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Gao L, Wu L, Zhang M, Zhao X, Cheng H, Mi J. Gender-specific association of the rs6499640 polymorphism in the FTO gene with plasma lipid levels in Chinese children. Genet Mol Biol 2018; 41:397-402. [PMID: 29870569 PMCID: PMC6082231 DOI: 10.1590/1678-4685-gmb-2017-0107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 10/25/2017] [Indexed: 11/25/2022] Open
Abstract
The fat mass- and obesity-associated gene (FTO) is significantly
associated with obesity, but the associations of FTO with
obesity-related traits are not fully described. We aimed to investigate the
association of the FTO single nucleotide polymorphism (SNP)
rs6499640 with lipid levels in Chinese children. A total of 3503 children aged
6-18 years were included in the present study. Lipid levels were analyzed and
the SNP rs6499640 was genotyped using the TaqMan Allelic Discrimination Assay.
Statistically significant associations were found between rs6499640 and
low-density lipoprotein cholesterol (LDL-C) (p = 0.008), total
cholesterol (TC) (p = 0.005), and triglycerides (TG)
(p < 0.001) in girls under a dominant model adjusted for
age and BMI. No statistical significance was found between the SNP and lipid
levels in boys. We demonstrated for the first time that the SNP rs6499640 in
FTO is associated with LDL-C, TC, and TG in Chinese girls.
Our study identified a new risk locus for lipid levels in children.
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Affiliation(s)
- Liwang Gao
- Department of Epidemiology, Capital Institute of Pediatrics, Beijing, China
| | - Lijun Wu
- Department of Epidemiology, Capital Institute of Pediatrics, Beijing, China
| | - Meixian Zhang
- Department of Epidemiology, Capital Institute of Pediatrics, Beijing, China
| | - Xiaoyuan Zhao
- Department of Epidemiology, Capital Institute of Pediatrics, Beijing, China
| | - Hong Cheng
- Department of Epidemiology, Capital Institute of Pediatrics, Beijing, China
| | - Jie Mi
- Department of Epidemiology, Capital Institute of Pediatrics, Beijing, China
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Znf202 affects high density lipoprotein cholesterol levels and promotes hepatosteatosis in hyperlipidemic mice. PLoS One 2013; 8:e57492. [PMID: 23469003 PMCID: PMC3585336 DOI: 10.1371/journal.pone.0057492] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Accepted: 01/22/2013] [Indexed: 11/19/2022] Open
Abstract
Background The zinc finger protein Znf202 is a transcriptional suppressor of lipid related genes and has been linked to hypoalphalipoproteinemia. A functional role of Znf202 in lipid metabolism in vivo still remains to be established. Methodology and Principal Findings We generated mouse Znf202 expression vectors, the functionality of which was established in several in vitro systems. Next, effects of adenoviral znf202 overexpression in vivo were determined in normo- as well as hyperlipidemic mouse models. Znf202 overexpression in mouse hepatoma cells mhAT3F2 resulted in downregulation of members of the Apoe/c1/c2 and Apoa1/c3/a4 gene cluster. The repressive activity of Znf202 was firmly confirmed in an apoE reporter assay and Znf202 responsive elements within the ApoE promoter were identified. Adenoviral Znf202 transfer to Ldlr−/− mice resulted in downregulation of apoe, apoc1, apoa1, and apoc3 within 24 h after gene transfer. Interestingly, key genes in bile flux (abcg5/8 and bsep) and in bile acid synthesis (cyp7a1) were also downregulated. At 5 days post-infection, the expression of the aforementioned genes was normalized, but mice had developed severe hepatosteatosis accompanied by hypercholesterolemia and hypoalphalipoproteinemia. A much milder phenotype was observed in wildtype mice after 5 days of hepatic Znf202 overexpression. Interestingly and similar to Ldl−/− mice, HDL-cholesterol levels in wildtype mice were lowered after hepatic Znf202 overexpression. Conclusion/Significance Znf202 overexpression in vivo reveals an important role of this transcriptional regulator in liver lipid homeostasis, while firmly establishing the proposed key role in the control of HDL levels.
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Razzaghi H, Santorico SA, Kamboh MI. Population-Based Resequencing of LIPG and ZNF202 Genes in Subjects with Extreme HDL Levels. Front Genet 2012; 3:89. [PMID: 22723803 PMCID: PMC3375090 DOI: 10.3389/fgene.2012.00089] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Accepted: 05/03/2012] [Indexed: 11/26/2022] Open
Abstract
Endothelial lipase (LIPG) and zinc finger protein 202
(ZNF202) are two pivotal genes in high density lipoprotein (HDL
metabolism). We sought to determine their genetic contribution to variation in
HDL-cholesterol levels by comprehensive resequencing of both genes in 235 individuals with
high or low HDL-C levels. The selected subjects were 141 Whites (High HDL Group:
n = 68, x¯=76.90mg/dl; Low HDL Group:
n = 73, x¯=32.55mg/dl) and 94 Hispanics (High HDL Group:
n = 46, x¯=74.85mg/dl; Low HDL Group:
n = 48, x¯=29.95mg/dl). We identified a total of 185 and 122 sequence variants in
LIPG and ZNF202, respectively. We found only two
missense variants in LIPG (T111I and N396S) and two in
ZNF202 (A154V and K259E). In both genes, there were several variants
unique to either the low or high HDL group. For LIPG, the proportion of
unique variants differed between the high and low HDL groups in both Whites
(p = 0.022) and Hispanics
(p = 0.017), but for ZNF202 this
difference was observed only in Hispanics
(p = 0.021). We also identified a common
haplotype in ZNF202 among Whites that was significantly associated with
the high HDL group (p = 0.013). These findings
provide insights into the genetics of LIPG and ZNF202,
and suggest that sequence variants occurring with high frequency in non-exonic regions may
play a prominent role in modulating HDL-C levels in the general population.
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Affiliation(s)
- Hamid Razzaghi
- Division of Cardiology, Department of Medicine, University of Colorado Denver Aurora, CO, USA
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Daneshpour MS, Rebai A, Houshmand M, Alfadhli S, Zeinali S, Hedayati M, Zarkesh M, Azizi F. 8q24.3 and 11q25 chromosomal loci association with low HDL-C in metabolic syndrome. Eur J Clin Invest 2011; 41:1105-12. [PMID: 21443751 DOI: 10.1111/j.1365-2362.2011.02516.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND High-density lipoprotein cholesterol (HDL-C) levels are low in Iranians. Low HDL-C is the most frequent phenotype in metabolic syndrome (MetS) among the Iranian population (32%). This has been claimed to be related to genetic factors. MATERIALS AND METHODS To investigate possible genes linked to this disorder, 12 microsatellite markers were selected. They were used in 107 families with MetS and low HDL-C to analyse relevant association and linkage signals. RESULT Family-based association tests under the biallelic mode gave many positive association signals. Higher association - after correction for multiple testing - was found to be linked with marker D8S1743 and D11S1304 (P < 0·003). The obtained results suggested evidence for association with regions on chromosome 8, 11 and to a lesser degree on chromosome 16. Nonparametric linkage analysis performed by Merlin software gave no significant correlation for any of the chromosomal regions. By considering only families with positive Nonparametric Logarithm of odds (LOD) scores, higher association can clearly be visible with D16S3096 and D11S934. CONCLUSIONS These results suggest that 8q22-24; 11q23-25 and 16q23-24 regions are very likely to contain genes that control HDL-C level in Iranian families with metabolic syndrome.
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Affiliation(s)
- Maryam Sadat Daneshpour
- Obesity Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti MC, Tehran, Iran
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Daneshpour MS, Alfadhli S, Houshmand M, Zeinali S, Hedayati M, Zarkesh M, Azizi F. Allele frequency distribution for D11S1304, D11S1998, and D11S934 and metabolic syndrome in TLGS. EUR J LIPID SCI TECH 2010. [DOI: 10.1002/ejlt.201000340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Maryam Sadat Daneshpour
- Department of Medical Genetics, National Institute for Genetic Engineering and Biotechnology, Tehran, Iran
- Obesity Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti university of Medical Science, Tehran, Iran
| | - Suad Alfadhli
- Faculty of Allied Health Sciences, Department of Medical Laboratory Sciences, Kuwait University, Kuwait
| | - Massoud Houshmand
- Department of Medical Genetics, National Institute for Genetic Engineering and Biotechnology, Tehran, Iran
| | - Sirous Zeinali
- Biotechnology Research Centre, Pasteur Institute of Iran, Teheran, Iran
| | - Mehdi Hedayati
- Obesity Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti university of Medical Science, Tehran, Iran
| | - Maryam Zarkesh
- Obesity Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti university of Medical Science, Tehran, Iran
| | - Fereidoun Azizi
- Obesity Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti university of Medical Science, Tehran, Iran
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Weissglas-Volkov D, Pajukanta P. Genetic causes of high and low serum HDL-cholesterol. J Lipid Res 2010; 51:2032-57. [PMID: 20421590 DOI: 10.1194/jlr.r004739] [Citation(s) in RCA: 147] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Plasma levels of HDL cholesterol (HDL-C) have a strong inherited basis with heritability estimates of 40-60%. The well-established inverse relationship between plasma HDL-C levels and the risk of coronary artery disease (CAD) has led to an extensive search for genetic factors influencing HDL-C concentrations. Over the past 30 years, candidate gene, genome-wide linkage, and most recently genome-wide association (GWA) studies have identified several genetic variations for plasma HDL-C levels. However, the functional role of several of these variants remains unknown, and they do not always correlate with CAD. In this review, we will first summarize what is known about HDL metabolism, monogenic disorders associated with both low and high HDL-C levels, and candidate gene studies. Then we will focus this review on recent genetic findings from the GWA studies and future strategies to elucidate the remaining substantial proportion of HDL-C heritability. Comprehensive investigation of the genetic factors conferring to low and high HDL-C levels using integrative approaches is important to unravel novel pathways and their relations to CAD, so that more effective means of diagnosis, treatment, and prevention will be identified.
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7
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Cannon DS, Miller JS, Robison RJ, Villalobos ME, Wahmhoff NK, Allen-Brady K, McMahon WM, Coon H. Genome-wide linkage analyses of two repetitive behavior phenotypes in Utah pedigrees with autism spectrum disorders. Mol Autism 2010; 1:3. [PMID: 20678246 PMCID: PMC2907569 DOI: 10.1186/2040-2392-1-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2009] [Accepted: 02/22/2010] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND It has been suggested that efforts to identify genetic risk markers of autism spectrum disorder (ASD) would benefit from the analysis of more narrowly defined ASD phenotypes. Previous research indicates that 'insistence on sameness' (IS) and 'repetitive sensory-motor actions' (RSMA) are two factors within the ASD 'repetitive and stereotyped behavior' domain. The primary aim of this study was to identify genetic risk markers of both factors to allow comparison of those markers with one another and with markers found in the same set of pedigrees using ASD diagnosis as the phenotype. Thus, we empirically addresses the possibilities that more narrowly defined phenotypes improve linkage analysis signals and that different narrowly defined phenotypes are associated with different loci. Secondary aims were to examine the correlates of IS and RSMA and to assess the heritability of both scales. METHODS A genome-wide linkage analysis was conducted with a sample of 70 multiplex ASD pedigrees using IS and RSMA as phenotypes. Genotyping services were provided by the Center for Inherited Disease Research using the 6 K single nucleotide polymorphism linkage panel. Analysis was done using the multipoint linkage software program MCLINK, a Markov chain Monte Carlo (MCMC) method that allows for multilocus linkage analysis on large extended pedigrees. RESULTS Genome-wide significance was observed for IS at 2q37.1-q37.3 (dominant model heterogeneity lod score (hlod) 3.42) and for RSMA at 15q13.1-q14 (recessive model hlod 3.93). We found some linkage signals that overlapped and others that were not observed in our previous linkage analysis of the ASD phenotype in the same pedigrees, and regions varied in the range of phenotypes with which they were linked. A new finding with respect to IS was that it is positively associated with IQ if the IS-RSMA correlation is statistically controlled. CONCLUSIONS The finding that IS and RSMA are linked to different regions that only partially overlap regions previously identified with ASD as the phenotype supports the value of including multiple, narrowly defined phenotypes in ASD genetic research. Further, we replicated previous reports indicating that RSMA is more strongly associated than IS with measures of ASD severity.
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Affiliation(s)
- Dale S Cannon
- Utah Autism Research Project, Department of Psychiatry, University of Utah, 650 Komas Drive, Suite 206, Salt Lake City, UT, 84108-3528, USA
| | - Judith S Miller
- Utah Autism Research Project, Department of Psychiatry, University of Utah, 650 Komas Drive, Suite 206, Salt Lake City, UT, 84108-3528, USA
| | - Reid J Robison
- Utah Autism Research Project, Department of Psychiatry, University of Utah, 650 Komas Drive, Suite 206, Salt Lake City, UT, 84108-3528, USA
| | - Michele E Villalobos
- Utah Autism Research Project, Department of Psychiatry, University of Utah, 650 Komas Drive, Suite 206, Salt Lake City, UT, 84108-3528, USA
| | - Natalie K Wahmhoff
- Utah Autism Research Project, Department of Psychiatry, University of Utah, 650 Komas Drive, Suite 206, Salt Lake City, UT, 84108-3528, USA
| | - Kristina Allen-Brady
- Utah Autism Research Project, Department of Psychiatry, University of Utah, 650 Komas Drive, Suite 206, Salt Lake City, UT, 84108-3528, USA
| | - William M McMahon
- Utah Autism Research Project, Department of Psychiatry, University of Utah, 650 Komas Drive, Suite 206, Salt Lake City, UT, 84108-3528, USA
| | - Hilary Coon
- Utah Autism Research Project, Department of Psychiatry, University of Utah, 650 Komas Drive, Suite 206, Salt Lake City, UT, 84108-3528, USA
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Yang R, Li L, Seidelmann SB, Shen GQ, Sharma S, Rao S, Abdullah KG, Mackinlay KG, Elston RC, Chen Q, Topol EJ, Wang QK. A genome-wide linkage scan identifies multiple quantitative trait loci for HDL-cholesterol levels in families with premature CAD and MI. J Lipid Res 2010; 51:1442-51. [PMID: 20075193 DOI: 10.1194/jlr.m004325] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Plasma HDL cholesterol levels (HDL-C) are an independent predictor of coronary artery disease (CAD). We have completed a genome-wide linkage scan for HDL-C in a US cohort consisting of 388 multiplex families with premature CAD (GeneQuest). The heritability of HDL-C in GeneQuest was 0.37 with gender and age as covariates (P = 5.1 x 10(-4)). Two major quantitative trait loci (QTL) for log-transformed HDL-C adjusted for age and gender were identified onto chromosomes 7p22 and 15q25 with maximum multipoint logarithm of odds (LOD) scores of 3.76 and 6.69, respectively. Fine mapping decreased the 7p22 LOD score to a nonsignificant level of 3.09 and split the 15q25 QTL into two loci, one minor QTL on 15q22 (LOD = 2.73) that spanned the LIPC gene, and the other at 15q25 (LOD = 5.63). A family-based quantitative transmission disequilibrium test (QTDT) revealed significant association between variant rs1800588 in LIPC and HDL-C in the GeneQuest population (P = 0.0067), which may account for the minor QTL on 15q22. The 15q25 QTL is the most significant locus identified for HDL-C to date, and these results provide a framework for the ultimate identification of the underlying HDL-C variant and gene on chromosomes 15q25, which will provide insights into novel regulatory mechanisms of HDL-C metabolism.
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Affiliation(s)
- Rong Yang
- Department of Molecular Cardiology, Lerner Research Institute, The Cleveland Clinic Foundation, Center for Cardiovascular Genetics, Cleveland, OH 44195, USA
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9
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Turner ST, Fornage M, Jack CR, Mosley TH, Knopman DS, Kardia SLR, Boerwinkle E, de Andrade M. Genomic susceptibility Loci for brain atrophy, ventricular volume, and leukoaraiosis in hypertensive sibships. ACTA ACUST UNITED AC 2009; 66:847-57. [PMID: 19597086 DOI: 10.1001/archneurol.2009.110] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
OBJECTIVE To localize susceptibility genes for alterations in brain structure associated with risk of stroke and dementia. We conducted genomewide linkage analyses for magnetic resonance imaging (MRI) measures of brain atrophy, ventricular, and subcortical white matter hyperintensity (leukoaraiosis) in 689 non-Hispanic white (673 sibling pairs; median age, 61 years) and 544 non-Hispanic black participants (503 sibling pairs; median age, 64 years) from sibships with at least 2 members with essential hypertension. DESIGN, SETTING, AND PATIENTS We determined brain, ventricular, and leukoaraiosis volumes from axial fluid-attenuated inversion recovery MRI; we calculated brain atrophy as the difference between total intracranial and brain volumes. Microsatellite markers (n = 451) distributed across the 22 autosomes were genotyped, and we used variance components methods to estimate heritability and assess evidence of genetic linkage for each MRI measure. MAIN OUTCOME MEASURES Brain atrophy ventricular volume, and leukoaraiosis determined from fluid-attenuated inversion recovery MRI. RESULTS In both races, the heritability of each MRI measure was statistically greater than 0 (P < .001), ranging in magnitude from 0.42 (for ventricular volume in blacks) to 0.69 (for brain atrophy in blacks). Based on multipoint logarithm of odds scores (MLS), the strongest evidence of genetic linkage was observed for brain atrophy on chromosomes 1 (MLS, 3.49 at 161 cM; P < .001) and 17 (MLS, 3.08 at 18 cM; P < .001) in whites; for ventricular volume on chromosome 12 (MLS, 3.67 at 49 cM; P < .001) in blacks and chromosome 10 (MLS, 2.47 at 110 cM; P < .001) in whites; and for leukoaraiosis on chromosome 11 (MLS, 2.21 at 118 cM; P < .001) in whites and chromosome 22 (MLS, 2.02 at 36 cM; P = .001) in blacks. CONCLUSIONS The MRI measures of structural brain injury are heritable in non-Hispanic black and white sibships ascertained through hypertensive sibling pairs. The susceptibility loci for brain atrophy, ventricular volume, and leukoaraiosis identified by linkage analyses differ among MRI measures and between races.
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Affiliation(s)
- Stephen T Turner
- Division of Nephrology and Hypertension, Department of Internal Medicine, Mayo Clinic and Foundation, Rochester, Minnesota 55905, USA.
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Gallardo D, Pena RN, Amills M, Varona L, Ramírez O, Reixach J, Díaz I, Tibau J, Soler J, Prat-Cuffi JM, Noguera JL, Quintanilla R. Mapping of quantitative trait loci for cholesterol, LDL, HDL, and triglyceride serum concentrations in pigs. Physiol Genomics 2008; 35:199-209. [DOI: 10.1152/physiolgenomics.90249.2008] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The fine mapping of polymorphisms influencing cholesterol (CT), triglyceride (TG), and lipoprotein serum levels in human and mouse has provided a wealth of knowledge about the complex genetic architecture of these traits. The extension of these genetic analyses to pigs would be of utmost importance since they constitute a valuable biological and clinical model for the study of coronary artery disease and myocardial infarction. In the present work, we performed a whole genome scan for serum lipid traits in a half-sib Duroc pig population of 350 individuals. Phenotypic registers included total CT, TG, and low (LDL)- and high (HDL)-density lipoprotein serum concentrations at 45 and 190 days of age. This approach allowed us to identify two genomewide significant quantitative trait loci (QTL) for HDL-to-LDL ratio at 45 days (SSC6, 84 cM) and for TG at 190 days (SSC4, 23 cM) as well as a number of chromosomewide significant QTL. The comparison of QTL locations at 45 and 190 days revealed a notable lack of concordance at these two time points, suggesting that the effects of these QTL are age specific. Moreover, we have observed a considerable level of correspondence among the locations of the most significant porcine lipid QTL and those identified in humans. This finding might suggest that, in mammals, diverse polymorphisms located in a common set of genes are involved in the genetic variation of serum lipid levels.
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Affiliation(s)
- David Gallardo
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra
| | - Ramona N. Pena
- Genètica i Millora Animal, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Lleida
| | - Marcel Amills
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra
| | - Luis Varona
- Genètica i Millora Animal, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Lleida
| | - Oscar Ramírez
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra
| | | | | | - Joan Tibau
- Control i Avaluació de Porcí, IRTA, Monells
| | | | | | - José L. Noguera
- Genètica i Millora Animal, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Lleida
| | - Raquel Quintanilla
- Genètica i Millora Animal, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Lleida
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Stene MCA, Frikke-Schmidt R, Nordestgaard BG, Grande P, Schnohr P, Tybjaerg-Hansen A. Functional promoter variant in zinc finger protein 202 predicts severe atherosclerosis and ischemic heart disease. J Am Coll Cardiol 2008; 52:369-77. [PMID: 18652945 DOI: 10.1016/j.jacc.2008.03.059] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2007] [Revised: 02/08/2008] [Accepted: 03/25/2008] [Indexed: 11/17/2022]
Abstract
OBJECTIVES This study was designed to test the hypotheses that single nucleotide polymorphisms (SNPs), in zinc finger protein 202 (ZNF202), predict severe atherosclerosis and ischemic heart disease (IHD). BACKGROUND ZNF202 is a transcriptional repressor controlling promoter elements in genes involved in vascular maintenance and lipid metabolism. METHODS We first determined genotype association for 9 ZNF202 SNPs with severe atherosclerosis (ankle brachial index >0.7 vs. <or=0.7) in a cross-sectional study of 5,355 individuals from the Danish general population. We then determined genotype association with IHD in 10,431 individuals from the Danish general population, the CCHS (Copenhagen City Heart Study), including 1,511 incident IHD events during 28 years of follow-up. Results were verified in 2 independent case-control studies including, respectively, 942 and 1,549 cases with IHD and 8,998 controls. Finally, we determined whether g.-660A>G altered transcriptional activity of the ZNF202 promoter in vitro. RESULTS Cross-sectionally, ZNF202 g.-660 GG versus AA homozygosity predicted an odds ratio for severe atherosclerosis of 2.01 (95% confidence interval [CI]: 1.34 to 3.01). Prospectively, GG versus AA homozygosity predicted a hazard ratio for IHD of 1.21 (95% CI: 1.02 to 1.43). In the 2 case-control studies, the equivalent odds ratios for IHD were 1.29 (95% CI: 1.02 to 1.62) and 1.60 (95% CI: 1.34 to 1.92), confirming the results from the prospective study. Only 2 other SNPs, which were highly correlated with g.-660A>G, also predicted risk of severe atherosclerosis and IHD. Finally, ZNF202 g.-660G versus g.-660A was associated with a 60% reduction in transcriptional activity in vitro, whereas none of the 2 correlated SNPs were predicted to be functional. CONCLUSIONS Homozygosity for a common functional promoter variant in ZNF202 predicts severe atherosclerosis and an increased risk of IHD.
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Affiliation(s)
- Maria C A Stene
- Department of Clinical Biochemistry, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
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Samudrala N, Farook VS, Dodd GD, Puppala S, Schneider J, Fowler S, Granato R, Dyer TD, Arya R, Almasy L, Jenkinson CP, Diehl AK, Blangero J, Duggirala R. Autosomal Genome-Wide Linkage Analysis to Identify Loci for Gallbladder Wall Thickness in Mexican Americans. Hum Biol 2008; 80:11-28. [DOI: 10.3378/1534-6617(2008)80[11:aglati]2.0.co;2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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13
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Familial occurrence of abnormalities of high-density lipoprotein cholesterol. J Clin Lipidol 2007; 1:31-40. [DOI: 10.1016/j.jacl.2007.01.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2007] [Accepted: 01/25/2007] [Indexed: 11/23/2022]
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Abstract
PURPOSE OF REVIEW High-density lipoproteins have multi-factorial anti-atherosclerosis properties: they have potent anti-oxidant effects and prevent the oxidation of low-density lipoproteins; they have anti-inflammatory effects; they modulate vascular endothelial cell function and transport cholesterol back to the liver for excretion into the bile - a process called reverse cholesterol transport. The present review focuses on genetic aspects of high-density lipoprotein metabolism, with genomic approaches used to identify genes that regulate high-density lipoproteins in humans. RECENT FINDINGS Disorders of the many genes that code for proteins, including transporters, enzymes, receptors, transfer proteins and lipases, involved in high-density lipoprotein metabolism have been identified in humans as causing extremes of high-density lipoprotein cholesterol, and provide potential novel therapeutic avenues. These, however, explain fewer than 5% of the causes of low high-density lipoprotein cholesterol in the general population. SUMMARY Genome-wide linkage studies of large cohorts, with discrete as well as quantitative trait loci analyses, followed by association studies have enabled the identification of large chromosomal regions that may harbor genes that modulate high-density lipoprotein cholesterol levels in humans. Using mouse genetics, the results of the HapMap project and novel genetic approaches will allow the discovery of novel genes in high-density lipoprotein metabolism.
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Affiliation(s)
- Zari Dastani
- Cardiovascular Genetics Laboratory, Division of Cardiology, McGill University Health Centre/Royal Victoria Hospital, Montréal, Québec, Canada
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15
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Abstract
Longitudinal population studies have confirmed plasma levels of high-density lipoprotein (HDL) cholesterol to be an important inverse coronary risk factor. Although environmental influences are known to regulate HDL cholesterol levels, genetic factors are also known to be important, and over 25 candidate genes have been proposed to be associated with variation in HDL cholesterol levels. A variety of monogenic conditions of extremely low or high HDL cholesterol has helped to delineate the physiology of HDL cholesterol metabolism in humans, which has led to the development of new therapeutic approaches to HDL cholesterol. However, most causes of genetic variation in HDL cholesterol in the general population are likely oligogenic or polygenic. We review the monogenic disorders associated with both high and low HDL cholesterol and the relevance of mutations and polymorphisms in these genes to variation in HDL cholesterol levels in the general population.
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Affiliation(s)
- Atif Qasim
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, 421 Curie Boulevard, Philadelphia, PA 19104, USA
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16
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Stene MC, Frikke-Schmidt R, Nordestgaard BG, Tybjaerg-Hansen A. Zinc Finger Protein 202, genetic variation, and HDL cholesterol in the general population. J Lipid Res 2006; 47:944-52. [PMID: 16467280 DOI: 10.1194/jlr.m500521-jlr200] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Zinc Finger Protein 202 (ZNF202) is a transcriptional repressor that binds elements found predominantly in genes involved in HDL metabolism. We tested the following hypotheses: 1) frequencies of single-nucleotide polymorphisms (SNPs) and haplotypes in ZNF202 differ between individuals with low and high HDL cholesterol; and 2) SNPs in ZNF202 affect HDL cholesterol levels in the general population. We screened the promoter and protein-coding exons of ZNF202 in individuals with the highest 1% (n = 95) and lowest 1% (n = 95) HDL cholesterol among 9,259 Danish adults. None of the 10 SNPs identified differed in frequency as single sites or as haplotypes between low and high HDL cholesterol groups. In accordance with this, seven mutations were equally frequent (4-5%) in individuals with low or high HDL cholesterol. Finally, for all five SNPs identified in the coding region, we determined the association of genotype with HDL cholesterol in 9,259 individuals from the general population. Four SNPs were not associated with variation in HDL cholesterol, although c.*2T>G homozygosity was associated with a discrete effect on HDL cholesterol in men. We show that genetic variation in ZNF202 is common in the general population. However, SNPs in the protein-coding region of ZNF202 do not make a major contribution to HDL cholesterol levels.
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Affiliation(s)
- Maria C Stene
- Department of Clinical Biochemistry, Rigshospitalet, Copenhagen University Hospital, Denmark
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17
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Camp NJ, Farnham JM, Cannon Albright LA. Genomic search for prostate cancer predisposition loci in Utah pedigrees. Prostate 2005; 65:365-74. [PMID: 16037989 DOI: 10.1002/pros.20287] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
BACKGROUND We report a genome linkage scan in extended Utah pedigrees, utilizing a pedigree-splitting approach to reduce intra-familial heterogeneity. METHODS Fifty-nine pedigrees with at least four Prostate cancer (PrCa) cases and no more than two meioses separating PrCa cases were analyzed using the CIDR genomic search STRP marker set. Parametric linkage analyses using dominant and recessive models were performed on four datasets resulting from a pedigree splitting algorithm. In addition, age at diagnosis subset analyses were performed. RESULTS Four regions of interest (LODs>1.9) were identified on chromosomes 1p, 3q, 5q, and 22q. The linkage peaks on 1p, 3q, and 22q have been previously implicated for PrCa, though not significantly. The 1p region was supported by a single large Utah pedigree with a multipoint LOD score of 3.1. An additional 10 regions gave LOD scores>1.22 (nominal linkage evidence), including moderate evidence supporting the HPC20 region with a recessive model. CONCLUSIONS Our genome-wide search in the informative, extended Utah pedigrees continues to illustrate an ability to identify and replicate linkage peaks, and supports four regions of interest for PrCa predisposition genes.
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Affiliation(s)
- Nicola J Camp
- Genetic Epidemiology, Department of Medical Informatics, University of Utah, Salt Lake City, Utah 84108, USA
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Dastani Z, Quiogue L, Plaisier C, Engert JC, Marcil M, Genest J, Pajukanta P. Evidence for a gene influencing high-density lipoprotein cholesterol on chromosome 4q31.21. Arterioscler Thromb Vasc Biol 2005; 26:392-7. [PMID: 16322534 DOI: 10.1161/01.atv.0000198243.83781.a3] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
OBJECTIVE A low level of plasma high-density lipoprotein cholesterol (HDL-C) is a major risk factor for coronary atherosclerosis. To identify novel genes regulating plasma HDL-C levels, we investigated 13 multigenerational French Canadian families with an average of 12 affected individuals per family for genome-wide signals, which we subsequently fine mapped. METHODS AND RESULTS We genotyped a total of 362 individuals, including 151 affected subjects for 485 autosomal microsatellite markers. In parametric 2-point linkage analyses, the highest 2-point logarithm of odds (lod) score of 4.6 was observed with marker D4S424 on chromosome 4q31.21 (at approximately 142 Mb). The multipoint analysis of this region resulted in a lod score of 3.8 and a lod -1 region of 12.2 cM, containing 40 known genes. The results were obtained by allowing for genetic heterogeneity among these extended pedigrees, and approximately 50% of families were linked to this region with the highest single-pedigree lod score being 3.6. We further restricted the linked region from 12.2 to 2.9 cM (2.37 Mb) by genotyping 15 additional markers in the 3 families with the highest lod scores. We sequenced 4 genes with a likely role in lipid metabolism as well as 2 genes residing directly under the linkage peak but found no evidence for a causative variant. None of the genes residing in the significantly restricted 2.37-Mb region has been associated previously with HDL-C metabolism. CONCLUSIONS This study provides significant evidence for a gene influencing HDL-C on chromosome 4q31.21.
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Affiliation(s)
- Zari Dastani
- Department of Medicine, McGill University, Montreal, Canada
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19
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Edelstein LC, Collins T. The SCAN domain family of zinc finger transcription factors. Gene 2005; 359:1-17. [PMID: 16139965 DOI: 10.1016/j.gene.2005.06.022] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2005] [Revised: 05/26/2005] [Accepted: 06/03/2005] [Indexed: 12/29/2022]
Abstract
Zinc finger transcription factor genes represent a significant portion of the genes in the vertebrate genome. Some Cys2His2 type zinc fingers are associated with conserved protein domains that help to define these regulators. A novel domain of this type, the SCAN domain, is a highly conserved 84-residue motif that is found near the N-terminus of a subfamily of C2H2 zinc finger proteins. The SCAN domain, which is also known as the leucine rich region, functions as a protein interaction domain, mediating self-association or selective association with other proteins. Here we define the mouse SCAN domain and annotate the mouse SCAN family members. In addition to a single SCAN domain, some of the members of the mouse SCAN family members have a conserved N-terminal motif, a KRAB domain, SANT domains and a variable number of C2H2 type zinc fingers (3-14). The genes encoding mouse SCAN domains are clustered, often in tandem arrays, and are capable of generating isoforms that may affect the function of family members. Although the function of most of the family members is not known, an overview of selected members of this group of transcription factors suggests that some of the mouse SCAN domain family members play roles in cell survival and differentiation.
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Affiliation(s)
- Leonard C Edelstein
- Department of Pathology, Children's Hospital Boston and Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
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20
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Yu Y, Wyszynski DF, Waterworth DM, Wilton SD, Barter PJ, Kesäniemi YA, Mahley RW, McPherson R, Waeber G, Bersot TP, Ma Q, Sharma SS, Montgomery DS, Middleton LT, Sundseth SS, Mooser V, Grundy SM, Farrer LA. Multiple QTLs influencing triglyceride and HDL and total cholesterol levels identified in families with atherogenic dyslipidemia. J Lipid Res 2005; 46:2202-13. [PMID: 16061952 DOI: 10.1194/jlr.m500137-jlr200] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We conducted a genome-wide scan using variance components linkage analysis to localize quantitative-trait loci (QTLs) influencing triglyceride (TG), high density lipoprotein-cholesterol (HDL-C), low density lipoprotein-cholesterol, and total cholesterol (TC) levels in 3,071 subjects from 459 families with atherogenic dyslipidemia. The most significant evidence for linkage to TG levels was found in a subset of Turkish families at 11q22 [logarithm of the odds ratio (LOD)=3.34] and at 17q12 (LOD=3.44). We performed sequential oligogenic linkage analysis to examine whether multiple QTLs jointly influence TG levels in the Turkish families. These analyses revealed loci at 20q13 that showed strong epistatic effects with 11q22 (conditional LOD=3.15) and at 7q36 that showed strong epistatic effects with 17q12 (conditional LOD=3.21). We also found linkage on the 8p21 region for TG in the entire group of families (LOD=3.08). For HDL-C levels, evidence of linkage was identified on chromosome 15 in the Turkish families (LOD=3.05) and on chromosome 5 in the entire group of families (LOD=2.83). Linkage to QTLs for TC was found at 8p23 in the entire group of families (LOD=4.05) and at 5q13 in a subset of Turkish and Mediterranean families (LOD=3.72). These QTLs provide important clues for the further investigation of genes responsible for these complex lipid phenotypes. These data also indicate that a large proportion of the variance of TG levels in the Turkish population is explained by the interaction of multiple genetic loci.
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Affiliation(s)
- Yi Yu
- Department of Medicine (Genetics Program), Boston University School of Medicine, Boston, MA, USA
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Gagnon F, Jarvik GP, Badzioch MD, Motulsky AG, Brunzell JD, Wijsman EM. Genome scan for quantitative trait loci influencing HDL levels: evidence for multilocus inheritance in familial combined hyperlipidemia. Hum Genet 2005; 117:494-505. [PMID: 15959807 DOI: 10.1007/s00439-005-1338-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2004] [Accepted: 04/27/2005] [Indexed: 11/25/2022]
Abstract
Several genome scans in search of high-density lipoprotein (HDL) quantitative trait loci (QTLs) have been performed. However, to date the actual identification of genes implicated in the regulation of common forms of HDL abnormalities remains unsuccessful. This may be due, in part, to the oligogenic and multivariate nature of HDL regulation, and potentially, pleiotropy affecting HDL and other lipid-related traits. Using a Bayesian Markov Chain Monte Carlo (MCMC) approach, we recently provided evidence of linkage of HDL level variation to the APOA1-C3-A4-A5 gene complex, in familial combined hyperlipidemia pedigrees, with an estimated number of two to three large QTLs remaining to be identified. We also presented results consistent with pleiotropy affecting HDL and triglycerides at the APOA1-C3-A4-A5 gene complex. Here we use the same MCMC analytic strategy, which allows for oligogenic trait models, as well as simultaneous incorporation of covariates, in the context of multipoint analysis. We now present results from a genome scan in search for the additional HDL QTLs in these pedigrees. We provide evidence of linkage for additional HDL QTLs on chromosomes 3p14 and 13q32, with results on chromosome 3 further supported by maximum parametric and variance component LOD scores of 3.0 and 2.6, respectively. Weaker evidence of linkage was also obtained for 7q32, 12q12, 14q31-32 and 16q23-24.
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Affiliation(s)
- France Gagnon
- Department of Epidemiology and Community Medicine, University of Ottawa, Ottawa, Ontario, Canada
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22
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Pajukanta P. Do DNA sequence variants in ABCA1 contribute to HDL cholesterol levels in the general population? J Clin Invest 2004; 114:1244-7. [PMID: 15520856 PMCID: PMC524241 DOI: 10.1172/jci23466] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
HDL has a key role in reverse cholesterol transport, mobilizing cholesterol from the peripheral tissues to liver. In this process, the ABC transporter A1 (ABCA1) protein controls the efflux of intracellular cholesterol to apoAI, the major apolipoprotein of HDL. Since ABCA1 mutations were discovered to cause Tangier disease, a rare recessive HDL deficiency, it has been speculated that sequence variants in ABCA1 might also contribute to variations in plasma HDL cholesterol levels in the general population. A new study provides genetic evidence supporting this hypothesis.
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Affiliation(s)
- Päivi Pajukanta
- Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, California 90095-7088, USA.
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Farnham JM, Camp NJ, Swensen J, Tavtigian SV, Albright LAC. Confirmation of the HPCX prostate cancer predisposition locus in large Utah prostate cancer pedigrees. Hum Genet 2004; 116:179-85. [PMID: 15592687 DOI: 10.1007/s00439-004-1220-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2004] [Accepted: 11/03/2004] [Indexed: 11/28/2022]
Abstract
Several genetic predisposition loci for prostate cancer have been identified through linkage analysis, and it is now generally recognized that no single gene is responsible for more than a small proportion of prostate cancers. However, published confirmations of these loci have been few, and failures to confirm have been frequent. The genetic etiology of prostate cancer is clearly complex and includes significant genetic heterogeneity, phenocopies, and reduced penetrance. Powerful analyses that involve robust statistics and methods to reduce genetic heterogeneity are therefore necessary. We have performed linkage analysis on 143 Utah pedigrees for the previously published Xq27-28 (HPCX) prostate cancer susceptibility locus. We employed a robust multipoint statistic (TLOD) and a novel splitting algorithm to reduce intra-familial heterogeneity by iteratively removing the top generation from the large Utah pedigrees. In a dataset containing pedigrees having no more than five generations, we observed a multipoint TLOD of 2.74 (P=0.0002), which is statistically significant after correction for multiple testing. For both the full-structure pedigrees (up to seven generations) and the smaller sub-pedigrees, the linkage evidence was much reduced. This study thus represents the first significant confirmation of HPCX (Xq27-28) and argues for the continued utility of large pedigrees in linkage analyses for complex diseases.
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Affiliation(s)
- James M Farnham
- Genetic Epidemiology, Department of Medical Informatics, University of Utah, Salt Lake City, UT 84108, USA
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24
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Pajukanta P. Do DNA sequence variants in ABCA1 contribute to HDL cholesterol levels in the general population? J Clin Invest 2004. [DOI: 10.1172/jci200423466] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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25
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Wallis RH, Wallace KJ, Collins SC, McAteer M, Argoud K, Bihoreau MT, Kaisaki PJ, Gauguier D. Enhanced insulin secretion and cholesterol metabolism in congenic strains of the spontaneously diabetic (Type 2) Goto Kakizaki rat are controlled by independent genetic loci in rat chromosome 8. Diabetologia 2004; 47:1096-106. [PMID: 15164172 DOI: 10.1007/s00125-004-1416-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2004] [Accepted: 03/03/2004] [Indexed: 10/26/2022]
Abstract
AIMS/HYPOTHESIS Genetic investigations in the spontaneously diabetic (Type 2) Goto Kakizaki (GK) rat have identified quantitative trait loci (QTL) for diabetes-related phenotypes. The aims of this study were to refine the chromosomal mapping of a QTL ( Nidd/gk5) identified in chromosome 8 of the GK rat and to define a pathophysiological profile of GK gene variants underlying the QTL effects in congenics. METHODS Genetic linkage analysis was carried out with chromosome 8 markers genotyped in a GKxBN F2 intercross previously used to map diabetes QTL. Two congenic strains were designed to contain GK haplotypes in the region of Nidd/gk5 transferred onto a Brown Norway (BN) genetic background, and a broad spectrum of diabetes phenotypes were characterised in the animals. RESULTS Results from QTL mapping suggest that variations in glucose-stimulated insulin secretion in vivo, and in body weight are controlled by different chromosome 8 loci (LOD3.53; p=0.0004 and LOD4.19; p=0.00007, respectively). Extensive physiological screening in male and female congenics at 12 and 24 weeks revealed the existence of GK variants at the locus Nidd/gk5, independently responsible for significantly enhanced insulin secretion and increased levels of plasma triglycerides, phospholipids and HDL, LDL and total cholesterol. Sequence polymorphisms detected between the BN and GK strains in genes encoding ApoAI, AIV, CIII and Lipc do not account for these effects. CONCLUSIONS/INTERPRETATION We refined the localisation of the QTL Nidd/gk5 and its pathophysiological characteristics in congenic strains derived for the locus. These congenic strains provide novel models for testing the contribution of a subset of GK alleles on diabetes phenotypes and for identifying diabetes susceptibility genes.
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Affiliation(s)
- R H Wallis
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Headington, Oxford OX3 7BN, UK
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26
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Lyons MA, Korstanje R, Li R, Walsh KA, Churchill GA, Carey MC, Paigen B. Genetic contributors to lipoprotein cholesterol levels in an intercross of 129S1/SvImJ and RIIIS/J inbred mice. Physiol Genomics 2004; 17:114-21. [PMID: 14872007 DOI: 10.1152/physiolgenomics.00168.2003] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
To determine the genetic contribution to variation among lipoprotein cholesterol levels, we performed quantitative trait locus (QTL) analyses on an intercross between mouse strains RIIIS/J and 129S1/SvImJ. Male mice of the parental strains and the reciprocal F1and F2populations were fed a high-cholesterol, cholic acid-containing diet for 8–12 wk. At the end of the feeding period, plasma total, high-density lipoprotein (HDL), and non-HDL cholesterol were determined. For HDL cholesterol, we identified three significant QTLs on chromosomes (Chrs) 1 ( D1Mit507, 88 cM, 72–105 cM, 4.8 LOD), 9 ( D11Mit149, 14 cM, 10–25 cM, 9.4 LOD), and 12 ( D12Mit60, 20 cM, 0–50 cM, 5.0 LOD). These QTLs were considered identical to QTLs previously named Hdlq5, Hdlq17, and Hdlq18, respectively, in crosses sharing strain 129. For total cholesterol, we identified two significant QTLs on Chrs 1 and 9, which were named Chol10 ( D1Mit507, 88 cM, 10–105 cM, 3.9 LOD) and Chol11 ( D11Mit149, 14 cM, 0–30 cM, 4.4 LOD), respectively. In addition, for total cholesterol, we identified two suggestive QTLs on Chrs 12 (distal) and 17, which remain unnamed. For non-HDL cholesterol, we identified and named one new QTL on Chr 17, Nhdlq3 ( D17Mit221, 58 cM, 45–60 cM, 3.4 LOD). Nhdlq3 colocalized with orthologous human QTLs for lipoprotein phenotypes, and with Abcg5 and Abcg8. Overall, we detected eight QTLs for lipoprotein cholesterol concentrations on Chrs 1, 9, 12, and 17 (each two per chromosome), including a new QTL for non-HDL cholesterol, Nhdlq3, on Chr 17.
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Schmitz G, Heimerl S, Langmann T. Zinc finger protein ZNF202 structure and function in transcriptional control of HDL metabolism. Curr Opin Lipidol 2004; 15:199-208. [PMID: 15017363 DOI: 10.1097/00041433-200404000-00013] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW The zinc finger protein ZNF202 is a transcriptional repressor controlling promoter elements predominantly found in genes involved in lipid metabolism and energy homeostasis. Here we summarize the structure, regulation and modulation of ZNF202 function by protein interactions. RECENT FINDINGS We review recent data and discuss the importance of the steadily growing list of ZNF202 target genes, defining a central role for ZNF202 as a key transcriptional regulator in metabolic disorders. Furthermore, we provide an interlink between transcriptional repression by ZNF202 and enhancement of gene activation via nuclear receptor coactivation by SCAN domain protein 1. SUMMARY The novel findings suggest that ZNF202 together with other SCAN domain proteins orchestrates a complex transcriptional regulatory network, which justifies a further exploration of its potential as a therapeutic target in lipid disorders such as atherosclerosis and associated metabolic syndromes.
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Affiliation(s)
- Gerd Schmitz
- Institute of Clinical Chemistry and Laboratory Medicine, University of Regensburg, Regensburg, Germany.
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Bossé Y, Chagnon YC, Després JP, Rice T, Rao DC, Bouchard C, Pérusse L, Vohl MC. Genome-wide linkage scan reveals multiple susceptibility loci influencing lipid and lipoprotein levels in the Quebec Family Study. J Lipid Res 2003; 45:419-26. [PMID: 14679165 DOI: 10.1194/jlr.m300401-jlr200] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A genome-wide linkage study was performed to identify chromosomal regions harboring genes influencing lipid and lipoprotein levels. Linkage analyses were conducted for four quantitative lipoprotein/lipid traits, i.e., total cholesterol, triglyceride, HDL-cholesterol (HDL-C), and LDL-C concentrations, in 930 subjects enrolled in the Québec Family Study. A maximum of 534 pairs of siblings from 292 nuclear families were available. Linkage was tested using both allele-sharing and variance-component linkage methods. The strongest evidence of linkage was found on chromosome 12q14.1 at marker D12S334 for HDL-C, with a logarithm of the odds (LOD) score of 4.06. Chromosomal regions harboring quantitative trait loci (QTLs) for LDL-C included 1q43 (LOD = 2.50), 11q23.2 (LOD = 3.22), 15q26.1 (LOD = 3.11), and 19q13.32 (LOD = 3.59). In the case of triglycerides, three markers located on 2p14, 11p13, and 11q24.1 provided suggestive evidence of linkage (LOD > 1.75). Tests for total cholesterol levels yielded significant evidence of linkage at 15q26.1 and 18q22.3 with the allele-sharing linkage method, but the results were nonsignificant with the variance-component method. In conclusion, this genome scan provides evidence for several QTLs influencing lipid and lipoprotein levels. Promising candidate genes were located in the vicinity of the genomic regions showing evidence of linkage.
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Affiliation(s)
- Y Bossé
- Lipid Research Center, Laval University Medical Research Center, and Department of Food Science and Nutrition, Laval University, Québec, Canada
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Abkevich V, Camp NJ, Hensel CH, Neff CD, Russell DL, Hughes DC, Plenk AM, Lowry MR, Richards RL, Carter C, Frech GC, Stone S, Rowe K, Chau CA, Cortado K, Hunt A, Luce K, O'Neil G, Poarch J, Potter J, Poulsen GH, Saxton H, Bernat-Sestak M, Thompson V, Gutin A, Skolnick MH, Shattuck D, Cannon-Albright L. Predisposition locus for major depression at chromosome 12q22-12q23.2. Am J Hum Genet 2003; 73:1271-81. [PMID: 14606042 PMCID: PMC1180393 DOI: 10.1086/379978] [Citation(s) in RCA: 146] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2003] [Accepted: 09/12/2003] [Indexed: 11/03/2022] Open
Abstract
Major depression disorder is a common psychiatric disease with a major economic impact on society. In many cases, no effective treatment is available. The etiology of major depression is complex, but it is clear that the disease is, to a large extent, determined genetically, especially among individuals with a familial history of major depression, presumably through the involvement of multiple predisposition genes in addition to an environmental component. As a first step toward identification of chromosomal loci contributing to genetic predisposition to major depression, we have conducted a genomewide scan by using 628 microsatellite markers on 1,890 individuals from 110 Utah pedigrees with a strong family history of major depression. We identified significant linkage to major depression in males at marker D12S1300 (multipoint heterogeneity LOD score 4.6; P=.00003 after adjustment for multiple testing). With additional markers, the linkage evidence became highly significant, with the multipoint heterogeneity LOD score at marker D12S1706 increasing to 6.1 (P=.0000007 after adjustment for multiple testing). This study confirms the presence of one or more genes involved in psychiatric diseases on the q arm of chromosome 12 and provides strong evidence for the existence of a sex-specific predisposition gene to major depression at 12q22-q23.2.
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Langmann T, Schumacher C, Morham SG, Honer C, Heimerl S, Moehle C, Schmitz G. ZNF202 is inversely regulated with its target genes ABCA1 and apoE during macrophage differentiation and foam cell formation. J Lipid Res 2003; 44:968-77. [PMID: 12611910 DOI: 10.1194/jlr.m300016-jlr200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The zinc finger protein ZNF202 is a transcriptional repressor that binds to promoter elements predominantly found in genes involved in lipid metabolism. Here we demonstrate that ZNF202 mRNA expression is inversely correlated with ATP binding cassette A1 (ABCA1), ABCG1, and apolipoprotein E (apoE) in human monocytes. Upregulation of ABCA1, ABCG1, and apoE expression during monocyte differentiation and foam cell formation was accompanied by a simultaneous downregulation of both ZNF202 mRNA isoforms m1 and m3. Conversely, deloading of macrophage foam cells with HDL3 caused upregulation of ZNF202 mRNA. To further characterize the transcriptional regulation of the ZNF202 gene, comparative genomic sequence analysis and reporter gene assays were performed. The ZNF202 core promoter region resides within 247 bp upstream of the transcription initiation site and is highly active in THP-1 monocytes, yet downregulated upon macrophage differentiation. Using site-directed mutagenesis, we show that two highly conserved transcription factor binding sites, a GC-box and an Ets-binding motif, are required for ZNF202 gene expression. Furthermore, electrophoretic mobility shift assays demonstrate in vitro binding of PU.1 and GC-box binding proteins to the ZNF202 proximal promoter. We conclude that the inversely correlated transcriptional activity of ZNF202 and its target genes during macrophage differentiation may reflect a direct regulatory interdependence and thus provide further evidence for ZNF202 as an important gatekeeper of lipid efflux.
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Affiliation(s)
- Thomas Langmann
- Novartis Institute for Biomedical Research, Summit, NJ 07901, USA
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Lilja HE, Soro A, Ylitalo K, Nuotio I, Viikari JSA, Salomaa V, Vartiainen E, Taskinen MR, Peltonen L, Pajukanta P. A candidate gene study in low HDL-cholesterol families provides evidence for the involvement of the APOA2 gene and the APOA1C3A4 gene cluster. Atherosclerosis 2002; 164:103-11. [PMID: 12119199 DOI: 10.1016/s0021-9150(02)00040-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In patients with premature coronary heart disease, the most common lipoprotein abnormality is high-density lipoprotein (HDL) deficiency. To assess the genetic background of the low HDL-cholesterol trait, we performed a candidate gene study in 25 families with low HDL, collected from the genetically isolated population of Finland. We studied 21 genes encoding essential proteins involved in the HDL metabolism by genotyping intragenic and flanking markers for these genes. We found suggestive evidence for linkage in two candidate regions: Marker D1S2844, in the apolipoprotein A-II (APOA2) region, yielded a LOD score of 2.14 and marker D11S939 flanking the apolipoprotein A-I/C-III/A-IV gene cluster (APOA1C3A4) produced a LOD score of 1.69. Interestingly, we identified potential shared haplotypes in these two regions in a subset of low HDL families. These families also contributed to the obtained positive LOD scores, whereas the rest of the families produced negative LOD scores. None of the remaining candidate regions provided any evidence for linkage. Since only a limited number of loci were tested in this candidate gene study, these LOD scores suggest significant involvement of the APOA2 gene and the APOA1C3A4 gene cluster, or loci in their immediate vicinity, in the pathogenesis of low HDL.
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Affiliation(s)
- Heidi E Lilja
- Department of Human Molecular Genetics, National Public Health Institute, Helsinki, Finland
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Kronenberg F, Coon H, Gutin A, Abkevich V, Samuels ME, Ballinger DG, Hopkins PN, Hunt SC. A genome scan for loci influencing anti-atherogenic serum bilirubin levels. Eur J Hum Genet 2002; 10:539-46. [PMID: 12173031 DOI: 10.1038/sj.ejhg.5200842] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2001] [Revised: 05/14/2002] [Accepted: 05/16/2002] [Indexed: 01/19/2023] Open
Abstract
Epidemiological studies have shown an association of decreased serum bilirubin levels with coronary artery disease. Two segregation analyses in large pedigrees have suggested a major gene responsible for high bilirubin levels occurring in about 12% of the population. Based on a recessive model from a previous segregation analysis, we performed a genome scan using 587 markers genotyped in 862 individuals from 48 Utah pedigrees to detect loci linked to high bilirubin levels. As a complementary approach, non-parametric linkage (NPL) analysis was performed. These two methods identified four regions showing evidence for linkage. The first region is on chromosome 2q34-37 with multipoint LOD and NPL scores of 3.01 and 3.22, respectively, for marker D2S1363. This region contains a previously described gene, uridine diphosphate glycosyltransferase 1, which has been associated with high bilirubin levels. A polymorphism in the promoter of this gene was recently shown to be responsible for Gilbert syndrome which is associated with mild hyperbilirubinemia. The other regions were found on chromosomes 9q21, 10q25-26, and 18q12 with maximum NPL scores of 2.39, 1.55, and 2.79, respectively. Furthermore, we investigated in these pedigrees the association between bilirubin levels and coronary artery disease. One-hundred and sixty-one male and 41 female subjects had already suffered a coronary artery disease event. Male patients showed significantly lower bilirubin concentrations than age-matched controls. This association, however, was not observed in females. These results provide evidence that loci influencing bilirubin variation exist on chromosomes 2q34-37, 9q21, 10q25-26, and 18q12 and confirms the association of low bilirubin levels with coronary artery disease in males.
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Wang X, Paigen B. Quantitative trait loci and candidate genes regulating HDL cholesterol: a murine chromosome map. Arterioscler Thromb Vasc Biol 2002; 22:1390-401. [PMID: 12231556 DOI: 10.1161/01.atv.0000030201.29121.a3] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
OBJECTIVE Summarizing the many discovered mouse and human quantitative trait loci (QTL) for high density lipoprotein (HDL) cholesterol (HDL-C) levels is important for guiding future research on the genetic regulation of HDL concentrations and for finding gene targets for upregulating HDL levels in mice and humans. METHODS AND RESULTS We summarized the 27 QTL and candidate genes associated with HDL-C concentrations in mice and plotted them on a mouse chromosome map. We also summarized the 22 human QTL for HDL-C levels and compared them with those of the mouse by comparative genomics. At least part of the mouse homologies for 18 of the 22 human HDL-C QTL were within the murine HDL-C QTL. CONCLUSIONS Murine QTL for HDL-C levels may predict their homologous location in humans, and their underlying genes may be appropriate genes to test in humans.
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Annilo T, Tammur J, Hutchinson A, Rzhetsky A, Dean M, Allikmets R. Human and mouse orthologs of a new ATP-binding cassette gene, ABCG4. Cytogenet Genome Res 2002; 94:196-201. [PMID: 11856881 DOI: 10.1159/000048816] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We characterized a new ATP-binding cassette (ABC) transporter gene from human and mouse that is highly expressed in the brain. The gene, ABCG4, produces several transcripts that differ at the 5' end and encode proteins of various lengths. The ABCG4 protein is closely related to the Drosophila white and human ABCG1 genes, and belongs to the ABCG subfamily several members of which are involved in cholesterol transport. All representatives of this "reverse transporter" subfamily, including ABCG4, have a single ATP-binding domain at the N-terminus and a single C-terminal set of transmembrane segments. ABCG4 maps to human chromosome 11q23, between the markers D11S939 and D11S924, and Abcg4 to a conserved syntenic region on mouse chromosome 9. The abundant expression of this gene in the brain and close evolutionary relationship to the other members of the subfamily suggests a potential role for ABCG4 in cholesterol transport processes in this tissue.
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Affiliation(s)
- T Annilo
- Laboratory of Genomic Diversity, NCI-FCRDC, Frederick, MD, USA
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Elbein SC, Hasstedt SJ. Quantitative trait linkage analysis of lipid-related traits in familial type 2 diabetes: evidence for linkage of triglyceride levels to chromosome 19q. Diabetes 2002; 51:528-35. [PMID: 11812765 DOI: 10.2337/diabetes.51.2.528] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Macrovascular disease is a major complication of type 2 diabetes. Epidemiological data suggest that the risk of macrovascular complications may predate the onset of hyperglycemia. Hypertriglyceridemia, low levels of HDL cholesterol, and an atherogenic profile characterize the insulin resistance/metabolic syndrome that is also prevalent among nondiabetic members of familial type 2 diabetic kindreds. To identify the genes for lipid-related traits, we first performed a 10-cM genome scan using 440 markers in 379 members of 19 multiplex families ascertained for two diabetic siblings (screening study). We then extended findings for three regions with initial logarithm of odds (LOD) scores >1.5 to an additional 23 families, for a total of 576 genotyped individuals (extended study). We found heritabilities for all lipid measures in the range of 0.31 to 0.52, similar to those reported by others in unselected families. However, we found the strongest evidence for linkage of triglyceride levels to chromosome 19q13.2, very close to the ApoC2/ApoE/ApoC1/ApoC4 gene cluster (LOD 2.56) in the screening study; the LOD increased to 3.16 in the extended study. Triglyceride-to-HDL cholesterol ratios showed slightly lower LOD scores (2.73, extended family) in this same location. Other regions with LOD scores >2.0 included HDL linkage to chromosome 1q21-q23, where susceptibility loci for both familial type 2 diabetes and familial combined hyperlipidemia have been mapped, and to chromosome 2q in the region of the NIDDM1 locus. Neither region showed stronger evidence for linkage in the extended studies, however. Our results suggest that genes in or near the ApoE/ApoC2/ApoC1/ApoC4 cluster on 19q13.2 may contribute to the commonly observed hypertriglyceridemia and low HDL seen in diabetic family members and their offspring, and thus may be a candidate locus for the insulin resistance syndrome.
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Affiliation(s)
- S C Elbein
- Department of Endocrinology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205-7199, USA.
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Hegele RA. Monogenic dyslipidemias: window on determinants of plasma lipoprotein metabolism. Am J Hum Genet 2001; 69:1161-77. [PMID: 11704922 PMCID: PMC1235529 DOI: 10.1086/324647] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2001] [Accepted: 09/27/2001] [Indexed: 12/19/2022] Open
Affiliation(s)
- R A Hegele
- John P. Robarts Research Institute, London, Ontario, Canada.
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Peacock JM, Arnett DK, Atwood LD, Myers RH, Coon H, Rich SS, Province MA, Heiss G. Genome scan for quantitative trait loci linked to high-density lipoprotein cholesterol: The NHLBI Family Heart Study. Arterioscler Thromb Vasc Biol 2001; 21:1823-8. [PMID: 11701472 DOI: 10.1161/hq1101.097804] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We conducted a genome-wide linkage scan for quantitative trait loci influencing total HDL-cholesterol (HDL-C) concentration in a sample of 1027 whites from 101 families participating in the NHLBI Family Heart Study. To maximize the relative contribution of genetic components of variance to the total variance of HDL-C, the HDL-C phenotype was adjusted for age, age(2), body mass index, and Family Heart Study field center, and standardized HDL-C residuals were created separately for men and women. All analyses were completed by the variance components method, as implemented in the program GENEHUNTER using 383 anonymous markers typed at the NHLBI Mammalian Genotyping Service in Marshfield, Wis. Evidence for linkage of residual HDL-C was detected near marker D5S1470 at location 39.9 cM from the p-terminal of chromosome 5 (LOD=3.64). Suggestive linkage was detected near marker D13S1493 at location 27.5 cM on chromosome 13 (LOD=2.36). We conclude that at least 1 genomic region is likely to harbor a gene that influences interindividual variation in HDL cholesterol.
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Affiliation(s)
- J M Peacock
- Division of Epidemiology, School of Public Health, University of Minnesota, Minneapolis, Minnesota, USA
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Affiliation(s)
- T Collins
- Department of Pathology, Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.
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Abstract
The role of the ATP-binding cassette transporter 1 (ABCA1) in cellular lipid efflux and high density lipoprotein metabolism has been recently documented by mutations in genetic HDL deficiency syndromes such as classical Tangier disease. Analysis of ABCA1 knockout mice and overexpression studies have established the importance of ABCA1 as a major determinant of HDL cholesterol in plasma. These studies also indicate that ABCA1 is critically involved in cellular trafficking of cholesterol and choline-phospholipids and in total body lipid homeostasis, such as intestinal cholesterol and fat-soluble vitamin absorption and in the modulation of steroidogenesis. First insights into the upregulation of ABCA1 gene expression by cellular cholesterol and cAMP have identified critical ABCA1 promoter elements, which bind the transcription factors liver X receptor, retinoid X receptor, Sp1 and E-box proteins. The finding that a lipid sensitive subgroup of ABC transporters is able to translocate cholesterol and phospholipids supports the concept that in ABCA1 deficiency, compensatory mechanisms possibly involving MDR1, MDR3 and MRP-family members could be active. This suggests that a network of ABC transporters involved in cellular lipid transport exists, which is under the tight control of energy pathways directly linked to high density lipoprotein metabolism and atherogenesis.
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Affiliation(s)
- G Schmitz
- Institute for Clinical Chemistry and Laboratory Medicine, University of Regensburg, Regensburg, Germany.
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Samuels ME, Forbey KC, Reid JE, Abkevich V, Bulka K, Wardell BR, Bowen BR, Hopkins PN, Hunt SC, Ballinger DG, Skolnick MH, Wagner S. Identification of a common variant in the lipoprotein lipase gene in a large Utah kindred ascertained for coronary heart disease: the -93G/D9N variant predisposes to low HDL-C/high triglycerides. Clin Genet 2001; 59:88-98. [PMID: 11260209 DOI: 10.1034/j.1399-0004.2001.590205.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Defects in the lipoprotein lipase (LPL) gene are associated with dyslipidemia in the general population. Several rare mutations in the gene, as well as two common coding region polymorphisms, D9N and N291S, exhibit deleterious effects on circulating lipid levels. Using a linkage-based approach, we have identified a large Utah kindred segregating the D9N variant in the LPL gene. The kindred was ascertained for premature coronary heart disease and was expanded based on familial dyslipidemia. A genomic scan identified a region of linkage including LPL, and mutation screening identified the segregating variant. In the kindred, the variant shows high penetrance for a hypoalphalipoproteinemia phenotype, but is also associated with hypertriglyceridemia and elevated insulin levels. The strength of linkage was dependent on the combination of phenotype definition and model parameters, favoring the use of a MOD score approach. Most other studies of LPL have proceeded by mutation screening of randomly chosen individuals or selected affected probands; this is the first example identifying a segregating LPL mutation using direct linkage.
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Affiliation(s)
- M E Samuels
- Myriad Genetics Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA
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