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Munn‐Chernoff MA, Johnson EC, Chou Y, Coleman JR, Thornton LM, Walters RK, Yilmaz Z, Baker JH, Hübel C, Gordon S, Medland SE, Watson HJ, Gaspar HA, Bryois J, Hinney A, Leppä VM, Mattheisen M, Ripke S, Yao S, Giusti‐Rodríguez P, Hanscombe KB, Adan RA, Alfredsson L, Ando T, Andreassen OA, Berrettini WH, Boehm I, Boni C, Boraska Perica V, Buehren K, Burghardt R, Cassina M, Cichon S, Clementi M, Cone RD, Courtet P, Crow S, Crowley JJ, Danner UN, Davis OS, Zwaan M, Dedoussis G, Degortes D, DeSocio JE, Dick DM, Dikeos D, Dina C, Dmitrzak‐Weglarz M, Docampo E, Duncan LE, Egberts K, Ehrlich S, Escaramís G, Esko T, Estivill X, Farmer A, Favaro A, Fernández‐Aranda F, Fichter MM, Fischer K, Föcker M, Foretova L, Forstner AJ, Forzan M, Franklin CS, Gallinger S, Giegling I, Giuranna J, Gonidakis F, Gorwood P, Gratacos Mayora M, Guillaume S, Guo Y, Hakonarson H, Hatzikotoulas K, Hauser J, Hebebrand J, Helder SG, Herms S, Herpertz‐Dahlmann B, Herzog W, Huckins LM, Hudson JI, Imgart H, Inoko H, Janout V, Jiménez‐Murcia S, Julià A, Kalsi G, Kaminská D, Karhunen L, Karwautz A, Kas MJ, Kennedy JL, Keski‐Rahkonen A, Kiezebrink K, Kim Y, Klump KL, Knudsen GPS, La Via MC, Le Hellard S, Levitan RD, Li D, Lilenfeld L, Lin BD, Lissowska J, Luykx J, Magistretti PJ, Maj M, Mannik K, Marsal S, Marshall CR, Mattingsdal M, McDevitt S, McGuffin P, Metspalu A, Meulenbelt I, Micali N, Mitchell K, Monteleone AM, Monteleone P, Nacmias B, Navratilova M, Ntalla I, O'Toole JK, Ophoff RA, Padyukov L, Palotie A, Pantel J, Papezova H, Pinto D, Rabionet R, Raevuori A, Ramoz N, Reichborn‐Kjennerud T, Ricca V, Ripatti S, Ritschel F, Roberts M, Rotondo A, Rujescu D, Rybakowski F, Santonastaso P, Scherag A, Scherer SW, Schmidt U, Schork NJ, Schosser A, Seitz J, Slachtova L, Slagboom PE, Slof‐Op't Landt MC, Slopien A, Sorbi S, Świątkowska B, Szatkiewicz JP, Tachmazidou I, Tenconi E, Tortorella A, Tozzi F, Treasure J, Tsitsika A, Tyszkiewicz‐Nwafor M, Tziouvas K, Elburg AA, Furth EF, Wagner G, Walton E, Widen E, Zeggini E, Zerwas S, Zipfel S, Bergen AW, Boden JM, Brandt H, Crawford S, Halmi KA, Horwood LJ, Johnson C, Kaplan AS, Kaye WH, Mitchell J, Olsen CM, Pearson JF, Pedersen NL, Strober M, Werge T, Whiteman DC, Woodside DB, Grove J, Henders AK, Larsen JT, Parker R, Petersen LV, Jordan J, Kennedy MA, Birgegård A, Lichtenstein P, Norring C, Landén M, Mortensen PB, Polimanti R, McClintick JN, Adkins AE, Aliev F, Bacanu S, Batzler A, Bertelsen S, Biernacka JM, Bigdeli TB, Chen L, Clarke T, Degenhardt F, Docherty AR, Edwards AC, Foo JC, Fox L, Frank J, Hack LM, Hartmann AM, Hartz SM, Heilmann‐Heimbach S, Hodgkinson C, Hoffmann P, Hottenga J, Konte B, Lahti J, Lahti‐Pulkkinen M, Lai D, Ligthart L, Loukola A, Maher BS, Mbarek H, McIntosh AM, McQueen MB, Meyers JL, Milaneschi Y, Palviainen T, Peterson RE, Ryu E, Saccone NL, Salvatore JE, Sanchez‐Roige S, Schwandt M, Sherva R, Streit F, Strohmaier J, Thomas N, Wang J, Webb BT, Wedow R, Wetherill L, Wills AG, Zhou H, Boardman JD, Chen D, Choi D, Copeland WE, Culverhouse RC, Dahmen N, Degenhardt L, Domingue BW, Frye MA, Gäebel W, Hayward C, Ising M, Keyes M, Kiefer F, Koller G, Kramer J, Kuperman S, Lucae S, Lynskey MT, Maier W, Mann K, Männistö S, Müller‐Myhsok B, Murray AD, Nurnberger JI, Preuss U, Räikkönen K, Reynolds MD, Ridinger M, Scherbaum N, Schuckit MA, Soyka M, Treutlein J, Witt SH, Wodarz N, Zill P, Adkins DE, Boomsma DI, Bierut LJ, Brown SA, Bucholz KK, Costello EJ, Wit H, Diazgranados N, Eriksson JG, Farrer LA, Foroud TM, Gillespie NA, Goate AM, Goldman D, Grucza RA, Hancock DB, Harris KM, Hesselbrock V, Hewitt JK, Hopfer CJ, Iacono WG, Johnson EO, Karpyak VM, Kendler KS, Kranzler HR, Krauter K, Lind PA, McGue M, MacKillop J, Madden PA, Maes HH, Magnusson PK, Nelson EC, Nöthen MM, Palmer AA, Penninx BW, Porjesz B, Rice JP, Rietschel M, Riley BP, Rose RJ, Shen P, Silberg J, Stallings MC, Tarter RE, Vanyukov MM, Vrieze S, Wall TL, Whitfield JB, Zhao H, Neale BM, Wade TD, Heath AC, Montgomery GW, Martin NG, Sullivan PF, Kaprio J, Breen G, Gelernter J, Edenberg HJ, Bulik CM, Agrawal A. Shared genetic risk between eating disorder‐ and substance‐use‐related phenotypes: Evidence from genome‐wide association studies. Addict Biol 2021; 26:e12880. [DOI: 10.1111/adb.12880] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 12/09/2019] [Accepted: 01/13/2020] [Indexed: 02/01/2023]
Affiliation(s)
- Melissa A. Munn‐Chernoff
- Department of Psychiatry University of North Carolina at Chapel Hill Chapel Hill North Carolina USA
| | - Emma C. Johnson
- Department of Psychiatry Washington University School of Medicine Saint Louis Missouri USA
| | - Yi‐Ling Chou
- Department of Psychiatry Washington University School of Medicine Saint Louis Missouri USA
| | - Jonathan R.I. Coleman
- Social, Genetic and Developmental Psychiatry (SGDP) Centre, Institute of Psychiatry, Psychology and Neuroscience King's College London London UK
- National Institute for Health Research Biomedical Research Centre King's College London and South London and Maudsley National Health Service Trust London UK
| | - Laura M. Thornton
- Department of Psychiatry University of North Carolina at Chapel Hill Chapel Hill North Carolina USA
| | - Raymond K. Walters
- Analytic and Translational Genetics Unit, Department of Medicine Massachusetts General Hospital and Harvard Medical School Boston Massachusetts USA
- Stanley Center for Psychiatric Research Broad Institute of MIT and Harvard Cambridge Massachusetts USA
| | - Zeynep Yilmaz
- Department of Psychiatry University of North Carolina at Chapel Hill Chapel Hill North Carolina USA
- Department of Genetics University of North Carolina at Chapel Hill Chapel Hill North Carolina USA
| | - Jessica H. Baker
- Department of Psychiatry University of North Carolina at Chapel Hill Chapel Hill North Carolina USA
| | - Christopher Hübel
- Social, Genetic and Developmental Psychiatry (SGDP) Centre, Institute of Psychiatry, Psychology and Neuroscience King's College London London UK
- National Institute for Health Research Biomedical Research Centre King's College London and South London and Maudsley National Health Service Trust London UK
- Department of Medical Epidemiology and Biostatistics Karolinska Institutet Stockholm Sweden
| | - Scott Gordon
- QIMR Berghofer Medical Research Institute Brisbane Queensland Australia
| | - Sarah E. Medland
- QIMR Berghofer Medical Research Institute Brisbane Queensland Australia
| | - Hunna J. Watson
- Department of Psychiatry University of North Carolina at Chapel Hill Chapel Hill North Carolina USA
- School of Psychology Curtin University Perth Western Australia Australia
- School of Paediatrics and Child Health University of Western Australia Perth Western Australia Australia
| | - Héléna A. Gaspar
- Social, Genetic and Developmental Psychiatry (SGDP) Centre, Institute of Psychiatry, Psychology and Neuroscience King's College London London UK
- National Institute for Health Research Biomedical Research Centre King's College London and South London and Maudsley National Health Service Trust London UK
| | - Julien Bryois
- Department of Medical Epidemiology and Biostatistics Karolinska Institutet Stockholm Sweden
| | - Anke Hinney
- Department of Child and Adolescent Psychiatry University Hospital Essen, University of Duisburg‐Essen Essen Germany
| | - Virpi M. Leppä
- Department of Medical Epidemiology and Biostatistics Karolinska Institutet Stockholm Sweden
| | - Manuel Mattheisen
- Department of Biomedicine Aarhus University Aarhus Denmark
- Department of Clinical Neuroscience Karolinska Institutet Stockholm Sweden
- Center for Psychiatry Research, Stockholm Health Care Services Stockholm County Council Stockholm Sweden
- Department of Psychiatry, Psychosomatics and Psychotherapy University of Würzburg Germany
| | - Stephan Ripke
- Analytic and Translational Genetics Unit, Department of Medicine Massachusetts General Hospital and Harvard Medical School Boston Massachusetts USA
- Stanley Center for Psychiatric Research Broad Institute of MIT and Harvard Cambridge Massachusetts USA
- Department of Psychiatry and Psychotherapy Charité ‐ Universitätsmedizin Berlin Germany
| | - Shuyang Yao
- Department of Medical Epidemiology and Biostatistics Karolinska Institutet Stockholm Sweden
| | - Paola Giusti‐Rodríguez
- Department of Genetics University of North Carolina at Chapel Hill Chapel Hill North Carolina USA
| | - Ken B. Hanscombe
- Department of Medical and Molecular Genetics King's College London, Guy's Hospital London UK
| | - Roger A.H. Adan
- Department of Translational Neuroscience, Brain Center Rudolf Magnus University Medical Center Utrecht Utrecht The Netherlands
- Center for Eating Disorders Rintveld Altrecht Mental Health Institute Zeist The Netherlands
- Sahlgrenska Academy University of Gothenburg Gothenburg Sweden
| | - Lars Alfredsson
- Institute of Environmental Medicine Karolinska Institutet Stockholm Sweden
| | - Tetsuya Ando
- Department of Behavioral Medicine, National Institute of Mental Health National Center of Neurology and Psychiatry Kodaira Tokyo Japan
| | - Ole A. Andreassen
- NORMENT Centre, Division of Mental Health and Addiction, NORMENT Centre University of Oslo, Oslo University Hospital Oslo Norway
| | - Wade H. Berrettini
- Department of Psychiatry, Center for Neurobiology and Behavior University of Pennsylvania Perelman School of Medicine Philadelphia Pennsylvania USA
| | - Ilka Boehm
- Division of Psychological and Social Medicine and Developmental Neurosciences, Faculty of Medicine Technische Universität Dresden Dresden Germany
| | - Claudette Boni
- Centre of Psychiatry and Neuroscience INSERM U894 Paris France
| | - Vesna Boraska Perica
- Wellcome Sanger Institute, Wellcome Genome Campus Hinxton Cambridge UK
- Department of Medical Biology, School of Medicine University of Split Split Croatia
| | - Katharina Buehren
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy RWTH Aachen University Aachen Germany
| | | | - Matteo Cassina
- Clinical Genetics Unit, Department of Woman and Child Health University of Padova Italy
| | - Sven Cichon
- Institute of Medical Genetics and Pathology University Hospital Basel Basel Switzerland
- Department of Biomedicine University of Basel Basel Switzerland
- Institute of Neuroscience and Medicine (INM‐1) Research Center Juelich Germany
| | - Maurizio Clementi
- Clinical Genetics Unit, Department of Woman and Child Health University of Padova Italy
| | - Roger D. Cone
- Department of Molecular and Integrative Physiology, Life Sciences Institute University of Michigan Ann Arbor Michigan USA
| | - Philippe Courtet
- Department of Emergency Psychiatry and Post‐Acute Care, CHRU Montpellier University of Montpellier Montpellier France
| | - Scott Crow
- Department of Psychiatry University of Minnesota Minneapolis Minnesota USA
| | - James J. Crowley
- Department of Genetics University of North Carolina at Chapel Hill Chapel Hill North Carolina USA
- Department of Clinical Neuroscience Karolinska Institutet Stockholm Sweden
| | - Unna N. Danner
- Altrecht Eating Disorders Rintveld Altrecht Mental Health Institute Zeist The Netherlands
| | - Oliver S.P. Davis
- MRC Integrative Epidemiology Unit University of Bristol Bristol UK
- School of Social and Community Medicine University of Bristol Bristol UK
| | - Martina Zwaan
- Department of Psychosomatic Medicine and Psychotherapy Hannover Medical School Hannover Germany
| | - George Dedoussis
- Department of Nutrition and Dietetics Harokopio University Athens Greece
| | | | | | - Danielle M. Dick
- Department of Psychology Virginia Commonwealth University Richmond Virginia USA
- College Behavioral and Emotional Health Institute Virginia Commonwealth University Richmond Virginia USA
- Department of Human & Molecular Genetics Virginia Commonwealth University Richmond Virginia USA
| | - Dimitris Dikeos
- Department of Psychiatry, Athens University Medical School Athens University Athens Greece
| | - Christian Dina
- l'institut du thorax INSERM, CNRS, Univ Nantes Nantes France
| | | | - Elisa Docampo
- Barcelona Institute of Science and Technology Barcelona Spain
- Universitat Pompeu Fabra Barcelona Spain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP) Barcelona Spain
| | - Laramie E. Duncan
- Department of Psychiatry and Behavioral Sciences Stanford University Stanford California USA
| | - Karin Egberts
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Centre for Mental Health University Hospital of Würzburg Würzburg Germany
| | - Stefan Ehrlich
- Division of Psychological and Social Medicine and Developmental Neurosciences, Faculty of Medicine Technische Universität Dresden Dresden Germany
| | - Geòrgia Escaramís
- Barcelona Institute of Science and Technology Barcelona Spain
- Universitat Pompeu Fabra Barcelona Spain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP) Barcelona Spain
| | - Tõnu Esko
- Estonian Genome Center University of Tartu Tartu Estonia
- Program in Medical and Population Genetics Broad Institute of MIT and Harvard Cambridge Massachusetts USA
| | - Xavier Estivill
- Barcelona Institute of Science and Technology Barcelona Spain
- Universitat Pompeu Fabra Barcelona Spain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP) Barcelona Spain
- Genomics and Disease, Bioinformatics and Genomics Programme Centre for Genomic Regulation Barcelona Spain
| | - Anne Farmer
- Social, Genetic and Developmental Psychiatry (SGDP) Centre, Institute of Psychiatry, Psychology and Neuroscience King's College London London UK
| | - Angela Favaro
- Department of Neurosciences University of Padova Padova Italy
| | - Fernando Fernández‐Aranda
- Department of Psychiatry University Hospital of Bellvitge –IDIBELL and CIBERobn Barcelona Spain
- Department of Clinical Sciences, School of Medicine University of Barcelona Barcelona Spain
| | - Manfred M. Fichter
- Department of Psychiatry and Psychotherapy Ludwig‐Maximilians‐University Munich Germany
- Schön Klinik Roseneck affiliated with the Medical Faculty of the University of Munich Munich Germany
| | - Krista Fischer
- Estonian Genome Center University of Tartu Tartu Estonia
| | - Manuel Föcker
- Department of Child and Adolescent Psychiatry University of Münster Münster Germany
| | - Lenka Foretova
- Department of Cancer, Epidemiology and Genetics Masaryk Memorial Cancer Institute Brno Czech Republic
| | - Andreas J. Forstner
- Department of Biomedicine University of Basel Basel Switzerland
- Centre for Human Genetics University of Marburg Marburg Germany
- Institute of Human Genetics School of Medicine & University Hospital Bonn, University of Bonn Bonn Germany
- Department of Psychiatry (UPK) University of Basel Basel Switzerland
| | - Monica Forzan
- Clinical Genetics Unit, Department of Woman and Child Health University of Padova Italy
| | | | - Steven Gallinger
- Department of Surgery, Faculty of Medicine University of Toronto Toronto Ontario Canada
| | - Ina Giegling
- Department of Psychiatry, Psychotherapy and Psychosomatics Martin‐Luther‐University Halle‐Wittenberg Halle (Saale) Germany
| | - Johanna Giuranna
- Department of Child and Adolescent Psychiatry University Hospital Essen, University of Duisburg‐Essen Essen Germany
| | - Fragiskos Gonidakis
- 1st Psychiatric Department National and Kapodistrian University of Athens, Medical School, Eginition Hospital Athens Greece
| | - Philip Gorwood
- Institute of Psychiatry and Neuroscience of Paris INSERM U1266 Paris France
- CMME (GHU Paris Psychiatrie et Neurosciences), Paris Descartes University Paris France
| | - Monica Gratacos Mayora
- Barcelona Institute of Science and Technology Barcelona Spain
- Universitat Pompeu Fabra Barcelona Spain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP) Barcelona Spain
| | - Sébastien Guillaume
- Department of Emergency Psychiatry and Post‐Acute Care, CHRU Montpellier University of Montpellier Montpellier France
| | - Yiran Guo
- Center for Applied Genomics Children's Hospital of Philadelphia Philadelphia Pennsylvania USA
| | - Hakon Hakonarson
- Center for Applied Genomics Children's Hospital of Philadelphia Philadelphia Pennsylvania USA
- Department of Pediatrics University of Pennsylvania Perelman School of Medicine Philadelphia Pennsylvania USA
| | - Konstantinos Hatzikotoulas
- Wellcome Sanger Institute, Wellcome Genome Campus Hinxton Cambridge UK
- Institute of Translational Genomics, Helmholtz Zentrum München ‐ German Research Centre for Environmental Health Neuherberg Germany
| | - Joanna Hauser
- Department of Adult Psychiatry Poznan University of Medical Sciences Poznan Poland
| | - Johannes Hebebrand
- Department of Child and Adolescent Psychiatry University Hospital Essen, University of Duisburg‐Essen Essen Germany
| | - Sietske G. Helder
- Social, Genetic and Developmental Psychiatry (SGDP) Centre, Institute of Psychiatry, Psychology and Neuroscience King's College London London UK
- Zorg op Orde Delft The Netherlands
| | - Stefan Herms
- Institute of Medical Genetics and Pathology University Hospital Basel Basel Switzerland
- Department of Biomedicine University of Basel Basel Switzerland
| | - Beate Herpertz‐Dahlmann
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy RWTH Aachen University Aachen Germany
| | - Wolfgang Herzog
- Department of General Internal Medicine and Psychosomatics Heidelberg University Hospital, Heidelberg University Heidelberg Germany
| | - Laura M. Huckins
- Wellcome Sanger Institute, Wellcome Genome Campus Hinxton Cambridge UK
- Department of Psychiatry, and Genetics and Genomics Sciences, Division of Psychiatric Genomics Icahn School of Medicine at Mount Sinai New York New York USA
| | - James I. Hudson
- Biological Psychiatry Laboratory McLean Hospital/Harvard Medical School Boston Massachusetts USA
| | - Hartmut Imgart
- Eating Disorders Unit Parklandklinik Bad Wildungen Germany
| | - Hidetoshi Inoko
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, School of Medicine Tokai University Isehara Japan
| | - Vladimir Janout
- Faculty of Health Sciences Palacky University Olomouc Czech Republic
| | - Susana Jiménez‐Murcia
- Department of Psychiatry University Hospital of Bellvitge –IDIBELL and CIBERobn Barcelona Spain
- Department of Clinical Sciences, School of Medicine University of Barcelona Barcelona Spain
| | - Antonio Julià
- Rheumatology Research Group Vall d'Hebron Research Institute Barcelona Spain
| | - Gursharan Kalsi
- Social, Genetic and Developmental Psychiatry (SGDP) Centre, Institute of Psychiatry, Psychology and Neuroscience King's College London London UK
| | - Deborah Kaminská
- Department of Psychiatry, First Faculty of Medicine Charles University Prague Czech Republic
| | - Leila Karhunen
- Department of Clinical Nutrition, Institute of Public Health and Clinical Nutrition University of Eastern Finland Kuopio Finland
| | - Andreas Karwautz
- Eating Disorders Unit, Department of Child and Adolescent Psychiatry Medical University of Vienna Vienna Austria
| | - Martien J.H. Kas
- Department of Translational Neuroscience, Brain Center Rudolf Magnus University Medical Center Utrecht Utrecht The Netherlands
- Groningen Institute for Evolutionary Life Sciences University of Groningen Groningen The Netherlands
| | - James L. Kennedy
- Centre for Addiction and Mental Health Toronto Ontario Canada
- Institute of Medical Science University of Toronto Toronto Ontario Canada
- Department of Psychiatry University of Toronto Toronto Ontario Canada
| | | | - Kirsty Kiezebrink
- Institute of Applied Health Sciences, School of Medicine, Medical Sciences and Nutrition University of Aberdeen Aberdeen UK
| | - Youl‐Ri Kim
- Department of Psychiatry Seoul Paik Hospital, Inje University Seoul Korea
| | - Kelly L. Klump
- Department of Psychology Michigan State University East Lansing Michigan USA
| | | | - Maria C. La Via
- Department of Psychiatry University of North Carolina at Chapel Hill Chapel Hill North Carolina USA
| | - Stephanie Le Hellard
- Department of Clinical Science, Norwegian Centre for Mental Disorders Research (NORMENT) University of Bergen Bergen Norway
- Dr. Einar Martens Research Group for Biological Psychiatry, Center for Medical Genetics and Molecular Medicine Haukeland University Hospital Bergen Norway
- Department of Clinical Medicine, Laboratory Building Haukeland University Hospital Bergen Norway
| | - Robert D. Levitan
- Centre for Addiction and Mental Health Toronto Ontario Canada
- Institute of Medical Science University of Toronto Toronto Ontario Canada
- Department of Psychiatry University of Toronto Toronto Ontario Canada
| | - Dong Li
- Center for Applied Genomics Children's Hospital of Philadelphia Philadelphia Pennsylvania USA
| | - Lisa Lilenfeld
- The Chicago School of Professional Psychology, Washington DC Campus Washington District of Columbia USA
| | - Bochao Danae Lin
- Department of Translational Neuroscience, Brain Center Rudolf Magnus University Medical Center Utrecht Utrecht The Netherlands
| | - Jolanta Lissowska
- Department of Cancer Epidemiology and Prevention M Skłodowska‐Curie Cancer Center ‐ Oncology Center Warsaw Poland
| | - Jurjen Luykx
- Department of Translational Neuroscience, Brain Center Rudolf Magnus University Medical Center Utrecht Utrecht The Netherlands
| | - Pierre J. Magistretti
- BESE Division King Abdullah University of Science and Technology Thuwal Saudi Arabia
- Department of Psychiatry University of Lausanne‐University Hospital of Lausanne (UNIL‐CHUV) Lausanne Switzerland
| | - Mario Maj
- Department of Psychiatry University of Campania "Luigi Vanvitelli" Naples Italy
| | - Katrin Mannik
- Estonian Genome Center University of Tartu Tartu Estonia
- Center for Integrative Genomics University of Lausanne Lausanne Switzerland
| | - Sara Marsal
- Rheumatology Research Group Vall d'Hebron Research Institute Barcelona Spain
| | - Christian R. Marshall
- Department of Paediatric Laboratory Medicine, Division of Genome Diagnostics The Hospital for Sick Children Toronto Ontario Canada
| | - Morten Mattingsdal
- NORMENT KG Jebsen Centre, Division of Mental Health and Addiction University of Oslo, Oslo University Hospital Oslo Norway
| | - Sara McDevitt
- Department of Psychiatry University College Cork Cork Ireland
- Eist Linn Adolescent Unit, Bessborough Health Service Executive South Cork Ireland
| | - Peter McGuffin
- Social, Genetic and Developmental Psychiatry (SGDP) Centre, Institute of Psychiatry, Psychology and Neuroscience King's College London London UK
| | - Andres Metspalu
- Estonian Genome Center University of Tartu Tartu Estonia
- Institute of Molecular and Cell Biology University of Tartu Tartu Estonia
| | - Ingrid Meulenbelt
- Molecular Epidemiology Section (Department of Biomedical Datasciences) Leiden University Medical Centre Leiden The Netherlands
| | - Nadia Micali
- Department of Psychiatry, Faculty of Medicine University of Geneva Geneva Switzerland
- Division of Child and Adolescent Psychiatry Geneva University Hospital Geneva Switzerland
| | - Karen Mitchell
- National Center for PTSD VA Boston Healthcare System Boston Massachusetts USA
- Department of Psychiatry Boston University School of Medicine Boston Massachusetts USA
| | | | - Palmiero Monteleone
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana" University of Salerno Salerno Italy
| | - Benedetta Nacmias
- Department of Neuroscience, Psychology, Drug Research and Child Health (NEUROFARBA) University of Florence Florence Italy
| | - Marie Navratilova
- Department of Cancer, Epidemiology and Genetics Masaryk Memorial Cancer Institute Brno Czech Republic
| | - Ioanna Ntalla
- Department of Nutrition and Dietetics Harokopio University Athens Greece
| | | | - Roel A. Ophoff
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior University of California Los Angeles Los Angeles California USA
- Department of Psychiatry, Erasmus MC University Medical Center Rotterdam Rotterdam The Netherlands
| | - Leonid Padyukov
- Department of Medicine, Center for Molecular Medicine, Division of Rheumatology Karolinska Institutet and Karolinska University Hospital Stockholm Sweden
| | - Aarno Palotie
- Program in Medical and Population Genetics Broad Institute of MIT and Harvard Cambridge Massachusetts USA
- Institute for Molecular Medicine FIMM, HiLIFE University of Helsinki Helsinki Finland
- Center for Human Genome Research Massachusetts General Hospital Boston Massachusetts USA
| | - Jacques Pantel
- Centre of Psychiatry and Neuroscience INSERM U894 Paris France
| | - Hana Papezova
- Department of Psychiatry, First Faculty of Medicine Charles University Prague Czech Republic
| | - Dalila Pinto
- Department of Psychiatry, and Genetics and Genomics Sciences, Division of Psychiatric Genomics Icahn School of Medicine at Mount Sinai New York New York USA
| | - Raquel Rabionet
- Saint Joan de Déu Research Institute Saint Joan de Déu Barcelona Children's Hospital Barcelona Spain
- Institute of Biomedicine (IBUB) University of Barcelona Barcelona Spain
- Department of Genetics, Microbiology and Statistics University of Barcelona Barcelona Spain
| | - Anu Raevuori
- Department of Public Health University of Helsinki Helsinki Finland
| | - Nicolas Ramoz
- Institute of Psychiatry and Neuroscience of Paris INSERM U1266 Paris France
| | - Ted Reichborn‐Kjennerud
- Department of Mental Disorders Norwegian Institute of Public Health Oslo Norway
- Institute of Clinical Medicine University of Oslo Oslo Norway
| | - Valdo Ricca
- Department of Health Science University of Florence Florence Italy
| | - Samuli Ripatti
- Department of Biometry University of Helsinki Helsinki Finland
| | - Franziska Ritschel
- Division of Psychological and Social Medicine and Developmental Neurosciences, Faculty of Medicine Technische Universität Dresden Dresden Germany
- Department of Child and Adolescent Psychiatry, Faculty of Medicine, Eating Disorders Research and Treatment Center Technische Universität Dresden Dresden Germany
| | - Marion Roberts
- Social, Genetic and Developmental Psychiatry (SGDP) Centre, Institute of Psychiatry, Psychology and Neuroscience King's College London London UK
| | - Alessandro Rotondo
- Department of Psychiatry, Neurobiology, Pharmacology, and Biotechnologies University of Pisa Pisa Italy
| | - Dan Rujescu
- Department of Psychiatry, Psychotherapy and Psychosomatics Martin‐Luther‐University Halle‐Wittenberg Halle (Saale) Germany
| | - Filip Rybakowski
- Department of Psychiatry Poznan University of Medical Sciences Poznan Poland
| | - Paolo Santonastaso
- Department of Neurosciences, Padua Neuroscience Center University of Padova Padova Italy
| | - André Scherag
- Institute of Medical Statistics, Computer and Data Sciences Jena University Hospital Jena Germany
| | - Stephen W. Scherer
- Department of Genetics and Genomic Biology The Hospital for Sick Children Toronto Ontario Canada
- McLaughlin Centre University of Toronto Toronto Ontario Canada
| | - Ulrike Schmidt
- Department of Psychological Medicine, Institute of Psychiatry, Psychology and Neuroscience King's College London London UK
| | | | - Alexandra Schosser
- Department of Psychiatry and Psychotherapy Medical University of Vienna Vienna Austria
| | - Jochen Seitz
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy RWTH Aachen University Aachen Germany
| | - Lenka Slachtova
- Department of Pediatrics and Center of Applied Genomics, First Faculty of Medicine Charles University Prague Czech Republic
| | - P. Eline Slagboom
- Molecular Epidemiology Section (Department of Medical Statistics) Leiden University Medical Centre Leiden The Netherlands
| | - Margarita C.T. Slof‐Op't Landt
- Center for Eating Disorders Ursula Rivierduinen Leiden The Netherlands
- Department of Psychiatry Leiden University Medical Centre Leiden The Netherlands
| | - Agnieszka Slopien
- Department of Child and Adolescent Psychiatry Poznan University of Medical Sciences Poznan Poland
| | - Sandro Sorbi
- Department of Neuroscience, Psychology, Drug Research and Child Health (NEUROFARBA) University of Florence Florence Italy
- IRCCS Fondazione Don Carlo Gnocchi Florence Italy
| | - Beata Świątkowska
- Department of Environmental Epidemiology Nofer Institute of Occupational Medicine Lodz Poland
| | - Jin P. Szatkiewicz
- Department of Genetics University of North Carolina at Chapel Hill Chapel Hill North Carolina USA
| | | | - Elena Tenconi
- Department of Neurosciences University of Padova Padova Italy
| | - Alfonso Tortorella
- Department of Psychiatry University of Naples SUN Naples Italy
- Department of Psychiatry University of Perugia Perugia Italy
| | - Federica Tozzi
- Brain Sciences Department Stremble Ventures Limassol Cyprus
| | - Janet Treasure
- Department of Psychological Medicine, Institute of Psychiatry, Psychology and Neuroscience King's College London London UK
| | - Artemis Tsitsika
- Adolescent Health Unit, Second Department of Pediatrics "P. & A. Kyriakou" Children's Hospital, University of Athens Athens Greece
| | - Marta Tyszkiewicz‐Nwafor
- Department of Child and Adolescent Psychiatry Poznan University of Medical Sciences Poznan Poland
| | - Konstantinos Tziouvas
- Pediatric Intensive Care Unit "P. & A. Kyriakou" Children's Hospital, University of Athens Athens Greece
| | - Annemarie A. Elburg
- Center for Eating Disorders Rintveld Altrecht Mental Health Institute Zeist The Netherlands
- Faculty of Social and Behavioral Sciences Utrecht University Utrecht The Netherlands
| | - Eric F. Furth
- Center for Eating Disorders Ursula Rivierduinen Leiden The Netherlands
- Department of Psychiatry Leiden University Medical Centre Leiden The Netherlands
| | - Gudrun Wagner
- Eating Disorders Unit, Department of Child and Adolescent Psychiatry Medical University of Vienna Vienna Austria
| | - Esther Walton
- Division of Psychological and Social Medicine and Developmental Neurosciences, Faculty of Medicine Technische Universität Dresden Dresden Germany
| | - Elisabeth Widen
- Institute for Molecular Medicine FIMM, HiLIFE University of Helsinki Helsinki Finland
| | - Eleftheria Zeggini
- Wellcome Sanger Institute, Wellcome Genome Campus Hinxton Cambridge UK
- Institute of Translational Genomics, Helmholtz Zentrum München ‐ German Research Centre for Environmental Health Neuherberg Germany
| | - Stephanie Zerwas
- Department of Psychiatry University of North Carolina at Chapel Hill Chapel Hill North Carolina USA
| | - Stephan Zipfel
- Department of Internal Medicine VI, Psychosomatic Medicine and Psychotherapy University Medical Hospital Tuebingen Tuebingen Germany
| | - Andrew W. Bergen
- BioRealm, LLC Walnut California USA
- Oregon Research Institute Eugene Oregon USA
| | - Joseph M. Boden
- Christchurch Health and Development Study University of Otago Christchurch New Zealand
| | - Harry Brandt
- The Center for Eating Disorders at Sheppard Pratt Baltimore Maryland USA
| | - Steven Crawford
- The Center for Eating Disorders at Sheppard Pratt Baltimore Maryland USA
| | - Katherine A. Halmi
- Department of Psychiatry Weill Cornell Medical College New York New York USA
| | - L. John Horwood
- Christchurch Health and Development Study University of Otago Christchurch New Zealand
| | | | - Allan S. Kaplan
- Centre for Addiction and Mental Health Toronto Ontario Canada
- Institute of Medical Science University of Toronto Toronto Ontario Canada
- Department of Psychiatry University of Toronto Toronto Ontario Canada
| | - Walter H. Kaye
- Department of Psychiatry University of California San Diego La Jolla California USA
| | - James Mitchell
- Department of Psychiatry and Behavioral Science University of North Dakota School of Medicine and Health Sciences Fargo North Dakota USA
| | - Catherine M. Olsen
- Population Health Department QIMR Berghofer Medical Research Institute Brisbane Queensland Australia
| | - John F. Pearson
- Biostatistics and Computational Biology Unit University of Otago Christchurch New Zealand
| | - Nancy L. Pedersen
- Department of Medical Epidemiology and Biostatistics Karolinska Institutet Stockholm Sweden
| | - Michael Strober
- Department of Psychiatry and Biobehavioral Science, Semel Institute for Neuroscience and Human Behavior University of California Los Angeles Los Angeles California USA
- David Geffen School of Medicine University of California Los Angeles Los Angeles California USA
| | - Thomas Werge
- Department of Clinical Medicine University of Copenhagen Copenhagen Denmark
| | - David C. Whiteman
- Population Health Department QIMR Berghofer Medical Research Institute Brisbane Queensland Australia
| | - D. Blake Woodside
- Institute of Medical Science University of Toronto Toronto Ontario Canada
- Department of Psychiatry University of Toronto Toronto Ontario Canada
- Centre for Mental Health University Health Network Toronto Ontario Canada
- Program for Eating Disorders University Health Network Toronto Ontario Canada
| | - Jakob Grove
- Department of Biomedicine Aarhus University Aarhus Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH) Aarhus Denmark
- Centre for Integrative Sequencing, iSEQ Aarhus University Aarhus Denmark
- Bioinformatics Research Centre Aarhus University Aarhus Denmark
| | - Anjali K. Henders
- Institute for Molecular Bioscience University of Queensland Brisbane Queensland Australia
| | - Janne T. Larsen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH) Aarhus Denmark
- National Centre for Register‐Based Research, Aarhus BSS Aarhus University Aarhus Denmark
- Centre for Integrated Register‐based Research (CIRRAU) Aarhus University Aarhus Denmark
| | - Richard Parker
- QIMR Berghofer Medical Research Institute Brisbane Queensland Australia
| | - Liselotte V. Petersen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH) Aarhus Denmark
- National Centre for Register‐Based Research, Aarhus BSS Aarhus University Aarhus Denmark
- Centre for Integrated Register‐based Research (CIRRAU) Aarhus University Aarhus Denmark
| | - Jennifer Jordan
- Department of Psychological Medicine University of Otago Christchurch New Zealand
- Canterbury District Health Board Christchurch New Zealand
| | - Martin A. Kennedy
- Department of Pathology and Biomedical Science University of Otago Christchurch New Zealand
| | - Andreas Birgegård
- Department of Medical Epidemiology and Biostatistics Karolinska Institutet Stockholm Sweden
- Department of Clinical Neuroscience Karolinska Institutet Stockholm Sweden
- Center for Psychiatry Research, Stockholm Health Care Services Stockholm County Council Stockholm Sweden
| | - Paul Lichtenstein
- Department of Medical Epidemiology and Biostatistics Karolinska Institutet Stockholm Sweden
| | - Claes Norring
- Department of Clinical Neuroscience Karolinska Institutet Stockholm Sweden
- Center for Psychiatry Research, Stockholm Health Care Services Stockholm County Council Stockholm Sweden
| | - Mikael Landén
- Department of Medical Epidemiology and Biostatistics Karolinska Institutet Stockholm Sweden
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology The Sahlgrenska Academy at the University of Gothenburg Gothenburg Sweden
| | - Preben Bo Mortensen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH) Aarhus Denmark
- National Centre for Register‐Based Research, Aarhus BSS Aarhus University Aarhus Denmark
- Centre for Integrated Register‐based Research (CIRRAU) Aarhus University Aarhus Denmark
| | - Renato Polimanti
- Department of Psychiatry, Division of Human Genetics Yale School of Medicine New Haven Connecticut USA
- Veterans Affairs Connecticut Healthcare System West Haven Connecticut USA
| | - Jeanette N. McClintick
- Department of Biochemistry and Molecular Biology Indiana University School of Medicine Indianapolis Indiana USA
| | - Amy E. Adkins
- Department of Psychology Virginia Commonwealth University Richmond Virginia USA
- College Behavioral and Emotional Health Institute Virginia Commonwealth University Richmond Virginia USA
| | - Fazil Aliev
- Department of Psychology Virginia Commonwealth University Richmond Virginia USA
- Faculty of Business Karabuk University Karabuk Turkey
| | - Silviu‐Alin Bacanu
- Virginia Commonwealth University Alcohol Research Center Virginia Commonwealth University Richmond Virginia USA
- Virginia Institute for Psychiatric and Behavioral Genetics Virginia Commonwealth University Richmond Virginia USA
- Department of Psychiatry Virginia Commonwealth University Richmond Virginia USA
| | - Anthony Batzler
- Psychiatric Genomics and Pharmacogenomics Program Mayo Clinic Rochester Minnesota USA
| | - Sarah Bertelsen
- Department of Neuroscience Icahn School of Medicine at Mount Sinai New York New York USA
| | - Joanna M. Biernacka
- Department of Health Sciences Research Mayo Clinic Rochester Minnesota USA
- Department of Psychiatry and Psychology Mayo Clinic Rochester Minnesota USA
| | - Tim B. Bigdeli
- Department of Psychiatry and Behavioral Sciences State University of New York Downstate Medical Center Brooklyn New York USA
| | - Li‐Shiun Chen
- Department of Psychiatry Washington University School of Medicine Saint Louis Missouri USA
| | | | - Franziska Degenhardt
- Institute of Human Genetics University of Bonn School of Medicine & University Hospital Bonn Bonn Germany
| | - Anna R. Docherty
- Department of Psychiatry University of Utah Salt Lake City Utah USA
| | - Alexis C. Edwards
- Virginia Institute for Psychiatric and Behavioral Genetics Virginia Commonwealth University Richmond Virginia USA
- Department of Psychiatry Virginia Commonwealth University Richmond Virginia USA
| | - Jerome C. Foo
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim Heidelberg University Mannheim Germany
| | - Louis Fox
- Department of Psychiatry Washington University School of Medicine Saint Louis Missouri USA
| | - Josef Frank
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim Heidelberg University Mannheim Germany
| | - Laura M. Hack
- Department of Psychiatry and Behavioral Sciences Stanford University Stanford California USA
| | - Annette M. Hartmann
- Department of Psychiatry, Psychotherapy and Psychosomatics Martin‐Luther‐University Halle‐Wittenberg Halle (Saale) Germany
| | - Sarah M. Hartz
- Department of Psychiatry Washington University School of Medicine Saint Louis Missouri USA
| | - Stefanie Heilmann‐Heimbach
- Institute of Human Genetics University of Bonn School of Medicine & University Hospital Bonn Bonn Germany
| | | | - Per Hoffmann
- Institute of Medical Genetics and Pathology University Hospital Basel Basel Switzerland
- Institute of Human Genetics School of Medicine & University Hospital Bonn, University of Bonn Bonn Germany
- Human Genomics Research Group, Department of Biomedicine University of Basel Basel Switzerland
| | - Jouke‐Jan Hottenga
- Department of Biological Psychology, Amsterdam Public Health Research Institute Vrije Universiteit Amsterdam Amsterdam The Netherlands
| | - Bettina Konte
- Department of Psychiatry, Psychotherapy and Psychosomatics Martin‐Luther‐University Halle‐Wittenberg Halle (Saale) Germany
| | - Jari Lahti
- Turku Institute for Advanced Studies University of Turku Turku Finland
| | | | - Dongbing Lai
- Department of Medical and Molecular Genetics Indiana University School of Medicine Indianapolis Indiana USA
| | - Lannie Ligthart
- Department of Biological Psychology, Amsterdam Public Health Research Institute Vrije Universiteit Amsterdam Amsterdam The Netherlands
| | - Anu Loukola
- Institute for Molecular Medicine FIMM, HiLIFE University of Helsinki Helsinki Finland
| | - Brion S. Maher
- Johns Hopkins Bloomberg School of Public Health Baltimore Maryland USA
| | - Hamdi Mbarek
- Department of Biological Psychology, Amsterdam Public Health Research Institute Vrije Universiteit Amsterdam Amsterdam The Netherlands
| | - Andrew M. McIntosh
- Division of Psychiatry, Centre for Cognitive Ageing and Cognitive Epidemiology University of Edinburgh Edinburgh UK
| | - Matthew B. McQueen
- Department of Integrative Physiology University of Colorado Boulder Boulder Colorado USA
| | - Jacquelyn L. Meyers
- Department of Psychiatry and Behavioral Sciences, Henri Begleiter Neurodynamics Laboratory SUNY Downstate Medical Center Brooklyn New York USA
| | - Yuri Milaneschi
- Department of Psychiatry, Amsterdam Public Health Research Institute VU University Medical Center/GGz inGeest Amsterdam The Netherlands
| | - Teemu Palviainen
- Institute for Molecular Medicine FIMM, HiLIFE University of Helsinki Helsinki Finland
| | - Roseann E. Peterson
- Virginia Institute for Psychiatric and Behavioral Genetics Virginia Commonwealth University Richmond Virginia USA
- Department of Psychiatry Virginia Commonwealth University Richmond Virginia USA
| | - Euijung Ryu
- Department of Health Sciences Research Mayo Clinic Rochester Minnesota USA
| | - Nancy L. Saccone
- Department of Genetics Washington University School of Medicine Saint Louis Missouri USA
| | - Jessica E. Salvatore
- Department of Psychology Virginia Commonwealth University Richmond Virginia USA
- Virginia Institute for Psychiatric and Behavioral Genetics Virginia Commonwealth University Richmond Virginia USA
- Department of Psychiatry Virginia Commonwealth University Richmond Virginia USA
| | - Sandra Sanchez‐Roige
- Department of Psychiatry University of California San Diego La Jolla California USA
| | | | - Richard Sherva
- Department of Medicine (Biomedical Genetics) Boston University School of Medicine Boston Massachusetts USA
| | - Fabian Streit
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim Heidelberg University Mannheim Germany
| | - Jana Strohmaier
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim Heidelberg University Mannheim Germany
| | - Nathaniel Thomas
- Department of Psychology Virginia Commonwealth University Richmond Virginia USA
- College Behavioral and Emotional Health Institute Virginia Commonwealth University Richmond Virginia USA
| | - Jen‐Chyong Wang
- Department of Neuroscience Icahn School of Medicine at Mount Sinai New York New York USA
| | - Bradley T. Webb
- Virginia Commonwealth University Alcohol Research Center Virginia Commonwealth University Richmond Virginia USA
- Virginia Institute for Psychiatric and Behavioral Genetics Virginia Commonwealth University Richmond Virginia USA
- Department of Psychiatry Virginia Commonwealth University Richmond Virginia USA
| | - Robbee Wedow
- Analytic and Translational Genetics Unit, Department of Medicine Massachusetts General Hospital and Harvard Medical School Boston Massachusetts USA
- Stanley Center for Psychiatric Research Broad Institute of MIT and Harvard Cambridge Massachusetts USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health Harvard University Cambridge Massachusetts USA
- Department of Sociology Harvard University Cambridge Massachusetts USA
| | - Leah Wetherill
- Department of Medical and Molecular Genetics Indiana University School of Medicine Indianapolis Indiana USA
| | - Amanda G. Wills
- Department of Pharmacology University of Colorado School of Medicine Aurora Colorado USA
| | - Hang Zhou
- Department of Psychiatry, Division of Human Genetics Yale School of Medicine New Haven Connecticut USA
- Veterans Affairs Connecticut Healthcare System West Haven Connecticut USA
| | - Jason D. Boardman
- Institute of Behavioral Science University of Colorado Boulder Colorado USA
- Department of Sociology University of Colorado Boulder Colorado USA
| | - Danfeng Chen
- Stanley Center for Psychiatric Research Broad Institute of MIT and Harvard Cambridge Massachusetts USA
| | - Doo‐Sup Choi
- Department of Molecular Pharmacology and Experimental Therapeutics Mayo Clinic Rochester Minnesota USA
| | - William E. Copeland
- Department of Psychiatry University of Vermont Medical Center Burlington Vermont USA
| | - Robert C. Culverhouse
- Department of Medicine, Division of Biostatistics Washington University School of Medicine Saint Louis Missouri USA
| | - Norbert Dahmen
- Department of Psychiatry University of Mainz Mainz Germany
| | - Louisa Degenhardt
- National Drug and Alcohol Research Centre University of New South Wales Sydney New South Wales Australia
| | - Benjamin W. Domingue
- Stanford University Graduate School of Education Stanford University Stanford California USA
| | - Mark A. Frye
- Department of Psychiatry and Psychology Mayo Clinic Rochester Minnesota USA
| | - Wolfgang Gäebel
- Department of Psychiatry and Psychotherapy University of Düsseldorf Duesseldorf Germany
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine University of Edinburgh Edinburgh UK
| | - Marcus Ising
- Max‐Planck‐Institute of Psychiatry Munich Germany
| | - Margaret Keyes
- Department of Psychology University of Minnesota Minneapolis Minnesota USA
| | - Falk Kiefer
- Department of Addictive Behavior and Addiction Medicine, Central Institute of Mental Health, Medical Faculty Mannheim Heidelberg University Mannheim Germany
| | - Gabriele Koller
- Department of Psychiatry and Psychotherapy University Hospital, LMU Munich Munich Germany
| | - John Kramer
- Department of Psychiatry University of Iowa Roy J and Lucille A Carver College of Medicine Iowa City Iowa USA
| | - Samuel Kuperman
- Department of Psychiatry University of Iowa Roy J and Lucille A Carver College of Medicine Iowa City Iowa USA
| | | | - Michael T. Lynskey
- Addictions Department, Institute of Psychiatry, Psychology & Neuroscience King's College London London UK
| | - Wolfgang Maier
- Department of Psychiatry University of Bonn Bonn Germany
| | - Karl Mann
- Department of Addictive Behavior and Addiction Medicine, Central Institute of Mental Health, Medical Faculty Mannheim Heidelberg University Mannheim Germany
| | - Satu Männistö
- Department of Public Health Solutions National Institute for Health and Welfare Helsinki Finland
| | - Bertram Müller‐Myhsok
- Department of Statistical Genetics Max‐Planck‐Institute of Psychiatry München Germany
| | - Alison D. Murray
- Aberdeen Biomedical Imaging Centre, School of Medicine, Medical Sciences & Nutrition University of Aberdeen Foresterhill Aberdeen UK
| | - John I. Nurnberger
- Department of Medical and Molecular Genetics Indiana University School of Medicine Indianapolis Indiana USA
- Department of Psychiatry Indiana University School of Medicine Indianapolis Indiana USA
| | - Ulrich Preuss
- Department of Psychiatry, Psychotherapy and Psychosomatics Martin‐Luther‐University Halle‐Wittenberg Herborn Germany
- Department of Psychiatry and Psychotherapy Vitos Hospital Herborn Herborn Germany
| | - Katri Räikkönen
- Department of Psychology and Logopedics University of Helsinki Helsinki Finland
| | | | - Monika Ridinger
- Department of Psychiatry and Psychotherapy University of Regensburg Psychiatric Health Care Aargau Regensburg Germany
| | - Norbert Scherbaum
- Department of Psychiatry and Psychotherapy and Department of Addictive Behaviour and Addiction Medicine, Medical Faculty LVR‐Hospital Essen, University of Duisburg‐Essen Essen Germany
| | - Marc A. Schuckit
- Department of Psychiatry University of California San Diego La Jolla California USA
| | - Michael Soyka
- Medical Park Chiemseeblick in Bernau‐Felden Ludwig‐Maximilians‐University Bernau am Chiemsee Germany
- Psychiatric Hospital, Ludwig‐Maximilians‐University Bernau am Chiemsee Germany
| | - Jens Treutlein
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim Heidelberg University Mannheim Germany
| | - Stephanie H. Witt
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim Heidelberg University Mannheim Germany
| | - Norbert Wodarz
- Department of Psychiatry and Psychotherapy University of Regensburg Regensburg Germany
| | - Peter Zill
- Department of Psychiatry Psychiatric Hospital, Ludwig‐Maximilians‐University Munich Germany
| | - Daniel E. Adkins
- Department of Psychiatry University of Utah Salt Lake City Utah USA
- Department of Sociology University of Utah Salt Lake City Utah USA
| | - Dorret I. Boomsma
- Department of Biological Psychology, Amsterdam Public Health Research Institute Vrije Universiteit Amsterdam Amsterdam The Netherlands
| | - Laura J. Bierut
- Department of Psychiatry Washington University School of Medicine Saint Louis Missouri USA
| | - Sandra A. Brown
- Department of Psychiatry University of California San Diego La Jolla California USA
- Department of Psychology University of California San Diego La Jolla California USA
| | - Kathleen K. Bucholz
- Department of Psychiatry Washington University School of Medicine Saint Louis Missouri USA
| | - E. Jane Costello
- Department of Psychiatry and Behavioral Sciences Duke University Medical Center Durham North Carolina USA
| | - Harriet Wit
- Department of Psychiatry and Behavioral Neuroscience University of Chicago Chicago Illinois USA
| | | | - Johan G. Eriksson
- Department of General Practice and Primary Health Care University of Helsinki Helsinki Finland
- National Institute for Health and Welfare Helsinki Finland
| | - Lindsay A. Farrer
- Department of Medicine (Biomedical Genetics) Boston University School of Medicine Boston Massachusetts USA
- Department of Neurology Boston University School of Medicine Boston Massachusetts USA
- Department of Ophthalmology Boston University School of Medicine Boston Massachusetts USA
- Department of Epidemiology, School of Public Health Boston University Boston Massachusetts USA
- Department of Biostatistics, School of Public Health Boston University Boston Massachusetts USA
| | - Tatiana M. Foroud
- Department of Medical and Molecular Genetics Indiana University School of Medicine Indianapolis Indiana USA
| | - Nathan A. Gillespie
- Virginia Institute for Psychiatric and Behavioral Genetics Virginia Commonwealth University Richmond Virginia USA
| | - Alison M. Goate
- Department of Neuroscience Icahn School of Medicine at Mount Sinai New York New York USA
| | - David Goldman
- Laboratory of Neurogenetics NIH/NIAAA Bethesda Maryland USA
- Office of the Clinical Director NIH/NIAAA Besthesda Maryland USA
| | - Richard A. Grucza
- Department of Psychiatry Washington University School of Medicine Saint Louis Missouri USA
| | - Dana B. Hancock
- Center for Omics Discovery and Epidemiology, Behavioral Health Research Division RTI International Research Triangle Park North Carolina USA
| | - Kathleen Mullan Harris
- Department of Sociology University of North Carolina at Chapel Hill Chapel Hill North Carolina USA
- Carolina Population Center University of North Carolina at Chapel Hill Chapel Hill North Carolina USA
| | - Victor Hesselbrock
- Department of Psychiatry University of Connecticut School of Medicine Farmington Connecticut USA
| | - John K. Hewitt
- Institute for Behavioral Genetics University of Colorado Boulder Boulder Colorado USA
| | | | - William G. Iacono
- Department of Psychology University of Minnesota Minneapolis Minnesota USA
| | - Eric O. Johnson
- Center for Omics Discovery and Epidemiology, Behavioral Health Research Division RTI International Research Triangle Park North Carolina USA
- Fellow Program RTI International Research Triangle Park North Carolina USA
| | - Victor M. Karpyak
- Department of Psychiatry and Psychology Mayo Clinic Rochester Minnesota USA
| | - Kenneth S. Kendler
- Virginia Institute for Psychiatric and Behavioral Genetics Virginia Commonwealth University Richmond Virginia USA
- Department of Psychiatry Virginia Commonwealth University Richmond Virginia USA
| | - Henry R. Kranzler
- Center for Studies of Addiction University of Pennsylvania Perelman School of Medicine Philadelphia Pennsylvania USA
- VISN 4 MIRECC Crescenz VAMC Philadelphia Pennsylvania USA
| | - Kenneth Krauter
- Department of Molecular, Cellular, and Developmental Biology University of Colorado Boulder Boulder Colorado USA
| | - Penelope A. Lind
- QIMR Berghofer Medical Research Institute Brisbane Queensland Australia
| | - Matt McGue
- Department of Psychology University of Minnesota Minneapolis Minnesota USA
| | - James MacKillop
- Peter Boris Centre for Addictions Research McMaster University/St. Joseph's Healthcare Hamilton Hamilton Ontario Canada
- Michael G. DeGroote Centre for Medicinal Cannabis Research McMaster University/St. Joseph's Healthcare Hamilton Hamilton Ontario Canada
| | - Pamela A.F. Madden
- Department of Psychiatry Washington University School of Medicine Saint Louis Missouri USA
| | - Hermine H. Maes
- Virginia Institute for Psychiatric and Behavioral Genetics Virginia Commonwealth University Richmond Virginia USA
| | - Patrik K.E. Magnusson
- Department of Medical Epidemiology and Biostatistics Karolinska Institutet Stockholm Sweden
| | - Elliot C. Nelson
- Department of Psychiatry Washington University School of Medicine Saint Louis Missouri USA
| | - Markus M. Nöthen
- Institute of Human Genetics University of Bonn School of Medicine & University Hospital Bonn Bonn Germany
| | - Abraham A. Palmer
- Department of Psychiatry University of California San Diego La Jolla California USA
- Institute for Genomic Medicine University of California San Diego La Jolla California USA
| | - Brenda W.J.H. Penninx
- Department of Psychiatry, Amsterdam UMC VU University and GGZinGeest Amsterdam The Netherlands
| | - Bernice Porjesz
- Department of Psychiatry and Behavioral Sciences, Henri Begleiter Neurodynamics Laboratory SUNY Downstate Medical Center Brooklyn New York USA
| | - John P. Rice
- Department of Psychiatry Washington University School of Medicine Saint Louis Missouri USA
| | - Marcella Rietschel
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim Heidelberg University Mannheim Germany
| | - Brien P. Riley
- Virginia Commonwealth University Alcohol Research Center Virginia Commonwealth University Richmond Virginia USA
- Virginia Institute for Psychiatric and Behavioral Genetics Virginia Commonwealth University Richmond Virginia USA
- Department of Psychiatry Virginia Commonwealth University Richmond Virginia USA
| | - Richard J. Rose
- Department of Psychological & Brain Sciences Indiana University Bloomington Bloomington Indiana USA
| | - Pei‐Hong Shen
- Laboratory of Neurogenetics NIH/NIAAA Bethesda Maryland USA
| | - Judy Silberg
- Virginia Institute for Psychiatric and Behavioral Genetics Virginia Commonwealth University Richmond Virginia USA
- Department of Psychiatry Virginia Commonwealth University Richmond Virginia USA
| | - Michael C. Stallings
- Institute for Behavioral Genetics University of Colorado Boulder Boulder Colorado USA
| | - Ralph E. Tarter
- School of Pharmacy University of Pittsburgh Pittsburgh Pennsylvania USA
| | | | - Scott Vrieze
- Department of Psychology University of Minnesota Minneapolis Minnesota USA
| | - Tamara L. Wall
- Department of Psychiatry University of California San Diego La Jolla California USA
| | - John B. Whitfield
- QIMR Berghofer Medical Research Institute Brisbane Queensland Australia
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health Yale University New Haven Connecticut USA
| | - Benjamin M. Neale
- Analytic and Translational Genetics Unit, Department of Medicine Massachusetts General Hospital and Harvard Medical School Boston Massachusetts USA
- Stanley Center for Psychiatric Research Broad Institute of MIT and Harvard Cambridge Massachusetts USA
| | - Tracey D. Wade
- School of Psychology Flinders University Adelaide South Australia Australia
| | - Andrew C. Heath
- Department of Psychiatry Washington University School of Medicine Saint Louis Missouri USA
| | - Grant W. Montgomery
- QIMR Berghofer Medical Research Institute Brisbane Queensland Australia
- Institute for Molecular Bioscience University of Queensland Brisbane Queensland Australia
- Queensland Brain Institute University of Queensland Brisbane Queensland Australia
| | | | - Patrick F. Sullivan
- Department of Psychiatry University of North Carolina at Chapel Hill Chapel Hill North Carolina USA
- Department of Genetics University of North Carolina at Chapel Hill Chapel Hill North Carolina USA
- Department of Medical Epidemiology and Biostatistics Karolinska Institutet Stockholm Sweden
| | - Jaakko Kaprio
- Department of Public Health University of Helsinki Helsinki Finland
- Institute for Molecular Medicine FIMM, HiLIFE University of Helsinki Helsinki Finland
| | - Gerome Breen
- Social, Genetic and Developmental Psychiatry (SGDP) Centre, Institute of Psychiatry, Psychology and Neuroscience King's College London London UK
- National Institute for Health Research Biomedical Research Centre King's College London and South London and Maudsley National Health Service Trust London UK
| | - Joel Gelernter
- Department of Psychiatry, Division of Human Genetics Yale School of Medicine New Haven Connecticut USA
- Veterans Affairs Connecticut Healthcare System West Haven Connecticut USA
- Department of Genetics Yale School of Medicine New Haven Connecticut USA
- Department of Neuroscience Yale School of Medicine New Haven Connecticut USA
| | - Howard J. Edenberg
- Department of Biochemistry and Molecular Biology Indiana University School of Medicine Indianapolis Indiana USA
- Department of Medical and Molecular Genetics Indiana University School of Medicine Indianapolis Indiana USA
| | - Cynthia M. Bulik
- Department of Psychiatry University of North Carolina at Chapel Hill Chapel Hill North Carolina USA
- Department of Medical Epidemiology and Biostatistics Karolinska Institutet Stockholm Sweden
- Department of Nutrition University of North Carolina at Chapel Hill Chapel Hill North Carolina USA
| | - Arpana Agrawal
- Department of Psychiatry Washington University School of Medicine Saint Louis Missouri USA
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Johnson EC, Demontis D, Thorgeirsson TE, Walters RK, Polimanti R, Hatoum AS, Sanchez-Roige S, Paul SE, Wendt FR, Clarke TK, Lai D, Reginsson GW, Zhou H, He J, Baranger DAA, Gudbjartsson DF, Wedow R, Adkins DE, Adkins AE, Alexander J, Bacanu SA, Bigdeli TB, Boden J, Brown SA, Bucholz KK, Bybjerg-Grauholm J, Corley RP, Degenhardt L, Dick DM, Domingue BW, Fox L, Goate AM, Gordon SD, Hack LM, Hancock DB, Hartz SM, Hickie IB, Hougaard DM, Krauter K, Lind PA, McClintick JN, McQueen MB, Meyers JL, Montgomery GW, Mors O, Mortensen PB, Nordentoft M, Pearson JF, Peterson RE, Reynolds MD, Rice JP, Runarsdottir V, Saccone NL, Sherva R, Silberg JL, Tarter RE, Tyrfingsson T, Wall TL, Webb BT, Werge T, Wetherill L, Wright MJ, Zellers S, Adams MJ, Bierut LJ, Boardman JD, Copeland WE, Farrer LA, Foroud TM, Gillespie NA, Grucza RA, Harris KM, Heath AC, Hesselbrock V, Hewitt JK, Hopfer CJ, Horwood J, Iacono WG, Johnson EO, Kendler KS, Kennedy MA, Kranzler HR, Madden PAF, Maes HH, Maher BS, Martin NG, McGue M, McIntosh AM, Medland SE, Nelson EC, Porjesz B, Riley BP, Stallings MC, Vanyukov MM, Vrieze S, Davis LK, Bogdan R, Gelernter J, Edenberg HJ, Stefansson K, Børglum AD, Agrawal A. A large-scale genome-wide association study meta-analysis of cannabis use disorder. Lancet Psychiatry 2020; 7:1032-1045. [PMID: 33096046 PMCID: PMC7674631 DOI: 10.1016/s2215-0366(20)30339-4] [Citation(s) in RCA: 144] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/15/2020] [Accepted: 07/16/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND Variation in liability to cannabis use disorder has a strong genetic component (estimated twin and family heritability about 50-70%) and is associated with negative outcomes, including increased risk of psychopathology. The aim of the study was to conduct a large genome-wide association study (GWAS) to identify novel genetic variants associated with cannabis use disorder. METHODS To conduct this GWAS meta-analysis of cannabis use disorder and identify associations with genetic loci, we used samples from the Psychiatric Genomics Consortium Substance Use Disorders working group, iPSYCH, and deCODE (20 916 case samples, 363 116 control samples in total), contrasting cannabis use disorder cases with controls. To examine the genetic overlap between cannabis use disorder and 22 traits of interest (chosen because of previously published phenotypic correlations [eg, psychiatric disorders] or hypothesised associations [eg, chronotype] with cannabis use disorder), we used linkage disequilibrium score regression to calculate genetic correlations. FINDINGS We identified two genome-wide significant loci: a novel chromosome 7 locus (FOXP2, lead single-nucleotide polymorphism [SNP] rs7783012; odds ratio [OR] 1·11, 95% CI 1·07-1·15, p=1·84 × 10-9) and the previously identified chromosome 8 locus (near CHRNA2 and EPHX2, lead SNP rs4732724; OR 0·89, 95% CI 0·86-0·93, p=6·46 × 10-9). Cannabis use disorder and cannabis use were genetically correlated (rg 0·50, p=1·50 × 10-21), but they showed significantly different genetic correlations with 12 of the 22 traits we tested, suggesting at least partially different genetic underpinnings of cannabis use and cannabis use disorder. Cannabis use disorder was positively genetically correlated with other psychopathology, including ADHD, major depression, and schizophrenia. INTERPRETATION These findings support the theory that cannabis use disorder has shared genetic liability with other psychopathology, and there is a distinction between genetic liability to cannabis use and cannabis use disorder. FUNDING National Institute of Mental Health; National Institute on Alcohol Abuse and Alcoholism; National Institute on Drug Abuse; Center for Genomics and Personalized Medicine and the Centre for Integrative Sequencing; The European Commission, Horizon 2020; National Institute of Child Health and Human Development; Health Research Council of New Zealand; National Institute on Aging; Wellcome Trust Case Control Consortium; UK Research and Innovation Medical Research Council (UKRI MRC); The Brain & Behavior Research Foundation; National Institute on Deafness and Other Communication Disorders; Substance Abuse and Mental Health Services Administration (SAMHSA); National Institute of Biomedical Imaging and Bioengineering; National Health and Medical Research Council (NHMRC) Australia; Tobacco-Related Disease Research Program of the University of California; Families for Borderline Personality Disorder Research (Beth and Rob Elliott) 2018 NARSAD Young Investigator Grant; The National Child Health Research Foundation (Cure Kids); The Canterbury Medical Research Foundation; The New Zealand Lottery Grants Board; The University of Otago; The Carney Centre for Pharmacogenomics; The James Hume Bequest Fund; National Institutes of Health: Genes, Environment and Health Initiative; National Institutes of Health; National Cancer Institute; The William T Grant Foundation; Australian Research Council; The Virginia Tobacco Settlement Foundation; The VISN 1 and VISN 4 Mental Illness Research, Education, and Clinical Centers of the US Department of Veterans Affairs; The 5th Framework Programme (FP-5) GenomEUtwin Project; The Lundbeck Foundation; NIH-funded Shared Instrumentation Grant S10RR025141; Clinical Translational Sciences Award grants; National Institute of Neurological Disorders and Stroke; National Heart, Lung, and Blood Institute; National Institute of General Medical Sciences.
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Affiliation(s)
- Emma C Johnson
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA.
| | - Ditte Demontis
- Department of Biomedicine-Human Genetics and Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark; Center for Genomics and Personalized Medicine, Aarhus, Denmark
| | | | - Raymond K Walters
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Renato Polimanti
- Division of Human Genetics, Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA; Veterans Affairs Connecticut Healthcare System, West Haven, CT, USA
| | - Alexander S Hatoum
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
| | - Sandra Sanchez-Roige
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA; Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Sarah E Paul
- Department of Psychological and Brain Sciences, Washington University in Saint Louis, St. Louis, MO, USA
| | - Frank R Wendt
- Division of Human Genetics, Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA; Veterans Affairs Connecticut Healthcare System, West Haven, CT, USA
| | - Toni-Kim Clarke
- Division of Psychiatry, University of Edinburgh, Edinburgh, UK
| | - Dongbing Lai
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | | | - Hang Zhou
- Division of Human Genetics, Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA; Veterans Affairs Connecticut Healthcare System, West Haven, CT, USA
| | - June He
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
| | - David A A Baranger
- Department of Psychiatry, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Daniel F Gudbjartsson
- Statistics Department, Reykjavik, Iceland; School of Engineering and Natural Sciences, Iceland University, Reykjavik, Iceland
| | - Robbee Wedow
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel E Adkins
- Department of Psychiatry, University of Utah, Salt Lake City, UT, USA; Department of Psychology, Virginia Commonwealth University, Richmond, VA, USA; College Behavioral and Emotional Health Institute, Virginia Commonwealth University, Richmond, VA, USA
| | - Amy E Adkins
- Department of Psychiatry, University of Utah, Salt Lake City, UT, USA; Department of Psychology, Virginia Commonwealth University, Richmond, VA, USA; College Behavioral and Emotional Health Institute, Virginia Commonwealth University, Richmond, VA, USA
| | - Jeffry Alexander
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Silviu-Alin Bacanu
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Tim B Bigdeli
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Joseph Boden
- Department of Psychological Medicine, University of Otago, Christchurch, New Zealand
| | - Sandra A Brown
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA; Department of Psychology and Office of Research Affairs, University of California San Diego, La Jolla, CA, USA
| | - Kathleen K Bucholz
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
| | - Jonas Bybjerg-Grauholm
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark; Department for Congenital Disorders, Center for Neonatal Screening, Statens Serum Institut, Copenhagen, Denmark
| | - Robin P Corley
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
| | - Louisa Degenhardt
- National Drug and Alcohol Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Danielle M Dick
- Department of Psychology, Virginia Commonwealth University, Richmond, VA, USA; Department of Human & Molecular Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - Benjamin W Domingue
- Stanford University Graduate School of Education, Stanford University, Stanford, CA, USA
| | - Louis Fox
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
| | - Alison M Goate
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Scott D Gordon
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Laura M Hack
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Dana B Hancock
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, Durham, NC, USA
| | - Sarah M Hartz
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
| | - Ian B Hickie
- Brain and Mind Centre, University of Sydney, Sydney, Australia
| | - David M Hougaard
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark; Department for Congenital Disorders, Center for Neonatal Screening, Statens Serum Institut, Copenhagen, Denmark
| | - Kenneth Krauter
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA; University of Colorado Boulder, Boulder, CO, USA
| | - Penelope A Lind
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Jeanette N McClintick
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Matthew B McQueen
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Jacquelyn L Meyers
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY, USA; Henri Begleiter Neurodynamics Laboratory, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Grant W Montgomery
- Institute for Molecular Bioscience, University of Queensland, QLD, Australia
| | - Ole Mors
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark; Psychosis Research Unit, Aarhus University Hospital, Aarhus, Denmark
| | - Preben B Mortensen
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark; Centre for Integrated Register-based Research, Aarhus University, Aarhus, Denmark; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
| | - Merete Nordentoft
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark; Mental Health Services in the Capital Region of Denmark, Mental Health Center Copenhagen, University of Copenhagen, Copenhagen, Denmark
| | - John F Pearson
- Biostatistics and Computational Biology Unit, University of Otago, Christchurch, New Zealand; Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Roseann E Peterson
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | | | - John P Rice
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
| | | | - Nancy L Saccone
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA; Division of Biostatistics, Washington University School of Medicine, St Louis, MO, USA
| | - Richard Sherva
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - Judy L Silberg
- Department of Human & Molecular Genetics, Virginia Commonwealth University, Richmond, VA, USA; Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - Ralph E Tarter
- School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Tamara L Wall
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Bradley T Webb
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Thomas Werge
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark; Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Copenhagen, Denmark; Department of Clinical Medicine, and Center for GeoGenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Leah Wetherill
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Margaret J Wright
- Queensland Brain Institute, University of Queensland, QLD, Australia
| | - Stephanie Zellers
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | - Mark J Adams
- Division of Psychiatry, University of Edinburgh, Edinburgh, UK
| | - Laura J Bierut
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
| | - Jason D Boardman
- Institute of Behavioral Science and Department of Sociology, University of Colorado Boulder, Boulder, CO, USA
| | - William E Copeland
- Department of Psychiatry, University of Vermont Medical Center, Burlington, VT, USA
| | - Lindsay A Farrer
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - Tatiana M Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Nathan A Gillespie
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - Richard A Grucza
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
| | - Kathleen Mullan Harris
- Department of Sociology, and The Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Andrew C Heath
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
| | - Victor Hesselbrock
- Department of Psychiatry, University of Connecticut School of Medicine, Farmington, CT, USA
| | - John K Hewitt
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
| | - Christian J Hopfer
- Department of Psychiatry, University of Colorado Denver, Aurora, CO, USA
| | - John Horwood
- Department of Psychological Medicine, University of Otago, Christchurch, New Zealand
| | - William G Iacono
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | - Eric O Johnson
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, Durham, NC, USA
| | - Kenneth S Kendler
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - Martin A Kennedy
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Henry R Kranzler
- Center for Studies of Addiction, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; VISN 4 MIRECC, Crescenz VAMC, Philadelphia, PA, USA
| | - Pamela A F Madden
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
| | - Hermine H Maes
- Department of Human & Molecular Genetics, Virginia Commonwealth University, Richmond, VA, USA; Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - Brion S Maher
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Matthew McGue
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | | | - Sarah E Medland
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Elliot C Nelson
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
| | - Bernice Porjesz
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY, USA; Henri Begleiter Neurodynamics Laboratory, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Brien P Riley
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Michael C Stallings
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
| | | | - Scott Vrieze
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | - Lea K Davis
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Psychiatry and Behavioral Sciences, and Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ryan Bogdan
- Department of Psychological and Brain Sciences, Washington University in Saint Louis, St. Louis, MO, USA
| | - Joel Gelernter
- Division of Human Genetics, Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA; Department of Genetics, and Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA; Veterans Affairs Connecticut Healthcare System, West Haven, CT, USA
| | - Howard J Edenberg
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kari Stefansson
- deCODE Genetics/Amgen, Reykjavik, Iceland; Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Anders D Børglum
- Department of Biomedicine-Human Genetics and Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark; Center for Genomics and Personalized Medicine, Aarhus, Denmark
| | - Arpana Agrawal
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
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3
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Orschell CM, Skaar TC, DeFord ME, Ybe J, Driscol J, Drury C, Reeves L, Willis MS, Reiter JL, York J, Orr R, McClintick JN, Sors TG, Hunt J, Cornetta K, Shekhar A. The Access Technology Program of the Indiana Clinical Translational Sciences Institute (CTSI): A model to facilitate access to cutting-edge technologies across a state. J Clin Transl Sci 2020; 5:e33. [PMID: 33948256 PMCID: PMC8057440 DOI: 10.1017/cts.2020.525] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 07/31/2020] [Accepted: 08/12/2020] [Indexed: 11/07/2022] Open
Abstract
INTRODUCTION Access to cutting-edge technologies is essential for investigators to advance translational research. The Indiana Clinical and Translational Sciences Institute (CTSI) spans three major and preeminent universities, four large academic campuses across the state of Indiana, and is mandate to provide best practices to a whole state. METHODS To address the need to facilitate the availability of innovative technologies to its investigators, the Indiana CTSI implemented the Access Technology Program (ATP). The activities of the ATP, or any program of the Indiana CTSI, are challenged to connect technologies and investigators on the multiple Indiana CTSI campuses by the geographical distances between campuses (1-4 hr driving time). RESULTS Herein, we describe the initiatives developed by the ATP to increase the availability of state-of-the-art technologies to its investigators on all Indiana CTSI campuses, and the methods developed by the ATP to bridge the distance between campuses, technologies, and investigators for the advancement of clinical translational research. CONCLUSIONS The methods and practices described in this publication may inform other approaches to enhance translational research, dissemination, and usage of innovative technologies by translational investigators, especially when distance or multi-campus cultural differences are factors to efficient application.
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Affiliation(s)
- Christie M. Orschell
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
- Indiana CTSI Access Technology Program, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Todd C. Skaar
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
- Indiana CTSI Access Technology Program, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Melanie E. DeFord
- Notre Dame Research and Indiana CTSI Access Technology Program, University of Notre Dame, Notre Dame, IN, USA
| | - Joel Ybe
- Office of the Vice Provost for Research and Indiana CTSI Access Technology Program, Indiana University School of Public Health, Bloomington, IN, USA
| | - Julie Driscol
- Indiana CTSI Translational Research Development Program, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Christine Drury
- Indiana CTSI Research Communications, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Lilith Reeves
- Indiana CTSI Access Technology Program, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Monte S. Willis
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Jill L. Reiter
- Indiana CTSI Access Technology Program, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Jenna York
- Indiana CTSI Access Technology Program, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Rob Orr
- Indiana CTSI Access Technology Program, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Jeanette N. McClintick
- Indiana CTSI Access Technology Program, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Thomas G. Sors
- Institute of Inflammation, Immunology and Infectious Disease and Indiana CTSI Access Technology Program, Purdue University, West Lafayette, IN, USA
| | - Joe Hunt
- Indiana CTSI Tracking and Evaluation Program, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kenneth Cornetta
- Indiana CTSI Access Technology Program, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Anantha Shekhar
- Indiana CTSI, Indiana University School of Medicine, Indianapolis, IN, USA
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4
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Polimanti R, Walters RK, Johnson EC, McClintick JN, Adkins AE, Adkins DE, Bacanu SA, Bierut LJ, Bigdeli TB, Brown S, Bucholz KK, Copeland WE, Costello EJ, Degenhardt L, Farrer LA, Foroud TM, Fox L, Goate AM, Grucza R, Hack LM, Hancock DB, Hartz SM, Heath AC, Hewitt JK, Hopfer CJ, Johnson EO, Kendler KS, Kranzler HR, Krauter K, Lai D, Madden PAF, Martin NG, Maes HH, Nelson EC, Peterson RE, Porjesz B, Riley BP, Saccone N, Stallings M, Wall TL, Webb BT, Wetherill L, Edenberg HJ, Agrawal A, Gelernter J. Leveraging genome-wide data to investigate differences between opioid use vs. opioid dependence in 41,176 individuals from the Psychiatric Genomics Consortium. Mol Psychiatry 2020; 25:1673-1687. [PMID: 32099098 PMCID: PMC7392789 DOI: 10.1038/s41380-020-0677-9] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 01/15/2020] [Accepted: 01/30/2020] [Indexed: 01/17/2023]
Abstract
To provide insights into the biology of opioid dependence (OD) and opioid use (i.e., exposure, OE), we completed a genome-wide analysis comparing 4503 OD cases, 4173 opioid-exposed controls, and 32,500 opioid-unexposed controls, including participants of European and African descent (EUR and AFR, respectively). Among the variants identified, rs9291211 was associated with OE (exposed vs. unexposed controls; EUR z = -5.39, p = 7.2 × 10-8). This variant regulates the transcriptomic profiles of SLC30A9 and BEND4 in multiple brain tissues and was previously associated with depression, alcohol consumption, and neuroticism. A phenome-wide scan of rs9291211 in the UK Biobank (N > 360,000) found association of this variant with propensity to use dietary supplements (p = 1.68 × 10-8). With respect to the same OE phenotype in the gene-based analysis, we identified SDCCAG8 (EUR + AFR z = 4.69, p = 10-6), which was previously associated with educational attainment, risk-taking behaviors, and schizophrenia. In addition, rs201123820 showed a genome-wide significant difference between OD cases and unexposed controls (AFR z = 5.55, p = 2.9 × 10-8) and a significant association with musculoskeletal disorders in the UK Biobank (p = 4.88 × 10-7). A polygenic risk score (PRS) based on a GWAS of risk-tolerance (n = 466,571) was positively associated with OD (OD vs. unexposed controls, p = 8.1 × 10-5; OD cases vs. exposed controls, p = 0.054) and OE (exposed vs. unexposed controls, p = 3.6 × 10-5). A PRS based on a GWAS of neuroticism (n = 390,278) was positively associated with OD (OD vs. unexposed controls, p = 3.2 × 10-5; OD vs. exposed controls, p = 0.002) but not with OE (p = 0.67). Our analyses highlight the difference between dependence and exposure and the importance of considering the definition of controls in studies of addiction.
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Affiliation(s)
- Renato Polimanti
- Department of Psychiatry, Yale University School of Medicine, Veterans Affairs Connecticut Healthcare Center, West Haven, CT, USA
| | - Raymond K Walters
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Emma C Johnson
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
| | - Jeanette N McClintick
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Amy E Adkins
- Department of Psychology, Virginia Commonwealth University, Richmond, VA, USA
| | - Daniel E Adkins
- Department of Psychiatry, University of Utah, Salt Lake City, UT, USA
| | - Silviu-Alin Bacanu
- Virginia Commonwealth University Alcohol Research Center, Virginia Institute for Psychiatric and Behavioral Genetics, Richmond, VA, USA
| | - Laura J Bierut
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
| | - Tim B Bigdeli
- Department of Psychiatry and Behavioral Sciences, State University of New York Downstate Medical Center, Brooklyn, NY, USA
| | - Sandra Brown
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Kathleen K Bucholz
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
| | - William E Copeland
- Department of Psychiatry, University of Vermont Medical Center, Burlington, VT, USA
| | - E Jane Costello
- Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, NC, USA
| | - Louisa Degenhardt
- National Drug and Alcohol Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Lindsay A Farrer
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - Tatiana M Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Louis Fox
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
| | - Alison M Goate
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Richard Grucza
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
| | - Laura M Hack
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Dana B Hancock
- Center for Omics Discovery and Epidemiology, RTI International, Research Triangle Park, NC, USA
| | - Sarah M Hartz
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
| | - Andrew C Heath
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
| | - John K Hewitt
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
| | - Christian J Hopfer
- Department of Psychiatry, University of Colorado Denver, Aurora, CO, USA
| | - Eric O Johnson
- Center for Omics Discovery and Epidemiology, RTI International, Research Triangle Park, NC, USA
| | - Kenneth S Kendler
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - Henry R Kranzler
- Center for Studies of Addiction, University of Pennsylvania Perelman School of Medicine, VISN 4 MIRECC, Crescenz VAMC, Philadelphia, PA, USA
| | - Kenneth Krauter
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Dongbing Lai
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Pamela A F Madden
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
| | | | - Hermine H Maes
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - Elliot C Nelson
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
| | - Roseann E Peterson
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - Bernice Porjesz
- Department of Psychiatry and Behavioral Sciences, State University of New York Downstate Medical Center, Brooklyn, NY, USA
| | - Brien P Riley
- Virginia Commonwealth University Alcohol Research Center, Virginia Institute for Psychiatric and Behavioral Genetics, Richmond, VA, USA
| | - Nancy Saccone
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA
| | - Michael Stallings
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
| | - Tamara L Wall
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Bradley T Webb
- Virginia Commonwealth University Alcohol Research Center, Virginia Institute for Psychiatric and Behavioral Genetics, Richmond, VA, USA
| | - Leah Wetherill
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Howard J Edenberg
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Arpana Agrawal
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
| | - Joel Gelernter
- Department of Psychiatry, Yale University School of Medicine, Veterans Affairs Connecticut Healthcare Center, West Haven, CT, USA.
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5
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McClintick JN, Thapa K, Liu Y, Xuei X, Edenberg HJ. Effects of chronic intermittent ethanol exposure and withdrawal on neuroblastoma cell transcriptome. Alcohol 2020; 85:119-126. [PMID: 31923563 PMCID: PMC7237278 DOI: 10.1016/j.alcohol.2019.12.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 09/24/2019] [Revised: 12/08/2019] [Accepted: 12/22/2019] [Indexed: 02/06/2023]
Abstract
Cycles of heavy drinking and abstinence can lead to alcohol use disorder. We studied the effects of chronic intermittent ethanol exposure (CIE) over 3 weeks on neuroblastoma cells, using an ethanol concentration frequently attained in binge drinking (40 mM, 184 mg/dL). There were many changes in gene expression but most were small. CIE affected pathways instrumental in the development or plasticity of neurons, including axonal guidance, reelin signaling, and synaptogenesis. Genes involved in dopamine and serotonin signaling were also affected. Changes in transporters and receptors could dampen both NMDA and norepinephrine transmissions. Decreased expression of the GABA transporter SLC6A11 could increase GABA transmission and has been associated with a switch from sweet drinking to ethanol consumption in rats. Ethanol increased stress responses such as the unfolded protein response. TGF-β and NFκB signaling were increased. Most of the genes involved in cholesterol biosynthesis were decreased in expression. Withdrawal for 24 h after CIE caused most of the CIE-induced expression changes to move back toward unexposed levels.
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Affiliation(s)
- Jeanette N McClintick
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Kriti Thapa
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Yunlong Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Xiaoling Xuei
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Howard J Edenberg
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States.
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6
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Sarmah S, Srivastava R, McClintick JN, Janga SC, Edenberg HJ, Marrs JA. Embryonic ethanol exposure alters expression of sox2 and other early transcripts in zebrafish, producing gastrulation defects. Sci Rep 2020; 10:3951. [PMID: 32127575 PMCID: PMC7054311 DOI: 10.1038/s41598-020-59043-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 11/01/2019] [Accepted: 01/21/2020] [Indexed: 01/10/2023] Open
Abstract
Ethanol exposure during prenatal development causes fetal alcohol spectrum disorder (FASD), the most frequent preventable birth defect and neurodevelopmental disability syndrome. The molecular targets of ethanol toxicity during development are poorly understood. Developmental stages surrounding gastrulation are very sensitive to ethanol exposure. To understand the effects of ethanol on early transcripts during embryogenesis, we treated zebrafish embryos with ethanol during pre-gastrulation period and examined the transcripts by Affymetrix GeneChip microarray before gastrulation. We identified 521 significantly dysregulated genes, including 61 transcription factors in ethanol-exposed embryos. Sox2, the key regulator of pluripotency and early development was significantly reduced. Functional annotation analysis showed enrichment in transcription regulation, embryonic axes patterning, and signaling pathways, including Wnt, Notch and retinoic acid. We identified all potential genomic targets of 25 dysregulated transcription factors and compared their interactions with the ethanol-dysregulated genes. This analysis predicted that Sox2 targeted a large number of ethanol-dysregulated genes. A gene regulatory network analysis showed that many of the dysregulated genes are targeted by multiple transcription factors. Injection of sox2 mRNA partially rescued ethanol-induced gene expression, epiboly and gastrulation defects. Additional studies of this ethanol dysregulated network may identify therapeutic targets that coordinately regulate early development.
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Affiliation(s)
- Swapnalee Sarmah
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Rajneesh Srivastava
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Jeanette N McClintick
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Sarath C Janga
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Howard J Edenberg
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - James A Marrs
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA.
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7
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McClintick JN, Tischfield JA, Deng L, Kapoor M, Xuei X, Edenberg HJ. Ethanol activates immune response in lymphoblastoid cells. Alcohol 2019; 79:81-91. [PMID: 30639126 PMCID: PMC6616005 DOI: 10.1016/j.alcohol.2019.01.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 10/04/2018] [Revised: 12/21/2018] [Accepted: 01/03/2019] [Indexed: 12/25/2022]
Abstract
The short-term effects of alcohol on gene expression in brain tissue cannot directly be studied in humans. Because neuroimmune signaling is altered by alcohol, immune cells are a logical, accessible choice to study and may provide biomarkers. RNAseq was used to study the effects of 48-h exposure to ethanol on lymphoblastoid cell lines (LCLs) from 20 alcoholic subjects and 20 control subjects. Ethanol exposure resulted in differential expression of 4456 of the 12,503 genes detectably expressed in the LCLs (FDR [false discovery rate] ≤ 0.05); 52% of these showed increased expression. Cells from alcoholic subjects and control subjects responded similarly. The genes whose expression changed fell into many pathways: NFκB, neuroinflammation, IL6, IL2, IL8, and dendritic cell maturation pathways were activated, consistent with increased signaling by NFκB, TNF, IL1, IL4, IL18, TLR4, and LPS. Signaling by Interferons A and B decreased, as did EIF2 signaling, phospholipase C signaling, and glycolysis. Baseline gene expression patterns were similar in LCLs from alcoholic subjects and control subjects. At relaxed stringency (p < 0.05), 465 genes differed, 230 of which were also affected by ethanol. There was a suggestion of compensation because baseline differences (no ethanol) were in the opposite direction of differences due to ethanol exposure in 78% of these genes. Pathways with IL8, phospholipase C, and α-adrenergic signaling were significant. The pattern of expression was consistent with increased signaling by several cytokines, including interferons, TLR2, and TLR3 in alcoholics. Expression of genes in the cholesterol biosynthesis pathway, including the rate-limiting enzyme HMGCR, was lower in alcoholic subjects. LCLs show many effects of ethanol exposure, some of which might provide biomarkers for alcohol use disorders. Identifying genes and pathways altered by ethanol can aid in interpreting which genes within loci identified by GWAS might play functional roles.
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Affiliation(s)
- Jeanette N McClintick
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, United States.
| | - Jay A Tischfield
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, United States
| | - Li Deng
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, United States
| | - Manav Kapoor
- Departments of Neuroscience, Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, United States
| | - Xiaoling Xuei
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, United States
| | - Howard J Edenberg
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, United States; Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, United States
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8
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Edenberg HJ, McClintick JN. Alcohol Dehydrogenases, Aldehyde Dehydrogenases, and Alcohol Use Disorders: A Critical Review. Alcohol Clin Exp Res 2018; 42:2281-2297. [PMID: 30320893 PMCID: PMC6286250 DOI: 10.1111/acer.13904] [Citation(s) in RCA: 132] [Impact Index Per Article: 22.0] [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: 08/03/2018] [Accepted: 10/07/2018] [Indexed: 12/20/2022]
Abstract
Alcohol use disorders (AUDs) are complex traits, meaning that variations in many genes contribute to the risk, as does the environment. Although the total genetic contribution to risk is substantial, most individual variations make only very small contributions. By far the strongest contributors are functional variations in 2 genes involved in alcohol (ethanol [EtOH]) metabolism. A functional variant in alcohol dehydrogenase 1B (ADH1B) is protective in people of European and Asian descent, and a different functional variant in the same gene is protective in those of African descent. A strongly protective variant in aldehyde dehydrogenase 2 (ALDH2) is essentially only found in Asians. This highlights the need to study a wide range of populations. The likely mechanism of protection against heavy drinking and AUDs in both cases is alteration in the rate of metabolism of EtOH that at least transiently elevates acetaldehyde. Other ADH and ALDH variants, including functional variations in ADH1C, have also been implicated in affecting drinking behavior and risk for alcoholism. The pattern of linkage disequilibrium in the ADH region and the differences among populations complicate analyses, particularly of regulatory variants. This critical review focuses upon the ADH and ALDH genes as they affect AUDs.
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Affiliation(s)
- Howard J. Edenberg
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
| | - Jeanette N. McClintick
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN
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9
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Walters RK, Polimanti R, Johnson EC, McClintick JN, Adams MJ, Adkins AE, Aliev F, Bacanu SA, Batzler A, Bertelsen S, Biernacka JM, Bigdeli TB, Chen LS, Clarke TK, Chou YL, Degenhardt F, Docherty AR, Edwards AC, Fontanillas P, Foo JC, Fox L, Frank J, Giegling I, Gordon S, Hack LM, Hartmann AM, Hartz SM, Heilmann-Heimbach S, Herms S, Hodgkinson C, Hoffmann P, Jan Hottenga J, Kennedy MA, Alanne-Kinnunen M, Konte B, Lahti J, Lahti-Pulkkinen M, Lai D, Ligthart L, Loukola A, Maher BS, Mbarek H, McIntosh AM, McQueen MB, Meyers JL, Milaneschi Y, Palviainen T, Pearson JF, Peterson RE, Ripatti S, Ryu E, Saccone NL, Salvatore JE, Sanchez-Roige S, Schwandt M, Sherva R, Streit F, Strohmaier J, Thomas N, Wang JC, Webb BT, Wedow R, Wetherill L, Wills AG, Boardman JD, Chen D, Choi DS, Copeland WE, Culverhouse RC, Dahmen N, Degenhardt L, Domingue BW, Elson SL, Frye MA, Gäbel W, Hayward C, Ising M, Keyes M, Kiefer F, Kramer J, Kuperman S, Lucae S, Lynskey MT, Maier W, Mann K, Männistö S, Müller-Myhsok B, Murray AD, Nurnberger JI, Palotie A, Preuss U, Räikkönen K, Reynolds MD, Ridinger M, Scherbaum N, Schuckit MA, Soyka M, Treutlein J, Witt S, Wodarz N, Zill P, Adkins DE, Boden JM, Boomsma DI, Bierut LJ, Brown SA, Bucholz KK, Cichon S, Costello EJ, de Wit H, Diazgranados N, Dick DM, Eriksson JG, Farrer LA, Foroud TM, Gillespie NA, Goate AM, Goldman D, Grucza RA, Hancock DB, Harris KM, Heath AC, Hesselbrock V, Hewitt JK, Hopfer CJ, Horwood J, Iacono W, Johnson EO, Kaprio JA, Karpyak VM, Kendler KS, Kranzler HR, Krauter K, Lichtenstein P, Lind PA, McGue M, MacKillop J, Madden PAF, Maes HH, Magnusson P, Martin NG, Medland SE, Montgomery GW, Nelson EC, Nöthen MM, Palmer AA, Pedersen NL, Penninx BWJH, Porjesz B, Rice JP, Rietschel M, Riley BP, Rose R, Rujescu D, Shen PH, Silberg J, Stallings MC, Tarter RE, Vanyukov MM, Vrieze S, Wall TL, Whitfield JB, Zhao H, Neale BM, Gelernter J, Edenberg HJ, Agrawal A. Transancestral GWAS of alcohol dependence reveals common genetic underpinnings with psychiatric disorders. Nat Neurosci 2018; 21:1656-1669. [PMID: 30482948 PMCID: PMC6430207 DOI: 10.1038/s41593-018-0275-1] [Citation(s) in RCA: 367] [Impact Index Per Article: 61.2] [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: 01/22/2018] [Accepted: 10/12/2018] [Indexed: 01/21/2023]
Abstract
Liability to alcohol dependence (AD) is heritable, but little is known about its complex polygenic architecture or its genetic relationship with other disorders. To discover loci associated with AD and characterize the relationship between AD and other psychiatric and behavioral outcomes, we carried out the largest genome-wide association study to date of DSM-IV-diagnosed AD. Genome-wide data on 14,904 individuals with AD and 37,944 controls from 28 case-control and family-based studies were meta-analyzed, stratified by genetic ancestry (European, n = 46,568; African, n = 6,280). Independent, genome-wide significant effects of different ADH1B variants were identified in European (rs1229984; P = 9.8 × 10-13) and African ancestries (rs2066702; P = 2.2 × 10-9). Significant genetic correlations were observed with 17 phenotypes, including schizophrenia, attention deficit-hyperactivity disorder, depression, and use of cigarettes and cannabis. The genetic underpinnings of AD only partially overlap with those for alcohol consumption, underscoring the genetic distinction between pathological and nonpathological drinking behaviors.
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Affiliation(s)
- Raymond K Walters
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Renato Polimanti
- Department of Psychiatry, Yale School of Medicine and Veterans Affairs Connecticut Healthcare Center, West Haven, CT, USA
| | - Emma C Johnson
- Washington University School of Medicine, Department of Psychiatry, St. Louis, MO, USA
| | - Jeanette N McClintick
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Mark J Adams
- University of Edinburgh, Division of Psychiatry, Edinburgh, UK
| | - Amy E Adkins
- Department of Psychology & College Behavioral and Emotional Health Institute, Virginia Commonwealth University, Richmond, VA, USA
| | - Fazil Aliev
- Virginia Commonwealth University, Department of Psychology, Richmond, VA, USA
| | - Silviu-Alin Bacanu
- Virginia Commonwealth University Alcohol Research Center; Virginia Institute for Psychiatric and Behavioral Genetics; Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - Anthony Batzler
- Mayo Clinic, Psychiatric Genomics and Pharmacogenomics Program, Rochester, MN, USA
| | - Sarah Bertelsen
- Icahn School of Medicine at Mount Sinai, Department of Neuroscience, New York, NY, USA
| | - Joanna M Biernacka
- Mayo Clinic, Department of Health Sciences Research, and Department of Psychiatry and Psychology, Rochester, MN, USA
| | - Tim B Bigdeli
- Department of Psychiatry and Behavioral Sciences, State University of New York Downstate Medical Center, Brooklyn, NY, USA
| | - Li-Shiun Chen
- Washington University School of Medicine, Department of Psychiatry, St. Louis, MO, USA
| | - Toni-Kim Clarke
- University of Edinburgh, Division of Psychiatry, Edinburgh, UK
| | - Yi-Ling Chou
- Washington University School of Medicine, Department of Psychiatry, St. Louis, MO, USA
| | - Franziska Degenhardt
- Institute of Human Genetics, University of Bonn; and Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Anna R Docherty
- University of Utah, Department of Psychiatry, Salt Lake City, UT, USA
| | - Alexis C Edwards
- Virginia Commonwealth University, Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Richmond, VA, USA
| | | | - Jerome C Foo
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Louis Fox
- Washington University School of Medicine, Department of Psychiatry, St. Louis, MO, USA
| | - Josef Frank
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Ina Giegling
- Martin-Luther-University Halle-Wittenberg, Department of Psychiatry, Psychotherapy and Psychosomatics, Halle, Germany
| | - Scott Gordon
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Laura M Hack
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Annette M Hartmann
- Martin-Luther-University Halle-Wittenberg, Department of Psychiatry, Psychotherapy and Psychosomatics, Halle, Germany
| | - Sarah M Hartz
- Washington University School of Medicine, Department of Psychiatry, St. Louis, MO, USA
| | - Stefanie Heilmann-Heimbach
- Institute of Human Genetics, University of Bonn; and Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Stefan Herms
- Institute of Human Genetics, University of Bonn; and Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
- Human Genomics Research Group, Department of Biomedicine, University of Basel Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | | | - Per Hoffmann
- Institute of Human Genetics, University of Bonn; and Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
- Human Genomics Research Group, Department of Biomedicine, University of Basel Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Jouke Jan Hottenga
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | | | - Mervi Alanne-Kinnunen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Bettina Konte
- Martin-Luther-University Halle-Wittenberg, Department of Psychiatry, Psychotherapy and Psychosomatics, Halle, Germany
| | - Jari Lahti
- Helsinki Collegium for Advanced Studies, University of Helsinki, Helsinki, Finland
- Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
| | | | - Dongbing Lai
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Lannie Ligthart
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Anu Loukola
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Brion S Maher
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Hamdi Mbarek
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Andrew M McIntosh
- University of Edinburgh, Division of Psychiatry, Centre for Cognitive Ageing and Cognitive Epidemiology, Edinburgh, UK
| | - Matthew B McQueen
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Jacquelyn L Meyers
- Henri Begleiter Neurodynamics Laboratory, Department of Psychiatry and Behavioral Sciences, SUNY Downstate Medical Center, Brooklyn, NY, USA
| | - Yuri Milaneschi
- Department of Psychiatry, Amsterdam Public Health Research Institute, VU University Medical Center/GGz inGeest, Amsterdam, The Netherlands
| | - Teemu Palviainen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - John F Pearson
- Biostatistics and Computational Biology Unit, University of Otago, Christchurch, New Zealand
| | - Roseann E Peterson
- Virginia Commonwealth University, Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Richmond, VA, USA
| | - Samuli Ripatti
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Euijung Ryu
- Mayo Clinic, Department of Health Sciences Research, Rochester, MN, USA
| | - Nancy L Saccone
- Washington University School of Medicine, Department of Genetics, St. Louis, MO, USA
| | - Jessica E Salvatore
- Virginia Commonwealth University, Department of Psychology, Richmond, VA, USA
- Virginia Commonwealth University, Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Richmond, VA, USA
| | - Sandra Sanchez-Roige
- University of California San Diego, Department of Psychiatry, San Diego, CA, USA
| | | | - Richard Sherva
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - Fabian Streit
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Jana Strohmaier
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Nathaniel Thomas
- Department of Psychology & College Behavioral and Emotional Health Institute, Virginia Commonwealth University, Richmond, VA, USA
| | - Jen-Chyong Wang
- Icahn School of Medicine at Mount Sinai, Department of Neuroscience, New York, NY, USA
| | - Bradley T Webb
- Virginia Commonwealth University Alcohol Research Center; Virginia Institute for Psychiatric and Behavioral Genetics; Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - Robbee Wedow
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Sociology, Harvard University, Cambridge, MA, USA
| | - Leah Wetherill
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Amanda G Wills
- University of Colorado School of Medicine, Department of Pharmacology, Aurora, CO, USA
| | - Jason D Boardman
- Institute of Behavioral Science and Department of Sociology, University of Colorado, Boulder, CO, USA
| | - Danfeng Chen
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Doo-Sup Choi
- Mayo Clinic, Department of Molecular Pharmacology and Experimental Therapeutics, Rochester, MN, USA
| | - William E Copeland
- Duke University Medical Center, Department of Psychiatry and Behavioral Sciences, Durham, NC, USA
| | - Robert C Culverhouse
- Washington University School of Medicine, Department of Medicine and Division of Biostatistics, St. Louis, MO, USA
| | - Norbert Dahmen
- Department of Psychiatry, University of Mainz, Mainz, Germany
| | - Louisa Degenhardt
- National Drug and Alcohol Research Centre, University of New South Wales, Sydney, New South Wales, Australia
| | | | | | - Mark A Frye
- Mayo Clinic, Department of Psychiatry and Psychology, Rochester, MN, USA
| | - Wolfgang Gäbel
- Department of Psychiatry and Psychotherapy, University of Düsseldorf, Düsseldorf, Germany
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Marcus Ising
- Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Margaret Keyes
- University of Minnesota, Department of Psychology, Minneapolis, MN, USA
| | - Falk Kiefer
- Department of Addictive Behavior and Addiction Medicine, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - John Kramer
- University of Iowa Roy J and Lucille A Carver College of Medicine, Department of Psychiatry, Iowa City, IA, USA
| | - Samuel Kuperman
- University of Iowa Roy J and Lucille A Carver College of Medicine, Department of Psychiatry, Iowa City, IA, USA
| | | | - Michael T Lynskey
- Addictions Department, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Wolfgang Maier
- Department of Psychiatry, University of Bonn, Bonn, Germany
| | - Karl Mann
- Department of Addictive Behavior and Addiction Medicine, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | | | - Bertram Müller-Myhsok
- Department of Statistical Genetics, Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Alison D Murray
- The Institute of Medical Sciences, Aberdeen Biomedical Imaging Centre, University of Aberdeen, Aberdeen, UK
| | - John I Nurnberger
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Aarno Palotie
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Department of Medicine, Department of Neurology and Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Ulrich Preuss
- Martin-Luther-University Halle-Wittenberg, Department of Psychiatry, Psychotherapy and Psychosomatics, Halle, Germany
- Vitos Hospital Herborn, Department of Psychiatry and Psychotherapy, Herborn, Germany
| | - Katri Räikkönen
- Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
| | | | - Monika Ridinger
- Department of Psychiatry and Psychotherapy, University of Regensburg Psychiatric Health Care Aargau, Regensburg, Germany
| | - Norbert Scherbaum
- LVR-Hospital Essen, Department of Psychiatry and Psychotherapy, Department of Addictive Behaviour and Addiction Medicine, Medical Faculty, University of Duisburg-Essen, Duisburg, Germany
| | - Marc A Schuckit
- University of California San Diego, Department of Psychiatry, San Diego, CA, USA
| | - Michael Soyka
- Medical Park Chiemseeblick in Bernau-Felden, Chiemsee, Germany
- Psychiatric Hospital, Ludwig-Maximilians-University, Munich, Germany
| | - Jens Treutlein
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Stephanie Witt
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Norbert Wodarz
- Department of Psychiatry and Psychotherapy, University of Regensburg, Regensburg, Germany
| | - Peter Zill
- Psychiatric Hospital, Ludwig-Maximilians-University, Munich, Germany
| | - Daniel E Adkins
- University of Utah, Department of Psychiatry, Salt Lake City, UT, USA
- University of Utah, Department of Sociology, Salt Lake City, UT, USA
| | | | - Dorret I Boomsma
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Laura J Bierut
- Washington University School of Medicine, Department of Psychiatry, St. Louis, MO, USA
| | - Sandra A Brown
- University of California San Diego, Department of Psychiatry, San Diego, CA, USA
- University of California, San Diego School of Medicine, Department of Psychology, San Diego, CA, USA
| | - Kathleen K Bucholz
- Washington University School of Medicine, Department of Psychiatry, St. Louis, MO, USA
| | - Sven Cichon
- Human Genomics Research Group, Department of Biomedicine, University of Basel Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - E Jane Costello
- Duke University Medical Center, Department of Psychiatry and Behavioral Sciences, Durham, NC, USA
| | | | | | - Danielle M Dick
- Department of Psychology & College Behavioral and Emotional Health Institute, Virginia Commonwealth University, Richmond, VA, USA
- Department of Human & Molecular Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - Johan G Eriksson
- Department of General Practice and Primary Health Care, University of Helsinki, and National Institute for Health and Welfare, Helsinki, Finland
| | - Lindsay A Farrer
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
- Departments of Neurology, Ophthalmology, Epidemiology, and Biostatistics, Boston University Schools of Medicine and Public Health, Boston, MA, USA
| | - Tatiana M Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Nathan A Gillespie
- Virginia Commonwealth University, Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Richmond, VA, USA
| | - Alison M Goate
- Icahn School of Medicine at Mount Sinai, Department of Neuroscience, New York, NY, USA
| | - David Goldman
- NIH/NIAAA, Laboratory of Neurogenetics, Bethesda, MD, USA
- NIH/NIAAA, Office of the Clinical Director, Bethesda, MD, USA
| | - Richard A Grucza
- Washington University School of Medicine, Department of Psychiatry, St. Louis, MO, USA
| | - Dana B Hancock
- Center for Omics Discovery and Epidemiology, Behavioral Health Research Division, RTI International, Research Triangle Park, NC, USA
| | - Kathleen Mullan Harris
- Department of Sociology and Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Andrew C Heath
- Washington University School of Medicine, Department of Psychiatry, St. Louis, MO, USA
| | - Victor Hesselbrock
- University of Connecticut School of Medicine, Department of Psychiatry, Farmington, CT, USA
| | - John K Hewitt
- University of Colorado Boulder, Institute for Behavioral Genetics, Boulder, CO, USA
| | | | | | - William Iacono
- University of Minnesota, Department of Psychology, Minneapolis, MN, USA
| | - Eric O Johnson
- RTI International, Fellows Program, Research Triangle Park, NC, USA
| | - Jaakko A Kaprio
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Victor M Karpyak
- Mayo Clinic, Department of Psychiatry and Psychology, Rochester, MN, USA
| | - Kenneth S Kendler
- Virginia Commonwealth University Alcohol Research Center; Virginia Institute for Psychiatric and Behavioral Genetics; Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - Henry R Kranzler
- University of Pennsylvania Perelman School of Medicine, Center for Studies of Addiction, Department of Psychiatry and VISN 4 MIRECC, Crescenz VAMC, Philadelphia, PA, USA
| | - Kenneth Krauter
- University of Colorado Boulder, Department of Molecular, Cellular, and Developmental Biology, Boulder, CO, USA
| | - Paul Lichtenstein
- Department of Medical Epidemiology and Biostatistics, Karolinska Instituet, Stockholm, Sweden
| | - Penelope A Lind
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Matt McGue
- University of Minnesota, Department of Psychology, Minneapolis, MN, USA
| | - James MacKillop
- Peter Boris Centre for Addictions Research, McMaster University/St. Joseph's Healthcare Hamilton; Michael G. DeGroote Centre for Medicinal Cannabis Research, Hamilton, Ontario, Canada
| | - Pamela A F Madden
- Washington University School of Medicine, Department of Psychiatry, St. Louis, MO, USA
| | - Hermine H Maes
- Virginia Commonwealth University, Virginia Institute for Psychiatric and Behavioral Genetics, Richmond, VA, USA
| | - Patrik Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Instituet, Stockholm, Sweden
| | - Nicholas G Martin
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Sarah E Medland
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Grant W Montgomery
- The Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Elliot C Nelson
- Washington University School of Medicine, Department of Psychiatry, St. Louis, MO, USA
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Abraham A Palmer
- University of California San Diego, Department of Psychiatry, San Diego, CA, USA
- University of California San Diego, Institute for Genomic Medicine, San Diego, CA, USA
| | - Nancy L Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Instituet, Stockholm, Sweden
| | - Brenda W J H Penninx
- Department of Psychiatry, Amsterdam Public Health Research Institute, VU University Medical Center/GGz inGeest, Amsterdam, The Netherlands
| | - Bernice Porjesz
- Henri Begleiter Neurodynamics Laboratory, Department of Psychiatry and Behavioral Sciences, SUNY Downstate Medical Center, Brooklyn, NY, USA
| | - John P Rice
- Washington University School of Medicine, Department of Psychiatry, St. Louis, MO, USA
| | - Marcella Rietschel
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Brien P Riley
- Virginia Commonwealth University Alcohol Research Center; Virginia Institute for Psychiatric and Behavioral Genetics; Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - Richard Rose
- Department of Psychological & Brain Sciences, Indiana University Bloomington, Bloomington, IN, USA
| | - Dan Rujescu
- Martin-Luther-University Halle-Wittenberg, Department of Psychiatry, Psychotherapy and Psychosomatics, Halle, Germany
| | - Pei-Hong Shen
- NIH/NIAAA, Laboratory of Neurogenetics, Bethesda, MD, USA
| | - Judy Silberg
- Virginia Commonwealth University, Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Richmond, VA, USA
| | - Michael C Stallings
- University of Colorado Boulder, Institute for Behavioral Genetics, Boulder, CO, USA
| | - Ralph E Tarter
- University of Pittsburgh, School of Pharmacy, Pittsburgh, PA, USA
| | | | - Scott Vrieze
- University of Minnesota, Department of Psychology, Minneapolis, MN, USA
| | - Tamara L Wall
- University of California San Diego, Department of Psychiatry, San Diego, CA, USA
| | - John B Whitfield
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Benjamin M Neale
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joel Gelernter
- Departments of Psychiatry, Genetics, and Neuroscience, Yale University School of Medicine, Veterans Affairs Connecticut Healthcare System, New Haven, CT, USA.
| | - Howard J Edenberg
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA.
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Arpana Agrawal
- Washington University School of Medicine, Department of Psychiatry, St. Louis, MO, USA.
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10
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Frump AL, Albrecht ME, McClintick JN, Lahm T. Estrogen receptor-dependent attenuation of hypoxia-induced changes in the lung genome of pulmonary hypertension rats. Pulm Circ 2017; 7:232-243. [PMID: 28680582 PMCID: PMC5448529 DOI: 10.1177/2045893217702055] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 12/27/2016] [Indexed: 12/19/2022] Open
Abstract
17β-estradiol (E2) exerts complex and context-dependent effects in pulmonary hypertension. In hypoxia-induced pulmonary hypertension (HPH), E2 attenuates lung vascular remodeling through estrogen receptor (ER)-dependent effects; however, ER target genes in the hypoxic lung remain unknown. In order to identify the genome regulated by the E2-ER axis in the hypoxic lung, we performed a microarray analysis in lungs from HPH rats treated with E2 (75 mcg/kg/day) ± ER-antagonist ICI182,780 (3 mg/kg/day). Untreated HPH rats and normoxic rats served as controls. Using a false discovery rate of 10%, we identified a significantly differentially regulated genome in E2-treated versus untreated hypoxia rats. Genes most upregulated by E2 encoded matrix metalloproteinase 8, S100 calcium binding protein A8, and IgA Fc receptor; genes most downregulated by E2 encoded olfactory receptor 63, secreted frizzled-related protein 2, and thrombospondin 2. Several genes affected by E2 changed in the opposite direction after ICI182,780 co-treatment, indicating an ER-regulated genome in HPH lungs. The bone morphogenetic protein antagonist Grem1 (gremlin 1) was upregulated by hypoxia, but found to be among the most downregulated genes after E2 treatment. Gremlin 1 protein was reduced in E2-treated versus untreated hypoxic animals, and ER-blockade abolished the inhibitory effect of E2 on Grem1 mRNA and protein. In conclusion, E2 ER-dependently regulates several genes involved in proliferative and inflammatory processes during hypoxia. Gremlin 1 is a novel target of the E2-ER axis in HPH. Understanding the mechanisms of E2 gene regulation in HPH may allow for selectively harnessing beneficial transcriptional activities of E2 for therapeutic purposes.
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Affiliation(s)
- Andrea L Frump
- Department of Medicine; Division of Pulmonary, Critical Care, Sleep and Occupational Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Marjorie E Albrecht
- Department of Medicine; Division of Pulmonary, Critical Care, Sleep and Occupational Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Jeanette N McClintick
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA.,Center for Medical Genomics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Tim Lahm
- Department of Medicine; Division of Pulmonary, Critical Care, Sleep and Occupational Medicine, Indiana University School of Medicine, Indianapolis, IN, USA.,Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, IN, USA.,Richard L. Roudebush Veterans Affairs Medical Center, Indianapolis, IN, USA
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11
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Herring BP, Hoggatt AM, Griffith SL, McClintick JN, Gallagher PJ. Inflammation and vascular smooth muscle cell dedifferentiation following carotid artery ligation. Physiol Genomics 2016; 49:115-126. [PMID: 28039430 PMCID: PMC5374455 DOI: 10.1152/physiolgenomics.00095.2016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 12/21/2016] [Accepted: 12/21/2016] [Indexed: 11/22/2022] Open
Abstract
Following vascular injury medial smooth muscle cells dedifferentiate and migrate through the internal elastic lamina where they form a neointima. The goal of the current study was to identify changes in gene expression that occur before the development of neointima and are associated with the early response to injury. Vascular injury was induced in C57BL/6 mice and in Myh11-creER(T2) mTmG reporter mice by complete ligation of the left carotid artery. Reporter mice were used to visualize cellular changes in the injured vessels. Total RNA was isolated from control carotid arteries or from carotid arteries 3 days following ligation of C57BL/6 mice and analyzed by Affymetrix microarray and quantitative RT-PCR. This analysis revealed decreased expression of mRNAs encoding smooth muscle-specific contractile proteins that was accompanied by a marked increase in a host of mRNAs encoding inflammatory cytokines following injury. There was also marked decrease in molecules associated with BMP, Wnt, and Hedgehog signaling and an increase in those associated with B cell, T cell, and macrophage signaling. Expression of a number of noncoding RNAs were also altered following injury with microRNAs 143/145 being dramatically downregulated and microRNAs 1949 and 142 upregulated. Several long noncoding RNAs showed altered expression that mirrored the expression of their nearest coding genes. These data demonstrate that following carotid artery ligation an inflammatory cascade is initiated that is associated with the downregulation of coding and noncoding RNAs that are normally required to maintain smooth muscle cells in a differentiated state.
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Affiliation(s)
- B Paul Herring
- Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, Indiana; and
| | - April M Hoggatt
- Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, Indiana; and
| | - Sarah L Griffith
- Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, Indiana; and
| | - Jeanette N McClintick
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Patricia J Gallagher
- Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, Indiana; and
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12
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Anand A, McClintick JN, Murrell J, Karne H, Nurnberger JI, Edenberg HJ. Effects of Lithium Monotherapy for Bipolar Disorder on Gene Expression in Peripheral Lymphocytes. Mol Neuropsychiatry 2016; 2:115-123. [PMID: 27867936 DOI: 10.1159/000446348] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 04/20/2016] [Indexed: 11/19/2022]
Abstract
BACKGROUND This study investigated the effect of lithium monotherapy on peripheral lymphocyte gene expression in bipolar disorder (BD). METHOD Twenty-two medication-free bipolar subjects (11 hypomanic, 11 depressed) were started on lithium monotherapy. Closely matched healthy subjects (n = 15) were included as controls but did not receive treatment. Blood RNA samples were collected at baseline and after 2 and 8 weeks of treatment. RNA expression was measured using the Affymetrix GeneChip® Human Gene 1.0 ST Array followed by Ingenuity pathways analysis. The results for the contrast of weeks 2 and 8 were not significantly different and were combined. RESULTS In BD subjects, 56 genes showed significant (false discovery rate <0.1) expression changes from baseline; the effect sizes and directions for all of these were similar at weeks 2 and 8. Among these were immune-related genes (IL5RA, MOK, IFI6, and RFX2), purinergic receptors (P2RY14, P2RY2, and ADORA3) and signal transduction-related genes (CAMK1 and PIK3R6). Pathway and upstream regulator analysis also revealed that lithium altered several immune- and signal transduction-related functions. Differentially expressed genes did not correlate with week 8 clinical response, but other genes involved in protein synthesis and degradation did. CONCLUSION Peripheral gene expression may serve as a biomarker of lithium effect.
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Affiliation(s)
- Amit Anand
- Center for Behavioral Health, Cleveland Clinic, Cleveland, Ohio, USA; Department of Psychiatry, Indiana University School of Medicine, Indianapolis, Ind., USA
| | - Jeanette N McClintick
- Department of Biochemistry and Molecular Biology and Center for Medical Genomics, Indiana University School of Medicine, Indianapolis, Ind., USA
| | - Jill Murrell
- Department of Biochemistry and Molecular Biology and Center for Medical Genomics, Indiana University School of Medicine, Indianapolis, Ind., USA
| | - Harish Karne
- Center for Behavioral Health, Cleveland Clinic, Cleveland, Ohio, USA; Department of Psychiatry, Indiana University School of Medicine, Indianapolis, Ind., USA
| | - John I Nurnberger
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, Ind., USA
| | - Howard J Edenberg
- Department of Biochemistry and Molecular Biology and Center for Medical Genomics, Indiana University School of Medicine, Indianapolis, Ind., USA
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13
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Sassoon DJ, Goodwill AG, Noblet JN, Conteh AM, Herring BP, McClintick JN, Tune JD, Mather KJ. Obesity alters molecular and functional cardiac responses to ischemia/reperfusion and glucagon-like peptide-1 receptor agonism. Basic Res Cardiol 2016; 111:43. [PMID: 27234258 DOI: 10.1007/s00395-016-0563-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [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: 02/23/2016] [Accepted: 05/18/2016] [Indexed: 12/22/2022]
Abstract
This study tested the hypothesis that obesity alters the cardiac response to ischemia/reperfusion and/or glucagon like peptide-1 (GLP-1) receptor activation, and that these differences are associated with alterations in the obese cardiac proteome and microRNA (miRNA) transcriptome. Ossabaw swine were fed normal chow or obesogenic diet for 6 months. Cardiac function was assessed at baseline, during a 30-minutes coronary occlusion, and during 2 hours of reperfusion in anesthetized swine treated with saline or exendin-4 for 24 hours. Cardiac biopsies were obtained from normal and ischemia/reperfusion territories. Fat-fed animals were heavier, and exhibited hyperinsulinemia, hyperglycemia, and hypertriglyceridemia. Plasma troponin-I concentration (index of myocardial injury) was increased following ischemia/reperfusion and decreased by exendin-4 treatment in both groups. Ischemia/reperfusion produced reductions in systolic pressure and stroke volume in lean swine. These indices were higher in obese hearts at baseline and relatively maintained throughout ischemia/reperfusion. Exendin-4 administration increased systolic pressure in lean swine but did not affect the blood pressure in obese swine. End-diastolic volume was reduced by exendin-4 following ischemia/reperfusion in obese swine. These divergent physiologic responses were associated with obesity-related differences in proteins related to myocardial structure/function (e.g. titin) and calcium handling (e.g. SERCA2a, histidine-rich Ca(2+) binding protein). Alterations in expression of cardiac miRs in obese hearts included miR-15, miR-27, miR-130, miR-181, and let-7. Taken together, these observations validate this discovery approach and reveal novel associations that suggest previously undiscovered mechanisms contributing to the effects of obesity on the heart and contributing to the actions of GLP-1 following ischemia/reperfusion.
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Affiliation(s)
- Daniel J Sassoon
- Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, USA
| | - Adam G Goodwill
- Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, USA
| | - Jillian N Noblet
- Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, USA
| | - Abass M Conteh
- Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, USA
| | - B Paul Herring
- Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, USA
| | - Jeanette N McClintick
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, USA
| | - Johnathan D Tune
- Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, USA
| | - Kieren J Mather
- Department of Medicine, Indiana University School of Medicine, 1120 W. Michigan St., Suite CL365, Indianapolis, IN, 46202, USA.
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14
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McClintick JN, McBride WJ, Bell RL, Ding ZM, Liu Y, Xuei X, Edenberg HJ. Gene Expression Changes in Glutamate and GABA-A Receptors, Neuropeptides, Ion Channels, and Cholesterol Synthesis in the Periaqueductal Gray Following Binge-Like Alcohol Drinking by Adolescent Alcohol-Preferring (P) Rats. Alcohol Clin Exp Res 2016; 40:955-68. [PMID: 27061086 DOI: 10.1111/acer.13056] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 02/28/2016] [Indexed: 12/31/2022]
Abstract
BACKGROUND Binge drinking of alcohol during adolescence is a serious public health concern with long-term consequences, including increased pain, fear, and anxiety. The periaqueductal gray (PAG) is involved in processing pain, fear, and anxiety. The effects of adolescent binge drinking on gene expression in this region have yet to be studied. METHODS Male adolescent alcohol-preferring (P) rats were exposed to repeated binge drinking (three 1-hour sessions/d during the dark/cycle, 5 days/wk for 3 weeks starting at 28 days of age; ethanol intakes of 2.5 to 3 g/kg/session). We used RNA sequencing to assess the effects of ethanol intake on gene expression. RESULTS Ethanol significantly altered the expression of 1,670 of the 12,123 detected genes: 877 (53%) decreased. In the glutamate system, 23 genes were found to be altered, including reduction in 7 of 10 genes for metabotropic and NMDA receptors. Subunit changes in the NMDA receptor may make it less sensitive to ethanol. Changes in GABAA genes would most likely increase the ability of the PAG to produce tonic inhibition. Five serotonin receptor genes, 6 acetylcholine receptor genes, and 4 glycine receptor genes showed decreased expression in the alcohol-drinking rats. Opioid genes (e.g., Oprk1, Oprm1) and genes for neuropeptides linked to anxiety and panic behaviors (e.g., Npy1r) had mostly decreased expression. Genes for 27 potassium, 10 sodium, and 5 calcium ion channels were found to be differentially expressed. Nine genes in the cholesterol synthesis pathway had decreased expression, including Hmgcr, encoding the rate-limiting enzyme. Genes involved in the production of myelin also had decreased expression. CONCLUSIONS The results demonstrate that binge alcohol drinking during adolescence produces developmental changes in the expression of key genes within the PAG; many of these changes point to increased susceptibility to pain, fear, and anxiety, which could contribute to excessive drinking to relieve these negative effects.
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Affiliation(s)
- Jeanette N McClintick
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana.,Center for Medical Genomics, Indiana University School of Medicine, Indianapolis, Indiana
| | - William J McBride
- Institute of Psychiatric Research, Department of Psychiatry, Indiana University School of Medicine, Indianapolis, Indiana
| | - Richard L Bell
- Institute of Psychiatric Research, Department of Psychiatry, Indiana University School of Medicine, Indianapolis, Indiana
| | - Zheng-Ming Ding
- Institute of Psychiatric Research, Department of Psychiatry, Indiana University School of Medicine, Indianapolis, Indiana
| | - Yunlong Liu
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Xiaoling Xuei
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana.,Center for Medical Genomics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Howard J Edenberg
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana.,Center for Medical Genomics, Indiana University School of Medicine, Indianapolis, Indiana.,Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
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15
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Blue EK, Sheehan BM, Nuss ZV, Boyle FA, Hocutt CM, Gohn CR, Varberg KM, McClintick JN, Haneline LS. Epigenetic Regulation of Placenta-Specific 8 Contributes to Altered Function of Endothelial Colony-Forming Cells Exposed to Intrauterine Gestational Diabetes Mellitus. Diabetes 2015; 64:2664-75. [PMID: 25720387 PMCID: PMC4477353 DOI: 10.2337/db14-1709] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 02/15/2015] [Indexed: 12/19/2022]
Abstract
Intrauterine exposure to gestational diabetes mellitus (GDM) is linked to development of hypertension, obesity, and type 2 diabetes in children. Our previous studies determined that endothelial colony-forming cells (ECFCs) from neonates exposed to GDM exhibit impaired function. The current goals were to identify aberrantly expressed genes that contribute to impaired function of GDM-exposed ECFCs and to evaluate for evidence of altered epigenetic regulation of gene expression. Genome-wide mRNA expression analysis was conducted on ECFCs from control and GDM pregnancies. Candidate genes were validated by quantitative RT-PCR and Western blotting. Bisulfite sequencing evaluated DNA methylation of placenta-specific 8 (PLAC8). Proliferation and senescence assays of ECFCs transfected with siRNA to knockdown PLAC8 were performed to determine functional impact. Thirty-eight genes were differentially expressed between control and GDM-exposed ECFCs. PLAC8 was highly expressed in GDM-exposed ECFCs, and PLAC8 expression correlated with maternal hyperglycemia. Methylation status of 17 CpG sites in PLAC8 negatively correlated with mRNA expression. Knockdown of PLAC8 in GDM-exposed ECFCs improved proliferation and senescence defects. This study provides strong evidence in neonatal endothelial progenitor cells that GDM exposure in utero leads to altered gene expression and DNA methylation, suggesting the possibility of altered epigenetic regulation.
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Affiliation(s)
- Emily K Blue
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN
| | - BreAnn M Sheehan
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN
| | - Zia V Nuss
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN
| | - Frances A Boyle
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN
| | - Caleb M Hocutt
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN
| | - Cassandra R Gohn
- Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, IN
| | - Kaela M Varberg
- Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, IN
| | - Jeanette N McClintick
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN
| | - Laura S Haneline
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, IN Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN Indiana University Melvin and Bren Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN
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16
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Chaturvedi P, Chen NX, O'Neill K, McClintick JN, Moe SM, Janga SC. Differential miRNA Expression in Cells and Matrix Vesicles in Vascular Smooth Muscle Cells from Rats with Kidney Disease. PLoS One 2015; 10:e0131589. [PMID: 26115487 PMCID: PMC4482652 DOI: 10.1371/journal.pone.0131589] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [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: 02/18/2015] [Accepted: 06/02/2015] [Indexed: 01/14/2023] Open
Abstract
Vascular calcification is a complex process and has been associated with aging, diabetes, chronic kidney disease (CKD). Although there have been several studies that examine the role of miRNAs (miRs) in bone osteogenesis, little is known about the role of miRs in vascular calcification and their role in the pathogenesis of vascular abnormalities. Matrix vesicles (MV) are known to play in important role in initiating vascular smooth muscle cell (VSMC) calcification. In the present study, we performed miRNA microarray analysis to identify the dysregulated miRs between MV and VSMC derived from CKD rats to understand the role of post-transcriptional regulatory networks governed by these miRNAs in vascular calcification and to uncover the differential miRNA content of MV. The percentage of miRNA to total RNA was increased in MV compared to VSMC. Comparison of expression profiles of miRNA by microarray demonstrated 33 miRs to be differentially expressed with the majority (~ 57%) of them down-regulated. Target genes controlled by differentially expressed miRNAs were identified utilizing two different complementary computational approaches Miranda and Targetscan to understand the functions and pathways that may be affected due to the production of MV from calcifying VSMC thereby contributing to the regulation of genes by miRs. We found several processes including vascular smooth muscle contraction, response to hypoxia and regulation of muscle cell differentiation to be enriched. Signaling pathways identified included MAP-kinase and wnt signaling that have previously been shown to be important in vascular calcification. In conclusion, our results demonstrate that miRs are concentrated in MV from calcifying VSMC, and that important functions and pathways are affected by the miRs dysregulation between calcifying VSMC and the MV they produce. This suggests that miRs may play a very important regulatory role in vascular calcification in CKD by controlling an extensive network of post-transcriptional targets.
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Affiliation(s)
- Praneet Chaturvedi
- Department of Biohealth Informatics, School of Informatics and Computing, Indiana University Purdue University, Indianapolis, Indiana, United States of America
| | - Neal X Chen
- Division of Nephrology, Department of Medicine, School of Medicine, Indiana University, Indianapolis, Indiana, United States of America
| | - Kalisha O'Neill
- Division of Nephrology, Department of Medicine, School of Medicine, Indiana University, Indianapolis, Indiana, United States of America
| | - Jeanette N McClintick
- Division of Nephrology, Department of Medicine, School of Medicine, Indiana University, Indianapolis, Indiana, United States of America
| | - Sharon M Moe
- Division of Nephrology, Department of Medicine, School of Medicine, Indiana University, Indianapolis, Indiana, United States of America; Roudebush VA Medical Center, Indianapolis, Indiana, United States of America
| | - Sarath Chandra Janga
- Department of Biohealth Informatics, School of Informatics and Computing, Indiana University Purdue University, Indianapolis, Indiana, United States of America; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 5021 Health Information and Translational Sciences (HITS), Indianapolis, Indiana, United States of America; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Medical Research and Library Building, Indianapolis, Indiana, United States of America
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17
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Salvatore JE, Edwards AC, McClintick JN, Bigdeli TB, Adkins A, Aliev F, Edenberg HJ, Foroud T, Hesselbrock V, Kramer J, Nurnberger JI, Schuckit M, Tischfield JA, Xuei X, Dick DM. Genome-wide association data suggest ABCB1 and immune-related gene sets may be involved in adult antisocial behavior. Transl Psychiatry 2015; 5:e558. [PMID: 25918995 PMCID: PMC4462601 DOI: 10.1038/tp.2015.36] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 02/09/2015] [Indexed: 11/09/2022] Open
Abstract
Adult antisocial behavior (AAB) is moderately heritable, relatively common and has adverse consequences for individuals and society. We examined the molecular genetic basis of AAB in 1379 participants from a case-control study in which the cases met criteria for alcohol dependence. We also examined whether genes of interest were expressed in human brain. AAB was measured using a count of the number of Antisocial Personality Disorder criteria endorsed under criterion A from the Diagnostic and Statistical Manual of Mental Disorders, 4th Edition (DSM-IV). Participants were genotyped on the Illumina Human 1M BeadChip. In total, all single-nucleotide polymorphisms (SNPs) accounted for 25% of the variance in AAB, although this estimate was not significant (P=0.09). Enrichment tests indicated that more significantly associated genes were over-represented in seven gene sets, and most were immune related. Our most highly associated SNP (rs4728702, P=5.77 × 10(-7)) was located in the protein-coding adenosine triphosphate-binding cassette, sub-family B (MDR/TAP), member 1 (ABCB1). In a gene-based test, ABCB1 was genome-wide significant (q=0.03). Expression analyses indicated that ABCB1 was robustly expressed in the brain. ABCB1 has been implicated in substance use, and in post hoc tests we found that variation in ABCB1 was associated with DSM-IV alcohol and cocaine dependence criterion counts. These results suggest that ABCB1 may confer risk across externalizing behaviors, and are consistent with previous suggestions that immune pathways are associated with externalizing behaviors. The results should be tempered by the fact that we did not replicate the associations for ABCB1 or the gene sets in a less-affected independent sample.
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Affiliation(s)
- J E Salvatore
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - A C Edwards
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - J N McClintick
- Department of Biochemistry and Molecular Biology, Indiana University, Indianapolis, IN, USA
| | - T B Bigdeli
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - A Adkins
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - F Aliev
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
- Department of Statistics and Institute of Biotechnology, Ankara University, Ankara, Turkey
| | - H J Edenberg
- Department of Biochemistry and Molecular Biology, Indiana University, Indianapolis, IN, USA
| | - T Foroud
- Department of Medical and Molecular Genetics, Indiana University, Indianapolis, IN, USA
| | - V Hesselbrock
- Department of Psychiatry, University of Connecticut, Farmington, CT, USA
| | - J Kramer
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - J I Nurnberger
- Department of Psychiatry, Indiana University, Indianapolis, IN, USA
| | - M Schuckit
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - J A Tischfield
- Department of Genetics, Rutgers University, Piscataway, NJ, USA
| | - X Xuei
- Department of Biochemistry and Molecular Biology, Indiana University, Indianapolis, IN, USA
| | - D M Dick
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
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Cheng S, Swanson K, Eliaz I, McClintick JN, Sandusky GE, Sliva D. Pachymic acid inhibits growth and induces apoptosis of pancreatic cancer in vitro and in vivo by targeting ER stress. PLoS One 2015; 10:e0122270. [PMID: 25915041 PMCID: PMC4411097 DOI: 10.1371/journal.pone.0122270] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 02/12/2015] [Indexed: 12/17/2022] Open
Abstract
Pachymic acid (PA) is a purified triterpene extracted from medicinal fungus Poria cocos. In this paper, we investigated the anticancer effect of PA on human chemotherapy resistant pancreatic cancer. PA triggered apoptosis in gemcitabine-resistant pancreatic cancer cells PANC-1 and MIA PaCa-2. Comparative gene expression array analysis demonstrated that endoplasmic reticulum (ER) stress was induced by PA through activation of heat shock response and unfolded protein response related genes. Induced ER stress was confirmed by increasing expression of XBP-1s, ATF4, Hsp70, CHOP and phospho-eIF2α. Moreover, ER stress inhibitor tauroursodeoxycholic acid (TUDCA) blocked PA induced apoptosis. In addition, 25 mg kg-1 of PA significantly suppressed MIA PaCa-2 tumor growth in vivo without toxicity, which correlated with induction of apoptosis and expression of ER stress related proteins in tumor tissues. Taken together, growth inhibition and induction of apoptosis by PA in gemcitabine-resistant pancreatic cancer cells were associated with ER stress activation both in vitro and in vivo. PA may be potentially exploited for the use in treatment of chemotherapy resistant pancreatic cancer.
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Affiliation(s)
- Shujie Cheng
- Cancer Research Laboratory, Methodist Research Institute, Indiana University Health, Indianapolis, Indiana, United States of America
| | - Kristen Swanson
- Cancer Research Laboratory, Methodist Research Institute, Indiana University Health, Indianapolis, Indiana, United States of America
| | - Isaac Eliaz
- Amitabha Medical Clinic and Healing Center, Santa Rosa, California, United States of America
| | - Jeanette N. McClintick
- Departments of Biochemistry and Molecular Biology, School of Medicine, Indiana University, Indianapolis, Indiana, United States of America
| | - George E. Sandusky
- Departments of Pathology, School of Medicine, Indiana University, Indianapolis, Indiana, United States of America
| | - Daniel Sliva
- Cancer Research Laboratory, Methodist Research Institute, Indiana University Health, Indianapolis, Indiana, United States of America
- Departments of Medicine, School of Medicine, Indiana University, Indianapolis, Indiana, United States of America
- DSTest Laboratories, Purdue Research Park, Indianapolis, Indiana, United States of America
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McClintick JN, McBride WJ, Bell RL, Ding ZM, Liu Y, Xuei X, Edenberg HJ. Gene expression changes in serotonin, GABA-A receptors, neuropeptides and ion channels in the dorsal raphe nucleus of adolescent alcohol-preferring (P) rats following binge-like alcohol drinking. Pharmacol Biochem Behav 2014; 129:87-96. [PMID: 25542586 PMCID: PMC4302739 DOI: 10.1016/j.pbb.2014.12.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [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: 11/12/2014] [Revised: 12/13/2014] [Accepted: 12/17/2014] [Indexed: 12/31/2022]
Abstract
Alcohol binge-drinking during adolescence is a serious public health concern with long-term consequences. We used RNA sequencing to assess the effects of excessive adolescent ethanol binge-drinking on gene expression in the dorsal raphe nucleus (DRN) of alcohol preferring (P) rats. Repeated binges across adolescence (three 1h sessions across the dark-cycle per day, 5 days per week for 3 weeks starting at 28 days of age; ethanol intakes of 2.5-3 g/kg/session) significantly altered the expression of approximately one-third of the detected genes. Multiple neurotransmitter systems were altered, with the largest changes in the serotonin system (21 of 23 serotonin-related genes showed decreased expression) and GABA-A receptors (8 decreased and 2 increased). Multiple neuropeptide systems were also altered, with changes in the neuropeptide Y and corticotropin-releasing hormone systems similar to those associated with increased drinking and decreased resistance to stress. There was increased expression of 21 of 32 genes for potassium channels. Expression of downstream targets of CREB signaling was increased. There were also changes in expression of genes involved in inflammatory processes, axonal guidance, growth factors, transcription factors, and several intracellular signaling pathways. These widespread changes indicate that excessive binge drinking during adolescence alters the functioning of the DRN and likely its modulation of many regions of the central nervous system, including the mesocorticolimbic system.
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Affiliation(s)
- Jeanette N McClintick
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, United States; Center for Medical Genomics, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - William J McBride
- Institute of Psychiatric Research, Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - Richard L Bell
- Institute of Psychiatric Research, Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - Zheng-Ming Ding
- Institute of Psychiatric Research, Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - Yunlong Liu
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - Xiaoling Xuei
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, United States; Center for Medical Genomics, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - Howard J Edenberg
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, United States; Center for Medical Genomics, Indiana University School of Medicine, Indianapolis, IN 46202, United States; Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, United States.
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20
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McClintick JN, Brooks AI, Deng L, Liang L, Wang JC, Kapoor M, Xuei X, Foroud T, Tischfield JA, Edenberg HJ. Ethanol treatment of lymphoblastoid cell lines from alcoholics and non-alcoholics causes many subtle changes in gene expression. Alcohol 2014; 48:603-10. [PMID: 25129674 PMCID: PMC4730944 DOI: 10.1016/j.alcohol.2014.07.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [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: 12/14/2022]
Abstract
To elucidate the effects of a controlled exposure to ethanol on gene expression, we studied lymphoblastoid cell lines (LCLs) from 21 alcoholics and 21 controls. We cultured each cell line for 24 h with and without 75 mM ethanol and measured gene expression using microarrays. Differences in expression between LCLs from alcoholics and controls included 13 genes previously identified as associated with alcoholism or related traits, including KCNA3, DICER1, ZNF415, CAT, SLC9A9, and PPARGC1B. The paired design allowed us to detect very small changes due to ethanol treatment: ethanol altered the expression of 37% of the probe sets (51% of the unique named genes) expressed in these LCLs, most by modest amounts. Ninety-nine percent of the named genes expressed in the LCLs were also expressed in brain. Key pathways affected by ethanol include cytokine, TNF, and NFκB signaling. Among the genes affected by ethanol were ANK3, EPHB1, SLC1A1, SLC9A9, NRD1, and SH3BP5, which were reported to be associated with alcoholism or related phenotypes in 2 genome-wide association studies. Genes that either differed in expression between alcoholics and controls or were affected by ethanol exposure are candidates for further study.
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Affiliation(s)
- Jeanette N McClintick
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Andrew I Brooks
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Li Deng
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Li Liang
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Jen C Wang
- Department of Psychiatry, B8134, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO 63110, USA
| | - Manav Kapoor
- Department of Psychiatry, B8134, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO 63110, USA
| | - Xiaoling Xuei
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Tatiana Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Jay A Tischfield
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Howard J Edenberg
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA.
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Baird TD, Palam LR, Fusakio ME, Willy JA, Davis CM, McClintick JN, Anthony TG, Wek RC. Selective mRNA translation during eIF2 phosphorylation induces expression of IBTKα. Mol Biol Cell 2014; 25:1686-97. [PMID: 24648495 PMCID: PMC4019499 DOI: 10.1091/mbc.e14-02-0704] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
This study measured changes in global mRNA translation in response to ER stress. The analysis suggests that translation of a majority of gene transcripts is either repressed or resistant, whereas select key regulators are subject to preferential translation. From this last group, IBTKα is identified as a novel target of the UPR central to cell fate. Disruption of protein folding in the endoplasmic reticulum (ER) triggers the unfolded protein response (UPR), a transcriptional and translational control network designed to restore protein homeostasis. Central to the UPR is PKR-like ER kinase (PERK/EIF2AK3) phosphorylation of the α subunit of eIF2 (eIF2α∼P), which represses global translation coincident with preferential translation of mRNAs, such as activating transcription factor 4 (ATF4) and C/EBP-homologous protein (CHOP), that serve to implement UPR transcriptional regulation. In this study, we used sucrose gradient ultracentrifugation and a genome-wide microarray approach to measure changes in mRNA translation during ER stress. Our analysis suggests that translational efficiencies vary over a broad range during ER stress, with the majority of transcripts being either repressed or resistant to eIF2α∼P, whereas a notable cohort of key regulators are subject to preferential translation. From the latter group, we identified the α isoform of inhibitor of Bruton's tyrosine kinase (IBTKα) as being subject to both translational and transcriptional induction during eIF2α∼P in both cell lines and a mouse model of ER stress. Translational regulation of IBTKα mRNA involves stress-induced relief of two inhibitory upstream open reading frames in the 5′-leader of the transcript. Depletion of IBTKα by short hairpin RNA reduced viability of cultured cells coincident with increased caspase 3/7 cleavage, suggesting that IBTKα is a key regulator in determining cell fate during the UPR.
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Affiliation(s)
- Thomas D Baird
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Lakshmi Reddy Palam
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Michael E Fusakio
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Jeffrey A Willy
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202Investigative Toxicology, Lilly Research Laboratories, Indianapolis, IN 46285
| | - Christopher M Davis
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Jeanette N McClintick
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Tracy G Anthony
- Department of Nutritional Sciences, Rutgers University, New Brunswick, NJ 08901
| | - Ronald C Wek
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202
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22
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Wang JC, Foroud T, Hinrichs AL, Le NXH, Bertelsen S, Budde JP, Harari O, Koller DL, Wetherill L, Agrawal A, Almasy L, Brooks AI, Bucholz K, Dick D, Hesselbrock V, Johnson EO, Kang S, Kapoor M, Kramer J, Kuperman S, Madden PAF, Manz N, Martin NG, McClintick JN, Montgomery GW, Nurnberger JI, Rangaswamy M, Rice J, Schuckit M, Tischfield JA, Whitfield JB, Xuei X, Porjesz B, Heath AC, Edenberg HJ, Bierut LJ, Goate AM. A genome-wide association study of alcohol-dependence symptom counts in extended pedigrees identifies C15orf53. Mol Psychiatry 2013; 18:1218-24. [PMID: 23089632 PMCID: PMC3752321 DOI: 10.1038/mp.2012.143] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Revised: 07/26/2012] [Accepted: 09/04/2012] [Indexed: 11/09/2022]
Abstract
Several studies have identified genes associated with alcohol-use disorders (AUDs), but the variation in each of these genes explains only a small portion of the genetic vulnerability. The goal of the present study was to perform a genome-wide association study (GWAS) in extended families from the Collaborative Study on the Genetics of Alcoholism to identify novel genes affecting risk for alcohol dependence (AD). To maximize the power of the extended family design, we used a quantitative endophenotype, measured in all individuals: number of alcohol-dependence symptoms endorsed (symptom count (SC)). Secondary analyses were performed to determine if the single nucleotide polymorphisms (SNPs) associated with SC were also associated with the dichotomous phenotype, DSM-IV AD. This family-based GWAS identified SNPs in C15orf53 that are strongly associated with DSM-IV alcohol-dependence symptom counts (P=4.5 × 10(-8), inflation-corrected P=9.4 × 10(-7)). Results with DSM-IV AD in the regions of interest support our findings with SC, although the associations were less significant. Attempted replications of the most promising association results were conducted in two independent samples: nonoverlapping subjects from the Study of Addiction: Genes and Environment (SAGE) and the Australian Twin Family Study of AUDs (OZALC). Nominal association of C15orf53 with SC was observed in SAGE. The variant that showed strongest association with SC, rs12912251 and its highly correlated variants (D'=1, r(2) 0.95), have previously been associated with risk for bipolar disorder.
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Affiliation(s)
- Jen-Chyong Wang
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO
| | - Tatiana Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
| | - Anthony L Hinrichs
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO
| | - Nhung XH Le
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO
| | - Sarah Bertelsen
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO
| | - John P Budde
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO
| | - Oscar Harari
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO
| | - Daniel L Koller
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
| | - Leah Wetherill
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
| | - Arpana Agrawal
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO
| | - Laura Almasy
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | | | - Kathleen Bucholz
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO
| | - Danielle Dick
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA
| | - Victor Hesselbrock
- Department of Psychiatry, University of Connecticut Health Center, Farmington, CT
| | - Eric O Johnson
- Division of Health, Social and Economic Research, Research Triangle Institute International, Research Triangle Park, NC
| | - Sun Kang
- Henri Begleiter Neurodynamics Laboratory, Department of Psychiatry and Behavioral Sciences, SUNY Downstate Medical Center, Brooklyn, NY
| | - Manav Kapoor
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO
| | - John Kramer
- Department of Psychiatry, University of Iowa College of Medicine, Iowa City, IA
| | - Samuel Kuperman
- Division of Child Psychiatry, University of Iowa Hospitals, Iowa City, IA
| | - Pamela AF Madden
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO
| | - Niklas Manz
- Henri Begleiter Neurodynamics Laboratory, Department of Psychiatry and Behavioral Sciences, SUNY Downstate Medical Center, Brooklyn, NY
| | | | - Jeanette N McClintick
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN
| | | | - John I Nurnberger
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN
| | - Madhavi Rangaswamy
- Henri Begleiter Neurodynamics Laboratory, Department of Psychiatry and Behavioral Sciences, SUNY Downstate Medical Center, Brooklyn, NY
| | - John Rice
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO
| | - Marc Schuckit
- Department of Psychiatry, University of California-San Diego, La Jolla, CA
| | - Jay A Tischfield
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | | | - Xiaoling Xuei
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN
| | - Bernice Porjesz
- Henri Begleiter Neurodynamics Laboratory, Department of Psychiatry and Behavioral Sciences, SUNY Downstate Medical Center, Brooklyn, NY
| | - Andrew C Heath
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO
| | - Howard J Edenberg
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN
| | - Laura J Bierut
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO
| | - Alison M Goate
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO
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McClintick JN, Xuei X, Tischfield JA, Goate A, Foroud T, Wetherill L, Ehringer MA, Edenberg HJ. Stress-response pathways are altered in the hippocampus of chronic alcoholics. Alcohol 2013; 47:505-15. [PMID: 23981442 DOI: 10.1016/j.alcohol.2013.07.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 07/02/2013] [Accepted: 07/09/2013] [Indexed: 12/26/2022]
Abstract
The chronic high-level alcohol consumption seen in alcoholism leads to dramatic effects on the hippocampus, including decreased white matter, loss of oligodendrocytes and other glial cells, and inhibition of neurogenesis. Examining gene expression in post mortem hippocampal tissue from 20 alcoholics and 19 controls allowed us to detect differentially expressed genes that may play a role in the risk for alcoholism or whose expression is modified by chronic consumption of alcohol. We identified 639 named genes whose expression significantly differed between alcoholics and controls at a False Discovery Rate (FDR) ≤ 0.20; 52% of these genes differed by at least 1.2-fold. Differentially expressed genes included the glucocorticoid receptor and the related gene FK506 binding protein 5 (FKBP5), UDP glycosyltransferase 8 (UGT8), urea transporter (SLC14A1), zinc transporter (SLC39A10), Interleukin 1 receptor type 1 (IL1R1), thioredoxin interacting protein (TXNIP), and many metallothioneins. Pathways related to inflammation, hypoxia, and stress showed activation, and pathways that play roles in neurogenesis and myelination showed decreases. The cortisol pathway dysregulation and increased inflammation identified here are seen in other stress-related conditions such as depression and post-traumatic stress disorder and most likely play a role in addiction. Many of the detrimental effects on the hippocampus appear to be mediated through NF-κB signaling. Twenty-four of the differentially regulated genes were previously identified by genome-wide association studies of alcohol use disorders; this raises the potential interest of genes not normally associated with alcoholism, such as suppression of tumorigenicity 18 (ST18), BCL2-associated athanogene 3 (BAG3), and von Willebrand factor (VWF).
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McBride WJ, Kimpel MW, McClintick JN, Ding ZM, Hyytia P, Colombo G, Liang T, Edenberg HJ, Lumeng L, Bell RL. Gene expression within the extended amygdala of 5 pairs of rat lines selectively bred for high or low ethanol consumption. Alcohol 2013; 47:517-29. [PMID: 24157127 DOI: 10.1016/j.alcohol.2013.08.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 08/30/2013] [Accepted: 08/30/2013] [Indexed: 11/25/2022]
Abstract
The objectives of this study were to determine innate differences in gene expression in 2 regions of the extended amygdala between 5 different pairs of lines of male rats selectively bred for high or low ethanol consumption: a) alcohol-preferring (P) vs. alcohol-non-preferring (NP) rats, b) high-alcohol-drinking (HAD) vs. low-alcohol-drinking (LAD) rats (replicate line-pairs 1 and 2), c) ALKO alcohol (AA) vs. nonalcohol (ANA) rats, and d) Sardinian alcohol-preferring (sP) vs. Sardinian alcohol-nonpreferring (sNP) rats, and then to determine if these differences are common across the line-pairs. Microarray analysis revealed up to 1772 unique named genes in the nucleus accumbens shell (AcbSh) and 494 unique named genes in the central nucleus of the amygdala (CeA) that significantly differed [False Discovery Rate (FDR) = 0.10; fold-change at least 1.2] in expression between the individual line-pairs. Analysis using Gene Ontology (GO) and Ingenuity Pathways information indicated significant categories and networks in common for up to 3 or 4 line-pairs, but not for all 5 line-pairs. However, there were almost no individual genes in common within these categories and networks. ANOVAs of the combined data for the 5 line-pairs indicated 1014 and 731 significant (p < 0.01) differences in expression of named genes in the AcbSh and CeA, respectively. There were 4-6 individual named genes that significantly differed across up to 3 line-pairs in both regions; only 1 gene (Gsta4 in the CeA) differed in as many as 4 line-pairs. Overall, the findings suggest that a) some biological categories or networks (e.g., cell-to-cell signaling, cellular stress response, cellular organization, etc.) may be in common for subsets of line-pairs within either the AcbSh or CeA, and b) regulation of different genes and/or combinations of multiple biological systems may be contributing to the disparate alcohol drinking behaviors of these line-pairs.
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Sarmah S, Muralidharan P, Curtis CL, McClintick JN, Buente BB, Holdgrafer DJ, Ogbeifun O, Olorungbounmi OC, Patino L, Lucas R, Gilbert S, Groninger ES, Arciero J, Edenberg HJ, Marrs JA. Ethanol exposure disrupts extraembryonic microtubule cytoskeleton and embryonic blastomere cell adhesion, producing epiboly and gastrulation defects. Biol Open 2013; 2:1013-21. [PMID: 24167711 PMCID: PMC3798184 DOI: 10.1242/bio.20135546] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [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: 05/20/2013] [Accepted: 07/07/2013] [Indexed: 11/20/2022] Open
Abstract
Fetal alcohol spectrum disorder (FASD) occurs when pregnant mothers consume alcohol, causing embryonic ethanol exposure and characteristic birth defects that include craniofacial, neural and cardiac defects. Gastrulation is a particularly sensitive developmental stage for teratogen exposure, and zebrafish is an outstanding model to study gastrulation and FASD. Epiboly (spreading blastomere cells over the yolk cell), prechordal plate migration and convergence/extension cell movements are sensitive to early ethanol exposure. Here, experiments are presented that characterize mechanisms of ethanol toxicity on epiboly and gastrulation. Epiboly mechanisms include blastomere radial intercalation cell movements and yolk cell microtubule cytoskeleton pulling the embryo to the vegetal pole. Both of these processes were disrupted by ethanol exposure. Ethanol effects on cell migration also indicated that cell adhesion was affected, which was confirmed by cell aggregation assays. E-cadherin cell adhesion molecule expression was not affected by ethanol exposure, but E-cadherin distribution, which controls epiboly and gastrulation, was changed. E-cadherin was redistributed into cytoplasmic aggregates in blastomeres and dramatically redistributed in the extraembryonic yolk cell. Gene expression microarray analysis was used to identify potential causative factors for early development defects, and expression of the cell adhesion molecule protocadherin-18a (pcdh18a), which controls epiboly, was significantly reduced in ethanol exposed embryos. Injecting pcdh18a synthetic mRNA in ethanol treated embryos partially rescued epiboly cell movements, including enveloping layer cell shape changes. Together, data show that epiboly and gastrulation defects induced by ethanol are multifactorial, and include yolk cell (extraembryonic tissue) microtubule cytoskeleton disruption and blastomere adhesion defects, in part caused by reduced pcdh18a expression.
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Affiliation(s)
- Swapnalee Sarmah
- Department of Biology, Indiana University-Purdue University Indianapolis , 723 West Michigan Street, Indianapolis, IN 46202-5130 , USA
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26
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McBride WJ, Kimpel MW, McClintick JN, Ding ZM, Hauser SR, Edenberg HJ, Bell RL, Rodd ZA. Changes in gene expression within the ventral tegmental area following repeated excessive binge-like alcohol drinking by alcohol-preferring (P) rats. Alcohol 2013; 47:367-80. [PMID: 23714385 DOI: 10.1016/j.alcohol.2013.04.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [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: 01/18/2013] [Revised: 04/02/2013] [Accepted: 04/17/2013] [Indexed: 12/11/2022]
Abstract
The objective of this study was to detect changes in gene expression in the ventral tegmental area (VTA) following repeated excessive binge-like ('loss-of-control') alcohol drinking by alcohol-preferring (P) rats. Adult female P rats (n = 7) were given concurrent access to 10, 20, and 30% EtOH for 4 1-h sessions daily for 10 weeks followed by 2 cycles of 2 weeks of abstinence and 2 weeks of EtOH access. Rats were sacrificed by decapitation 3 h after the 4th daily EtOH-access session at the end of the second 2-week relapse period. A water-control group of female P rats (n = 8) was also sacrificed. RNA was prepared from micro-punch samples of the VTA from individual rats; analyses were conducted with Affymetrix Rat 230.2 GeneChips. Ethanol intakes were 1.2-1.7 g/kg per session, resulting in blood levels >200 mg% at the end of the 4th session. There were 211 unique named genes that significantly differed (FDR = 0.1) between the water and EtOH groups. Bioinformatics analyses indicated alterations in a) transcription factors that reduced excitation-coupled transcription and promoted excitotoxic neuronal damage involving clusters of genes associated with Nfkbia, Fos, and Srebf1, b) genes that reduced cholesterol and fatty acid synthesis, and increased protein degradation, and c) genes involved in cell-to-cell interactions and regulation of the actin cytoskeleton. Among the named genes, there were 62 genes that showed differences between alcohol-naïve P and non-preferring (NP) rats, with 43 of the genes changing toward NP-like expression levels following excessive binge-like drinking in the P rats. These genes are involved in a pro-inflammatory response, and enhanced response to glucocorticoids and steroid hormones. Overall, the results of this study indicate that the repeated excessive binge-like alcohol drinking can change the expression of genes that may alter neuronal function in several ways, some of which may be deleterious.
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Affiliation(s)
- William J McBride
- Institute of Psychiatric Research, Department of Psychiatry, Indiana University School of Medicine, Indiana University-Purdue University at Indianapolis, Indianapolis, IN 46202, USA.
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27
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Unthank JL, McClintick JN, Labarrere CA, Li L, Distasi MR, Miller SJ. Molecular basis for impaired collateral artery growth in the spontaneously hypertensive rat: insight from microarray analysis. Physiol Rep 2013; 1:e0005. [PMID: 24303120 PMCID: PMC3831906 DOI: 10.1002/phy2.5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [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: 05/07/2013] [Accepted: 05/08/2013] [Indexed: 01/08/2023] Open
Abstract
Analysis of global gene expression in mesenteric control and collateral arteries was used to investigate potential molecules, pathways, and mechanisms responsible for impaired collateral growth in the Spontaneously Hypertensive Rat (SHR). A fundamental difference was observed in overall gene expression pattern in SHR versus Wistar Kyoto (WKY) collaterals; only 6% of genes altered in collaterals were similar between rat strains. Ingenuity® Pathway Analysis (IPA) identified major differences between WKY and SHR in networks and biological functions related to cell growth and proliferation and gene expression. In SHR control arteries, several mechano-sensitive and redox-dependent transcription regulators were downregulated including JUN (-5.2×, P = 0.02), EGR1 (-4.1×, P = 0.01), and NFĸB1 (-1.95×, P = 0.04). Predicted binding sites for NFĸB and AP-1 were present in genes altered in WKY but not SHR collaterals. Immunostaining showed increased NFĸB nuclear translocation in collateral arteries of WKY and apocynin-treated SHR, but not in untreated SHR. siRNA for the p65 subunit suppressed collateral growth in WKY, confirming a functional role of NFkB. Canonical pathways identified by IPA in WKY but not SHR included nitric oxide and renin-angiotensin system signaling. The angiotensin type 1 receptor (AGTR1) exhibited upregulation in WKY collaterals, but downregulation in SHR; pharmacological blockade of AGTR1 with losartan prevented collateral luminal expansion in WKY. Together, these results suggest that collateral growth impairment results from an abnormality in a fundamental regulatory mechanism that occurs at a level between signal transduction and gene transcription and implicate redox-dependent modulation of mechano-sensitive transcription factors such as NFĸB as a potential mechanism.
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Affiliation(s)
- Joseph L Unthank
- Department of Surgery, Indiana University School of Medicine Indianapolis, Indiana, 46202 ; Department of Cellular and Integrative Physiology, Indiana University School of Medicine Indianapolis, Indiana, 46202 ; Indiana Center for Vascular Biology and Medicine, Indiana University School of Medicine Indianapolis, Indiana, 46202
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Chambers RA, McClintick JN, Sentir AM, Berg SA, Runyan M, Choi KH, Edenberg HJ. Cortical-striatal gene expression in neonatal hippocampal lesion (NVHL)-amplified cocaine sensitization. Genes Brain Behav 2013; 12:564-75. [PMID: 23682998 DOI: 10.1111/gbb.12051] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 05/01/2013] [Accepted: 05/14/2013] [Indexed: 11/30/2022]
Abstract
Cortical-striatal circuit dysfunction in mental illness may enhance addiction vulnerability. Neonatal ventral hippocampal lesions (NVHL) model this dual diagnosis causality by producing a schizophrenia syndrome with enhanced responsiveness to addictive drugs. Rat genome-wide microarrays containing >24 000 probesets were used to examine separate and co-occurring effects of NVHLs and cocaine sensitization (15 mg/kg/day × 5 days) on gene expression within medial prefrontal cortex (MPFC), nucleus accumbens (NAC), and caudate-putamen (CAPU). Two weeks after NVHLs robustly amplified cocaine behavioral sensitization, brains were harvested for genes of interest defined as those altered at P < 0.001 by NVHL or cocaine effects or interactions. Among 135 genes so impacted, NVHLs altered twofold more than cocaine, with half of all changes in the NAC. Although no genes were changed in the same direction by both NVHL and cocaine history, the anatomy and directionality of significant changes suggested synergy on the neural circuit level generative of compounded behavioral phenotypes: NVHL predominantly downregulated expression in MPFC and NAC while NVHL and cocaine history mostly upregulated CAPU expression. From 75 named genes altered by NVHL or cocaine, 27 had expression levels that correlated significantly with degree of behavioral sensitization, including 11 downregulated by NVHL in MPFC/NAC, and 10 upregulated by NVHL or cocaine in CAPU. These findings suggest that structural and functional impoverishment of prefrontal-cortical-accumbens circuits in mental illness is associated with abnormal striatal plasticity compounding with that in addictive disease. Polygenetic interactions impacting neuronal signaling and morphology within these networks likely contribute to addiction vulnerability in mental illness.
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Affiliation(s)
- R A Chambers
- Lab for Translational Neuroscience of Dual Diagnosis & Development, Department of Psychiatry, Institute for Psychiatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
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Teske BF, Fusakio ME, Zhou D, Shan J, McClintick JN, Kilberg MS, Wek RC. CHOP induces activating transcription factor 5 (ATF5) to trigger apoptosis in response to perturbations in protein homeostasis. Mol Biol Cell 2013; 24:2477-90. [PMID: 23761072 PMCID: PMC3727939 DOI: 10.1091/mbc.e13-01-0067] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [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] [Indexed: 01/12/2023] Open
Abstract
Environmental stresses that disrupt protein homeostasis induce phosphorylation of eIF2, triggering repression of global protein synthesis coincident with preferential translation of ATF4, a transcriptional activator of the integrated stress response (ISR). Depending on the extent of protein disruption, ATF4 may not be able to restore proteostatic control and instead switches to a terminal outcome that features elevated expression of the transcription factor CHOP (GADD153/DDIT3). The focus of this study is to define the mechanisms by which CHOP directs gene regulatory networks that determine cell fate. We find that in response to proteasome inhibition, CHOP enhances the expression of a collection of genes encoding transcription regulators, including ATF5, which is preferentially translated during eIF2 phosphorylation. Transcriptional expression of ATF5 is directly induced by both CHOP and ATF4. Knockdown of ATF5 increases cell survival in response to proteasome inhibition, supporting the idea that both ATF5 and CHOP have proapoptotic functions. Transcriptome analysis of ATF5-dependent genes reveals targets involved in apoptosis, including NOXA, which is important for inducing cell death during proteasome inhibition. This study suggests that the ISR features a feedforward loop of stress-induced transcriptional regulators, each subject to transcriptional and translational control, which can switch cell fate toward apoptosis.
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Affiliation(s)
- Brian F Teske
- Department of Biochemistry and Molecular Biology, School of Medicine, Indiana University, Indianapolis, IN 46202, USA
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McBride WJ, Kimpel MW, McClintick JN, Ding ZM, Hyytia P, Colombo G, Edenberg HJ, Lumeng L, Bell RL. Gene expression in the ventral tegmental area of 5 pairs of rat lines selectively bred for high or low ethanol consumption. Pharmacol Biochem Behav 2012; 102:275-85. [PMID: 22579914 PMCID: PMC3383357 DOI: 10.1016/j.pbb.2012.04.016] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Revised: 04/20/2012] [Accepted: 04/30/2012] [Indexed: 12/28/2022]
Abstract
The objective of this study was to determine if there are common innate differences in gene expression or gene pathways in the ventral tegmental area (VTA) among 5 different pairs of rat lines selectively bred for high (HEC) or low (LEC) ethanol consumption: (a) alcohol-preferring (P) vs. alcohol-non-preferring (NP) rats; (b) high-alcohol-drinking (HAD) vs. low-alcohol-drinking (LAD) rats (replicate line pairs 1 and 2); (c) ALKO alcohol (AA) vs. nonalcohol (ANA) rats; and (d) Sardinian alcohol-preferring (sP) vs. alcohol-nonpreferring (sNP) rats. Microarray analysis revealed between 370 and 1340 unique named genes that significantly differed in expression between the individual line-pairs. Analysis using Gene Ontology (GO) and Ingenuity Pathways information indicated significant categories and networks in common for up to 3 line-pairs, but not for all 5 line-pairs; moreover, there were few genes in common in these categories and networks. ANOVA of the combined data for the 5 line-pairs indicated 1295 significant (p<0.01) differences in expression of named genes. Although no individual named gene was significant across all 5 line-pairs, there were 22 genes that overlapped in the same direction in 3 or 4 of the line-pairs. Overall, the findings suggest that (a) some biological categories or networks may be in common for subsets of line-pairs; and (b) regulation of different genes and/or combinations of multiple biological systems (e.g., transcription, synaptic function, intracellular signaling and protection against oxidative stress) within the VTA (possibly involving dopamine and glutamate) may be contributing to the disparate alcohol drinking behaviors of these line-pairs.
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Affiliation(s)
- William J McBride
- Institute of Psychiatric Research, Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN 46202-4887, USA.
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DiStasi MR, Labarrere CA, McClintick JN, Li L, Miller SJ, Unthank J. Abstract 267: Redox-Dependent Transcriptional Regulation: A Potential Mechanism for Collateral Growth Impairment During Chronic Oxidative Stress. Arterioscler Thromb Vasc Biol 2012. [DOI: 10.1161/atvb.32.suppl_1.a267] [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] [Indexed: 11/16/2022]
Abstract
Vascular risk factors characterized by oxidative stress are correlated with impaired collateral growth through mechanisms largely unknown. Spontaneously hypertensive rats (SHR) with increased oxidative stress were used to investigate potential mechanisms mediating impaired collateral compensation. Microarray analysis of global gene expression was performed with control and collateral mesenteric artery samples (n=4) from SHR and their normotensive controls (WKY) 24 hours after model creation. In SHR control arteries, several mechano-sensitive and redox-dependent transcription regulators were down-regulated including Jun (-5.2X, P=0.02), Egr-1 (-4.1X, P=0.01), and NFkB1 (-1.95X, P=0.04). Collateral arteries of WKY and SHR exhibited a fundamentally different gene expression pattern (<7% overlap), especially for molecules regulating cell growth and proliferation and gene expression. Predicted binding sites for NFkB and AP-1 were present in the genes altered in WKY but not SHR collaterals. Immunostaining demonstrated increased NFkB nuclear translocation in WKY but not in SHR collaterals (see figure). Increased NFkB nuclear translocation was also seen in collaterals of SHR pretreated with the anti-oxidant apocynin (Apo), which we have previously shown to restore a normal redox status and collateral growth. Based upon these results, we propose redox-dependent modulation of mechano-sensitive transcription factors as a mechanism to explain, at least in part, the fundamental differences in collateral gene expression between WKY and SHR and the impairment of collateral growth during chronic oxidative stress.
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Affiliation(s)
| | | | | | - Lang Li
- Computational Biology and Bioinformatics, Indiana Univ Med Ctr, Indianapolis, IN
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Teske BF, Wek SA, Bunpo P, Cundiff JK, McClintick JN, Anthony TG, Wek RC. The eIF2 kinase PERK and the integrated stress response facilitate activation of ATF6 during endoplasmic reticulum stress. Mol Biol Cell 2011; 22:4390-405. [PMID: 21917591 PMCID: PMC3216664 DOI: 10.1091/mbc.e11-06-0510] [Citation(s) in RCA: 273] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
This study shows that the eIF2 kinase PERK is required not only for translational control but also for activation of ATF6 and its target genes in the unfolded protein response. The PERK pathway facilitates both the synthesis of ATF6 and trafficking of ATF6 from the endoplasmic reticulum to the Golgi for intramembrane proteolysis and activation of ATF6. Disruptions of the endoplasmic reticulum (ER) that perturb protein folding cause ER stress and elicit an unfolded protein response (UPR) that involves translational and transcriptional changes in gene expression aimed at expanding the ER processing capacity and alleviating cellular injury. Three ER stress sensors (PERK, ATF6, and IRE1) implement the UPR. PERK phosphorylation of the α subunit of eIF2 during ER stress represses protein synthesis, which prevents further influx of ER client proteins. Phosphorylation of eIF2α (eIF2α∼P) also induces preferential translation of ATF4, a transcription activator of the integrated stress response. In this study we show that the PERK/eIF2α∼P/ATF4 pathway is required not only for translational control, but also for activation of ATF6 and its target genes. The PERK pathway facilitates both the synthesis of ATF6 and trafficking of ATF6 from the ER to the Golgi for intramembrane proteolysis and activation of ATF6. As a consequence, liver-specific depletion of PERK significantly reduces both the translational and transcriptional phases of the UPR, leading to reduced protein chaperone expression, disruptions of lipid metabolism, and enhanced apoptosis. These findings show that the regulatory networks of the UPR are fully integrated and help explain the diverse biological defects associated with loss of PERK.
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Affiliation(s)
- Brian F Teske
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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Herbert BS, Chanoux RA, Liu Y, Baenziger PH, Goswami CP, McClintick JN, Edenberg HJ, Pennington RE, Lipkin SM, Kopelovich L. A molecular signature of normal breast epithelial and stromal cells from Li-Fraumeni syndrome mutation carriers. Oncotarget 2011; 1:405-22. [PMID: 21311097 DOI: 10.18632/oncotarget.101004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Specific changes in gene expression during cancer initiation should enable discovery of biomarkers for risk assessment, early detection and targets for chemoprevention. It has been previously demonstrated that altered mRNA and proteome signatures of morphologically normal cells bearing a single inherited "hit" in a tumor suppressor gene parallel many changes observed in the corresponding sporadic cancer. Here, we report on the global gene expression profile of morphologically normal, cultured primary breast epithelial and stromal cells from Li-Fraumeni syndrome (LFS) TP53 mutation carriers. Our analyses identified multiple changes in gene expression in both morphologically normal breast epithelial and stromal cells associated with TP53 haploinsufficiency, as well as interlocking pathways. Notably, a dysregulated p53 signaling pathway was readily detectable. Pharmacological intervention with the p53 rescue compounds CP-31398 and PRIMA-1 provided further evidence in support of the central role of p53 in affecting these changes in LFS cells and treatment for this cancer. Because loss of signaling mediated by TP53 is associated with the development and survival of many human tumors, identification of gene expression profiles in morphologically normal cells that carry "one-hit" p53 mutations may reveal novel biomarkers, enabling the discovery of potential targets for chemoprevention of sporadic tumors as well.
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Affiliation(s)
- Brittney-Shea Herbert
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA.
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Zhou FC, Zhao Q, Liu Y, Goodlett CR, Liang T, McClintick JN, Edenberg HJ, Li L. Alteration of gene expression by alcohol exposure at early neurulation. BMC Genomics 2011; 12:124. [PMID: 21338521 PMCID: PMC3056799 DOI: 10.1186/1471-2164-12-124] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [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: 09/06/2010] [Accepted: 02/21/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND We have previously demonstrated that alcohol exposure at early neurulation induces growth retardation, neural tube abnormalities, and alteration of DNA methylation. To explore the global gene expression changes which may underline these developmental defects, microarray analyses were performed in a whole embryo mouse culture model that allows control over alcohol and embryonic variables. RESULT Alcohol caused teratogenesis in brain, heart, forelimb, and optic vesicle; a subset of the embryos also showed cranial neural tube defects. In microarray analysis (accession number GSM9545), adopting hypothesis-driven Gene Set Enrichment Analysis (GSEA) informatics and intersection analysis of two independent experiments, we found that there was a collective reduction in expression of neural specification genes (neurogenin, Sox5, Bhlhe22), neural growth factor genes [Igf1, Efemp1, Klf10 (Tieg), and Edil3], and alteration of genes involved in cell growth, apoptosis, histone variants, eye and heart development. There was also a reduction of retinol binding protein 1 (Rbp1), and de novo expression of aldehyde dehydrogenase 1B1 (Aldh1B1). Remarkably, four key hematopoiesis genes (glycophorin A, adducin 2, beta-2 microglobulin, and ceruloplasmin) were absent after alcohol treatment, and histone variant genes were reduced. The down-regulation of the neurospecification and the neurotrophic genes were further confirmed by quantitative RT-PCR. Furthermore, the gene expression profile demonstrated distinct subgroups which corresponded with two distinct alcohol-related neural tube phenotypes: an open (ALC-NTO) and a closed neural tube (ALC-NTC). Further, the epidermal growth factor signaling pathway and histone variants were specifically altered in ALC-NTO, and a greater number of neurotrophic/growth factor genes were down-regulated in the ALC-NTO than in the ALC-NTC embryos. CONCLUSION This study revealed a set of genes vulnerable to alcohol exposure and genes that were associated with neural tube defects during early neurulation.
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Affiliation(s)
- Feng C Zhou
- Department of Anatomy and Cell Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA.
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Mitra R, Lee J, Jo J, Milani M, McClintick JN, Edenberg HJ, Kesler KA, Rieger KM, Badve S, Cummings OW, Mohiuddin A, Thomas DG, Luo X, Juliar BE, Li L, Mesaros C, Blair IA, Srirangam A, Kratzke RA, McDonald CJ, Kim J, Potter DA. Prediction of postoperative recurrence-free survival in non-small cell lung cancer by using an internationally validated gene expression model. Clin Cancer Res 2011; 17:2934-46. [PMID: 21242119 DOI: 10.1158/1078-0432.ccr-10-1803] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
PURPOSE This study was performed to discover prognostic genomic markers associated with postoperative outcome of stage I to III non-small cell lung cancer (NSCLC) that are reproducible between geographically distant and demographically distinct patient populations. EXPERIMENTAL DESIGN American patients (n = 27) were stratified on the basis of recurrence and microarray profiling of their tumors was performed to derive a training set of 44 genes. A larger Korean patient validation cohort (n = 138) was also stratified by recurrence and screened for these genes. Four reproducible genes were identified and used to construct genomic and clinicogenomic Cox models for both cohorts. RESULTS Four genomic markers, DBN1 (drebrin 1), CACNB3 (calcium channel beta 3), FLAD1 (PP591; flavin adenine dinucleotide synthetase), and CCND2 (cyclin D2), exhibited highly significant differential expression in recurrent tumors in the training set (P < 0.001). In the validation set, DBN1, FLAD1 (PP591), and CACNB3 were significant by Cox univariate analysis (P ≤ 0.035), whereas only DBN1 was significant by multivariate analysis. Genomic and clinicogenomic models for recurrence-free survival (RFS) were equally effective for risk stratification of stage I to II or I to III patients (all models P < 0.0001). For stage I to II or I to III patients, 5-year RFS of the low- and high-risk patients was approximately 70% versus 30% for both models. The genomic model for overall survival of stage I to III patients was improved by addition of pT and pN stage (P < 0.0013 vs. 0.010). CONCLUSION A 4-gene prognostic model incorporating the multivariate marker DBN1 exhibits potential clinical utility for risk stratification of stage I to III NSCLC patients.
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Affiliation(s)
- Ranjana Mitra
- Division of Hematology, Department of Medicine, School of Public Health, University of Minnesota, Minneapolis, Minnesota 55455, USA
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36
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Herbert BS, Chanoux RA, Liu Y, Baenziger PH, Goswami CP, McClintick JN, Edenberg HJ, Pennington RE, Lipkin SM, Kopelovich L. A molecular signature of normal breast epithelial and stromal cells from Li-Fraumeni syndrome mutation carriers. Oncotarget 2010; 1:405-422. [PMID: 21311097 PMCID: PMC3039408 DOI: 10.18632/oncotarget.175] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [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: 08/11/2010] [Accepted: 10/05/2010] [Indexed: 11/25/2022] Open
Abstract
Specific changes in gene expression during cancer initiation should enable discovery of biomarkers for risk assessment, early detection and targets for chemoprevention. It has been previously demonstrated that altered mRNA and proteome signatures of morphologically normal cells bearing a single inherited "hit" in a tumor suppressor gene parallel many changes observed in the corresponding sporadic cancer. Here, we report on the global gene expression profile of morphologically normal, cultured primary breast epithelial and stromal cells from Li-Fraumeni syndrome (LFS) TP53 mutation carriers. Our analyses identified multiple changes in gene expression in both morphologically normal breast epithelial and stromal cells associated with TP53 haploinsufficiency, as well as interlocking pathways. Notably, a dysregulated p53 signaling pathway was readily detectable. Pharmacological intervention with the p53 rescue compounds CP-31398 and PRIMA-1 provided further evidence in support of the central role of p53 in affecting these changes in LFS cells and treatment for this cancer. Because loss of signaling mediated by TP53 is associated with the development and survival of many human tumors, identification of gene expression profiles in morphologically normal cells that carry "one-hit" p53 mutations may reveal novel biomarkers, enabling the discovery of potential targets for chemoprevention of sporadic tumors as well.
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MESH Headings
- Adolescent
- Adult
- Aza Compounds/pharmacology
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Breast Neoplasms/genetics
- Breast Neoplasms/pathology
- Bridged Bicyclo Compounds, Heterocyclic/pharmacology
- Carcinoma, Ductal, Breast/genetics
- Carcinoma, Ductal, Breast/pathology
- Cells, Cultured
- Epithelial Cells/metabolism
- Female
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- Genetic Predisposition to Disease
- Germ-Line Mutation/genetics
- Haploinsufficiency
- Humans
- Li-Fraumeni Syndrome/genetics
- Neoplasm Proteins/genetics
- Oligonucleotide Array Sequence Analysis
- Pyrimidines/pharmacology
- RNA, Messenger/genetics
- Reverse Transcriptase Polymerase Chain Reaction
- Stromal Cells/metabolism
- Tumor Suppressor Protein p53/antagonists & inhibitors
- Tumor Suppressor Protein p53/genetics
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Affiliation(s)
- Brittney-Shea Herbert
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
- Indiana University Melvin and Bren Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Rebecca A. Chanoux
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Yunlong Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
- Division of Biostatistics, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
- Center for Medical Genomics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Peter H. Baenziger
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Chirayu P. Goswami
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Jeanette N. McClintick
- Center for Medical Genomics, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Howard J. Edenberg
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
- Center for Medical Genomics, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Robert E. Pennington
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Steven M. Lipkin
- Departments of Medicine and Genetic Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Levy Kopelovich
- Division of Cancer Prevention, National Cancer Institute, Bethesda, MD, USA
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Staschke KA, Dey S, Zaborske JM, Palam LR, McClintick JN, Pan T, Edenberg HJ, Wek RC. Integration of general amino acid control and target of rapamycin (TOR) regulatory pathways in nitrogen assimilation in yeast. J Biol Chem 2010; 285:16893-911. [PMID: 20233714 DOI: 10.1074/jbc.m110.121947] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Two important nutrient-sensing and regulatory pathways, the general amino acid control (GAAC) and the target of rapamycin (TOR), participate in the control of yeast growth and metabolism during changes in nutrient availability. Amino acid starvation activates the GAAC through Gcn2p phosphorylation of translation factor eIF2 and preferential translation of GCN4, a transcription activator. TOR senses nitrogen availability and regulates transcription factors such as Gln3p. We used microarray analyses to address the integration of the GAAC and TOR pathways in directing the yeast transcriptome during amino acid starvation and rapamycin treatment. We found that GAAC is a major effector of the TOR pathway, with Gcn4p and Gln3p each inducing a similar number of genes during rapamycin treatment. Although Gcn4p activates a common core of 57 genes, the GAAC directs significant variations in the transcriptome during different stresses. In addition to inducing amino acid biosynthetic genes, Gcn4p in conjunction with Gln3p activates genes required for the assimilation of secondary nitrogen sources such as gamma-aminobutyric acid (GABA). Gcn2p activation upon shifting to secondary nitrogen sources is suggested to occur by means of a dual mechanism. First, Gcn2p is induced by the release of TOR repression through a mechanism involving Sit4p protein phosphatase. Second, this eIF2 kinase is activated by select uncharged tRNAs, which were shown to accumulate during the shift to the GABA medium. This study highlights the mechanisms by which the GAAC and TOR pathways are integrated to recognize changing nitrogen availability and direct the transcriptome for optimal growth adaptation.
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Affiliation(s)
- Kirk A Staschke
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
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McBride WJ, Kimpel MW, Schultz JA, McClintick JN, Edenberg HJ, Bell RL. Changes in gene expression in regions of the extended amygdala of alcohol-preferring rats after binge-like alcohol drinking. Alcohol 2010; 44:171-83. [PMID: 20116196 DOI: 10.1016/j.alcohol.2009.12.001] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [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: 08/06/2009] [Revised: 11/13/2009] [Accepted: 12/14/2009] [Indexed: 01/05/2023]
Abstract
The objective of this study was to determine time-course changes in gene expression within two regions of the extended amygdala after binge-like alcohol drinking by alcohol-preferring (P) rats. Adult male P rats were given 1-h access to 15 and 30% ethanol three times daily for 8 weeks. Rats (n = 10/time point for ethanol and n = 6/time point for water) were killed by decapitation 1, 6, and 24 h after the last drinking episode. RNA was prepared from individual micropunch samples of the nucleus accumbens shell (ACB-shell) and central nucleus of the amygdala (CeA); analyses were conducted with Affymetrix Rat Genome 230.2 GeneChips. Ethanol intakes were 1.5-2 g/kg for each of the three sessions. There were no genes that were statistically different between the ethanol and water control groups at any individual time point. Therefore, an overall effect, comparing the water control and ethanol groups, was determined. In the ACB-shell and CeA, there were 276 and 402 probe sets for named genes, respectively, that differed between the two groups. There were 1.5-3.6-fold more genes with increased expression than with decreased expression in the ethanol-drinking group, with most differences between 1.1- and 1.2-fold. Among the differences between the ethanol and water control groups were several significant biological processes categories that were in common between the two regions (e.g., synaptic transmission, neurite development); however, within these categories, there were few genes in common between the two regions. Overall, the results indicate that binge-like alcohol drinking by P rats produces region-dependent changes in the expression of genes that could alter transcription, synaptic function, and neuronal plasticity in the ACB-shell and CeA; within each region, different mechanisms may underlie these alterations because there were few common ethanol-responsive genes between the ACB-shell and CeA.
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Affiliation(s)
- William J McBride
- Department of Psychiatry, Institute of Psychiatric Research, Indiana University-Purdue University at Indianapolis, Indianapolis, 46202-4887, USA.
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Liang T, Kimpel MW, McClintick JN, Skillman AR, McCall K, Edenberg HJ, Carr LG. Candidate genes for alcohol preference identified by expression profiling in alcohol-preferring and -nonpreferring reciprocal congenic rats. Genome Biol 2010; 11:R11. [PMID: 20128895 PMCID: PMC2872871 DOI: 10.1186/gb-2010-11-2-r11] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [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: 09/18/2009] [Revised: 01/21/2010] [Accepted: 02/03/2010] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Selectively bred alcohol-preferring (P) and alcohol-nonpreferring (NP) rats differ greatly in alcohol preference, in part due to a highly significant quantitative trait locus (QTL) on chromosome 4. Alcohol consumption scores of reciprocal chromosome 4 congenic strains NP.P and P.NP correlated with the introgressed interval. The goal of this study was to identify candidate genes that may influence alcohol consumption by comparing gene expression in five brain regions of alcohol-naïve inbred alcohol-preferring and P.NP congenic rats: amygdala, nucleus accumbens, hippocampus, caudate putamen, and frontal cortex. RESULTS Within the QTL region, 104 cis-regulated probe sets were differentially expressed in more than one region, and an additional 53 were differentially expressed in a single region. Fewer trans-regulated probe sets were detected, and most differed in only one region. Analysis of the average expression values across the 5 brain regions yielded 141 differentially expressed cis-regulated probe sets and 206 trans-regulated probe sets. Comparing the present results from inbred alcohol-preferring vs. congenic P.NP rats to earlier results from the reciprocal congenic NP.P vs. inbred alcohol-nonpreferring rats demonstrated that 74 cis-regulated probe sets were differentially expressed in the same direction and with a consistent magnitude of difference in at least one brain region. CONCLUSIONS Cis-regulated candidate genes for alcohol consumption that lie within the chromosome 4 QTL were identified and confirmed by consistent results in two independent experiments with reciprocal congenic rats. These genes are strong candidates for affecting alcohol preference in the inbred alcohol-preferring and inbred alcohol-nonpreferring rats.
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Affiliation(s)
- Tiebing Liang
- Indiana University School of Medicine, Department of Medicine, IB424G, 975 West Walnut Street, Indianapolis, IN 46202, USA.
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Bell RL, Kimpel MW, McClintick JN, Strother WN, Carr LG, Liang T, Rodd ZA, Mayfield RD, Edenberg HJ, McBride WJ. Gene expression changes in the nucleus accumbens of alcohol-preferring rats following chronic ethanol consumption. Pharmacol Biochem Behav 2009; 94:131-47. [PMID: 19666046 DOI: 10.1016/j.pbb.2009.07.019] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2008] [Revised: 07/21/2009] [Accepted: 07/28/2009] [Indexed: 12/16/2022]
Abstract
The objective of this study was to determine the effects of binge-like alcohol drinking on gene expression changes in the nucleus accumbens (ACB) of alcohol-preferring (P) rats. Adult male P rats were given ethanol under multiple scheduled access (MSA; three 1-h dark cycle sessions/day) conditions for 8 weeks. For comparison purposes, a second ethanol drinking group was given continuous/daily alcohol access (CA; 24h/day). A third group was ethanol-naïve (W group). Average ethanol intakes for the CA and MSA groups were approximately 9.5 and 6.5 g/kg/day, respectively. Fifteen hours after the last drinking episode, rats were euthanized, the brains extracted, and the ACB dissected. RNA was extracted and purified for microarray analysis. The only significant differences were between the CA and W groups (p<0.01; Storey false discovery rate=0.15); there were 374 differences in named genes between these 2 groups. There were 20 significant Gene Ontology (GO) categories, which included negative regulation of protein kinase activity, anti-apoptosis, and regulation of G-protein coupled receptor signaling. Ingenuity analysis indicated a network of transcription factors, involving oncogenes (Fos, Jun, Junb had higher expression in the ACB of the CA group), suggesting increased neuronal activity. There were 43 genes located within rat QTLs for alcohol consumption and preference; 4 of these genes (Tgfa, Hspa5, Mtus1 and Creb3l2) are involved in anti-apoptosis and increased transcription, suggesting that they may be contributing to cellular protection and maintaining high alcohol intakes. Overall, these findings suggest that chronic CA drinking results in genomic changes that can be observed during the early acute phase of ethanol withdrawal. Conversely, chronic MSA drinking, with its associated protracted withdrawal periods, results in genomic changes that may be masked by tight regulation of these genes following repeated experiences of ethanol withdrawal.
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Affiliation(s)
- Richard L Bell
- Department of Psychiatry, Indiana University Purdue University at Indianapolis, Indianapolis, IN 46202, USA.
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Taylor MW, Tsukahara T, McClintick JN, Edenberg HJ, Kwo P. Cyclic changes in gene expression induced by Peg-interferon alfa-2b plus ribavirin in peripheral blood monocytes (PBMC) of hepatitis C patients during the first 10 weeks of treatment. J Transl Med 2008; 6:66. [PMID: 18986530 PMCID: PMC2613871 DOI: 10.1186/1479-5876-6-66] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [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: 09/16/2008] [Accepted: 11/05/2008] [Indexed: 01/21/2023] Open
Abstract
Background and Aims This study determined the kinetics of gene expression during the first 10 weeks of therapy with Pegylated-interferon-alfa2b (PegIntron™) and ribavirin (administered by weight) in HCV patients and compared it with the recently completed Virahep C study [1,2] in which Peginterferon-alfa2a (Pegasys™) and ribavirin were administered. Methods RNA was isolated from peripheral blood monocytes (PBMC) from twenty treatment-naïve patients just before treatment (day 1) and at days 3, 6, 10, 13, 27, 42 and 70 days after treatment. Gene expression at each time was measured using Affymetrix microarrays and compared to that of day 1. Results The expression of many genes differed significantly (p ≤ 0.001 and changed at least 1.5-fold) at days 3 (290 probes) and 10 (255 probes), but the number dropped at days 6 (165) and 13 (142). Most genes continued to be up regulated throughout the trial period. A second group of genes, including CXCL10, CMKLR1 (chemokine receptor 1), TRAIL, IL1Rα and genes associated with complement and lipid metabolism, was transiently induced early in treatment. CDKN1C (cyclin kinase inhibitor 1) was induced early but repressed at later times. Genes induced at later times were mostly related to blood chemistry and oxygen transport. By week 10, 11 of the patients demonstrated a positive response to therapy, and the final sustained viral response (SVR) was 35%. The levels of gene induction or decrease was very similar to that previously reported with Pegasys/ribavirin treatment. Conclusion The response to Pegintron/ribavirin was similar to that reported for Pegasys/ribavirin despite some differences in the amount administered. We did not detect major differences at the genomic level between patients responding to treatment or non-responders, perhaps because of limited power. Gene induction occurred in a cyclic fashion, peaking right after administration of interferon and declining between administrations of the drug. Our data suggest that more than once a week dosing might be desirable early during treatment to maintain high levels of response as measured by gene expression.
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Affiliation(s)
- Milton W Taylor
- Department of Biology, Indiana University, Bloomington, IN 47401, USA.
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Taylor MW, Tsukahara T, McClintick JN, Edenberg HJ, Kwo P. 178 Changes in gene expression induced by Pegintron plus ribavirin in PBMC of Hepatitis C patients during the first 10 weeks of treatment. Cytokine 2008. [DOI: 10.1016/j.cyto.2008.07.240] [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: 10/21/2022]
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Carr LG, Kimpel MW, Liang T, McClintick JN, McCall K, Morse M, Edenberg HJ. Identification of candidate genes for alcohol preference by expression profiling of congenic rat strains. Alcohol Clin Exp Res 2007; 31:1089-98. [PMID: 17451403 PMCID: PMC4455872 DOI: 10.1111/j.1530-0277.2007.00397.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [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] [Indexed: 01/02/2023]
Abstract
BACKGROUND A highly significant quantitative trait locus (QTL) on chromosome 4 that influenced alcohol preference was identified by analyzing crosses between the iP and iNP rats. Congenic strains in which the iP chromosome 4 QTL interval was transferred to the iNP (NP.P) exhibited the expected increase in alcohol consumption compared with the iNP background strain. This study was undertaken to identify genes in the chromosome 4 QTL interval that might contribute to the differences in alcohol consumption between the alcohol-naïve congenic and background strains. METHODS RNA from 5 brain regions from each of 6 NP.P and 6 iNP rats was labeled and analyzed separately on an Affymetrix Rat Genome 230 2.0 microarray to look for both cis-regulated and trans-regulated genes. Expression levels were normalized using robust multi-chip average (RMA). Differential gene expression was validated using quantitative real-time polymerase chain reaction. Five individual brain regions (nucleus accumbens, frontal cortex, amygdala, hippocampus, and striatum) were analyzed to detect differential expression of genes within the introgressed QTL interval, as well as genes outside that region. To increase the power to detect differentially expressed genes, combined analyses (averaging data from the 5 discrete brain regions of each animal) were also carried out. RESULTS Analyses within individual brain regions that focused on genes within the QTL interval detected differential expression in all 5 brain regions; a total of 35 genes were detected in at least 1 region, ranging from 6 genes in the nucleus accumbens to 22 in the frontal cortex. Analysis of the whole genome detected very few differentially expressed genes outside the QTL. Combined analysis across brain regions was more powerful. Analysis focused on the genes within the QTL interval confirmed 19 of the genes detected in individual regions and detected 15 additional genes. Whole genome analysis detected 1 differentially expressed gene outside the interval. CONCLUSIONS Cis-regulated candidate genes for alcohol consumption were identified using microarray profiling of gene expression differences in congenic animals carrying a QTL for alcohol preference.
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Affiliation(s)
- Lucinda G Carr
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
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Kimpel MW, Strother WN, McClintick JN, Carr LG, Liang T, Edenberg HJ, McBride WJ. Functional gene expression differences between inbred alcohol-preferring and -non-preferring rats in five brain regions. Alcohol 2007; 41:95-132. [PMID: 17517326 PMCID: PMC1976291 DOI: 10.1016/j.alcohol.2007.03.003] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.6] [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: 11/29/2006] [Revised: 03/01/2007] [Accepted: 03/08/2007] [Indexed: 01/23/2023]
Abstract
The objective of this study was to determine if there are innate differences in gene expression in selected CNS regions between inbred alcohol-preferring (iP) and -non-preferring (iNP) rats. Gene expression was determined in the nucleus accumbens (ACB), amygdala (AMYG), frontal cortex (FC), caudate-putamen (CPU), and hippocampus (HIPP) of alcohol-naïve adult male iP and iNP rats, using Affymetrix Rat Genome U34A microarrays (n = 6/strain). Using Linear Modeling for Microarray Analysis with a false discovery rate threshold of 0.1, there were 16 genes with differential expression in the ACB, 54 in the AMYG, 8 in the FC, 24 in the CPU, and 21 in the HIPP. When examining the main effect of strain across regions, 296 genes were differentially expressed. Although the relatively small number of genes found significant within individual regions precluded a powerful analysis for over-represented Gene Ontology categories, the much larger list resulting from the main effect of strain analysis produced 17 over-represented categories (P < .05), including axon guidance, gliogenesis, negative regulation of programmed cell death, regulation of programmed cell death, regulation of synapse structure function, and transmission of nerve impulse. Co-citation analysis and graphing of significant genes revealed a network involved in the neuropeptide Y (NPY) transmitter system. Correlation of all significant genes with those located within previously established rat alcohol QTLs revealed that of the total of 313 significant genes, 71 are located within such QTLs. The many regional and overall gene expression differences between the iP and iNP rat lines may contribute to the divergent alcohol drinking phenotypes of these rats.
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Affiliation(s)
- Mark W Kimpel
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN 46202-4887, USA.
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Taylor MW, Tsukahara T, Brodsky L, Schaley J, Sanda C, Stephens MJ, McClintick JN, Edenberg HJ, Li L, Tavis JE, Howell C, Belle SH. Changes in gene expression during pegylated interferon and ribavirin therapy of chronic hepatitis C virus distinguish responders from nonresponders to antiviral therapy. J Virol 2007; 81:3391-401. [PMID: 17267482 PMCID: PMC1866036 DOI: 10.1128/jvi.02640-06] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Treating chronic hepatitis C virus (HCV) infection using pegylated alpha interferon and ribavirin leads to sustained clearance of virus and clinical improvement in approximately 50% of patients. Response rates are lower among patients with genotype 1 than with genotypes 2 and 3 and among African-American (AA) patients compared to Caucasian (CA) patients. Using DNA microarrays, gene expression was assessed for a group of 33 African-American and 36 Caucasian American patients with chronic HCV genotype 1 infection during the first 28 days of treatment. Results were examined with respect to treatment responses and to race. Patients showed a response to treatment at the gene expression level in RNA isolated from peripheral blood mononuclear cells irrespective of degree of decrease in HCV RNA levels. However, gene expression responses were relatively blunted in patients with poor viral response (<1.5 log(10)-IU/ml decrease at 28 days) compared to those in patients with a marked (>3.5 log(10)-IU/ml decrease) or intermediate (1.5 to 3.5 log(10)-IU/ml decrease) response. The number of genes that were up- or down-regulated by pegylated interferon and ribavirin treatment was fewer in patients with a poor response than in those with an intermediate or marked viral response. However AA patients had a stronger interferon response than CA patients in general. The induced levels of known interferon-stimulated genes such as the 2'5'-oligoadenylate synthetase, MX1, IRF-7, and toll-like receptor TLR-7 genes was lower in poor-response patients than in marked- or intermediate-response patients. Thus, the relative lack of viral response to interferon therapy of hepatitis C virus infection is associated with blunted interferon cell signaling. No specific regulatory gene could be identified as responsible for this global blunting or the racial differences.
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Affiliation(s)
- Milton W Taylor
- Department of Biology, Indiana University, Bloomington, IN 47401, USA.
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Sanda C, Weitzel P, Tsukahara T, Schaley J, Edenberg HJ, Stephens MA, McClintick JN, Blatt LM, Li L, Brodsky L, Taylor MW. Differential gene induction by type I and type II interferons and their combination. J Interferon Cytokine Res 2006; 26:462-72. [PMID: 16800785 DOI: 10.1089/jir.2006.26.462] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.8] [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] [Indexed: 11/12/2022] Open
Abstract
Type I and type II interferons (IFNs) bind to different cell surface receptors but activate overlapping signal transduction pathways. We examined the effects of a type I IFN (IFN-alphacon1) and a type II IFN (IFN-gamma1b) on gene expression in A549 cells and demonstrate that there is a common set of genes modulated by both IFNs as well as a set of genes specifically regulated by each, reflecting the activation of different signaling pathways. In particular, IFN-gamma induced many more genes of the signaling pathways, apoptosis, and cytokine interactions than did IFN-alpha. Even with genes induced by both IFNs there were distinctive quantitative differences in expression. IFN-gamma1b plays a major role in the induction and regulation of the complement pathway. Previous work has shown a synergistic antiviral and antiproliferative effect of type I and type II IFNs in cell culture and in the treatment of tumors in mice. We demonstrate that a majority of genes showed an additive effect of IFN-alphacon1 and IFN-gamma1b, but a subset of genes is synergistically induced; these include ISG20, MX2, OAS2, and other genes known to be involved in the antiviral response, TRAIL (TNFSF10) and caspases involved in apoptosis and chemokine genes RANTES, CXCL10, and CXCL11. Greater than additive transcription of some of these genes in the presence of both IFNs was confirmed by real-time kinetic RT-PCR. Elevated induction of many of these genes may be sufficient to explain the synergistic antiviral and antitumor effects of this combination of IFNs in vivo.
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Affiliation(s)
- Corneliu Sanda
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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McClintick JN, Crabb DW, Tian H, Pinaire J, Smith JR, Jerome RE, Edenberg HJ. Global effects of vitamin A deficiency on gene expression in rat liver: evidence for hypoandrogenism. J Nutr Biochem 2006; 17:345-55. [PMID: 16214324 DOI: 10.1016/j.jnutbio.2005.08.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [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: 06/21/2005] [Revised: 07/29/2005] [Accepted: 08/16/2005] [Indexed: 10/25/2022]
Abstract
Vitamin A (retinol) metabolites are ligands for transcription factors that regulate many genes. The liver is the main storage depot for retinol and plays a role in vitamin A homeostasis. To better understand the effects of vitamin A deficiency on liver gene expression, we produced retinol deficiency in male rats by feeding a diet low in retinol for 53 days after weaning and examined the effects on gene expression in liver using Affymetrix oligonucleotide microarrays. We detected expression of 41% of the 8799 probe sets represented on the RGU-34A GeneChips. Vitamin A deficiency resulted in major changes in liver gene expression: 805 genes (22% of all genes detected) differed at P<or=.05 (false discovery rate <0.143). Genes involved in fatty acid metabolism, peroxisomal function, glycolysis, glutamate metabolism and the urea cycle were altered. The expression of many sexually dimorphic genes was altered toward a feminized or senescent pattern of gene expression in the liver. Retinol deficiency also produces a shift toward increased protein and fat catabolism and decreased fatty acid synthesis.
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Affiliation(s)
- Jeanette N McClintick
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202-5251, USA
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Abstract
Background Affymetrix GeneChips® are widely used for expression profiling of tens of thousands of genes. The large number of comparisons can lead to false positives. Various methods have been used to reduce false positives, but they have rarely been compared or quantitatively evaluated. Here we describe and evaluate a simple method that uses the detection (Present/Absent) call generated by the Affymetrix microarray suite version 5 software (MAS5) to remove data that is not reliably detected before further analysis, and compare this with filtering by expression level. We explore the effects of various thresholds for removing data in experiments of different size (from 3 to 10 arrays per treatment), as well as their relative power to detect significant differences in expression. Results Our approach sets a threshold for the fraction of arrays called Present in at least one treatment group. This method removes a large percentage of probe sets called Absent before carrying out the comparisons, while retaining most of the probe sets called Present. It preferentially retains the more significant probe sets (p ≤ 0.001) and those probe sets that are turned on or off, and improves the false discovery rate. Permutations to estimate false positives indicate that probe sets removed by the filter contribute a disproportionate number of false positives. Filtering by fraction Present is effective when applied to data generated either by the MAS5 algorithm or by other probe-level algorithms, for example RMA (robust multichip average). Experiment size greatly affects the ability to reproducibly detect significant differences, and also impacts the effect of filtering; smaller experiments (3–5 samples per treatment group) benefit from more restrictive filtering (≥50% Present). Conclusion Use of a threshold fraction of Present detection calls (derived by MAS5) provided a simple method that effectively eliminated from analysis probe sets that are unlikely to be reliable while preserving the most significant probe sets and those turned on or off; it thereby increased the ratio of true positives to false positives.
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Affiliation(s)
- Jeanette N McClintick
- Department of Medical and Molecular Genetics, Indiana University, Indianapolis, Indiana, USA
- Center for Medical Genomics, Indiana University, Indianapolis, Indiana, USA
| | - Howard J Edenberg
- Department of Medical and Molecular Genetics, Indiana University, Indianapolis, Indiana, USA
- Center for Medical Genomics, Indiana University, Indianapolis, Indiana, USA
- Department of Biochemistry and Molecular Biology, Indiana University, Indianapolis, Indiana, USA
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Fong SL, Criswell MH, Belecky-Adams T, Fong WB, McClintick JN, Kao WW, Edenberg HJ. Characterization of a transgenic mouse line lacking photoreceptor development within the ventral retina. Exp Eye Res 2005; 81:376-88. [PMID: 16054133 DOI: 10.1016/j.exer.2005.06.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2005] [Revised: 05/24/2005] [Accepted: 06/08/2005] [Indexed: 11/27/2022]
Abstract
A unique transgenic mouse line was generated by incorporating a minigene that contained a cone-specific human cone transducin alpha-subunit (GNAT2) promoter, an attenuated diphtheria toxin A (DTA) gene, and an enhancer element from human interphotoreceptor retinoid-binding protein (IRBP) gene. This transgenic mouse line is designated h-GNAT2pro-DTA. During postnatal retinal development, both transgenic and non-transgenic retinas showed similar morphology and thickness at P1. Between ages P8 and P30, all retinal layers became recognizable in non-transgenic and also in transgenic dorsal retinas. However, in the ventral retina of the transgenic mice the photoreceptor layers did not develop. This aberration occurred as a result of abnormal cellular development, rather than as a consequence of retinal degeneration. In adult transgenic animals, approximately 44% of the retina located dorsally appeared morphologically normal, whereas 32% of the retina located ventrally was completely lacking photoreceptor development. The 24% mid-retinal region exhibited transitional morphology containing malformed photoreceptors. At P360 or older, the thickness of retina layers was reduced in both dorsal and ventral regions. The abnormality observed in transgenic retinas involved mainly the photoreceptors; the other retinal cell types were all present in both dorsal and ventral retinas. Since the DTA gene was only expressed in cone cells, the absence of cone photoreceptors in the transgenic retina was to be expected. However, what was unexpected was the concomitant absence of rod photoreceptors in the ventral retina, suggesting that the presence of cones may be important for the development of rods. This new transgenic line can lead to better understanding of photoreceptor development, and may serve as a new animal model for studying photoreceptor-related retinal diseases.
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Affiliation(s)
- Shao-Ling Fong
- Department of Ophthalmology, Indiana University, 702 Rotary Circle, Indianapolis, IN 46202, USA.
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Edenberg HJ, Strother WN, McClintick JN, Tian H, Stephens M, Jerome RE, Lumeng L, Li TK, McBride WJ. Gene expression in the hippocampus of inbred alcohol-preferring and -nonpreferring rats. Genes Brain Behav 2005; 4:20-30. [PMID: 15660665 DOI: 10.1111/j.1601-183x.2004.00091.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The hippocampus is sensitive to the effects of ethanol and appears to have a role in the development of alcohol tolerance. The objective of this study was to test the hypothesis that there are innate differences in gene expression in the hippocampus of inbred alcohol-preferring (iP) and -nonpreferring (iNP) rats that may contribute to differences in sensitivity to ethanol and/or in the development of tolerance. Affymetrix microarrays were used to measure gene expression in the hippocampus of alcohol-naive male iP and iNP rats in two experiments (n=4 and 6 per strain in the two experiments). Combining data from the two experiments, there were 137 probesets representing 129 genes that significantly differed (P < or = 0.01); 62 probesets differed at P < or = 0.001. Among the 36% of the genes that were expressed more in the iP than iNP rat at this level of significance, many were involved in cell growth and adhesion, cellular stress reduction and anti-oxidation, protein trafficking, regulation of gene expression, synaptic function and metabolism. Among the 64% of the genes that had lower expression in the hippocampus of iP than iNP rats were genes involved in metabolic pathways, cellular signaling systems, protein trafficking, cell death and neurotransmission. Overall, the data indicate that there are significant innate differences in gene expression in the hippocampus between iP and iNP rats, some of which might contribute to the differences observed in the development of alcohol tolerance between the selectively bred P and NP lines.
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Affiliation(s)
- H J Edenberg
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202-4887, USA
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