Johan Björkegren

Johan Björkegren

Principal Researcher | Docent
Visiting address: Novum, Blickagången 6, 14157 Huddinge/Stockholm
Postal address: H7 Medicin, Huddinge, H7 Metabolism/ICMC Björkegren, 171 77 Stockholm
Part of:

About me

  • Professor Genetics and Genomic Sciences, Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York (2013)

    Professor Medicine and Cardiology, Mount Sinai Hospital and the Cardiovascular Research Center of Icahn School of Medicine at Mount Sinai (2013)

    Associate Professor of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden (2003)

    Visiting Professor, University of Tartu, Estonia (2015) and Tokyo College, Tokyo Univeristy, Japan (2024)

     

  • Focusing on cardiovascular diseases, the goal of my research is to use 

  • multi-modal big data analysis to create reliable network models of human biology and disease. Network models have enormous potential to improve our ability to predict disease risk, identify new therapeutic targets, and to 
  • monitor molecular effects of treatments. To achieve this goal, I have designed and generated a range of clinical datasets of cardiovascular disease 
  • that combine detailed clinical characteristics with imaging, genomics, proteomics, and other types of data. My research has long focused on cardiovascular disease. My early work explored the role of triglyceride-rich lipoproteins in coronary artery disease (CAD), and my postdoctoral studies in mouse models established the hepatic gene microsomal triglyceride transfer protein as a key target to lower plasma cholesterol levels and reduce atherosclerosis. Since then, my primary focus has been systems analyses to generate network models from large genomic datasets—both from CAD patients in the clinic and from cellular and mouse models of atherosclerosis progression and regression in the laboratory. Throughout the last decade, I have designed and led a range of clinical and mouse model studies to elucidate the inherit complexity of CAD. As one of the first clinical scientists to apply the emerging technologies of molecular profiling to large patient cohorts, I have revealed the role of functionally associated genes in several molecular networks that drive CAD. A common complex disease such as CAD cannot be understood nor cured by targeting isolated genes. Rather, the focus needs to be on molecular disease processes mirrored by regulatory-gene networks that capture the combined effects of many genetic and environmental risk factors. To this end, at Karolinska Institutet and Tartu University Hospital, much of my time has gone into gathering a truly unique biobank from CAD patients undergoing different forms of heart surgery. The Stockholm-Tartu Atherosclerosis Reverse Network Engineering Task (STARNET) is a joint study initiative between the cardiovascular chief surgeon at the Tartu University Hospital in Estonia, Dr. Arno Ruusalepp, and myself. Using the STARNET bio-bank, I have since 2013 been mainly active at the Department of Genetics and Genomic Sciences at Mount Sinai where we have generated RNA sequence data from up to nine CAD-relevant tissues isolated from near 2000 clinically well–characterized patients. This unprecedented dataset is the main resource for our current efforts to generate network models that predict the risk for and clinical outcomes of CAD. My entrepreneurial ambitions have focused on translating the results of our systems genetic research into new therapies and diagnostics for patients at risk for or suffering CAD. I have launched several entrepreneurial projects. Of particular importance is Clinical Gene Networks AB—the first Bio-IT company in Sweden, founded in 2003 with the goal of exploring “clinical” networks to generate the next generation of diagnostics and therapies based 
  • on network models of complex diseases. 
  • According to Stanford University's list of "World's Top 2%" scientists, our clinical systems genetics appraoch has led to publications putting me among the top 2 % of scientists all categories across the globe in 2024.

Research

  • I use multi-modal big data analysis to create new and reliable network models of human molecular biology in health and disease that can lead to better disease prediction, monitoring and therapies. To this effort I have created clinical datasets of mainly cardiovascular disease patients in Sweden,  

  • Estonia and the US that are enriched for many of these data modalities including genetics, -omics (epigenetics, RNA, proteins, metabolites andlipids) combined with detailed clinical characteristics including imaging. I have a broad background in the design and analysis of clinical studies 
  • apprehending and applying the new screening and bioinformatics analysis tools to elucidate the true complexity of common diseases. The focus of these studies has been the role of functionally associated genes in molecular networks driving disease. Vital to this approach of a more granular 
  • understanding of complex disease biology is to originate these studies in humans suffering the disease whereas animal and cell disease model systems are used for the purpose of validating key disease drivers and processes first identified in humans (i.e. a top-down vs. bottom-up approach).


    This effort has now resulted in one of the world’s most unique cardiometabolic disease (CMD)-related dataset, STARNET (Stockholm-Tartu Atherosclerosis Reverse Network Engineering Task), published in leading journals. Currently, we are expanding STARNET (v2) with >

  • 1500 coronary artery disease (CAD)-affected subjects and >
  • 400 subjects verified to be CAD-free (nonCAD)) by preprocessing arterial wall (atherosclerotic and non-atherosclerotic) and metabolic (liver, skeletal muscle, visceral abdominal, and subcutaneous fat) samples allowing for multi-omics analyses (epigenomics, transcriptomics and proteomics) that besides whole tissue also includes single nucleus isolation for subsequent snATAC/snRNAseq and spatial RNAseq analyses. From some of these patients, we are also collecting samples from the portal vein and gut microbiome.

     

  • Moving forward, I am highly driven, motivated and focused to expand the central theme of my research strategies

  •  
  • a mechanistic framework of gene-regulatory networks providing a global understanding of the regulatory landscape that 1) combines pathways into organ functions and 2) explain organ-organ interactions. In the end, this new knowledge will be required to enable diagnostics and therapies of molecularly-defined subcategories of CMD patients (i.e. enabling precision medicine). 

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Teaching

  • I am devoted to teaching. Prior to my years at Moint Sinai Hospital (2013-) I regulary teached medical student in the field of cardiometabolic disease.

    I also teached in several PhD programs including "Bioinformatics in Medicine", "An overview of the process of Atherosclerosis", "Clinical Sciences from gene to 

  • disease", and at the Biomedical School, “Molecular Medicine”. I also actively take part in educating the public like in numerous Swedish radio and televesion apparences involving matters like “Personal Genetic Testing", “Consequences of Clinical Genomics on Health Care in Sweden”, “Food a matter of the heart” and ”Where is medical research heading—consequences for the health industry”. During my years at Mount Sinai I was hired to focus 100% of my time to leading clinical omiics research initiatives working with Mount Sinai clinicians to establish new human disease-focused 
  • omics biobanks. I supervised FoAss (n=3), post-docs (n=11) and PhD-students (n=12 (6 as main supervisor)) as well as master students (n=9)..

     

Selected publications

Articles

All other publications

Grants

  • MIRACLE - European Union’s Horizon Europe (European Innovation Council
    European Union’s Horizon Europe (European Innovation Council)
    1 October 2023 - 1 October 2027
  • AtheroGen - Fondation Leducq
    Fondation Leducq
    1 January 2023 - 31 December 2026
  • Swedish Heart-Lung Foundation
    1 January 2021 - 31 December 2023
  • PlaqueOmics: Novel Roles of Smooth Muscle and Other Matrix Producing Cells in Atherosclerotic Plaque Stability and Rupture
    Foundation Leducq
    1 January 2020 - 1 January 2025
  • The Swedish Heart-Lung Foundation - Project grant
    The Swedish Heart-Lung Foundation
    1 January 2018
  • National Institutes of Health R21
    National Institutes of Health
    1 January 2017 - 1 January 2019
  • National Institutes of Health -RO1
    National Institutes of Health
    1 January 2016 - 1 January 2020
  • 1 January 2015 - 1 January 2019
  • CADgenomics: Understanding CAD Genes, Leducq Foundation
    Transatalantic Network, the Leducq Foundation
    1 January 2014 - 1 January 2017
  • CVgenes@target -FP7 European Commission Integrated project
    FP7 -European Commission Integrated project
    1 January 2014 - 1 January 2017
  • American Heart Association - Family-Based Approach in a Minority Community Integrating Systems–Biology for Promotion of Health (FAMILIA)
    American Heart Association
    1 January 2014 - 1 January 2018
  • The Swedish Heart-Lung Foundation - Project grant
    The Swedish Heart-Lung Foundation
    1 January 2013
  • Karolinska-AstraZeneca Center for Translation Science
    Karolinska Astra-Zeneca Center for Translation Science
    1 January 2013 - 1 January 2016
  • Center for Translation Genomics, University of Tartu
    Center for translation genomics, University of Tartu
    1 January 2012 - 1 January 2015
  • Swedish Heart-Lung Foundation - FoASS
    Swedish Heart-Lung Foundation
    1 January 2010
  • Swedish Research Council-Project grant
    Swedish Research Council
    1 January 2008
  • Swedish Heart-Lung Foundation - Project grant
    Swedish Heart-Lung Foundation
    1 January 2008
  • Show more

Employments

  • Principal Researcher, Department of Medicine, Huddinge, Karolinska Institutet, 2022-
  • Tenure Professorship, Genetics and Genomic Sciences, Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 2013-2023
  • Professor, Medicine-Cardiology, Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, 2013-2023
  • Chief Clinical Science Officer, Clinical systems genetics, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, 2013-2020

Degrees and Education

  • Docent, Karolinska Institutet, 2003
  • PhD, Degree of Doctor, Postprandial triglyceride-rich lipoproteins and atherosclerosis, Medicine, Solna, Karolinska Institutet, 1998
  • University Medical Degree, Karolinska Institutet, 1995
  • BA, Business School, Stockholm University, 1989

Leadership and responsibility assignments

  • Director of studies, Clinical systems genetics studies, Department of Genetics and Genomic Sciences, Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, 2013-2020
  • CEO and Chair, Clinical Gene Networks AB, Clinical Gene Networks (Sweden), http://clinicalgenenetworks.com/, 2003-

Distinction and awards

  • Visiting Professor at Tokyo College, University of Tokyo, 2024
  • Senior investigator award, Swedish Heart-Lung Foundation, 2010
  • Senior investigator award, Karolinska Institutet, 2008
  • Research Assistant award, Swedish Research Council, 2004
  • Finalist in the Young Investigator Award, International Society of Atherosclerosis, 2003
  • Fogarty fellowship, University of San Francisco, 1999

Committee work

  • Member, Affymetrix Inc/Karolinska Institutet collaboration, Karolinska Institutet, 2005-
  • Member, Assessment of access to biobanks in relation to new Swedish legislation, Karolinska Institutet, 2005-2006
  • Chair, Examination committees for PhD theses, Karolinska Institutet, 2003-2012

Visiting research fellowships

  • Post-doc, Gladstone Institutes, Post-doc using mouse models of atherosclerosis and cardiometabolic diseases, 1999-2001

Thesis evaluation

  • Katharina Slätis, Opponent, Department of Medicine, Karolinska Institutet, 2009
  • Margareta Jernås, Opponent, Sahlgrenska University Hospital, 2008

Other expert reviewer/evaluation assignment

  • Evaluator of research applications in international competition, External Evaluator, Danish Council for Strategic Research, 2008-2013
  • Evaluator of research applications in international competition, External Evaluator, European Science Foundation, 2008-2013
  • Reviewer or advisor for other scientific bodies, Scientific Evaluator, University of Tromsö, 2003

News from KI

Events from KI

News from external media

Presentations

  • Presentation (slides etc.): 2022
    Invited speaker to the Finnish Atherosclerosis Society (SATY). Title: STARNET- A World-Leading Functional Database for Studies of Cardiometabolic Disorders and Coronary Artery Disease.
    Björkegren J
  • Presentation (slides etc.): 2020
    Plenary speaker, European Atherosclerosis Society (EAS). Title: Implementing systems biology to personalize medicine.
    Björkegren J
  • Presentation (slides etc.): 2020
    Invited speaker to Columbia University, Cardiovascular Seminar Series. Title: A systems medicine approach to unravel key disease network drivers and biomarkers in cardiometabolic and coronary artery disease
    Björkegren J
  • Presentation (slides etc.): 2020
    Inivited keynote speaker, The 1st International Symposium on Human InformatiX. Title: A systems medicine approach to unravel key disease network drivers and biomarkers in cardiometabolic and coronary artery disease
    Björkegren J
  • Presentation (slides etc.): 2019
    Riskgener som driver åderförkalkning - ett gennätverks perspektiv, Temadag Kolesterol och Åderförkalkning, Karolinska Institutet
    Björkegren J
  • Presentation (slides etc.): 2018
    Invited Keynote speaker, GENMED workshop. “From GWAS to genetically regulated tissue-specified coding and non-coding genes in CAD-causal networks and pathways – a Systems Genetics Approach”
    Björkegren J
  • Presentation (slides etc.): 2018
    Invited Keynote speaker, Keystone Symposium of Atherosclerosis. “Cardiometabolic risk loci share downstream cis- and trans-gene regulation across tissues and diseases”
    Björkegren J
  • Presentation (slides etc.): 2018
    Invited Keynote speaker, 10 years of GWAS, Looking back – looking forward. Title: “Systems genetic approaches to coronary artery disease”
    Björkegren J
  • Presentation (slides etc.): 2016
    Invited speaker and chair at the 6th Conference on Systems Biology of the Mammalian Cells. Title of talk “Systems Genetic Approaches to Coronary Artery Disease - Toward Diagnostics and Therapies of Molecularly Defined Subcategories of Patients”,
    Björkegren J
  • Presentation (slides etc.): 2016
    Invited speaker EBRC SEMINAR- THE ROSLIN INSTITUTE “Systems Genetic Approaches to Coronary Artery Disease Towards Diagnostics and Therapies of Patients in Molecularly Defined Subcategories”.
    Björkegren J
  • Presentation (slides etc.): 2015
    Invited speaker and part of the Expert Panel Advisory Board for the HIGH SCIENCE HDL FORUM: THE ROLE OF HDL MODIFYING THERAPY FOR THE PREVENTION OF CARDIOVASCULAR DISEASE Title of the talk: “Systems Biology in the evaluation of genetically determined risk”
    Björkegren J
  • Presentation (slides etc.): 2013
    Invited speaker to the Symposium - Genetics of Atherosclerosis - Update 2013
    Björkegren J
  • Presentation (slides etc.): 2012
    Invited keynote speaker at the conference “Complex Traits: Genomics and Computational Approaches”, Keystone Conference (B5)
    Björkegren J
  • Presentation (slides etc.): 2012
    Invited speaker at the conference GeneForum
    Björkegren J
  • Presentation (slides etc.): 2010
    Invited keynote speaker at the “Advances in Molecular Mechanisms of Atherosclerosis (J7)” organized by the Keystone Conferences organization
    Björkegren J
  • Presentation (slides etc.): 2009
    Invited speaker to the “Genetics and Genomics of Cardiovascular Disease Workshop” organized by the North American Vascular Biology Organization (NAVBO)
    Björkegren J
  • Presentation (slides etc.): 2008
    Program Committee of the International Conference on Systems Biology (ICSB). Moderator of workshop on Cardiovascular Systems Biology
    Björkegren J
  • Presentation (slides etc.): 2008
    Organizer and keynote speaker, ESF Exploratory Workshop on Computational Disease Modeling
    Björkegren J
  • Presentation (slides etc.): 2004
    Speaker at the XV International Symposium on Drugs Affecting Lipid Metabolism
    Björkegren J
  • Presentation (slides etc.): 2003
    Atheroma Club 1992-2006
    Björkegren J
  • Presentation (slides etc.): 2003
    Speaker at the International Symposium on Atherosclerosis
    Björkegren J
  • Presentation (slides etc.): 2002
    Invited speaker to the British Atherosclerosis Society
    Björkegren J
  • Presentation (slides etc.): 2002
    Speaker at the 42nd Annual Conference on Cardiovascular Disease Epidemiology and Prevention
    Björkegren J
  • Presentation (slides etc.): 2002
    Speaker at the Annual Scandinavian Atherosclerosis Conference, 2002, 2003, 2204
    Björkegren J
  • Presentation (slides etc.): 1998
    Invited speaker to European Lipoprotein Club 1998, 2001
    Björkegren J
  • Presentation (slides etc.): 1998
    Speaker at the International Symposium on Atherosclerosis (IAS)
    Björkegren J