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Bayer S, Reik A, von Hesler L, Hauner H, Holzapfel C. Association between Genotype and the Glycemic Response to an Oral Glucose Tolerance Test: A Systematic Review. Nutrients 2023; 15:nu15071695. [PMID: 37049537 PMCID: PMC10096950 DOI: 10.3390/nu15071695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/21/2023] [Accepted: 03/22/2023] [Indexed: 04/03/2023] Open
Abstract
The inter-individual variability of metabolic response to foods may be partly due to genetic variation. This systematic review aims to assess the associations between genetic variants and glucose response to an oral glucose tolerance test (OGTT). Three databases (PubMed, Web of Science, Embase) were searched for keywords in the field of genetics, OGTT, and metabolic response (PROSPERO: CRD42021231203). Inclusion criteria were available data on single nucleotide polymorphisms (SNPs) and glucose area under the curve (gAUC) in a healthy study cohort. In total, 33,219 records were identified, of which 139 reports met the inclusion criteria. This narrative synthesis focused on 49 reports describing gene loci for which several reports were available. An association between SNPs and the gAUC was described for 13 gene loci with 53 different SNPs. Three gene loci were mostly investigated: transcription factor 7 like 2 (TCF7L2), peroxisome proliferator-activated receptor gamma (PPARγ), and potassium inwardly rectifying channel subfamily J member 11 (KCNJ11). In most reports, the associations were not significant or single findings were not replicated. No robust evidence for an association between SNPs and gAUC after an OGTT in healthy persons was found across the identified studies. Future studies should investigate the effect of polygenic risk scores on postprandial glucose levels.
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Affiliation(s)
- Sandra Bayer
- Institute for Nutritional Medicine, School of Medicine, University Hospital “Klinikum Rechts der Isar”, Technical University of Munich, 80992 Munich, Germany
| | - Anna Reik
- Institute for Nutritional Medicine, School of Medicine, University Hospital “Klinikum Rechts der Isar”, Technical University of Munich, 80992 Munich, Germany
| | - Lena von Hesler
- Institute for Nutritional Medicine, School of Medicine, University Hospital “Klinikum Rechts der Isar”, Technical University of Munich, 80992 Munich, Germany
| | - Hans Hauner
- Institute for Nutritional Medicine, School of Medicine, University Hospital “Klinikum Rechts der Isar”, Technical University of Munich, 80992 Munich, Germany
- Else Kröner-Fresenius-Center for Nutritional Medicine, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Christina Holzapfel
- Institute for Nutritional Medicine, School of Medicine, University Hospital “Klinikum Rechts der Isar”, Technical University of Munich, 80992 Munich, Germany
- Department of Nutritional, Food and Consumer Sciences, Fulda University of Applied Sciences, 36037 Fulda, Germany
- Correspondence:
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Ng NHJ, Jasmen JB, Lim CS, Lau HH, Krishnan VG, Kadiwala J, Kulkarni RN, Ræder H, Vallier L, Hoon S, Teo AKK. HNF4A Haploinsufficiency in MODY1 Abrogates Liver and Pancreas Differentiation from Patient-Derived Induced Pluripotent Stem Cells. iScience 2019; 16:192-205. [PMID: 31195238 PMCID: PMC6562146 DOI: 10.1016/j.isci.2019.05.032] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 11/20/2018] [Accepted: 05/22/2019] [Indexed: 01/01/2023] Open
Abstract
Maturity-onset diabetes of the young 1 (MODY1) is a monogenic diabetes condition caused by heterozygous HNF4A mutations. We investigate how HNF4A haploinsufficiency from a MODY1/HNF4A mutation influences the development of foregut-derived liver and pancreatic cells through differentiation of human induced pluripotent stem cells from a MODY1 family down the foregut lineage. In MODY1-derived hepatopancreatic progenitors, which expressed reduced HNF4A levels and mislocalized HNF4A, foregut genes were downregulated, whereas hindgut-specifying HOX genes were upregulated. MODY1-derived hepatocyte-like cells were found to exhibit altered morphology. Hepatic and β cell gene signatures were also perturbed in MODY1-derived hepatocyte-like and β-like cells, respectively. As mutant HNF4A (p.Ile271fs) did not undergo complete nonsense-mediated decay or exert dominant negativity, HNF4A-mediated loss of function is likely due to impaired transcriptional activation of target genes. Our results suggest that in MODY1, liver and pancreas development is perturbed early on, contributing to altered hepatic proteins and β cell defects in patients. HNF4A is downregulated and predominantly mislocalized in the cytoplasm in MODY1 Foregut markers, pancreatic and hepatic genes, were downregulated in MODY1-HPPs A reciprocal upregulation of hindgut HOX genes was observed in MODY1-HPPs Mutant HNF4A resulted in loss of transcriptional activation of target genes
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Affiliation(s)
- Natasha Hui Jin Ng
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore
| | - Joanita Binte Jasmen
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore
| | - Chang Siang Lim
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore
| | - Hwee Hui Lau
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | | | - Juned Kadiwala
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Anne McLaren Laboratory, Department of Surgery, University of Cambridge, Cambridge CB2 0SZ, UK
| | - Rohit N Kulkarni
- Section of Islet Cell and Regenerative Biology, Joslin Diabetes Center, Harvard Stem Cell Institute, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA 02215, USA
| | - Helge Ræder
- Department of Pediatrics, Haukeland University Hospital, 5021 Bergen, Norway; KG Jebsen Center for Diabetes Research, Department of Clinical Science, Faculty of Medicine, University of Bergen, 5020 Bergen, Norway
| | - Ludovic Vallier
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Anne McLaren Laboratory, Department of Surgery, University of Cambridge, Cambridge CB2 0SZ, UK; Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Shawn Hoon
- Molecular Engineering Lab, A*STAR, Singapore 138673, Singapore
| | - Adrian Kee Keong Teo
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore; Department of Biochemistry and Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore.
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Wu L, Wang CC. Genetic variants in promoter regions associated with type 2 diabetes mellitus: A large-scale meta-analysis and subgroup analysis. J Cell Biochem 2019; 120:13012-13025. [PMID: 30860284 DOI: 10.1002/jcb.28572] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 02/20/2019] [Indexed: 12/15/2022]
Abstract
BACKGROUND Promoter plays important roles in regulating transcription of genes. Association studies of genetic variants in promoter region with type 2 diabetes (T2D) risk have been reported, but most were limited to small number of individual genetic variants and insufficient sample sizes. In addition, the effect of study populations and demographic characteristics were often neglected. METHODS In this study, we conducted a large-scale meta-analysis and subgroup analysis of T2D associated genetic variants in the promoter regions to evaluate their contribution to the susceptibility in T2D. Alleles and genotypes from cohort or case-controlled studies were extracted for future study. Total 41 742 cases and 50 493 controls for three loci were involved in 70 articles. RESULTS Seventy case-controlled studies of three genes with 41 742 cases and 50 493 controls were included. Meta-analysis showed only rs266729 and rs17300539 of ADIPOQ, and rs1884613, rs2144908, and rs4810424 of HNF4A were significantly associated with T2D risk. Subgroup analysis showed that both rs266729 and rs17300539 of ADIPOQ were associated with the risk of T2D in Caucasian population, but only rs266729 of ADIPOQ in Asian population and rs2144908 in other population including multinational North American. For diagnostic criteria, rs266729 of ADIPOQ and rs2144908 of HNF4A were associated with T2D risk when WHO/ADA diagnostic criteria were used. For genotyping methods, both rs266729 of ADIPOQ and rs2144908 of HNF4A were associated with T2D risk when other than Taqman and Sequencing methods were used. CONCLUSIONS T2D was significantly associated with promoter rs266729, rs17300539, rs1884613, rs2144908, and rs4810424, and the association of T2D risk were affected by study population, diagnostic criteria, and genotype methods.
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Affiliation(s)
- Ling Wu
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong
| | - Chi Chiu Wang
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong.,School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong
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Chen W, Liu Q, Lv Y, Xu D, Chen W, Yu J. Special role of JUN in papillary thyroid carcinoma based on bioinformatics analysis. World J Surg Oncol 2017; 15:119. [PMID: 28673327 PMCID: PMC5496398 DOI: 10.1186/s12957-017-1190-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 06/22/2017] [Indexed: 01/05/2023] Open
Abstract
Background Papillary thyroid carcinoma (PTC) is the most common malignancy in thyroid tissue, and the number of patients with PTC has been increasing in recent years. Discovering the mechanism of PTC genesis and progression and finding new potential diagnostic biomarkers/therapeutic target genes of PTC are of great significance. Methods In this work, the datasets GSE3467 and GSE3678 were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were identified with the limma package in R. GO function and KEGG pathway enrichment were conducted with DAVID tool. The interaction network of the DEGs and other genes was performed with Cytoscape plugin BisoGenet, while clustering analysis was performed with Cytoscape plugin ClusterOne. Results A total of 1800 overlapped DEGs were detected in two datasets. Enrichment analysis of the DEGs found that the top three enriched GO terms in three ontologies and four significantly enriched KEGG pathways were mainly concerned with intercellular junction and extracellular matrix components. Interaction network analysis found that transcription factor hepatocyte nuclear factor 4, alpha (HNF4A) and DEG JUN had higher connection degrees. Clustering analysis indicated that two function modules, in which JUN was playing a central role, were highly relevant to PTC genesis and progression. Conclusions JUN may be used as a specific diagnostic biomarker/therapeutic molecular target of PTC. However, further experiments are still needed to confirm our results.
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Affiliation(s)
- Wenzheng Chen
- Department of Thyroid and Neck Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, 330006, China
| | - Qingfeng Liu
- Department of General Surgery, The People's Hospital of Liaoning Province, Shenyang, 110016, China
| | - Yunxia Lv
- Department of Thyroid and Neck Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, 330006, China
| | - Debin Xu
- Department of Thyroid and Neck Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, 330006, China
| | - Wanzhi Chen
- Department of Thyroid and Neck Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, 330006, China
| | - Jichun Yu
- Department of Thyroid and Neck Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, 330006, China.
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Hepatocyte nuclear factor 4 alpha polymorphisms and the metabolic syndrome in French-Canadian youth. PLoS One 2015; 10:e0117238. [PMID: 25671620 PMCID: PMC4325000 DOI: 10.1371/journal.pone.0117238] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Accepted: 12/19/2014] [Indexed: 01/18/2023] Open
Abstract
Objectives Hepatocyte nuclear factor 4 alpha (HNF4α) is a transcription factor involved in the regulation of serum glucose and lipid levels. Several HNF4A gene variants have been associated with the risk of developing type 2 diabetes mellitus. However, no study has yet explored its association with insulin resistance and the cardiometabolic risk in children. We aimed to investigate the relationship between HNF4A genetic variants and the presence of metabolic syndrome (MetS) and metabolic parameters in a pediatric population. Design and Methods Our study included 1,749 French-Canadians aged 9, 13 and 16 years and evaluated 24 HNF4A polymorphisms that were previously identified by sequencing. Results Analyses revealed that, after correction for multiple testing, one SNP (rs736824; P<0.022) and two haplotypes (P1 promoter haplotype rs6130608-rs2425637; P<0.032 and intronic haplotype rs736824-rs745975-rs3212183; P<0.025) were associated with the risk of MetS. Additionally, a significant association was found between rs3212172 and apolipoprotein B levels (coefficient: -0.14 ± 0.05; P<0.022). These polymorphisms are located in HNF4A P1 promoter or in intronic regions. Conclusions Our study demonstrates that HNF4α genetic variants are associated with the MetS and metabolic parameters in French Canadian children and adolescents. This study, the first exploring the relation between HNF4A genetic variants and MetS and metabolic variables in a pediatric cohort, suggests that HNF4α could represent an early marker for the risk of developing type 2 diabetes mellitus.
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Prediabetes is associated with HNF-4 α P2 promoter polymorphism rs1884613: a case-control study in Han Chinese population and an updated meta-analysis. DISEASE MARKERS 2014; 2014:231736. [PMID: 25400315 PMCID: PMC4226192 DOI: 10.1155/2014/231736] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2014] [Accepted: 09/11/2014] [Indexed: 11/18/2022]
Abstract
BACKGROUND Controversy remains for the association between hepatocyte nuclear factor 4α (HNF-4α) P2 promoter polymorphism rs1884613 and type 2 diabetes (T2D). There was no association test of this polymorphism with prediabetes and T2D in the Chinese population. Moreover, an updated meta-analysis in various ethnic groups is needed to establish the contribution of rs1884613 to T2D risk. METHODS Using the Sequenom MassARRAY platform approach, we genotyped rs1884613 of HNF-4α in the P2 promoter region among 490 T2D patients, 471 individuals with prediabetes, and 575 healthy controls. All the individuals were recruited from 16 community health service centers in Nanshan district in Shenzhen province. Using STATA 11.0 software, meta-analysis was performed to summarize the overall contribution of rs1884613 to T2D risk. RESULTS Polymorphism rs1884613 was associated with genetic susceptibility to prediabetes in the whole samples (OR = 1.40, 95% CI = 1.16-1.68, P = 0.0001) and the female subgrouped samples (OR = 1.48, 95% CI = 1.14-1.92, P = 0.003) after adjusting for age and body mass index (BMI). In contrast, there was no association of rs1884613 with T2D in the whole samples and male in our case-control study and meta-analysis. CONCLUSIONS Our results suggest that rs1884613 contributes to susceptibility to prediabetes, whereas this polymorphism may not play an important role in the development of T2D.
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Kupfer DM, White VL, Strayer DL, Crouch DJ, Burian D. Microarray characterization of gene expression changes in blood during acute ethanol exposure. BMC Med Genomics 2013; 6:26. [PMID: 23883607 PMCID: PMC3750403 DOI: 10.1186/1755-8794-6-26] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 07/17/2013] [Indexed: 11/29/2022] Open
Abstract
Background As part of the civil aviation safety program to define the adverse effects of ethanol on flying performance, we performed a DNA microarray analysis of human whole blood samples from a five-time point study of subjects administered ethanol orally, followed by breathalyzer analysis, to monitor blood alcohol concentration (BAC) to discover significant gene expression changes in response to the ethanol exposure. Methods Subjects were administered either orange juice or orange juice with ethanol. Blood samples were taken based on BAC and total RNA was isolated from PaxGene™ blood tubes. The amplified cDNA was used in microarray and quantitative real-time polymerase chain reaction (RT-qPCR) analyses to evaluate differential gene expression. Microarray data was analyzed in a pipeline fashion to summarize and normalize and the results evaluated for relative expression across time points with multiple methods. Candidate genes showing distinctive expression patterns in response to ethanol were clustered by pattern and further analyzed for related function, pathway membership and common transcription factor binding within and across clusters. RT-qPCR was used with representative genes to confirm relative transcript levels across time to those detected in microarrays. Results Microarray analysis of samples representing 0%, 0.04%, 0.08%, return to 0.04%, and 0.02% wt/vol BAC showed that changes in gene expression could be detected across the time course. The expression changes were verified by qRT-PCR. The candidate genes of interest (GOI) identified from the microarray analysis and clustered by expression pattern across the five BAC points showed seven coordinately expressed groups. Analysis showed function-based networks, shared transcription factor binding sites and signaling pathways for members of the clusters. These include hematological functions, innate immunity and inflammation functions, metabolic functions expected of ethanol metabolism, and pancreatic and hepatic function. Five of the seven clusters showed links to the p38 MAPK pathway. Conclusions The results of this study provide a first look at changing gene expression patterns in human blood during an acute rise in blood ethanol concentration and its depletion because of metabolism and excretion, and demonstrate that it is possible to detect changes in gene expression using total RNA isolated from whole blood. The analysis approach for this study serves as a workflow to investigate the biology linked to expression changes across a time course and from these changes, to identify target genes that could serve as biomarkers linked to pilot performance.
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Affiliation(s)
- Doris M Kupfer
- Civil Aerospace Medical Institute, AAM 610, Federal Aviation Administration, Bioaeronautical Sciences Research Laboratory, Oklahoma City, OK 73169, USA.
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Ho JSK, Germer S, Tam CHT, So WY, Martin M, Ma RCW, Chan JCN, Ng MCY. Association of the PPARG Pro12Ala polymorphism with type 2 diabetes and incident coronary heart disease in a Hong Kong Chinese population. Diabetes Res Clin Pract 2012; 97:483-91. [PMID: 22515931 DOI: 10.1016/j.diabres.2012.03.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2012] [Revised: 03/04/2012] [Accepted: 03/15/2012] [Indexed: 11/18/2022]
Abstract
AIMS We examined the risk association between single nucleotide polymorphisms (SNPs) in eleven candidate genes with type 2 diabetes (T2D). T2D-associated polymorphisms were also examined for prediction of incident CHD. METHODS 113 tagging SNPs were genotyped in stage 1 (467 T2D cases, 290 controls), and 15 SNPs were analyzed in the final cohort (1462 T2D cases, 600 controls). Three T2D-associated SNPs were further tested for prediction of CHD within a subset of 1417 T2D cases free of CHD at enrolment. RESULTS In the case-control analysis, PPARG rs1801282 (Pro12Ala) (OR=1.48 (1.02-2.16)), ADIPOQ rs1063539 (OR=1.17 (1.01-1.35)), and HNF4A rs1884614 (OR=1.16 (1.00-1.32) were associated with T2D (P(allelic)<0.05). Joint analysis of rs1801282-C, rs1063539-G, and rs1884614-T risk alleles showed an additive dosage effect (P for trend=0.001). Moreover, carriers with two PPARG rs1801282-C risk alleles were associated with an increased risk of incident CHD (HR=4.38 (1.03-18.57), P=0.045) in T2D patients in the prospective analysis. CONCLUSIONS Genetic variants of PPARG, ADIPOQ and HNF4A were individually and jointly associated with T2D in Hong Kong Chinese. The PPARG Pro12 risk allele contributed to increased risk for both T2D and CHD.
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Affiliation(s)
- Janice S K Ho
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong
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Peltsverger MY, Celi FS. Cardiovascular Risk in the Old Order Amish. CURRENT CARDIOVASCULAR RISK REPORTS 2011. [DOI: 10.1007/s12170-011-0163-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Brouwers MCGJ, de Graaf J, van Greevenbroek MMJ, Schaper N, Stehouwer CDA, Stalenhoef AFH. Novel drugs in familial combined hyperlipidemia: lessons from type 2 diabetes mellitus. Curr Opin Lipidol 2010; 21:530-8. [PMID: 20739883 DOI: 10.1097/mol.0b013e32833ea9ec] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
PURPOSE OF REVIEW Familial combined hyperlipidemia (FCHL) and type 2 diabetes mellitus (T2DM) are prevalent entities that share many features of the metabolic syndrome. Recent findings suggest that FCHL and T2DM are less distinct than initially anticipated, which could offer new insights for their therapeutic approach. RECENT FINDINGS Genetic association studies have provided evidence for a common genetic background (upstream transcription factor 1, activating transcription factor 6, transcription factor 7-like 2 and hepatocyte nuclear factor 4 alpha) between FCHL and T2DM. The metabolic overlap can be illustrated by the presence of ectopic fat accumulation and insulin resistance (muscle, adipose tissue and liver). We have shown that FCHL patients are at increased risk to develop T2DM. This indicates that both entities are not static, but instead the former is able to migrate to the latter as insulin resistance progresses. Given these new findings, it can be anticipated that FCHL patients could also benefit from insulin-sensitizing therapy such as pioglitazone and metformin. Indeed, pilot studies have demonstrated that pioglitazone might be advantageous in FCHL patients. SUMMARY Recent studies suggest that FCHL patients have an increased risk to develop T2DM, which has important clinical implications. Further studies are necessary to evaluate whether FCHL patients can be protected from new-onset T2DM and premature cardiovascular events with insulin-sensitizing therapy.
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MESH Headings
- Adipose Tissue/drug effects
- Adipose Tissue/metabolism
- Cholesterol, LDL/genetics
- Cholesterol, LDL/metabolism
- Diabetes Mellitus, Type 2/complications
- Diabetes Mellitus, Type 2/drug therapy
- Diabetes Mellitus, Type 2/genetics
- Diabetes Mellitus, Type 2/metabolism
- Drug Discovery
- Fatty Liver/genetics
- Fatty Liver/metabolism
- Genetic Predisposition to Disease
- Humans
- Hyperlipidemia, Familial Combined/complications
- Hyperlipidemia, Familial Combined/drug therapy
- Hyperlipidemia, Familial Combined/genetics
- Hyperlipidemia, Familial Combined/metabolism
- Insulin/metabolism
- Insulin Resistance/genetics
- Male
- Metabolic Syndrome/etiology
- Metabolic Syndrome/genetics
- Metabolic Syndrome/metabolism
- Metformin/administration & dosage
- Models, Biological
- Obesity/genetics
- Obesity/metabolism
- Pioglitazone
- Risk Factors
- Thiazolidinediones/administration & dosage
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Triglycerides/genetics
- Triglycerides/metabolism
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Affiliation(s)
- Martijn C G J Brouwers
- Laboratory of Vascular Medicine and Metabolism, Department of Internal Medicine, Divisions of General Internal Medicine and Endocrinology, Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, The Netherlands
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Chen Z, Zhang D, Liu Y, Zhou D, Zhao T, Yang Y, He L, Xu H. Variants in hepatocyte nuclear factor 4alpha gene promoter region and type 2 diabetes risk in Chinese. Exp Biol Med (Maywood) 2010; 235:857-61. [PMID: 20558840 DOI: 10.1258/ebm.2010.010024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
As a key regulator of insulin secretion and metabolism of glucose, cholesterol and fatty acid, hepatocyte nuclear factor 4alpha (HNF4A) was suggested as a candidate gene for type 2 diabetes (T2D); however, no association study between HNF4A and T2D in the Chinese population has been conducted before. To address this issue, we evaluated the impact of the HNF4A variants (rs1884614 and rs2425637) on T2D and metabolic traits in 1912 unrelated patients and 2041 control subjects in the Chinese Han population. Our results suggested that no individual single nucleotide polymorphisms of HNF4A was significantly associated with T2D at either allele or genotype level. However, rs2425637 in the promoter region of HNF4A was found to have an effect on total cholesterol and high-density lipoprotein before multiple testing correction. To summarize, our investigation did not confirm the effects of HNF4A variants (rs1884614 and rs2425637) on T2D risk, but found that the risk HNF4A contributed to T2D might be population specific.
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Affiliation(s)
- Zhuo Chen
- Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 294 Taiyuan Road, Shanghai, PR China
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Cattaert T, Urrea V, Naj AC, De Lobel L, De Wit V, Fu M, Mahachie John JM, Shen H, Calle ML, Ritchie MD, Edwards TL, Van Steen K. FAM-MDR: a flexible family-based multifactor dimensionality reduction technique to detect epistasis using related individuals. PLoS One 2010; 5:e10304. [PMID: 20421984 PMCID: PMC2858665 DOI: 10.1371/journal.pone.0010304] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Accepted: 03/01/2010] [Indexed: 12/05/2022] Open
Abstract
We propose a novel multifactor dimensionality reduction method for epistasis detection in small or extended pedigrees, FAM-MDR. It combines features of the Genome-wide Rapid Association using Mixed Model And Regression approach (GRAMMAR) with Model-Based MDR (MB-MDR). We focus on continuous traits, although the method is general and can be used for outcomes of any type, including binary and censored traits. When comparing FAM-MDR with Pedigree-based Generalized MDR (PGMDR), which is a generalization of Multifactor Dimensionality Reduction (MDR) to continuous traits and related individuals, FAM-MDR was found to outperform PGMDR in terms of power, in most of the considered simulated scenarios. Additional simulations revealed that PGMDR does not appropriately deal with multiple testing and consequently gives rise to overly optimistic results. FAM-MDR adequately deals with multiple testing in epistasis screens and is in contrast rather conservative, by construction. Furthermore, simulations show that correcting for lower order (main) effects is of utmost importance when claiming epistasis. As Type 2 Diabetes Mellitus (T2DM) is a complex phenotype likely influenced by gene-gene interactions, we applied FAM-MDR to examine data on glucose area-under-the-curve (GAUC), an endophenotype of T2DM for which multiple independent genetic associations have been observed, in the Amish Family Diabetes Study (AFDS). This application reveals that FAM-MDR makes more efficient use of the available data than PGMDR and can deal with multi-generational pedigrees more easily. In conclusion, we have validated FAM-MDR and compared it to PGMDR, the current state-of-the-art MDR method for family data, using both simulations and a practical dataset. FAM-MDR is found to outperform PGMDR in that it handles the multiple testing issue more correctly, has increased power, and efficiently uses all available information.
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Affiliation(s)
- Tom Cattaert
- Montefiore Institute, University of Liège, Liège, Belgium.
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Wallerman O, Motallebipour M, Enroth S, Patra K, Bysani MSR, Komorowski J, Wadelius C. Molecular interactions between HNF4a, FOXA2 and GABP identified at regulatory DNA elements through ChIP-sequencing. Nucleic Acids Res 2010; 37:7498-508. [PMID: 19822575 PMCID: PMC2794179 DOI: 10.1093/nar/gkp823] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Gene expression is regulated by combinations of transcription factors, which can be mapped to regulatory elements on a genome-wide scale using ChIP experiments. In a previous ChIP-chip study of USF1 and USF2 we found evidence also of binding of GABP, FOXA2 and HNF4a within the enriched regions. Here, we have applied ChIP-seq for these transcription factors and identified 3064 peaks of enrichment for GABP, 7266 for FOXA2 and 18783 for HNF4a. Distal elements with USF2 signal was frequently bound also by HNF4a and FOXA2. GABP peaks were found at transcription start sites, whereas 94% of FOXA2 and 90% of HNF4a peaks were located at other positions. We developed a method to accurately define TFBS within peaks, and found the predicted sites to have an elevated conservation level compared to peak centers; however the majority of bindings were not evolutionary conserved. An interaction between HNF4a and GABP was seen at TSS, with one-third of the HNF4a positive promoters being bound also by GABP, and this interaction was verified by co-immunoprecipitations.
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Affiliation(s)
- Ola Wallerman
- Department of Genetics and Pathology, Rudbeck Laboratory, SE-751 85 Uppsala, Sweden
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14
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Leak TS, Langefeld CD, Keene KL, Gallagher CJ, Lu L, Mychaleckyj JC, Rich SS, Freedman BI, Bowden DW, Sale MM. Chromosome 7p linkage and association study for diabetes related traits and type 2 diabetes in an African-American population enriched for nephropathy. BMC MEDICAL GENETICS 2010; 11:22. [PMID: 20144192 PMCID: PMC2829011 DOI: 10.1186/1471-2350-11-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2009] [Accepted: 02/08/2010] [Indexed: 12/21/2022]
Abstract
BACKGROUND Previously we performed a linkage scan of 638 African American affected sibling pairs (ASP) with type 2 diabetes (T2D) enriched for end-stage renal disease (ESRD). Ordered subset linkage analysis (OSA) revealed a linkage peak on chromosome 7p in the subset of families with earlier age of T2D diagnosis. METHODS We fine mapped this region by genotyping 11 additional polymorphic markers in the same ASP and investigated a total of 68 single nucleotide polymorphisms (SNPs) in functional candidate genes (GCK1, IL6, IGFBP1 and IGFBP3) for association with age of T2D diagnosis, age of ESRD diagnosis, duration of T2D to onset of ESRD, body mass index (BMI) in African American cases and T2D-ESRD in an African American case-control cohort. OSA of fine mapping markers supported linkage at 28 cM on 7p (near D7S3051) in early-onset T2D families (max. LOD = 3.61, P = 0.002). SNPs in candidate genes and 70 ancestry-informative markers (AIMs) were evaluated in 577 African American T2D-ESRD cases and 596 African American controls. RESULTS The most significant association was observed between ESRD age of diagnosis and SNP rs730497, located in intron 1 of the GCK1 gene (recessive T2D age-adjusted P = 0.0006). Nominal associations were observed with GCK1 SNPs and T2D age of diagnosis (BMI-adjusted P = 0.014 to 0.032). Also, one IGFBP1 and four IGFBP3 SNPs showed nominal genotypic association with T2D-ESRD (P = 0.002-0.049). After correcting for multiple tests, only rs730497 remanined significant. CONCLUSION Variant rs730947 in the GCK1 gene appears to play a role in early ESRD onset in African Americans.
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Affiliation(s)
- Tennille S Leak
- Center for Human Genomics, Wake Forest University School of Medicine, Winston-Salem, NC, USA
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Carl D Langefeld
- Department of Biostatistical Sciences, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Keith L Keene
- Center for Human Genomics, Wake Forest University School of Medicine, Winston-Salem, NC, USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Carla J Gallagher
- Center for Human Genomics, Wake Forest University School of Medicine, Winston-Salem, NC, USA
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC, USA
- Milton S Hershey Medical Center, Pennsylvania State University, Hershey, PA, USA
| | - Lingyi Lu
- Department of Biostatistical Sciences, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Josyf C Mychaleckyj
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Barry I Freedman
- Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Donald W Bowden
- Center for Human Genomics, Wake Forest University School of Medicine, Winston-Salem, NC, USA
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC, USA
- Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Michèle M Sale
- Center for Human Genomics, Wake Forest University School of Medicine, Winston-Salem, NC, USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
- Department of Medicine, University of Virginia, Charlottesville, VA, USA
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15
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Sookoian S, Gemma C, Pirola CJ. Influence of hepatocyte nuclear factor 4alpha (HNF4alpha) gene variants on the risk of type 2 diabetes: a meta-analysis in 49,577 individuals. Mol Genet Metab 2010; 99:80-9. [PMID: 19748811 DOI: 10.1016/j.ymgme.2009.08.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2009] [Revised: 08/14/2009] [Accepted: 08/14/2009] [Indexed: 12/19/2022]
Abstract
BACKGROUND The nuclear receptor hepatocyte nuclear factor 4alpha (HNF4alpha) contributes to the regulation of a large fraction of liver and pancreatic islet transcriptomes. AIM To evaluate the influence of HNF4alpha polymorphisms across the entire locus on the occurrence of type 2 diabetes (T2D) by means of a meta-analysis. METHODS We evaluated haplotype block structure of HNF4alpha variants owing to linkage disequilibrium (LD). From 1455 reports, we evaluated 21 observational studies. RESULTS Six haplotype blocks of LD were constructed with SNPs with r(2)>0.8; there were also 14 unlinked SNPs. Overall, we included 22,920 cases and 26.657 controls. Among 17 heterogeneous studies (21,881 cases and 24,915 controls), including 3 SNPs of P2 promoter region in block 1, we observed a significant association with T2D in fixed (OR 0.94, 95%CI: 0.905-0.975, p=0.001) and random (OR 0.988, 95%CI: 0.880-0.948, p=0.000012) model. Three homogeneous studies were evaluated in block 2 (2684 cases and 2059 controls), and a significant association with T2D was also observed: OR: 1.121, 95%CI 1.013-1.241, p=0.027. Three additional variants were associated with T2D: two intronic SNPs (rs4810424: OR: 1.080, 95%CI: 1.010-1.154, p<0.03 and rs3212183: OR: 0.843, 95%CI: 0.774-0.918, p<0.00009) and one missense variant (rs1800961: OR: 0.770, 95%CI: 0.595-0.995, p<0.05, 6562 cases and 6723 controls). CONCLUSIONS In addition to HNF4alpha variants in the promoter region, other SNPs may be involved on the occurrence of T2D.
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Affiliation(s)
- Silvia Sookoian
- Molecular Genetics and Biology of Complex Diseases Department, Institute of Medical Research A. Lanari, University of Buenos Aires--National Council of Scientific and Technological Research, Combatientes de Malvinas 3150, Buenos Aires (1427), Argentina
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16
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Naj AC, Kao WHL, O’Connell JR, Mitchell BD, Silver KD. Sequence variation in IGF1R is associated with differences in insulin levels in nondiabetic Old Order Amish. Diabetes Metab Res Rev 2009; 25:773-9. [PMID: 19877134 PMCID: PMC2837841 DOI: 10.1002/dmrr.1044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
BACKGROUND Insulin growth factor-1 receptor (IGF1R) encodes the insulin-like growth factor 1 receptor, a transmembrane tyrosine kinase receptor located on chromosome 15q26.3, in a region of linkage (LOD = 2.53, P = 0.00032) to Insulin30 on an OGTT in the Old Order Amish. Mouse models with beta-cell-specific deficiency of IGF1R demonstrate defects in glucose-stimulated insulin secretion. METHODS To test the hypothesis that genetic variation in IGF1R is associated with impaired insulin secretion, we genotyped 54 SNPs in 778 nondiabetic subjects from the AFDS who had undergone OGTTs and tested them for association with ln Insulin30 and ISI. RESULTS No individual SNPs were significantly associated with ln Insulin30 or ISI using a multiple hypothesis testing adjusted P < 0.002. Tests of association of 4-SNP haplotypes constructed by a windowing approach revealed an association of the CTTG-variant of a 4-SNP haplotype found in intron 20 (rs1784195-rs2715439-rs8034284-rs12440962) with lower ISI levels (beta = 0.18, SE(beta) = 0.05, P = 0.001). CONCLUSIONS Sequence variation in IGF1R may influence insulin secretory function, although further studies in other populations will be needed to confirm these findings.
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Affiliation(s)
- Adam C. Naj
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
- Welch Center for Epidemiology, Prevention, and Clinical Research, Baltimore, MD
| | - Wen-Hong L. Kao
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
- Welch Center for Epidemiology, Prevention, and Clinical Research, Baltimore, MD
| | - Jeffrey R. O’Connell
- Division of Endocrinology, Diabetes, and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD
| | - Braxton D. Mitchell
- Division of Endocrinology, Diabetes, and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD
| | - Kristi D. Silver
- Division of Endocrinology, Diabetes, and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD
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17
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Abstract
Type 2 diabetes mellitus is a complex metabolic disease that is caused by insulin resistance and beta-cell dysfunction. Furthermore, type 2 diabetes has an evident genetic component and represents a polygenic disease. During the last decade, considerable progress was made in the identification of type 2 diabetes risk genes. This was crucially influenced by the development of affordable high-density single nucleotide polymorphism (SNP) arrays that prompted several successful genome-wide association scans in large case-control cohorts. Subsequent to the identification of type 2 diabetes risk SNPs, cohorts thoroughly phenotyped for prediabetic traits with elaborate in vivo methods allowed an initial characterization of the pathomechanisms of these SNPs. Although the underlying molecular mechanisms are still incompletely understood, a surprising result of these pathomechanistic investigations was that most of the risk SNPs affect beta-cell function. This favors a beta-cell-centric view on the genetics of type 2 diabetes. The aim of this review is to summarize the current knowledge about the type 2 diabetes risk genes and their variants' pathomechanisms.
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Affiliation(s)
- Harald Staiger
- Department of Internal Medicine, Division of Endocrinology, Diabetology, Angiology, Nephrology, and Clinical Chemistry, University Hospital Tübingen, D-72076 Tübingen, Germany
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Ruchat SM, Weisnagel JS, Rankinen T, Bouchard C, Vohl MC, Pérusse L. Interaction between HNF4A polymorphisms and physical activity in relation to type 2 diabetes-related traits: results from the Quebec Family Study. Diabetes Res Clin Pract 2009; 84:211-8. [PMID: 19406499 DOI: 10.1016/j.diabres.2009.03.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2008] [Revised: 03/10/2009] [Accepted: 03/17/2009] [Indexed: 11/17/2022]
Abstract
AIMS To test for associations between type 2 diabetes mellitus (T2DM)-related traits and polymorphisms (SNPs) in the hepatocyte nuclear factor 4-alpha gene (HNF4A) in the Quebec Family Study cohort, and determine whether these associations are modulated by physical activity (PA). METHODS Two HNF4A SNPs (rs1885088 G>A; rs745975 C>T), previously reported to be associated with T2DM, were studied in 528 non-diabetic subjects who underwent a 75g oral glucose tolerance test (OGTT). Glucose, insulin and C-peptide plasma levels, measured in the fasting state and during the OGTT, were used in the analysis. The amount (hours per week) of PA was assessed by questionnaire. RESULTS The HNF4A rs1885088 SNP was not independently associated with T2DM-related traits, whereas the rs745975 was associated with fasting insulin, HOMA-IR and 2-h glucose levels (p<0.05 for all). Genotype by PA interactions were found for glucose homeostasis (p<0.0001) and insulin secretion (p<or=0.03). When subjects were stratified by PA level (according to the median value), we found that high level of PA (>2h/week) was associated with smaller glucose area under the curve (AUC) and 2-h glucose levels in rs1885088 A/A homozygotes and with lower fasting C-peptide and insulin AUC in rs745975 T/T homozygotes. CONCLUSION These results indicate that the associations of HNF4A rs1885088 with glucose tolerance and rs745975 with insulin secretion are modulated by PA. Our finding therefore suggests that the effect of HNF4A polymorphisms on the risk of T2DM is influenced by PA.
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19
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Wang C, Hu C, Zhang R, Bao Y, Ma X, Lu J, Qin W, Shao X, Lu J, Xu J, Lu H, Xiang K, Jia W. Common variants of hepatocyte nuclear factor 1beta are associated with type 2 diabetes in a Chinese population. Diabetes 2009; 58:1023-7. [PMID: 19168595 PMCID: PMC2661584 DOI: 10.2337/db08-1064] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2008] [Accepted: 01/13/2009] [Indexed: 11/13/2022]
Abstract
OBJECTIVE Hepatocyte nuclear factor 1beta (HNF1beta) is a transcription factor that is critical for pancreatic cell formation and glucose homeostasis. Previous studies have reported that common variants of HNF1beta were associated with type 2 diabetes in Caucasians and West Africans. However, analysis in the subjects from the Botnia study and Malmö Preventive Project produced conflicting results, and the role for HNF1beta in type 2 diabetes susceptibility remains unclear. We therefore investigated common variants across the HNF1beta gene in a Chinese population. RESEARCH DESIGN AND METHODS Fifteen tagging single nucleotide polymorphisms (SNPs) were analyzed for association with type 2 diabetes in subjects with type 2 diabetes (n = 1,859) and normal glucose regulation (n = 1,785). RESULTS Consistent with the initial study, we observed evidence that the risk G allele of rs4430796 in intron 2 was significantly associated with type 2 diabetes (odds ratio 1.16 [95% CI 1.05-1.29], P = 0.0035, empirical P = 0.0475). Furthermore, the at-risk G allele was associated with earlier age at diagnosis in the type 2 diabetic subjects (P = 0.0228). CONCLUSIONS The result of this study provides evidence that variants in the HNF1beta region contribute to susceptibility to type 2 diabetes in the Chinese population.
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Affiliation(s)
- Congrong Wang
- Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai Diabetes Institute, Shanghai Clinical Center for Diabetes, Shanghai, China
| | - Cheng Hu
- Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai Diabetes Institute, Shanghai Clinical Center for Diabetes, Shanghai, China
| | - Rong Zhang
- Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai Diabetes Institute, Shanghai Clinical Center for Diabetes, Shanghai, China
| | - Yuqian Bao
- Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai Diabetes Institute, Shanghai Clinical Center for Diabetes, Shanghai, China
| | - Xiaojing Ma
- Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai Diabetes Institute, Shanghai Clinical Center for Diabetes, Shanghai, China
| | - Jingyi Lu
- Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai Diabetes Institute, Shanghai Clinical Center for Diabetes, Shanghai, China
| | - Wen Qin
- Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai Diabetes Institute, Shanghai Clinical Center for Diabetes, Shanghai, China
| | - Xinyu Shao
- Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai Diabetes Institute, Shanghai Clinical Center for Diabetes, Shanghai, China
| | - Junxi Lu
- Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai Diabetes Institute, Shanghai Clinical Center for Diabetes, Shanghai, China
| | - Jing Xu
- Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai Diabetes Institute, Shanghai Clinical Center for Diabetes, Shanghai, China
| | - Huijuan Lu
- Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai Diabetes Institute, Shanghai Clinical Center for Diabetes, Shanghai, China
| | - Kunsan Xiang
- Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai Diabetes Institute, Shanghai Clinical Center for Diabetes, Shanghai, China
| | - Weiping Jia
- Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai Diabetes Institute, Shanghai Clinical Center for Diabetes, Shanghai, China
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Chen R, Morgan AA, Dudley J, Deshpande T, Li L, Kodama K, Chiang AP, Butte AJ. FitSNPs: highly differentially expressed genes are more likely to have variants associated with disease. Genome Biol 2008; 9:R170. [PMID: 19061490 PMCID: PMC2646274 DOI: 10.1186/gb-2008-9-12-r170] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2008] [Revised: 09/26/2008] [Accepted: 12/05/2008] [Indexed: 12/18/2022] Open
Abstract
Differential expressed genes are more likely to have variants associated with disease. A new tool, fitSNP, prioritizes candidate SNPs from association studies. Background Candidate single nucleotide polymorphisms (SNPs) from genome-wide association studies (GWASs) were often selected for validation based on their functional annotation, which was inadequate and biased. We propose to use the more than 200,000 microarray studies in the Gene Expression Omnibus to systematically prioritize candidate SNPs from GWASs. Results We analyzed all human microarray studies from the Gene Expression Omnibus, and calculated the observed frequency of differential expression, which we called differential expression ratio, for every human gene. Analysis conducted in a comprehensive list of curated disease genes revealed a positive association between differential expression ratio values and the likelihood of harboring disease-associated variants. By considering highly differentially expressed genes, we were able to rediscover disease genes with 79% specificity and 37% sensitivity. We successfully distinguished true disease genes from false positives in multiple GWASs for multiple diseases. We then derived a list of functionally interpolating SNPs (fitSNPs) to analyze the top seven loci of Wellcome Trust Case Control Consortium type 1 diabetes mellitus GWASs, rediscovered all type 1 diabetes mellitus genes, and predicted a novel gene (KIAA1109) for an unexplained locus 4q27. We suggest that fitSNPs would work equally well for both Mendelian and complex diseases (being more effective for cancer) and proposed candidate genes to sequence for their association with 597 syndromes with unknown molecular basis. Conclusions Our study demonstrates that highly differentially expressed genes are more likely to harbor disease-associated DNA variants. FitSNPs can serve as an effective tool to systematically prioritize candidate SNPs from GWASs.
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Affiliation(s)
- Rong Chen
- Stanford Center for Biomedical Informatics Research, 251 Cmpus Drive, Stanford, CA 94305, USA.
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21
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Tokunaga A, Horikawa Y, Fukuda-Akita E, Okita K, Iwahashi H, Shimomura I, Takeda J, Yamagata K. A common P2 promoter polymorphism of the hepatocyte nuclear factor-4alpha gene is associated with insulin secretion in non-obese Japanese with type 2 diabetes. Endocr J 2008; 55:999-1004. [PMID: 18654034 DOI: 10.1507/endocrj.k08e-083] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
AIMS Heterozygous mutations of the hepatocyte nuclear factor (HNF)-4alpha gene cause a particular form of maturity-onset diabetes of the young (MODY1). Recent genetic studies have shown that single nucleotide polymorphisms (SNPs) of the beta-cell type P2 promoter of the HNF-4alpha gene are associated with type 2 diabetes in some populations. In the Japanese population, a haplotype consisting of two SNPs (rs1884614 and rs2144908) in the P2 promoter region is reported to show a significant association with type 2 diabetes. METHODS Both rs1884614 and rs2144908 were genotyped in 349 type 2 diabetic patients and 203 non-diabetic controls. The relation of these SNPs to clinical characteristics was also examined in the diabetic subjects. RESULTS There were no differences in the genotype distribution of the two SNPs between the control and diabetic subjects, and the haplotype distribution was also similar in the two groups. However, the rs1884614 T/T genotype was significantly associated with a smaller area under the plasma insulin curve (AUC) during the OGTT in non-obese (BMI <25 kg/m(2)) patients (p=0.0272; adjusted for age and sex). CONCLUSIONS SNP rs1884614 in the P2 promoter region of the HNF-4alpha gene may influence insulin secretion in non-obese Japanese subjects with type 2 diabetes.
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Affiliation(s)
- Ayumi Tokunaga
- Department of Metabolic Medicine, Graduate School of Medicine, Osaka University, Osaka, Japan
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22
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Barroso I, Luan J, Wheeler E, Whittaker P, Wasson J, Zeggini E, Weedon MN, Hunt S, Venkatesh R, Frayling TM, Delgado M, Neuman RJ, Zhao J, Sherva R, Glaser B, Walker M, Hitman G, McCarthy MI, Hattersley AT, Permutt MA, Wareham NJ, Deloukas P. Population-specific risk of type 2 diabetes conferred by HNF4A P2 promoter variants: a lesson for replication studies. Diabetes 2008; 57:3161-5. [PMID: 18728231 PMCID: PMC2570416 DOI: 10.2337/db08-0719] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
OBJECTIVE Single nucleotide polymorphisms (SNPs) in the P2 promoter region of HNF4A were originally shown to be associated with predisposition for type 2 diabetes in Finnish, Ashkenazi, and, more recently, Scandinavian populations, but they generated conflicting results in additional populations. We aimed to investigate whether data from a large-scale mapping approach would replicate this association in novel Ashkenazi samples and in U.K. populations and whether these data would allow us to refine the association signal. RESEARCH DESIGN AND METHODS Using a dense linkage disequilibrium map of 20q, we selected SNPs from a 10-Mb interval centered on HNF4A. In a staged approach, we first typed 4,608 SNPs in case-control populations from four U.K. populations and an Ashkenazi population (n = 2,516). In phase 2, a subset of 763 SNPs was genotyped in 2,513 additional samples from the same populations. RESULTS Combined analysis of both phases demonstrated association between HNF4A P2 SNPs (rs1884613 and rs2144908) and type 2 diabetes in the Ashkenazim (n = 991; P < 1.6 x 10(-6)). Importantly, these associations are significant in a subset of Ashkenazi samples (n = 531) not previously tested for association with P2 SNPs (odds ratio [OR] approximately 1.7; P < 0.002), thus providing replication within the Ashkenazim. In the U.K. populations, this association was not significant (n = 4,022; P > 0.5), and the estimate for the OR was much smaller (OR 1.04; [95%CI 0.91-1.19]). CONCLUSIONS These data indicate that the risk conferred by HNF4A P2 is significantly different between U.K. and Ashkenazi populations (P < 0.00007), suggesting that the underlying causal variant remains unidentified. Interactions with other genetic or environmental factors may also contribute to this difference in risk between populations.
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Affiliation(s)
- Inês Barroso
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.
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Kempf K, Rathmann W, Herder C. Impaired glucose regulation and type 2 diabetes in children and adolescents. Diabetes Metab Res Rev 2008; 24:427-37. [PMID: 18551709 DOI: 10.1002/dmrr.869] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Diabetes mellitus in paediatric patients used to be almost exclusively type 1, but in recent years, case series as well as hospital-based and population-based studies indicated that the number of children and adolescents with type 2 diabetes (T2DM) has been increasing. This development is alarming since T2DM in youth is usually not an isolated condition, but accompanied by other cardiovascular risk factors such as obesity, dyslipidaemia, hypertension and low-grade inflammation. In adults, numerous studies provided detailed data on prevalence, incidence and risk factors for the development of T2DM, but for children and adolescents clinical and experimental data are still rather limited. This review provides an overview about the epidemiology and pathogenesis of T2DM in youth and about impaired glucose regulation as major risk factor for diabetes development with a special focus on the recent literature on clinical and lifestyle-related risk factors. Differences in incidence and prevalence across different populations indicate that ethnic background and genetic pre-disposition may be important risk determinants. In addition, epigenetic factors and foetal programming appear to confer additional risk before birth. Among the environmental and lifestyle-related risk factors there is evidence that obesity, hypercaloric diet, physical inactivity, socio-economic position (SEP), smoking, low-grade inflammation, psychosocial stress and sleeping patterns contribute to the risk for T2DM. However, the assessment of the relevance of risk factors and of incidence or prevalence estimates in youth is complicated by methodological issues that are also discussed.
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Affiliation(s)
- Kerstin Kempf
- Institute for Clinical Diabetes Research, German Diabetes Centre, Leibniz Institute at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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24
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Black MH, Fingerlin TE, Allayee H, Zhang W, Xiang AH, Trigo E, Hartiala J, Lehtinen AB, Haffner SM, Bergman RN, McEachin RC, Kjos SL, Lawrence JM, Buchanan TA, Watanabe RM. Evidence of interaction between PPARG2 and HNF4A contributing to variation in insulin sensitivity in Mexican Americans. Diabetes 2008; 57:1048-56. [PMID: 18162503 PMCID: PMC4447520 DOI: 10.2337/db07-0848] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
OBJECTIVE We hypothesized that interaction between PPARG2 Pro12Ala and variants in the promoter region of HNF4A are associated with type 2 diabetes-related quantitative traits in Mexican-American families of a proband with previous gestational diabetes. RESEARCH DESIGN AND METHODS The BetaGene project genotyped PPARG2 Pro12Ala and nine HNF4A single nucleotide polymorphisms (SNPs) in 473 individuals in 89 families. Members of the proband generation had fasting glucose <126 mg/dl and were phenotyped by oral and intravenous glucose tolerance tests. RESULTS Neither PPARG2 Pro12Ala nor any of the nine HNF4A SNPs were independently associated with type 2 diabetes-related quantitative traits. However, the interaction between PPARG2 Pro12Ala and HNF4A rs2144908 was significantly associated with both insulin sensitivity (S(I)) (Bonferroni P = 0.0006) and 2-h insulin (Bonferroni P = 0.039). Subjects with at least one PPARG2 Ala allele and homozygous for the HNF4A rs2144908 A allele had 40% higher S(I) compared with individuals with at least one G allele. S(I) did not vary by rs2144908 genotype among PPARG2 Pro/Pro. The interaction result for S(I) was replicated by the Insulin Resistance Atherosclerosis Family Study (P = 0.018) in their San Antonio sample (n = 484) where subjects with at least one PPARG2 Ala allele and homozygous for the HNF4A rs2144908 A allele had a 29% higher S(I) compared with individuals with at least one G allele. However, the interaction was not replicated in their San Luis Valley sample (n = 496; P = 0.401). CONCLUSIONS Together, these results suggest that variation in PPARG2 and HNF4A may interact to regulate insulin sensitivity in Mexican Americans at risk for type 2 diabetes.
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Affiliation(s)
- Mary Helen Black
- Department of Preventive Medicine, Division of Biostatistics, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Tasha E. Fingerlin
- Department of Preventive Medicine and Biometrics, University of Colorado at Denver and Health Sciences Center, Denver, Colorado
| | - Hooman Allayee
- Department of Preventive Medicine, Division of Biostatistics, Keck School of Medicine, University of Southern California, Los Angeles, California
- Institute for Genetic Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Weiming Zhang
- Department of Preventive Medicine and Biometrics, University of Colorado at Denver and Health Sciences Center, Denver, Colorado
| | - Anny H. Xiang
- Department of Preventive Medicine, Division of Biostatistics, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Enrique Trigo
- Department of Medicine, Division of Diabetes and Endocrinology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Jaana Hartiala
- Department of Preventive Medicine, Division of Biostatistics, Keck School of Medicine, University of Southern California, Los Angeles, California
- Institute for Genetic Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Allison B. Lehtinen
- Department of Biochemistry and Center for Human Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | - Steven M. Haffner
- Department of Medicine, Division of Clinical Epidemiology, University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Richard N. Bergman
- Department of Physiology and Biophysics, Keck School of Medicine of University of Southern California, Los Angeles, California
| | - Richard C. McEachin
- Department of Psychiatry, University of Michigan Medical School, Ann Arbor, Michigan
| | - Siri L. Kjos
- Department of Obstetrics and Gynecology, Harbor-UCLA Medical Center, Los Angeles, California
| | - Jean M. Lawrence
- Research and Evaluation, Kaiser Permanente Southern California, Pasadena, California
| | - Thomas A. Buchanan
- Department of Medicine, Division of Diabetes and Endocrinology, Keck School of Medicine, University of Southern California, Los Angeles, California
- Department of Physiology and Biophysics, Keck School of Medicine of University of Southern California, Los Angeles, California
| | - Richard M. Watanabe
- Department of Preventive Medicine, Division of Biostatistics, Keck School of Medicine, University of Southern California, Los Angeles, California
- Department of Physiology and Biophysics, Keck School of Medicine of University of Southern California, Los Angeles, California
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Jongjaroenprasert W, Chanprasertyothin S, Kongsuksai A, Bunnag P, Puavilai G, Ongphiphadhanakul B. Association of genetic variations near P2 promoter of the hepatocyte nuclear factor-4alpha gene and insulin secretion index in Thais. Acta Diabetol 2007; 44:227-32. [PMID: 17805472 DOI: 10.1007/s00592-007-0008-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2007] [Accepted: 06/18/2007] [Indexed: 10/22/2022]
Abstract
This study was aimed to assess the association of the two single nucleotide polymorphisms (SNPs) near P2 promoter (rs1884614 and rs2144908) of hepatocyte nuclear factor-4alpha (HNF4A) with insulin secretion index and type 2 diabetes in Thais. Participants were categorized into three groups; unrelated type 2 diabetes (N = 219), prediabetes subjects (N = 228), and normal glucose tolerant controls (N = 203). Homeostasis model assessment was calculated for individual insulin secretion and insulin sensitivity index. Genotyping of both SNPs was done by allele-specific PCR technique. Difference of SNP allele frequencies between groups were computed using the chi (2)-statistic. Multivariate regression analysis was performed to determine the effect of SNPs on insulin secretion index. The clinical features of all groups were similar. We demonstrated genotype TT at rs1884614, BMI, and waist circumference were significantly associated with insulin secretion index (P = 0.023) but not with diabetes phenotype.
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Affiliation(s)
- W Jongjaroenprasert
- Endocrine and Metabolism Unit, Department of Medicine, Ramathibodi Hospital, Mahidol University, Rama 6 Road, Rajthevi, Bangkok 10400, Thailand.
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26
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Johansson S, Raeder H, Eide SA, Midthjell K, Hveem K, Søvik O, Molven A, Njølstad PR. Studies in 3,523 Norwegians and meta-analysis in 11,571 subjects indicate that variants in the hepatocyte nuclear factor 4 alpha (HNF4A) P2 region are associated with type 2 diabetes in Scandinavians. Diabetes 2007; 56:3112-7. [PMID: 17827402 DOI: 10.2337/db07-0513] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
OBJECTIVE Recent publications have found an association between common variants near the hepatocyte nuclear factor 4 alpha (HNF4A) P2 promoter and type 2 diabetes in some populations but not in others, and the role for HNF4A in type 2 diabetes has remained unclear. In an attempt to address these inconsistencies, we investigated HNF4A single nucleotide polymorphisms (SNPs) in a large population-based sample and included a meta-analysis of published studies. RESEARCH DESIGN AND METHODS We genotyped 12 SNPs in the HNF4A region in a Norwegian population-based sample of 1,644 individuals with type 2 diabetes and 1,879 control subjects (the Nord-Trøndelag Health Study [HUNT] 2). We combined our data with all previously published case/control studies and performed a meta-analysis. RESULTS Consistent with initial studies, we found a trend toward association for the SNPs rs1884613 (odds ratio [OR] 1.17 [95% CI 1.03-1.35]) and rs2144908 (1.21 [1.05-1.38]) in the P2 region and for rs4812831 (1.21 [1.02-1.44]), located 34 kb downstream of the P2 promoter. Meta-analysis, comprising 12,292 type 2 diabetic case and 15,519 control subjects, revealed a nonsignificant OR of 1.05 (95% CI 0.98-1.12) but with significant heterogeneity between the populations. We therefore performed a subanalysis including only the data for subjects from Scandinavia. Among the 4,000 case and 7,571 control Scandinavian subjects, a pooled OR of 1.14 (1.06-1.23), P = 0.0004, was found for the SNP rs1884613. CONCLUSIONS Our results suggest that variation in the HNF4A region is associated with type 2 diabetes in Scandinavians, highlighting the importance of exploring small genetic effects in large, homogenous populations.
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Affiliation(s)
- Stefan Johansson
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
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27
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Rampersaud E, Damcott CM, Fu M, Shen H, McArdle P, Shi X, Shelton J, Yin J, Chang YPC, Ott SH, Zhang L, Zhao Y, Mitchell BD, O'Connell J, Shuldiner AR. Identification of novel candidate genes for type 2 diabetes from a genome-wide association scan in the Old Order Amish: evidence for replication from diabetes-related quantitative traits and from independent populations. Diabetes 2007; 56:3053-62. [PMID: 17846126 DOI: 10.2337/db07-0457] [Citation(s) in RCA: 143] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
OBJECTIVE We sought to identify type 2 diabetes susceptibility genes through a genome-wide association scan (GWAS) in the Amish. RESEARCH DESIGN AND METHODS DNA from 124 type 2 diabetic case subjects and 295 control subjects with normal glucose tolerance were genotyped on the Affymetrix 100K single nucleotide polymorphism (SNP) array. A total of 82,485 SNPs were tested for association with type 2 diabetes. Type 2 diabetes-associated SNPs were further prioritized by the following: 1) associations with 5 oral glucose tolerance test (OGTT) traits in 427 nondiabetic Amish subjects, and 2) in silico replication from three independent 100L SNP GWASs (Framingham Heart Study Caucasians, Pima Indians, and Mexican Americans) and a 500K GWAS in Scandinavians. RESULTS The strongest association (P = 1.07 x 10(-5)) was for rs2237457, which is located in growth factor receptor-bound protein 10 (Grb10), an adaptor protein that regulate insulin receptor signaling. rs2237457 was also strongly associated with OGTT glucose area under the curve in nondiabetic subjects (P = 0.001). Of the 1,093 SNPs associated with type 2 diabetes at P < 0.01, 67 SNPs demonstrated associations with at least one OGTT trait in nondiabetic individuals; 80 SNPs were nominally associated with type 2 diabetes in one of the three independent 100K GWASs, 3 SNPs (rs2540317 in MFSD9, rs10515353 on chromosome 5, and rs2242400 in BCAT1 were associated with type 2 diabetes in more than one population), and 11 SNPs were nominally associated with type 2 diabetes in Scandinavians. One type 2 diabetes-associated SNP (rs3845971, located in FHIT) showed replication with OGTT traits and also in another population. CONCLUSIONS Our GWAS of type 2 diabetes identified several gene variants associated with type 2 diabetes, some of which are worthy of further study.
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Affiliation(s)
- Evadnie Rampersaud
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, 660 West Redwood St., Room 494, Baltimore, MD 21201, USA
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28
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Abstract
PURPOSE OF REVIEW Variants in the hepatocyte nuclear factor 4alpha (HNF4A) gene play a role in the development of diabetes mellitus. Although genetic variation in and around HNF4A regulatory regions has received considerable attention, the significance of these variants in the common type 2 diabetes varies in the literature. This review will provide a general overview of recent genetic studies involving the evaluation of HNF4A as a contributor to the risk and pathophysiology of diabetes mellitus and related risk factors. RECENT FINDINGS These studies report newly identified variants, evaluate previously reported polymorphisms that were associated with type 2 diabetes in several distinct populations with maturity-onset diabetes of the young, type 2 diabetes, gestational diabetes, and diabetes related risk factors, and propose a role for HNF4A in insulin secretion via the potassium ATP channel. SUMMARY HNF4A variants identified so far appear to modestly contribute to predisposition for type 2 diabetes. Continued identification and especially functional characterization of variants, however, will be critical in future studies to enhance our understanding of the metabolic impact of this gene.
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Affiliation(s)
- Latisha Love-Gregory
- Nutritional Sciences, Endocrinology, Metabolism and Lipid Research, Department of Medicine, Washington University School of Medicine, St Louis, Missouri 63110, USA
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29
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Watanabe RM, Black MH, Xiang AH, Allayee H, Lawrence JM, Buchanan TA. Genetics of gestational diabetes mellitus and type 2 diabetes. Diabetes Care 2007; 30 Suppl 2:S134-40. [PMID: 17596461 PMCID: PMC2925642 DOI: 10.2337/dc07-s205] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Richard M Watanabe
- Department of Preventive Medicine, Keck School of Medicine of USC, Los Angeles, CA 90089-9011, USA.
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30
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Abstract
Diabetes mellitus is widely recognized as one of the leading causes of death and disability. While insulin insensitivity is an early phenomenon partly related to obesity, pancreatic beta-cell function declines gradually over time even before the onset of clinical hyperglycemia. Several mechanisms have been proposed to be responsible for insulin resistance, including increased non-esterified fatty acids, inflammatory cytokines, adipokines, and mitochondrial dysfunction, as well as glucotoxicity, lipotoxicity, and amyloid formation for beta-cell dysfunction. Moreover, the disease has a strong genetic component, although only a handful of genes have been identified so far. Diabetic management includes diet, exercise and combinations of antihyperglycemic drug treatment with lipid-lowering, antihypertensive, and antiplatelet therapy. Since many persons with type 2 diabetes are insulin resistant and overweight, nutrition therapy often begins with lifestyle strategies to reduce energy intake and increase energy expenditure through physical activity. These strategies should be implemented as soon as diabetes or impaired glucose homoeostasis (pre-diabetes) is diagnosed.
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Affiliation(s)
- George V Z Dedoussis
- Department of Nutrition and Dietetics, Harokopio University of Athens, 70 El. Venizelou Str., 17671 Kallithea-Athens, Greece
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31
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Rahib L, MacLennan NK, Horvath S, Liao JC, Dipple KM. Glycerol kinase deficiency alters expression of genes involved in lipid metabolism, carbohydrate metabolism, and insulin signaling. Eur J Hum Genet 2007; 15:646-57. [PMID: 17406644 DOI: 10.1038/sj.ejhg.5201801] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Glycerol kinase (GK) is at the interface of fat and carbohydrate metabolism and has been implicated in insulin resistance and type 2 diabetes mellitus. To define GK's role in insulin resistance, we examined gene expression in brown adipose tissue in a glycerol kinase knockout (KO) mouse model using microarray analysis. Global gene expression profiles of KO mice were distinct from wild type with 668 differentially expressed genes. These include genes involved in lipid metabolism, carbohydrate metabolism, insulin signaling, and insulin resistance. Real-time polymerase chain reaction analysis confirmed the differential expression of selected genes involved in lipid and carbohydrate metabolism. PathwayAssist analysis confirmed direct and indirect connections between glycerol kinase and genes in lipid metabolism, carbohydrate metabolism, insulin signaling, and insulin resistance. Network component analysis (NCA) showed that the transcription factors (TFs) PPAR-gamma, SREBP-1, SREBP-2, STAT3, STAT5, SP1, CEBPalpha, CREB, GR and PPAR-alpha have altered activity in the KO mice. NCA also revealed the individual contribution of these TFs on the expression of genes altered in the microarray data. This study elucidates the complex network of glycerol kinase and further confirms a possible role for glycerol kinase deficiency, a simple Mendelian disorder, in insulin resistance, and type 2 diabetes mellitus, a common complex genetic disorder.
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Affiliation(s)
- Lola Rahib
- Biomedical Engineering, Interdepartmental Program, Henry Samueli School of Engineering and Applied Science at UCLA, Los Angeles, CA 90095, USA
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32
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Winckler W, Weedon MN, Graham RR, McCarroll SA, Purcell S, Almgren P, Tuomi T, Gaudet D, Boström KB, Walker M, Hitman G, Hattersley AT, McCarthy MI, Ardlie KG, Hirschhorn JN, Daly MJ, Frayling TM, Groop L, Altshuler D. Evaluation of common variants in the six known maturity-onset diabetes of the young (MODY) genes for association with type 2 diabetes. Diabetes 2007; 56:685-93. [PMID: 17327436 DOI: 10.2337/db06-0202] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
An important question in human genetics is the extent to which genes causing monogenic forms of disease harbor common variants that may contribute to the more typical form of that disease. We aimed to comprehensively evaluate the extent to which common variation in the six known maturity-onset diabetes of the young (MODY) genes, which cause a monogenic form of type 2 diabetes, is associated with type 2 diabetes. Specifically, we determined patterns of common sequence variation in the genes encoding Gck, Ipf1, Tcf2, and NeuroD1 (MODY2 and MODY4-MODY6, respectively), selected a comprehensive set of 107 tag single nucleotide polymorphisms (SNPs) that captured common variation, and genotyped each in 4,206 patients and control subjects from Sweden, Finland, and Canada (including family-based studies and unrelated case-control subjects). All SNPs with a nominal P value <0.1 for association to type 2 diabetes in this initial screen were then genotyped in an additional 4,470 subjects from North America and Poland. Of 30 nominally significant SNPs from the initial sample, 8 achieved consistent results in the replication sample. We found the strongest effect at rs757210 in intron 2 of TCF2, with corrected P values <0.01 for an odds ratio (OR) of 1.13. This association was observed again in an independent sample of 5,891 unrelated case and control subjects and 500 families from the U.K., for an overall OR of 1.12 and a P value <10(-6) in >15,000 samples. We combined these results with our previous studies on HNF4alpha and TCF1 and explicitly tested for gene-gene interactions among these variants and with several known type 2 diabetes susceptibility loci, and we found no genetic interactions between these six genes. We conclude that although rare variants in these six genes explain most cases of MODY, common variants in these same genes contribute very modestly, if at all, to the common form of type 2 diabetes.
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Affiliation(s)
- Wendy Winckler
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
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33
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Lehman DM, Richardson DK, Jenkinson CP, Hunt KJ, Dyer TD, Leach RJ, Arya R, Abboud HE, Blangero J, Duggirala R, Stern MP. P2 promoter variants of the hepatocyte nuclear factor 4alpha gene are associated with type 2 diabetes in Mexican Americans. Diabetes 2007; 56:513-7. [PMID: 17259399 DOI: 10.2337/db06-0881] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Common and rare variants of the hepatocyte nuclear factor 4alpha (HNF4A) gene have been associated with type 2 diabetes and related traits in several populations suggesting the involvement of this transcription factor in diabetes pathogenesis. Single nucleotide polymorphisms (SNPs) within a large haplotype block surrounding the alternate P2 promoter, located approximately 45 kb upstream from the coding region, have been investigated in several populations of varying ethnicity with inconsistent results. Additionally, SNPs located within the P1 promoter and coding region have also been inconsistently associated with type 2 diabetes. Characterization of variation across this gene region in Mexican-American populations has not been reported. We therefore examined polymorphisms across the HNF4A gene in a cohort of Mexican-American pedigrees and assessed their association with type 2 diabetes. We observed evidence for association of SNPs in the P2 promoter region with type 2 diabetes (P = 0.003) and its age at diagnosis (P = 0.003). The risk allele frequency (53%) was intermediate to that reported in Caucasian populations (20-27%) and Pima Indians (83%). No other SNPs were associated with either trait. These results support the possibility that a variant in the P2 promoter region of HNF4A, or variants in linkage disequilibrium within this region, contributes to susceptibility to type 2 diabetes in many ethnic populations including Mexican Americans.
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Affiliation(s)
- Donna M Lehman
- Department of Medicine/Clinical Epidemiology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA.
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34
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Harries LW. Alternate mRNA processing of the hepatocyte nuclear factor genes and its role in monogenic diabetes. Expert Rev Endocrinol Metab 2006; 1:715-726. [PMID: 30754156 DOI: 10.1586/17446651.1.6.715] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Variation in mRNA processing has the capacity to exert fine control over gene expression in most cell types. The hepatic nuclear factor genes, like approximately 74% of the genome, produce multiple transcripts. Hepatic nuclear factor isoforms exhibit both spatial and temporal variation in expression. In this review, the known isoforms of the hepatocyte nuclear factor-1α, hepatocyte nuclear factor-1β and hepatocyte nuclear factor-4α genes are described and their properties are compared. Finally, data are discussed regarding the influence of hepatocyte nuclear factor-1α alternate mRNA processing on the clinical phenotype of maturity-onset diabetes of the young.
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Affiliation(s)
- Lorna W Harries
- a RCUK Diabetes and Metabolism Academic Fellow, Institute of Biomedical and Clinical Sciences, Peninsula Medical School, Barrack Road, Exeter, EX2 5DW, UK.
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35
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Bonnycastle LL, Willer CJ, Conneely KN, Jackson AU, Burrill CP, Watanabe RM, Chines PS, Narisu N, Scott LJ, Enloe ST, Swift AJ, Duren WL, Stringham HM, Erdos MR, Riebow NL, Buchanan TA, Valle TT, Tuomilehto J, Bergman RN, Mohlke KL, Boehnke M, Collins FS. Common variants in maturity-onset diabetes of the young genes contribute to risk of type 2 diabetes in Finns. Diabetes 2006; 55:2534-40. [PMID: 16936201 DOI: 10.2337/db06-0178] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Prior reports have suggested that variants in the genes for maturity-onset diabetes of the young (MODY) may confer susceptibility to type 2 diabetes, but results have been conflicting and coverage of the MODY genes has been incomplete. To complement our previous studies of HNF4A, we examined the other five known MODY genes for association with type 2 diabetes in Finnish individuals. For each of the five genes, we selected 1) nonredundant single nucleotide polymorphisms (SNPs) (r(2)< 0.8 with other SNPs) from the HapMap database or another linkage disequilibrium map, 2) SNPs with previously reported type 2 diabetes association, and 3) nonsynonymous coding SNPs. We tested 128 SNPs for association with type 2 diabetes in 786 index cases from type 2 diabetic families and 619 normal glucose-tolerant control subjects. We followed up 35 of the most significant SNPs by genotyping them on another 384 case subjects and 366 control subjects from Finland. We also supplemented our previous HNF4A results by genotyping 12 SNPs on additional Finnish samples. After correcting for testing multiple correlated SNPs within a gene, we find evidence of type 2 diabetes association with SNPs in five of the six known MODY genes: GCK, HNF1A, HNF1B, NEUROD1, and HNF4A. Our data suggest that common variants in several MODY genes play a modest role in type 2 diabetes susceptibility.
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Affiliation(s)
- Lori L Bonnycastle
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892-2152, USA
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36
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Andrulionyte L, Laukkanen O, Chiasson JL, Laakso M. Single nucleotide polymorphisms of the HNF4alpha gene are associated with the conversion to type 2 diabetes mellitus: the STOP-NIDDM trial. J Mol Med (Berl) 2006; 84:701-8. [PMID: 16838170 DOI: 10.1007/s00109-006-0063-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2005] [Accepted: 02/22/2006] [Indexed: 10/24/2022]
Abstract
Hepatocyte nuclear factor 4alpha (HNF4alpha) is a transcription factor, which is necessary for normal function of human liver and pancreatic islets. We investigated whether single nucleotide polymorphisms (SNPs) of HNF4A, encoding HNF4alpha, influenced the conversion from impaired glucose tolerance (IGT) to type 2 diabetes mellitus in subjects of the STOP-NIDDM trial. This trial aimed at evaluating the effect of acarbose compared to placebo in the prevention of type 2 diabetes mellitus. Eight SNPs covering the intragenic and alternate P2 promoter regions of HNF4A were genotyped in study samples using the TaqMan Allelic Discrimination Assays. Three SNPs in the P2 promoter region (rs4810424, rs1884614, and rs2144908) were in almost complete association (D'>0.97, r (2)>0.95) and, therefore, only rs4810424 was included in further analyses. Female carriers of the less frequent C allele of rs4810424 had a 1.7-fold elevated risk [95% confidence interval (CI) 1.09-2.66; P=0.020] for the conversion to diabetes compared to women with the common genotype after the adjustment for age, treatment group (placebo or acarbose), smoking, weight at baseline, and weight change. No association was found in men. Haplotype analysis based on three SNPs (rs4810424, rs2071197, and rs3818247) representing the linkage disequilibrium blocks in our study population indicated that the conversion to type 2 diabetes mellitus was dependent on the number of risk alleles in different haplotypes in women. Our results suggest that SNPs of HNF4A and their haplotypes predispose to type 2 diabetes mellitus in female subjects of the STOP-NIDDM study population.
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Huang QY, Cheng MR, Ji SL. Linkage and Association Studies of the Susceptibility Genes for Type 2 Diabetes. ACTA ACUST UNITED AC 2006; 33:573-89. [PMID: 16875315 DOI: 10.1016/s0379-4172(06)60087-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Type 2 diabetes mellitus (T2DM) is a complex disease characterized by hyperglycemia, insulin resistance, and impaired insulin secretion. T2DM is under strong genetic control. Identification and characterization of genes involved in determining T2DM will contribute to a greater understanding of the pathogenesis of T2DM, and ultimately might lead to the development of better diagnosis, prevention and treatment strategies. Efforts to identify T2DM susceptibility genes have focused on candidate gene approach (association studies) and genome-wide scans (linkage analyses). In this article, we review the current status for mapping and identification of genes for T2DM, with a focus on some promising regions (or genes) and future prospects.
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Affiliation(s)
- Qing-Yang Huang
- College of Life Science, Central China Normal University, Wuhan 430079, China.
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38
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Weissglas-Volkov D, Huertas-Vazquez A, Suviolahti E, Lee J, Plaisier C, Canizales-Quinteros S, Tusie-Luna T, Aguilar-Salinas C, Taskinen MR, Pajukanta P. Common hepatic nuclear factor-4alpha variants are associated with high serum lipid levels and the metabolic syndrome. Diabetes 2006; 55:1970-7. [PMID: 16804065 DOI: 10.2337/db06-0035] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Hepatic nuclear factor-4alpha (HNF-4alpha), a transcription factor involved in the regulation of serum lipid and glucose levels, has recently been associated with type 2 diabetes. The HNF-4alpha gene (HNF4A) resides on chromosome 20q12-q13.1, which, in addition to type 2 diabetes, has also previously been linked to high triglycerides in Finnish familial combined hyperlipidemia (FCHL) families. FCHL, characterized by elevated levels of serum total cholesterol, triglycerides, or both, is a common dyslipidemia observed in up to 20% of patients with premature coronary heart disease. Considering the clear phenotypic overlap between type 2 diabetes and FCHL, both predisposing to high serum triglycerides and glucose intolerance, we tested this gene for association in dyslipidemic families originating from two distinct populations, Finnish and Mexican, and comprising 1,447 subjects. Our data show that common HNF4A variants and haplotypes are associated with elevated serum lipid levels and the metabolic syndrome (P = 0.008-0.04), as well as with elevated glucose parameters (P = 0.008-0.03), using family-based association analysis. Importantly, both Finnish and Mexican families shared two common lipid-associated HNF4A haplotypes (P = 0.005 for total cholesterol and 0.006 for triglycerides). In conclusion, we show for the first time that common HNF4A variants are associated with high serum lipid levels and the metabolic syndrome.
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Affiliation(s)
- Daphna Weissglas-Volkov
- UCLA, Department of Human Genetics, Gonda Neuroscience and Genetics Research Center, 695 Charles E. Young Dr. South, Los Angeles, CA 90095-7088, USA
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39
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Raeder H, Bjørkhaug L, Johansson S, Mangseth K, Sagen JV, Hunting A, Følling I, Johansen O, Bjørgaas M, Paus PN, Søvik O, Molven A, Njølstad PR. A hepatocyte nuclear factor-4 alpha gene (HNF4A) P2 promoter haplotype linked with late-onset diabetes: studies of HNF4A variants in the Norwegian MODY registry. Diabetes 2006; 55:1899-903. [PMID: 16731861 DOI: 10.2337/db05-1677] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Variants in hepatocyte nuclear factor (HNF)-4alpha cause maturity-onset diabetes of the young, type 1 (MODY1) and may also be risk factors for type 2 diabetes. We sequenced the HNF4A gene of 95 MODY3-negative probands from the Norwegian MODY Registry. We found three novel coding variants in exon 8 of HNF4A: G326R, T339I, and W340X. In intron 7, we noted a single nucleotide polymorphism in the binding site of a previously published primer pair, which in some cases caused allelic drop out when amplifying exon 8. We also detected two novel sequence variants of the P2 promoter region, of which P2 -192C>G showed linkage with diabetes in two families (maximal logarithm of odds score of 3.1 and 0.8, respectively). This variant and a surrounding haplotype restricted by 3.7 Mb was also found in two Danish MODY pedigrees. The age of onset was higher in the P2 -192C>G carriers (median 45 years) compared with that reported for other MODY1 individuals. We could not support a biological role of the P2 promoter variant by in vitro transfection assays. In conclusion, we have identified three novel HNF4A mutations and a 3.7-Mb haplotype, including the HNF4A P2 promoter, which was linked with diabetes.
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Affiliation(s)
- Helge Raeder
- Section for Pediatrics, Department of Clinical Medicine, University of Bergen, N-5020 Bergen, Norway
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Ek J, Hansen SP, Lajer M, Nicot C, Boesgaard TW, Pruhova S, Johansen A, Albrechtsen A, Yderstraede K, Lauenborg J, Parrizas M, Boj SF, Jørgensen T, Borch-Johnsen K, Damm P, Ferrer J, Lebl J, Pedersen O, Hansen T. A novel -192c/g mutation in the proximal P2 promoter of the hepatocyte nuclear factor-4 alpha gene (HNF4A) associates with late-onset diabetes. Diabetes 2006; 55:1869-73. [PMID: 16731855 DOI: 10.2337/db05-1684] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Recently, it has been shown that mutations in the P2 promoter of the hepatocyte nuclear factor (HNF)-4 alpha gene (HNF4A) cause maturity-onset diabetes of the young (MODY), while single nucleotide polymorphisms in this locus are associated with type 2 diabetes. In this study, we examined 1,189 bp of the P2 promoter and the associated exon 1D of HNF4A for variations associated with diabetes in 114 patients with type 2 diabetes, 72 MODYX probands, and 85 women with previous gestational diabetes mellitus. A -192c/g mutation was found in five patients. We screened 1,587 diabetic subjects and 4,812 glucose-tolerant subjects for the -192c/g mutation and identified 5 diabetic and 1 glucose-tolerant mutation carriers (P=0.004). Examination of the families showed that carriers of the -192c/g mutation had a significantly impaired glucose-stimulated insulin release and lower levels of serum total cholesterol compared with matched control subjects. Furthermore, the mutation disrupted the binding of an unidentified sequence-specific DNA binding complex present in human islet extracts. Also, two novel linked polymorphisms in the P2 promoter at positions -1107g/t and -858c/t were identified. These variants were not significantly associated with type 2 diabetes or any pre-diabetic traits. In conclusion, a rare, novel mutation that disrupts a protein binding site in the pancreatic HNF4A promoter associates with late-onset diabetes.
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Affiliation(s)
- Jakob Ek
- Steno Diabetes Center and Hagedorn Research Institute, Gentofte, Denmark
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Hara K, Horikoshi M, Kitazato H, Ito C, Noda M, Ohashi J, Froguel P, Tokunaga K, Tobe K, Nagai R, Kadowaki T. Hepatocyte nuclear factor-4alpha P2 promoter haplotypes are associated with type 2 diabetes in the Japanese population. Diabetes 2006; 55:1260-4. [PMID: 16644680 DOI: 10.2337/db05-0620] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Hepatocyte nuclear factor (HNF)-4alpha is a transcription factor known as a key molecule in the development and functions of the beta-cells. In a previously performed genome-wide scan of Japanese type 2 diabetic sibpairs, we observed linkage of type 2 diabetes to chromosome 20q12-q13, a region in which the HNF4A gene is located. Recent studies have reported associations between type 2 diabetes and polymorphisms in the P2 promoter region specific to beta-cells. In this study, we attempted to assess whether the HNF4A gene plays a role in the genetic susceptibility to type 2 diabetes in the Japanese population by analyzing polymorphisms and haplotypes of the HNF4A gene. Linkage disequilibrium across the P2 promoter region was preserved in the Japanese population, consistent with previous reports. Although none of the individual polymorphisms examined showed any significant association with type 2 diabetes, we found very strong evidence of the association between type 2 diabetes and the haplotype consisting of two polymorphisms in the P2 promoter region of the HNF4A gene (P = 3.82 x 10(-4)). In contrast, there was no association between type 2 diabetes and haplotypes consisting of polymorphisms not located in the P2 promoter region, suggesting that the type 2 diabetes susceptibility loci are localized in the P2 promoter region of the HNF4A gene. The association was replicated using two additional cohorts (P = 1.51 x 10(-4) and 0.019, respectively). The results of the present analysis revealed that the HNF4A gene might be a type 2 diabetes susceptibility gene common to different ethnic groups. The study also suggested the possible existence of an as-yet-unidentified but functional polymorphism in the P2 promoter region of the HNF4A gene that directly influences susceptibility to type 2 diabetes.
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Affiliation(s)
- Kazuo Hara
- Department of Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
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Abstract
Type 2 Diabetes results from a complex physiologic process that includes the pancreatic beta cells, peripheral glucose uptake in muscle, the secretion of multiple cytokines and hormone-like molecules from adipocytes, hepatic glucose production, and likely the central nervous system. Consistent with the complex web of physiologic defects, the emerging picture of the genetics will involve a large number of risk susceptibility genes, each individually with relatively small effect (odds ratios below 1.2 in most cases). The challenge for the future will include cataloging and confirming the genetic risk factors, and understanding how these risk factors interact with each other and with the known environmental and lifestyle risk factors that increase the propensity to type 2 diabetes.
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Affiliation(s)
- Swapan Kumar Das
- University of Arkansas for Medical Sciences and Central Arkansas Veterans Healthcare System, Little Rock, Arkansas
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Abstract
PURPOSE OF REVIEW Familial combined hyperlipidemia is a common complex disease that accounts for up to 20% of premature coronary heart disease. The upstream transcription factor 1, located on 1q21, was recently shown to be linked and associated with familial combined hyperlipidemia in Finnish families. Upstream transcription factor 1 is the first gene identified by positional cloning for familial combined hyperlipidemia. Replication studies are critical to investigation of complex diseases because only they can verify the importance of the original findings. We review recent studies that examine the genetic contribution and functional consequence of upstream transcription factor 1 variants to familial combined hyperlipidemia and type 2 diabetes mellitus. Aiming beyond upstream transcription factor 1, we also evaluate novel strategies that have made it possible to globally examine the genome and the transcriptome. RECENT FINDINGS Three independent studies support the role of upstream transcription factor 1 in familial combined hyperlipidemia. The results for type 2 diabetes mellitus and the metabolic syndrome have been less conclusive highlight novel strategies for gene identification in familial combined hyperlipidemia. SUMMARY Currently, genetic and functional evidence is supportive of a role for upstream transcription factor 1 in the etiology of familial combined hyperlipidemia and its component traits, although the mechanism of causality still remains largely unknown.
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Affiliation(s)
- Jenny C Lee
- Department of Human Genetics bDepartment of Medicine/Division of Cardiology, University of California Los Angeles, Los Angeles, California 90095, USA
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44
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Abstract
Familial combined hyperlipidemia (FCHL) constitutes a substantial risk factor for atherosclerosis since it is observed in about 20% of coronary heart disease (CHD) patients under 60 years. FCHL, characterized by elevated levels of total cholesterol (TC) and triglycerides (TGs), or both, is also one of the most common familial hyperlipidemias with a prevalence of 1%-6% in Western populations. Numerous studies have been performed to identify genes contributing to FCHL. The recent linkage and association studies and their replications are beginning to elucidate the genetic variations underlying the susceptibility to FCHL. Three chromosomal regions on 1q21-23, 11p and 16q22-24.1 have been replicated in different study samples, offering targets for gene hunting. In addition, several candidate gene studies have replicated the influence of the lipoprotein lipase (LPL) gene and apolipoprotein A1/C3/A4/A5 (APOA1/C3/A4/A5) gene cluster in FCHL. Recently, the linked region on chromosome 1q21 was successfully fine-mapped and the upstream transcription factor 1 (USF1) gene identified as the underlying gene for FCHL. This finding has now been replicated in independent FCHL samples. However, the total number of variants, the risk related to each variant and their relative contributions to the disease susceptibility are not known yet.
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Affiliation(s)
- Elina Suviolahti
- Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA 90095-7088, USA
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Muller YL, Infante AM, Hanson RL, Love-Gregory L, Knowler W, Bogardus C, Baier LJ. Variants in hepatocyte nuclear factor 4alpha are modestly associated with type 2 diabetes in Pima Indians. Diabetes 2005; 54:3035-9. [PMID: 16186411 PMCID: PMC1351112 DOI: 10.2337/diabetes.54.10.3035] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Single nucleotide polymorphisms (SNPs) within the hepatocyte nuclear factor 4alpha (HNF4alpha) gene are associated with type 2 diabetes in Finns and Ashkenazi Jews. Previous studies in both populations have reported linkage to type 2 diabetes near the HNF4alpha locus on chromosome 20q12-13. To investigate whether HNF4alpha is a diabetes susceptibility gene in Pima Indians, a population with the highest reported prevalence of type 2 diabetes but with no evidence for linkage of the disease on chromosome 20q, 19 SNPs across the promoter and coding region of HNF4alpha were genotyped for association analysis. In a group of 1,037 Pima Indians (573 diabetic and 464 nondiabetic subjects), three SNPs in HNF4alpha (rs3212183 and rs2071197 located in introns 3 and 1, respectively, and rs6031558, an extremely rare SNP located in the P2 promoter region) were modestly associated with type 2 diabetes (rs3212183 odds ratio [OR] 1.34 [95% CI 1.07-1.67], P = 0.009; rs2071197 1.34 [1.07-1.66], P = 0.008; and rs6031558 3.18 [1.03-9.84], P = 0.04, adjusted for age, sex, birth year, heritage, and family membership). We conclude that variants in HNF4alpha do not appear to be major determinants for type 2 diabetes in Pima Indians; however, HNF4alpha may have a minor role in type 2 diabetes susceptibility within this Native American population.
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Affiliation(s)
- Yunhua Li Muller
- From the Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Phoenix, Arizona; and
| | - Aniello M. Infante
- From the Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Phoenix, Arizona; and
| | - Robert L. Hanson
- From the Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Phoenix, Arizona; and
| | | | - William Knowler
- From the Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Phoenix, Arizona; and
| | - Clifton Bogardus
- From the Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Phoenix, Arizona; and
| | - Leslie J. Baier
- From the Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Phoenix, Arizona; and
- Address correspondence and reprint requests to Leslie Baier, PhD, Clinical Diabetes and Nutrition Section, NIDDK, NIH, 4212 N. 16th St., Phoenix, AZ 85016. E-mail:
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Current literature in diabetes. Diabetes Metab Res Rev 2005; 21:475-82. [PMID: 16114072 DOI: 10.1002/dmrr.587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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47
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Mohlke KL, Skol AD, Scott LJ, Valle TT, Bergman RN, Tuomilehto J, Boehnke M, Collins FS. Evaluation of SLC2A10 (GLUT10) as a candidate gene for type 2 diabetes and related traits in Finns. Mol Genet Metab 2005; 85:323-7. [PMID: 15936967 DOI: 10.1016/j.ymgme.2005.04.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2005] [Revised: 04/16/2005] [Accepted: 04/19/2005] [Indexed: 12/21/2022]
Abstract
The SLC2A10 gene encodes a glucose transporter and is located on chromosome 20q13, where evidence has been found for linkage to type 2 diabetes (T2D) in multiple studies. We investigated SLC2A10 as a T2D candidate gene in Finns. We did not confirm the previously reported association between Ala206Thr and fasting insulin and we observed no statistically significant evidence for T2D association with any single marker. We tested haplotypes for association with diabetes-related traits and observed no excess of significant results.
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Affiliation(s)
- Karen L Mohlke
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, MD, USA.
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Abstract
Genes influence susceptibility to type 2 diabetes mellitus (T2DM), and both positional cloning and candidate gene approaches have been used to identify these genes. Linkage analysis has generated evidence for T2DM-predisposing variants on chromosome 20q in studies of Caucasians, Asians, and Africans, and fine-mapping recently identified a likely susceptibility gene, hepatocyte nuclear factor 4-alpha (HNF4A). Rare loss-of-function mutations in HNF4A cause maturity-onset diabetes of the young and now common noncoding variants have been found to be associated with T2DM.
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Affiliation(s)
- Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599-7264, USA.
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