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Abstract
PURPOSE OF REVIEW Residual cardiovascular disease risk and increasing metabolic syndrome risk underscores a need for novel therapeutics targeting lipid metabolism in humans. Unbiased human genetic screens have proven powerful in identifying novel genomic loci, and this review discusses recent developments in such discovery. RECENT FINDINGS Recent human genome-wide association studies have been completed in incredibly large, detailed cohorts, allowing for the identification of more than 300 genomic loci that participate in the regulation of plasma lipid metabolism. However, the discovery of these loci has greatly outpaced the elucidation of the underlying functional mechanisms. The identification of novel roles for long noncoding RNAs, such as CHROME, LeXis, and MeXis, in lipid metabolism suggests that noncoding RNAs should be included in the functional translation of GWAS loci. SUMMARY Unbiased genetic studies appear to have unearthed a great deal of novel biology with respect to lipid metabolism, yet translation of these findings into actionable mechanisms has been slow. Increased focus on the translation, rather than the discovery, of these loci, with new attention paid to lncRNAs, can help spur the development of novel therapeutics targeting lipid metabolism.
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Affiliation(s)
- Elizabeth E. Ha
- Cardiometabolic Genomics Program, Division of Cardiology, Department of
Medicine, Columbia University, New York, NY, 10032
| | - Andrew G. Van Camp
- Cardiometabolic Genomics Program, Division of Cardiology, Department of
Medicine, Columbia University, New York, NY, 10032
| | - Robert C. Bauer
- Cardiometabolic Genomics Program, Division of Cardiology, Department of
Medicine, Columbia University, New York, NY, 10032
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2
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Hennessy EJ, van Solingen C, Scacalossi KR, Ouimet M, Afonso MS, Prins J, Koelwyn GJ, Sharma M, Ramkhelawon B, Carpenter S, Busch A, Chernogubova E, Matic LP, Hedin U, Maegdefessel L, Caffrey BE, Hussein MA, Ricci EP, Temel RE, Garabedian MJ, Berger JS, Vickers KC, Kanke M, Sethupathy P, Teupser D, Holdt LM, Moore KJ. The long noncoding RNA CHROME regulates cholesterol homeostasis in primate. Nat Metab 2019; 1:98-110. [PMID: 31410392 PMCID: PMC6691505 DOI: 10.1038/s42255-018-0004-9] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The human genome encodes thousands of long non-coding RNAs (lncRNAs), the majority of which are poorly conserved and uncharacterized. Here we identify a primate-specific lncRNA (CHROME), elevated in the plasma and atherosclerotic plaques of individuals with coronary artery disease, that regulates cellular and systemic cholesterol homeostasis. LncRNA CHROME expression is influenced by dietary and cellular cholesterol via the sterol-activated liver X receptor transcription factors, which control genes mediating responses to cholesterol overload. Using gain- and loss-of-function approaches, we show that CHROME promotes cholesterol efflux and HDL biogenesis by curbing the actions of a set of functionally related microRNAs that repress genes in those pathways. CHROME knockdown in human hepatocytes and macrophages increases levels of miR-27b, miR-33a, miR-33b and miR-128, thereby reducing expression of their overlapping target gene networks and associated biologic functions. In particular, cells lacking CHROME show reduced expression of ABCA1, which regulates cholesterol efflux and nascent HDL particle formation. Collectively, our findings identify CHROME as a central component of the non-coding RNA circuitry controlling cholesterol homeostasis in humans.
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Affiliation(s)
- Elizabeth J. Hennessy
- Department of Medicine, Leon H. Charney Division of
Cardiology, New York University School of Medicine, New York, New York, USA
| | - Coen van Solingen
- Department of Medicine, Leon H. Charney Division of
Cardiology, New York University School of Medicine, New York, New York, USA
| | - Kaitlyn R. Scacalossi
- Department of Medicine, Leon H. Charney Division of
Cardiology, New York University School of Medicine, New York, New York, USA
| | - Mireille Ouimet
- Department of Medicine, Leon H. Charney Division of
Cardiology, New York University School of Medicine, New York, New York, USA
| | - Milessa S. Afonso
- Department of Medicine, Leon H. Charney Division of
Cardiology, New York University School of Medicine, New York, New York, USA
| | - Jurrien Prins
- Department of Internal Medicine (Nephrology), Einthoven
Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center,
Leiden, The Netherlands
| | - Graeme J. Koelwyn
- Department of Medicine, Leon H. Charney Division of
Cardiology, New York University School of Medicine, New York, New York, USA
| | - Monika Sharma
- Department of Medicine, Leon H. Charney Division of
Cardiology, New York University School of Medicine, New York, New York, USA
| | - Bhama Ramkhelawon
- Department of Medicine, Leon H. Charney Division of
Cardiology, New York University School of Medicine, New York, New York, USA
| | - Susan Carpenter
- Department of Molecular, Cell and Developmental Biology,
University of California, Santa Cruz, California, USA
| | - Albert Busch
- Department of Molecular Medicine and Surgery, Karolinska
Institute, Stockholm, Sweden
- Department of Vascular and Endovascular Surgery, Klinikum
Rechts der Isar, Technical University Munich, Munich, Germany
| | | | - Ljubica Perisic Matic
- Department of Molecular Medicine and Surgery, Karolinska
Institute, Stockholm, Sweden
| | - Ulf Hedin
- Department of Molecular Medicine and Surgery, Karolinska
Institute, Stockholm, Sweden
| | - Lars Maegdefessel
- Department of Molecular Medicine and Surgery, Karolinska
Institute, Stockholm, Sweden
- Department of Vascular and Endovascular Surgery, Klinikum
Rechts der Isar, Technical University Munich, Munich, Germany
| | | | - Maryem A. Hussein
- Department of Microbiology, New York University School of
Medicine, New York, New York, USA
| | - Emiliano P. Ricci
- INSERM U1111, Centre International de Recherche en
Infectiologie, Ecole Normale Supérieure de Lyon, Université de Lyon,
Lyon, France
| | - Ryan E. Temel
- Saha Cardiovascular Research Center, University of
Kentucky, Lexington, Kentucky, USA
| | - Michael J. Garabedian
- Department of Microbiology, New York University School of
Medicine, New York, New York, USA
| | - Jeffrey S. Berger
- Department of Medicine, Leon H. Charney Division of
Cardiology, New York University School of Medicine, New York, New York, USA
| | - Kasey C. Vickers
- Department of Medicine, Vanderbilt University Medical
Center, Nashville, Tenessee, USA
| | - Matthew Kanke
- Department of Biomedical Sciences, College of Veterinary
Medicine, Cornell University Ithaca, New York, USA
| | - Praveen Sethupathy
- Department of Biomedical Sciences, College of Veterinary
Medicine, Cornell University Ithaca, New York, USA
| | - Daniel Teupser
- Institute of Laboratory Medicine,
Ludwig-Maximilians-University Munich, Munich, Germany
| | - Lesca M. Holdt
- Institute of Laboratory Medicine,
Ludwig-Maximilians-University Munich, Munich, Germany
| | - Kathryn J. Moore
- Department of Medicine, Leon H. Charney Division of
Cardiology, New York University School of Medicine, New York, New York, USA
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3
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Cox LA, Olivier M, Spradling-Reeves K, Karere GM, Comuzzie AG, VandeBerg JL. Nonhuman Primates and Translational Research-Cardiovascular Disease. ILAR J 2018; 58:235-250. [PMID: 28985395 DOI: 10.1093/ilar/ilx025] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Indexed: 12/18/2022] Open
Abstract
Cardiovascular disease (CVD) is the leading cause of morbidity and mortality in the United States. Human epidemiological studies provide challenges for understanding mechanisms that regulate initiation and progression of CVD due to variation in lifestyle, diet, and other environmental factors. Studies describing metabolic and physiologic aspects of CVD, and those investigating genetic and epigenetic mechanisms influencing CVD initiation and progression, have been conducted in multiple Old World nonhuman primate (NHP) species. Major advantages of NHPs as models for understanding CVD are their genetic, metabolic, and physiologic similarities with humans, and the ability to control diet, environment, and breeding. These NHP species are also genetically and phenotypically heterogeneous, providing opportunities to study gene by environment interactions that are not feasible in inbred animal models. Each Old World NHP species included in this review brings unique strengths as models to better understand human CVD. All develop CVD without genetic manipulation providing multiple models to discover genetic variants that influence CVD risk. In addition, as each of these NHP species age, their age-related comorbidities such as dyslipidemia and diabetes are accelerated proportionally 3 to 4 times faster than in humans.In this review, we discuss current CVD-related research in NHPs focusing on selected aspects of CVD for which nonprimate model organism studies have left gaps in our understanding of human disease. We include studies on current knowledge of genetics, epigenetics, calorie restriction, maternal calorie restriction and offspring health, maternal obesity and offspring health, nonalcoholic steatohepatitis and steatosis, Chagas disease, microbiome, stem cells, and prevention of CVD.
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Affiliation(s)
- Laura A Cox
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas.,Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas
| | - Michael Olivier
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas.,Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas
| | | | - Genesio M Karere
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas
| | - Anthony G Comuzzie
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas
| | - John L VandeBerg
- South Texas Diabetes and Obesity Center, School of Medicine, University of Texas Rio Grande Valley, Edinburg/Harlingen/Brownsville, Texas
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4
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Ouimet M, Hennessy EJ, van Solingen C, Koelwyn GJ, Hussein MA, Ramkhelawon B, Rayner KJ, Temel RE, Perisic L, Hedin U, Maegdefessel L, Garabedian MJ, Holdt LM, Teupser D, Moore KJ. miRNA Targeting of Oxysterol-Binding Protein-Like 6 Regulates Cholesterol Trafficking and Efflux. Arterioscler Thromb Vasc Biol 2016; 36:942-951. [PMID: 26941018 DOI: 10.1161/atvbaha.116.307282] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 02/19/2016] [Indexed: 02/06/2023]
Abstract
OBJECTIVE Cholesterol homeostasis is fundamental to human health and is, thus, tightly regulated. MicroRNAs exert potent effects on biological pathways, including cholesterol metabolism, by repressing genes with related functions. We reasoned that this mode of pathway regulation could be exploited to identify novel genes involved in cholesterol homeostasis. APPROACH AND RESULTS Here, we identify oxysterol-binding protein-like 6 (OSBPL6) as a novel target of 2 miRNA hubs regulating cholesterol homeostasis: miR-33 and miR-27b. Characterization of OSBPL6 revealed that it is transcriptionally regulated in macrophages and hepatocytes by liver X receptor and in response to cholesterol loading and in mice and nonhuman primates by Western diet feeding. OSBPL6 encodes the OSBPL-related protein 6 (ORP6), which contains dual membrane- and endoplasmic reticulum-targeting motifs. Subcellular localization studies showed that ORP6 is associated with the endolysosomal network and endoplasmic reticulum, suggesting a role for ORP6 in cholesterol trafficking between these compartments. Accordingly, knockdown of OSBPL6 results in aberrant clustering of endosomes and promotes the accumulation of free cholesterol in these structures, resulting in reduced cholesterol esterification at the endoplasmic reticulum. Conversely, ORP6 overexpression enhances cholesterol trafficking and efflux in macrophages and hepatocytes. Moreover, we show that hepatic expression of OSBPL6 is positively correlated with plasma levels of high-density lipoprotein cholesterol in a cohort of 200 healthy individuals, whereas its expression is reduced in human atherosclerotic plaques. CONCLUSIONS These studies identify ORP6 as a novel regulator of cholesterol trafficking that is part of the miR-33 and miR-27b target gene networks that contribute to the maintenance of cholesterol homeostasis.
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Affiliation(s)
- Mireille Ouimet
- Marc and Ruti Bell Vascular Biology and Disease Program, Leon H. Charney Division of Cardiology, Department of Medicine, New York University School of Medicine, New York, NY 10016
| | - Elizabeth J Hennessy
- Marc and Ruti Bell Vascular Biology and Disease Program, Leon H. Charney Division of Cardiology, Department of Medicine, New York University School of Medicine, New York, NY 10016
| | - Coen van Solingen
- Marc and Ruti Bell Vascular Biology and Disease Program, Leon H. Charney Division of Cardiology, Department of Medicine, New York University School of Medicine, New York, NY 10016
| | - Graeme J Koelwyn
- Marc and Ruti Bell Vascular Biology and Disease Program, Leon H. Charney Division of Cardiology, Department of Medicine, New York University School of Medicine, New York, NY 10016
| | - Maryem A Hussein
- Department of Microbiology, New York University School of Medicine, New York, NY 10016
| | - Bhama Ramkhelawon
- Marc and Ruti Bell Vascular Biology and Disease Program, Leon H. Charney Division of Cardiology, Department of Medicine, New York University School of Medicine, New York, NY 10016
| | - Katey J Rayner
- University of Ottawa Heart Institute, Ottawa, ON, Canada
| | - Ryan E Temel
- Saha Cardiovascular Research Center, Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY 40536
| | - Ljubica Perisic
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - Ulf Hedin
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | | | - Michael J Garabedian
- Department of Microbiology, New York University School of Medicine, New York, NY 10016
| | - Lesca M Holdt
- Institute of Laboratory Medicine, Ludwig-Maximilians-University Munich, Marchioninistraße 15, 81377 Munich, Germany
| | - Daniel Teupser
- Institute of Laboratory Medicine, Ludwig-Maximilians-University Munich, Marchioninistraße 15, 81377 Munich, Germany
| | - Kathryn J Moore
- Marc and Ruti Bell Vascular Biology and Disease Program, Leon H. Charney Division of Cardiology, Department of Medicine, New York University School of Medicine, New York, NY 10016
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5
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Farrer L, Logue M. Collection of clinical and epidemiological data for genetic linkage and association studies. CURRENT PROTOCOLS IN HUMAN GENETICS 2012; Chapter 1:Unit1.1. [PMID: 22241654 DOI: 10.1002/0471142905.hg0101s72] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Modern gene-mapping can include linkage studies, which correlate the presence of disease to broad genomic regions in either small or large family units, and association studies, which can narrow the location of a disease-predisposing trait to a single gene using either case-control or family data. This unit provides an overview of key concepts and presents guidelines for collecting diagnostic, epidemiological, and genealogical data from potential study participants. The commentary discusses the use of publicly available data from online resources, methods for evaluating evidence of genetic versus environmental influences in a disease or disease-related endophenotype, and use of e-forms to capture data electronically.
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Affiliation(s)
- Lindsay Farrer
- Boston University School of Medicine, Boston, Massachusetts, USA
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6
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Chadwick W, Zhou Y, Park SS, Wang L, Mitchell N, Stone MD, Becker KG, Martin B, Maudsley S. Minimal peroxide exposure of neuronal cells induces multifaceted adaptive responses. PLoS One 2010; 5:e14352. [PMID: 21179406 PMCID: PMC3003681 DOI: 10.1371/journal.pone.0014352] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Accepted: 11/24/2010] [Indexed: 12/20/2022] Open
Abstract
Oxidative exposure of cells occurs naturally and may be associated with cellular damage and dysfunction. Protracted low level oxidative exposure can induce accumulated cell disruption, affecting multiple cellular functions. Accumulated oxidative exposure has also been proposed as one of the potential hallmarks of the physiological/pathophysiological aging process. We investigated the multifactorial effects of long-term minimal peroxide exposure upon SH-SY5Y neural cells to understand how they respond to the continued presence of oxidative stressors. We show that minimal protracted oxidative stresses induce complex molecular and physiological alterations in cell functionality. Upon chronic exposure to minimal doses of hydrogen peroxide, SH-SY5Y cells displayed a multifactorial response to the stressor. To fully appreciate the peroxide-mediated cellular effects, we assessed these adaptive effects at the genomic, proteomic and cellular signal processing level. Combined analyses of these multiple levels of investigation revealed a complex cellular adaptive response to the protracted peroxide exposure. This adaptive response involved changes in cytoskeletal structure, energy metabolic shifts towards glycolysis and selective alterations in transmembrane receptor activity. Our analyses of the global responses to chronic stressor exposure, at multiple biological levels, revealed a viable neural phenotype in-part reminiscent of aged or damaged neural tissue. Our paradigm indicates how cellular physiology can subtly change in different contexts and potentially aid the appreciation of stress response adaptations.
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Affiliation(s)
- Wayne Chadwick
- Receptor Pharmacology Unit, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Yu Zhou
- Receptor Pharmacology Unit, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Sung-Soo Park
- Receptor Pharmacology Unit, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Liyun Wang
- Receptor Pharmacology Unit, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Nicholas Mitchell
- Department of Biology, Saint Bonaventure University, Saint Bonaventure, New York, United States of America
| | - Matthew D. Stone
- Receptor Pharmacology Unit, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Kevin G. Becker
- Gene Expression and Genomics Unit, Research Resources Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Bronwen Martin
- Metabolism Unit, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Stuart Maudsley
- Receptor Pharmacology Unit, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
- * E-mail:
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7
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Farrer L. Collection of clinical and epidemiological data for linkage studies. CURRENT PROTOCOLS IN HUMAN GENETICS 2008; Chapter 1:Unit 1.1. [PMID: 18428351 DOI: 10.1002/0471142905.hg0101s40] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Accurate assessment of the genetic basis for a disorder is necessary to determine if linkage studies will be meaningful. This unit provides an overview of key concepts and presents guidelines for collecting diagnostic, epidemiological, and genealogical data from potential study participants. The commentary discusses methods for evaluating evidence of genetic versus environmental influences in a disease and for assessing individual pedigrees.
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Affiliation(s)
- Lindsay Farrer
- Boston University School of Medicine and Harvard Medical School, Boston, Massachusetts, USA
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8
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Arnett DK, Baird AE, Barkley RA, Basson CT, Boerwinkle E, Ganesh SK, Herrington DM, Hong Y, Jaquish C, McDermott DA, O'Donnell CJ. Relevance of Genetics and Genomics for Prevention and Treatment of Cardiovascular Disease. Circulation 2007; 115:2878-901. [PMID: 17515457 DOI: 10.1161/circulationaha.107.183679] [Citation(s) in RCA: 156] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Atherosclerotic cardiovascular disease (CVD) is a major health problem in the United States and around the world. Evidence accumulated over decades convincingly demonstrates that family history in a parent or a sibling is associated with atherosclerotic CVD, manifested as coronary heart disease, stroke, and/or peripheral arterial disease. Although there are several mendelian disorders that contribute to CVD, most common forms of CVD are believed to be multifactorial and to result from many genes, each with a relatively small effect working alone or in combination with modifier genes and/or environmental factors. The identification and the characterization of these genes and their modifiers would enhance prediction of CVD risk and improve prevention, treatment, and quality of care. This scientific statement describes the approaches researchers are using to advance understanding of the genetic basis of CVD and details the current state of knowledge regarding the genetics of myocardial infarction, atherosclerotic CVD, hypercholesterolemia, and hypertension. Current areas of interest and investigation--including gene-environment interaction, pharmacogenetics, and genetic counseling--are also discussed. The statement concludes with a list of specific recommendations intended to help incorporate usable knowledge into current clinical and public health practice, foster and guide future research, and prepare both researchers and practitioners for the changes likely to occur as molecular genetics moves from the laboratory to clinic.
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9
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Lynch AI, Arnett DK, Pankow JS, Miller MB, North KE, Eckfeldt JH, Hunt SC, Rao DC, Djoussé L. Sex-specific effects of ACE I/D and AGT-M235T on pulse pressure: the HyperGEN Study. Hum Genet 2007; 122:33-40. [PMID: 17492314 DOI: 10.1007/s00439-007-0370-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2007] [Accepted: 04/18/2007] [Indexed: 12/01/2022]
Abstract
Evidence shows that an elevated pulse pressure (PP) may lead to an increased risk of cardiovascular morbidity and mortality. There is also evidence that PP is a sexually dimorphic trait, and that genetic factors influence inter-individual variation in PP. The aim of this project was to assess the genotype-by-sex interaction on PP in a sample of mostly hypertensive African American and White participants using candidate genes involved in the renin-angiotensin-aldosterone system. Subjects were participants in the HyperGEN Study, including men (43%) and women (57%) over the age of 55 years (mean age = 65). Candidate gene polymorphisms used were ACE insertion/deletion (1,789 subjects genotyped) and AGT-M235T (1,800 subjects genotyped). We employed linear regression methods to assess the genotype-by-sex interaction. For ACE, genotype-by-sex interaction on PP was detected (P = 0.04): the "D/D" genotype predicted a 2.2 mmHg higher pulse pressure among women, but a 1.2 mmHg lower PP among men, compared to those with an "I" allele, after adjusting for age, weight, height, ethnicity, and antihypertension medication use. A similar interaction was found for systolic blood pressure. The genotype-by-sex interaction was consistent across ethnicity. The interaction was evident among those on antihypertensive medications (P = 0.05), but not among those not taking such medications (P = 0.55). In our analysis of AGT, no evidence of a genotype-by-sex interaction affecting PP, SBP, or DBP was detected. This evidence for a genotype-by-sex interaction helps our understanding of the complex genetic underpinnings of blood pressure phenotypes.
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Affiliation(s)
- Amy I Lynch
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
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10
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Diego VP, Rainwater DL, Wang XL, Cole SA, Curran JE, Johnson MP, Jowett JBM, Dyer TD, Williams JT, Moses EK, Comuzzie AG, Maccluer JW, Mahaney MC, Blangero J. Genotype x adiposity interaction linkage analyses reveal a locus on chromosome 1 for lipoprotein-associated phospholipase A2, a marker of inflammation and oxidative stress. Am J Hum Genet 2007; 80:168-77. [PMID: 17160904 PMCID: PMC1785310 DOI: 10.1086/510497] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2006] [Accepted: 10/24/2006] [Indexed: 12/30/2022] Open
Abstract
Because obesity leads to a state of chronic, low-grade inflammation and oxidative stress, we hypothesized that the contribution of genes to variation in a biomarker of these two processes may be influenced by the degree of adiposity. We tested this hypothesis using samples from the San Antonio Family Heart Study that were assayed for activity of lipoprotein-associated phospholipase A(2) (Lp-PLA(2)), a marker of inflammation and oxidative stress. Using an approach to model discrete genotypexenvironment (GxE) interaction, we assigned individuals to one of two discrete diagnostic states (or "adiposity environments"): nonobese or obese, according to criteria suggested by the World Health Organization. We found a genomewide maximum LOD of 3.39 at 153 cM on chromosome 1 for Lp-PLA(2). Significant GxE interaction for Lp-PLA(2) at the genomewide maximum (P=1.16 x 10(-4)) was also found. Microarray gene-expression data were analyzed within the 1-LOD interval of the linkage signal on chromosome 1. We found two transcripts--namely, for Fc gamma receptor IIA and heat-shock protein (70 kDa)--that were significantly associated with Lp-PLA(2) (P<.001 for both) and showed evidence of cis-regulation with nominal LOD scores of 2.75 and 13.82, respectively. It would seem that there is a significant genetic response to the adiposity environment in this marker of inflammation and oxidative stress. Additionally, we conclude that GxE interaction analyses can improve our ability to identify and localize quantitative-trait loci.
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Affiliation(s)
- Vincent P Diego
- Department of Genetics, Southwest Foundation for Biomedical Research, San Antonio, TX, 78245-0549, USA.
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11
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Nsengimana J, Samani NJ, Hall AS, Balmforth AJ, Mangino M, Yuldasheva N, Maqbool A, Braund P, Burton P, Bishop DT, Ball SG, Barrett JH. Enhanced linkage of a locus on chromosome 2 to premature coronary artery disease in the absence of hypercholesterolemia. Eur J Hum Genet 2006; 15:313-9. [PMID: 17149386 DOI: 10.1038/sj.ejhg.5201752] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Linkage studies of complex diseases have so far had limited success in producing significant and replicable results, in part owing to genetic heterogeneity. We recently reported the results of a large genome-wide linkage scan for coronary artery disease (CAD) based on 1933 families. The greatest evidence for linkage was to a region of chromosome 2, with a logarithm of odds (LOD) score of 1.86, based on the non-parametric S(ALL) statistic, which did not reach genome-wide significance (P>0.3). Inclusion of a covariate in linkage analysis can be a powerful method of accounting for disease heterogeneity. As CAD is a heterogeneous disease, we carried out a linkage analysis of chromosome 2 incorporating covariates. Increased evidence for linkage was found when hypercholesterolemia was considered (LOD score including covariate of 4.4) reaching genome-wide significance as assessed by simulation (P=0.04). Results showed that the original evidence for linkage was largely attributable to the subset of 108 non-hypercholesterolemic affected sibling pairs. In separate linkage analyses of subsets of hypercholesterolemic and non-hypercholesterolemic sibling pairs, the maximum LOD scores were 1.09 in the former group and 3.74 in the latter. This result illustrates the potential to increase the power of linkage analysis in the presence of heterogeneity by inclusion of covariates. This linked locus on chromosome 2 should now be investigated further to identify the gene(s) influencing risk of CAD in subjects with a normal level of total cholesterol. Candidate genes include the interleukin 1 cluster and two potential regulators of high-density lipoprotein cholesterol level, PLA2R1 and OSBPL6.
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Affiliation(s)
- Jérémie Nsengimana
- Genetic Epidemiology Division, Leeds Institute of Molecular Medicine, University of Leeds, Leeds, UK
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12
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Thapar A, Langley K, O'donovan M, Owen M. Refining the attention deficit hyperactivity disorder phenotype for molecular genetic studies. Mol Psychiatry 2006; 11:714-20. [PMID: 16702977 DOI: 10.1038/sj.mp.4001831] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
It is well established that attention deficit hyperactivity disorder (ADHD) is a familial and highly heritable disorder. Consequently, much effort is being directed towards searching for specific susceptibility genes. There is a growing trend, across the field of complex disease genetics, towards undertaking secondary analyses based on refined phenotypic definitions and in testing whether specific susceptibility genes modify the phenotypic presentation of the disorder in question. It is crucial that good, empirically derived arguments are made before undertaking multiple analyses on different phenotype refinements. In this review article, we consider the evidence from genetic epidemiological studies as well as key clinical studies that provide guidance on examining the ADHD phenotype for the purpose of molecular genetic studies. Specifically, findings on categorical versus dimensional conceptualisations of ADHD, reporter effects, comorbidity, ADHD subtypes and persistence are reviewed. Current evidence suggests that for the purpose of identifying susceptibility genes for ADHD, parent and teachers should be used as informants and that focusing on the clinical diagnosis of ADHD is useful. There is also good empirical support in favour of examining antisocial behaviour in ADHD. Genetic studies of dimensional ADHD are useful for other complementary purposes.
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Affiliation(s)
- A Thapar
- Department of Psychological Medicine, Cardiff University, School of Medicine, Heath Park, Cardiff, Wales, UK.
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13
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Abstract
Plasma high-density lipoprotein cholesterol (HDL-C) concentrations are genetically determined to a great extent, and quantitative trait locus (QTL) analysis has been used to identify chromosomal regions containing genes regulating HDL-C levels. We discuss new genes found to participate in HDL metabolism. We also summarize 37 mouse and 30 human QTLs for plasma HDL-C levels, finding that all but three of the mouse QTLs have been confirmed by a second cross or a homologous human QTL, that the mouse QTL map is almost saturated because 92% of recently reported QTLs are repeats of those already found, and that 28 of the 30 human QTLs are located in regions homologous to mouse QTLs. This high degree of concordance between mouse and human QTLs suggests that the underlying genes may be the same. Strategies to more rapidly identify genes underlying mouse and human QTLs for HDL-C include focusing on the mouse and using mouse–human homologies, combining crosses, and haplotyping to narrow the region. Sequence analysis and expression studies can distinguish candidate genes consistent across multiple mouse crosses, and testing the candidate genes in human association studies can provide additional evidence for the candidacy of a gene. Together these strategies can accelerate the pace of finding genes that regulate HDL.
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Affiliation(s)
- Xiaosong Wang
- Jackson Laboratory, 600 Main St, Bar Harbor, ME 04609, USA.
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14
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Zhao W, Ma C, Cheverud JM, Wu R. A unifying statistical model for QTL mapping of genotype × sex interaction for developmental trajectories. Physiol Genomics 2004; 19:218-27. [PMID: 15304622 DOI: 10.1152/physiolgenomics.00129.2004] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Most organisms display remarkable differences in morphological, anatomical, and developmental features between the two sexes. It has been recognized that these sex-dependent differences are controlled by an array of specific genetic factors, mediated through various environmental stimuli. In this paper, we present a unifying statistical model for mapping quantitative trait loci (QTL) that are responsible for sexual differences in growth trajectories during ontogenetic development. This model is derived within the maximum likelihood context, incorporated by sex-stimulated differentiation in growth form that is described by mathematical functions. A typical structural model is implemented to approximate time-dependent covariance matrices for longitudinal traits. This model allows for a number of biologically meaningful hypothesis tests regarding the effects of QTL on overall growth trajectories or particular stages of development. It is particularly powerful to test whether and how the genetic effects of QTL are expressed differently in different sexual backgrounds. Our model has been employed to map QTL affecting body mass growth trajectories in both male and female mice of an F2population derived from the large (LG/J) and small (SM/J) mouse strains. We detected four growth QTL on chromosomes 6, 7, 11, and 15, two of which trigger different effects on growth curves between the two sexes. All the four QTL display significant genotype-sex interaction effects on the timing of maximal growth rate in the ontogenetic growth of mice. The implications of our model for studying the genetic architecture of growth trajectories and its extensions to some more general situations are discussed.
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Affiliation(s)
- Wei Zhao
- Department of Statistics, University of Florida, Gainesville, Florida 32611, USA
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15
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Lilja HE, Suviolahti E, Soro-Paavonen A, Hiekkalinna T, Day A, Lange K, Sobel E, Taskinen MR, Peltonen L, Perola M, Pajukanta P. Locus for quantitative HDL-cholesterol on chromosome 10q in Finnish families with dyslipidemia. J Lipid Res 2004; 45:1876-84. [PMID: 15258200 DOI: 10.1194/jlr.m400141-jlr200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Decreased HDL-cholesterol (HDL-C) and familial combined hyperlipidemia (FCHL) are the two most common familial dyslipidemias predisposing to premature coronary heart disease (CHD). These dyslipidemias share many phenotypic features, suggesting a partially overlapping molecular pathogenesis. This was supported by our previous pooled data analysis of the genome scans for low HDL-C and FCHL, which identified three shared chromosomal regions for a qualitative HDL-C trait on 8q23.1, 16q23.3, and 20q13.32. This study further investigates these regions as well as two other loci we identified earlier for premature CHD on 2q31 and Xq24 and a locus for high serum triglycerides (TGs) on 10q11. We analyzed 67 microsatellite markers in an extended study sample of 1,109 individuals from 92 low HDL-C or FCHL families using both qualitative and quantitative lipid phenotypes. These analyses provided evidence for linkage (a logarithm of odds score of 3.2) on 10q11 using a quantitative HDL-C trait. Importantly, this region, previously linked to TGs, body mass index, and obesity, provided evidence for association for quantitative TGs (P = 0.0006) and for a combined trait of HDL-C and TGs (P = 0.008) with marker D10S546. Suggestive evidence for linkage also emerged for HDL-C on 2q31 and for TGs on 20q13.32. Finnish families ascertained for dyslipidemias thus suggest that 10q11, 2q31, and 20q13.32 harbor loci for HDL-C and TGs.
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Affiliation(s)
- Heidi E Lilja
- Department of Molecular Medicine, National Public Health Institute, Helsinki, Finland
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16
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Goldin LR, Camp NJ, Keen KJ, Martin LJ, Moslehi R, Ghosh S, North KE, Wyszynski DF, Blacker D. Analysis of metabolic syndrome phenotypes in Framingham Heart Study families from Genetic Analysis Workshop 13. Genet Epidemiol 2003; 25 Suppl 1:S78-89. [PMID: 14635173 DOI: 10.1002/gepi.10288] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Twelve teams of investigators constituted a group which analyzed phenotypes related to metabolic syndrome, making use of the available longitudinal measurements from the family component of the Framingham Heart Study or the simulated data, as distributed by Genetic Analysis Workshop 13 (GAW13). Body mass index, obesity, lipid abnormalities, glucose, or combinations of these traits were analyzed by this group. A wide variety of approaches were taken to construct phenotypes from the longitudinal measurements, including considering single or multiple cross-sectional time points, single ages, minimum values, maximum values, means, other lifetime values, ever/never dichotomy, or age at onset of some threshold value. Approaches also differed in the family structures utilized (sib pairs to full extended pedigrees), the genetic data considered (two-point or multipoint), and the statistics calculated (model-free and parametric), and led to a diverse set of analyses being performed. Inferences were made about heritability, and attempts were made to map underlying genes. Over 40 genome-wide linkage analyses were conducted. Despite the broad range of approaches, several regions of the genome were repeatedly identified across multiple analyses.
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Affiliation(s)
- Lynn R Goldin
- Genetic Epidemiology Branch, DCEG, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-7236, USA.
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