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Nagarajan P, Winkler TW, Bentley AR, Miller CL, Kraja AT, Schwander K, Lee S, Wang W, Brown MR, Morrison JL, Giri A, O’Connell JR, Bartz TM, de las Fuentes L, Gudmundsdottir V, Guo X, Harris SE, Huang Z, Kals M, Kho M, Lefevre C, Luan J, Lyytikäinen LP, Mangino M, Milaneschi Y, Palmer ND, Rao V, Rauramaa R, Shen B, Stadler S, Sun Q, Tang J, Thériault S, van der Graaf A, van der Most PJ, Wang Y, Weiss S, Westerman KE, Yang Q, Yasuharu T, Zhao W, Zhu W, Altschul D, Ansari MAY, Anugu P, Argoty-Pantoja AD, Arzt M, Aschard H, Attia JR, Bazzanno L, Breyer MA, Brody JA, Cade BE, Chen HH, Ida Chen YD, Chen Z, de Vries PS, Dimitrov LM, Do A, Du J, Dupont CT, Edwards TL, Evans MK, Faquih T, Felix SB, Fisher-Hoch SP, Floyd JS, Graff M, Gu C, Gu D, Hairston KG, Hanley AJ, Heid IM, Heikkinen S, Highland HM, Hood MM, Kähönen M, Karvonen-Gutierrez CA, Kawaguchi T, Kazuya S, Kelly TN, Komulainen P, Levy D, Lin HJ, Liu PY, Marques-Vidal P, McCormick JB, Mei H, Meigs JB, Menni C, Nam K, Nolte IM, Pacheco NL, Petty LE, Polikowsky HG, Province MA, Psaty BM, Raffield LM, Raitakari OT, Rich SS, Riha RL, Risch L, Risch M, Ruiz-Narvaez EA, Scott RJ, Sitlani CM, Smith JA, Sofer T, Teder-Laving M, Völker U, Vollenweider P, Wang G, van Dijk KW, Wilson OD, Xia R, Yao J, Young KL, Zhang R, Zhu X, Below JE, Böger CA, Conen D, Cox SR, Dörr M, Feitosa MF, Fox ER, Franceschini N, Gharib SA, Gudnason V, Harlow SD, He J, Holliday EG, Kutalik Z, Lakka TA, Lawlor DA, Lee S, Lehtimäki T, Li C, Liu CT, Mägi R, Matsuda F, Morrison AC, Penninx BWJH, Peyser PA, Rotter JI, Snieder H, Spector TD, Wagenknecht LE, Wareham NJ, Zonderman AB, North KE, Fornage M, Hung AM, Manning AK, Gauderman J, Chen H, Munroe PB, Rao DC, van Heemst D, Redline S, Noordam R, Wang H. A Large-Scale Genome-Wide Study of Gene-Sleep Duration Interactions for Blood Pressure in 811,405 Individuals from Diverse Populations. medRxiv 2024:2024.03.07.24303870. [PMID: 38496537 PMCID: PMC10942520 DOI: 10.1101/2024.03.07.24303870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Although both short and long sleep duration are associated with elevated hypertension risk, our understanding of their interplay with biological pathways governing blood pressure remains limited. To address this, we carried out genome-wide cross-population gene-by-short-sleep and long-sleep duration interaction analyses for three blood pressure traits (systolic, diastolic, and pulse pressure) in 811,405 individuals from diverse population groups. We discover 22 novel gene-sleep duration interaction loci for blood pressure, mapped to genes involved in neurological, thyroidal, bone metabolism, and hematopoietic pathways. Non-overlap between short sleep (12) and long sleep (10) interactions underscores the plausibility of distinct influences of both sleep duration extremes in cardiovascular health. With several of our loci reflecting specificity towards population background or sex, our discovery sheds light on the importance of embracing granularity when addressing heterogeneity entangled in gene-environment interactions, and in therapeutic design approaches for blood pressure management.
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Affiliation(s)
- Pavithra Nagarajan
- Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Thomas W Winkler
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Amy R Bentley
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, US National Institutes of Health, Bethesda, MD, USA
| | - Clint L Miller
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesvil le, VA, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville ,VA, USA
| | - Aldi T Kraja
- University of Mississippi Medical Center, Jackson, MS, USA
| | - Karen Schwander
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Songmi Lee
- Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX, USA
| | - Wenyi Wang
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Michael R Brown
- Human Genetics Center, Department of Epidemiology, University of Texas Health Science Center at Houston School of Public Health, Houston, TX, USA
| | - John L Morrison
- Division of Biostatistics, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA
| | - Ayush Giri
- Division of Quantitative Sciences, Department of Obstetrics & Gynecology, Vanderbilt University Medical Center, Nashville, TN, USA
- Biomedical Laboratory Research and Development, Tennessee Valley Healthcare System (626), Department of Veterans Affairs/ Nashville, TN, USA
| | - Jeffrey R O’Connell
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Traci M Bartz
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Lisa de las Fuentes
- Cardiovascular Division, Department of Medicine, Washington University School of Medicine in St. Louis, MO, USA
- Center for Biostatistics and Data Science, Institute for Informatics, Data Science, and Biostatistics, Washington University in St. Louis, School of Medicine, St. Louis, MO, USA
| | - Valborg Gudmundsdottir
- Icelandic Heart Association, Kopavogur, Iceland
- Faculty of Medicine, Department of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Sarah E Harris
- Department of Psychology, The University of Edinburgh, Edinburgh, UK
| | - Zhijie Huang
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, US
| | - Mart Kals
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Minjung Kho
- Graduate School of Data Science, Seoul National University, Seoul, South Korea
| | - Christophe Lefevre
- Department of Data Sciences, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Jian’an Luan
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
- Finnish Cardiovascular Research Center - Tampere, Department of Clinical Chemistry, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere, Finland
| | - Massimo Mangino
- Department of Twin Research, King’s College London, London, UK
- National Heart & Lung Institute, Cardiovascular Genomics and Precision Medicine, Imperial College London, London, UK
| | - Yuri Milaneschi
- Department of Psychiatry, Amsterdam UMC/Vrije universiteit, Amsterdam, Netherlands
- GGZ inGeest, Amsterdam, Netherlands
| | - Nicholette D Palmer
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Varun Rao
- Division of Nephrology, Department of Medicine, University of Illinois Chicago, Chicago, USA
| | - Rainer Rauramaa
- Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
| | - Botong Shen
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, Maryland
| | - Stefan Stadler
- Department of Internal Medicine II, University Hospital Regensburg, Regensburg, Germany
| | - Quan Sun
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jingxian Tang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Sébastien Thériault
- Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Quebec City, Qc, Canada
| | - Adriaan van der Graaf
- Statistical Genetics Group, Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Peter J van der Most
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Yujie Wang
- Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Stefan Weiss
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
| | - Kenneth E Westerman
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Clinical and Translational Epidemiology Unit, Mongan Institute, Massachusetts General Hospital, Boston, MA, USA
| | - Qian Yang
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Tabara Yasuharu
- Graduate School of Public Health, Shizuoka Graduate University of Public Health, Shizuoka, Japan
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Wei Zhao
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Wanying Zhu
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Drew Altschul
- Department of Psychology, The University of Edinburgh, Edinburgh, UK
| | - Md Abu Yusuf Ansari
- Department of Data Science, University of Mississippi Medical Center, Jackson, MS, USA
| | - Pramod Anugu
- Jackson Heart Study, University of Mississippi Medical Center, Jackson, MS, USA
| | - Anna D Argoty-Pantoja
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Michael Arzt
- Department of Internal Medicine II, University Hospital Regensburg, Regensburg, Germany
| | - Hugues Aschard
- Department of Computational Biology, F-75015 Paris, France Institut Pasteur, Université Paris Cité, Paris, France
- Department of Epidemiology, Harvard TH School of Public Health, Boston, MA, USA
| | - John R Attia
- School of Medicine and Public Health, College of Health Medicine and Wellbeing, University of Newcastle, New Lambton Heights, NSW, Australia
| | - Lydia Bazzanno
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, US
| | - Max A Breyer
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Brian E Cade
- Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Hung-hsin Chen
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Zekai Chen
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Paul S de Vries
- Human Genetics Center, Department of Epidemiology, University of Texas Health Science Center at Houston School of Public Health, Houston, TX, USA
| | - Latchezar M Dimitrov
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Anh Do
- Center for Biostatistics and Data Science, Institute for Informatics, Data Science, and Biostatistics, Washington University in St. Louis, School of Medicine, St. Louis, MO, USA
| | - Jiawen Du
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Charles T Dupont
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Todd L Edwards
- Biomedical Laboratory Research and Development, Tennessee Valley Healthcare System (626), Department of Veterans Affairs/ Nashville, TN, USA
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, US A
| | - Michele K Evans
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, Maryland
| | - Tariq Faquih
- Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Stephan B Felix
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
- Cardiology, Pneumology, Infectious Diseases, Intensive Care Medicine, Department of Internal Medicine B, Un iversity Medicine Greifswald, Greifswald, Germany
| | - Susan P Fisher-Hoch
- School of Public Health, The University of Texas Health Science Center at Houston (UTHealth), Brownsville, TX, USA
| | - James S Floyd
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Mariaelisa Graff
- Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Charles Gu
- Center for Biostatistics and Data Science, Institute for Informatics, Data Science, and Biostatistics, Washington University in St. Louis, School of Medicine, St. Louis, MO, USA
| | - Dongfeng Gu
- Shenzhen Key Laboratory of Cardiovascular Health and Precision Medicine, Southern University of Science an d Technology, Shenzhen, China
| | - Kristen G Hairston
- Department of Endocrinology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Anthony J Hanley
- Department of Nutritional Sciences, University of Toronto, Toronto, ON, Canada
| | - Iris M Heid
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Sami Heikkinen
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Kuopio
| | - Heather M Highland
- Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michelle M Hood
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Mika Kähönen
- Finnish Cardiovascular Research Center - Tampere, Department of Clinical Chemistry, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere, Finland
- Department of Clinical Physiology, Tampere University Hospital, Tampere, Finland
| | | | - Takahisa Kawaguchi
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Setoh Kazuya
- Graduate School of Public Health, Shizuoka Graduate University of Public Health, Shizuoka, Japan
| | - Tanika N Kelly
- Division of Nephrology, Department of Medicine, University of Illinois Chicago, Chicago, USA
| | | | - Daniel Levy
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
- Framingham Heart Study, Framingham, MA, USA
| | - Henry J Lin
- The Institute for Translational Genomics and Population Sciences, Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Peter Y Liu
- The Institute for Translational Genomics and Population Sciences, Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Pedro Marques-Vidal
- Department of Medicine, Internal Medicine, Lausanne University Hospital (CHUV), Lausanne, Switzerland
- Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Joseph B McCormick
- School of Public Health, The University of Texas Health Science Center at Houston (UTHealth), Brownsville, TX, USA
| | - Hao Mei
- Department of Data Science, University of Mississippi Medical Center, Jackson, MS, USA
| | - James B Meigs
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Cristina Menni
- Department of Twin Research, King’s College London, London, UK
| | - Kisung Nam
- Graduate School of Data Science, Seoul National University, Seoul, South Korea
| | - Ilja M Nolte
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Natasha L Pacheco
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, Maryland
| | - Lauren E Petty
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Hannah G Polikowsky
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Michael A Province
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Olli T Raitakari
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, and Department of Clinical Physiology and Nuclear Medicine, University of Turku, and Turku University Hospital, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Renata L Riha
- Department of Sleep Medicine, The University of Edinburgh, Edinburgh, UK
| | - Lorenz Risch
- Faculty of Medical Sciences , Institute for Laboratory Medicine, Private University in the Principality of Liecht enstein, Vaduz, Liechtenstein
- Center of Laboratory Medicine, Institute of Clinical Chemistry, University of Bern and Inselspital, Bern, Switze rland
| | - Martin Risch
- Central Laboratory, Cantonal Hospital Graubünden, Chur, Switzerland
- Medical Laboratory, Dr. Risch Anstalt, Vaduz, Liechtenstein
| | | | - Rodney J Scott
- School of Biomedical Sciences and Pharmacy, College of Health Medicine and Wellbeing, University of Newcastle, New Lambton Heights, NSW, Australia
| | - Colleen M Sitlani
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Jennifer A Smith
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Tamar Sofer
- Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- CardioVascular Institute (CVI), Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Maris Teder-Laving
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Uwe Völker
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
| | - Peter Vollenweider
- Department of Medicine, Internal Medicine, Lausanne University Hospital (CHUV), Lausanne, Switzerland
- Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Guanchao Wang
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ko Willems van Dijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
- Department of Internal Medicine, Division of Endocrinology, Leiden, Netherlands
| | - Otis D Wilson
- Biomedical Laboratory Research and Development, Tennessee Valley Healthcare System (626), Department of Veterans Affairs/ Nashville, TN, USA
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rui Xia
- Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX, USA
| | - Jie Yao
- The Institute for Translational Genomics and Population Sciences, Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Kristin L Young
- Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ruiyuan Zhang
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, US
| | - Xiaofeng Zhu
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Jennifer E Below
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Carsten A Böger
- Department of Nephrology, University Hospital Regensburg, Regensburg, Germany
- Department of Nephrology and Rheumatology, Kliniken Südostbayern, Traunstein, Germany
- KfH Kidney Centre Traunstein, Traunstein, Germany
| | - David Conen
- Population Health Research Institute, Medicine, McMaster University, Hamilton, On, Canada
| | - Simon R Cox
- Department of Psychology, The University of Edinburgh, Edinburgh, UK
| | - Marcus Dörr
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
- Cardiology, Pneumology, Infectious Diseases, Intensive Care Medicine, Department of Internal Medicine B, Un iversity Medicine Greifswald, Greifswald, Germany
| | - Mary F Feitosa
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Ervin R Fox
- Jackson Heart Study, Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Nora Franceschini
- Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sina A Gharib
- Pulmonary, Critical Care and Sleep Medicine, Medicine, University of Washington, Seattle, WA, USA
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland
- Faculty of Medicine, Department of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Sioban D Harlow
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Jiang He
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, US
- Tulane University Translational Sciences Institute, New Orleans, LA , USA
| | - Elizabeth G Holliday
- School of Medicine and Public Health, College of Health Medicine and Wellbeing, University of Newcastle, New Lambton Heights, NSW, Australia
| | - Zoltan Kutalik
- Statistical Genetics Group, Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Center for Primary Care and Public Health, University of Lausanne, Lausanne, Switzerland
| | - Timo A Lakka
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Kuopio
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, Kuopio, Finland
- Foundation for Research in Health Exercise and Nutrition, Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
| | - Deborah A Lawlor
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Seunggeun Lee
- Graduate School of Data Science, Seoul National University, Seoul, South Korea
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
- Finnish Cardiovascular Research Center - Tampere, Department of Clinical Chemistry, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere, Finland
| | - Changwei Li
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, US
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Reedik Mägi
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, University of Texas Health Science Center at Houston School of Public Health, Houston, TX, USA
| | - Brenda WJH Penninx
- Department of Psychiatry, Amsterdam UMC/Vrije universiteit, Amsterdam, Netherlands
- GGZ inGeest, Amsterdam, Netherlands
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Tim D Spector
- Department of Twin Research, King’s College London, London, UK
| | - Lynne E Wagenknecht
- Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | | | - Alan B Zonderman
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, Maryland
| | - Kari E North
- Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX, USA
- Human Genetics Center, Department of Epidemiology, University of Texas Health Science Center at Houston School of Public Health, Houston, TX, USA
| | | | - Adriana M Hung
- Biomedical Laboratory Research and Development, Tennessee Valley Healthcare System (626), Department of Veterans Affairs/ Nashville, TN, USA
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Alisa K Manning
- Clinical and Translational Epidemiology Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Metabolism Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - James Gauderman
- Division of Biostatistics, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA
| | - Han Chen
- Human Genetics Center, Department of Epidemiology, University of Texas Health Science Center at Houston School of Public Health, Houston, TX, USA
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Patricia B Munroe
- Clinical Pharmacology and Precision Medicine, Queen Mary University of London, London, UK
| | - Dabeeru C Rao
- Center for Biostatistics and Data Science, Institute for Informatics, Data Science, and Biostatistics, Washington University in St. Louis, School of Medicine, St. Louis, MO, USA
| | - Diana van Heemst
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Lei den, Netherlands
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Raymond Noordam
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Lei den, Netherlands
| | - Heming Wang
- Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
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Lu H, Lary CW, Hodonsky CJ, Peyser PA, Bos D, van der Laan SW, Miller CL, Rivadeneira F, Kiel DP, Kavousi M, Medina-Gomez C. Association between bone mineral density and coronary artery calcification: an observational and Mendelian randomization study. J Bone Miner Res 2024:zjae022. [PMID: 38477752 DOI: 10.1093/jbmr/zjae022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 01/10/2024] [Accepted: 02/02/2024] [Indexed: 03/14/2024]
Abstract
Observational studies have reported inconsistent associations between bone mineral density (BMD) and coronary artery calcification (CAC). We examined the observational association of BMD with CAC in two large population-based studies and evaluated the evidence for a potential causal relation between BMD and CAC using polygenic risk scores (PRS), 1- and 2-sample Mendelian randomization (MR) approaches. Our study populations comprised 1414 individuals (mean age 69.9 years, 52.0% women) from the Rotterdam Study and 2233 individuals (mean age 56.5 years, 50.9% women) from the Framingham Heart Study with complete information on CAC and BMD measurements at the total body (TB-), lumbar spine (LS-), and femoral neck (FN-). We used linear regression models to evaluate the observational association between BMD and CAC. Subsequently, we compared the mean CAC across PRSBMD quintile groups at different skeletal sites. In addition, we used the 2-stage least squares regression (2SLS) and the inverse variance weighted (IVW) model as primary methods for 1- and 2-sample MR to test evidence for a potentially causal association. We did not observe robust associations between measured BMD levels and CAC. These results were consistent with a uniform random distribution of mean CAC across PRSBMD quintile groups (p-value >0.05). Moreover, neither 1- nor 2-sample MR supported the possible causal association between BMD and CAC. Our results do not support the contention that lower BMD is (causally) associated with an increased CAC risk. These findings suggest that previously reported epidemiological associations of BMD with CAC are likely explained by unmeasured confounders or shared etiology, rather than by causal pathways underlying both osteoporosis and vascular calcification processes.
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Affiliation(s)
- Haojie Lu
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Christine W Lary
- Roux Institute at Northeastern University, Portland, ME, United States
| | - Chani J Hodonsky
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - Daniel Bos
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Radiology and Nuclear Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Sander W van der Laan
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Clint L Miller
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, United States
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Douglas P Kiel
- Hinda and Arthur Marcus Institute for Aging Research, Hebrew Senior Life Boston, MA, United States
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Maryam Kavousi
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Carolina Medina-Gomez
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
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3
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Hodonsky CJ, Turner AW, Khan MD, Barrientos NB, Methorst R, Ma L, Lopez NG, Mosquera JV, Auguste G, Farber E, Ma WF, Wong D, Onengut-Gumuscu S, Kavousi M, Peyser PA, van der Laan SW, Leeper NJ, Kovacic JC, Björkegren JLM, Miller CL. Multi-ancestry genetic analysis of gene regulation in coronary arteries prioritizes disease risk loci. Cell Genom 2024; 4:100465. [PMID: 38190101 PMCID: PMC10794848 DOI: 10.1016/j.xgen.2023.100465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 09/07/2023] [Accepted: 11/19/2023] [Indexed: 01/09/2024]
Abstract
Genome-wide association studies (GWASs) have identified hundreds of risk loci for coronary artery disease (CAD). However, non-European populations are underrepresented in GWASs, and the causal gene-regulatory mechanisms of these risk loci during atherosclerosis remain unclear. We incorporated local ancestry and haplotypes to identify quantitative trait loci for expression (eQTLs) and splicing (sQTLs) in coronary arteries from 138 ancestrally diverse Americans. Of 2,132 eQTL-associated genes (eGenes), 47% were previously unreported in coronary artery; 19% exhibited cell-type-specific expression. Colocalization revealed subgroups of eGenes unique to CAD and blood pressure GWAS. Fine-mapping highlighted additional eGenes, including TBX20 and IL5. We also identified sQTLs for 1,690 genes, among which TOR1AIP1 and ULK3 sQTLs demonstrated the importance of evaluating splicing to accurately identify disease-relevant isoform expression. Our work provides a patient-derived coronary artery eQTL resource and exemplifies the need for diverse study populations and multifaceted approaches to characterize gene regulation in disease processes.
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Affiliation(s)
- Chani J Hodonsky
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Adam W Turner
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Mohammad Daud Khan
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Nelson B Barrientos
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA; Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Ruben Methorst
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, the Netherlands
| | - Lijiang Ma
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nicolas G Lopez
- Division of Vascular Surgery, Department of Surgery, Stanford University, Stanford, CA 94305, USA
| | - Jose Verdezoto Mosquera
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA; Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - Gaëlle Auguste
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Emily Farber
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Wei Feng Ma
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA; Medical Scientist Training Program, Department of Pathology, University of Virginia, Charlottesville, VA 22908, USA
| | - Doris Wong
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA; Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - Suna Onengut-Gumuscu
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Maryam Kavousi
- Department of Epidemiology, Erasmus University Medical Center, 3000 CA Rotterdam, the Netherlands
| | - Patricia A Peyser
- Department of Epidemiology, University of Michigan, Ann Arbor, MI 48019, USA
| | - Sander W van der Laan
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, the Netherlands
| | - Nicholas J Leeper
- Division of Vascular Surgery, Department of Surgery, Stanford University, Stanford, CA 94305, USA
| | - Jason C Kovacic
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia; St. Vincent's Clinical School, University of New South Wales, Sydney, NSW 2052, Australia
| | - Johan L M Björkegren
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Huddinge, Karolinska Institutet, 141 52 Huddinge, Sweden
| | - Clint L Miller
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA; Division of Vascular Surgery, Department of Surgery, Stanford University, Stanford, CA 94305, USA; Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA.
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4
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Cornelissen A, Gadhoke NV, Ryan K, Hodonsky CJ, Mitchell R, Bihlmeyer NA, Duong T, Chen Z, Dikongue A, Sakamoto A, Sato Y, Kawakami R, Mori M, Kawai K, Fernandez R, Ghosh SKB, Braumann R, Abebe B, Kutys R, Kutyna M, Romero ME, Kolodgie FD, Miller CL, Hong CC, Grove ML, Brody JA, Sotoodehnia N, Arking DE, Schunkert H, Mitchell BD, Guo L, Virmani R, Finn AV. Polygenic Risk Score Associates With Atherosclerotic Plaque Characteristics at Autopsy. Arterioscler Thromb Vasc Biol 2024; 44:300-313. [PMID: 37916415 DOI: 10.1161/atvbaha.123.319818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 10/19/2023] [Indexed: 11/03/2023]
Abstract
BACKGROUND Polygenic risk scores (PRSs) for coronary artery disease (CAD) potentially improve cardiovascular risk prediction. However, their relationship with histopathologic features of CAD has never been examined systematically. METHODS From 4327 subjects referred to CVPath by the State of Maryland Office Chief Medical Examiner for sudden death between 1994 and 2015, 2455 cases were randomly selected for genotyping. We generated PRS from 291 known CAD risk loci. Detailed histopathologic examination of the coronary arteries was performed in all subjects. The primary study outcome measurements were histopathologic plaque features determining severity of atherosclerosis, including %stenosis, calcification, thin-cap fibroatheromas, and thrombotic CAD. RESULTS After exclusion of cases with insufficient DNA sample quality or with missing data, 954 cases (mean age, 48.8±14.7 years; 75.7% men) remained in the final study cohort. Subjects in the highest PRS quintile exhibited more severe atherosclerosis compared with subjects in the lowest quintile, with greater %stenosis (80.3%±27.0% versus 50.4%±38.7%; adjusted P<0.001) and a higher frequency of calcification (69.6% versus 35.8%; adjusted P=0.004) and thin-cap fibroatheroma (26.7% versus 9.5%; adjusted P=0.007). Even after adjustment for traditional CAD risk factors, subjects within the highest PRS quintile had higher odds of severe atherosclerosis (ie, ≥75% stenosis; adjusted odds ratio, 3.77 [95% CI, 2.10-6.78]; P<0.001) and plaque rupture (adjusted odds ratio, 4.05 [95% CI, 2.26-7.24]; P<0.001). Moreover, subjects within the highest quintile had higher odds of CAD-associated cause of death, especially among those aged ≤50 years (adjusted odds ratio, 4.08 [95% CI, 2.01-8.30]; P<0.001). No statistically significant associations were observed with plaque erosion after adjusting for covariates. CONCLUSIONS This is the first autopsy study investigating associations between PRS and atherosclerosis severity at the histopathologic level in subjects with sudden death. Our pathological analysis suggests PRS correlates with plaque burden and features of advanced atherosclerosis and may be useful as a method for CAD risk stratification, especially in younger subjects.
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Affiliation(s)
- Anne Cornelissen
- CVPath Institute, Gaithersburg, MD (A.C., N.V.G., A.D., A.S., Y.S., R. Kawakami, M.M., K.K., R.F., S.K.B.G., R.B., B.A., R. Kutys, M.K., M.E.R., F.D.K., L.G., R.V., A.V.F.)
- Department of Cardiology, University Hospital RWTH Aachen, Germany (A.C.)
| | - Neel V Gadhoke
- CVPath Institute, Gaithersburg, MD (A.C., N.V.G., A.D., A.S., Y.S., R. Kawakami, M.M., K.K., R.F., S.K.B.G., R.B., B.A., R. Kutys, M.K., M.E.R., F.D.K., L.G., R.V., A.V.F.)
| | - Kathleen Ryan
- Department of Medicine, University of Maryland School of Medicine, Baltimore (K.R., C.C.H., B.D.M., A.V.F.)
| | - Chani J Hodonsky
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville (C.J.H., C.L.M.)
| | - Rebecca Mitchell
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD (R.M., N.A.B., T.D., M.L.G., N.S., D.E.A.)
| | - Nathan A Bihlmeyer
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD (R.M., N.A.B., T.D., M.L.G., N.S., D.E.A.)
| | - ThuyVy Duong
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD (R.M., N.A.B., T.D., M.L.G., N.S., D.E.A.)
| | - Zhifen Chen
- Department of Cardiology, Deutsches Herzzentrum München, Technische Universität München, Munich, Germany (Z.C., H.S.)
- Deutsches Zentrum für Herz-und Kreislauferkrankungen (DZHK), Partner Site Munich Heart Alliance, Germany (Z.C., H.S.)
| | - Armelle Dikongue
- CVPath Institute, Gaithersburg, MD (A.C., N.V.G., A.D., A.S., Y.S., R. Kawakami, M.M., K.K., R.F., S.K.B.G., R.B., B.A., R. Kutys, M.K., M.E.R., F.D.K., L.G., R.V., A.V.F.)
| | - Atsushi Sakamoto
- CVPath Institute, Gaithersburg, MD (A.C., N.V.G., A.D., A.S., Y.S., R. Kawakami, M.M., K.K., R.F., S.K.B.G., R.B., B.A., R. Kutys, M.K., M.E.R., F.D.K., L.G., R.V., A.V.F.)
| | - Yu Sato
- CVPath Institute, Gaithersburg, MD (A.C., N.V.G., A.D., A.S., Y.S., R. Kawakami, M.M., K.K., R.F., S.K.B.G., R.B., B.A., R. Kutys, M.K., M.E.R., F.D.K., L.G., R.V., A.V.F.)
| | - Rika Kawakami
- CVPath Institute, Gaithersburg, MD (A.C., N.V.G., A.D., A.S., Y.S., R. Kawakami, M.M., K.K., R.F., S.K.B.G., R.B., B.A., R. Kutys, M.K., M.E.R., F.D.K., L.G., R.V., A.V.F.)
| | - Masayuki Mori
- CVPath Institute, Gaithersburg, MD (A.C., N.V.G., A.D., A.S., Y.S., R. Kawakami, M.M., K.K., R.F., S.K.B.G., R.B., B.A., R. Kutys, M.K., M.E.R., F.D.K., L.G., R.V., A.V.F.)
| | - Kenji Kawai
- CVPath Institute, Gaithersburg, MD (A.C., N.V.G., A.D., A.S., Y.S., R. Kawakami, M.M., K.K., R.F., S.K.B.G., R.B., B.A., R. Kutys, M.K., M.E.R., F.D.K., L.G., R.V., A.V.F.)
| | - Raquel Fernandez
- CVPath Institute, Gaithersburg, MD (A.C., N.V.G., A.D., A.S., Y.S., R. Kawakami, M.M., K.K., R.F., S.K.B.G., R.B., B.A., R. Kutys, M.K., M.E.R., F.D.K., L.G., R.V., A.V.F.)
| | - Saikat Kumar B Ghosh
- CVPath Institute, Gaithersburg, MD (A.C., N.V.G., A.D., A.S., Y.S., R. Kawakami, M.M., K.K., R.F., S.K.B.G., R.B., B.A., R. Kutys, M.K., M.E.R., F.D.K., L.G., R.V., A.V.F.)
| | - Ryan Braumann
- CVPath Institute, Gaithersburg, MD (A.C., N.V.G., A.D., A.S., Y.S., R. Kawakami, M.M., K.K., R.F., S.K.B.G., R.B., B.A., R. Kutys, M.K., M.E.R., F.D.K., L.G., R.V., A.V.F.)
| | - Biniyam Abebe
- CVPath Institute, Gaithersburg, MD (A.C., N.V.G., A.D., A.S., Y.S., R. Kawakami, M.M., K.K., R.F., S.K.B.G., R.B., B.A., R. Kutys, M.K., M.E.R., F.D.K., L.G., R.V., A.V.F.)
| | - Robert Kutys
- CVPath Institute, Gaithersburg, MD (A.C., N.V.G., A.D., A.S., Y.S., R. Kawakami, M.M., K.K., R.F., S.K.B.G., R.B., B.A., R. Kutys, M.K., M.E.R., F.D.K., L.G., R.V., A.V.F.)
| | - Matthew Kutyna
- CVPath Institute, Gaithersburg, MD (A.C., N.V.G., A.D., A.S., Y.S., R. Kawakami, M.M., K.K., R.F., S.K.B.G., R.B., B.A., R. Kutys, M.K., M.E.R., F.D.K., L.G., R.V., A.V.F.)
| | - Maria E Romero
- CVPath Institute, Gaithersburg, MD (A.C., N.V.G., A.D., A.S., Y.S., R. Kawakami, M.M., K.K., R.F., S.K.B.G., R.B., B.A., R. Kutys, M.K., M.E.R., F.D.K., L.G., R.V., A.V.F.)
| | - Frank D Kolodgie
- CVPath Institute, Gaithersburg, MD (A.C., N.V.G., A.D., A.S., Y.S., R. Kawakami, M.M., K.K., R.F., S.K.B.G., R.B., B.A., R. Kutys, M.K., M.E.R., F.D.K., L.G., R.V., A.V.F.)
| | - Clint L Miller
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville (C.J.H., C.L.M.)
| | - Charles C Hong
- Department of Medicine, University of Maryland School of Medicine, Baltimore (K.R., C.C.H., B.D.M., A.V.F.)
| | - Megan L Grove
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD (R.M., N.A.B., T.D., M.L.G., N.S., D.E.A.)
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle (J.A.B.)
| | - Nona Sotoodehnia
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD (R.M., N.A.B., T.D., M.L.G., N.S., D.E.A.)
| | - Dan E Arking
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD (R.M., N.A.B., T.D., M.L.G., N.S., D.E.A.)
| | - Heribert Schunkert
- Department of Cardiology, Deutsches Herzzentrum München, Technische Universität München, Munich, Germany (Z.C., H.S.)
- Deutsches Zentrum für Herz-und Kreislauferkrankungen (DZHK), Partner Site Munich Heart Alliance, Germany (Z.C., H.S.)
| | - Braxton D Mitchell
- Department of Medicine, University of Maryland School of Medicine, Baltimore (K.R., C.C.H., B.D.M., A.V.F.)
- Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, MD (B.D.M.)
| | - Liang Guo
- CVPath Institute, Gaithersburg, MD (A.C., N.V.G., A.D., A.S., Y.S., R. Kawakami, M.M., K.K., R.F., S.K.B.G., R.B., B.A., R. Kutys, M.K., M.E.R., F.D.K., L.G., R.V., A.V.F.)
| | - Renu Virmani
- CVPath Institute, Gaithersburg, MD (A.C., N.V.G., A.D., A.S., Y.S., R. Kawakami, M.M., K.K., R.F., S.K.B.G., R.B., B.A., R. Kutys, M.K., M.E.R., F.D.K., L.G., R.V., A.V.F.)
| | - Aloke V Finn
- CVPath Institute, Gaithersburg, MD (A.C., N.V.G., A.D., A.S., Y.S., R. Kawakami, M.M., K.K., R.F., S.K.B.G., R.B., B.A., R. Kutys, M.K., M.E.R., F.D.K., L.G., R.V., A.V.F.)
- Department of Medicine, University of Maryland School of Medicine, Baltimore (K.R., C.C.H., B.D.M., A.V.F.)
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5
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Mosquera JV, Auguste G, Wong D, Turner AW, Hodonsky CJ, Alvarez-Yela AC, Song Y, Cheng Q, Lino Cardenas CL, Theofilatos K, Bos M, Kavousi M, Peyser PA, Mayr M, Kovacic JC, Björkegren JLM, Malhotra R, Stukenberg PT, Finn AV, van der Laan SW, Zang C, Sheffield NC, Miller CL. Integrative single-cell meta-analysis reveals disease-relevant vascular cell states and markers in human atherosclerosis. Cell Rep 2023; 42:113380. [PMID: 37950869 DOI: 10.1016/j.celrep.2023.113380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 09/12/2023] [Accepted: 10/20/2023] [Indexed: 11/13/2023] Open
Abstract
Coronary artery disease (CAD) is characterized by atherosclerotic plaque formation in the arterial wall. CAD progression involves complex interactions and phenotypic plasticity among vascular and immune cell lineages. Single-cell RNA-seq (scRNA-seq) studies have highlighted lineage-specific transcriptomic signatures, but human cell phenotypes remain controversial. Here, we perform an integrated meta-analysis of 22 scRNA-seq libraries to generate a comprehensive map of human atherosclerosis with 118,578 cells. Besides characterizing granular cell-type diversity and communication, we leverage this atlas to provide insights into smooth muscle cell (SMC) modulation. We integrate genome-wide association study data and uncover a critical role for modulated SMC phenotypes in CAD, myocardial infarction, and coronary calcification. Finally, we identify fibromyocyte/fibrochondrogenic SMC markers (LTBP1 and CRTAC1) as proxies of atherosclerosis progression and validate these through omics and spatial imaging analyses. Altogether, we create a unified atlas of human atherosclerosis informing cell state-specific mechanistic and translational studies of cardiovascular diseases.
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Affiliation(s)
- Jose Verdezoto Mosquera
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA; Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Gaëlle Auguste
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Doris Wong
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA; Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Adam W Turner
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Chani J Hodonsky
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | | | - Yipei Song
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA; Department of Computer Engineering, University of Virginia, Charlottesville, VA 22908, USA
| | - Qi Cheng
- CVPath Institute, Gaithersburg, MD 20878, USA
| | - Christian L Lino Cardenas
- Cardiovascular Research Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA
| | | | - Maxime Bos
- Department of Epidemiology, Erasmus University Medical Center, 3000 CA Rotterdam, the Netherlands
| | - Maryam Kavousi
- Department of Epidemiology, Erasmus University Medical Center, 3000 CA Rotterdam, the Netherlands
| | - Patricia A Peyser
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI 48019, USA
| | - Manuel Mayr
- King's British Heart Foundation Centre, King's College London, London WC2R 2LS, UK; National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
| | - Jason C Kovacic
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia; St. Vincent's Clinical School, University of New South Wales, Sydney, NSW 2052, Australia
| | - Johan L M Björkegren
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Karolinska Institutet, 141 52 Huddinge, Sweden
| | - Rajeev Malhotra
- Cardiovascular Research Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA
| | - P Todd Stukenberg
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | | | - Sander W van der Laan
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, the Netherlands
| | - Chongzhi Zang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA; Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA; Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA; Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA
| | - Nathan C Sheffield
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA; Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA; Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA; Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA
| | - Clint L Miller
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA; Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA; Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA; Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA.
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Lino Cardenas CL, Jiang W, Kajuluri LP, Singh K, Ostrom K, Li R, Cherbonneau F, Boerboom S, Birchenough C, Roh K, Chou EL, Shahrooz Z, Nicholson C, Johnson AL, Lee S, Ichinose F, Bloch DB, Nigwekar S, Ellinor PT, Musolino P, Lindsay ME, Dou Z, Miller CL, Malhotra R. Treatment of calcific arterial disease via enhancement of autophagy using GSK343. iScience 2023; 26:108360. [PMID: 38033629 PMCID: PMC10681952 DOI: 10.1016/j.isci.2023.108360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/31/2023] [Accepted: 10/25/2023] [Indexed: 12/02/2023] Open
Abstract
Vascular calcification is a hallmark of atherosclerotic disease and serves as a strong predictor and risk factor for cardiovascular events. Growing evidence suggests that autophagy may play a protective role in early atherosclerosis. The precise effects of autophagy on VSMC-mediated calcification remain unknown. In this study, we utilized multi-omic profiling to investigate impaired autophagy at the transcriptional level as a key driver of VSMC calcification. Our findings revealed that impaired autophagy is an essential determinant of VSMC calcification. We observed that an osteogenic environment affects the open chromatin status of VSMCs, compromising the transcriptional activation of autophagy initiation genes. In vivo experiments involve pharmacological and genetic activation of autophagy using mouse models of spontaneous large (Mgp-/-) and small (Abcc6-/-) artery calcification. Taken together, these data advance our mechanistic understanding of vascular calcification and provide important insights for a broad range of cardiovascular diseases involving VSMC phenotype switch.
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Affiliation(s)
- Christian L. Lino Cardenas
- Cardiovascular Research Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Wanlin Jiang
- Cardiovascular Research Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Lova P. Kajuluri
- Cardiovascular Research Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Kuldeep Singh
- Cardiovascular Research Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Katrina Ostrom
- Cardiovascular Research Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Rebecca Li
- Cardiovascular Research Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Francois Cherbonneau
- Cardiovascular Research Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Sophie Boerboom
- Cardiovascular Research Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Claire Birchenough
- Cardiovascular Research Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Kangsan Roh
- Cardiovascular Research Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Elizabeth L. Chou
- Cardiovascular Research Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Division of Vascular and Endovascular Surgery, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Zarbafian Shahrooz
- Cardiovascular Research Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Christopher Nicholson
- Cardiovascular Research Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Adam L. Johnson
- Cardiovascular Research Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Sujin Lee
- Cardiovascular Research Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Fumito Ichinose
- Department of Anesthesia, Critical Care and Pain Medicine at Massachusetts General Hospital, Boston, MA 02114, USA
| | - Donald B. Bloch
- Department of Anesthesia, Critical Care and Pain Medicine at Massachusetts General Hospital, Boston, MA 02114, USA
- Division of Rheumatology, Allergy, and Immunology, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Sagar Nigwekar
- Division of Nephrology, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Patrick T. Ellinor
- Cardiovascular Research Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Patricia Musolino
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Mark E. Lindsay
- Cardiovascular Research Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Zhixun Dou
- Center for Regenerative Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Clint L. Miller
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA
| | - Rajeev Malhotra
- Cardiovascular Research Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
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7
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de Las Fuentes L, Schwander KL, Brown MR, Bentley AR, Winkler TW, Sung YJ, Munroe PB, Miller CL, Aschard H, Aslibekyan S, Bartz TM, Bielak LF, Chai JF, Cheng CY, Dorajoo R, Feitosa MF, Guo X, Hartwig FP, Horimoto A, Kolčić I, Lim E, Liu Y, Manning AK, Marten J, Musani SK, Noordam R, Padmanabhan S, Rankinen T, Richard MA, Ridker PM, Smith AV, Vojinovic D, Zonderman AB, Alver M, Boissel M, Christensen K, Freedman BI, Gao C, Giulianini F, Harris SE, He M, Hsu FC, Kühnel B, Laguzzi F, Li X, Lyytikäinen LP, Nolte IM, Poveda A, Rauramaa R, Riaz M, Robino A, Sofer T, Takeuchi F, Tayo BO, van der Most PJ, Verweij N, Ware EB, Weiss S, Wen W, Yanek LR, Zhan Y, Amin N, Arking DE, Ballantyne C, Boerwinkle E, Brody JA, Broeckel U, Campbell A, Canouil M, Chai X, Chen YDI, Chen X, Chitrala KN, Concas MP, de Faire U, de Mutsert R, de Silva HJ, de Vries PS, Do A, Faul JD, Fisher V, Floyd JS, Forrester T, Friedlander Y, Girotto G, Gu CC, Hallmans G, Heikkinen S, Heng CK, Homuth G, Hunt S, Ikram MA, Jacobs DR, Kavousi M, Khor CC, Kilpeläinen TO, Koh WP, Komulainen P, Langefeld CD, Liang J, Liu K, Liu J, Lohman K, Mägi R, Manichaikul AW, McKenzie CA, Meitinger T, Milaneschi Y, Nauck M, Nelson CP, O'Connell JR, Palmer ND, Pereira AC, Perls T, Peters A, Polašek O, Raitakari OT, Rice K, Rice TK, Rich SS, Sabanayagam C, Schreiner PJ, Shu XO, Sidney S, Sims M, Smith JA, Starr JM, Strauch K, Tai ES, Taylor KD, Tsai MY, Uitterlinden AG, van Heemst D, Waldenberger M, Wang YX, Wei WB, Wilson G, Xuan D, Yao J, Yu C, Yuan JM, Zhao W, Becker DM, Bonnefond A, Bowden DW, Cooper RS, Deary IJ, Divers J, Esko T, Franks PW, Froguel P, Gieger C, Jonas JB, Kato N, Lakka TA, Leander K, Lehtimäki T, Magnusson PKE, North KE, Ntalla I, Penninx B, Samani NJ, Snieder H, Spedicati B, van der Harst P, Völzke H, Wagenknecht LE, Weir DR, Wojczynski MK, Wu T, Zheng W, Zhu X, Bouchard C, Chasman DI, Evans MK, Fox ER, Gudnason V, Hayward C, Horta BL, Kardia SLR, Krieger JE, Mook-Kanamori DO, Peyser PA, Province MM, Psaty BM, Rudan I, Sim X, Smith BH, van Dam RM, van Duijn CM, Wong TY, Arnett DK, Rao DC, Gauderman J, Liu CT, Morrison AC, Rotter JI, Fornage M. Gene-educational attainment interactions in a multi-population genome-wide meta-analysis identify novel lipid loci. Front Genet 2023; 14:1235337. [PMID: 38028628 PMCID: PMC10651736 DOI: 10.3389/fgene.2023.1235337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 09/27/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction: Educational attainment, widely used in epidemiologic studies as a surrogate for socioeconomic status, is a predictor of cardiovascular health outcomes. Methods: A two-stage genome-wide meta-analysis of low-density lipoprotein cholesterol (LDL), high-density lipoprotein cholesterol (HDL), and triglyceride (TG) levels was performed while accounting for gene-educational attainment interactions in up to 226,315 individuals from five population groups. We considered two educational attainment variables: "Some College" (yes/no, for any education beyond high school) and "Graduated College" (yes/no, for completing a 4-year college degree). Genome-wide significant (p < 5 × 10-8) and suggestive (p < 1 × 10-6) variants were identified in Stage 1 (in up to 108,784 individuals) through genome-wide analysis, and those variants were followed up in Stage 2 studies (in up to 117,531 individuals). Results: In combined analysis of Stages 1 and 2, we identified 18 novel lipid loci (nine for LDL, seven for HDL, and two for TG) by two degree-of-freedom (2 DF) joint tests of main and interaction effects. Four loci showed significant interaction with educational attainment. Two loci were significant only in cross-population analyses. Several loci include genes with known or suggested roles in adipose (FOXP1, MBOAT4, SKP2, STIM1, STX4), brain (BRI3, FILIP1, FOXP1, LINC00290, LMTK2, MBOAT4, MYO6, SENP6, SRGAP3, STIM1, TMEM167A, TMEM30A), and liver (BRI3, FOXP1) biology, highlighting the potential importance of brain-adipose-liver communication in the regulation of lipid metabolism. An investigation of the potential druggability of genes in identified loci resulted in five gene targets shown to interact with drugs approved by the Food and Drug Administration, including genes with roles in adipose and brain tissue. Discussion: Genome-wide interaction analysis of educational attainment identified novel lipid loci not previously detected by analyses limited to main genetic effects.
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Affiliation(s)
- Lisa de Las Fuentes
- Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, United States
| | - Karen L Schwander
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, United States
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, United States
| | - Michael R Brown
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Amy R Bentley
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Thomas W Winkler
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Yun Ju Sung
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, United States
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States
| | - Patricia B Munroe
- Clinical Pharmacology, Queen Mary University of London, London, United Kingdom
- National Institute for Health Research Barts Cardiovascular Biomedical Research Unit, Queen Mary University of London, London, United Kingdom
| | - Clint L Miller
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, United States
- Biochemistry and Molecular Genetics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, United States
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States
| | - Hugo Aschard
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, United States
- Département de Génomes et Génétique, Institut Pasteur de Lille, Université de Lille, Lille, France
| | - Stella Aslibekyan
- School of Public Health, Epidemiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Traci M Bartz
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, United States
- Department of Biostatistics, University of Washington, Seattle, WA, United States
| | - Lawrence F Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - Jin Fang Chai
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Ching-Yu Cheng
- Ocular Epidemiology, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program, Medical School, Duke-National University of Singapore, Singapore, Singapore
| | - Rajkumar Dorajoo
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Mary F Feitosa
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, United States
| | - Xiuqing Guo
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Los Angeles, CA, United States
| | - Fernando P Hartwig
- Postgraduate Programme in Epidemiology, Faculty of Medicine, Federal University of Pelotas, Pelotas, RS, Brazil
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
| | - Andrea Horimoto
- Laboratory of Genetics and Molecular Cardiology, Heart Institute, University of Sao Paulo Medical School, Sao Paulo, SP, Brazil
| | - Ivana Kolčić
- University of Split School of Medicine, Split, Croatia
- Algebra University College, Zagreb, Croatia
| | - Elise Lim
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, United States
| | - Yongmei Liu
- Division of Cardiology, Department of Medicine, Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, United States
| | - Alisa K Manning
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, United States
- Department of Medicine, Harvard Medical School, Boston, MA, United States
| | - Jonathan Marten
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Solomon K Musani
- Jackson Heart Study, Department of Medicine, University of Mississippi Medical Center, Jackson, MS, United States
| | - Raymond Noordam
- Section of Gerontology and Geriatrics, Department of Internal Medicine, Leiden University Medical Center, Leiden, Netherlands
| | - Sandosh Padmanabhan
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Tuomo Rankinen
- Human Genomics Laboratory, Pennington Biomedical Research Center, Baton Rouge, LA, United States
| | - Melissa A Richard
- Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Paul M Ridker
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Albert V Smith
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, United States
- Icelandic Heart Association, Kopavogur, Iceland
| | - Dina Vojinovic
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, Netherlands
| | - Alan B Zonderman
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
- National Institutes of Health, Baltimore, MD, United States
| | - Maris Alver
- Estonian Genome Center, Insititute of Genomics, University of Tartu, Tartu, Estonia
| | - Mathilde Boissel
- European Genomic Institute for Diabetes, Institut Pasteur de Lille, Lille, France
- University of Lille, Lille University Hospital, Lille, France
| | - Kaare Christensen
- Unit of Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Barry I Freedman
- Nephrology Division, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Chuan Gao
- Molecular Genetics and Genomics Program, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Franco Giulianini
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, United States
| | - Sarah E Harris
- Department of Psychology, The University of Edinburgh, Edinburgh, United Kingdom
- Centre for Cognitive Ageing and Cognitive Epidemiology, The University of Edinburgh, Edinburgh, United Kingdom
| | - Meian He
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fang-Chi Hsu
- Department of Biostatistics and Data Science, Division of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC, United States
| | - Brigitte Kühnel
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Federica Laguzzi
- Cardiovascular and Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Xiaoyin Li
- Department of Population and Quantitative Health Sciences, Cleveland, OH, United States
- Department of Mathematics and Statistics, St. Cloud State University, St. Cloud, MN, United States
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, University of Tampere, Tampere, Finland
- Finnish Cardiovascular Research Center, University of Tampere, Tampere, Finland
| | - Ilja M Nolte
- Unit of Genetic Epidemiology and Bioinformatics, Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Alaitz Poveda
- Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Skåne University Hospital, Lund University, Malmö, Sweden
| | - Rainer Rauramaa
- Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
| | - Muhammad Riaz
- Department of Cardiovascular Sciences, University of Leicester, Leicester, United Kingdom
- NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, United Kingdom
| | - Antonietta Robino
- Institute for Maternal and Child Health-IRCCS Burlo Garofolo, Trieste, Italy
| | - Tamar Sofer
- Biostatistics, Department of Medicine, Brigham and Women's Hospital, Harvard University, Boston, MA, United States
| | - Fumihiko Takeuchi
- Department of Gene Diagnostics and Therapeutics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Bamidele O Tayo
- Department of Public Health Sciences, Loyola University Chicago, Maywood, IL, United States
| | - Peter J van der Most
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Niek Verweij
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Erin B Ware
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, United States
| | - Stefan Weiss
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald and University of Greifswald, Greifswald, Germany
- German Center for Cardiovascular Research, Greifswald, Germany
| | - Wanqing Wen
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Lisa R Yanek
- Division of General Internal Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Yiqiang Zhan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Najaf Amin
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Dan E Arking
- Department of Genetic Medicine, McKusick-Nathans Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Christie Ballantyne
- Section of Cardiovascular Research, Baylor College of Medicine, Houston, TX, United States
- Houston Methodist Debakey Heart and Vascular Center, Houston, TX, United States
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, United States
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, United States
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, United States
| | - Ulrich Broeckel
- Section on Genomic Pediatrics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, United Kingdom
- Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, United Kingdom
| | - Mickaël Canouil
- European Genomic Institute for Diabetes, Institut Pasteur de Lille, Lille, France
- University of Lille, Lille University Hospital, Lille, France
| | - Xiaoran Chai
- Data Science Unit, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Yii-Der Ida Chen
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Los Angeles, CA, United States
| | - Xu Chen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Kumaraswamy Naidu Chitrala
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Maria Pina Concas
- Institute for Maternal and Child Health-IRCCS Burlo Garofolo, Trieste, Italy
| | - Ulf de Faire
- Cardiovascular and Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Renée de Mutsert
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, Netherlands
| | - H Janaka de Silva
- Department of Medicine, Faculty of Medicine, University of Kelaniya, Ragama, Sri Lanka
| | - Paul S de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Ahn Do
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, United States
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, United States
| | - Jessica D Faul
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, United States
| | - Virginia Fisher
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, United States
| | - James S Floyd
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, United States
| | - Terrence Forrester
- Tropical Medicine Research Institute, University of the West Indies, Mona, Jamaica
| | - Yechiel Friedlander
- Braun School of Public Health, Hadassah Medical Center, Hebrew University, Jerusalem, Israel
| | - Giorgia Girotto
- Institute for Maternal and Child Health-IRCCS Burlo Garofolo, Trieste, Italy
| | - C Charles Gu
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, United States
| | - Göran Hallmans
- Section for Nutritional Research, Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Sami Heikkinen
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Chew-Kiat Heng
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Khoo Teck Puat National University Children's Medical Institute, National University Health System, Singapore, Singapore
| | - Georg Homuth
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald and University of Greifswald, Greifswald, Germany
| | - Steven Hunt
- Department of Internal Medicine, University of Utah, Salt Lake City, UT, United States
- Department of Genetic Medicine, Weill Cornell Medicine in Qatar, Doha, Qatar
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - David R Jacobs
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, United States
| | - Maryam Kavousi
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Chiea Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Tuomas O Kilpeläinen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Environmental Medicine and Public Health, The Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Woon-Puay Koh
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Singapore Institute for Clinical Sciences, Agency for Science Technology and Research (A*STAR), Singapore, Singapore
| | | | - Carl D Langefeld
- Department of Biostatistics and Data Science, Division of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC, United States
| | - Jingjing Liang
- Department of Population and Quantitative Health Sciences, Cleveland, OH, United States
| | - Kiang Liu
- Epidemiology, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Jianjun Liu
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Kurt Lohman
- Division of Cardiology, Department of Medicine, Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, United States
| | - Reedik Mägi
- Estonian Genome Center, Insititute of Genomics, University of Tartu, Tartu, Estonia
| | - Ani W Manichaikul
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, United States
| | - Colin A McKenzie
- Tropical Medicine Research Institute, University of the West Indies, Mona, Jamaica
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Human Genetics, Technische Universität München, Munich, Germany
| | | | - Matthias Nauck
- German Center for Cardiovascular Research, Greifswald, Germany
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Christopher P Nelson
- Department of Cardiovascular Sciences, University of Leicester, Leicester, United Kingdom
- NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, United Kingdom
| | - Jeffrey R O'Connell
- Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD, United States
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Nicholette D Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Alexandre C Pereira
- Laboratory of Genetics and Molecular Cardiology, Heart Institute, University of Sao Paulo Medical School, Sao Paulo, SP, Brazil
| | - Thomas Perls
- Geriatrics Section, Department of Medicine, Boston University School of Medicine, Boston, MA, United States
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Cardiovascular Research, Neuherberg, Germany
| | - Ozren Polašek
- University of Split School of Medicine, Split, Croatia
- Algebra University College, Zagreb, Croatia
| | - Olli T Raitakari
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
| | - Kenneth Rice
- Department of Biostatistics, University of Washington, Seattle, WA, United States
| | - Treva K Rice
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, United States
| | - Stephen S Rich
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, United States
| | - Charumathi Sabanayagam
- Ocular Epidemiology, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program, Medical School, Duke-National University of Singapore, Singapore, Singapore
| | - Pamela J Schreiner
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, United States
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Stephen Sidney
- Division of Research, Kaiser Permanente of Northern California, Oakland, CA, United States
| | - Mario Sims
- Jackson Heart Study, Department of Medicine, University of Mississippi Medical Center, Jackson, MS, United States
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, United States
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, United States
| | - John M Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, The University of Edinburgh, Edinburgh, United Kingdom
- Alzheimer Scotland Dementia Research Centre, The University of Edinburgh, Edinburgh, United Kingdom
| | - Konstantin Strauch
- German Research Center for Environmental Health, Helmholtz Zentrum München, Institute of Genetic Epidemiology, Neuherberg, Germany
- Institute of Medical Informatics Biometry and Epidemiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - E Shyong Tai
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
- Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Kent D Taylor
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Los Angeles, CA, United States
| | - Michael Y Tsai
- Department of Laboratory Medicine and Pathology, Minneapolis, MN, United States
| | - André G Uitterlinden
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Diana van Heemst
- Section of Gerontology and Geriatrics, Department of Internal Medicine, Leiden University Medical Center, Leiden, Netherlands
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Ya-Xing Wang
- Beijing Ophthalmology and Visual Science Key Lab, Beijing Tongren Eye Center, Beijing Tongren Hospital, Beijing Institute of Ophthalmology, Capital Medical University, Beijing, China
| | - Wen-Bin Wei
- Beijing Ophthalmology and Visual Science Key Lab, Beijing Tongren Eye Center, Beijing Tongren Hospital, Beijing Institute of Ophthalmology, Capital Medical University, Beijing, China
| | - Gregory Wilson
- Jackson Heart Study Graduate Training Center, School of Public, Jackson State University, Jackson, MS, United States
| | - Deng Xuan
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, United States
| | - Jie Yao
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Los Angeles, CA, United States
| | - Caizheng Yu
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jian-Min Yuan
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
- Division of Cancer Control and Population Sciences, University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center, Pittsburgh, PA, United States
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - Diane M Becker
- Division of General Internal Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Amélie Bonnefond
- European Genomic Institute for Diabetes, Institut Pasteur de Lille, Lille, France
- University of Lille, Lille University Hospital, Lille, France
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
| | - Donald W Bowden
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Richard S Cooper
- Department of Public Health Sciences, Loyola University Chicago, Maywood, IL, United States
| | - Ian J Deary
- Department of Psychology, The University of Edinburgh, Edinburgh, United Kingdom
- Centre for Cognitive Ageing and Cognitive Epidemiology, The University of Edinburgh, Edinburgh, United Kingdom
| | - Jasmin Divers
- Department of Biostatistics and Data Science, Division of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC, United States
| | - Tõnu Esko
- Estonian Genome Center, Insititute of Genomics, University of Tartu, Tartu, Estonia
- Broad Institute, Massachusetts Institute of Technology and Harvard University, Boston, MA, United States
| | - Paul W Franks
- Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Skåne University Hospital, Lund University, Malmö, Sweden
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
- Department of Nutrition, Harvard Chan School of Public Health, Boston, MA, United States
| | - Philippe Froguel
- European Genomic Institute for Diabetes, Institut Pasteur de Lille, Lille, France
- University of Lille, Lille University Hospital, Lille, France
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research, Neuherberg, Germany
| | - Jost B Jonas
- Beijing Ophthalmology and Visual Science Key Lab, Beijing Tongren Eye Center, Beijing Tongren Hospital, Beijing Institute of Ophthalmology, Capital Medical University, Beijing, China
- Department of Ophthalmology, Medical Faculty Mannheim, University Heidelberg, Mannheim, Germany
- Institute of Molecular and Clinical Ophthalmology, Basel, Switzerland
| | - Norihiro Kato
- Department of Gene Diagnostics and Therapeutics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Timo A Lakka
- Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, Kuopio, Finland
| | - Karin Leander
- Cardiovascular and Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Terho Lehtimäki
- Department of Clinical Chemistry, University of Tampere, Tampere, Finland
- Finnish Cardiovascular Research Center, University of Tampere, Tampere, Finland
| | - Patrik K E Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Kari E North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Ioanna Ntalla
- Clinical Pharmacology, Queen Mary University of London, London, United Kingdom
- Celgene, Bristol Myers Squibb, Mississauga, ON, Canada
| | | | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester, Leicester, United Kingdom
- NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, United Kingdom
| | - Harold Snieder
- Unit of Genetic Epidemiology and Bioinformatics, Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Beatrice Spedicati
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Pim van der Harst
- Division Heart and Lungs, Department of Cardiology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Henry Völzke
- German Center for Cardiovascular Research, Greifswald, Germany
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Lynne E Wagenknecht
- Department of Biostatistics and Data Science, Division of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC, United States
| | - David R Weir
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, United States
| | - Mary K Wojczynski
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, United States
| | - Tangchun Wu
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Xiaofeng Zhu
- Department of Population and Quantitative Health Sciences, Cleveland, OH, United States
| | - Claude Bouchard
- Human Genomics Laboratory, Pennington Biomedical Research Center, Baton Rouge, LA, United States
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Michele K Evans
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
- National Institute on Aging, National Institutes of Health, Bethesda, MD, United States
| | - Ervin R Fox
- Division of Cardiology, Department of Medicine, University of Mississippi Medical Center, Jackson, MS, United States
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Bernardo L Horta
- Postgraduate Programme in Epidemiology, Faculty of Medicine, Federal University of Pelotas, Pelotas, RS, Brazil
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - Jose Eduardo Krieger
- Laboratory of Genetics and Molecular Cardiology, Heart Institute, University of Sao Paulo Medical School, Sao Paulo, SP, Brazil
| | - Dennis O Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, Netherlands
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - Michael M Province
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, United States
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, United States
- Department of Epidemiology, University of Washington, Seattle, WA, United States
- Department of Health Systems and Population Health, University of Washington, Seattle, WA, United States
| | - Igor Rudan
- Centre for Global Health, The Usher Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Blair H Smith
- Division of Population Health and Genomics, Ninewells Hospital and Medical School, University of Dundee, Dundee, United Kingdom
| | - Rob M van Dam
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
- Department of Exercise and Nutrition Sciences, Milken Institute School of Public Health, The George Washington University, Washington, DC, United States
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
- Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Tien Yin Wong
- Ocular Epidemiology, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program, Medical School, Duke-National University of Singapore, Singapore, Singapore
| | - Donna K Arnett
- College of Public Health, Dean's Office, University of Kentucky, Lexington, KY, United States
| | - Dabeeru C Rao
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, United States
| | - James Gauderman
- Division of Biostatistics, Population and Public Health Sciences, University of Southern California, Los Angeles, CA, United States
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, United States
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Jerome I Rotter
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Los Angeles, CA, United States
| | - Myriam Fornage
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, United States
- Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, United States
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8
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Mekke JM, Sakkers TR, Verwer MC, van den Dungen NAM, Song Y, Miller CL, Finn AV, Pasterkamp G, Mokry M, den Ruijter HM, Vink A, de Kleijn DPV, de Borst GJ, Haitjema S, van der Laan SW. The accumulation of erythrocytes quantified and visualized by Glycophorin C in carotid atherosclerotic plaque reflects intraplaque hemorrhage and pre-procedural neurological symptoms. Sci Rep 2023; 13:17104. [PMID: 37816779 PMCID: PMC10564864 DOI: 10.1038/s41598-023-43369-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 09/22/2023] [Indexed: 10/12/2023] Open
Abstract
The accumulation of erythrocyte membranes within an atherosclerotic plaque may contribute to the deposition of free cholesterol and thereby the enlargement of the necrotic core. Erythrocyte membranes can be visualized and quantified in the plaque by immunostaining for the erythrocyte marker glycophorin C. Hence, we theorized that the accumulation of erythrocytes quantified by glycophorin C could function as a marker for plaque vulnerability, possibly reflecting intraplaque hemorrhage (IPH), and offering predictive value for pre-procedural neurological symptoms. We employed the CellProfiler-integrated slideToolKit workflow to visualize and quantify glycophorin C, defined as the total plaque area that is positive for glycophorin C, in single slides of culprit lesions obtained from the Athero-Express Biobank of 1819 consecutive asymptomatic and symptomatic patients who underwent carotid endarterectomy. Our assessment included the evaluation of various parameters such as lipid core, calcifications, collagen content, SMC content, and macrophage burden. These parameters were evaluated using a semi-quantitative scoring method, and the resulting data was dichotomized as predefined criteria into categories of no/minor or moderate/heavy staining. In addition, the presence or absence of IPH was also scored. The prevalence of IPH and pre-procedural neurological symptoms were 62.4% and 87.1%, respectively. The amount of glycophorin staining was significantly higher in samples from men compared to samples of women (median 7.15 (IQR:3.37, 13.41) versus median 4.06 (IQR:1.98, 8.32), p < 0.001). Glycophorin C was associated with IPH adjusted for clinical confounders (OR 1.90; 95% CI 1.63, 2.21; p = < 0.001). Glycophorin C was significantly associated with ipsilateral pre-procedural neurological symptoms (OR:1.27, 95%CI:1.06-1.41, p = 0.005). Sex-stratified analysis, showed that this was also the case for men (OR 1.37; 95%CI 1.12, 1.69; p = 0.003), but not for women (OR 1.15; 95%CI 0.77, 1.73; p = 0.27). Glycophorin C was associated with classical features of a vulnerable plaque, such as a larger lipid core, a higher macrophage burden, less calcifications, a lower collagen and SMC content. There were marked sex differences, in men, glycophorin C was associated with calcifications and collagen while these associations were not found in women. To conclude, the accumulation of erythrocytes in atherosclerotic plaque quantified and visualized by glycophorin C was independently associated with the presence of IPH, preprocedural symptoms in men, and with a more vulnerable plaque composition in both men and women. These results strengthen the notion that the accumulation of erythrocytes quantified by glycophorin C can be used as a marker for plaque vulnerability.
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Affiliation(s)
- Joost M Mekke
- Division of Surgical Specialties, Department of Vascular Surgery, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3508 GA, Utrecht, The Netherlands
| | - Tim R Sakkers
- Laboratory of Experimental Cardiology, Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3508 GA, Utrecht, The Netherlands
| | - Maarten C Verwer
- Division of Surgical Specialties, Department of Vascular Surgery, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3508 GA, Utrecht, The Netherlands
| | - Noortje A M van den Dungen
- Central Diagnostic Laboratory, Division Laboratories, Pharmacy and Biomedical genetics, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Yipei Song
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Clint L Miller
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22908, USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, 22908, USA
| | | | - Gerard Pasterkamp
- Central Diagnostic Laboratory, Division Laboratories, Pharmacy and Biomedical genetics, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Michal Mokry
- Laboratory of Experimental Cardiology, Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3508 GA, Utrecht, The Netherlands
- Division Heart and Lungs, Department of Cardiology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3508 GA, Utrecht, The Netherlands
| | - Hester M den Ruijter
- Laboratory of Experimental Cardiology, Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3508 GA, Utrecht, The Netherlands
| | - Aryan Vink
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3508 GA, Utrecht, The Netherlands
| | - Dominique P V de Kleijn
- Division of Surgical Specialties, Department of Vascular Surgery, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3508 GA, Utrecht, The Netherlands
- Netherlands Heart Institute, Moreelsepark 1, 3511 EP, Utrecht, The Netherlands
| | - Gert J de Borst
- Division of Surgical Specialties, Department of Vascular Surgery, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3508 GA, Utrecht, The Netherlands
| | - Saskia Haitjema
- Central Diagnostic Laboratory, Division Laboratories, Pharmacy and Biomedical genetics, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Sander W van der Laan
- Central Diagnostic Laboratory, Division Laboratories, Pharmacy and Biomedical genetics, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands.
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22908, USA.
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9
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Kavousi M, Bos MM, Barnes HJ, Lino Cardenas CL, Wong D, Lu H, Hodonsky CJ, Landsmeer LPL, Turner AW, Kho M, Hasbani NR, de Vries PS, Bowden DW, Chopade S, Deelen J, Benavente ED, Guo X, Hofer E, Hwang SJ, Lutz SM, Lyytikäinen LP, Slenders L, Smith AV, Stanislawski MA, van Setten J, Wong Q, Yanek LR, Becker DM, Beekman M, Budoff MJ, Feitosa MF, Finan C, Hilliard AT, Kardia SLR, Kovacic JC, Kral BG, Langefeld CD, Launer LJ, Malik S, Hoesein FAAM, Mokry M, Schmidt R, Smith JA, Taylor KD, Terry JG, van der Grond J, van Meurs J, Vliegenthart R, Xu J, Young KA, Zilhão NR, Zweiker R, Assimes TL, Becker LC, Bos D, Carr JJ, Cupples LA, de Kleijn DPV, de Winther M, den Ruijter HM, Fornage M, Freedman BI, Gudnason V, Hingorani AD, Hokanson JE, Ikram MA, Išgum I, Jacobs DR, Kähönen M, Lange LA, Lehtimäki T, Pasterkamp G, Raitakari OT, Schmidt H, Slagboom PE, Uitterlinden AG, Vernooij MW, Bis JC, Franceschini N, Psaty BM, Post WS, Rotter JI, Björkegren JLM, O'Donnell CJ, Bielak LF, Peyser PA, Malhotra R, van der Laan SW, Miller CL. Multi-ancestry genome-wide study identifies effector genes and druggable pathways for coronary artery calcification. Nat Genet 2023; 55:1651-1664. [PMID: 37770635 PMCID: PMC10601987 DOI: 10.1038/s41588-023-01518-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 08/29/2023] [Indexed: 09/30/2023]
Abstract
Coronary artery calcification (CAC), a measure of subclinical atherosclerosis, predicts future symptomatic coronary artery disease (CAD). Identifying genetic risk factors for CAC may point to new therapeutic avenues for prevention. Currently, there are only four known risk loci for CAC identified from genome-wide association studies (GWAS) in the general population. Here we conducted the largest multi-ancestry GWAS meta-analysis of CAC to date, which comprised 26,909 individuals of European ancestry and 8,867 individuals of African ancestry. We identified 11 independent risk loci, of which eight were new for CAC and five had not been reported for CAD. These new CAC loci are related to bone mineralization, phosphate catabolism and hormone metabolic pathways. Several new loci harbor candidate causal genes supported by multiple lines of functional evidence and are regulators of smooth muscle cell-mediated calcification ex vivo and in vitro. Together, these findings help refine the genetic architecture of CAC and extend our understanding of the biological and potential druggable pathways underlying CAC.
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Affiliation(s)
- Maryam Kavousi
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.
| | - Maxime M Bos
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Hanna J Barnes
- Cardiovascular Research Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Christian L Lino Cardenas
- Cardiovascular Research Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Doris Wong
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Haojie Lu
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Chani J Hodonsky
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Lennart P L Landsmeer
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Adam W Turner
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Minjung Kho
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Graduate School of Data Science, Seoul National University, Seoul, Republic of Korea
| | - Natalie R Hasbani
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Center at Houston, Houston, TX, USA
| | - Paul S de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Center at Houston, Houston, TX, USA
| | - Donald W Bowden
- Department of Biochemistry, Wake Forest University Health Sciences, Winston-Salem, NC, USA
| | - Sandesh Chopade
- Institute of Cardiovascular Science, Faculty of Population Health, University College London, London, UK
- University College London British Heart Foundation Research Accelerator Centre, London, UK
| | - Joris Deelen
- Biomedical Data Sciences, Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- Max Planck Institute for Biology of Aging, Cologne, Germany
| | - Ernest Diez Benavente
- Laboratory of Experimental Cardiology, Division of Heart and Lungs, University Medical Center Utrecht and Utrecht University, Utrecht, The Netherlands
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation (formerly Los Angeles Biomedical Research Institute) at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Edith Hofer
- Department of Neurology, Clinical Division of Neurogeriatrics, Medical University of Graz, Graz, Austria
- Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, Austria
| | | | - Sharon M Lutz
- Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care, Boston, MA, USA
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Lotte Slenders
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Albert V Smith
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Icelandic Heart Association, Kopavogur, Iceland
| | - Maggie A Stanislawski
- Department of Biomedical Informatics, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Jessica van Setten
- Department of Cardiology, Division of Heart and Lungs, University Medical Center Utrecht and Utrecht University, Utrecht, The Netherlands
| | - Quenna Wong
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Lisa R Yanek
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Diane M Becker
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Marian Beekman
- Biomedical Data Sciences, Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Matthew J Budoff
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation (formerly Los Angeles Biomedical Research Institute) at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Mary F Feitosa
- Department of Genetics, Division of Statistical Genomics, Washington University School of Medicine, St. Louis, MO, USA
| | - Chris Finan
- Institute of Cardiovascular Science, Faculty of Population Health, University College London, London, UK
- University College London British Heart Foundation Research Accelerator Centre, London, UK
- Department of Cardiology, Division of Heart and Lungs, University Medical Center Utrecht and Utrecht University, Utrecht, The Netherlands
| | | | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Jason C Kovacic
- Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia
- St Vincent's Clinical School, University of NSW, Sydney, New South Wales, Australia
- The Zena and Michael A. Wiener Cardiovascular Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Brian G Kral
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Carl D Langefeld
- Department of Biostatistical Sciences and Data Science, Wake Forest University Health Sciences, Winston-Salem, NC, USA
| | - Lenore J Launer
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Shaista Malik
- Susan Samueli Integrative Health Institute, Department of Medicine, University of California Irvine, Irvine, CA, USA
| | | | - Michal Mokry
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Laboratory of Experimental Cardiology, Division of Heart and Lungs, University Medical Center Utrecht and Utrecht University, Utrecht, The Netherlands
| | - Reinhold Schmidt
- Department of Neurology, Clinical Division of Neurogeriatrics, Medical University of Graz, Graz, Austria
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation (formerly Los Angeles Biomedical Research Institute) at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - James G Terry
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jeroen van der Grond
- Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Joyce van Meurs
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Rozemarijn Vliegenthart
- Department of Radiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jianzhao Xu
- Department of Biochemistry, Wake Forest University Health Sciences, Winston-Salem, NC, USA
| | - Kendra A Young
- Department of Epidemiology, University of Colorado, Anschutz Medical Campus, Denver, CO, USA
| | | | - Robert Zweiker
- Department of Internal Medicine, Division of Cardiology, Medical University of Graz, Graz, Austria
| | - Themistocles L Assimes
- VA Palo Alto Healthcare System, Palo Alto, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Lewis C Becker
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Daniel Bos
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Radiology and Nuclear Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - J Jeffrey Carr
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - L Adrienne Cupples
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
| | - Dominique P V de Kleijn
- Department of Vascular Surgery, University Medical Center Utrecht and Utrecht University, Utrecht, The Netherlands
| | - Menno de Winther
- Department of Medical Biochemistry, Experimental Vascular Biology, Amsterdam Cardiovascular Sciences: Atherosclerosis and Ischemic syndromes, Amsterdam Infection and Immunity: Inflammatory diseases, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Hester M den Ruijter
- Laboratory of Experimental Cardiology, Division of Heart and Lungs, University Medical Center Utrecht and Utrecht University, Utrecht, The Netherlands
| | - Myriam Fornage
- Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Barry I Freedman
- Department of Internal Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, USA
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland
- Faculty of Medicine, School of Public Health, University of Iceland, Reykjavik, Iceland
| | - Aroon D Hingorani
- Institute of Cardiovascular Science, Faculty of Population Health, University College London, London, UK
- University College London British Heart Foundation Research Accelerator Centre, London, UK
| | - John E Hokanson
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Ivana Išgum
- Image Sciences Institute, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Biomedical Engineering and Physics, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - David R Jacobs
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital and Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Leslie A Lange
- Department of Biomedical Informatics, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Gerard Pasterkamp
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Olli T Raitakari
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
| | - Helena Schmidt
- Gottfried Schatz Research Center (for Cell Signaling, Metabolism and Aging), Medical University of Graz, Graz, Austria
| | - P Eline Slagboom
- Biomedical Data Sciences, Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - André G Uitterlinden
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Meike W Vernooij
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Vascular Surgery, University Medical Center Utrecht and Utrecht University, Utrecht, The Netherlands
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Departments of Epidemiology, and Health Systems and Population Health, University of Washington, Seattle, WA, USA
| | - Wendy S Post
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation (formerly Los Angeles Biomedical Research Institute) at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Johan L M Björkegren
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Department of Medicine, Integrated Cardio Metabolic Centre, Karolinska Institutet, Huddinge, Sweden
| | - Christopher J O'Donnell
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Cardiology Section, Department of Medicine, Veterans Affairs Boston Healthcare System, Boston, MA, USA
| | - Lawrence F Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Rajeev Malhotra
- Cardiovascular Research Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Sander W van der Laan
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Clint L Miller
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA.
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA.
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA.
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10
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Zheng J, Wheeler E, Pietzner M, Andlauer TFM, Yau MS, Hartley AE, Brumpton BM, Rasheed H, Kemp JP, Frysz M, Robinson J, Reppe S, Prijatelj V, Gautvik KM, Falk L, Maerz W, Gergei I, Peyser PA, Kavousi M, de Vries PS, Miller CL, Bos M, van der Laan SW, Malhotra R, Herrmann M, Scharnagl H, Kleber M, Dedoussis G, Zeggini E, Nethander M, Ohlsson C, Lorentzon M, Wareham N, Langenberg C, Holmes MV, Davey Smith G, Tobias JH. Lowering of Circulating Sclerostin May Increase Risk of Atherosclerosis and Its Risk Factors: Evidence From a Genome-Wide Association Meta-Analysis Followed by Mendelian Randomization. Arthritis Rheumatol 2023; 75:1781-1792. [PMID: 37096546 PMCID: PMC10586470 DOI: 10.1002/art.42538] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 03/22/2023] [Accepted: 04/18/2023] [Indexed: 04/26/2023]
Abstract
OBJECTIVE In this study, we aimed to establish the causal effects of lowering sclerostin, target of the antiosteoporosis drug romosozumab, on atherosclerosis and its risk factors. METHODS A genome-wide association study meta-analysis was performed of circulating sclerostin levels in 33,961 European individuals. Mendelian randomization (MR) was used to predict the causal effects of sclerostin lowering on 15 atherosclerosis-related diseases and risk factors. RESULTS We found that 18 conditionally independent variants were associated with circulating sclerostin. Of these, 1 cis signal in SOST and 3 trans signals in B4GALNT3, RIN3, and SERPINA1 regions showed directionally opposite signals for sclerostin levels and estimated bone mineral density. Variants with these 4 regions were selected as genetic instruments. MR using 5 correlated cis-SNPs suggested that lower sclerostin increased the risk of type 2 diabetes mellitus (DM) (odds ratio [OR] 1.32 [95% confidence interval (95% CI) 1.03-1.69]) and myocardial infarction (MI) (OR 1.35 [95% CI 1.01-1.79]); sclerostin lowering was also suggested to increase the extent of coronary artery calcification (CAC) (β = 0.24 [95% CI 0.02-0.45]). MR using both cis and trans instruments suggested that lower sclerostin increased hypertension risk (OR 1.09 [95% CI 1.04-1.15]), but otherwise had attenuated effects. CONCLUSION This study provides genetic evidence to suggest that lower levels of sclerostin may increase the risk of hypertension, type 2 DM, MI, and the extent of CAC. Taken together, these findings underscore the requirement for strategies to mitigate potential adverse effects of romosozumab treatment on atherosclerosis and its related risk factors.
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Affiliation(s)
- Jie Zheng
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China, and Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the People's Republic of China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China, and MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of BristolBristolUK
| | - Eleanor Wheeler
- MRC Epidemiology Unit, Institute of Metabolic ScienceUniversity of Cambridge School of Clinical MedicineCambridgeUK
| | - Maik Pietzner
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK, and Computational Medicine, Berlin Institute of Health at Charité–Universitätsmedizin BerlinBerlinGermany
| | - Till F. M. Andlauer
- Department of Neurology, Klinikum rechts der Isar, School of MedicineTechnical University of MunichMunichGermany
| | - Michelle S. Yau
- Marcus Institute for Aging Research, Hebrew SeniorLifeHarvard Medical SchoolBostonMassachusetts
| | | | - Ben Michael Brumpton
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, and HUNT Research Centre, Department of Public Health and Nursing, NTNUNorwegian University of Science and TechnologyLevangerNorway
| | - Humaira Rasheed
- MRC IEU, Bristol Medical School, University of Bristol, Bristol, UK, and HUNT Research Centre, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Levanger, Norway, and Division of Medicine and Laboratory Sciences, Faculty of MedicineUniversity of OsloOsloNorway
| | - John P. Kemp
- MRC IEU, Bristol Medical School, University of Bristol, Bristol, UK, and Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia, and The University of Queensland Diamantina InstituteThe University of QueenslandBrisbaneQueenslandAustralia
| | - Monika Frysz
- MRC IEU, Bristol Medical School, University of Bristol, and Musculoskeletal Research UnitUniversity of BristolBristolUK
| | - Jamie Robinson
- MRC IEU, Bristol Medical SchoolUniversity of BristolBristolUK
| | - Sjur Reppe
- Unger‐Vetlesen Institute, Lovisenberg Diaconal Hospital and Department of Plastic and Reconstructive Surgery, Oslo University Hospital and Department of Medical BiochemistryOslo University HospitalOsloNorway
| | - Vid Prijatelj
- Department of Internal MedicineErasmus MC University Medical CenterRotterdamThe Netherlands
| | | | - Louise Falk
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK, and Computational Medicine, Berlin Institute of Health at Charité–Universitätsmedizin BerlinBerlinGermany
| | - Winfried Maerz
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Austria, and SYNLAB Academy, SYNLAB Holding Deutschland GmbH and Vth Department of Medicine (Nephrology, Hypertensiology, Rheumatology, Endocrinology, Diabetology), Medical Faculty MannheimUniversity of HeidelbergMannheimGermany
| | - Ingrid Gergei
- Vth Department of Medicine (Nephrology, Hypertensiology, Rheumatology, Endocrinology, Diabetology), Medical Faculty Mannheim, University of Heidelberg, Mannheim, and Therapeutic Area Cardiovascular MedicineBoehringer Ingelheim International GmbHIngelheimGermany
| | - Patricia A. Peyser
- Department of Epidemiology, School of Public HealthUniversity of MichiganAnn Arbor
| | - Maryam Kavousi
- Department of Epidemiology, Erasmus MCUniversity Medical CenterRotterdamThe Netherlands
| | - Paul S. de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public HealthThe University of Texas Health Science Center at Houston
| | - Clint L. Miller
- Center for Public Health Genomics, Department of Public Health SciencesUniversity of VirginiaCharlottesville
| | - Maxime Bos
- Department of Epidemiology, Erasmus MCUniversity Medical CenterRotterdamThe Netherlands
| | - Sander W. van der Laan
- Central Diagnostics Laboratory, Division of Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center UtrechtUtrecht UniversityUtrechtthe Netherlands
| | - Rajeev Malhotra
- Cardiology Division, Department of MedicineMassachusetts General HospitalBoston
| | - Markus Herrmann
- Clinical Institute of Medical and Chemical Laboratory DiagnosticsMedical University of GrazGrazAustria
| | - Hubert Scharnagl
- Clinical Institute of Medical and Chemical Laboratory DiagnosticsMedical University of GrazGrazAustria
| | - Marcus Kleber
- SYNLAB Academy, SYNLAB Holding Deutschland GmbHMannheimGermany
| | - George Dedoussis
- Department of Nutrition and Dietetics, School of Health Science and EducationHarokopio UniversityAthensGreece
| | - Eleftheria Zeggini
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, and Technical University of Munich (TUM) and Klinikum Rechts der IsarTUM School of MedicineMunichGermany
| | - Maria Nethander
- Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, University of Gothenburg and Bioinformatics and Data Centre, Sahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - Claes Ohlsson
- Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research, Department of Internal Medicine and Clinical Nutrition, Institute of MedicineUniversity of GothenburgGothenburgSweden
| | - Mattias Lorentzon
- Sahlgrenska Osteoporosis Centre, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden, and Region Västra Götaland, Geriatric Medicine, Sahlgrenska University Hospital, Mölndal, Sweden, and Mary McKillop Institute for Health ResearchAustralian Catholic UniversityMelbourneVictoriaAustralia
| | - Nick Wareham
- MRC Epidemiology Unit, Institute of Metabolic ScienceUniversity of Cambridge School of Clinical MedicineCambridgeUK
| | - Claudia Langenberg
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK, and Computational Medicine, Berlin Institute of Health at Charité–Universitätsmedizin BerlinBerlinGermany
| | - Michael V. Holmes
- MRC IEU, Bristol Medical School, University of Bristol, and Medical Research Council Population Health Research Unit, University of Oxford, and Clinical Trial Service Unit & Epidemiological Studies Unit, Nuffield Department of Population HealthUniversity of Oxford, and National Institute for Health Research, Oxford Biomedical Research Centre, Oxford University HospitalOxfordUK
| | | | - Jonathan H. Tobias
- MRC IEU, Bristol Medical School, University of Bristol, and Musculoskeletal Research UnitUniversity of BristolBristolUK
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11
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von Scheidt M, Bauer S, Ma A, Hao K, Kessler T, Vilne B, Wang Y, Hodonsky CJ, Ghosh SK, Mokry M, Gao H, Kawai K, Sakamoto A, Kaiser J, Bongiovanni D, Fleig J, Oldenbuettel L, Chen Z, Moggio A, Sager HB, Hecker JS, Bassermann F, Maegdefessel L, Miller CL, Koenig W, Zeiher AM, Dimmeler S, Graw M, Braun C, Ruusalepp A, Leeper NJ, Kovacic JC, Björkegren JL, Schunkert H. Leukocytes carrying Clonal Hematopoiesis of Indeterminate Potential (CHIP) Mutations invade Human Atherosclerotic Plaques. medRxiv 2023:2023.07.22.23292754. [PMID: 37546840 PMCID: PMC10402238 DOI: 10.1101/2023.07.22.23292754] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Background Leukocyte progenitors derived from clonal hematopoiesis of undetermined potential (CHIP) are associated with increased cardiovascular events. However, the prevalence and functional relevance of CHIP in coronary artery disease (CAD) are unclear, and cells affected by CHIP have not been detected in human atherosclerotic plaques. Methods CHIP mutations in blood and tissues were identified by targeted deep-DNA-sequencing (DNAseq: coverage >3,000) and whole-genome-sequencing (WGS: coverage >35). CHIP-mutated leukocytes were visualized in human atherosclerotic plaques by mutaFISH™. Functional relevance of CHIP mutations was studied by RNAseq. Results DNAseq of whole blood from 540 deceased CAD patients of the Munich cardIovaScular StudIes biObaNk (MISSION) identified 253 (46.9%) CHIP mutation carriers (mean age 78.3 years). DNAseq on myocardium, atherosclerotic coronary and carotid arteries detected identical CHIP mutations in 18 out of 25 mutation carriers in tissue DNA. MutaFISH™ visualized individual macrophages carrying DNMT3A CHIP mutations in human atherosclerotic plaques. Studying monocyte-derived macrophages from Stockholm-Tartu Atherosclerosis Reverse Networks Engineering Task (STARNET; n=941) by WGS revealed CHIP mutations in 14.2% (mean age 67.1 years). RNAseq of these macrophages revealed that expression patterns in CHIP mutation carriers differed substantially from those of non-carriers. Moreover, patterns were different depending on the underlying mutations, e.g. those carrying TET2 mutations predominantly displayed upregulated inflammatory signaling whereas ASXL1 mutations showed stronger effects on metabolic pathways. Conclusions Deep-DNA-sequencing reveals a high prevalence of CHIP mutations in whole blood of CAD patients. CHIP-affected leukocytes invade plaques in human coronary arteries. RNAseq data obtained from macrophages of CHIP-affected patients suggest that pro-atherosclerotic signaling differs depending on the underlying mutations. Further studies are necessary to understand whether specific pathways affected by CHIP mutations may be targeted for personalized treatment.
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Affiliation(s)
- Moritz von Scheidt
- Department of Cardiology, German Heart Center Munich, Technical University Munich, Munich, Germany
- Deutsches Zentrum für Herz- und Kreislaufforschung (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Sabine Bauer
- Department of Cardiology, German Heart Center Munich, Technical University Munich, Munich, Germany
- Deutsches Zentrum für Herz- und Kreislaufforschung (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Angela Ma
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Thorsten Kessler
- Department of Cardiology, German Heart Center Munich, Technical University Munich, Munich, Germany
- Deutsches Zentrum für Herz- und Kreislaufforschung (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Baiba Vilne
- Deutsches Zentrum für Herz- und Kreislaufforschung (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
- Bioinformatics Lab, Riga Stradiņš University, Riga, Latvia
- SIA Net-OMICS, Riga, Latvia
| | - Ying Wang
- Department of Pathology and Laboratory Medicine, Centre for Heart Lung Innovation, University of British Columbia, Vancouver, Canada
| | - Chani J. Hodonsky
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | | | - Michal Mokry
- Laboratory of Experimental Cardiology, Department of Cardiology, University Medical Center Utrecht, University Utrecht, Utrecht, Netherlands
- Central Diagnostics Laboratory, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Hua Gao
- Division of Vascular Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, USA
| | | | - Atsushi Sakamoto
- CVPath Institute, Inc, Gaithersburg, USA
- Division of Cardiology, Internal Medicine III, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Juliane Kaiser
- Institute of Legal Medicine, Faculty of Medicine, LMU Munich, Germany
| | - Dario Bongiovanni
- Department of Internal Medicine I, Cardiology, University Hospital Augsburg, University of Augsburg, Germany
- Department of Cardiovascular Medicine, Humanitas Clinical and Research Center IRCCS and Humanitas University, Rozzano, Milan, Italy
| | - Julia Fleig
- Department of Cardiology, German Heart Center Munich, Technical University Munich, Munich, Germany
| | - Lilith Oldenbuettel
- Department of Cardiology, German Heart Center Munich, Technical University Munich, Munich, Germany
| | - Zhifen Chen
- Department of Cardiology, German Heart Center Munich, Technical University Munich, Munich, Germany
- Deutsches Zentrum für Herz- und Kreislaufforschung (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Aldo Moggio
- Department of Cardiology, German Heart Center Munich, Technical University Munich, Munich, Germany
- Deutsches Zentrum für Herz- und Kreislaufforschung (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Hendrik B. Sager
- Department of Cardiology, German Heart Center Munich, Technical University Munich, Munich, Germany
- Deutsches Zentrum für Herz- und Kreislaufforschung (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Judith S. Hecker
- Department of Medicine III, Technical University of Munich (TUM), Klinikum rechts der Isar, Munich, Germany
| | - Florian Bassermann
- Department of Medicine III, Technical University of Munich (TUM), Klinikum rechts der Isar, Munich, Germany
| | - Lars Maegdefessel
- Deutsches Zentrum für Herz- und Kreislaufforschung (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
- Department for Vascular and Endovascular Surgery, Klinikum Rechts der Isar, Technical University Munich, Munich, Germany
| | - Clint L. Miller
- Center for Public Health Genomics, Department of Public Health Sciences, Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Wolfgang Koenig
- Department of Cardiology, German Heart Center Munich, Technical University Munich, Munich, Germany
- Deutsches Zentrum für Herz- und Kreislaufforschung (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Andreas M. Zeiher
- Institute for Cardiovascular Regeneration, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
| | - Stefanie Dimmeler
- Institute for Cardiovascular Regeneration, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
| | - Matthias Graw
- Institute of Legal Medicine, Faculty of Medicine, LMU Munich, Germany
| | - Christian Braun
- Institute of Legal Medicine, Faculty of Medicine, LMU Munich, Germany
| | - Arno Ruusalepp
- Department of Cardiac Surgery, The Heart Clinic, Tartu University Hospital, Tartu, Estonia
- Clinical Gene Networks AB, Stockholm, Sweden
- Institute of Clinical Medicine, Faculty of Medicine, Tartu University, Tartu, Estonia
| | - Nicholas J. Leeper
- Central Diagnostics Laboratory, University Medical Center Utrecht, Utrecht, The Netherlands
- Stanford Cardiovascular Institute, Stanford University, Stanford, USA
| | - Jason C. Kovacic
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia
- St. Vincent’s Clinical School, University of New South Wales, Sydney, Australia
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Johan L.M. Björkegren
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, USA
- Clinical Gene Networks AB, Stockholm, Sweden
- Department of Medicine, Huddinge, Karolinska Institutet, Karolinska Universitetssjukhuset, Stockholm, Sweden
| | - Heribert Schunkert
- Department of Cardiology, German Heart Center Munich, Technical University Munich, Munich, Germany
- Deutsches Zentrum für Herz- und Kreislaufforschung (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
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12
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Cornelissen A, Gadhoke NV, Ryan K, Hodonsky CJ, Mitchell R, Bihlmeyer N, Duong T, Chen Z, Dikongue A, Sakamoto A, Sato Y, Kawakami R, Mori M, Kawai K, Fernandez R, Ghosh SKB, Braumann R, Abebe B, Kutys R, Kutyna M, Romero ME, Kolodgie FD, Miller CL, Hong CC, Grove ML, Brody JA, Sotoodehnia N, Arking DE, Schunkert H, Mitchell BD, Guo L, Virmani R, Finn AV. Polygenic Risk Score Associates with Atherosclerotic Plaque Characteristics at Autopsy. bioRxiv 2023:2023.07.05.547891. [PMID: 37461703 PMCID: PMC10350003 DOI: 10.1101/2023.07.05.547891] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
Background Polygenic risk scores (PRS) for coronary artery disease (CAD) potentially improve cardiovascular risk prediction. However, their relationship with histopathologic features of CAD has never been examined systematically. Methods From 4,327 subjects referred to CVPath by the State of Maryland Office Chief Medical Examiner (OCME) for sudden death between 1994 and 2015, 2,455 cases were randomly selected for genotyping. We generated PRS from 291 known CAD risk loci. Detailed histopathologic examination of the coronary arteries was performed in all subjects. The primary study outcome measurements were histopathologic plaque features determining severity of atherosclerosis, including %stenosis, calcification, thin-cap fibroatheromas (TCFA), and thrombotic CAD. Results After exclusion of cases with insufficient DNA sample quality or with missing data, 954 cases (mean age 48.8±14.7; 75.7% men) remained in the final study cohort. Subjects in the highest PRS quintile exhibited more severe atherosclerosis compared to subjects in the lowest quintile, with greater %stenosis (80.3%±27.0% vs. 50.4%±38.7%; adjusted p<0.001) and a higher frequency of calcification (69.6% vs. 35.8%; adjusted p=0.004) and TCFAs (26.7% vs. 9.5%; adjusted p=0.007). Even after adjustment for traditional CAD risk factors subjects within the highest PRS quintile had higher odds of severe atherosclerosis (i.e., ≥75% stenosis; adjusted OR 3.77; 95%CI 2.10-6.78; p<0.001) and plaque rupture (adjusted OR 4.05; 95%CI 2.26-7.24; p<0.001). Moreover, subjects within the highest quintile had higher odds of CAD-associated cause of death, especially among those aged 50 years and younger (adjusted OR 4.08; 95%CI 2.01-8.30; p<0.001). No associations were observed with plaque erosion. Conclusions This is the first autopsy study investigating associations between PRS and atherosclerosis severity at the histopathologic level in subjects with sudden death. Our pathological analysis suggests PRS correlates with plaque burden and features of advanced atherosclerosis and may be useful as a method for CAD risk stratification, especially in younger subjects. Highlights In this autopsy study including 954 subjects within the CVPath Sudden Death Registry, high PRS correlated with plaque burden and atherosclerosis severity.The PRS showed differential associations with plaque rupture and plaque erosion, suggesting different etiologies to these two causes of thrombotic CAD.PRS may be useful for risk stratification, particularly in the young. Further examination of individual risk loci and their association with plaque morphology may help understand molecular mechanisms of atherosclerosis, potentially revealing new therapy targets of CAD. Graphic Abstract A polygenic risk score, generated from 291 known CAD risk loci, was assessed in 954 subjects within the CVPath Sudden Death Registry. Histopathologic examination of the coronary arteries was performed in all subjects. Subjects in the highest PRS quintile exhibited more severe atherosclerosis as compared to subjects in the lowest quintile, with a greater plaque burden, more calcification, and a higher frequency of plaque rupture.
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13
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Zhang W, Zhao J, Deng L, Ishimwe N, Pauli J, Wu W, Shan S, Kempf W, Ballantyne MD, Kim D, Lyu Q, Bennett M, Rodor J, Turner AW, Lu YW, Gao P, Choi M, Warthi G, Kim HW, Barroso MM, Bryant WB, Miller CL, Weintraub NL, Maegdefessel L, Miano JM, Baker AH, Long X. INKILN is a Novel Long Noncoding RNA Promoting Vascular Smooth Muscle Inflammation via Scaffolding MKL1 and USP10. Circulation 2023. [PMID: 37199168 DOI: 10.1161/circulationaha.123.063760] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
BACKGROUND Activation of vascular smooth muscle cell (VSMC) inflammation is vital to initiate vascular disease. The role of human-specific long noncoding RNAs in VSMC inflammation is poorly understood. METHODS Bulk RNA sequencing in differentiated human VSMCs revealed a novel human-specific long noncoding RNA called inflammatory MKL1 (megakaryoblastic leukemia 1) interacting long noncoding RNA (INKILN). INKILN expression was assessed in multiple in vitro and ex vivo models of VSMC phenotypic modulation as well as human atherosclerosis and abdominal aortic aneurysm. The transcriptional regulation of INKILN was verified through luciferase reporter and chromatin immunoprecipitation assays. Loss-of-function and gain-of-function studies and multiple RNA-protein and protein-protein interaction assays were used to uncover a mechanistic role of INKILN in the VSMC proinflammatory gene program. Bacterial artificial chromosome transgenic mice were used to study INKILN expression and function in ligation injury-induced neointimal formation. RESULTS INKILN expression is downregulated in contractile VSMCs and induced in human atherosclerosis and abdominal aortic aneurysm. INKILN is transcriptionally activated by the p65 pathway, partially through a predicted NF-κB (nuclear factor kappa B) site within its proximal promoter. INKILN activates proinflammatory gene expression in cultured human VSMCs and ex vivo cultured vessels. INKILN physically interacts with and stabilizes MKL1, a key activator of VSMC inflammation through the p65/NF-κB pathway. INKILN depletion blocks interleukin-1β-induced nuclear localization of both p65 and MKL1. Knockdown of INKILN abolishes the physical interaction between p65 and MKL1 and the luciferase activity of an NF-κB reporter. Furthermore, INKILN knockdown enhances MKL1 ubiquitination through reduced physical interaction with the deubiquitinating enzyme USP10 (ubiquitin-specific peptidase 10). INKILN is induced in injured carotid arteries and exacerbates ligation injury-induced neointimal formation in bacterial artificial chromosome transgenic mice. CONCLUSIONS These findings elucidate an important pathway of VSMC inflammation involving an INKILN/MKL1/USP10 regulatory axis. Human bacterial artificial chromosome transgenic mice offer a novel and physiologically relevant approach for investigating human-specific long noncoding RNAs under vascular disease conditions.
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Affiliation(s)
- Wei Zhang
- Vascular Biology Center, Medical College of Georgia at Augusta University (W.Z., N.I., S.S., D.K., Q.L., G.W., H.W.K., W.B.B., N.L.W., J.M.M., X.L.)
| | - Jinjing Zhao
- Vascular Biology Center, Medical College of Georgia at Augusta University (W.Z., N.I., S.S., D.K., Q.L., G.W., H.W.K., W.B.B., N.L.W., J.M.M., X.L.)
- Department of Molecular and Cellular Physiology, Albany Medical College, NY (J.Z., W.W., Y.W.L., P.G., M.C., M.M.B., X.L.)
| | - Lin Deng
- Centre for Cardiovascular Science, University of Edinburgh, Scotland (L.D., M.D.B., M.B., J.R., A.H.B.)
| | - Nestor Ishimwe
- Vascular Biology Center, Medical College of Georgia at Augusta University (W.Z., N.I., S.S., D.K., Q.L., G.W., H.W.K., W.B.B., N.L.W., J.M.M., X.L.)
| | - Jessica Pauli
- Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technical University Munich, Germany (J.P., W.K., L.M.)
| | - Wen Wu
- Department of Molecular and Cellular Physiology, Albany Medical College, NY (J.Z., W.W., Y.W.L., P.G., M.C., M.M.B., X.L.)
| | - Shengshuai Shan
- Vascular Biology Center, Medical College of Georgia at Augusta University (W.Z., N.I., S.S., D.K., Q.L., G.W., H.W.K., W.B.B., N.L.W., J.M.M., X.L.)
| | - Wolfgang Kempf
- Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technical University Munich, Germany (J.P., W.K., L.M.)
| | - Margaret D Ballantyne
- Centre for Cardiovascular Science, University of Edinburgh, Scotland (L.D., M.D.B., M.B., J.R., A.H.B.)
| | - David Kim
- Vascular Biology Center, Medical College of Georgia at Augusta University (W.Z., N.I., S.S., D.K., Q.L., G.W., H.W.K., W.B.B., N.L.W., J.M.M., X.L.)
| | - Qing Lyu
- Vascular Biology Center, Medical College of Georgia at Augusta University (W.Z., N.I., S.S., D.K., Q.L., G.W., H.W.K., W.B.B., N.L.W., J.M.M., X.L.)
| | - Matthew Bennett
- Centre for Cardiovascular Science, University of Edinburgh, Scotland (L.D., M.D.B., M.B., J.R., A.H.B.)
| | - Julie Rodor
- Centre for Cardiovascular Science, University of Edinburgh, Scotland (L.D., M.D.B., M.B., J.R., A.H.B.)
| | - Adam W Turner
- Centre for Cardiovascular Science, University of Edinburgh, Scotland (L.D., M.D.B., M.B., J.R., A.H.B.)
- Center for Public Health Genomics, University of Virginia, Charlottesville. (A.W.T., C.L.M.)
| | - Yao Wei Lu
- Department of Molecular and Cellular Physiology, Albany Medical College, NY (J.Z., W.W., Y.W.L., P.G., M.C., M.M.B., X.L.)
| | - Ping Gao
- Department of Molecular and Cellular Physiology, Albany Medical College, NY (J.Z., W.W., Y.W.L., P.G., M.C., M.M.B., X.L.)
| | - Mihyun Choi
- Department of Molecular and Cellular Physiology, Albany Medical College, NY (J.Z., W.W., Y.W.L., P.G., M.C., M.M.B., X.L.)
| | - Ganesh Warthi
- Vascular Biology Center, Medical College of Georgia at Augusta University (W.Z., N.I., S.S., D.K., Q.L., G.W., H.W.K., W.B.B., N.L.W., J.M.M., X.L.)
| | - Ha Won Kim
- Vascular Biology Center, Medical College of Georgia at Augusta University (W.Z., N.I., S.S., D.K., Q.L., G.W., H.W.K., W.B.B., N.L.W., J.M.M., X.L.)
| | - Margarida M Barroso
- Department of Molecular and Cellular Physiology, Albany Medical College, NY (J.Z., W.W., Y.W.L., P.G., M.C., M.M.B., X.L.)
| | - William B Bryant
- Vascular Biology Center, Medical College of Georgia at Augusta University (W.Z., N.I., S.S., D.K., Q.L., G.W., H.W.K., W.B.B., N.L.W., J.M.M., X.L.)
| | - Clint L Miller
- Center for Public Health Genomics, University of Virginia, Charlottesville. (A.W.T., C.L.M.)
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville. (C.L.M.)
| | - Neal L Weintraub
- Vascular Biology Center, Medical College of Georgia at Augusta University (W.Z., N.I., S.S., D.K., Q.L., G.W., H.W.K., W.B.B., N.L.W., J.M.M., X.L.)
| | - Lars Maegdefessel
- Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technical University Munich, Germany (J.P., W.K., L.M.)
- German Center for Cardiovascular Research (DZHK, partner site Munich), Germany (L.M.)
- Department of Medicine, Karolinska Institute, Stockholm, Sweden (L.M.)
| | - Joseph M Miano
- Vascular Biology Center, Medical College of Georgia at Augusta University (W.Z., N.I., S.S., D.K., Q.L., G.W., H.W.K., W.B.B., N.L.W., J.M.M., X.L.)
| | - Andrew H Baker
- Centre for Cardiovascular Science, University of Edinburgh, Scotland (L.D., M.D.B., M.B., J.R., A.H.B.)
| | - Xiaochun Long
- Vascular Biology Center, Medical College of Georgia at Augusta University (W.Z., N.I., S.S., D.K., Q.L., G.W., H.W.K., W.B.B., N.L.W., J.M.M., X.L.)
- Department of Molecular and Cellular Physiology, Albany Medical College, NY (J.Z., W.W., Y.W.L., P.G., M.C., M.M.B., X.L.)
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14
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Safabakhsh S, Ma WF, Miller CL, Laksman Z. Cardiovascular utility of single cell RNA-Seq. Curr Opin Cardiol 2023; 38:193-200. [PMID: 36728943 DOI: 10.1097/hco.0000000000001014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
PURPOSE OF REVIEW Cardiovascular diseases remain the leading causes of morbidity and mortality globally. Single-cell RNA sequencing has the potential to improve diagnostics, risk stratification, and provide novel therapeutic targets that have the potential to improve patient outcomes. RECENT FINDINGS Here, we provide an overview of the basic processes underlying single-cell RNA sequencing, including library preparation, data processing, and downstream analyses. We briefly discuss how the technique has been adapted to related medical disciplines, including hematology and oncology, with short term translational impact. We discuss potential applications of this technology within cardiology as well as recent innovative research within the field. We also discuss future directions to translate this technology to other high impact clinical areas. SUMMARY The use of single-cell RNA sequencing technology has made significant advancements in the field of cardiology, with ongoing growth in terms of applications and uptake. Most of the current research has focused on structural or atherosclerotic heart disease. Future areas that stand to benefit from this technology include cardiac electrophysiology and cardio-oncology.
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Affiliation(s)
- Sina Safabakhsh
- Division of Cardiology
- Centre for Heart Lung Innovation
- Centre for Cardiovascular Innovation, University of British Columbia, Vancouver, BC, Canada
| | - Wei Feng Ma
- Center for Public Health Genomics, Department of Public Health Sciences
- Medical Scientist Training Program, University of Virginia, Charlottesville, Virginia, USA
| | - Clint L Miller
- Center for Public Health Genomics, Department of Public Health Sciences
| | - Zachary Laksman
- Division of Cardiology
- Centre for Heart Lung Innovation
- Centre for Cardiovascular Innovation, University of British Columbia, Vancouver, BC, Canada
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15
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Wong D, Auguste G, Cardenas CLL, Turner AW, Chen Y, Song Y, Ma L, Perry RN, Aherrahrou R, Kuppusamy M, Yang C, Mosquera JV, Dube CJ, Khan MD, Palmore M, Kalra JK, Kavousi M, Peyser PA, Matic L, Hedin U, Manichaikul A, Sonkusare SK, Civelek M, Kovacic JC, Björkegren JL, Malhotra R, Miller CL. FHL5 Controls Vascular Disease-Associated Gene Programs in Smooth Muscle Cells. Circ Res 2023; 132:1144-1161. [PMID: 37017084 PMCID: PMC10147587 DOI: 10.1161/circresaha.122.321692] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 03/21/2023] [Indexed: 04/06/2023]
Abstract
BACKGROUND Genome-wide association studies have identified hundreds of loci associated with common vascular diseases, such as coronary artery disease, myocardial infarction, and hypertension. However, the lack of mechanistic insights for many GWAS loci limits their translation into the clinic. Among these loci with unknown functions is UFL1-four-and-a-half LIM (LIN-11, Isl-1, MEC-3) domain 5 (FHL5; chr6q16.1), which reached genome-wide significance in a recent coronary artery disease/ myocardial infarction GWAS meta-analysis. UFL1-FHL5 is also associated with several vascular diseases, consistent with the widespread pleiotropy observed for GWAS loci. METHODS We apply a multimodal approach leveraging statistical fine-mapping, epigenomic profiling, and ex vivo analysis of human coronary artery tissues to implicate FHL5 as the top candidate causal gene. We unravel the molecular mechanisms of the cross-phenotype genetic associations through in vitro functional analyses and epigenomic profiling experiments in coronary artery smooth muscle cells. RESULTS We prioritized FHL5 as the top candidate causal gene at the UFL1-FHL5 locus through expression quantitative trait locus colocalization methods. FHL5 gene expression was enriched in the smooth muscle cells and pericyte population in human artery tissues with coexpression network analyses supporting a functional role in regulating smooth muscle cell contraction. Unexpectedly, under procalcifying conditions, FHL5 overexpression promoted vascular calcification and dysregulated processes related to extracellular matrix organization and calcium handling. Lastly, by mapping FHL5 binding sites and inferring FHL5 target gene function using artery tissue gene regulatory network analyses, we highlight regulatory interactions between FHL5 and downstream coronary artery disease/myocardial infarction loci, such as FOXL1 and FN1 that have roles in vascular remodeling. CONCLUSIONS Taken together, these studies provide mechanistic insights into the pleiotropic genetic associations of UFL1-FHL5. We show that FHL5 mediates vascular disease risk through transcriptional regulation of downstream vascular remodeling gene programs. These transacting mechanisms may explain a portion of the heritable risk for complex vascular diseases.
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Affiliation(s)
- Doris Wong
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
- Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, Virginia, USA
| | - Gaëlle Auguste
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Christian L. Lino Cardenas
- Cardiovascular Research Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Adam W. Turner
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Yixuan Chen
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Yipei Song
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Lijiang Ma
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, USA
| | - R. Noah Perry
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
- Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, Virginia, USA
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, USA
| | - Redouane Aherrahrou
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Maniselvan Kuppusamy
- Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, Virginia, USA
| | - Chaojie Yang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Jose Verdezoto Mosquera
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Collin J. Dube
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Mohammad Daud Khan
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Meredith Palmore
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Jaspreet K. Kalra
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Maryam Kavousi
- Department of Epidemiology, Erasmus University Medical Center, The Netherlands
| | | | - Ljubica Matic
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Ulf Hedin
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Ani Manichaikul
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, USA
| | - Swapnil K. Sonkusare
- Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, Virginia, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Mete Civelek
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
- Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, Virginia, USA
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, USA
| | - Jason C. Kovacic
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, USA
- Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia
- St. Vincent’s Clinical School, University of New South Wales, Sydney, Australia
| | - Johan L.M. Björkegren
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, USA
- Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Rajeev Malhotra
- Cardiovascular Research Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Clint L. Miller
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
- Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, Virginia, USA
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
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16
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Zhang M, Li J, Wang Q, Urabe G, Tang R, Huang Y, Mosquera JV, Kent KC, Wang B, Miller CL, Guo LW. Gene-repressing epigenetic reader EED unexpectedly enhances cyclinD1 gene activation. Mol Ther Nucleic Acids 2023; 31:717-729. [PMID: 36923952 PMCID: PMC10009644 DOI: 10.1016/j.omtn.2023.02.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 02/16/2023] [Indexed: 02/23/2023]
Abstract
Epigenetically switched, proliferative vascular smooth muscle cells (SMCs) form neointima, engendering stenotic diseases. Histone-3 lysine-27 trimethylation (H3K27me3) and acetylation (H3K27ac) marks are associated with gene repression and activation, respectively. The polycomb protein embryonic ectoderm development (EED) reads H3K27me3 and also enhances its deposition, hence is a canonical gene repressor. However, herein we found an unexpected role for EED in activating the bona fide pro-proliferative gene Ccnd1 (cyclinD1). EED overexpression in SMCs increased Ccnd1 mRNA, seemingly contradicting its gene-repressing function. However, consistently, EED co-immunoprecipitated with gene-activating H3K27ac reader BRD4, and they co-occupied at both mitogen-activated Ccnd1 and mitogen-repressed P57 (bona fide anti-proliferative gene), as indicated by chromatin immunoprecipitation qPCR. These results were abolished by an inhibitor of either the EED/H3K27me3 or BRD4/H3K27ac reader function. In accordance, elevating BRD4 increased H3K27me3. In vivo, while EED was upregulated in rat and human neointimal lesions, selective EED inhibition abated angioplasty-induced neointima and reduced cyclinD1 in rat carotid arteries. Thus, results uncover a previously unknown role for EED in Ccnd1 activation, likely via its cooperativity with BRD4 that enhances each other's reader function; i.e., activating pro-proliferative Ccnd1 while repressing anti-proliferative P57. As such, this study confers mechanistic implications for the epigenetic intervention of neointimal pathology.
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Affiliation(s)
- Mengxue Zhang
- Department of Surgery, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Jing Li
- Department of Surgery, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Qingwei Wang
- Department of Surgery, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Go Urabe
- Department of Surgery, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Runze Tang
- Department of Surgery, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Yitao Huang
- Department of Surgery, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Jose Verdezoto Mosquera
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA.,Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - K Craig Kent
- Department of Surgery, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Bowen Wang
- Department of Surgery, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Clint L Miller
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA.,Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA.,Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA.,Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA 22908, USA
| | - Lian-Wang Guo
- Department of Surgery, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA.,Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA 22908, USA.,Department of Molecular Physiology and Biological Physics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
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17
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Sakamoto A, Kawakami R, Mori M, Guo L, Paek KH, Mosquera JV, Cornelissen A, Ghosh SKB, Kawai K, Konishi T, Fernandez R, Fuller DT, Xu W, Vozenilek AE, Sato Y, Jinnouchi H, Torii S, Turner AW, Akahori H, Kuntz S, Weinkauf CC, Lee PJ, Kutys R, Harris K, Killey AL, Mayhew CM, Ellis M, Weinstein LM, Gadhoke NV, Dhingra R, Ullman J, Dikongue A, Romero ME, Kolodgie FD, Miller CL, Virmani R, Finn AV. CD163+ macrophages restrain vascular calcification, promoting the development of high-risk plaque. JCI Insight 2023; 8:e154922. [PMID: 36719758 PMCID: PMC10077470 DOI: 10.1172/jci.insight.154922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 01/20/2023] [Indexed: 02/01/2023] Open
Abstract
Vascular calcification (VC) is concomitant with atherosclerosis, yet it remains uncertain why rupture-prone high-risk plaques do not typically show extensive calcification. Intraplaque hemorrhage (IPH) deposits erythrocyte-derived cholesterol, enlarging the necrotic core and promoting high-risk plaque development. Pro-atherogenic CD163+ alternative macrophages engulf hemoglobin:haptoglobin (HH) complexes at IPH sites. However, their role in VC has never been examined to our knowledge. Here we show, in human arteries, the distribution of CD163+ macrophages correlated inversely with VC. In vitro experiments using vascular smooth muscle cells (VSMCs) cultured with HH-exposed human macrophage - M(Hb) - supernatant reduced calcification, while arteries from ApoE-/- CD163-/- mice showed greater VC. M(Hb) supernatant-exposed VSMCs showed activated NF-κB, while blocking NF-κB attenuated the anticalcific effect of M(Hb) on VSMCs. CD163+ macrophages altered VC through NF-κB-induced transcription of hyaluronan synthase (HAS), an enzyme that catalyzes the formation of the extracellular matrix glycosaminoglycan, hyaluronan, within VSMCs. M(Hb) supernatants enhanced HAS production in VSMCs, while knocking down HAS attenuated its anticalcific effect. NF-κB blockade in ApoE-/- mice reduced hyaluronan and increased VC. In human arteries, hyaluronan and HAS were increased in areas of CD163+ macrophage presence. Our findings highlight an important mechanism by which CD163+ macrophages inhibit VC through NF-κB-induced HAS augmentation and thus promote the high-risk plaque development.
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Affiliation(s)
| | | | | | - Liang Guo
- CVPath Institute, Inc., Gaithersburg, Maryland, USA
| | - Ka Hyun Paek
- CVPath Institute, Inc., Gaithersburg, Maryland, USA
| | - Jose Verdezoto Mosquera
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA
| | | | | | - Kenji Kawai
- CVPath Institute, Inc., Gaithersburg, Maryland, USA
| | | | | | | | - Weili Xu
- CVPath Institute, Inc., Gaithersburg, Maryland, USA
| | | | - Yu Sato
- CVPath Institute, Inc., Gaithersburg, Maryland, USA
| | | | - Sho Torii
- CVPath Institute, Inc., Gaithersburg, Maryland, USA
| | - Adam W. Turner
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Hirokuni Akahori
- Department of Cardiovascular and Renal Medicine, Hyogo Medical University, Nishinomiya, Hyogo, Japan
| | - Salome Kuntz
- CVPath Institute, Inc., Gaithersburg, Maryland, USA
| | - Craig C. Weinkauf
- Division of Vascular and Endovascular Surgery, University of Arizona, Tucson, Arizona, USA
| | | | - Robert Kutys
- CVPath Institute, Inc., Gaithersburg, Maryland, USA
| | - Kathryn Harris
- University of Maryland School of Medicine, Baltimore, Maryland, USA
| | | | | | | | | | | | - Roma Dhingra
- CVPath Institute, Inc., Gaithersburg, Maryland, USA
| | | | | | | | | | - Clint L. Miller
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Renu Virmani
- CVPath Institute, Inc., Gaithersburg, Maryland, USA
| | - Aloke V. Finn
- CVPath Institute, Inc., Gaithersburg, Maryland, USA
- University of Maryland School of Medicine, Baltimore, Maryland, USA
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18
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Hodonsky CJ, Turner AW, Khan MD, Barrientos NB, Methorst R, Ma L, Lopez NG, Mosquera JV, Auguste G, Farber E, Ma WF, Wong D, Onengut-Gumuscu S, Kavousi M, Peyser PA, van der Laan SW, Leeper NJ, Kovacic JC, Björkegren JLM, Miller CL. Integrative multi-ancestry genetic analysis of gene regulation in coronary arteries prioritizes disease risk loci. medRxiv 2023:2023.02.09.23285622. [PMID: 36824883 PMCID: PMC9949190 DOI: 10.1101/2023.02.09.23285622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Genome-wide association studies (GWAS) have identified hundreds of genetic risk loci for coronary artery disease (CAD). However, non-European populations are underrepresented in GWAS and the causal gene-regulatory mechanisms of these risk loci during atherosclerosis remain unclear. We incorporated local ancestry and haplotype information to identify quantitative trait loci (QTL) for gene expression and splicing in coronary arteries obtained from 138 ancestrally diverse Americans. Of 2,132 eQTL-associated genes (eGenes), 47% were previously unreported in coronary arteries and 19% exhibited cell-type-specific expression. Colocalization analysis with GWAS identified subgroups of eGenes unique to CAD and blood pressure. Fine-mapping highlighted additional eGenes of interest, including TBX20 and IL5 . Splicing (s)QTLs for 1,690 genes were also identified, among which TOR1AIP1 and ULK3 sQTLs demonstrated the importance of evaluating splicing events to accurately identify disease-relevant gene expression. Our work provides the first human coronary artery eQTL resource from a patient sample and exemplifies the necessity of diverse study populations and multi-omic approaches to characterize gene regulation in critical disease processes. Study Design Overview
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19
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Aherrahrou R, Lue D, Perry RN, Aberra YT, Khan MD, Soh JY, Örd T, Singha P, Yang Q, Gilani H, Benavente ED, Wong D, Hinkle J, Ma L, Sheynkman GM, den Ruijter HM, Miller CL, Björkegren JLM, Kaikkonen MU, Civelek M. Genetic Regulation of SMC Gene Expression and Splicing Predict Causal CAD Genes. Circ Res 2023; 132:323-338. [PMID: 36597873 PMCID: PMC9898186 DOI: 10.1161/circresaha.122.321586] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 12/20/2022] [Indexed: 01/05/2023]
Abstract
BACKGROUND Coronary artery disease (CAD) is the leading cause of death worldwide. Recent meta-analyses of genome-wide association studies have identified over 175 loci associated with CAD. The majority of these loci are in noncoding regions and are predicted to regulate gene expression. Given that vascular smooth muscle cells (SMCs) play critical roles in the development and progression of CAD, we aimed to identify the subset of the CAD loci associated with the regulation of transcription in distinct SMC phenotypes. METHODS We measured gene expression in SMCs isolated from the ascending aortas of 151 heart transplant donors of various genetic ancestries in quiescent or proliferative conditions and calculated the association of their expression and splicing with ~6.3 million imputed single-nucleotide polymorphism markers across the genome. RESULTS We identified 4910 expression and 4412 splicing quantitative trait loci (sQTLs) representing regions of the genome associated with transcript abundance and splicing. A total of 3660 expression quantitative trait loci (eQTLs) had not been observed in the publicly available Genotype-Tissue Expression dataset. Further, 29 and 880 eQTLs were SMC-specific and sex-biased, respectively. We made these results available for public query on a user-friendly website. To identify the effector transcript(s) regulated by CAD loci, we used 4 distinct colocalization approaches. We identified 84 eQTL and 164 sQTL that colocalized with CAD loci, highlighting the importance of genetic regulation of mRNA splicing as a molecular mechanism for CAD genetic risk. Notably, 20% and 35% of the eQTLs were unique to quiescent or proliferative SMCs, respectively. One CAD locus colocalized with a sex-specific eQTL (TERF2IP), and another locus colocalized with SMC-specific eQTL (ALKBH8). The most significantly associated CAD locus, 9p21, was an sQTL for the long noncoding RNA CDKN2B-AS1, also known as ANRIL, in proliferative SMCs. CONCLUSIONS Collectively, our results provide evidence for the molecular mechanisms of genetic susceptibility to CAD in distinct SMC phenotypes.
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Affiliation(s)
- Rédouane Aherrahrou
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America
| | - Dillon Lue
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America
| | - R Noah Perry
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America
| | - Yonathan Tamrat Aberra
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America
| | - Mohammad Daud Khan
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Joon Yuhl Soh
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America
| | - Tiit Örd
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Prosanta Singha
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Qianyi Yang
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Huda Gilani
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Ernest Diez Benavente
- Laboratory of Experimental Cardiology, University Medical Center Utrecht, Utrecht University, The Netherlands
| | - Doris Wong
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Jameson Hinkle
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Lijiang Ma
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States of America
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States of America
| | - Gloria M Sheynkman
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
- Cancer Center, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Hester M den Ruijter
- Laboratory of Experimental Cardiology, University Medical Center Utrecht, Utrecht University, The Netherlands
| | - Clint L Miller
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Johan LM Björkegren
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States of America
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States of America
- Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset, Huddinge, Sweden
| | - Minna U Kaikkonen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Mete Civelek
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America
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20
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Zhang W, Zhao J, Deng L, Ishimwe N, Pauli J, Wu W, Shan S, Kempf W, Ballantyne MD, Kim D, Lyu Q, Bennett M, Rodor J, Turner AW, Lu YW, Gao P, Choi M, Warthi G, Kim HW, Barroso MM, Bryant WB, Miller CL, Weintraub NL, Maegdefessel L, Miano JM, Baker AH, Long X. INKILN is a novel long noncoding RNA promoting vascular smooth muscle inflammation via scaffolding MKL1 and USP10. bioRxiv 2023:2023.01.07.522948. [PMID: 36711681 PMCID: PMC9881896 DOI: 10.1101/2023.01.07.522948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Background Activation of vascular smooth muscle cells (VSMCs) inflammation is vital to initiate vascular disease. However, the role of human-specific long noncoding RNAs (lncRNAs) in VSMC inflammation is poorly understood. Methods Bulk RNA-seq in differentiated human VSMCs revealed a novel human-specific lncRNA called IN flammatory M K L1 I nteracting L ong N oncoding RNA ( INKILN ). INKILN expression was assessed in multiple in vitro and ex vivo models of VSMC phenotypic modulation and human atherosclerosis and abdominal aortic aneurysm (AAA) samples. The transcriptional regulation of INKILN was determined through luciferase reporter system and chromatin immunoprecipitation assay. Both loss- and gain-of-function approaches and multiple RNA-protein and protein-protein interaction assays were utilized to uncover the role of INKILN in VSMC proinflammatory gene program and underlying mechanisms. Bacterial Artificial Chromosome (BAC) transgenic (Tg) mice were utilized to study INKLIN expression and function in ligation injury-induced neointimal formation. Results INKILN expression is downregulated in contractile VSMCs and induced by human atherosclerosis and abdominal aortic aneurysm. INKILN is transcriptionally activated by the p65 pathway, partially through a predicted NF-κB site within its proximal promoter. INKILN activates the proinflammatory gene expression in cultured human VSMCs and ex vivo cultured vessels. Mechanistically, INKILN physically interacts with and stabilizes MKL1, a key activator of VSMC inflammation through the p65/NF-κB pathway. INKILN depletion blocks ILIβ-induced nuclear localization of both p65 and MKL1. Knockdown of INKILN abolishes the physical interaction between p65 and MKL1, and the luciferase activity of an NF-κB reporter. Further, INKILN knockdown enhances MKL1 ubiquitination, likely through the reduced physical interaction with the deubiquitinating enzyme, USP10. INKILN is induced in injured carotid arteries and exacerbates ligation injury-induced neointimal formation in BAC Tg mice. Conclusions These findings elucidate an important pathway of VSMC inflammation involving an INKILN /MKL1/USP10 regulatory axis. Human BAC Tg mice offer a novel and physiologically relevant approach for investigating human-specific lncRNAs under vascular disease conditions.
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21
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Mokry M, Boltjes A, Slenders L, Bel-Bordes G, Cui K, Brouwer E, Mekke JM, Depuydt MA, Timmerman N, Waissi F, Verwer MC, Turner AW, Khan MD, Hodonsky CJ, Benavente ED, Hartman RJ, van den Dungen NAM, Lansu N, Nagyova E, Prange KH, Kovacic JC, Björkegren JL, Pavlos E, Andreakos E, Schunkert H, Owens GK, Monaco C, Finn AV, Virmani R, Leeper NJ, de Winther MP, Kuiper J, de Borst GJ, Stroes ES, Civelek M, de Kleijn DP, den Ruijter HM, Asselbergs FW, van der Laan SW, Miller CL, Pasterkamp G. Transcriptomic-based clustering of human atherosclerotic plaques identifies subgroups with different underlying biology and clinical presentation. Nat Cardiovasc Res 2022; 1:1140-1155. [PMID: 37920851 PMCID: PMC10621615 DOI: 10.1038/s44161-022-00171-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 10/20/2022] [Indexed: 11/04/2023]
Abstract
Histopathological studies have revealed key processes of atherosclerotic plaque thrombosis. However, the diversity and complexity of lesion types highlight the need for improved sub-phenotyping. Here we analyze the gene expression profiles of 654 advanced human carotid plaques. The unsupervised, transcriptome-driven clustering revealed five dominant plaque types. These plaque phenotypes were associated with clinical presentation and showed differences in cellular compositions. Validation in coronary segments showed that the molecular signature of these plaques was linked to coronary ischemia. One of the plaque types with the most severe clinical symptoms pointed to both inflammatory and fibrotic cell lineages. Further, we did a preliminary analysis of potential circulating biomarkers that mark the different plaques phenotypes. In conclusion, the definition of the plaque at risk for a thrombotic event can be fine-tuned by in-depth transcriptomic-based phenotyping. These differential plaque phenotypes prove clinically relevant for both carotid and coronary artery plaques and point to distinct underlying biology of symptomatic lesions.
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Affiliation(s)
- Michal Mokry
- Central Diagnostics Laboratory, University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
- Laboratory of Experimental Cardiology, Department of Cardiology, University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
| | - Arjan Boltjes
- Central Diagnostics Laboratory, University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
| | - Lotte Slenders
- Central Diagnostics Laboratory, University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
| | - Gemma Bel-Bordes
- Central Diagnostics Laboratory, University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
| | - Kai Cui
- Laboratory of Experimental Cardiology, Department of Cardiology, University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
| | - Eli Brouwer
- Central Diagnostics Laboratory, University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
| | - Joost M. Mekke
- Department of Vascular Surgery, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Marie A.C. Depuydt
- Leiden Academic Centre for Drug Research, Division of Biotherapeutics, Leiden University, Leiden, The Netherlands
| | - Nathalie Timmerman
- Department of Vascular Surgery, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Farahnaz Waissi
- Department of Vascular Surgery, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Maarten C Verwer
- Department of Vascular Surgery, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Adam W. Turner
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Mohammad Daud Khan
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Chani J. Hodonsky
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Ernest Diez Benavente
- Laboratory of Experimental Cardiology, Department of Cardiology, University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
| | - Robin J.G. Hartman
- Laboratory of Experimental Cardiology, Department of Cardiology, University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
| | - Noortje A M van den Dungen
- Central Diagnostics Laboratory, University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
| | - Nico Lansu
- Central Diagnostics Laboratory, University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
| | - Emilia Nagyova
- Central Diagnostics Laboratory, University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
| | - Koen H.M. Prange
- Amsterdam University Medical Centers – location AMC, University of Amsterdam, Experimental Vascular Biology, Department of Medical Biochemistry, Amsterdam Cardiovascular Sciences, Amsterdam Infection and Immunity, Amsterdam, The Netherlands
| | - Jason C. Kovacic
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia; and St Vincent’s Clinical School, University of New South Wales, Australia
| | - Johan L.M. Björkegren
- Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset, Huddinge, Sweden
- Department of Genetics & Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029-6574, USA
| | - Eleftherios Pavlos
- Laboratory of Immunobiology, Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Evangelos Andreakos
- Laboratory of Immunobiology, Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Heribert Schunkert
- Department of Cardiology, German Heart Centre Munich, Technical University of Munich, Munich, Germany
- German Centre for Cardiovascular Research (DZHK e.V.), Partner Site Munich Heart Alliance, Munich, Germany
| | - Gary K. Owens
- Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Claudia Monaco
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford
| | | | | | - Nicholas J. Leeper
- Department of Surgery, Division of Vascular Surgery, Stanford University School of Medicine, Stanford, CA
| | - Menno P.J. de Winther
- Amsterdam University Medical Centers – location AMC, University of Amsterdam, Experimental Vascular Biology, Department of Medical Biochemistry, Amsterdam Cardiovascular Sciences, Amsterdam Infection and Immunity, Amsterdam, The Netherlands
| | - Johan Kuiper
- Leiden Academic Centre for Drug Research, Division of Biotherapeutics, Leiden University, Leiden, The Netherlands
| | - Gert J. de Borst
- Department of Vascular Surgery, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Erik S.G. Stroes
- Department of Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Amsterdam, the Netherlands
| | - Mete Civelek
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | | | - Hester M. den Ruijter
- Laboratory of Experimental Cardiology, Department of Cardiology, University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
| | - Folkert W. Asselbergs
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- Health Data Research UK and Institute of Health Informatics, University College London, London, United Kingdom
| | - Sander W. van der Laan
- Central Diagnostics Laboratory, University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
| | - Clint L. Miller
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Biomedical Engineering, Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Gerard Pasterkamp
- Central Diagnostics Laboratory, University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
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22
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Cornelissen A, Gadhoke NV, Ryan K, Hodonsky CJ, Duong TV, Dikongue A, Sakamoto A, Sato Y, Miller CL, Hong CC, Arking DE, Mitchell BD, Guo L, Virmani R, Finn AV. Polygenic risk score associates with atherosclerosis severity at autopsy. Eur Heart J 2022. [DOI: 10.1093/eurheartj/ehac544.2267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
Polygenic risk scores (PRS) for coronary artery disease (CAD) are emerging as a potential method to improve cardiovascular risk prediction. Questions remain about their applicability to diverse populations as well as their correlation with coronary histopathology.
Purpose
To assess whether high genetic risk associates with histopathologic coronary plaque morphology.
Methods
We assessed 122 known CAD risk loci in 954 Black and White subjects within our sudden death registry to generate a PRS. The cohort was divided into quintiles according to z-score-standardized PRS, both in a race-stratified fashion and in the pooled sample. Detailed histopathologic examination of the coronary arteries was performed in all subjects.
Results
Subjects in the highest PRS quintile exhibited more severe atherosclerosis compared to subjects in the lowest quintile, with greater mean cross-sectional luminal narrowing (71.5% (95% CI, 66.6%-76.5%) vs. 56.6% (95% CI, 51.1%-62.1%); adjusted p<0.001; Figure 1) and a higher frequency of calcification (adjusted OR 2.19; 95% CI 1.31–3.68; p=0.003) after adjustment for the first 10 principal components, age, sex, and race. Higher z-score-standardized PRS was predictive for the finding of severe atherosclerosis (i.e., ≥75% cross-sectional luminal narrowing) even after additional controlling for traditional CAD risk factors including hypertension, smoking, diabetes mellitus, and hyperlipidemia (adjusted OR 1.39; 95% CI 1.19–1.63; p<0.001; Figure 2). Among Black subjects, higher PRS was associated with higher odds of plaque rupture (adjusted OR 1.31; 95% CI 1.03–1.66; p=0.03) and predicted CAD-associated cause of death among subjects younger than 50 years old (adjusted OR 1.26; 95% CI 1.01–1.58; p=0.04).
Conclusions
This is the first autopsy study investigating associations between PRS and atherosclerotic plaque morphology at a histopathologic level. Our pathological analysis suggests PRS correlates with plaque burden and coronary artery calcification and may be useful as a method for CAD risk stratification, especially in younger subjects.
Funding Acknowledgement
Type of funding sources: Foundation. Main funding source(s): R01 HL141425 Leducq Foundation Grant
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Affiliation(s)
- A Cornelissen
- RWTH University Hospital Aachen, Cardiology , Aachen , Germany
| | - N V Gadhoke
- CVPath Institute , Gaithersburg , United States of America
| | - K Ryan
- University of Maryland , Baltimore , United States of America
| | - C J Hodonsky
- University of Virginia , Charlottesville , United States of America
| | - T V Duong
- Johns Hopkins University School of Medicine , Baltimore , United States of America
| | - A Dikongue
- CVPath Institute , Gaithersburg , United States of America
| | - A Sakamoto
- CVPath Institute , Gaithersburg , United States of America
| | - Y Sato
- CVPath Institute , Gaithersburg , United States of America
| | - C L Miller
- University of Virginia , Charlottesville , United States of America
| | - C C Hong
- University of Maryland , Baltimore , United States of America
| | - D E Arking
- Johns Hopkins University School of Medicine , Baltimore , United States of America
| | - B D Mitchell
- University of Maryland , Baltimore , United States of America
| | - L Guo
- CVPath Institute , Gaithersburg , United States of America
| | - R Virmani
- CVPath Institute , Gaithersburg , United States of America
| | - A V Finn
- CVPath Institute , Gaithersburg , United States of America
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23
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Ma WF, Turner AW, Gancayco C, Wong D, Song Y, Mosquera JV, Auguste G, Hodonsky CJ, Prabhakar A, Ekiz HA, van der Laan SW, Miller CL. PlaqView 2.0: A comprehensive web portal for cardiovascular single-cell genomics. Front Cardiovasc Med 2022; 9:969421. [PMID: 36003902 PMCID: PMC9393487 DOI: 10.3389/fcvm.2022.969421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 07/21/2022] [Indexed: 11/13/2022] Open
Abstract
Single-cell RNA-seq (scRNA-seq) is a powerful genomics technology to interrogate the cellular composition and behaviors of complex systems. While the number of scRNA-seq datasets and available computational analysis tools have grown exponentially, there are limited systematic data sharing strategies to allow rapid exploration and re-analysis of single-cell datasets, particularly in the cardiovascular field. We previously introduced PlaqView, an open-source web portal for the exploration and analysis of published atherosclerosis single-cell datasets. Now, we introduce PlaqView 2.0 (www.plaqview.com), which provides expanded features and functionalities as well as additional cardiovascular single-cell datasets. We showcase improved PlaqView functionality, backend data processing, user-interface, and capacity. PlaqView brings new or improved tools to explore scRNA-seq data, including gene query, metadata browser, cell identity prediction, ad hoc RNA-trajectory analysis, and drug-gene interaction prediction. PlaqView serves as one of the largest central repositories for cardiovascular single-cell datasets, which now includes data from human aortic aneurysm, gene-specific mouse knockouts, and healthy references. PlaqView 2.0 brings advanced tools and high-performance computing directly to users without the need for any programming knowledge. Lastly, we outline steps to generalize and repurpose PlaqView's framework for single-cell datasets from other fields.
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Affiliation(s)
- Wei Feng Ma
- Medical Scientist Training Program, University of Virginia, Charlottesville, VA, United States
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
| | - Adam W. Turner
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
| | - Christina Gancayco
- Research Computing, University of Virginia, Charlottesville, VA, United States
| | - Doris Wong
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States
| | - Yipei Song
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
- Department of Computer Engineering, University of Virginia, Charlottesville, VA, United States
| | - Jose Verdezoto Mosquera
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
- Research Computing, University of Virginia, Charlottesville, VA, United States
| | - Gaëlle Auguste
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
| | - Chani J. Hodonsky
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
| | - Ajay Prabhakar
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
| | - H. Atakan Ekiz
- Department of Molecular Biology and Genetics, Izmir Institute of Technology, Gülbahçe, Turkey
| | - Sander W. van der Laan
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Clint L. Miller
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, United States
- *Correspondence: Clint L. Miller
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24
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Ma L, Bryce NS, Turner AW, Di Narzo AF, Rahman K, Xu Y, Ermel R, Sukhavasi K, d’Escamard V, Chandel N, V’Gangula B, Wolhuter K, Kadian-Dodov D, Franzen O, Ruusalepp A, Hao K, Miller CL, Björkegren JLM, Kovacic JC. The HDAC9-associated risk locus promotes coronary artery disease by governing TWIST1. PLoS Genet 2022; 18:e1010261. [PMID: 35714152 PMCID: PMC9246173 DOI: 10.1371/journal.pgen.1010261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 06/30/2022] [Accepted: 05/17/2022] [Indexed: 11/18/2022] Open
Abstract
Genome wide association studies (GWAS) have identified thousands of single nucleotide polymorphisms (SNPs) associated with the risk of common disorders. However, since the large majority of these risk SNPs reside outside gene-coding regions, GWAS generally provide no information about causal mechanisms regarding the specific gene(s) that are affected or the tissue(s) in which these candidate gene(s) exert their effect. The ‘gold standard’ method for understanding causal genes and their mechanisms of action are laborious basic science studies often involving sophisticated knockin or knockout mouse lines, however, these types of studies are impractical as a high-throughput means to understand the many risk variants that cause complex diseases like coronary artery disease (CAD). As a solution, we developed a streamlined, data-driven informatics pipeline to gain mechanistic insights on complex genetic loci. The pipeline begins by understanding the SNPs in a given locus in terms of their relative location and linkage disequilibrium relationships, and then identifies nearby expression quantitative trait loci (eQTLs) to determine their relative independence and the likely tissues that mediate their disease-causal effects. The pipeline then seeks to understand associations with other disease-relevant genes, disease sub-phenotypes, potential causality (Mendelian randomization), and the regulatory and functional involvement of these genes in gene regulatory co-expression networks (GRNs). Here, we applied this pipeline to understand a cluster of SNPs associated with CAD within and immediately adjacent to the gene encoding HDAC9. Our pipeline demonstrated, and validated, that this locus is causal for CAD by modulation of TWIST1 expression levels in the arterial wall, and by also governing a GRN related to metabolic function in skeletal muscle. Our results reconciled numerous prior studies, and also provided clear evidence that this locus does not govern HDAC9 expression, structure or function. This pipeline should be considered as a powerful and efficient way to understand GWAS risk loci in a manner that better reflects the highly complex nature of genetic risk associated with common disorders.
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Affiliation(s)
- Lijiang Ma
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Nicole S. Bryce
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia; St Vincent’s Clinical School, University of NSW, Sydney, Australia
| | - Adam W. Turner
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, Virginia, Unites States of America
| | - Antonio F. Di Narzo
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Karishma Rahman
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Yang Xu
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Raili Ermel
- Department of Cardiac Surgery and The Heart Clinic, Tartu University Hospital, Tartu, Estonia
| | - Katyayani Sukhavasi
- Department of Cardiac Surgery and The Heart Clinic, Tartu University Hospital, Tartu, Estonia
| | - Valentina d’Escamard
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Nirupama Chandel
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Bhargavi V’Gangula
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Kathryn Wolhuter
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia; St Vincent’s Clinical School, University of NSW, Sydney, Australia
| | - Daniella Kadian-Dodov
- Zena and Michael A. Wiener Cardiovascular Institute and Marie-Josée and Henry R, Kravis Center for Cardiovascular Health Icahn School of Medicine at Mount Sinai, New York, New York, Unites States of America
| | - Oscar Franzen
- Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset, Huddinge, Sweden
| | - Arno Ruusalepp
- Department of Cardiac Surgery and The Heart Clinic, Tartu University Hospital, Tartu, Estonia
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Respiratory Medicine, Shanghai Tenth People’s Hospital, Tongji University, Shanghai, China
| | - Clint L. Miller
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, Virginia, Unites States of America
| | - Johan L. M. Björkegren
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset, Huddinge, Sweden
| | - Jason C. Kovacic
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia; St Vincent’s Clinical School, University of NSW, Sydney, Australia
- Zena and Michael A. Wiener Cardiovascular Institute and Marie-Josée and Henry R, Kravis Center for Cardiovascular Health Icahn School of Medicine at Mount Sinai, New York, New York, Unites States of America
- * E-mail:
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25
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Turner AW, Hu SS, Mosquera JV, Ma WF, Hodonsky CJ, Wong D, Auguste G, Song Y, Sol-Church K, Farber E, Kundu S, Kundaje A, Lopez NG, Ma L, Ghosh SKB, Onengut-Gumuscu S, Ashley EA, Quertermous T, Finn AV, Leeper NJ, Kovacic JC, Björkgren JLM, Zang C, Miller CL. Single-nucleus chromatin accessibility profiling highlights regulatory mechanisms of coronary artery disease risk. Nat Genet 2022; 54:804-816. [PMID: 35590109 PMCID: PMC9203933 DOI: 10.1038/s41588-022-01069-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 03/31/2022] [Indexed: 12/24/2022]
Abstract
Coronary artery disease (CAD) is a complex inflammatory disease involving genetic influences across cell types. Genome-wide association studies (GWAS) have identified over 200 loci associated with CAD, where the majority of risk variants reside in noncoding DNA sequences impacting cis-regulatory elements (CREs). Here, we applied single-nucleus ATAC-seq to profile 28,316 nuclei across coronary artery segments from 41 patients with varying stages of CAD, which revealed 14 distinct cellular clusters. We mapped ~320,000 accessible sites across all cells, identified cell type-specific elements, transcription factors, and prioritized functional CAD risk variants. . We identified elements in smooth muscle cell (SMC) transition states (e.g. fibromyocytes) and functional variants predicted to alter SMC and macrophage-specific regulation of MRAS (3q22) and LIPA (10q23), respectively. We further nominated key driver transcription factors such as PRDM16 and TBX2. Together, this single nucleus atlas provides a critical step towards interpreting regulatory mechanisms across the continuum of CAD risk.
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Affiliation(s)
- Adam W Turner
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Shengen Shawn Hu
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Jose Verdezoto Mosquera
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA.,Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Wei Feng Ma
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA.,Medical Scientist Training Program, University of Virginia, Charlottesville, VA, USA.,Department of Pathology, University of Virginia, Charlottesville, VA, USA
| | - Chani J Hodonsky
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA.,Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA, USA
| | - Doris Wong
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA.,Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA.,Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA, USA
| | - Gaëlle Auguste
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Yipei Song
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Katia Sol-Church
- Department of Pathology, University of Virginia, Charlottesville, VA, USA.,Genome Analysis & Technology Core, University of Virginia, Charlottesville, VA, USA
| | - Emily Farber
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA.,Genome Sciences Laboratory, University of Virginia, Charlottesville, VA, USA
| | - Soumya Kundu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.,Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Nicolas G Lopez
- Division of Vascular Surgery, Department of Surgery, Stanford University, Stanford, CA, USA
| | - Lijiang Ma
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Suna Onengut-Gumuscu
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA.,Genome Sciences Laboratory, University of Virginia, Charlottesville, VA, USA.,Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Euan A Ashley
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.,Division of Cardiovascular Medicine, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Thomas Quertermous
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University, Stanford, CA, USA
| | | | - Nicholas J Leeper
- Division of Vascular Surgery, Department of Surgery, Stanford University, Stanford, CA, USA
| | - Jason C Kovacic
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia.,St. Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Johan L M Björkgren
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Chongzhi Zang
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA. .,Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA. .,Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA.
| | - Clint L Miller
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA. .,Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA. .,Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA, USA. .,Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA.
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26
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Hao K, Ermel R, Sukhavasi K, Cheng H, Ma L, Li L, Amadori L, Koplev S, Franzén O, d’Escamard V, Chandel N, Wolhuter K, Bryce NS, Venkata VRM, Miller CL, Ruusalepp A, Schunkert H, Björkegren JL, Kovacic JC. Integrative Prioritization of Causal Genes for Coronary Artery Disease. Circ Genom Precis Med 2022; 15:e003365. [PMID: 34961328 PMCID: PMC8847335 DOI: 10.1161/circgen.121.003365] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
BACKGROUND Hundreds of candidate genes have been associated with coronary artery disease (CAD) through genome-wide association studies. However, a systematic way to understand the causal mechanism(s) of these genes, and a means to prioritize them for further study, has been lacking. This represents a major roadblock for developing novel disease- and gene-specific therapies for patients with CAD. Recently, powerful integrative genomics analyses pipelines have emerged to identify and prioritize candidate causal genes by integrating tissue/cell-specific gene expression data with genome-wide association study data sets. METHODS We aimed to develop a comprehensive integrative genomics analyses pipeline for CAD and to provide a prioritized list of causal CAD genes. To this end, we leveraged several complimentary informatics approaches to integrate summary statistics from CAD genome-wide association studies (from UK Biobank and CARDIoGRAMplusC4D) with transcriptomic and expression quantitative trait loci data from 9 cardiometabolic tissue/cell types in the STARNET study (Stockholm-Tartu Atherosclerosis Reverse Network Engineering Task). RESULTS We identified 162 unique candidate causal CAD genes, which exerted their effect from between one and up to 7 disease-relevant tissues/cell types, including the arterial wall, blood, liver, skeletal muscle, adipose, foam cells, and macrophages. When their causal effect was ranked, the top candidate causal CAD genes were CDKN2B (associated with the 9p21.3 risk locus) and PHACTR1; both exerting their causal effect in the arterial wall. A majority of candidate causal genes were represented in cross-tissue gene regulatory co-expression networks that are involved with CAD, with 22/162 being key drivers in those networks. CONCLUSIONS We identified and prioritized candidate causal CAD genes, also localizing their tissue(s) of causal effect. These results should serve as a resource and facilitate targeted studies to identify the functional impact of top causal CAD genes.
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Affiliation(s)
- Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY,Sema4, Stamford, CT
| | - Raili Ermel
- Department of Cardiac Surgery and The Heart Clinic, Tartu University Hospital, Tartu, Estonia
| | - Katyayani Sukhavasi
- Department of Cardiac Surgery and The Heart Clinic, Tartu University Hospital, Tartu, Estonia
| | - Haoxiang Cheng
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Lijiang Ma
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY,Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Ling Li
- Department of Cardiology, Deutsches Herzzentrum München, Technische Universität München, Munich, Germany,Center for Doctoral Studies in Informatics and its Applications, Dept of Informatics, Technische Universität München, Munich, Germany,Deutsches Zentrum für Herz- und Kreislaufforschung (DZHK), Munich Heart Alliance, Munich, Germany
| | - Letizia Amadori
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY,Current affiliation: New York University Cardiovascular Research Center, Department of Medicine, Leon H. Charney Division of Cardiology, New York University Grossman School of Medicine, New York University Langone Health, New York, NY
| | - Simon Koplev
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
| | - Oscar Franzén
- Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset, Huddinge, Sweden
| | - Valentina d’Escamard
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Nirupama Chandel
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Kathryn Wolhuter
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia,University of New South Wales, Faculty of Medicine and Health, Sydney, Australia
| | - Nicole S. Bryce
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia,University of New South Wales, Faculty of Medicine and Health, Sydney, Australia
| | | | - Clint L. Miller
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA
| | - Arno Ruusalepp
- Department of Cardiac Surgery and The Heart Clinic, Tartu University Hospital, Tartu, Estonia,Department of Cardiology, Institute of Clinical Medicine, Tartu University
| | - Heribert Schunkert
- Department of Cardiology, Deutsches Herzzentrum München, Technische Universität München, Munich, Germany,Deutsches Zentrum für Herz- und Kreislaufforschung (DZHK), Munich Heart Alliance, Munich, Germany
| | - Johan L.M. Björkegren
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY,Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset, Huddinge, Sweden
| | - Jason C. Kovacic
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY,Victor Chang Cardiac Research Institute, Darlinghurst, Australia,St Vincent's Clinical School, University of New South Wales, Sydney, Australia
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27
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Slenders L, Landsmeer LPL, Cui K, Depuydt MAC, Verwer M, Mekke J, Timmerman N, van den Dungen NAM, Kuiper J, de Winther MPJ, Prange KHM, Ma WF, Miller CL, Aherrahrou R, Civelek M, de Borst GJ, de Kleijn DPV, Asselbergs FW, den Ruijter HM, Boltjes A, Pasterkamp G, van der Laan SW, Mokry M. Intersecting single-cell transcriptomics and genome-wide association studies identifies crucial cell populations and candidate genes for atherosclerosis. Eur Heart J Open 2022; 2:oeab043. [PMID: 35174364 PMCID: PMC8841481 DOI: 10.1093/ehjopen/oeab043] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/15/2021] [Indexed: 12/14/2022]
Abstract
Aims Genome-wide association studies (GWASs) have discovered hundreds of common genetic variants for atherosclerotic disease and cardiovascular risk factors. The translation of susceptibility loci into biological mechanisms and targets for drug discovery remains challenging. Intersecting genetic and gene expression data has led to the identification of candidate genes. However, previously studied tissues are often non-diseased and heterogeneous in cell composition, hindering accurate candidate prioritization. Therefore, we analysed single-cell transcriptomics from atherosclerotic plaques for cell-type-specific expression to identify atherosclerosis-associated candidate gene–cell pairs. Methods and results We applied gene-based analyses using GWAS summary statistics from 46 atherosclerotic and cardiovascular disease, risk factors, and other traits. We then intersected these candidates with single-cell RNA sequencing (scRNA-seq) data to identify genes specific for individual cell (sub)populations in atherosclerotic plaques. The coronary artery disease (CAD) loci demonstrated a prominent signal in plaque smooth muscle cells (SMCs) (SKI, KANK2, and SORT1) P-adj. = 0.0012, and endothelial cells (ECs) (SLC44A1, ATP2B1) P-adj. = 0.0011. Finally, we used liver-derived scRNA-seq data and showed hepatocyte-specific enrichment of genes involved in serum lipid levels. Conclusion We discovered novel and known gene–cell pairs pointing to new biological mechanisms of atherosclerotic disease. We highlight that loci associated with CAD reveal prominent association levels in mainly plaque SMC and EC populations. We present an intuitive single-cell transcriptomics-driven workflow rooted in human large-scale genetic studies to identify putative candidate genes and affected cells associated with cardiovascular traits. Collectively, our workflow allows for the identification of cell-specific targets relevant for atherosclerosis and can be universally applied to other complex genetic diseases and traits.
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Affiliation(s)
- Lotte Slenders
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, University Utrecht, Heidelberglaan 100, 3508 GA Utrecht, The Netherlands
| | - Lennart P L Landsmeer
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, University Utrecht, Heidelberglaan 100, 3508 GA Utrecht, The Netherlands
| | - Kai Cui
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, University Utrecht, Heidelberglaan 100, 3508 GA Utrecht, The Netherlands
| | - Marie A C Depuydt
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Maarten Verwer
- Department of Vascular Surgery, University Medical Centre Utrecht, University Utrecht, Heidelberglaan 100, 3508 GA Utrecht, The Netherlands
| | - Joost Mekke
- Department of Vascular Surgery, University Medical Centre Utrecht, University Utrecht, Heidelberglaan 100, 3508 GA Utrecht, The Netherlands
| | - Nathalie Timmerman
- Department of Vascular Surgery, University Medical Centre Utrecht, University Utrecht, Heidelberglaan 100, 3508 GA Utrecht, The Netherlands
| | - Noortje A M van den Dungen
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, University Utrecht, Heidelberglaan 100, 3508 GA Utrecht, The Netherlands
| | - Johan Kuiper
- Department of Medical Biochemistry, Amsterdam University Medical Centers-Location AMC, University of Amsterdam, Experimental Vascular Biology, Amsterdam Cardiovascular Sciences, Meibergdreef 9, Amsterdam, The Netherlands
| | - Menno P J de Winther
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Koen H M Prange
- Department of Medical Biochemistry, Amsterdam University Medical Centers-Location AMC, University of Amsterdam, Experimental Vascular Biology, Amsterdam Cardiovascular Sciences, Meibergdreef 9, Amsterdam, The Netherlands
| | - Wei Feng Ma
- Medical Scientist Training Program, University of Virginia, 200 Jeanette Lancaster Way, Charlottesville, VA 22908, USA.,Center for Public Health Genomics, University of Virginia, West Complex, 1335 Lee St, Charlottesville, VA 22908, USA
| | - Clint L Miller
- Center for Public Health Genomics, University of Virginia, West Complex, 1335 Lee St, Charlottesville, VA 22908, USA.,Department of Biochemistry and Molecular Genetics, University of Virginia, 1340 Jefferson Rark Avenue, Charlottesville, VA 22908, USA.,Department of Public Health Sciences, University of Virginia, West Complex Rm 3181, Charlottesville, VA 22908, USA
| | - Redouane Aherrahrou
- Center for Public Health Genomics, University of Virginia, West Complex, 1335 Lee St, Charlottesville, VA 22908, USA
| | - Mete Civelek
- Center for Public Health Genomics, University of Virginia, West Complex, 1335 Lee St, Charlottesville, VA 22908, USA.,Department of Biomedical Engineering, University of Virginia, 415 Lane Road, Charlottesville, VA 22908, USA
| | - Gert J de Borst
- Department of Vascular Surgery, University Medical Centre Utrecht, University Utrecht, Heidelberglaan 100, 3508 GA Utrecht, The Netherlands
| | - Dominique P V de Kleijn
- Department of Vascular Surgery, University Medical Centre Utrecht, University Utrecht, Heidelberglaan 100, 3508 GA Utrecht, The Netherlands
| | - Folkert W Asselbergs
- Laboratory of Experimental Cardiology, Department of Cardiology, University Medical Center Utrecht, University Utrecht, Heidelberglaan 100, Utrecht 3508 GA, The Netherlands
| | - Hester M den Ruijter
- Laboratory of Experimental Cardiology, Department of Cardiology, University Medical Center Utrecht, University Utrecht, Heidelberglaan 100, Utrecht 3508 GA, The Netherlands
| | - Arjan Boltjes
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, University Utrecht, Heidelberglaan 100, 3508 GA Utrecht, The Netherlands
| | - Gerard Pasterkamp
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, University Utrecht, Heidelberglaan 100, 3508 GA Utrecht, The Netherlands
| | - Sander W van der Laan
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, University Utrecht, Heidelberglaan 100, 3508 GA Utrecht, The Netherlands
| | - Michal Mokry
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, University Utrecht, Heidelberglaan 100, 3508 GA Utrecht, The Netherlands.,Laboratory of Experimental Cardiology, Department of Cardiology, University Medical Center Utrecht, University Utrecht, Heidelberglaan 100, Utrecht 3508 GA, The Netherlands
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28
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Ma WF, Hodonsky CJ, Turner AW, Wong D, Song Y, Mosquera JV, Ligay AV, Slenders L, Gancayco C, Pan H, Barrientos NB, Mai D, Alencar GF, Owsiany K, Owens GK, Reilly MP, Li M, Pasterkamp G, Mokry M, van der Laan SW, Khomtchouk BB, Miller CL. Enhanced single-cell RNA-seq workflow reveals coronary artery disease cellular cross-talk and candidate drug targets. Atherosclerosis 2022; 340:12-22. [PMID: 34871816 PMCID: PMC8919504 DOI: 10.1016/j.atherosclerosis.2021.11.025] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 11/19/2021] [Accepted: 11/24/2021] [Indexed: 01/03/2023]
Abstract
BACKGROUND AND AIMS The atherosclerotic plaque microenvironment is highly complex, and selective agents that modulate plaque stability are not yet available. We sought to develop a scRNA-seq analysis workflow to investigate this environment and uncover potential therapeutic approaches. We designed a user-friendly, reproducible workflow that will be applicable to other disease-specific scRNA-seq datasets. METHODS Here we incorporated automated cell labeling, pseudotemporal ordering, ligand-receptor evaluation, and drug-gene interaction analysis into a ready-to-deploy workflow. We applied this pipeline to further investigate a previously published human coronary single-cell dataset by Wirka et al. Notably, we developed an interactive web application to enable further exploration and analysis of this and other cardiovascular single-cell datasets. RESULTS We revealed distinct derivations of fibroblast-like cells from smooth muscle cells (SMCs), and showed the key changes in gene expression along their de-differentiation path. We highlighted several key ligand-receptor interactions within the atherosclerotic environment through functional expression profiling and revealed several avenues for future pharmacological development for precision medicine. Further, our interactive web application, PlaqView (www.plaqview.com), allows lay scientists to explore this and other datasets and compare scRNA-seq tools without prior coding knowledge. CONCLUSIONS This publicly available workflow and application will allow for more systematic and user-friendly analysis of scRNA datasets in other disease and developmental systems. Our analysis pipeline provides many hypothesis-generating tools to unravel the etiology of coronary artery disease. We also highlight potential mechanisms for several drugs in the atherosclerotic cellular environment. Future releases of PlaqView will feature more scRNA-seq and scATAC-seq atherosclerosis-related datasets to provide a critical resource for the field, and to promote data harmonization and biological interpretation.
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Affiliation(s)
- Wei Feng Ma
- Medical Scientist Training Program, University of Virginia, Charlottesville, VA, 22908, USA; Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Chani J Hodonsky
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Adam W Turner
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Doris Wong
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA; Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA , 22908, USA
| | - Yipei Song
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA; Department of Computer Engineering, University of Virginia, Charlottesville, VA, 22908, USA
| | - Jose Verdezoto Mosquera
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA; Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA , 22908, USA
| | - Alexandra V Ligay
- Master of Science in Biomedical Informatics (MScBMI) Program, University of Chicago, Chicago, IL, 60637, USA
| | - Lotte Slenders
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, 3584, CX, Utrecht, the Netherlands
| | - Christina Gancayco
- Research Computing, University of Virginia, Charlottesville, VA, 22908, USA
| | - Huize Pan
- Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, Irving Institute for Clinical and Translational Research, Columbia University, New York, NY, 10032, USA
| | - Nelson B Barrientos
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - David Mai
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Gabriel F Alencar
- Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA, 22908, USA
| | - Katherine Owsiany
- Medical Scientist Training Program, University of Virginia, Charlottesville, VA, 22908, USA; Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA, 22908, USA
| | - Gary K Owens
- Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA, 22908, USA; Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Muredach P Reilly
- Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, Irving Institute for Clinical and Translational Research, Columbia University, New York, NY, 10032, USA
| | - Mingyao Li
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Gerard Pasterkamp
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, 3584, CX, Utrecht, the Netherlands
| | - Michal Mokry
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, 3584, CX, Utrecht, the Netherlands; Department of Experimental Cardiology, University Medical Center Utrecht, 3584, CX, Utrecht, the Netherlands
| | - Sander W van der Laan
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, 3584, CX, Utrecht, the Netherlands
| | - Bohdan B Khomtchouk
- Department of Medicine, Section of Computational Biomedicine and Biomedical Data Science, Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL , 60637, USA.
| | - Clint L Miller
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA; Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA , 22908, USA; Department of Public Health Sciences, University of Virginia, Charlottesville, VA, 22908, USA.
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29
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Wang Y, Gao H, Wang F, Ye Z, Mokry M, Turner AW, Ye J, Koplev S, Luo L, Alsaigh T, Adkar SS, Elishaev M, Gao X, Maegdefessel L, Björkegren JLM, Pasterkamp G, Miller CL, Ross EG, Leeper NJ. Dynamic changes in chromatin accessibility are associated with the atherogenic transitioning of vascular smooth muscle cells. Cardiovasc Res 2021; 118:2792-2804. [PMID: 34849613 PMCID: PMC9586565 DOI: 10.1093/cvr/cvab347] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 11/18/2021] [Indexed: 11/13/2022] Open
Abstract
AIMS De-differentiation and activation of pro-inflammatory pathways are key transitions vascular smooth muscle cells (SMCs) make during atherogenesis. Here, we explored the upstream regulators of this 'atherogenic transition'. METHODS AND RESULTS Genome-wide sequencing studies, including ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) and RNA-seq, were performed on cells isolated from both murine SMC-lineage tracing models of atherosclerosis and human atherosclerotic lesions. At the bulk level, alterations in chromatin accessibility were associated with the atherogenic transitioning of lesional SMCs, especially in relation to genes that govern differentiation status and complement-dependent inflammation. Using computational biology, we observed that a transcription factor previously related to coronary artery disease, ATF3 (Activating transcription factor 3), was predicted to be an upstream regulator of genes altered during the transition. At the single-cell level, our results indicated that ATF3 is a key repressor of SMC transitioning towards the subset of cells that promote vascular inflammation by activating the complement cascade. The expression of ATF3 and complement component C3 were negatively correlated in SMCs from human atherosclerotic lesions, suggesting translational relevance. Phenome-wide association studies indicated that genetic variation that results in reduced expression of ATF3 is correlated with an increased risk for atherosclerosis, and the expression of ATF3 was significantly downregulated in humans with advanced vascular disease. CONCLUSION Our study indicates that the plasticity of atherosclerotic SMCs may in part be explained by dynamic changes in their chromatin architecture, which in turn may contribute to their maladaptive response to inflammation-induced stress. TRANSLATIONAL PERSPECTIVE The recent CANTOS and COLCOT trials have shown that targeting inflammatory pathways lowers the risk of major adverse cardiovascular events. However, more specific targets are needed to avoid immunosuppressive side effects. Our data identify an upstream regulator of pro-inflammatory SMCs, ATF3, which is involved in the initial atherogenic transitioning of lesional SMCs. Restoring ATF3 activity may prevent the de-differentiation of SMCs and offer a novel translational approach for the suppression of complement-dependent inflammation in atherosclerotic lesions.
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Affiliation(s)
- Ying Wang
- Department of Surgery, Division of Vascular Surgery, Stanford University School of Medicine, Stanford, California, United States of America.,Stanford Cardiovascular Institute, Stanford University, Stanford, California, United States of America
| | - Hua Gao
- Department of Surgery, Division of Vascular Surgery, Stanford University School of Medicine, Stanford, California, United States of America.,Stanford Cardiovascular Institute, Stanford University, Stanford, California, United States of America
| | - Fudi Wang
- Department of Surgery, Division of Vascular Surgery, Stanford University School of Medicine, Stanford, California, United States of America.,Stanford Cardiovascular Institute, Stanford University, Stanford, California, United States of America
| | - Zhongde Ye
- Department of Surgery, Division of Vascular Surgery, Stanford University School of Medicine, Stanford, California, United States of America.,Stanford Cardiovascular Institute, Stanford University, Stanford, California, United States of America
| | - Michal Mokry
- Department of Cardiology and Laboratory of Clinical Chemistry, University Medical Center Utrecht, the Netherlands
| | - Adam W Turner
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, United States of America
| | - Jianqin Ye
- Department of Surgery, Division of Vascular Surgery, Stanford University School of Medicine, Stanford, California, United States of America
| | - Simon Koplev
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Lingfeng Luo
- Department of Surgery, Division of Vascular Surgery, Stanford University School of Medicine, Stanford, California, United States of America.,Stanford Cardiovascular Institute, Stanford University, Stanford, California, United States of America
| | - Tom Alsaigh
- Department of Surgery, Division of Vascular Surgery, Stanford University School of Medicine, Stanford, California, United States of America.,Department of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Shaunak S Adkar
- Department of Surgery, Division of Vascular Surgery, Stanford University School of Medicine, Stanford, California, United States of America
| | - Maria Elishaev
- Department of Pathology and Laboratory Medicine, Centre for Heart Lung Innvoation, University of British Columbia, Vancouver, Canada
| | - Xiangyu Gao
- Department of Pathology and Laboratory Medicine, Centre for Heart Lung Innvoation, University of British Columbia, Vancouver, Canada
| | - Lars Maegdefessel
- Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technical University Munich, and the German Center for Cardiovascular Research (DZHK partner site), Munich, Germany.,Department of Internal Medicine, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
| | - Johan L M Björkegren
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States of America
| | - Gerard Pasterkamp
- Department of Cardiology and Laboratory of Clinical Chemistry, University Medical Center Utrecht, the Netherlands
| | - Clint L Miller
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, United States of America
| | - Elsie G Ross
- Department of Surgery, Division of Vascular Surgery, Stanford University School of Medicine, Stanford, California, United States of America.,Stanford Cardiovascular Institute, Stanford University, Stanford, California, United States of America
| | - Nicholas J Leeper
- Department of Surgery, Division of Vascular Surgery, Stanford University School of Medicine, Stanford, California, United States of America.,Stanford Cardiovascular Institute, Stanford University, Stanford, California, United States of America
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30
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Aguilar-Pineda JA, Vera-Lopez KJ, Shrivastava P, Chávez-Fumagalli MA, Nieto-Montesinos R, Alvarez-Fernandez KL, Goyzueta Mamani LD, Davila Del-Carpio G, Gomez-Valdez B, Miller CL, Malhotra R, Lindsay ME, Lino Cardenas CL. Vascular smooth muscle cell dysfunction contribute to neuroinflammation and Tau hyperphosphorylation in Alzheimer disease. iScience 2021; 24:102993. [PMID: 34505007 PMCID: PMC8417400 DOI: 10.1016/j.isci.2021.102993] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 06/17/2021] [Accepted: 08/13/2021] [Indexed: 11/21/2022] Open
Abstract
Despite the emerging evidence implying early vascular contributions to neurodegenerative syndromes, the role of vascular smooth muscle cells (VSMCs) in the pathogenesis of Alzheimer disease (AD) is still not well understood. Herein, we show that VSMCs in brains of patients with AD and animal models of the disease are deficient in multiple VSMC contractile markers which correlated with Tau accumulation in brain arterioles. Ex vivo and in vitro experiments demonstrated that VSMCs undergo dramatic phenotypic transitions under AD-like conditions, adopting pro-inflammatory phenotypes. Notably, these changes coincided with Tau hyperphosphorylation at residues Y18, T205, and S262. We also observed that VSMC dysfunction occurred in an age-dependent manner and that expression of Sm22α protein was inversely correlated with CD68 and Tau expression in brain arterioles of the 3xTg-AD and 5xFAD mice. Together, these findings further support the contribution of dysfunctional VSMCs in AD pathogenesis and nominate VSMCs as a potential therapeutic target in AD. Loss of VSMC contractile phenotypes correlates with Tau accumulation in brain arterioles VSMC dysfunction promotes the hyperphosphorylation of Tau protein at multiple residues VSMC dysfunction occurs in an age-dependent manner in brain arterioles of patients with AD Vascular smooth muscle cell is a promising therapeutic target in AD
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Affiliation(s)
- Jorge A Aguilar-Pineda
- Laboratory of Genomics and Neurovascular Diseases, Vicerrectorado de investigacion, Universidad Catolica de Santa Maria, Arequipa, Peru
| | - Karin J Vera-Lopez
- Laboratory of Genomics and Neurovascular Diseases, Vicerrectorado de investigacion, Universidad Catolica de Santa Maria, Arequipa, Peru
| | - Pallavi Shrivastava
- Laboratory of Genomics and Neurovascular Diseases, Vicerrectorado de investigacion, Universidad Catolica de Santa Maria, Arequipa, Peru
| | - Miguel A Chávez-Fumagalli
- Laboratory of Genomics and Neurovascular Diseases, Vicerrectorado de investigacion, Universidad Catolica de Santa Maria, Arequipa, Peru
| | - Rita Nieto-Montesinos
- Laboratory of Genomics and Neurovascular Diseases, Vicerrectorado de investigacion, Universidad Catolica de Santa Maria, Arequipa, Peru
| | - Karla L Alvarez-Fernandez
- Laboratory of Genomics and Neurovascular Diseases, Vicerrectorado de investigacion, Universidad Catolica de Santa Maria, Arequipa, Peru
| | - Luis D Goyzueta Mamani
- Laboratory of Genomics and Neurovascular Diseases, Vicerrectorado de investigacion, Universidad Catolica de Santa Maria, Arequipa, Peru
| | - Gonzalo Davila Del-Carpio
- Laboratory of Genomics and Neurovascular Diseases, Vicerrectorado de investigacion, Universidad Catolica de Santa Maria, Arequipa, Peru
| | - Badhin Gomez-Valdez
- Laboratory of Genomics and Neurovascular Diseases, Vicerrectorado de investigacion, Universidad Catolica de Santa Maria, Arequipa, Peru
| | - Clint L Miller
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA
| | - Rajeev Malhotra
- Cardiovascular Research Center, Cardiology Division, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Mark E Lindsay
- Cardiovascular Research Center, Cardiology Division, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Christian L Lino Cardenas
- Cardiovascular Research Center, Cardiology Division, Massachusetts General Hospital, Boston, MA 02114, USA.,Laboratory of Genomics and Neurovascular Diseases, Vicerrectorado de investigacion, Universidad Catolica de Santa Maria, Arequipa, Peru
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31
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Wong D, Turner A, Khan MD, Palmore M, Perry N, kuppusamy M, Ottolini M, Matic L, Hedin U, Ma L, Sonkusare SK, Civelek M, Kovacic JC, Bjorkegren J, Miller CL. Abstract MP39:
FHL5
, A Novel Cofactor Associated With Coronary Artery Disease, Regulates Smooth Muscle Cell Function Through A Transcriptional Network Linking Multiple Risk Loci. Arterioscler Thromb Vasc Biol 2021. [DOI: 10.1161/atvb.41.suppl_1.mp39] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Introduction:
Coronary artery disease (CAD) is the leading cause of death worldwide with an estimated heritability of ~50%. The most recent genome wide association study (GWAS) for CAD and myocardial infarction (MI) identified over 200 loci. One such novel CAD/MI locus,
UFL1-FHL5
(P = 1.1E-8), is associated with additional vascular pathologies, including hypertension, migraines, and coronary calcification. We previously showed through statistical fine-mapping that
FHL5
is the top candidate causal gene underlying each of these vascular trait associations and highly enriched in the contractile mural cell populations in the artery. These preliminary studies motivate our hypothesis that FHL5 functions as a transcriptional regulator of SMC contractility to affect vascular disease risk.
Methods and Results:
Given the reported role of FHL5 as a cofactor, we mapped 17,201 candidate FHL5 binding sites in coronary artery SMCs using the Cleavage Under Targets and Release Using Nuclease (CUT&RUN) method. Binding sites were enriched for AP-1 family motifs and strongly overlapped CREB binding sites and H3K27ac enhancer marks. FHL5 target genes were functionally enriched in well characterized CAD pathways, such as extracellular matrix organization (P=5.2E-15, OR=2.1) and TGF-beta signaling (P=8.0E-5, OR=2.0). Interestingly, FHL5 binding sites were also enriched for CAD (P=1.8E-7, OR=2.3) and blood pressure (BP) risk variants (P=0.04, OR=1.2), thereby linking FHL5 with the regulation of multiple downstream CAD/BP loci. Weighted gene co-expression network and key driver analyses of human coronary artery transcriptomic data further support this regulatory role. Lastly, we validated these findings by performing confocal based calcium imaging and collagen gel contraction assays. Consistent with our functional genomic analyses, overexpression of FHL5 elevated intracellular calcium levels 2.5X and increased SMC contractility by ~45%.
Conclusion:
Taken together, our results provide evidence that
FHL5
may impact CAD risk by regulating a network of disease-associated genes mediating SMC functions. These findings further contribute to our understanding of the heritable risk for multiple vascular diseases.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Ulf Hedin
- KAROLINSKA INSTITUTE, Stockholm, Sweden
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32
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Turner AW, Hu SE, Verdezoto Mosquera JE, Ma WF, Hodonsky CJ, Wong D, Auguste GE, sol-church K, Farber E, Kundu S, Kundaje AB, Lopez NG, Ma L, Ghosh S, Onengut-Gumuscu S, Ashley EA, Quertermous T, Finn A, Leeper NJ, Kovacic JC, Bjorkegren JL, Zang C, Miller CL. Abstract 113: Cell-specific Chromatin Landscape Of Human Coronary Artery Resolves Mechanisms Of Disease Risk. Arterioscler Thromb Vasc Biol 2021. [DOI: 10.1161/atvb.41.suppl_1.113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Coronary artery disease (CAD) is a complex inflammatory disease involving genetic influences across several cell types. Genome-wide association studies (GWAS) have identified over 170 loci associated with CAD, where the majority of risk variants reside in noncoding DNA sequences impacting
cis
-regulatory elements (CREs). Here, we applied single-cell ATAC-seq to profile 28,316 cells across coronary artery segments from 41 patients with varying stages of CAD, which revealed 14 distinct cellular clusters. We mapped over 320,000 accessible sites across all cells, identified cell type-specific elements, transcription factors, and prioritized functional CAD risk variants via quantitative trait locus and sequence-based predictive modeling. Using differential peak analyses we identified a number of candidate mechanisms for smooth muscle cell transition states (e.g. fibromyocytes). By integrating these profiles with GWAS meta-analysis summary data we resolved cell type-specific putative binding sites for the majority of CAD risk variants. In particular, we prioritized functional variants predicted to alter MEF2 binding in smooth muscle cells at the MRAS locus. We also identify variants predicted to alter macrophage-specific regulation of LIPA. We further employed DNA to gene linkage to nominate disease-associated key driver transcription factors such as PRDM16 and TBX2. Together, this single cell atlas provides a critical step towards interpreting
cis
-regulatory mechanisms in the vessel wall across the continuum of CAD risk.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Lijiang Ma
- Icahn Sch of Medicine at Mount Sinai, New York, NY
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33
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Hartiala JA, Han Y, Jia Q, Hilser JR, Huang P, Gukasyan J, Schwartzman WS, Cai Z, Biswas S, Trégouët DA, Smith NL, Seldin M, Pan C, Mehrabian M, Lusis AJ, Bazeley P, Sun YV, Liu C, Quyyumi AA, Scholz M, Thiery J, Delgado GE, Kleber ME, März W, Howe LJ, Asselbergs FW, van Vugt M, Vlachojannis GJ, Patel RS, Lyytikäinen LP, Kähönen M, Lehtimäki T, Nieminen TVM, Kuukasjärvi P, Laurikka JO, Chang X, Heng CK, Jiang R, Kraus WE, Hauser ER, Ferguson JF, Reilly MP, Ito K, Koyama S, Kamatani Y, Komuro I, Stolze LK, Romanoski CE, Khan MD, Turner AW, Miller CL, Aherrahrou R, Civelek M, Ma L, Björkegren JLM, Kumar SR, Tang WHW, Hazen SL, Allayee H. Genome-wide analysis identifies novel susceptibility loci for myocardial infarction. Eur Heart J 2021; 42:919-933. [PMID: 33532862 DOI: 10.1093/eurheartj/ehaa1040] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 09/18/2020] [Accepted: 12/07/2020] [Indexed: 12/27/2022] Open
Abstract
AIMS While most patients with myocardial infarction (MI) have underlying coronary atherosclerosis, not all patients with coronary artery disease (CAD) develop MI. We sought to address the hypothesis that some of the genetic factors which establish atherosclerosis may be distinct from those that predispose to vulnerable plaques and thrombus formation. METHODS AND RESULTS We carried out a genome-wide association study for MI in the UK Biobank (n∼472 000), followed by a meta-analysis with summary statistics from the CARDIoGRAMplusC4D Consortium (n∼167 000). Multiple independent replication analyses and functional approaches were used to prioritize loci and evaluate positional candidate genes. Eight novel regions were identified for MI at the genome wide significance level, of which effect sizes at six loci were more robust for MI than for CAD without the presence of MI. Confirmatory evidence for association of a locus on chromosome 1p21.3 harbouring choline-like transporter 3 (SLC44A3) with MI in the context of CAD, but not with coronary atherosclerosis itself, was obtained in Biobank Japan (n∼165 000) and 16 independent angiography-based cohorts (n∼27 000). Follow-up analyses did not reveal association of the SLC44A3 locus with CAD risk factors, biomarkers of coagulation, other thrombotic diseases, or plasma levels of a broad array of metabolites, including choline, trimethylamine N-oxide, and betaine. However, aortic expression of SLC44A3 was increased in carriers of the MI risk allele at chromosome 1p21.3, increased in ischaemic (vs. non-diseased) coronary arteries, up-regulated in human aortic endothelial cells treated with interleukin-1β (vs. vehicle), and associated with smooth muscle cell migration in vitro. CONCLUSIONS A large-scale analysis comprising ∼831 000 subjects revealed novel genetic determinants of MI and implicated SLC44A3 in the pathophysiology of vulnerable plaques.
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Affiliation(s)
- Jaana A Hartiala
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, 2250 Alcazar Street, CSC202, Los Angeles, CA 90033, USA
| | - Yi Han
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, 2250 Alcazar Street, CSC202, Los Angeles, CA 90033, USA.,Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Qiong Jia
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, 2250 Alcazar Street, CSC202, Los Angeles, CA 90033, USA.,Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - James R Hilser
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, 2250 Alcazar Street, CSC202, Los Angeles, CA 90033, USA.,Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Pin Huang
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, 2250 Alcazar Street, CSC202, Los Angeles, CA 90033, USA.,Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Janet Gukasyan
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, 2250 Alcazar Street, CSC202, Los Angeles, CA 90033, USA.,Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - William S Schwartzman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, 2250 Alcazar Street, CSC202, Los Angeles, CA 90033, USA.,Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Zhiheng Cai
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, 2250 Alcazar Street, CSC202, Los Angeles, CA 90033, USA.,Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Subarna Biswas
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, 2250 Alcazar Street, CSC202, Los Angeles, CA 90033, USA
| | - David-Alexandre Trégouët
- Institut National pour la Santé et la Recherche Médicale (INSERM) UMR_S 1219, Bordeaux Population Health Research Center, University of Bordeaux, 33076 Bordeaux, France
| | - Nicholas L Smith
- Department of Epidemiology, University of Washington, Seattle, WA 98101, USA.,Department of Veterans Affairs, Seattle Epidemiologic Research and Information Center, Office of Research and Development, Seattle, WA 98108, USA.,Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, WA 98101, USA
| | | | | | | | - Marcus Seldin
- Department of Biological Chemistry and Center for Epigenetics and Metabolism, UC Irvine School of Medicine, Irvine, CA 92697, USA
| | - Calvin Pan
- Department of Human Genetics, David Geffen School of Medicine of UCLA, Los Angeles, CA 90095, USA
| | - Margarete Mehrabian
- Department of Medicine, David Geffen School of Medicine of UCLA, Los Angeles, CA 90095, USA
| | - Aldons J Lusis
- Department of Human Genetics, David Geffen School of Medicine of UCLA, Los Angeles, CA 90095, USA.,Department of Medicine, David Geffen School of Medicine of UCLA, Los Angeles, CA 90095, USA.,Department of Microbiology, Immunology, & Molecular Genetics, David Geffen School of Medicine of UCLA, Los Angeles, CA 90095, USA
| | - Peter Bazeley
- Center for Clinical Genomics, Cleveland Clinic, Cleveland, OH 44195, USA.,Department of Cardiovascular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA.,Department of Cardiovascular & Metabolic Sciences, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Yan V Sun
- Department of Epidemiology, Emory University Rollins School of Public Health, 1518 Clifton Rd. NE, Atlanta, GA 30322, USA.,Department of Biomedical Informatics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Chang Liu
- Department of Epidemiology, Emory University Rollins School of Public Health, 1518 Clifton Rd. NE, Atlanta, GA 30322, USA.,Division of Cardiology, Department of Medicine, Emory Clinical Cardiovascular Research Institute, Emory University School of Medicine, 1462 Clifton Rd NE, Suite # 507, Atlanta, GA 30322, USA
| | - Arshed A Quyyumi
- Division of Cardiology, Department of Medicine, Emory Clinical Cardiovascular Research Institute, Emory University School of Medicine, 1462 Clifton Rd NE, Suite # 507, Atlanta, GA 30322, USA
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, 04107 Leipzig, Germany.,LIFE Research Center for Civilization Diseases, University of Leipzig, 04103 Leipzig, Germany
| | - Joachim Thiery
- LIFE Research Center for Civilization Diseases, University of Leipzig, 04103 Leipzig, Germany.,Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital, 04103 Leipzig, Germany
| | - Graciela E Delgado
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
| | - Marcus E Kleber
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
| | - Winfried März
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany.,SYNLAB Academy, SYNLAB Holding Deutschland GmbH, 86156 Augsburg, Germany.,Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, 8036 Graz, Austria
| | - Laurence J Howe
- Institute of Cardiovascular Science, Faculty of Population Health Sciences, University College London, London WC1E 6HX, UK
| | - Folkert W Asselbergs
- Institute of Cardiovascular Science, Faculty of Population Health Sciences, University College London, London WC1E 6HX, UK.,Health Data Research UK and Institute of Health Informatics, University College London, London NW1 2DA, UK.,Division Heart & Lungs, Department of Cardiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, the Netherlands
| | - Marion van Vugt
- Division Heart & Lungs, Department of Cardiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, the Netherlands
| | - Georgios J Vlachojannis
- Division Heart & Lungs, Department of Cardiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, the Netherlands
| | - Riyaz S Patel
- Institute of Cardiovascular Science, Faculty of Population Health Sciences, University College London, London WC1E 6HX, UK.,Bart's Heart Centre, St Bartholomew's Hospital, London EC1A 2DA, UK
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere 33520, Finland.,Department of Clinical Chemistry, Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere 33014, Finland.,Department of Cardiology, Heart Center, Tampere University Hospital, Tampere 33521, Finland
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, Tampere 33521, Finland.,Department of Clinical Physiology, Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere 33014, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere 33520, Finland.,Department of Clinical Chemistry, Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere 33014, Finland
| | - Tuomo V M Nieminen
- Department of Internal Medicine, Päijät-Häme Central Hospital, Lahti 15850, Finland
| | - Pekka Kuukasjärvi
- Department of Cardio-Thoracic Surgery, Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere 33014, Finland
| | - Jari O Laurikka
- Department of Cardio-Thoracic Surgery, Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere 33014, Finland.,Department of Cardio-Thoracic Surgery, Heart Center, Tampere University Hospital, Tampere 33521, Finland
| | - Xuling Chang
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore.,Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore 119074, Singapore
| | - Chew-Kiat Heng
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore.,Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore 119074, Singapore
| | - Rong Jiang
- Department of Psychiatry & Behavioral Sciences, Duke University School of Medicine Durham, NC 27710, USA
| | - William E Kraus
- Duke Molecular Physiology Institute, Duke University School of Medicine Durham, NC 27710, USA.,Department of Medicine, Duke University School of Medicine Durham, NC 27710, USA
| | - Elizabeth R Hauser
- Duke Molecular Physiology Institute, Duke University School of Medicine Durham, NC 27710, USA.,Department of Biostatistics & Bioinformatics, Duke University School of Medicine Durham, NC 27710, USA
| | - Jane F Ferguson
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Muredach P Reilly
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA.,Irving Institute for Clinical and Translational Research, Columbia University, New York, NY 10032, USA
| | - Kaoru Ito
- Laboratory for Cardiovascular Genomics and Informatics, RIKEN Center for Integrative Medical Sciences, Kanagawa 230-0045, Japan
| | - Satoshi Koyama
- Laboratory for Cardiovascular Genomics and Informatics, RIKEN Center for Integrative Medical Sciences, Kanagawa 230-0045, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Kanagawa 230-0045, Japan.,Human Disease Genomics, Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan.,Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo 108-0071, Japan
| | - Issei Komuro
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | | | - Lindsey K Stolze
- Department of Cellular and Molecular Medicine, University of Arizona College of Medicine, Tucson, AZ 85721, USA
| | - Casey E Romanoski
- Department of Cellular and Molecular Medicine, University of Arizona College of Medicine, Tucson, AZ 85721, USA
| | - Mohammad Daud Khan
- Center for Public Health Genomics, University of Virginia, Charlottesville University of Virginia, Charlottesville, VA 22904, USA.,Department of Biomedical Engineering, University of Virginia, Charlottesville University of Virginia, Charlottesville, VA 22904, USA.,Department of Biochemistry & Molecular Genetics, University of Virginia, Charlottesville University of Virginia, Charlottesville, VA 22904, USA.,Department of Public Health Sciences, University of Virginia, Charlottesville University of Virginia, Charlottesville, VA 22904, USA
| | - Adam W Turner
- Center for Public Health Genomics, University of Virginia, Charlottesville University of Virginia, Charlottesville, VA 22904, USA.,Department of Biomedical Engineering, University of Virginia, Charlottesville University of Virginia, Charlottesville, VA 22904, USA.,Department of Biochemistry & Molecular Genetics, University of Virginia, Charlottesville University of Virginia, Charlottesville, VA 22904, USA.,Department of Public Health Sciences, University of Virginia, Charlottesville University of Virginia, Charlottesville, VA 22904, USA
| | - Clint L Miller
- Center for Public Health Genomics, University of Virginia, Charlottesville University of Virginia, Charlottesville, VA 22904, USA.,Department of Biomedical Engineering, University of Virginia, Charlottesville University of Virginia, Charlottesville, VA 22904, USA.,Department of Biochemistry & Molecular Genetics, University of Virginia, Charlottesville University of Virginia, Charlottesville, VA 22904, USA.,Department of Public Health Sciences, University of Virginia, Charlottesville University of Virginia, Charlottesville, VA 22904, USA
| | - Redouane Aherrahrou
- Center for Public Health Genomics, University of Virginia, Charlottesville University of Virginia, Charlottesville, VA 22904, USA.,Department of Biomedical Engineering, University of Virginia, Charlottesville University of Virginia, Charlottesville, VA 22904, USA
| | - Mete Civelek
- Center for Public Health Genomics, University of Virginia, Charlottesville University of Virginia, Charlottesville, VA 22904, USA.,Department of Biomedical Engineering, University of Virginia, Charlottesville University of Virginia, Charlottesville, VA 22904, USA
| | - Lijiang Ma
- Department of Genetics & Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Johan L M Björkegren
- Department of Genetics & Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset, 141 57 Huddinge, Sweden
| | - S Ram Kumar
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - W H Wilson Tang
- Center for Clinical Genomics, Cleveland Clinic, Cleveland, OH 44195, USA.,Department of Cardiovascular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA.,Department of Cardiovascular & Metabolic Sciences, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Stanley L Hazen
- Department of Cardiovascular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA.,Department of Cardiovascular & Metabolic Sciences, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Hooman Allayee
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, 2250 Alcazar Street, CSC202, Los Angeles, CA 90033, USA.,Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
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Cornelissen A, Fuller DT, Fernandez R, Zhao X, Kutys R, Binns-Roemer E, Delsante M, Sakamoto A, Paek KH, Sato Y, Kawakami R, Mori M, Kawai K, Yoshida T, Latt KZ, Miller CL, de Vries PS, Kolodgie FD, Virmani R, Shin MK, Hoek M, Heymann J, Kopp JB, Rosenberg AZ, Davis HR, Guo L, Finn AV. APOL1 Genetic Variants Are Associated With Increased Risk of Coronary Atherosclerotic Plaque Rupture in the Black Population. Arterioscler Thromb Vasc Biol 2021; 41:2201-2214. [PMID: 34039022 DOI: 10.1161/atvbaha.120.315788] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Anne Cornelissen
- CVPath Institute, Gaithersburg, MD (A.C., D.T.F., R.F., X.Z., R. Kutys, A.S, K.H.P., Y.S., R. Kawakami, M.M., K.K., F.D.K., R.V., H.R.D., L.G., A.V.F.).,Department of Cardiology, University Hospital RWTH Aachen, Germany (A.C.)
| | - Daniela T Fuller
- CVPath Institute, Gaithersburg, MD (A.C., D.T.F., R.F., X.Z., R. Kutys, A.S, K.H.P., Y.S., R. Kawakami, M.M., K.K., F.D.K., R.V., H.R.D., L.G., A.V.F.)
| | - Raquel Fernandez
- CVPath Institute, Gaithersburg, MD (A.C., D.T.F., R.F., X.Z., R. Kutys, A.S, K.H.P., Y.S., R. Kawakami, M.M., K.K., F.D.K., R.V., H.R.D., L.G., A.V.F.)
| | - Xiaoqing Zhao
- CVPath Institute, Gaithersburg, MD (A.C., D.T.F., R.F., X.Z., R. Kutys, A.S, K.H.P., Y.S., R. Kawakami, M.M., K.K., F.D.K., R.V., H.R.D., L.G., A.V.F.)
| | - Robert Kutys
- CVPath Institute, Gaithersburg, MD (A.C., D.T.F., R.F., X.Z., R. Kutys, A.S, K.H.P., Y.S., R. Kawakami, M.M., K.K., F.D.K., R.V., H.R.D., L.G., A.V.F.)
| | - Elizabeth Binns-Roemer
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD (E.B.-R.)
| | - Marco Delsante
- Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD (M.D., T.Y., K.Z.L., J.H., J.B.K., A.Z.R.).,Dipartimento di Medicina e Chirurgia Università di Parma, UO Nefrologia, Azienda Ospedaliera-Universitaria, Italy (M.D.)
| | - Atsushi Sakamoto
- CVPath Institute, Gaithersburg, MD (A.C., D.T.F., R.F., X.Z., R. Kutys, A.S, K.H.P., Y.S., R. Kawakami, M.M., K.K., F.D.K., R.V., H.R.D., L.G., A.V.F.)
| | - Ka Hyun Paek
- CVPath Institute, Gaithersburg, MD (A.C., D.T.F., R.F., X.Z., R. Kutys, A.S, K.H.P., Y.S., R. Kawakami, M.M., K.K., F.D.K., R.V., H.R.D., L.G., A.V.F.)
| | | | - Rika Kawakami
- CVPath Institute, Gaithersburg, MD (A.C., D.T.F., R.F., X.Z., R. Kutys, A.S, K.H.P., Y.S., R. Kawakami, M.M., K.K., F.D.K., R.V., H.R.D., L.G., A.V.F.)
| | - Masayuki Mori
- CVPath Institute, Gaithersburg, MD (A.C., D.T.F., R.F., X.Z., R. Kutys, A.S, K.H.P., Y.S., R. Kawakami, M.M., K.K., F.D.K., R.V., H.R.D., L.G., A.V.F.)
| | - Kenji Kawai
- CVPath Institute, Gaithersburg, MD (A.C., D.T.F., R.F., X.Z., R. Kutys, A.S, K.H.P., Y.S., R. Kawakami, M.M., K.K., F.D.K., R.V., H.R.D., L.G., A.V.F.)
| | - Teruhiko Yoshida
- Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD (M.D., T.Y., K.Z.L., J.H., J.B.K., A.Z.R.)
| | - Khun Zaw Latt
- Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD (M.D., T.Y., K.Z.L., J.H., J.B.K., A.Z.R.)
| | - Clint L Miller
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville (C.L.M.)
| | - Paul S de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston (P.S.d.V.)
| | - Frank D Kolodgie
- CVPath Institute, Gaithersburg, MD (A.C., D.T.F., R.F., X.Z., R. Kutys, A.S, K.H.P., Y.S., R. Kawakami, M.M., K.K., F.D.K., R.V., H.R.D., L.G., A.V.F.)
| | | | | | | | - Jurgen Heymann
- Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD (M.D., T.Y., K.Z.L., J.H., J.B.K., A.Z.R.)
| | - Jeffrey B Kopp
- Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD (M.D., T.Y., K.Z.L., J.H., J.B.K., A.Z.R.)
| | - Avi Z Rosenberg
- Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD (M.D., T.Y., K.Z.L., J.H., J.B.K., A.Z.R.).,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD (A.Z.R.)
| | - Harry R Davis
- CVPath Institute, Gaithersburg, MD (A.C., D.T.F., R.F., X.Z., R. Kutys, A.S, K.H.P., Y.S., R. Kawakami, M.M., K.K., F.D.K., R.V., H.R.D., L.G., A.V.F.)
| | - Liang Guo
- CVPath Institute, Gaithersburg, MD (A.C., D.T.F., R.F., X.Z., R. Kutys, A.S, K.H.P., Y.S., R. Kawakami, M.M., K.K., F.D.K., R.V., H.R.D., L.G., A.V.F.)
| | - Aloke V Finn
- CVPath Institute, Gaithersburg, MD (A.C., D.T.F., R.F., X.Z., R. Kutys, A.S, K.H.P., Y.S., R. Kawakami, M.M., K.K., F.D.K., R.V., H.R.D., L.G., A.V.F.).,School of Medicine, University of Maryland School of Medicine, Baltimore (A.V.F.)
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Miller CL, Zhang H. Clarifying the Distinct Roles of Smooth Muscle Cell-Derived Versus Macrophage Foam Cells and the Implications in Atherosclerosis. Arterioscler Thromb Vasc Biol 2021; 41:2035-2037. [PMID: 33853350 DOI: 10.1161/atvbaha.121.316287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Clint L Miller
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville (C.L.M.)
| | - Hanrui Zhang
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York (H.Z.)
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36
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Gillespie TC, Roberts SA, Brunelle CL, Bucci LK, Bernstein MC, Daniell KM, Naoum GN, Miller CL, Taghian AG. Comparison of perometry-based volumetric arm measurements and bioimpedance spectroscopy for early identification of lymphedema in a prospectively-screened cohort of breast cancer patients. Lymphology 2021; 54:1-11. [PMID: 34506083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Breast cancer-related lymphedema (BCRL) affects more than one in five women treated for breast cancer, and women remain at lifelong risk. Screening for BCRL is recommended by several national and international organizations for women at risk of BCRL, and multiple methods of objective screening measurement exist. The goal of this study was to compare the use of perometry and bioimpedance spectroscopy (BIS) for early identification of BCRL in a cohort of 138 prospectivelyscreened patients. At each screening visit, a patient's relative volume change (RVC) from perometer measurements and change in L-Dex from baseline (ΔL-Dex) using BIS was calculated. There was a negligible correlation between RVC and ΔL-Dex (r=0.195). Multiple thresholds of BCRL were examined: RVC ≥5% and ≥10% as well as and ΔL-Dex ≥6.5 and ≥10. While some patients developed an elevated RVC and ΔL-Dex, many demonstrated elevations in only one threshold category. Moreover, the majority of patients with RVC ≥5%, ΔL-Dex ≥6.5, or ΔL-Dex ≥10 regressed to non-elevated measurements without intervention. These findings suggest a role for combining multiple screening methods for early identification of BCRL; furthermore, BCRL diagnosis must incorporate patient symptoms and clinical evaluation with objective measurements obtained from techniques such as perometry and bioimpedance spectroscopy.
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Affiliation(s)
- T C Gillespie
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - S A Roberts
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - C L Brunelle
- Department of Physical and Occupational Therapy, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - L K Bucci
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - M C Bernstein
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - K M Daniell
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - G N Naoum
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - C L Miller
- Department of General Surgery, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - A G Taghian
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
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37
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Aherrahrou R, Guo L, Nagraj VP, Aguhob A, Hinkle J, Chen L, Yuhl Soh J, Lue D, Alencar GF, Boltjes A, van der Laan SW, Farber E, Fuller D, Anane-Wae R, Akingbesote N, Manichaikul AW, Ma L, Kaikkonen MU, Björkegren JLM, Önengüt-Gümüşcü S, Pasterkamp G, Miller CL, Owens GK, Finn A, Navab M, Fogelman AM, Berliner JA, Civelek M. Genetic Regulation of Atherosclerosis-Relevant Phenotypes in Human Vascular Smooth Muscle Cells. Circ Res 2020; 127:1552-1565. [PMID: 33040646 DOI: 10.1161/circresaha.120.317415] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
RATIONALE Coronary artery disease (CAD) is a major cause of morbidity and mortality worldwide. Recent genome-wide association studies revealed 163 loci associated with CAD. However, the precise molecular mechanisms by which the majority of these loci increase CAD risk are not known. Vascular smooth muscle cells (VSMCs) are critical in the development of CAD. They can play either beneficial or detrimental roles in lesion pathogenesis, depending on the nature of their phenotypic changes. OBJECTIVE To identify genetic variants associated with atherosclerosis-relevant phenotypes in VSMCs. METHODS AND RESULTS We quantified 12 atherosclerosis-relevant phenotypes related to calcification, proliferation, and migration in VSMCs isolated from 151 multiethnic heart transplant donors. After genotyping and imputation, we performed association mapping using 6.3 million genetic variants. We demonstrated significant variations in calcification, proliferation, and migration. These phenotypes were not correlated with each other. We performed genome-wide association studies for 12 atherosclerosis-relevant phenotypes and identified 4 genome-wide significant loci associated with at least one VSMC phenotype. We overlapped the previously identified CAD loci with our data set and found nominally significant associations at 79 loci. One of them was the chromosome 1q41 locus, which harbors MIA3. The G allele of the lead risk single nucleotide polymorphism (SNP) rs67180937 was associated with lower VSMC MIA3 expression and lower proliferation. Lentivirus-mediated silencing of MIA3 (melanoma inhibitory activity protein 3) in VSMCs resulted in lower proliferation, consistent with human genetics findings. Furthermore, we observed a significant reduction of MIA3 protein in VSMCs in thin fibrous caps of late-stage atherosclerotic plaques compared to early fibroatheroma with thick and protective fibrous caps in mice and humans. CONCLUSIONS Our data demonstrate that genetic variants have significant influences on VSMC function relevant to the development of atherosclerosis. Furthermore, high MIA3 expression may promote atheroprotective VSMC phenotypic transitions, including increased proliferation, which is essential in the formation or maintenance of a protective fibrous cap.
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MESH Headings
- Animals
- Aryl Hydrocarbon Receptor Nuclear Translocator/genetics
- Aryl Hydrocarbon Receptor Nuclear Translocator/metabolism
- Atherosclerosis/genetics
- Atherosclerosis/metabolism
- Atherosclerosis/pathology
- Cell Movement
- Cell Proliferation
- Cells, Cultured
- Disease Models, Animal
- Female
- Fibrosis
- Genetic Predisposition to Disease
- Genetic Variation
- Genome-Wide Association Study
- Humans
- Male
- Mice, Knockout, ApoE
- Muscle, Smooth, Vascular/metabolism
- Muscle, Smooth, Vascular/pathology
- Myocytes, Smooth Muscle/metabolism
- Myocytes, Smooth Muscle/pathology
- Phenotype
- Plaque, Atherosclerotic
- Polymorphism, Single Nucleotide
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Affiliation(s)
- Redouane Aherrahrou
- Center for Public Health Genomics (R.A., A.A., J.H., L.C., J.Y.S., D.L., E.F., R.A.-W., N.A., A.W.M., S.O.-G., C.L.M., M.C.), University of Virginia, Charlottesville
| | - Liang Guo
- CVPath Institute, Inc, Gaithersburg, MD (L.G., D.F., A.F.)
| | - V Peter Nagraj
- School of Medicine Research Computing (V.P.N.), University of Virginia, Charlottesville
| | - Aaron Aguhob
- Center for Public Health Genomics (R.A., A.A., J.H., L.C., J.Y.S., D.L., E.F., R.A.-W., N.A., A.W.M., S.O.-G., C.L.M., M.C.), University of Virginia, Charlottesville
- Biomedical Engineering (A.A., L.C., D.L., R.A.-W., M.C.), University of Virginia, Charlottesville
| | - Jameson Hinkle
- Center for Public Health Genomics (R.A., A.A., J.H., L.C., J.Y.S., D.L., E.F., R.A.-W., N.A., A.W.M., S.O.-G., C.L.M., M.C.), University of Virginia, Charlottesville
| | - Lisa Chen
- Center for Public Health Genomics (R.A., A.A., J.H., L.C., J.Y.S., D.L., E.F., R.A.-W., N.A., A.W.M., S.O.-G., C.L.M., M.C.), University of Virginia, Charlottesville
- Biomedical Engineering (A.A., L.C., D.L., R.A.-W., M.C.), University of Virginia, Charlottesville
| | - Joon Yuhl Soh
- Center for Public Health Genomics (R.A., A.A., J.H., L.C., J.Y.S., D.L., E.F., R.A.-W., N.A., A.W.M., S.O.-G., C.L.M., M.C.), University of Virginia, Charlottesville
| | - Dillon Lue
- Center for Public Health Genomics (R.A., A.A., J.H., L.C., J.Y.S., D.L., E.F., R.A.-W., N.A., A.W.M., S.O.-G., C.L.M., M.C.), University of Virginia, Charlottesville
- Biomedical Engineering (A.A., L.C., D.L., R.A.-W., M.C.), University of Virginia, Charlottesville
| | - Gabriel F Alencar
- Molecular Physiology, Biological Physics, Medicine, Division of Cardiology, Robert M. Berne Cardiovascular Research Center (G.F.A., G.K.O.), University of Virginia, Charlottesville
| | - Arjan Boltjes
- Laboratory of Clinical Chemistry and Hematology, University Medical Center Utrecht, University of Utrecht (A.B., S.W.v.d.L., G.P.)
| | - Sander W van der Laan
- Laboratory of Clinical Chemistry and Hematology, University Medical Center Utrecht, University of Utrecht (A.B., S.W.v.d.L., G.P.)
| | - Emily Farber
- Center for Public Health Genomics (R.A., A.A., J.H., L.C., J.Y.S., D.L., E.F., R.A.-W., N.A., A.W.M., S.O.-G., C.L.M., M.C.), University of Virginia, Charlottesville
| | - Daniela Fuller
- CVPath Institute, Inc, Gaithersburg, MD (L.G., D.F., A.F.)
| | - Rita Anane-Wae
- Center for Public Health Genomics (R.A., A.A., J.H., L.C., J.Y.S., D.L., E.F., R.A.-W., N.A., A.W.M., S.O.-G., C.L.M., M.C.), University of Virginia, Charlottesville
- Biomedical Engineering (A.A., L.C., D.L., R.A.-W., M.C.), University of Virginia, Charlottesville
| | - Ngozi Akingbesote
- Center for Public Health Genomics (R.A., A.A., J.H., L.C., J.Y.S., D.L., E.F., R.A.-W., N.A., A.W.M., S.O.-G., C.L.M., M.C.), University of Virginia, Charlottesville
| | - Ani W Manichaikul
- Center for Public Health Genomics (R.A., A.A., J.H., L.C., J.Y.S., D.L., E.F., R.A.-W., N.A., A.W.M., S.O.-G., C.L.M., M.C.), University of Virginia, Charlottesville
| | - Lijiang Ma
- Genetics and Genomic Sciences (L.M., J.L.M.B.), Icahn School of Medicine at Mount Sinai, NY
- Icahn Institute of Genomics and Multiscale Biology (L.M., J.L.M.B.), Icahn School of Medicine at Mount Sinai, NY
| | - Minna U Kaikkonen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland (M.U.K.)
| | - Johan L M Björkegren
- Genetics and Genomic Sciences (L.M., J.L.M.B.), Icahn School of Medicine at Mount Sinai, NY
- Icahn Institute of Genomics and Multiscale Biology (L.M., J.L.M.B.), Icahn School of Medicine at Mount Sinai, NY
- Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet (J.L.M.B.)
| | - Suna Önengüt-Gümüşcü
- Center for Public Health Genomics (R.A., A.A., J.H., L.C., J.Y.S., D.L., E.F., R.A.-W., N.A., A.W.M., S.O.-G., C.L.M., M.C.), University of Virginia, Charlottesville
| | - Gerard Pasterkamp
- Laboratory of Clinical Chemistry and Hematology, University Medical Center Utrecht, University of Utrecht (A.B., S.W.v.d.L., G.P.)
| | - Clint L Miller
- Center for Public Health Genomics (R.A., A.A., J.H., L.C., J.Y.S., D.L., E.F., R.A.-W., N.A., A.W.M., S.O.-G., C.L.M., M.C.), University of Virginia, Charlottesville
| | - Gary K Owens
- Molecular Physiology, Biological Physics, Medicine, Division of Cardiology, Robert M. Berne Cardiovascular Research Center (G.F.A., G.K.O.), University of Virginia, Charlottesville
| | - Aloke Finn
- CVPath Institute, Inc, Gaithersburg, MD (L.G., D.F., A.F.)
| | - Mohamad Navab
- Medicine, David Geffen School of Medicine, University of California, Los Angeles (M.N., A.M.F., J.A.B.)
| | - Alan M Fogelman
- Medicine, David Geffen School of Medicine, University of California, Los Angeles (M.N., A.M.F., J.A.B.)
| | - Judith A Berliner
- Medicine, David Geffen School of Medicine, University of California, Los Angeles (M.N., A.M.F., J.A.B.)
| | - Mete Civelek
- Center for Public Health Genomics (R.A., A.A., J.H., L.C., J.Y.S., D.L., E.F., R.A.-W., N.A., A.W.M., S.O.-G., C.L.M., M.C.), University of Virginia, Charlottesville
- Biomedical Engineering (A.A., L.C., D.L., R.A.-W., M.C.), University of Virginia, Charlottesville
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Wang Y, Nanda V, Direnzo D, Ye J, Xiao S, Kojima Y, Howe KL, Jarr KU, Flores AM, Tsantilas P, Tsao N, Rao A, Newman AAC, Eberhard AV, Priest JR, Ruusalepp A, Pasterkamp G, Maegdefessel L, Miller CL, Lind L, Koplev S, Björkegren JLM, Owens GK, Ingelsson E, Weissman IL, Leeper NJ. Clonally expanding smooth muscle cells promote atherosclerosis by escaping efferocytosis and activating the complement cascade. Proc Natl Acad Sci U S A 2020; 117:15818-15826. [PMID: 32541024 PMCID: PMC7354942 DOI: 10.1073/pnas.2006348117] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Atherosclerosis is the process underlying heart attack and stroke. Despite decades of research, its pathogenesis remains unclear. Dogma suggests that atherosclerotic plaques expand primarily via the accumulation of cholesterol and inflammatory cells. However, recent evidence suggests that a substantial portion of the plaque may arise from a subset of "dedifferentiated" vascular smooth muscle cells (SMCs) which proliferate in a clonal fashion. Herein we use multicolor lineage-tracing models to confirm that the mature SMC can give rise to a hyperproliferative cell which appears to promote inflammation via elaboration of complement-dependent anaphylatoxins. Despite being extensively opsonized with prophagocytic complement fragments, we find that this cell also escapes immune surveillance by neighboring macrophages, thereby exacerbating its relative survival advantage. Mechanistic studies indicate this phenomenon results from a generalized opsonin-sensing defect acquired by macrophages during polarization. This defect coincides with the noncanonical up-regulation of so-called don't eat me molecules on inflamed phagocytes, which reduces their capacity for programmed cell removal (PrCR). Knockdown or knockout of the key antiphagocytic molecule CD47 restores the ability of macrophages to sense and clear opsonized targets in vitro, allowing for potent and targeted suppression of clonal SMC expansion in the plaque in vivo. Because integrated clinical and genomic analyses indicate that similar pathways are active in humans with cardiovascular disease, these studies suggest that the clonally expanding SMC may represent a translational target for treating atherosclerosis.
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Affiliation(s)
- Ying Wang
- Division of Vascular Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA 94305
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305
| | - Vivek Nanda
- Division of Vascular Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA 94305
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305
- Department of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Daniel Direnzo
- Division of Vascular Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA 94305
| | - Jianqin Ye
- Division of Vascular Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA 94305
| | - Sophia Xiao
- Division of Vascular Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA 94305
| | - Yoko Kojima
- Division of Vascular Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA 94305
| | - Kathryn L Howe
- Division of Vascular Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA 94305
| | - Kai-Uwe Jarr
- Division of Vascular Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA 94305
| | - Alyssa M Flores
- Division of Vascular Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA 94305
| | - Pavlos Tsantilas
- Division of Vascular Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA 94305
| | - Noah Tsao
- Division of Vascular Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA 94305
| | - Abhiram Rao
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305
- Department of Bioengineering, Stanford University, Stanford, CA 94305
| | - Alexandra A C Newman
- Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA 22904
| | - Anne V Eberhard
- Division of Vascular Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA 94305
| | - James R Priest
- Division of Pediatric Cardiology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305
| | - Arno Ruusalepp
- Department of Cardiac Surgery, Tartu University Hospital, Tartu, Estonia 50406
| | - Gerard Pasterkamp
- Department of Cardiology, University Medical Center Utrecht, 3584CX Utrecht, the Netherlands
- Laboratory of Clinical Chemistry, University Medical Center Utrecht, 3584CX Utrecht, the Netherlands
| | - Lars Maegdefessel
- Department for Vascular and Endovascular Surgery, Klinikum Rechts der Isar, Technical University Munich, 80333 Munich, Germany
- German Center for Cardiovascular Research (DZHK partner site), 10785 Munich, Germany
| | - Clint L Miller
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22904
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22904
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22904
| | - Lars Lind
- Department of Medical Sciences, Uppsala University, SE-751 05 Uppsala, Sweden
| | - Simon Koplev
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574
| | - Johan L M Björkegren
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574
| | - Gary K Owens
- Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA 22904
| | - Erik Ingelsson
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305
- Department of Medical Sciences, Uppsala University, SE-751 05 Uppsala, Sweden
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - Irving L Weissman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - Nicholas J Leeper
- Division of Vascular Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA 94305;
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305
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Abstract
Coronary artery disease is a complex cardiovascular disease involving an interplay of genetic and environmental influences over a lifetime. Although considerable progress has been made in understanding lifestyle risk factors, genetic factors identified from genome-wide association studies may capture additional hidden risk undetected by traditional clinical tests. These genetic discoveries have highlighted many candidate genes and pathways dysregulated in the vessel wall, including those involving smooth muscle cell phenotypic modulation and injury responses. Here, we summarize experimental evidence for a few genome-wide significant loci supporting their roles in smooth muscle cell biology and disease. We also discuss molecular quantitative trait locus mapping as a powerful discovery and fine-mapping approach applied to smooth muscle cell and coronary artery disease-relevant tissues. We emphasize the critical need for alternative genetic strategies, including cis/trans-regulatory network analysis, genome editing, and perturbations, as well as single-cell sequencing in smooth muscle cell tissues and model organisms, under both normal and disease states. By integrating multiple experimental and analytical modalities, these multidimensional datasets should improve the interpretation of coronary artery disease genome-wide association studies and molecular quantitative trait locus signals and inform candidate targets for therapeutic intervention or risk prediction.
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Affiliation(s)
- Doris Wong
- From the Center for Public Health Genomics (D.W., A.W.T., C.L.M.), University of Virginia, Charlottesville.,Department of Biochemistry and Molecular Genetics (D.W., C.L.M.), University of Virginia, Charlottesville
| | - Adam W Turner
- From the Center for Public Health Genomics (D.W., A.W.T., C.L.M.), University of Virginia, Charlottesville
| | - Clint L Miller
- From the Center for Public Health Genomics (D.W., A.W.T., C.L.M.), University of Virginia, Charlottesville.,Department of Biochemistry and Molecular Genetics (D.W., C.L.M.), University of Virginia, Charlottesville.,Department of Biomedical Engineering (C.L.M.), University of Virginia, Charlottesville.,Department of Public Health Sciences (C.L.M.), University of Virginia, Charlottesville
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40
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Rykaczewska U, Suur BE, Röhl S, Razuvaev A, Lengquist M, Sabater-Lleal M, van der Laan SW, Miller CL, Wirka RC, Kronqvist M, Gonzalez Diez M, Vesterlund M, Gillgren P, Odeberg J, Lindeman JH, Veglia F, Humphries SE, de Faire U, Baldassarre D, Tremoli E, Lehtiö J, Hansson GK, Paulsson-Berne G, Pasterkamp G, Quertermous T, Hamsten A, Eriksson P, Hedin U, Matic L. PCSK6 Is a Key Protease in the Control of Smooth Muscle Cell Function in Vascular Remodeling. Circ Res 2020; 126:571-585. [PMID: 31893970 DOI: 10.1161/circresaha.119.316063] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
RATIONALE PCSKs (Proprotein convertase subtilisins/kexins) are a protease family with unknown functions in vasculature. Previously, we demonstrated PCSK6 upregulation in human atherosclerotic plaques associated with smooth muscle cells (SMCs), inflammation, extracellular matrix remodeling, and mitogens. OBJECTIVE Here, we applied a systems biology approach to gain deeper insights into the PCSK6 role in normal and diseased vessel wall. METHODS AND RESULTS Genetic analyses revealed association of intronic PCSK6 variant rs1531817 with maximum internal carotid intima-media thickness progression in high-cardiovascular risk subjects. This variant was linked with PCSK6 mRNA expression in healthy aortas and plaques but also with overall plaque SMA+ cell content and pericyte fraction. Increased PCSK6 expression was found in several independent human cohorts comparing atherosclerotic lesions versus healthy arteries, using transcriptomic and proteomic datasets. By immunohistochemistry, PCSK6 was localized to fibrous cap SMA+ cells and neovessels in plaques. In human, rat, and mouse intimal hyperplasia, PCSK6 was expressed by proliferating SMA+ cells and upregulated after 5 days in rat carotid balloon injury model, with positive correlation to PDGFB (platelet-derived growth factor subunit B) and MMP (matrix metalloprotease) 2/MMP14. Here, PCSK6 was shown to colocalize and cointeract with MMP2/MMP14 by in situ proximity ligation assay. Microarrays of carotid arteries from Pcsk6-/- versus control mice revealed suppression of contractile SMC markers, extracellular matrix remodeling enzymes, and cytokines/receptors. Pcsk6-/- mice showed reduced intimal hyperplasia response upon carotid ligation in vivo, accompanied by decreased MMP14 activation and impaired SMC outgrowth from aortic rings ex vivo. PCSK6 silencing in human SMCs in vitro leads to downregulation of contractile markers and increase in MMP2 expression. Conversely, PCSK6 overexpression increased PDGFBB (platelet-derived growth factor BB)-induced cell proliferation and particularly migration. CONCLUSIONS PCSK6 is a novel protease that induces SMC migration in response to PDGFB, mechanistically via modulation of contractile markers and MMP14 activation. This study establishes PCSK6 as a key regulator of SMC function in vascular remodeling. Visual Overview: An online visual overview is available for this article.
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Affiliation(s)
- Urszula Rykaczewska
- From the Department of Molecular Medicine and Surgery, Karolinska Institute and Karolinska University Hospital Solna, Stockholm, Sweden (U.R., B.E.S., S.R., A.R., M.L., M.K., U.H., L.M.)
| | - Bianca E Suur
- From the Department of Molecular Medicine and Surgery, Karolinska Institute and Karolinska University Hospital Solna, Stockholm, Sweden (U.R., B.E.S., S.R., A.R., M.L., M.K., U.H., L.M.)
| | - Samuel Röhl
- From the Department of Molecular Medicine and Surgery, Karolinska Institute and Karolinska University Hospital Solna, Stockholm, Sweden (U.R., B.E.S., S.R., A.R., M.L., M.K., U.H., L.M.)
| | - Anton Razuvaev
- From the Department of Molecular Medicine and Surgery, Karolinska Institute and Karolinska University Hospital Solna, Stockholm, Sweden (U.R., B.E.S., S.R., A.R., M.L., M.K., U.H., L.M.)
| | - Mariette Lengquist
- From the Department of Molecular Medicine and Surgery, Karolinska Institute and Karolinska University Hospital Solna, Stockholm, Sweden (U.R., B.E.S., S.R., A.R., M.L., M.K., U.H., L.M.)
| | - Maria Sabater-Lleal
- Department of Medicine Solna, Karolinska Institute and Karolinska University Hospital Solna, Stockholm, Sweden (M.S.-L., M.G.D., G.P.-B., G.K.H., A.H., P.E., J.O.).,Unit of Genomics of Complex Diseases, Institut de Recerca Hospital de Sant Pau (IIB-Sant Pau), Barcelona, Spain (M.S.-L.)
| | - Sander W van der Laan
- Central Diagnostics Laboratory, Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, The Netherlands (S.v.d.L.)
| | - Clint L Miller
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville (C.L.M.).,Division of Cardiovascular Medicine, Stanford University School of Medicine, CA (C.L.M., R.C.W., T.Q.)
| | - Robert C Wirka
- Division of Cardiovascular Medicine, Stanford University School of Medicine, CA (C.L.M., R.C.W., T.Q.)
| | - Malin Kronqvist
- From the Department of Molecular Medicine and Surgery, Karolinska Institute and Karolinska University Hospital Solna, Stockholm, Sweden (U.R., B.E.S., S.R., A.R., M.L., M.K., U.H., L.M.)
| | - Maria Gonzalez Diez
- Department of Medicine Solna, Karolinska Institute and Karolinska University Hospital Solna, Stockholm, Sweden (M.S.-L., M.G.D., G.P.-B., G.K.H., A.H., P.E., J.O.)
| | - Mattias Vesterlund
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institute, Sweden (M.V., J.L.)
| | - Peter Gillgren
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, and Department of Vascular Surgery, Södersjukhuset, Stockholm, Sweden (P.G.)
| | - Jacob Odeberg
- Department of Medicine Solna, Karolinska Institute and Karolinska University Hospital Solna, Stockholm, Sweden (M.S.-L., M.G.D., G.P.-B., G.K.H., A.H., P.E., J.O.).,Science for Life Laboratory, Department of Proteomics, School of Chemistry Biotechnology and Health (CBH), KTH, Stockholm, Sweden (J.O.)
| | - Jan H Lindeman
- Department of Vascular Surgery, Leiden University Medical Center, The Netherlands (J.H.N.L.)
| | - Fabrizio Veglia
- Centro Cardiologico Monzino, IRCCS, Milan, Italy (F.V., D.B., E.T.)
| | - Steve E Humphries
- Cardiovascular Genetics, Institute Cardiovascular Science, University College of London, Department of Medicine, Rayne Building, United Kingdom (S.E.H.)
| | - Ulf de Faire
- Division of Cardiovascular Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Sweden (H.d.F.)
| | - Damiano Baldassarre
- Centro Cardiologico Monzino, IRCCS, Milan, Italy (F.V., D.B., E.T.).,Department of Medical Biotechnology and Translational Medicine, Università di Milano, Milan, Italy (D.B.)
| | - Elena Tremoli
- Centro Cardiologico Monzino, IRCCS, Milan, Italy (F.V., D.B., E.T.)
| | | | - Janne Lehtiö
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institute, Sweden (M.V., J.L.)
| | - Göran K Hansson
- Department of Medicine Solna, Karolinska Institute and Karolinska University Hospital Solna, Stockholm, Sweden (M.S.-L., M.G.D., G.P.-B., G.K.H., A.H., P.E., J.O.)
| | - Gabrielle Paulsson-Berne
- Department of Medicine Solna, Karolinska Institute and Karolinska University Hospital Solna, Stockholm, Sweden (M.S.-L., M.G.D., G.P.-B., G.K.H., A.H., P.E., J.O.)
| | - Gerard Pasterkamp
- Laboratory of Experimental Cardiology, Division Heart & Lungs, University Medical Center Utrecht, The Netherlands (G.P.)
| | - Thomas Quertermous
- Division of Cardiovascular Medicine, Stanford University School of Medicine, CA (C.L.M., R.C.W., T.Q.)
| | - Anders Hamsten
- Department of Medicine Solna, Karolinska Institute and Karolinska University Hospital Solna, Stockholm, Sweden (M.S.-L., M.G.D., G.P.-B., G.K.H., A.H., P.E., J.O.)
| | - Per Eriksson
- Department of Medicine Solna, Karolinska Institute and Karolinska University Hospital Solna, Stockholm, Sweden (M.S.-L., M.G.D., G.P.-B., G.K.H., A.H., P.E., J.O.)
| | - Ulf Hedin
- From the Department of Molecular Medicine and Surgery, Karolinska Institute and Karolinska University Hospital Solna, Stockholm, Sweden (U.R., B.E.S., S.R., A.R., M.L., M.K., U.H., L.M.)
| | - Ljubica Matic
- From the Department of Molecular Medicine and Surgery, Karolinska Institute and Karolinska University Hospital Solna, Stockholm, Sweden (U.R., B.E.S., S.R., A.R., M.L., M.K., U.H., L.M.)
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Wang Z, Civelek M, Miller CL, Sheffield NC, Guertin MJ, Zang C. BART: a transcription factor prediction tool with query gene sets or epigenomic profiles. Bioinformatics 2019; 34:2867-2869. [PMID: 29608647 DOI: 10.1093/bioinformatics/bty194] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 03/27/2018] [Indexed: 01/09/2023] Open
Abstract
Summary Identification of functional transcription factors that regulate a given gene set is an important problem in gene regulation studies. Conventional approaches for identifying transcription factors, such as DNA sequence motif analysis, are unable to predict functional binding of specific factors and not sensitive enough to detect factors binding at distal enhancers. Here, we present binding analysis for regulation of transcription (BART), a novel computational method and software package for predicting functional transcription factors that regulate a query gene set or associate with a query genomic profile, based on more than 6000 existing ChIP-seq datasets for over 400 factors in human or mouse. This method demonstrates the advantage of utilizing publicly available data for functional genomics research. Availability and implementation BART is implemented in Python and available at http://faculty.virginia.edu/zanglab/bart. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Zhenjia Wang
- Center for Public Health Genomics, Charlottesville, VA, USA
| | - Mete Civelek
- Center for Public Health Genomics, Charlottesville, VA, USA.,Department of Biomedical Engineering, Charlottesville, VA, USA
| | - Clint L Miller
- Center for Public Health Genomics, Charlottesville, VA, USA.,Department of Biomedical Engineering, Charlottesville, VA, USA.,Department of Public Health Sciences, Charlottesville, VA, USA.,Department of Biochemistry and Molecular Genetics, Charlottesville, VA, USA
| | - Nathan C Sheffield
- Center for Public Health Genomics, Charlottesville, VA, USA.,Department of Biomedical Engineering, Charlottesville, VA, USA.,Department of Public Health Sciences, Charlottesville, VA, USA.,Department of Biochemistry and Molecular Genetics, Charlottesville, VA, USA
| | - Michael J Guertin
- Center for Public Health Genomics, Charlottesville, VA, USA.,Department of Biochemistry and Molecular Genetics, Charlottesville, VA, USA
| | - Chongzhi Zang
- Center for Public Health Genomics, Charlottesville, VA, USA.,Department of Biomedical Engineering, Charlottesville, VA, USA.,Department of Public Health Sciences, Charlottesville, VA, USA.,Department of Biochemistry and Molecular Genetics, Charlottesville, VA, USA.,Cancer Center, University of Virginia, Charlottesville, VA, USA
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Xu S, Xu Y, Liu P, Zhang S, Liu H, Slavin S, Kumar S, Koroleva M, Luo J, Wu X, Rahman A, Pelisek J, Jo H, Si S, Miller CL, Jin ZG. The novel coronary artery disease risk gene JCAD/KIAA1462 promotes endothelial dysfunction and atherosclerosis. Eur Heart J 2019; 40:2398-2408. [PMID: 31539914 PMCID: PMC6698662 DOI: 10.1093/eurheartj/ehz303] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 12/30/2018] [Accepted: 05/03/2019] [Indexed: 01/12/2023] Open
Abstract
AIMS Recent genome-wide association studies (GWAS) have identified that the JCAD locus is associated with risk of coronary artery disease (CAD) and myocardial infarction (MI). However, the mechanisms whereby candidate gene JCAD confers disease risk remain unclear. We addressed whether and how JCAD affects the development of atherosclerosis, the common cause of CAD. METHODS AND RESULTS By mining data in the Genotype-Tissue Expression (GTEx) database, we found that CAD-associated risk variants at the JCAD locus are linked to increased JCAD gene expression in human arteries, implicating JCAD as a candidate causal CAD gene. We therefore generated global and endothelial cell (EC) specific-JCAD knockout mice, and observed that JCAD deficiency attenuated high fat diet-induced atherosclerosis in ApoE-deficient mice. JCAD-deficiency in mice also improved endothelium-dependent relaxation. Genome-wide transcriptional profiling of JCAD-depleted human coronary artery ECs showed that JCAD depletion inhibited the activation of YAP/TAZ pathway, and the expression of downstream pro-atherogenic genes, including CTGF and Cyr61. As a result, JCAD-deficient ECs attracted fewer monocytes in response to lipopolysaccharide (LPS) stimulation. Moreover, JCAD expression in ECs was decreased under unidirectional laminar flow in vitro and in vivo. Proteomics studies suggest that JCAD regulates YAP/TAZ activation by interacting with actin-binding protein TRIOBP, thereby stabilizing stress fiber formation. Finally, we observed that endothelial JCAD expression was increased in mouse and human atherosclerotic plaques. CONCLUSION The present study demonstrates that the GWAS-identified CAD risk gene JCAD promotes endothelial dysfunction and atherosclerosis, thus highlighting the possibility of new therapeutic strategies for CAD by targeting JCAD.
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Affiliation(s)
- Suowen Xu
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Yanni Xu
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Peking Union Medical College and Chinese Academy of Medical Sciences (CAMS), Beijing, China
| | - Peng Liu
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Peking Union Medical College and Chinese Academy of Medical Sciences (CAMS), Beijing, China
| | - Shuya Zhang
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, Department of Biochemistry and Molecular Biology, Ningxia Medical University, Yinchuan, China
| | - Huan Liu
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, Department of Biochemistry and Molecular Biology, Ningxia Medical University, Yinchuan, China
| | - Spencer Slavin
- Department of Pediatrics, Lung Biology and Disease Program, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Sandeep Kumar
- Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, USA
- Department of Cardiology, Emory University, Atlanta, GA, USA
| | - Marina Koroleva
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Jinque Luo
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Peking Union Medical College and Chinese Academy of Medical Sciences (CAMS), Beijing, China
| | - Xiaoqian Wu
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Arshad Rahman
- Department of Pediatrics, Lung Biology and Disease Program, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Jaroslav Pelisek
- Department of Vascular and Endovascular Surgery, Klinikum rechts der Isar der Technischen Universitaet Muenchen, Germany
| | - Hanjoong Jo
- Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, USA
- Department of Cardiology, Emory University, Atlanta, GA, USA
| | - Shuyi Si
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Peking Union Medical College and Chinese Academy of Medical Sciences (CAMS), Beijing, China
| | - Clint L Miller
- Center for Public Health Genomics, Department of Public Sciences, University of Virginia, Charlottesville, VA, USA
| | - Zheng Gen Jin
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
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Jaffré F, Miller CL, Schänzer A, Evans T, Roberts AE, Hahn A, Kontaridis MI. Inducible Pluripotent Stem Cell-Derived Cardiomyocytes Reveal Aberrant Extracellular Regulated Kinase 5 and Mitogen-Activated Protein Kinase Kinase 1/2 Signaling Concomitantly Promote Hypertrophic Cardiomyopathy in RAF1-Associated Noonan Syndrome. Circulation 2019; 140:207-224. [PMID: 31163979 DOI: 10.1161/circulationaha.118.037227] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND More than 90% of individuals with Noonan syndrome (NS) with mutations clustered in the CR2 domain of RAF1 present with severe and often lethal hypertrophic cardiomyopathy (HCM). The signaling pathways by which NS RAF1 mutations promote HCM remain elusive, and so far, there is no known treatment for NS-associated HCM. METHODS We used patient-derived RAF1S257L/+ and CRISPR-Cas9-generated isogenic control inducible pluripotent stem cell (iPSC)-derived cardiomyocytes to model NS RAF1-associated HCM and to further delineate the molecular mechanisms underlying the disease. RESULTS We show that mutant iPSC-derived cardiomyocytes phenocopy the pathology seen in hearts of patients with NS by exhibiting hypertrophy and structural defects. Through pharmacological and genetic targeting, we identify 2 perturbed concomitant pathways that, together, mediate HCM in RAF1 mutant iPSC-derived cardiomyocytes. Hyperactivation of mitogen-activated protein kinase kinase 1/2 (MEK1/2), but not extracellular regulated kinase 1/2, causes myofibrillar disarray, whereas the enlarged cardiomyocyte phenotype is a direct consequence of increased extracellular regulated kinase 5 (ERK5) signaling, a pathway not previously known to be involved in NS. RNA-sequencing reveals genes with abnormal expression in RAF1 mutant iPSC-derived cardiomyocytes and identifies subsets of genes dysregulated by aberrant MEK1/2 or ERK5 pathways that could contribute to the NS-associated HCM. CONCLUSIONS Taken together, the results of our study identify the molecular mechanisms by which NS RAF1 mutations cause HCM and reveal downstream effectors that could serve as therapeutic targets for treatment of NS and perhaps other, more common, congenital HCM disorders.
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Affiliation(s)
- Fabrice Jaffré
- Department of Medicine, Division of Cardiology, Beth Israel Deaconess Medical Center (F.J., M.I.K.).,Harvard Medical School, Boston, MA (F.J., M.I.K.).,Department of Surgery, Weill Cornell Medical College, New York, NY (F.J., T.E.)
| | - Clint L Miller
- Center for Public Health Genomics, Department of Public Health Sciences, Biochemistry and Molecular Genetics, and Biomedical Engineering, University of Virginia, Charlottesville (C.L.M.)
| | - Anne Schänzer
- Institute of Neuropathology (A.S.), University Hospital Giessen, Justus Liebig University Giessen, Germany
| | - Todd Evans
- Department of Surgery, Weill Cornell Medical College, New York, NY (F.J., T.E.)
| | - Amy E Roberts
- Department of Cardiology, Division of Genetics, Boston Children's Hospital, MA (A.E.R.)
| | - Andreas Hahn
- Department of Child Neurology (A.H.), University Hospital Giessen, Justus Liebig University Giessen, Germany
| | - Maria I Kontaridis
- Department of Medicine, Division of Cardiology, Beth Israel Deaconess Medical Center (F.J., M.I.K.).,Department of Biological Chemistry and Molecular Pharmacology (M.I.K.).,Harvard Medical School, Boston, MA (F.J., M.I.K.).,Harvard Stem Cell Institute, Harvard University, Cambridge, MA (M.I.K.).,Masonic Medical Research Institute, Utica, NY (M.I.K.)
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44
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Zhao Q, Wirka R, Nguyen T, Nagao M, Cheng P, Miller CL, Kim JB, Pjanic M, Quertermous T. TCF21 and AP-1 interact through epigenetic modifications to regulate coronary artery disease gene expression. Genome Med 2019; 11:23. [PMID: 31014396 PMCID: PMC6480881 DOI: 10.1186/s13073-019-0635-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 04/03/2019] [Indexed: 12/11/2022] Open
Abstract
Background Genome-wide association studies have identified over 160 loci that are associated with coronary artery disease. As with other complex human diseases, risk in coronary disease loci is determined primarily by altered expression of the causal gene, due to variation in binding of transcription factors and chromatin-modifying proteins that directly regulate the transcriptional apparatus. We have previously identified a coronary disease network downstream of the disease-associated transcription factor TCF21, and in work reported here extends these studies to investigate the mechanisms by which it interacts with the AP-1 transcription complex to regulate local epigenetic effects in these downstream coronary disease loci. Methods Genomic studies, including chromatin immunoprecipitation sequencing, RNA sequencing, and protein-protein interaction studies, were performed in human coronary artery smooth muscle cells. Results We show here that TCF21 and JUN regulate expression of two presumptive causal coronary disease genes, SMAD3 and CDKN2B-AS1, in part by interactions with histone deacetylases and acetyltransferases. Genome-wide TCF21 and JUN binding is jointly localized and particularly enriched in coronary disease loci where they broadly modulate H3K27Ac and chromatin state changes linked to disease-related processes in vascular cells. Heterozygosity at coronary disease causal variation, or genome editing of these variants, is associated with decreased binding of both JUN and TCF21 and loss of expression in cis, supporting a transcriptional mechanism for disease risk. Conclusions These data show that the known chromatin remodeling and pioneer functions of AP-1 are a pervasive aspect of epigenetic control of transcription, and thus, the risk in coronary disease-associated loci, and that interaction of AP-1 with TCF21 to control epigenetic features, contributes to the genetic risk in loci where they co-localize. Electronic supplementary material The online version of this article (10.1186/s13073-019-0635-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Quanyi Zhao
- Division of Cardiovascular Medicine and Cardiovascular Institute, School of Medicine, Stanford University, 300 Pasteur Dr., Falk CVRC, Stanford, CA, 94305, USA
| | - Robert Wirka
- Division of Cardiovascular Medicine and Cardiovascular Institute, School of Medicine, Stanford University, 300 Pasteur Dr., Falk CVRC, Stanford, CA, 94305, USA
| | - Trieu Nguyen
- Division of Cardiovascular Medicine and Cardiovascular Institute, School of Medicine, Stanford University, 300 Pasteur Dr., Falk CVRC, Stanford, CA, 94305, USA
| | - Manabu Nagao
- Division of Cardiovascular Medicine and Cardiovascular Institute, School of Medicine, Stanford University, 300 Pasteur Dr., Falk CVRC, Stanford, CA, 94305, USA
| | - Paul Cheng
- Division of Cardiovascular Medicine and Cardiovascular Institute, School of Medicine, Stanford University, 300 Pasteur Dr., Falk CVRC, Stanford, CA, 94305, USA
| | - Clint L Miller
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, 22908, USA.,Center for Public Health Genomics, Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA.,Center for Public Health Genomics, Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Juyong Brian Kim
- Division of Cardiovascular Medicine and Cardiovascular Institute, School of Medicine, Stanford University, 300 Pasteur Dr., Falk CVRC, Stanford, CA, 94305, USA
| | - Milos Pjanic
- Division of Cardiovascular Medicine and Cardiovascular Institute, School of Medicine, Stanford University, 300 Pasteur Dr., Falk CVRC, Stanford, CA, 94305, USA
| | - Thomas Quertermous
- Division of Cardiovascular Medicine and Cardiovascular Institute, School of Medicine, Stanford University, 300 Pasteur Dr., Falk CVRC, Stanford, CA, 94305, USA.
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Kojima Y, Werner N, Ye J, Nanda V, Tsao N, Wang Y, Flores AM, Miller CL, Weissman I, Deng H, Xu B, Dalman RL, Eken SM, Pelisek J, Li Y, Maegdefessel L, Leeper NJ. Proefferocytic Therapy Promotes Transforming Growth Factor-β Signaling and Prevents Aneurysm Formation. Circulation 2019; 137:750-753. [PMID: 29440201 DOI: 10.1161/circulationaha.117.030389] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Yoko Kojima
- Department of Surgery, Division of Vascular Surgery (Y.K., N.W., J.Y., V.N., N.T., Y.W., A.M.F., H.D., B.X., R.L.D., N.J.L.)
| | - Norna Werner
- Department of Surgery, Division of Vascular Surgery (Y.K., N.W., J.Y., V.N., N.T., Y.W., A.M.F., H.D., B.X., R.L.D., N.J.L.)
| | - Jianqin Ye
- Department of Surgery, Division of Vascular Surgery (Y.K., N.W., J.Y., V.N., N.T., Y.W., A.M.F., H.D., B.X., R.L.D., N.J.L.)
| | - Vivek Nanda
- Department of Surgery, Division of Vascular Surgery (Y.K., N.W., J.Y., V.N., N.T., Y.W., A.M.F., H.D., B.X., R.L.D., N.J.L.)
| | - Noah Tsao
- Department of Surgery, Division of Vascular Surgery (Y.K., N.W., J.Y., V.N., N.T., Y.W., A.M.F., H.D., B.X., R.L.D., N.J.L.)
| | - Ying Wang
- Department of Surgery, Division of Vascular Surgery (Y.K., N.W., J.Y., V.N., N.T., Y.W., A.M.F., H.D., B.X., R.L.D., N.J.L.)
| | - Alyssa M Flores
- Department of Surgery, Division of Vascular Surgery (Y.K., N.W., J.Y., V.N., N.T., Y.W., A.M.F., H.D., B.X., R.L.D., N.J.L.)
| | - Clint L Miller
- Department of Medicine, Division of Cardiovascular Medicine (C.L.M., N.J.L.)
| | - Irving Weissman
- Institute for Stem Cell Biology and Regenerative Medicine (I.W.)
| | - Hongping Deng
- Department of Surgery, Division of Vascular Surgery (Y.K., N.W., J.Y., V.N., N.T., Y.W., A.M.F., H.D., B.X., R.L.D., N.J.L.)
| | - Baohui Xu
- Department of Surgery, Division of Vascular Surgery (Y.K., N.W., J.Y., V.N., N.T., Y.W., A.M.F., H.D., B.X., R.L.D., N.J.L.)
| | - Ronald L Dalman
- Department of Surgery, Division of Vascular Surgery (Y.K., N.W., J.Y., V.N., N.T., Y.W., A.M.F., H.D., B.X., R.L.D., N.J.L.)
| | - Suzanne M Eken
- Stanford University School of Medicine, CA. Department of Medicine, Karolinska Institute, Stockholm, Sweden (S.M.E., L.M.)
| | - Jaroslav Pelisek
- Department of Vascular and Endovascular Surgery, Klinikum Rechts der Isar, Technical University Munich and German Center for Cardiovascular Research Partner Site Munich, Munich, Germany (J.P., Y.L., L.M.)
| | - Yuhuang Li
- Department of Vascular and Endovascular Surgery, Klinikum Rechts der Isar, Technical University Munich and German Center for Cardiovascular Research Partner Site Munich, Munich, Germany (J.P., Y.L., L.M.)
| | - Lars Maegdefessel
- Stanford University School of Medicine, CA. Department of Medicine, Karolinska Institute, Stockholm, Sweden (S.M.E., L.M.).,Department of Vascular and Endovascular Surgery, Klinikum Rechts der Isar, Technical University Munich and German Center for Cardiovascular Research Partner Site Munich, Munich, Germany (J.P., Y.L., L.M.)
| | - Nicholas J Leeper
- Department of Surgery, Division of Vascular Surgery (Y.K., N.W., J.Y., V.N., N.T., Y.W., A.M.F., H.D., B.X., R.L.D., N.J.L.) .,Department of Medicine, Division of Cardiovascular Medicine (C.L.M., N.J.L.)
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46
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Turner AW, Wong D, Khan MD, Dreisbach CN, Palmore M, Miller CL. Multi-Omics Approaches to Study Long Non-coding RNA Function in Atherosclerosis. Front Cardiovasc Med 2019; 6:9. [PMID: 30838214 PMCID: PMC6389617 DOI: 10.3389/fcvm.2019.00009] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Accepted: 01/30/2019] [Indexed: 12/15/2022] Open
Abstract
Atherosclerosis is a complex inflammatory disease of the vessel wall involving the interplay of multiple cell types including vascular smooth muscle cells, endothelial cells, and macrophages. Large-scale genome-wide association studies (GWAS) and the advancement of next generation sequencing technologies have rapidly expanded the number of long non-coding RNA (lncRNA) transcripts predicted to play critical roles in the pathogenesis of the disease. In this review, we highlight several lncRNAs whose functional role in atherosclerosis is well-documented through traditional biochemical approaches as well as those identified through RNA-sequencing and other high-throughput assays. We describe novel genomics approaches to study both evolutionarily conserved and divergent lncRNA functions and interactions with DNA, RNA, and proteins. We also highlight assays to resolve the complex spatial and temporal regulation of lncRNAs. Finally, we summarize the latest suite of computational tools designed to improve genomic and functional annotation of these transcripts in the human genome. Deep characterization of lncRNAs is fundamental to unravel coronary atherosclerosis and other cardiovascular diseases, as these regulatory molecules represent a new class of potential therapeutic targets and/or diagnostic markers to mitigate both genetic and environmental risk factors.
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Affiliation(s)
- Adam W. Turner
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
| | - Doris Wong
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States
| | - Mohammad Daud Khan
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
| | - Caitlin N. Dreisbach
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
- School of Nursing, University of Virginia, Charlottesville, VA, United States
- Data Science Institute, University of Virginia, Charlottesville, VA, United States
| | - Meredith Palmore
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
| | - Clint L. Miller
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States
- Data Science Institute, University of Virginia, Charlottesville, VA, United States
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, United States
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, United States
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47
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Nanda V, Wang T, Pjanic M, Liu B, Nguyen T, Matic LP, Hedin U, Koplev S, Ma L, Franzén O, Ruusalepp A, Schadt EE, Björkegren JLM, Montgomery SB, Snyder MP, Quertermous T, Leeper NJ, Miller CL. Functional regulatory mechanism of smooth muscle cell-restricted LMOD1 coronary artery disease locus. PLoS Genet 2018; 14:e1007755. [PMID: 30444878 PMCID: PMC6268002 DOI: 10.1371/journal.pgen.1007755] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 11/30/2018] [Accepted: 10/10/2018] [Indexed: 12/28/2022] Open
Abstract
Recent genome-wide association studies (GWAS) have identified multiple new loci which appear to alter coronary artery disease (CAD) risk via arterial wall-specific mechanisms. One of the annotated genes encodes LMOD1 (Leiomodin 1), a member of the actin filament nucleator family that is highly enriched in smooth muscle-containing tissues such as the artery wall. However, it is still unknown whether LMOD1 is the causal gene at this locus and also how the associated variants alter LMOD1 expression/function and CAD risk. Using epigenomic profiling we recently identified a non-coding regulatory variant, rs34091558, which is in tight linkage disequilibrium (LD) with the lead CAD GWAS variant, rs2820315. Herein we demonstrate through expression quantitative trait loci (eQTL) and statistical fine-mapping in GTEx, STARNET, and human coronary artery smooth muscle cell (HCASMC) datasets, rs34091558 is the top regulatory variant for LMOD1 in vascular tissues. Position weight matrix (PWM) analyses identify the protective allele rs34091558-TA to form a conserved Forkhead box O3 (FOXO3) binding motif, which is disrupted by the risk allele rs34091558-A. FOXO3 chromatin immunoprecipitation and reporter assays show reduced FOXO3 binding and LMOD1 transcriptional activity by the risk allele, consistent with effects of FOXO3 downregulation on LMOD1. LMOD1 knockdown results in increased proliferation and migration and decreased cell contraction in HCASMC, and immunostaining in atherosclerotic lesions in the SMC lineage tracing reporter mouse support a key role for LMOD1 in maintaining the differentiated SMC phenotype. These results provide compelling functional evidence that genetic variation is associated with dysregulated LMOD1 expression/function in SMCs, together contributing to the heritable risk for CAD.
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Affiliation(s)
- Vivek Nanda
- Department of Surgery, Division of Vascular Surgery, Stanford University School of Medicine, Stanford, California, United States of America
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, United States of America
| | - Ting Wang
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Milos Pjanic
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Boxiang Liu
- Department of Biology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Trieu Nguyen
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Ljubica Perisic Matic
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Ulf Hedin
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Simon Koplev
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States of America
| | - Lijiang Ma
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States of America
| | - Oscar Franzén
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States of America
- Clinical Gene Networks AB, Stockholm, Sweden
| | - Arno Ruusalepp
- Clinical Gene Networks AB, Stockholm, Sweden
- Department of Cardiac Surgery, Tartu University Hospital, Tartu, Estonia
| | - Eric E. Schadt
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States of America
| | - Johan L. M. Björkegren
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States of America
- Department of Medical Biochemistry and Biophysics, Vascular Biology Unit, Karolinska Institutet, Stockholm, Sweden
- Department of Physiology, Institute of Biomedicine and Translation Medicine, University of Tartu, Tartu, Estonia
| | - Stephen B. Montgomery
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Michael P. Snyder
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Thomas Quertermous
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Nicholas J. Leeper
- Department of Surgery, Division of Vascular Surgery, Stanford University School of Medicine, Stanford, California, United States of America
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, United States of America
| | - Clint L. Miller
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California, United States of America
- Center for Public Health Genomics, Department of Public Health Sciences, Department of Biochemistry and Molecular Genetics, and Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America
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48
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Iyer D, Zhao Q, Wirka R, Naravane A, Nguyen T, Liu B, Nagao M, Cheng P, Miller CL, Kim JB, Pjanic M, Quertermous T. Coronary artery disease genes SMAD3 and TCF21 promote opposing interactive genetic programs that regulate smooth muscle cell differentiation and disease risk. PLoS Genet 2018; 14:e1007681. [PMID: 30307970 PMCID: PMC6198989 DOI: 10.1371/journal.pgen.1007681] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 10/23/2018] [Accepted: 09/07/2018] [Indexed: 12/13/2022] Open
Abstract
Although numerous genetic loci have been associated with coronary artery disease (CAD) with genome wide association studies, efforts are needed to identify the causal genes in these loci and link them into fundamental signaling pathways. Recent studies have investigated the disease mechanism of CAD associated gene SMAD3, a central transcription factor (TF) in the TGFβ pathway, investigating its role in smooth muscle biology. In vitro studies in human coronary artery smooth muscle cells (HCASMC) revealed that SMAD3 modulates cellular phenotype, promoting expression of differentiation marker genes while inhibiting proliferation. RNA sequencing and chromatin immunoprecipitation sequencing studies in HCASMC identified downstream genes that reside in pathways which mediate vascular development and atherosclerosis processes in this cell type. HCASMC phenotype, and gene expression patterns promoted by SMAD3 were noted to have opposing direction of effect compared to another CAD associated TF, TCF21. At sites of SMAD3 and TCF21 colocalization on DNA, SMAD3 binding was inversely correlated with TCF21 binding, due in part to TCF21 locally blocking chromatin accessibility at the SMAD3 binding site. Further, TCF21 was able to directly inhibit SMAD3 activation of gene expression in transfection reporter gene studies. In contrast to TCF21 which is protective toward CAD, SMAD3 expression in HCASMC was shown to be directly correlated with disease risk. We propose that the pro-differentiation action of SMAD3 inhibits dedifferentiation that is required for HCASMC to expand and stabilize disease plaque as they respond to vascular stresses, counteracting the protective dedifferentiating activity of TCF21 and promoting disease risk.
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Affiliation(s)
- Dharini Iyer
- Department of Medicine and Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, United States of America
| | - Quanyi Zhao
- Department of Medicine and Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, United States of America
| | - Robert Wirka
- Department of Medicine and Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, United States of America
| | - Ameay Naravane
- Department of Medicine and Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, United States of America
| | - Trieu Nguyen
- Department of Medicine and Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, United States of America
| | - Boxiang Liu
- Department of Medicine and Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, United States of America
| | - Manabu Nagao
- Department of Medicine and Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, United States of America
| | - Paul Cheng
- Department of Medicine and Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, United States of America
| | - Clint L. Miller
- Departments of Public Health Sciences, Biochemistry and Genetics, and Biomedical Engineering, University of Virginia, Charlottesville, VA, United States of America
| | - Juyong Brian Kim
- Department of Medicine and Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, United States of America
| | - Milos Pjanic
- Department of Medicine and Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, United States of America
| | - Thomas Quertermous
- Department of Medicine and Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, United States of America
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49
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Liu B, Pjanic M, Wang T, Nguyen T, Gloudemans M, Rao A, Castano VG, Nurnberg S, Rader DJ, Elwyn S, Ingelsson E, Montgomery SB, Miller CL, Quertermous T. Genetic Regulatory Mechanisms of Smooth Muscle Cells Map to Coronary Artery Disease Risk Loci. Am J Hum Genet 2018; 103:377-388. [PMID: 30146127 PMCID: PMC6128252 DOI: 10.1016/j.ajhg.2018.08.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Accepted: 08/01/2018] [Indexed: 12/30/2022] Open
Abstract
Coronary artery disease (CAD) is the leading cause of death globally. Genome-wide association studies (GWASs) have identified more than 95 independent loci that influence CAD risk, most of which reside in non-coding regions of the genome. To interpret these loci, we generated transcriptome and whole-genome datasets using human coronary artery smooth muscle cells (HCASMCs) from 52 unrelated donors, as well as epigenomic datasets using ATAC-seq on a subset of 8 donors. Through systematic comparison with publicly available datasets from GTEx and ENCODE projects, we identified transcriptomic, epigenetic, and genetic regulatory mechanisms specific to HCASMCs. We assessed the relevance of HCASMCs to CAD risk using transcriptomic and epigenomic level analyses. By jointly modeling eQTL and GWAS datasets, we identified five genes (SIPA1, TCF21, SMAD3, FES, and PDGFRA) that may modulate CAD risk through HCASMCs, all of which have relevant functional roles in vascular remodeling. Comparison with GTEx data suggests that SIPA1 and PDGFRA influence CAD risk predominantly through HCASMCs, while other annotated genes may have multiple cell and tissue targets. Together, these results provide tissue-specific and mechanistic insights into the regulation of a critical vascular cell type associated with CAD in human populations.
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Affiliation(s)
- Boxiang Liu
- Department of Biology, School of Humanities and Sciences, Stanford University, Stanford, CA 94305, USA; Cardiovascular Institute, Stanford School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA
| | - Milos Pjanic
- Cardiovascular Institute, Stanford School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA; Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Ting Wang
- Cardiovascular Institute, Stanford School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Trieu Nguyen
- Cardiovascular Institute, Stanford School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA; Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Michael Gloudemans
- Biomedical Informatics Training Program, Stanford School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA
| | - Abhiram Rao
- Cardiovascular Institute, Stanford School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Victor G Castano
- Cardiovascular Institute, Stanford School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA; Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Sylvia Nurnberg
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Daniel J Rader
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Susannah Elwyn
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Erik Ingelsson
- Cardiovascular Institute, Stanford School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA; Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Stephen B Montgomery
- Cardiovascular Institute, Stanford School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Clint L Miller
- Center for Public Health Genomics, Department of Public Health Sciences, Biochemistry and Genetics, and Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA
| | - Thomas Quertermous
- Cardiovascular Institute, Stanford School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA; Department of Medicine, Stanford University, Stanford, CA 94305, USA.
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50
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Turner AW, Wong D, Dreisbach CN, Miller CL. GWAS Reveal Targets in Vessel Wall Pathways to Treat Coronary Artery Disease. Front Cardiovasc Med 2018; 5:72. [PMID: 29988570 PMCID: PMC6026658 DOI: 10.3389/fcvm.2018.00072] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 05/29/2018] [Indexed: 12/22/2022] Open
Abstract
Coronary artery disease (CAD) is the leading cause of mortality worldwide and poses a considerable public health burden. Recent genome-wide association studies (GWAS) have revealed >100 genetic loci associated with CAD susceptibility in humans. While a number of these loci harbor gene targets of currently approved therapies, such as statins and PCSK9 inhibitors, the majority of the annotated genes at these loci encode for proteins involved in vessel wall function with no known drugs available. Importantly many of the associated genes linked to vascular (smooth muscle, endothelial, and macrophage) cell processes are now organized into distinct functional pathways, e.g., vasodilation, growth factor responses, extracellular matrix and plaque remodeling, and inflammation. In this mini-review, we highlight the most recently identified loci that have predicted roles in the vessel wall and provide genetic context for pre-existing therapies as well as new drug targets informed from GWAS. With the development of new modalities to target these pathways, (e.g., antisense oligonucleotides, CRISPR/Cas9, and RNA interference) as well as the computational frameworks to prioritize or reposition therapeutics, there is great opportunity to close the gap from initial genetic discovery to clinical translation for many patients affected by this common disease.
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Affiliation(s)
- Adam W Turner
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
| | - Doris Wong
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States.,Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States
| | - Caitlin N Dreisbach
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States.,Data Science Institute, University of Virginia, Charlottesville, VA, United States
| | - Clint L Miller
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States.,Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States.,Data Science Institute, University of Virginia, Charlottesville, VA, United States.,Department of Public Health Sciences, University of Virginia, Charlottesville, VA, United States
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