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Lanore A, Basset A, Lesage S. A machine learning approach for gene prioritization in Parkinson's disease. Brain 2024; 147:743-745. [PMID: 38428999 DOI: 10.1093/brain/awae043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 02/08/2024] [Indexed: 03/03/2024] Open
Abstract
This scientific commentary refers to ‘Machine learning nominates the inositol pathway and novel genes in Parkinson’s disease’ by Yu et al. (https://doi.org/10.1093/brain/awad345).
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Affiliation(s)
- Aymeric Lanore
- Sorbonne Université, Institut du Cerveau, Paris Brain Institute, ICM, Inserm, CNRS, Paris, France
- Assistance Publique Hôpitaux de Paris, Département de Neurologie, CIC Neurosciences, Hôpital Pitié-Salpêtrière, Paris, France
| | - Aymeric Basset
- Sorbonne Université, Institut du Cerveau, Paris Brain Institute, ICM, Inserm, CNRS, Paris, France
| | - Suzanne Lesage
- Sorbonne Université, Institut du Cerveau, Paris Brain Institute, ICM, Inserm, CNRS, Paris, France
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Koromina M, Ravi A, Panagiotaropoulou G, Schilder BM, Humphrey J, Braun A, Bidgeli T, Chatzinakos C, Coombes B, Kim J, Liu X, Terao C, O.’Connell KS, Adams M, Adolfsson R, Alda M, Alfredsson L, Andlauer TFM, Andreassen OA, Antoniou A, Baune BT, Bengesser S, Biernacka J, Boehnke M, Bosch R, Cairns M, Carr VJ, Casas M, Catts S, Cichon S, Corvin A, Craddock N, Dafnas K, Dalkner N, Dannlowski U, Degenhardt F, Di Florio A, Dikeos D, Fellendorf FT, Ferentinos P, Forstner AJ, Forty L, Frye M, Fullerton JM, Gawlik M, Gizer IR, Gordon-Smith K, Green MJ, Grigoroiu-Serbanescu M, Guzman-Parra J, Hahn T, Henskens F, Hillert J, Jablensky AV, Jones L, Jones I, Jonsson L, Kelsoe JR, Kircher T, Kirov G, Kittel-Schneider S, Kogevinas M, Landén M, Leboyer M, Lenger M, Lissowska J, Lochner C, Loughland C, MacIntyre D, Martin NG, Maratou E, Mathews CA, Mayoral F, McElroy SL, McGregor NW, McIntosh A, McQuillin A, Michie P, Milanova V, Mitchell PB, Moutsatsou P, Mowry B, Müller-Myhsok B, Myers R, Nenadić I, Nöthen MM, O’Donovan C, O’Donovan M, Ophoff RA, Owen MJ, Pantelis C, Pato C, Pato MT, Patrinos GP, Pawlak JM, Perlis RH, Porichi E, Posthuma D, Ramos-Quiroga JA, Reif A, Reininghaus EZ, Ribasés M, Rietschel M, Schall U, Schulze TG, Scott L, Scott RJ, Serretti A, Weickert CS, Smoller JW, Artigas MS, Stein DJ, Streit F, Toma C, Tooney P, Vieta E, Vincent JB, Waldman ID, Weickert T, Witt SH, Hong KS, Ikeda M, Iwata N, Świątkowska B, Won HH, Edenberg HJ, Ripke S, Raj T, Coleman JRI, Mullins N. Fine-mapping genomic loci refines bipolar disorder risk genes. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.12.24302716. [PMID: 38405768 PMCID: PMC10889003 DOI: 10.1101/2024.02.12.24302716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Bipolar disorder (BD) is a heritable mental illness with complex etiology. While the largest published genome-wide association study identified 64 BD risk loci, the causal SNPs and genes within these loci remain unknown. We applied a suite of statistical and functional fine-mapping methods to these loci, and prioritized 22 likely causal SNPs for BD. We mapped these SNPs to genes, and investigated their likely functional consequences by integrating variant annotations, brain cell-type epigenomic annotations, brain quantitative trait loci, and results from rare variant exome sequencing in BD. Convergent lines of evidence supported the roles of SCN2A, TRANK1, DCLK3, INSYN2B, SYNE1, THSD7A, CACNA1B, TUBBP5, PLCB3, PRDX5, KCNK4, AP001453.3, TRPT1, FKBP2, DNAJC4, RASGRP1, FURIN, FES, YWHAE, DPH1, GSDMB, MED24, THRA, EEF1A2, and KCNQ2 in BD. These represent promising candidates for functional experiments to understand biological mechanisms and therapeutic potential. Additionally, we demonstrated that fine-mapping effect sizes can improve performance and transferability of BD polygenic risk scores across ancestrally diverse populations, and present a high-throughput fine-mapping pipeline (https://github.com/mkoromina/SAFFARI).
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Affiliation(s)
- Maria Koromina
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ashvin Ravi
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Brian M. Schilder
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jack Humphrey
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alice Braun
- Department of Psychiatry and Psychotherapy, Charité - Universitätsmedizin, Berlin, Germany
| | | | | | - Brandon Coombes
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Jaeyoung Kim
- Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Samsung Medical Center, Seoul, Republic of Korea
- Samsung Genome Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Xiaoxi Liu
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
- The Department of Applied Genetics, The School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Kevin S. O.’Connell
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
- NORMENT, University of Oslo, Oslo, Norway
| | - Mark Adams
- Division of Psychiatry, Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh, UK
| | - Rolf Adolfsson
- Department of Clinical Sciences, Psychiatry, Umeå, University Medical Faculty, Umeå, Sweden
| | - Martin Alda
- Department 20 of Psychiatry, Dalhousie University, Halifax, NS, Canada
- National Institute of Mental Health, Klecany, Czech Republic
| | - Lars Alfredsson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Till F. M. Andlauer
- Department of Neurology, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Ole A. Andreassen
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
- NORMENT, University of Oslo, Oslo, Norway
| | - Anastasia Antoniou
- National Kapodistrian University of Athens, 2nd Department of Psychiatry, Attikon General Hospital, Athens, Greece
| | - Bernhard T. Baune
- Department of Psychiatry, University of Münster, Münster, Germany
- Department of Psychiatry, Melbourne Medical School, The University of Melbourne, Melbourne, VIC, Australia
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia
| | - Susanne Bengesser
- Medical University of Graz, Division of Psychiatry and Psychotherapeutic Medicine, Graz, Austria
| | - Joanna Biernacka
- Department of Quantitative Health Sciences Research, Mayo Clinic, Rochester, MN, USA
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA
| | - Michael Boehnke
- Center for Statistical Genetics and Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Rosa Bosch
- Instituto de Salud Carlos III, Biomedical Network Research Centre on Mental Health (CIBERSAM), Madrid, Spain
- Programa SJD MIND Escoles, Hospital Sant Joan de Déu, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Spain
| | | | - Vaughan J. Carr
- School of Clinical Medicine, Discipline of Psychiatry and Mental Health, University of New South Wales, Sydney, NSW, Australia
| | - Miquel Casas
- Instituto de Salud Carlos III, Biomedical Network Research Centre on Mental Health (CIBERSAM), Madrid, Spain
- Programa SJD MIND Escoles, Hospital Sant Joan de Déu, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Spain
| | | | - Sven Cichon
- Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
- Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany
| | - Aiden Corvin
- Neuropsychiatric Genetics Research Group, Dept of Psychiatry and Trinity Translational Medicine Institute, Trinity College Dublin, Dublin, Ireland
| | - Nicholas Craddock
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Konstantinos Dafnas
- National Kapodistrian University of Athens, 2nd Department of Psychiatry, Attikon General Hospital, Athens, Greece
| | - Nina Dalkner
- Medical University of Graz, Division of Psychiatry and Psychotherapeutic Medicine, Graz, Austria
| | - Udo Dannlowski
- Institute for Translatiol Psychiatry, University of Münster, Münster, Germany
| | - Franziska Degenhardt
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Duisburg, Germany
| | - Arianna Di Florio
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
- Department of Psychiatry, University of North Caroli at Chapel Hill, Chapel Hill, NC, USA
| | - Dimitris Dikeos
- National Kapodistrian University of Athens, 2nd Department of Psychiatry, Attikon General Hospital, Athens, Greece
| | | | - Panagiotis Ferentinos
- National Kapodistrian University of Athens, 2nd Department of Psychiatry, Attikon General Hospital, Athens, Greece
- Social, Genetic and Developmental Psychiatry Centre, King’s College London, London, UK
| | - Andreas J. Forstner
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
- Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany
- Centre for Human Genetics, University of Marburg, Marburg, Germany
| | - Liz Forty
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Mark Frye
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA
| | - Janice M. Fullerton
- Neuroscience Research Australia, Sydney, NSW, Australia
- School of Biomedical Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Micha Gawlik
- Department of Psychiatry, Psychosomatics and Psychotherapy, Center of Mental Health, University Hospital Würzburg, Würzburg, Germany
| | - Ian R. Gizer
- Department of Psychological Sciences, University of Missouri, Columbia, MO, USA
| | | | - Melissa J. Green
- Neuroscience Research Australia, Sydney, NSW, Australia
- Discipline of Psychiatry and Mental Health, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
| | - Maria Grigoroiu-Serbanescu
- Biometric Psychiatric Genetics Research Unit, Alexandru Obregia Clinical Psychiatric Hospital, Bucharest, Romania
| | - José Guzman-Parra
- Mental Health Department, University Regional Hospital, Biomedicine Institute (IBIMA), Málaga, Spain
| | - Tim Hahn
- Institute for Translatiol Psychiatry, University of Münster, Münster, Germany
| | | | - Jan Hillert
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | | | - Lisa Jones
- Psychological Medicine, University of Worcester, Worcester, UK
| | - Ian Jones
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Lina Jonsson
- Institute of Neuroscience and Physiology, University of Gothenburg, Gothenburg, Sweden
| | - John R. Kelsoe
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Tilo Kircher
- Department of Psychiatry and Psychotherapy, University of Marburg, Germany
| | - George Kirov
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Sarah Kittel-Schneider
- Department of Psychiatry, Psychosomatics and Psychotherapy, Center of Mental Health, University Hospital Würzburg, Würzburg, Germany
- Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, University Hospital Frankfurt, Frankfurt am Main, Germany
- Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland
| | | | - Mikael Landén
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Marion Leboyer
- Université Paris Est Créteil, INSERM, IMRB, Translational Neuropsychiatry, Créteil, France
- Department of Psychiatry and Addiction Medicine, Assistance Publique - Hôpitaux de Paris, Paris, France
| | - Melanie Lenger
- Medical University of Graz, Division of Psychiatry and Psychotherapeutic Medicine, Graz, Austria
| | - Jolanta Lissowska
- Cancer Epidemiology and Prevention, M. Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Christine Lochner
- SA MRC Unit on Risk and Resilience in Mental Disorders, Dept of Psychiatry, Stellenbosch University, Stellenbosch, South Africa
| | | | - Donald MacIntyre
- Division of Psychiatry, Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh, UK
| | - Nicholas G. Martin
- Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Psychology, The University of Queensland, Brisbane, QLD, Australia
| | - Eirini Maratou
- National and Kapodistrian University of Athens, Medical School, Clinical Biochemistry Laboratory, Attikon General Hospital, Athens, Greece
| | - Carol A. Mathews
- Department of Psychiatry and Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Fermin Mayoral
- Mental Health Department, University Regional Hospital, Biomedicine Institute (IBIMA), Málaga, Spain
| | | | - Nathaniel W. McGregor
- Systems Genetics Working Group, Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| | - Andrew McIntosh
- Division of Psychiatry, Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh, UK
| | | | | | - Vihra Milanova
- Psychiatric Clinic, Alexander University Hospital, Bulgaria
| | - Philip B. Mitchell
- Discipline of Psychiatry and Mental Health, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
| | - Paraskevi Moutsatsou
- National Kapodistrian University of Athens, Medical School, Clinical Biochemistry Laboratory, Attikon General Hospital, Athens, Greece
| | - Bryan Mowry
- University of Queensland, Brisbane, QLD, Australia
| | - Bertram Müller-Myhsok
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Richard Myers
- Hudsolpha Institute for Biotechnology, Huntsville, AL, USA
| | - Igor Nenadić
- Department of Psychiatry and Psychotherapy, University of Marburg, Marburg, Germany
- Center for Mind, Brain and Behavior (CMBB), University of Marburg and Justus Liebig University Giessen, Giessen, Germany
| | - Markus M. Nöthen
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Claire O’Donovan
- Department 20 of Psychiatry, Dalhousie University, Halifax, NS, Canada
| | - Michael O’Donovan
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Roel A. Ophoff
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Department of Psychiatry, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Psychiatry and Biobehavioral Science, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Michael J Owen
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | | | - Carlos Pato
- Institute for Genomic Health, SUNY Downstate Medical Center College of Medicine, Brooklyn, NY, USA
| | - Michele T. Pato
- Institute for Genomic Health, SUNY Downstate Medical Center College of Medicine, Brooklyn, NY, USA
| | - George P. Patrinos
- University of Patras, School of Health Sciences, Department of Pharmacy, Laboratory of Pharmacogenomics and Individualized Therapy, Patras, Greece
- United Arab Emirates University, College of Medicine and Health Sciences, Department of Genetics and Genomics, Al-Ain, United Arab Emirates
- United Arab Emirates University, Zayed Center for Health Sciences, Al-Ain, United Arab Emirates
| | - Joanna M. Pawlak
- Department of Psychiatry, Departmet of Psychiatric Genetics, Poznan University of Medical Sciences, Poznan, Poland
| | - Roy H. Perlis
- Psychiatry, Harvard Medical School, Boston, MA, USA
- Division of Clinical Research, Massachusetts General Hospital, Boston, MA, USA
| | - Evgenia Porichi
- National and Kapodistrian University of Athens, 2nd Department of Psychiatry, Attikon General Hospital, Athens, Greece
| | - Danielle Posthuma
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Department of Clinical Genetics, Amsterdam Neuroscience, Vrije Universiteit Medical Center, Amsterdam, The Netherlands
| | - Josep Antoni Ramos-Quiroga
- Instituto de Salud Carlos III, Biomedical Network Research Centre on Mental Health (CIBERSAM), Madrid, Spain
- Department of Psychiatry, Hospital Universitari Vall d´Hebron, Barcelo, Spain
- Department of Psychiatry and Forensic Medicine, Universitat Autònoma de Barcelo, Barcelo, Spain
- Psychiatric Genetics Unit, Group of Psychiatry Mental Health and Addictions, Vall d´Hebron Research Institut (VHIR), Universitat Autònoma de Barcelo, Barcelo, Spain
| | - Andreas Reif
- Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Eva Z. Reininghaus
- Medical University of Graz, Division of Psychiatry and Psychotherapeutic Medicine, Graz, Austria
| | - Marta Ribasés
- Instituto de Salud Carlos III, Biomedical Network Research Centre on Mental Health (CIBERSAM), Madrid, Spain
- Department of Psychiatry, Hospital Universitari Vall d´Hebron, Barcelona, Spain
- Psychiatric Genetics Unit, Group of Psychiatry Mental Health and Addictions, Vall d´Hebron Research Institut (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
- Department of Genetics, Microbiology, and Statistics, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain. Department of Genetics, Microbiology and Statistics, Faculty of Biology, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Marcella Rietschel
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | | | - Thomas G. Schulze
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Institute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU Munich, Munich, Germany
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Göttingen, Germany
- Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Laura Scott
- Center for Statistical Genetics and Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | | | - Alessandro Serretti
- Department of Biomedical and NeuroMotor Sciences, University of Bologna, Bologna, Italy
| | - Cynthia Shannon Weickert
- Discipline of Psychiatry and Mental Health, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
- Department of Neuroscience, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Jordan W. Smoller
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
- Psychiatric and Neurodevelopmental Genetics Unit (PNGU), Massachusetts General Hospital, Boston, MA, USA
| | - Maria Soler Artigas
- Instituto de Salud Carlos III, Biomedical Network Research Centre on Mental Health (CIBERSAM), Madrid, Spain
- Department of Psychiatry, Hospital Universitari Vall d´Hebron, Barcelo, Spain
- Psychiatric Genetics Unit, Group of Psychiatry Mental Health and Addictions, Vall d´Hebron Research Institut (VHIR), Universitat Autònoma de Barcelo, Barcelo, Spain
- Department of Genetics, Microbiology, and Statistics, Faculty of Biology, Universitat de Barcelo, Barcelo, Spain
| | - Dan J. Stein
- SAMRC Unit on Risk and Resilience in Mental Disorders, Dept of Psychiatry and Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Fabian Streit
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Claudio Toma
- Neuroscience Research Australia, Sydney, NSW, Australia
- Discipline of Psychiatry and Mental Health, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid and CSIC, Madrid, Spain
| | - Paul Tooney
- University of Newcastle, Newcastle, NSW, Australia
| | - Eduard Vieta
- Clinical Institute of Neuroscience, Hospital Clinic, University of Barcelona, IDIBAPS, CIBERSAM, Barcelona, Spain
| | - John B. Vincent
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | | | - Thomas Weickert
- Discipline of Psychiatry and Mental Health, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
- Department of Neuroscience, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Stephanie H. Witt
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Kyung Sue Hong
- Department of Psychiatry, Sungkyunkwan University School of Medicine, Samsung Medical Center, Seoul, South Korea
| | - Masashi Ikeda
- Department of Psychiatry, Fujita Health University School of Medicine, Toyoake, Japan
| | - Nakao Iwata
- Department of Psychiatry, Fujita Health University School of Medicine, Toyoake, Japan
| | - Beata Świątkowska
- Department of Environmental Epidemiology, Nofer Institute of Occupational Medicine, Lodz, Poland
| | - Hong-Hee Won
- Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Samsung Medical Center, Seoul, Republic of Korea
| | - Howard J. Edenberg
- Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Medical and Molecular Genetics, Indiana University, Indianapolis, IN, USA
| | - Stephan Ripke
- Department of Psychiatry and Psychotherapy, Charité - Universitätsmedizin, Berlin, Germany
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Towfique Raj
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jonathan R. I. Coleman
- Social, Genetic and Developmental Psychiatry Centre, King’s College London, London, UK
- NIHR Maudsley Biomedical Research Centre, South London and Maudsley NHS Foundation Trust, London, UK
| | - Niamh Mullins
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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3
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Liao Y, Yu H, Zhang Y, Lu Z, Sun Y, Guo L, Guo J, Kang Z, Feng X, Sun Y, Wang G, Su Z, Lu T, Yang Y, Li W, Lv L, Yan H, Zhang D, Yue W. Genome-wide association study implicates lipid pathway dysfunction in antipsychotic-induced weight gain: multi-ancestry validation. Mol Psychiatry 2024:10.1038/s41380-024-02447-2. [PMID: 38336841 DOI: 10.1038/s41380-024-02447-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 01/21/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024]
Abstract
Antipsychotic-induced weight gain (AIWG) is a common side effect of antipsychotic medication and may contribute to diabetes and coronary heart disease. To expand the unclear genetic mechanism underlying AIWG, we conducted a two-stage genome-wide association study in Han Chinese patients with schizophrenia. The study included a discovery cohort of 1936 patients and a validation cohort of 534 patients, with an additional 630 multi-ancestry patients from the CATIE study for external validation. We applied Mendelian randomization (MR) analysis to investigate the relationship between AIWG and antipsychotic-induced lipid changes. Our results identified two novel genome-wide significant loci associated with AIWG: rs10422861 in PEPD (P = 1.373 × 10-9) and rs3824417 in PTPRD (P = 3.348 × 10-9) in Chinese Han samples. The association of rs10422861 was validated in the European samples. Fine-mapping and functional annotation revealed that PEPD and PTPRD are potentially causal genes for AIWG, with their proteins being prospective therapeutic targets. Colocalization analysis suggested that AIWG and type 2 diabetes (T2D) shared a causal variant in PEPD. Polygenic risk scores (PRSs) for AIWG and T2D significantly predicted AIWG in multi-ancestry samples. Furthermore, MR revealed a risky causal effect of genetically predicted changes in low-density lipoprotein cholesterol (P = 7.58 × 10-4) and triglycerides (P = 2.06 × 10-3) caused by acute-phase of antipsychotic treatment on AIWG, which had not been previously reported. Our model, incorporating antipsychotic-induced lipid changes, PRSs, and clinical predictors, significantly predicted BMI percentage change after 6-month antipsychotic treatment (AUC = 0.79, R2 = 0.332). Our results highlight that the mechanism of AIWG involves lipid pathway dysfunction and may share a genetic basis with T2D through PEPD. Overall, this study provides new insights into the pathogenesis of AIWG and contributes to personalized treatment of schizophrenia.
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Affiliation(s)
- Yundan Liao
- Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, 100191, China
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, 100191, China
- NHC Key Laboratory of Mental Health (Peking University), Beijing, 100191, China
| | - Hao Yu
- Department of Psychiatry, Jining Medical University, Jining, Shandong, 272067, China
| | - Yuyanan Zhang
- Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, 100191, China.
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, 100191, China.
- NHC Key Laboratory of Mental Health (Peking University), Beijing, 100191, China.
| | - Zhe Lu
- Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, 100191, China
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, 100191, China
- NHC Key Laboratory of Mental Health (Peking University), Beijing, 100191, China
| | - Yaoyao Sun
- Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, 100191, China
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, 100191, China
- NHC Key Laboratory of Mental Health (Peking University), Beijing, 100191, China
| | - Liangkun Guo
- Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, 100191, China
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, 100191, China
- NHC Key Laboratory of Mental Health (Peking University), Beijing, 100191, China
| | - Jing Guo
- Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, 100191, China
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, 100191, China
- NHC Key Laboratory of Mental Health (Peking University), Beijing, 100191, China
| | - Zhewei Kang
- Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, 100191, China
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, 100191, China
- NHC Key Laboratory of Mental Health (Peking University), Beijing, 100191, China
| | - Xiaoyang Feng
- Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, 100191, China
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, 100191, China
- NHC Key Laboratory of Mental Health (Peking University), Beijing, 100191, China
| | - Yutao Sun
- No.5 Hospital, Tangshan, Hebei, 063000, China
| | - Guishan Wang
- The Second Affiliated Hospital of Jining Medical College, Jining, 272051, China
| | - Zhonghua Su
- The Second Affiliated Hospital of Jining Medical College, Jining, 272051, China
| | - Tianlan Lu
- Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, 100191, China
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, 100191, China
- NHC Key Laboratory of Mental Health (Peking University), Beijing, 100191, China
| | - Yongfeng Yang
- The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, 453002, Henan, China
| | - Wenqiang Li
- The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, 453002, Henan, China
| | - Luxian Lv
- The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, 453002, Henan, China
| | - Hao Yan
- Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, 100191, China
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, 100191, China
- NHC Key Laboratory of Mental Health (Peking University), Beijing, 100191, China
| | - Dai Zhang
- Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, 100191, China
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, 100191, China
- NHC Key Laboratory of Mental Health (Peking University), Beijing, 100191, China
- Chinese Institute for Brain Research, Beijing, 102206, China
- Institute for Brain Research and Rehabilitation (IBRR), Guangdong Key Laboratory of Mental Health and Cognitive Science, South China Normal University, Guangzhou, 510631, China
| | - Weihua Yue
- Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, 100191, China.
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, 100191, China.
- NHC Key Laboratory of Mental Health (Peking University), Beijing, 100191, China.
- Chinese Institute for Brain Research, Beijing, 102206, China.
- PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing, 100871, China.
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4
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Schilder BM, Murphy AE, Skene NG. rworkflows: automating reproducible practices for the R community. Nat Commun 2024; 15:149. [PMID: 38167858 PMCID: PMC10761765 DOI: 10.1038/s41467-023-44484-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 12/14/2023] [Indexed: 01/05/2024] Open
Abstract
Despite calls to improve reproducibility in research, achieving this goal remains elusive even within computational fields. Currently, >50% of R packages are distributed exclusively through GitHub. While the trend towards sharing open-source software has been revolutionary, GitHub does not have any default built-in checks for minimal coding standards or software usability. This makes it difficult to assess the current quality R packages, or to consistently use them over time and across platforms. While GitHub-native solutions are technically possible, they require considerable time and expertise for each developer to write, implement, and maintain. To address this, we develop rworkflows; a suite of tools to make robust continuous integration and deployment ( https://github.com/neurogenomics/rworkflows ). rworkflows can be implemented by developers of all skill levels using a one-time R function call which has both sensible defaults and extensive options for customisation. Once implemented, any updates to the GitHub repository automatically trigger parallel workflows that install all software dependencies, run code checks, generate a dedicated documentation website, and deploy a publicly accessible containerised environment. By making the rworkflows suite free, automated, and simple to use, we aim to promote widespread adoption of reproducible practices across a continually growing R community.
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Affiliation(s)
- Brian M Schilder
- Department of Brain Sciences, Faculty of Medicine, Imperial College London, London, W12 0BZ, UK.
- UK Dementia Research Institute at Imperial College London, London, W12 0BZ, UK.
| | - Alan E Murphy
- Department of Brain Sciences, Faculty of Medicine, Imperial College London, London, W12 0BZ, UK
- UK Dementia Research Institute at Imperial College London, London, W12 0BZ, UK
| | - Nathan G Skene
- Department of Brain Sciences, Faculty of Medicine, Imperial College London, London, W12 0BZ, UK.
- UK Dementia Research Institute at Imperial College London, London, W12 0BZ, UK.
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5
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Burstein D, Griffen TC, Therrien K, Bendl J, Venkatesh S, Dong P, Modabbernia A, Zeng B, Mathur D, Hoffman G, Sysko R, Hildebrandt T, Voloudakis G, Roussos P. Genome-wide analysis of a model-derived binge eating disorder phenotype identifies risk loci and implicates iron metabolism. Nat Genet 2023; 55:1462-1470. [PMID: 37550530 PMCID: PMC10947608 DOI: 10.1038/s41588-023-01464-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 06/29/2023] [Indexed: 08/09/2023]
Abstract
Binge eating disorder (BED) is the most common eating disorder, yet its genetic architecture remains largely unknown. Studying BED is challenging because it is often comorbid with obesity, a common and highly polygenic trait, and it is underdiagnosed in biobank data sets. To address this limitation, we apply a supervised machine-learning approach (using 822 cases of individuals diagnosed with BED) to estimate the probability of each individual having BED based on electronic medical records from the Million Veteran Program. We perform a genome-wide association study of individuals of African (n = 77,574) and European (n = 285,138) ancestry while controlling for body mass index to identify three independent loci near the HFE, MCHR2 and LRP11 genes and suggest APOE as a risk gene for BED. We identify shared heritability between BED and several neuropsychiatric traits, and implicate iron metabolism in the pathophysiology of BED. Overall, our findings provide insights into the genetics underlying BED and suggest directions for future translational research.
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Affiliation(s)
- David Burstein
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mental Illness Research, Education, and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, New York, NY, USA
| | - Trevor C Griffen
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center of Excellence in Eating and Weight Disorders, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
| | - Karen Therrien
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mental Illness Research, Education, and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, New York, NY, USA
| | - Jaroslav Bendl
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sanan Venkatesh
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mental Illness Research, Education, and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, New York, NY, USA
| | - Pengfei Dong
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Biao Zeng
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Deepika Mathur
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gabriel Hoffman
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robyn Sysko
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center of Excellence in Eating and Weight Disorders, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tom Hildebrandt
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center of Excellence in Eating and Weight Disorders, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Georgios Voloudakis
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Mental Illness Research, Education, and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, New York, NY, USA.
| | - Panos Roussos
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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6
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Martinez-Carrasco A, Real R, Lawton M, Iwaki H, Tan MMX, Wu L, Williams NM, Carroll C, Hu MTM, Grosset DG, Hardy J, Ryten M, Foltynie T, Ben-Shlomo Y, Shoai M, Morris HR. Genetic meta-analysis of levodopa induced dyskinesia in Parkinson's disease. NPJ Parkinsons Dis 2023; 9:128. [PMID: 37652906 PMCID: PMC10471743 DOI: 10.1038/s41531-023-00573-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 08/16/2023] [Indexed: 09/02/2023] Open
Abstract
The genetic basis of levodopa-induced-dyskinesia (LiD) is poorly understood, and there have been few well-powered genome-wide studies. We performed a genome-wide survival meta-analyses to study the effect of genetic variation on the development of LiD in five separate longitudinal cohorts, and meta-analysed the results. We included 2784 PD patients, of whom 14.6% developed LiD. We found female sex (HR = 1.35, SE = 0.11, P = 0.007) and younger age at onset (HR = 1.8, SE = 0.14, P = 2 × 10-5) increased the probability of developing LiD. We identified three genetic loci significantly associated with time-to-LiD onset. rs72673189 on chromosome 1 (HR = 2.77, SE = 0.18, P = 1.53 × 10-8) located at the LRP8 locus, rs189093213 on chromosome 4 (HR = 3.06, SE = 0.19, P = 2.81 × 10-9) in the non-coding RNA LINC02353 locus, and rs180924818 on chromosome 16 (HR = 3.13, SE = 0.20, P = 6.27 × 10-9) in the XYLT1 locus. Based on a functional annotation analysis on chromosome 1, we determined that changes in DNAJB4 gene expression, close to LRP8, are an additional potential cause of increased susceptibility to LiD. Baseline anxiety status was significantly associated with LiD (OR = 1.14, SE = 0.03, P = 7.4 × 10-5). Finally, we performed a candidate variant analysis of previously reported loci, and found that genetic variability in ANKK1 (rs1800497, HR = 1.27, SE = 0.09, P = 8.89 × 10-3) and BDNF (rs6265, HR = 1.21, SE = 0.10, P = 4.95 × 10-2) loci were significantly associated with time to LiD in our large meta-analysis.
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Affiliation(s)
- Alejandro Martinez-Carrasco
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK.
- UCL Movement Disorders Centre, University College London, London, UK.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA.
| | - Raquel Real
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
- UCL Movement Disorders Centre, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Michael Lawton
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Hirotaka Iwaki
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International, Glen Echo, MD, USA
| | - Manuela M X Tan
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Lesley Wu
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
- UCL Movement Disorders Centre, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Nigel M Williams
- Institute of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Camille Carroll
- Faculty of Health, University of Plymouth, Plymouth, UK
- Translational and Clinical Research Institute, Newcastle University, Newcastle, UK
| | - Michele T M Hu
- Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, University of Oxford, Oxford, UK
- Oxford Parkinson's Disease Centre, University of Oxford, Oxford, UK
| | - Donald G Grosset
- School of Neuroscience and Psychology, University of Glasgow, Glasgow, UK
| | - John Hardy
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
- Department of Neurodegenerative Diseases, UCL Queen Square Institute of Neurology, University College London, London, UK
- UK Dementia Research Institute, University College London, London, UK
- Reta Lila Weston Institute, UCL Queen Square Institute of Neurology, London, UK
- National Institute for Health Research (NIHR) University College London Hospitals Biomedical Research Centre, London, UK
- Institute for Advanced Study, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Mina Ryten
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
| | - Tom Foltynie
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Yoav Ben-Shlomo
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Maryam Shoai
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
- Department of Neurodegenerative Diseases, UCL Queen Square Institute of Neurology, University College London, London, UK
- UK Dementia Research Institute, University College London, London, UK
| | - Huw R Morris
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK.
- UCL Movement Disorders Centre, University College London, London, UK.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA.
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7
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Rosoff DB, Mavromatis LA, Bell AS, Wagner J, Jung J, Marioni RE, Davey Smith G, Horvath S, Lohoff FW. Multivariate genome-wide analysis of aging-related traits identifies novel loci and new drug targets for healthy aging. NATURE AGING 2023; 3:1020-1035. [PMID: 37550455 PMCID: PMC10432278 DOI: 10.1038/s43587-023-00455-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 06/07/2023] [Indexed: 08/09/2023]
Abstract
The concept of aging is complex, including many related phenotypes such as healthspan, lifespan, extreme longevity, frailty and epigenetic aging, suggesting shared biological underpinnings; however, aging-related endpoints have been primarily assessed individually. Using data from these traits and multivariate genome-wide association study methods, we modeled their underlying genetic factor ('mvAge'). mvAge (effective n = ~1.9 million participants of European ancestry) identified 52 independent variants in 38 genomic loci. Twenty variants were novel (not reported in input genome-wide association studies). Transcriptomic imputation identified age-relevant genes, including VEGFA and PHB1. Drug-target Mendelian randomization with metformin target genes showed a beneficial impact on mvAge (P value = 8.41 × 10-5). Similarly, genetically proxied thiazolidinediones (P value = 3.50 × 10-10), proprotein convertase subtilisin/kexin 9 inhibition (P value = 1.62 × 10-6), angiopoietin-like protein 4, beta blockers and calcium channel blockers also had beneficial Mendelian randomization estimates. Extending the drug-target Mendelian randomization framework to 3,947 protein-coding genes prioritized 122 targets. Together, these findings will inform future studies aimed at improving healthy aging.
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Affiliation(s)
- Daniel B Rosoff
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
- NIH-Oxford-Cambridge Scholars Program; Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
| | - Lucas A Mavromatis
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Andrew S Bell
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Josephin Wagner
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Jeesun Jung
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - George Davey Smith
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
| | - Steve Horvath
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- San Diego Institute of Science, Alto Labs, San Diego, CA, USA
| | - Falk W Lohoff
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA.
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8
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Toker L, Nido GS, Tzoulis C. Not every estimate counts - evaluation of cell composition estimation approaches in brain bulk tissue data. Genome Med 2023; 15:41. [PMID: 37287013 DOI: 10.1186/s13073-023-01195-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 05/22/2023] [Indexed: 06/09/2023] Open
Abstract
BACKGROUND Variation in cell composition can dramatically impact analyses in bulk tissue samples. A commonly employed approach to mitigate this issue is to adjust statistical models using estimates of cell abundance derived directly from omics data. While an arsenal of estimation methods exists, the applicability of these methods to brain tissue data and whether or not cell estimates can sufficiently account for confounding cellular composition has not been adequately assessed. METHODS We assessed the correspondence between different estimation methods based on transcriptomic (RNA sequencing, RNA-seq) and epigenomic (DNA methylation and histone acetylation) data from brain tissue samples of 49 individuals. We further evaluated the impact of different estimation approaches on the analysis of H3K27 acetylation chromatin immunoprecipitation sequencing (ChIP-seq) data from entorhinal cortex of individuals with Alzheimer's disease and controls. RESULTS We show that even closely adjacent tissue samples from the same Brodmann area vary greatly in their cell composition. Comparison across different estimation methods indicates that while different estimation methods applied to the same data produce highly similar outcomes, there is a surprisingly low concordance between estimates based on different omics data modalities. Alarmingly, we show that cell type estimates may not always sufficiently account for confounding variation in cell composition. CONCLUSIONS Our work indicates that cell composition estimation or direct quantification in one tissue sample should not be used as a proxy to the cellular composition of another tissue sample from the same brain region of an individual-even if the samples are directly adjacent. The highly similar outcomes observed among vastly different estimation methods, highlight the need for brain benchmark datasets and better validation approaches. Finally, unless validated through complementary experiments, the interpretation of analyses outcomes based on data confounded by cell composition should be done with great caution, and ideally avoided all together.
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Affiliation(s)
- Lilah Toker
- Neuro-SysMed Center of Excellence, Department of Neurology, Department of Clinical Medicine, Haukeland University Hospital, University of Bergen, 5021, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Pb 7804, 5020, Bergen, Norway
- K.G Jebsen Center for Translational Research in Parkinson's Disease, University of Bergen, Bergen, Norway
| | - Gonzalo S Nido
- Neuro-SysMed Center of Excellence, Department of Neurology, Department of Clinical Medicine, Haukeland University Hospital, University of Bergen, 5021, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Pb 7804, 5020, Bergen, Norway
- K.G Jebsen Center for Translational Research in Parkinson's Disease, University of Bergen, Bergen, Norway
| | - Charalampos Tzoulis
- Neuro-SysMed Center of Excellence, Department of Neurology, Department of Clinical Medicine, Haukeland University Hospital, University of Bergen, 5021, Bergen, Norway.
- Department of Clinical Medicine, University of Bergen, Pb 7804, 5020, Bergen, Norway.
- K.G Jebsen Center for Translational Research in Parkinson's Disease, University of Bergen, Bergen, Norway.
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9
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Martinez-Carrasco A, Real R, Lawton M, Iwaki H, Tan MMX, Wu L, Williams NM, Carroll C, Hu MT, Grosset DG, Hardy J, Ryten M, Foltynie T, Ben-Shlomo Y, Shoai M, Morris HR. Genetic meta-analysis of levodopa induced dyskinesia in Parkinson's disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.24.23290362. [PMID: 37425912 PMCID: PMC10327264 DOI: 10.1101/2023.05.24.23290362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Importance Forty percent of Parkinson's disease patients develop levodopa-induced-dyskinesia (LiD) within 4 years of starting levodopa. The genetic basis of LiD remains poorly understood, and there have been few well powered studies. Objective To discover common genetic variants in the PD population that increase the probability of developing LiD. Design setting and Participants We performed survival analyses to study the development of LiD in 5 separate longitudinal cohorts. We performed a meta-analysis to combine the results of genetic association from each study based on a fixed effects model weighting the effect sizes by the inverse of their standard error. The selection criteria was specific to each cohort. We studied individuals that were genotyped from each cohort and that passed our analysis specific inclusion criteria. Main Outcomes and Measures We measured the time for PD patients on levodopa treatment to develop LiD as defined by reaching a score higher or equal than 2 from the MDS-UPDRS part IV, item 1, which is equivalent to a range of 26%-50% of the waking time with dyskinesia. We carried out a genome-wide analysis of the hazard ratio and the association of genome-wide SNPs with the probability of developing LiD using cox proportional hazard models (CPH). Results This study included 2,784 PD patients of European ancestry, of whom 14.6% developed LiD. Consistent with previous studies, we found female gender (HR = 1.35, SE = 0.11, P = 0.007) and younger age at onset (HR = 1.8, SE = 0.14, P = 2 × 10 -5 ) to increase the probability of developing LiD. We identified three loci significantly associated with time-to-LiD onset. rs72673189 on chromosome 1 (HR = 2.77, SE = 0.18, P = 1.53 × 10 -8 ) located in the LRP8 locus, rs189093213 on chromosome 4 (HR = 3.06,, SE = 0.19, P = 2.81 × 10 -9 ) in the non-coding RNA LINC02353 locus, and rs180924818 on chromosome 16 (HR = 3.13, SE = 0.20, P = 6.27 × 10 -9 ) in the XYLT1 locus. Subsequent colocalization analyses on chromosome 1 identified DNAJB4 as a candidate gene associated with LiD through a change in gene expression. We computed a PRS based on our GWAS meta-analysis and found high accuracy to stratify between PD-LID and PD (AUC 83.9). We also performed a stepwise regression analysis for baseline features selection associated with LiD status. We found baseline anxiety status to be significantly associated with LiD (OR = 1.14, SE = 0.03, P = 7.4 × 10 -5 ). Finally, we performed a candidate variant analysis and found that genetic variability in ANKK1 ( rs1800497 , Beta = 0.24, SE = 0.09, P = 8.89 × 10 -3 ) and BDNF ( rs6265 , Beta = 0.19, SE = 0.10, P = 4.95 × 10 -2 ) loci were significantly associated with time to LiD in our large meta-analysis. Conclusion In this association study, we have found three novel genetic variants associated with LiD, as well as confirming reports that variability in ANKK1 and BDNF loci were significantly associated with LiD probability. A PRS nominated from our time-to-LiD meta-analysis significantly differentiated between PD-LiD and PD. In addition, we have found female gender, young PD onset and anxiety to be significantly associated with LiD.
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Affiliation(s)
- Alejandro Martinez-Carrasco
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, UK
- UCL Movement Disorders Centre, University College London, London, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
| | - Raquel Real
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, UK
- UCL Movement Disorders Centre, University College London, London, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
| | - Michael Lawton
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Hirotaka Iwaki
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International, Glen Echo, Maryland, USA
| | | | - Lesley Wu
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, UK
- UCL Movement Disorders Centre, University College London, London, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
| | - Nigel M. Williams
- Institute of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Camille Carroll
- Faculty of Health, University of Plymouth, Plymouth, UK; Translational and Clinical Research Institute, Newcastle University, Newcastle, UK
| | - Michele T.M. Hu
- Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, University of Oxford, Oxford, UK
- Oxford Parkinson’s Disease Centre, University of Oxford, Oxford, UK
| | - Donald G. Grosset
- School of Neuroscience and Psychology, University of Glasgow, Glasgow, UK
| | - John Hardy
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
- Department of Neurodegenerative Diseases, UCL Queen Square Institute of Neurology, University College London, London, UK
- UK Dementia Research Institute, University College London, London, UK
- Reta Lila Weston Institute, UCL Queen Square Institute of Neurology, London, UK
- National Institute for Health Research (NIHR) University College London Hospitals Biomedical Research Centre, London, UK
- Institute for Advanced Study, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Mina Ryten
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
| | - Tom Foltynie
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, UK
| | - Yoav Ben-Shlomo
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Maryam Shoai
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
- Department of Neurodegenerative Diseases, UCL Queen Square Institute of Neurology, University College London, London, UK
- UK Dementia Research Institute, University College London, London, UK
| | - Huw R. Morris
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, UK
- UCL Movement Disorders Centre, University College London, London, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
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10
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Kim M, Vo DD, Kumagai ME, Jops CT, Gandal MJ. GeneticsMakie.jl: a versatile and scalable toolkit for visualizing locus-level genetic and genomic data. Bioinformatics 2023; 39:6887175. [PMID: 36495218 PMCID: PMC9825774 DOI: 10.1093/bioinformatics/btac786] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 10/29/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
SUMMARY With the continued deluge of results from genome-wide association and functional genomic studies, it has become increasingly imperative to quickly combine and visualize different layers of genetic and genomic data within a given locus to facilitate exploratory and integrative data analyses. While several tools have been developed to visualize locus-level genetic results, the limited speed, scalability and flexibility of current approaches remain a significant bottleneck. Here, we present a Julia package for high-performance genetics and genomics-related data visualization that enables fast, simultaneous plotting of hundreds of association results along with multiple relevant genomic annotations. Leveraging the powerful plotting and layout utilities from Makie.jl facilitates the customization and extensibility of every component of a plot, enabling generation of publication-ready figures. AVAILABILITY AND IMPLEMENTATION The GeneticsMakie.jl package is open source and distributed under the MIT license via GitHub (https://github.com/mmkim1210/GeneticsMakie.jl). The GitHub repository contains installation instructions as well as examples and documentation for built-in functions. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Minsoo Kim
- To whom correspondence should be addressed. or
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11
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Pan S, Kang H, Liu X, Lin S, Yuan N, Zhang Z, Bao Y, Jia P. Brain Catalog: a comprehensive resource for the genetic landscape of brain-related traits. Nucleic Acids Res 2022; 51:D835-D844. [PMID: 36243988 PMCID: PMC9825493 DOI: 10.1093/nar/gkac895] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/13/2022] [Accepted: 10/08/2022] [Indexed: 01/30/2023] Open
Abstract
A broad range of complex phenotypes are related to dysfunctions in brain (hereafter referred to as brain-related traits), including various mental and behavioral disorders and diseases of the nervous system. These traits in general share overlapping symptoms, pathogenesis, and genetic components. Here, we present Brain Catalog (https://ngdc.cncb.ac.cn/braincatalog), a comprehensive database aiming to delineate the genetic components of more than 500 GWAS summary statistics datasets for brain-related traits from multiple aspects. First, Brain Catalog provides results of candidate causal variants, causal genes, and functional tissues and cell types for each trait identified by multiple methods using comprehensive annotation datasets (58 QTL datasets spanning 6 types of QTLs). Second, Brain Catalog estimates the SNP-based heritability, the partitioning heritability based on functional annotations, and genetic correlations among traits. Finally, through bidirectional Mendelian randomization analyses, Brain Catalog presents inference of risk factors that are likely causal to each trait. In conclusion, Brain Catalog presents a one-stop shop for the genetic components of brain-related traits, potentially serving as a valuable resource for worldwide researchers to advance the understanding of how GWAS signals may contribute to the biological etiology of brain-related traits.
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Affiliation(s)
| | | | | | - Shiqi Lin
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Na Yuan
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Zhang Zhang
- Correspondence may also be addressed to Zhang Zhang.
| | - Yiming Bao
- Correspondence may also be addressed to Yiming Bao.
| | - Peilin Jia
- To whom correspondence should be addressed. Tel: +86 1084097798; ;
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12
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Khatri B, Tessneer KL, Rasmussen A, Aghakhanian F, Reksten TR, Adler A, Alevizos I, Anaya JM, Aqrawi LA, Baecklund E, Brun JG, Bucher SM, Eloranta ML, Engelke F, Forsblad-d’Elia H, Glenn SB, Hammenfors D, Imgenberg-Kreuz J, Jensen JL, Johnsen SJA, Jonsson MV, Kvarnström M, Kelly JA, Li H, Mandl T, Martín J, Nocturne G, Norheim KB, Palm Ø, Skarstein K, Stolarczyk AM, Taylor KE, Teruel M, Theander E, Venuturupalli S, Wallace DJ, Grundahl KM, Hefner KS, Radfar L, Lewis DM, Stone DU, Kaufman CE, Brennan MT, Guthridge JM, James JA, Scofield RH, Gaffney PM, Criswell LA, Jonsson R, Eriksson P, Bowman SJ, Omdal R, Rönnblom L, Warner B, Rischmueller M, Witte T, Farris AD, Mariette X, Alarcon-Riquelme ME, Shiboski CH, Wahren-Herlenius M, Ng WF, Sivils KL, Adrianto I, Nordmark G, Lessard CJ. Genome-wide association study identifies Sjögren's risk loci with functional implications in immune and glandular cells. Nat Commun 2022; 13:4287. [PMID: 35896530 PMCID: PMC9329286 DOI: 10.1038/s41467-022-30773-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 05/17/2022] [Indexed: 02/06/2023] Open
Abstract
Sjögren's disease is a complex autoimmune disease with twelve established susceptibility loci. This genome-wide association study (GWAS) identifies ten novel genome-wide significant (GWS) regions in Sjögren's cases of European ancestry: CD247, NAB1, PTTG1-MIR146A, PRDM1-ATG5, TNFAIP3, XKR6, MAPT-CRHR1, RPTOR-CHMP6-BAIAP6, TYK2, SYNGR1. Polygenic risk scores yield predictability (AUROC = 0.71) and relative risk of 12.08. Interrogation of bioinformatics databases refine the associations, define local regulatory networks of GWS SNPs from the 95% credible set, and expand the implicated gene list to >40. Many GWS SNPs are eQTLs for genes within topologically associated domains in immune cells and/or eQTLs in the main target tissue, salivary glands.
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Affiliation(s)
- Bhuwan Khatri
- grid.274264.10000 0000 8527 6890Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - Kandice L. Tessneer
- grid.274264.10000 0000 8527 6890Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - Astrid Rasmussen
- grid.274264.10000 0000 8527 6890Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - Farhang Aghakhanian
- grid.274264.10000 0000 8527 6890Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - Tove Ragna Reksten
- grid.274264.10000 0000 8527 6890Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA ,grid.7914.b0000 0004 1936 7443Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Adam Adler
- grid.274264.10000 0000 8527 6890NGS Core Laboratory, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - Ilias Alevizos
- grid.419633.a0000 0001 2205 0568Salivary Disorder Unit, National Institute of Dental and Craniofacial Research, Bethesda, MD USA
| | - Juan-Manuel Anaya
- grid.412191.e0000 0001 2205 5940Center for Autoimmune Diseases Research (CREA), Universidad del Rosario, Bogotá, Colombia
| | - Lara A. Aqrawi
- grid.5510.10000 0004 1936 8921Department of Oral Surgery and Oral Medicine, Faculty of Dentistry, University of Oslo, Oslo, Norway ,grid.457625.70000 0004 0383 3497Department of Health Sciences, Kristiania University College, Oslo, Norway
| | - Eva Baecklund
- grid.8993.b0000 0004 1936 9457Department of Medical Sciences, Rheumatology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Johan G. Brun
- grid.7914.b0000 0004 1936 7443Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Sara Magnusson Bucher
- grid.15895.300000 0001 0738 8966Department of Rheumatology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Maija-Leena Eloranta
- grid.8993.b0000 0004 1936 9457Department of Medical Sciences, Rheumatology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Fiona Engelke
- grid.10423.340000 0000 9529 9877Department of Rheumatology and Immunology, Hannover Medical School, Hannover, Germany
| | - Helena Forsblad-d’Elia
- grid.8761.80000 0000 9919 9582Department of Rheumatology and Inflammation Research, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Stuart B. Glenn
- grid.274264.10000 0000 8527 6890Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - Daniel Hammenfors
- grid.412008.f0000 0000 9753 1393Department of Rheumatology, Haukeland University Hospital, Bergen, Norway
| | - Juliana Imgenberg-Kreuz
- grid.8993.b0000 0004 1936 9457Department of Medical Sciences, Rheumatology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Janicke Liaaen Jensen
- grid.5510.10000 0004 1936 8921Department of Oral Surgery and Oral Medicine, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Svein Joar Auglænd Johnsen
- grid.412835.90000 0004 0627 2891Department of Internal Medicine, Clinical Immunology Unit, Stavanger University Hospital, Stavanger, Norway
| | - Malin V. Jonsson
- grid.7914.b0000 0004 1936 7443Department of Clinical Science, University of Bergen, Bergen, Norway ,grid.7914.b0000 0004 1936 7443Section for Oral and Maxillofacial Radiology, Department of Clinical Dentistry, Medical Faculty, University of Bergen, Bergen, Norway
| | - Marika Kvarnström
- grid.4714.60000 0004 1937 0626Rheumatology Unity, Department of Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden ,grid.425979.40000 0001 2326 2191Academic Specialist Center, Center for Rheumatology and Studieenheten, Stockholm Health Services, Region Stockholm, Sweden
| | - Jennifer A. Kelly
- grid.274264.10000 0000 8527 6890Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - He Li
- grid.274264.10000 0000 8527 6890Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA ,grid.505430.7Translational Sciences, The Janssen Pharmaceutical Companies of Johnson & Johnson, Spring House, PA USA
| | - Thomas Mandl
- grid.4514.40000 0001 0930 2361Rheumatology, Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
| | - Javier Martín
- grid.4711.30000 0001 2183 4846Instituto de Biomedicina y Parasitología López-Neyra, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Gaétane Nocturne
- grid.413784.d0000 0001 2181 7253Université Paris-Saclay, Assistance Publique–Hôpitaux de Paris (AP-HP), Hôpital Bicêtre, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR1184, Le Kremlin Bicêtre, France
| | - Katrine Brække Norheim
- grid.7914.b0000 0004 1936 7443Department of Clinical Science, University of Bergen, Bergen, Norway ,grid.412835.90000 0004 0627 2891Department of Rheumatology, Stavanger University Hospital, Stavanger, Norway
| | - Øyvind Palm
- grid.5510.10000 0004 1936 8921Department of Rheumatology, University of Oslo, Oslo, Norway
| | - Kathrine Skarstein
- grid.7914.b0000 0004 1936 7443Department of Clinical Science, University of Bergen, Bergen, Norway ,grid.412008.f0000 0000 9753 1393Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Anna M. Stolarczyk
- grid.274264.10000 0000 8527 6890Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - Kimberly E. Taylor
- grid.266102.10000 0001 2297 6811Department of Medicine, Russell/Engleman Rheumatology Research Center, University of California San Francisco, San Francisco, California USA
| | - Maria Teruel
- grid.4489.10000000121678994Genyo, Center for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, Granada, Spain
| | - Elke Theander
- grid.411843.b0000 0004 0623 9987Department of Rheumatology, Skåne University Hospital, Malmö, Sweden ,Medical Affairs, Jannsen-Cilag EMEA (Europe/Middle East/Africa), Beerse, Belgium
| | - Swamy Venuturupalli
- grid.50956.3f0000 0001 2152 9905Division of Rheumatology, Cedars-Sinai Medical Center, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA USA
| | - Daniel J. Wallace
- grid.50956.3f0000 0001 2152 9905Division of Rheumatology, Cedars-Sinai Medical Center, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA USA
| | - Kiely M. Grundahl
- grid.274264.10000 0000 8527 6890Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | | | - Lida Radfar
- grid.266900.b0000 0004 0447 0018Oral Diagnosis and Radiology Department, University of Oklahoma College of Dentistry, Oklahoma City, OK USA
| | - David M. Lewis
- grid.266900.b0000 0004 0447 0018Department of Oral and Maxillofacial Pathology, University of Oklahoma College of Dentistry, Oklahoma City, OK USA
| | - Donald U. Stone
- grid.266902.90000 0001 2179 3618Department of Ophthalmology, Dean McGee Eye Institute, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
| | - C. Erick Kaufman
- grid.266902.90000 0001 2179 3618Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
| | - Michael T. Brennan
- grid.239494.10000 0000 9553 6721Department of Oral Medicine/Oral & Maxillofacial Surgery, Atrium Health Carolinas Medical Center, Charlotte, NC USA ,grid.241167.70000 0001 2185 3318Department of Otolaryngology/Head and Neck Surgery, Wake Forest University School of Medicine, Winston-Salem, NC USA
| | - Joel M. Guthridge
- grid.274264.10000 0000 8527 6890Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA ,grid.266902.90000 0001 2179 3618Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
| | - Judith A. James
- grid.274264.10000 0000 8527 6890Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA ,grid.266902.90000 0001 2179 3618Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
| | - R. Hal Scofield
- grid.274264.10000 0000 8527 6890Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA ,grid.266902.90000 0001 2179 3618Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA ,grid.413864.c0000 0004 0420 2582US Department of Veterans Affairs Medical Center, Oklahoma City, OK USA
| | - Patrick M. Gaffney
- grid.274264.10000 0000 8527 6890Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - Lindsey A. Criswell
- grid.266102.10000 0001 2297 6811Department of Medicine, Russell/Engleman Rheumatology Research Center, University of California San Francisco, San Francisco, California USA ,grid.266102.10000 0001 2297 6811Institute of Human Genetics (IHG), University of California San Francisco, San Francisco, CA USA ,grid.280128.10000 0001 2233 9230Genomics of Autoimmune Rheumatic Disease Section, National Human Genome Research Institute, NIH, Bethesda, MD USA
| | - Roland Jonsson
- grid.7914.b0000 0004 1936 7443Department of Clinical Science, University of Bergen, Bergen, Norway ,grid.412008.f0000 0000 9753 1393Department of Rheumatology, Haukeland University Hospital, Bergen, Norway
| | - Per Eriksson
- grid.5640.70000 0001 2162 9922Department of Biomedical and Clinical Sciences, Division of Inflammation and Infection, Linköping University, Linköping, Sweden
| | - Simon J. Bowman
- grid.412563.70000 0004 0376 6589Rheumatology Department, University Hospital Birmingham NHS Foundation Trust, Birmingham, UK ,grid.6572.60000 0004 1936 7486Rheumatology Research Group, Institute of Inflammation & Ageing, University of Birmingham, Birmingham, UK ,grid.415667.7Rheumatology Department, Milton Keynes University Hospital, Milton Keynes, UK
| | - Roald Omdal
- grid.7914.b0000 0004 1936 7443Department of Clinical Science, University of Bergen, Bergen, Norway ,grid.412835.90000 0004 0627 2891Department of Internal Medicine, Clinical Immunology Unit, Stavanger University Hospital, Stavanger, Norway
| | - Lars Rönnblom
- grid.8993.b0000 0004 1936 9457Department of Medical Sciences, Rheumatology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Blake Warner
- grid.419633.a0000 0001 2205 0568Salivary Disorder Unit, National Institute of Dental and Craniofacial Research, Bethesda, MD USA
| | - Maureen Rischmueller
- grid.278859.90000 0004 0486 659XRheumatology Department, The Queen Elizabeth Hospital, Woodville, South Australia ,grid.1010.00000 0004 1936 7304University of Adelaide, Adelaide, South Australia
| | - Torsten Witte
- grid.10423.340000 0000 9529 9877Department of Rheumatology and Immunology, Hannover Medical School, Hannover, Germany
| | - A. Darise Farris
- grid.274264.10000 0000 8527 6890Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - Xavier Mariette
- grid.413784.d0000 0001 2181 7253Université Paris-Saclay, Assistance Publique–Hôpitaux de Paris (AP-HP), Hôpital Bicêtre, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR1184, Le Kremlin Bicêtre, France
| | - Marta E. Alarcon-Riquelme
- grid.4489.10000000121678994Genyo, Center for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, Granada, Spain
| | | | - Caroline H. Shiboski
- grid.266102.10000 0001 2297 6811Department of Orofacial Sciences, University of California San Francisco, San Francisco, CA USA
| | | | - Marie Wahren-Herlenius
- grid.7914.b0000 0004 1936 7443Department of Clinical Science, University of Bergen, Bergen, Norway ,grid.4714.60000 0004 1937 0626Rheumatology Unity, Department of Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Wan-Fai Ng
- grid.1006.70000 0001 0462 7212Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK ,grid.420004.20000 0004 0444 2244NIHR Newcastle Biomedical Centre and NIHR Newcastle Clinical Research Facility, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | | | - Kathy L. Sivils
- grid.274264.10000 0000 8527 6890Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA ,grid.505430.7Translational Sciences, The Janssen Pharmaceutical Companies of Johnson & Johnson, Spring House, PA USA
| | - Indra Adrianto
- grid.239864.20000 0000 8523 7701Center for Bioinformatics, Department of Public Health Sciences, Henry Ford Health System, Detroit, MI USA
| | - Gunnel Nordmark
- grid.8993.b0000 0004 1936 9457Department of Medical Sciences, Rheumatology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Christopher J. Lessard
- grid.274264.10000 0000 8527 6890Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA ,grid.266902.90000 0001 2179 3618Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
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13
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Zhou F, Butterworth AS, Asimit JL. Flashfm-ivis: interactive visualization for fine-mapping of multiple quantitative traits. Bioinformatics 2022; 38:4238-4242. [PMID: 35792838 PMCID: PMC9438951 DOI: 10.1093/bioinformatics/btac453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/31/2022] [Accepted: 07/05/2022] [Indexed: 12/24/2022] Open
Abstract
SUMMARY flashfm-ivis provides a suite of interactive visualization plots to view potential causal genetic variants that underlie associations that are shared or distinct between multiple quantitative traits and compares results between single- and multi-trait fine-mapping. Unique features include network diagrams that show joint effects between variants for each trait and regional association plots that integrate fine-mapping results, all with user-controlled zoom features for an interactive exploration of potential causal variants across traits. AVAILABILITY AND IMPLEMENTATION flashfm-ivis is an open-source software under the MIT license. It is available as an interactive web-based tool (http://shiny.mrc-bsu.cam.ac.uk/apps/flashfm-ivis/) and as an R package. Code and documentation are available at https://github.com/fz-cambridge/flashfm-ivis and https://zenodo.org/record/6376244#.YjnarC-l2X0. Additional features can be downloaded as standalone R libraries to encourage reuse. SUPPLEMENTARY INFORMATION Supplementary information are available at Bioinformatics online.
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Affiliation(s)
- Feng Zhou
- To whom correspondence should be addressed. or
| | - Adam S Butterworth
- British Heart Foundation, Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK,National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics University of Cambridge, Cambridge CB1 8RN, UK,British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge CB1 8RN, UK,Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge CB10 1SA, UK
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14
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Ahmed WUR, Kleeman S, Ng M, Wang W, Auton A, Lee R, Handa A, Zondervan KT, Wiberg A, Furniss D. Genome-wide association analysis and replication in 810,625 individuals with varicose veins. Nat Commun 2022; 13:3065. [PMID: 35654884 PMCID: PMC9163161 DOI: 10.1038/s41467-022-30765-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 05/17/2022] [Indexed: 12/30/2022] Open
Abstract
Varicose veins affect one-third of Western society, with a significant subset of patients developing venous ulceration, costing $14.9 billion annually in the USA. Current management consists of either compression stockings, or surgical ablation for more advanced disease. Most varicose veins patients report a positive family history, and heritability is ~17%. We describe the largest two-stage genome-wide association study of varicose veins in 401,656 individuals from UK Biobank, and replication in 408,969 individuals from 23andMe (total 135,514 cases and 675,111 controls). Forty-nine signals at 46 susceptibility loci were discovered. We map 237 genes to these loci, several of which are biologically plausible and tractable to therapeutic targeting. Pathway analysis identified enrichment in extracellular matrix biology, inflammation, (lymph)angiogenesis, vascular smooth muscle cell migration, and apoptosis. Using a polygenic risk score (PRS) derived in an independent cohort, we demonstrate its predictive utility and correlation with varicose veins surgery.
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Affiliation(s)
- Waheed-Ul-Rahman Ahmed
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Botnar Research Centre, Windmill Road, Oxford, OX3 7LD, UK
| | - Sam Kleeman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Michael Ng
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Botnar Research Centre, Windmill Road, Oxford, OX3 7LD, UK
| | - Wei Wang
- 23andMe, Inc., Sunnyvale, CA, USA
| | | | | | - Regent Lee
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Ashok Handa
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Krina T Zondervan
- Nuffield Department of Women's & Reproductive Health, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK.,Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Akira Wiberg
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Botnar Research Centre, Windmill Road, Oxford, OX3 7LD, UK.,Department of Plastic and Reconstructive Surgery, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Dominic Furniss
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Botnar Research Centre, Windmill Road, Oxford, OX3 7LD, UK. .,Department of Plastic and Reconstructive Surgery, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, OX3 9DU, UK.
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15
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Lopes KDP, Snijders GJL, Humphrey J, Allan A, Sneeboer MAM, Navarro E, Schilder BM, Vialle RA, Parks M, Missall R, van Zuiden W, Gigase FAJ, Kübler R, van Berlekom AB, Hicks EM, Bӧttcher C, Priller J, Kahn RS, de Witte LD, Raj T. Genetic analysis of the human microglial transcriptome across brain regions, aging and disease pathologies. Nat Genet 2022; 54:4-17. [PMID: 34992268 PMCID: PMC9245609 DOI: 10.1038/s41588-021-00976-y] [Citation(s) in RCA: 82] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 10/19/2021] [Indexed: 12/12/2022]
Abstract
Microglia have emerged as important players in brain aging and pathology. To understand how genetic risk for neurological and psychiatric disorders is related to microglial function, large transcriptome studies are essential. Here, we describe the transcriptome analysis of 255 primary human microglia samples isolated at autopsy from multiple brain regions of 100 human subjects. We performed systematic analyses to investigate various aspects of microglial heterogeneities, including brain region and aging. We mapped expression and splicing quantitative trait loci and showed that many neurological disease susceptibility loci are mediated through gene expression or splicing in microglia. Fine-mapping of these loci nominated candidate causal variants that are within microglia-specific enhancers, finding associations with microglia expression of USP6NL for Alzheimer’s disease and P2RY12 for Parkinson’s disease. We have built the most comprehensive catalog to date of genetic effects on the microglia transcriptome and propose candidate functional variants in neurological and psychiatric disorders.
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Affiliation(s)
- Katia de Paiva Lopes
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gijsje J L Snijders
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Mental Illness Research, Education and Clinical Center, James J Peters VA Medical Center, New York, NY, USA
| | - Jack Humphrey
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Amanda Allan
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marjolein A M Sneeboer
- Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, the Netherlands
| | - Elisa Navarro
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brian M Schilder
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ricardo A Vialle
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Madison Parks
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Roy Missall
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Welmoed van Zuiden
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Frederieke A J Gigase
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Mental Illness Research, Education and Clinical Center, James J Peters VA Medical Center, New York, NY, USA
| | - Raphael Kübler
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Amber Berdenis van Berlekom
- Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, the Netherlands
| | - Emily M Hicks
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Chotima Bӧttcher
- Department of Neuropsychiatry and Laboratory of Molecular Psychiatry, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Josef Priller
- Department of Neuropsychiatry and Laboratory of Molecular Psychiatry, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - René S Kahn
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Mental Illness Research, Education and Clinical Center, James J Peters VA Medical Center, New York, NY, USA
| | - Lot D de Witte
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Mental Illness Research, Education and Clinical Center, James J Peters VA Medical Center, New York, NY, USA.
| | - Towfique Raj
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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16
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Schilder BM, Navarro E, Raj T. Multi-omic insights into Parkinson's Disease: From genetic associations to functional mechanisms. Neurobiol Dis 2021; 163:105580. [PMID: 34871738 PMCID: PMC10101343 DOI: 10.1016/j.nbd.2021.105580] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/17/2021] [Accepted: 12/02/2021] [Indexed: 02/07/2023] Open
Abstract
Genome-Wide Association Studies (GWAS) have elucidated the genetic components of Parkinson's Disease (PD). However, because the vast majority of GWAS association signals fall within non-coding regions, translating these results into an interpretable, mechanistic understanding of the disease etiology remains a major challenge in the field. In this review, we provide an overview of the approaches to prioritize putative causal variants and genes as well as summarise the primary findings of previous studies. We then discuss recent efforts to integrate multi-omics data to identify likely pathogenic cell types and biological pathways implicated in PD pathogenesis. We have compiled full summary statistics of cell-type, tissue, and phentoype enrichment analyses from multiple studies of PD GWAS and provided them in a standardized format as a resource for the research community (https://github.com/RajLabMSSM/PD_omics_review). Finally, we discuss the experimental, computational, and conceptual advances that will be necessary to fully elucidate the effects of functional variants and genes on cellular dysregulation and disease risk.
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Affiliation(s)
- Brian M Schilder
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Department of Brain Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom; UK Dementia Research Institute at Imperial College London, London, United Kingdom.
| | - Elisa Navarro
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Sección Departamental de Bioquímica y Biología Molecular, Facultad de Medicina, Universidad Complutense de Madrid, Madrid, Spain
| | - Towfique Raj
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.
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17
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Schilder BM, Raj T. Fine-mapping of Parkinson's disease susceptibility loci identifies putative causal variants. Hum Mol Genet 2021; 31:888-900. [PMID: 34617105 PMCID: PMC8947317 DOI: 10.1093/hmg/ddab294] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 09/05/2021] [Accepted: 09/11/2021] [Indexed: 12/13/2022] Open
Abstract
Recent genome-wide association studies have identified 78 loci associated with Parkinson’s disease susceptibility but the underlying mechanisms remain largely unclear. To identify likely causal variants for disease risk, we fine-mapped these Parkinson’s-associated loci using four different fine-mapping methods. We then integrated multi-assay cell type–specific epigenomic profiles to pinpoint the likely mechanism of action of each variant, allowing us to identify Consensus single nucleotide polymorphism (SNPs) that disrupt LRRK2 and FCGR2A regulatory elements in microglia, an MBNL2 enhancer in oligodendrocytes, and a DYRK1A enhancer in neurons. This genome-wide functional fine-mapping investigation of Parkinson’s disease substantially advances our understanding of the causal mechanisms underlying this complex disease while avoiding focus on spurious, non-causal mechanisms. Together, these results provide a robust, comprehensive list of the likely causal variants, genes and cell-types underlying Parkinson’s disease risk as demonstrated by consistently greater enrichment of our fine-mapped SNPs relative to lead GWAS SNPs across independent functional impact annotations. In addition, our approach prioritized an average of 3/85 variants per locus as putatively causal, making downstream experimental studies both more tractable and more likely to yield disease-relevant, actionable results. Large-scale studies comparing individuals with Parkinson’s disease to age-matched controls have identified many regions of the genome associated with the disease. However, there is widespread correlation between different parts of the genome, making it difficult to tell which genetic variants cause Parkinson’s and which are simply co-inherited with causal variants. We therefore applied a suite of statistical models to identify the most likely causal genetic variants (i.e. fine-mapping). We then linked these genetic variants with epigenomic and gene expression signatures across a wide variety of tissues and cell types to identify how these variants cause disease. Therefore, this study provides a comprehensive and robust list of cellular and molecular mechanisms that may serve as targets in the development of more effective Parkinson’s therapeutics.
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Affiliation(s)
- Brian M Schilder
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America.,Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America.,Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Towfique Raj
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America.,Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America.,Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
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18
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Navarro E, Udine E, de Paiva Lopes K, Parks M, Riboldi G, Schilder BM, Humphrey J, Snijders GJL, Vialle RA, Zhuang M, Sikder T, Argyrou C, Allan A, Chao MJ, Farrell K, Henderson B, Simon S, Raymond D, Elango S, Ortega RA, Shanker V, Swan M, Zhu CW, Ramdhani R, Walker RH, Tse W, Sano M, Pereira AC, Ahfeldt T, Goate AM, Bressman S, Crary JF, de Witte L, Frucht S, Saunders-Pullman R, Raj T. Dysregulation of mitochondrial and proteolysosomal genes in Parkinson's disease myeloid cells. NATURE AGING 2021; 1:850-863. [PMID: 35005630 PMCID: PMC8728893 DOI: 10.1038/s43587-021-00110-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 08/05/2021] [Indexed: 12/11/2022]
Abstract
An increasing number of identified Parkinson's disease (PD) risk loci contain genes highly expressed in innate immune cells, yet their role in pathology is not understood. We hypothesize that PD susceptibility genes modulate disease risk by influencing gene expression within immune cells. To address this, we have generated transcriptomic profiles of monocytes from 230 individuals with sporadic PD and healthy subjects. We observed a dysregulation of mitochondrial and proteasomal pathways. We also generated transcriptomic profiles of primary microglia from brains of 55 subjects and observed discordant transcriptomic signatures of mitochondrial genes in PD monocytes and microglia. We further identified 17 PD susceptibility genes whose expression, relative to each risk allele, is altered in monocytes. These findings reveal widespread transcriptomic alterations in PD monocytes, with some being distinct from microglia, and facilitate efforts to understand the roles of myeloid cells in PD as well as the development of biomarkers.
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Affiliation(s)
- Elisa Navarro
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Evan Udine
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Katia de Paiva Lopes
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Madison Parks
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Giulietta Riboldi
- The Marlene and Paolo Fresco Institute for Parkinson's Disease and Movement Disorders, New York University Langone Health, New York, NY, United States of America
- Universita degli Studi di Milano, Molecular and Translational Medicine, Milan, Italy
| | - Brian M. Schilder
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Jack Humphrey
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Gijsje J. L. Snijders
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, United States of America
- Mental Illness Research Education Clinical, Centers of Excellence, VA, Mental Health, Veterans, Bronx, United States of America
| | - Ricardo A. Vialle
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Maojuan Zhuang
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Tamjeed Sikder
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Neuropathology Brain Bank & Research CoRE, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Charalambos Argyrou
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Amanda Allan
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Michael J. Chao
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Kurt Farrell
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Neuropathology Brain Bank & Research CoRE, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Brooklyn Henderson
- The Marlene and Paolo Fresco Institute for Parkinson's Disease and Movement Disorders, New York University Langone Health, New York, NY, United States of America
| | - Sarah Simon
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Neurology, Mount Sinai Beth Israel, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Deborah Raymond
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Neurology, Mount Sinai Beth Israel, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Sonya Elango
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Neurology, Mount Sinai Beth Israel, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Roberto A. Ortega
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Neurology, Mount Sinai Beth Israel, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Vicki Shanker
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Neurology, Mount Sinai Beth Israel, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Matthew Swan
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Neurology, Mount Sinai Beth Israel, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Carolyn W. Zhu
- Department of Geriatrics and Palliative Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Geriatric Research, Education and Clinical Centers (GRECC), James J. Peters VA Medical Center, Bronx, New York, NY, United States of America
- Alzheimer's Disease Research Center (ADRC), Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Ritesh Ramdhani
- Department of Neurology, Zucker School of Medicine at Hofstra Northwell, New York, NY, United States of America
| | - Ruth H. Walker
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Neurology, James J. Peters VA Medical Center, Bronx, NY, United States of America
| | - Winona Tse
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Mary Sano
- Department of Geriatrics and Palliative Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Geriatric Research, Education and Clinical Centers (GRECC), James J. Peters VA Medical Center, Bronx, New York, NY, United States of America
- Alzheimer's Disease Research Center (ADRC), Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Ana C. Pereira
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Tim Ahfeldt
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Alison M. Goate
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Susan Bressman
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Neurology, Mount Sinai Beth Israel, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - John F. Crary
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Neuropathology Brain Bank & Research CoRE, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Lotje de Witte
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, United States of America
- Mental Illness Research Education Clinical, Centers of Excellence, VA, Mental Health, Veterans, Bronx, United States of America
| | - Steven Frucht
- The Marlene and Paolo Fresco Institute for Parkinson's Disease and Movement Disorders, New York University Langone Health, New York, NY, United States of America
| | - Rachel Saunders-Pullman
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Neurology, Mount Sinai Beth Israel, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Towfique Raj
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
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