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Pazokitoroudi A, Liu Z, Dahl A, Zaitlen N, Rosset S, Sankararaman S. A scalable and robust variance components method reveals insights into the architecture of gene-environment interactions underlying complex traits. Am J Hum Genet 2024:S0002-9297(24)00178-2. [PMID: 38866020 DOI: 10.1016/j.ajhg.2024.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 05/15/2024] [Accepted: 05/15/2024] [Indexed: 06/14/2024] Open
Abstract
Understanding the contribution of gene-environment interactions (GxE) to complex trait variation can provide insights into disease mechanisms, explain sources of heritability, and improve genetic risk prediction. While large biobanks with genetic and deep phenotypic data hold promise for obtaining novel insights into GxE, our understanding of GxE architecture in complex traits remains limited. We introduce a method to estimate the proportion of trait variance explained by GxE (GxE heritability) and additive genetic effects (additive heritability) across the genome and within specific genomic annotations. We show that our method is accurate in simulations and computationally efficient for biobank-scale datasets. We applied our method to common array SNPs (MAF ≥1%), fifty quantitative traits, and four environmental variables (smoking, sex, age, and statin usage) in unrelated white British individuals in the UK Biobank. We found 68 trait-E pairs with significant genome-wide GxE heritability (p<0.05/200) with a ratio of GxE to additive heritability of ≈6.8% on average. Analyzing ≈8 million imputed SNPs (MAF ≥0.1%), we documented an approximate 28% increase in genome-wide GxE heritability compared to array SNPs. We partitioned GxE heritability across minor allele frequency (MAF) and local linkage disequilibrium (LD) values, revealing that, like additive allelic effects, GxE allelic effects tend to increase with decreasing MAF and LD. Analyzing GxE heritability near genes highly expressed in specific tissues, we find significant brain-specific enrichment for body mass index (BMI) and basal metabolic rate in the context of smoking and adipose-specific enrichment for waist-hip ratio (WHR) in the context of sex.
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Affiliation(s)
- Ali Pazokitoroudi
- Department of Computer Science, UCLA, Los Angeles, CA, USA; Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Zhengtong Liu
- Department of Computer Science, UCLA, Los Angeles, CA, USA
| | - Andrew Dahl
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Noah Zaitlen
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Department of Neurology, UCLA, Los Angeles, CA, USA
| | - Saharon Rosset
- Department of Statistics, Tel-Aviv University, Tel-Aviv, Israel
| | - Sriram Sankararaman
- Department of Computer Science, UCLA, Los Angeles, CA, USA; Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
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2
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Mitok KA, Keller MP, Attie AD. Sorting through the extensive and confusing roles of sortilin in metabolic disease. J Lipid Res 2022; 63:100243. [PMID: 35724703 PMCID: PMC9356209 DOI: 10.1016/j.jlr.2022.100243] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 01/06/2023] Open
Abstract
Sortilin is a post-Golgi trafficking receptor homologous to the yeast vacuolar protein sorting receptor 10 (VPS10). The VPS10 motif on sortilin is a 10-bladed β-propeller structure capable of binding more than 50 proteins, covering a wide range of biological functions including lipid and lipoprotein metabolism, neuronal growth and death, inflammation, and lysosomal degradation. Sortilin has a complex cellular trafficking itinerary, where it functions as a receptor in the trans-Golgi network, endosomes, secretory vesicles, multivesicular bodies, and at the cell surface. In addition, sortilin is associated with hypercholesterolemia, Alzheimer's disease, prion diseases, Parkinson's disease, and inflammation syndromes. The 1p13.3 locus containing SORT1, the gene encoding sortilin, carries the strongest association with LDL-C of all loci in human genome-wide association studies. However, the mechanism by which sortilin influences LDL-C is unclear. Here, we review the role sortilin plays in cardiovascular and metabolic diseases and describe in detail the large and often contradictory literature on the role of sortilin in the regulation of LDL-C levels.
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Affiliation(s)
- Kelly A Mitok
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Mark P Keller
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Alan D Attie
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
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3
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Shi J, Swanson SA, Kraft P, Rosner B, De Vivo I, Hernán MA. Mendelian Randomization With Repeated Measures of a Time-varying Exposure: An Application of Structural Mean Models. Epidemiology 2022; 33:84-94. [PMID: 34847085 PMCID: PMC9067358 DOI: 10.1097/ede.0000000000001417] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Mendelian randomization (MR) is often used to estimate effects of time-varying exposures on health outcomes using observational data. However, MR studies typically use a single measurement of exposure and apply conventional instrumental variable (IV) methods designed to handle time-fixed exposures. As such, MR effect estimates for time-varying exposures are often biased, and interpretations are unclear. We describe the instrumental conditions required for IV estimation with a time-varying exposure, and the additional conditions required to causally interpret MR estimates as a point effect, a period effect or a lifetime effect depending on whether researchers have measurements at a single or multiple time points. We propose methods to incorporate time-varying exposures in MR analyses based on g-estimation of structural mean models, and demonstrate its application by estimating the period effect of alcohol intake, high-density lipoprotein cholesterol and low-density lipoprotein cholesterol on intermediate coronary heart disease outcomes using data from the Framingham Heart Study. We use this data example to highlight the challenges of interpreting MR estimates as causal effects, and describe other extensions of structural mean models for more complex data scenarios.
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Affiliation(s)
- Joy Shi
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Sonja A. Swanson
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Bernard Rosner
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Immaculata De Vivo
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Miguel A. Hernán
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, Massachusetts, USA
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4
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Feofanova EV, Lim E, Chen H, Lee M, Liu CT, Cupples LA, Boerwinkle E. Exome sequence association study of levels and longitudinal change of cardiovascular risk factor phenotypes in European Americans and African Americans from the Atherosclerosis Risk in Communities Study. Genet Epidemiol 2021; 45:651-663. [PMID: 34167169 PMCID: PMC9047057 DOI: 10.1002/gepi.22390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 04/09/2021] [Accepted: 05/04/2021] [Indexed: 12/21/2022]
Abstract
Cardiovascular disease (CVD) is responsible for 31% of all deaths worldwide. Among CVD risk factors are age, race, increased systolic blood pressure (BP), and dyslipidemia. Both BP and blood lipids levels change with age, with a dose-dependent relationship between the cumulative exposure to hyperlipidemia and the risk of CVD. We performed an exome sequence association study using longitudinal data with up to 7805 European Americans (EAs) and 3171 African Americans (AAs) from the Atherosclerosis Risk in Communities (ARIC) study. We assessed associations of common (minor allele frequency > 5%) nonsynonymous and splice-site variants and gene-based sets of rare variants with levels and with longitudinal change of seven CVD risk factor phenotypes (BP traits: systolic BP, diastolic BP, pulse pressure; lipids traits: triglycerides, total cholesterol, high-density lipoprotein cholesterol [HDL-C], low-density lipoprotein cholesterol [LDL-C]). Furthermore, we investigated the relationship of the identified variants and genes with select CVD endpoints. We identified two novel genes: DCLK3 associated with the change of HDL-C levels in AAs and RAB7L1 associated with the change of LDL-C levels in EAs. RAB7L1 is further associated with an increased risk of heart failure in ARIC EAs. Investigation of the contribution of genetic factors to the longitudinal change of CVD risk factor phenotypes promotes our understanding of the etiology of CVD outcomes, stressing the importance of incorporating the longitudinal structure of the cohort data in future analyses.
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Affiliation(s)
- Elena V. Feofanova
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Elise Lim
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Han Chen
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Center for Precision Health, School of Public Health & School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - MinJae Lee
- Division of Biostatistics, Department of Population & Data Sciences, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - L. Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Framingham Heart Study, Framingham, MA, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
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5
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Sorlí JV, Barragán R, Coltell O, Portolés O, Pascual EC, Ortega-Azorín C, González JI, Estruch R, Saiz C, Pérez-Fidalgo A, Ordovas JM, Corella D. Chronological Age Interacts with the Circadian Melatonin Receptor 1B Gene Variation, Determining Fasting Glucose Concentrations in Mediterranean Populations. Additional Analyses on Type-2 Diabetes Risk. Nutrients 2020; 12:nu12113323. [PMID: 33138317 PMCID: PMC7692445 DOI: 10.3390/nu12113323] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/21/2020] [Accepted: 10/24/2020] [Indexed: 12/25/2022] Open
Abstract
Gene-age interactions have not been systematically investigated on metabolic phenotypes and this modulation will be key for a better understanding of the temporal regulation in nutrigenomics. Taking into account that aging is typically associated with both impairment of the circadian system and a decrease in melatonin secretion, we focused on the melatonin receptor 1B (MTNR1B)-rs10830963 C>G variant that has been associated with fasting glucose concentrations, gestational diabetes, and type-2 diabetes. Therefore, our main aim was to investigate whether the association between the MTNR1B-rs10830963 polymorphism and fasting glucose is age dependent. Our secondary aims were to analyze the polymorphism association with type-2 diabetes and explore the gene-pregnancies interactions on the later type-2 diabetes risk. Three Mediterranean cohorts (n = 2823) were analyzed. First, a cross-sectional study in the discovery cohort consisting of 1378 participants (aged 18 to 80 years; mean age 41 years) from the general population was carried out. To validate and extend the results, two replication cohorts consisting of elderly individuals were studied. In the discovery cohort, we observed a strong gene-age interaction (p = 0.001), determining fasting glucose in such a way that the increasing effect of the risk G-allele was much greater in young (p = 5.9 × 10-10) than in elderly participants (p = 0.805). Consistently, the association of the MTNR1B-rs10830963 polymorphism with fasting glucose concentrations in the two replication cohorts (mean age over 65 years) did not reach statistical significance (p > 0.05 for both). However, in the elderly cohorts, significant associations between the polymorphism and type-2 diabetes at baseline were found. Moreover, in one of the cohorts, we obtained a statistically significant interaction between the MTNR1B polymorphism and the number of pregnancies, retrospectively assessed, on the type-2 diabetes risk. In conclusion, the association of the MTNR1B-rs10830963 polymorphism with fasting glucose is age-dependent, having a greater effect in younger people. However, in elderly subjects, associations of the polymorphism with type-2 diabetes were observed and our exploratory analysis suggested a modulatory effect of the number of past pregnancies on the future type-2 diabetes genetic risk.
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Affiliation(s)
- Jose V. Sorlí
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain; (J.V.S.); (R.B.); (O.P.); (E.C.P.); (C.O.-A.); (J.I.G.); (C.S.); (A.P.-F.)
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (O.C.); (R.E.)
| | - Rocío Barragán
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain; (J.V.S.); (R.B.); (O.P.); (E.C.P.); (C.O.-A.); (J.I.G.); (C.S.); (A.P.-F.)
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (O.C.); (R.E.)
- Department of Medicine, Sleep Center of Excellence, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Oscar Coltell
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (O.C.); (R.E.)
- Department of Computer Languages and Systems, Universitat Jaume I, 12071 Castellón, Spain
| | - Olga Portolés
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain; (J.V.S.); (R.B.); (O.P.); (E.C.P.); (C.O.-A.); (J.I.G.); (C.S.); (A.P.-F.)
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (O.C.); (R.E.)
| | - Eva C. Pascual
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain; (J.V.S.); (R.B.); (O.P.); (E.C.P.); (C.O.-A.); (J.I.G.); (C.S.); (A.P.-F.)
| | - Carolina Ortega-Azorín
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain; (J.V.S.); (R.B.); (O.P.); (E.C.P.); (C.O.-A.); (J.I.G.); (C.S.); (A.P.-F.)
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (O.C.); (R.E.)
| | - José I. González
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain; (J.V.S.); (R.B.); (O.P.); (E.C.P.); (C.O.-A.); (J.I.G.); (C.S.); (A.P.-F.)
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (O.C.); (R.E.)
| | - Ramon Estruch
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (O.C.); (R.E.)
- Department of Internal Medicine, Hospital Clinic, Institut d’Investigació Biomèdica August Pi i Sunyer (IDIBAPS), University of Barcelona, Villarroel, 170, 08036 Barcelona, Spain
| | - Carmen Saiz
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain; (J.V.S.); (R.B.); (O.P.); (E.C.P.); (C.O.-A.); (J.I.G.); (C.S.); (A.P.-F.)
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (O.C.); (R.E.)
| | - Alejandro Pérez-Fidalgo
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain; (J.V.S.); (R.B.); (O.P.); (E.C.P.); (C.O.-A.); (J.I.G.); (C.S.); (A.P.-F.)
- CIBER Cáncer, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Jose M. Ordovas
- Nutrition and Genomics Laboratory, JM-USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA 02111, USA;
- Precision Nutrition and Obesity Program, IMDEA Alimentación, 28049 Madrid, Spain
| | - Dolores Corella
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain; (J.V.S.); (R.B.); (O.P.); (E.C.P.); (C.O.-A.); (J.I.G.); (C.S.); (A.P.-F.)
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (O.C.); (R.E.)
- Correspondence: ; Tel.: +34-96-386-4800
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6
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Su X, Peng D. New insight into sortilin in controlling lipid metabolism and the risk of atherogenesis. Biol Rev Camb Philos Soc 2020; 95:232-243. [PMID: 31625271 DOI: 10.1111/brv.12561] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 09/16/2019] [Accepted: 09/18/2019] [Indexed: 01/24/2023]
Affiliation(s)
- Xin Su
- Department of Cardiovascular Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Daoquan Peng
- Department of Cardiovascular Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
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7
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Labrecque JA, Swanson SA. Interpretation and Potential Biases of Mendelian Randomization Estimates With Time-Varying Exposures. Am J Epidemiol 2019; 188:231-238. [PMID: 30239571 DOI: 10.1093/aje/kwy204] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 09/05/2018] [Indexed: 01/08/2023] Open
Abstract
Mendelian randomization (MR) is used to answer a variety of epidemiologic questions. One stated advantage of MR is that it estimates a "lifetime effect" of exposure, though this term remains vaguely defined. Instrumental variable analysis, on which MR is based, has focused on estimating the effects of point or time-fixed exposures rather than "lifetime effects." Here we use an empirical example with data from the Rotterdam Study (Rotterdam, the Netherlands, 2009-2013) to demonstrate how confusion can arise when estimating "lifetime effects." We provide one possible definition of a lifetime effect: the average change in outcome measured at time t when the entire exposure trajectory from conception to time t is shifted by 1 unit. We show that MR only estimates this type of lifetime effect under specific conditions-for example, when the effect of the genetic variants used on exposure does not change over time. Lastly, we simulate the magnitude of bias that would result in realistic scenarios that use genetic variants with effects that change over time. We recommend that investigators in future MR studies carefully consider the effect of interest and how genetic variants whose effects change with time may impact the interpretability and validity of their results.
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Affiliation(s)
| | - Sonja A Swanson
- Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands
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8
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Miettinen ME, Smart MC, Kinnunen L, Keinänen-Kiukaanniemi S, Moilanen L, Puolijoki H, Saltevo J, Oksa H, Hitman GA, Tuomilehto J, Peltonen M. The effect of age and gender on the genetic regulation of serum 25-hydroxyvitamin D - the FIN-D2D population-based study. J Steroid Biochem Mol Biol 2018; 178:229-233. [PMID: 29287921 DOI: 10.1016/j.jsbmb.2017.12.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 12/20/2017] [Accepted: 12/23/2017] [Indexed: 01/19/2023]
Abstract
In addition to sunlight and dietary sources, several genes in the metabolic pathway of vitamin D affect serum 25-hydroxyvitamin D (25OHD) concentration. It is not known whether this genetic regulation is influenced by host characteristics. We investigated the effect of age and gender on the genetic regulation of serum 25OHD concentration. In total, 2868 Finnish men and women aged 45-74 years participated in FIN-D2D population-based health survey in 2007. Of the 2822 participants that had serum 25OHD concentration available, 2757 were successfully genotyped. Age and gender-dependent association of SNPs with serum 25OHD concentration was studied in 10 SNPs with previously found association with vitamin D metabolites. Associations of 3 SNPs with serum 25OHD concentration were dependent on age with greater effects on younger (≤60 y) than older (>60 y) adults (rs10783219 in VDR, rs12512631 in GC and rs3794060 in NADSYN1/DHCR7; pinteraction = 0.03, 0.02 and 0.01, respectively). The results suggested a novel association between serum 25OHD concentration and rs8082391 in STAT5B gene in men but not in women (pinteraction = 0.01). After multiple testing correction with false discovery rate method, two age-dependent interactions (rs3794060 in NADSYN1/DHCR7 gene and rs12512631 in GC gene) remained statistically significant. This is the first study to suggest that genetic regulation of serum 25OHD concentration is age-dependent. Our results also indicated a novel association between serum 25OHD concentration and SNP in STAT5B gene in men. The results need to be confirmed in future studies preferably in a larger sample.
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Affiliation(s)
- Maija E Miettinen
- Chronic Disease Prevention Unit, National Institute for Health and Welfare, 00271, Helsinki, Finland.
| | - Melissa C Smart
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, E1 4NS, UK; University of Essex, Colchester, CO4 3SQ, UK
| | - Leena Kinnunen
- Genomics and Biomarkers Unit, National Institute for Health and Welfare, 00271 Helsinki, Finland
| | - Sirkka Keinänen-Kiukaanniemi
- Faculty of Medicine, Center for Life Course Health Research, University of Oulu, 90014 Oulu, Finland; MRC and Unit of Primary Care, Oulu University Hospital, 90220, Oulu, Finland; Health Center of Oulu, Oulu, Finland
| | - Leena Moilanen
- Department of Medicine, Kuopio University Hospital, Northern Savo Hospital District, Kuopio Campus, 70210, Kuopio, Finland
| | - Hannu Puolijoki
- Central Hospital of Southern Ostrobothnia, 60220, Seinäjoki, Finland
| | - Juha Saltevo
- Central Finland Central Hospital, 40620, Jyväskylä, Finland
| | - Heikki Oksa
- Pirkanmaa Hospital District, Finland, Tampere University Hospital, 33521, Tampere, Finland
| | - Graham A Hitman
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, E1 4NS, UK
| | - Jaakko Tuomilehto
- Chronic Disease Prevention Unit, National Institute for Health and Welfare, 00271, Helsinki, Finland; Central Hospital of Southern Ostrobothnia, 60220, Seinäjoki, Finland; Center for Vascular Prevention, Danube-University Krems, 3500, Krems an Der Donau, Austria; Diabetes Research Group, King Abdulaziz University, Jeddah, 23218, Saudi Arabia; Dasman Diabetes Institute, Kuwait City, 1180, Kuwait
| | - Markku Peltonen
- Chronic Disease Prevention Unit, National Institute for Health and Welfare, 00271, Helsinki, Finland
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9
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Andersson CH, Hansson O, Minthon L, Andreasen N, Blennow K, Zetterberg H, Skoog I, Wallin A, Nilsson S, Kettunen P. A Genetic Variant of the Sortilin 1 Gene is Associated with Reduced Risk of Alzheimer's Disease. J Alzheimers Dis 2018; 53:1353-63. [PMID: 27392867 PMCID: PMC5147507 DOI: 10.3233/jad-160319] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Alzheimer’s disease (AD) is a neurodegenerative disorder represented by the accumulation of intracellular tau protein and extracellular deposits of amyloid-β (Aβ) in the brain. The gene sortilin 1 (SORT1) has previously been associated with cardiovascular disease in gene association studies. It has also been proposed to be involved in AD pathogenesis through facilitating Aβ clearance by binding apoE/Aβ complexes prior to cellular uptake. However, the neuropathological role of SORT1 in AD is not fully understood. To evaluate the associations between gene variants of SORT1 and risk of AD, we performed genetic analyses in a Swedish case-control cohort. Ten single nucleotide polymorphisms (SNPs), covering the whole SORT1 gene, were selected and genotyped in 620 AD patients and 1107 controls. The SNP rs17646665, located in a non-coding region of the SORT1 gene, remained significantly associated with decreased risk of AD after multiple testing (pc = 0.0061). In addition, other SNPs were found to be nominally associated with risk of AD, as well as altered cognitive function and the CSF biomarker Aβ42, but these associations did not survive correction for multiple testing. The fact that SORT1 has been strongly associated with risk of cardiovascular disease is intriguing as cardiovascular disease is also regarded as a risk factor for AD. Finally, increased knowledge about SORT1 function has a potential to increase our understanding of APOE, the strongest risk factor for AD.
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Affiliation(s)
- Carl-Henrik Andersson
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Oskar Hansson
- Clinical Memory Research Unit, Department of Clinical Sciences Malmö, Faculty of Medicine, Lund University, Sweden.,Memory Clinic, Skåne University Hospital, Malmö, Sweden
| | - Lennart Minthon
- Clinical Memory Research Unit, Department of Clinical Sciences Malmö, Faculty of Medicine, Lund University, Sweden.,Memory Clinic, Skåne University Hospital, Malmö, Sweden
| | - Niels Andreasen
- Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet, Stockholm, Sweden
| | - Kaj Blennow
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Henrik Zetterberg
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,UCL Institute of Neurology, Queen Square, London, United Kingdom
| | - Ingmar Skoog
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anders Wallin
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Staffan Nilsson
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Sweden
| | - Petronella Kettunen
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Neuropathology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
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10
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Goettsch C, Kjolby M, Aikawa E. Sortilin and Its Multiple Roles in Cardiovascular and Metabolic Diseases. Arterioscler Thromb Vasc Biol 2017; 38:19-25. [PMID: 29191923 DOI: 10.1161/atvbaha.117.310292] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 11/16/2017] [Indexed: 12/24/2022]
Abstract
Cardiovascular disease is a leading cause of morbidity and mortality in the Western world. Studies of sortilin's influence on cardiovascular and metabolic diseases goes far beyond the genome-wide association studies that have revealed an association between cardiovascular diseases and the 1p13 locus that encodes sortilin. Emerging evidence suggests a significant role of sortilin in the pathogenesis of vascular and metabolic diseases; this includes type II diabetes mellitus via regulation of insulin resistance, atherosclerosis through arterial wall inflammation and calcification, and dysregulated lipoprotein metabolism. Sortilin is also known for its functional role in neurological disorders. It serves as a key receptor for cytokines, lipids, and enzymes and participates in pathological cargo loading to and trafficking of extracellular vesicles. This article provides a comprehensive review of sortilin's contributions to cardiovascular and metabolic diseases but focuses particularly on atherosclerosis. We summarize recent clinical findings that suggest that sortilin may be a cardiovascular risk biomarker and also discuss sortilin as a potential drug target.
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Affiliation(s)
- Claudia Goettsch
- From the Department of Internal Medicine I-Cardiology, RWTH Aachen University, Germany (C.G.); The Danish Research Institute of Translational Neuroscience, Nordic European Molecular Biology Laboratory Partnership for Molecular Medicine, Danish Diabetes Academy, Denmark (M.K.); Department of Biomedicine (M.K.) and Department of Cardiology (M.K.), Aarhus University, Denmark; and Center for Interdisciplinary Cardiovascular Sciences (E.A.) and Center for Excellence in Vascular Biology, Division of Cardiovascular Medicine (E.A.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Mads Kjolby
- From the Department of Internal Medicine I-Cardiology, RWTH Aachen University, Germany (C.G.); The Danish Research Institute of Translational Neuroscience, Nordic European Molecular Biology Laboratory Partnership for Molecular Medicine, Danish Diabetes Academy, Denmark (M.K.); Department of Biomedicine (M.K.) and Department of Cardiology (M.K.), Aarhus University, Denmark; and Center for Interdisciplinary Cardiovascular Sciences (E.A.) and Center for Excellence in Vascular Biology, Division of Cardiovascular Medicine (E.A.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Elena Aikawa
- From the Department of Internal Medicine I-Cardiology, RWTH Aachen University, Germany (C.G.); The Danish Research Institute of Translational Neuroscience, Nordic European Molecular Biology Laboratory Partnership for Molecular Medicine, Danish Diabetes Academy, Denmark (M.K.); Department of Biomedicine (M.K.) and Department of Cardiology (M.K.), Aarhus University, Denmark; and Center for Interdisciplinary Cardiovascular Sciences (E.A.) and Center for Excellence in Vascular Biology, Division of Cardiovascular Medicine (E.A.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA.
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11
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Paththinige CS, Sirisena ND, Dissanayake V. Genetic determinants of inherited susceptibility to hypercholesterolemia - a comprehensive literature review. Lipids Health Dis 2017; 16:103. [PMID: 28577571 PMCID: PMC5457620 DOI: 10.1186/s12944-017-0488-4] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 05/17/2017] [Indexed: 02/08/2023] Open
Abstract
Hypercholesterolemia is a strong determinant of mortality and morbidity associated with cardiovascular diseases and a major contributor to the global disease burden. Mutations in four genes (LDLR, APOB, PCSK9 and LDLRAP1) account for the majority of cases with familial hypercholesterolemia. However, a substantial proportion of adults with hypercholesterolemia do not have a mutation in any of these four genes. This indicates the probability of having other genes with a causative or contributory role in the pathogenesis of hypercholesterolemia and suggests a polygenic inheritance of this condition. Here in, we review the recent evidence of association of the genetic variants with hypercholesterolemia and the three lipid traits; total cholesterol (TC), HDL-cholesterol (HDL-C) and LDL-cholesterol (LDL-C), their biological pathways and the associated pathogenetic mechanisms. Nearly 80 genes involved in lipid metabolism (encoding structural components of lipoproteins, lipoprotein receptors and related proteins, enzymes, lipid transporters, lipid transfer proteins, and activators or inhibitors of protein function and gene transcription) with single nucleotide variants (SNVs) that are recognized to be associated with hypercholesterolemia and serum lipid traits in genome-wide association studies and candidate gene studies were identified. In addition, genome-wide association studies in different populations have identified SNVs associated with TC, HDL-C and LDL-C in nearly 120 genes within or in the vicinity of the genes that are not known to be involved in lipid metabolism. Over 90% of the SNVs in both these groups are located outside the coding regions of the genes. These findings indicates that there might be a considerable number of unrecognized processes and mechanisms of lipid homeostasis, which when disrupted, would lead to hypercholesterolemia. Knowledge of these molecular pathways will enable the discovery of novel treatment and preventive methods as well as identify the biochemical and molecular markers for the risk prediction and early detection of this common, yet potentially debilitating condition.
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Affiliation(s)
- C S Paththinige
- Human Genetics Unit, Faculty of Medicine, University of Colombo, Kynsey Road, Colombo, 00800, Sri Lanka.
| | - N D Sirisena
- Human Genetics Unit, Faculty of Medicine, University of Colombo, Kynsey Road, Colombo, 00800, Sri Lanka
| | - Vhw Dissanayake
- Human Genetics Unit, Faculty of Medicine, University of Colombo, Kynsey Road, Colombo, 00800, Sri Lanka
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12
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Osmak GJ, Lvovs D, Titov BV, Matveeva NA, Favorova OO, Favorov AV. The combined effects of myocardial infarction risk factors: Simulation of the combined effects of gene variants, age, and smoking and an analysis of their interaction. Biophysics (Nagoya-shi) 2017. [DOI: 10.1134/s0006350917010146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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13
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He QC, Hu YY, Zhang QP, Tan LL, Liu YH, Liu T, Hu YQ, Li Q, Liang N. A meta-analysis of three identified single nucleotide polymorphisms at 1p13.3 and 1q41 and their associations with lipid levels and coronary artery disease. Kaohsiung J Med Sci 2016; 33:1-10. [PMID: 28088267 DOI: 10.1016/j.kjms.2016.10.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 10/19/2016] [Accepted: 10/24/2016] [Indexed: 12/19/2022] Open
Abstract
The aim of this meta-analysis was to detect whether three identified single nucleotide polymorphisms (SNPs) (rs646776, rs599839, and rs17465637) at 1p13.3 and 1q41 are associated with lipid levels and the risk of coronary artery disease (CAD). Databases of MEDLINE, EMBASE, the Cochrane Library, and BIOSIS were systematically searched. The pooled effects were expressed as odds ratio or standardized mean difference or mean difference with 95% confidence intervals. A total of 14 studies with 57,916 patients were included in the meta-analysis. Pooled effects showed that the AA group of 1p13.3 rs599839 had higher total cholesterol (TC) and low-density lipoprotein cholesterol (LDLC), and lower high-density lipoprotein cholesterol (HDLC) levels than the GA/GG group, and the CAD group had higher AA genotype frequency than the control group. The TT group of 1p13.3 rs646776 had higher TC and LDLC levels and lower HDLC levels than the CT/CC group. The CAD group also had higher CC genotype frequency of 1q41 rs17465637 than the control group. The SNPs of 1p13 rs599839 and rs646776 were associated with serum lipid levels. The genetic variants of 1p13 rs599839 and 1q41 rs17465637 SNPs were prominently related to CAD, and the genetic variants of chromosome 1p13 promote the risk of CAD by increased TC and LDLC levels and decreased HDLC levels.
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Affiliation(s)
- Qian-Chao He
- Department of Encephalopathy Division I, The First Affiliated Hospital of Guangxi University of Chinese Medicine, Guangxi, People's Republic of China
| | - Yu-Ying Hu
- Department of Encephalopathy Division I, The First Affiliated Hospital of Guangxi University of Chinese Medicine, Guangxi, People's Republic of China
| | - Qing-Ping Zhang
- Department of Encephalopathy Division I, The First Affiliated Hospital of Guangxi University of Chinese Medicine, Guangxi, People's Republic of China
| | - Lu-Lu Tan
- Department of Encephalopathy Division I, The First Affiliated Hospital of Guangxi University of Chinese Medicine, Guangxi, People's Republic of China
| | - Yong-Hui Liu
- Department of Encephalopathy Division I, The First Affiliated Hospital of Guangxi University of Chinese Medicine, Guangxi, People's Republic of China
| | - Tai Liu
- Department of Encephalopathy Division I, The First Affiliated Hospital of Guangxi University of Chinese Medicine, Guangxi, People's Republic of China
| | - Yue-Qiang Hu
- Department of Encephalopathy Division I, The First Affiliated Hospital of Guangxi University of Chinese Medicine, Guangxi, People's Republic of China
| | - Qing Li
- Department of Internal Medicine, Affiliated Shanghai First People's Hospital, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Ni Liang
- Department of Encephalopathy Division I, The First Affiliated Hospital of Guangxi University of Chinese Medicine, Guangxi, People's Republic of China.
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14
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Shahid SU, ᅟ S, Cooper JA, Beaney KE, Li K, Rehman A, Humphries SE. Effect of SORT1, APOB and APOE polymorphisms on LDL-C and coronary heart disease in Pakistani subjects and their comparison with Northwick Park Heart Study II. Lipids Health Dis 2016; 15:83. [PMID: 27112212 PMCID: PMC4845441 DOI: 10.1186/s12944-016-0253-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Accepted: 04/19/2016] [Indexed: 12/26/2022] Open
Abstract
Background Many SNPs have been identified in genes regulating LDL-C metabolism, but whether their influence is similar in subjects from different ethnicities is unclear. Effect of 4 such SNPs on LDL-C and coronary heart disease (CHD) was examined in Pakistani subjects and was compared with middle aged UK men from Northwick Park Heart Study II (NPHSII). Methods One thousand nine hundred sixty-five (1770 non CHD, 195 CHD) UK and 623 (219 non CHD, 404 CHD) Pakistani subjects were enrolled in the study. The SNPs SORT1 rs646776, APOB rs1042031 and APOE rs429358, rs7412 were genotyped by TaqMan/KASPar technique and their gene score was calculated. LDL-C was calculated by Friedewald equation, results were analyzed using SPSS. Results Allele frequencies were significantly different (p = <0.05) between UK and Pakistani subjects. However, the SNPs were associated with LDL-C in both groups. In UK non CHD, UK CHD, Pakistani non CHD and Pakistani CHD respectively, for rs646776, per risk allele increase in LDL-C(mmol/l) was 0.18(0.04), 0.06(0.11), 0.15(0.04) and 0.27(0.06) respectively. For rs1042031, per risk allele increase in LDL-C in four groups was 0.11(0.04), 0.04(0.14), 0.15(0.06) and 0.25(0.09) respectively. For APOE genotypes, compared to Ɛ3, each Ɛ2 decreased LDL-C by 0.11(0.06), 0.07(0.15), 0.20(0.08) and 0.38(0.09), while each Ɛ4 increased LDL-C by 0.43(0.06), 0.39(0.21), 0.19(0.11) and 0.39(0.14) respectively. Overall gene score explained a considerable proportion of sample variance in four groups (3.8 %, 1.26 % 13.7 % and 12.3 %). Gene score in both non-CHD groups was significantly lower than CHD subjects. Conclusions The SNPs show a dose response association with LDL-C levels and risk of CHD in both populations. Electronic supplementary material The online version of this article (doi:10.1186/s12944-016-0253-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Saleem Ullah Shahid
- Department of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan.
| | - Shabana ᅟ
- Department of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
| | - Jackie A Cooper
- Centre for Cardiovascular Genetics, British Heart Foundation Laboratories, University College London, London, WC1E6JF, UK
| | - Katherine E Beaney
- Centre for Cardiovascular Genetics, British Heart Foundation Laboratories, University College London, London, WC1E6JF, UK
| | - Kawah Li
- Centre for Cardiovascular Genetics, British Heart Foundation Laboratories, University College London, London, WC1E6JF, UK
| | - Abdul Rehman
- Department of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
| | - Stephen Eric Humphries
- Centre for Cardiovascular Genetics, British Heart Foundation Laboratories, University College London, London, WC1E6JF, UK
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15
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Sortilin, Encoded by the Cardiovascular Risk Gene SORT1, and Its Suggested Functions in Cardiovascular Disease. Curr Atheroscler Rep 2015; 17:496. [DOI: 10.1007/s11883-015-0496-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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16
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Connors KE, Karlos AE, Gnatiuk EA, Shearer J, Reimer RA, Hittel DS. SORT1
Protective Allele Is Associated With Attenuated Postprandial. ACTA ACUST UNITED AC 2014; 7:576-82. [DOI: 10.1161/circgenetics.114.000534] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background—
Elevated levels of lipids and lipoproteins have strong genetic determinants and are recognized as key risk factors for atherogenesis and cardiovascular disease, particularly in the postprandial state. The aim of the study to determine whether young adults, when stratified by genotype at the rs646776 variant of the 1p13 locus, displayed differential postprandial responses to an oral fat tolerance test.
Methods and Results—
Participants (n=30) received a high-fat mixed meal (91 g; 55% kcal from fat) after an overnight fast and a fat-exclusion meal (3.9 g; 6% kcal from fat) at 8 hours postprandially. Blood samples were obtained at
t
=0, 2, 4, 6, 8, and 24 hours for lipoprotein analyses via nuclear magnetic resonance profiling. Carriers of the minor, protective allele (TC/CC) displayed lower fasting (TC/CC, 30.1±3.0 nmol/L versus TT, 48.8±5.1 nmol/L;
P
<0.01) and mean postprandial (TC/CC, 44.2±3.1 nmol/L versus TT, 57.0±4.5 nmol/L;
P
=0.03) very low-density lipoprotein and chylomicron particle number in addition to triglyceride content when compared with individuals homozygous for the major, risk allele (TT).
Conclusions—
We report a novel association between the
SORT1
1p13 locus and extent of postprandial lipaemia. These results provide evidence of decreased exposure to atherogenic particles in carriers of the minor
SORT1
allele, suggesting relative protection against cardiovascular disease when compared with TT homozygotes.
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Affiliation(s)
- Kimberly E. Connors
- From the Faculty of Kinesiology (K.E.C., E.A.G., J.S., R.A.R.), Faculty of Medicine (A.E.K., J.S., R.A.R.), Department of Biochemistry and Molecular Biology within the Faculty of Medicine (J.S., R.A.R., D.S.H.), University of Calgary, Calgary, Alberta, Canada
| | - Angela E. Karlos
- From the Faculty of Kinesiology (K.E.C., E.A.G., J.S., R.A.R.), Faculty of Medicine (A.E.K., J.S., R.A.R.), Department of Biochemistry and Molecular Biology within the Faculty of Medicine (J.S., R.A.R., D.S.H.), University of Calgary, Calgary, Alberta, Canada
| | - Elizabeth A. Gnatiuk
- From the Faculty of Kinesiology (K.E.C., E.A.G., J.S., R.A.R.), Faculty of Medicine (A.E.K., J.S., R.A.R.), Department of Biochemistry and Molecular Biology within the Faculty of Medicine (J.S., R.A.R., D.S.H.), University of Calgary, Calgary, Alberta, Canada
| | - Jane Shearer
- From the Faculty of Kinesiology (K.E.C., E.A.G., J.S., R.A.R.), Faculty of Medicine (A.E.K., J.S., R.A.R.), Department of Biochemistry and Molecular Biology within the Faculty of Medicine (J.S., R.A.R., D.S.H.), University of Calgary, Calgary, Alberta, Canada
| | - Raylene A. Reimer
- From the Faculty of Kinesiology (K.E.C., E.A.G., J.S., R.A.R.), Faculty of Medicine (A.E.K., J.S., R.A.R.), Department of Biochemistry and Molecular Biology within the Faculty of Medicine (J.S., R.A.R., D.S.H.), University of Calgary, Calgary, Alberta, Canada
| | - Dustin S. Hittel
- From the Faculty of Kinesiology (K.E.C., E.A.G., J.S., R.A.R.), Faculty of Medicine (A.E.K., J.S., R.A.R.), Department of Biochemistry and Molecular Biology within the Faculty of Medicine (J.S., R.A.R., D.S.H.), University of Calgary, Calgary, Alberta, Canada
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17
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Klein MS, Connors KE, Shearer J, Vogel HJ, Hittel DS. Metabolomics reveals the sex-specific effects of the SORT1 low-density lipoprotein cholesterol locus in healthy young adults. J Proteome Res 2014; 13:5063-70. [PMID: 25182463 DOI: 10.1021/pr500659r] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Metabolite profiles of individuals possessing either the cardiovascular risk or protective variants of the low-density lipoprotein cholesterol (LDL-C) associated 1p13.3 locus of the SORT1 gene (rs646776) were analyzed. Serum metabolites and lipids were assessed using LC-MS-based metabolomics in a healthy young population (n = 138: 95 males, 43 females). Although no significant differences were observed in the combined cohort, divergent sex effects were identified. Females carrying the protective allele showed increased phosphatidylcholines, very long chain fatty acids (>C20), and unsaturated fatty acids. Unsaturated fatty acids are considered to be protective against cardiovascular disease. In contrast, males carrying the protective allele exhibited decreased long-chain fatty acids (≤C20) and sphingomyelins, which is similarly considered to decrease cardiovascular disease risk. No significant changes in clinically assessed lipids such as LDL-C, high-density lipoprotein (HDL-C), total cholesterol, or triglycerides were observed in females, whereas only LDL-C was significantly changed in males. This indicates that, apart from reducing LDL-C, other mechanisms may contribute to the protective effect of the SORT1 locus. Thus, the analysis of metabolic biomarkers might reveal early disease development that may be overlooked by relying on standard clinical parameters.
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Affiliation(s)
- Matthias S Klein
- Faculty of Kinesiology, ‡Department of Biochemistry and Molecular Biology, Faculty of Medicine, and §Department of Biological Sciences, University of Calgary , Calgary, Alberta T2N 1N4, Canada
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18
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Simino J, Kume R, Kraja AT, Turner ST, Hanis CL, Sheu W, Chen I, Jaquish C, Cooper RS, Chakravarti A, Quertermous T, Boerwinkle E, Hunt SC, Rao DC. Linkage analysis incorporating gene-age interactions identifies seven novel lipid loci: the Family Blood Pressure Program. Atherosclerosis 2014; 235:84-93. [PMID: 24819747 PMCID: PMC4322916 DOI: 10.1016/j.atherosclerosis.2014.04.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 04/07/2014] [Accepted: 04/09/2014] [Indexed: 01/16/2023]
Abstract
OBJECTIVE To detect novel loci with age-dependent effects on fasting (≥ 8 h) levels of total cholesterol, high-density lipoprotein, low-density lipoprotein, and triglycerides using 3600 African Americans, 1283 Asians, 3218 European Americans, and 2026 Mexican Americans from the Family Blood Pressure Program (FBPP). METHODS Within each subgroup (defined by network, race, and sex), we employed stepwise linear regression (retention p ≤ 0.05) to adjust lipid levels for age, age-squared, age-cubed, body-mass-index, current smoking status, current drinking status, field center, estrogen therapy (females only), as well as antidiabetic, antihypertensive, and antilipidemic medication use. For each trait, we pooled the standardized male and female residuals within each network and race and fit a generalized variance components model that incorporated gene-age interactions. We conducted FBPP-wide and race-specific meta-analyses by combining the p-values of each linkage marker across subgroups using a modified Fisher's method. RESULTS We identified seven novel loci with age-dependent effects; four total cholesterol loci from the meta-analysis of Mexican Americans (on chromosomes 2q24.1, 4q21.21, 8q22.2, and 12p11.23) and three high-density lipoprotein loci from the meta-analysis of all FBPP subgroups (on chromosomes 1p12, 14q11.2, and 21q21.1). These loci lacked significant genome-wide linkage or association evidence in the literature and had logarithm of odds (LOD) score ≥ 3 in the meta-analysis with LOD ≥ 1 in at least two network and race subgroups (exclusively of non-European descent). CONCLUSION Incorporating gene-age interactions into the analysis of lipids using multi-ethnic cohorts can enhance gene discovery. These interaction loci can guide the selection of families for sequencing studies of lipid-associated variants.
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Affiliation(s)
- Jeannette Simino
- Division of Biostatistics, Washington University in St. Louis, School of Medicine, Saint Louis, Missouri, USA
| | - Rezart Kume
- Division of Biostatistics, Washington University in St. Louis, School of Medicine, Saint Louis, Missouri, USA
| | - Aldi T. Kraja
- Division of Statistical Genomics Washington University in St. Louis, School of Medicine, Saint Louis, Missouri, USA
| | - Stephen T. Turner
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA
| | - Craig L. Hanis
- Human Genetics Center, University of Texas Health Science Center, Houston, Texas, USA
| | - Wayne Sheu
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Ida Chen
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, CA 90502
| | - Cashell Jaquish
- Division of Cardiovascular Sciences, National Heart, Lung, Blood Institute, Bethesda, Maryland, USA
| | - Richard S. Cooper
- Department of Preventive Medicine and Epidemiology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
| | - Aravinda Chakravarti
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Thomas Quertermous
- Department of Geriatric Medicine, John A. Burns School of Medicine, University of Hawaii, Honolulu, USA
| | - Eric Boerwinkle
- Human Genetics Center, University of Texas Health Science Center, Houston, Texas, USA
| | - Steven C. Hunt
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah, USA
| | - DC Rao
- Division of Biostatistics, Washington University in St. Louis, School of Medicine, Saint Louis, Missouri, USA
- Also Departments of Genetics, Psychiatry, and Mathematics, Washington University in St. Louis, School of Medicine, Missouri, USA
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19
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Dumitrescu L, Carty CL, Franceschini N, Hindorff LA, Cole SA, Bůžková P, Schumacher FR, Eaton CB, Goodloe RJ, Duggan DJ, Haessler J, Cochran B, Henderson BE, Cheng I, Johnson KC, Carlson CS, Love SA, Brown-Gentry K, Nato AQ, Quibrera M, Anderson G, Shohet RV, Ambite JL, Wilkens LR, Le Marchand L, Haiman CA, Buyske S, Kooperberg C, North KE, Fornage M, Crawford DC. Post-genome-wide association study challenges for lipid traits: describing age as a modifier of gene-lipid associations in the Population Architecture using Genomics and Epidemiology (PAGE) study. Ann Hum Genet 2013; 77:416-25. [PMID: 23808484 PMCID: PMC3796061 DOI: 10.1111/ahg.12027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 03/28/2013] [Indexed: 11/27/2022]
Abstract
Numerous common genetic variants that influence plasma high-density lipoprotein cholesterol, low-density lipoprotein cholesterol (LDL-C), and triglyceride distributions have been identified via genome-wide association studies (GWAS). However, whether or not these associations are age-dependent has largely been overlooked. We conducted an association study and meta-analysis in more than 22,000 European Americans between 49 previously identified GWAS variants and the three lipid traits, stratified by age (males: <50 or ≥50 years of age; females: pre- or postmenopausal). For each variant, a test of heterogeneity was performed between the two age strata and significant Phet values were used as evidence of age-specific genetic effects. We identified seven associations in females and eight in males that displayed suggestive heterogeneity by age (Phet < 0.05). The association between rs174547 (FADS1) and LDL-C in males displayed the most evidence for heterogeneity between age groups (Phet = 1.74E-03, I(2) = 89.8), with a significant association in older males (P = 1.39E-06) but not younger males (P = 0.99). However, none of the suggestive modifying effects survived adjustment for multiple testing, highlighting the challenges of identifying modifiers of modest SNP-trait associations despite large sample sizes.
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Affiliation(s)
- Logan Dumitrescu
- Center for Human Genetics Research, Vanderbilt University, Nashville, TN
| | - Cara L. Carty
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC
| | - Lucia A. Hindorff
- Office of Population Genomics, National Human Genome Research Institute, Bethesda, MD
| | - Shelley A. Cole
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Petra Bůžková
- Department of Biostatistics, University of Washington, Seattle, WA
| | - Fredrick R. Schumacher
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Charles B. Eaton
- Department of Family Medicine, Warren Alpert Medical School, Brown University, Providence, RI
| | - Robert J. Goodloe
- Center for Human Genetics Research, Vanderbilt University, Nashville, TN
| | | | - Jeff Haessler
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | - Brian E. Henderson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Iona Cheng
- Cancer Prevention Institute of California, Fremont, CA
| | - Karen C. Johnson
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN
| | - Chris S. Carlson
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Shelly-Ann Love
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC
| | | | | | - Miguel Quibrera
- Gillings School of Public Health, University of North Carolina, Chapel Hill, NC
| | - Garnet Anderson
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Ralph V. Shohet
- John A. Burns School of Medicine, University of Hawaii, Honolulu, HI
| | - José Luis Ambite
- Information Sciences Institute, University of Southern California, Marina del Rey, CA
| | - Lynne R. Wilkens
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI
| | - Loïc Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI
| | - Christopher A. Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Steven Buyske
- Department of Genetics and Department of Statistics, Rutgers University, Piscataway, NJ
| | - Charles Kooperberg
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Kari E. North
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Myriam Fornage
- Division of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, University of Texas Health Sciences Center at Houston, TX
- Institute of Molecular Medicine, University of Texas Health Sciences Center at Houston, TX
| | - Dana C. Crawford
- Center for Human Genetics Research, Vanderbilt University, Nashville, TN
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN
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Schooling CM, Au Yeung SL, Yeung SL, Freeman G. Mendelian randomization estimates may be inflated. J Am Coll Cardiol 2013; 61:1931. [PMID: 23500241 DOI: 10.1016/j.jacc.2012.12.049] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 12/19/2012] [Indexed: 02/07/2023]
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Ackert-Bicknell C, Paigen B, Korstanje R. Recalculation of 23 mouse HDL QTL datasets improves accuracy and allows for better candidate gene analysis. J Lipid Res 2013; 54:984-94. [PMID: 23393305 DOI: 10.1194/jlr.m033035] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
In the past 15 years, the quantitative trait locus (QTL) mapping approach has been applied to crosses between different inbred mouse strains to identify genetic loci associated with plasma HDL cholesterol levels. Although successful, a disadvantage of this method is low mapping resolution, as often several hundred candidate genes fall within the confidence interval for each locus. Methods have been developed to narrow these loci by combining the data from the different crosses, but they rely on the accurate mapping of the QTL and the treatment of the data in a consistent manner. We collected 23 raw datasets used for the mapping of previously published HDL QTL and reanalyzed the data from each cross using a consistent method and the latest mouse genetic map. By utilizing this approach, we identified novel QTL and QTL that were mapped to the wrong part of chromosomes. Our new HDL QTL map allows for reliable combining of QTL data and candidate gene analysis, which we demonstrate by identifying Grin3a and Etv6, as candidate genes for QTL on chromosomes 4 and 6, respectively. In addition, we were able to narrow a QTL on Chr 19 to five candidates.
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Yokoyama A, Yokoyama T, Matsui T, Mizukami T, Kimura M, Matsushita S, Higuchi S, Maruyama K. Trends in gastrectomy and ADH1B and ALDH2 genotypes in Japanese alcoholic men and their gene-gastrectomy, gene-gene and gene-age interactions for risk of alcoholism. Alcohol Alcohol 2013; 48:146-52. [PMID: 23296215 DOI: 10.1093/alcalc/ags135] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
AIMS The life-time drinking profiles of Japanese alcoholics have shown that gastrectomy increases susceptibility to alcoholism. We investigated the trends in gastrectomy and alcohol dehydrogenase-1B (ADH1B) and aldehyde dehydrogenase-2 (ALDH2) genotypes and their interactions in alcoholics. METHODS This survey was conducted on 4879 Japanese alcoholic men 40 years of age or older who underwent routine gastrointestinal endoscopic screening during the period 1996-2010. ADH1B/ALDH2 genotyping was performed in 3702 patients. RESULTS A history of gastrectomy was found in 508 (10.4%) patients. The reason for the gastrectomy was peptic ulcer in 317 patients and gastric cancer in 187 patients. The frequency of gastrectomy had gradually decreased from 13.3% in 1996-2000 to 10.5% in 2001-2005 and to 7.8% in 2006-2010 (P < 0.0001). ADH1B*1/*1 was less frequent in the gastrectomy group than in the non-gastrectomy group (age-adjusted prevalence: 20.4 vs. 27.6%, P = 0.006). ALDH2 genotype distribution did not differ between the two groups. The frequency of inactive ALDH2*1/*2 heterozygotes increased slightly from 13.0% in 1996-2000 to 14.0% in 2001-2005 and to 15.4% in 2006-2010 (P < 0.08). Two alcoholism-susceptibility genotypes, ADH1B*1/*1 and ALDH2*1/*1, modestly but significantly tended not to occur in the same individual (P = 0.026). The frequency of ADH1B*1/*1 decreased with ascending age groups. CONCLUSIONS The high frequency of history of gastrectomy suggested that gastrectomy is still a risk factor for alcoholism, although the percentage decreased during the period. The alcoholism-susceptibility genotype ADH1B*1/*1 was less frequent in the gastrectomy group, suggesting a competitive gene-gastrectomy interaction for alcoholism. A gene-gene interaction and gene-age interactions regarding the ADH1B genotype were observed.
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Affiliation(s)
- Akira Yokoyama
- National Hospital Organization Kurihama Medical and Addiction Center, 5-3-1 Nobi, Yokosuka, Kanagawa 239-0841, Japan.
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Karlos A, Shearer J, Gnatiuk E, Onyewu C, Many G, Hoffman EP, Hittel DS. Effect of the SORT1 low-density lipoprotein cholesterol locus is sex-specific in a fit, Canadian young-adult population. Appl Physiol Nutr Metab 2012; 38:188-93. [PMID: 23438231 DOI: 10.1139/apnm-2012-0231] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The SORT1 locus was originally identified by genome-wide association studies of low-density lipoprotein cholesterol (LDL-C) in adults. Although the effect sizes of this locus are relatively small, we hypothesized that a younger population would show a greater genetic effect because of fewer confounding variables. As such, we investigated the association between the SORT1 locus and LDL-C in a group of healthy young adults. Subjects (n = 122, mean age = 23.2 years) were recruited from the University of Calgary. Lipid measures and genomic DNA were collected from peripheral blood after an overnight fast. Blood pressure, percent body fat (%BF), and maximal oxygen consumption were also measured. Associations between genotype and LDL-C were investigated using linear regression. Nearly one half (42.9%) of the female and 21.7% of the male subjects had a %BF that was above a healthy range. More than one quarter of the subjects had LDL-C values that were considered nonoptimal. Although the association was not significant when both sexes were combined, a significant association was observed between the SORT1 locus (GG: 2.46 ± 0.11 mmol·L(-1) vs. GT-TT: 2.06 ± 0.12 mmol·L(-1), p = 0.016) and LDL-C in male subjects, with genotype explaining 3.0% of the variability in LDL-C. A high prevalence of nonoptimal LDL-C exists in this young population even though it is otherwise fit and healthy. A significant association was found between LDL-C and the minor SORT1 allele in male subjects, with an effect size larger than previously reported in older populations. SORT1 is a valuable target for identifying individuals who would most benefit from early interventions to prevent cardiovascular disease.
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Affiliation(s)
- Angela Karlos
- Faculty of Kinesiology, University of Calgary, 2500 University Drive, Calgary, AB T2N 1N4, Canada
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Current world literature. Curr Opin Nephrol Hypertens 2012; 21:557-66. [PMID: 22874470 DOI: 10.1097/mnh.0b013e3283574c3b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Maouche S, Schunkert H. Strategies beyond genome-wide association studies for atherosclerosis. Arterioscler Thromb Vasc Biol 2012; 32:170-81. [PMID: 22258900 DOI: 10.1161/atvbaha.111.232652] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Atherosclerotic diseases, including coronary artery disease (CAD) and myocardial infarction (MI), are the leading causes of death in the world. The genetic basis of CAD and MI, which are caused by multiple interacting endogenous and exogenous factors, has gained considerable interest in the last years as genome-wide association studies (GWASs) have identified many new susceptibility loci for CAD and MI, and the underlying genes provide new insights into the genetic architecture of these diseases. Here we summarize the recent findings from GWASs of atherosclerosis and discuss their functional and biological implications. We also discuss the different post-GWAS strategies that are currently used for refining the location of causal variants, understanding their role, and shedding light on molecular mechanisms explaining their association to CAD. We finally discuss potential clinical translations of GWAS findings for individual risk prediction, advanced clinical strategies, and personalized treatments.
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Affiliation(s)
- Seraya Maouche
- Universität zu Lübeck, Medizinische Klinik II, Ratzeburger Allee 160, 23538 Lübeck, Germany
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Shirts BH, Howard MT, Hasstedt SJ, Nanjee MN, Knight S, Carlquist JF, Anderson JL, Hopkins PN, Hunt SC. Vitamin D dependent effects of APOA5 polymorphisms on HDL cholesterol. Atherosclerosis 2012; 222:167-74. [PMID: 22425169 DOI: 10.1016/j.atherosclerosis.2012.02.030] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Revised: 02/01/2012] [Accepted: 02/20/2012] [Indexed: 12/17/2022]
Abstract
OBJECTIVES Vitamin D and serum lipid levels are risk factors for cardiovascular disease. We sought to determine if vitamin D (25OHD) interacts at established lipid loci potentially explaining additional variance in lipids. METHODS 1060 individuals from Utah families were used to screen 14 loci for SNPs potentially interacting with dietary 25OHD on lipid levels. Identified putative interactions were evaluated for (1) greater effect size in subsamples with winter measures, (2) replication in an independent sample, and (3) lack of gene-environment interaction for other correlated dietary factors. Maximum likelihood models were used to evaluate interactions. The replicate sample consisted of 2890 individuals from the Family Heart Study. Putative 25OHD receptor binding site modifying SNPs were identified and allele-specific, 25OHD-dependent APOA5 promoter activity examined using luciferase expression assays. An additional sample with serum 25OHD measures was analyzed. RESULTS An rs3135506-25OHD interaction influencing HDL-C was identified. The rs3135506 minor allele was more strongly associated with low HDL-C in individuals with low winter dietary 25OHD in initial and replicate samples (p=0.0003 Utah, p=0.002 Family Heart); correlated dietary factors did not explain the interaction. SNP rs10750097 was identified as a putative causative polymorphism, was associated with 25OHD-dependent changes in APOA5 promoter activity in HEP3B and HEK293 cells (p<0.01), and showed similar interactions to rs3135506 in family cohorts. Linear interactions were not significant in samples with serum 25OHD measures; however, genotype-specific differences were seen at deficient 25OHD levels. CONCLUSIONS A 25OHD receptor binding site modifying APOA5 promoter polymorphism is associated with lower HDL-C in 25OHD deficient individuals.
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Affiliation(s)
- Brian H Shirts
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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