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Jiang C, Wang R, Zong B, Wei P, Lu W, Han B, Xu Y. Subgroup Identification with Gene Expression Profiles of Adipose Tissue in Patients with Coronary Artery Disease. Int Heart J 2021; 62:1199-1206. [PMID: 34744146 DOI: 10.1536/ihj.21-189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Among many diseases, coronary artery disease (CAD) is the primary cause of mortality and morbidity worldwide. With the aim of revealing the underlying genetic characteristics of the CAD subtypes, we recruited patients with CAD and categorized them into subgroups according to the transcriptome expression profiles of the adipose tissue.With the removal of the batch effect, consensus clustering was employed to determine the subgroup numbers. Subgroup-specific genes were determined to conduct analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Weighted gene co-expression network analysis (WGCNA) revealed the subgroup-specific WGCNA modules. Moreover, gene set enrichment analysis (GSEA) was conducted. Overrepresentation enrichment analysis (OEA) of subgroup-specific signatures was also conducted to reveal the significant gene module associated with the corresponding clinical characteristics.After the removal of the batch effect, 77 CAD objects were divided into three subgroups. It was observed that the patients in subgroup III tended to be fat. After analyzing the dominant pathways of each subgroup, we discovered that the protein digestion and absorption pathway was specifically upregulated in subgroup I, which might result from the lowest proportion of the epicardial adipose tissue (EAT) sample. Moreover, subgroup II patients had genetic characteristics of high expression of complement and coagulation cascades and TNF signaling pathway. Furthermore, Th17 cell differentiation was significantly upregulated in subgroup III, indicating that Th17 cell differentiation is related to the clinical characteristics of body mass index (BMI).In conclusion, the genetic classification of CAD subjects indicated that subjects from different subgroups may exhibit specific gene expression patterns, suggesting that more personalized treatment should be applied to patients in each subgroup.
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Affiliation(s)
- Chunying Jiang
- Department of Cardiology, The Xuzhou School of Clinical Medicine of Nanjing Medical University; Xuzhou Central Hospital
| | - Rui Wang
- Department of Ultrasound, The Third Affiliated Hospital of Xuzhou Medical University
| | - Bin Zong
- Department of Cardiology, The Xuzhou School of Clinical Medicine of Nanjing Medical University; Xuzhou Central Hospital
| | - Peng Wei
- Department of Cardiology, The Xuzhou School of Clinical Medicine of Nanjing Medical University; Xuzhou Central Hospital
| | - Wen Lu
- Department of Cardiology, The Xuzhou School of Clinical Medicine of Nanjing Medical University; Xuzhou Central Hospital
| | - Bing Han
- Department of Cardiology, The Xuzhou School of Clinical Medicine of Nanjing Medical University; Xuzhou Central Hospital
| | - Yawei Xu
- Department of Cardiology, Shanghai Tenth Clinical Medical School of Nanjing Medical University; Shanghai Tenth People's Hospital
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2
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Wang N, Tong R, Xu J, Tian Y, Pan J, Cui J, Chen H, Peng Y, Fei S, Yang S, Wang L, Yao J, Cui W. PDX1 and MC4R genetic polymorphisms are associated with type 2 diabetes mellitus risk in the Chinese Han population. BMC Med Genomics 2021; 14:249. [PMID: 34696776 PMCID: PMC8543917 DOI: 10.1186/s12920-021-01037-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/01/2021] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Diabetes mellitus (DM) is a complex metabolic disease that is caused by a complex interplay between genetic and environmental factors. This research aimed to investigate the association of genetic polymorphisms in PDX1 and MC4R with T2DM risk. METHODS The genotypes of 10 selected SNPs in PDX1 and MC4R were identified using the Agena MassARRAY platform. We utilized odds ratio (OR) and 95% confidence intervals (CIs) to assess the correlation between genetic polymorphisms and T2DM risk. RESULTS We found that PDX1-rs9581943 decreased susceptibility to T2DM among in a Chinese Han population (OR = 0.76, p = 0.045). We also found that selected genetic polymorphisms in PDX1 and MC4R could modify the risk of T2DM, which might also be influenced by age, sex, BMI, smoking status, and drinking status (p < 0.05). CONCLUSIONS We concluded that PDX1 and MC4R genetic variants were significantly associated with T2DM risk in a Chinese Han population. These single polymorphic markers may be considered to be new targets in the assessment and prevention of T2DM among Chinese Han people.
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Affiliation(s)
- Ning Wang
- Department of Endocrinology and Second Department of Geriatrics, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, 710061, Shaanxi, China
| | - Rui Tong
- Department of Endocrinology and Second Department of Geriatrics, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, 710061, Shaanxi, China
| | - Jing Xu
- Department of Endocrinology and Second Department of Geriatrics, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, 710061, Shaanxi, China
| | - Yanni Tian
- Department of Oncology, East Branch of the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710089, Shaanxi, China
| | - Juan Pan
- Department of Endocrinology, Xianyang Central Hospital, Xianyang, 712000, Shaanxi, China
| | - Jiaqi Cui
- Department of Endocrinology and Second Department of Geriatrics, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, 710061, Shaanxi, China
| | - Huan Chen
- Department of Endocrinology and Second Department of Geriatrics, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, 710061, Shaanxi, China
| | - Yanqi Peng
- Department of Endocrinology and Second Department of Geriatrics, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, 710061, Shaanxi, China
| | - Sijia Fei
- Department of Endocrinology and Second Department of Geriatrics, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, 710061, Shaanxi, China
| | - Shujun Yang
- Department of Endocrinology and Second Department of Geriatrics, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, 710061, Shaanxi, China
| | - Lu Wang
- Department of Endocrinology and Second Department of Geriatrics, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, 710061, Shaanxi, China
| | - Juanchuan Yao
- Department of Endocrinology and Second Department of Geriatrics, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, 710061, Shaanxi, China
| | - Wei Cui
- Department of Endocrinology and Second Department of Geriatrics, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, 710061, Shaanxi, China.
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3
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Heterozygous Nme7 Mutation Affects Glucose Tolerance in Male Rats. Genes (Basel) 2021; 12:genes12071087. [PMID: 34356103 PMCID: PMC8305224 DOI: 10.3390/genes12071087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/15/2021] [Accepted: 07/17/2021] [Indexed: 12/28/2022] Open
Abstract
Complex metabolic conditions such as type 2 diabetes and obesity result from the interaction of numerous genetic and environmental factors. While the family of Nme proteins has been connected so far mostly to development, proliferation, or ciliary functions, several lines of evidence from human and experimental studies point to the potential involvement of one of its members, NME7 (non-metastatic cells 7, nucleoside diphosphate kinase 7) in carbohydrate and lipid metabolism. As a complete lack of Nme7 is semilethal in rats, we compared morphometric, metabolic, and transcriptomic profiles of standard diet-fed heterozygous Nme7+/− on male rats vs. their wild-type Nme7+/+ controls. Nme7+/− animals showed increased body weight, adiposity, higher insulin levels together with decreased glucose tolerance. Moreover, they displayed pancreatic islet fibrosis and kidney tubular damage. Despite no signs of overt liver steatosis or dyslipidemia, we found significant changes in the hepatic transcriptome of Nme7+/− male rats with a concerted increase of expression of lipogenic enzymes including Scd1, Fads1, Dhcr7 and a decrease of Cyp7b1 and Nme7. Network analyses suggested possible links between Nme7 and the activation of Srebf1 and Srebf2 upstream regulators. These results further support the implication of NME7 in the pathogenesis of glucose intolerance and adiposity.
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Veturi Y, Lucas A, Bradford Y, Hui D, Dudek S, Theusch E, Verma A, Miller JE, Kullo I, Hakonarson H, Sleiman P, Schaid D, Stein CM, Edwards DRV, Feng Q, Wei WQ, Medina MW, Krauss R, Hoffmann TJ, Risch N, Voight BF, Rader DJ, Ritchie MD. A unified framework identifies new links between plasma lipids and diseases from electronic medical records across large-scale cohorts. Nat Genet 2021; 53:972-981. [PMID: 34140684 PMCID: PMC8555954 DOI: 10.1038/s41588-021-00879-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 05/05/2021] [Indexed: 02/05/2023]
Abstract
Plasma lipids are known heritable risk factors for cardiovascular disease, but increasing evidence also supports shared genetics with diseases of other organ systems. We devised a comprehensive three-phase framework to identify new lipid-associated genes and study the relationships among lipids, genotypes, gene expression and hundreds of complex human diseases from the Electronic Medical Records and Genomics (347 traits) and the UK Biobank (549 traits). Aside from 67 new lipid-associated genes with strong replication, we found evidence for pleiotropic SNPs/genes between lipids and diseases across the phenome. These include discordant pleiotropy in the HLA region between lipids and multiple sclerosis and putative causal paths between triglycerides and gout, among several others. Our findings give insights into the genetic basis of the relationship between plasma lipids and diseases on a phenome-wide scale and can provide context for future prevention and treatment strategies.
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Affiliation(s)
- Yogasudha Veturi
- Department of Genetics and Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Anastasia Lucas
- Department of Genetics and Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yuki Bradford
- Department of Genetics and Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel Hui
- Department of Genetics and Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Scott Dudek
- Department of Genetics and Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Elizabeth Theusch
- Department of Pediatrics, University of California San Francisco, Oakland, CA, USA
| | - Anurag Verma
- Department of Genetics and Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jason E. Miller
- Department of Genetics and Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Iftikhar Kullo
- Division of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children’s Hospital of Philadelphia, PA, USA
| | - Patrick Sleiman
- Center for Applied Genomics, Children’s Hospital of Philadelphia, PA, USA
| | - Daniel Schaid
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Charles M. Stein
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Digna R. Velez Edwards
- Department of Biomedical Informatics in School of Medicine, Vanderbilt University, Nashville, TN, USA.,Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA.,Division of Quantitative Science, Department of Obstetrics and Gynecology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - QiPing Feng
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Wei-Qi Wei
- Department of Biomedical Informatics in School of Medicine, Vanderbilt University, Nashville, TN, USA
| | - Marisa W. Medina
- Department of Pediatrics, University of California San Francisco, Oakland, CA, USA
| | - Ronald Krauss
- Department of Pediatrics, University of California San Francisco, Oakland, CA, USA
| | - Thomas J. Hoffmann
- Institute for Human Genetics, and Department of Epidemiology & Biostatistics, University of California and San Francisco, San Francisco, CA, USA
| | - Neil Risch
- Institute for Human Genetics, and Department of Epidemiology & Biostatistics, University of California and San Francisco, San Francisco, CA, USA
| | - Benjamin F. Voight
- Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Institute of Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel J. Rader
- Department of Genetics and Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Marylyn D. Ritchie
- Department of Genetics and Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,
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5
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Nikpay M, McPherson R. Convergence of biomarkers and risk factor trait loci of coronary artery disease at 3p21.31 and HLA region. NPJ Genom Med 2021; 6:12. [PMID: 33574266 PMCID: PMC7878768 DOI: 10.1038/s41525-021-00174-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 01/06/2021] [Indexed: 12/13/2022] Open
Abstract
Here we seek to identify molecular biomarkers that mediate the effect of risk factors on coronary artery disease (CAD). We perform a SNP-based multiomics data analysis to find biomarkers (probes) causally associated with the risk of CAD within known genomic loci for its risk factors. We identify 78 biomarkers, the majority (64%) of which are methylation probes. We detect the convergence of several CNS and lifestyle trait loci and their biomarkers at the 3p21.31 and human leukocyte antigen (HLA) regions. The 3p21.31 locus was the most populated region in the convergence of biomarkers and risk factors. In this region, we noted as the BSN gene becomes methylated the level of stomatin (STOM) in blood increases and this contributes to higher risk of CAD. In the HLA locus, we identify several methylation biomarkers associated with various CAD risk factors. SNPs in the CFB gene display a trans-regulatory impact on the GRIA4 protein level. A methylation site upstream of the APOE gene is associated with a higher protein level of S100A13 which in turn leads to higher LDL-C and greater CAD risk. We find UHRF1BP1 and ILRUN mediate the effect of obesity on CAD whereas methylation sites within NOS3 and CKM mediate the effect of their associated-risk factors on CAD. This study provides further insight into the biology of CAD and identifies a list of biomarkers that mediate the impact of risk factors on CAD. A SNP-based initiative can unite data from various fields of omics into a single network of knowledge.
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Affiliation(s)
- Majid Nikpay
- Ruddy Canadian Cardiovascular Genetics Centre, University of Ottawa Heart Institute, Ottawa, ON, Canada.
| | - Ruth McPherson
- Ruddy Canadian Cardiovascular Genetics Centre, University of Ottawa Heart Institute, Ottawa, ON, Canada. .,Atherogenomics Laboratory, University of Ottawa Heart Institute, Ottawa, ON, Canada.
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6
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Karunakaran D, Turner AW, Duchez AC, Soubeyrand S, Rasheed A, Smyth D, Cook DP, Nikpay M, Kandiah JW, Pan C, Geoffrion M, Lee R, Boytard L, Wyatt H, Nguyen MA, Lau P, Laakso M, Ramkhelawon B, Alvarez M, Pietiläinen KH, Pajukanta P, Vanderhyden BC, Liu P, Berger SB, Gough PJ, Bertin J, Harper ME, Lusis AJ, McPherson R, Rayner KJ. RIPK1 gene variants associate with obesity in humans and can be therapeutically silenced to reduce obesity in mice. Nat Metab 2020; 2:1113-1125. [PMID: 32989316 PMCID: PMC8362891 DOI: 10.1038/s42255-020-00279-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 08/10/2020] [Indexed: 12/13/2022]
Abstract
Obesity is a major public health burden worldwide and is characterized by chronic low-grade inflammation driven by the cooperation of the innate immune system and dysregulated metabolism in adipose tissue and other metabolic organs. Receptor-interacting serine/threonine-protein kinase 1 (RIPK1) is a central regulator of inflammatory cell function that coordinates inflammation, apoptosis and necroptosis in response to inflammatory stimuli. Here we show that genetic polymorphisms near the human RIPK1 locus associate with increased RIPK1 gene expression and obesity. We show that one of these single nucleotide polymorphisms is within a binding site for E4BP4 and increases RIPK1 promoter activity and RIPK1 gene expression in adipose tissue. Therapeutic silencing of RIPK1 in vivo in a mouse model of diet-induced obesity dramatically reduces fat mass, total body weight and improves insulin sensitivity, while simultaneously reducing macrophage and promoting invariant natural killer T cell accumulation in adipose tissue. These findings demonstrate that RIPK1 is genetically associated with obesity, and reducing RIPK1 expression is a potential therapeutic approach to target obesity and related diseases.
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Affiliation(s)
- Denuja Karunakaran
- Cardiometabolic microRNA Laboratory, University of Ottawa Heart Institute, Ottawa, Ontario, Canada.
- Cardiac Function Laboratory, University of Ottawa Heart Institute, Ottawa, Ontario, Canada.
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia.
| | - Adam W Turner
- Atherogenomics Laboratory, University of Ottawa Heart Institute, Ottawa, Ontario, Canada
| | - Anne-Claire Duchez
- Cardiometabolic microRNA Laboratory, University of Ottawa Heart Institute, Ottawa, Ontario, Canada
| | - Sebastien Soubeyrand
- Atherogenomics Laboratory, University of Ottawa Heart Institute, Ottawa, Ontario, Canada
| | - Adil Rasheed
- Cardiometabolic microRNA Laboratory, University of Ottawa Heart Institute, Ottawa, Ontario, Canada
| | - David Smyth
- Cardiac Function Laboratory, University of Ottawa Heart Institute, Ottawa, Ontario, Canada
| | - David P Cook
- Ottawa Hospital Research Institute, Centre for Cancer Therapeutics, Ottawa, Ontario, Canada
| | - Majid Nikpay
- Atherogenomics Laboratory, University of Ottawa Heart Institute, Ottawa, Ontario, Canada
| | - Joshua W Kandiah
- Cardiometabolic microRNA Laboratory, University of Ottawa Heart Institute, Ottawa, Ontario, Canada
| | - Calvin Pan
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Michele Geoffrion
- Cardiometabolic microRNA Laboratory, University of Ottawa Heart Institute, Ottawa, Ontario, Canada
| | - Richard Lee
- Cardiovascular Antisense Drug Discovery Group, Ionis Pharmaceuticals, Carlsbad, CA, USA
| | - Ludovic Boytard
- New York University Langone Medical Center, New York, NY, USA
| | - Hailey Wyatt
- Cardiometabolic microRNA Laboratory, University of Ottawa Heart Institute, Ottawa, Ontario, Canada
| | - My-Anh Nguyen
- Cardiometabolic microRNA Laboratory, University of Ottawa Heart Institute, Ottawa, Ontario, Canada
| | - Paulina Lau
- Atherogenomics Laboratory, University of Ottawa Heart Institute, Ottawa, Ontario, Canada
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | | | - Marcus Alvarez
- Department of Human Genetics, and Institute for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Kirsi H Pietiläinen
- Obesity Research Unit, Research Program for Clinical and Molecular Metabolism and Obesity Center, Endocrinology, Abdominal Center, Helsinki University Central Hospital, University of Helsinki, Helsinki, Finland
| | - Päivi Pajukanta
- Department of Human Genetics, and Institute for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Barbara C Vanderhyden
- Ottawa Hospital Research Institute, Centre for Cancer Therapeutics, Ottawa, Ontario, Canada
| | - Peter Liu
- Cardiac Function Laboratory, University of Ottawa Heart Institute, Ottawa, Ontario, Canada
| | - Scott B Berger
- Pattern Recognition Receptor DPU, GlaxoSmithKline, Collegeville, PA, USA
| | - Peter J Gough
- Pattern Recognition Receptor DPU, GlaxoSmithKline, Collegeville, PA, USA
| | - John Bertin
- Pattern Recognition Receptor DPU, GlaxoSmithKline, Collegeville, PA, USA
| | - Mary-Ellen Harper
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Aldons J Lusis
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ruth McPherson
- Atherogenomics Laboratory, University of Ottawa Heart Institute, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Katey J Rayner
- Cardiometabolic microRNA Laboratory, University of Ottawa Heart Institute, Ottawa, Ontario, Canada.
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada.
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7
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Nikpay M, Soubeyrand S, Tahmasbi R, McPherson R. Multiomics Screening Identifies Molecular Biomarkers Causally Associated With the Risk of Coronary Artery Disease. CIRCULATION-GENOMIC AND PRECISION MEDICINE 2020; 13:e002876. [PMID: 32969717 DOI: 10.1161/circgen.119.002876] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND In this study, we aimed to investigate functional mechanisms underlying coronary artery disease (CAD) loci and find molecular biomarkers for CAD. METHODS We devised a multiomics data analysis approach based on Mendelian randomization and utilized it to search for molecular biomarkers causally associated with the risk of CAD within genomic regions known to be associated with CAD. RESULTS Through our CAD-centered multiomics data analysis approach, we identified 33 molecular biomarkers (probes) that were causally associated with the risk of CAD. The majority of these (N=19) were methylation probes; moreover, methylation was often behind the causal effect of expression/protein probes. We identified a number of novel loci that have a causal impact on CAD including C5orf38, SF3A3, DHX36, and MRPL33. Furthermore, by integrating the risk factors of CAD in our analysis, we were able to investigate the clinical pathways whereby several of our probes exert their effect. We found that the SELE protein level in the blood is under the trans-regulatory impact of methylation sites within the ABO gene and that SELE exerts its effect on CAD through immune, glycemic, and lipid metabolism, making it a candidate of interest for therapeutic interventions. We found the methylation site, cg05126514 within the BSN gene exert its effect on CAD through central nervous system-lifestyle risk factors. Finally, genes with a transcriptional regulatory role (SF3A3, ILF3, and N4BP2L2) exert their effect on CAD through height. CONCLUSIONS We demonstrate that multiomics data analysis is a powerful approach to unravel the functional mechanisms underlying CAD loci and to identify novel molecular biomarkers. Our results indicate epigenetic modifications are important in the pathogenesis of CAD and identifying and targeting these sites is of potential therapeutic interest to address the detrimental effects of both environmental and genetic factors.
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Affiliation(s)
- Majid Nikpay
- Ruddy Canadian Cardiovascular Genetics Centre (M.N., R.M.), University of Ottawa Heart Institute, Ottawa, Ontario, Canada
| | - Sebastien Soubeyrand
- Atherogenomics Laboratory (S.S., R.M.), University of Ottawa Heart Institute, Ottawa, Ontario, Canada
| | - Rasool Tahmasbi
- Institute for Behavioral Genetics, University of Colorado, Boulder, Colorado (R.T.)
| | - Ruth McPherson
- Ruddy Canadian Cardiovascular Genetics Centre (M.N., R.M.), University of Ottawa Heart Institute, Ottawa, Ontario, Canada.,Atherogenomics Laboratory (S.S., R.M.), University of Ottawa Heart Institute, Ottawa, Ontario, Canada
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8
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Nikpay M, Lau P, Soubeyrand S, Whytock KL, Beehler K, Pileggi C, Ghosh S, Harper ME, Dent R, McPherson R. SGCG rs679482 Associates With Weight Loss Success in Response to an Intensively Supervised Outpatient Program. Diabetes 2020; 69:2017-2026. [PMID: 32527767 DOI: 10.2337/db20-0219] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 06/07/2020] [Indexed: 02/07/2023]
Abstract
Weight loss in response to energy restriction is highly variable, and identification of genetic contributors can provide insights into underlying biology. Leveraging 1000 Genomes imputed genotypes, we carried out genome-wide association study (GWAS) analysis in 551 unrelated obese subjects of European ancestry who participated in an intensively supervised weight loss program with replication of promising signals in an independent sample of 1,331 obese subjects who completed the program at a later date. By single nucleotide polymorphism-based and sib-pair analysis, we show that that weight loss is a heritable trait, with estimated heritability (h 2 = 0.49) within the range reported for obesity. We find rs679482, intronic to SGCG (sarcoglycan γ), highly expressed in skeletal muscle, to concordantly associate with weight loss in discovery and replication samples reaching GWAS significance in the combined meta-analysis (β = -0.35, P = 1.7 × 10-12). Located in a region of open chromatin, rs679482 is predicted to bind DMRT2, and allele-specific transcription factor binding analysis indicates preferential binding of DMRT2 to rs679482-A. Concordantly, rs679482-A impairs native repressor activity and increases basal and DMRT2-mediated enhancer activity. These findings confirm that weight loss is a heritable trait and provide evidence by which a novel variant in SGCG, rs679482, leads to impaired diet response.
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Affiliation(s)
- Majid Nikpay
- Ruddy Canadian Cardiovascular Genetics Centre, University of Ottawa Heart Institute, Ottawa, Canada
| | - Paulina Lau
- Atherogenomics Laboratory, University of Ottawa Heart Institute, Ottawa, Canada
| | | | - Katey L Whytock
- Translational Research Institute for Metabolism and Diabetes, AdventHealth, Orlando, FL
| | - Kaitlyn Beehler
- Atherogenomics Laboratory, University of Ottawa Heart Institute, Ottawa, Canada
| | - Chantal Pileggi
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Sujoy Ghosh
- Duke-NUS Medical School, Singapore, Singapore
| | - Mary-Ellen Harper
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Robert Dent
- Weight Management Clinic, The Ottawa Hospital, Ottawa, Canada
| | - Ruth McPherson
- Ruddy Canadian Cardiovascular Genetics Centre, University of Ottawa Heart Institute, Ottawa, Canada
- Atherogenomics Laboratory, University of Ottawa Heart Institute, Ottawa, Canada
- Division of Cardiology, University of Ottawa Heart Institute, Ottawa, Canada
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9
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Sull JW, Kim G, Jee SH. Association of MC4R (rs17782313) with diabetes and cardiovascular disease in Korean men and women. BMC MEDICAL GENETICS 2020; 21:160. [PMID: 32807123 PMCID: PMC7433161 DOI: 10.1186/s12881-020-01100-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 08/03/2020] [Indexed: 01/26/2023]
Abstract
Background Diabetes is mostly assessed by the fasting glucose level. Several studies reported that serum fasting glucose levels and cardiovascular disease are associated with MC4R. Methods A total of 4294 subjects participated in this study. There were 1810 subjects with cardiovascular disease among the 4294 subjects. We used multivariate linear regression models and multiple logistic regression analysis. Results Individuals with the TC/CC genotype had a 1.29-fold higher risk of diabetes than did those with the TT genotype when adjusting for age, sex, and BMI (OR, 1.29; 95% CI, 1.04–1.60). For healthy subjects, the association was significant in women (OR, 1.99; 95% CI, 1.01–3.93). Men with the TC/CC genotype had a 1.21-fold higher risk of cardiovascular disease than did those with the TT genotype when adjusting for age, sex, and BMI (OR, 1.21; 95% CI, 1.04–1.41). The relationship between MC4R and cardiovascular disease was stronger in lean men (OR, 1.40; 95% CI, 1.12–1.74, p = 0.0028) than in overweight men. Conclusions This study suggests that the rs17782313 SNP in MC4R is related to diabetes and the SNP is also associated with cardiovascular disease in lean men.
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Affiliation(s)
- Jae Woong Sull
- Department of Biomedical Laboratory Science, College of Health Sciences, Eulji University, Seongnam, Korea
| | - Gitae Kim
- Department of Biomedical Laboratory Science, College of Health Sciences, Eulji University, Seongnam, Korea
| | - Sun Ha Jee
- Department of Epidemiology and Health Promotion, Institute for Health Promotion, Graduate School of Public Health, Yonsei University, Seoul, Korea.
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Christou MA, Ntritsos G, Markozannes G, Koskeridis F, Nikas SN, Karasik D, Kiel DP, Evangelou E, Ntzani EE. A genome-wide scan for pleiotropy between bone mineral density and nonbone phenotypes. Bone Res 2020; 8:26. [PMID: 32637184 PMCID: PMC7329904 DOI: 10.1038/s41413-020-0101-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 03/04/2020] [Accepted: 04/07/2020] [Indexed: 12/11/2022] Open
Abstract
Osteoporosis is the most common metabolic bone disorder globally and is characterized by skeletal fragility and microarchitectural deterioration. Genetic pleiotropy occurs when a single genetic element is associated with more than one phenotype. We aimed to identify pleiotropic loci associated with bone mineral density (BMD) and nonbone phenotypes in genome-wide association studies. In the discovery stage, the NHGRI-EBI Catalog was searched for genome-wide significant associations (P value < 5 × 10-8), excluding bone-related phenotypes. SNiPA was used to identify proxies of the significantly associated single nucleotide polymorphisms (SNPs) (r 2 = 1). We then assessed putative genetic associations of this set of SNPs with femoral neck (FN) and lumbar spine (LS) BMD data from the GEFOS Consortium. Pleiotropic variants were claimed at a false discovery rate < 1.4 × 10-3 for FN-BMD and < 1.5 × 10-3 for LS-BMD. Replication of these genetic markers was performed among more than 400 000 UK Biobank participants of European ancestry with available genetic and heel bone ultrasound data. In the discovery stage, 72 BMD-related pleiotropic SNPs were identified, and 12 SNPs located in 11 loci on 8 chromosomes were replicated in the UK Biobank. These SNPs were associated, in addition to BMD, with 14 different phenotypes. Most pleiotropic associations were exhibited by rs479844 (AP5B1, OVOL1 genes), which was associated with dermatological and allergic diseases, and rs4072037 (MUC1 gene), which was associated with magnesium levels and gastroenterological cancer. In conclusion, 12 BMD-related genome-wide significant SNPs showed pleiotropy with nonbone phenotypes. Pleiotropic associations can deepen the genetic understanding of bone-related diseases by identifying shared biological mechanisms with other diseases or traits.
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Affiliation(s)
- Maria A. Christou
- Department of Hygiene and Epidemiology, Clinical and Molecular Epidemiology Unit, School of Medicine, University of Ioannina, Ioannina, Greece
| | - Georgios Ntritsos
- Department of Hygiene and Epidemiology, Clinical and Molecular Epidemiology Unit, School of Medicine, University of Ioannina, Ioannina, Greece
| | - Georgios Markozannes
- Department of Hygiene and Epidemiology, Clinical and Molecular Epidemiology Unit, School of Medicine, University of Ioannina, Ioannina, Greece
| | - Fotis Koskeridis
- Department of Hygiene and Epidemiology, Clinical and Molecular Epidemiology Unit, School of Medicine, University of Ioannina, Ioannina, Greece
| | - Spyros N. Nikas
- Department of Hygiene and Epidemiology, Clinical and Molecular Epidemiology Unit, School of Medicine, University of Ioannina, Ioannina, Greece
| | - David Karasik
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Hinda and Arthur Marcus Institute for Aging Research, Hebrew SeniorLife, and the Broad Institute of MIT & Harvard, Cambridge, MA USA
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Douglas P. Kiel
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Hinda and Arthur Marcus Institute for Aging Research, Hebrew SeniorLife, and the Broad Institute of MIT & Harvard, Cambridge, MA USA
| | - Evangelos Evangelou
- Department of Hygiene and Epidemiology, Clinical and Molecular Epidemiology Unit, School of Medicine, University of Ioannina, Ioannina, Greece
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
| | - Evangelia E. Ntzani
- Department of Hygiene and Epidemiology, Clinical and Molecular Epidemiology Unit, School of Medicine, University of Ioannina, Ioannina, Greece
- Department of Health Services, Policy and Practice, Center for Research Synthesis in Health, School of Public Health, Brown University, Providence, RI USA
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11
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Zheng H, Zeng Z, Wen H, Wang P, Huang C, Huang P, Chen Q, Gong D, Qiu X. Application of Genome-Wide Association Studies in Coronary Artery Disease. Curr Pharm Des 2020; 25:4274-4286. [PMID: 31692429 DOI: 10.2174/1381612825666191105125148] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 10/30/2019] [Indexed: 01/10/2023]
Abstract
Coronary artery disease (CAD) is a complex disease caused by the combination of environmental and genetic factors. It is one of the leading causes of death and disability in the world. Much research has been focussed on CAD genetic mechanism. In recent years, genome-wide association study (GWAS) has developed rapidly around the world. Medical researchers around the world have successfully discovered a series of CAD genetic susceptibility genes or susceptible loci using medical research strategies, leading CAD research toward a new stage. This paper briefly summarizes the important progress made by GWAS for CAD in the world in recent years, and then analyzes the challenges faced by GWAS at this stage and the development trend of future research, to promote the transformation of genetic research results into clinical practice and provide guidance for further exploration of the genetic mechanism of CAD.
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Affiliation(s)
- Huilei Zheng
- Department of Medical Examination & Health Management, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China.,Guangxi Key Laboratory of Precision Medicine in Cardio-cerebrovascular Diseases Control and Prevention, Nanning, Guangxi, China.,Guangxi Clinical Research Center for Cardio-cerebrovascular Diseases, Nanning, Guangxi, China
| | - Zhiyu Zeng
- Guangxi Key Laboratory of Precision Medicine in Cardio-cerebrovascular Diseases Control and Prevention, Nanning, Guangxi, China.,Guangxi Clinical Research Center for Cardio-cerebrovascular Diseases, Nanning, Guangxi, China.,Elderly Cardiology Ward, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Hong Wen
- Guangxi Key Laboratory of Precision Medicine in Cardio-cerebrovascular Diseases Control and Prevention, Nanning, Guangxi, China.,Guangxi Clinical Research Center for Cardio-cerebrovascular Diseases, Nanning, Guangxi, China.,Elderly Comprehensive Ward, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Peng Wang
- Department of Medical Examination & Health Management, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Chunxia Huang
- Department of Medical Examination & Health Management, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Ping Huang
- Department of Medical Examination & Health Management, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Qingyun Chen
- Department of Medical Examination & Health Management, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Danping Gong
- Guangxi Key Laboratory of Precision Medicine in Cardio-cerebrovascular Diseases Control and Prevention, Nanning, Guangxi, China.,Guangxi Clinical Research Center for Cardio-cerebrovascular Diseases, Nanning, Guangxi, China.,Elderly Cardiology Ward, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Xiaoling Qiu
- Department of Population Health Science, Duke University School of Medicine, Durham, North Carolina, NC27708, United States.,Guangxi Key Laboratory of Precision Medicine in Cardio-cerebrovascular Diseases Control and Prevention, Nanning, Guangxi, China.,Guangxi Clinical Research Center for Cardio-cerebrovascular Diseases, Nanning, Guangxi, China
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12
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Nikpay M, Mohammadzadeh S. Phenome-wide screening for traits causally associated with the risk of coronary artery disease. J Hum Genet 2020; 65:371-380. [PMID: 31907388 DOI: 10.1038/s10038-019-0716-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 11/29/2019] [Accepted: 12/17/2019] [Indexed: 12/17/2022]
Abstract
Using two independent approaches, Mendelian randomization and Polygenic risk score in a sample of 6194 CAD cases and 4287 controls of European ancestry, we did a comprehensive phenome-wide search (PheWAS) for traits that causally associated with the risk of CAD. We found 46 risk factors that represented diverse categories including cardiovascular, CNS (central nervous system), diabetes, lipids, immune, anthropometry, and life style features; moreover, we noted numerous evidences of genetic correlations and causal associations between risk factors from different categories. Among the identified risk factors, CAD showed highest genetic relatedness with thrombotic conditions. The most represented category was life style features (29%) with evidence of strong genetic overlap with CNS traits. Genetic variants associated with higher cognition were associated with life style characteristics and cardiometabolic features that lower the risk of CAD. Conditional analysis indicated this trend is in part attributed to higher age of first sexual intercourse (AFS) in those with higher cognition. Lower AFS was concordantly associated with higher risk of CAD in males, females, and the combined sample; furthermore, lower AFS was causally associated with several CAD-risk factors including, higher fasting insulin, fasting glucose, LDL, immature reticulocyte fraction, HbA1c levels, as well as, higher risk of T2D and pulmonary embolism but lower levels of HDL. These results indicate CAD is the outcome of several phenotypically distinct but genetically interrelated sources; moreover, we identified lower AFS as an independent causal risk factor of CAD and revealed its role in mediating the effect of other risk factors.
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Affiliation(s)
- Majid Nikpay
- Ruddy Canadian Cardiovascular Genetics Centre, University of Ottawa Heart Institute, Ottawa, ON, K1Y 4W7, Canada.
| | - Sara Mohammadzadeh
- Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, 6714967346, Iran
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13
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Nikpay M, Beehler K, Valsesia A, Hager J, Harper ME, Dent R, McPherson R. Genome-wide identification of circulating-miRNA expression quantitative trait loci reveals the role of several miRNAs in the regulation of cardiometabolic phenotypes. Cardiovasc Res 2019; 115:1629-1645. [DOI: 10.1093/cvr/cvz030] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 12/18/2018] [Accepted: 01/29/2019] [Indexed: 11/13/2022] Open
Abstract
Abstract
Aims
To identify genetic variants that have a regulatory impact on circulating microRNAs (miRNAs) and to connect genetic risk to blood traits/biomarkers through the circulating miRNAs.
Methods and results
Leveraging miRNA-Seq data and the 1000 Genomes imputed genotypes, we carried out genome-wide association analysis for SNPs that regulate the expression of circulating miRNAs in a sample of 710 unrelated subjects of European ancestry. Wherever possible, we used data from the Framingham and the Geuvadis studies to replicate our findings. We found at least one genome-wide significant (P < 5e−8) miRNA-eQTL (mirQTL) for 143 circulating miRNAs. Overall each mirQTL explained a small portion (<1%) of variation in miRNA levels; however, we identified a few mirQTLs that explained 4% to 20% of variation in miRNA levels in plasma. Unlike trans-mirQTLs (P = 0.7), cis-mirQTLs tend to be also associated with their counterpart mature miRNAs (P < 0.0001), this suggests trans-mirQTLs exert their effect through processes that affect the stability of mature miRNAs; whereas, cis-mirQTLs mainly regulate the expression of primary-miRNAs. Next, we used the identified mirQTLs to investigate the links between circulating miRNAs with blood traits/biomarkers through Mendelian randomization analysis. We found miR-1908-5p plays an important role in regulating low-density lipoprotein (LDL), total cholesterol (TC), fasting glucose, HbA1c, and several lipid-metabolites in blood, whereas, miR-10b-5p mediates the trans-regulatory effect of the ABO locus on several blood proteins, coronary artery disease, and TC. Moreover, we demonstrated that a higher plasma level of miR-199a is causally associated with lower levels of LDL and TC. Finally, we found miR-143-3p and miR-145-5p are functionally related and mediate the effect of ZFPM2 on a number of its protein targets in blood including VEGFA, SERPINE1, and PDGFs.
Conclusions
This study identifies SNPs that have a regulatory impact on circulating miRNAs, and underlines the role of several circulating miRNAs in mediating the effect of a number of GWAS loci on cardiometabolic phenotypes.
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Affiliation(s)
- Majid Nikpay
- Ruddy Canadian Cardiovascular Genetics Centre, University of Ottawa Heart Institute, 40 Ruskin St – H4208, Ottawa, Canada
| | - Kaitlyn Beehler
- Atherogenomics Laboratory, University of Ottawa Heart Institute, 40 Ruskin St – H4203, Ottawa, Canada
| | - Armand Valsesia
- Nestle Institute of Health Sciences, EPFL Innovation Park, 1015 Lausanne, Switzerland
| | - Jorg Hager
- Nestle Institute of Health Sciences, EPFL Innovation Park, 1015 Lausanne, Switzerland
| | - Mary-Ellen Harper
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Roger Guindon Hall, Room 4220, Ottawa, Canada
| | - Robert Dent
- Ottawa Hospital Weight Management Clinic, 1053 Carling Avenue, Ottawa, Canada
| | - Ruth McPherson
- Ruddy Canadian Cardiovascular Genetics Centre, University of Ottawa Heart Institute, 40 Ruskin St – H4208, Ottawa, Canada
- Atherogenomics Laboratory, University of Ottawa Heart Institute, 40 Ruskin St – H4203, Ottawa, Canada
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