene and linked to increased susceptibility to type 2 diabetes, was associated with progression from MCI to probable AD.
Collapse
Affiliation(s)
- Hugo Girard
- Centre de recherche CERVO de l'Institut universitaire en santé mentale de Québec, Québec, Canada; Département de radiologie, Faculté de médecine, Université Laval, Québec, Canada
| | - Olivier Potvin
- Centre de recherche CERVO de l'Institut universitaire en santé mentale de Québec, Québec, Canada
| | - Scott Nugent
- Centre de recherche CERVO de l'Institut universitaire en santé mentale de Québec, Québec, Canada
| | - Caroline Dallaire-Théroux
- Centre de recherche CERVO de l'Institut universitaire en santé mentale de Québec, Québec, Canada; Faculté de médecine, Université Laval, Québec, Canada
| | - Stephen Cunnane
- Département de médecine, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Canada
| | - Simon Duchesne
- Centre de recherche CERVO de l'Institut universitaire en santé mentale de Québec, Québec, Canada; Département de radiologie, Faculté de médecine, Université Laval, Québec, Canada.
| | | |
Collapse
|
15
|
Khella MS, Hamdy NM, Amin AI, El-Mesallamy HO. The (FTO) gene polymorphism is associated with metabolic syndrome risk in Egyptian females: a case- control study. BMC MEDICAL GENETICS 2017; 18:101. [PMID: 28915859 PMCID: PMC5603034 DOI: 10.1186/s12881-017-0461-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Accepted: 09/08/2017] [Indexed: 02/07/2023]
Abstract
Background Variations within fat mass and obesity associated (FTO) gene had crosstalk with obesity risk in European and some Asian populations. This study was designed to investigate FTO rs9939609 association with metabolic syndrome (MetS) as well as biochemical parameters as plasma glucose, serum triacylglycerol (TAG), total cholesterol (TC) and transaminases enzymes in Arab female population from Egypt. Methods In order to achieve that, FTO gene rs9939609 (A < T) was genotyped using TaqMan SNP Genotyping Assay in a total of 197 females which were enrolled in this study. Fasting levels of serum insulin, lipid profile and plasma glucose, in addition to liver transaminases were measured. The association between the genotype distribution and MetS risk was evaluated using Chi-square and logistic regression tests in a case-control design under different genetic models. Results The association of genotype distribution with MetS was significant (χ2 = 8.6/P = 0.014) with an increased odds ratio under dominant model (OR = 1.97, P = 0.029 and 95%C.I = 1.07–3.6) and recessive model (OR = 2.95, P = 0.017 and 95%C.I = 1.22–7.22). Moreover, (AA) subjects showed significant lower HDL-C levels (P = 0.009) when compared to (TT) ones. In addition, interestingly subjects with (AA) genotype have significantly higher ALT levels (P = 0.02) that remained significant after correction of major confounders as body mass index and serum triacylglycerols but not after conservative Bonferroni adjustment. Conclusions The present study shows for first time that FTO gene rs9939609 is genetic risk factor for metabolic syndrome in Egyptian population which may help in understanding the biology of this complex syndrome and highlighted that this association may be through HDL-C component. The association of this genetic polymorphism with ALT levels needs to be studied in other populations with larger sample size.
Collapse
Affiliation(s)
- Mina S Khella
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, African Union Organization Street, Abbassia, Cairo, 11566, Egypt
| | - Nadia M Hamdy
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, African Union Organization Street, Abbassia, Cairo, 11566, Egypt
| | - Ashraf I Amin
- Clinical Pathology and Laboratory Department, National Institute of Diabetes and Endocrinology (NIDE), Cairo, Egypt
| | - Hala O El-Mesallamy
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, African Union Organization Street, Abbassia, Cairo, 11566, Egypt.
| |
Collapse
|
16
|
Tan LJ, Zhu H, He H, Wu KH, Li J, Chen XD, Zhang JG, Shen H, Tian Q, Krousel-Wood M, Papasian CJ, Bouchard C, Pérusse L, Deng HW. Replication of 6 obesity genes in a meta-analysis of genome-wide association studies from diverse ancestries. PLoS One 2014; 9:e96149. [PMID: 24879436 PMCID: PMC4039436 DOI: 10.1371/journal.pone.0096149] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 04/03/2014] [Indexed: 12/30/2022] Open
Abstract
Obesity is a major public health problem with a significant genetic component. Multiple DNA polymorphisms/genes have been shown to be strongly associated with obesity, typically in populations of European descent. The aim of this study was to verify the extent to which 6 confirmed obesity genes (FTO, CTNNBL1, ADRB2, LEPR, PPARG and UCP2 genes) could be replicated in 8 different samples (n = 11,161) and to explore whether the same genes contribute to obesity-susceptibility in populations of different ancestries (five Caucasian, one Chinese, one African-American and one Hispanic population). GWAS-based data sets with 1000 G imputed variants were tested for association with obesity phenotypes individually in each population, and subsequently combined in a meta-analysis. Multiple variants at the FTO locus showed significant associations with BMI, fat mass (FM) and percentage of body fat (PBF) in meta-analysis. The strongest association was detected at rs7185735 (P-value = 1.01×10(-7) for BMI, 1.80×10(-6) for FM, and 5.29×10(-4) for PBF). Variants at the CTNNBL1, LEPR and PPARG loci demonstrated nominal association with obesity phenotypes (meta-analysis P-values ranging from 1.15×10(-3) to 4.94×10(-2)). There was no evidence of association with variants at ADRB2 and UCP2 genes. When stratified by sex and ethnicity, FTO variants showed sex-specific and ethnic-specific effects on obesity traits. Thus, it is likely that FTO has an important role in the sex- and ethnic-specific risk of obesity. Our data confirmed the role of FTO, CTNNBL1, LEPR and PPARG in obesity predisposition. These findings enhanced our knowledge of genetic associations between these genes and obesity-related phenotypes, and provided further justification for pursuing functional studies of these genes in the pathophysiology of obesity. Sex and ethnic differences in genetic susceptibility across populations of diverse ancestries may contribute to a more targeted prevention and customized treatment of obesity.
Collapse
Affiliation(s)
- Li-Jun Tan
- Laboratory of Molecular and Statistical Genetics and Key Laboratory of Protein Chemistry and Developmental Biology of the Ministry of Education, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Hu Zhu
- Laboratory of Molecular and Statistical Genetics and Key Laboratory of Protein Chemistry and Developmental Biology of the Ministry of Education, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Hao He
- School of Public Health and Tropical Medicine and/or School of Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Ke-Hao Wu
- Laboratory of Molecular and Statistical Genetics and Key Laboratory of Protein Chemistry and Developmental Biology of the Ministry of Education, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Jian Li
- School of Public Health and Tropical Medicine and/or School of Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Xiang-Ding Chen
- Laboratory of Molecular and Statistical Genetics and Key Laboratory of Protein Chemistry and Developmental Biology of the Ministry of Education, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Ji-Gang Zhang
- School of Public Health and Tropical Medicine and/or School of Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Hui Shen
- School of Public Health and Tropical Medicine and/or School of Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Qing Tian
- School of Public Health and Tropical Medicine and/or School of Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Marie Krousel-Wood
- School of Public Health and Tropical Medicine and/or School of Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Christopher J. Papasian
- School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, United States of America
| | - Claude Bouchard
- Human Genomics Laboratory, Pennington Biomedical Research Center, Baton Rouge, Louisiana, United States of America
| | - Louis Pérusse
- Department of Kinesiology, Laval University, Québec, Québec, Canada
| | - Hong-Wen Deng
- Laboratory of Molecular and Statistical Genetics and Key Laboratory of Protein Chemistry and Developmental Biology of the Ministry of Education, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
- School of Public Health and Tropical Medicine and/or School of Medicine, Tulane University, New Orleans, Louisiana, United States of America
| |
Collapse
|
17
|
Simonson MA, McQueen MB, Keller MC. Whole-genome pathway analysis on 132,497 individuals identifies novel gene-sets associated with body mass index. PLoS One 2014; 9:e78546. [PMID: 24497910 PMCID: PMC3908858 DOI: 10.1371/journal.pone.0078546] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 09/14/2013] [Indexed: 01/28/2023] Open
Abstract
Whole genome pathway analysis is a powerful tool for the exploration of the combined effects of gene-sets within biological pathways. This study applied Interval Based Enrichment Analysis (INRICH) to perform whole-genome pathway analysis of body-mass index (BMI). We used a discovery set composed of summary statistics from a meta-analysis of 123,865 subjects performed by the GIANT Consortium, and an independent sample of 8,632 subjects to assess replication of significant pathways. We examined SNPs within nominally significant pathways using linear mixed models to estimate their contribution to overall BMI heritability. Six pathways replicated as having significant enrichment for association after correcting for multiple testing, including the previously unknown relationships between BMI and the Reactome regulation of ornithine decarboxylase pathway, the KEGG lysosome pathway, and the Reactome stabilization of P53 pathway. Two non-overlapping sets of genes emerged from the six significant pathways. The clustering of shared genes based on previously identified protein-protein interactions listed in PubMed and OMIM supported the relatively independent biological effects of these two gene-sets. We estimate that the SNPs located in examined pathways explain ∼20% of the heritability for BMI that is tagged by common SNPs (3.35% of the 16.93% total).
Collapse
Affiliation(s)
- Matthew A. Simonson
- Department of Psychology and Neuroscience, Institute for Behavioral Genetics, University of Colorado, Boulder, Colorado, United States of America
- Mayo Clinic, Department of Health Sciences, Division of Biomedical Statistics and Informatics, Rochester, Minnesota, United States of America
- * E-mail:
| | - Matthew B. McQueen
- Department of Integrative Physiology, Institute for Behavioral Genetics, University of Colorado, Boulder, Colorado, United States of America
| | - Matthew C. Keller
- Department of Psychology and Neuroscience, Institute for Behavioral Genetics, University of Colorado, Boulder, Colorado, United States of America
| |
Collapse
|
18
|
Development of GMDR-GPU for gene-gene interaction analysis and its application to WTCCC GWAS data for type 2 diabetes. PLoS One 2013; 8:e61943. [PMID: 23626757 PMCID: PMC3633958 DOI: 10.1371/journal.pone.0061943] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 03/15/2013] [Indexed: 12/27/2022] Open
Abstract
Although genome-wide association studies (GWAS) have identified a significant number of single-nucleotide polymorphisms (SNPs) associated with many complex human traits, the susceptibility loci identified so far can explain only a small fraction of the genetic risk. Among other possible explanations, the lack of a comprehensive examination of gene–gene interaction (G×G) is often considered a source of the missing heritability. Previously, we reported a model-free Generalized Multifactor Dimensionality Reduction (GMDR) approach for detecting G×G in both dichotomous and quantitative phenotypes. However, the computational burden and less efficient implementation of the original programs make them impossible to use for GWAS. In this study, we developed a graphics processing unit (GPU)-based GMDR program (named GWAS-GPU), which is able not only to analyze GWAS data but also to run much faster than the earlier version of the GMDR program. As a demonstration of the program, we used the GMDR-GPU software to analyze a publicly available GWAS dataset on type 2 diabetes (T2D) from the Wellcome Trust Case Control Consortium. Through an exhaustive search of pair-wise interactions and a selected search of three- to five-way interactions conditioned on significant pair-wise results, we identified 24 core SNPs in six genes (FTO: rs9939973, rs9940128, rs9922047, rs1121980, rs9939609, rs9930506; TSPAN8: rs1495377; TCF7L2: rs4074720, rs7901695, rs4506565, rs4132670, rs10787472, rs11196205, rs10885409, rs11196208; L3MBTL3: rs10485400, rs4897366; CELF4: rs2852373, rs608489; RUNX1: rs445984, rs1040328, rs990074, rs2223046, rs2834970) that appear to be important for T2D. Of these core SNPs, 11 in FTO, TSPAN8, and TCF7L2 have been reported to be associated with T2D, obesity, or both, providing an independent replication of previously reported SNPs. Importantly, we identified three new susceptibility genes; i.e., L3MBTL3, CELF4, and RUNX1, for T2D, a finding that warrants further investigation with independent samples.
Collapse
|
19
|
Reitz C, Tosto G, Mayeux R, Luchsinger JA. Genetic variants in the Fat and Obesity Associated (FTO) gene and risk of Alzheimer's disease. PLoS One 2012; 7:e50354. [PMID: 23251365 PMCID: PMC3520931 DOI: 10.1371/journal.pone.0050354] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Accepted: 10/24/2012] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Recent studies showed that polymorphisms in the Fat and Obesity-Associated (FTO) gene have robust effects on obesity, obesity-related traits and endophenotypes associated with Alzheimer's disease (AD). METHODS We used 1,877 Caucasian cases and controls from the NIA-LOAD study and 1,093 Caribbean Hispanics to further explore the association of FTO with AD. Using logistic regression, we assessed 42 SNPs in introns 1 and 2, the region previously reported to be associated with AD endophenotypes, which had been derived by genome-wide screenings. In addition, we performed gene expression analyses of neuropathologically confirmed AD cases and controls of two independent datasets (19 AD cases, 10 controls; 176 AD cases, 188 controls) using within- and between-group factors ANOVA of log(10) transformed rank invariant normalized expression data. RESULTS In the NIALOAD study, one SNP was significantly associated with AD and three additional markers were close to significance (rs6499640, rs10852521, rs16945088, rs8044769, FDR p-value: 0.05 0.9) with the previously reported SNPs. In the Caribbean Hispanic dataset, we identified three SNPs (rs17219084, rs11075996, rs11075997, FDR p-value: 0.009 CONCLUSIONS Our data support the notion that genetic variation in Introns 1 and 2 of the FTO gene may contribute to AD risk.
Collapse
Affiliation(s)
- Christiane Reitz
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, New York, United States of America
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, New York, United States of America
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, New York, United States of America
| | - Giuseppe Tosto
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, New York, United States of America
| | - Richard Mayeux
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, New York, United States of America
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, New York, United States of America
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, New York, United States of America
- Department of Psychiatry, College of Physicians and Surgeons, Columbia University, New York, New York, United States of America
- Department of Medicine, Pathology, College of Physicians and Surgeons, Columbia University, New York, New York, United States of America
| | - Jose A. Luchsinger
- Department of Medicine, Pathology, College of Physicians and Surgeons, Columbia University, New York, New York, United States of America
| | | |
Collapse
|
20
|
Zhang G, Karns R, Sun G, Indugula SR, Cheng H, Havas-Augustin D, Novokmet N, Durakovic Z, Missoni S, Chakraborty R, Rudan P, Deka R. Finding missing heritability in less significant Loci and allelic heterogeneity: genetic variation in human height. PLoS One 2012; 7:e51211. [PMID: 23251454 PMCID: PMC3521016 DOI: 10.1371/journal.pone.0051211] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Accepted: 11/05/2012] [Indexed: 11/19/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified many common variants associated with complex traits in human populations. Thus far, most reported variants have relatively small effects and explain only a small proportion of phenotypic variance, leading to the issues of 'missing' heritability and its explanation. Using height as an example, we examined two possible sources of missing heritability: first, variants with smaller effects whose associations with height failed to reach genome-wide significance and second, allelic heterogeneity due to the effects of multiple variants at a single locus. Using a novel analytical approach we examined allelic heterogeneity of height-associated loci selected from SNPs of different significance levels based on the summary data of the GIANT (stage 1) studies. In a sample of 1,304 individuals collected from an island population of the Adriatic coast of Croatia, we assessed the extent of height variance explained by incorporating the effects of less significant height loci and multiple effective SNPs at the same loci. Our results indicate that approximately half of the 118 loci that achieved stringent genome-wide significance (p-value<5×10(-8)) showed evidence of allelic heterogeneity. Additionally, including less significant loci (i.e., p-value<5×10(-4)) and accounting for effects of allelic heterogeneity substantially improved the variance explained in height.
Collapse
Affiliation(s)
- Ge Zhang
- Human Genetics Division, Cincinnati Children's Hospital, Cincinnati, Ohio, United States of America
| | - Rebekah Karns
- Center for Genome Information, Department of Environmental Health, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Guangyun Sun
- Center for Genome Information, Department of Environmental Health, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Subba Rao Indugula
- Center for Genome Information, Department of Environmental Health, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Hong Cheng
- Center for Genome Information, Department of Environmental Health, University of Cincinnati, Cincinnati, Ohio, United States of America
| | | | | | | | - Sasa Missoni
- Institute for Anthropological Research, Zagreb, Croatia
| | - Ranajit Chakraborty
- Center for Computational Genomics, Institute of Applied Genetics, University of North Texas Health Science Center, Forth Worth, Texas, United States of America
| | - Pavao Rudan
- Institute for Anthropological Research, Zagreb, Croatia
| | - Ranjan Deka
- Center for Genome Information, Department of Environmental Health, University of Cincinnati, Cincinnati, Ohio, United States of America
- * E-mail:
| |
Collapse
|
21
|
Moore SC, Gunter MJ, Daniel CR, Reddy KS, George PS, Yurgalevitch S, Devasenapathy N, Ramakrishnan L, Chatterjee N, Chanock SJ, Berndt SI, Mathew A, Prabhakaran D, Sinha R. Common genetic variants and central adiposity among Asian-Indians. Obesity (Silver Spring) 2012; 20:1902-8. [PMID: 21799482 PMCID: PMC3429696 DOI: 10.1038/oby.2011.238] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Recent studies have identified common genetic variants that are unequivocally associated with central adiposity, BMI, and/or fasting plasma glucose among individuals of European descent. Our objective was to evaluate these associations in a population of Asian-Indians. We examined 16 single-nucleotide polymorphisms (SNPs) from loci previously linked to waist circumference, BMI, or fasting glucose in 1,129 Asian-Indians from New Delhi and Trivandrum. Trained medical staff measured waist circumference, height, and weight. Fasting plasma glucose was measured from collected blood specimens. Genotype-phenotype associations were evaluated using linear regression, with adjustments for age, gender, religion, and study region. For gene-environment interaction tests, total physical activity (PA) during the past 7 days was assessed by the International Physical Activity Questionnaire (IPAQ). The T allele at the FTO rs3751812 locus was associated with increased waist circumference (per allele effect of +1.58 cm, P(trend) = 0.0015) after Bonferroni adjustment for multiple testing (P(adj) = 0.04). We also found a nominally statistically significant FTO-PA interaction (P(interaction) = 0.008). Among participants with <81 metabolic equivalent (MET)-h/wk of PA, the rs3751812 variant was associated with increased waist size (+2.68 cm; 95% confidence interval (CI) = 1.24, 4.12), but not among those with 212+ MET-h/wk (-1.79 cm; 95% CI = -4.17, 0.58). No other variant had statistically significant associations, although statistical power was modest. In conclusion, we confirmed that an FTO variant associated with central adiposity in European populations is associated with central adiposity among Asian-Indians and corroborated prior reports indicating that high PA attenuates FTO-related genetic susceptibility to adiposity.
Collapse
Affiliation(s)
- Steven C Moore
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Rockville, Maryland, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Apalasamy YD, Ming MF, Rampal S, Bulgiba A, Mohamed Z. Genetic association of SNPs in the FTO gene and predisposition to obesity in Malaysian Malays. Braz J Med Biol Res 2012; 45:1119-26. [PMID: 22911346 PMCID: PMC3854209 DOI: 10.1590/s0100-879x2012007500134] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 08/09/2012] [Indexed: 12/18/2022] Open
Abstract
The common variants in the fat mass- and obesity-associated (FTO) gene have been previously found to be associated with obesity in various adult populations. The objective of the present study was to investigate whether the single nucleotide polymorphisms (SNPs) and linkage disequilibrium (LD) blocks in various regions of the FTO gene are associated with predisposition to obesity in Malaysian Malays. Thirty-one FTO SNPs were genotyped in 587 (158 obese and 429 non-obese) Malaysian Malay subjects. Obesity traits and lipid profiles were measured and single-marker association testing, LD testing, and haplotype association analysis were performed. LD analysis of the FTO SNPs revealed the presence of 57 regions with complete LD (D' = 1.0). In addition, we detected the association of rs17817288 with low-density lipoprotein cholesterol. The FTO gene may therefore be involved in lipid metabolism in Malaysian Malays. Two haplotype blocks were present in this region of the FTO gene, but no particular haplotype was found to be significantly associated with an increased risk of obesity in Malaysian Malays.
Collapse
Affiliation(s)
- Y D Apalasamy
- Pharmacogenomics Laboratory, Department of Pharmacology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
| | | | | | | | | |
Collapse
|
23
|
Association of FTO polymorphisms with early age of obesity in obese Italian subjects. EXPERIMENTAL DIABETES RESEARCH 2012; 2012:872176. [PMID: 22454631 PMCID: PMC3290805 DOI: 10.1155/2012/872176] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Revised: 12/10/2011] [Accepted: 12/10/2011] [Indexed: 12/18/2022]
Abstract
Obesity is recognized as a major health problem worldwide. Genetic factors play a major role in obesity, and genomewide association studies have provided evidence that several common variants within the fat mass- and obesity-associated (FTO) gene are significantly associated with obesity. Very limited data is available on FTO in the Italian population.
Aims of our study are to investigate: (1) the association of FTO gene SNPs rs9939609 and rs9930506 with body mass index (BMI) and obesity-related parameters in a large cohort (n = 752) of Italian obese subjects; (2) the association between the two FTO SNPs and age of onset of obesity.
Our results demonstrate a strong association between FTO SNPs rs9939609 (P < 0.043) and rs9930506 (P < 0.029) with BMI in the Italian population. FTO rs9930506 was significantly associated with higher BMI in a G allele dose-dependent manner (BMI + 1.4 kg/m2 per G allele). We also observed that the association with BMI of the two FTO variants varied with age, with the carriers of the risk alleles developing an increase in body weight earlier in life. In conclusion, our study further demonstrates a role of the genetic variability in FTO on BMI in a large Italian population.
Collapse
|
24
|
Karns R, Zhang G, Sun G, Rao Indugula S, Cheng H, Havas-Augustin D, Novokmet N, Rudan D, Durakovic Z, Missoni S, Chakraborty R, Rudan P, Deka R. Genome-wide association of serum uric acid concentration: replication of sequence variants in an island population of the Adriatic coast of Croatia. Ann Hum Genet 2012; 76:121-7. [PMID: 22229870 DOI: 10.1111/j.1469-1809.2011.00698.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A genome-wide association study of serum uric acid (SUA) laevels was performed in a relatively isolated population of European descent from an island of the Adriatic coast of Croatia. The study sample included 532 unrelated and 768 related individuals from 235 pedigrees. Inflation due to relatedness was controlled by using genomic control. Genetic association was assessed with 2,241,249 single nucleotide polymorphisms (SNPs) in 1300 samples after adjusting for age and gender. Our study replicated four previously reported SUA loci (SLC2A9, ABCG2, RREB1, and SLC22A12). The strongest association was found with a SNP in SLC2A9 (rs13129697, P=2.33×10(-19)), which exhibited significant gender-specific effects, 35.76 μmol/L (P=2.11×10(-19)) in females and 19.58 μmol/L (P=5.40×10(-5)) in males. Within this region of high linkage disequilibrium, we also detected a strong association with a nonsynonymous SNP, rs16890979 (P=2.24×10(-17)), a putative causal variant for SUA variation. In addition, we identified several novel loci suggestive of association with uric acid levels (SEMA5A, TMEM18, SLC28A2, and ODZ2), although the P-values (P<5×10(-6)) did not reach the threshold of genome-wide significance. Together, these findings provide further confirmation of previously reported uric-acid-related genetic variants and highlight suggestive new loci for additional investigation.
Collapse
Affiliation(s)
- Rebekah Karns
- Center for Genome Information, Department of Environmental Health, University of Cincinnati, and Cincinnati Children's Hospital, Cincinnati, OH 45267, USA
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Zhang G, Karns R, Sun G, Indugula SR, Cheng H, Havas-Augustin D, Novokmet N, Rudan D, Durakovic Z, Missoni S, Chakraborty R, Rudan P, Deka R. Extent of height variability explained by known height-associated genetic variants in an isolated population of the Adriatic coast of Croatia. PLoS One 2011; 6:e29475. [PMID: 22216288 PMCID: PMC3246488 DOI: 10.1371/journal.pone.0029475] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Accepted: 11/29/2011] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Human height is a classical example of a polygenic quantitative trait. Recent large-scale genome-wide association studies (GWAS) have identified more than 200 height-associated loci, though these variants explain only 2∼10% of overall variability of normal height. The objective of this study was to investigate the variance explained by these loci in a relatively isolated population of European descent with limited admixture and homogeneous genetic background from the Adriatic coast of Croatia. METHODOLOGY/PRINCIPAL FINDINGS In a sample of 1304 individuals from the island population of Hvar, Croatia, we performed genome-wide SNP typing and assessed the variance explained by genetic scores constructed from different panels of height-associated SNPs extracted from five published studies. The combined information of the 180 SNPs reported by Lango Allen el al. explained 7.94% of phenotypic variation in our sample. Genetic scores based on 20~50 SNPs reported by the remaining individual GWA studies explained 3~5% of height variance. These percentages of variance explained were within ranges comparable to the original studies and heterogeneity tests did not detect significant differences in effect size estimates between our study and the original reports, if the estimates were obtained from populations of European descent. CONCLUSIONS/SIGNIFICANCE We have evaluated the portability of height-associated loci and the overall fitting of estimated effect sizes reported in large cohorts to an isolated population. We found proportions of explained height variability were comparable to multiple reference GWAS in cohorts of European descent. These results indicate similar genetic architecture and comparable effect sizes of height loci among populations of European descent.
Collapse
Affiliation(s)
- Ge Zhang
- Human Genetics Division, Cincinnati Children's Hospital, Cincinnati, Ohio, United States of America
| | - Rebekah Karns
- Center for Genome Information, Department of Environmental Health, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Guangyun Sun
- Center for Genome Information, Department of Environmental Health, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Subba Rao Indugula
- Center for Genome Information, Department of Environmental Health, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Hong Cheng
- Center for Genome Information, Department of Environmental Health, University of Cincinnati, Cincinnati, Ohio, United States of America
| | | | | | - Dusko Rudan
- Institute for Anthropological Research, Zagreb, Croatia
| | | | - Sasa Missoni
- Institute for Anthropological Research, Zagreb, Croatia
| | - Ranajit Chakraborty
- Center for Computational Genomics, Institute of Investigative Genetics, University of North Texas Health Science Center, Forth Worth, Texas, United States of America
| | - Pavao Rudan
- Institute for Anthropological Research, Zagreb, Croatia
| | - Ranjan Deka
- Center for Genome Information, Department of Environmental Health, University of Cincinnati, Cincinnati, Ohio, United States of America
- * E-mail:
| |
Collapse
|
26
|
Rask-Andersen M, Almén MS, Olausen HR, Olszewski PK, Eriksson J, Chavan RA, Levine AS, Fredriksson R, Schiöth HB. Functional coupling analysis suggests link between the obesity gene FTO and the BDNF-NTRK2 signaling pathway. BMC Neurosci 2011; 12:117. [PMID: 22087873 PMCID: PMC3248879 DOI: 10.1186/1471-2202-12-117] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Accepted: 11/16/2011] [Indexed: 11/24/2022] Open
Abstract
Background The Fat mass and obesity gene (FTO) has been identified through genome wide association studies as an important genetic factor contributing to a higher body mass index (BMI). However, the molecular context in which this effect is mediated has yet to be determined. We investigated the potential molecular network for FTO by analyzing co-expression and protein-protein interaction databases, Coxpresdb and IntAct, as well as the functional coupling predicting multi-source database, FunCoup. Hypothalamic expression of FTO-linked genes defined with this bioinformatics approach was subsequently studied using quantitative real time-PCR in mouse feeding models known to affect FTO expression. Results We identified several candidate genes for functional coupling to FTO through database studies and selected nine for further study in animal models. We observed hypothalamic expression of Profilin 2 (Pfn2), cAMP-dependent protein kinase catalytic subunit beta (Prkacb), Brain derived neurotrophic factor (Bdnf), neurotrophic tyrosine kinase, receptor, type 2 (Ntrk2), Signal transducer and activator of transcription 3 (Stat3), and Btbd12 to be co-regulated in concert with Fto. Pfn2 and Prkacb have previously not been linked to feeding regulation. Conclusions Gene expression studies validate several candidates generated through database studies of possible FTO-interactors. We speculate about a wider functional role for FTO in the context of current and recent findings, such as in extracellular ligand-induced neuronal plasticity via NTRK2/BDNF, possibly via interaction with the transcription factor CCAAT/enhancer binding protein β (C/EBPβ).
Collapse
Affiliation(s)
- Mathias Rask-Andersen
- Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Uppsala SE 75124, Sweden
| | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Chauhan G, Tabassum R, Mahajan A, Dwivedi OP, Mahendran Y, Kaur I, Nigam S, Dubey H, Varma B, Madhu SV, Mathur SK, Ghosh S, Tandon N, Bharadwaj D. Common variants of FTO and the risk of obesity and type 2 diabetes in Indians. J Hum Genet 2011; 56:720-6. [PMID: 21814223 DOI: 10.1038/jhg.2011.87] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Common variants of fat mass and obesity-associated gene (FTO, fat mass- and obesity-associated gene) have been shown to be associated with obesity and type 2 diabetes in population of European and non-European ethnicity. However, studies in Indian population have provided inconsistent results. Here, we examined association of eight FTO variants (rs1421085, rs8050136, rs9939609, rs9930506, rs1861867, rs9926180, rs2540769 and rs708277) with obesity and type 2 diabetes in 5364 North Indians (2474 type 2 diabetes patients and 2890 non-diabetic controls) in two stages. None of the variants including previously reported intron 1 variants (rs1421085, rs8050136, rs9939609 and rs9930506) showed body mass index (BMI)-dependent/independent association with type 2 diabetes. However, rs1421085, rs8050136 and rs9939609 were associated with obesity status and measures of obesity (BMI, waist circumference and waist-to-hip ratio) in stage 2 and combined study population. Meta-analysis of the two study population results also revealed that rs1421085, rs8050136 and rs9939609 were significantly associated with BMI both under the random- and fixed-effect models (P (random/fixed)=0.02/0.0001, 0.004/0.0006 and 0.01/0.01, respectively). In conclusion, common variants of FTO were associated with obesity, but not with type 2 diabetes in North Indian population.
Collapse
Affiliation(s)
- Ganesh Chauhan
- Genomics and Molecular Medicine Unit, Institute of Genomics and Integrative Biology (CSIR), Delhi, India
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Abstract
Genome-wide association studies have been very powerful, uncovering potentially new biology that would not have been possible using a candidate gene approach. A prime example of this is the gene FTO (fat mass and obesity associated), which first came to light in 2007, when single nucleotide polymorphisms in its first intron were robustly associated with body mass index and obesity. Subsequently, as it became clear that this association with body weight, and increasingly food intake, was replicable across multiple populations and different age groups, attention was turned to studying the biology of FTO, about which absolutely nothing was known. This review focuses on the genetic and biochemical approaches as well as animal models that have been used by us and others since 2007 to try and uncover the complex biology of FTO.
Collapse
Affiliation(s)
- Yi-Chun Loraine Tung
- University of Cambridge Metabolic Research Labs, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, United Kingdom
| | | |
Collapse
|
29
|
Karns R, Zhang G, Jeran N, Havas-Augustin D, Missoni S, Niu W, Indugula SR, Sun G, Durakovic Z, Narancic NS, Rudan P, Chakraborty R, Deka R. Replication of genetic variants from genome-wide association studies with metabolic traits in an island population of the Adriatic coast of Croatia. Eur J Hum Genet 2010; 19:341-6. [PMID: 21150882 DOI: 10.1038/ejhg.2010.178] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Twenty-two single-nucleotide polymorphisms (SNPs) in 10 gene regions previously identified in obesity and type 2 diabetes (T2D) genome-wide association studies (GWAS) were evaluated for association with metabolic traits in a sample from an island population of European descent. We performed a population-based study using 18 anthropometric and biochemical traits considered as continuous variables in a sample of 843 unrelated subjects (360 men and 483 women) aged 18-80 years old from the island of Hvar on the eastern Adriatic coast of Croatia. All eight GWAS SNPs in FTO were significantly associated with weight, body mass index, waist circumference and hip circumference; 20 of the 32 nominal P-values remained significant after permutation testing for multiple corrections. The strongest associations were found between the two TCF7L2 GWAS SNPs with fasting plasma glucose and HbA1c levels, all four P-values remained significant after permutation tests. Nominally significant associations were found between several SNPs and other metabolic traits; however, the significance did not hold after permutation tests. Although the sample size was modest, our study strongly replicated the association of FTO variants with obesity-related measures and TCF7L2 variants with T2D-related traits. The estimated effect sizes of these variants were larger or comparable to published studies. This is likely attributable to the homogenous genetic background of the relatively isolated study population.
Collapse
Affiliation(s)
- Rebekah Karns
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0056, USA
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|