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Liu H, Xin X, Gan J, Huang J. The long-term effects of blood urea nitrogen levels on cardiovascular disease and all-cause mortality in diabetes: a prospective cohort study. BMC Cardiovasc Disord 2024; 24:256. [PMID: 38755538 PMCID: PMC11097526 DOI: 10.1186/s12872-024-03928-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 05/08/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND The long-term effects of blood urea nitrogen(BUN) in patients with diabetes remain unknown. Current studies reporting the target BUN level in patients with diabetes are also limited. Hence, this prospective study aimed to explore the relationship of BUN with all-cause and cardiovascular mortalities in patients with diabetes. METHODS In total, 10,507 participants with diabetes from the National Health and Nutrition Examination Survey (1999-2018) were enrolled. The causes and numbers of deaths were determined based on the National Death Index mortality data from the date of NHANES interview until follow-up (December 31, 2019). Multivariate Cox proportional hazard regression models were used to calculate the hazard ratios (HRs) and 95% confidence interval (CIs) of mortality. RESULTS Of the adult participants with diabetes, 4963 (47.2%) were female. The median (interquartile range) BUN level of participants was 5 (3.93-6.43) mmol/L. After 86,601 person-years of follow-up, 2,441 deaths were documented. After adjusting for variables, the HRs of cardiovascular disease (CVD) and all-cause mortality in the highest BUN level group were 1.52 and 1.35, respectively, compared with those in the lowest BUN level group. With a one-unit increment in BUN levels, the HRs of all-cause and CVD mortality rates were 1.07 and 1.08, respectively. The results remained robust when several sensitivity and stratified analyses were performed. Moreover, BUN showed a nonlinear association with all-cause and CVD mortality. Their curves all showed that the inflection points were close to the BUN level of 5 mmol/L. CONCLUSION BUN had a nonlinear association with all-cause and CVD mortality in patients with diabetes. The inflection point was at 5 mmol/L.
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Affiliation(s)
- Hongfang Liu
- Electrocardiography Department, Ganzhou Maternal and Child Health Hospital, Ganzhou, Jiangxi Province, 341000, China
| | - Xiaoqin Xin
- Department of Clinical Laboratory, Ganzhou People's Hospital, Ganzhou, Jiangxi Province, 341000, China
| | - Jinghui Gan
- Department of Medical Genetic, Ganzhou Maternal and Child Health Hospital, Ganzhou, Jiangxi Province, 341000, China
| | - Jungao Huang
- Department of Medical Genetic, Ganzhou Maternal and Child Health Hospital, Ganzhou, Jiangxi Province, 341000, China.
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2
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Zhang Z, Cui Y, Su V, Wang D, Tol MJ, Cheng L, Wu X, Kim J, Rajbhandari P, Zhang S, Li W, Tontonoz P, Villanueva CJ, Sallam T. A PPARγ/long noncoding RNA axis regulates adipose thermoneutral remodeling in mice. J Clin Invest 2023; 133:e170072. [PMID: 37909330 PMCID: PMC10617768 DOI: 10.1172/jci170072] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 09/06/2023] [Indexed: 11/03/2023] Open
Abstract
Interplay between energy-storing white adipose cells and thermogenic beige adipocytes contributes to obesity and insulin resistance. Irrespective of specialized niche, adipocytes require the activity of the nuclear receptor PPARγ for proper function. Exposure to cold or adrenergic signaling enriches thermogenic cells though multiple pathways that act synergistically with PPARγ; however, the molecular mechanisms by which PPARγ licenses white adipose tissue to preferentially adopt a thermogenic or white adipose fate in response to dietary cues or thermoneutral conditions are not fully elucidated. Here, we show that a PPARγ/long noncoding RNA (lncRNA) axis integrates canonical and noncanonical thermogenesis to restrain white adipose tissue heat dissipation during thermoneutrality and diet-induced obesity. Pharmacologic inhibition or genetic deletion of the lncRNA Lexis enhances uncoupling protein 1-dependent (UCP1-dependent) and -independent thermogenesis. Adipose-specific deletion of Lexis counteracted diet-induced obesity, improved insulin sensitivity, and enhanced energy expenditure. Single-nuclei transcriptomics revealed that Lexis regulates a distinct population of thermogenic adipocytes. We systematically map Lexis motif preferences and show that it regulates the thermogenic program through the activity of the metabolic GWAS gene and WNT modulator TCF7L2. Collectively, our studies uncover a new mode of crosstalk between PPARγ and WNT that preserves white adipose tissue plasticity.
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Affiliation(s)
- Zhengyi Zhang
- Division of Cardiology, Department of Medicine
- Department of Physiology, and
- Molecular Biology Institute, UCLA, Los Angeles, California, USA
| | - Ya Cui
- Division of Computational Biomedicine, Biological Chemistry, University of California, Irvine, Irvine, California, USA
| | - Vivien Su
- Division of Cardiology, Department of Medicine
- Department of Physiology, and
- Molecular Biology Institute, UCLA, Los Angeles, California, USA
| | - Dan Wang
- Division of Cardiology, Department of Medicine
- Department of Physiology, and
- Molecular Biology Institute, UCLA, Los Angeles, California, USA
| | - Marcus J. Tol
- Molecular Biology Institute, UCLA, Los Angeles, California, USA
- Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, California, USA
| | - Lijing Cheng
- Division of Cardiology, Department of Medicine
- Department of Physiology, and
- Molecular Biology Institute, UCLA, Los Angeles, California, USA
| | - Xiaohui Wu
- Division of Cardiology, Department of Medicine
- Department of Physiology, and
- Molecular Biology Institute, UCLA, Los Angeles, California, USA
| | - Jason Kim
- Division of Cardiology, Department of Medicine
- Department of Physiology, and
- Molecular Biology Institute, UCLA, Los Angeles, California, USA
| | - Prashant Rajbhandari
- Diabetes, Obesity, and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Sicheng Zhang
- Molecular Biology Institute, UCLA, Los Angeles, California, USA
| | - Wei Li
- Division of Computational Biomedicine, Biological Chemistry, University of California, Irvine, Irvine, California, USA
| | - Peter Tontonoz
- Molecular Biology Institute, UCLA, Los Angeles, California, USA
- Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, California, USA
- Department of Biological Chemistry and
| | - Claudio J. Villanueva
- Molecular Biology Institute, UCLA, Los Angeles, California, USA
- Department of Integrative Biology and Physiology, College of Life Sciences, UCLA, Los Angeles, California, USA
| | - Tamer Sallam
- Division of Cardiology, Department of Medicine
- Department of Physiology, and
- Molecular Biology Institute, UCLA, Los Angeles, California, USA
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3
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Majeed SR, Omara AM, Al-Koofee DA. Association of interferon-induced helicase (IFIH1) gene polymorphism rs1990760 with type two diabetes mellitus in Iraqi population. Meta Gene 2021. [DOI: 10.1016/j.mgene.2021.100952] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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4
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Leak-Johnson T, Yan F, Daniels P. What the Jackson Heart Study Has Taught Us About Diabetes and Cardiovascular Disease in the African American Community: a 20-year Appreciation. Curr Diab Rep 2021; 21:39. [PMID: 34495422 DOI: 10.1007/s11892-021-01413-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/25/2021] [Indexed: 01/10/2023]
Abstract
PURPOSE OF REVIEW The burden of cardiometabolic diseases such as cardiovascular disease (CVD) and type 2 diabetes (T2D) is pronounced among African Americans. Research has shown that behavioral, social, metabolic, psychosocial, and genetic risk factors of CVD and T2D are closely interwoven. Approximately 20 years ago, the Jackson Heart Study (JHS) was established to investigate this constellation of risk factors. RECENT FINDINGS Findings from neighborhood studies emphasize the importance of social cohesion and physical environment in the context CVD and T2D risk. Socioeconomic status factors such as income and education were significant predictors for CVD and T2D. Behavioral studies indicate that modifiable risk factors such as smoking, physical inactivity, lack of sleep, and poor nutrition are associated with CVD risk and all-cause mortality. Mental health also was found to be associated with CVD and T2D. Genetic influences are associated with disease etiology. This review summarizes the joint contributions of CVD and cardiometabolic risk factors in an African American population.
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Affiliation(s)
- Tennille Leak-Johnson
- Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, GA, 30310, USA.
- Department of Physiology, Morehouse School of Medicine, Atlanta, GA, USA.
| | - Fengxia Yan
- The Research Design and Biostatistics Core, Morehouse School of Medicine, Atlanta, GA, USA
- Community Health & Preventive Medicine, Morehouse School of Medicine, Atlanta, GA, USA
| | - Pamela Daniels
- The Research Design and Biostatistics Core, Morehouse School of Medicine, Atlanta, GA, USA
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5
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Al-Kashwan TA, Algenabi AHA, Omara AM, Kaftan AN. Association of vitamin D receptor gene polymorphisms BsmI (rs 1544410) and TaqI rs (731236) with the type 2 diabetes mellitus in Iraqi Patients from the middle Euphrates region. Meta Gene 2021. [DOI: 10.1016/j.mgene.2021.100854] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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6
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Rasouli N, Younes N, Utzschneider KM, Inzucchi SE, Balasubramanyam A, Cherrington AL, Ismail-Beigi F, Cohen RM, Olson DE, DeFronzo RA, Herman WH, Lachin JM, Kahn SE. Association of Baseline Characteristics With Insulin Sensitivity and β-Cell Function in the Glycemia Reduction Approaches in Diabetes: A Comparative Effectiveness (GRADE) Study Cohort. Diabetes Care 2021; 44:340-349. [PMID: 33334808 PMCID: PMC7818323 DOI: 10.2337/dc20-1787] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 11/11/2020] [Indexed: 02/03/2023]
Abstract
OBJECTIVE We investigated sex and racial differences in insulin sensitivity, β-cell function, and glycated hemoglobin (HbA1c) and the associations with selected phenotypic characteristics. RESEARCH DESIGN AND METHODS This is a cross-sectional analysis of baseline data from 3,108 GRADE (Glycemia Reduction Approaches in Diabetes: A Comparative Effectiveness Study) participants. All had type 2 diabetes diagnosed <10 years earlier and were on metformin monotherapy. Insulin sensitivity and β-cell function were evaluated using the HOMA of insulin sensitivity and estimates from oral glucose tolerance tests, including the Matsuda Index, insulinogenic index, C-peptide index, and oral disposition index (DI). RESULTS The cohort was 56.6 ± 10 years of age (mean ± SD), 63.8% male, with BMI 34.2 ± 6.7 kg/m2, HbA1c 7.5 ± 0.5%, and type 2 diabetes duration 4.0 ± 2.8 years. Women had higher DI than men but similar insulin sensitivity. DI was the highest in Black/African Americans, followed by American Indians/Alaska Natives, Asians, and Whites in descending order. Compared with Whites, American Indians/Alaska Natives had significantly higher HbA1c, but Black/African Americans and Asians had lower HbA1c. However, when adjusted for glucose levels, Black/African Americans had higher HbA1c than Whites. Insulin sensitivity correlated inversely with BMI, waist-to-hip ratio, triglyceride-to-HDL-cholesterol ratio (TG/HDL-C), and the presence of metabolic syndrome, whereas DI was associated directly with age and inversely with BMI, HbA1c, and TG/HDL-C. CONCLUSIONS In the GRADE cohort, β-cell function differed by sex and race and was associated with the concurrent level of HbA1c. HbA1c also differed among the races, but not by sex. Age, BMI, and TG/HDL-C were associated with multiple measures of β-cell function and insulin sensitivity.
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Affiliation(s)
- Neda Rasouli
- Division of Endocrinology, Metabolism and Diabetes, Department of Medicine, University of Colorado School of Medicine, Aurora, CO
- VA Eastern Colorado Health Care System, Aurora, CO
| | - Naji Younes
- The Biostatistics Center, Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, The George Washington University, Rockville, MD
| | - Kristina M Utzschneider
- Division of Metabolism, Endocrinology and Nutrition, Department of Medicine, VA Puget Sound Health Care System and the University of Washington, Seattle, WA
| | | | - Ashok Balasubramanyam
- Division of Diabetes, Endocrinology and Metabolism, Baylor College of Medicine, Houston, TX
| | | | - Faramarz Ismail-Beigi
- Department of Medicine, Case Western Reserve University and Louis Stokes Cleveland VA Medical Center, Cleveland, OH
| | - Robert M Cohen
- Division of Endocrinology, Diabetes and Metabolism, University of Cincinnati College of Medicine and Cincinnati VA Medical Center, Cincinnati, OH
| | - Darin E Olson
- Atlanta VA Health Care System and Division of Endocrinology, Metabolism, and Lipids, Department of Medicine, Emory University School of Medicine, Atlanta, GA
| | - Ralph A DeFronzo
- University of Texas Health Science Center at San Antonio, San Antonio, TX
| | - William H Herman
- Departments of Internal Medicine and Epidemiology, University of Michigan, Ann Arbor, MI
| | - John M Lachin
- The Biostatistics Center, Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, The George Washington University, Rockville, MD
| | - Steven E Kahn
- Division of Metabolism, Endocrinology and Nutrition, Department of Medicine, VA Puget Sound Health Care System and the University of Washington, Seattle, WA
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7
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Ganmore I, Livny A, Ravona-Springer R, Cooper I, Alkelai A, Shelly S, Tsarfaty G, Heymann A, Schnaider Beeri M, Greenbaum L. TCF7L2 polymorphisms are associated with amygdalar volume in elderly individuals with Type 2 Diabetes. Sci Rep 2019; 9:15818. [PMID: 31676834 PMCID: PMC6825182 DOI: 10.1038/s41598-019-48899-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 08/08/2019] [Indexed: 02/06/2023] Open
Abstract
The association between several Single Nucleotide Polymorphisms (SNPs) within the transcription factor 7-like 2 (TCF7L2) gene and Type 2 Diabetes (T2D) as well as additional T2D-related traits is well established. Since alteration in total and regional brain volumes are consistent findings among T2D individuals, we studied the association of four T2D susceptibility SNPS within TCF7L2 (rs7901695, rs7903146, rs11196205, and rs12255372) with volumes of white matter hyperintensities (WMH), gray matter, and regional volumes of amygdala and hippocampus obtained from structural MRI among 191 T2D elderly Jewish individuals. Under recessive genetic model (controlling for age, sex and intracranial volume), we found that for all four SNPs, carriers of two copies of the T2D risk allele (homozygous genotype) had significantly smaller amygdalar volume: rs7901695- CC genotype vs. CT + TT genotypes, p = 0.002; rs7903146-TT vs. TC + CC, p = 0.003; rs11196205- CC vs. CG + GG, p = 0.0003; and rs12255372- TT vs. TG + GG, p = 0.003. Adjusting also for T2D-related covariates, body mass index (BMI), and ancestry did not change the results substantively (rs7901695, p = 0.003; rs7903146, p = 0.005; rs11196205, p = 0.001; and rs12255372, p = 0.005). Conditional analysis demonstrated that only rs11196205 was independently associated with amygdalar volume at a significant level. Separate analysis of left and right amygdala revealed stronger results for left amygdalar volume. Taken together, we report association of TCF7L2 SNPs with amygdalar volume among T2D elderly Jewish patients. Further studies in other populations are required to support these findings and reach more definitive conclusions.
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Affiliation(s)
- Ithamar Ganmore
- Department of Neurology, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel. .,The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel. .,Memory clinic, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel. .,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Abigail Livny
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Department of Diagnostic Imaging, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ramit Ravona-Springer
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Memory clinic, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Itzik Cooper
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Anna Alkelai
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - Shahar Shelly
- Department of Neurology, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Department of Neurology, Mayo Clinic, Rochester, Minnesota, USA
| | - Galia Tsarfaty
- Department of Diagnostic Imaging, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Anthony Heymann
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Maccabi Healthcare Services, Tel Aviv, Israel
| | - Michal Schnaider Beeri
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lior Greenbaum
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
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8
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Chen J, Sun M, Adeyemo A, Pirie F, Carstensen T, Pomilla C, Doumatey AP, Chen G, Young EH, Sandhu M, Morris AP, Barroso I, McCarthy MI, Mahajan A, Wheeler E, Rotimi CN, Motala AA. Genome-wide association study of type 2 diabetes in Africa. Diabetologia 2019; 62:1204-1211. [PMID: 31049640 PMCID: PMC6560001 DOI: 10.1007/s00125-019-4880-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 03/22/2019] [Indexed: 02/02/2023]
Abstract
AIMS/HYPOTHESIS Genome-wide association studies (GWAS) for type 2 diabetes have uncovered >400 risk loci, primarily in populations of European and Asian ancestry. Here, we aimed to discover additional type 2 diabetes risk loci (including African-specific variants) and fine-map association signals by performing genetic analysis in African populations. METHODS We conducted two type 2 diabetes genome-wide association studies in 4347 Africans from South Africa, Nigeria, Ghana and Kenya and meta-analysed both studies together. Likely causal variants were identified using fine-mapping approaches. RESULTS The most significantly associated variants mapped to the widely replicated type 2 diabetes risk locus near TCF7L2 (p = 5.3 × 10-13). Fine-mapping of the TCF7L2 locus suggested one type 2 diabetes association signal shared between Europeans and Africans (indexed by rs7903146) and a distinct African-specific signal (indexed by rs17746147). We also detected one novel signal, rs73284431, near AGMO (p = 5.2 × 10-9, minor allele frequency [MAF] = 0.095; monomorphic in most non-African populations), distinct from previously reported signals in the region. In analyses focused on 100 published type 2 diabetes risk loci, we identified 21 with shared causal variants in African and non-African populations. CONCLUSIONS/INTERPRETATION These results demonstrate the value of performing GWAS in Africans, provide a resource to larger consortia for further discovery and fine-mapping and indicate that additional large-scale efforts in Africa are warranted to gain further insight in to the genetic architecture of type 2 diabetes.
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Affiliation(s)
- Ji Chen
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Meng Sun
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Adebowale Adeyemo
- Center for Research on Genomics and Global Heath, National Human Genome Research Institute, National Institute of Health, Bethesda, MD, USA
| | - Fraser Pirie
- Department of Diabetes and Endocrinology, University of KwaZulu-Natal, Durban, 4013, South Africa
| | - Tommy Carstensen
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Cristina Pomilla
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Ayo P Doumatey
- Center for Research on Genomics and Global Heath, National Human Genome Research Institute, National Institute of Health, Bethesda, MD, USA
| | - Guanjie Chen
- Center for Research on Genomics and Global Heath, National Human Genome Research Institute, National Institute of Health, Bethesda, MD, USA
| | - Elizabeth H Young
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Manjinder Sandhu
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Andrew P Morris
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
- Department of Biostatistics, University of Liverpool, Liverpool, UK
| | - Inês Barroso
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Mark I McCarthy
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
- Oxford NIHR Biomedical Research Centre, Oxford, UK
| | - Anubha Mahajan
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK.
| | - Eleanor Wheeler
- Wellcome Sanger Institute, Hinxton, Cambridge, UK.
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK.
| | - Charles N Rotimi
- Center for Research on Genomics and Global Heath, National Human Genome Research Institute, National Institute of Health, Bethesda, MD, USA.
| | - Ayesha A Motala
- Department of Diabetes and Endocrinology, University of KwaZulu-Natal, Durban, 4013, South Africa.
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9
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Geoghegan G, Simcox J, Seldin MM, Parnell TJ, Stubben C, Just S, Begaye L, Lusis AJ, Villanueva CJ. Targeted deletion of Tcf7l2 in adipocytes promotes adipocyte hypertrophy and impaired glucose metabolism. Mol Metab 2019; 24:44-63. [PMID: 30948248 PMCID: PMC6531814 DOI: 10.1016/j.molmet.2019.03.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 03/02/2019] [Accepted: 03/09/2019] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVE Activation of the Wnt-signaling pathway is known to inhibit differentiation in adipocytes. However, there is a gap in our understanding of the transcriptional network regulated by components of the Wnt-signaling pathway during adipogenesis and in adipocytes during postnatal life. The key intracellular effectors of the Wnt-signaling pathway occur through TCF transcription factors such as TCF7L2 (transcription factor-7-like 2). Several genetic variants in proximity to TCF7L2 have been linked to type 2 diabetes through genome-wide association studies in various human populations. Our work aims to functionally characterize the adipocyte specific gene program regulated by TCF7L2 and understand how this program regulates metabolism. METHODS We generated Tcf7l2F/F mice and assessed TCF7L2 function in isolated adipocytes and adipose specific knockout mice. ChIP-sequencing and RNA-sequencing was performed on the isolated adipocytes with control and TCF7L2 knockout cells. Adipose specific TCF7L2 knockout mice were challenged with high fat diet and assessed for body weight, glucose tolerance, and lipolysis. RESULTS Here we report that TCF7L2 regulates adipocyte size, endocrine function, and glucose metabolism. Tcf7l2 is highly expressed in white adipose tissue, and its expression is suppressed in genetic and diet-induced models of obesity. Genome-wide distribution of TCF7L2 binding and gene expression analysis in adipocytes suggests that TCF7L2 directly regulates genes implicated in cellular metabolism and cell cycle control. When challenged with a high-fat diet, conditional deletion of TCF7L2 in adipocytes led to impaired glucose tolerance, impaired insulin sensitivity, promoted weight gain, and increased adipose tissue mass. This was accompanied by reduced expression of triglyceride hydrolase, reduced fasting-induced free fatty acid release, and adipocyte hypertrophy in subcutaneous adipose tissue. CONCLUSIONS Together our studies support that TCF7L2 is a central transcriptional regulator of the adipocyte metabolic program by directly regulating the expression of genes involved in lipid and glucose metabolism.
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Affiliation(s)
- Gisela Geoghegan
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Judith Simcox
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Marcus M Seldin
- Department of Human Genetics/Medicine, University of California, Los Angeles, CA, USA; Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, USA
| | - Timothy J Parnell
- Bioinformatics Shared Resources, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Chris Stubben
- Bioinformatics Shared Resources, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Steven Just
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Lori Begaye
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Aldons J Lusis
- Department of Human Genetics/Medicine, University of California, Los Angeles, CA, USA; Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, USA
| | - Claudio J Villanueva
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA.
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11
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Keaton JM, Gao C, Guan M, Hellwege JN, Palmer ND, Pankow JS, Fornage M, Wilson JG, Correa A, Rasmussen-Torvik LJ, Rotter JI, Chen YDI, Taylor KD, Rich SS, Wagenknecht LE, Freedman BI, Ng MCY, Bowden DW. Genome-wide interaction with the insulin secretion locus MTNR1B reveals CMIP as a novel type 2 diabetes susceptibility gene in African Americans. Genet Epidemiol 2018; 42:559-570. [PMID: 29691896 PMCID: PMC6160319 DOI: 10.1002/gepi.22126] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 02/27/2018] [Accepted: 03/16/2018] [Indexed: 11/09/2022]
Abstract
Although type 2 diabetes (T2D) results from metabolic defects in insulin secretion and insulin sensitivity, most of the genetic risk loci identified to date relates to insulin secretion. We reported that T2D loci influencing insulin sensitivity may be identified through interactions with insulin secretion loci, thereby leading to T2D. Here, we hypothesize that joint testing of variant main effects and interaction effects with an insulin secretion locus increases power to identify genetic interactions leading to T2D. We tested this hypothesis with an intronic MTNR1B SNP, rs10830963, which is associated with acute insulin response to glucose, a dynamic measure of insulin secretion. rs10830963 was tested for interaction and joint (main + interaction) effects with genome-wide data in African Americans (2,452 cases and 3,772 controls) from five cohorts. Genome-wide genotype data (Affymetrix Human Genome 6.0 array) was imputed to a 1000 Genomes Project reference panel. T2D risk was modeled using logistic regression with rs10830963 dosage, age, sex, and principal component as predictors. Joint effects were captured using the Kraft two degrees of freedom test. Genome-wide significant (P < 5 × 10-8 ) interaction with MTNR1B and joint effects were detected for CMIP intronic SNP rs17197883 (Pinteraction = 1.43 × 10-8 ; Pjoint = 4.70 × 10-8 ). CMIP variants have been nominally associated with T2D, fasting glucose, and adiponectin in individuals of East Asian ancestry, with high-density lipoprotein, and with waist-to-hip ratio adjusted for body mass index in Europeans. These data support the hypothesis that additional genetic factors contributing to T2D risk, including insulin sensitivity loci, can be identified through interactions with insulin secretion loci.
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Affiliation(s)
- Jacob M Keaton
- Molecular Genetics and Genomics Program, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Chuan Gao
- Molecular Genetics and Genomics Program, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Meijian Guan
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Jacklyn N Hellwege
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Nicholette D Palmer
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - James S Pankow
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Myriam Fornage
- Institute of Molecular Medicine and Human Genetics Center, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - James G Wilson
- Department of Medicine, University of Mississippi Medical Center, Jackson, Mississipi, United States of America
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, Mississipi, United States of America
| | - Laura J Rasmussen-Torvik
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Yii-Der I Chen
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Kent D Taylor
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Lynne E Wagenknecht
- Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Barry I Freedman
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- Department of Internal Medicine - Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Maggie C Y Ng
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Donald W Bowden
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
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12
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Adams JD, Vella A. What Can Diabetes-Associated Genetic Variation in TCF7L2 Teach Us About the Pathogenesis of Type 2 Diabetes? Metab Syndr Relat Disord 2018; 16:383-389. [PMID: 29993315 DOI: 10.1089/met.2018.0024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Type 2 diabetes mellitus (T2DM) is a polygenic metabolic disorder characterized by hyperglycemia occurring as a result of impaired insulin secretion and/or insulin resistance. Among the various genetic factors associated with T2DM, a common genetic variant within the transcription factor 7-like 2 locus (TCF7L2) confers the greatest genetic risk for development of the disease. However, the mechanism(s) by which TCF7L2 predisposes to diabetes remain uncertain. Here we review the current literature pertaining to the potential mechanisms by which TCF7L2 confers risk of T2DM, using genetic variation as a probe to understand the pathogenesis of the disease.
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Affiliation(s)
- J D Adams
- Endocrine Research Unit, Department of Endocrinology, Diabetes and Nutrition, Mayo Clinic College of Medicine , Rochester, Minnesota
| | - Adrian Vella
- Endocrine Research Unit, Department of Endocrinology, Diabetes and Nutrition, Mayo Clinic College of Medicine , Rochester, Minnesota
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13
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Huang ZQ, Liao YQ, Huang RZ, Chen JP, Sun HL. Possible role of TCF7L2 in the pathogenesis of type 2 diabetes mellitus. BIOTECHNOL BIOTEC EQ 2018; 32:830-834. [DOI: 10.1080/13102818.2018.1438211] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 02/05/2018] [Indexed: 01/17/2023] Open
Affiliation(s)
- Zhi-qiu Huang
- Department of Endocrinology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, PR China
| | - Yao-qi Liao
- Department of Endocrinology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, PR China
| | - Run-ze Huang
- Department of Endocrinology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, PR China
| | - Jin-peng Chen
- Department of Endocrinology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, PR China
| | - Hui-lin Sun
- Department of Endocrinology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, PR China
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14
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Rotimi CN, Bentley AR, Doumatey AP, Chen G, Shriner D, Adeyemo A. The genomic landscape of African populations in health and disease. Hum Mol Genet 2017; 26:R225-R236. [PMID: 28977439 PMCID: PMC6075021 DOI: 10.1093/hmg/ddx253] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 06/19/2017] [Accepted: 06/29/2017] [Indexed: 12/12/2022] Open
Abstract
A deeper appreciation of the complex architecture of African genomes is critical to the global effort to understand human history, biology and differential distribution of disease by geography and ancestry. Here, we report on how the growing engagement of African populations in genome science is providing new insights into the forces that shaped human genomes before and after the Out-of-Africa migrations. As a result of this human evolutionary history, African ancestry populations have the greatest genomic diversity in the world, and this diversity has important ramifications for genomic research. In the case of pharmacogenomics, for instance, variants of consequence are not limited to those identified in other populations, and diversity within African ancestry populations precludes summarizing risk across different African ethnic groups. Exposure of Africans to fatal pathogens, such as Plasmodium falciparum, Lassa Virus and Trypanosoma brucei rhodesiense, has resulted in elevated frequencies of alleles conferring survival advantages for infectious diseases, but that are maladaptive in modern-day environments. Illustrating with cardiometabolic traits, we show that while genomic research in African ancestry populations is still in early stages, there are already many examples of novel and African ancestry-specific disease loci that have been discovered. Furthermore, the shorter haplotypes in African genomes have facilitated fine-mapping of loci discovered in other human ancestry populations. Given the insights already gained from the interrogation of African genomes, it is imperative to continue and increase our efforts to describe genomic risk in and across African ancestry populations.
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Affiliation(s)
- Charles N. Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Amy R. Bentley
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Ayo P. Doumatey
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Guanjie Chen
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Daniel Shriner
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD 20892, USA
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15
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Wang XF, Lin X, Li DY, Zhou R, Greenbaum J, Chen YC, Zeng CP, Peng LP, Wu KH, Ao ZX, Lu JM, Guo YF, Shen J, Deng HW. Linking Alzheimer's disease and type 2 diabetes: Novel shared susceptibility genes detected by cFDR approach. J Neurol Sci 2017; 380:262-272. [PMID: 28870582 DOI: 10.1016/j.jns.2017.07.044] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 06/29/2017] [Accepted: 07/28/2017] [Indexed: 02/08/2023]
Abstract
BACKGROUND Both type 2 diabetes (T2D) and Alzheimer's disease (AD) occur commonly in the aging populations and T2D has been considered as an important risk factor for AD. The heritability of both diseases is estimated to be over 50%. However, common pleiotropic single-nucleotide polymorphisms (SNPs)/loci have not been well-defined. The aim of this study is to analyze two large public accessible GWAS datasets to identify novel common genetic loci for T2D and/or AD. METHODS AND MATERIALS The recently developed novel conditional false discovery rate (cFDR) approach was used to analyze the summary GWAS datasets from International Genomics of Alzheimer's Project (IGAP) and Diabetes Genetics Replication And Meta-analysis (DIAGRAM) to identify novel susceptibility genes for AD and T2D. RESULTS We identified 78 SNPs (including 58 novel SNPs) that were associated with AD in Europeans conditional on T2D (cFDR<0.05). 66 T2D SNPs (including 40 novel SNPs) were identified by conditioning on SNPs association with AD (cFDR<0.05). A conjunction-cFDR (ccFDR) analysis detected 8 pleiotropic SNPs with a significance threshold of ccFDR<0.05 for both AD and T2D, of which 5 SNPs (rs6982393, rs4734295, rs7812465, rs10510109, rs2421016) were novel findings. Furthermore, among the 8 SNPs annotated at 6 different genes, 3 corresponding genes TP53INP1, TOMM40 and C8orf38 were related to mitochondrial dysfunction, critically involved in oxidative stress, which potentially contribute to the etiology of both AD and T2D. CONCLUSION Our study provided evidence for shared genetic loci between T2D and AD in European subjects by using cFDR and ccFDR analyses. These results may provide novel insight into the etiology and potential therapeutic targets of T2D and/or AD.
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Affiliation(s)
- Xia-Fang Wang
- Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, PR China
| | - Xu Lin
- Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, PR China
| | - Ding-You Li
- Department of Gastroenterology, Children's Mercy Kansas City, University of Missouri Kansas City School of Medicine, Kansas City MO 64108, USA
| | - Rou Zhou
- Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, PR China
| | - Jonathan Greenbaum
- Center for Bioinformatics and Genomics, Department of Global Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Yuan-Cheng Chen
- Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, PR China
| | - Chun-Ping Zeng
- Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, PR China
| | - Lin-Ping Peng
- Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, PR China
| | - Ke-Hao Wu
- Center for Bioinformatics and Genomics, Department of Global Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Zeng-Xin Ao
- Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, PR China
| | - Jun-Min Lu
- Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, PR China
| | - Yan-Fang Guo
- Institute of Bioinformatics, School of Basic Medical Science, Southern Medical University, Guangzhou, Guangdong 510515, PR China
| | - Jie Shen
- Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, PR China
| | - Hong-Wen Deng
- Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, PR China; Center for Bioinformatics and Genomics, Department of Global Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA.
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16
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Manach C, Milenkovic D, Van de Wiele T, Rodriguez‐Mateos A, de Roos B, Garcia‐Conesa MT, Landberg R, Gibney ER, Heinonen M, Tomás‐Barberán F, Morand C. Addressing the inter-individual variation in response to consumption of plant food bioactives: Towards a better understanding of their role in healthy aging and cardiometabolic risk reduction. Mol Nutr Food Res 2017; 61:1600557. [PMID: 27687784 PMCID: PMC5484307 DOI: 10.1002/mnfr.201600557] [Citation(s) in RCA: 141] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Revised: 09/08/2016] [Accepted: 09/13/2016] [Indexed: 12/21/2022]
Abstract
Bioactive compounds in plant-based foods have health properties that contribute to the prevention of age-related chronic diseases, particularly cardiometabolic disorders. Conclusive proof and understanding of these benefits in humans is essential in order to provide effective dietary recommendations but, so far, the evidence obtained from human intervention trials is limited and contradictory. This is partly due to differences between individuals in the absorption, distribution, metabolism and excretion of bioactive compounds, as well as to heterogeneity in their biological response regarding cardiometabolic health outcomes. Identifying the main factors underlying inter-individual differences, as well as developing new and innovative methodologies to account for such variability constitute an overarching goal to ultimately optimize the beneficial health effects of plant food bioactives for each and every one of us. In this respect, this position paper from the COST Action FA1403-POSITIVe examines the main factors likely to affect the individual responses to consumption of plant food bioactives and presents perspectives for assessment and consideration of inter-individual variability.
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Affiliation(s)
- Claudine Manach
- INRA, UMR 1019, UNH, CRNH Auvergne, F‐63000 Clermont‐Ferrand; Clermont UniversitéUniversité d'AuvergneUnité de Nutrition HumaineBP 10448F‐63000Clermont‐FerrandFrance
| | - Dragan Milenkovic
- INRA, UMR 1019, UNH, CRNH Auvergne, F‐63000 Clermont‐Ferrand; Clermont UniversitéUniversité d'AuvergneUnité de Nutrition HumaineBP 10448F‐63000Clermont‐FerrandFrance
| | - Tom Van de Wiele
- Center for Microbial Ecology and Technology (CMET)Ghent UniversityGhentBelgium
| | - Ana Rodriguez‐Mateos
- Division of Cardiology, Pulmonology and Vascular MedicineMedical FacultyUniversity of DüsseldorfGermany
| | - Baukje de Roos
- Rowett Institute of Nutrition and HealthUniversity of AberdeenAberdeenUK
| | - Maria Teresa Garcia‐Conesa
- Research Group on Quality, Safety and Bioactivity of Plant FoodsCEBAS‐CSICCampus de EspinardoMurciaSpain
| | - Rikard Landberg
- Department of Food ScienceSwedish University of Agricultural SciencesUppsalaSweden
- Nutritional Epidemiology UnitInstitute of Environmental MedicineKarolinska InstitutetSolnaSweden
| | - Eileen R. Gibney
- UCD Institute of Food and HealthUniversity College DublinDublinRepublic of Ireland
| | - Marina Heinonen
- Department of Food and Environmental SciencesFood ChemistryUniversity of HelsinkiFinland
| | - Francisco Tomás‐Barberán
- Research Group on Quality, Safety and Bioactivity of Plant FoodsCEBAS‐CSICCampus de EspinardoMurciaSpain
| | - Christine Morand
- INRA, UMR 1019, UNH, CRNH Auvergne, F‐63000 Clermont‐Ferrand; Clermont UniversitéUniversité d'AuvergneUnité de Nutrition HumaineBP 10448F‐63000Clermont‐FerrandFrance
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17
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Xia Q, Chesi A, Manduchi E, Johnston BT, Lu S, Leonard ME, Parlin UW, Rappaport EF, Huang P, Wells AD, Blobel GA, Johnson ME, Grant SFA. The type 2 diabetes presumed causal variant within TCF7L2 resides in an element that controls the expression of ACSL5. Diabetologia 2016; 59:2360-2368. [PMID: 27539148 DOI: 10.1007/s00125-016-4077-2] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 07/22/2016] [Indexed: 01/27/2023]
Abstract
AIMS/HYPOTHESIS One of the most strongly associated type 2 diabetes loci reported to date resides within the TCF7L2 gene. Previous studies point to the T allele of rs7903146 in intron 3 as the causal variant at this locus. We aimed to identify the actual gene(s) under the influence of this variant. METHODS Using clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein-9 nuclease, we generated a 1.4 kb deletion of the genomic region harbouring rs7903146 in the HCT116 cell line, followed by global gene expression analysis. We then carried out a combination of circularised chromosome conformation capture (4C) and Capture C in cell lines, HCT116 and NCM460 in order to ascertain which promoters of these perturbed genes made consistent physical contact with this genomic region. RESULTS We observed 99 genes with significant differential expression (false discovery rate [FDR] cut-off:10%) and an effect size of at least twofold. The subsequent promoter contact analyses revealed just one gene, ACSL5, which resides in the same topologically associating domain as TCF7L2. The generation of additional, smaller deletions (66 bp and 104 bp) comprising rs7903146 showed consistently reduced ACSL5 mRNA levels across all three deletions of up to 30-fold, with commensurate loss of acyl-CoA synthetase long-chain family member 5 (ACSL5) protein. Notably, the deletion of this single-nucleotide polymorphism region abolished significantly detectable chromatin contacts with the ACSL5 promoter. We went on to confirm that contacts between rs7903146 and the ACSL5 promoter regions were conserved in human colon tissue. ACSL5 encodes ACSL5, an enzyme with known roles in fatty acid metabolism. CONCLUSIONS/INTERPRETATION This 'variant to gene mapping' effort implicates the genomic location harbouring rs7903146 as a regulatory region for ACSL5.
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Affiliation(s)
- Qianghua Xia
- Divisions of Human Genetics and Endocrinology, The Children's Hospital of Philadelphia, 3615 Civic Center Boulevard, Room 1102D, Philadelphia, PA, 19104, USA
| | - Alessandra Chesi
- Divisions of Human Genetics and Endocrinology, The Children's Hospital of Philadelphia, 3615 Civic Center Boulevard, Room 1102D, Philadelphia, PA, 19104, USA
| | - Elisabetta Manduchi
- Divisions of Human Genetics and Endocrinology, The Children's Hospital of Philadelphia, 3615 Civic Center Boulevard, Room 1102D, Philadelphia, PA, 19104, USA
- Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Brian T Johnston
- Divisions of Human Genetics and Endocrinology, The Children's Hospital of Philadelphia, 3615 Civic Center Boulevard, Room 1102D, Philadelphia, PA, 19104, USA
| | - Sumei Lu
- Divisions of Human Genetics and Endocrinology, The Children's Hospital of Philadelphia, 3615 Civic Center Boulevard, Room 1102D, Philadelphia, PA, 19104, USA
| | - Michelle E Leonard
- Divisions of Human Genetics and Endocrinology, The Children's Hospital of Philadelphia, 3615 Civic Center Boulevard, Room 1102D, Philadelphia, PA, 19104, USA
| | - Ursula W Parlin
- Divisions of Human Genetics and Endocrinology, The Children's Hospital of Philadelphia, 3615 Civic Center Boulevard, Room 1102D, Philadelphia, PA, 19104, USA
| | - Eric F Rappaport
- NAPCore, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Peng Huang
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Andrew D Wells
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Gerd A Blobel
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew E Johnson
- Divisions of Human Genetics and Endocrinology, The Children's Hospital of Philadelphia, 3615 Civic Center Boulevard, Room 1102D, Philadelphia, PA, 19104, USA
| | - Struan F A Grant
- Divisions of Human Genetics and Endocrinology, The Children's Hospital of Philadelphia, 3615 Civic Center Boulevard, Room 1102D, Philadelphia, PA, 19104, USA.
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Institute of Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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18
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Lacroix S, Cantin J, Nigam A. Contemporary issues regarding nutrition in cardiovascular rehabilitation. Ann Phys Rehabil Med 2016; 60:36-42. [PMID: 27641779 DOI: 10.1016/j.rehab.2016.07.262] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 06/23/2016] [Accepted: 07/07/2016] [Indexed: 12/20/2022]
Abstract
In this article, we discuss certain contemporary and controversial topics in cardiovascular (CV) nutrition including recent data regarding the health benefits of the Mediterranean diet, the role of saturated fatty acids, red meat and the microbiome in CV disease and the current role of personalized CV nutrition. Findings from the PREDIMED study now demonstrate the health benefits of the Mediterranean diet even in the absence of heart disease. The study highlighted that even small, sustained and easily implementable changes to diet can provide significant health benefits even in Mediterranean regions. Likewise, observational data in secondary prevention show that increased adherence to the Mediterranean diet is associated with good long-term clinical outcomes among subjects with stable coronary heart disease. The role of saturated fats in the development of CV disease remains controversial, although data suggest that these fats are associated with modestly increased risk of CV events. In contrast, the obesity epidemic currently driving the CV risk worldwide is in large part due to excess consumption of refined carbohydrates. Furthermore, a growing body of evidence suggests that the intestinal microbiome is highly sensitive to lifestyle choices and may play a pivotal role in modulating CV disease development. For example, recent evidence linking processed and unprocessed meats to increased CV risk pointed to the gut microbial metabolite trimethylamine N-oxide as a potential culprit. Finally, given the high interindividual variability in response to interventions including diet, personalized nutrition has potential to play a major role in tailoring diets based on genetic make-up to maximize health benefits. This approach is still in its infancy but is highly promising.
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Affiliation(s)
- Sébastien Lacroix
- The Microsoft Research, University of Trento Centre for Computational Systems Biology (COSBI), Piazza Manifattura 1, 38068 Rovereto, Italy; Cardiovascular Prevention and Rehabilitation Centre, Montreal Heart Institute, Montreal, Quebec, Canada H1T 1C8; Research Centre, Montreal Heart Institute, Canada; Department of Nutrition, Faculty of Medicine, Université de Montréal, Montréal, Québec, Canada H3T 1A8
| | - Jennifer Cantin
- Cardiovascular Prevention and Rehabilitation Centre, Montreal Heart Institute, Montreal, Quebec, Canada H1T 1C8; Research Centre, Montreal Heart Institute, Canada; Department of Nutrition, Faculty of Medicine, Université de Montréal, Montréal, Québec, Canada H3T 1A8
| | - Anil Nigam
- Cardiovascular Prevention and Rehabilitation Centre, Montreal Heart Institute, Montreal, Quebec, Canada H1T 1C8; Research Centre, Montreal Heart Institute, Canada; Department of Nutrition, Faculty of Medicine, Université de Montréal, Montréal, Québec, Canada H3T 1A8; Department of Medicine, Université de Montréal, Montréal, Québec, Canada H3T 1J4; PERFORM Centre, Concordia University, Montreal, Quebec, Canada H4B 1R6.
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19
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Ravera A, Carubelli V, Sciatti E, Bonadei I, Gorga E, Cani D, Vizzardi E, Metra M, Lombardi C. Nutrition and Cardiovascular Disease: Finding the Perfect Recipe for Cardiovascular Health. Nutrients 2016; 8:E363. [PMID: 27314382 PMCID: PMC4924204 DOI: 10.3390/nu8060363] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 05/05/2016] [Accepted: 05/23/2016] [Indexed: 02/07/2023] Open
Abstract
The increasing burden of cardiovascular disease (CVD) despite the progress in management entails the need of more effective preventive and curative strategies. As dietary-associated risk is the most important behavioral factor influencing global health, it appears the best target in the challenge against CVD. Although for many years, since the formulation of the cholesterol hypothesis, a nutrient-based approach was attempted for CVD prevention and treatment, in recent years a dietary-based approach resulted more effective in reducing cardiovascular risk worldwide. After the publication of randomized trials on the remarkable effects of the Mediterranean diet and the Dietary Approach to Stop Hypertension (DASH) diet on CVD, new efforts were put on research about the effects of complex dietary interventions on CVD. The purpose of this paper is to review the evidence on dietary interventions in the prevention and disease modification of CVD, focusing on coronary artery disease and heart failure, the main disease responsible for the enormous toll taken by CVD worldwide.
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Affiliation(s)
- Alice Ravera
- Division of Cardiology, Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University and Civil Hospital of Brescia, Brescia 25123, Italy.
| | - Valentina Carubelli
- Division of Cardiology, Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University and Civil Hospital of Brescia, Brescia 25123, Italy.
| | - Edoardo Sciatti
- Division of Cardiology, Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University and Civil Hospital of Brescia, Brescia 25123, Italy.
| | - Ivano Bonadei
- Division of Cardiology, Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University and Civil Hospital of Brescia, Brescia 25123, Italy.
| | - Elio Gorga
- Division of Cardiology, Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University and Civil Hospital of Brescia, Brescia 25123, Italy.
| | - Dario Cani
- Division of Cardiology, Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University and Civil Hospital of Brescia, Brescia 25123, Italy.
| | - Enrico Vizzardi
- Division of Cardiology, Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University and Civil Hospital of Brescia, Brescia 25123, Italy.
| | - Marco Metra
- Division of Cardiology, Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University and Civil Hospital of Brescia, Brescia 25123, Italy.
| | - Carlo Lombardi
- Division of Cardiology, Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University and Civil Hospital of Brescia, Brescia 25123, Italy.
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20
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Jin T. Current Understanding on Role of the Wnt Signaling Pathway Effector TCF7L2 in Glucose Homeostasis. Endocr Rev 2016; 37:254-77. [PMID: 27159876 DOI: 10.1210/er.2015-1146] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The role of the Wnt signaling pathway in metabolic homeostasis has drawn our intensive attention, especially after the genome-wide association study discovery that certain polymorphisms of its key effector TCF7L2 are strongly associated with the susceptibility to type 2 diabetes. For a decade, great efforts have been made in determining the function of TCF7L2 in various metabolic organs, which have generated both considerable achievements and disputes. In this review, I will briefly introduce the canonical Wnt signaling pathway, focusing on its effector β-catenin/TCF, including emphasizing the bidirectional feature of TCFs and β-catenin post-translational modifications. I will then summarize the observations on the association between TCF7L2 polymorphisms and type 2 diabetes risk. The main content, however, is on the intensive functional exploration of the metabolic role of TCF7L2, including the disputes generated on determining its role in the pancreas and liver with various transgenic mouse lines. Finally, I will discuss those achievements and disputes and present my future perspectives.
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Affiliation(s)
- Tianru Jin
- Division of Advanced Diagnostics, Toronto General Research Institute, University Health Network, Toronto, ON M5G 2C4, Canada
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Ding Y, Hu Z, Yuan S, Xie P, Liu Q. Association between transcription factor 7-like 2 rs7903146 polymorphism and diabetic retinopathy in type 2 diabetes mellitus: A meta-analysis. Diab Vasc Dis Res 2015; 12:436-44. [PMID: 26316572 DOI: 10.1177/1479164115598274] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
As one of the vascular complications of type 2 diabetes mellitus, the incidence of diabetes retinopathy is greatly increasing worldwide. Both genetic and environmental factors are involved in the pathologies. A meta-analysis was conducted to assess the association between transcription factor 7-like 2 polymorphism (rs7903146) and type 2 diabetic retinopathy. Published literature from PubMed, Web of Science and China National Knowledge Infrastructure were retrieved. Pooled odds ratios with 95% confidence intervals were calculated to estimate the strength of the association. Eight studies including 6422 participants were included in the final meta-analysis. Our analysis provides substantial evidence that the rs7903146 variant is significantly associated with the risk of diabetic retinopathy in Caucasian populations while not in East Asian populations. The variant of rs7903146 appeared more likely to be a promising genetic biomarker of diabetic retinopathy in Caucasians.
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Affiliation(s)
- Yuzhi Ding
- The First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Zizhong Hu
- The First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Songtao Yuan
- The First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Ping Xie
- The First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Qinghuai Liu
- The First Affiliated Hospital, Nanjing Medical University, Nanjing, China
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Abstract
Type 2 diabetes (T2D) is a global health problem showing substantial ethnic disparity in disease prevalence. African Americans have one of the highest prevalence of T2D in the USA but little is known about their genetic risks. This review summarizes the findings of genetic regions and loci associated with T2D and related glycemic traits using linkage, admixture, and association approaches in populations of African ancestry. In particular, findings from genome-wide association and exome chip studies suggest the presence of both ancestry-specific and shared loci for T2D and glycemic traits. Among the European-identified loci that are transferable to individuals of African ancestry, allelic heterogeneity as well as differential linkage disequilibrium and risk allele frequencies pose challenges and opportunities for fine mapping and identification of causal variant(s) by trans-ancestry meta-analysis. More genetic research is needed in African ancestry populations including the next-generation sequencing to improve the understanding of genetic architecture of T2D.
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Affiliation(s)
- Maggie C Y Ng
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC, USA,
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Cheng PW, Chen YY, Cheng WH, Lu PJ, Chen HH, Chen BR, Yeh TC, Sun GC, Hsiao M, Tseng CJ. Wnt Signaling Regulates Blood Pressure by Downregulating a GSK-3β-Mediated Pathway to Enhance Insulin Signaling in the Central Nervous System. Diabetes 2015; 64:3413-24. [PMID: 25883115 DOI: 10.2337/db14-1439] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Accepted: 04/08/2015] [Indexed: 11/13/2022]
Abstract
Aberrant Wnt signaling appears to play an important role in the onset of diabetes. Moreover, the insulin signaling pathway is defective in the nucleus tractus solitarii (NTS) of spontaneously hypertensive rats (SHRs) and fructose-fed rats. Nevertheless, the relationships between Wnt signaling and the insulin pathway and the related modulation of blood pressure (BP) in the central nervous system have yet to be established. The aim of this study was to investigate the potential signaling pathways involved in Wnt-mediated BP regulation in the NTS. Pretreatment with the LDL receptor-related protein (LRP) antagonist Dickkopf-1 (DKK1) significantly attenuated the Wnt3a-induced depressor effect and nitric oxide production. Additionally, the inhibition of LRP6 activity using DKK1 significantly abolished Wnt3a-induced glycogen synthase kinase 3β (GSK-3β)(S9), extracellular signal-regulated kinases 1/2(T202/Y204), ribosomal protein S6 kinase(T359/S363), and Akt(S473) phosphorylation; and increased insulin receptor substrate 1 (IRS1)(S332) phosphorylation. GSK-3β was also found to bind directly to IRS1 and to induce the phosphorylation of IRS1 at serine 332 in the NTS. By contrast, administration of the GSK-3β inhibitor TWS119 into the brain decreased the BP of hypertensive rats by enhancing IRS1 activity. Taken together, these results suggest that the GSK-3β-IRS1 pathway may play a significant role in Wnt-mediated central BP regulation.
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Affiliation(s)
- Pei-Wen Cheng
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Republic of China
| | - Ying-Ying Chen
- Department of Ophthalmology, Kaohsiung Veterans General Hospital, Kaohsiung, Republic of China
| | - Wen-Han Cheng
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Republic of China
| | - Pei-Jung Lu
- Institute of Clinical Medicine, National Cheng Kung University, Tainan, Republic of China
| | - Hsin-Hung Chen
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, Republic of China
| | - Bo-Rong Chen
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Republic of China
| | - Tung-Chen Yeh
- Department of Internal Medicine, Division of Cardiology, Kaohsiung Veterans General Hospital, Kaohsiung, Republic of China
| | - Gwo-Ching Sun
- Institute of Clinical Medicine, National Cheng Kung University, Tainan, Republic of China
| | - Michael Hsiao
- Genomics Research Center, Academia Sinica, Taipei, Republic of China
| | - Ching-Jiunn Tseng
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Republic of China Institute of Clinical Medicine, National Yang-Ming University, Taipei, Republic of China Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Republic of China
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Assmann TS, Duarte GCK, Rheinheimer J, Cruz LA, Canani LH, Crispim D. The TCF7L2 rs7903146 (C/T) polymorphism is associated with risk to type 2 diabetes mellitus in Southern-Brazil. ACTA ACUST UNITED AC 2015; 58:918-25. [PMID: 25627047 DOI: 10.1590/0004-2730000003510] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 09/14/2014] [Indexed: 02/26/2023]
Abstract
OBJECTIVE The aim of this study was to investigate the association between the rs7903146 (C/T) polymorphism in the TCF7L2 gene and type 2 diabetes mellitus, in a Southern-Brazilian population. MATERIALS AND METHODS The TCF7L2 rs7903146 polymorphism was genotyped in 953 type 2 diabetic patients and 535 non-diabetic subjects. All subjects were white. The polymorphism was genotyped by Real-Time PCR using TaqMan MGB probes (Life Technologies). Odds ratios (OR) and 95% confidence intervals (CI) were calculated for additive, recessive and dominant inheritance models. RESULTS Genotype and allele frequencies of the rs7903146 polymorphism differed significantly between type 2 diabetic patients and non-diabetic subjects (P = 0.001 and P = 0.0001, respectively). The frequency of the minor allele was 38% in type 2 diabetes group and 31% in non-diabetic subjects, and this allele was significantly associated with type 2 diabetes risk (OR = 1.42, 95% CI 1.15 - 1.76 for the dominant model of inheritance). Moreover, the T/T genotype was associated with a higher risk for type 2 diabetes (OR = 1.83, 95% CI 1.3-2.5) than the presence of only one copy of the T allele (OR = 1.31, 95% CI 1.1-1.6). Both results were adjusted for age and gender. CONCLUSIONS Our results confirm the association between the TCF7L2 rs7903146 polymorphism and increase risk for type 2 diabetes in Southern-Brazil.
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Affiliation(s)
- Taís S Assmann
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Guilherme C K Duarte
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Jakeline Rheinheimer
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Lavínia A Cruz
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Luís H Canani
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Daisy Crispim
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
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Maggadottir SM, Li J, Glessner JT, Li YR, Wei Z, Chang X, Mentch FD, Thomas KA, Kim CE, Zhao Y, Hou C, Wang F, Jørgensen SF, Perez EE, Sullivan KE, Orange JS, Karlsen TH, Chapel H, Cunningham-Rundles C, Hakonarson H. Rare variants at 16p11.2 are associated with common variable immunodeficiency. J Allergy Clin Immunol 2015; 135:1569-77. [PMID: 25678086 PMCID: PMC4461447 DOI: 10.1016/j.jaci.2014.12.1939] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 12/24/2014] [Accepted: 12/31/2014] [Indexed: 12/27/2022]
Abstract
BACKGROUND Common variable immunodeficiency (CVID) is characterized clinically by inadequate quantity and quality of serum immunoglobulins with increased susceptibility to infections, resulting in significant morbidity and mortality. Only a few genes have been uncovered, and the genetic background of CVID remains elusive to date for the majority of patients. OBJECTIVE We sought to seek novel associations of genes and genetic variants with CVID. METHODS We performed association analyses in a discovery cohort of 164 patients with CVID and 19,542 healthy control subjects genotyped on the Immuno BeadChip from Illumina platform; replication of findings was examined in an independent cohort of 135 patients with CVID and 2,066 healthy control subjects, followed by meta-analysis. RESULTS We identified 11 single nucleotide polymorphisms (SNPs) at the 16p11.2 locus associated with CVID at a genome-wide significant level in the discovery cohort. The most significant SNP, rs929867 (P = 6.21 × 10(-9)), is in the gene fused-in-sarcoma (FUS), with 4 other SNPs mapping to integrin CD11b (ITGAM). Results were confirmed in our replication cohort. Conditional association analysis suggests a single association signal at the 16p11.2 locus. A strong trend of association was also seen for 38 SNPs (P < 5 × 10(-5)) in the MHC region, supporting that this is a genuine CVID locus. Interestingly, we found that 80% of patients with the rare ITGAM variants have reduced switched memory B-cell counts. CONCLUSION We report a novel association of CVID with rare variants at the FUS/ITGAM (CD11b) locus on 16p11.2. The association signal is enriched for promoter/enhancer markers in the ITGAM gene. ITGAM encodes the integrin CD11b, a part of complement receptor 3, a novel candidate gene implicated here for the first time in the pathogenesis of CVID.
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Affiliation(s)
- S Melkorka Maggadottir
- Division of Allergy and Immunology, Children's Hospital of Philadelphia, Philadelphia, Pa; Center for Applied Genomics, Abramson Research Center, Children's Hospital of Philadelphia, Philadelphia, Pa
| | - Jin Li
- Center for Applied Genomics, Abramson Research Center, Children's Hospital of Philadelphia, Philadelphia, Pa
| | - Joseph T Glessner
- Center for Applied Genomics, Abramson Research Center, Children's Hospital of Philadelphia, Philadelphia, Pa
| | - Yun Rose Li
- Center for Applied Genomics, Abramson Research Center, Children's Hospital of Philadelphia, Philadelphia, Pa; Medical Scientist Training Program, Perelman School of Medicine Philadelphia, University of Pennsylvania, Philadelphia, Pa
| | - Zhi Wei
- Department of Computer Science, New Jersey Institute of Technology, Newark, NJ
| | - Xiao Chang
- Center for Applied Genomics, Abramson Research Center, Children's Hospital of Philadelphia, Philadelphia, Pa
| | - Frank D Mentch
- Center for Applied Genomics, Abramson Research Center, Children's Hospital of Philadelphia, Philadelphia, Pa
| | - Kelly A Thomas
- Center for Applied Genomics, Abramson Research Center, Children's Hospital of Philadelphia, Philadelphia, Pa
| | - Cecilia E Kim
- Center for Applied Genomics, Abramson Research Center, Children's Hospital of Philadelphia, Philadelphia, Pa
| | - Yan Zhao
- Center for Applied Genomics, Abramson Research Center, Children's Hospital of Philadelphia, Philadelphia, Pa
| | - Cuiping Hou
- Center for Applied Genomics, Abramson Research Center, Children's Hospital of Philadelphia, Philadelphia, Pa
| | - Fengxiang Wang
- Center for Applied Genomics, Abramson Research Center, Children's Hospital of Philadelphia, Philadelphia, Pa
| | - Silje F Jørgensen
- K.G. Jebsen Inflammation Research Centre, Research Institute of Internal Medicine, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Elena E Perez
- Division of Allergy, Immunology and Rheumatology, Department of Pediatrics, University of South Florida, St Petersburg, Fla
| | - Kathleen E Sullivan
- Division of Allergy and Immunology, Children's Hospital of Philadelphia, Philadelphia, Pa
| | - Jordan S Orange
- Section of Immunology, Allergy and Rheumatology, Texas Children's Hospital, Houston, Tex
| | - Tom H Karlsen
- K.G. Jebsen Inflammation Research Centre, Research Institute of Internal Medicine, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Helen Chapel
- Nuffield Department of Medicine, University of Oxford and Oxford Radcliffe Hospital, Oxford, United Kingdom
| | | | - Hakon Hakonarson
- Center for Applied Genomics, Abramson Research Center, Children's Hospital of Philadelphia, Philadelphia, Pa; Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pa; Department of Pediatrics, Perelman School of Medicine Philadelphia, University of Pennsylvania, Philadelphia, Pa.
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Gaillard TR, Osei K. Racial Disparities in the Pathogenesis of Type 2 Diabetes and its Subtypes in the African Diaspora: A New Paradigm. J Racial Ethn Health Disparities 2015; 3:117-28. [PMID: 26896111 DOI: 10.1007/s40615-015-0121-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 04/22/2015] [Accepted: 04/24/2015] [Indexed: 01/23/2023]
Abstract
The global epidemic of diabetes has extended to the developing countries including Sub-Sahara Africa. In this context, blacks with type 2 diabetes in the African Diaspora continue to manifest 1.5-2 times higher prevalent rates than in their white counterparts. Previous studies have demonstrated that blacks with and without type 2 diabetes have alterations in hepatic and peripheral insulin sensitivity, beta-cell function, and hepatic insulin clearance as well as hepatic glucose dysregulation when compared to whites. In addition, non-diabetic blacks in the African Diaspora manifest multiple metabolic mediators that predict type 2 diabetes and its subtypes. These pathogenic modifiers include differences in subclinical inflammation, oxidative stress burden, and adipocytokines in blacks in the African Diaspora prior to clinical diagnosis. Consequently, blacks in the African Diaspora manifest subtypes of type 2 diabetes, including ketosis-prone diabetes and J type diabetes. Given the diversity of type 2 diabetes in blacks in the African Diaspora, we hypothesize that blacks manifest multiple early pathogenic defects prior to the diagnosis of type 2 diabetes and its subtypes. These metabolic alterations have strong genetic component, which appears to play pivotal and primary role in the pathogenesis of type 2 diabetes and its subtypes in blacks in the African Diaspora. However, environmental factors must also be considered as major contributors to the higher prevalence of type 2 diabetes and its subtypes in blacks in the African Diaspora. These multiple alterations should be targets for early prevention of type 2 diabetes in blacks in the African Diaspora.
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Affiliation(s)
- Trudy R Gaillard
- Division of Endocrinology Diabetes and Metabolism, The Ohio State University Wexner Medical Center, 561 McCampbell Hall, South, 1581 Dodd Drive, Columbus, OH, 43210, USA.
| | - Kwame Osei
- The Ohio State University Wexner Medical Center, 561 McCampbell Hall, 5th Floor South, 1581 Dodd Hall, Columbus, OH, 43210, USA.
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Castelli F, Tomasoni LR, El Hamad I. Migration and chronic noncommunicable diseases: is the paradigm shifting? J Cardiovasc Med (Hagerstown) 2015; 15:693-5. [PMID: 25083580 DOI: 10.2459/jcm.0000000000000096] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Francesco Castelli
- aDepartment of Clinical and Experimental Sciences, University of Brescia bUniversity Division of Infectious Diseases, University of Brescia and Brescia Spedali Civili General Hospital cUnit for Imported and Tropical Diseases dDivision of Infectious Diseases, Spedali Civili General Hospital, Brescia, Italy
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Al-Daghri NM, Al-Attas OS, Krishnaswamy S, Mohammed AK, Alenad AM, Chrousos GP, Alokail MS. Association of Type 2 Diabetes Mellitus related SNP genotypes with altered serum adipokine levels and metabolic syndrome phenotypes. Int J Clin Exp Med 2015; 8:4464-4471. [PMID: 26064370 PMCID: PMC4443204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 02/28/2015] [Indexed: 06/04/2023]
Abstract
The pathogenesis of T2DM involves secretion of several pro-inflammatory molecules by the dramatically increased adipocytes, both by number and size, and associated macrophages of adipose tissue. Since T2DM is usually preceded by obesity and chronic systemic inflammation, the objective of this study was to explore for any association between genetic variants of previously established 36 T2DM-associated SNPs and altered serum adipocytokine levels and metabolic syndrome phenotypes. Study consisted of 566 subjects (284 males and 282 females) of whom 147 were T2DM patients and 419 healthy controls. Study subjects were genotyped for 36 T2DM-linked single nucleotide polymorphisms (SNPs) using the KASPar SNP Genotyping System and grouped into different genotypes for each SNP. Various anthropometric and biochemical parameters were measured following standard procedures. The mean values of serum levels of individual adipocytokines and the presence/absence of metabolic syndrome phenotypes corresponding to various genotypes were compared by determining the odds ratios. Genotypic variants of five and seven of the 36 T2DM-related SNPs were significantly associated with altered serum levels of adiponectin and aPAI, respectively. Six variants of the 36 SNPs were associated with metabolic syndrome manifestations. This study identified positive associations between genotypic variants of five and seven of the 36 T2DM related SNPs and altered serum levels of adiponectin and aPAI, respectively. Six of 36 SNPs were also associated with metabolic syndrome in the studied population. The relation between specific SNPs and individual phenotypic traits may be useful in explaining the causal mechanisms of hereditary component of T2DM.
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Affiliation(s)
- Nasser M Al-Daghri
- Department of Biochemistry, Biomarkers Research Program, College of Science, King Saud UniversityRiyadh, KSA
- Prince Mutaib Chair for Biomarkers of Osteoporosis, King Saud UniversityRiyadh, KSA
| | - Omar S Al-Attas
- Department of Biochemistry, Biomarkers Research Program, College of Science, King Saud UniversityRiyadh, KSA
- Prince Mutaib Chair for Biomarkers of Osteoporosis, King Saud UniversityRiyadh, KSA
| | - Soundararajan Krishnaswamy
- Department of Biochemistry, Biomarkers Research Program, College of Science, King Saud UniversityRiyadh, KSA
- Prince Mutaib Chair for Biomarkers of Osteoporosis, King Saud UniversityRiyadh, KSA
| | - Abdul Khader Mohammed
- Department of Biochemistry, Biomarkers Research Program, College of Science, King Saud UniversityRiyadh, KSA
- Prince Mutaib Chair for Biomarkers of Osteoporosis, King Saud UniversityRiyadh, KSA
| | - Amal M Alenad
- School of Biological Sciences, University of SouthamptonSouthampton SO17 1BJ, UK
| | - George P Chrousos
- First Department of Pediatrics, Athens University Medical SchoolAthens, Greece
| | - Majed S Alokail
- Department of Biochemistry, Biomarkers Research Program, College of Science, King Saud UniversityRiyadh, KSA
- Prince Mutaib Chair for Biomarkers of Osteoporosis, King Saud UniversityRiyadh, KSA
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Ghassibe-Sabbagh M, Haber M, Salloum AK, Al-Sarraj Y, Akle Y, Hirbli K, Romanos J, Mouzaya F, Gauguier D, Platt DE, El-Shanti H, Zalloua PA. T2DM GWAS in the Lebanese population confirms the role of TCF7L2 and CDKAL1 in disease susceptibility. Sci Rep 2014; 4:7351. [PMID: 25483131 PMCID: PMC5376673 DOI: 10.1038/srep07351] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 11/14/2014] [Indexed: 12/30/2022] Open
Abstract
Genome-wide association studies (GWAS) of multiple populations with distinctive genetic and lifestyle backgrounds are crucial to the understanding of Type 2 Diabetes Mellitus (T2DM) pathophysiology. We report a GWAS on the genetic basis of T2DM in a 3,286 Lebanese participants. More than 5,000,000 SNPs were directly genotyped or imputed using the 1000 Genomes Project reference panels. We identify genome-wide significant variants in two loci CDKAL1 and TCF7L2, independent of sex, age and BMI, with leading variants rs7766070 (OR = 1.39, P = 4.77 × 10(-9)) and rs34872471 (OR = 1.35, P = 1.01 × 10(-8)) respectively. The current study is the first GWAS to find genomic regions implicated in T2DM in the Lebanese population. The results support a central role of CDKAL1 and TCF7L2 in T2DM susceptibility in Southwest Asian populations and provide a plausible component for understanding molecular mechanisms involved in the disease.
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Affiliation(s)
| | - Marc Haber
- Lebanese American University, School of Medicine, Beirut 1102 2801, Lebanon
| | | | | | - Yasmine Akle
- Centre Hospitalier du Nord-CHN, Zgharta, Lebanon
| | - Kamal Hirbli
- 1] Lebanese American University, School of Medicine, Beirut 1102 2801, Lebanon [2] University Medical Center - Rizk Hospital (UMC-RH), Lebanon
| | - Jihane Romanos
- Lebanese American University, School of Medicine, Beirut 1102 2801, Lebanon
| | - Francis Mouzaya
- Lebanese American University, School of Medicine, Beirut 1102 2801, Lebanon
| | | | - Daniel E Platt
- Bioinformatics and Pattern Discovery, IBM T. J. Watson Research Centre, Yorktown Hgts, NY 10598, USA
| | - Hatem El-Shanti
- 1] Shafallah Medical Genetics Center, Doha, Qatar [2] University of Iowa Carver College of Medicine, Iowa City
| | - Pierre A Zalloua
- 1] Lebanese American University, School of Medicine, Beirut 1102 2801, Lebanon [2] Harvard School of Public Health, Boston MA 02215, USA
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Konstantinidou V, Daimiel L, Ruiz LAD, Ordovás JM. Personalized nutrition and cardiovascular disease prevention: From Framingham to PREDIMED. Adv Nutr 2014; 5:368S-71S. [PMID: 24829490 PMCID: PMC4013195 DOI: 10.3945/an.113.005686] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Diet is considered the cornerstone for the prevention of age-related diseases, and a low-fat diet has been considered for decades as the most suitable alternative to achieve this goal. However, mounting evidence supports the efficacy of other alternatives, such as the Mediterranean diet. Nevertheless, it is well known that people present a dramatic range of responses to similar environmental challenges, and it has been shown that some of this variability is rooted in the genome. In fact, this knowledge is driving the field of nutrigenetics. The finding of interactions between diet and genetic variants has led to intense research and debate about the effectiveness of personalized nutrition as a more suitable tool for the prevention of chronic diseases than the traditional 1-size-fits-all recommendations. Here, we provide some of our own examples that illustrate the progression of nutrigenetics through the years, from the initial studies within the Framingham Heart Study, to the most recent use of large consortia, such as the Cohorts for Heart and Aging Research in Genomic Epidemiology, and ending up with large dietary intervention studies, such as the PREDIMED (Prevención con Dieta Mediterránea) study. These recent approaches are providing more robust and clinically relevant gene-diet interactions. Therefore, although the current evidence level of applying genomic information to tailoring is at its early stages, the prospect of widespread incorporation of nutrigenetics to the clinical practice is encouraging.
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Affiliation(s)
| | | | | | - Jose M Ordovás
- Madrid Institute for Advanced Studies-Food, Madrid, Spain; Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA; and National Center of Cardiovascular Research, Madrid, Spain
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Xia Q, Deliard S, Yuan CX, Johnson ME, Grant SFA. Characterization of the transcriptional machinery bound across the widely presumed type 2 diabetes causal variant, rs7903146, within TCF7L2. Eur J Hum Genet 2014; 23:103-9. [PMID: 24667787 DOI: 10.1038/ejhg.2014.48] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 02/13/2014] [Accepted: 02/19/2014] [Indexed: 12/29/2022] Open
Abstract
Resolving the underlying functional mechanism to a given genetic association has proven extremely challenging. However, the strongest associated type 2 diabetes (T2D) locus reported to date, TCF7L2, presents an opportunity for translational analyses, as many studies in multiple ethnicities strongly point to SNP rs7903146 in intron 3 as being the causal variant within this gene. We carried out oligo pull-down combined with mass spectrophotometry (MS) to elucidate the specific transcriptional machinery across this SNP using protein extracts from HCT116 cells. We observed that poly (ADP-ribose) polymerase 1 (PARP-1) is by far the most abundant binding factor. Pursuing the possibility of a feedback mechanism, we observed that PARP-1, along with the next most abundant binding proteins, DNA topoisomerase I and ATP-dependent RNA helicase A, dimerize with the TCF7L2 protein and with each other. We uncovered further evidence of a feedback mechanism using a luciferase reporter approach, including observing expression differences between alleles for rs7903146. We also found that there was an allelic difference in the MS results for proteins with less abundant binding, namely X-ray repair cross-complementing 5 and RPA/p70. Our results point to a protein complex binding across rs7903146 within TCF7L2 and suggests a possible mechanism by which this locus confers its T2D risk.
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Affiliation(s)
- Qianghua Xia
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sandra Deliard
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Chao-Xing Yuan
- Department of Proteomics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew E Johnson
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Struan F A Grant
- 1] Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA [2] Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA [3] Institute of Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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Al-Daghri NM, Alkharfy KM, Al-Attas OS, Krishnaswamy S, Mohammed AK, Albagha OM, Alenad AM, Chrousos GP, Alokail MS. Association between type 2 diabetes mellitus-related SNP variants and obesity traits in a Saudi population. Mol Biol Rep 2014; 41:1731-40. [PMID: 24435973 DOI: 10.1007/s11033-014-3022-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 01/02/2014] [Indexed: 10/25/2022]
Abstract
Obesity, commonly measured as body mass index (BMI), has been on a rapid rise around the world and is an underlying cause of several chronic non-communicable diseases, including type 2 diabetes mellitus (T2DM). In addition to the environmental factors, genetic factors may also contribute to the ongoing obesity epidemic in Saudi Arabia. This study investigated the association between variants of 36 previously established T2DM SNPs and obesity phenotypes in a population of Saudi subjects. Study subjects consisted of 975 obese (BMI: ≥30), 825 overweight (25-30) and 423 lean controls (18-25) and of these 927 had a history of T2DM. Subjects were genotyped for 36 SNPs, which have been previously proved to be T2DM linked, using the KASPar method and the means of BMI and waist circumference (WC) corresponding to each of the genotypes were compared by additive, recessive and dominant genetic models. Five and seven of 36 T2DM-related SNPs were significantly associated with the BMI and WC, respectively. Variants of SNPs rs7903146, rs1552224 and rs11642841 in the control group and rs7903146 in T2DM group showed significant association with both BMI and WC. Variant of SNP rs10440833 was significantly associated with BMI in T2DM group of both males [OR = 1.8 (1.0, 3.3); P = 0.04] and females [OR = 2.0 (1.0, 3.9); P = 0.04]. Genetic risk scores explained 19 and 14% of WC and hip size variance in this population. Variants of a number of established T2DM related SNPs were associated with obesity phenotypes and may be significant hereditary factors in the pathogenesis of T2DM.
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Affiliation(s)
- Nasser M Al-Daghri
- Biomarkers Research Program, Biochemistry Department, College of Science, King Saud University, Riyadh, Kingdom of Saudi Arabia,
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Basile KJ, Johnson ME, Xia Q, Grant SFA. Genetic susceptibility to type 2 diabetes and obesity: follow-up of findings from genome-wide association studies. Int J Endocrinol 2014; 2014:769671. [PMID: 24719615 PMCID: PMC3955626 DOI: 10.1155/2014/769671] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 01/17/2014] [Accepted: 01/20/2014] [Indexed: 12/13/2022] Open
Abstract
Elucidating the underlying genetic variations influencing various complex diseases is one of the major challenges currently facing clinical genetic research. Although these variations are often difficult to uncover, approaches such as genome-wide association studies (GWASs) have been successful at finding statistically significant associations between specific genomic loci and disease susceptibility. GWAS has been especially successful in elucidating genetic variants that influence type 2 diabetes (T2D) and obesity/body mass index (BMI). Specifically, several GWASs have confirmed that a variant in transcription factor 7-like 2 (TCF7L2) confers risk for T2D, while a variant in fat mass and obesity-associated protein (FTO) confers risk for obesity/BMI; indeed both of these signals are considered the most statistically associated loci discovered for these respective traits to date. The discovery of these two key loci in this context has been invaluable for providing novel insight into mechanisms of heritability and disease pathogenesis. As follow-up studies of TCF7L2 and FTO have typically lead the way in how to follow up a GWAS discovery, we outline what has been learned from such investigations and how they have implications for the myriad of other loci that have been subsequently reported in this disease context.
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Affiliation(s)
- Kevin J. Basile
- Division of Human Genetics, The Children's Hospital of Philadelphia Research Institute, 34th and Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Matthew E. Johnson
- Division of Human Genetics, The Children's Hospital of Philadelphia Research Institute, 34th and Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Qianghua Xia
- Division of Human Genetics, The Children's Hospital of Philadelphia Research Institute, 34th and Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Struan F. A. Grant
- Division of Human Genetics, The Children's Hospital of Philadelphia Research Institute, 34th and Civic Center Boulevard, Philadelphia, PA 19104, USA
- Center for Applied Genomics, The Children's Hospital of Philadelphia Research Institute, 34th and Civic Center Boulevard, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- 1216F Children's Hospital of Philadelphia Research Institute, 34th and Civic Center Boulevard, Philadelphia, PA 19104, USA
- *Struan F. A. Grant:
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Corella D, Carrasco P, Sorlí JV, Estruch R, Rico-Sanz J, Martínez-González MÁ, Salas-Salvadó J, Covas MI, Coltell O, Arós F, Lapetra J, Serra-Majem L, Ruiz-Gutiérrez V, Warnberg J, Fiol M, Pintó X, Ortega-Azorín C, Muñoz MÁ, Martínez JA, Gómez-Gracia E, González JI, Ros E, Ordovás JM. Mediterranean diet reduces the adverse effect of the TCF7L2-rs7903146 polymorphism on cardiovascular risk factors and stroke incidence: a randomized controlled trial in a high-cardiovascular-risk population. Diabetes Care 2013; 36:3803-11. [PMID: 23942586 PMCID: PMC3816851 DOI: 10.2337/dc13-0955] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 06/17/2013] [Indexed: 02/03/2023]
Abstract
OBJECTIVE Transcription factor 7-like 2 (TCF7L2) polymorphisms are strongly associated with type 2 diabetes, but controversially with plasma lipids and cardiovascular disease. Interactions of the Mediterranean diet (MedDiet) on these associations are unknown. We investigated whether the TCF7L2-rs7903146 (C>T) polymorphism associations with type 2 diabetes, glucose, lipids, and cardiovascular disease incidence were modulated by MedDiet. RESEARCH DESIGN AND METHODS A randomized trial (two MedDiet intervention groups and a control group) with 7,018 participants in the PREvención con DIetaMEDiterránea study was undertaken and major cardiovascular events assessed. Data were analyzed at baseline and after a median follow-up of 4.8 years. Multivariable-adjusted Cox regression was used to estimate hazard ratios (HRs) for cardiovascular events. RESULTS The TCF7L2-rs7903146 polymorphism was associated with type 2 diabetes (odds ratio 1.87 [95% CI 1.62-2.17] for TT compared with CC). MedDiet interacted significantly with rs7903146 on fasting glucose at baseline (P interaction = 0.004). When adherence to the MedDiet was low, TT had higher fasting glucose concentrations (132.3 ± 3.5 mg/dL) than CC+CT (127.3 ± 3.2 mg/dL) individuals (P = 0.001). Nevertheless, when adherence was high, this increase was not observed (P = 0.605). This modulation was also detected for total cholesterol, LDL cholesterol, and triglycerides (P interaction < 0.05 for all). Likewise, in the randomized trial, TT subjects had a higher stroke incidence in the control group (adjusted HR 2.91 [95% CI 1.36-6.19]; P = 0.006 compared with CC), whereas dietary intervention with MedDiet reduced stroke incidence in TT homozygotes (adjusted HR 0.96 [95% CI 0.49-1.87]; P = 0.892 for TT compared with CC). CONCLUSIONS Our novel results suggest that MedDiet may not only reduce increased fasting glucose and lipids in TT individuals, but also stroke incidence.
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Yu X, Sun S. Comparing a few SNP calling algorithms using low-coverage sequencing data. BMC Bioinformatics 2013; 14:274. [PMID: 24044377 PMCID: PMC3848615 DOI: 10.1186/1471-2105-14-274] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 09/12/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Many Single Nucleotide Polymorphism (SNP) calling programs have been developed to identify Single Nucleotide Variations (SNVs) in next-generation sequencing (NGS) data. However, low sequencing coverage presents challenges to accurate SNV identification, especially in single-sample data. Moreover, commonly used SNP calling programs usually include several metrics in their output files for each potential SNP. These metrics are highly correlated in complex patterns, making it extremely difficult to select SNPs for further experimental validations. RESULTS To explore solutions to the above challenges, we compare the performance of four SNP calling algorithm, SOAPsnp, Atlas-SNP2, SAMtools, and GATK, in a low-coverage single-sample sequencing dataset. Without any post-output filtering, SOAPsnp calls more SNVs than the other programs since it has fewer internal filtering criteria. Atlas-SNP2 has stringent internal filtering criteria; thus it reports the least number of SNVs. The numbers of SNVs called by GATK and SAMtools fall between SOAPsnp and Atlas-SNP2. Moreover, we explore the values of key metrics related to SNVs' quality in each algorithm and use them as post-output filtering criteria to filter out low quality SNVs. Under different coverage cutoff values, we compare four algorithms and calculate the empirical positive calling rate and sensitivity. Our results show that: 1) the overall agreement of the four calling algorithms is low, especially in non-dbSNPs; 2) the agreement of the four algorithms is similar when using different coverage cutoffs, except that the non-dbSNPs agreement level tends to increase slightly with increasing coverage; 3) SOAPsnp, SAMtools, and GATK have a higher empirical calling rate for dbSNPs compared to non-dbSNPs; and 4) overall, GATK and Atlas-SNP2 have a relatively higher positive calling rate and sensitivity, but GATK calls more SNVs. CONCLUSIONS Our results show that the agreement between different calling algorithms is relatively low. Thus, more caution should be used in choosing algorithms, setting filtering parameters, and designing validation studies. For reliable SNV calling results, we recommend that users employ more than one algorithm and use metrics related to calling quality and coverage as filtering criteria.
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Affiliation(s)
- Xiaoqing Yu
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio 44106, USA.
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Affiliation(s)
- Valeriya Lyssenko
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University, Malmö, Sweden.
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Coin LJM, Cao D, Ren J, Zuo X, Sun L, Yang S, Zhang X, Cui Y, Li Y, Jin X, Wang J. An exome sequencing pipeline for identifying and genotyping common CNVs associated with disease with application to psoriasis. Bioinformatics 2013; 28:i370-i374. [PMID: 22962454 PMCID: PMC3436806 DOI: 10.1093/bioinformatics/bts379] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Motivation: Despite the prevalence of copy number variation (CNV) in the human genome, only a handful of confirmed associations have been reported between common CNVs and complex disease. This may be partially attributed to the difficulty in accurately genotyping CNVs in large cohorts using array-based technologies. Exome sequencing is now widely being applied to case–control cohorts and presents an exciting opportunity to look for common CNVs associated with disease. Results: We developed ExoCNVTest: an exome sequencing analysis pipeline to identify disease-associated CNVs and to generate absolute copy number genotypes at putatively associated loci. Our method re-discovered the LCE3B_LCE3C CNV association with psoriasis (P-value = 5 × 10e−6) while controlling inflation of test statistics (λ < 1). ExoCNVTest-derived absolute CNV genotypes were 97.4% concordant with PCR-derived genotypes at this locus. Availability and implementation: ExoCNVTest has been implemented in Java and R and is freely available from www1.imperial.ac.uk/medicine/people/l.coin/. Contact:wangj@genomics.org.cn or Lachlan.J.M.Coin@genomics.org.cn
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Ng MCY, Saxena R, Li J, Palmer ND, Dimitrov L, Xu J, Rasmussen-Torvik LJ, Zmuda JM, Siscovick DS, Patel SR, Crook ED, Sims M, Chen YDI, Bertoni AG, Li M, Grant SFA, Dupuis J, Meigs JB, Psaty BM, Pankow JS, Langefeld CD, Freedman BI, Rotter JI, Wilson JG, Bowden DW. Transferability and fine mapping of type 2 diabetes loci in African Americans: the Candidate Gene Association Resource Plus Study. Diabetes 2013; 62:965-76. [PMID: 23193183 PMCID: PMC3581206 DOI: 10.2337/db12-0266] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Accepted: 08/21/2012] [Indexed: 01/08/2023]
Abstract
Type 2 diabetes (T2D) disproportionally affects African Americans (AfA) but, to date, genetic variants identified from genome-wide association studies (GWAS) are primarily from European and Asian populations. We examined the single nucleotide polymorphism (SNP) and locus transferability of 40 reported T2D loci in six AfA GWAS consisting of 2,806 T2D case subjects with or without end-stage renal disease and 4,265 control subjects from the Candidate Gene Association Resource Plus Study. Our results revealed that seven index SNPs at the TCF7L2, KLF14, KCNQ1, ADCY5, CDKAL1, JAZF1, and GCKR loci were significantly associated with T2D (P < 0.05). The strongest association was observed at TCF7L2 rs7903146 (odds ratio [OR] 1.30; P = 6.86 × 10⁻⁸). Locus-wide analysis demonstrated significant associations (P(emp) < 0.05) at regional best SNPs in the TCF7L2, KLF14, and HMGA2 loci as well as suggestive signals in KCNQ1 after correction for the effective number of SNPs at each locus. Of these loci, the regional best SNPs were in differential linkage disequilibrium (LD) with the index and adjacent SNPs. Our findings suggest that some loci discovered in prior reports affect T2D susceptibility in AfA with similar effect sizes. The reduced and differential LD pattern in AfA compared with European and Asian populations may facilitate fine mapping of causal variants at loci shared across populations.
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Affiliation(s)
- Maggie C Y Ng
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA.
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McCormack S, Grant SFA. Genetics of obesity and type 2 diabetes in African Americans. J Obes 2013; 2013:396416. [PMID: 23577239 PMCID: PMC3614120 DOI: 10.1155/2013/396416] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 02/13/2013] [Indexed: 12/21/2022] Open
Abstract
Obesity and type 2 diabetes are highly prevalent and lead to significant morbidity and mortality. In the United States, the impact of these conditions may be worse on historically underserved minorities, particularly African Americans. Genetic ancestry and differences in physiology are unlikely to be the sole or primary determinants of these disparities. In addition, research in this area has the ethically problematic possibility of conflating race with biology. Despite these important considerations and the challenges of conducting this work, population-based approaches for investigating the etiology of obesity and T2D may yield useful information about the pathophysiology of disease, and have implications that extend to all affected individuals. The purpose of this paper is to describe what is understood about the genetic variation that underlies obesity and T2D in African Americans and other individuals of more recent African descent and to highlight several examples that illustrate how ensuring adequate minority representation in genetic research improves its quality. For a variety of reasons a number of unique insights have been possible as a result of these efforts.
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Affiliation(s)
- Shana McCormack
- Division of Endocrinology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Struan F. A. Grant
- Division of Human Genetics, The Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
- Center for Applied Genomics, The Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
- *Struan F. A. Grant:
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Zhu W, Deng Y, Jie K, Luo D, Liu Z, Yu L, Zeng E, Wan F. Detection of single nucleotide polymorphisms by PCR conformation-difference gel electrophoresis. Biotechnol Lett 2012; 35:515-22. [DOI: 10.1007/s10529-012-1115-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 11/28/2012] [Indexed: 11/30/2022]
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Long J, Edwards T, Signorello LB, Cai Q, Zheng W, Shu XO, Blot WJ. Evaluation of genome-wide association study-identified type 2 diabetes loci in African Americans. Am J Epidemiol 2012; 176:995-1001. [PMID: 23144361 DOI: 10.1093/aje/kws176] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Type 2 diabetes (T2D) is up to twice as prevalent among African Americans as Caucasians. Recent genome-wide association studies (GWAS) have identified multiple common genetic risk variants for T2D; however, none of these studies were conducted exclusively among subjects of African ancestry. Investigating these known loci in other populations would be an expedient way to evaluate the generalizability of the current findings. The authors evaluated 29 known T2D loci in a large southeastern US cohort study including 4,288 African Americans (1,554 cases and 2,734 controls) enrolled during 2002-2009. Seven of the 29 single nucleotide polymorphisms (SNPs) examined were found to be associated with T2D risk at P ≤ 0.05, including rs6769511 (IGF2BP2), 2 SNPs in the WFS1 gene (rs4689388 and rs1801214), rs7903146 (TCF7L2), and 3 SNPs in the KCNQ1 gene (rs231362, rs2237892, and rs2237897). Notably, the association for rs7903146 reached the GWAS significance level (P = 3.6 × 10(-8)), with an odds ratio per T allele of 1.32 (95% confidence interval: 1.20, 1.46). Regional analyses using GWAS data from Vanderbilt University's BioVU DNA biobank showed significant associations (P < 0.05) with 9 loci, though no association was observed for the index SNPs reported in European- or Asian-ancestry populations. These results extend some of the recent GWAS findings to African Americans and may guide future efforts to identify causal variants for T2D.
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Affiliation(s)
- Jirong Long
- Division of Epidemiology, Departmentof Medicine, School of Medicine, Vanderbilt University, Nashville, Tennessee 37203-1738, USA.
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Peng S, Zhu Y, Lü B, Xu F, Li X, Lai M. TCF7L2 gene polymorphisms and type 2 diabetes risk: a comprehensive and updated meta-analysis involving 121,174 subjects. Mutagenesis 2012. [PMID: 23188737 DOI: 10.1093/mutage/ges048] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Recently, many new loci associated with type 2 diabetes have been uncovered by genetic association studies and genome-wide association studies. As more reports are made, particularly with respect to varying ethnicities, there is a need to determine more precisely the effect sizes in each major racial group. In addition, some reports have claimed ethnic-specific associations with alternative single-nucleotide polymorphisms (SNPs), and to that end there has been a degree of confusion. We conducted a meta-analysis using an additive genetic model. Eight polymorphisms in 155 studies with 121174 subjects (53385 cases and 67789 controls) were addressed in this meta-analysis. Significant associations were found between type 2 diabetes and rs7903146, rs12255372, rs11196205, rs7901695, rs7895340 and rs4506565, with summary odds ratios (ORs) (95% confidence interval) of 1.39 (1.34-1.45), 1.33 (1.27-1.40), 1.20 (1.14-1.26), 1.32 (1.25-1.39), 1.21 (1.13-1.29) and 1.39 (1.29-1.49), respectively. In addition, no significant associations were found between the two polymorphisms (rs290487 and rs11196218) and type 2 diabetes. The summary ORs for the six statistically significant associations (P < 0.05) were further evaluated by estimating the false-positive report probability, with results indicating that all of the six significant associations were considered noteworthy, and may plausibly be true associations. Significant associations were found between the six polymorphisms (rs7903146, rs12255372, rs11196205, rs7901695, rs7895340 and rs4506565) in the TCF7L2 gene and type 2 diabetes risk, and the other two polymorphisms (rs11196218 and rs290487) were not found to be significantly associated with type 2 diabetes. Subgroups analyses show that significant associations are not found between the six SNPs (rs7903146, rs12255372, rs11196205, rs7901695, rs7895340, and rs4506565) and the type 2 diabetes in some ethnic populations.
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Affiliation(s)
- Sihua Peng
- Department of Pathology, Zhejiang University School of Medicine, Hangzhou 310058, PR China
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Liu CT, Ng MCY, Rybin D, Adeyemo A, Bielinski SJ, Boerwinkle E, Borecki I, Cade B, Chen YDI, Djousse L, Fornage M, Goodarzi MO, Grant SFA, Guo X, Harris T, Kabagambe E, Kizer JR, Liu Y, Lunetta KL, Mukamal K, Nettleton JA, Pankow JS, Patel SR, Ramos E, Rasmussen-Torvik L, Rich SS, Rotimi CN, Sarpong D, Shriner D, Sims M, Zmuda JM, Redline S, Kao WH, Siscovick D, Florez JC, Rotter JI, Dupuis J, Wilson JG, Bowden DW, Meigs JB. Transferability and fine-mapping of glucose and insulin quantitative trait loci across populations: CARe, the Candidate Gene Association Resource. Diabetologia 2012; 55:2970-84. [PMID: 22893027 PMCID: PMC3804308 DOI: 10.1007/s00125-012-2656-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 06/14/2012] [Indexed: 01/22/2023]
Abstract
AIMS/HYPOTHESIS Hyperglycaemia disproportionately affects African-Americans (AfAs). We tested the transferability of 18 single-nucleotide polymorphisms (SNPs) associated with glycaemic traits identified in European ancestry (EuA) populations in 5,984 non-diabetic AfAs. METHODS We meta-analysed SNP associations with fasting glucose (FG) or insulin (FI) in AfAs from five cohorts in the Candidate Gene Association Resource. We: (1) calculated allele frequency differences, variations in linkage disequilibrium (LD), fixation indices (F(st)s) and integrated haplotype scores (iHSs); (2) tested EuA SNPs in AfAs; and (3) interrogated within ± 250 kb around each EuA SNP in AfAs. RESULTS Allele frequency differences ranged from 0.6% to 54%. F(st) exceeded 0.15 at 6/16 loci, indicating modest population differentiation. All iHSs were <2, suggesting no recent positive selection. For 18 SNPs, all directions of effect were the same and 95% CIs of association overlapped when comparing EuA with AfA. For 17 of 18 loci, at least one SNP was nominally associated with FG in AfAs. Four loci were significantly associated with FG (GCK, p = 5.8 × 10(-8); MTNR1B, p = 8.5 × 10(-9); and FADS1, p = 2.2 × 10(-4)) or FI (GCKR, p = 5.9 × 10(-4)). At GCK and MTNR1B the EuA and AfA SNPs represented the same signal, while at FADS1, and GCKR, the EuA and best AfA SNPs were weakly correlated (r(2) <0.2), suggesting allelic heterogeneity for association with FG at these loci. CONCLUSIONS/INTERPRETATION Few glycaemic SNPs showed strict evidence of transferability from EuA to AfAs. Four loci were significantly associated in both AfAs and those with EuA after accounting for varying LD across ancestral groups, with new signals emerging to aid fine-mapping.
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Affiliation(s)
- C.-T. Liu
- Department of Biostatistics, Boston University School of Public
Health, Boston, MA, USA
| | - M. C. Y. Ng
- Center for Genomics and Personalized Medicine Research, Center for
Diabetes Research, Wake Forest University School of Medicine, Winston-Salem,
NC, USA
| | - D. Rybin
- Boston University Data Coordinating Center, Boston, MA, USA
| | - A. Adeyemo
- National Human Genome Research Institute, Bethesda, MD, USA
| | | | - E. Boerwinkle
- University of Texas Health Science Center at Houston, Houston, TX,
USA
| | - I. Borecki
- Washington University, St Louis, MO, USA
| | - B. Cade
- Brigham and Women's Hospital, Boston, MA, USA
| | | | - L. Djousse
- Brigham and Women's Hospital, Boston, MA, USA; Department
of Medicine, Harvard Medical School, Boston, MA, USA; Boston VA Healthcare
System, Boston, MA, USA
| | - M. Fornage
- University of Texas Health Science Center at Houston, Houston, TX,
USA
| | | | - S. F. A. Grant
- Children's Hospital of Philadelphia, Philadelphia, PA,
USA
| | - X. Guo
- Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - T. Harris
- National Institute on Aging, Bethesda, MD, USA
| | | | | | - Y. Liu
- Center for Genomics and Personalized Medicine Research, Center for
Diabetes Research, Wake Forest University School of Medicine, Winston-Salem,
NC, USA; Department of Epidemiology and Prevention, Wake Forest University,
Winston-Salem, North Carolina, USA
| | - K. L. Lunetta
- Department of Biostatistics, Boston University School of Public
Health, Boston, MA, USA; National Heart, Lung, and Blood Institute'
Framingham Heart Study, Framingham, MA, USA
| | - K. Mukamal
- Department of Medicine, Harvard Medical School, Boston, MA,
USA
| | - J. A. Nettleton
- University of Texas Health Science Center at Houston, Houston, TX,
USA
| | | | - S. R. Patel
- Brigham and Women's Hospital, Boston, MA, USA
| | - E. Ramos
- National Human Genome Research Institute, Bethesda, MD, USA
| | | | - S. S. Rich
- University of Virginia, Charlottesville, VA, USA
| | - C. N. Rotimi
- National Human Genome Research Institute, Bethesda, MD, USA
| | - D. Sarpong
- Jackson State University, Jackson, MS, USA
| | - D. Shriner
- National Human Genome Research Institute, Bethesda, MD, USA
| | - M. Sims
- University of Mississippi Medical Center, Jackson, MS, USA
| | - J. M. Zmuda
- University of Pittsburgh, Graduate School of Public Health,
Pittsburgh, PA, USA
| | - S. Redline
- Brigham and Women's Hospital, Boston, MA, USA
| | - W. H. Kao
- Johns Hopkins University, Baltimore, MD, USA
| | | | - J. C. Florez
- Department of Medicine, Harvard Medical School, Boston, MA, USA;
Diabetes Unit and Center for Human Genetic Research, Massachusetts General
Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad
Institute, Cambridge, MA, USA
| | - J. I. Rotter
- Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - J. Dupuis
- Department of Biostatistics, Boston University School of Public
Health, Boston, MA, USA; National Heart, Lung, and Blood Institute's
Framingham Heart Study, Framingham, MA, USA
| | - J. G. Wilson
- University of Mississippi Medical Center, Jackson, MS, USA
| | - D. W. Bowden
- Center for Genomics and Personalized Medicine Research, Center for
Diabetes Research, Wake Forest University School of Medicine, Winston-Salem,
NC, USA; Departments of Biochemistry and Internal Medicine, Wake Forest
University School of Medicine, Winston-Salem, NC, USA
| | - J. B. Meigs
- Department of Medicine, Harvard Medical School, Boston, MA, USA;
General Medicine Division, Massachusetts General Hospital, 50 Staniford
Street, 9th Flr, Boston, MA, USA
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Mattei J, Qi Q, Hu FB, Sacks FM, Qi L. TCF7L2 genetic variants modulate the effect of dietary fat intake on changes in body composition during a weight-loss intervention. Am J Clin Nutr 2012; 96:1129-36. [PMID: 23034957 PMCID: PMC3471200 DOI: 10.3945/ajcn.112.038125] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND TCF7L2 gene variants have been associated with increased risk of type 2 diabetes and higher adiposity. Observational studies and short-term trials have suggested that macronutrients may modify these effects. However, to our knowledge, this has yet to be verified in long-term interventions. OBJECTIVE In a long-term intervention setting, we investigated the effects of TCF7L2 polymorphisms rs7903146 and rs12255372 and dietary total fat on changes in body composition and subsequent glycemic control. DESIGN Data were analyzed for 591 participants in the Preventing Overweight Using Novel Dietary Strategies (Pounds Lost) trial, which is a 2-y weight-loss randomized clinical trial of diets that differed in macronutrient proportions. Adjusted means for changes in body composition at 6 and 24 mo were obtained for gene main effects and interactions with a low-fat diet (20% from energy) compared with a high-fat diet (40% from energy). Interactions with protein and carbohydrate intakes were also tested. Predicted changes in glycemic control from changes in adiposity were determined by genotype and diet type. RESULTS Significant interactions were observed for rs12255372 TT (risk genotype) and fat intake for changes in BMI, total fat mass, and trunk fat mass (all P/q < 0.05) at 6 mo, with nonsignificant larger decreases for TT carriers on a low-fat diet. No significant associations were observed at 24 mo or for other macronutrients. Changes in body composition for TT carriers predicted reductions in plasma glucose and insulin only on the low-fat diet. CONCLUSIONS Individuals with the TCF7L2 rs12255372 risk genotype may reduce body adiposity by consuming a diet lower in total fat. These reductions may induce better glycemic control for such individuals predisposed to type 2 diabetes. The Pounds Lost trial was registered at clinicaltrials.gov as NCT00072995.
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Affiliation(s)
- Josiemer Mattei
- Department of Nutrition, Harvard School of Public Health, Boston, MA 02115, USA
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Vassy JL, Durant NH, Kabagambe EK, Carnethon MR, Rasmussen-Torvik LJ, Fornage M, Lewis CE, Siscovick DS, Meigs JB. A genotype risk score predicts type 2 diabetes from young adulthood: the CARDIA study. Diabetologia 2012; 55:2604-2612. [PMID: 22782289 PMCID: PMC3434294 DOI: 10.1007/s00125-012-2637-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2012] [Accepted: 06/15/2012] [Indexed: 12/29/2022]
Abstract
AIMS/HYPOTHESIS Genotype does not change over the life course and may thus facilitate earlier identification of individuals at high risk for type 2 diabetes. We hypothesised that a genotype score predicts incident type 2 diabetes from young adulthood and improves diabetes prediction models based on clinical risk factors alone. METHODS The Coronary Artery Risk Development in Young Adults (CARDIA) study followed young adults (aged 18-30 years, mean age 25) serially into middle adulthood. We used Cox regression to build nested prediction models for incident type 2 diabetes based on clinical risk factors assessed in young adulthood (age, sex, race, parental history of diabetes, BMI, mean arterial pressure, fasting glucose, HDL-cholesterol and triacylglyercol), without and with a 38-variant genotype score. Models were compared with C statistics and continuous net reclassification improvement indices (NRI). RESULTS Of 2,439 participants, 830 (34%) were black and 249 (10%) had a BMI ≥ 30 kg/m(2) at baseline. Over a mean 23.9 years of follow-up, 215 (8.8%) participants developed type 2 diabetes. The genotype score significantly predicted incident diabetes in all models, with an HR of 1.08 per risk allele (95% CI 1.04, 1.13) in the full model. The addition of the score to the full model modestly improved reclassification (continuous NRI 0.285; 95% CI 0.126, 0.433) but not discrimination (C statistics 0.824 and 0.829 in full models with and without score). Race-stratified analyses were similar. CONCLUSIONS/INTERPRETATION Knowledge of genotype predicts type 2 diabetes over 25 years in white and black young adults but may not improve prediction over routine clinical measurements.
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Affiliation(s)
- J L Vassy
- General Medicine Division, Massachusetts General Hospital, 50 Staniford Street, 9th floor, Boston, MA, 02114, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
| | - N H Durant
- Division of Pediatrics and Adolescent Medicine, Department of Pediatrics, University of Alabama Birmingham School of Medicine, Birmingham, AL, USA
| | - E K Kabagambe
- Department of Epidemiology, University of Alabama Birmingham School of Public Health, Birmingham, AL, USA
| | - M R Carnethon
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - L J Rasmussen-Torvik
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - M Fornage
- Institute of Molecular Medicine Research Center for Human Genetics, The University of Texas Health Science Center, Houston, TX, USA
| | - C E Lewis
- Division of Preventive Medicine, Department of Medicine, University of Alabama Birmingham, Birmingham, AL, USA
| | - D S Siscovick
- Cardiovascular Health Research Unit, Departments of Medicine and Epidemiology, University of Washington, Seattle, WA, USA
| | - J B Meigs
- General Medicine Division, Massachusetts General Hospital, 50 Staniford Street, 9th floor, Boston, MA, 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
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Haiman CA, Fesinmeyer MD, Spencer KL, Buzková P, Voruganti VS, Wan P, Haessler J, Franceschini N, Monroe KR, Howard BV, Jackson RD, Florez JC, Kolonel LN, Buyske S, Goodloe RJ, Liu S, Manson JE, Meigs JB, Waters K, Mukamal KJ, Pendergrass SA, Shrader P, Wilkens LR, Hindorff LA, Ambite JL, North KE, Peters U, Crawford DC, Le Marchand L, Pankow JS. Consistent directions of effect for established type 2 diabetes risk variants across populations: the population architecture using Genomics and Epidemiology (PAGE) Consortium. Diabetes 2012; 61:1642-7. [PMID: 22474029 PMCID: PMC3357304 DOI: 10.2337/db11-1296] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Common genetic risk variants for type 2 diabetes (T2D) have primarily been identified in populations of European and Asian ancestry. We tested whether the direction of association with 20 T2D risk variants generalizes across six major racial/ethnic groups in the U.S. as part of the Population Architecture using Genomics and Epidemiology Consortium (16,235 diabetes case and 46,122 control subjects of European American, African American, Hispanic, East Asian, American Indian, and Native Hawaiian ancestry). The percentage of positive (odds ratio [OR] >1 for putative risk allele) associations ranged from 69% in American Indians to 100% in European Americans. Of the nine variants where we observed significant heterogeneity of effect by racial/ethnic group (P(heterogeneity) < 0.05), eight were positively associated with risk (OR >1) in at least five groups. The marked directional consistency of association observed for most genetic variants across populations implies a shared functional common variant in each region. Fine-mapping of all loci will be required to reveal markers of risk that are important within and across populations.
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Affiliation(s)
- Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, California, USA.
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Franceschini N, Shara NM, Wang H, Voruganti VS, Laston S, Haack K, Lee ET, Best LG, Maccluer JW, Cochran BJ, Dyer TD, Howard BV, Cole SA, North KE, Umans JG. The association of genetic variants of type 2 diabetes with kidney function. Kidney Int 2012; 82:220-5. [PMID: 22513821 PMCID: PMC3664521 DOI: 10.1038/ki.2012.107] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Type 2 diabetes is highly prevalent and is the major cause of progressive chronic kidney disease in American Indians. Genome-wide association studies identified several loci associated with diabetes but their impact on susceptibility to diabetic complications is unknown. We studied the association of 18 type 2 diabetes genome-wide association single-nucleotide polymorphisms (SNPs) with estimated glomerular filtration rate (eGFR; MDRD equation) and urine albumin-to-creatinine ratio in 6958 Strong Heart Study family and cohort participants. Center-specific residuals of eGFR and log urine albumin-to-creatinine ratio, obtained from linear regression models adjusted for age, sex, and body mass index, were regressed onto SNP dosage using variance component models in family data and linear regression in unrelated individuals. Estimates were then combined across centers. Four diabetic loci were associated with eGFR and one locus with urine albumin-to-creatinine ratio. A SNP in the WFS1 gene (rs10010131) was associated with higher eGFR in younger individuals and with increased albuminuria. SNPs in the FTO, KCNJ11, and TCF7L2 genes were associated with lower eGFR, but not albuminuria, and were not significant in prospective analyses. Our findings suggest a shared genetic risk for type 2 diabetes and its kidney complications, and a potential role for WFS1 in early-onset diabetic nephropathy in American Indian populations.
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Včelák J, Vejražková D, Vaňková M, Lukášová P, Bradnová O, Hálková T, Bešťák J, Andělová K, Kvasničková H, Hoskovcová P, Vondra K, Vrbíková J, Bendlová B. T2D risk haplotypes of the TCF7L2 gene in the Czech population sample: the association with free fatty acids composition. Physiol Res 2012; 61:229-40. [PMID: 22480428 DOI: 10.33549/physiolres.932272] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The association of transcription factor 7-like 2 (TCF7L2) gene variants with the pathogenesis of T2D, gestational diabetes and polycystic ovary syndrome (PCOS) was examined. The study involved 1460 individuals: 347 T2D patients (D); 261 gestational diabetics (G); 147 offspring of T2D (O); 329 women with PCOS, and 376 controls (C). The SNPs: rs7901695; rs7903146; rs12255372 in the TCF7L2 gene were genotyped. Anthropometric and biochemical parameters, oGTT derived indices were assessed. In addition, free fatty acids (FFAs) were evaluated in 183 non-diabetic women. The CTT haplotype showed the strongest association with T2D with OR 1.57, p=0.0003. The frequency of the CTT/CTT haplotype was decreasing in following order: D 10.6, O 9.5, G 6.1, C 5.3 and PCOS 4.9 [%]. Among CTT carriers, significantly decreased levels of oGTT-stimulated insulin and C-peptide as well as proportions of fasting PUFAs were observed. The carriership of CTG/TCG was associated with gestational diabetes, OR 2.59, p=0.036. The association of TCF7L2 haplotypes with T2D and gestational diabetes but not with PCOS was confirmed. Novel association of TCF7L2 with FFAs composition was found.
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Affiliation(s)
- J Včelák
- Department of Molecular Endocrinology, Institute of Endocrinology, Prague, Czech Republic.
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Abstract
The early identification of individuals at risk for type 2 diabetes (T2D) enables prevention. Recent genome-wide association studies (GWAS) have added at least 40 genetic variants to the list of already well characterized T2D risk predictors, including family history, obesity, and elevated fasting plasma glucose levels. Although these variants can significantly predict T2D alone and as a part of genotype risk scores, they do not yet offer clinical discrimination beyond that achieved with common clinical measurements. Future progress on at least two research fronts may improve the predictive performance of genotype information. First, expanded GWAS efforts in non-European populations will allow targeted sequencing of risk loci and the identification of true causal variants. Second, studies with longer prediction time horizons may demonstrate that genotype information performs better than clinical risk predictors over a longer period of the life course. At present, however, genetic testing cannot be recommended for clinical T2D risk prediction in adults.
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Affiliation(s)
- Jason L Vassy
- General Medicine Division, Massachusetts General Hospital, Boston, 02114, USA.
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