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Solomon O, Lanata CM, Adams C, Nititham J, Taylor KE, Chung SA, Yazdany J, Dall’Era M, Pons-Estel BA, Tusié-Luna T, Tsao B, Morand E, Alarcón-Riquelme ME, Barcellos LF, Criswell LA. Local Ancestry at the Major Histocompatibility Complex Region is Not a Major Contributor to Disease Heterogeneity in a Multiethnic Lupus Cohort. Arthritis Rheumatol 2024; 76:614-619. [PMID: 38073021 PMCID: PMC10965360 DOI: 10.1002/art.42766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 11/14/2023] [Accepted: 11/27/2023] [Indexed: 01/31/2024]
Abstract
OBJECTIVE Systemic lupus erythematosus (SLE) is an autoimmune disease resulting in debilitating clinical manifestations that vary in severity by race and ethnicity with a disproportionate burden in African American, Mestizo, and Asian populations compared with populations of European descent. Differences in global and local genetic ancestry may shed light on the underlying mechanisms contributing to these disparities, including increased prevalence of lupus nephritis, younger age of symptom onset, and presence of autoantibodies. METHODS A total of 1,139 European, African American, and Mestizos patients with SLE were genotyped using the Affymetrix LAT1 World array. Global ancestry proportions were estimated using ADMIXTURE, and local ancestry was estimated using RFMIXv2.0. We investigated associations between lupus nephritis, age at onset, and autoantibody status with both global and local ancestry proportions within the Major Histocompatibility Complex region. RESULTS Our results showed small effect sizes that did not meet the threshold for statistical significance for global or local ancestry proportions in either African American or Mestizo patients with SLE who presented with the clinical manifestations of interest compared with those who did not. CONCLUSION These findings suggest that local genetic ancestry within the Major Histocompatibility Complex region is not a major contributor to these SLE manifestations among patients with SLE from admixed populations.
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Affiliation(s)
- Olivia Solomon
- University of California, Berkeley, Genetic Epidemiology and Genomic Laboratory
| | | | - Cameron Adams
- University of California, Berkeley, Genetic Epidemiology and Genomic Laboratory
| | - Joanne Nititham
- National Human Genome Research Institute, NIH, Bethesda, Maryland
| | - Kimberly E. Taylor
- Russell/Engleman Rheumatology Research Center, University of California, San Francisco
| | - Sharon A. Chung
- Russell/Engleman Rheumatology Research Center, University of California, San Francisco
| | - Jinoos Yazdany
- Russell/Engleman Rheumatology Research Center, University of California, San Francisco
| | - Maria Dall’Era
- Russell/Engleman Rheumatology Research Center, University of California, San Francisco
| | - Bernado A. Pons-Estel
- Centro Regional de Enfermedades Autoinmunes y Reumaticas (GO-CREAR), Rosario, Argentina
| | - Teresa Tusié-Luna
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán and Instituto de Investigaciones Biomédicas de la Universidad Nacional Autonoma de México, Mexico City, Mexico
| | - Betty Tsao
- Medical University of South Carolina, Charleston, South Carolina
| | - Eric Morand
- Monash University Faculty of Medicine, Nursing & Health Sciences, Melbourne, Australia
| | - Marta E. Alarcón-Riquelme
- Center for Genomics and Oncological Research (GENYO). Pfizer—University of Granada—Andalusian Government, Parque Tecnologico de la Salud, Granada, Spain
| | - Lisa F. Barcellos
- University of California, Berkeley, Genetic Epidemiology and Genomic Laboratory
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Ziaei A, Solomon O, Casper TC, Waltz M, Weinstock-Guttman B, Aaen G, Wheeler Y, Graves J, Benson L, Gorman M, Rensel M, Mar S, Lotze T, Greenberg B, Chitnis T, Waldman AT, Krupp L, James JA, Hart J, Barcellos LF, Waubant E. Gene-environment interactions: Epstein-Barr virus infection and risk of pediatric-onset multiple sclerosis. Mult Scler 2024; 30:308-315. [PMID: 38332747 PMCID: PMC11093131 DOI: 10.1177/13524585231224685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
BACKGROUND AND OBJECTIVE Prior Epstein-Barr virus (EBV) infection is associated with an increased risk of pediatric-onset multiple sclerosis (POMS) and adult-onset multiple sclerosis (MS). It has been challenging to elucidate the biological mechanisms underlying this association. We examined the interactions between candidate human leukocyte antigen (HLA) and non-HLA variants and childhood EBV infection as it may provide mechanistic insights into EBV-associated MS. METHODS Cases and controls were enrolled in the Environmental and Genetic Risk Factors for Pediatric MS study of the US Network of Pediatric MS Centers. Participants were categorized as seropositive and seronegative for EBV-viral capsid antigen (VCA). The association between prior EBV infection and having POMS was estimated with logistic regression. Interactions between EBV serostatus, major HLA MS risk factors, and non-HLA POMS risk variants associated with response to EBV infection were also evaluated with logistic regression. Models were adjusted for sex, age, genetic ancestry, and the mother's education. Additive interactions were calculated using relative risk due to interaction (RERI) and attributable proportions (APs). RESULTS A total of 473 POMS cases and 702 controls contributed to the analyses. Anti-VCA seropositivity was significantly higher in POMS cases compared to controls (94.6% vs 60.7%, p < 0.001). There was evidence for additive interaction between childhood EBV infection and the presence of the HLA-DRB1*15 allele (RERI = 10.25, 95% confidence interval (CI) = 3.78 to 16.72; AP = 0.61, 95% CI = 0.47 to 0.75). There was evidence for multiplicative interaction (p < 0.05) between childhood EBV infection and the presence of DRB1*15 alleles (odds ratio (OR) = 3.43, 95% CI = 1.06 to 11.07). Among the pediatric MS variants also associated with EBV infection, we detected evidence for additive interaction (p = 0.02) between prior EBV infection and the presence of the GG genotype in risk variant (rs2255214) within CD86 (AP = 0.30, 95% CI = 0.03 to 0.58). CONCLUSION We report evidence for interactions between childhood EBV infection and DRB1*15 and the GG genotype of CD86 POMS risk variant. Our results suggest an important role of antigen-presenting cells (APCs) in EBV-associated POMS risk.
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Affiliation(s)
- Amin Ziaei
- University of California San Francisco, San Francisco, CA, USA/Department of Pathology & Laboratory Medicine, University of California, Irvine Medical Center (UCIMC), Orange, CA, USA
| | - Olivia Solomon
- Division of Epidemiology and Genetic Epidemiology and Genomics Laboratory, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | | | | | | | - Greg Aaen
- Loma Linda University Children's Hospital, Loma Linda, CA, USA
| | - Yolanda Wheeler
- The University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Leslie Benson
- Pediatric Multiple Sclerosis and Related Disorders Program, Boston Children's Hospital, Boston, MA, USA
| | - Mark Gorman
- Pediatric Multiple Sclerosis and Related Disorders Program, Boston Children's Hospital, Boston, MA, USA
| | | | - Soe Mar
- Washington University in St. Louis, St. Louis, MO, USA
| | - Tim Lotze
- Texas Children's Hospital, Houston, TX, USA
| | | | - Tanuja Chitnis
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Amy T Waldman
- Division of Child Neurology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Lauren Krupp
- New York University Medical Center, New York, NY, USA
| | - Judith A James
- Oklahoma Medical Research Foundation, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Janace Hart
- University of California San Francisco, San Francisco, CA, USA
| | - Lisa F Barcellos
- Division of Epidemiology and Genetic Epidemiology and Genomics Laboratory, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
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Kadalayil L, Alam MZ, White CH, Ghantous A, Walton E, Gruzieva O, Merid SK, Kumar A, Roy RP, Solomon O, Huen K, Eskenazi B, Rzehak P, Grote V, Langhendries JP, Verduci E, Ferre N, Gruszfeld D, Gao L, Guan W, Zeng X, Schisterman EF, Dou JF, Bakulski KM, Feinberg JI, Soomro MH, Pesce G, Baiz N, Isaevska E, Plusquin M, Vafeiadi M, Roumeliotaki T, Langie SAS, Standaert A, Allard C, Perron P, Bouchard L, van Meel ER, Felix JF, Jaddoe VWV, Yousefi PD, Ramlau-Hansen CH, Relton CL, Tobi EW, Starling AP, Yang IV, Llambrich M, Santorelli G, Lepeule J, Salas LA, Bustamante M, Ewart SL, Zhang H, Karmaus W, Röder S, Zenclussen AC, Jin J, Nystad W, Page CM, Magnus M, Jima DD, Hoyo C, Maguire RL, Kvist T, Czamara D, Räikkönen K, Gong T, Ullemar V, Rifas-Shiman SL, Oken E, Almqvist C, Karlsson R, Lahti J, Murphy SK, Håberg SE, London S, Herberth G, Arshad H, Sunyer J, Grazuleviciene R, Dabelea D, Steegers-Theunissen RPM, Nohr EA, Sørensen TIA, Duijts L, Hivert MF, Nelen V, Popovic M, Kogevinas M, Nawrot TS, Herceg Z, Annesi-Maesano I, Fallin MD, Yeung E, Breton CV, Koletzko B, Holland N, Wiemels JL, Melén E, Sharp GC, Silver MJ, Rezwan FI, Holloway JW. Analysis of DNA methylation at birth and in childhood reveals changes associated with season of birth and latitude. Clin Epigenetics 2023; 15:148. [PMID: 37697338 PMCID: PMC10496224 DOI: 10.1186/s13148-023-01542-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 07/27/2023] [Indexed: 09/13/2023] Open
Abstract
BACKGROUND Seasonal variations in environmental exposures at birth or during gestation are associated with numerous adult traits and health outcomes later in life. Whether DNA methylation (DNAm) plays a role in the molecular mechanisms underlying the associations between birth season and lifelong phenotypes remains unclear. METHODS We carried out epigenome-wide meta-analyses within the Pregnancy And Childhood Epigenetic Consortium to identify associations of DNAm with birth season, both at differentially methylated probes (DMPs) and regions (DMRs). Associations were examined at two time points: at birth (21 cohorts, N = 9358) and in children aged 1-11 years (12 cohorts, N = 3610). We conducted meta-analyses to assess the impact of latitude on birth season-specific associations at both time points. RESULTS We identified associations between birth season and DNAm (False Discovery Rate-adjusted p values < 0.05) at two CpGs at birth (winter-born) and four in the childhood (summer-born) analyses when compared to children born in autumn. Furthermore, we identified twenty-six differentially methylated regions (DMR) at birth (winter-born: 8, spring-born: 15, summer-born: 3) and thirty-two in childhood (winter-born: 12, spring and summer: 10 each) meta-analyses with few overlapping DMRs between the birth seasons or the two time points. The DMRs were associated with genes of known functions in tumorigenesis, psychiatric/neurological disorders, inflammation, or immunity, amongst others. Latitude-stratified meta-analyses [higher (≥ 50°N), lower (< 50°N, northern hemisphere only)] revealed differences in associations between birth season and DNAm by birth latitude. DMR analysis implicated genes with previously reported links to schizophrenia (LAX1), skin disorders (PSORS1C, LTB4R), and airway inflammation including asthma (LTB4R), present only at birth in the higher latitudes (≥ 50°N). CONCLUSIONS In this large epigenome-wide meta-analysis study, we provide evidence for (i) associations between DNAm and season of birth that are unique for the seasons of the year (temporal effect) and (ii) latitude-dependent variations in the seasonal associations (spatial effect). DNAm could play a role in the molecular mechanisms underlying the effect of birth season on adult health outcomes.
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Affiliation(s)
- Latha Kadalayil
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK
| | - Md Zahangir Alam
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
| | - Cory Haley White
- Merck Exploratory Science Center in Cambridge MA, Merck Research Laboratories, Cambridge, MA, 02141, USA
| | - Akram Ghantous
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer, Lyon, France
| | - Esther Walton
- Department of Psychology, University of Bath, Bath, UK
| | - Olena Gruzieva
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Centre for Occupational and Environmental Medicine, Region Stockholm, Sweden
| | - Simon Kebede Merid
- Centre for Occupational and Environmental Medicine, Region Stockholm, Sweden
| | - Ashish Kumar
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - Ritu P Roy
- Helen Diller Family Comprehensive Cancer Center University of California, San Francisco, CA, 94143, USA
- Computational Biology and Informatics Core, University of California, San Francisco, CA, 94143, USA
| | - Olivia Solomon
- Children's Environmental Health Laboratory, University of California, Berkeley, CA, USA
| | - Karen Huen
- Children's Environmental Health Laboratory, University of California, Berkeley, CA, USA
| | - Brenda Eskenazi
- Children's Environmental Health Laboratory, University of California, Berkeley, CA, USA
| | - Peter Rzehak
- Division of Metabolic and Nutritional Medicine, Dr. von Hauner Children's Hospital, Ludwig-Maximilians Universität München (LMU), Munich, Germany
| | - Veit Grote
- Division of Metabolic and Nutritional Medicine, Dr. von Hauner Children's Hospital, Ludwig-Maximilians Universität München (LMU), Munich, Germany
| | | | - Elvira Verduci
- Department of Pediatrics, Vittore Buzzi Children Hospital, University of Milan, Milan, Italy
| | - Natalia Ferre
- Pediatric Nutrition and Human Development Research Unit, Universitat Rovira i Virgili, IISPV, Reus, Spain
| | - Darek Gruszfeld
- Neonatal Department, Children's Memorial Health Institute, Warsaw, Poland
| | - Lu Gao
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Weihua Guan
- Division of Biostatistics, School of Public Health, University of Minnesota, A460 Mayo Building, MMC 303, 420 Delaware St. SE, Minneapolis, MN, 55455, USA
| | | | - Enrique F Schisterman
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, 423 Guardian Drive, Philadelphia, PA, 19104, USA
| | - John F Dou
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, USA
| | - Kelly M Bakulski
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, USA
| | - Jason I Feinberg
- Wendy Klag Center for Autism and Developmental Disabilities Johns Hopkins University, Baltimore, MD, USA
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Munawar Hussain Soomro
- Sorbonne Université and INSERM, Epidemiology of Allergic and Respiratory Diseases Department, Pierre Louis Institute of Epidemiology and Public Health (IPLESP UMRS 1136), Saint-Antoine Medical School, Paris Cedex 12, France
- Department of Community Medicine and Public Health, SMBB Medical University, Larkana, Pakistan
| | - Giancarlo Pesce
- Sorbonne Université and INSERM, Epidemiology of Allergic and Respiratory Diseases Department, Pierre Louis Institute of Epidemiology and Public Health (IPLESP UMRS 1136), Saint-Antoine Medical School, Paris Cedex 12, France
| | - Nour Baiz
- Institut Desbrest de Santé Publique (IDESP), INSERM and Montpellier University, Montpellier, France
| | - Elena Isaevska
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, CPO Piemonte, Italy
| | - Michelle Plusquin
- Center for Environmental Sciences, University of Hasselt, 3590, Diepenbeek, Belgium
| | - Marina Vafeiadi
- Department of Social Medicine, School of Medicine, University of Crete, Heraklion, Greece
| | - Theano Roumeliotaki
- Department of Social Medicine, School of Medicine, University of Crete, Heraklion, Greece
| | - Sabine A S Langie
- Unit Health, Flemish Institute for Technological Research (VITO), Mol, Belgium
- Faculty of Sciences, Hasselt University, Diepenbeek, Belgium
- Department of Pharmacology and Toxicology, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, Limburg, The Netherlands
| | - Arnout Standaert
- Unit Health, Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Catherine Allard
- Centre de Recherche du Centre Hospitalier de l'Universite de Sherbrooke, Sherbrooke, Canada
| | - Patrice Perron
- Department of Medicine, Universite de Sherbrooke, Sherbrooke, Canada
| | - Luigi Bouchard
- Department of Biochemistry and Functional Genomics, Universite de Sherbrooke, Sherbrooke, Canada
- Clinical Department of Laboratory Medicine, Centre intégré universitaire de santé et de services sociaux (CIUSSS) du Saguenay-Lac-Saint-Jean - Hôpital de Chicoutimi, Chicoutimi, Canada
| | - Evelien R van Meel
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Division of Respiratory Medicine and Allergology, Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Vincent W V Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Paul D Yousefi
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | | | - Caroline L Relton
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | - Elmar W Tobi
- Periconceptional Epidemiology, Department of Obstetrics and Gynecology, Erasmus MC, University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Anne P Starling
- Life Course Epidemiology of Adiposity and Diabetes (LEAD) Center, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ivana V Yang
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
| | - Maria Llambrich
- Institute for Global Health (ISGlobal), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | | | - Johanna Lepeule
- Institute for Advanced Biosciences, University Grenoble-Alpes, INSERM, CNRS, Grenoble, France
| | - Lucas A Salas
- Institute for Global Health (ISGlobal), Barcelona, Spain
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA
- Center for Molecular Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA
- Children's Environmental Health and Disease Prevention Research Center at Dartmouth, Lebanon, NH, USA
| | - Mariona Bustamante
- Institute for Global Health (ISGlobal), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Susan L Ewart
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, USA
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, USA
| | - Stefan Röder
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Ana Claudia Zenclussen
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Jianping Jin
- 2530 Meridian Pkwy, Suite 200, Durham, NC 27713, USA
| | - Wenche Nystad
- Department of Chronic Diseases and Ageing, Norwegian Institute of Public Health, Oslo, Norway
| | - Christian M Page
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Section for Statistics and Data Science, Department of Mathematics, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Maria Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Dereje D Jima
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Cathrine Hoyo
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Rachel L Maguire
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Department of Obstetrics and Gynaecology, Duke University Medical Center, Durham, NC, USA
| | - Tuomas Kvist
- Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
| | - Darina Czamara
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, 80804, Munich, Germany
| | - Katri Räikkönen
- Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
| | - Tong Gong
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Vilhelmina Ullemar
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Sheryl L Rifas-Shiman
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, USA
| | - Emily Oken
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, USA
| | - Catarina Almqvist
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Pediatric Allergy and Pulmonology Unit at Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Robert Karlsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Jari Lahti
- Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
| | - Susan K Murphy
- Department of Obstetrics and Gynaecology, Duke University Medical Center, Durham, NC, USA
| | - Siri E Håberg
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Stephanie London
- Department of Health and Human Services, National Institute of Environmental Health Sciences, National Institutes of Health, RTP, NC, 27709, USA
| | - Gunda Herberth
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Hasan Arshad
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- David Hide Asthma and Allergy Research Centre, Isle of Wight, UK
- NIHR Southampton Biomedical Research Centre, Southampton General Hospital, Southampton, UK
| | - Jordi Sunyer
- Institute for Global Health (ISGlobal), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Regina Grazuleviciene
- Department of Environmental Science, Vytautas Magnus University, 44248, Kaunas, Lithuania
| | - Dana Dabelea
- Life Course Epidemiology of Adiposity and Diabetes (LEAD) Center, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Pediatrics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Régine P M Steegers-Theunissen
- Periconceptional Epidemiology, Department of Obstetrics and Gynecology, Erasmus MC, University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Ellen A Nohr
- Department of Clinical Research, Odense Universitetshospital, Odense, 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 Public Health, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Liesbeth Duijts
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Division of Respiratory Medicine and Allergology, Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Division of Neonatology, Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Marie-France Hivert
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Vera Nelen
- Provincial Institute for Hygiene, Antwerp, Belgium
| | - Maja Popovic
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, CPO Piemonte, Italy
| | | | - Tim S Nawrot
- Center for Environmental Sciences, University of Hasselt, 3590, Diepenbeek, Belgium
- Department of Public Health and Primary Care, Leuven University, Louvain, Belgium
| | - Zdenko Herceg
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer, Lyon, France
| | - Isabella Annesi-Maesano
- Institut Desbrest de Santé Publique (IDESP), INSERM and Montpellier University, Montpellier, France
| | - M Daniele Fallin
- Wendy Klag Center for Autism and Developmental Disabilities Johns Hopkins University, Baltimore, MD, USA
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Edwina Yeung
- Epidemiology Branch, Division of Population Health Research, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, 6710B Rockledge Dr, MSC 7004, Bethesda, MD, USA
| | - Carrie V Breton
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Berthold Koletzko
- Division of Metabolic and Nutritional Medicine, Dr. von Hauner Children's Hospital, Ludwig-Maximilians Universität München (LMU), Munich, Germany
| | - Nina Holland
- Children's Environmental Health Laboratory, CERCH, Berkeley Public Health, University of California, 2121 Berkeley Way #5216, Berkeley, CA, 94720, USA
| | - Joseph L Wiemels
- Center for Genetic Epidemiology, University of Southern California, Los Angeles, CA, 90033, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90033, USA
| | - Erik Melén
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
- Sachs' Children and Youth Hospital, Södersjukhuset, Stockholm, Sweden
| | - Gemma C Sharp
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- School of Psychology, University of Exeter, Exeter, UK
| | - Matt J Silver
- Medical Research Council Unit, The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
- Medical Research Council Unit, The Gambia at the London School of Hygiene and Tropical Medicine, London, UK
| | - Faisal I Rezwan
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK
- Department of Computer Science, Aberystwyth University, Aberystwyth, Ceredigion, UK
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK.
- NIHR Southampton Biomedical Research Centre, Southampton General Hospital, Southampton, UK.
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Chi C, Solomon O, Shiboski C, Taylor KE, Quach H, Quach D, Barcellos LF, Criswell LA. Identification of Sjögren's syndrome patient subgroups by clustering of labial salivary gland DNA methylation profiles. PLoS One 2023; 18:e0281891. [PMID: 36862625 PMCID: PMC9980741 DOI: 10.1371/journal.pone.0281891] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 02/02/2023] [Indexed: 03/03/2023] Open
Abstract
Heterogeneity in Sjögren's syndrome (SS), increasingly called Sjögren's disease, suggests the presence of disease subtypes, which poses a major challenge for the diagnosis, management, and treatment of this autoimmune disorder. Previous work distinguished patient subgroups based on clinical symptoms, but it is not clear to what extent symptoms reflect underlying pathobiology. The purpose of this study was to discover clinical meaningful subtypes of SS based on genome-wide DNA methylation data. We performed a cluster analysis of genome-wide DNA methylation data from labial salivary gland (LSG) tissue collected from 64 SS cases and 67 non-cases. Specifically, hierarchical clustering was performed on low dimensional embeddings of DNA methylation data extracted from a variational autoencoder to uncover unknown heterogeneity. Clustering revealed clinically severe and mild subgroups of SS. Differential methylation analysis revealed that hypomethylation at the MHC and hypermethylation at other genome regions characterize the epigenetic differences between these SS subgroups. Epigenetic profiling of LSGs in SS yields new insights into mechanisms underlying disease heterogeneity. The methylation patterns at differentially methylated CpGs are different in SS subgroups and support the role of epigenetic contributions to the heterogeneity in SS. Biomarker data derived from epigenetic profiling could be explored in future iterations of the classification criteria for defining SS subgroups.
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Affiliation(s)
- Calvin Chi
- Division of Computing, Center for Computational Biology, Data Science and Society, University of California Berkeley, Berkeley, California, United States of America
- Genetic Epidemiology and Genomics Laboratory, School of Public Health, University of California Berkeley, Berkeley, California, United States of America
| | - Olivia Solomon
- Genetic Epidemiology and Genomics Laboratory, School of Public Health, University of California Berkeley, Berkeley, California, United States of America
| | - Caroline Shiboski
- Department of Orofacial Sciences, School of Dentistry, University of California San Francisco, San Francisco, California, United States of America
| | - Kimberly E. Taylor
- Department of Medicine, Russell/Engleman Rheumatology Research Center, University of California San Francisco, San Francisco, California, United States of America
| | - Hong Quach
- Genetic Epidemiology and Genomics Laboratory, School of Public Health, University of California Berkeley, Berkeley, California, United States of America
| | - Diana Quach
- Genetic Epidemiology and Genomics Laboratory, School of Public Health, University of California Berkeley, Berkeley, California, United States of America
| | - Lisa F. Barcellos
- Division of Computing, Center for Computational Biology, Data Science and Society, University of California Berkeley, Berkeley, California, United States of America
- Genetic Epidemiology and Genomics Laboratory, School of Public Health, University of California Berkeley, Berkeley, California, United States of America
- * E-mail:
| | - Lindsey A. Criswell
- Genomics of Autoimmune Rheumatic Disease Section, National Human Genome Research Institute, National Institute of Health, Bethesda, Maryland, United States of America
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Lanata CM, Nititham J, Taylor KE, Solomon O, Chung SA, Blazer A, Trupin L, Katz P, Dall'Era M, Yazdany J, Sirota M, Barcellos LF, Criswell LA. Dynamics of Methylation of CpG Sites Associated With Systemic Lupus Erythematosus Subtypes in a Longitudinal Cohort. Arthritis Rheumatol 2022; 74:1676-1686. [PMID: 35635730 PMCID: PMC9529797 DOI: 10.1002/art.42237] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 04/28/2022] [Accepted: 05/12/2022] [Indexed: 01/11/2023]
Abstract
OBJECTIVE Findings from cross-sectional studies have revealed associations between DNA methylation and systemic lupus erythematosus (SLE) outcomes. This study was undertaken to investigate the dynamics of DNA methylation by examining participants from an SLE longitudinal cohort using samples collected at 2 time points. METHODS A total of 101 participants from the California Lupus Epidemiology Study were included in our analysis. DNA was extracted from blood samples collected at the time of enrolment in the cohort and samples collected after 2 years and was analyzed using Illumina EPIC BeadChip kit. Paired t-tests were used to identify genome-wide changes which included 256 CpG sites previously found to be associated with SLE subtypes. Linear mixed models were developed to understand the relationship between DNA methylation and disease activity, medication use, and sample cell-type proportions, adjusted for age, sex, and genetic principal components. RESULTS The majority of CpGs that were previously determined to be associated with SLE subtypes remained stable over 2 years (185 CpGs [72.3%]; t-test false discovery rate >0.05). Compared to background genome-wide methylation, there was an enrichment of SLE subtype-associated CpGs that changed over time (27.7% versus 0.34%). Changes in cell-type proportions were associated with changes at 67 CpGs (P < 2.70 × 10-5 ), and 15 CpGs had at least 1 significant association with immunosuppressant use. CONCLUSION In this longitudinal SLE cohort, we identified a subset of SLE subtype-associated CpGs that remained stable over time and may be useful as biomarkers of disease subtypes. Another subset of SLE subtype-associated CpGs changed at a higher proportion compared to the genome-wide methylome. Additional studies are needed to understand the etiology and impact of these changes on methylation of SLE-associated CpGs.
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Affiliation(s)
| | - Joanne Nititham
- National Human Genome Research Institute, NIH, Bethesda, Maryland
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Adams C, Horton M, Solomon O, Wong M, Wu SL, Fuller S, Shao X, Fedrigo I, Quach HL, Quach DL, Meas M, Lopez L, Broughton A, Barcellos AL, Shim J, Seymens Y, Hernandez S, Montoya M, Johnson DM, Beckman KB, Busch MP, Coloma J, Lewnard JA, Harris E, Barcellos LF. Health inequities in SARS-CoV-2 infection, seroprevalence, and COVID-19 vaccination: Results from the East Bay COVID-19 study. PLOS Glob Public Health 2022; 2:e0000647. [PMID: 36962725 PMCID: PMC10022102 DOI: 10.1371/journal.pgph.0000647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 06/29/2022] [Indexed: 11/18/2022]
Abstract
Comprehensive data on transmission mitigation behaviors and both SARS-CoV-2 infection and serostatus are needed from large, community-based cohorts to identify COVID-19 risk factors and the impact of public health measures. We conducted a longitudinal, population-based study in the East Bay Area of Northern California. From July 2020-March 2021, approximately 5,500 adults were recruited and followed over three data collection rounds to investigate the association between geographic and demographic characteristics and transmission mitigation behavior with SARS-CoV-2 prevalence. We estimated the populated-adjusted prevalence of antibodies from SARS-CoV-2 infection and COVID-19 vaccination, and self-reported COVID-19 test positivity. Population-adjusted SARS-CoV-2 seroprevalence was low, increasing from 1.03% (95% CI: 0.50-1.96) in Round 1 (July-September 2020), to 1.37% (95% CI: 0.75-2.39) in Round 2 (October-December 2020), to 2.18% (95% CI: 1.48-3.17) in Round 3 (February-March 2021). Population-adjusted seroprevalence of COVID-19 vaccination was 21.64% (95% CI: 19.20-24.34) in Round 3, with White individuals having 4.35% (95% CI: 0.35-8.32) higher COVID-19 vaccine seroprevalence than individuals identifying as African American or Black, American Indian or Alaskan Native, Asian, Hispanic, two or more races, or other. No evidence for an association between transmission mitigation behavior and seroprevalence was observed. Despite >99% of participants reporting wearing masks individuals identifying as African American or Black, American Indian or Alaskan Native, Asian, Hispanic, two or more races, or other, as well as those in lower-income households, and lower-educated individuals had the highest SARS-CoV-2 seroprevalence and lowest vaccination seroprevalence. Results demonstrate that more effective policies are needed to address these disparities and inequities.
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Affiliation(s)
- Cameron Adams
- School of Public Health, University of California, Berkeley, California, United States of America
| | - Mary Horton
- School of Public Health, University of California, Berkeley, California, United States of America
| | - Olivia Solomon
- School of Public Health, University of California, Berkeley, California, United States of America
| | - Marcus Wong
- School of Public Health, University of California, Berkeley, California, United States of America
| | - Sean L Wu
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, Washington, United States of America
| | - Sophia Fuller
- School of Public Health, University of California, Berkeley, California, United States of America
| | - Xiaorong Shao
- School of Public Health, University of California, Berkeley, California, United States of America
| | - Indro Fedrigo
- School of Public Health, University of California, Berkeley, California, United States of America
| | - Hong L Quach
- School of Public Health, University of California, Berkeley, California, United States of America
| | - Diana L Quach
- School of Public Health, University of California, Berkeley, California, United States of America
| | - Michelle Meas
- School of Public Health, University of California, Berkeley, California, United States of America
| | - Luis Lopez
- School of Public Health, University of California, Berkeley, California, United States of America
| | - Abigail Broughton
- School of Public Health, University of California, Berkeley, California, United States of America
| | - Anna L Barcellos
- School of Public Health, University of California, Berkeley, California, United States of America
| | - Joan Shim
- School of Public Health, University of California, Berkeley, California, United States of America
| | - Yusef Seymens
- School of Public Health, University of California, Berkeley, California, United States of America
| | - Samantha Hernandez
- School of Public Health, University of California, Berkeley, California, United States of America
| | - Magelda Montoya
- School of Public Health, University of California, Berkeley, California, United States of America
| | - Darrell M Johnson
- University of Minnesota Genomics Center, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Kenneth B Beckman
- University of Minnesota Genomics Center, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Michael P Busch
- Vitalant Research Institute, San Francisco, California, United States of America
| | - Josefina Coloma
- School of Public Health, University of California, Berkeley, California, United States of America
| | - Joseph A Lewnard
- School of Public Health, University of California, Berkeley, California, United States of America
| | - Eva Harris
- School of Public Health, University of California, Berkeley, California, United States of America
| | - Lisa F Barcellos
- School of Public Health, University of California, Berkeley, California, United States of America
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7
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Solomon O, Huen K, Yousefi P, Küpers LK, González JR, Suderman M, Reese SE, Page CM, Gruzieva O, Rzehak P, Gao L, Bakulski KM, Novoloaca A, Allard C, Pappa I, Llambrich M, Vives M, Jima DD, Kvist T, Baccarelli A, White C, Rezwan FI, Sharp GC, Tindula G, Bergström A, Grote V, Dou JF, Isaevska E, Magnus MC, Corpeleijn E, Perron P, Jaddoe VWV, Nohr EA, Maitre L, Foraster M, Hoyo C, Håberg SE, Lahti J, DeMeo DL, Zhang H, Karmaus W, Kull I, Koletzko B, Feinberg JI, Gagliardi L, Bouchard L, Ramlau-Hansen CH, Tiemeier H, Santorelli G, Maguire RL, Czamara D, Litonjua AA, Langhendries JP, Plusquin M, Lepeule J, Binder EB, Verduci E, Dwyer T, Carracedo Á, Ferre N, Eskenazi B, Kogevinas M, Nawrot TS, Munthe-Kaas MC, Herceg Z, Relton C, Melén E, Gruszfeld D, Breton C, Fallin MD, Ghantous A, Nystad W, Heude B, Snieder H, Hivert MF, Felix JF, Sørensen TIA, Bustamante M, Murphy SK, Raikkönen K, Oken E, Holloway JW, Arshad SH, London SJ, Holland N. Meta-analysis of epigenome-wide association studies in newborns and children show widespread sex differences in blood DNA methylation. Mutat Res Rev Mutat Res 2022; 789:108415. [PMID: 35690418 PMCID: PMC9623595 DOI: 10.1016/j.mrrev.2022.108415] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 02/27/2022] [Accepted: 03/08/2022] [Indexed: 11/26/2022]
Abstract
BACKGROUND Among children, sex-specific differences in disease prevalence, age of onset, and susceptibility have been observed in health conditions including asthma, immune response, metabolic health, some pediatric and adult cancers, and psychiatric disorders. Epigenetic modifications such as DNA methylation may play a role in the sexual differences observed in diseases and other physiological traits. METHODS We performed a meta-analysis of the association of sex and cord blood DNA methylation at over 450,000 CpG sites in 8438 newborns from 17 cohorts participating in the Pregnancy And Childhood Epigenetics (PACE) Consortium. We also examined associations of child sex with DNA methylation in older children ages 5.5-10 years from 8 cohorts (n = 4268). RESULTS In newborn blood, sex was associated at Bonferroni level significance with differences in DNA methylation at 46,979 autosomal CpG sites (p < 1.3 × 10-7) after adjusting for white blood cell proportions and batch. Most of those sites had lower methylation levels in males than in females. Of the differentially methylated CpG sites identified in newborn blood, 68% (31,727) met look-up level significance (p < 1.1 × 10-6) in older children and had methylation differences in the same direction. CONCLUSIONS This is a large-scale meta-analysis examining sex differences in DNA methylation in newborns and older children. Expanding upon previous studies, we replicated previous findings and identified additional autosomal sites with sex-specific differences in DNA methylation. Differentially methylated sites were enriched in genes involved in cancer, psychiatric disorders, and cardiovascular phenotypes.
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Affiliation(s)
- Olivia Solomon
- Children's Environmental Health Laboratory, Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
| | - Karen Huen
- Children's Environmental Health Laboratory, Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA.
| | - Paul Yousefi
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK; MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, BS8 2BN, UK
| | - Leanne K Küpers
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands
| | - Juan R González
- ISGlobal, Barcelona Institute for Global Health, Dr Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Matthew Suderman
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, BS8 2BN, UK
| | - Sarah E Reese
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Christian M Page
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway; Oslo Centre for Biostatistics and Epidemiology, Oslo University Hospital, Oslo, Norway
| | - Olena Gruzieva
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Center for Occupational and Environmental Medicine, Region Stockholm, Sweden
| | - Peter Rzehak
- Div. Metabolic and Nutritional Medicine, Dept. Pediatrics, Dr. von Hauner Children's Hospital, Ludwig-Maximilians Universität München (LMU), Munich, Germany
| | - Lu Gao
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Kelly M Bakulski
- School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Catherine Allard
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, QC, Canada
| | - Irene Pappa
- Department of Child and Adolescent Psychiatry/ Psychology, Erasmus Medical Center, Sophia Children's Hospital, P.O. Box 2060, 3000 CB Rotterdam, The Netherlands; The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, P.O. Box 2060, 3000 CB Rotterdam, The Netherlands
| | - Maria Llambrich
- ISGlobal, Barcelona Institute for Global Health, Dr Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Marta Vives
- ISGlobal, Barcelona Institute for Global Health, Dr Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Dereje D Jima
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27606, USA; Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27606, USA
| | - Tuomas Kvist
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Finland
| | - Andrea Baccarelli
- Laboratory of Precision Environmental Biosciences, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Cory White
- Merck Exploratory Science Center, Merck Research Laboratories, Cambridge, MA 02141, USA
| | - Faisal I Rezwan
- Department of Computer Science, Aberystwyth University, Aberystwyth, Ceredigion, SY23 3DB, United Kingdom; Human Development and Health, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK
| | - Gemma C Sharp
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, BS8 2BN, UK
| | - Gwen Tindula
- Children's Environmental Health Laboratory, Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
| | - Anna Bergström
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Center for Occupational and Environmental Medicine, Region Stockholm, Sweden
| | - Veit Grote
- Div. Metabolic and Nutritional Medicine, Dept. Pediatrics, Dr. von Hauner Children's Hospital, Ludwig-Maximilians Universität München (LMU), Munich, Germany
| | - John F Dou
- School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Elena Isaevska
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Maria C Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Eva Corpeleijn
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands
| | - Patrice Perron
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, QC, Canada; Department of Medicine, Universite de Sherbrooke, QC, Canada
| | - Vincent W V Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, P.O. Box 2060, 3000 CB Rotterdam, The Netherlands; Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, P.O. Box 2060, 3000 CB Rotterdam, The Netherlands
| | - Ellen A Nohr
- Institute of Clinical Research, University of Southern Denmark, Odense, Denmark; Centre of Women's, Family and Child Health, University of South-Eastern Norway, Kongsberg, Norway
| | - Lea Maitre
- ISGlobal, Barcelona Institute for Global Health, Dr Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Maria Foraster
- ISGlobal, Barcelona Institute for Global Health, Dr Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; PHAGEX Research Group, Blanquerna School of Health Science, Universitat Ramon Llull, Barcelona, Spain
| | - Cathrine Hoyo
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27606, USA; Department of Biological Sciences, North Carolina State University, NC, USA
| | - Siri E Håberg
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Jari Lahti
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Finland
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, USA
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, USA
| | - Inger Kull
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden; Sachs' Children and Youth Hospital, Södersjukhuset, Stockholm, Sweden
| | - Berthold Koletzko
- Div. Metabolic and Nutritional Medicine, Dept. Pediatrics, Dr. von Hauner Children's Hospital, Ludwig-Maximilians Universität München (LMU), Munich, Germany
| | - Jason I Feinberg
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Luigi Gagliardi
- Department of Woman and Child Health, Ospedale Versilia, Azienda USL Toscana Nord Ovest, Viareggio, Italy
| | - Luigi Bouchard
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, QC, Canada; Department of Medical Biology, CIUSSS Saguenay-Lac-Saint-Jean, Chicoutimi Hospital, Saguenay, QC, Canada
| | | | - Henning Tiemeier
- Department of Child and Adolescent Psychiatry/ Psychology, Erasmus Medical Center, Sophia Children's Hospital, P.O. Box 2060, 3000 CB Rotterdam, The Netherlands; Department of Social and Behavioral Science, Harvard TH Chan School of Public Health, 677 Huntington Ave, Boston, MA, USA
| | - Gillian Santorelli
- Bradford Institute of Health Research, Bradford Royal Infirmary, Bradford BD9 6RJ, UK
| | - Rachel L Maguire
- Department of Biological Sciences, North Carolina State University, NC, USA; Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC 27701, USA
| | - Darina Czamara
- Dept. Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Augusto A Litonjua
- Division of Pediatric Pulmonology, Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA
| | | | - Michelle Plusquin
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Johanna Lepeule
- Univ. Grenoble Alpes, Inserm, CNRS, Team of Environmental Epidemiology Applied to Reproduction and Respiratory Health, IAB, 38000 Grenoble, France
| | - Elisabeth B Binder
- Dept. Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany; Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, USA
| | - Elvira Verduci
- Department of Pediatrics, Ospedale dei Bambini Vittore Buzzi, University of Milan, Milan, Italy; Department of Health Sciences, University of Milan, Milan, Italy
| | - Terence Dwyer
- Clinical Sciences, Heart Group, Murdoch Children's Research Institute, Melbourne, Australia; Department of Pediatrics, University of Melbourne, Melbourne, Australia; Nuffield Department of Women's & Reproductive Health, University of Oxford, Oxford, UK
| | - Ángel Carracedo
- Grupo de Medicina Xenómica, Fundación Pública Galega de Merdicina Xenómica, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), SERGAS, Santiago de Compostela, Spain; Centro de Investigación en Red de Enfermedades Raras (CIBERER) y Centro Nacional de Genotipado (CEGEN-PRB3), Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - Natalia Ferre
- Pediatric Nutrition and Human Development Research Unit, Universitat Rovira i Virgili, IISPV, Reus, Spain
| | - Brenda Eskenazi
- Center for Environmental Research and Children's Health, School of Public Health, University of California, Berkeley, CA, USA
| | - Manolis Kogevinas
- ISGlobal, Barcelona Institute for Global Health, Dr Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; IMIM (Hospital del Mar Medical Research Institute), Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Tim S Nawrot
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium; Department Public Health & Primary care, Leuven University, Belgium
| | - Monica C Munthe-Kaas
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway; Department of Pediatric Oncology and Hematology, Oslo University Hospital, Norway
| | - Zdenko Herceg
- International Agency for Research on Cancer, Lyon, France
| | - Caroline Relton
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, BS8 2BN, UK
| | - Erik Melén
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden; Sachs' Children and Youth Hospital, Södersjukhuset, Stockholm, Sweden
| | - Dariusz Gruszfeld
- Neonatal Department, Children's Memorial Health Institute, Warsaw, Poland
| | - Carrie Breton
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - M D Fallin
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Akram Ghantous
- International Agency for Research on Cancer, Lyon, France
| | - Wenche Nystad
- Department of Chronic Diseases and Ageing, Division of Mental and Physical Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Barbara Heude
- Université de Paris, Centre for Research in Epidemiology and Statistics (CRESS), INSERM, INRAE, F-75004 Paris, France
| | - Harold Snieder
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands
| | - Marie-France Hivert
- Department of Medicine, Universite de Sherbrooke, QC, Canada; Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA, USA; Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, P.O. Box 2060, 3000 CB Rotterdam, The Netherlands; Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, P.O. Box 2060, 3000 CB Rotterdam, The Netherlands
| | - Thorkild I A Sørensen
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK; MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, BS8 2BN, UK; Department of Public Health, Section of Epidemiology, University of Copenhagen, Copenhagen, Denmark; The Novo Nordisk Foundation Center for Basic Metabolic Research, Section on Metabolic Genetics, Faculty of Medical and Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mariona Bustamante
- ISGlobal, Barcelona Institute for Global Health, Dr Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Susan K Murphy
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC 27701, USA
| | - Katri Raikkönen
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Finland
| | - Emily Oken
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK; Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Syed Hasan Arshad
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK; David Hide Asthma and Allergy Research Centre, Isle of Wight, UK
| | - Stephanie J London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Nina Holland
- Children's Environmental Health Laboratory, Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
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8
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Ha Y, Ochoa LF, Solomon O, Shi S, Villarreal PP, Li S, Buscho S, Vargas G, Zhang W. Light-Sheet Microscopy of the Optic Nerve Reveals Axonal Degeneration and Microglial Activation in NMDA-Induced Retinal Injury. EC Ophthalmol 2021; 12:23-31. [PMID: 36108311 PMCID: PMC9450914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
PURPOSE Optic nerve degeneration is a feature of neurodegenerative eye diseases and causes irreversible vision loss. Therefore, understanding the degenerating patterns of the optic nerve is critical to find the potential therapeutic target for optic neuropathy. However, the traditional method of optic nerve degeneration has the limitations of losing spatiotemporal tissue information. Light sheet fluorescence microscopy (LSFM) is a fluorescence microscopy technique that allows capturing 3D images rapidly with a high spatial optical resolution. In this study, we evaluated the availability of LSFM on the optic nerve with NMDA injected Thy1-CFP mice. METHODS NMDA injected to both eyes of Thy1-CFP mice. After 7 days from the injection, the retina and optic nerve were collected and immunostained with anti-Iba1 antibody. NMDA excitotoxicity induced RGC, and its axon loss and microglial activation in the retina were observed using confocal microscopy. The immunostained optic nerve was completed the optical clearing process with TDE and mounted for LSFM imaging. RESULTS We found that retinal flatmounts confirmed significant loss of CFP-expressing RGC and axon degradation and loss in Thy1-CFP mice at 7 days after NMDA injection. Together with these data verifying that NMDA induces RGC and its axon loss, we confirmed that NMDA excitotoxicity induced microglia activation and leukostasis, such as increased microglia number, transform its morphology to ameboid or round, and increase in attached leukocytes in vessels. Using LSFM, we observed that CFP expressing nerve fiber was well organized and arranged parallel in vehicle treated optic nerve, whileas NMDA injected optic nerve showed axon swelling and fragmentation and loss of axon density from the anterior to the posterior regions. Furthermore, LSFM enabled the observation of microglia phenotype transformation in the entire optic nerve. Unlike microglia in vehicle injected optic nerve, microglia in NMDA injected optic nerve displayed larger soma and short process with high Iba1 expression through the entire optic nerve from the anterior to posterior. CONCLUSIONS In summary, we examined the applicability of the modified optic clearing protocol for the optic nerve and verified it enabled to acquiring of the 3D images of the optic nerve successfully revealing the complex spatial relationships between the axons, microglia and vasculature throughout the entire organ with single acquisitions. With these optimized techniques, we successfully obtained the high-resolution 3D images of NMDA-induced optic neuropathy, including the clues for optic nerve degeneration such as axon swelling, axonal fragmentation, and microglia activation. Overall, we believe that our current study could help understand the pathology of the optic nerve in neurodegenerative diseases, and it will be the basis for translational research.
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Affiliation(s)
- Yonju Ha
- Department of Ophthalmology and Visual Sciences, University of Texas Medical Branch, Galveston, Texas, USA
| | - Lorenzo F Ochoa
- Department of Neuroscience, Cell Biology and Anatomy, University of Texas Medical Branch, Galveston, Texas, USA
| | - Olivia Solomon
- Department of Neuroscience, Cell Biology and Anatomy, University of Texas Medical Branch, Galveston, Texas, USA
- Human Pathophysiology and Translational Medicine Graduate Program, University of Texas Medical Branch, Galveston, Texas, USA
| | - Shuizhen Shi
- Department of Ophthalmology and Visual Sciences, University of Texas Medical Branch, Galveston, Texas, USA
| | - Paula P Villarreal
- Department of Neuroscience, Cell Biology and Anatomy, University of Texas Medical Branch, Galveston, Texas, USA
| | - Shengguo Li
- Department of Ophthalmology and Visual Sciences, University of Texas Medical Branch, Galveston, Texas, USA
| | - Seth Buscho
- Department of Ophthalmology and Visual Sciences, University of Texas Medical Branch, Galveston, Texas, USA
| | - Gracie Vargas
- Department of Neuroscience, Cell Biology and Anatomy, University of Texas Medical Branch, Galveston, Texas, USA
| | - Wenbo Zhang
- Department of Ophthalmology and Visual Sciences, University of Texas Medical Branch, Galveston, Texas, USA
- Department of Neuroscience, Cell Biology and Anatomy, University of Texas Medical Branch, Galveston, Texas, USA
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Ferrarotto R, Rauch R, Leibovich T, Shitrit A, Solomon O, Herz E, Walker R, Ho A, Kaye J. 1789P The gamma secretase inhibitor AL101 combined with other drugs for dual targeting of Notch dysregulated tumors. Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.08.1732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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Solomon O, Macisaac JL, Tindula G, Kobor MS, Eskenazi B, Holland N. 5-Hydroxymethylcytosine in cord blood and associations of DNA methylation with sex in newborns. Mutagenesis 2020; 34:315-322. [PMID: 31587037 DOI: 10.1093/mutage/gez023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 08/20/2019] [Indexed: 11/14/2022] Open
Abstract
DNA methylation has been widely studied for associations with exposures and health outcomes. Both 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) are epigenetic marks that may function differently to impact gene expression; however, the most commonly used technology to assess methylation for population studies in blood use are the Illumina 450K and EPIC BeadChips, for which the traditional bisulfite conversion does not differentiate 5mC and 5hmC marks. We used a modified protocol originally developed by Stewart et al. to analyse oxidative bisulfite-converted and conventional bisulfite-converted DNA for the same subject in parallel by the EPIC chip, allowing us to isolate the two measures. We measured 5mC and 5hmC in cord blood of 41 newborn participants of the Center for Health Assessment of Mothers and Children of Salinas (CHAMACOS) birth cohort and investigated differential methylation of 5mC + 5hmC, isolated 5mC and isolated 5hmC with sex at birth as an example of a biological variable previously associated with DNA methylation. Results showed low levels of 5hmC throughout the epigenome in the cord blood samples in comparison to 5mC. The concordance of autosomal hits between 5mC + 5hmC and exclusive 5mC analyses were low (25%); however, overlap was larger with increased effect size difference. There were 43 autosomal cytosine nucleotide followed by a guanine nucleotide (CpG) sites where 5hmC was associated with sex, 21 of which were unique to 5hmC after adjustment for cell composition. 5hmC only accounts for a small portion of overall methylation in cord blood; however, it has the potential to impact interpretation of combined 5hmC + 5mC studies in cord blood, especially given that effect sizes of differential methylation analyses are often small. Several significant CpG sites were unique to 5hmC, suggesting some functions distinct from 5mC. More studies of genome-wide 5hmC in children are warranted.
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Affiliation(s)
- Olivia Solomon
- School of Public Health, Center for Environmental Research and Children's Health (CERCH), University of California, Berkeley, Berkeley, CA, USA
| | - Julia L Macisaac
- University of British Columbia, BC Children's Hospital Research, Vancouver, BC, Canada
| | - Gwen Tindula
- School of Public Health, Center for Environmental Research and Children's Health (CERCH), University of California, Berkeley, Berkeley, CA, USA
| | - Michael S Kobor
- University of British Columbia, BC Children's Hospital Research, Vancouver, BC, Canada
| | - Brenda Eskenazi
- School of Public Health, Center for Environmental Research and Children's Health (CERCH), University of California, Berkeley, Berkeley, CA, USA
| | - Nina Holland
- School of Public Health, Center for Environmental Research and Children's Health (CERCH), University of California, Berkeley, Berkeley, CA, USA
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11
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Merid SK, Novoloaca A, Sharp GC, Küpers LK, Kho AT, Roy R, Gao L, Annesi-Maesano I, Jain P, Plusquin M, Kogevinas M, Allard C, Vehmeijer FO, Kazmi N, Salas LA, Rezwan FI, Zhang H, Sebert S, Czamara D, Rifas-Shiman SL, Melton PE, Lawlor DA, Pershagen G, Breton CV, Huen K, Baiz N, Gagliardi L, Nawrot TS, Corpeleijn E, Perron P, Duijts L, Nohr EA, Bustamante M, Ewart SL, Karmaus W, Zhao S, Page CM, Herceg Z, Jarvelin MR, Lahti J, Baccarelli AA, Anderson D, Kachroo P, Relton CL, Bergström A, Eskenazi B, Soomro MH, Vineis P, Snieder H, Bouchard L, Jaddoe VW, Sørensen TIA, Vrijheid M, Arshad SH, Holloway JW, Håberg SE, Magnus P, Dwyer T, Binder EB, DeMeo DL, Vonk JM, Newnham J, Tantisira KG, Kull I, Wiemels JL, Heude B, Sunyer J, Nystad W, Munthe-Kaas MC, Räikkönen K, Oken E, Huang RC, Weiss ST, Antó JM, Bousquet J, Kumar A, Söderhäll C, Almqvist C, Cardenas A, Gruzieva O, Xu CJ, Reese SE, Kere J, Brodin P, Solomon O, Wielscher M, Holland N, Ghantous A, Hivert MF, Felix JF, Koppelman GH, London SJ, Melén E. Epigenome-wide meta-analysis of blood DNA methylation in newborns and children identifies numerous loci related to gestational age. Genome Med 2020; 12:25. [PMID: 32114984 PMCID: PMC7050134 DOI: 10.1186/s13073-020-0716-9] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 01/30/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Preterm birth and shorter duration of pregnancy are associated with increased morbidity in neonatal and later life. As the epigenome is known to have an important role during fetal development, we investigated associations between gestational age and blood DNA methylation in children. METHODS We performed meta-analysis of Illumina's HumanMethylation450-array associations between gestational age and cord blood DNA methylation in 3648 newborns from 17 cohorts without common pregnancy complications, induced delivery or caesarean section. We also explored associations of gestational age with DNA methylation measured at 4-18 years in additional pediatric cohorts. Follow-up analyses of DNA methylation and gene expression correlations were performed in cord blood. DNA methylation profiles were also explored in tissues relevant for gestational age health effects: fetal brain and lung. RESULTS We identified 8899 CpGs in cord blood that were associated with gestational age (range 27-42 weeks), at Bonferroni significance, P < 1.06 × 10- 7, of which 3343 were novel. These were annotated to 4966 genes. After restricting findings to at least three significant adjacent CpGs, we identified 1276 CpGs annotated to 325 genes. Results were generally consistent when analyses were restricted to term births. Cord blood findings tended not to persist into childhood and adolescence. Pathway analyses identified enrichment for biological processes critical to embryonic development. Follow-up of identified genes showed correlations between gestational age and DNA methylation levels in fetal brain and lung tissue, as well as correlation with expression levels. CONCLUSIONS We identified numerous CpGs differentially methylated in relation to gestational age at birth that appear to reflect fetal developmental processes across tissues. These findings may contribute to understanding mechanisms linking gestational age to health effects.
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Affiliation(s)
- Simon Kebede Merid
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Sciences and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - Alexei Novoloaca
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Gemma C Sharp
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Leanne K Küpers
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Division of Human Nutrition and Health, Wageningen University & Research, Wageningen, the Netherlands
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Alvin T Kho
- Computational Health Informatics Program, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Ritu Roy
- Computational Biology And Informatics, University of California, San Francisco, San Francisco, CA, USA
- HDF Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Lu Gao
- Department of Preventive Medicine, University of Southern California, Los Angeles, USA
| | - Isabella Annesi-Maesano
- Sorbonne Université and INSERM, Epidemiology of Allergic and Respiratory Diseases Department (EPAR), Pierre Louis Institute of Epidemiology and Public Health (IPLESP UMRS 1136), Saint-Antoine Medical School, Paris, France
| | - Pooja Jain
- NIHR-Health Protection Research Unit, Respiratory Infections and Immunity, Imperial College London, London, UK
- Department of Epidemiology and Biostatistics, The School of Public Health, Imperial College London, London, UK
| | - Michelle Plusquin
- NIHR-Health Protection Research Unit, Respiratory Infections and Immunity, Imperial College London, London, UK
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Manolis Kogevinas
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Catherine Allard
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CHUS), Sherbrooke, QC, Canada
| | - Florianne O Vehmeijer
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Nabila Kazmi
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Lucas A Salas
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, USA
| | - Faisal I Rezwan
- School of Water, Energy and Environment, Cranfield University, Cranfield, Bedfordshire, MK43 0AL, UK
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, USA
| | - Sylvain Sebert
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Department of Genomic of Complex diseases, School of Public Health, Imperial College London, London, UK
| | - Darina Czamara
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Sheryl L Rifas-Shiman
- Division of Chronic Disease Research Across the Lifecourse (CoRAL), Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Phillip E Melton
- School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin University, Bentley, Australia
- Curtin/UWA Centre for Genetic Origins of Health and Disease, School of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Western Australia, Perth, Australia
| | - Debbie A Lawlor
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Bristol NIHR Biomedical Research Centre, Bristol, UK
| | - Göran Pershagen
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Centre for Occupational and Environmental Medicine, Stockholm, Stockholm Region, Sweden
| | - Carrie V Breton
- Department of Preventive Medicine, University of Southern California, Los Angeles, USA
| | - Karen Huen
- Children's Environmental Health Laboratory, University of California, Berkeley, Berkeley, CA, USA
| | - Nour Baiz
- Sorbonne Université and INSERM, Epidemiology of Allergic and Respiratory Diseases Department (EPAR), Pierre Louis Institute of Epidemiology and Public Health (IPLESP UMRS 1136), Saint-Antoine Medical School, Paris, France
| | - Luigi Gagliardi
- Division of Neonatology and Pediatrics, Ospedale Versilia, Viareggio, AUSL Toscana Nord Ovest, Pisa, Italy
| | - Tim S Nawrot
- NIHR-Health Protection Research Unit, Respiratory Infections and Immunity, Imperial College London, London, UK
- Department of Public Health & Primary Care, Leuven University, Leuven, Belgium
| | - Eva Corpeleijn
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Patrice Perron
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CHUS), Sherbrooke, QC, Canada
- Department of Medicine, Université de Sherbrooke, Sherbrooke, Canada
| | - Liesbeth Duijts
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Ellen Aagaard Nohr
- Research Unit for Gynaecology and Obstetrics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Mariona Bustamante
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Susan L Ewart
- College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, USA
| | - Shanshan Zhao
- Department of Health and Human Services, National Institute of Environmental Health Sciences, National Institutes of Health, RTP, Durham, NC, USA
| | | | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Marjo-Riitta Jarvelin
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, UK
- Unit of Primary Care, Oulu University Hospital, Oulu, Finland
| | - Jari Lahti
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Turku Institute for Advanced Studies, University of Turku, Turku, Finland
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University Medical Center, New York, NY, USA
| | - Denise Anderson
- Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Priyadarshini Kachroo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Bristol NIHR Biomedical Research Centre, Bristol, UK
| | - Anna Bergström
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Centre for Occupational and Environmental Medicine, Stockholm, Stockholm Region, Sweden
| | - Brenda Eskenazi
- Center for Environmental Research and Children's Health (CERCH), University of California, Berkeley, Berkeley, CA, USA
| | - Munawar Hussain Soomro
- Sorbonne Université and INSERM, Epidemiology of Allergic and Respiratory Diseases Department (EPAR), Pierre Louis Institute of Epidemiology and Public Health (IPLESP UMRS 1136), Saint-Antoine Medical School, Paris, France
| | - Paolo Vineis
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Luigi Bouchard
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CHUS), Sherbrooke, QC, Canada
- Department of Biochemistry, Université de Sherbrooke, Sherbrooke, QC, Canada
- Department of medical biology, CIUSSS-SLSJ, Saguenay, QC, Canada
| | - Vincent W Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Thorkild I A Sørensen
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section on Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Public Health, Section of Epidemiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Martine Vrijheid
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - S Hasan Arshad
- Clinical & Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- The David Hide Asthma and Allergy Research Centre, Newport, Isle of Wight, UK
| | - John W Holloway
- Human Development & Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | | | - Per Magnus
- Norwegian Institute of Public Health, Oslo, Norway
| | - Terence Dwyer
- Nuffield Department of Women's and Reproductive Health, University of Oxford, Oxford, UK
- Murdoch Children's Research Institute, Australia Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia
| | - Elisabeth B Binder
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, USA
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Judith M Vonk
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
| | - John Newnham
- Faculty of Health and Medical Sciences, UWA Medical School, University of Western Australia, Perth, Australia
| | - Kelan G Tantisira
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Inger Kull
- Department of Clinical Sciences and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
- Sachs' Children's Hospital, Södersjukhuset, 118 83, Stockholm, Sweden
| | - Joseph L Wiemels
- Center for Genetic Epidemiology, University of Southern California, Los Angeles, USA
| | - Barbara Heude
- INSERM, UMR1153 Epidemiology and Biostatistics Sorbonne Paris Cité Center (CRESS), Research Team on Early life Origins of Health (EarOH), Paris Descartes University, Paris, France
| | - Jordi Sunyer
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | | | - Monica C Munthe-Kaas
- Norwegian Institute of Public Health, Oslo, Norway
- Department of Pediatric Oncology and Hematology, Oslo University Hospital, Oslo, Norway
| | | | - Emily Oken
- Division of Chronic Disease Research Across the Lifecourse (CoRAL), Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Rae-Chi Huang
- Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Scott T Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Josep Maria Antó
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Jean Bousquet
- University Hospital, Montpellier, France
- Department of Dermatology, Charité, Berlin, Germany
| | - Ashish Kumar
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- University of Basel, Basel, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Cilla Söderhäll
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Catarina Almqvist
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Pediatric Allergy and Pulmonology Unit at Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Andres Cardenas
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Olena Gruzieva
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Centre for Occupational and Environmental Medicine, Stockholm, Stockholm Region, Sweden
| | - Cheng-Jian Xu
- University of Groningen, University Medical Center Groningen, Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, GRIAC Research Institute Groningen, Groningen, The Netherlands
| | - Sarah E Reese
- Department of Health and Human Services, National Institute of Environmental Health Sciences, National Institutes of Health, RTP, Durham, NC, USA
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- Folkhälsa Research Institute, Helsinki, and Stem Cells and Metabolism Research Program, University of Helsinki Finland, Helsinki, Finland
| | - Petter Brodin
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
- Department of Newborn Medicine, Karolinska University Hospital, Stockholm, Sweden
- Science for Life Laboratory, Stockholm, Sweden
| | - Olivia Solomon
- Children's Environmental Health Laboratory, University of California, Berkeley, Berkeley, CA, USA
| | - Matthias Wielscher
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, UK
| | - Nina Holland
- Children's Environmental Health Laboratory, University of California, Berkeley, Berkeley, CA, USA
| | - Akram Ghantous
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Marie-France Hivert
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CHUS), Sherbrooke, QC, Canada
- Division of Chronic Disease Research Across the Lifecourse (CoRAL), Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Gerard H Koppelman
- University of Groningen, University Medical Center Groningen, Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, GRIAC Research Institute Groningen, Groningen, The Netherlands
| | - Stephanie J London
- Department of Health and Human Services, National Institute of Environmental Health Sciences, National Institutes of Health, RTP, Durham, NC, USA
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.
- Department of Clinical Sciences and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden.
- Sachs' Children's Hospital, South General Hospital, Stockholm, Sweden.
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Küpers LK, Monnereau C, Sharp GC, Yousefi P, Salas LA, Ghantous A, Page CM, Reese SE, Wilcox AJ, Czamara D, Starling AP, Novoloaca A, Lent S, Roy R, Hoyo C, Breton CV, Allard C, Just AC, Bakulski KM, Holloway JW, Everson TM, Xu CJ, Huang RC, van der Plaat DA, Wielscher M, Merid SK, Ullemar V, Rezwan FI, Lahti J, van Dongen J, Langie SAS, Richardson TG, Magnus MC, Nohr EA, Xu Z, Duijts L, Zhao S, Zhang W, Plusquin M, DeMeo DL, Solomon O, Heimovaara JH, Jima DD, Gao L, Bustamante M, Perron P, Wright RO, Hertz-Picciotto I, Zhang H, Karagas MR, Gehring U, Marsit CJ, Beilin LJ, Vonk JM, Jarvelin MR, Bergström A, Örtqvist AK, Ewart S, Villa PM, Moore SE, Willemsen G, Standaert ARL, Håberg SE, Sørensen TIA, Taylor JA, Räikkönen K, Yang IV, Kechris K, Nawrot TS, Silver MJ, Gong YY, Richiardi L, Kogevinas M, Litonjua AA, Eskenazi B, Huen K, Mbarek H, Maguire RL, Dwyer T, Vrijheid M, Bouchard L, Baccarelli AA, Croen LA, Karmaus W, Anderson D, de Vries M, Sebert S, Kere J, Karlsson R, Arshad SH, Hämäläinen E, Routledge MN, Boomsma DI, Feinberg AP, Newschaffer CJ, Govarts E, Moisse M, Fallin MD, Melén E, Prentice AM, Kajantie E, Almqvist C, Oken E, Dabelea D, Boezen HM, Melton PE, Wright RJ, Koppelman GH, Trevisi L, Hivert MF, Sunyer J, Munthe-Kaas MC, Murphy SK, Corpeleijn E, Wiemels J, Holland N, Herceg Z, Binder EB, Davey Smith G, Jaddoe VWV, Lie RT, Nystad W, London SJ, Lawlor DA, Relton CL, Snieder H, Felix JF. Meta-analysis of epigenome-wide association studies in neonates reveals widespread differential DNA methylation associated with birthweight. Nat Commun 2019; 10:1893. [PMID: 31015461 PMCID: PMC6478731 DOI: 10.1038/s41467-019-09671-3] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 02/18/2019] [Indexed: 12/16/2022] Open
Abstract
Birthweight is associated with health outcomes across the life course, DNA methylation may be an underlying mechanism. In this meta-analysis of epigenome-wide association studies of 8,825 neonates from 24 birth cohorts in the Pregnancy And Childhood Epigenetics Consortium, we find that DNA methylation in neonatal blood is associated with birthweight at 914 sites, with a difference in birthweight ranging from -183 to 178 grams per 10% increase in methylation (PBonferroni < 1.06 x 10-7). In additional analyses in 7,278 participants, <1.3% of birthweight-associated differential methylation is also observed in childhood and adolescence, but not adulthood. Birthweight-related CpGs overlap with some Bonferroni-significant CpGs that were previously reported to be related to maternal smoking (55/914, p = 6.12 x 10-74) and BMI in pregnancy (3/914, p = 1.13x10-3), but not with those related to folate levels in pregnancy. Whether the associations that we observe are causal or explained by confounding or fetal growth influencing DNA methylation (i.e. reverse causality) requires further research.
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Affiliation(s)
- Leanne K Küpers
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands
- Division of Human Nutrition and Health, Wageningen University, Wageningen, The Netherlands
| | - Claire Monnereau
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Gemma C Sharp
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- School of Oral and Dental Sciences, University of Bristol, Bristol, UK
| | - Paul Yousefi
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Children's Environmental Health Laboratory, Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
| | - Lucas A Salas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA
- ISGlobal, Bacelona Institute for Global Health, Barcelona, Spain
| | - Akram Ghantous
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Christian M Page
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Oslo Centre for Biostatisitcs and Epidemology, Oslo University Hospital, Oslo, Norway
| | - Sarah E Reese
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Service, Research Triangle Park, Durham, NC, USA
| | - Allen J Wilcox
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Service, Research Triangle Park, Durham, NC, USA
| | - Darina Czamara
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Anne P Starling
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Alexei Novoloaca
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Samantha Lent
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Ritu Roy
- HDF Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Computational Biology and Informatics, UCSF, San Francisco, CA, USA
| | - Cathrine Hoyo
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
| | - Carrie V Breton
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Catherine Allard
- Centre de recherche du Centre hospitalier universitaire de Sherbrooke, Sherbrooke, QC, Canada
| | - Allan C Just
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kelly M Bakulski
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - John W Holloway
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK
| | - Todd M Everson
- Department of Environmental Health, Rollins School of Public Health at Emory University, Atlanta, GA, USA
| | - Cheng-Jian Xu
- University of Groningen, University Medical Center Groningen, Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Rae-Chi Huang
- Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Diana A van der Plaat
- University of Groningen, University Medical Center Groningen, Department of Epidemiology and Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
| | - Matthias Wielscher
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, UK
| | - Simon Kebede Merid
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Vilhelmina Ullemar
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Faisal I Rezwan
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK
| | - Jari Lahti
- Helsinki Collegium for Advanced Studies, University of Helsinki, Helsinki, Finland
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jenny van Dongen
- Department of Biological Psychology, Netherlands Twin Register, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Sabine A S Langie
- VITO - Health, Mol, Belgium
- Theoretical Physics, Faculty of Sciences, Hasselt University, Hasselt, Belgium
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Tom G Richardson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Maria C Magnus
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Ellen A Nohr
- Research Unit for Gynaecology and Obstetrics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Zongli Xu
- Department of Pediatrics, Division of Respiratory Medicine and Allergology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Liesbeth Duijts
- Division of Human Nutrition and Health, Wageningen University, Wageningen, The Netherlands
- Department of Pediatrics, Division of Respiratory Medicine and Allergology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Division of Neonatology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Shanshan Zhao
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, Durham, NC, USA
| | - Weiming Zhang
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Michelle Plusquin
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
- MRC/PHE Centre for Environment and Health School of Public Health Imperial College London, St Mary's Campus, Norfolk Place, London, UK
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Olivia Solomon
- School of Oral and Dental Sciences, University of Bristol, Bristol, UK
| | - Joosje H Heimovaara
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands
| | - Dereje D Jima
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Lu Gao
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Mariona Bustamante
- ISGlobal, Bacelona Institute for Global Health, Barcelona, Spain
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Patrice Perron
- Centre de recherche du Centre hospitalier universitaire de Sherbrooke, Sherbrooke, QC, Canada
- Department of Medicine, Universite de Sherbrooke, Sherbrooke, QC, Canada
| | - Robert O Wright
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Irva Hertz-Picciotto
- Department of Public Health Sciences, School of Medicine, University of California Davis MIND Institute, Sacramento, CA, USA
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Margaret R Karagas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA
- Children's Environmental Health & Disease Prevention Research Center at Dartmouth, Hanover, NH, USA
| | - Ulrike Gehring
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
| | - Carmen J Marsit
- Department of Environmental Health, Rollins School of Public Health at Emory University, Atlanta, GA, USA
| | | | - Judith M Vonk
- University of Groningen, University Medical Center Groningen, Department of Epidemiology and Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, UK
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, 90014, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Unit of Primary Care, Oulu University Hospital, Oulu, Finland
| | - Anna Bergström
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Center for Occupational and Environmental Medicine, Stockholm County Council, Stockholm, Sweden
| | - Anne K Örtqvist
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Susan Ewart
- College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
| | - Pia M Villa
- Obstetrics and Gynaecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Sophie E Moore
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, UK
- Department of Women and Children's Health, King's College London, London, UK
| | - Gonneke Willemsen
- Department of Biological Psychology, Netherlands Twin Register, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | | | - Siri E Håberg
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Thorkild I A Sørensen
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Public Health, Section of Epidemiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jack A Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Service, Research Triangle Park, Durham, NC, USA
| | - Katri Räikkönen
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Ivana V Yang
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Katerina Kechris
- Department of Pediatrics, Division of Neonatology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Tim S Nawrot
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
- Department of Public Health & Primary Care, Leuven University, Leuven, Belgium
| | - Matt J Silver
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, UK
| | - Yun Yun Gong
- School of Food Sciences and Nutrition, University of Leeds, Leeds, UK
| | - Lorenzo Richiardi
- Department of Medical Sciences, University of Turin, Turin, Italy
- AOU Citta della Salute e della Sceinza, CPO Piemonte, Turin, Italy
| | - Manolis Kogevinas
- ISGlobal, Bacelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Augusto A Litonjua
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Brenda Eskenazi
- Children's Environmental Health Laboratory, Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
- Center for Environmental Research and Children's Health, School of Public Health, University of California, Berkeley, CA, USA
| | - Karen Huen
- Children's Environmental Health Laboratory, Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
| | - Hamdi Mbarek
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Rachel L Maguire
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Department of Community and Family Medicine, Duke University Medical Center, Raleigh, NC, USA
| | - Terence Dwyer
- The George Institute for Global Health, Nuffield Department of Women's & Reproductive Health, University of Oxford, Oxford, UK
| | - Martine Vrijheid
- ISGlobal, Bacelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Luigi Bouchard
- Department of Biochemistry, Université de Sherbrooke, Sherbrooke, QC, Canada
- ECOGENE-21 Biocluster, Chicoutimi Hospital, Saguenay, QC, Canada
| | - Andrea A Baccarelli
- Laboratory of Precision Environmental Biosciences, Columbia University Mailman School of Public Health, New York, NY, USA
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Lisa A Croen
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Denise Anderson
- Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Maaike de Vries
- University of Groningen, University Medical Center Groningen, Department of Epidemiology and Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
| | - Sylvain Sebert
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, 90014, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Department for Genomics of Common Diseases, School of Public Health, Imperial College London, London, UK
| | - Juha Kere
- Folkhälsan Institute of Genetics, Helsinki, and Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- School of Basic and Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Robert Karlsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Syed Hasan Arshad
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- David Hide Asthma and Allergy Research Centre, Isle of Wight, UK
| | - Esa Hämäläinen
- HUSLAB and the Department of Clinical Chemistry, University of Helsinki, Helsinki, Finland
| | | | - Dorret I Boomsma
- Department of Biological Psychology, Netherlands Twin Register, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MA, USA
| | | | | | - Matthieu Moisse
- KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), Leuven, Belgium
- VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, Leuven, Belgium
| | - M Daniele Fallin
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Sachs' Children's Hospital, Stockholm, Sweden
| | - Andrew M Prentice
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, UK
| | - Eero Kajantie
- National Institute for Health and Welfare, Helsinki and Oulu, Oulu, Finland
- Hospital for Children and Adolescents, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
- PEDEGO Research Unit, MRC Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Catarina Almqvist
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Pediatric Allergy and Pulmonology Unit at Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Emily Oken
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Dana Dabelea
- Department of Epidemiology, Colorado School of Public Health, and Department of Pediatrics, University of Colorado School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - H Marike Boezen
- University of Groningen, University Medical Center Groningen, Department of Epidemiology and Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
| | - Phillip E Melton
- Centre for Genetic Origins of Health and Disease, School of Biomedical Sciences, University of Western Australia, Perth, Australia
- School of Pharmacy and Biomedical Sciences, Curtin University, Perth, Australia
| | - Rosalind J Wright
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gerard H Koppelman
- University of Groningen, University Medical Center Groningen, Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands
| | - Letizia Trevisi
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA
| | - Marie-France Hivert
- Department of Medicine, Universite de Sherbrooke, Sherbrooke, QC, Canada
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Jordi Sunyer
- ISGlobal, Bacelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Monica C Munthe-Kaas
- Norwegian Institute of Public Health, Oslo, Norway
- Department of Pediatric Oncology and Hematology, Oslo University Hospital, Oslo, Norway
| | - Susan K Murphy
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, USA
| | - Eva Corpeleijn
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands
| | - Joseph Wiemels
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Nina Holland
- Children's Environmental Health Laboratory, Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Elisabeth B Binder
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Altanta, GA, USA
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Vincent W V Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Rolv T Lie
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Wenche Nystad
- Department for Non-Communicable Diseases, Norwegian Institute for Public Health, Oslo, Norway
| | - Stephanie J London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Service, Research Triangle Park, Durham, NC, USA
| | - Debbie A Lawlor
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.
| | - Harold Snieder
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands.
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.
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Mouton M, Boulton A, Solomon O, Rock MJ. 'When the dog bites': What can we learn about health geography from newspaper coverage in a 'model city' for dog-bite prevention? Health Place 2019; 57:70-73. [PMID: 30999259 DOI: 10.1016/j.healthplace.2019.03.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 01/29/2019] [Accepted: 03/25/2019] [Indexed: 11/28/2022]
Abstract
Despite calls for the adoption of 'One-Health' approaches, dog-bite injuries remain neglected in healthcare and public health, and our study may help to understand why. Media coverage can influence policy directions, including policies that address dogs. We collected articles (n = 65) published in two local newspapers, 2012-2017, then carried out an ethnographically-informed discourse analysis of the dog-bite reports. The newspapers portrayed dog-bites mainly as matters of public disorder, as opposed to priorities for healthcare and public health. Even as our study took place in a city that has shown dog-bite reductions without recourse to 'breed bans' or restrictions (i.e., breed-specific legislation), journalists still tended to emphasize dog breed as a narrative element in explaining dog-bite incidents. Nonetheless, the news coverage did not reproduce a 'nature versus nurture' dichotomy. Rather, the journalists presented dog breed, and presumably associated aggressive behaviour, as entanglements with social, economic, and cultural contexts. Meanwhile, the news stories reduced contextual complexity to geographic locations, as codes for community reputation, in attributing causality and morality.
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Affiliation(s)
- M Mouton
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Canada.
| | - A Boulton
- Faculty of Social Work, University of Calgary, Canada
| | - O Solomon
- University of Southern California University Center for Excellence in Developmental Disabilities at Children's Hospital Los Angeles, USA; Department of Pediatrics, Keck School of Medicine, University of Southern California, USA
| | - M J Rock
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Canada; Faculty of Social Work, University of Calgary, Canada
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Huen K, Solomon O, Kogut K, Eskenazi B, Holland N. PON1 DNA methylation and neurobehavior in Mexican-American children with prenatal organophosphate exposure. Environ Int 2018; 121:31-40. [PMID: 30172926 PMCID: PMC6242297 DOI: 10.1016/j.envint.2018.08.044] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 08/17/2018] [Accepted: 08/18/2018] [Indexed: 06/08/2023]
Abstract
PON1 is a multifunctional enzyme involved in oxidative stress and detoxification of some organophosphate (OP) pesticides. It has been associated with nervous system diseases like Alzheimer's disease, amyotrophic lateral sclerosis, Parkinson's disease, and autism. We previously found that PON1 susceptible genotypes were associated with lower IQ scores in children. Epigenetic marks, such as DNA methylation, can regulate gene expression. Yet, data on whether DNA methylation may influence the relationship between PON1 levels and neurobehavior are limited. In this study, we used Illumina 450K and EPIC BeadChip arrays to assess PON1 DNA methylation in blood specimens collected from children (n = 238) at birth (cord blood) and age 7 years and examined their relationship with cognitive outcomes. The Wechsler Intelligence Scale for Children was used to assess Full Scale IQ and four composite measures (Verbal Comprehension, Perceptual Reasoning, Working Memory, and Processing Speed Indexes) in 7-year-old children. We observed a consistent yet nonsignificant inverse relationship of methylation at several CpG sites close to the PON1 transcription start site with Full Scale IQ and other composite measures of cognition. We also found an inverse relationship between cord blood methylation at cg15887283 with working memory and a positive association of 7-year-old methylation at cg22798737 with processing speed, independent of OP exposure. However, none of the associations remained significant after accounting for multiple comparisons. This study provides some evidence of the role DNA methylation may play in the known relationship between PON1 and neurobehavior in children, however it appears to be only suggestive and warrants additional research.
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Affiliation(s)
- Karen Huen
- Children's Environmental Health Laboratory, Global Berkeley Campus, 1301 S. 46th Street, Bldg 112, Richmond, CA 94804, USA.
| | - Olivia Solomon
- Children's Environmental Health Laboratory, Global Berkeley Campus, 1301 S. 46th Street, Bldg 112, Richmond, CA 94804, USA
| | - Katherine Kogut
- Center for Children's Environmental Health, School of Public Health, University of California, Berkeley, 1995 University Avenue Suite 265, Berkeley, CA 94720, USA
| | - Brenda Eskenazi
- Center for Children's Environmental Health, School of Public Health, University of California, Berkeley, 1995 University Avenue Suite 265, Berkeley, CA 94720, USA
| | - Nina Holland
- Children's Environmental Health Laboratory, Global Berkeley Campus, 1301 S. 46th Street, Bldg 112, Richmond, CA 94804, USA
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Solomon O, MacIsaac J, Quach H, Tindula G, Kobor MS, Huen K, Meaney MJ, Eskenazi B, Barcellos LF, Holland N. Comparison of DNA methylation measured by Illumina 450K and EPIC BeadChips in blood of newborns and 14-year-old children. Epigenetics 2018; 13:655-664. [PMID: 30044683 PMCID: PMC6140901 DOI: 10.1080/15592294.2018.1497386] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Analysis of DNA methylation helps to understand the effects of environmental exposures as well as the role of epigenetics in human health. Illumina, Inc. recently replaced the HumanMethylation450 BeadChip (450K) with the EPIC BeadChip, which nearly doubles the measured CpG sites to >850,000. Although the new chip uses the same underlying technology, it is important to establish if data between the two platforms are comparable within cohorts and for meta-analyses. DNA methylation was assessed by 450K and EPIC using whole blood from newborn (n = 109) and 14-year-old (n = 86) participants of the Center for the Health Assessment of Mothers and Children of Salinas. The overall per-sample correlations were very high (r >0.99), although many individual CpG sites, especially those with low variance of methylation, had lower correlations (median r = 0.24). There was also a small subset of CpGs with large mean methylation β-value differences between platforms, in both the newborn and 14-year datasets. However, estimates of cell type proportion prediction by 450K and EPIC were highly correlated at both ages. Finally, differentially methylated positions between boys and girls replicated very well by both platforms in newborns and older children. These findings are encouraging for application of combined data from EPIC and 450K platforms for birth cohorts and other population studies. These data in children corroborate recent comparisons of the two BeadChips in adults and in cancer cell lines. However, researchers should be cautious when characterizing individual CpG sites and consider independent methods for validation of significant hits.
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Affiliation(s)
- Olivia Solomon
- a School of Public Health, Center for Environmental Research and Children's Health (CERCH) , University of California, Berkeley , Berkeley , CA , USA
| | - Julie MacIsaac
- b BC Children's Hospital Research , University of British Columbia , Vancouver , Canada
| | - Hong Quach
- c Genetic Epidemiology and Genomics Laboratory, School of Public Health , University of California, Berkeley , Berkeley , CA , USA
| | - Gwen Tindula
- a School of Public Health, Center for Environmental Research and Children's Health (CERCH) , University of California, Berkeley , Berkeley , CA , USA
| | - Michael S Kobor
- b BC Children's Hospital Research , University of British Columbia , Vancouver , Canada
| | - Karen Huen
- a School of Public Health, Center for Environmental Research and Children's Health (CERCH) , University of California, Berkeley , Berkeley , CA , USA
| | - Michael J Meaney
- d Ludmer Centre for Neuroinformatics & Mental Health, Douglas University Mental Health Research Institute , McGill University , Montreal , Canada
| | - Brenda Eskenazi
- a School of Public Health, Center for Environmental Research and Children's Health (CERCH) , University of California, Berkeley , Berkeley , CA , USA
| | - Lisa F Barcellos
- c Genetic Epidemiology and Genomics Laboratory, School of Public Health , University of California, Berkeley , Berkeley , CA , USA
| | - Nina Holland
- a School of Public Health, Center for Environmental Research and Children's Health (CERCH) , University of California, Berkeley , Berkeley , CA , USA
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Solomon O, Yousefi P, Huen K, Gunier RB, Escudero-Fung M, Barcellos LF, Eskenazi B, Holland N. Prenatal phthalate exposure and altered patterns of DNA methylation in cord blood. Environ Mol Mutagen 2017; 58:398-410. [PMID: 28556291 PMCID: PMC6488305 DOI: 10.1002/em.22095] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 04/11/2017] [Accepted: 04/12/2017] [Indexed: 05/18/2023]
Abstract
Epigenetic changes such as DNA methylation may be a molecular mechanism through which environmental exposures affect health. Phthalates are known endocrine disruptors with ubiquitous exposures in the general population including pregnant women, and they have been linked with a number of adverse health outcomes. We examined the association between in utero phthalate exposure and altered patterns of cord blood DNA methylation in 336 Mexican-American newborns. Concentrations of 11 phthalate metabolites were analyzed in maternal urine samples collected at 13 and 26 weeks gestation as a measure of fetal exposure. DNA methylation was assessed using the Infinium HumanMethylation 450K BeadChip adjusting for cord blood cell composition. To identify differentially methylated regions (DMRs) that may be more informative than individual CpG sites, we used two different approaches, DMRcate and comb-p. Regional assessment by both methods identified 27 distinct DMRs, the majority of which were in relation to multiple phthalate metabolites. Most of the significant DMRs (67%) were observed for later pregnancy (26 weeks gestation). Further, 51% of the significant DMRs were associated with the di-(2-ethylhexyl) phthalate metabolites. Five individual CpG sites were associated with phthalate metabolite concentrations after multiple comparisons adjustment (FDR), all showing hypermethylation. Genes with DMRs were involved in inflammatory response (IRAK4 and ESM1), cancer (BRCA1 and LASP1), endocrine function (CNPY1), and male fertility (IFT140, TESC, and PRDM8). These results on differential DNA methylation in newborns with prenatal phthalate exposure provide new insights and targets to explore mechanism of adverse effects of phthalates on human health. Environ. Mol. Mutagen. 58:398-410, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Olivia Solomon
- School of Public Health, Center for Environmental Research and Children’s Health (CERCH), University
of California, Berkeley, Berkeley, CA 94720, USA
| | - Paul Yousefi
- School of Public Health, Center for Environmental Research and Children’s Health (CERCH), University
of California, Berkeley, Berkeley, CA 94720, USA
| | - Karen Huen
- School of Public Health, Center for Environmental Research and Children’s Health (CERCH), University
of California, Berkeley, Berkeley, CA 94720, USA
| | - Robert B. Gunier
- School of Public Health, Center for Environmental Research and Children’s Health (CERCH), University
of California, Berkeley, Berkeley, CA 94720, USA
| | - Maria Escudero-Fung
- School of Public Health, Center for Environmental Research and Children’s Health (CERCH), University
of California, Berkeley, Berkeley, CA 94720, USA
| | - Lisa F. Barcellos
- School of Public Health, Center for Environmental Research and Children’s Health (CERCH), University
of California, Berkeley, Berkeley, CA 94720, USA
| | - Brenda Eskenazi
- School of Public Health, Center for Environmental Research and Children’s Health (CERCH), University
of California, Berkeley, Berkeley, CA 94720, USA
| | - Nina Holland
- School of Public Health, Center for Environmental Research and Children’s Health (CERCH), University
of California, Berkeley, Berkeley, CA 94720, USA
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Mok A, Solomon O, Nayak RR, Coit P, Quach HL, Nititham J, Sawalha AH, Barcellos LF, Criswell LA, Chung SA. Genome-wide profiling identifies associations between lupus nephritis and differential methylation of genes regulating tissue hypoxia and type 1 interferon responses. Lupus Sci Med 2016; 3:e000183. [PMID: 28074145 PMCID: PMC5174796 DOI: 10.1136/lupus-2016-000183] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 11/09/2016] [Accepted: 11/11/2016] [Indexed: 11/04/2022]
Abstract
OBJECTIVE Previous studies have shown that differential DNA methylation is associated with SLE susceptibility. How DNA methylation affects the clinical heterogeneity of SLE has not been fully defined. We conducted this study to identify differentially methylated CpG sites associated with nephritis among women with SLE. METHODS The methylation status of 428 229 CpG sites across the genome was characterised for peripheral blood cells from 322 women of European descent with SLE, 80 of whom had lupus nephritis, using the Illumina HumanMethylation450 BeadChip. Multivariable linear regression adjusting for population substructure and leucocyte cell proportions was used to identify differentially methylated sites associated with lupus nephritis. The influence of genetic variation on methylation status was investigated using data from a genome-wide association study of SLE. Pathway analyses were used to identify biological processes associated with lupus nephritis. RESULTS We identified differential methylation of 19 sites in 18 genomic regions that was associated with nephritis among patients with SLE (false discovery rate q<0.05). Associations for four sites in HIF3A, IFI44 and PRR4 were replicated when examining methylation data derived from CD4+ T cells collected from an independent set of patients with SLE. These associations were not driven by genetic variation within or around the genomic regions. In addition, genes associated with lupus nephritis in a prior genome-wide association study were not differentially methylated in this epigenome-wide study. Pathway analysis indicated that biological processes involving type 1 interferon responses and the development of the immune system were associated with nephritis in patients with SLE. CONCLUSIONS Differential methylation of genes regulating the response to tissue hypoxia and interferon-mediated signalling is associated with lupus nephritis among women with SLE. These findings have not been identified in genetic studies of lupus nephritis, suggesting that epigenome-wide association studies can help identify the genomic differences that underlie the clinical heterogeneity of SLE.
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Affiliation(s)
- Amanda Mok
- Genetic Epidemiology and Genomics Laboratory, School of Public Health, University of California, Berkeley, Berkeley, California, USA
| | - Olivia Solomon
- Genetic Epidemiology and Genomics Laboratory, School of Public Health, University of California, Berkeley, Berkeley, California, USA
| | - Renuka R Nayak
- Russell/Engleman Rheumatology Research Center, University of California, San Francisco , San Francisco, California , USA
| | - Patrick Coit
- Division of Rheumatology, Department of Internal Medicine , University of Michigan , Ann Arbor, Michigan , USA
| | - Hong L Quach
- Genetic Epidemiology and Genomics Laboratory, School of Public Health, University of California, Berkeley, Berkeley, California, USA
| | - Joanne Nititham
- Russell/Engleman Rheumatology Research Center, University of California, San Francisco , San Francisco, California , USA
| | - Amr H Sawalha
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA; Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Lisa F Barcellos
- Genetic Epidemiology and Genomics Laboratory, School of Public Health, University of California, Berkeley, Berkeley, California, USA
| | - Lindsey A Criswell
- Russell/Engleman Rheumatology Research Center, University of California, San Francisco , San Francisco, California , USA
| | - Sharon A Chung
- Russell/Engleman Rheumatology Research Center, University of California, San Francisco , San Francisco, California , USA
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