51
|
Wills L, Ables JL, Braunscheidel KM, Caligiuri SPB, Elayouby KS, Fillinger C, Ishikawa M, Moen JK, Kenny PJ. Neurobiological Mechanisms of Nicotine Reward and Aversion. Pharmacol Rev 2022; 74:271-310. [PMID: 35017179 PMCID: PMC11060337 DOI: 10.1124/pharmrev.121.000299] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 08/24/2021] [Indexed: 12/27/2022] Open
Abstract
Neuronal nicotinic acetylcholine receptors (nAChRs) regulate the rewarding actions of nicotine contained in tobacco that establish and maintain the smoking habit. nAChRs also regulate the aversive properties of nicotine, sensitivity to which decreases tobacco use and protects against tobacco use disorder. These opposing behavioral actions of nicotine reflect nAChR expression in brain reward and aversion circuits. nAChRs containing α4 and β2 subunits are responsible for the high-affinity nicotine binding sites in the brain and are densely expressed by reward-relevant neurons, most notably dopaminergic, GABAergic, and glutamatergic neurons in the ventral tegmental area. High-affinity nAChRs can incorporate additional subunits, including β3, α6, or α5 subunits, with the resulting nAChR subtypes playing discrete and dissociable roles in the stimulatory actions of nicotine on brain dopamine transmission. nAChRs in brain dopamine circuits also participate in aversive reactions to nicotine and the negative affective state experienced during nicotine withdrawal. nAChRs containing α3 and β4 subunits are responsible for the low-affinity nicotine binding sites in the brain and are enriched in brain sites involved in aversion, including the medial habenula, interpeduncular nucleus, and nucleus of the solitary tract, brain sites in which α5 nAChR subunits are also expressed. These aversion-related brain sites regulate nicotine avoidance behaviors, and genetic variation that modifies the function of nAChRs in these sites increases vulnerability to tobacco dependence and smoking-related diseases. Here, we review the molecular, cellular, and circuit-level mechanisms through which nicotine elicits reward and aversion and the adaptations in these processes that drive the development of nicotine dependence. SIGNIFICANCE STATEMENT: Tobacco use disorder in the form of habitual cigarette smoking or regular use of other tobacco-related products is a major cause of death and disease worldwide. This article reviews the actions of nicotine in the brain that contribute to tobacco use disorder.
Collapse
Affiliation(s)
- Lauren Wills
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, New York
| | - Jessica L Ables
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, New York
| | - Kevin M Braunscheidel
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, New York
| | - Stephanie P B Caligiuri
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, New York
| | - Karim S Elayouby
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, New York
| | - Clementine Fillinger
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, New York
| | - Masago Ishikawa
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, New York
| | - Janna K Moen
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, New York
| | - Paul J Kenny
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, New York
| |
Collapse
|
52
|
Clark KC, Kwitek AE. Multi-Omic Approaches to Identify Genetic Factors in Metabolic Syndrome. Compr Physiol 2021; 12:3045-3084. [PMID: 34964118 PMCID: PMC9373910 DOI: 10.1002/cphy.c210010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Metabolic syndrome (MetS) is a highly heritable disease and a major public health burden worldwide. MetS diagnosis criteria are met by the simultaneous presence of any three of the following: high triglycerides, low HDL/high LDL cholesterol, insulin resistance, hypertension, and central obesity. These diseases act synergistically in people suffering from MetS and dramatically increase risk of morbidity and mortality due to stroke and cardiovascular disease, as well as certain cancers. Each of these component features is itself a complex disease, as is MetS. As a genetically complex disease, genetic risk factors for MetS are numerous, but not very powerful individually, often requiring specific environmental stressors for the disease to manifest. When taken together, all sequence variants that contribute to MetS disease risk explain only a fraction of the heritable variance, suggesting additional, novel loci have yet to be discovered. In this article, we will give a brief overview on the genetic concepts needed to interpret genome-wide association studies (GWAS) and quantitative trait locus (QTL) data, summarize the state of the field of MetS physiological genomics, and to introduce tools and resources that can be used by the physiologist to integrate genomics into their own research on MetS and any of its component features. There is a wealth of phenotypic and molecular data in animal models and humans that can be leveraged as outlined in this article. Integrating these multi-omic QTL data for complex diseases such as MetS provides a means to unravel the pathways and mechanisms leading to complex disease and promise for novel treatments. © 2022 American Physiological Society. Compr Physiol 12:1-40, 2022.
Collapse
Affiliation(s)
- Karen C Clark
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Anne E Kwitek
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| |
Collapse
|
53
|
Alsulami S, Cruvinel NT, da Silva NR, Antoneli AC, Lovegrove JA, Horst MA, Vimaleswaran KS. Effect of dietary fat intake and genetic risk on glucose and insulin-related traits in Brazilian young adults. J Diabetes Metab Disord 2021; 20:1337-1347. [PMID: 34900785 PMCID: PMC8630327 DOI: 10.1007/s40200-021-00863-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 07/16/2021] [Indexed: 12/27/2022]
Abstract
PURPOSE The development of metabolic diseases such as type 2 diabetes (T2D) is closely linked to a complex interplay between genetic and dietary factors. The prevalence of abdominal obesity, hyperinsulinemia, dyslipidaemia, and high blood pressure among Brazilian adolescents is increasing and hence, early lifestyle interventions targeting these factors might be an effective strategy to prevent or slow the progression of T2D. METHODS We aimed to assess the interaction between dietary and genetic factors on metabolic disease-related traits in 200 healthy Brazilian young adults. Dietary intake was assessed using 3-day food records. Ten metabolic disease-related single nucleotide polymorphisms (SNPs) were used to construct a metabolic-genetic risk score (metabolic-GRS). RESULTS We found significant interactions between the metabolic-GRS and total fat intake on fasting insulin level (Pinteraction = 0.017), insulin-glucose ratio (Pinteraction = 0.010) and HOMA-B (Pinteraction = 0.002), respectively, in addition to a borderline GRS-fat intake interaction on HOMA-IR (Pinteraction = 0.051). Within the high-fat intake category [37.98 ± 3.39% of total energy intake (TEI)], individuals with ≥ 5 risk alleles had increased fasting insulin level (P = 0.021), insulin-glucose ratio (P = 0.010), HOMA-B (P = 0.001) and HOMA-IR (P = 0.053) than those with < 5 risk alleles. CONCLUSION Our study has demonstrated a novel GRS-fat intake interaction in young Brazilian adults, where individuals with higher genetic risk and fat intake had increased glucose and insulin-related traits than those with lower genetic risk. Large intervention and follow-up studies with an objective assessment of dietary factors are needed to confirm our findings. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s40200-021-00863-7.
Collapse
Affiliation(s)
- Sooad Alsulami
- Department of Food and Nutritional Sciences, Hugh Sinclair Unit of Human Nutrition, University of Reading, Reading, RG6 6DZ UK
- Department of Clinical Nutrition, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Nathália Teixeira Cruvinel
- Nutritional Genomics Research Group, Faculty of Nutrition, Federal University of Goiás (UFG), Goiania, Goiás, Brazil
| | - Nara Rubia da Silva
- Nutritional Genomics Research Group, Faculty of Nutrition, Federal University of Goiás (UFG), Goiania, Goiás, Brazil
| | - Ana Carolina Antoneli
- Nutritional Genomics Research Group, Faculty of Nutrition, Federal University of Goiás (UFG), Goiania, Goiás, Brazil
| | - Julie A. Lovegrove
- Department of Food and Nutritional Sciences, Hugh Sinclair Unit of Human Nutrition, University of Reading, Reading, RG6 6DZ UK
- Institute for Cardiovascular and Metabolic Research, University of Reading, Reading, UK
| | - Maria Aderuza Horst
- Nutritional Genomics Research Group, Faculty of Nutrition, Federal University of Goiás (UFG), Goiania, Goiás, Brazil
| | - Karani Santhanakrishnan Vimaleswaran
- Department of Food and Nutritional Sciences, Hugh Sinclair Unit of Human Nutrition, University of Reading, Reading, RG6 6DZ UK
- Institute for Cardiovascular and Metabolic Research, University of Reading, Reading, UK
- Institute for Food, Nutrition, and Health, University of Reading, Reading, UK
| |
Collapse
|
54
|
Pessoa Rodrigues C, Chatterjee A, Wiese M, Stehle T, Szymanski W, Shvedunova M, Akhtar A. Histone H4 lysine 16 acetylation controls central carbon metabolism and diet-induced obesity in mice. Nat Commun 2021; 12:6212. [PMID: 34707105 PMCID: PMC8551339 DOI: 10.1038/s41467-021-26277-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 09/21/2021] [Indexed: 12/26/2022] Open
Abstract
Noncommunicable diseases (NCDs) account for over 70% of deaths world-wide. Previous work has linked NCDs such as type 2 diabetes (T2D) to disruption of chromatin regulators. However, the exact molecular origins of these chronic conditions remain elusive. Here, we identify the H4 lysine 16 acetyltransferase MOF as a critical regulator of central carbon metabolism. High-throughput metabolomics unveil a systemic amino acid and carbohydrate imbalance in Mof deficient mice, manifesting in T2D predisposition. Oral glucose tolerance testing (OGTT) reveals defects in glucose assimilation and insulin secretion in these animals. Furthermore, Mof deficient mice are resistant to diet-induced fat gain due to defects in glucose uptake in adipose tissue. MOF-mediated H4K16ac deposition controls expression of the master regulator of glucose metabolism, Pparg and the entire downstream transcriptional network. Glucose uptake and lipid storage can be reconstituted in MOF-depleted adipocytes in vitro by ectopic Glut4 expression, PPARγ agonist thiazolidinedione (TZD) treatment or SIRT1 inhibition. Hence, chronic imbalance in H4K16ac promotes a destabilisation of metabolism triggering the development of a metabolic disorder, and its maintenance provides an unprecedented regulatory epigenetic mechanism controlling diet-induced obesity.
Collapse
Affiliation(s)
- Cecilia Pessoa Rodrigues
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104, Freiburg, Germany
- International Max Planck Research School for Molecular and Cellular Biology (IMPRS-MCB), Freiburg, Germany
| | - Aindrila Chatterjee
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Meike Wiese
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Thomas Stehle
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Witold Szymanski
- Proteomics Facility, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Maria Shvedunova
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Asifa Akhtar
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany.
- Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104, Freiburg, Germany.
| |
Collapse
|
55
|
Borisevich D, Schnurr TM, Engelbrechtsen L, Rakitko A, Ängquist L, Ilinsky V, Aadahl M, Grarup N, Pedersen O, Sørensen TIA, Hansen T. Non-linear interaction between physical activity and polygenic risk score of body mass index in Danish and Russian populations. PLoS One 2021; 16:e0258748. [PMID: 34662357 PMCID: PMC8523041 DOI: 10.1371/journal.pone.0258748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 10/04/2021] [Indexed: 11/19/2022] Open
Abstract
Body mass index (BMI) is a highly heritable polygenic trait. It is also affected by various environmental and behavioral risk factors. We used a BMI polygenic risk score (PRS) to study the interplay between the genetic and environmental factors defining BMI. First, we generated a BMI PRS that explained more variance than a BMI genetic risk score (GRS), which was using only genome-wide significant BMI-associated variants (R2 = 13.1% compared to 6.1%). Second, we analyzed interactions between BMI PRS and seven environmental factors. We found a significant interaction between physical activity and BMI PRS, even when the well-known effect of the FTO region was excluded from the PRS, using a small dataset of 6,179 samples. Third, we stratified the study population into two risk groups using BMI PRS. The top 22% of the studied populations were included in a high PRS risk group. Engagement in self-reported physical activity was associated with a 1.66 kg/m2 decrease in BMI in this group, compared to a 0.84 kg/m2 decrease in BMI in the rest of the population. Our results (i) confirm that genetic background strongly affects adult BMI in the general population, (ii) show a non-linear interaction between BMI genetics and physical activity, and (iii) provide a standardized framework for future gene-environment interaction analyses.
Collapse
Affiliation(s)
- Dmitrii Borisevich
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
| | - Theresia M. Schnurr
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Line Engelbrechtsen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Gynecology and Obstetrics, Herlev Hospital, Herlev, Denmark
| | | | - Lars Ängquist
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Mette Aadahl
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, Frederiksberg, Denmark
- Department of Public Health, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thorkild I. A. Sørensen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Public Health, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
56
|
Wolf JM, Westra J, Tintle N. Using Summary Statistics to Model Multiplicative Combinations of Initially Analyzed Phenotypes With a Flexible Choice of Covariates. Front Genet 2021; 12:745901. [PMID: 34712269 PMCID: PMC8546319 DOI: 10.3389/fgene.2021.745901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/23/2021] [Indexed: 12/03/2022] Open
Abstract
While the promise of electronic medical record and biobank data is large, major questions remain about patient privacy, computational hurdles, and data access. One promising area of recent development is pre-computing non-individually identifiable summary statistics to be made publicly available for exploration and downstream analysis. In this manuscript we demonstrate how to utilize pre-computed linear association statistics between individual genetic variants and phenotypes to infer genetic relationships between products of phenotypes (e.g., ratios; logical combinations of binary phenotypes using "and" and "or") with customized covariate choices. We propose a method to approximate covariate adjusted linear models for products and logical combinations of phenotypes using only pre-computed summary statistics. We evaluate our method's accuracy through several simulation studies and an application modeling ratios of fatty acids using data from the Framingham Heart Study. These studies show consistent ability to recapitulate analysis results performed on individual level data including maintenance of the Type I error rate, power, and effect size estimates. An implementation of this proposed method is available in the publicly available R package pcsstools.
Collapse
Affiliation(s)
- Jack M. Wolf
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, United States
| | - Jason Westra
- Department of Mathematics, Computer Science, and Statistics, Dordt University, Sioux Center, IA, United States
| | - Nathan Tintle
- Department of Mathematics, Computer Science, and Statistics, Dordt University, Sioux Center, IA, United States
- Department of Population Health Nursing Science, College of Nursing, University of Illinois Chicago, Chicago, IL, United States
| |
Collapse
|
57
|
Amador C, Zeng Y, Barber M, Walker RM, Campbell A, McIntosh AM, Evans KL, Porteous DJ, Hayward C, Wilson JF, Navarro P, Haley CS. Genome-wide methylation data improves dissection of the effect of smoking on body mass index. PLoS Genet 2021; 17:e1009750. [PMID: 34499657 PMCID: PMC8428545 DOI: 10.1371/journal.pgen.1009750] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/28/2021] [Indexed: 11/18/2022] Open
Abstract
Variation in obesity-related traits has a genetic basis with heritabilities between 40 and 70%. While the global obesity pandemic is usually associated with environmental changes related to lifestyle and socioeconomic changes, most genetic studies do not include all relevant environmental covariates, so the genetic contribution to variation in obesity-related traits cannot be accurately assessed. Some studies have described interactions between a few individual genes linked to obesity and environmental variables but there is no agreement on their total contribution to differences between individuals. Here we compared self-reported smoking data and a methylation-based proxy to explore the effect of smoking and genome-by-smoking interactions on obesity related traits from a genome-wide perspective to estimate the amount of variance they explain. Our results indicate that exploiting omic measures can improve models for complex traits such as obesity and can be used as a substitute for, or jointly with, environmental records to better understand causes of disease.
Collapse
Affiliation(s)
- Carmen Amador
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Yanni Zeng
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, China
| | - Michael Barber
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Rosie M. Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Clinical Brain Sciences, Chancellor’s Building, 49 Little France Crescent, Edinburgh BioQuarter, Edinburgh, United Kingdom
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Andrew M. McIntosh
- Division of Psychiatry, University of Edinburgh, Edinburgh, United Kingdom
| | - Kathryn L. Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - David J. Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - James F. Wilson
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Pau Navarro
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Chris S. Haley
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| |
Collapse
|
58
|
Haslam DE, Peloso GM, Guirette M, Imamura F, Bartz TM, Pitsillides AN, Wang CA, Li-Gao R, Westra JM, Pitkänen N, Young KL, Graff M, Wood AC, Braun KVE, Luan J, Kähönen M, Kiefte-de Jong JC, Ghanbari M, Tintle N, Lemaitre RN, Mook-Kanamori DO, North K, Helminen M, Mossavar-Rahmani Y, Snetselaar L, Martin LW, Viikari JS, Oddy WH, Pennell CE, Rosendall FR, Ikram MA, Uitterlinden AG, Psaty BM, Mozaffarian D, Rotter JI, Taylor KD, Lehtimäki T, Raitakari OT, Livingston KA, Voortman T, Forouhi NG, Wareham NJ, de Mutsert R, Rich SS, Manson JE, Mora S, Ridker PM, Merino J, Meigs JB, Dashti HS, Chasman DI, Lichtenstein AH, Smith CE, Dupuis J, Herman MA, McKeown NM. Sugar-Sweetened Beverage Consumption May Modify Associations Between Genetic Variants in the CHREBP (Carbohydrate Responsive Element Binding Protein) Locus and HDL-C (High-Density Lipoprotein Cholesterol) and Triglyceride Concentrations. CIRCULATION-GENOMIC AND PRECISION MEDICINE 2021; 14:e003288. [PMID: 34270325 PMCID: PMC8373451 DOI: 10.1161/circgen.120.003288] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Supplemental Digital Content is available in the text. Background: ChREBP (carbohydrate responsive element binding protein) is a transcription factor that responds to sugar consumption. Sugar-sweetened beverage (SSB) consumption and genetic variants in the CHREBP locus have separately been linked to HDL-C (high-density lipoprotein cholesterol) and triglyceride concentrations. We hypothesized that SSB consumption would modify the association between genetic variants in the CHREBP locus and dyslipidemia. Methods: Data from 11 cohorts from the Cohorts for Heart and Aging Research in Genomic Epidemiology consortium (N=63 599) and the UK Biobank (N=59 220) were used to quantify associations of SSB consumption, genetic variants, and their interaction on HDL-C and triglyceride concentrations using linear regression models. A total of 1606 single nucleotide polymorphisms within or near CHREBP were considered. SSB consumption was estimated from validated questionnaires, and participants were grouped by their estimated intake. Results: In a meta-analysis, rs71556729 was significantly associated with higher HDL-C concentrations only among the highest SSB consumers (β, 2.12 [95% CI, 1.16–3.07] mg/dL per allele; P<0.0001), but not significantly among the lowest SSB consumers (P=0.81; PDiff <0.0001). Similar results were observed for 2 additional variants (rs35709627 and rs71556736). For triglyceride, rs55673514 was positively associated with triglyceride concentrations only among the highest SSB consumers (β, 0.06 [95% CI, 0.02–0.09] ln-mg/dL per allele, P=0.001) but not the lowest SSB consumers (P=0.84; PDiff=0.0005). Conclusions: Our results identified genetic variants in the CHREBP locus that may protect against SSB-associated reductions in HDL-C and other variants that may exacerbate SSB-associated increases in triglyceride concentrations. Registration: URL: https://www.clinicaltrials.gov; Unique identifier: NCT00005133, NCT00005121, NCT00005487, and NCT00000479.
Collapse
Affiliation(s)
- Danielle E Haslam
- Nutritional Epidemiology Program (D.E.H., M. Guirette, K.A.L., N.M.M.), Tufts University, Boston, MA.,Channing Division of Network Medicine (D.E.H., J.E.M.), Brigham and Women's Hospital and Harvard Medical School, Boston, MA.,Department of Nutrition (D.E.H.), Harvard T.H. Chan School of Public Health, Boston, MA
| | - Gina M Peloso
- Department of Biostatistics, Boston University School of Public Health, MA (G.M.P., A.N.P., J.D.)
| | - Melanie Guirette
- Nutritional Epidemiology Program (D.E.H., M. Guirette, K.A.L., N.M.M.), Tufts University, Boston, MA
| | - Fumiaki Imamura
- Medical Research Council Epidemiology Unit, University of Cambridge, United Kingdom (F.I., J.L., N.G.F., N.J.W.)
| | - Traci M Bartz
- Cardiovascular Health Research Unit, Departments of Biostatistics (T.M.B.), University of Washington, Seattle.,Department of Medicine (T.M.B., R.N.L., B.M.P.), University of Washington, Seattle
| | - Achilleas N Pitsillides
- Department of Biostatistics, Boston University School of Public Health, MA (G.M.P., A.N.P., J.D.)
| | - Carol A Wang
- School of Medicine and Public Health, Faculty of Medicine and Health, The University of Newcastle, NSW, Australia (C.A.W., C.E.P.)
| | - Ruifang Li-Gao
- Department of Clinical Epidemiology (R.L.G., D.O.M.-K., F.R.R., R.dM.), Leiden University Medical Center, the Netherlands
| | | | - Niina Pitkänen
- Auria Biobank (N.P.), University of Turku, Finland.,Research Centre of Applied and Preventive Cardiovascular Medicine (N.P., O.T.R.), University of Turku, Finland
| | - Kristin L Young
- Department of Epidemiology, Gillings School of Global Public Health (K.L.Y., M. Graff, K.N.), University of North Carolina, Chapel Hill
| | - Mariaelisa Graff
- Department of Epidemiology, Gillings School of Global Public Health (K.L.Y., M. Graff, K.N.), University of North Carolina, Chapel Hill
| | - Alexis C Wood
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX (A.C.W.)
| | - Kim V E Braun
- Department of Epidemiology (K.V.E.B., J.C.K.-d.J., M. Ghanbari, M.A.I.), Erasmus MC University Medical Center Rotterdam, the Netherlands
| | - Jian'an Luan
- Medical Research Council Epidemiology Unit, University of Cambridge, United Kingdom (F.I., J.L., N.G.F., N.J.W.)
| | - Mika Kähönen
- Department of Clinical Physiology (M.K.), Tampere University Hospital, Finland.,Department of Clinical Physiology (M.K.), Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Life Sciences, University of Tampere, Finland
| | - Jessica C Kiefte-de Jong
- Department of Public Health and Primary Care (J.C.L.d.J., D.O.M.-K.), Leiden University Medical Center, the Netherlands.,Department of Epidemiology (K.V.E.B., J.C.K.-d.J., M. Ghanbari, M.A.I.), Erasmus MC University Medical Center Rotterdam, the Netherlands
| | - Mohsen Ghanbari
- Department of Epidemiology (K.V.E.B., J.C.K.-d.J., M. Ghanbari, M.A.I.), Erasmus MC University Medical Center Rotterdam, the Netherlands
| | | | - Rozenn N Lemaitre
- Department of Medicine (T.M.B., R.N.L., B.M.P.), University of Washington, Seattle
| | - Dennis O Mook-Kanamori
- Department of Clinical Epidemiology (R.L.G., D.O.M.-K., F.R.R., R.dM.), Leiden University Medical Center, the Netherlands.,Department of Public Health and Primary Care (J.C.L.d.J., D.O.M.-K.), Leiden University Medical Center, the Netherlands
| | - Kari North
- Department of Epidemiology, Gillings School of Global Public Health (K.L.Y., M. Graff, K.N.), University of North Carolina, Chapel Hill.,Carolina Center for Genome Science (K.N.), University of North Carolina, Chapel Hill
| | - Mika Helminen
- Research Development and Innovation Centre (M.H.), Tampere University Hospital, Finland.,Faculty of Social Sciences, Health Sciences, Tampere University, Finland (M.H.)
| | - Yasmin Mossavar-Rahmani
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY (Y.M.-R.)
| | - Linda Snetselaar
- Department of Epidemiology, University of Iowa, Iowa City (L.S.)
| | - Lisa W Martin
- George Washington University School of Medicine and Health Sciences, Washington, D.C. (L.W.M.)
| | - Jorma S Viikari
- Department of Medicine (J.S.V.), University of Turku, Finland.,Division of Medicine (J.S.V.), Turku University Hospital, Finland
| | - Wendy H Oddy
- Menzies Institute for Medical Research, University of Tasmania, HOB, Australia (W.H.O.)
| | - Craig E Pennell
- Nutrition and Genomics Laboratory (C.E.S.), Tufts University, Boston, MA.,School of Medicine and Public Health, Faculty of Medicine and Health, The University of Newcastle, NSW, Australia (C.A.W., C.E.P.)
| | - Frits R Rosendall
- Department of Clinical Epidemiology (R.L.G., D.O.M.-K., F.R.R., R.dM.), Leiden University Medical Center, the Netherlands
| | - M Arfan Ikram
- Department of Epidemiology (K.V.E.B., J.C.K.-d.J., M. Ghanbari, M.A.I.), Erasmus MC University Medical Center Rotterdam, the Netherlands
| | - Andre G Uitterlinden
- Department of Internal Medicine (A.G.U.), Erasmus MC University Medical Center Rotterdam, the Netherlands
| | - Bruce M Psaty
- Department of Medicine (T.M.B., R.N.L., B.M.P.), University of Washington, Seattle.,Departments of Epidemiology and Health Services (B.M.P.), University of Washington, Seattle.,Kaiser Permanente Washington Health Research Institute, Seattle, WA (B.M.P.)
| | - Dariush Mozaffarian
- Jean Mayer U.S. Department of Agriculture Human Nutrition Research Center on Aging, and Friedman School of Nutrition Science and Policy (D.M.), Tufts University, Boston, MA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA (J.I.R., K.D.T.)
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA (J.I.R., K.D.T.)
| | - Terho Lehtimäki
- Department of Clinical Chemistry (T.L.), Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Life Sciences, University of Tampere, Finland.,Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland (T.L.)
| | - Olli T Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine (N.P., O.T.R.), University of Turku, Finland.,Centre for Population Health Research (O.T.R.), University of Turku, Finland.,Department of Clinical Physiology and Nuclear Medicine (O.T.R.), Turku University Hospital, Finland
| | - Kara A Livingston
- Nutritional Epidemiology Program (D.E.H., M. Guirette, K.A.L., N.M.M.), Tufts University, Boston, MA
| | | | - Nita G Forouhi
- Medical Research Council Epidemiology Unit, University of Cambridge, United Kingdom (F.I., J.L., N.G.F., N.J.W.)
| | - Nick J Wareham
- Medical Research Council Epidemiology Unit, University of Cambridge, United Kingdom (F.I., J.L., N.G.F., N.J.W.)
| | - Renée de Mutsert
- Department of Clinical Epidemiology (R.L.G., D.O.M.-K., F.R.R., R.dM.), Leiden University Medical Center, the Netherlands
| | - Steven S Rich
- Center for Public Health Genomics and Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville (S.S.R.)
| | - JoAnn E Manson
- Channing Division of Network Medicine (D.E.H., J.E.M.), Brigham and Women's Hospital and Harvard Medical School, Boston, MA.,Division of Preventive Medicine (J.E.M., S.M., P.M.R., D.I.C.), Brigham and Women's Hospital and Harvard Medical School, Boston, MA.,Department of Epidemiology (J.E.M.), Harvard T.H. Chan School of Public Health, Boston, MA
| | - Samia Mora
- Division of Preventive Medicine (J.E.M., S.M., P.M.R., D.I.C.), Brigham and Women's Hospital and Harvard Medical School, Boston, MA.,Cardiovascular Division of Medicine and Center for Lipid Metabolomics (S.M., P.M.R.), Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Paul M Ridker
- Division of Preventive Medicine (J.E.M., S.M., P.M.R., D.I.C.), Brigham and Women's Hospital and Harvard Medical School, Boston, MA.,Cardiovascular Division of Medicine and Center for Lipid Metabolomics (S.M., P.M.R.), Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Jordi Merino
- Program in Medical and Population Genetics (J.M., J.B.M., H.S.D.), Broad Institute of MIT and Harvard, Cambridge, MA.,Program in Metabolism (J.M., J.B.M.), Broad Institute of MIT and Harvard, Cambridge, MA.,Department of Medicine, Harvard Medical School, Boston, MA (J.M., J.B.M.).,Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus, Spain (J.M.).,Diabetes Unit and Center for Genomic Medicine (J.M., H.S.D.), Massachusetts General Hospital and Harvard Medical School, Boston
| | - James B Meigs
- Program in Medical and Population Genetics (J.M., J.B.M., H.S.D.), Broad Institute of MIT and Harvard, Cambridge, MA.,Program in Metabolism (J.M., J.B.M.), Broad Institute of MIT and Harvard, Cambridge, MA.,Department of Medicine, Harvard Medical School, Boston, MA (J.M., J.B.M.).,Division of General Internal Medicine (J.B.M.), Massachusetts General Hospital and Harvard Medical School, Boston
| | - Hassan S Dashti
- Program in Medical and Population Genetics (J.M., J.B.M., H.S.D.), Broad Institute of MIT and Harvard, Cambridge, MA.,Diabetes Unit and Center for Genomic Medicine (J.M., H.S.D.), Massachusetts General Hospital and Harvard Medical School, Boston.,Department of Anesthesia, Critical Care and Pain Medicine (H.S.D.), Massachusetts General Hospital and Harvard Medical School, Boston
| | - Daniel I Chasman
- Division of Preventive Medicine (J.E.M., S.M., P.M.R., D.I.C.), Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | | | | | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, MA (G.M.P., A.N.P., J.D.)
| | - Mark A Herman
- Division Of Endocrinology, Metabolism, and Nutrition, Department of Medicine and Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC (M.A.H.)
| | - Nicola M McKeown
- Nutritional Epidemiology Program (D.E.H., M. Guirette, K.A.L., N.M.M.), Tufts University, Boston, MA
| |
Collapse
|
59
|
Lin E, Tsai SJ, Kuo PH, Liu YL, Yang AC, Conomos MP, Thornton TA. Genome-wide association study in the Taiwan biobank identifies four novel genes for human height: NABP2, RASA2, RNF41 and SLC39A5. Hum Mol Genet 2021; 30:2362-2369. [PMID: 34270706 DOI: 10.1093/hmg/ddab202] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 06/13/2021] [Accepted: 07/12/2021] [Indexed: 11/13/2022] Open
Abstract
Numerous genome-wide association studies (GWASs) have been conducted for the identification of genetic variants involved with human height. The vast majority of these studies, however, have been conducted in populations of European ancestry. Here, we report the first GWAS of adult height in the Taiwan Biobank using a discovery sample of 14 571 individuals and an independent replication sample of 20 506 individuals. From our analysis we generalize to the Taiwanese population genome-wide significant associations with height and 18 previously identified genes in European and non-Taiwanese East Asian populations. We also identify and replicate, at the genome-wide significance level, associated variants for height in four novel genes at two loci that have not previously been reported: RASA2 on chromosome 3 and NABP2, RNF41, and SLC39A5 at 12q13.3 on chromosome 12. RASA2 and RNF41 are strong candidates for having a role in height with copy number and loss of function variants in RASA2 previously found to be associated with short stature disorders, and decreased expression of the RNF41 gene resulting in insulin resistance in skeletal muscle. The results from our analysis of the Taiwan Biobank underscore the potential for the identification of novel genetic discoveries in underrepresented worldwide populations, even for traits, such as height, that have been extensively investigated in large-scale studies of European ancestry populations.
Collapse
Affiliation(s)
- Eugene Lin
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA.,Department of Electrical & Computer Engineering, University of Washington, Seattle, WA 98195, USA.,Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
| | - Shih-Jen Tsai
- Department of Psychiatry, Taipei Veterans General Hospital, Taipei, Taiwan.,Division of Psychiatry, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Po-Hsiu Kuo
- Department of Public Health, Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan
| | - Yu-Li Liu
- Center for Neuropsychiatric Research, National Health Research Institutes, Miaoli County, Taiwan
| | - Albert C Yang
- Institute of Brain Science, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Division of Interdisciplinary Medicine and Biotechnology, Beth Israel Deaconess Medical Center/Harvard Medical School, Boston, MA 02215, USA
| | - Matthew P Conomos
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Timothy A Thornton
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| |
Collapse
|
60
|
Justice AE, Young K, Gogarten SM, Sofer T, Graff M, Love SAM, Wang Y, Klimentidis YC, Cruz M, Guo X, Hartwig F, Petty L, Yao J, Allison MA, Below JE, Buchanan TA, Chen YDI, Goodarzi MO, Hanis C, Highland HM, Hsueh WA, Ipp E, Parra E, Palmas W, Raffel LJ, Rotter JI, Tan J, Taylor KD, Valladares A, Xiang AH, Sánchez-Johnsen L, Isasi CR, North KE. Genome-wide association study of body fat distribution traits in Hispanics/Latinos from the HCHS/SOL. Hum Mol Genet 2021; 30:2190-2204. [PMID: 34165540 PMCID: PMC8561424 DOI: 10.1093/hmg/ddab166] [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: 03/11/2021] [Revised: 06/16/2021] [Accepted: 06/17/2021] [Indexed: 01/02/2023] Open
Abstract
Central obesity is a leading health concern with a great burden carried by ethnic minority populations, especially Hispanics/Latinos. Genetic factors contribute to the obesity burden overall and to inter-population differences. We aimed to identify the loci associated with central adiposity measured as waist-to-hip ratio (WHR), waist circumference (WC) and hip circumference (HIP) adjusted for body mass index (adjBMI) by using the Hispanic Community Health Study/Study of Latinos (HCHS/SOL); determine if differences in associations differ by background group within HCHS/SOL and determine whether previously reported associations generalize to HCHS/SOL. Our analyses included 7472 women and 5200 men of mainland (Mexican, Central and South American) and Caribbean (Puerto Rican, Cuban and Dominican) background residing in the USA. We performed genome-wide association analyses stratified and combined across sexes using linear mixed-model regression. We identified 16 variants for waist-to-hip ratio adjusted for body mass index (WHRadjBMI), 22 for waist circumference adjusted for body mass index (WCadjBMI) and 28 for hip circumference adjusted for body mass index (HIPadjBMI), which reached suggestive significance (P < 1 × 10-6). Many loci exhibited differences in strength of associations by ethnic background and sex. We brought a total of 66 variants forward for validation in cohorts (N = 34 161) with participants of Hispanic/Latino, African and European descent. We confirmed four novel loci (P < 0.05 and consistent direction of effect, and P < 5 × 10-8 after meta-analysis), including two for WHRadjBMI (rs13301996, rs79478137); one for WCadjBMI (rs3168072) and one for HIPadjBMI (rs28692724). Also, we generalized previously reported associations to HCHS/SOL, (8 for WHRadjBMI, 10 for WCadjBMI and 12 for HIPadjBMI). Our study highlights the importance of large-scale genomic studies in ancestrally diverse Hispanic/Latino populations for identifying and characterizing central obesity susceptibility that may be ancestry-specific.
Collapse
Affiliation(s)
- Anne E Justice
- Department of Population Health Sciences, Geisinger Health System, Danville, PA 17822, USA,Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA,To whom correspondence should be addressed at: Department of Population Health Sciences, Geisinger Health System, Danville, PA 17822, USA. Tel: +1 5702141009; Fax: +1 5702143071;
| | - Kristin Young
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | | | - Tamar Sofer
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Misa Graff
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Shelly Ann M Love
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Yujie Wang
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Yann C Klimentidis
- Department of Epidemiology and Biostatistics, University of Arizona, Tucson, AZ 85724, USA
| | - Miguel Cruz
- Unidad de Investigacion Medica en Bioquimica, Hospital de Especialidades, Centro Medico Nacional Siglo XXI (CMNSXX1)-IMSS, Mexico City 06720, Mexico
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Fernando Hartwig
- Center for Epidemiological Research, Universidade Federal de Pelotas, Pelotas 96020, Brazil
| | - Lauren Petty
- Division of Genetic Medicine, Department of Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jie Yao
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Matthew A Allison
- Division of Preventive Medicine, Department of Family Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Jennifer E Below
- Division of Genetic Medicine, Department of Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Thomas A Buchanan
- Department of Medicine, Keck School of Medicine and Diabetes and Obesity Research Institute, University of Southern California, Los Angeles, CA 90033, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Mark O Goodarzi
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Craig Hanis
- 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 77030, USA
| | - Heather M Highland
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Willa A Hsueh
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Wexner Medical Center, The Ohio State University, Columbus, OH 43210, USA
| | - Eli Ipp
- Department of Medicine, Endocrinology, Diabetes & Metabolism, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Esteban Parra
- Department of Anthropology, University of Toronto at Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Walter Palmas
- Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Leslie J Raffel
- Department of PediatrIcs, Division of Genetic and Genomic Medicine, University of California, Irvine, CA 92868, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Jingyi Tan
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Adan Valladares
- Unidad de Investigacion Medica en Bioquimica, Hospital de Especialidades, Centro Medico Nacional Siglo XXI (CMNSXX1)-IMSS, Mexico City 06720, Mexico
| | - Anny H Xiang
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA 91101, USA
| | - Lisa Sánchez-Johnsen
- Department of Family Medicine, Rush University Medical Center, Chicago, IL 60612, USA
| | - Carmen R Isasi
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY 10467, USA,Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY 10467, USA
| | - Kari E North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| |
Collapse
|
61
|
Abstract
Peripheral artery disease-atherosclerosis of the abdominal aorta and lower extremity vascular bed-is a complex disease with both environmental and genetic determinants. Unmitigated disease is associated with major functional decline and can lead to chronic limb-threatening ischemia, amputation, and increased mortality. Over the last 10 years, major advances have been made in identifying the genetic basis of this common, complex disease. In this review, we provide an overview of the primary types of genetic analyses performed for peripheral artery disease, including heritability and linkage studies, and more recently biobank-based genome-wide association studies. Looking forward, we highlight areas of future study including efforts to identify causal peripheral artery disease genes, rare variant and structural variant analyses using whole-exome and whole-genome sequencing data, and the need to include individuals of diverse genetic ancestries.
Collapse
Affiliation(s)
- Derek Klarin
- Malcolm Randall VA Medical Center, Gainesville, FL (D.K.).,Division of Vascular Surgery and Endovascular Therapy, University of Florida College of Medicine, Gainesville (D.K.).,Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston (D.K.).,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA (D.K.)
| | - Philip S Tsao
- VA Palo Alto Health Care System, CA (P.S.T.).,Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, CA (P.S.T.)
| | - Scott M Damrauer
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA (S.M.D.).,Department of Surgery, Perlman School of Medicine, University of Pennsylvania, Philadelphia (S.M.D.)
| |
Collapse
|
62
|
Wang J, Zhao Q, Bowden J, Hemani G, Davey Smith G, Small DS, Zhang NR. Causal inference for heritable phenotypic risk factors using heterogeneous genetic instruments. PLoS Genet 2021; 17:e1009575. [PMID: 34157017 PMCID: PMC8301661 DOI: 10.1371/journal.pgen.1009575] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 07/23/2021] [Accepted: 05/04/2021] [Indexed: 12/25/2022] Open
Abstract
Over a decade of genome-wide association studies (GWAS) have led to the finding of extreme polygenicity of complex traits. The phenomenon that "all genes affect every complex trait" complicates Mendelian Randomization (MR) studies, where natural genetic variations are used as instruments to infer the causal effect of heritable risk factors. We reexamine the assumptions of existing MR methods and show how they need to be clarified to allow for pervasive horizontal pleiotropy and heterogeneous effect sizes. We propose a comprehensive framework GRAPPLE to analyze the causal effect of target risk factors with heterogeneous genetic instruments and identify possible pleiotropic patterns from data. By using GWAS summary statistics, GRAPPLE can efficiently use both strong and weak genetic instruments, detect the existence of multiple pleiotropic pathways, determine the causal direction and perform multivariable MR to adjust for confounding risk factors. With GRAPPLE, we analyze the effect of blood lipids, body mass index, and systolic blood pressure on 25 disease outcomes, gaining new information on their causal relationships and potential pleiotropic pathways involved.
Collapse
Affiliation(s)
- Jingshu Wang
- Department of Statistics, University of Chicago, Chicago, Illinois, United States of America
| | - Qingyuan Zhao
- Department of Pure Mathematics and Mathematical Statistics, University of Cambridge, Cambridge, United Kingdom
| | - Jack Bowden
- College of Medicine and Health, University of Exeter, Exeter, United Kingdom
| | - Gibran Hemani
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
| | - Dylan S. Small
- Department of Statistics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Nancy R. Zhang
- Department of Statistics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| |
Collapse
|
63
|
Wang H, Goodman MO, Sofer T, Redline S. Cutting the fat: advances and challenges in sleep apnoea genetics. Eur Respir J 2021; 57:57/5/2004644. [PMID: 33958377 DOI: 10.1183/13993003.04644-2020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 02/10/2021] [Indexed: 01/25/2023]
Affiliation(s)
- Heming Wang
- Division of Sleep and Circadian Disorders, Dept of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Matthew O Goodman
- Division of Sleep and Circadian Disorders, Dept of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Tamar Sofer
- Division of Sleep and Circadian Disorders, Dept of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Dept of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| |
Collapse
|
64
|
Peng H, Wu X, Wen Y, Lin J. Association between elevated body mass index in non-smokers and autoimmune diseases: A two-sample Mendelian randomization analysis. Autoimmun Rev 2021; 20:102853. [PMID: 33971344 DOI: 10.1016/j.autrev.2021.102853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 02/15/2021] [Accepted: 02/20/2021] [Indexed: 10/21/2022]
Affiliation(s)
- Haoxin Peng
- Nanshan School, Guangzhou Medical University, Jingxiu Road, Panyu District, Guangzhou 511436, China.
| | - Xiangrong Wu
- Nanshan School, Guangzhou Medical University, Jingxiu Road, Panyu District, Guangzhou 511436, China
| | - Yaokai Wen
- Nanshan School, Guangzhou Medical University, Jingxiu Road, Panyu District, Guangzhou 511436, China
| | - Jinsheng Lin
- Nanshan School, Guangzhou Medical University, Jingxiu Road, Panyu District, Guangzhou 511436, China
| |
Collapse
|
65
|
Thio CHL, van Zon SKR, van der Most PJ, Snieder H, Bültmann U, Gansevoort RT. Associations of Genetic Factors, Educational Attainment, and Their Interaction With Kidney Function Outcomes. Am J Epidemiol 2021; 190:864-874. [PMID: 33089864 PMCID: PMC8096480 DOI: 10.1093/aje/kwaa237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 10/02/2020] [Accepted: 10/19/2020] [Indexed: 11/16/2022] Open
Abstract
Both genetic predisposition and low educational attainment (EA) are associated with higher risk of chronic kidney disease. We examined the interaction of EA and genetic risk in kidney function outcomes. We included 3,597 participants from the Prevention of Renal and Vascular End-Stage Disease Cohort Study, a longitudinal study in a community-based sample from Groningen, the Netherlands (median follow-up, 11 years; 1997–2012). Kidney function was approximated by obtaining estimated glomerular filtration rate (eGFR) from serum creatinine and cystatin C. Individual longitudinal linear eGFR trajectories were derived from linear mixed models. Genotype data on 63 single-nucleotide polymorphisms, with known associations with eGFR, were used to calculate an allele-weighted genetic score (WGS). EA was categorized into high, medium, and low. In ordinary least squares analysis, higher WGS and lower EA showed additive effects on reduced baseline eGFR; the interaction term was nonsignificant. In analysis of eGFR decline, the significant interaction term suggested amplification of genetic risk by low EA. Adjustment for known renal risk factors did not affect our results. This study presents the first evidence of gene-environment interaction between EA and a WGS for eGFR decline and provides population-level insights into the mechanisms underlying socioeconomic disparities in chronic kidney disease.
Collapse
Affiliation(s)
- Chris H L Thio
- Correspondence to Dr. Chris H. L. Thio, Unit of Genetic Epidemiology and Bioinformatics, Department of Epidemiology (HPC FA40), University Medical Center Groningen, University of Groningen Hanzeplein 1, PO Box 30.001, 9700RB Groningen, the Netherlands (e-mail: )
| | | | | | | | | | | |
Collapse
|
66
|
Xu H, Schwander K, Brown MR, Wang W, Waken RJ, Boerwinkle E, Cupples LA, de Las Fuentes L, van Heemst D, Osazuwa-Peters O, de Vries PS, van Dijk KW, Sung YJ, Zhang X, Morrison AC, Rao DC, Noordam R, Liu CT. Lifestyle Risk Score: handling missingness of individual lifestyle components in meta-analysis of gene-by-lifestyle interactions. Eur J Hum Genet 2021; 29:839-850. [PMID: 33500576 PMCID: PMC8110957 DOI: 10.1038/s41431-021-00808-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 11/30/2020] [Accepted: 01/05/2021] [Indexed: 01/29/2023] Open
Abstract
Recent studies consider lifestyle risk score (LRS), an aggregation of multiple lifestyle exposures, in identifying association of gene-lifestyle interaction with disease traits. However, not all cohorts have data on all lifestyle factors, leading to increased heterogeneity in the environmental exposure in collaborative meta-analyses. We compared and evaluated four approaches (Naïve, Safe, Complete and Moderator Approaches) to handle the missingness in LRS-stratified meta-analyses under various scenarios. Compared to "benchmark" results with all lifestyle factors available for all cohorts, the Complete Approach, which included only cohorts with all lifestyle components, was underpowered due to lower sample size, and the Naïve Approach, which utilized all available data and ignored the missingness, was slightly inflated. The Safe Approach, which used all data in LRS-exposed group and only included cohorts with all lifestyle factors available in the LRS-unexposed group, and the Moderator Approach, which handled missingness via moderator meta-regression, were both slightly conservative and yielded almost identical p values. We also evaluated the performance of the Safe Approach under different scenarios. We observed that the larger the proportion of cohorts without missingness included, the more accurate the results compared to "benchmark" results. In conclusion, we generally recommend the Safe Approach, a straightforward and non-inflated approach, to handle heterogeneity among cohorts in the LRS based genome-wide interaction meta-analyses.
Collapse
Affiliation(s)
- Hanfei Xu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA.
| | - Karen Schwander
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Michael R Brown
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, the University of Texas School of Public health, Houston, TX, USA
| | - Wenyi Wang
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - R J Waken
- Field and Environmental Data Science, Benson Hill Inc, St. Louis, MO, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, the University of Texas School of Public health, Houston, TX, USA
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - L Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- NHLBI and Boston University Framingham Heart Study, Framingham, MA, USA
| | - Lisa de Las Fuentes
- Department of Medicine, Cardiovascular Division, Washington University School of Medicine, St. Louis, MO, USA
| | - Diana van Heemst
- Section of Gerontology and Geriatrics, Department of Internal Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Paul S de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, the University of Texas School of Public health, Houston, TX, USA
| | - Ko Willems van Dijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
- Division of Endocrinology, Department of Internal Medicine, Leiden University Medical Center, Leiden, the Netherlands
- Leiden Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Yun Ju Sung
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Xiaoyu Zhang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, the University of Texas School of Public health, Houston, TX, USA
| | - D C Rao
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Raymond Noordam
- Section of Gerontology and Geriatrics, Department of Internal Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA.
| |
Collapse
|
67
|
Katus U, Villa I, Ringmets I, Veidebaum T, Harro J. Neuropeptide Y gene variants in obesity, dietary intake, blood pressure, lipid and glucose metabolism: A longitudinal birth cohort study. Peptides 2021; 139:170524. [PMID: 33652060 DOI: 10.1016/j.peptides.2021.170524] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 02/24/2021] [Accepted: 02/24/2021] [Indexed: 12/29/2022]
Abstract
OBJECTIVE Neuropeptide Y affects several physiological functions, notably appetite regulation. We analysed the association between four single nucleotide polymorphisms (SNP) in the NPY gene (rs5574, rs16147, rs16139, rs17149106) and measures of obesity, dietary intake, physical activity, blood pressure, glucose and lipid metabolism from adolescence to young adulthood. METHODS The sample included both birth cohorts of the Estonian Children Personality Behaviour and Health Study at ages 15 (n = 1075 with available complete data), 18 (n = 913) and 25 (n = 926) years. Linear mixed-effects regression models were used for longitudinal association between NPY SNP-s and variables of interest. Associations at ages 15, 18 and 25 were analysed by ANOVA. RESULTS Rs5574 CC-homozygotes had a greater increase per year in waist-to-hip ratio (WHR) and a smaller decrease in daily energy intake and carbohydrate intake from age 15-25 years; fasting glucose and cholesterol were higher in rs5574 CC-homozygotes. Rs16147 TT-homozygotes had higher body weight and a greater increase in sum of 5 skinfolds, waist circumference, WHR and waist-to-height ratio; however, they had lower carbohydrate intake throughout the observation period. Rs16147 TT-homozygotes and both rs16139 and rs17149106 heterozygotes had higher triglyceride levels. All NPY SNP-s were associated with blood pressure: rs5574 TT-and rs16147 CC-homozygotes had a smaller increase in diastolic blood pressure, while rs16139 and rs17149106 heterozygous had lower blood pressure throughout the study. CONCLUSION Variants of the NPY gene were associated with measures of obesity, dietary intake, glucose and lipid metabolism and blood pressure from adolescence to young adulthood.
Collapse
Affiliation(s)
- Urmeli Katus
- Department of Family Medicine and Public Health, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Inga Villa
- Department of Family Medicine and Public Health, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Inge Ringmets
- Department of Family Medicine and Public Health, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Toomas Veidebaum
- Department of Chronic Diseases, National Institute for Health Development, Tallinn, Estonia
| | - Jaanus Harro
- Chair of Neuropsychopharmacology, Institute of Chemistry, University of Tartu, Tartu, Estonia.
| |
Collapse
|
68
|
Schnurr TM, Stallknecht BM, Sørensen TIA, Kilpeläinen TO, Hansen T. Evidence for shared genetics between physical activity, sedentary behaviour and adiposity-related traits. Obes Rev 2021; 22:e13182. [PMID: 33354910 DOI: 10.1111/obr.13182] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/23/2020] [Accepted: 11/25/2020] [Indexed: 12/20/2022]
Abstract
Observational, cross-sectional and longitudinal studies showed that physical activity and sedentary behaviour are associated with adiposity-related traits, apparently in a bidirectional manner. Physical activity is also suggested to suppress the genetic risk of adiposity. Since phenotypic associations with genetic variants are not subject to reverse causation or confounding, they may be used as tools to shed light on cause and effect in this complex interdependency. We review the evidence for shared genetics of physical activity and adiposity-related traits and for gene-by-physical activity interactions on adiposity-related traits in human studies. We outline limitations, challenges and opportunities in studying and understanding of these relationships. In summary, physical activity and sedentary behaviour are genetically correlated with body mass index and fat percentage but may not be correlated with lean body mass. Mendelian randomisation analyses show that physical activity and sedentary behaviour have bidirectional relationships with adiposity. Several studies suggest that physical activity suppresses genetic risk of adiposity. No studies have yet tested whether adiposity enhances genetic predisposition to sedentariness. The complexity of the comprehensive causal model makes the assessment of the single or combined components challenging. Substantial progress in this field may need long-term intervention studies.
Collapse
Affiliation(s)
- Theresia M Schnurr
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Bente M Stallknecht
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thorkild I A Sørensen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Public Health, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tuomas O Kilpeläinen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
69
|
Moccia C, Popovic M, Isaevska E, Fiano V, Trevisan M, Rusconi F, Polidoro S, Richiardi L. Birthweight DNA methylation signatures in infant saliva. Clin Epigenetics 2021; 13:57. [PMID: 33741061 PMCID: PMC7980592 DOI: 10.1186/s13148-021-01053-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 03/09/2021] [Indexed: 11/17/2022] Open
Abstract
Background Low birthweight has been repeatedly associated with long-term adverse health outcomes and many non-communicable diseases. Our aim was to look-up cord blood birthweight-associated CpG sites identified by the PACE Consortium in infant saliva, and to explore saliva-specific DNA methylation signatures of birthweight. Methods DNA methylation was assessed using Infinium HumanMethylation450K array in 135 saliva samples collected from children of the NINFEA birth cohort at an average age of 10.8 (range 7–17) months. The association analyses between birthweight and DNA methylation variations were carried out using robust linear regression models both in the exploratory EWAS analyses and in the look-up of the PACE findings in infant saliva. Results None of the cord blood birthweight-associated CpGs identified by the PACE Consortium was associated with birthweight when analysed in infant saliva. In saliva EWAS analyses, considering a false discovery rate p-values < 0.05, birthweight as continuous variable was associated with DNA methylation in 44 CpG sites; being born small for gestational age (SGA, lower 10th percentile of birthweight for gestational age according to WHO reference charts) was associated with DNA methylation in 44 CpGs, with only one overlapping CpG between the two analyses. Despite no overlap with PACE results at the CpG level, two of the top saliva birthweight CpGs mapped at genes associated with birthweight with the same direction of the effect also in the PACE Consortium (MACROD1 and RPTOR). Conclusion Our study provides an indication of the birthweight and SGA epigenetic salivary signatures in children around 10 months of age. DNA methylation signatures in cord blood may not be comparable with saliva DNA methylation signatures at about 10 months of age, suggesting that the birthweight epigenetic marks are likely time and tissue specific. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01053-1.
Collapse
Affiliation(s)
- Chiara Moccia
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin and CPO Piemonte, Via Santena 7, 10126, Turin, Italy.
| | - Maja Popovic
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin and CPO Piemonte, Via Santena 7, 10126, Turin, Italy
| | - Elena Isaevska
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin and CPO Piemonte, Via Santena 7, 10126, Turin, Italy
| | - Valentina Fiano
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin and CPO Piemonte, Via Santena 7, 10126, Turin, Italy
| | - Morena Trevisan
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin and CPO Piemonte, Via Santena 7, 10126, Turin, Italy
| | - Franca Rusconi
- Unit of Epidemiology, 'Anna Meyer' Children's University Hospital, Florence, Italy
| | - Silvia Polidoro
- Italian Institute for Genomic Medicine (IIGM), Candiolo, Italy.,MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College, London, UK
| | - Lorenzo Richiardi
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin and CPO Piemonte, Via Santena 7, 10126, Turin, Italy
| |
Collapse
|
70
|
Iwase M, Matsuo K, Nakatochi M, Oze I, Ito H, Koyanagi Y, Ugai T, Kasugai Y, Hishida A, Takeuchi K, Okada R, Kubo Y, Shimanoe C, Tanaka K, Ikezaki H, Murata M, Takezaki T, Nishimoto D, Kuriyama N, Ozaki E, Suzuki S, Watanabe M, Mikami H, Nakamura Y, Uemura H, Katsuura-Kamano S, Kuriki K, Kita Y, Takashima N, Nagino M, Momozawa Y, Kubo M, Wakai K. Differential Effect of Polymorphisms on Body Mass Index Across the Life Course of Japanese: The Japan Multi-Institutional Collaborative Cohort Study. J Epidemiol 2021; 31:172-179. [PMID: 32147644 PMCID: PMC7878711 DOI: 10.2188/jea.je20190296] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 02/24/2020] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Obesity is a reported risk factor for various health problems. Genome-wide association studies (GWASs) have identified numerous independent loci associated with body mass index (BMI). However, most of these have been focused on Europeans, and little evidence is available on the genetic effects across the life course of other ethnicities. METHODS We conducted a cross-sectional study to examine the associations of 282 GWAS-identified single nucleotide polymorphisms with three BMI-related traits, current BMI, BMI at 20 years old (BMI at 20), and change in BMI (BMI change), among 11,586 Japanese individuals enrolled in the Japan Multi-Institutional Collaborative Cohort study. Associations were examined using multivariable linear regression models. RESULTS We found a significant association (P < 0.05/282 = 1.77 × 10-4) between BMI and 11 polymorphisms in or near FTO, BDNF, TMEM18, HS6ST3, and BORCS7. The trend was similar between current BMI and BMI change, but differed from that of the BMI at 20. Among the significant variants, those on FTO were associated with all BMI traits, whereas those on TMEM18 and HS6SR3 were only associated with BMI at 20. The association of FTO loci with BMI remained, even after additional adjustment for dietary energy intake. CONCLUSIONS Previously reported BMI-associated loci discovered in Europeans were also identified in the Japanese population. Additionally, our results suggest that the effects of each loci on BMI may vary across the life course and that this variation may be caused by the differential effects of individual genes on BMI via different pathways.
Collapse
Affiliation(s)
- Madoka Iwase
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan
- Department of Surgical Oncology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Keitaro Matsuo
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan
- Division of Cancer Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Masahiro Nakatochi
- Department of Nursing, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Isao Oze
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Hidemi Ito
- Division of Cancer Information and Control, Aichi Cancer Center Research Institute, Nagoya, Japan
- Division of Descriptive Cancer Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuriko Koyanagi
- Division of Cancer Information and Control, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Tomotaka Ugai
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Yumiko Kasugai
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Asahi Hishida
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kenji Takeuchi
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Rieko Okada
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoko Kubo
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | | | - Keitaro Tanaka
- Department of Preventive Medicine, Faculty of Medicine, Saga University, Saga, Japan
| | - Hiroaki Ikezaki
- Department of General Internal Medicine, Kyushu University Hospital, Fukuoka, Japan
| | - Masayuki Murata
- Department of General Internal Medicine, Kyushu University Hospital, Fukuoka, Japan
| | - Toshiro Takezaki
- Department of International Island and Community Medicine, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Daisaku Nishimoto
- School of Health Sciences, Faculty of Medicine, Kagoshima University, Kagoshima, Japan
| | - Nagato Kuriyama
- Department of Epidemiology for Community Health and Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Etsuko Ozaki
- Department of Epidemiology for Community Health and Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Sadao Suzuki
- Department of Public Health, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Miki Watanabe
- Department of Public Health, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Haruo Mikami
- Cancer Prevention Center, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Yohko Nakamura
- Cancer Prevention Center, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Hirokazu Uemura
- Department of Preventive Medicine, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Sakurako Katsuura-Kamano
- Department of Preventive Medicine, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Kiyonori Kuriki
- Laboratory of Public Health, University of Shizuoka, Shizuoka, Japan
| | - Yoshikuni Kita
- Faculty of Nursing Science, Tsuruga Nursing University, Fukui, Japan
| | - Naoyuki Takashima
- Department of Public Health, Faculty of Medicine, Kindai University, Osaka, Japan
| | - Masato Nagino
- Department of Surgical Oncology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kenji Wakai
- Division of Descriptive Cancer Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| |
Collapse
|
71
|
Lu Y, Xu Z, Georgakis MK, Wang Z, Lin H, Zheng L. Smoking and heart failure: a Mendelian randomization and mediation analysis. ESC Heart Fail 2021; 8:1954-1965. [PMID: 33656795 PMCID: PMC8120408 DOI: 10.1002/ehf2.13248] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 01/15/2021] [Accepted: 01/26/2021] [Indexed: 12/31/2022] Open
Abstract
Aims We performed a Mendelian randomization (MR) study to elucidate the associations of ever smoking, lifelong smoking duration, and smoking cessation with heart failure (HF) risk. Methods and results We extracted genetic variants associated with smoking initiation, age at initiation of regular smoking, cigarettes per day, and smoking cessation from the genome‐wide association study and Sequencing Consortium of Alcohol and Nicotine use (1.2 million individuals), as well as a composite lifetime smoking index from the UK Biobank (462 690 individuals). The associations between smoking phenotypes and HF were explored in the Heart Failure Molecular Epidemiology for Therapeutic Targets Consortium (47 309 cases; 930 014 controls) employing inverse variance‐weighted meta‐analysis and multivariable MR. The mediation effects of coronary artery disease and atrial fibrillation on smoking–HF risk were explored using mediation analysis. The odds ratios (ORs) for HF were 1.28 [95% confidence interval (CI), 1.22–1.36; P = 1.5 × 10−18] for ever regular smokers compared with never smokers and 1.25 (95% CI, 1.09–1.44; P = 1.6 × 10−3) for current smokers vs. former smokers. Genetic liability to smoking more cigarettes per day (OR, 1.37; 95% CI, 1.20–1.58; P = 6.4 × 10−6) and a higher composite lifetime smoking index (OR, 1.49; 95% CI, 1.31–1.70; P = 2.5 × 10−9) were associated with a higher risk of HF. The results were robust and consistent in all sensitivity analyses and multivariable MR after adjusting for HF risk factors, and their associations were independent of coronary artery disease and atrial fibrillation. Conclusions Genetic liability to ever smoking and a higher lifetime smoking burden are associated with a higher risk of HF.
Collapse
Affiliation(s)
- Yunlong Lu
- Department of Cardiology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
| | - Zhouming Xu
- Huzhou Maternal and Child Health Care Hospital, Huzhou, Zhejiang, China
| | - Marios K Georgakis
- Institute for Stroke and Dementia Research (ISD), University Hospital, Ludwig Maximilian University of Munich (LMU), Munich, Germany
| | - Zhen Wang
- Department of Cardiology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
| | - Hefeng Lin
- The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Liangrong Zheng
- Department of Cardiology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
| |
Collapse
|
72
|
Identification of genetic loci affecting body mass index through interaction with multiple environmental factors using structured linear mixed model. Sci Rep 2021; 11:5001. [PMID: 33654129 PMCID: PMC7925554 DOI: 10.1038/s41598-021-83684-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 02/05/2021] [Indexed: 11/08/2022] Open
Abstract
Multiple environmental factors could interact with a single genetic factor to affect disease phenotypes. We used Struct-LMM to identify genetic variants that interacted with environmental factors related to body mass index (BMI) using data from the Korea Association Resource. The following factors were investigated: alcohol consumption, education, physical activity metabolic equivalent of task (PAMET), income, total calorie intake, protein intake, carbohydrate intake, and smoking status. Initial analysis identified 7 potential single nucleotide polymorphisms (SNPs) that interacted with the environmental factors (P value < 5.00 × 10-6). Of the 8 environmental factors, PAMET score was excluded for further analysis since it had an average Bayes Factor (BF) value < 1 (BF = 0.88). Interaction analysis using 7 environmental factors identified 11 SNPs (P value < 5.00 × 10-6). Of these, rs2391331 had the most significant interaction (P value = 7.27 × 10-9) and was located within the intron of EFNB2 (Chr 13). In addition, the gene-based genome-wide association study verified EFNB2 gene significantly interacting with 7 environmental factors (P value = 5.03 × 10-10). BF analysis indicated that most environmental factors, except carbohydrate intake, contributed to the interaction of rs2391331 on BMI. Although the replication of the results in other cohorts is warranted, these findings proved the usefulness of Struct-LMM to identify the gene-environment interaction affecting disease.
Collapse
|
73
|
Virani SS, Alonso A, Aparicio HJ, Benjamin EJ, Bittencourt MS, Callaway CW, Carson AP, Chamberlain AM, Cheng S, Delling FN, Elkind MSV, Evenson KR, Ferguson JF, Gupta DK, Khan SS, Kissela BM, Knutson KL, Lee CD, Lewis TT, Liu J, Loop MS, Lutsey PL, Ma J, Mackey J, Martin SS, Matchar DB, Mussolino ME, Navaneethan SD, Perak AM, Roth GA, Samad Z, Satou GM, Schroeder EB, Shah SH, Shay CM, Stokes A, VanWagner LB, Wang NY, Tsao CW. Heart Disease and Stroke Statistics-2021 Update: A Report From the American Heart Association. Circulation 2021; 143:e254-e743. [PMID: 33501848 DOI: 10.1161/cir.0000000000000950] [Citation(s) in RCA: 3172] [Impact Index Per Article: 1057.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND The American Heart Association, in conjunction with the National Institutes of Health, annually reports the most up-to-date statistics related to heart disease, stroke, and cardiovascular risk factors, including core health behaviors (smoking, physical activity, diet, and weight) and health factors (cholesterol, blood pressure, and glucose control) that contribute to cardiovascular health. The Statistical Update presents the latest data on a range of major clinical heart and circulatory disease conditions (including stroke, congenital heart disease, rhythm disorders, subclinical atherosclerosis, coronary heart disease, heart failure, valvular disease, venous disease, and peripheral artery disease) and the associated outcomes (including quality of care, procedures, and economic costs). METHODS The American Heart Association, through its Statistics Committee, continuously monitors and evaluates sources of data on heart disease and stroke in the United States to provide the most current information available in the annual Statistical Update. The 2021 Statistical Update is the product of a full year's worth of effort by dedicated volunteer clinicians and scientists, committed government professionals, and American Heart Association staff members. This year's edition includes data on the monitoring and benefits of cardiovascular health in the population, an enhanced focus on social determinants of health, adverse pregnancy outcomes, vascular contributions to brain health, the global burden of cardiovascular disease, and further evidence-based approaches to changing behaviors related to cardiovascular disease. RESULTS Each of the 27 chapters in the Statistical Update focuses on a different topic related to heart disease and stroke statistics. CONCLUSIONS The Statistical Update represents a critical resource for the lay public, policy makers, media professionals, clinicians, health care administrators, researchers, health advocates, and others seeking the best available data on these factors and conditions.
Collapse
|
74
|
Campbell PT, Lin Y, Bien SA, Figueiredo JC, Harrison TA, Guinter MA, Berndt SI, Brenner H, Chan AT, Chang-Claude J, Gallinger SJ, Gapstur SM, Giles GG, Giovannucci E, Gruber SB, Gunter M, Hoffmeister M, Jacobs EJ, Jenkins MA, Le Marchand L, Li L, McLaughlin JR, Murphy N, Milne RL, Newcomb PA, Newton C, Ogino S, Potter JD, Rennert G, Rennert HS, Robinson J, Sakoda LC, Slattery ML, Song Y, White E, Woods MO, Casey G, Hsu L, Peters U. Association of Body Mass Index With Colorectal Cancer Risk by Genome-Wide Variants. J Natl Cancer Inst 2021; 113:38-47. [PMID: 32324875 PMCID: PMC7781451 DOI: 10.1093/jnci/djaa058] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 02/27/2020] [Accepted: 04/17/2020] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Body mass index (BMI) is a complex phenotype that may interact with genetic variants to influence colorectal cancer risk. METHODS We tested multiplicative statistical interactions between BMI (per 5 kg/m2) and approximately 2.7 million single nucleotide polymorphisms with colorectal cancer risk among 14 059 colorectal cancer case (53.2% women) and 14 416 control (53.8% women) participants. All analyses were stratified by sex a priori. Statistical methods included 2-step (ie, Cocktail method) and single-step (ie, case-control logistic regression and a joint 2-degree of freedom test) procedures. All statistical tests were two-sided. RESULTS Each 5 kg/m2 increase in BMI was associated with higher risks of colorectal cancer, less so for women (odds ratio [OR] = 1.14, 95% confidence intervals [CI] = 1.11 to 1.18; P = 9.75 × 10-17) than for men (OR = 1.26, 95% CI = 1.20 to 1.32; P = 2.13 × 10-24). The 2-step Cocktail method identified an interaction for women, but not men, between BMI and a SMAD7 intronic variant at 18q21.1 (rs4939827; Pobserved = .0009; Pthreshold = .005). A joint 2-degree of freedom test was consistent with this finding for women (joint P = 2.43 × 10-10). Each 5 kg/m2 increase in BMI was more strongly associated with colorectal cancer risk for women with the rs4939827-CC genotype (OR = 1.24, 95% CI = 1.16 to 1.32; P = 2.60 × 10-10) than for women with the CT (OR = 1.14, 95% CI = 1.09 to 1.19; P = 1.04 × 10-8) or TT (OR = 1.07, 95% CI = 1.01 to 1.14; P = .02) genotypes. CONCLUSION These results provide novel insights on a potential mechanism through which a SMAD7 variant, previously identified as a susceptibility locus for colorectal cancer, and BMI may influence colorectal cancer risk for women.
Collapse
Affiliation(s)
- Peter T Campbell
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, USA
| | - Yi Lin
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Stephanie A Bien
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jane C Figueiredo
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Tabitha A Harrison
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Mark A Guinter
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ), and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andrew T Chan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- University Medical Centre Hamburg-Eppendorf, University Cancer Centre Hamburg (UCCH), Hamburg, Germany
| | - Steven J Gallinger
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Susan M Gapstur
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, USA
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Edward Giovannucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Stephen B Gruber
- Center for Precision Medicine and Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Marc Gunter
- Section of Nutrition and Metabolism, International Agency for Research on Cancer, Lyon, France
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Eric J Jacobs
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, USA
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | | | - Li Li
- Department of Family Medicine and Cancer Center, University of Virginia, Charlottesville, VA, USA
| | - John R McLaughlin
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Neil Murphy
- Section of Nutrition and Metabolism, International Agency for Research on Cancer, Lyon, France
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Polly A Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Christina Newton
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, USA
| | - Shuji Ogino
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham & Women’s Hospital, and Harvard Medical School, Boston, MA, USA
| | - John D Potter
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Gad Rennert
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
- Clalit National Cancer Control Center, Haifa, Israel
| | - Hedy S Rennert
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
- Clalit National Cancer Control Center, Haifa, Israel
| | - Jennifer Robinson
- Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, IA, USA
| | - Lori C Sakoda
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Martha L Slattery
- Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
| | - Yiqing Song
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Indiana University, Indianapolis, IN, USA
| | - Emily White
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington School of Public Health, Seattle, WA, USA
| | - Michael O Woods
- Discipline of Genetics, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Li Hsu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington School of Public Health, Seattle, WA, USA
| |
Collapse
|
75
|
Marcos-Pasero H, Aguilar-Aguilar E, Ikonomopoulou MP, Loria-Kohen V. BDNF Gene as a Precision Skill of Obesity Management. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1331:233-248. [PMID: 34453302 DOI: 10.1007/978-3-030-74046-7_15] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The scarcity of the results obtained for the treatment of obesity leads us to consider new strategies, contemplating all the factors involved in the development of the disease. One of the key molecules for controlling body weight and energy homeostasis is the brain-derived neurotrophic factor (BDNF). This work summarizes the mechanisms in which BDNF gene regulates this multifactorial disease. In addition, we discuss the role of other BDNF polymorphisms as genetic determinants of obesity. In this context, a total of 14 SNPs near or inside BDNF/BDNF-AS related to BMI were identified in various GWASs. Finally, we assess gene-diet interaction as a novel tool to prevent obesity and formulate solid and personalized nutritional management. Our research group has performed the first study on the association of BDNF-AS rs925946 polymorphism and calcium intake as potential modulators of the nutritional status. Although these results should be confirmed in future studies, they open the path for new prevention opportunities.
Collapse
Affiliation(s)
- Helena Marcos-Pasero
- Nutrition and Clinical Trials Unit, GENYAL Platform, IMDEA-Food Institute, CEI UAM + CSIC, Madrid, Spain
| | - Elena Aguilar-Aguilar
- Nutrition and Clinical Trials Unit, GENYAL Platform, IMDEA-Food Institute, CEI UAM + CSIC, Madrid, Spain
| | - Maria P Ikonomopoulou
- Translational Venomics Group, IMDEA-Food, CEI UAM+CSIC, Madrid, Spain.,Institute for Molecular Bioscience, The University of Queensland, St Lucia, Australia
| | - Viviana Loria-Kohen
- Nutrition and Clinical Trials Unit, GENYAL Platform, IMDEA-Food Institute, CEI UAM + CSIC, Madrid, Spain. .,Department of Nutrition and Food Science, Faculty of Pharmacy, Complutense University of Madrid, Madrid, Spain.
| |
Collapse
|
76
|
Brandts L, van Poppel FW, van den Brandt PA. Parental lifespan and the likelihood of reaching the age of 90 years in the Netherlands Cohort Study. Geriatr Gerontol Int 2020; 21:215-221. [PMID: 33368897 PMCID: PMC7898670 DOI: 10.1111/ggi.14120] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 10/12/2020] [Accepted: 11/29/2020] [Indexed: 12/16/2022]
Abstract
Aim Growing evidence suggests an association between parental longevity and lifespan of subsequent generations. We aimed to reproduce earlier findings, showing a positive association between parental longevity and offspring's longevity. Additionally, we investigated whether this is mainly driven by the maternal or paternal germline in male and female offspring. Methods For these analyses, data from the oldest birth cohort (1916–17) of the Netherlands Cohort Study was used. Participants filled in a baseline questionnaire in 1986 (at age 68–70 years). Follow up for vital status information until the age of 90 years (2006–07) was >99.9% complete. Multivariable‐adjusted Cox regression analyses with a fixed follow‐up time were based on 2368 men and 2657 women with complete parental survival data and relevant confounders to calculate risk ratios (RR) of reaching longevity. Results In age‐adjusted models, paternal and maternal age at death were significantly positively associated with reaching 90 years in both male and female offspring. In male offspring, paternal age at death (≥90 years vs <80 years) showed the strongest association with survival to 90 years (RR 1.42, 95% CI 1.07–1.89), after confounder correction. In female offspring, maternal age at death (≥90 years vs <80 years) showed the strongest association with survival to 90 years (RR 1.20, 95% CI 1.04–1.40). Discussion After confounder adjustment, stronger and significant associations were observed between paternal lifespan and male offspring longevity, and maternal lifespan and female offspring longevity. Future research should investigate through which pathways a longer lifespan of parents is transmitted to their offspring. Geriatr Gerontol Int 2021; 21: 215–221.
Collapse
Affiliation(s)
- Lloyd Brandts
- GROW - School for Oncology and Developmental Biology, Department of Epidemiology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Frans Wa van Poppel
- Netherlands Interdisciplinary Demographic Institute (NIDI)/Royal Netherlands Academy of Arts and Sciences (KNAW), The Hague, the Netherlands
| | - Piet A van den Brandt
- GROW - School for Oncology and Developmental Biology, Department of Epidemiology, Maastricht University Medical Center, Maastricht, the Netherlands.,CAPHRI - School for Public Health and Primary Care, Department of Epidemiology, Maastricht University Medical Center, Maastricht, the Netherlands
| |
Collapse
|
77
|
Xiao L, Yuan Z, Jin S, Wang T, Huang S, Zeng P. Multiple-Tissue Integrative Transcriptome-Wide Association Studies Discovered New Genes Associated With Amyotrophic Lateral Sclerosis. Front Genet 2020; 11:587243. [PMID: 33329728 PMCID: PMC7714931 DOI: 10.3389/fgene.2020.587243] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 10/26/2020] [Indexed: 12/12/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified multiple causal genes associated with amyotrophic lateral sclerosis (ALS); however, the genetic architecture of ALS remains completely unknown and a large number of causal genes have yet been discovered. To full such gap in part, we implemented an integrative analysis of transcriptome-wide association study (TWAS) for ALS to prioritize causal genes with summary statistics from 80,610 European individuals and employed 13 GTEx brain tissues as reference transcriptome panels. The summary-level TWAS analysis with single brain tissue was first undertaken and then a flexible p-value combination strategy, called summary data-based Cauchy Aggregation TWAS (SCAT), was proposed to pool association signals from single-tissue TWAS analysis while protecting against highly positive correlation among tests. Extensive simulations demonstrated SCAT can produce well-calibrated p-value for the control of type I error and was often much more powerful to identify association signals across various scenarios compared with single-tissue TWAS analysis. Using SCAT, we replicated three ALS-associated genes (i.e., ATXN3, SCFD1, and C9orf72) identified in previous GWASs and discovered additional five genes (i.e., SLC9A8, FAM66D, TRIP11, JUP, and RP11-529H20.6) which were not reported before. Furthermore, we discovered the five associations were largely driven by genes themselves and thus might be new genes which were likely related to the risk of ALS. However, further investigations are warranted to verify these results and untangle the pathophysiological function of the genes in developing ALS.
Collapse
Affiliation(s)
- Lishun Xiao
- Department of Epidemiology and Biostatistics, Xuzhou Medical University, Xuzhou, China
| | - Zhongshang Yuan
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Siyi Jin
- Department of Epidemiology and Biostatistics, Xuzhou Medical University, Xuzhou, China
| | - Ting Wang
- Department of Epidemiology and Biostatistics, Xuzhou Medical University, Xuzhou, China
| | - Shuiping Huang
- Department of Epidemiology and Biostatistics, Xuzhou Medical University, Xuzhou, China.,Center for Medical Statistics and Data Analysis, School of Public Health, Xuzhou Medical University, Xuzhou, China
| | - Ping Zeng
- Department of Epidemiology and Biostatistics, Xuzhou Medical University, Xuzhou, China.,Center for Medical Statistics and Data Analysis, School of Public Health, Xuzhou Medical University, Xuzhou, China
| |
Collapse
|
78
|
Sikkink SK, Mine S, Freis O, Danoux L, Tobin DJ. Stress-sensing in the human greying hair follicle: Ataxia Telangiectasia Mutated (ATM) depletion in hair bulb melanocytes in canities-prone scalp. Sci Rep 2020; 10:18711. [PMID: 33128003 PMCID: PMC7603349 DOI: 10.1038/s41598-020-75334-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 10/12/2020] [Indexed: 02/06/2023] Open
Abstract
Canities (or hair greying) is an age-linked loss of the natural pigment called melanin from hair. While the specific cause(s) underlying the loss of melanogenically-active melanocytes from the anagen hair bulbs of affected human scalp remains unclear, oxidative stress sensing appears to be a key factor involved. In this study, we examined the follicular melanin unit in variably pigmented follicles from the aging human scalp of healthy individuals (22-70 years). Over 20 markers were selected within the following categories: melanocyte-specific, apoptosis, cell cycle, DNA repair/damage, senescence and oxidative stress. As expected, a reduction in melanocyte-specific markers in proportion to the extent of canities was observed. A major finding of our study was the intense and highly specific nuclear expression of Ataxia Telangiectasia Mutated (ATM) protein within melanocytes in anagen hair follicle bulbs. ATM is a serine/threonine protein kinase that is recruited and activated by DNA double-strand breaks and functions as an important sensor of reactive oxygen species (ROS) in human cells. The incidence and expression level of ATM correlated with pigmentary status in canities-affected hair follicles. Moreover, increased staining of the redox-associated markers 8-OHdG, GADD45 and GP-1 were also detected within isolated bulbar melanocytes, although this change was not clearly associated with donor age or canities extent. Surprisingly, we were unable to detect any specific change in the expression of other markers of oxidative stress, senescence or DNA damage/repair in the canities-affected melanocytes compared to surrounding bulbar keratinocytes. By contrast, several markers showed distinct expression of markers for oxidative stress and apoptosis/differentiation in the inner root sheath (IRS) as well as other parts of the hair follicle. Using our in vitro model of primary human scalp hair follicle melanocytes, we showed that ATM expression increased after incubation with the pro-oxidant hydrogen peroxide (H2O2). In addition, this ATM increase was prevented by pre-incubation of cells with antioxidants. The relationship between ATM and redox stress sensing was further evidenced as we observed that the inhibition of ATM expression by chemical inhibition promoted the loss of melanocyte viability induced by oxidative stress. Taken together these new findings illustrate the key role of ATM in the protection of human hair follicle melanocytes from oxidative stress/damage within the human scalp hair bulb. In conclusion, these results highlight the remarkable complexity and role of redox sensing in the status of human hair follicle growth, differentiation and pigmentation.
Collapse
Affiliation(s)
- Stephen K Sikkink
- Centre for Skin Sciences, School of Life Sciences, University of Bradford, Richmond Rd., Bradford, BD7 1DP, West Yorkshire, UK.
| | - Solene Mine
- BASF Beauty Care Solutions France S.A.S., Pulnoy, France
| | - Olga Freis
- BASF Beauty Care Solutions France S.A.S., Pulnoy, France
| | - Louis Danoux
- BASF Beauty Care Solutions France S.A.S., Pulnoy, France
| | - Desmond J Tobin
- Centre for Skin Sciences, School of Life Sciences, University of Bradford, Richmond Rd., Bradford, BD7 1DP, West Yorkshire, UK. .,The Charles Institute of Dermatology, School of Medicine, University College Dublin, Dublin 4, Ireland.
| |
Collapse
|
79
|
Kim W, Prokopenko D, Sakornsakolpat P, Hobbs BD, Lutz SM, Hokanson JE, Wain LV, Melbourne CA, Shrine N, Tobin MD, Silverman EK, Cho MH, Beaty TH. Genome-Wide Gene-by-Smoking Interaction Study of Chronic Obstructive Pulmonary Disease. Am J Epidemiol 2020; 190:875-885. [PMID: 33106845 PMCID: PMC8096488 DOI: 10.1093/aje/kwaa227] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 09/28/2020] [Accepted: 10/13/2020] [Indexed: 01/20/2023] Open
Abstract
Risk of chronic obstructive pulmonary disease (COPD) is determined by both cigarette smoking and genetic susceptibility, but little is known about gene-by-smoking interactions. We performed a genome-wide association analysis of 179,689 controls and 21,077 COPD cases from UK Biobank subjects of European ancestry recruited from 2006 to 2010, considering genetic main effects and gene-by-smoking interaction effects simultaneously (2-degrees-of-freedom (df) test) as well as interaction effects alone (1-df interaction test). We sought to replicate significant results in COPDGene (United States, 2008-2010) and SpiroMeta Consortium (multiple countries, 1947-2015) data. We considered 2 smoking variables: 1) ever/never and 2) current/noncurrent. In the 1-df test, we identified 1 genome-wide significant locus on 15q25.1 (cholinergic receptor nicotinic β4 subunit, or CHRNB4) for ever- and current smoking and identified PI*Z allele (rs28929474) of serpin family A member 1 (SERPINA1) for ever-smoking and 3q26.2 (MDS1 and EVI1 complex locus, or MECOM) for current smoking in an analysis of previously reported COPD loci. In the 2-df test, most of the significant signals were also significant for genetic marginal effects, aside from 16q22.1 (sphingomyelin phosphodiesterase 3, or SMPD3) and 19q13.2 (Egl-9 family hypoxia inducible factor 2, or EGLN2). The significant effects at 15q25.1 and 19q13.2 loci, both previously described in prior genome-wide association studies of COPD or smoking, were replicated in COPDGene and SpiroMeta. We identified interaction effects at previously reported COPD loci; however, we failed to identify novel susceptibility loci.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Terri H Beaty
- Correspondence to Dr. Terri H. Beaty, Department of Epidemiology, Johns Hopkins School of Public Health, 615 N. Wolfe Street, Baltimore, MD 21205 (e-mail: )
| |
Collapse
|
80
|
Stefanovics EA, Potenza MN, Pietrzak RH. Smoking, obesity, and their co-occurrence in the U.S. military veterans: results from the national health and resilience in veterans study. J Affect Disord 2020; 274:354-362. [PMID: 32469827 DOI: 10.1016/j.jad.2020.04.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 01/24/2020] [Accepted: 04/09/2020] [Indexed: 12/18/2022]
Abstract
BACKGROUND Smoking and obesity are major public health concerns, though little is known about the mental and physical health burden of co-occurring obesity and smoking. METHODS Using a nationally representative sample of U.S. military veterans, we examined the prevalence of mental and physical co-morbidities, physical and mental functioning, and quality of life between obese only; smoking only; and obese smokers. RESULTS Among current smokers, 31.7% were obese; among obese veterans, 16.4% were current smokers; and in the total sample, 5.4% were obese and current smokers. Relative to the obese-only group, obese smokers were more likely to be younger, male, non-white, non-married, unemployed and VA-served, and have lower household incomes. These also reported higher levels of perceived stress and trauma and were more likely to endorsed current suicidal ideation and lifetime suicide attempts (odds ratio [OR]=2.0), medical (2.3<=OR<=3.9) and psychiatric (1.5<=OR<=2.9) comorbidities, and lower overall health status and quality of life. Compared to the smoking-only group, obese smokers were more likely to endorse current suicidal ideation (OR=2.0) and nicotine dependence (OR=1.5), and reported poorer physical health and overall quality of life. Analyses were adjusted for sociodemographic and military characteristics. LIMITATIONS The cross-sectional study design precludes causal inference. CONCLUSIONS These findings suggest that co-occurring obesity and smoking is associated with substantial mental and physical health burden in U.S. veterans. Collectively, they underscore the importance of multicomponent interventions targeting, obesity, smoking, and co-occurring issues, such as trauma and internalizing disorders, in this population.
Collapse
Affiliation(s)
- Elina A Stefanovics
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA.; U.S. Department of Veteran Affairs New England Mental Illness Research and Education Clinical Center (MIRECC), Connecticut Healthcare System, West Haven, CT, USA..
| | - Marc N Potenza
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA.; Department of Neuroscience and Child Study Center, Yale University School of Medicine, New Haven, CT, USA.; Connecticut Council on Problem Gambling, Connecticut Council on Problem Gambling, Wethersfield, CT, USA.; Connecticut Mental Health Center, New Haven, CT, USA
| | - Robert H Pietrzak
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA.; U.S. Department of Veterans Affairs National Center for Posttraumatic Stress Disorder, VA Connecticut Healthcare System, West Haven, CT, USA
| |
Collapse
|
81
|
Conditional and unconditional genome-wide association study reveal complicate genetic architecture of human body weight and impacts of smoking. Sci Rep 2020; 10:12136. [PMID: 32699216 PMCID: PMC7376032 DOI: 10.1038/s41598-020-68935-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 07/03/2020] [Indexed: 12/20/2022] Open
Abstract
To reveal the impacts of smoking on genetic architecture of human body weight, we conducted a genome-wide association study on 5,336 subjects in four ethnic populations from MESA (The Multi-Ethnic Study of Atherosclerosis) data. A full genetic model was applied to association mapping for analyzing genetic effects of additive, dominance, epistasis, and their ethnicity-specific effects. Both the unconditional model (base) and conditional model including smoking as a cofactor were investigated. There were 10 SNPs involved in 96 significant genetic effects detected by the base model, which accounted for a high heritability (61.78%). Gene ontology analysis revealed that a number of genetic factors are related to the metabolic pathway of benzopyrene, a main compound in cigarettes. Smoking may play important roles in genetic effects of dominance, dominance-related epistasis, and gene-ethnicity interactions on human body weight. Gene effect prediction shows that the genetic effects of smoking cessation on body weight vary from different populations.
Collapse
|
82
|
Translating GWAS-identified loci for cardiac rhythm and rate using an in vivo image- and CRISPR/Cas9-based approach. Sci Rep 2020; 10:11831. [PMID: 32678143 PMCID: PMC7367351 DOI: 10.1038/s41598-020-68567-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 06/29/2020] [Indexed: 02/07/2023] Open
Abstract
A meta-analysis of genome-wide association studies (GWAS) identified eight loci that are associated with heart rate variability (HRV), but candidate genes in these loci remain uncharacterized. We developed an image- and CRISPR/Cas9-based pipeline to systematically characterize candidate genes for HRV in live zebrafish embryos. Nine zebrafish orthologues of six human candidate genes were targeted simultaneously in eggs from fish that transgenically express GFP on smooth muscle cells (Tg[acta2:GFP]), to visualize the beating heart. An automated analysis of repeated 30 s recordings of beating atria in 381 live, intact zebrafish embryos at 2 and 5 days post-fertilization highlighted genes that influence HRV (hcn4 and si:dkey-65j6.2 [KIAA1755]); heart rate (rgs6 and hcn4); and the risk of sinoatrial pauses and arrests (hcn4). Exposure to 10 or 25 µM ivabradine—an open channel blocker of HCNs—for 24 h resulted in a dose-dependent higher HRV and lower heart rate at 5 days post-fertilization. Hence, our screen confirmed the role of established genes for heart rate and rhythm (RGS6 and HCN4); showed that ivabradine reduces heart rate and increases HRV in zebrafish embryos, as it does in humans; and highlighted a novel gene that plays a role in HRV (KIAA1755).
Collapse
|
83
|
Prevalence and correlates of overweight and abdominal adiposity amongst adults residing in Madeira Autonomous Region: a cross-sectional, population-based study. Porto Biomed J 2020; 5:e067. [PMID: 32734010 PMCID: PMC7386548 DOI: 10.1097/j.pbj.0000000000000067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 03/29/2020] [Indexed: 11/26/2022] Open
Abstract
Background: Data on nutritional status and its risk factors amongst the adult population of the Madeira Autonomous Region (RAM) is scarce. This study aims to investigate the prevalence of, and risk factors associated with overweight and abdominal adiposity, assessed through measuring body mass index (BMI), waist circumference (WC), and waist-to-height ratio (WHtR) indexes. Methods: Cross-sectional study using a representative sample of 911 subjects (18–64 years) from the RAM Dietary Habits of Adult Population Study. Logistic regression models were conducted to investigate the association between body mass index, WC, and WHtR indexes, with sociodemographic and lifestyle characteristics. Results: The prevalence of overweight amongst adults was 60.0% [95% confidence interval (CI): 56.8–63.2]. The prevalence of abdominal adiposity, assessed by WC and WHtR indexes, was 62.6% (95% CI: 59.4–65.7) and 71.9% (95% CI: 69.0–74.8), respectively. In adjusted models, age and self-reported chronic diseases were associated with both overweight and abdominal adiposity. Women were less likely to be overweight [odds ratio (OR) = 0.7 (95% CI: 0.5–0.9); P = .012] but more likely to have increased WC [OR = 2.9 (95% CI: 2.1–4.0); P < .001], compared to men. Being married was positively associated to being overweight [OR = 1.5 (95% CI: 1.1–2.1); P = .013] and increased WC [OR = 1.8 (95% CI: 1.3–2.6); P < .001], but not with WHtR index. Education level was only associated with WHtR index. Inverse associations were found for each abdominal obesity indicators and smoking status. Conclusions: Overweight and abdominal adiposity should be considered 2 major public health problems, amongst adult population of the RAM. Older less educated adults, with smoking habits may be considered a target group for health promotion interventions.
Collapse
|
84
|
Cheng W, Ramachandran S, Crawford L. Estimation of non-null SNP effect size distributions enables the detection of enriched genes underlying complex traits. PLoS Genet 2020; 16:e1008855. [PMID: 32542026 PMCID: PMC7316356 DOI: 10.1371/journal.pgen.1008855] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 06/25/2020] [Accepted: 05/13/2020] [Indexed: 12/22/2022] Open
Abstract
Traditional univariate genome-wide association studies generate false positives and negatives due to difficulties distinguishing associated variants from variants with spurious nonzero effects that do not directly influence the trait. Recent efforts have been directed at identifying genes or signaling pathways enriched for mutations in quantitative traits or case-control studies, but these can be computationally costly and hampered by strict model assumptions. Here, we present gene-ε, a new approach for identifying statistical associations between sets of variants and quantitative traits. Our key insight is that enrichment studies on the gene-level are improved when we reformulate the genome-wide SNP-level null hypothesis to identify spurious small-to-intermediate SNP effects and classify them as non-causal. gene-ε efficiently identifies enriched genes under a variety of simulated genetic architectures, achieving greater than a 90% true positive rate at 1% false positive rate for polygenic traits. Lastly, we apply gene-ε to summary statistics derived from six quantitative traits using European-ancestry individuals in the UK Biobank, and identify enriched genes that are in biologically relevant pathways.
Collapse
Affiliation(s)
- Wei Cheng
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
| | - Sohini Ramachandran
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
- * E-mail: (SR); (LC)
| | - Lorin Crawford
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
- Department of Biostatistics, Brown University, Providence, Rhode Island, United States of America
- Center for Statistical Sciences, Brown University, Providence, Rhode Island, United States of America
- * E-mail: (SR); (LC)
| |
Collapse
|
85
|
Marenne G, Hendricks AE, Perdikari A, Bounds R, Payne F, Keogh JM, Lelliott CJ, Henning E, Pathan S, Ashford S, Bochukova EG, Mistry V, Daly A, Hayward C, Wareham NJ, O'Rahilly S, Langenberg C, Wheeler E, Zeggini E, Farooqi IS, Barroso I. Exome Sequencing Identifies Genes and Gene Sets Contributing to Severe Childhood Obesity, Linking PHIP Variants to Repressed POMC Transcription. Cell Metab 2020; 31:1107-1119.e12. [PMID: 32492392 PMCID: PMC7267775 DOI: 10.1016/j.cmet.2020.05.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 03/06/2020] [Accepted: 05/09/2020] [Indexed: 12/12/2022]
Abstract
Obesity is genetically heterogeneous with monogenic and complex polygenic forms. Using exome and targeted sequencing in 2,737 severely obese cases and 6,704 controls, we identified three genes (PHIP, DGKI, and ZMYM4) with an excess burden of very rare predicted deleterious variants in cases. In cells, we found that nuclear PHIP (pleckstrin homology domain interacting protein) directly enhances transcription of pro-opiomelanocortin (POMC), a neuropeptide that suppresses appetite. Obesity-associated PHIP variants repressed POMC transcription. Our demonstration that PHIP is involved in human energy homeostasis through transcriptional regulation of central melanocortin signaling has potential diagnostic and therapeutic implications for patients with obesity and developmental delay. Additionally, we found an excess burden of predicted deleterious variants involving genes nearest to loci from obesity genome-wide association studies. Genes and gene sets influencing obesity with variable penetrance provide compelling evidence for a continuum of causality in the genetic architecture of obesity, and explain some of its missing heritability.
Collapse
Affiliation(s)
- Gaëlle Marenne
- Wellcome Sanger Institute, Cambridge, UK; Inserm, Univ Brest, EFS, UMR 1078, GGB, 29200 Brest, France
| | - Audrey E Hendricks
- Wellcome Sanger Institute, Cambridge, UK; Mathematical and Statistical Sciences, University of Colorado Denver, Denver, CO, USA
| | - Aliki Perdikari
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK
| | - Rebecca Bounds
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK
| | | | - Julia M Keogh
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK
| | | | - Elana Henning
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK
| | - Saad Pathan
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK
| | - Sofie Ashford
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK
| | - Elena G Bochukova
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK
| | - Vanisha Mistry
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK
| | - Allan Daly
- Wellcome Sanger Institute, Cambridge, UK
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK; Generation Scotland, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Nicholas J Wareham
- University of Cambridge MRC Epidemiology Unit, Wellcome Trust-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK
| | - Stephen O'Rahilly
- MRC Metabolic Diseases Unit, Wellcome-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK
| | - Claudia Langenberg
- University of Cambridge MRC Epidemiology Unit, Wellcome Trust-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK
| | - Eleanor Wheeler
- Wellcome Sanger Institute, Cambridge, UK; University of Cambridge MRC Epidemiology Unit, Wellcome Trust-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK
| | - Eleftheria Zeggini
- Wellcome Sanger Institute, Cambridge, UK; Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - I Sadaf Farooqi
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK.
| | - Inês Barroso
- Wellcome Sanger Institute, Cambridge, UK; University of Cambridge MRC Epidemiology Unit, Wellcome Trust-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK.
| |
Collapse
|
86
|
Ouidir M, Zeng X, Workalemahu T, Shrestha D, Grantz KL, Mendola P, Zhang C, Tekola-Ayele F. Early pregnancy dyslipidemia is associated with placental DNA methylation at loci relevant for cardiometabolic diseases. Epigenomics 2020; 12:921-934. [PMID: 32677467 PMCID: PMC7466909 DOI: 10.2217/epi-2019-0293] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 04/07/2020] [Indexed: 02/07/2023] Open
Abstract
Aim: To identify placental DNA methylation changes that are associated with early pregnancy maternal dyslipidemia. Materials & methods: We analyzed placental genome-wide DNA methylation (n = 262). Genes annotating differentially methylated CpGs were evaluated for gene expression in placenta (n = 64). Results: We found 11 novel significant differentially methylated CpGs associated with high total cholesterol, low-density lipoprotein cholesterol and triglycerides, and low high-density lipoprotein cholesterol. High triglycerides were associated with decreased methylation of cg02785814 (ALX4) and decreased expression of ALX4 in placenta. Genes annotating the differentially methylated CpGs play key roles in lipid metabolism and were enriched in dyslipidemia pathways. Functional annotation found cis-methylation quantitative trait loci for genetic loci in ALX4 and EXT2. Conclusion: Our findings lend novel insights into potential placental epigenetic mechanisms linked with maternal dyslipidemia. Trial Registration: ClinicalTrials.gov, NCT00912132.
Collapse
Affiliation(s)
- Marion Ouidir
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health & Human Development, National Institutes of Health, Bethesda, MD 20892-7004, USA
| | - Xuehuo Zeng
- Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health & Human Development, National Institutes of Health, Bethesda, MD 20892-7004, USA
| | - Tsegaselassie Workalemahu
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health & Human Development, National Institutes of Health, Bethesda, MD 20892-7004, USA
| | - Deepika Shrestha
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health & Human Development, National Institutes of Health, Bethesda, MD 20892-7004, USA
| | - Katherine L. Grantz
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health & Human Development, National Institutes of Health, Bethesda, MD 20892-7004, USA
| | - Pauline Mendola
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health & Human Development, National Institutes of Health, Bethesda, MD 20892-7004, USA
| | - Cuilin Zhang
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health & Human Development, National Institutes of Health, Bethesda, MD 20892-7004, USA
| | - Fasil Tekola-Ayele
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health & Human Development, National Institutes of Health, Bethesda, MD 20892-7004, USA
| |
Collapse
|
87
|
Buniello A, MacArthur JAL, Cerezo M, Harris LW, Hayhurst J, Malangone C, McMahon A, Morales J, Mountjoy E, Sollis E, Suveges D, Vrousgou O, Whetzel PL, Amode R, Guillen JA, Riat HS, Trevanion SJ, Hall P, Junkins H, Flicek P, Burdett T, Hindorff LA, Cunningham F, Parkinson H. The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019. Nucleic Acids Res 2020; 47:D1005-D1012. [PMID: 30445434 PMCID: PMC6323933 DOI: 10.1093/nar/gky1120] [Citation(s) in RCA: 2449] [Impact Index Per Article: 612.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 10/25/2018] [Indexed: 02/06/2023] Open
Abstract
The GWAS Catalog delivers a high-quality curated collection of all published genome-wide association studies enabling investigations to identify causal variants, understand disease mechanisms, and establish targets for novel therapies. The scope of the Catalog has also expanded to targeted and exome arrays with 1000 new associations added for these technologies. As of September 2018, the Catalog contains 5687 GWAS comprising 71673 variant-trait associations from 3567 publications. New content includes 284 full P-value summary statistics datasets for genome-wide and new targeted array studies, representing 6 × 109 individual variant-trait statistics. In the last 12 months, the Catalog's user interface was accessed by ∼90000 unique users who viewed >1 million pages. We have improved data access with the release of a new RESTful API to support high-throughput programmatic access, an improved web interface and a new summary statistics database. Summary statistics provision is supported by a new format proposed as a community standard for summary statistics data representation. This format was derived from our experience in standardizing heterogeneous submissions, mapping formats and in harmonizing content. Availability: https://www.ebi.ac.uk/gwas/.
Collapse
Affiliation(s)
- Annalisa Buniello
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jacqueline A L MacArthur
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Maria Cerezo
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Laura W Harris
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - James Hayhurst
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Cinzia Malangone
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Aoife McMahon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Joannella Morales
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Edward Mountjoy
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.,Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.,JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, Wellcome Centre for Human Genetics, University of Oxford, NIHR Oxford Biomedical Research Centre, Nuffield Department of Medicine, Oxford, UK
| | - Elliot Sollis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel Suveges
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Olga Vrousgou
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Patricia L Whetzel
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ridwan Amode
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jose A Guillen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Harpreet S Riat
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Stephen J Trevanion
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Peggy Hall
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Heather Junkins
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Tony Burdett
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Lucia A Hindorff
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| |
Collapse
|
88
|
Wu P, Rybin D, Bielak LF, Feitosa MF, Franceschini N, Li Y, Lu Y, Marten J, Musani SK, Noordam R, Raghavan S, Rose LM, Schwander K, Smith AV, Tajuddin SM, Vojinovic D, Amin N, Arnett DK, Bottinger EP, Demirkan A, Florez JC, Ghanbari M, Harris TB, Launer LJ, Liu J, Liu J, Mook-Kanamori DO, Murray AD, Nalls MA, Peyser PA, Uitterlinden AG, Voortman T, Bouchard C, Chasman D, Correa A, de Mutsert R, Evans MK, Gudnason V, Hayward C, Kao L, Kardia SLR, Kooperberg C, Loos RJF, Province MM, Rankinen T, Redline S, Ridker PM, Rotter JI, Siscovick D, Smith BH, van Duijn C, Zonderman AB, Rao DC, Wilson JG, Dupuis J, Meigs JB, Liu CT, Vassy JL. Smoking-by-genotype interaction in type 2 diabetes risk and fasting glucose. PLoS One 2020; 15:e0230815. [PMID: 32379818 PMCID: PMC7205201 DOI: 10.1371/journal.pone.0230815] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 03/09/2020] [Indexed: 02/07/2023] Open
Abstract
Smoking is a potentially causal behavioral risk factor for type 2 diabetes (T2D), but not all smokers develop T2D. It is unknown whether genetic factors partially explain this variation. We performed genome-environment-wide interaction studies to identify loci exhibiting potential interaction with baseline smoking status (ever vs. never) on incident T2D and fasting glucose (FG). Analyses were performed in participants of European (EA) and African ancestry (AA) separately. Discovery analyses were conducted using genotype data from the 50,000-single-nucleotide polymorphism (SNP) ITMAT-Broad-CARe (IBC) array in 5 cohorts from from the Candidate Gene Association Resource Consortium (n = 23,189). Replication was performed in up to 16 studies from the Cohorts for Heart Aging Research in Genomic Epidemiology Consortium (n = 74,584). In meta-analysis of discovery and replication estimates, 5 SNPs met at least one criterion for potential interaction with smoking on incident T2D at p<1x10-7 (adjusted for multiple hypothesis-testing with the IBC array). Two SNPs had significant joint effects in the overall model and significant main effects only in one smoking stratum: rs140637 (FBN1) in AA individuals had a significant main effect only among smokers, and rs1444261 (closest gene C2orf63) in EA individuals had a significant main effect only among nonsmokers. Three additional SNPs were identified as having potential interaction by exhibiting a significant main effects only in smokers: rs1801232 (CUBN) in AA individuals, rs12243326 (TCF7L2) in EA individuals, and rs4132670 (TCF7L2) in EA individuals. No SNP met significance for potential interaction with smoking on baseline FG. The identification of these loci provides evidence for genetic interactions with smoking exposure that may explain some of the heterogeneity in the association between smoking and T2D.
Collapse
Affiliation(s)
- Peitao Wu
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, MA, United States of America
| | - Denis Rybin
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, MA, United States of America
| | - Lawrence F. Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, United States of America
| | - Mary F. Feitosa
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Nora Franceschini
- University of North Carolina, Chapel Hill, NC, United States of America
| | - Yize Li
- Division of Biostatistics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Yingchang Lu
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Jonathan Marten
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Solomon K. Musani
- Jackson Heart Study, University of Mississippi Medical Center, MS, United States of America
| | - Raymond Noordam
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
| | - Sridharan Raghavan
- Section of Hospital Medicine, Veterans Affairs Eastern Colorado Healthcare System, Denver, CO, United States of America
- Division of General Internal Medicine, University of Colorado School of Medicine, Aurora, CO, United States of America
- Colorado Cardiovascular Outcomes Research Consortium, Aurora, CO, United States of America
| | - Lynda M. Rose
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, United States of America
| | - Karen Schwander
- Division of Biostatistics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Albert V. Smith
- Icelandic Heart Association, Kopavogur, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Salman M. Tajuddin
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States of America
| | - Dina Vojinovic
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Najaf Amin
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Donna K. Arnett
- Dean's Office, University of Kentucky College of Public Health, Lexington, Kentucky, United States of America
| | - Erwin P. Bottinger
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Ayse Demirkan
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jose C. Florez
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Massachusetts General Hospital, Boston, MA, United States of America
- Programs in Metabolism and Medical & Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Department of Medicine, Harvard Medical School, Boston, MA, United States of America
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Genetics, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Tamara B. Harris
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Intramural Research Program, National Institutes of Health, Bethesda, MD, United States of America
| | - Lenore J. Launer
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Intramural Research Program, National Institutes of Health, Bethesda, MD, United States of America
| | - Jingmin Liu
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Jun Liu
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Dennis O. Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, The Netherlands
| | - Alison D. Murray
- The Institute of Medical Sciences, Aberdeen Biomedical Imaging Centre, University of Aberdeen, Aberdeen, United Kingdom
| | - Mike A. Nalls
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, United States of America
- Data Tecnica International LLC, Glen Echo, MD, United States of America
| | - Patricia A. Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, United States of America
| | - André G. Uitterlinden
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Trudy Voortman
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Claude Bouchard
- Human Genomics Laboratory, Pennington Biomedical Research Center, Louisiana State University System, Baton Rouge, LA, United States of America
| | - Daniel Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, United States of America
- Harvard Medical School, Boston, MA, United States of America
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, United States of America
| | - Renée de Mutsert
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Michele K. Evans
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States of America
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland
- University of Iceland, Reykjavik, Iceland
| | - Caroline Hayward
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Linda Kao
- Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, United States of America
- Welch Center for Prevention, Epidemiology and Clinical Research, Johns Hopkins University, Baltimore, MD, United States of America
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States of America
| | - Sharon L. R. Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, United States of America
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Ruth J. F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- The Mindich Child Health and Development Institute, Ichan School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Michael M. Province
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Tuomo Rankinen
- Human Genomics Laboratory, Pennington Biomedical Research Center, Louisiana State University System, Baton Rouge, LA, United States of America
| | - Susan Redline
- Harvard Medical School, Boston, MA, United States of America
- Departments of Medicine, Brigham and Women's Hospital, Boston, MA, United States of America
- Beth Israel Deaconess Medical Center, Boston, MA, United States of America
| | - Paul M. Ridker
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, United States of America
- Harvard Medical School, Boston, MA, United States of America
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, United States of America
| | - David Siscovick
- The New York Academy of Medicine, New York, NY, United States of America
| | - Blair H. Smith
- Division of Population Health and Genomics, University of Dundee, Dundee, United Kingdom
| | - Cornelia van Duijn
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Alan B. Zonderman
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States of America
| | - D. C. Rao
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, United States of America
| | - James G. Wilson
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, United States of America
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, MA, United States of America
- The National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, MA, United States of America
| | - James B. Meigs
- Programs in Metabolism and Medical & Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Division of General Internal Medicine Division, Massachusetts General Hospital, Boston, MA, United States of America
- Department of Medicine, Harvard Medical School, Boston, MA, United States of America
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, MA, United States of America
| | - Jason L. Vassy
- Department of Medicine, Harvard Medical School, Boston, MA, United States of America
- VA Boston Healthcare System, Boston, MA, United States of America
| |
Collapse
|
89
|
Trifonova EA, Popovich AA, Bocharova AV, Vagaitseva KV, Stepanov VA. The Role of Natural Selection in the Formation of the Genetic Structure of Populations by SNP Markers in Association with Body Mass Index and Obesity. Mol Biol 2020. [DOI: 10.1134/s0026893320030176] [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]
|
90
|
Olafsdottir T, Thorleifsson G, Sulem P, Stefansson OA, Medek H, Olafsson K, Ingthorsson O, Gudmundsson V, Jonsdottir I, Halldorsson GH, Kristjansson RP, Frigge ML, Stefansdottir L, Sigurdsson JK, Oddsson A, Sigurdsson A, Eggertsson HP, Melsted P, Halldorsson BV, Lund SH, Styrkarsdottir U, Steinthorsdottir V, Gudmundsson J, Holm H, Tragante V, Asselbergs FW, Thorsteinsdottir U, Gudbjartsson DF, Jonsdottir K, Rafnar T, Stefansson K. Genome-wide association identifies seven loci for pelvic organ prolapse in Iceland and the UK Biobank. Commun Biol 2020; 3:129. [PMID: 32184442 PMCID: PMC7078216 DOI: 10.1038/s42003-020-0857-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 02/25/2020] [Indexed: 12/17/2022] Open
Abstract
Pelvic organ prolapse (POP) is a downward descent of one or more of the pelvic organs, resulting in a protrusion of the vaginal wall and/or uterus. We performed a genome-wide association study of POP using data from Iceland and the UK Biobank, a total of 15,010 cases with hospital-based diagnosis code and 340,734 female controls, and found eight sequence variants at seven loci associating with POP (P < 5 × 10-8); seven common (minor allele frequency >5%) and one with minor allele frequency of 4.87%. Some of the variants associating with POP also associated with traits of similar pathophysiology. Of these, rs3820282, which may alter the estrogen-based regulation of WNT4, also associates with leiomyoma of uterus, gestational duration and endometriosis. Rs3791675 at EFEMP1, a gene involved in connective tissue homeostasis, also associates with hernias and carpal tunnel syndrome. Our results highlight the role of connective tissue metabolism and estrogen exposure in the etiology of POP.
Collapse
Affiliation(s)
| | | | - Patrick Sulem
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland
| | | | - Helga Medek
- Department of Obstetrics and Gynecology, Landspitali University Hospital, 101, Reykjavik, Iceland
| | - Karl Olafsson
- Department of Obstetrics and Gynecology, Landspitali University Hospital, 101, Reykjavik, Iceland
| | - Orri Ingthorsson
- Department of Obstetrics and Gynecology, Akureyri Hospital, 600, Akureyri, Iceland
| | - Valur Gudmundsson
- Department of Obstetrics and Gynecology, Akureyri Hospital, 600, Akureyri, Iceland
| | - Ingileif Jonsdottir
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, 101, Reykjavik, Iceland
- Department of Immunology, Landspitali University Hospital, 101, Reykjavik, Iceland
| | | | | | | | | | | | | | | | | | - Pall Melsted
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, 101, Reykjavik, Iceland
| | - Bjarni V Halldorsson
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland
- School of Science and Engineering, Reykjavik University, 101, Reykjavik, Iceland
| | - Sigrun H Lund
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland
| | | | | | | | - Hilma Holm
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland
| | - Vinicius Tragante
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Folkert W Asselbergs
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Institute of Cardiovascular Science, Faculty of Population Health Sciences, University College London, London, UK
- Health Data Research UK and Institute of Health Informatics, University College London, London, UK
| | - Unnur Thorsteinsdottir
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, 101, Reykjavik, Iceland
| | - Daniel F Gudbjartsson
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, 101, Reykjavik, Iceland
| | - Kristin Jonsdottir
- Department of Obstetrics and Gynecology, Landspitali University Hospital, 101, Reykjavik, Iceland
| | - Thorunn Rafnar
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland
| | - Kari Stefansson
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland.
- Faculty of Medicine, School of Health Sciences, University of Iceland, 101, Reykjavik, Iceland.
| |
Collapse
|
91
|
Lim E, Chen H, Dupuis J, Liu CT. A unified method for rare variant analysis of gene-environment interactions. Stat Med 2020; 39:801-813. [PMID: 31799744 PMCID: PMC7261513 DOI: 10.1002/sim.8446] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 11/19/2019] [Accepted: 11/21/2019] [Indexed: 01/17/2023]
Abstract
Advanced technology in whole-genome sequencing has offered the opportunity to comprehensively investigate the genetic contribution, particularly rare variants, to complex traits. Several region-based tests have been developed to jointly model the marginal effect of rare variants, but methods to detect gene-environment (GE) interactions are underdeveloped. Identifying the modification effects of environmental factors on genetic risk poses a considerable challenge. To tackle this challenge, we develop a method to detect GE interactions for rare variants using generalized linear mixed effect model. The proposed method can accommodate either binary or continuous traits in related or unrelated samples. Under this model, genetic main effects, GE interactions, and sample relatedness are modeled as random effects. We adopt a kernel-based method to leverage the joint information across rare variants and implement variance component score tests to reduce the computational burden. Our simulation studies of continuous and binary traits show that the proposed method maintains correct type I error rates and appropriate power under various scenarios, such as genotype main effects and GE interaction effects in opposite directions and varying the proportion of causal variants in the model. We apply our method in the Framingham Heart Study to test GE interaction of smoking on body mass index or overweight status and replicate the Cholinergic Receptor Nicotinic Beta 4 gene association reported in previous large consortium meta-analysis of single nucleotide polymorphism-smoking interaction. Our proposed set-based GE test is computationally efficient and is applicable to both binary and continuous phenotypes, while appropriately accounting for familial or cryptic relatedness.
Collapse
Affiliation(s)
- Elise Lim
- Department of Biostatistics, Boston University, Boston, Massachusetts
| | - 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, Texas
- Center for Precision Health, School of Public Health and School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Josée Dupuis
- Department of Biostatistics, Boston University, Boston, Massachusetts
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University, Boston, Massachusetts
| |
Collapse
|
92
|
Campos AI, García-Marín LM, Byrne EM, Martin NG, Cuéllar-Partida G, Rentería ME. Insights into the aetiology of snoring from observational and genetic investigations in the UK Biobank. Nat Commun 2020; 11:817. [PMID: 32060260 PMCID: PMC7021827 DOI: 10.1038/s41467-020-14625-1] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 01/22/2020] [Indexed: 12/15/2022] Open
Abstract
Although snoring is common in the general population, its aetiology has been largely understudied. Here we report a genetic study on snoring (n ~ 408,000; snorers ~ 152,000) using data from the UK Biobank. We identify 42 genome-wide significant loci, with an SNP-based heritability estimate of ~10% on the liability scale. Genetic correlations with body mass index, alcohol intake, smoking, schizophrenia, anorexia nervosa and neuroticism are observed. Gene-based associations identify 173 genes, including DLEU7, MSRB3 and POC5, highlighting genes expressed in the brain, cerebellum, lungs, blood and oesophagus. We use polygenic scores (PGS) to predict recent snoring and probable obstructive sleep apnoea (OSA) in an independent Australian sample (n ~ 8000). Mendelian randomization analyses suggest a potential causal relationship between high BMI and snoring. Altogether, our results uncover insights into the aetiology of snoring as a complex sleep-related trait and its role in health and disease beyond it being a cardinal symptom of OSA. Snoring is common in the population and tends to be more prevalent in older and/or male individuals. Here, the authors perform GWAS for habitual snoring, identify 41 genomic loci and explore potential causal relationships with anthropometric and cardiometabolic disease traits.
Collapse
Affiliation(s)
- Adrián I Campos
- Genetic Epidemiology Lab, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Luis M García-Marín
- Genetic Epidemiology Lab, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,Tecnológico de Monterrey, Escuela de Ingeniería y Ciencias, Zapopan, Jalisco, México
| | - Enda M Byrne
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Nicholas G Martin
- Genetic Epidemiology Lab, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Gabriel Cuéllar-Partida
- Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia. .,University of Queensland Diamantina Institute, Brisbane, QLD, Australia.
| | - Miguel E Rentería
- Genetic Epidemiology Lab, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia. .,Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia.
| |
Collapse
|
93
|
Boua PR, Brandenburg JT, Choudhury A, Hazelhurst S, Sengupta D, Agongo G, Nonterah EA, Oduro AR, Tinto H, Mathew CG, Sorgho H, Ramsay M. Novel and Known Gene-Smoking Interactions With cIMT Identified as Potential Drivers for Atherosclerosis Risk in West-African Populations of the AWI-Gen Study. Front Genet 2020; 10:1354. [PMID: 32117412 PMCID: PMC7025492 DOI: 10.3389/fgene.2019.01354] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 12/10/2019] [Indexed: 12/22/2022] Open
Abstract
Introduction Atherosclerosis is a key contributor to the burden of cardiovascular diseases (CVDs) and many epidemiological studies have reported on the effect of smoking on carotid intima-media thickness (cIMT) and its subsequent effect on CVD risk. Gene-environment interaction studies have contributed towards understanding some of the missing heritability of genome-wide association studies. Gene-smoking interactions on cIMT have been studied in non-African populations (European, Latino-American, and African American) but no comparable African research has been reported. Our aim was to investigate smoking-SNP interactions on cIMT in two West African populations by genome-wide analysis. Materials and methods Only male participants from Burkina Faso (Nanoro = 993) and Ghana (Navrongo = 783) were included, as smoking was extremely rare among women. Phenotype and genotype data underwent stringent QC and genotype imputation was performed using the Sanger African Imputation Panel. Smoking prevalence among men was 13.3% in Nanoro and 42.5% in Navrongo. We analyzed gene-smoking interactions with PLINK after adjusting for covariates: age and 6 PCs (Model 1); age, BMI, blood pressure, fasting glucose, cholesterol levels, MVPA, and 6 PCs (Model 2). All analyses were performed at site level and for the combined data set. Results In Nanoro, we identified new gene-smoking interaction variants for cIMT within the previously described RCBTB1 region (rs112017404, rs144170770, and rs4941649) (Model 1: p = 1.35E-07; Model 2: p = 3.08E-08). In the combined sample, two novel intergenic interacting variants were identified, rs1192824 in the regulatory region of TBC1D8 (p = 5.90E-09) and rs77461169 (p = 4.48E-06) located in an upstream region of open chromatin. In silico functional analysis suggests the involvement of genes implicated in biological processes related to cell or biological adhesion and regulatory processes in gene-smoking interactions with cIMT (as evidenced by chromatin interactions and eQTLs). Discussion This is the first gene-smoking interaction study for cIMT, as a risk factor for atherosclerosis, in sub-Saharan African populations. In addition to replicating previously known signals for RCBTB1, we identified two novel genomic regions (TBC1D8, near BCHE) involved in this gene-environment interaction.
Collapse
Affiliation(s)
- Palwende Romuald Boua
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé, Nanoro, Burkina Faso.,Faculty of Health Sciences, Sydney Brenner Institute for Molecular Bioscience (SBIMB), University of the Witwatersrand, Johannesburg, South Africa.,Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jean-Tristan Brandenburg
- Faculty of Health Sciences, Sydney Brenner Institute for Molecular Bioscience (SBIMB), University of the Witwatersrand, Johannesburg, South Africa
| | - Ananyo Choudhury
- Faculty of Health Sciences, Sydney Brenner Institute for Molecular Bioscience (SBIMB), University of the Witwatersrand, Johannesburg, South Africa
| | - Scott Hazelhurst
- Faculty of Health Sciences, Sydney Brenner Institute for Molecular Bioscience (SBIMB), University of the Witwatersrand, Johannesburg, South Africa.,School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
| | - Dhriti Sengupta
- Faculty of Health Sciences, Sydney Brenner Institute for Molecular Bioscience (SBIMB), University of the Witwatersrand, Johannesburg, South Africa
| | - Godfred Agongo
- Faculty of Health Sciences, Sydney Brenner Institute for Molecular Bioscience (SBIMB), University of the Witwatersrand, Johannesburg, South Africa.,Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
| | - Engelbert A Nonterah
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana.,Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Abraham R Oduro
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
| | - Halidou Tinto
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé, Nanoro, Burkina Faso
| | - Christopher G Mathew
- Faculty of Health Sciences, Sydney Brenner Institute for Molecular Bioscience (SBIMB), University of the Witwatersrand, Johannesburg, South Africa.,Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Hermann Sorgho
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé, Nanoro, Burkina Faso
| | - Michèle Ramsay
- Faculty of Health Sciences, Sydney Brenner Institute for Molecular Bioscience (SBIMB), University of the Witwatersrand, Johannesburg, South Africa.,Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| |
Collapse
|
94
|
A Comprehensive Genome-Wide and Phenome-Wide Examination of BMI and Obesity in a Northern Nevadan Cohort. G3-GENES GENOMES GENETICS 2020; 10:645-664. [PMID: 31888951 PMCID: PMC7003082 DOI: 10.1534/g3.119.400910] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The aggregation of Electronic Health Records (EHR) and personalized genetics leads to powerful discoveries relevant to population health. Here we perform genome-wide association studies (GWAS) and accompanying phenome-wide association studies (PheWAS) to validate phenotype-genotype associations of BMI, and to a greater extent, severe Class 2 obesity, using comprehensive diagnostic and clinical data from the EHR database of our cohort. Three GWASs of 500,000 variants on the Illumina platform of 6,645 Healthy Nevada participants identified several published and novel variants that affect BMI and obesity. Each GWAS was followed with two independent PheWASs to examine associations between extensive phenotypes (incidence of diagnoses, condition, or disease), significant SNPs, BMI, and incidence of extreme obesity. The first GWAS examines associations with BMI in a cohort with no type 2 diabetics, focusing exclusively on BMI. The second GWAS examines associations with BMI in a cohort that includes type 2 diabetics. In the second GWAS, type 2 diabetes is a comorbidity, and thus becomes a covariate in the statistical model. The intersection of significant variants of these two studies is surprising. The third GWAS is a case vs. control study, with cases defined as extremely obese (Class 2 or 3 obesity), and controls defined as participants with BMI between 18.5 and 25. This last GWAS identifies strong associations with extreme obesity, including established variants in the FTO and NEGR1 genes, as well as loci not yet linked to obesity. The PheWASs validate published associations between BMI and extreme obesity and incidence of specific diagnoses and conditions, yet also highlight novel links. This study emphasizes the importance of our extensive longitudinal EHR database to validate known associations and identify putative novel links with BMI and obesity.
Collapse
|
95
|
Virani SS, Alonso A, Benjamin EJ, Bittencourt MS, Callaway CW, Carson AP, Chamberlain AM, Chang AR, Cheng S, Delling FN, Djousse L, Elkind MSV, Ferguson JF, Fornage M, Khan SS, Kissela BM, Knutson KL, Kwan TW, Lackland DT, Lewis TT, Lichtman JH, Longenecker CT, Loop MS, Lutsey PL, Martin SS, Matsushita K, Moran AE, Mussolino ME, Perak AM, Rosamond WD, Roth GA, Sampson UKA, Satou GM, Schroeder EB, Shah SH, Shay CM, Spartano NL, Stokes A, Tirschwell DL, VanWagner LB, Tsao CW. Heart Disease and Stroke Statistics-2020 Update: A Report From the American Heart Association. Circulation 2020; 141:e139-e596. [PMID: 31992061 DOI: 10.1161/cir.0000000000000757] [Citation(s) in RCA: 4927] [Impact Index Per Article: 1231.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND The American Heart Association, in conjunction with the National Institutes of Health, annually reports on the most up-to-date statistics related to heart disease, stroke, and cardiovascular risk factors, including core health behaviors (smoking, physical activity, diet, and weight) and health factors (cholesterol, blood pressure, and glucose control) that contribute to cardiovascular health. The Statistical Update presents the latest data on a range of major clinical heart and circulatory disease conditions (including stroke, congenital heart disease, rhythm disorders, subclinical atherosclerosis, coronary heart disease, heart failure, valvular disease, venous disease, and peripheral artery disease) and the associated outcomes (including quality of care, procedures, and economic costs). METHODS The American Heart Association, through its Statistics Committee, continuously monitors and evaluates sources of data on heart disease and stroke in the United States to provide the most current information available in the annual Statistical Update. The 2020 Statistical Update is the product of a full year's worth of effort by dedicated volunteer clinicians and scientists, committed government professionals, and American Heart Association staff members. This year's edition includes data on the monitoring and benefits of cardiovascular health in the population, metrics to assess and monitor healthy diets, an enhanced focus on social determinants of health, a focus on the global burden of cardiovascular disease, and further evidence-based approaches to changing behaviors, implementation strategies, and implications of the American Heart Association's 2020 Impact Goals. RESULTS Each of the 26 chapters in the Statistical Update focuses on a different topic related to heart disease and stroke statistics. CONCLUSIONS The Statistical Update represents a critical resource for the lay public, policy makers, media professionals, clinicians, healthcare administrators, researchers, health advocates, and others seeking the best available data on these factors and conditions.
Collapse
|
96
|
Benjamin EJ, Muntner P, Alonso A, Bittencourt MS, Callaway CW, Carson AP, Chamberlain AM, Chang AR, Cheng S, Das SR, Delling FN, Djousse L, Elkind MSV, Ferguson JF, Fornage M, Jordan LC, Khan SS, Kissela BM, Knutson KL, Kwan TW, Lackland DT, Lewis TT, Lichtman JH, Longenecker CT, Loop MS, Lutsey PL, Martin SS, Matsushita K, Moran AE, Mussolino ME, O'Flaherty M, Pandey A, Perak AM, Rosamond WD, Roth GA, Sampson UKA, Satou GM, Schroeder EB, Shah SH, Spartano NL, Stokes A, Tirschwell DL, Tsao CW, Turakhia MP, VanWagner LB, Wilkins JT, Wong SS, Virani SS. Heart Disease and Stroke Statistics-2019 Update: A Report From the American Heart Association. Circulation 2019; 139:e56-e528. [PMID: 30700139 DOI: 10.1161/cir.0000000000000659] [Citation(s) in RCA: 5401] [Impact Index Per Article: 1080.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
97
|
Liu L, Pei YF, Liu TL, Hu WZ, Yang XL, Li SC, Hai R, Ran S, Zhao LJ, Shen H, Tian Q, Xiao HM, Zhang K, Deng HW, Zhang L. Identification of a 1p21 independent functional variant for abdominal obesity. Int J Obes (Lond) 2019; 43:2480-2490. [PMID: 30944420 PMCID: PMC6776704 DOI: 10.1038/s41366-019-0350-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 12/08/2018] [Accepted: 01/25/2019] [Indexed: 12/11/2022]
Abstract
OBJECTIVES Aiming to uncover the genetic basis of abdominal obesity, we performed a genome-wide association study (GWAS) meta-analysis of trunk fat mass adjusted by trunk lean mass (TFMadj) and followed by a series of functional investigations. SUBJECTS A total of 11,569 subjects from six samples were included into the GWAS meta-analysis. METHODS Meta-analysis was performed by a weighted fixed-effects model. In silico replication analysis was performed in the UK-Biobank (UKB) sample (N = 331,093) and in the GIANT study (N up to 110,204). Cis-expression QTL (cis-eQTL) analysis, dual-luciferase reporter assay and electrophoresis mobility shift assay (EMSA) were conducted to examine the functional relevance of the identified SNPs. At last, differential gene expression analysis (DGEA) was performed. RESULTS We identified an independent SNP rs12409479 at 1p21 (MAF = 0.07, p = 7.26 × 10-10), whose association was replicated by the analysis of TFM in the UKB sample (one-sided p = 3.39 × 10-3), and was cross-validated by the analyses of BMI (one-sided p = 0.03) and WHRadj (one-sided p = 0.04) in the GIANT study. Cis-eQTL analysis demonstrated that allele A at rs12409479 was positively associated with PTBP2 expression level in subcutaneous adipose tissue (N = 385, p = 4.15 × 10-3). Dual-luciferase reporter assay showed that the region repressed PTBP2 gene expression by downregulating PTBP2 promoter activity (p < 0.001), and allele A at rs12409479 induced higher luciferase activity than allele G did (p = 4.15 × 10-3). EMSA experiment implied that allele A was more capable of binding to unknown transcription factors than allele G. Lastly, DGEA showed that the level of PTBP2 expression was higher in individuals with obesity than in individuals without obesity (N = 20 and 11, p = 0.04 and 9.22 × 10-3), suggesting a regulatory role in obesity development. CONCLUSIONS Taken together, we hypothesize a regulating path from rs12409479 to trunk fat mass development through its allelic specific regulation of PTBP2 gene expression, thus providing some novel insight into the genetic basis of abdominal obesity.
Collapse
Affiliation(s)
- Lu Liu
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Medical College of Soochow University, Suzhou, China
| | - Yu-Fang Pei
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Medical College of Soochow University, Suzhou, China
- Department of Epidemiology and Health Statistics, School of Public Health, Medical College of Soochow University, Suzhou, China
| | - Tao-Le Liu
- Center for Circadian Clock, School of Biology & Basic Medical Sciences, Medical College of Soochow University, Suzhou, China
| | - Wen-Zhu Hu
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Medical College of Soochow University, Suzhou, China
| | - Xiao-Lin Yang
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Medical College of Soochow University, Suzhou, China
| | - Shan-Cheng Li
- Department of Orthopedics, the Second Affiliated Hospital, Soochow University, Suzhou, China
| | - Rong Hai
- Inner Mongolia Autonomous Region People's Hospital, Hohhot, Inner Mongolia, China
| | - Shu Ran
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Lan Juan Zhao
- Tulane Center for Genomics and Bioinformatics, Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Hui Shen
- Tulane Center for Genomics and Bioinformatics, Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Qing Tian
- Tulane Center for Genomics and Bioinformatics, Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Hong-Mei Xiao
- School of Basic Medical Sciences, Central South University, 410000, Changsha, China
| | - Kun Zhang
- Department of Computer Science, Bioinformatics Facility of Xavier NIH RCMI Cancer Research Center, Xavier University of Louisiana, New Orleans, LA, 70125, USA
| | - Hong-Wen Deng
- Tulane Center for Genomics and Bioinformatics, Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA.
- School of Basic Medical Sciences, Central South University, 410000, Changsha, China.
| | - Lei Zhang
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, China.
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Medical College of Soochow University, Suzhou, China.
| |
Collapse
|
98
|
Noordam R, Bos MM, Wang H, Winkler TW, Bentley AR, Kilpeläinen TO, de Vries PS, Sung YJ, Schwander K, Cade BE, Manning A, Aschard H, Brown MR, Chen H, Franceschini N, Musani SK, Richard M, Vojinovic D, Aslibekyan S, Bartz TM, de Las Fuentes L, Feitosa M, Horimoto AR, Ilkov M, Kho M, Kraja A, Li C, Lim E, Liu Y, Mook-Kanamori DO, Rankinen T, Tajuddin SM, van der Spek A, Wang Z, Marten J, Laville V, Alver M, Evangelou E, Graff ME, He M, Kühnel B, Lyytikäinen LP, Marques-Vidal P, Nolte IM, Palmer ND, Rauramaa R, Shu XO, Snieder H, Weiss S, Wen W, Yanek LR, Adolfo C, Ballantyne C, Bielak L, Biermasz NR, Boerwinkle E, Dimou N, Eiriksdottir G, Gao C, Gharib SA, Gottlieb DJ, Haba-Rubio J, Harris TB, Heikkinen S, Heinzer R, Hixson JE, Homuth G, Ikram MA, Komulainen P, Krieger JE, Lee J, Liu J, Lohman KK, Luik AI, Mägi R, Martin LW, Meitinger T, Metspalu A, Milaneschi Y, Nalls MA, O'Connell J, Peters A, Peyser P, Raitakari OT, Reiner AP, Rensen PCN, Rice TK, Rich SS, Roenneberg T, Rotter JI, Schreiner PJ, Shikany J, Sidney SS, Sims M, Sitlani CM, Sofer T, Strauch K, Swertz MA, Taylor KD, Uitterlinden AG, van Duijn CM, Völzke H, Waldenberger M, Wallance RB, van Dijk KW, Yu C, Zonderman AB, Becker DM, Elliott P, Esko T, Gieger C, Grabe HJ, Lakka TA, Lehtimäki T, North KE, Penninx BWJH, Vollenweider P, Wagenknecht LE, Wu T, Xiang YB, Zheng W, Arnett DK, Bouchard C, Evans MK, Gudnason V, Kardia S, Kelly TN, Kritchevsky SB, Loos RJF, Pereira AC, Province M, Psaty BM, Rotimi C, Zhu X, Amin N, Cupples LA, Fornage M, Fox EF, Guo X, Gauderman WJ, Rice K, Kooperberg C, Munroe PB, Liu CT, Morrison AC, Rao DC, van Heemst D, Redline S. Multi-ancestry sleep-by-SNP interaction analysis in 126,926 individuals reveals lipid loci stratified by sleep duration. Nat Commun 2019; 10:5121. [PMID: 31719535 PMCID: PMC6851116 DOI: 10.1038/s41467-019-12958-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 10/04/2019] [Indexed: 12/12/2022] Open
Abstract
Both short and long sleep are associated with an adverse lipid profile, likely through different biological pathways. To elucidate the biology of sleep-associated adverse lipid profile, we conduct multi-ancestry genome-wide sleep-SNP interaction analyses on three lipid traits (HDL-c, LDL-c and triglycerides). In the total study sample (discovery + replication) of 126,926 individuals from 5 different ancestry groups, when considering either long or short total sleep time interactions in joint analyses, we identify 49 previously unreported lipid loci, and 10 additional previously unreported lipid loci in a restricted sample of European-ancestry cohorts. In addition, we identify new gene-sleep interactions for known lipid loci such as LPL and PCSK9. The previously unreported lipid loci have a modest explained variance in lipid levels: most notable, gene-short-sleep interactions explain 4.25% of the variance in triglyceride level. Collectively, these findings contribute to our understanding of the biological mechanisms involved in sleep-associated adverse lipid profiles. Sleep duration is associated with an adverse lipid profile. Here, the authors perform genome-wide gene-by-sleep interaction analysis and find 49 previously unreported lipid loci when considering short or long total sleep time.
Collapse
Affiliation(s)
- Raymond Noordam
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands.
| | - Maxime M Bos
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - Heming Wang
- Division of Sleep and Circadian Disorders, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Thomas W Winkler
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Amy R Bentley
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Tuomas O Kilpeläinen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark.,Department of Environmental Medicine and Public Health, The Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Paul S de Vries
- 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
| | - Yun Ju Sung
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Karen Schwander
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Brian E Cade
- Division of Sleep and Circadian Disorders, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Alisa Manning
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Hugues Aschard
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA.,Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Institut Pasteur, Paris, France
| | - Michael R Brown
- 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
| | - 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
| | - Nora Franceschini
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Solomon K Musani
- Jackson Heart Study, Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Melissa Richard
- Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Dina Vojinovic
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Stella Aslibekyan
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Traci M Bartz
- Cardiovascular Health Research Unit, Biostatistics and Medicine, University of Washington, Seattle, WA, USA
| | - Lisa de Las Fuentes
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA.,Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Mary Feitosa
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Andrea R Horimoto
- Laboratory of Genetics and Molecular Cardiology, Heart Institute (InCor), University of São Paulo Medical School, São Paulo, SP, Brazil
| | | | - Minjung Kho
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Aldi Kraja
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Changwei Li
- Epidemiology and Biostatistics, University of Georgia at Athens College of Public Health, Athens, GA, USA
| | - Elise Lim
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Yongmei Liu
- Public Health Sciences, Epidemiology and Prevention, Wake Forest University Health Sciences, Winston-Salem, NC, USA
| | - Dennis O Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, Netherlands.,Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, Netherlands
| | - Tuomo Rankinen
- Human Genomics Laboratory, Pennington Biomedical Research Center, Baton Rouge, LA, USA
| | - Salman M Tajuddin
- Health Disparities Research Section, Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Ashley van der Spek
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Zhe Wang
- 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
| | - Jonathan Marten
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Vincent Laville
- Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Institut Pasteur, Paris, France
| | - Maris Alver
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia.,Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Evangelos Evangelou
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK.,Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, Greece
| | - Maria E Graff
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Meian He
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Brigitte Kühnel
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland.,Department of Clinical Chemistry, Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Pedro Marques-Vidal
- Medicine, Internal Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Ilja M Nolte
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands
| | | | - Rainer Rauramaa
- Foundation for Research in Health Exercise and Nutrition, Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Harold Snieder
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands
| | - Stefan Weiss
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Wanqing Wen
- Division of Epidemiology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Lisa R Yanek
- Division of General Internal Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Correa Adolfo
- Jackson Heart Study, Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Christie Ballantyne
- Section of Cardiovascular Research, Baylor College of Medicine, Houston, TX, USA.,Houston Methodist Debakey Heart and Vascular Center, Houston, TX, USA
| | - Larry Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Nienke R Biermasz
- Department of Internal Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, The Netherlands.,Einthoven Laboratory for Experimental Vascular Medicine, Leiden, The Netherlands
| | - 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
| | - Niki Dimou
- Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, Greece
| | | | - Chuan Gao
- Molecular Genetics and Genomics Program, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Sina A Gharib
- Computational Medicine Core, Center for Lung Biology, UW Medicine Sleep Center, Medicine, University of Washington, Seattle, WA, USA
| | - Daniel J Gottlieb
- Division of Sleep and Circadian Disorders, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA.,VA Boston Healthcare System, Boston, MA, USA
| | - José Haba-Rubio
- Medicine, Sleep Laboratory, Lausanne University Hospital, Lausanne, Switzerland
| | - Tamara B Harris
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Sami Heikkinen
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland.,Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio Campus, Finland
| | - Raphaël Heinzer
- Medicine, Sleep Laboratory, Lausanne University Hospital, Lausanne, Switzerland
| | - James E Hixson
- 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
| | - Georg Homuth
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Radiology and Nuclear Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Pirjo Komulainen
- Foundation for Research in Health Exercise and Nutrition, Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
| | - Jose E Krieger
- Laboratory of Genetics and Molecular Cardiology, Heart Institute (InCor), University of São Paulo Medical School, São Paulo, SP, Brazil
| | - Jiwon Lee
- Division of Sleep and Circadian Disorders, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Jingmin Liu
- Fred Hutchinson Cancer Research Center, University of Washington School of Public Health, Seattle, WA, USA
| | - Kurt K Lohman
- Public Health Sciences, Biostatistical Sciences, Wake Forest University Health Sciences, Winston-Salem, NC, USA
| | - Annemarie I Luik
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Reedik Mägi
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Lisa W Martin
- Cardiology, School of Medicine and Health Sciences, George Washington University, Washington, D.C., USA
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Andres Metspalu
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia.,Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Yuri Milaneschi
- Cardiology, School of Medicine and Health Sciences, George Washington University, Washington, D.C., USA
| | - Mike A Nalls
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA.,Data Tecnica International, Glen Echo, MD, USA
| | - Jeff O'Connell
- Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD, USA.,Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Neuherberg, Germany
| | - Patricia Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Olli T Raitakari
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland.,University of Turku, Turku, Finland
| | - Alex P Reiner
- Fred Hutchinson Cancer Research Center, University of Washington School of Public Health, Seattle, WA, USA
| | - Patrick C N Rensen
- Department of Internal Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, The Netherlands.,Einthoven Laboratory for Experimental Vascular Medicine, Leiden, The Netherlands
| | - Treva K Rice
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Till Roenneberg
- Institute of Medical Psychology, Ludwig-Maximilians-Universitat Munchen, Munich, Germany
| | - Jerome I Rotter
- Genomic Outcomes, Department of Pediatrics, Institute for Translational Genomics and Population Sciences, LABioMed at Harbor-UCLA Medical Center, Torrance, CC, USA
| | - Pamela J Schreiner
- Division of Epidemiology & Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - James Shikany
- Division of Preventive Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Stephen S Sidney
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Mario Sims
- Jackson Heart Study, Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Colleen M Sitlani
- Cardiovascular Health Research Unit, Medicine, University of Washington, Seattle, WA, USA
| | - Tamar Sofer
- Division of Sleep and Circadian Disorders, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA.,Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Institute for Medical Informatics Biometry and Epidemiology, Ludwig-Maximilians-Universitat Munchen, Munich, Germany
| | - Morris A Swertz
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Kent D Taylor
- Genomic Outcomes, Department of Pediatrics, Institute for Translational Genomics and Population Sciences, LABioMed at Harbor-UCLA Medical Center, Torrance, CC, USA
| | - André G Uitterlinden
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Henry Völzke
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Neuherberg, Germany
| | - Robert B Wallance
- Department of Epidemiology, University of Iowa College of Public Health, Iowa City, IA, USA
| | - Ko Willems van Dijk
- Department of Internal Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, The Netherlands.,Einthoven Laboratory for Experimental Vascular Medicine, Leiden, The Netherlands.,Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Caizheng Yu
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Alan B Zonderman
- Behavioral Epidemiology Section, Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Diane M Becker
- Division of General Internal Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Paul Elliott
- Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.,MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK.,National Institute of Health Research Imperial College London Biomedical Research Centre, London, UK.,UK-DRI Dementia Research Institute at Imperial College London, London, UK
| | - Tõnu Esko
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia.,Broad Institute of the Massachusetts Institute of Technology and Harvard University, Boston, MA, USA
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Hans J Grabe
- Department Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
| | - Timo A Lakka
- Foundation for Research in Health Exercise and Nutrition, Kuopio Research Institute of Exercise Medicine, Kuopio, Finland.,Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio Campus, Finland.,Department of Clinical Phsiology and Nuclear Medicine, Kuopia University Hospital, Kuopio, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland.,Department of Clinical Chemistry, Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Kari E North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Brenda W J H Penninx
- Department of Psychiatry, Amsterdam Neuroscience and Amsterdam Public Health Research Institute, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - Peter Vollenweider
- Medicine, Internal Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Lynne E Wagenknecht
- Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Tangchun Wu
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yong-Bing Xiang
- SKLORG & Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, P. R. China
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Donna K Arnett
- Dean's Office, University of Kentucky College of Public Health, Lexington, KS, USA
| | - Claude Bouchard
- Human Genomics Laboratory, Pennington Biomedical Research Center, Baton Rouge, LA, USA
| | - Michele K Evans
- Health Disparities Research Section, Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland.,Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Sharon Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Tanika N Kelly
- Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Stephen B Kritchevsky
- Sticht Center for Healthy Aging and Rehabilitation, Gerontology and Geriatric Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, NY, USA.,The Mindich Child Health Development Institute, The Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexandre C Pereira
- Laboratory of Genetics and Molecular Cardiology, Heart Institute (InCor), University of São Paulo Medical School, São Paulo, SP, Brazil
| | - Mike Province
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Epidemiology, Medicine and Health Services, University of Washington, Seattle, WA, USA.,Kaiser Permanente Washington, Health Research Institute, Seattle, WA, USA
| | - Charles Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xiaofeng Zhu
- Department of Population Quantitative and Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Najaf Amin
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - L Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA.,NHLBI Framingham Heart Study, Framingham, MA, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Ervin F Fox
- Cardiology, Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Xiuqing Guo
- Genomic Outcomes, Department of Pediatrics, Institute for Translational Genomics and Population Sciences, LABioMed at Harbor-UCLA Medical Center, Torrance, CC, USA
| | - W James Gauderman
- Biostatistics, Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Kenneth Rice
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Charles Kooperberg
- Fred Hutchinson Cancer Research Center, University of Washington School of Public Health, Seattle, WA, USA
| | - Patricia B Munroe
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.,NIHR Barts Cardiovascular Biomedical Research Centre, Queen Mary University of London, London, London, UK
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Alanna C Morrison
- 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
| | - Dabeeru C Rao
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Diana van Heemst
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA. .,Division of Pulmonary Medicine, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
99
|
Trifonova EA, Popovich AA, Vagaitseva KV, Bocharova AV, Gavrilenko MM, Ivanov VV, Stepanov VA. The Multiplex Genotyping Method for Single-Nucleotide Polymorphisms of Genes Associated with Obesity and Body Mass Index. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419100144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
100
|
Castillejo-Lopez C, Pjanic M, Pirona AC, Hetty S, Wabitsch M, Wadelius C, Quertermous T, Arner E, Ingelsson E. Detailed Functional Characterization of a Waist-Hip Ratio Locus in 7p15.2 Defines an Enhancer Controlling Adipocyte Differentiation. iScience 2019; 20:42-59. [PMID: 31557715 PMCID: PMC6817687 DOI: 10.1016/j.isci.2019.09.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 07/10/2019] [Accepted: 09/05/2019] [Indexed: 12/22/2022] Open
Abstract
We combined CAGE sequencing in human adipocytes during differentiation with data from genome-wide association studies to identify an enhancer in the SNX10 locus on chromosome 7, presumably involved in body fat distribution. Using reporter assays and CRISPR-Cas9 gene editing in human cell lines, we characterized the role of the enhancer in adipogenesis. The enhancer was active during adipogenesis and responded strongly to insulin and isoprenaline. The allele associated with increased waist-hip ratio in human genetic studies was associated with higher enhancer activity. Mutations of the enhancer resulted in less adipocyte differentiation. RNA sequencing of cells with disrupted enhancer showed reduced expression of established adipocyte markers, such as ADIPOQ and LPL, and identified CHI3L1 on chromosome 1 as a potential gene involved in adipocyte differentiation. In conclusion, we identified and characterized an enhancer in the SNX10 locus and outlined its plausible mechanisms of action and downstream targets. An enhancer active during adipogenesis is located in an obesity GWAS locus The enhancer responded strongly to insulin and isoprenaline Mutation of the enhancer by CRISPR-Cas9 decreased adipocyte differentiation Knockout of CHI3L1 decreased adipocyte differentiation
Collapse
Affiliation(s)
- Casimiro Castillejo-Lopez
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Milos Pjanic
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Anna Chiara Pirona
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Susanne Hetty
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Martin Wabitsch
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Endocrinology and Diabetes, University of Ulm, Ulm, Germany
| | - Claes Wadelius
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Thomas Quertermous
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Erik Arner
- Laboratory for Applied Regulatory Genomics Network Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045 Japan
| | - Erik Ingelsson
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden; Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA; Stanford Diabetes Research Center, Stanford University, Stanford, CA 94305, USA.
| |
Collapse
|