1
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Milenkovic I, Santos Vieira HG, Lucas MC, Ruiz-Orera J, Patone G, Kesteven S, Wu J, Feneley M, Espadas G, Sabidó E, Hübner N, van Heesch S, Völkers M, Novoa EM. Dynamic interplay between RPL3- and RPL3L-containing ribosomes modulates mitochondrial activity in the mammalian heart. Nucleic Acids Res 2023; 51:5301-5324. [PMID: 36882085 PMCID: PMC10287911 DOI: 10.1093/nar/gkad121] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [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: 11/23/2022] [Revised: 01/31/2023] [Accepted: 02/09/2023] [Indexed: 03/09/2023] Open
Abstract
The existence of naturally occurring ribosome heterogeneity is now a well-acknowledged phenomenon. However, whether this heterogeneity leads to functionally diverse 'specialized ribosomes' is still a controversial topic. Here, we explore the biological function of RPL3L (uL3L), a ribosomal protein (RP) paralogue of RPL3 (uL3) that is exclusively expressed in skeletal muscle and heart tissues, by generating a viable homozygous Rpl3l knockout mouse strain. We identify a rescue mechanism in which, upon RPL3L depletion, RPL3 becomes up-regulated, yielding RPL3-containing ribosomes instead of RPL3L-containing ribosomes that are typically found in cardiomyocytes. Using both ribosome profiling (Ribo-seq) and a novel orthogonal approach consisting of ribosome pulldown coupled to nanopore sequencing (Nano-TRAP), we find that RPL3L modulates neither translational efficiency nor ribosome affinity towards a specific subset of transcripts. In contrast, we show that depletion of RPL3L leads to increased ribosome-mitochondria interactions in cardiomyocytes, which is accompanied by a significant increase in ATP levels, potentially as a result of fine-tuning of mitochondrial activity. Our results demonstrate that the existence of tissue-specific RP paralogues does not necessarily lead to enhanced translation of specific transcripts or modulation of translational output. Instead, we reveal a complex cellular scenario in which RPL3L modulates the expression of RPL3, which in turn affects ribosomal subcellular localization and, ultimately, mitochondrial activity.
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Affiliation(s)
- Ivan Milenkovic
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Helaine Graziele Santos Vieira
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Morghan C Lucas
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jorge Ruiz-Orera
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), D-13125 Berlin, Germany
| | - Giannino Patone
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), D-13125 Berlin, Germany
| | - Scott Kesteven
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | - Jianxin Wu
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | - Michael Feneley
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | - Guadalupe Espadas
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Eduard Sabidó
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Norbert Hübner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), D-13125 Berlin, Germany
- Charité -Universitätsmedizin, D-10117 Berlin, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Berlin, D-13347 Berlin, Germany
| | - Sebastiaan van Heesch
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | | | - Eva Maria Novoa
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
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2
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Konigorski S, Janke J, Patone G, Bergmann MM, Lippert C, Hübner N, Kaaks R, Boeing H, Pischon T. Correction to: Identification of novel genes whose expression in adipose tissue affects body fat mass and distribution: an RNA-Seq and Mendelian Randomization study. Eur J Hum Genet 2022:10.1038/s41431-022-01183-x. [PMID: 36038726 DOI: 10.1038/s41431-022-01183-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Stefan Konigorski
- Digital Health & Machine Learning Research Group, Hasso Plattner Institute for Digital Engineering, University of Potsdam, Potsdam, Germany.
- Molecular Epidemiology Research Group, Max Delbrück Center (MDC) for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Jürgen Janke
- Molecular Epidemiology Research Group, Max Delbrück Center (MDC) for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Giannino Patone
- Genetics and Genomics of Cardiovascular Diseases Research Group, Max Delbrück Center (MDC) for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Manuela M Bergmann
- German Institute of Human Nutrition Potsdam-Rehbrücke (DIfE), Nuthetal, Germany
| | - Christoph Lippert
- Digital Health & Machine Learning Research Group, Hasso Plattner Institute for Digital Engineering, University of Potsdam, Potsdam, Germany
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Norbert Hübner
- Genetics and Genomics of Cardiovascular Diseases Research Group, Max Delbrück Center (MDC) for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- DZHK (German Center for Cardiovascular Research) partner site Berlin, Berlin, Germany
- Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Rudolf Kaaks
- Department of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Heiner Boeing
- German Institute of Human Nutrition Potsdam-Rehbrücke (DIfE), Nuthetal, Germany
| | - Tobias Pischon
- Molecular Epidemiology Research Group, Max Delbrück Center (MDC) for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
- DZHK (German Center for Cardiovascular Research) partner site Berlin, Berlin, Germany.
- Charité Universitätsmedizin Berlin, Berlin, Germany.
- MDC Biobank, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany.
- BIH Biobank, Berlin Institute of Health, Berlin, Germany.
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3
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Konigorski S, Janke J, Patone G, Bergmann MM, Lippert C, Hübner N, Kaaks R, Boeing H, Pischon T. Identification of novel genes whose expression in adipose tissue affects body fat mass and distribution: an RNA-Seq and Mendelian Randomization study. Eur J Hum Genet 2022:10.1038/s41431-022-01161-3. [PMID: 35953519 DOI: 10.1038/s41431-022-01161-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 06/26/2022] [Accepted: 07/19/2022] [Indexed: 10/15/2022] Open
Abstract
Many studies have shown that abdominal adiposity is more strongly related to health risks than peripheral adiposity. However, the underlying pathways are still poorly understood. In this cross-sectional study using data from RNA-sequencing experiments and whole-body MRI scans of 200 participants in the EPIC-Potsdam cohort, our aim was to identify novel genes whose gene expression in subcutaneous adipose tissue has an effect on body fat mass (BFM) and body fat distribution (BFD). The analysis identified 625 genes associated with adiposity, of which 531 encode a known protein and 487 are novel candidate genes for obesity. Enrichment analyses indicated that BFM-associated genes were characterized by their higher than expected involvement in cellular, regulatory and immune system processes, and BFD-associated genes by their involvement in cellular, metabolic, and regulatory processes. Mendelian Randomization analyses suggested that the gene expression of 69 genes was causally related to BFM and BFD. Six genes were replicated in UK Biobank. In this study, we identified novel genes for BFM and BFD that are BFM- and BFD-specific, involved in different molecular processes, and whose up-/downregulated gene expression may causally contribute to obesity.
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Affiliation(s)
- Stefan Konigorski
- Digital Health & Machine Learning Research Group, Hasso Plattner Institute for Digital Engineering, University of Potsdam, Potsdam, Germany.
- Molecular Epidemiology Research Group, Max Delbrück Center (MDC) for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Jürgen Janke
- Molecular Epidemiology Research Group, Max Delbrück Center (MDC) for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Giannino Patone
- Genetics and Genomics of Cardiovascular Diseases Research Group, Max Delbrück Center (MDC) for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Manuela M Bergmann
- German Institute of Human Nutrition Potsdam-Rehbrücke (DIfE), Nuthetal, Germany
| | - Christoph Lippert
- Digital Health & Machine Learning Research Group, Hasso Plattner Institute for Digital Engineering, University of Potsdam, Potsdam, Germany
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Norbert Hübner
- Genetics and Genomics of Cardiovascular Diseases Research Group, Max Delbrück Center (MDC) for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- DZHK (German Center for Cardiovascular Research) partner site Berlin, Berlin, Germany
- Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Rudolf Kaaks
- Department of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Heiner Boeing
- German Institute of Human Nutrition Potsdam-Rehbrücke (DIfE), Nuthetal, Germany
| | - Tobias Pischon
- Molecular Epidemiology Research Group, Max Delbrück Center (MDC) for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
- DZHK (German Center for Cardiovascular Research) partner site Berlin, Berlin, Germany.
- Charité Universitätsmedizin Berlin, Berlin, Germany.
- MDC Biobank, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany.
- BIH Biobank, Berlin Institute of Health, Berlin, Germany.
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4
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Reichart D, Lindberg EL, Maatz H, Miranda AMA, Viveiros A, Shvetsov N, Gärtner A, Nadelmann ER, Lee M, Kanemaru K, Ruiz-Orera J, Strohmenger V, DeLaughter DM, Patone G, Zhang H, Woehler A, Lippert C, Kim Y, Adami E, Gorham JM, Barnett SN, Brown K, Buchan RJ, Chowdhury RA, Constantinou C, Cranley J, Felkin LE, Fox H, Ghauri A, Gummert J, Kanda M, Li R, Mach L, McDonough B, Samari S, Shahriaran F, Yapp C, Stanasiuk C, Theotokis PI, Theis FJ, van den Bogaerdt A, Wakimoto H, Ware JS, Worth CL, Barton PJR, Lee YA, Teichmann SA, Milting H, Noseda M, Oudit GY, Heinig M, Seidman JG, Hubner N, Seidman CE. Pathogenic variants damage cell composition and single cell transcription in cardiomyopathies. Science 2022; 377:eabo1984. [PMID: 35926050 PMCID: PMC9528698 DOI: 10.1126/science.abo1984] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Pathogenic variants in genes that cause dilated cardiomyopathy (DCM) and arrhythmogenic cardiomyopathy (ACM) convey high risks for the development of heart failure through unknown mechanisms. Using single-nucleus RNA sequencing, we characterized the transcriptome of 880,000 nuclei from 18 control and 61 failing, nonischemic human hearts with pathogenic variants in DCM and ACM genes or idiopathic disease. We performed genotype-stratified analyses of the ventricular cell lineages and transcriptional states. The resultant DCM and ACM ventricular cell atlas demonstrated distinct right and left ventricular responses, highlighting genotype-associated pathways, intercellular interactions, and differential gene expression at single-cell resolution. Together, these data illuminate both shared and distinct cellular and molecular architectures of human heart failure and suggest candidate therapeutic targets.
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Affiliation(s)
- Daniel Reichart
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Cardiovascular Division, Brigham and Women's Hospital, Boston, MA 02115, USA.,Department of Medicine I, University Hospital, LMU Munich, 80336 Munich, Germany
| | - Eric L Lindberg
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Henrike Maatz
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 10785 Berlin, Germany
| | - Antonio M A Miranda
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK.,British Heart Foundation Centre for Research Excellence and Centre for Regenerative Medicine, Imperial College London, London WC2R 2LS, UK
| | - Anissa Viveiros
- Division of Cardiology, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada.,Mazankowski Alberta Heart Institute, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Nikolay Shvetsov
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Anna Gärtner
- Erich and Hanna Klessmann Institute, Heart and Diabetes Center NRW, University Hospital of the Ruhr-University Bochum, 32545 Bad Oeynhausen, Germany
| | - Emily R Nadelmann
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Michael Lee
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
| | - Kazumasa Kanemaru
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Jorge Ruiz-Orera
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Viktoria Strohmenger
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Walter-Brendel-Centre of Experimental Medicine, Ludwig-Maximilian University of Munich, 81377 Munich, Germany
| | - Daniel M DeLaughter
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Bethesda, MD 20815, USA
| | - Giannino Patone
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Hao Zhang
- Division of Cardiology, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada.,Mazankowski Alberta Heart Institute, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Andrew Woehler
- Systems Biology Imaging Platform, Berlin Institute for Medical Systems Biology (BIMSB), Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 10115 Berlin, Germany
| | - Christoph Lippert
- Digital Health-Machine Learning group, Hasso Plattner Institute for Digital Engineering, University of Potsdam, 14482 Potsdam, Germany.,Hasso Plattner Institute for Digital Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yuri Kim
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Cardiovascular Division, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Eleonora Adami
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Joshua M Gorham
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Sam N Barnett
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
| | - Kemar Brown
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Cardiac Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Rachel J Buchan
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK.,Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK
| | - Rasheda A Chowdhury
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
| | | | - James Cranley
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Leanne E Felkin
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK.,Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK
| | - Henrik Fox
- Heart and Diabetes Center NRW, Clinic for Thoracic and Cardiovascular Surgery, University Hospital of the Ruhr-University, 32545 Bad Oeynhausen, Germany
| | - Ahla Ghauri
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Jan Gummert
- Heart and Diabetes Center NRW, Clinic for Thoracic and Cardiovascular Surgery, University Hospital of the Ruhr-University, 32545 Bad Oeynhausen, Germany
| | - Masatoshi Kanda
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany.,Department of Rheumatology and Clinical Immunology, Sapporo Medical University School of Medicine, Sapporo 060-8556, Japan
| | - Ruoyan Li
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Lukas Mach
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK.,Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK
| | - Barbara McDonough
- Cardiovascular Division, Brigham and Women's Hospital, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Bethesda, MD 20815, USA
| | - Sara Samari
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
| | - Farnoush Shahriaran
- Computational Health Center, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), 85764 Neuherberg, Germany
| | - Clarence Yapp
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Caroline Stanasiuk
- Erich and Hanna Klessmann Institute, Heart and Diabetes Center NRW, University Hospital of the Ruhr-University Bochum, 32545 Bad Oeynhausen, Germany
| | - Pantazis I Theotokis
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK.,MRC London Institute of Medical Sciences, Imperial College London, London W12 0NN, UK
| | - Fabian J Theis
- Computational Health Center, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), 85764 Neuherberg, Germany
| | | | - Hiroko Wakimoto
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - James S Ware
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK.,Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK.,MRC London Institute of Medical Sciences, Imperial College London, London W12 0NN, UK
| | - Catherine L Worth
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Paul J R Barton
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK.,Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK.,MRC London Institute of Medical Sciences, Imperial College London, London W12 0NN, UK
| | - Young-Ae Lee
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany.,Clinic for Pediatric Allergy, Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin, 13125 Berlin, Germany
| | - Sarah A Teichmann
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK.,Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, UK
| | - Hendrik Milting
- Erich and Hanna Klessmann Institute, Heart and Diabetes Center NRW, University Hospital of the Ruhr-University Bochum, 32545 Bad Oeynhausen, Germany
| | - Michela Noseda
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK.,British Heart Foundation Centre for Research Excellence and Centre for Regenerative Medicine, Imperial College London, London WC2R 2LS, UK
| | - Gavin Y Oudit
- Division of Cardiology, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada.,Mazankowski Alberta Heart Institute, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Matthias Heinig
- Computational Health Center, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), 85764 Neuherberg, Germany.,Department of Informatics, Technische Universitaet Muenchen (TUM), 85748 Munich, Germany.,DZHK (German Centre for Cardiovascular Research), Munich Heart Association, Partner Site Munich, 10785 Berlin, Germany
| | | | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 10785 Berlin, Germany.,Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Cardiovascular Division, Brigham and Women's Hospital, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Bethesda, MD 20815, USA
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5
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Axelsson Raja A, Wakimoto H, DeLaughter DM, Reichart D, Gorham J, Conner DA, Lun M, Probst CK, Sakai N, Knipe RS, Montesi SB, Shea B, Adam LP, Leinwand LA, Wan W, Choi ES, Lindberg EL, Patone G, Noseda M, Hübner N, Seidman CE, Tager AM, Seidman JG, Ho CY. Ablation of lysophosphatidic acid receptor 1 attenuates hypertrophic cardiomyopathy in a mouse model. Proc Natl Acad Sci U S A 2022; 119:e2204174119. [PMID: 35787042 PMCID: PMC9282378 DOI: 10.1073/pnas.2204174119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/25/2022] [Indexed: 01/07/2023] Open
Abstract
Myocardial fibrosis is a key pathologic feature of hypertrophic cardiomyopathy (HCM). However, the fibrotic pathways activated by HCM-causing sarcomere protein gene mutations are poorly defined. Because lysophosphatidic acid is a mediator of fibrosis in multiple organs and diseases, we tested the role of the lysophosphatidic acid pathway in HCM. Lysphosphatidic acid receptor 1 (LPAR1), a cell surface receptor, is required for lysophosphatidic acid mediation of fibrosis. We bred HCM mice carrying a pathogenic myosin heavy-chain variant (403+/-) with Lpar1-ablated mice to create mice carrying both genetic changes (403+/- LPAR1 -/-) and assessed development of cardiac hypertrophy and fibrosis. Compared with 403+/- LPAR1WT, 403+/- LPAR1 -/- mice developed significantly less hypertrophy and fibrosis. Single-nucleus RNA sequencing of left ventricular tissue demonstrated that Lpar1 was predominantly expressed by lymphatic endothelial cells (LECs) and cardiac fibroblasts. Lpar1 ablation reduced the population of LECs, confirmed by immunofluorescence staining of the LEC markers Lyve1 and Ccl21a and, by in situ hybridization, for Reln and Ccl21a. Lpar1 ablation also altered the distribution of fibroblast cell states. FB1 and FB2 fibroblasts decreased while FB0 and FB3 fibroblasts increased. Our findings indicate that Lpar1 is expressed predominantly by LECs and fibroblasts in the heart and is required for development of hypertrophy and fibrosis in an HCM mouse model. LPAR1 antagonism, including agents in clinical trials for other fibrotic diseases, may be beneficial for HCM.
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Affiliation(s)
- Anna Axelsson Raja
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Department of Cardiology, Copenhagen University Hospital Rigshospitalet, 2100 Copenhagen, Denmark
| | - Hiroko Wakimoto
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | | | - Daniel Reichart
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Joshua Gorham
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - David A. Conner
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Mingyue Lun
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Clemens K. Probst
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114
- Fibrosis Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114
| | - Norihiko Sakai
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114
- Fibrosis Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114
- Division of Nephrology, Kanazawa University, Kanazawa, 920-1192 Japan
| | - Rachel S. Knipe
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114
- Fibrosis Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114
| | - Sydney B. Montesi
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114
| | - Barry Shea
- Division of Pulmonary, Critical Care and Sleep Medicine, Albert Medical School of Brown University, Providence, RI 02903
| | - Leonard P. Adam
- Research and Development, Bristol-Myers Squibb Company, Princeton, NJ 08540
| | - Leslie A. Leinwand
- Biofrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80302
| | - William Wan
- Biofrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80302
| | - Esther Sue Choi
- Biofrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80302
| | - Eric L. Lindberg
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Giannino Patone
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Michela Noseda
- National Heart and Lung Institute, British Heart Foundation Centre of Regenerative Medicine, British Heart Foundation Centre of Research Excellence, Imperial College London, London SW7 2AZ, United Kingdom
| | - Norbert Hübner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
- Charité-Universitätsmedizin, Berlin Institute of Health, 10117 Berlin, Germany
- German Centre for Cardiovascular Research, Partner Site Berlin, 13347 Berlin, Germany
| | - Christine E. Seidman
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Division of Cardiovascular Medicine, Brigham and Women’s Hospital, Boston, MA 02115
- HHMI, Chevy Chase, MD 20815
| | - Andrew M. Tager
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114
- Fibrosis Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114
| | - J. G. Seidman
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Carolyn Y. Ho
- Division of Cardiovascular Medicine, Brigham and Women’s Hospital, Boston, MA 02115
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6
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Witte F, Ruiz-Orera J, Mattioli CC, Blachut S, Adami E, Schulz JF, Schneider-Lunitz V, Hummel O, Patone G, Mücke MB, Šilhavý J, Heinig M, Bottolo L, Sanchis D, Vingron M, Chekulaeva M, Pravenec M, Hubner N, van Heesch S. A trans locus causes a ribosomopathy in hypertrophic hearts that affects mRNA translation in a protein length-dependent fashion. Genome Biol 2021; 22:191. [PMID: 34183069 PMCID: PMC8240307 DOI: 10.1186/s13059-021-02397-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 06/02/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Little is known about the impact of trans-acting genetic variation on the rates with which proteins are synthesized by ribosomes. Here, we investigate the influence of such distant genetic loci on the efficiency of mRNA translation and define their contribution to the development of complex disease phenotypes within a panel of rat recombinant inbred lines. RESULTS We identify several tissue-specific master regulatory hotspots that each control the translation rates of multiple proteins. One of these loci is restricted to hypertrophic hearts, where it drives a translatome-wide and protein length-dependent change in translational efficiency, altering the stoichiometric translation rates of sarcomere proteins. Mechanistic dissection of this locus across multiple congenic lines points to a translation machinery defect, characterized by marked differences in polysome profiles and misregulation of the small nucleolar RNA SNORA48. Strikingly, from yeast to humans, we observe reproducible protein length-dependent shifts in translational efficiency as a conserved hallmark of translation machinery mutants, including those that cause ribosomopathies. Depending on the factor mutated, a pre-existing negative correlation between protein length and translation rates could either be enhanced or reduced, which we propose to result from mRNA-specific imbalances in canonical translation initiation and reinitiation rates. CONCLUSIONS We show that distant genetic control of mRNA translation is abundant in mammalian tissues, exemplified by a single genomic locus that triggers a translation-driven molecular mechanism. Our work illustrates the complexity through which genetic variation can drive phenotypic variability between individuals and thereby contribute to complex disease.
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Affiliation(s)
- Franziska Witte
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
- Present Address: NUVISAN ICB GmbH, Lead Discovery-Structrual Biology, 13353, Berlin, Germany
| | - Jorge Ruiz-Orera
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Camilla Ciolli Mattioli
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 10115, Berlin, Germany
- Present Address: Department of Biological Regulation, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Susanne Blachut
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Eleonora Adami
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
- Present Address: Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore, 169857, Singapore
| | - Jana Felicitas Schulz
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Valentin Schneider-Lunitz
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Oliver Hummel
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Giannino Patone
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Michael Benedikt Mücke
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 13347, Berlin, Germany
- Charité-Universitätsmedizin, 10117, Berlin, Germany
| | - Jan Šilhavý
- Institute of Physiology of the Czech Academy of Sciences, 4, 142 20, Praha, Czech Republic
| | - Matthias Heinig
- Institute of Computational Biology (ICB), HMGU, Ingolstaedter Landstr. 1, 85764 Neuherberg, Munich, Germany
- Department of Informatics, Technische Universitaet Muenchen (TUM), Boltzmannstr. 3, 85748 Garching, Munich, Germany
| | - Leonardo Bottolo
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
- The Alan Turing Institute, London, NW1 2DB, UK
- MRC Biostatistics Unit, University of Cambridge, Cambridge, CB2 0SR, UK
| | - Daniel Sanchis
- Institut de Recerca Biomedica de Lleida (IRBLLEIDA), Universitat de Lleida, Edifici Biomedicina-I. Av. Rovira Roure, 80, 25198, Lleida, Spain
| | - Martin Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Marina Chekulaeva
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 10115, Berlin, Germany
| | - Michal Pravenec
- Institute of Physiology of the Czech Academy of Sciences, 4, 142 20, Praha, Czech Republic
| | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany.
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 13347, Berlin, Germany.
- Charité-Universitätsmedizin, 10117, Berlin, Germany.
| | - Sebastiaan van Heesch
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany.
- Present Address: The Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.
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7
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Cuello F, Knaust AE, Saleem U, Loos M, Raabe J, Mosqueira D, Laufer S, Schweizer M, van der Kraak P, Flenner F, Ulmer BM, Braren I, Yin X, Theofilatos K, Ruiz‐Orera J, Patone G, Klampe B, Schulze T, Piasecki A, Pinto Y, Vink A, Hübner N, Harding S, Mayr M, Denning C, Eschenhagen T, Hansen A. Impairment of the ER/mitochondria compartment in human cardiomyocytes with PLN p.Arg14del mutation. EMBO Mol Med 2021; 13:e13074. [PMID: 33998164 PMCID: PMC8185541 DOI: 10.15252/emmm.202013074] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 03/31/2021] [Accepted: 04/07/2021] [Indexed: 12/28/2022] Open
Abstract
The phospholamban (PLN) p.Arg14del mutation causes dilated cardiomyopathy, with the molecular disease mechanisms incompletely understood. Patient dermal fibroblasts were reprogrammed to hiPSC, isogenic controls were established by CRISPR/Cas9, and cardiomyocytes were differentiated. Mutant cardiomyocytes revealed significantly prolonged Ca2+ transient decay time, Ca2+ -load dependent irregular beating pattern, and lower force. Proteomic analysis revealed less endoplasmic reticulum (ER) and ribosomal and mitochondrial proteins. Electron microscopy showed dilation of the ER and large lipid droplets in close association with mitochondria. Follow-up experiments confirmed impairment of the ER/mitochondria compartment. PLN p.Arg14del end-stage heart failure samples revealed perinuclear aggregates positive for ER marker proteins and oxidative stress in comparison with ischemic heart failure and non-failing donor heart samples. Transduction of PLN p.Arg14del EHTs with the Ca2+ -binding proteins GCaMP6f or parvalbumin improved the disease phenotype. This study identified impairment of the ER/mitochondria compartment without SR dysfunction as a novel disease mechanism underlying PLN p.Arg14del cardiomyopathy. The pathology was improved by Ca2+ -scavenging, suggesting impaired local Ca2+ cycling as an important disease culprit.
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8
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Jiang H, Hooper C, Kelly M, Steeples V, Simon JN, Beglov J, Azad AJ, Leinhos L, Bennett P, Ehler E, Kalisch-Smith JI, Sparrow DB, Fischer R, Heilig R, Isackson H, Ehsan M, Patone G, Huebner N, Davies B, Watkins H, Gehmlich K. Functional analysis of a gene-edited mouse model to gain insights into the disease mechanisms of a titin missense variant. Basic Res Cardiol 2021; 116:14. [PMID: 33637999 PMCID: PMC7910237 DOI: 10.1007/s00395-021-00853-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 02/10/2021] [Indexed: 11/03/2022]
Abstract
Titin truncating variants are a well-established cause of cardiomyopathy; however, the role of titin missense variants is less well understood. Here we describe the generation of a mouse model to investigate the underlying disease mechanism of a previously reported titin A178D missense variant identified in a family with non-compaction and dilated cardiomyopathy. Heterozygous and homozygous mice carrying the titin A178D missense variant were characterised in vivo by echocardiography. Heterozygous mice had no detectable phenotype at any time point investigated (up to 1 year). By contrast, homozygous mice developed dilated cardiomyopathy from 3 months. Chronic adrenergic stimulation aggravated the phenotype. Targeted transcript profiling revealed induction of the foetal gene programme and hypertrophic signalling pathways in homozygous mice, and these were confirmed at the protein level. Unsupervised proteomics identified downregulation of telethonin and four-and-a-half LIM domain 2, as well as the upregulation of heat shock proteins and myeloid leukaemia factor 1. Loss of telethonin from the cardiac Z-disc was accompanied by proteasomal degradation; however, unfolded telethonin accumulated in the cytoplasm, leading to a proteo-toxic response in the mice.We show that the titin A178D missense variant is pathogenic in homozygous mice, resulting in cardiomyopathy. We also provide evidence of the disease mechanism: because the titin A178D variant abolishes binding of telethonin, this leads to its abnormal cytoplasmic accumulation. Subsequent degradation of telethonin by the proteasome results in proteasomal overload, and activation of a proteo-toxic response. The latter appears to be a driving factor for the cardiomyopathy observed in the mouse model.
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Affiliation(s)
- He Jiang
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine and British Heart Foundation Centre of Research Excellence Oxford, University of Oxford, Oxford, OX3 9DU, UK
| | - Charlotte Hooper
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine and British Heart Foundation Centre of Research Excellence Oxford, University of Oxford, Oxford, OX3 9DU, UK
| | - Matthew Kelly
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine and British Heart Foundation Centre of Research Excellence Oxford, University of Oxford, Oxford, OX3 9DU, UK
| | - Violetta Steeples
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine and British Heart Foundation Centre of Research Excellence Oxford, University of Oxford, Oxford, OX3 9DU, UK
| | - Jillian N Simon
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine and British Heart Foundation Centre of Research Excellence Oxford, University of Oxford, Oxford, OX3 9DU, UK
| | - Julia Beglov
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine and British Heart Foundation Centre of Research Excellence Oxford, University of Oxford, Oxford, OX3 9DU, UK
| | - Amar J Azad
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine and British Heart Foundation Centre of Research Excellence Oxford, University of Oxford, Oxford, OX3 9DU, UK
| | - Lisa Leinhos
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine and British Heart Foundation Centre of Research Excellence Oxford, University of Oxford, Oxford, OX3 9DU, UK
| | - Pauline Bennett
- Randall Centre for Cell and Molecular Biophysics, School of Cardiovascular Medicine and Sciences, King's College London BHF Centre of Research Excellence, London, UK
| | - Elisabeth Ehler
- Randall Centre for Cell and Molecular Biophysics, School of Cardiovascular Medicine and Sciences, King's College London BHF Centre of Research Excellence, London, UK
| | | | - Duncan B Sparrow
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Roman Fischer
- Nuffield Department of Clinical Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
| | - Raphael Heilig
- Nuffield Department of Clinical Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
| | - Henrik Isackson
- Department of Medical Sciences, Cardiology, Uppsala University, Uppsala, Sweden
- Department of Medical Cell Biology, Integrative Physiology, Uppsala University, Uppsala, Sweden
| | - Mehroz Ehsan
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine and British Heart Foundation Centre of Research Excellence Oxford, University of Oxford, Oxford, OX3 9DU, UK
| | - Giannino Patone
- Max Delbrueck Centre for Molecular Medicine, Berlin, Germany
| | - Norbert Huebner
- Max Delbrueck Centre for Molecular Medicine, Berlin, Germany
| | - Benjamin Davies
- Transgenic Core, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Hugh Watkins
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine and British Heart Foundation Centre of Research Excellence Oxford, University of Oxford, Oxford, OX3 9DU, UK
| | - Katja Gehmlich
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine and British Heart Foundation Centre of Research Excellence Oxford, University of Oxford, Oxford, OX3 9DU, UK.
- Institute of Cardiovascular Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
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9
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Su X, Feng Y, Rahman SA, Wu S, Li G, Rüschendorf F, Zhao L, Cui H, Liang J, Fang L, Hu H, Froehler S, Yu Y, Patone G, Hummel O, Chen Q, Raile K, Luft FC, Bähring S, Hussain K, Chen W, Zhang J, Gong M. Phosphatidylinositol 4-kinase β mutations cause nonsyndromic sensorineural deafness and inner ear malformation. J Genet Genomics 2020; 47:618-626. [PMID: 33358777 DOI: 10.1016/j.jgg.2020.07.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 07/15/2020] [Accepted: 07/16/2020] [Indexed: 10/23/2022]
Abstract
Congenital hearing loss is a common disorder worldwide. Heterogeneous gene variation accounts for approximately 20-25% of such patients. We investigated a five-generation Chinese family with autosomal-dominant nonsyndromic sensorineural hearing loss (SNHL). No wave was detected in the pure-tone audiometry, and the auditory brainstem response was absent in all patients. Computed tomography of the patients, as well as of two sporadic SNHL cases, showed bilateral inner ear anomaly, cochlear maldevelopment, absence of the osseous spiral lamina, and an enlarged vestibular aqueduct. Such findings were absent in nonaffected persons. We used linkage analysis and exome sequencing and uncovered a heterozygous missense mutation in the PI4KB gene (p.Gln121Arg) encoding phosphatidylinositol 4-kinase β (PI4KB) from the patients in this family. In addition, 3 missense PI4KB (p.Val434Gly, p.Glu667Lys, and p.Met739Arg) mutations were identified in five patients with nonsyndromic SNHL from 57 sporadic cases. No such mutations were present within 600 Chinese controls, the 1000 genome project, gnomAD, or similar databases. Depleting pi4kb mRNA expression in zebrafish caused inner ear abnormalities and audiosensory impairment, mimicking the patient phenotypes. Moreover, overexpression of 4 human missense PI4KB mutant mRNAs in zebrafish embryos resulted in impaired hearing function, suggesting dominant-negative effects. Taken together, our results reveal that PI4KB mutations can cause SNHL and inner ear malformation. PI4KB should be included in neonatal deafness screening.
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Affiliation(s)
- Xiulan Su
- Clinical Medicine Research Center, Affiliated Hospital of Inner Mongolia Medical University, Huhhot, 010050, China
| | - Yufei Feng
- Affiliated Hospital of Guangdong Medical University & Key Laboratory of Zebrafish Model for Development and Disease of Guangdong Medical University, Zhanjiang, 524001, China; Marine Medical Research Institute of Guangdong Zhanjiang, Zhanjiang, 524023, China
| | - Sofia A Rahman
- Genomic Medicine Programme, UCL Institute of Child Health and Great Ormond Street Hospital for Children, 30 Guilford Street, London, WC1N 1EH, UK
| | - Shuilong Wu
- Affiliated Hospital of Guangdong Medical University & Key Laboratory of Zebrafish Model for Development and Disease of Guangdong Medical University, Zhanjiang, 524001, China; Marine Medical Research Institute of Guangdong Zhanjiang, Zhanjiang, 524023, China
| | - Guoan Li
- Affiliated Hospital of Guangdong Medical University & Key Laboratory of Zebrafish Model for Development and Disease of Guangdong Medical University, Zhanjiang, 524001, China; Marine Medical Research Institute of Guangdong Zhanjiang, Zhanjiang, 524023, China
| | - Franz Rüschendorf
- Max-Delbrueck-Center for Molecular Medicine (MDC), Robert-Roessle-Str.10, Berlin, 13125, Germany
| | - Lei Zhao
- Department of Radiology, Affiliated Hospital of Inner Mongolia Medical University, Huhhot, 010050, China
| | - Hongwei Cui
- Clinical Medicine Research Center, Affiliated Hospital of Inner Mongolia Medical University, Huhhot, 010050, China
| | - Junqing Liang
- Affiliated People Hospital of Inner Mongolia Medical University, Huhhot, 010050, China
| | - Liang Fang
- Max-Delbrueck-Center for Molecular Medicine (MDC), Robert-Roessle-Str.10, Berlin, 13125, Germany; Department of Biology, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Hao Hu
- Guangzhou Women and Children's Medical Center, Guangzhou, 510623, China
| | - Sebastian Froehler
- Max-Delbrueck-Center for Molecular Medicine (MDC), Robert-Roessle-Str.10, Berlin, 13125, Germany
| | - Yong Yu
- Max-Delbrueck-Center for Molecular Medicine (MDC), Robert-Roessle-Str.10, Berlin, 13125, Germany
| | - Giannino Patone
- Max-Delbrueck-Center for Molecular Medicine (MDC), Robert-Roessle-Str.10, Berlin, 13125, Germany
| | - Oliver Hummel
- Max-Delbrueck-Center for Molecular Medicine (MDC), Robert-Roessle-Str.10, Berlin, 13125, Germany
| | - Qinghua Chen
- Department of Radiology, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, China
| | - Klemens Raile
- Experimental and Clinical Research Center (ECRC), A Joint Cooperation Between the Charité Medical Faculty and the Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association (MDC), Lindenberger Weg.80, Berlin, 13125, Germany
| | - Friedrich C Luft
- Experimental and Clinical Research Center (ECRC), A Joint Cooperation Between the Charité Medical Faculty and the Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association (MDC), Lindenberger Weg.80, Berlin, 13125, Germany
| | - Sylvia Bähring
- Experimental and Clinical Research Center (ECRC), A Joint Cooperation Between the Charité Medical Faculty and the Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association (MDC), Lindenberger Weg.80, Berlin, 13125, Germany
| | - Khalid Hussain
- Department of Paediatric Medicine Division of Endocrinology, Sidra Medical & Research Center, OPC, Doha, C6-337, Qatar
| | - Wei Chen
- Department of Biology, Southern University of Science and Technology, Shenzhen, 518055, China; Medi-X Institute, SUSTec Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Jingjing Zhang
- Affiliated Hospital of Guangdong Medical University & Key Laboratory of Zebrafish Model for Development and Disease of Guangdong Medical University, Zhanjiang, 524001, China; Marine Medical Research Institute of Guangdong Zhanjiang, Zhanjiang, 524023, China.
| | - Maolian Gong
- Experimental and Clinical Research Center (ECRC), A Joint Cooperation Between the Charité Medical Faculty and the Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association (MDC), Lindenberger Weg.80, Berlin, 13125, Germany.
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10
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Litviňuková M, Talavera-López C, Maatz H, Reichart D, Worth CL, Lindberg EL, Kanda M, Polanski K, Heinig M, Lee M, Nadelmann ER, Roberts K, Tuck L, Fasouli ES, DeLaughter DM, McDonough B, Wakimoto H, Gorham JM, Samari S, Mahbubani KT, Saeb-Parsy K, Patone G, Boyle JJ, Zhang H, Zhang H, Viveiros A, Oudit GY, Bayraktar OA, Seidman JG, Seidman CE, Noseda M, Hubner N, Teichmann SA. Cells of the adult human heart. Nature 2020; 588:466-472. [PMID: 32971526 PMCID: PMC7681775 DOI: 10.1038/s41586-020-2797-4] [Citation(s) in RCA: 677] [Impact Index Per Article: 169.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 09/18/2020] [Indexed: 12/15/2022]
Abstract
Cardiovascular disease is the leading cause of death worldwide. Advanced insights into disease mechanisms and therapeutic strategies require a deeper understanding of the molecular processes involved in the healthy heart. Knowledge of the full repertoire of cardiac cells and their gene expression profiles is a fundamental first step in this endeavour. Here, using state-of-the-art analyses of large-scale single-cell and single-nucleus transcriptomes, we characterize six anatomical adult heart regions. Our results highlight the cellular heterogeneity of cardiomyocytes, pericytes and fibroblasts, and reveal distinct atrial and ventricular subsets of cells with diverse developmental origins and specialized properties. We define the complexity of the cardiac vasculature and its changes along the arterio-venous axis. In the immune compartment, we identify cardiac-resident macrophages with inflammatory and protective transcriptional signatures. Furthermore, analyses of cell-to-cell interactions highlight different networks of macrophages, fibroblasts and cardiomyocytes between atria and ventricles that are distinct from those of skeletal muscle. Our human cardiac cell atlas improves our understanding of the human heart and provides a valuable reference for future studies.
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Affiliation(s)
- Monika Litviňuková
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.,Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Carlos Talavera-López
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.,EMBL - EBI, Wellcome Genome Campus, Hinxton, UK
| | - Henrike Maatz
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Daniel Reichart
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Department of Cardiology, University Heart & Vascular Center, University of Hamburg, Hamburg, Germany
| | - Catherine L Worth
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Eric L Lindberg
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Masatoshi Kanda
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.,Department of Rheumatology and Clinical Immunology, Sapporo Medical University, Sapporo, Japan
| | - Krzysztof Polanski
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Matthias Heinig
- Institute of Computational Biology (ICB), HMGU, Neuherberg, Germany.,Department of Informatics, Technische Universitaet Muenchen (TUM), Munich, Germany
| | - Michael Lee
- National Heart and Lung Institute, Imperial College London, London, UK
| | | | - Kenny Roberts
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Liz Tuck
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Eirini S Fasouli
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Barbara McDonough
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Cardiovascular Division, Brigham and Women's Hospital, Boston, MA, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Hiroko Wakimoto
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Joshua M Gorham
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Sara Samari
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Krishnaa T Mahbubani
- Department of Surgery, University of Cambridge, NIHR Cambridge Biomedical Centre, Cambridge Biorepository for Translational Medicine, Cambridge, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge, NIHR Cambridge Biomedical Centre, Cambridge Biorepository for Translational Medicine, Cambridge, UK
| | - Giannino Patone
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Joseph J Boyle
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Hongbo Zhang
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.,Department of Histology and Embryology of Zhongshan School of Medicine, Sun-Yat Sen University, Guangzhou, China
| | - Hao Zhang
- Division of Cardiology, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada.,Mazankowski Alberta Heart Institute, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Anissa Viveiros
- Division of Cardiology, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada.,Mazankowski Alberta Heart Institute, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Gavin Y Oudit
- Division of Cardiology, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada.,Mazankowski Alberta Heart Institute, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Omer Ali Bayraktar
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - J G Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
| | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, USA. .,Cardiovascular Division, Brigham and Women's Hospital, Boston, MA, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Michela Noseda
- National Heart and Lung Institute, Imperial College London, London, UK. .,British Heart Foundation Centre of Regenerative Medicine, British Heart Foundation Centre of Research Excellence, Imperial College London, London, UK.
| | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany. .,DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany. .,Charité-Universitätsmedizin, Berlin, Germany. .,Berlin Institute of Health (BIH), Berlin, Germany.
| | - Sarah A Teichmann
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK. .,Deptartment of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK.
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11
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Grunwald SA, Popp O, Haafke S, Jedraszczak N, Grieben U, Saar K, Patone G, Kress W, Steinhagen-Thiessen E, Dittmar G, Spuler S. Statin-induced myopathic changes in primary human muscle cells and reversal by a prostaglandin F2 alpha analogue. Sci Rep 2020; 10:2158. [PMID: 32034223 PMCID: PMC7005895 DOI: 10.1038/s41598-020-58668-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 01/17/2020] [Indexed: 12/18/2022] Open
Abstract
Statin-related muscle side effects are a constant healthcare problem since patient compliance is dependent on side effects. Statins reduce plasma cholesterol levels and can prevent secondary cardiovascular diseases. Although statin-induced muscle damage has been studied, preventive or curative therapies are yet to be reported. We exposed primary human muscle cell populations (n = 22) to a lipophilic (simvastatin) and a hydrophilic (rosuvastatin) statin and analyzed their expressome. Data and pathway analyses included GOrilla, Reactome and DAVID. We measured mevalonate intracellularly and analyzed eicosanoid profiles secreted by human muscle cells. Functional assays included proliferation and differentiation quantification. More than 1800 transcripts and 900 proteins were differentially expressed after exposure to statins. Simvastatin had a stronger effect on the expressome than rosuvastatin, but both statins influenced cholesterol biosynthesis, fatty acid metabolism, eicosanoid synthesis, proliferation, and differentiation of human muscle cells. Cultured human muscle cells secreted ω-3 and ω-6 derived eicosanoids and prostaglandins. The ω-6 derived metabolites were found at higher levels secreted from simvastatin-treated primary human muscle cells. Eicosanoids rescued muscle cell differentiation. Our data suggest a new aspect on the role of skeletal muscle in cholesterol metabolism. For clinical practice, the addition of omega-n fatty acids might be suitable to prevent or treat statin-myopathy.
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Affiliation(s)
- Stefanie Anke Grunwald
- Muscle Research Unit, Experimental and Clinical Research Center, a joint cooperation between the Charité Universitätsmedizin and the Max Delbrück Center for Molecular Medicine, Berlin, 13125, Germany.
- Charité Universitätsmedizin Berlin, Berlin, 13125, Germany.
| | - Oliver Popp
- Mass Spectrometry Core Facility, Max Delbrück Center for Molecular Medicine in the Helmholtz Society, Berlin, 13125, Germany
- Mass Spectrometry Facility, Berlin Institute of Health, Berlin, 13125, Germany
| | - Stefanie Haafke
- Muscle Research Unit, Experimental and Clinical Research Center, a joint cooperation between the Charité Universitätsmedizin and the Max Delbrück Center for Molecular Medicine, Berlin, 13125, Germany
- Charité Universitätsmedizin Berlin, Berlin, 13125, Germany
| | - Nicole Jedraszczak
- Muscle Research Unit, Experimental and Clinical Research Center, a joint cooperation between the Charité Universitätsmedizin and the Max Delbrück Center for Molecular Medicine, Berlin, 13125, Germany
- Charité Universitätsmedizin Berlin, Berlin, 13125, Germany
| | - Ulrike Grieben
- Muscle Research Unit, Experimental and Clinical Research Center, a joint cooperation between the Charité Universitätsmedizin and the Max Delbrück Center for Molecular Medicine, Berlin, 13125, Germany
- Charité Universitätsmedizin Berlin, Berlin, 13125, Germany
| | - Kathrin Saar
- Genetics and Genomics of Cardiovascular Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Society, Berlin, 13125, Germany
| | - Giannino Patone
- Genetics and Genomics of Cardiovascular Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Society, Berlin, 13125, Germany
| | - Wolfram Kress
- Institute for Human Genetics, Julius-Maximilians-University of Würzburg, Würzburg, 97074, Germany
| | | | - Gunnar Dittmar
- Mass Spectrometry Core Facility, Max Delbrück Center for Molecular Medicine in the Helmholtz Society, Berlin, 13125, Germany
- Mass Spectrometry Facility, Berlin Institute of Health, Berlin, 13125, Germany
| | - Simone Spuler
- Muscle Research Unit, Experimental and Clinical Research Center, a joint cooperation between the Charité Universitätsmedizin and the Max Delbrück Center for Molecular Medicine, Berlin, 13125, Germany.
- Charité Universitätsmedizin Berlin, Berlin, 13125, Germany.
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12
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Chothani S, Schäfer S, Adami E, Viswanathan S, Widjaja AA, Langley SR, Tan J, Wang M, Quaife NM, Jian Pua C, D'Agostino G, Guna Shekeran S, George BL, Lim S, Yiqun Cao E, van Heesch S, Witte F, Felkin LE, Christodoulou EG, Dong J, Blachut S, Patone G, Barton PJR, Hubner N, Cook SA, Rackham OJL. Widespread Translational Control of Fibrosis in the Human Heart by RNA-Binding Proteins. Circulation 2019; 140:937-951. [PMID: 31284728 PMCID: PMC6749977 DOI: 10.1161/circulationaha.119.039596] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Supplemental Digital Content is available in the text. Fibrosis is a common pathology in many cardiac disorders and is driven by the activation of resident fibroblasts. The global posttranscriptional mechanisms underlying fibroblast-to-myofibroblast conversion in the heart have not been explored.
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Affiliation(s)
- Sonia Chothani
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore (S.C., S.S., E.A., S.V., A.W., S.L., M.W., G.D., S.G.S., B.L.G., S.L., E.Y.C., E.C., J.D., S.A.C., O.J.L.R.)
| | - Sebastian Schäfer
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore (S.C., S.S., E.A., S.V., A.W., S.L., M.W., G.D., S.G.S., B.L.G., S.L., E.Y.C., E.C., J.D., S.A.C., O.J.L.R.).,National Heart Centre Singapore, Singapore (S.S., S.L., J.T., C.J.P., S.A.C.)
| | - Eleonora Adami
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore (S.C., S.S., E.A., S.V., A.W., S.L., M.W., G.D., S.G.S., B.L.G., S.L., E.Y.C., E.C., J.D., S.A.C., O.J.L.R.).,Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (E.A., S.v.H., F.W., S.B., G.P., N.H.)
| | - Sivakumar Viswanathan
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore (S.C., S.S., E.A., S.V., A.W., S.L., M.W., G.D., S.G.S., B.L.G., S.L., E.Y.C., E.C., J.D., S.A.C., O.J.L.R.)
| | - Anissa A Widjaja
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore (S.C., S.S., E.A., S.V., A.W., S.L., M.W., G.D., S.G.S., B.L.G., S.L., E.Y.C., E.C., J.D., S.A.C., O.J.L.R.)
| | - Sarah R Langley
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore (S.C., S.S., E.A., S.V., A.W., S.L., M.W., G.D., S.G.S., B.L.G., S.L., E.Y.C., E.C., J.D., S.A.C., O.J.L.R.)
| | - Jessie Tan
- National Heart Centre Singapore, Singapore (S.S., S.L., J.T., C.J.P., S.A.C.)
| | - Mao Wang
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore (S.C., S.S., E.A., S.V., A.W., S.L., M.W., G.D., S.G.S., B.L.G., S.L., E.Y.C., E.C., J.D., S.A.C., O.J.L.R.)
| | - Nicholas M Quaife
- National Heart and Lung Institute, Imperial College London, United Kingdom (N.M.Q., L.E.F., P.J.R.B., S.A.C.).,Medical Research Council-London Institute of Medical Sciences, Hammersmith Hospital Campus, United Kingdom (N.M.Q, S.A.C.).,Cardiovascular Research Centre, Royal Brompton and Harefield National Health Serfice Trust, London, United Kingdom (N.M.Q, P.J.R.B.)
| | - Chee Jian Pua
- National Heart Centre Singapore, Singapore (S.S., S.L., J.T., C.J.P., S.A.C.)
| | - Giuseppe D'Agostino
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore (S.C., S.S., E.A., S.V., A.W., S.L., M.W., G.D., S.G.S., B.L.G., S.L., E.Y.C., E.C., J.D., S.A.C., O.J.L.R.)
| | - Shamini Guna Shekeran
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore (S.C., S.S., E.A., S.V., A.W., S.L., M.W., G.D., S.G.S., B.L.G., S.L., E.Y.C., E.C., J.D., S.A.C., O.J.L.R.)
| | - Benjamin L George
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore (S.C., S.S., E.A., S.V., A.W., S.L., M.W., G.D., S.G.S., B.L.G., S.L., E.Y.C., E.C., J.D., S.A.C., O.J.L.R.)
| | - Stella Lim
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore (S.C., S.S., E.A., S.V., A.W., S.L., M.W., G.D., S.G.S., B.L.G., S.L., E.Y.C., E.C., J.D., S.A.C., O.J.L.R.).,National Heart Centre Singapore, Singapore (S.S., S.L., J.T., C.J.P., S.A.C.)
| | - Elaine Yiqun Cao
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore (S.C., S.S., E.A., S.V., A.W., S.L., M.W., G.D., S.G.S., B.L.G., S.L., E.Y.C., E.C., J.D., S.A.C., O.J.L.R.)
| | - Sebastiaan van Heesch
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (E.A., S.v.H., F.W., S.B., G.P., N.H.)
| | - Franziska Witte
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (E.A., S.v.H., F.W., S.B., G.P., N.H.)
| | - Leanne E Felkin
- National Heart and Lung Institute, Imperial College London, United Kingdom (N.M.Q., L.E.F., P.J.R.B., S.A.C.)
| | - Eleni G Christodoulou
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore (S.C., S.S., E.A., S.V., A.W., S.L., M.W., G.D., S.G.S., B.L.G., S.L., E.Y.C., E.C., J.D., S.A.C., O.J.L.R.)
| | - Jinrui Dong
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore (S.C., S.S., E.A., S.V., A.W., S.L., M.W., G.D., S.G.S., B.L.G., S.L., E.Y.C., E.C., J.D., S.A.C., O.J.L.R.)
| | - Susanne Blachut
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (E.A., S.v.H., F.W., S.B., G.P., N.H.)
| | - Giannino Patone
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (E.A., S.v.H., F.W., S.B., G.P., N.H.)
| | - Paul J R Barton
- National Heart and Lung Institute, Imperial College London, United Kingdom (N.M.Q., L.E.F., P.J.R.B., S.A.C.).,Cardiovascular Research Centre, Royal Brompton and Harefield National Health Serfice Trust, London, United Kingdom (N.M.Q, P.J.R.B.)
| | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (E.A., S.v.H., F.W., S.B., G.P., N.H.).,German Centre for Cardiovascular Research, partner site Berlin, Germany (N.H.).,Charité-Universitätsmedizin, Berlin, Germany (N.H.).,Berlin Institute of Health, Germany (N.H.)
| | - Stuart A Cook
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore (S.C., S.S., E.A., S.V., A.W., S.L., M.W., G.D., S.G.S., B.L.G., S.L., E.Y.C., E.C., J.D., S.A.C., O.J.L.R.).,National Heart Centre Singapore, Singapore (S.S., S.L., J.T., C.J.P., S.A.C.).,National Heart and Lung Institute, Imperial College London, United Kingdom (N.M.Q., L.E.F., P.J.R.B., S.A.C.).,Medical Research Council-London Institute of Medical Sciences, Hammersmith Hospital Campus, United Kingdom (N.M.Q, S.A.C.)
| | - Owen J L Rackham
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore (S.C., S.S., E.A., S.V., A.W., S.L., M.W., G.D., S.G.S., B.L.G., S.L., E.Y.C., E.C., J.D., S.A.C., O.J.L.R.)
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13
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Schafer S, Viswanathan S, Widjaja AA, Lim WW, Moreno-Moral A, DeLaughter DM, Ng B, Patone G, Chow K, Khin E, Tan J, Chothani SP, Ye L, Rackham OJL, Ko NSJ, Sahib NE, Pua CJ, Zhen NTG, Xie C, Wang M, Maatz H, Lim S, Saar K, Blachut S, Petretto E, Schmidt S, Putoczki T, Guimarães-Camboa N, Wakimoto H, van Heesch S, Sigmundsson K, Lim SL, Soon JL, Chao VTT, Chua YL, Tan TE, Evans SM, Loh YJ, Jamal MH, Ong KK, Chua KC, Ong BH, Chakaramakkil MJ, Seidman JG, Seidman CE, Hubner N, Sin KYK, Cook SA. IL-11 is a crucial determinant of cardiovascular fibrosis. Nature 2017; 552:110-115. [PMID: 29160304 PMCID: PMC5807082 DOI: 10.1038/nature24676] [Citation(s) in RCA: 380] [Impact Index Per Article: 54.3] [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: 03/22/2017] [Accepted: 11/02/2017] [Indexed: 02/06/2023]
Abstract
Fibrosis is a common pathology in cardiovascular disease. In the heart, fibrosis causes mechanical and electrical dysfunction and in the kidney, it predicts the onset of renal failure. Transforming growth factor β1 (TGFβ1) is the principal pro-fibrotic factor, but its inhibition is associated with side effects due to its pleiotropic roles. We hypothesized that downstream effectors of TGFβ1 in fibroblasts could be attractive therapeutic targets and lack upstream toxicity. Here we show, using integrated imaging-genomics analyses of primary human fibroblasts, that upregulation of interleukin-11 (IL-11) is the dominant transcriptional response to TGFβ1 exposure and required for its pro-fibrotic effect. IL-11 and its receptor (IL11RA) are expressed specifically in fibroblasts, in which they drive non-canonical, ERK-dependent autocrine signalling that is required for fibrogenic protein synthesis. In mice, fibroblast-specific Il11 transgene expression or Il-11 injection causes heart and kidney fibrosis and organ failure, whereas genetic deletion of Il11ra1 protects against disease. Therefore, inhibition of IL-11 prevents fibroblast activation across organs and species in response to a range of important pro-fibrotic stimuli. These results reveal a central role of IL-11 in fibrosis and we propose that inhibition of IL-11 is a potential therapeutic strategy to treat fibrotic diseases.
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Affiliation(s)
- Sebastian Schafer
- National Heart Centre Singapore, Singapore
- Duke-National University of Singapore Medical School, Singapore
| | | | | | | | | | - Daniel M DeLaughter
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | | | - Giannino Patone
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rossle Strasse 10, 13125 Berlin, Germany
| | | | - Ester Khin
- Duke-National University of Singapore Medical School, Singapore
| | - Jessie Tan
- National Heart Centre Singapore, Singapore
| | | | - Lei Ye
- National Heart Centre Singapore, Singapore
| | | | - Nicole S J Ko
- Duke-National University of Singapore Medical School, Singapore
| | - Norliza E Sahib
- Duke-National University of Singapore Medical School, Singapore
| | | | | | - Chen Xie
- National Heart Centre Singapore, Singapore
| | - Mao Wang
- Duke-National University of Singapore Medical School, Singapore
| | - Henrike Maatz
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rossle Strasse 10, 13125 Berlin, Germany
| | - Shiqi Lim
- National Heart Centre Singapore, Singapore
| | - Kathrin Saar
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rossle Strasse 10, 13125 Berlin, Germany
| | - Susanne Blachut
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rossle Strasse 10, 13125 Berlin, Germany
| | - Enrico Petretto
- Duke-National University of Singapore Medical School, Singapore
| | - Sabine Schmidt
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rossle Strasse 10, 13125 Berlin, Germany
| | - Tracy Putoczki
- Inflammation Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3050, Australia
| | - Nuno Guimarães-Camboa
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - Hiroko Wakimoto
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Sebastiaan van Heesch
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rossle Strasse 10, 13125 Berlin, Germany
| | | | - See L Lim
- National Heart Centre Singapore, Singapore
| | - Jia L Soon
- National Heart Centre Singapore, Singapore
- Duke-National University of Singapore Medical School, Singapore
| | - Victor T T Chao
- National Heart Centre Singapore, Singapore
- Duke-National University of Singapore Medical School, Singapore
| | | | | | - Sylvia M Evans
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
- Department of Medicine, University of California at San Diego, La Jolla, California 92093, USA
- Department of Pharmacology, University of California at San Diego, La Jolla, California 92093, USA
| | - Yee J Loh
- National Heart Centre Singapore, Singapore
- Kandang Kerbau Women's and Children's Hospital, Singapore
| | | | - Kim K Ong
- National Heart Centre Singapore, Singapore
- Kandang Kerbau Women's and Children's Hospital, Singapore
| | - Kim C Chua
- National Heart Centre Singapore, Singapore
| | | | | | - Jonathan G Seidman
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Division of Cardiovascular Medicine, Brigham and Women's Hospital, Boston, Massachusettes 02115, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rossle Strasse 10, 13125 Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site, Berlin, Germany
- Charité-Universitätsmedizin, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Kenny Y K Sin
- National Heart Centre Singapore, Singapore
- Duke-National University of Singapore Medical School, Singapore
| | - Stuart A Cook
- National Heart Centre Singapore, Singapore
- Duke-National University of Singapore Medical School, Singapore
- National Heart and Lung Institute, Imperial College London, London, UK
- MRC-London Institute of Medical Sciences, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
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14
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Kammertoens T, Friese C, Arina A, Idel C, Briesemeister D, Rothe M, Ivanov A, Szymborska A, Patone G, Kunz S, Sommermeyer D, Engels B, Leisegang M, Textor A, Fehling HJ, Fruttiger M, Lohoff M, Herrmann A, Yu H, Weichselbaum R, Uckert W, Hübner N, Gerhardt H, Beule D, Schreiber H, Blankenstein T. Tumour ischaemia by interferon-γ resembles physiological blood vessel regression. Nature 2017; 545:98-102. [PMID: 28445461 PMCID: PMC5567674 DOI: 10.1038/nature22311] [Citation(s) in RCA: 166] [Impact Index Per Article: 23.7] [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: 02/02/2016] [Accepted: 03/30/2017] [Indexed: 12/11/2022]
Abstract
The relative contribution of the effector molecules produced by T cells to tumour rejection is unclear, but interferon-γ (IFNγ) is critical in most of the analysed models. Although IFNγ can impede tumour growth by acting directly on cancer cells, it must also act on the tumour stroma for effective rejection of large, established tumours. However, which stroma cells respond to IFNγ and by which mechanism IFNγ contributes to tumour rejection through stromal targeting have remained unknown. Here we use a model of IFNγ induction and an IFNγ-GFP fusion protein in large, vascularized tumours growing in mice that express the IFNγ receptor exclusively in defined cell types. Responsiveness to IFNγ by myeloid cells and other haematopoietic cells, including T cells or fibroblasts, was not sufficient for IFNγ-induced tumour regression, whereas responsiveness of endothelial cells to IFNγ was necessary and sufficient. Intravital microscopy revealed IFNγ-induced regression of the tumour vasculature, resulting in arrest of blood flow and subsequent collapse of tumours, similar to non-haemorrhagic necrosis in ischaemia and unlike haemorrhagic necrosis induced by tumour necrosis factor. The early events of IFNγ-induced tumour ischaemia resemble non-apoptotic blood vessel regression during development, wound healing or IFNγ-mediated, pregnancy-induced remodelling of uterine arteries. A better mechanistic understanding of how solid tumours are rejected may aid the design of more effective protocols for adoptive T-cell therapy.
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Affiliation(s)
- Thomas Kammertoens
- Institute of Immunology, Charité Campus Buch, 13125 Berlin, Germany
- Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Christian Friese
- Institute of Immunology, Charité Campus Buch, 13125 Berlin, Germany
- Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Ainhoa Arina
- Department of Radiation and Cellular Oncology, Ludwig Center for Metastasis Research, The University of Chicago, Chicago, Illinois 60637, USA
| | - Christian Idel
- Department of Pathology, The University of Chicago, Chicago, Illinois 60637, USA
| | - Dana Briesemeister
- Institute of Immunology, Charité Campus Buch, 13125 Berlin, Germany
- Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Michael Rothe
- Institute of Immunology, Charité Campus Buch, 13125 Berlin, Germany
- Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Andranik Ivanov
- Berlin Institute of Health, 10117 Berlin, Germany
- Charité - Universitätsmedizin, 10117 Berlin, Germany
| | - Anna Szymborska
- Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Giannino Patone
- Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Severine Kunz
- Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | | | - Boris Engels
- Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Matthias Leisegang
- Institute of Immunology, Charité Campus Buch, 13125 Berlin, Germany
- Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
- Berlin Institute of Health, 10117 Berlin, Germany
| | - Ana Textor
- Institute of Immunology, Charité Campus Buch, 13125 Berlin, Germany
- Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | | | - Marcus Fruttiger
- Institute of Ophthalmology, University College London, London EC1V 9EL, UK
| | - Michael Lohoff
- Institute for Medical Microbiology, University of Marburg, 35032 Marburg, Germany
| | - Andreas Herrmann
- Beckman Research Institute at the Comprehensive Cancer Center City of Hope, Los Angeles, California 91010-3000, USA
| | - Hua Yu
- Beckman Research Institute at the Comprehensive Cancer Center City of Hope, Los Angeles, California 91010-3000, USA
| | - Ralph Weichselbaum
- Department of Radiation and Cellular Oncology, Ludwig Center for Metastasis Research, The University of Chicago, Chicago, Illinois 60637, USA
| | - Wolfgang Uckert
- Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
- Berlin Institute of Health, 10117 Berlin, Germany
| | - Norbert Hübner
- Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
- Charité - Universitätsmedizin, 10117 Berlin, Germany
- DZHK (German Center for Cardiovascular Research), partner site Berlin, 13347 Berlin, Germany
| | - Holger Gerhardt
- Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
- Berlin Institute of Health, 10117 Berlin, Germany
- DZHK (German Center for Cardiovascular Research), partner site Berlin, 13347 Berlin, Germany
| | - Dieter Beule
- Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
- Berlin Institute of Health, 10117 Berlin, Germany
| | - Hans Schreiber
- Institute of Immunology, Charité Campus Buch, 13125 Berlin, Germany
- Department of Pathology, The University of Chicago, Chicago, Illinois 60637, USA
- Berlin Institute of Health, 10117 Berlin, Germany
| | - Thomas Blankenstein
- Institute of Immunology, Charité Campus Buch, 13125 Berlin, Germany
- Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
- Berlin Institute of Health, 10117 Berlin, Germany
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15
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Kannan S, Nicola Z, Overall RW, Ichwan M, Ramírez-Rodríguez G, N. Grzyb A, Patone G, Saar K, Hübner N, Kempermann G. Systems Genetics Analysis of a Recombinant Inbred Mouse Cell Culture Panel Reveals Wnt Pathway Member Lrp6 as a Regulator of Adult Hippocampal Precursor Cell Proliferation. Stem Cells 2016; 34:674-84. [DOI: 10.1002/stem.2313] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 09/28/2015] [Accepted: 10/25/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Suresh Kannan
- CRTD-Center for Regenerative Therapies Dresden; Technische Universität Dresden; Dresden Germany
- Department of Biomedical Sciences; Sri Ramachandra University; Porur Chennai India
| | - Zeina Nicola
- German Center for Neurodegenerative Diseases (DZNE) Dresden; Dresden Germany
| | - Rupert W. Overall
- CRTD-Center for Regenerative Therapies Dresden; Technische Universität Dresden; Dresden Germany
| | - Muhammad Ichwan
- CRTD-Center for Regenerative Therapies Dresden; Technische Universität Dresden; Dresden Germany
| | - Gerardo Ramírez-Rodríguez
- Laboratory of Neurogenesis, Division of Clinical Investigations; National Institute of Psychiatry “Ramón de la Fuente Muñiz; ” México D.F. México
| | - Anna N. Grzyb
- German Center for Neurodegenerative Diseases (DZNE) Dresden; Dresden Germany
| | | | - Kathrin Saar
- Max-Delbrück Center for Molecular Medicine; Berlin Germany
| | - Norbert Hübner
- Max-Delbrück Center for Molecular Medicine; Berlin Germany
| | - Gerd Kempermann
- CRTD-Center for Regenerative Therapies Dresden; Technische Universität Dresden; Dresden Germany
- German Center for Neurodegenerative Diseases (DZNE) Dresden; Dresden Germany
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16
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de Oliveira KAP, Kaergel E, Heinig M, Fontaine JF, Patone G, Muro EM, Mathas S, Hummel M, Andrade-Navarro MA, Hübner N, Scheidereit C. A roadmap of constitutive NF-κB activity in Hodgkin lymphoma: Dominant roles of p50 and p52 revealed by genome-wide analyses. Genome Med 2016; 8:28. [PMID: 26988706 PMCID: PMC4794921 DOI: 10.1186/s13073-016-0280-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [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: 11/16/2015] [Accepted: 02/17/2016] [Indexed: 12/02/2022] Open
Abstract
Background NF-κB is widely involved in lymphoid malignancies; however, the functional roles and specific transcriptomes of NF-κB dimers with distinct subunit compositions have been unclear. Methods Using combined ChIP-sequencing and microarray analyses, we determined the cistromes and target gene signatures of canonical and non-canonical NF-κB species in Hodgkin lymphoma (HL) cells. Results We found that the various NF-κB subunits are recruited to regions with redundant κB motifs in a large number of genes. Yet canonical and non-canonical NF-κB dimers up- and downregulate gene sets that are both distinct and overlapping, and are associated with diverse biological functions. p50 and p52 are formed through NIK-dependent p105 and p100 precursor processing in HL cells and are the predominant DNA binding subunits. Logistic regression analyses of combinations of the p50, p52, RelA, and RelB subunits in binding regions that have been assigned to genes they regulate reveal a cross-contribution of p52 and p50 to canonical and non-canonical transcriptomes. These analyses also indicate that the subunit occupancy pattern of NF-κB binding regions and their distance from the genes they regulate are determinants of gene activation versus repression. The pathway-specific signatures of activated and repressed genes distinguish HL from other NF-κB-associated lymphoid malignancies and inversely correlate with gene expression patterns in normal germinal center B cells, which are presumed to be the precursors of HL cells. Conclusions We provide insights that are relevant for lymphomas with constitutive NF-κB activation and generally for the decoding of the mechanisms of differential gene regulation through canonical and non-canonical NF-κB signaling. Electronic supplementary material The online version of this article (doi:10.1186/s13073-016-0280-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kivia A P de Oliveira
- Signal Transduction in Tumor Cells, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Eva Kaergel
- Signal Transduction in Tumor Cells, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Matthias Heinig
- Department of Computational Biology, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany.,Genetics and Genomics of Cardiovascular Diseases, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125, Berlin, Germany.,Institute of Computational Biology, Helmholtz Zentrum München, Ingolstädter Landstr.1, 85764, Neuherberg, Germany
| | - Jean-Fred Fontaine
- Computational Biology and Data Mining, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125, Berlin, Germany.,Present address: Johannes Gutenberg University, 55128, Mainz, Germany
| | - Giannino Patone
- Genetics and Genomics of Cardiovascular Diseases, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Enrique M Muro
- Computational Biology and Data Mining, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125, Berlin, Germany.,Present address: Johannes Gutenberg University, 55128, Mainz, Germany
| | - Stephan Mathas
- Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany.,Hematology, Oncology and Tumor Immunology, Charité-Universitätsmedizin Berlin, 13353, Berlin, Germany
| | - Michael Hummel
- Institute of Pathology, Charité-Universitätsmedizin Berlin, 10117, Berlin, Germany
| | - Miguel A Andrade-Navarro
- Computational Biology and Data Mining, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125, Berlin, Germany.,Present address: Johannes Gutenberg University, 55128, Mainz, Germany
| | - Norbert Hübner
- Genetics and Genomics of Cardiovascular Diseases, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Claus Scheidereit
- Signal Transduction in Tumor Cells, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125, Berlin, Germany.
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Rintisch C, Heinig M, Bauerfeind A, Schafer S, Mieth C, Patone G, Hummel O, Chen W, Cook S, Cuppen E, Colomé-Tatché M, Johannes F, Jansen RC, Neil H, Werner M, Pravenec M, Vingron M, Hubner N. Natural variation of histone modification and its impact on gene expression in the rat genome. Genome Res 2014; 24:942-53. [PMID: 24793478 PMCID: PMC4032858 DOI: 10.1101/gr.169029.113] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Histone modifications are epigenetic marks that play fundamental roles in many biological processes including the control of chromatin-mediated regulation of gene expression. Little is known about interindividual variability of histone modification levels across the genome and to what extent they are influenced by genetic variation. We annotated the rat genome with histone modification maps, identified differences in histone trimethyl-lysine levels among strains, and described their underlying genetic basis at the genome-wide scale using ChIP-seq in heart and liver tissues in a panel of rat recombinant inbred and their progenitor strains. We identified extensive variation of histone methylation levels among individuals and mapped hundreds of underlying cis- and trans-acting loci throughout the genome that regulate histone methylation levels in an allele-specific manner. Interestingly, most histone methylation level variation was trans-linked and the most prominent QTL identified influenced H3K4me3 levels at 899 putative promoters throughout the genome in the heart. Cis- acting variation was enriched in binding sites of distinct transcription factors in heart and liver. The integrated analysis of DNA variation together with histone methylation and gene expression levels showed that histoneQTLs are an important predictor of gene expression and that a joint analysis significantly enhanced the prediction of gene expression traits (eQTLs). Our data suggest that genetic variation has a widespread impact on histone trimethylation marks that may help to uncover novel genotype-phenotype relationships.
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Affiliation(s)
- Carola Rintisch
- Max-Delbrück-Center for Molecular Medicine (MDC), 13125 Berlin, Germany
| | - Matthias Heinig
- Max-Delbrück-Center for Molecular Medicine (MDC), 13125 Berlin, Germany; Department of Computational Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Anja Bauerfeind
- Max-Delbrück-Center for Molecular Medicine (MDC), 13125 Berlin, Germany
| | - Sebastian Schafer
- Max-Delbrück-Center for Molecular Medicine (MDC), 13125 Berlin, Germany
| | - Christin Mieth
- Max-Delbrück-Center for Molecular Medicine (MDC), 13125 Berlin, Germany
| | - Giannino Patone
- Max-Delbrück-Center for Molecular Medicine (MDC), 13125 Berlin, Germany
| | - Oliver Hummel
- Max-Delbrück-Center for Molecular Medicine (MDC), 13125 Berlin, Germany
| | - Wei Chen
- Max-Delbrück-Center for Molecular Medicine (MDC), 13125 Berlin, Germany
| | - Stuart Cook
- National Heart and Lung Institute, Cardiovascular Genetics and Genomics, London, SW3 6NP, United Kingdom; Duke-NUS Graduate Medical School, 169857 Singapore; National Heart Center Singapore, 169609 Singapore
| | - Edwin Cuppen
- Center for Molecular Medicine, University Medical Center Utrecht, Hubrecht Institute KNAW, 3584 CT Utrecht, The Netherlands
| | - Maria Colomé-Tatché
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, NL-9713 AV Groningen, The Netherlands
| | - Frank Johannes
- Groningen Bioinformatics Centre (GBIC), Groningen Biomolecular Sciences and Biotechnology Institute (GBB), 9747AG Groningen, The Netherlands
| | - Ritsert C Jansen
- Groningen Bioinformatics Centre (GBIC), Groningen Biomolecular Sciences and Biotechnology Institute (GBB), 9747AG Groningen, The Netherlands
| | - Helen Neil
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), iBiTec-S, Université Paris-Sud, CNRS FRE3377, F-91191 Gif-sur-Yvette cedex, France
| | - Michel Werner
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), iBiTec-S, Université Paris-Sud, CNRS FRE3377, F-91191 Gif-sur-Yvette cedex, France
| | - Michal Pravenec
- Institut of Physiology, Academy of Sciences of the Czech Republic, Videnska 1083, CZ-14220 Prague 4, Czech Republic
| | - Martin Vingron
- Department of Computational Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Norbert Hubner
- Max-Delbrück-Center for Molecular Medicine (MDC), 13125 Berlin, Germany; DZHK (German Centre for Cardiovascular Research), Partner site Berlin, 13125 Berlin, Germany
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18
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Yang C, Stingo FC, Ahn KW, Liu P, Vannucci M, Laud PW, Skelton M, O'Connor P, Kurth T, Ryan RP, Moreno C, Tsaih SW, Patone G, Hummel O, Jacob HJ, Liang M, Cowley AW. Increased proliferative cells in the medullary thick ascending limb of the loop of Henle in the Dahl salt-sensitive rat. Hypertension 2012. [PMID: 23184381 DOI: 10.1161/hypertensionaha.112.199380] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Studies of transcriptome profiles have provided new insights into mechanisms underlying the development of hypertension. Cell type heterogeneity in tissue samples, however, has been a significant hindrance in these studies. We performed a transcriptome analysis in medullary thick ascending limbs of the loop of Henle isolated from Dahl salt-sensitive rats. Genes differentially expressed between Dahl salt-sensitive rats and salt-insensitive consomic SS.13(BN) rats on either 0.4% or 7 days of 8.0% NaCl diet (n=4) were highly enriched for genes located on chromosome 13, the chromosome substituted in the SS.13(BN) rat. A pathway involving cell proliferation and cell cycle regulation was identified as one of the most highly ranked pathways based on differentially expressed genes and by a Bayesian model analysis. Immunofluorescent analysis indicated that just 1 week of a high-salt diet resulted in a severalfold increase in proliferative medullary thick ascending limb cells in both rat strains, and that Dahl salt-sensitive rats exhibited a significantly greater proportion of medullary thick ascending limb cells in a proliferative state than in SS.13(BN) rats (15.0±1.4% versus 10.1±0.6%; n=7-9; P<0.05). The total number of cells per medullary thick ascending limb section analyzed was not different between the 2 strains. The study revealed alterations in regulatory pathways in Dahl salt-sensitive rats in tissues highly enriched for a single cell type, leading to the unexpected finding of a greater increase in the number of proliferative medullary thick ascending limb cells in Dahl salt-sensitive rats on a high-salt diet.
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Affiliation(s)
- Chun Yang
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
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19
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Atanur SS, Birol I, Guryev V, Hirst M, Hummel O, Morrissey C, Behmoaras J, Fernandez-Suarez XM, Johnson MD, McLaren WM, Patone G, Petretto E, Plessy C, Rockland KS, Rockland C, Saar K, Zhao Y, Carninci P, Flicek P, Kurtz T, Cuppen E, Pravenec M, Hubner N, Jones SJM, Birney E, Aitman TJ. The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance. Genome Res 2010; 20:791-803. [PMID: 20430781 DOI: 10.1101/gr.103499.109] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The spontaneously hypertensive rat (SHR) is the most widely studied animal model of hypertension. Scores of SHR quantitative loci (QTLs) have been mapped for hypertension and other phenotypes. We have sequenced the SHR/OlaIpcv genome at 10.7-fold coverage by paired-end sequencing on the Illumina platform. We identified 3.6 million high-quality single nucleotide polymorphisms (SNPs) between the SHR/OlaIpcv and Brown Norway (BN) reference genome, with a high rate of validation (sensitivity 96.3%-98.0% and specificity 99%-100%). We also identified 343,243 short indels between the SHR/OlaIpcv and reference genomes. These SNPs and indels resulted in 161 gain or loss of stop codons and 629 frameshifts compared with the BN reference sequence. We also identified 13,438 larger deletions that result in complete or partial absence of 107 genes in the SHR/OlaIpcv genome compared with the BN reference and 588 copy number variants (CNVs) that overlap with the gene regions of 688 genes. Genomic regions containing genes whose expression had been previously mapped as cis-regulated expression quantitative trait loci (eQTLs) were significantly enriched with SNPs, short indels, and larger deletions, suggesting that some of these variants have functional effects on gene expression. Genes that were affected by major alterations in their coding sequence were highly enriched for genes related to ion transport, transport, and plasma membrane localization, providing insights into the likely molecular and cellular basis of hypertension and other phenotypes specific to the SHR strain. This near complete catalog of genomic differences between two extensively studied rat strains provides the starting point for complete elucidation, at the molecular level, of the physiological and pathophysiological phenotypic differences between individuals from these strains.
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Affiliation(s)
- Santosh S Atanur
- Physiological Genomics and Medicine Group, Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London W12 0NN, United Kingdom
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20
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Hubner N, Monti J, Fischer J, Paskas S, Heinig M, Schulz H, Goesele C, Heuser A, Fischer R, Schmidt C, Schirdewan A, Gross V, Hummel O, Maatz H, Patone G, Saar K, Vingron M, Weldon SM, Hammock BD, Rohde K, Dietz R, Cook SA, Schunck W, Luft FC. Soluble epoxide hydrolase (Ephx2) is a susceptibility gene for heart failure in a rat model of human disease 3044. FASEB J 2008. [DOI: 10.1096/fasebj.22.1_supplement.479.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Jan Monti
- Department of Clinical and Molecular CardiologyFranz‐Volhard ClinicHelios Clinics GmbHCharité Universitaetsmedizin BerlinBerlinGermany
| | | | | | | | | | | | - Arnd Heuser
- Max‐Delbruck‐Center for Molecular MedicineBerlinGermany
| | | | | | - Alexander Schirdewan
- Department of Clinical and Molecular CardiologyFranz‐Volhard ClinicHelios Clinics GmbHCharité Universitaetsmedizin BerlinBerlinGermany
| | - Volkmar Gross
- Max‐Delbruck‐Center for Molecular MedicineBerlinGermany
| | - Oliver Hummel
- Max‐Delbruck‐Center for Molecular MedicineBerlinGermany
| | - Henrike Maatz
- Max‐Delbruck‐Center for Molecular MedicineBerlinGermany
| | | | - Kathrin Saar
- Max‐Delbruck‐Center for Molecular MedicineBerlinGermany
| | - Martin Vingron
- Department of BioinformaticsMax‐Planck‐Institute for Molecular GeneticsBerlinGermany
| | | | - Bruce D. Hammock
- Departments of Entomology and Nutrition and Cancer Research CenterUC DavisSacramentoCA
| | - Klaus Rohde
- Max‐Delbruck‐Center for Molecular MedicineBerlinGermany
| | - Rainer Dietz
- Max‐Delbruck‐Center for Molecular MedicineBerlinGermany
| | - Stuart A. Cook
- MRC Clinical Sciences Centre Faculty of MedicineImperial CollegeLondonUnited Kingdom
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Abstract
The flight feathers and their coverts of a European kestrel Falco tinnunculus have been tested for their air transmissivity. The transmissivity was measured in both directions, i.e. from ventral to dorsal and vice versa; the mean difference between the two directions was less than 10 %. However, the transmissivity of the inner versus outer vanes of the remiges and coverts differed significantly, with the outer vanes being more transmissive than the inner vanes. A functional interpretation of the different transmissivities of the inner and outer vanes is given, and we propose that its significance lies in the formation of a smooth, continuous wing surface. The individual feathers are pushed firmly towards one another as a result of the different transmissivities, which cause a pressure gradient to build up from the less-transmissive inner vane towards the overlying, more-transmissive outer vane of the adjacent feather. In another test series, the transmissivity of the flight and covert feathers of 27 species was measured; the differences found between species were small.
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Affiliation(s)
- W MULler
- FG Bionik and Evolutionstechnik, Technische Universitat Berlin, Ackerstrasse 71-76 (ACK 1), Germany.
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