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Hawes E, Claxton D, Oeser J, O’Brien R. Identification of structural motifs critical for human G6PC2 function informed by sequence analysis and an AlphaFold2-predicted model. Biosci Rep 2024; 44:BSR20231851. [PMID: 38095063 PMCID: PMC10776900 DOI: 10.1042/bsr20231851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/22/2023] [Accepted: 12/12/2023] [Indexed: 01/10/2024] Open
Abstract
G6PC2 encodes a glucose-6-phosphatase (G6Pase) catalytic subunit, primarily expressed in pancreatic islet β cells, which modulates the sensitivity of insulin secretion to glucose and thereby regulates fasting blood glucose (FBG). Mutational analyses were conducted to validate an AlphaFold2 (AF2)-predicted structure of human G6PC2 in conjunction with a novel method to solubilize and purify human G6PC2 from a heterologous expression system. These analyses show that residues forming a predicted intramolecular disulfide bond are essential for G6PC2 expression and that residues forming part of a type 2 phosphatidic acid phosphatase (PAP2) motif are critical for enzyme activity. Additional mutagenesis shows that residues forming a predicted substrate cavity modulate enzyme activity and substrate specificity and residues forming a putative cholesterol recognition amino acid consensus (CRAC) motif influence protein expression or enzyme activity. This CRAC motif begins at residue 219, the site of a common G6PC2 non-synonymous single-nucleotide polymorphism (SNP), rs492594 (Val219Leu), though the functional impact of this SNP is disputed. In microsomal membrane preparations, the L219 variant has greater activity than the V219 variant, but this difference disappears when G6PC2 is purified in detergent micelles. We hypothesize that this was due to a differential association of the two variants with cholesterol. This concept was supported by the observation that the addition of cholesteryl hemi-succinate to the purified enzymes decreased the Vmax of the V219 and L219 variants ∼8-fold and ∼3 fold, respectively. We anticipate that these observations should support the rational development of G6PC2 inhibitors designed to lower FBG.
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Affiliation(s)
- Emily M. Hawes
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, U.S.A
| | - Derek P. Claxton
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, U.S.A
| | - James K. Oeser
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, U.S.A
| | - Richard M. O’Brien
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, U.S.A
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Keller MP, Hawes EM, Schueler KL, Stapleton DS, Mitok KA, Simonett SP, Oeser JK, Sampson LL, Attie AD, Magnuson MA, O’Brien RM. An Enhancer Within Abcb11 Regulates G6pc2 in C57BL/6 Mouse Pancreatic Islets. Diabetes 2023; 72:1621-1628. [PMID: 37552875 PMCID: PMC10588275 DOI: 10.2337/db23-0215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 08/01/2023] [Indexed: 08/10/2023]
Abstract
G6PC2 is predominantly expressed in pancreatic islet β-cells where it encodes a glucose-6-phosphatase catalytic subunit that modulates the sensitivity of insulin secretion to glucose by opposing the action of glucokinase, thereby regulating fasting blood glucose (FBG). Prior studies have shown that the G6pc2 promoter alone is unable to confer sustained islet-specific gene expression in mice, suggesting the existence of distal enhancers that regulate G6pc2 expression. Using information from both mice and humans and knowledge that single nucleotide polymorphisms (SNPs) both within and near G6PC2 are associated with variations in FBG in humans, we identified several putative enhancers 3' of G6pc2. One region, herein referred to as enhancer I, resides in the 25th intron of Abcb11 and binds multiple islet-enriched transcription factors. CRISPR-mediated deletion of enhancer I in C57BL/6 mice had selective effects on the expression of genes near the G6pc2 locus. In isolated islets, G6pc2 and Spc25 expression were reduced ∼50%, and Gm13613 expression was abolished, whereas Cers6 and nostrin expression were unaffected. This partial reduction in G6pc2 expression enhanced islet insulin secretion at basal glucose concentrations but did not affect FBG or glucose tolerance in vivo, consistent with the absence of a phenotype in G6pc2 heterozygous C57BL/6 mice. ARTICLE HIGHLIGHTS
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Affiliation(s)
- Mark P. Keller
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI
| | - Emily M. Hawes
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN
| | | | | | - Kelly A. Mitok
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI
| | - Shane P. Simonett
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI
| | - James K. Oeser
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN
| | - Leesa L. Sampson
- Center for Stem Cell Biology, Vanderbilt University School of Medicine, Nashville, TN
| | - Alan D. Attie
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI
- Department of Chemistry, University of Wisconsin–Madison, Madison, WI
- Department of Medicine, University of Wisconsin–Madison, Madison, WI
| | - Mark A. Magnuson
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN
- Center for Stem Cell Biology, Vanderbilt University School of Medicine, Nashville, TN
| | - Richard M. O’Brien
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN
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Overway EM, Bosma KJ, Claxton DP, Oeser JK, Singh K, Breidenbach LB, Mchaourab HS, Davis LK, O'Brien RM. Nonsynonymous single-nucleotide polymorphisms in the G6PC2 gene affect protein expression, enzyme activity, and fasting blood glucose. J Biol Chem 2022; 298:101534. [PMID: 34954144 PMCID: PMC8800118 DOI: 10.1016/j.jbc.2021.101534] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 12/30/2022] Open
Abstract
G6PC2 encodes a glucose-6-phosphatase (G6Pase) catalytic subunit that modulates the sensitivity of insulin secretion to glucose and thereby regulates fasting blood glucose (FBG). A common single-nucleotide polymorphism (SNP) in G6PC2, rs560887 is an important determinant of human FBG variability. This SNP has a subtle effect on G6PC2 RNA splicing, which raises the question as to whether nonsynonymous SNPs with a major impact on G6PC2 stability or enzyme activity might have a broader disease/metabolic impact. Previous attempts to characterize such SNPs were limited by the very low inherent G6Pase activity and expression of G6PC2 protein in islet-derived cell lines. In this study, we describe the use of a plasmid vector that confers high G6PC2 protein expression in islet cells, allowing for a functional analysis of 22 nonsynonymous G6PC2 SNPs, 19 of which alter amino acids that are conserved in mouse G6PC2 and the human and mouse variants of the related G6PC1 isoform. We show that 16 of these SNPs markedly impair G6PC2 protein expression (>50% decrease). These SNPs have variable effects on the stability of human and mouse G6PC1, despite the high sequence homology between these isoforms. Four of the remaining six SNPs impaired G6PC2 enzyme activity. Electronic health record-derived phenotype analyses showed an association between high-impact SNPs and FBG, but not other diseases/metabolites. While homozygous G6pc2 deletion in mice increases the risk of hypoglycemia, these human data reveal no evidence that the beneficial use of partial G6PC2 inhibitors to lower FBG would be associated with unintended negative consequences.
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Affiliation(s)
- Emily M Overway
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Karin J Bosma
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Derek P Claxton
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - James K Oeser
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Kritika Singh
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Lindsay B Breidenbach
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Lea K Davis
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA; Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Richard M O'Brien
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.
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Bartolomé A. Stem Cell-Derived β Cells: A Versatile Research Platform to Interrogate the Genetic Basis of β Cell Dysfunction. Int J Mol Sci 2022; 23:501. [PMID: 35008927 PMCID: PMC8745644 DOI: 10.3390/ijms23010501] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/27/2021] [Accepted: 12/29/2021] [Indexed: 02/07/2023] Open
Abstract
Pancreatic β cell dysfunction is a central component of diabetes progression. During the last decades, the genetic basis of several monogenic forms of diabetes has been recognized. Genome-wide association studies (GWAS) have also facilitated the identification of common genetic variants associated with an increased risk of diabetes. These studies highlight the importance of impaired β cell function in all forms of diabetes. However, how most of these risk variants confer disease risk, remains unanswered. Understanding the specific contribution of genetic variants and the precise role of their molecular effectors is the next step toward developing treatments that target β cell dysfunction in the era of personalized medicine. Protocols that allow derivation of β cells from pluripotent stem cells, represent a powerful research tool that allows modeling of human development and versatile experimental designs that can be used to shed some light on diabetes pathophysiology. This article reviews different models to study the genetic basis of β cell dysfunction, focusing on the recent advances made possible by stem cell applications in the field of diabetes research.
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Affiliation(s)
- Alberto Bartolomé
- Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, 28029 Madrid, Spain
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Liu Y, He S, Zhou R, Zhang X, Yang S, Deng D, Zhang C, Yu X, Chen Y, Su Z. Nuclear Factor-Y in Mouse Pancreatic β-Cells Plays a Crucial Role in Glucose Homeostasis by Regulating β-Cell Mass and Insulin Secretion. Diabetes 2021; 70:1703-1716. [PMID: 33980692 DOI: 10.2337/db20-1238] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 05/06/2021] [Indexed: 02/05/2023]
Abstract
Pancreatic β-cell mass and insulin secretion are determined by the dynamic change of transcription factor expression levels in response to altered metabolic demand. Nuclear factor-Y (NF-Y) is an evolutionarily conserved transcription factor playing critical roles in multiple cellular processes. However, the physiological role of NF-Y in pancreatic β-cells is poorly understood. The current study was undertaken in a conditional knockout of Nf-ya specifically in pancreatic β-cells (Nf-ya βKO) to define the essential physiological role of NF-Y in β-cells. Nf-ya βKO mice exhibited glucose intolerance without changes in insulin sensitivity. Reduced β-cell proliferation resulting in decreased β-cell mass was observed in these mice, which was associated with disturbed actin cytoskeleton. NF-Y-deficient β-cells also exhibited impaired insulin secretion with a reduced Ca2+ influx in response to glucose, which was associated with an inefficient glucose uptake into β-cells due to a decreased expression of GLUT2 and a reduction in ATP production resulting from the disruption of mitochondrial integrity. This study is the first to show that NF-Y is critical for pancreatic islet homeostasis and function through regulation in β-cell proliferation, glucose uptake into β-cells, and mitochondrial energy metabolism. Modulating NF-Y expression in β-cells may therefore offer an attractive approach for therapeutic intervention.
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Affiliation(s)
- Yin Liu
- Molecular Medicine Research Center and National Clinical Research Center for Geriatrics, West China Hospital, and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Siyuan He
- Molecular Medicine Research Center and National Clinical Research Center for Geriatrics, West China Hospital, and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Ruixue Zhou
- Molecular Medicine Research Center and National Clinical Research Center for Geriatrics, West China Hospital, and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Xueping Zhang
- Molecular Medicine Research Center and National Clinical Research Center for Geriatrics, West China Hospital, and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Shanshan Yang
- Molecular Medicine Research Center and National Clinical Research Center for Geriatrics, West China Hospital, and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Dan Deng
- Molecular Medicine Research Center and National Clinical Research Center for Geriatrics, West China Hospital, and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Caixia Zhang
- Molecular Medicine Research Center and National Clinical Research Center for Geriatrics, West China Hospital, and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Xiaoqian Yu
- Molecular Medicine Research Center and National Clinical Research Center for Geriatrics, West China Hospital, and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Yulong Chen
- Molecular Medicine Research Center and National Clinical Research Center for Geriatrics, West China Hospital, and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Zhiguang Su
- Molecular Medicine Research Center and National Clinical Research Center for Geriatrics, West China Hospital, and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
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Wang Y, Yang S, Guan Q, Chen J, Zhang X, Zhang Y, Yuan Y, Su Z. Effects of Genetic Variants of Nuclear Receptor Y on the Risk of Type 2 Diabetes Mellitus. J Diabetes Res 2019; 2019:4902301. [PMID: 31205951 PMCID: PMC6530108 DOI: 10.1155/2019/4902301] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 03/04/2019] [Indexed: 02/05/2023] Open
Abstract
Nuclear factor-Y (NF-Y) consists of three evolutionary conserved subunits including NF-YA, NF-YB, and NF-YC; it is a critical transcriptional regulator of lipid and glucose metabolism and adipokine biosynthesis that are associated with type 2 diabetes mellitus (T2DM) occurrence, while the impacts of genetic variants in the NF-Y gene on the risk of T2DM remain to be investigated. In the present study, we screened five single-nucleotide polymorphisms (SNPs) with the SNaPshot method in 427 patients with T2DM and 408 healthy individuals. Subsequently, we analyzed the relationships between genotypes and haplotypes constructed from these SNPs with T2DM under diverse genetic models. Furthermore, we investigated the allele effects on the quantitative metabolic traits. Of the five tagSNPs, we found that three SNPs (rs2268188, rs6918969, and rs28869187) exhibited nominal significant differences in allelic or genotypic frequency between patients with T2DM and healthy individuals. The minor alleles G, C, and C at rs2268188, rs6918969, and rs28869187, respectively, conferred a higher T2DM risk under a dominant genetic model, and the carriers of these risk alleles (either homozygotes of the minor allele or heterozygotes) had statistically higher levels of fasting plasma glucose, cholesterol, and triglycerides. Haplotype analysis showed that SNPs rs2268188, rs6918969, rs28869187, and rs35105472 formed a haplotype block, and haplotype TTAC was protective against T2DM (OR = 0.76, 95% CI = 0.33-0.82, P = 0.004), while haplotype GCCG was associated with an elevated susceptibility to T2DM (OR = 2.33, 95% CI = 1.43-3.57, P = 0.001). This study is the first ever observation to our knowledge that indicates the genetic variants of NF-YA might influence a Chinese Han individual's occurrence of T2DM.
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Affiliation(s)
- Ying Wang
- Department of Geriatric Medicine and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Shanshan Yang
- Molecular Medicine Research Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Qiuyue Guan
- Department of Geriatrics, People's Hospital of Sichuan Province, Chengdu, 610041 Sichuan, China
| | - Jinglu Chen
- Molecular Medicine Research Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xueping Zhang
- Molecular Medicine Research Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yuwei Zhang
- Division of Endocrinology and Metabolism, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yiming Yuan
- Department of Geriatric Medicine and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Zhiguang Su
- Molecular Medicine Research Center, West China Hospital, Sichuan University, Chengdu 610041, China
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Jung SY, Mancuso N, Yu H, Papp J, Sobel E, Zhang ZF. Genome-Wide Meta-analysis of Gene-Environmental Interaction for Insulin Resistance Phenotypes and Breast Cancer Risk in Postmenopausal Women. Cancer Prev Res (Phila) 2019; 12:31-42. [PMID: 30327367 DOI: 10.1158/1940-6207.capr-18-0180] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 09/14/2018] [Accepted: 10/09/2018] [Indexed: 11/16/2022]
Abstract
Insulin resistance (IR)-related genetic variants are possibly associated with breast cancer, and the gene-phenotype-cancer association could be modified by lifestyle factors including obesity, physical inactivity, and high-fat diet. Using data from postmenopausal women, a population highly susceptible to obesity, IR, and increased risk of breast cancer, we implemented a genome-wide association study (GWAS) in two steps: (1) GWAS meta-analysis of gene-environmental (i.e., behavioral) interaction (G*E) for IR phenotypes (hyperglycemia, hyperinsulinemia, and homeostatic model assessment-insulin resistance) and (2) after the G*E GWAS meta-analysis, the identified SNPs were tested for their associations with breast cancer risk in overall or subgroup population, where the SNPs were identified at genome-wide significance. We found 58 loci (55 novel SNPs; 5 index SNPs and 6 SNPs, independent of each other) that are associated with IR phenotypes in women overall or women stratified by obesity, physical activity, and high-fat diet; among those 58 loci, 29 (26 new loci; 2 index SNPs and 2 SNPs, independently) were associated with postmenopausal breast cancer. Our study suggests that a number of newly identified SNPs may have their effects on glucose intolerance by interplaying with obesity and other lifestyle factors, and a substantial proportion of these SNPs' susceptibility can also interact with the lifestyle factors to ultimately influence breast cancer risk. These findings may contribute to improved prediction accuracy for cancer and suggest potential intervention strategies for those women carrying genetic risk that will reduce their breast cancer risk.
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Affiliation(s)
- Su Yon Jung
- Translational Sciences Section, Jonsson Comprehensive Cancer Center, School of Nursing, University of California, Los Angeles, Los Angeles, California.
| | - Nick Mancuso
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Herbert Yu
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii
| | - Jeanette Papp
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Eric Sobel
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Zuo-Feng Zhang
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, California
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Spracklen CN, Shi J, Vadlamudi S, Wu Y, Zou M, Raulerson CK, Davis JP, Zeynalzadeh M, Jackson K, Yuan W, Wang H, Shou W, Wang Y, Luo J, Lange LA, Lange EM, Popkin BM, Gordon-Larsen P, Du S, Huang W, Mohlke KL. Identification and functional analysis of glycemic trait loci in the China Health and Nutrition Survey. PLoS Genet 2018; 14:e1007275. [PMID: 29621232 PMCID: PMC5886383 DOI: 10.1371/journal.pgen.1007275] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 02/23/2018] [Indexed: 12/17/2022] Open
Abstract
To identify genetic contributions to type 2 diabetes (T2D) and related glycemic traits (fasting glucose, fasting insulin, and HbA1c), we conducted genome-wide association analyses (GWAS) in up to 7,178 Chinese subjects from nine provinces in the China Health and Nutrition Survey (CHNS). We examined patterns of population structure within CHNS and found that allele frequencies differed across provinces, consistent with genetic drift and population substructure. We further validated 32 previously described T2D- and glycemic trait-loci, including G6PC2 and SIX3-SIX2 associated with fasting glucose. At G6PC2, we replicated a known fasting glucose-associated variant (rs34177044) and identified a second signal (rs2232326), a low-frequency (4%), probably damaging missense variant (S324P). A variant within the lead fasting glucose-associated signal at SIX3-SIX2 co-localized with pancreatic islet expression quantitative trait loci (eQTL) for SIX3, SIX2, and three noncoding transcripts. To identify variants functionally responsible for the fasting glucose association at SIX3-SIX2, we tested five candidate variants for allelic differences in regulatory function. The rs12712928-C allele, associated with higher fasting glucose and lower transcript expression level, showed lower transcriptional activity in reporter assays and increased binding to GABP compared to the rs12712928-G, suggesting that rs12712928-C contributes to elevated fasting glucose levels by disrupting an islet enhancer, resulting in reduced gene expression. Taken together, these analyses identified multiple loci associated with glycemic traits across China, and suggest a regulatory mechanism at the SIX3-SIX2 fasting glucose GWAS locus.
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Affiliation(s)
- Cassandra N. Spracklen
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jinxiu Shi
- Department of Genetics, Shanghai-MOST Key Laboratory of Heath and Disease Genomics, Chinese National Human Genome Center and Shanghai Industrial Technology Institute, Shanghai, China
| | - Swarooparani Vadlamudi
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Ying Wu
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Meng Zou
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Chelsea K. Raulerson
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - James P. Davis
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Monica Zeynalzadeh
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Kayla Jackson
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Wentao Yuan
- Department of Genetics, Shanghai-MOST Key Laboratory of Heath and Disease Genomics, Chinese National Human Genome Center and Shanghai Industrial Technology Institute, Shanghai, China
| | - Haifeng Wang
- Department of Genetics, Shanghai-MOST Key Laboratory of Heath and Disease Genomics, Chinese National Human Genome Center and Shanghai Industrial Technology Institute, Shanghai, China
| | - Weihua Shou
- Department of Genetics, Shanghai-MOST Key Laboratory of Heath and Disease Genomics, Chinese National Human Genome Center and Shanghai Industrial Technology Institute, Shanghai, China
| | - Ying Wang
- Department of Genetics, Shanghai-MOST Key Laboratory of Heath and Disease Genomics, Chinese National Human Genome Center and Shanghai Industrial Technology Institute, Shanghai, China
| | - Jingchun Luo
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Leslie A. Lange
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Ethan M. Lange
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Barry M. Popkin
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Penny Gordon-Larsen
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Shufa Du
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Wei Huang
- Department of Genetics, Shanghai-MOST Key Laboratory of Heath and Disease Genomics, Chinese National Human Genome Center and Shanghai Industrial Technology Institute, Shanghai, China
| | - Karen L. Mohlke
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail:
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Lakbakbi El Yaagoubi F, Charoute H, Morjane I, Sefri H, Rouba H, Ainahi A, Kandil M, Benrahma H, Barakat A. Association analysis of genetic variants with metabolic syndrome components in the Moroccan population. Curr Res Transl Med 2017; 65:121-125. [DOI: 10.1016/j.retram.2017.08.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/17/2017] [Accepted: 08/09/2017] [Indexed: 12/17/2022]
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10
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Meta-analyses of the association of G6PC2 allele variants with elevated fasting glucose and type 2 diabetes. PLoS One 2017; 12:e0181232. [PMID: 28704540 PMCID: PMC5509327 DOI: 10.1371/journal.pone.0181232] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 06/28/2017] [Indexed: 12/19/2022] Open
Abstract
Objective To collectively evaluate the association of glucose-6-phosphatase catalytic unit 2 (G6PC2) allele variants with elevated fasting glucose (FG) and type 2 diabetes (T2D). Design Meta-analysis Data sources PubMed, Web of Knowledge and Embase databases. Study selection Full text articles of studies that identified an association of G6PC2 with T2D and elevated FG. Patient involvement There was no T2D patient involvement in the analyses on the association of FG with G6PC2, there were T2D patients and non-diabetes patient involvement in the analyses on the association of T2D with G6PC2. Statistical analysis Random-effects meta-analyses were used to calculate the pool effect sizes. I2 metric and H2 tests were used to calculate the heterogeneity. Begg's funnel plot and Egger’s linear regression test were done to assess publication bias. Results Of the 423 studies identified, 21 were eligible and included. Data on three loci (rs560887, rs16856187 and rs573225) were available. The G allele at rs560887 in three ethnicities, the C allele at rs16856187 and the A allele at rs573225 all had a positive association with elevated FG. Per increment of G allele at rs560887 and A allele at rs573225 resulted in a FG 0.070 mmol/l and 0.075 mmol/l higher (ß (95% CI) = 0.070 (0.060, 0.079), p = 4.635e-50 and 0.075 (0.065, 0.085), p = 5.856e-48, respectively). With regard to the relationship of rs16856187 and FG, an increase of 0.152 (95% CI: 0.034–0.270; p = 0.011) and 0.317 (95% CI: 0.193–0.442, p = 6.046e-07) was found in the standardized mean difference (SMD) of FG for the AC and CC genotypes, respectively, when compared with the AA reference genotype. However, the G-allele of rs560887 in Caucasians under the additive model and the C-allele of rs16856187 under the allele and dominant models were associated with a decreased risk of T2D (OR (95% CI) = 0.964 (0.947, 0.981), p = 0.570e-4; OR (95% CI) = 0.892 (0.832, 0.956), p = 0.001; and OR (95% CI) = 0.923(0.892, 0.955), p = 5.301e-6, respectively). Conclusions Our meta-analyses demonstrate that all three allele variants of G6PC2 (rs560887, rs16856187 and rs573225) are associated with elevated FG, with two variants (rs560887 in the Caucasians subgroup and rs16856187 under the allele and dominant model) being associated with T2D as well. Further studies utilizing larger sample sizes and different ethnic populations are needed to extend and confirm these findings.
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Boortz KA, Syring KE, Pound LD, Mo H, Bastarache L, Oeser JK, McGuinness OP, Denny JC, O’Brien RM. Effects of G6pc2 deletion on body weight and cholesterol in mice. J Mol Endocrinol 2017; 58:127-139. [PMID: 28122818 PMCID: PMC5380368 DOI: 10.1530/jme-16-0202] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 01/24/2017] [Indexed: 11/08/2022]
Abstract
Genome-wide association study (GWAS) data have linked the G6PC2 gene to variations in fasting blood glucose (FBG). G6PC2 encodes an islet-specific glucose-6-phosphatase catalytic subunit that forms a substrate cycle with the beta cell glucose sensor glucokinase. This cycle modulates the glucose sensitivity of insulin secretion and hence FBG. GWAS data have not linked G6PC2 to variations in body weight but we previously reported that female C57BL/6J G6pc2-knockout (KO) mice were lighter than wild-type littermates on both a chow and high-fat diet. The purpose of this study was to compare the effects of G6pc2 deletion on FBG and body weight in both chow-fed and high-fat-fed mice on two other genetic backgrounds. FBG was reduced in G6pc2 KO mice largely independent of gender, genetic background or diet. In contrast, the effect of G6pc2 deletion on body weight was markedly influenced by these variables. Deletion of G6pc2 conferred a marked protection against diet-induced obesity in male mixed genetic background mice, whereas in 129SvEv mice deletion of G6pc2 had no effect on body weight. G6pc2 deletion also reduced plasma cholesterol levels in a manner dependent on gender, genetic background and diet. An association between G6PC2 and plasma cholesterol was also observed in humans through electronic health record-derived phenotype analyses. These observations suggest that the action of G6PC2 on FBG is largely independent of the influences of environment, modifier genes or epigenetic events, whereas the action of G6PC2 on body weight and cholesterol are influenced by unknown variables.
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Affiliation(s)
- Kayla A. Boortz
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Kristen E. Syring
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Lynley D. Pound
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Huan Mo
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - James K. Oeser
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Owen P. McGuinness
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Joshua C. Denny
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Richard M. O’Brien
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232
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12
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Boortz KA, Syring KE, Lee RA, Dai C, Oeser JK, McGuinness OP, Wang JC, O'Brien RM. G6PC2 Modulates the Effects of Dexamethasone on Fasting Blood Glucose and Glucose Tolerance. Endocrinology 2016; 157:4133-4145. [PMID: 27653037 PMCID: PMC5086534 DOI: 10.1210/en.2016-1678] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The glucose-6-phosphatase catalytic subunit 2 (G6PC2) gene encodes an islet-specific glucose-6-phosphatase catalytic subunit. G6PC2 forms a substrate cycle with glucokinase that determines the glucose sensitivity of insulin secretion. Consequently, deletion of G6pc2 lowers fasting blood glucose (FBG) without affecting fasting plasma insulin. Although chronic elevation of FBG is detrimental to health, glucocorticoids induce G6PC2 expression, suggesting that G6PC2 evolved to transiently modulate FBG under conditions of glucocorticoid-related stress. We show, using competition and mutagenesis experiments, that the synthetic glucocorticoid dexamethasone (Dex) induces G6PC2 promoter activity through a mechanism involving displacement of the islet-enriched transcription factor MafA by the glucocorticoid receptor. The induction of G6PC2 promoter activity by Dex is modulated by a single nucleotide polymorphism, previously linked to altered FBG in humans, that affects FOXA2 binding. A 5-day repeated injection paradigm was used to examine the chronic effect of Dex on FBG and glucose tolerance in wild-type (WT) and G6pc2 knockout mice. Acute Dex treatment only induces G6pc2 expression in 129SvEv but not C57BL/6J mice, but this chronic treatment induced G6pc2 expression in both. In 6-hour fasted C57BL/6J WT mice, Dex treatment lowered FBG and improved glucose tolerance, with G6pc2 deletion exacerbating the decrease in FBG and enhancing the improvement in glucose tolerance. In contrast, in 24-hour fasted C57BL/6J WT mice, Dex treatment raised FBG but still improved glucose tolerance, with G6pc2 deletion limiting the increase in FBG and enhancing the improvement in glucose tolerance. These observations demonstrate that G6pc2 modulates the complex effects of Dex on both FBG and glucose tolerance.
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Affiliation(s)
- Kayla A Boortz
- Departments of Molecular Physiology and Biophysics (K.A.B., K.E.S., J.K.O., O.P.M., R.M.O.) and Medicine (C.D.), Vanderbilt University School of Medicine, Nashville, Tennessee 37232; and Department of Nutritional Sciences and Toxicology (R.A.L., J.-C.W.), University of California at Berkeley, Berkeley, California 94720
| | - Kristen E Syring
- Departments of Molecular Physiology and Biophysics (K.A.B., K.E.S., J.K.O., O.P.M., R.M.O.) and Medicine (C.D.), Vanderbilt University School of Medicine, Nashville, Tennessee 37232; and Department of Nutritional Sciences and Toxicology (R.A.L., J.-C.W.), University of California at Berkeley, Berkeley, California 94720
| | - Rebecca A Lee
- Departments of Molecular Physiology and Biophysics (K.A.B., K.E.S., J.K.O., O.P.M., R.M.O.) and Medicine (C.D.), Vanderbilt University School of Medicine, Nashville, Tennessee 37232; and Department of Nutritional Sciences and Toxicology (R.A.L., J.-C.W.), University of California at Berkeley, Berkeley, California 94720
| | - Chunhua Dai
- Departments of Molecular Physiology and Biophysics (K.A.B., K.E.S., J.K.O., O.P.M., R.M.O.) and Medicine (C.D.), Vanderbilt University School of Medicine, Nashville, Tennessee 37232; and Department of Nutritional Sciences and Toxicology (R.A.L., J.-C.W.), University of California at Berkeley, Berkeley, California 94720
| | - James K Oeser
- Departments of Molecular Physiology and Biophysics (K.A.B., K.E.S., J.K.O., O.P.M., R.M.O.) and Medicine (C.D.), Vanderbilt University School of Medicine, Nashville, Tennessee 37232; and Department of Nutritional Sciences and Toxicology (R.A.L., J.-C.W.), University of California at Berkeley, Berkeley, California 94720
| | - Owen P McGuinness
- Departments of Molecular Physiology and Biophysics (K.A.B., K.E.S., J.K.O., O.P.M., R.M.O.) and Medicine (C.D.), Vanderbilt University School of Medicine, Nashville, Tennessee 37232; and Department of Nutritional Sciences and Toxicology (R.A.L., J.-C.W.), University of California at Berkeley, Berkeley, California 94720
| | - Jen-Chywan Wang
- Departments of Molecular Physiology and Biophysics (K.A.B., K.E.S., J.K.O., O.P.M., R.M.O.) and Medicine (C.D.), Vanderbilt University School of Medicine, Nashville, Tennessee 37232; and Department of Nutritional Sciences and Toxicology (R.A.L., J.-C.W.), University of California at Berkeley, Berkeley, California 94720
| | - Richard M O'Brien
- Departments of Molecular Physiology and Biophysics (K.A.B., K.E.S., J.K.O., O.P.M., R.M.O.) and Medicine (C.D.), Vanderbilt University School of Medicine, Nashville, Tennessee 37232; and Department of Nutritional Sciences and Toxicology (R.A.L., J.-C.W.), University of California at Berkeley, Berkeley, California 94720
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13
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Functional Analysis of Mouse G6pc1 Mutations Using a Novel In Situ Assay for Glucose-6-Phosphatase Activity and the Effect of Mutations in Conserved Human G6PC1/G6PC2 Amino Acids on G6PC2 Protein Expression. PLoS One 2016; 11:e0162439. [PMID: 27611587 PMCID: PMC5017610 DOI: 10.1371/journal.pone.0162439] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Accepted: 08/23/2016] [Indexed: 11/19/2022] Open
Abstract
Elevated fasting blood glucose (FBG) has been associated with increased risk for development of type 2 diabetes. Single nucleotide polymorphisms (SNPs) in G6PC2 are the most important common determinants of variations in FBG in humans. Studies using G6pc2 knockout mice suggest that G6pc2 regulates the glucose sensitivity of insulin secretion. G6PC2 and the related G6PC1 and G6PC3 genes encode glucose-6-phosphatase catalytic subunits. This study describes a functional analysis of 22 non-synonymous G6PC2 SNPs, that alter amino acids that are conserved in human G6PC1, mouse G6pc1 and mouse G6pc2, with the goal of identifying variants that potentially affect G6PC2 activity/expression. Published data suggest strong conservation of catalytically important amino acids between all four proteins and the related G6PC3 isoform. Because human G6PC2 has very low glucose-6-phosphatase activity we used an indirect approach, examining the effect of these SNPs on mouse G6pc1 activity. Using a novel in situ functional assay for glucose-6-phosphatase activity we demonstrate that the amino acid changes associated with the human G6PC2 rs144254880 (Arg79Gln), rs149663725 (Gly114Arg) and rs2232326 (Ser324Pro) SNPs reduce mouse G6pc1 enzyme activity without affecting protein expression. The Arg79Gln variant alters an amino acid mutation of which, in G6PC1, has previously been shown to cause glycogen storage disease type 1a. We also demonstrate that the rs368382511 (Gly8Glu), rs138726309 (His177Tyr), rs2232323 (Tyr207Ser) rs374055555 (Arg293Trp), rs2232326 (Ser324Pro), rs137857125 (Pro313Leu) and rs2232327 (Pro340Leu) SNPs confer decreased G6PC2 protein expression. In summary, these studies identify multiple G6PC2 variants that have the potential to be associated with altered FBG in humans.
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14
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Boortz KA, Syring KE, Dai C, Pound LD, Oeser JK, Jacobson DA, Wang JC, McGuinness OP, Powers AC, O'Brien RM. G6PC2 Modulates Fasting Blood Glucose In Male Mice in Response to Stress. Endocrinology 2016; 157:3002-8. [PMID: 27300767 PMCID: PMC4967123 DOI: 10.1210/en.2016-1245] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The glucose-6-phosphatase catalytic 2 (G6PC2) gene is expressed specifically in pancreatic islet beta cells. Genome-wide association studies have shown that single nucleotide polymorphisms in the G6PC2 gene are associated with variations in fasting blood glucose (FBG) but not fasting plasma insulin. Molecular analyses examining the functional effects of these single nucleotide polymorphisms demonstrate that elevated G6PC2 expression is associated with elevated FBG. Studies in mice complement these genome-wide association data and show that deletion of the G6pc2 gene lowers FBG without affecting fasting plasma insulin. This suggests that, together with glucokinase, G6PC2 forms a substrate cycle that determines the glucose sensitivity of insulin secretion. Because genome-wide association studies and mouse studies demonstrate that elevated G6PC2 expression raises FBG and because chronically elevated FBG is detrimental to human health, increasing the risk of type 2 diabetes, it is unclear why G6PC2 evolved. We show here that the synthetic glucocorticoid dexamethasone strongly induces human G6PC2 promoter activity and endogenous G6PC2 expression in isolated human islets. Acute treatment with dexamethasone selectively induces endogenous G6pc2 expression in 129SvEv but not C57BL/6J mouse pancreas and isolated islets. The difference is due to a single nucleotide polymorphism in the C57BL/6J G6pc2 promoter that abolishes glucocorticoid receptor binding. In 6-hour fasted, nonstressed 129SvEv mice, deletion of G6pc2 lowers FBG. In response to the stress of repeated physical restraint, which is associated with elevated plasma glucocorticoid levels, G6pc2 gene expression is induced and the difference in FBG between wild-type and knockout mice is enhanced. These data suggest that G6PC2 may have evolved to modulate FBG in response to stress.
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Affiliation(s)
- Kayla A Boortz
- Departments of Molecular Physiology and Biophysics (K.A.B., K.E.S., L.D.P., J.K.O., D.A.J., O.P.M., R.M.O.) and Medicine (C.D., A.C.P.), Vanderbilt University School of Medicine, and VA Tennessee Valley Healthcare System (A.C.P.), Nashville, Tennessee 37232-0615; and Department of Nutritional Sciences and Toxicology (J.-C.W.), University of California, Berkeley, Berkeley, California 94720-3104
| | - Kristen E Syring
- Departments of Molecular Physiology and Biophysics (K.A.B., K.E.S., L.D.P., J.K.O., D.A.J., O.P.M., R.M.O.) and Medicine (C.D., A.C.P.), Vanderbilt University School of Medicine, and VA Tennessee Valley Healthcare System (A.C.P.), Nashville, Tennessee 37232-0615; and Department of Nutritional Sciences and Toxicology (J.-C.W.), University of California, Berkeley, Berkeley, California 94720-3104
| | - Chunhua Dai
- Departments of Molecular Physiology and Biophysics (K.A.B., K.E.S., L.D.P., J.K.O., D.A.J., O.P.M., R.M.O.) and Medicine (C.D., A.C.P.), Vanderbilt University School of Medicine, and VA Tennessee Valley Healthcare System (A.C.P.), Nashville, Tennessee 37232-0615; and Department of Nutritional Sciences and Toxicology (J.-C.W.), University of California, Berkeley, Berkeley, California 94720-3104
| | - Lynley D Pound
- Departments of Molecular Physiology and Biophysics (K.A.B., K.E.S., L.D.P., J.K.O., D.A.J., O.P.M., R.M.O.) and Medicine (C.D., A.C.P.), Vanderbilt University School of Medicine, and VA Tennessee Valley Healthcare System (A.C.P.), Nashville, Tennessee 37232-0615; and Department of Nutritional Sciences and Toxicology (J.-C.W.), University of California, Berkeley, Berkeley, California 94720-3104
| | - James K Oeser
- Departments of Molecular Physiology and Biophysics (K.A.B., K.E.S., L.D.P., J.K.O., D.A.J., O.P.M., R.M.O.) and Medicine (C.D., A.C.P.), Vanderbilt University School of Medicine, and VA Tennessee Valley Healthcare System (A.C.P.), Nashville, Tennessee 37232-0615; and Department of Nutritional Sciences and Toxicology (J.-C.W.), University of California, Berkeley, Berkeley, California 94720-3104
| | - David A Jacobson
- Departments of Molecular Physiology and Biophysics (K.A.B., K.E.S., L.D.P., J.K.O., D.A.J., O.P.M., R.M.O.) and Medicine (C.D., A.C.P.), Vanderbilt University School of Medicine, and VA Tennessee Valley Healthcare System (A.C.P.), Nashville, Tennessee 37232-0615; and Department of Nutritional Sciences and Toxicology (J.-C.W.), University of California, Berkeley, Berkeley, California 94720-3104
| | - Jen-Chywan Wang
- Departments of Molecular Physiology and Biophysics (K.A.B., K.E.S., L.D.P., J.K.O., D.A.J., O.P.M., R.M.O.) and Medicine (C.D., A.C.P.), Vanderbilt University School of Medicine, and VA Tennessee Valley Healthcare System (A.C.P.), Nashville, Tennessee 37232-0615; and Department of Nutritional Sciences and Toxicology (J.-C.W.), University of California, Berkeley, Berkeley, California 94720-3104
| | - Owen P McGuinness
- Departments of Molecular Physiology and Biophysics (K.A.B., K.E.S., L.D.P., J.K.O., D.A.J., O.P.M., R.M.O.) and Medicine (C.D., A.C.P.), Vanderbilt University School of Medicine, and VA Tennessee Valley Healthcare System (A.C.P.), Nashville, Tennessee 37232-0615; and Department of Nutritional Sciences and Toxicology (J.-C.W.), University of California, Berkeley, Berkeley, California 94720-3104
| | - Alvin C Powers
- Departments of Molecular Physiology and Biophysics (K.A.B., K.E.S., L.D.P., J.K.O., D.A.J., O.P.M., R.M.O.) and Medicine (C.D., A.C.P.), Vanderbilt University School of Medicine, and VA Tennessee Valley Healthcare System (A.C.P.), Nashville, Tennessee 37232-0615; and Department of Nutritional Sciences and Toxicology (J.-C.W.), University of California, Berkeley, Berkeley, California 94720-3104
| | - Richard M O'Brien
- Departments of Molecular Physiology and Biophysics (K.A.B., K.E.S., L.D.P., J.K.O., D.A.J., O.P.M., R.M.O.) and Medicine (C.D., A.C.P.), Vanderbilt University School of Medicine, and VA Tennessee Valley Healthcare System (A.C.P.), Nashville, Tennessee 37232-0615; and Department of Nutritional Sciences and Toxicology (J.-C.W.), University of California, Berkeley, Berkeley, California 94720-3104
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Ray D, Pankow JS, Basu S. USAT: A Unified Score-Based Association Test for Multiple Phenotype-Genotype Analysis. Genet Epidemiol 2015; 40:20-34. [PMID: 26638693 DOI: 10.1002/gepi.21937] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 09/04/2015] [Accepted: 09/09/2015] [Indexed: 12/15/2022]
Abstract
Genome-wide association studies (GWASs) for complex diseases often collect data on multiple correlated endo-phenotypes. Multivariate analysis of these correlated phenotypes can improve the power to detect genetic variants. Multivariate analysis of variance (MANOVA) can perform such association analysis at a GWAS level, but the behavior of MANOVA under different trait models has not been carefully investigated. In this paper, we show that MANOVA is generally very powerful for detecting association but there are situations, such as when a genetic variant is associated with all the traits, where MANOVA may not have any detection power. In these situations, marginal model based methods, however, perform much better than multivariate methods. We investigate the behavior of MANOVA, both theoretically and using simulations, and derive the conditions where MANOVA loses power. Based on our findings, we propose a unified score-based test statistic USAT that can perform better than MANOVA in such situations and nearly as well as MANOVA elsewhere. Our proposed test reports an approximate asymptotic P-value for association and is computationally very efficient to implement at a GWAS level. We have studied through extensive simulations the performance of USAT, MANOVA, and other existing approaches and demonstrated the advantage of using the USAT approach to detect association between a genetic variant and multivariate phenotypes. We applied USAT to data from three correlated traits collected on 5, 816 Caucasian individuals from the Atherosclerosis Risk in Communities (ARIC, The ARIC Investigators []) Study and detected some interesting associations.
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Affiliation(s)
- Debashree Ray
- Division of Biostatistics, School of Public Health, University of Minnesota, Minnesota, United States of America
| | - James S Pankow
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minnesota, United States of America
| | - Saonli Basu
- Division of Biostatistics, School of Public Health, University of Minnesota, Minnesota, United States of America
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Wall ML, Pound LD, Trenary I, O'Brien RM, Young JD. Novel stable isotope analyses demonstrate significant rates of glucose cycling in mouse pancreatic islets. Diabetes 2015; 64:2129-37. [PMID: 25552595 PMCID: PMC4439557 DOI: 10.2337/db14-0745] [Citation(s) in RCA: 20] [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] [Received: 05/10/2014] [Accepted: 12/20/2014] [Indexed: 11/20/2022]
Abstract
A polymorphism located in the G6PC2 gene, which encodes an islet-specific glucose-6-phosphatase catalytic subunit, is the most important common determinant of variations in fasting blood glucose (FBG) levels in humans. Studies of G6pc2 knockout (KO) mice suggest that G6pc2 represents a negative regulator of basal glucose-stimulated insulin secretion (GSIS) that acts by hydrolyzing glucose-6-phosphate (G6P), thereby reducing glycolytic flux. However, this conclusion conflicts with the very low estimates for the rate of glucose cycling in pancreatic islets, as assessed using radioisotopes. We have reassessed the rate of glucose cycling in pancreatic islets using a novel stable isotope method. The data show much higher levels of glucose cycling than previously reported. In 5 mmol/L glucose, islets from C57BL/6J chow-fed mice cycled ∼16% of net glucose uptake. The cycling rate was further increased at 11 mmol/L glucose. Similar cycling rates were observed using islets from high fat-fed mice. Importantly, glucose cycling was abolished in G6pc2 KO mouse islets, confirming that G6pc2 opposes the action of the glucose sensor glucokinase by hydrolyzing G6P. The demonstration of high rates of glucose cycling in pancreatic islets explains why G6pc2 deletion enhances GSIS and why variants in G6PC2 affect FBG in humans.
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Affiliation(s)
- Martha L Wall
- Department of Chemical and Biomolecular Engineering, Vanderbilt School of Engineering, Nashville, TN
| | - Lynley D Pound
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical School, Nashville, TN
| | - Irina Trenary
- Department of Chemical and Biomolecular Engineering, Vanderbilt School of Engineering, Nashville, TN
| | - Richard M O'Brien
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical School, Nashville, TN
| | - Jamey D Young
- Department of Chemical and Biomolecular Engineering, Vanderbilt School of Engineering, Nashville, TN Department of Molecular Physiology and Biophysics, Vanderbilt University Medical School, Nashville, TN
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17
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Zheng C, Dalla Man C, Cobelli C, Groop L, Zhao H, Bale AE, Shaw M, Duran E, Pierpont B, Caprio S, Santoro N. A common variant in the MTNR1b gene is associated with increased risk of impaired fasting glucose (IFG) in youth with obesity. Obesity (Silver Spring) 2015; 23:1022-9. [PMID: 25919927 PMCID: PMC4414047 DOI: 10.1002/oby.21030] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 12/21/2014] [Indexed: 11/17/2022]
Abstract
OBJECTIVE To explore the role of MTNR1B rs10830963 and G6PC2 rs560887 variants in the pathogenesis of impaired fasting glucose (IFG) in obese adolescents. METHODS A total of 346 Caucasians, 218 African-Americans, and 217 Hispanics obese children and adolescents underwent an oral glucose tolerance test (OGTT) and 518 underwent the evaluation of insulin secretion by the oral minimal model (OMM). Also, 274 subjects underwent a second OGTT after 3.0 ± 2.1 years. RESULTS The MTNR1B rs10830963 variant was associated with higher fasting glucose levels and lower dynamic beta-cell response in Caucasians and Hispanics (P < 0.05) and conferred an increased risk of showing IFG to Caucasians (P = 0.05), African-Americans (P = 0.0066), and Hispanics (P = 0.024). Despite the association between the G6PC2 rs560887 and higher fasting glucose levels (P < 0.05), there was no association between this variant and IFG at baseline or at follow-up (all P > 0.10). CONCLUSIONS It has been shown for the first time in obese youth that the MTNR1B variant is associated with an increased risk of IFG.
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Affiliation(s)
- Chao Zheng
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT
- Department of Endocrinology, The 2 Affiliated Hospital & Yuying Children's Hospital of Wenzhou Medical University
| | - Chiara Dalla Man
- Department of Information Engineering, University of Padua, Padua, Italy
| | - Claudio Cobelli
- Department of Information Engineering, University of Padua, Padua, Italy
| | - Leif Groop
- Department of Clinical Sciences/Diabetes & Endocrinology and Lund University Diabetes Centre, Lund University, University Hospital, Malmoe, Malmoe, Sweden
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, New Haven, CT
| | - Allen E Bale
- Department of Genetics, Yale University School of Medicine, New Haven, CT
| | - Melissa Shaw
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT
| | - Elvira Duran
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT
| | - Bridget Pierpont
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT
| | - Sonia Caprio
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT
| | - Nicola Santoro
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT
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Silvestre-Roig C, Fernández P, Mansego ML, van Tiel CM, Viana R, Anselmi CV, Condorelli G, de Winter RJ, Martín-Fuentes P, Solanas-Barca M, Civeira F, Focaccio A, de Vries CJM, Chaves FJ, Andrés V. Genetic variants in CCNB1 associated with differential gene transcription and risk of coronary in-stent restenosis. ACTA ACUST UNITED AC 2014; 7:59-70. [PMID: 24395923 DOI: 10.1161/circgenetics.113.000305] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND The development of diagnostic tools to assess restenosis risk after stent deployment may enable the intervention to be tailored to the individual patient, for example, by targeting the use of drug-eluting stent to high-risk patients, with the goal of improving safety and reducing costs. The CCNB1 gene (encoding cyclin B1) positively regulates cell proliferation, a key component of in-stent restenosis. Therefore, we hypothesized that single-nucleotide polymorphisms in CCNB1 may serve as useful tools in risk stratification for in-stent restenosis. METHODS AND RESULTS We identified 3 single-nucleotide polymorphisms in CCNB1 associated with increased restenosis risk in a cohort of 284 patients undergoing coronary angioplasty and stent placement (rs350099: TT versus CC+TC; odds ratio [OR], 1.82; 95% confidence interval [CI], 1.09-3.03; P=0.023; rs350104: CC versus CT+TT; OR, 1.82; 95% CI, 1.02-3.26; P=0.040; and rs164390: GG versus GT+TT; OR, 2.27; 95% CI, 1.33-3.85; P=0.002). These findings were replicated in another cohort study of 715 patients (rs350099: TT versus CC+TC; OR, 1.88; 95% CI, 0.92-3.81; P=0.080; rs350104: CC versus CT+TT; OR, 2.23; 95% CI, 1.18-4.25; P=0.016; and rs164390: GG versus GT+TT; OR, 1.87; 95% CI, 1.03-3.47; P=0.040). Moreover, the haplotype containing all 3 risk alleles is associated with higher CCNB1 mRNA expression in circulating lymphocytes and increased in-stent restenosis risk (OR, 1.43; 95% CI, 1.00-1.823; P=0.039). The risk variants of rs350099, rs350104, and rs164390 are associated with increased reporter gene expression through binding of transcription factors nuclear factor-Y, activator protein 1, and specificity protein 1, respectively. CONCLUSIONS Allele-dependent transcriptional regulation of CCNB1 associated with rs350099, rs350104, and rs164390 affects the risk of in-stent restenosis. These findings reveal these common genetic variations as attractive diagnostic tools in risk stratification for restenosis.
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O'Brien RM. Moving on from GWAS: functional studies on the G6PC2 gene implicated in the regulation of fasting blood glucose. Curr Diab Rep 2013; 13:768-77. [PMID: 24142592 PMCID: PMC4041587 DOI: 10.1007/s11892-013-0422-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Genome-wide association studies (GWAS) have shown that single-nucleotide polymorphisms (SNPs) in G6PC2 are the most important common determinants of variations in fasting blood glucose (FBG) levels. Molecular studies examining the functional impact of these SNPs on G6PC2 gene transcription and splicing suggest that they affect FBG by directly modulating G6PC2 expression. This conclusion is supported by studies on G6pc2 knockout (KO) mice showing that G6pc2 represents a negative regulator of basal glucose-stimulated insulin secretion that acts by hydrolyzing glucose-6-phosphate, thereby reducing glycolytic flux and opposing the action of glucokinase. Suppression of G6PC2 activity might, therefore, represent a novel therapy for lowering FBG and the risk of cardiovascular-associated mortality. GWAS and G6pc2 KO mouse studies also suggest that G6PC2 affects other aspects of beta cell function. The evolutionary benefit conferred by G6PC2 remains unclear, but it is unlikely to be related to its ability to modulate FBG.
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Affiliation(s)
- Richard M O'Brien
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA,
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20
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Baerenwald DA, Bonnefond A, Bouatia-Naji N, Flemming BP, Umunakwe OC, Oeser JK, Pound LD, Conley NL, Cauchi S, Lobbens S, Eury E, Balkau B, Lantieri O, Dadi PK, Jacobson DA, Froguel P, O’Brien RM. Multiple functional polymorphisms in the G6PC2 gene contribute to the association with higher fasting plasma glucose levels. Diabetologia 2013; 56:1306-16. [PMID: 23508304 PMCID: PMC4106008 DOI: 10.1007/s00125-013-2875-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 01/28/2013] [Indexed: 01/14/2023]
Abstract
AIMS/HYPOTHESIS We previously identified the G6PC2 locus as a strong determinant of fasting plasma glucose (FPG) and showed that a common G6PC2 intronic single nucleotide polymorphism (SNP) (rs560887) and two common G6PC2 promoter SNPs (rs573225 and rs13431652) are highly associated with FPG. However, these promoter SNPs have complex effects on G6PC2 fusion gene expression, and our data suggested that only rs13431652 is a potentially causative SNP. Here we examine the effect of rs560887 on G6PC2 pre-mRNA splicing and the contribution of an additional common G6PC2 promoter SNP, rs2232316, to the association signal. METHODS Minigene analyses were used to characterise the effect of rs560887 on G6PC2 pre-mRNA splicing. Fusion gene and gel retardation analyses characterised the effect of rs2232316 on G6PC2 promoter activity and transcription factor binding. The genetic association of rs2232316 with FPG variation was assessed using regression adjusted for age, sex and BMI in 4,220 Europeans with normal FPG. RESULTS The rs560887-G allele was shown to enhance G6PC2 pre-mRNA splicing, whereas the rs2232316-A allele enhanced G6PC2 transcription by promoting Foxa2 binding. Genetic analyses provide evidence for association of the rs2232316-A allele with increased FPG (β = 0.04 mmol/l; p = 4.3 × 10(-3)) as part of the same signal as rs560887, rs573225 and rs13431652. CONCLUSIONS/INTERPRETATION As with rs13431652, the in situ functional data with rs560887 and rs2232316 are in accord with the putative function of G6PC2 in pancreatic islets, and suggest that all three are potentially causative SNPs that contribute to the association between G6PC2 and FPG.
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Affiliation(s)
- D. A. Baerenwald
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, 37232 Nashville, Tennessee, USA
| | - A. Bonnefond
- CNRS-UMR-8199, Institut Pasteur de Lille, F-59019, Lille, France
- University Lille Nord de France, F-59019 Lille, France
| | - N. Bouatia-Naji
- CNRS-UMR-8199, Institut Pasteur de Lille, F-59019, Lille, France
- University Lille Nord de France, F-59019 Lille, France
- INSERM U970, Paris Cardiovascular Research Center PARCC, 56 rue Leblanc, F-75015 Paris, France
| | - B. P. Flemming
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, 37232 Nashville, Tennessee, USA
| | - O. C. Umunakwe
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, 37232 Nashville, Tennessee, USA
| | - J. K. Oeser
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, 37232 Nashville, Tennessee, USA
| | - L. D. Pound
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, 37232 Nashville, Tennessee, USA
| | - N. L. Conley
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, 37232 Nashville, Tennessee, USA
| | - S. Cauchi
- CNRS-UMR-8199, Institut Pasteur de Lille, F-59019, Lille, France
- University Lille Nord de France, F-59019 Lille, France
| | - S. Lobbens
- CNRS-UMR-8199, Institut Pasteur de Lille, F-59019, Lille, France
- University Lille Nord de France, F-59019 Lille, France
| | - E. Eury
- CNRS-UMR-8199, Institut Pasteur de Lille, F-59019, Lille, France
- University Lille Nord de France, F-59019 Lille, France
| | - B. Balkau
- INSERM, Centre for research in Epidemiology and Population Health (CESP), U1018, Epidemiology of diabetes, obesity and chronic renal disease over the lifecourse, F-94807, Villejuif, France
- Université Paris-Sud 11, UMRS 1018, F-94807 Villejuif, France
| | - O. Lantieri
- Institut inter-régional pour la santé (IRSA), F-37521 La Riche, France
| | - MAGIC Investigators
- Meta-Analysis of Glucose and Insulin related traits Consortium Investigators (http://www.magicinvestigators.org/)
| | - P. K. Dadi
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, 37232 Nashville, Tennessee, USA
| | - D. A. Jacobson
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, 37232 Nashville, Tennessee, USA
| | - P. Froguel
- CNRS-UMR-8199, Institut Pasteur de Lille, F-59019, Lille, France
- University Lille Nord de France, F-59019 Lille, France
- Department of Genomics of Common Disease, School of Public Health, Imperial College London, W12 0NN London, UK
| | - R. M. O’Brien
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, 37232 Nashville, Tennessee, USA
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21
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Pound LD, Oeser JK, O’Brien TP, Wang Y, Faulman CJ, Dadi PK, Jacobson DA, Hutton JC, McGuinness OP, Shiota M, O’Brien RM. G6PC2: a negative regulator of basal glucose-stimulated insulin secretion. Diabetes 2013; 62:1547-56. [PMID: 23274894 PMCID: PMC3636628 DOI: 10.2337/db12-1067] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Elevated fasting blood glucose (FBG) is associated with increased risk for the development of type 2 diabetes and cardiovascular-associated mortality. Genome-wide association studies (GWAS) have linked polymorphisms in G6PC2 with variations in FBG and body fat, although not insulin sensitivity or glucose tolerance. G6PC2 encodes an islet-specific, endoplasmic reticulum-resident glucose-6-phosphatase catalytic subunit. A combination of in situ perfused pancreas, in vitro isolated islet, and in vivo analyses were used to explore the function of G6pc2 in mice. G6pc2 deletion had little effect on insulin sensitivity and glucose tolerance, whereas body fat was reduced in female G6pc2 knockout (KO) mice on both a chow and high-fat diet, observations that are all consistent with human GWAS data. G6pc2 deletion resulted in a leftward shift in the dose-response curve for glucose-stimulated insulin secretion (GSIS). As a consequence, under fasting conditions in which plasma insulin levels were identical, blood glucose levels were reduced in G6pc2 KO mice, again consistent with human GWAS data. Glucose-6-phosphatase activity was reduced, whereas basal cytoplasmic calcium levels were elevated in islets isolated from G6pc2 KO mice. These data suggest that G6pc2 represents a novel, negative regulator of basal GSIS that acts by hydrolyzing glucose-6-phosphate, thereby reducing glycolytic flux.
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Affiliation(s)
- Lynley D. Pound
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical School, Nashville, Tennessee
| | - James K. Oeser
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical School, Nashville, Tennessee
| | - Tracy P. O’Brien
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical School, Nashville, Tennessee
| | - Yingda Wang
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical School, Nashville, Tennessee
| | - Chandler J. Faulman
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical School, Nashville, Tennessee
| | - Prasanna K. Dadi
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical School, Nashville, Tennessee
| | - David A. Jacobson
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical School, Nashville, Tennessee
| | - John C. Hutton
- Barbara Davis Center for Childhood Diabetes, University of Colorado Health Sciences Center, Aurora, Colorado
| | - Owen P. McGuinness
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical School, Nashville, Tennessee
| | - Masakazu Shiota
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical School, Nashville, Tennessee
| | - Richard M. O’Brien
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical School, Nashville, Tennessee
- Corresponding author: Richard M. O’Brien,
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22
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Multiple roles of glucose-6-phosphatases in pathophysiology. Biochim Biophys Acta Gen Subj 2013; 1830:2608-18. [DOI: 10.1016/j.bbagen.2012.12.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Revised: 12/11/2012] [Accepted: 12/13/2012] [Indexed: 12/28/2022]
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Liu CT, Ng MCY, Rybin D, Adeyemo A, Bielinski SJ, Boerwinkle E, Borecki I, Cade B, Chen YDI, Djousse L, Fornage M, Goodarzi MO, Grant SFA, Guo X, Harris T, Kabagambe E, Kizer JR, Liu Y, Lunetta KL, Mukamal K, Nettleton JA, Pankow JS, Patel SR, Ramos E, Rasmussen-Torvik L, Rich SS, Rotimi CN, Sarpong D, Shriner D, Sims M, Zmuda JM, Redline S, Kao WH, Siscovick D, Florez JC, Rotter JI, Dupuis J, Wilson JG, Bowden DW, Meigs JB. Transferability and fine-mapping of glucose and insulin quantitative trait loci across populations: CARe, the Candidate Gene Association Resource. Diabetologia 2012; 55:2970-84. [PMID: 22893027 PMCID: PMC3804308 DOI: 10.1007/s00125-012-2656-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 06/14/2012] [Indexed: 01/22/2023]
Abstract
AIMS/HYPOTHESIS Hyperglycaemia disproportionately affects African-Americans (AfAs). We tested the transferability of 18 single-nucleotide polymorphisms (SNPs) associated with glycaemic traits identified in European ancestry (EuA) populations in 5,984 non-diabetic AfAs. METHODS We meta-analysed SNP associations with fasting glucose (FG) or insulin (FI) in AfAs from five cohorts in the Candidate Gene Association Resource. We: (1) calculated allele frequency differences, variations in linkage disequilibrium (LD), fixation indices (F(st)s) and integrated haplotype scores (iHSs); (2) tested EuA SNPs in AfAs; and (3) interrogated within ± 250 kb around each EuA SNP in AfAs. RESULTS Allele frequency differences ranged from 0.6% to 54%. F(st) exceeded 0.15 at 6/16 loci, indicating modest population differentiation. All iHSs were <2, suggesting no recent positive selection. For 18 SNPs, all directions of effect were the same and 95% CIs of association overlapped when comparing EuA with AfA. For 17 of 18 loci, at least one SNP was nominally associated with FG in AfAs. Four loci were significantly associated with FG (GCK, p = 5.8 × 10(-8); MTNR1B, p = 8.5 × 10(-9); and FADS1, p = 2.2 × 10(-4)) or FI (GCKR, p = 5.9 × 10(-4)). At GCK and MTNR1B the EuA and AfA SNPs represented the same signal, while at FADS1, and GCKR, the EuA and best AfA SNPs were weakly correlated (r(2) <0.2), suggesting allelic heterogeneity for association with FG at these loci. CONCLUSIONS/INTERPRETATION Few glycaemic SNPs showed strict evidence of transferability from EuA to AfAs. Four loci were significantly associated in both AfAs and those with EuA after accounting for varying LD across ancestral groups, with new signals emerging to aid fine-mapping.
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Affiliation(s)
- C.-T. Liu
- Department of Biostatistics, Boston University School of Public
Health, Boston, MA, USA
| | - M. C. Y. Ng
- Center for Genomics and Personalized Medicine Research, Center for
Diabetes Research, Wake Forest University School of Medicine, Winston-Salem,
NC, USA
| | - D. Rybin
- Boston University Data Coordinating Center, Boston, MA, USA
| | - A. Adeyemo
- National Human Genome Research Institute, Bethesda, MD, USA
| | | | - E. Boerwinkle
- University of Texas Health Science Center at Houston, Houston, TX,
USA
| | - I. Borecki
- Washington University, St Louis, MO, USA
| | - B. Cade
- Brigham and Women's Hospital, Boston, MA, USA
| | | | - L. Djousse
- Brigham and Women's Hospital, Boston, MA, USA; Department
of Medicine, Harvard Medical School, Boston, MA, USA; Boston VA Healthcare
System, Boston, MA, USA
| | - M. Fornage
- University of Texas Health Science Center at Houston, Houston, TX,
USA
| | | | - S. F. A. Grant
- Children's Hospital of Philadelphia, Philadelphia, PA,
USA
| | - X. Guo
- Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - T. Harris
- National Institute on Aging, Bethesda, MD, USA
| | | | | | - Y. Liu
- Center for Genomics and Personalized Medicine Research, Center for
Diabetes Research, Wake Forest University School of Medicine, Winston-Salem,
NC, USA; Department of Epidemiology and Prevention, Wake Forest University,
Winston-Salem, North Carolina, USA
| | - K. L. Lunetta
- Department of Biostatistics, Boston University School of Public
Health, Boston, MA, USA; National Heart, Lung, and Blood Institute'
Framingham Heart Study, Framingham, MA, USA
| | - K. Mukamal
- Department of Medicine, Harvard Medical School, Boston, MA,
USA
| | - J. A. Nettleton
- University of Texas Health Science Center at Houston, Houston, TX,
USA
| | | | - S. R. Patel
- Brigham and Women's Hospital, Boston, MA, USA
| | - E. Ramos
- National Human Genome Research Institute, Bethesda, MD, USA
| | | | - S. S. Rich
- University of Virginia, Charlottesville, VA, USA
| | - C. N. Rotimi
- National Human Genome Research Institute, Bethesda, MD, USA
| | - D. Sarpong
- Jackson State University, Jackson, MS, USA
| | - D. Shriner
- National Human Genome Research Institute, Bethesda, MD, USA
| | - M. Sims
- University of Mississippi Medical Center, Jackson, MS, USA
| | - J. M. Zmuda
- University of Pittsburgh, Graduate School of Public Health,
Pittsburgh, PA, USA
| | - S. Redline
- Brigham and Women's Hospital, Boston, MA, USA
| | - W. H. Kao
- Johns Hopkins University, Baltimore, MD, USA
| | | | - J. C. Florez
- Department of Medicine, Harvard Medical School, Boston, MA, USA;
Diabetes Unit and Center for Human Genetic Research, Massachusetts General
Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad
Institute, Cambridge, MA, USA
| | - J. I. Rotter
- Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - J. Dupuis
- Department of Biostatistics, Boston University School of Public
Health, Boston, MA, USA; National Heart, Lung, and Blood Institute's
Framingham Heart Study, Framingham, MA, USA
| | - J. G. Wilson
- University of Mississippi Medical Center, Jackson, MS, USA
| | - D. W. Bowden
- Center for Genomics and Personalized Medicine Research, Center for
Diabetes Research, Wake Forest University School of Medicine, Winston-Salem,
NC, USA; Departments of Biochemistry and Internal Medicine, Wake Forest
University School of Medicine, Winston-Salem, NC, USA
| | - J. B. Meigs
- Department of Medicine, Harvard Medical School, Boston, MA, USA;
General Medicine Division, Massachusetts General Hospital, 50 Staniford
Street, 9th Flr, Boston, MA, USA
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24
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Dolfini D, Gatta R, Mantovani R. NF-Y and the transcriptional activation of CCAAT promoters. Crit Rev Biochem Mol Biol 2011; 47:29-49. [PMID: 22050321 DOI: 10.3109/10409238.2011.628970] [Citation(s) in RCA: 171] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The CCAAT box promoter element and NF-Y, the transcription factor (TF) that binds to it, were among the first cis-elements and trans-acting factors identified; their interplay is required for transcriptional activation of a sizeable number of eukaryotic genes. NF-Y consists of three evolutionarily conserved subunits: a dimer of NF-YB and NF-YC which closely resembles a histone, and the "innovative" NF-YA. In this review, we will provide an update on the functional and biological features that make NF-Y a fundamental link between chromatin and transcription. The last 25 years have witnessed a spectacular increase in our knowledge of how genes are regulated: from the identification of cis-acting sequences in promoters and enhancers, and the biochemical characterization of the corresponding TFs, to the merging of chromatin studies with the investigation of enzymatic machines that regulate epigenetic states. Originally identified and studied in yeast and mammals, NF-Y - also termed CBF and CP1 - is composed of three subunits, NF-YA, NF-YB and NF-YC. The complex recognizes the CCAAT pentanucleotide and specific flanking nucleotides with high specificity (Dorn et al., 1997; Hatamochi et al., 1988; Hooft van Huijsduijnen et al, 1987; Kim & Sheffery, 1990). A compelling set of bioinformatics studies clarified that the NF-Y preferred binding site is one of the most frequent promoter elements (Suzuki et al., 2001, 2004; Elkon et al., 2003; Mariño-Ramírez et al., 2004; FitzGerald et al., 2004; Linhart et al., 2005; Zhu et al., 2005; Lee et al., 2007; Abnizova et al., 2007; Grskovic et al., 2007; Halperin et al., 2009; Häkkinen et al., 2011). The same consensus, as determined by mutagenesis and SELEX studies (Bi et al., 1997), was also retrieved in ChIP-on-chip analysis (Testa et al., 2005; Ceribelli et al., 2006; Ceribelli et al., 2008; Reed et al., 2008). Additional structural features of the CCAAT box - position, orientation, presence of multiple Transcriptional Start Sites - were previously reviewed (Dolfini et al., 2009) and will not be considered in detail here.
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Affiliation(s)
- Diletta Dolfini
- Dipartimento di Scienze Biomolecolari e Biotecnologie, Università degli Studi di Milano, Milan, Italy
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Abstract
Over the past 3 years, there has been a dramatic increase in the number of confirmed type 2 diabetes (T2D) susceptibility loci, most arising through the implementation of genome-wide association studies (GWAS). However, progress toward the understanding of disease mechanisms has been slowed by modest effect sizes and the fact that most GWAS signals map away from coding sequence: the presumption is that their effects are mediated through regulation of nearby transcripts, but the identities of the genes concerned are often far from clear. In this review we describe the progress that has been made to date in translating association signals into molecular mechanisms with a focus on the most tractable signals (eg, KCNJ11/ABCC8, SLC30A8, GCKR) and those in which human, animal, and cellular models (FTO, TCF7L2, G6PC2) have provided insights into the role in T2D pathogenesis. Finally, the challenges for the field with the advent of genome-scale next-generation resequencing efforts are discussed.
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Affiliation(s)
- Martijn van de Bunt
- Diabetes Research Laboratories, Oxford Centre for Diabetes Endocrinology & Metabolism, Churchill Hospital, University of Oxford, Headington, Oxford, OX3 7LJ, UK.
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