1
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Kmietczyk V, Riechert E, Gupta P, Kamuf-Schenk V, Katus H, Frey N, Völkers M. Cpeb4 regulates cardiomyocyte growth and function by the modulating the expression of Zeb1. J Mol Cell Cardiol 2022. [DOI: 10.1016/j.yjmcc.2022.08.211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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2
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Froese N, Cordero J, Abouissa A, Trogisch FA, Grein S, Szaroszyk M, Wang Y, Gigina A, Korf-Klingebiel M, Bosnjak B, Davenport CF, Wiehlmann L, Geffers R, Riechert E, Jürgensen L, Boileau E, Lin Y, Dieterich C, Förster R, Bauersachs J, Ola R, Dobreva G, Völkers M, Heineke J. Analysis of myocardial cellular gene expression during pressure overload reveals matrix based functional intercellular communication. iScience 2022; 25:103965. [PMID: 35281736 PMCID: PMC8908217 DOI: 10.1016/j.isci.2022.103965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/22/2021] [Accepted: 02/18/2022] [Indexed: 11/16/2022] Open
Abstract
To identify cellular mechanisms responsible for pressure overload triggered heart failure, we isolated cardiomyocytes, endothelial cells, and fibroblasts as most abundant cell types from mouse hearts in the subacute and chronic stages after transverse aortic constriction (TAC) and performed RNA-sequencing. We detected highly cell-type specific transcriptional responses with characteristic time courses and active intercellular communication. Cardiomyocytes after TAC exerted an early and sustained upregulation of inflammatory and matrix genes and a concomitant suppression of metabolic and ion channel genes. Fibroblasts, in contrast, showed transient early upregulation of inflammatory and matrix genes and downregulation of angiogenesis genes, but sustained induction of cell cycle and ion channel genes during TAC. Endothelial cells transiently induced cell cycle and extracellular matrix genes early after TAC, but exerted a long-lasting upregulation of inflammatory genes. As we found that matrix production by multiple cell types triggers pathological cellular responses, it might serve as a future therapeutic target. TAC induces matrix and growth, but reduces contraction genes in cardiomyocytes TAC induces genes related to matrix, inflammation, and cell cycle in endothelial cells TAC induces matrix and inflammation, but reduces angiogenesis genes in fibroblasts Matrix proteins trigger growth, proliferation, and migration in cardiac cells
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Affiliation(s)
- Natali Froese
- Department of Cardiology and Angiology, Hannover Medical School, 30625 Hannover, Germany
| | - Julio Cordero
- Department of Anatomy and Developmental Biology, European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University, 68167 Mannheim, Germany
| | - Aya Abouissa
- Department of Cardiovascular Physiology, European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University, Ludolf-Krehl-Str. 7-11, 68167 Mannheim, Germany
| | - Felix A Trogisch
- Department of Cardiovascular Physiology, European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University, Ludolf-Krehl-Str. 7-11, 68167 Mannheim, Germany
| | - Steve Grein
- Department of Cardiovascular Physiology, European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University, Ludolf-Krehl-Str. 7-11, 68167 Mannheim, Germany
| | - Malgorzata Szaroszyk
- Department of Cardiology and Angiology, Hannover Medical School, 30625 Hannover, Germany
| | - Yong Wang
- Department of Cardiology and Angiology, Hannover Medical School, 30625 Hannover, Germany
| | - Anna Gigina
- Department of Cardiology and Angiology, Hannover Medical School, 30625 Hannover, Germany
| | | | | | - Colin F Davenport
- Research Core Unit Genomics, Hannover Medical School, 30625 Hannover, Germany
| | - Lutz Wiehlmann
- Research Core Unit Genomics, Hannover Medical School, 30625 Hannover, Germany
| | - Robert Geffers
- Genome Analytics, Helmholtz Center for Infection Research, 38124 Braunschweig, Germany
| | - Eva Riechert
- Department of Internal Medicine III, Medical Faculty of Heidelberg, University of Heidelberg, 69120 Heidelberg, Germany
| | - Lonny Jürgensen
- Department of Internal Medicine III, Medical Faculty of Heidelberg, University of Heidelberg, 69120 Heidelberg, Germany
| | - Etienne Boileau
- Department of Internal Medicine III, Medical Faculty of Heidelberg, University of Heidelberg, 69120 Heidelberg, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany.,Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, 69120 Heidelberg, Germany
| | - Yanzhu Lin
- Department of Experimental Pharmacology, European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University, 68167 Mannheim, Germany
| | - Christoph Dieterich
- Department of Internal Medicine III, Medical Faculty of Heidelberg, University of Heidelberg, 69120 Heidelberg, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany.,Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, 69120 Heidelberg, Germany
| | | | - Johann Bauersachs
- Department of Cardiology and Angiology, Hannover Medical School, 30625 Hannover, Germany
| | - Roxana Ola
- Department of Experimental Pharmacology, European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University, 68167 Mannheim, Germany
| | - Gergana Dobreva
- Department of Anatomy and Developmental Biology, European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University, 68167 Mannheim, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - Mirko Völkers
- Department of Internal Medicine III, Medical Faculty of Heidelberg, University of Heidelberg, 69120 Heidelberg, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - Joerg Heineke
- Department of Cardiovascular Physiology, European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University, Ludolf-Krehl-Str. 7-11, 68167 Mannheim, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
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3
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Górska AA, Sandmann C, Riechert E, Hofmann C, Malovrh E, Varma E, Kmietczyk V, Ölschläger J, Jürgensen L, Kamuf-Schenk V, Stroh C, Furkel J, Konstandin MH, Sticht C, Boileau E, Dieterich C, Frey N, Katus HA, Doroudgar S, Völkers M. Muscle-specific Cand2 is translationally upregulated by mTORC1 and promotes adverse cardiac remodeling. EMBO Rep 2021; 22:e52170. [PMID: 34605609 PMCID: PMC8647021 DOI: 10.15252/embr.202052170] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 08/26/2021] [Accepted: 09/10/2021] [Indexed: 12/13/2022] Open
Abstract
The mechanistic target of rapamycin (mTOR) promotes pathological remodeling in the heart by activating ribosomal biogenesis and mRNA translation. Inhibition of mTOR in cardiomyocytes is protective; however, a detailed role of mTOR in translational regulation of specific mRNA networks in the diseased heart is unknown. We performed cardiomyocyte genome-wide sequencing to define mTOR-dependent gene expression control at the level of mRNA translation. We identify the muscle-specific protein Cullin-associated NEDD8-dissociated protein 2 (Cand2) as a translationally upregulated gene, dependent on the activity of mTOR. Deletion of Cand2 protects the myocardium against pathological remodeling. Mechanistically, we show that Cand2 links mTOR signaling to pathological cell growth by increasing Grk5 protein expression. Our data suggest that cell-type-specific targeting of mTOR might have therapeutic value against pathological cardiac remodeling.
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Affiliation(s)
- Agnieszka A Górska
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site, Heidelberg/Mannheim, Germany
| | - Clara Sandmann
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site, Heidelberg/Mannheim, Germany
| | - Eva Riechert
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site, Heidelberg/Mannheim, Germany
| | - Christoph Hofmann
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site, Heidelberg/Mannheim, Germany
| | - Ellen Malovrh
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site, Heidelberg/Mannheim, Germany
| | - Eshita Varma
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site, Heidelberg/Mannheim, Germany
| | - Vivien Kmietczyk
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site, Heidelberg/Mannheim, Germany
| | - Julie Ölschläger
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site, Heidelberg/Mannheim, Germany
| | - Lonny Jürgensen
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site, Heidelberg/Mannheim, Germany
| | - Verena Kamuf-Schenk
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site, Heidelberg/Mannheim, Germany
| | - Claudia Stroh
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site, Heidelberg/Mannheim, Germany
| | - Jennifer Furkel
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site, Heidelberg/Mannheim, Germany
| | - Mathias H Konstandin
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site, Heidelberg/Mannheim, Germany
| | - Carsten Sticht
- Medical Research Center, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Etienne Boileau
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site, Heidelberg/Mannheim, Germany.,Section of Bioinformatics and Systems Cardiology, Department of Cardiology, Angiology, and Pneumology and Klaus Tschira Institute for Integrative Computational Cardiology, University of Heidelberg, Heidelberg, Germany
| | - Christoph Dieterich
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site, Heidelberg/Mannheim, Germany.,Section of Bioinformatics and Systems Cardiology, Department of Cardiology, Angiology, and Pneumology and Klaus Tschira Institute for Integrative Computational Cardiology, University of Heidelberg, Heidelberg, Germany
| | - Norbert Frey
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site, Heidelberg/Mannheim, Germany
| | - Hugo A Katus
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site, Heidelberg/Mannheim, Germany
| | - Shirin Doroudgar
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site, Heidelberg/Mannheim, Germany
| | - Mirko Völkers
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site, Heidelberg/Mannheim, Germany
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4
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Boileau E, Doroudgar S, Riechert E, Jürgensen L, Ho TC, Katus HA, Völkers M, Dieterich C. Corrigendum: A Multi-Network Comparative Analysis of Transcriptome and Translatome Identifies Novel Hub Genes in Cardiac Remodeling. Front Genet 2021; 12:706542. [PMID: 34220968 PMCID: PMC8248784 DOI: 10.3389/fgene.2021.706542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 05/24/2021] [Indexed: 11/13/2022] Open
Abstract
[This corrects the article DOI: 10.3389/fgene.2020.583124.].
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Affiliation(s)
- Etienne Boileau
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg, Germany.,Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Berlin, Germany
| | - Shirin Doroudgar
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Berlin, Germany
| | - Eva Riechert
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Berlin, Germany
| | - Lonny Jürgensen
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Berlin, Germany
| | - Thanh Cao Ho
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, Heidelberg, Germany
| | - Hugo A Katus
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Berlin, Germany
| | - Mirko Völkers
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Berlin, Germany
| | - Christoph Dieterich
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg, Germany.,Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Berlin, Germany
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5
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Riechert E, Kmietczyk V, Stein F, Schwarzl T, Sekaran T, Jürgensen L, Kamuf-Schenk V, Varma E, Hofmann C, Rettel M, Gür K, Ölschläger J, Kühl F, Martin J, Ramirez-Pedraza M, Fernandez M, Doroudgar S, Méndez R, Katus HA, Hentze MW, Völkers M. Identification of dynamic RNA-binding proteins uncovers a Cpeb4-controlled regulatory cascade during pathological cell growth of cardiomyocytes. Cell Rep 2021; 35:109100. [PMID: 33979607 DOI: 10.1016/j.celrep.2021.109100] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 02/03/2021] [Accepted: 04/16/2021] [Indexed: 11/18/2022] Open
Abstract
RNA-binding proteins (RBPs) control critical aspects of cardiomyocyte function, but the repertoire of active RBPs in cardiomyocytes during the growth response is largely unknown. We define RBPs in healthy and diseased cardiomyocytes at a system-wide level by RNA interactome capture. This identifies 67 cardiomyocyte-specific RBPs, including several contractile proteins. Furthermore, we identify the cytoplasmic polyadenylation element-binding protein 4 (Cpeb4) as a dynamic RBP, regulating cardiac growth both in vitro and in vivo. We identify mRNAs bound to and regulated by Cpeb4 in cardiomyocytes. Cpeb4 regulates cardiac remodeling by differential expression of transcription factors. Among Cpeb4 target mRNAs, two zinc finger transcription factors (Zeb1 and Zbtb20) are discovered. We show that Cpeb4 regulates the expression of these mRNAs and that Cpeb4 depletion increases their expression. Thus, Cpeb4 emerges as a critical regulator of cardiomyocyte function by differential binding to specific mRNAs in response to pathological growth stimulation.
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Affiliation(s)
- Eva Riechert
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany; DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Germany
| | - Vivien Kmietczyk
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany; DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Germany
| | - Frank Stein
- Proteomics Core Facility, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Thomas Schwarzl
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Thileepan Sekaran
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Lonny Jürgensen
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany; DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Germany
| | - Verena Kamuf-Schenk
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany; DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Germany
| | - Eshita Varma
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany; DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Germany
| | - Christoph Hofmann
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany; DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Germany
| | - Mandy Rettel
- Proteomics Core Facility, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Kira Gür
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany; DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Germany
| | - Julie Ölschläger
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany; DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Germany
| | - Friederike Kühl
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany; DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Germany
| | - Judit Martin
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | | | | | - Shirin Doroudgar
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany; DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Germany
| | - Raúl Méndez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain; Institució Catalana de Recerca I Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Hugo A Katus
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany; DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Germany
| | - Matthias W Hentze
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Mirko Völkers
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany; DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Germany.
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6
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Boileau E, Doroudgar S, Riechert E, Jürgensen L, Ho TC, Katus HA, Völkers M, Dieterich C. A Multi-Network Comparative Analysis of Transcriptome and Translatome Identifies Novel Hub Genes in Cardiac Remodeling. Front Genet 2020; 11:583124. [PMID: 33304386 PMCID: PMC7701244 DOI: 10.3389/fgene.2020.583124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/09/2020] [Indexed: 12/03/2022] Open
Abstract
Our understanding of the transition from physiological to pathological cardiac hypertrophy remains elusive and largely based on reductionist hypotheses. Here, we profiled the translatomes of 15 mouse hearts to provide a molecular blueprint of altered gene networks in early cardiac remodeling. Using co-expression analysis, we showed how sub-networks are orchestrated into functional modules associated with pathological phenotypes. We discovered unappreciated hub genes, many undocumented for their role in cardiac hypertrophy, and genes in the transcriptional network that were rewired in the translational network, and associated with semantically different subsets of enriched functional terms, such as Fam210a, a novel musculoskeletal modulator, or Psmd12, implicated in protein quality control. Using their correlation structure, we found that transcriptome networks are only partially reproducible at the translatome level, providing further evidence of post-transcriptional control at the level of translation. Our results provide novel insights into the complexity of the organization of in vivo cardiac regulatory networks.
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Affiliation(s)
- Etienne Boileau
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg, Germany.,Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Berlin, Germany
| | - Shirin Doroudgar
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Berlin, Germany
| | - Eva Riechert
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Berlin, Germany
| | - Lonny Jürgensen
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Berlin, Germany
| | - Thanh Cao Ho
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, Heidelberg, Germany
| | - Hugo A Katus
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Berlin, Germany
| | - Mirko Völkers
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Berlin, Germany
| | - Christoph Dieterich
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg, Germany.,Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Berlin, Germany
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7
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Lerchenmüller C, Rabolli CP, Yeri A, Kitchen R, Salvador AM, Liu LX, Ziegler O, Danielson K, Platt C, Shah R, Damilano F, Kundu P, Riechert E, Katus HA, Saffitz JE, Keshishian H, Carr SA, Bezzerides VJ, Das S, Rosenzweig A. CITED4 Protects Against Adverse Remodeling in Response to Physiological and Pathological Stress. Circ Res 2020; 127:631-646. [PMID: 32418505 DOI: 10.1161/circresaha.119.315881] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
RATIONALE Cardiac CITED4 (CBP/p300-interacting transactivators with E [glutamic acid]/D [aspartic acid]-rich-carboxylterminal domain4) is induced by exercise and is sufficient to cause physiological hypertrophy and mitigate adverse ventricular remodeling after ischemic injury. However, the role of endogenous CITED4 in response to physiological or pathological stress is unknown. OBJECTIVE To investigate the role of CITED4 in murine models of exercise and pressure overload. METHODS AND RESULTS We generated cardiomyocyte-specific CITED4 knockout mice (C4KO) and subjected them to an intensive swim exercise protocol as well as transverse aortic constriction (TAC). Echocardiography, Western blotting, qPCR, immunohistochemistry, immunofluorescence, and transcriptional profiling for mRNA and miRNA (microRNA) expression were performed. Cellular crosstalk was investigated in vitro. CITED4 deletion in cardiomyocytes did not affect baseline cardiac size or function in young adult mice. C4KO mice developed modest cardiac dysfunction and dilation in response to exercise. After TAC, C4KOs developed severe heart failure with left ventricular dilation, impaired cardiomyocyte growth accompanied by reduced mTOR (mammalian target of rapamycin) activity and maladaptive cardiac remodeling with increased apoptosis, autophagy, and impaired mitochondrial signaling. Interstitial fibrosis was markedly increased in C4KO hearts after TAC. RNAseq revealed induction of a profibrotic miRNA network. miR30d was decreased in C4KO hearts after TAC and mediated crosstalk between cardiomyocytes and fibroblasts to modulate fibrosis. miR30d inhibition was sufficient to increase cardiac dysfunction and fibrosis after TAC. CONCLUSIONS CITED4 protects against pathological cardiac remodeling by regulating mTOR activity and a network of miRNAs mediating cardiomyocyte to fibroblast crosstalk. Our findings highlight the importance of CITED4 in response to both physiological and pathological stimuli.
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Affiliation(s)
- Carolin Lerchenmüller
- From the Corrigan Minehan Heart Center and Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston (C.L., C.P.R., A.Y., R.K., A.M.S., L.X.L., O.Z., K.D., C.P., R.S., F.D., P.K., S.D., A.R.).,Cardiology Department, University Hospital Heidelberg, Germany (C.L., E.R., H.A.K.).,German Center for Cardiovascular Research, Partner Site Heidelberg/Mannheim, Germany (C.L., E.R., H.A.K.)
| | - Charles P Rabolli
- From the Corrigan Minehan Heart Center and Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston (C.L., C.P.R., A.Y., R.K., A.M.S., L.X.L., O.Z., K.D., C.P., R.S., F.D., P.K., S.D., A.R.)
| | - Ashish Yeri
- From the Corrigan Minehan Heart Center and Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston (C.L., C.P.R., A.Y., R.K., A.M.S., L.X.L., O.Z., K.D., C.P., R.S., F.D., P.K., S.D., A.R.)
| | - Robert Kitchen
- From the Corrigan Minehan Heart Center and Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston (C.L., C.P.R., A.Y., R.K., A.M.S., L.X.L., O.Z., K.D., C.P., R.S., F.D., P.K., S.D., A.R.)
| | - Ane M Salvador
- From the Corrigan Minehan Heart Center and Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston (C.L., C.P.R., A.Y., R.K., A.M.S., L.X.L., O.Z., K.D., C.P., R.S., F.D., P.K., S.D., A.R.)
| | - Laura X Liu
- From the Corrigan Minehan Heart Center and Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston (C.L., C.P.R., A.Y., R.K., A.M.S., L.X.L., O.Z., K.D., C.P., R.S., F.D., P.K., S.D., A.R.)
| | - Olivia Ziegler
- From the Corrigan Minehan Heart Center and Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston (C.L., C.P.R., A.Y., R.K., A.M.S., L.X.L., O.Z., K.D., C.P., R.S., F.D., P.K., S.D., A.R.)
| | - Kirsty Danielson
- From the Corrigan Minehan Heart Center and Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston (C.L., C.P.R., A.Y., R.K., A.M.S., L.X.L., O.Z., K.D., C.P., R.S., F.D., P.K., S.D., A.R.)
| | - Colin Platt
- From the Corrigan Minehan Heart Center and Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston (C.L., C.P.R., A.Y., R.K., A.M.S., L.X.L., O.Z., K.D., C.P., R.S., F.D., P.K., S.D., A.R.)
| | - Ravi Shah
- From the Corrigan Minehan Heart Center and Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston (C.L., C.P.R., A.Y., R.K., A.M.S., L.X.L., O.Z., K.D., C.P., R.S., F.D., P.K., S.D., A.R.)
| | - Federico Damilano
- From the Corrigan Minehan Heart Center and Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston (C.L., C.P.R., A.Y., R.K., A.M.S., L.X.L., O.Z., K.D., C.P., R.S., F.D., P.K., S.D., A.R.)
| | - Piyusha Kundu
- From the Corrigan Minehan Heart Center and Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston (C.L., C.P.R., A.Y., R.K., A.M.S., L.X.L., O.Z., K.D., C.P., R.S., F.D., P.K., S.D., A.R.)
| | - Eva Riechert
- Cardiology Department, University Hospital Heidelberg, Germany (C.L., E.R., H.A.K.).,German Center for Cardiovascular Research, Partner Site Heidelberg/Mannheim, Germany (C.L., E.R., H.A.K.)
| | - Hugo A Katus
- Cardiology Department, University Hospital Heidelberg, Germany (C.L., E.R., H.A.K.).,German Center for Cardiovascular Research, Partner Site Heidelberg/Mannheim, Germany (C.L., E.R., H.A.K.)
| | - Jeffrey E Saffitz
- Pathology Department, Beth Israel Deaconess Medical Center, Boston, MA (J.E.S.)
| | | | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA (H.K., S.A.C.)
| | | | - Saumya Das
- From the Corrigan Minehan Heart Center and Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston (C.L., C.P.R., A.Y., R.K., A.M.S., L.X.L., O.Z., K.D., C.P., R.S., F.D., P.K., S.D., A.R.)
| | - Anthony Rosenzweig
- From the Corrigan Minehan Heart Center and Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston (C.L., C.P.R., A.Y., R.K., A.M.S., L.X.L., O.Z., K.D., C.P., R.S., F.D., P.K., S.D., A.R.)
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8
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Sanlialp A, Schumacher D, Kiper L, Varma E, Riechert E, Ho TC, Hofmann C, Kmietczyk V, Zimmermann F, Dlugosz S, Wirth A, Gorska AA, Burghaus J, Camacho Londoño JE, Katus HA, Doroudgar S, Freichel M, Völkers M. Saraf-dependent activation of mTORC1 regulates cardiac growth. J Mol Cell Cardiol 2020; 141:30-42. [PMID: 32173353 DOI: 10.1016/j.yjmcc.2020.03.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 03/03/2020] [Accepted: 03/09/2020] [Indexed: 10/24/2022]
Abstract
Pathological cardiac hypertrophy is an independent risk for heart failure (HF) and sudden death. Deciphering signaling pathways regulating intracellular Ca2+ homeostasis that control adaptive and pathological cardiac growth may enable identification of novel therapeutic targets. The objective of the present study is to determine the role of the store-operated calcium entry-associated regulatory factor (Saraf), encoded by the Tmem66 gene, on cardiac growth control in vitro and in vivo. Saraf is a single-pass membrane protein located at the sarco/endoplasmic reticulum and regulates intracellular calcium homeostasis. We found that Saraf expression was upregulated in the hypertrophied myocardium and was sufficient for cell growth in response to neurohumoral stimulation. Increased Saraf expression caused cell growth, which was associated with dysregulation of calcium-dependent signaling and sarcoplasmic reticulum calcium content. In vivo, Saraf augmented cardiac myocyte growth in response to angiotensin II and resulted in increased cardiac remodeling together with worsened cardiac function. Mechanistically, Saraf activated mTORC1 (mechanistic target of rapamycin complex 1) and increased protein synthesis, while mTORC1 inhibition blunted Saraf-dependent cell growth. In contrast, the hearts of Saraf knockout mice and Saraf-deficient myocytes did not show any morphological or functional alterations after neurohumoral stimulation, but Saraf depletion resulted in worsened cardiac function after acute pressure overload. SARAF knockout blunted transverse aortic constriction cardiac myocyte hypertrophy and impaired cardiac function, demonstrating a role for SARAF in compensatory myocyte growth. Collectively, these results reveal a novel link between sarcoplasmic reticulum calcium homeostasis and mTORC1 activation that is regulated by Saraf.
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Affiliation(s)
- Ayse Sanlialp
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, University of Heidelberg, Im Neuenheimer Feld 669, 69120 Heidelberg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - Dagmar Schumacher
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany; Institute of Pharmacology, University Hospital Heidelberg, University of Heidelberg, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany
| | - Leon Kiper
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, University of Heidelberg, Im Neuenheimer Feld 669, 69120 Heidelberg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - Eshita Varma
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, University of Heidelberg, Im Neuenheimer Feld 669, 69120 Heidelberg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - Eva Riechert
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, University of Heidelberg, Im Neuenheimer Feld 669, 69120 Heidelberg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - Thanh Cao Ho
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, University of Heidelberg, Im Neuenheimer Feld 669, 69120 Heidelberg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - Christoph Hofmann
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, University of Heidelberg, Im Neuenheimer Feld 669, 69120 Heidelberg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - Vivien Kmietczyk
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, University of Heidelberg, Im Neuenheimer Feld 669, 69120 Heidelberg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - Frank Zimmermann
- Interfacultary Biomedical Faculty (IBF), University of Heidelberg, Im Neuenheimer Feld 347, 69120 Heidelberg, Germany
| | - Sascha Dlugosz
- Interfacultary Biomedical Faculty (IBF), University of Heidelberg, Im Neuenheimer Feld 347, 69120 Heidelberg, Germany
| | - Angela Wirth
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany; Institute of Pharmacology, University Hospital Heidelberg, University of Heidelberg, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany
| | - Agnieszka A Gorska
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, University of Heidelberg, Im Neuenheimer Feld 669, 69120 Heidelberg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - Jana Burghaus
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, University of Heidelberg, Im Neuenheimer Feld 669, 69120 Heidelberg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - Juan E Camacho Londoño
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany; Institute of Pharmacology, University Hospital Heidelberg, University of Heidelberg, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany
| | - Hugo A Katus
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, University of Heidelberg, Im Neuenheimer Feld 669, 69120 Heidelberg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - Shirin Doroudgar
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, University of Heidelberg, Im Neuenheimer Feld 669, 69120 Heidelberg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - Marc Freichel
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany; Institute of Pharmacology, University Hospital Heidelberg, University of Heidelberg, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany
| | - Mirko Völkers
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, University of Heidelberg, Im Neuenheimer Feld 669, 69120 Heidelberg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany.
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9
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Grund A, Szaroszyk M, Korf-Klingebiel M, Malek Mohammadi M, Trogisch FA, Schrameck U, Gigina A, Tiedje C, Gaestel M, Kraft T, Hegermann J, Batkai S, Thum T, Perrot A, Remedios CD, Riechert E, Völkers M, Doroudgar S, Jungmann A, Bauer R, Yin X, Mayr M, Wollert KC, Pich A, Xiao H, Katus HA, Bauersachs J, Müller OJ, Heineke J. TIP30 counteracts cardiac hypertrophy and failure by inhibiting translational elongation. EMBO Mol Med 2019; 11:e10018. [PMID: 31468715 PMCID: PMC6783653 DOI: 10.15252/emmm.201810018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 08/01/2019] [Accepted: 08/06/2019] [Indexed: 12/17/2022] Open
Abstract
Pathological cardiac overload induces myocardial protein synthesis and hypertrophy, which predisposes to heart failure. To inhibit hypertrophy therapeutically, the identification of negative regulators of cardiomyocyte protein synthesis is needed. Here, we identified the tumor suppressor protein TIP30 as novel inhibitor of cardiac hypertrophy and dysfunction. Reduced TIP30 levels in mice entailed exaggerated cardiac growth during experimental pressure overload, which was associated with cardiomyocyte cellular hypertrophy, increased myocardial protein synthesis, reduced capillary density, and left ventricular dysfunction. Pharmacological inhibition of protein synthesis improved these defects. Our results are relevant for human disease, since we found diminished cardiac TIP30 levels in samples from patients suffering from end‐stage heart failure or hypertrophic cardiomyopathy. Importantly, therapeutic overexpression of TIP30 in mouse hearts inhibited cardiac hypertrophy and improved left ventricular function during pressure overload and in cardiomyopathic mdx mice. Mechanistically, we identified a previously unknown anti‐hypertrophic mechanism, whereby TIP30 binds the eukaryotic elongation factor 1A (eEF1A) to prevent the interaction with its essential co‐factor eEF1B2 and translational elongation. Therefore, TIP30 could be a therapeutic target to counteract cardiac hypertrophy.
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Affiliation(s)
- Andrea Grund
- Department for Cardiology and Angiology, Hannover Medical School, Hannover, Germany.,Department of Cardiovascular Research, European Center for Angioscience (ECAS), Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Malgorzata Szaroszyk
- Department for Cardiology and Angiology, Hannover Medical School, Hannover, Germany
| | | | - Mona Malek Mohammadi
- Department for Cardiology and Angiology, Hannover Medical School, Hannover, Germany.,Department of Cardiovascular Research, European Center for Angioscience (ECAS), Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Felix A Trogisch
- Department of Cardiovascular Research, European Center for Angioscience (ECAS), Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Ulrike Schrameck
- Department for Cardiology and Angiology, Hannover Medical School, Hannover, Germany
| | - Anna Gigina
- Department for Cardiology and Angiology, Hannover Medical School, Hannover, Germany
| | - Christopher Tiedje
- Institute of Cell Biochemistry, Hannover Medical School, Hannover, Germany
| | - Matthias Gaestel
- Institute of Cell Biochemistry, Hannover Medical School, Hannover, Germany
| | - Theresia Kraft
- Institute for Molecular and Cellphysiology, Hannover Medical School, Hannover, Germany
| | - Jan Hegermann
- Research Core Unit Electron Microscopy, Hannover Medical School, Hannover, Germany
| | - Sandor Batkai
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Hannover, Germany
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Hannover, Germany.,Cluster of Excellence Rebirth, Hannover Medical School, Hannover, Germany
| | - Andreas Perrot
- Experimental and Clinical Research Center, A Joint Cooperation of Max-Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany
| | | | - Eva Riechert
- Department of Cardiology, Angiology and Pneumology, Medical Faculty of Heidelberg, University of Heidelberg, Heidelberg, Germany
| | - Mirko Völkers
- Department of Cardiology, Angiology and Pneumology, Medical Faculty of Heidelberg, University of Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Shirin Doroudgar
- Department of Cardiology, Angiology and Pneumology, Medical Faculty of Heidelberg, University of Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Andreas Jungmann
- Department of Cardiology, Angiology and Pneumology, Medical Faculty of Heidelberg, University of Heidelberg, Heidelberg, Germany
| | - Ralf Bauer
- Department of Cardiology, Angiology and Pneumology, Medical Faculty of Heidelberg, University of Heidelberg, Heidelberg, Germany
| | - Xiaoke Yin
- King's British Heart Foundation Centre, King's College London, London, UK
| | - Manuel Mayr
- King's British Heart Foundation Centre, King's College London, London, UK
| | - Kai C Wollert
- Department for Cardiology and Angiology, Hannover Medical School, Hannover, Germany.,Cluster of Excellence Rebirth, Hannover Medical School, Hannover, Germany
| | - Andreas Pich
- Core Unit Proteomics, Hannover Medical School, Hannover, Germany
| | - Hua Xiao
- Department of Physiology, Michigan State University, East Lansing, MI, USA
| | - Hugo A Katus
- Department of Cardiology, Angiology and Pneumology, Medical Faculty of Heidelberg, University of Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Johann Bauersachs
- Department for Cardiology and Angiology, Hannover Medical School, Hannover, Germany.,Cluster of Excellence Rebirth, Hannover Medical School, Hannover, Germany
| | - Oliver J Müller
- Department of Cardiology, Angiology and Pneumology, Medical Faculty of Heidelberg, University of Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany.,Department of Internal Medicine III, Cardiology, Angiology and Intensive Care Medicine, Universitätsklinikum Schleswig-Holstein, Kiel, Germany
| | - Joerg Heineke
- Department for Cardiology and Angiology, Hannover Medical School, Hannover, Germany.,Department of Cardiovascular Research, European Center for Angioscience (ECAS), Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany.,Cluster of Excellence Rebirth, Hannover Medical School, Hannover, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
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10
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Doroudgar S, Hofmann C, Boileau E, Malone B, Riechert E, Gorska AA, Jakobi T, Sandmann C, Jürgensen L, Kmietczyk V, Malovrh E, Burghaus J, Rettel M, Stein F, Younesi F, Friedrich UA, Mauz V, Backs J, Kramer G, Katus HA, Dieterich C, Völkers M. Monitoring Cell-Type-Specific Gene Expression Using Ribosome Profiling In Vivo During Cardiac Hemodynamic Stress. Circ Res 2019; 125:431-448. [PMID: 31284834 PMCID: PMC6690133 DOI: 10.1161/circresaha.119.314817] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [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: 01/18/2023]
Abstract
Supplemental Digital Content is available in the text. Rationale: Gene expression profiles have been mainly determined by analysis of transcript abundance. However, these analyses cannot capture posttranscriptional gene expression control at the level of translation, which is a key step in the regulation of gene expression, as evidenced by the fact that transcript levels often poorly correlate with protein levels. Furthermore, genome-wide transcript profiling of distinct cell types is challenging due to the fact that lysates from tissues always represent a mixture of cells. Objectives: This study aimed to develop a new experimental method that overcomes both limitations and to apply this method to perform a genome-wide analysis of gene expression on the translational level in response to pressure overload. Methods and Results: By combining ribosome profiling (Ribo-seq) with a ribosome-tagging approach (Ribo-tag), it was possible to determine the translated transcriptome in specific cell types from the heart. After pressure overload, we monitored the cardiac myocyte translatome by purifying tagged cardiac myocyte ribosomes from cardiac lysates and subjecting the ribosome-protected mRNA fragments to deep sequencing. We identified subsets of mRNAs that are regulated at the translational level and found that translational control determines early changes in gene expression in response to cardiac stress in cardiac myocytes. Translationally controlled transcripts are associated with specific biological processes related to translation, protein quality control, and metabolism. Mechanistically, Ribo-seq allowed for the identification of upstream open reading frames in transcripts, which we predict to be important regulators of translation. Conclusions: This method has the potential to (1) provide a new tool for studying cell-specific gene expression at the level of translation in tissues, (2) reveal new therapeutic targets to prevent cellular remodeling, and (3) trigger follow-up studies that address both, the molecular mechanisms involved in the posttranscriptional control of gene expression in cardiac cells, and the protective functions of proteins expressed in response to cellular stress.
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Affiliation(s)
- Shirin Doroudgar
- From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).,DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.)
| | - Christoph Hofmann
- From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).,DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.)
| | - Etienne Boileau
- From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).,DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.).,Section of Bioinformatics and Systems Cardiology and Klaus Tschira Institute for Integrative Computational Cardiology, University of Heidelberg, Germany (E.B., B.M., T.J., C.D.)
| | - Brandon Malone
- From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).,DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.).,Section of Bioinformatics and Systems Cardiology and Klaus Tschira Institute for Integrative Computational Cardiology, University of Heidelberg, Germany (E.B., B.M., T.J., C.D.)
| | - Eva Riechert
- From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).,DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.)
| | - Agnieszka A Gorska
- From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).,DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.)
| | - Tobias Jakobi
- From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).,DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.).,Section of Bioinformatics and Systems Cardiology and Klaus Tschira Institute for Integrative Computational Cardiology, University of Heidelberg, Germany (E.B., B.M., T.J., C.D.)
| | - Clara Sandmann
- From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).,DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.)
| | - Lonny Jürgensen
- From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).,DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.)
| | - Vivien Kmietczyk
- From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).,DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.)
| | - Ellen Malovrh
- From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).,DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.)
| | - Jana Burghaus
- From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).,DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.)
| | - Mandy Rettel
- Proteomics Core Facility, EMBL Heidelberg, Germany (M.R., F.S.)
| | - Frank Stein
- Proteomics Core Facility, EMBL Heidelberg, Germany (M.R., F.S.)
| | - Fereshteh Younesi
- From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).,DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.)
| | - Ulrike A Friedrich
- Center for Molecular Biology of the University of Heidelberg (ZMBH) and German Cancer Research Center (DKFZ), Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Germany (G.K., U.A.F.)
| | - Victoria Mauz
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.).,Institute of Experimental Cardiology, Heidelberg, Germany (V.M., J. Backs)
| | - Johannes Backs
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.).,Institute of Experimental Cardiology, Heidelberg, Germany (V.M., J. Backs)
| | - Günter Kramer
- Center for Molecular Biology of the University of Heidelberg (ZMBH) and German Cancer Research Center (DKFZ), Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Germany (G.K., U.A.F.)
| | - Hugo A Katus
- From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).,DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.)
| | - Christoph Dieterich
- From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).,DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.).,Section of Bioinformatics and Systems Cardiology and Klaus Tschira Institute for Integrative Computational Cardiology, University of Heidelberg, Germany (E.B., B.M., T.J., C.D.)
| | - Mirko Völkers
- From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).,DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.)
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11
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Kmietczyk V, Riechert E, Kalinski L, Boileau E, Malovrh E, Malone B, Gorska A, Hofmann C, Varma E, Jürgensen L, Kamuf-Schenk V, Altmüller J, Tappu R, Busch M, Most P, Katus HA, Dieterich C, Völkers M. m 6A-mRNA methylation regulates cardiac gene expression and cellular growth. Life Sci Alliance 2019; 2:e201800233. [PMID: 30967445 PMCID: PMC6458851 DOI: 10.26508/lsa.201800233] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 03/22/2019] [Accepted: 03/22/2019] [Indexed: 01/25/2023] Open
Abstract
Conceptually similar to modifications of DNA, mRNAs undergo chemical modifications, which can affect their activity, localization, and stability. The most prevalent internal modification in mRNA is the methylation of adenosine at the N6-position (m6A). This returns mRNA to a role as a central hub of information within the cell, serving as an information carrier, modifier, and attenuator for many biological processes. Still, the precise role of internal mRNA modifications such as m6A in human and murine-dilated cardiac tissue remains unknown. Transcriptome-wide mapping of m6A in mRNA allowed us to catalog m6A targets in human and murine hearts. Increased m6A methylation was found in human cardiomyopathy. Knockdown and overexpression of the m6A writer enzyme Mettl3 affected cell size and cellular remodeling both in vitro and in vivo. Our data suggest that mRNA methylation is highly dynamic in cardiomyocytes undergoing stress and that changes in the mRNA methylome regulate translational efficiency by affecting transcript stability. Once elucidated, manipulations of methylation of specific m6A sites could be a powerful approach to prevent worsening of cardiac function.
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Affiliation(s)
- Vivien Kmietczyk
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, University of Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Eva Riechert
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, University of Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Laura Kalinski
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, University of Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Etienne Boileau
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, University of Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
- Section of Bioinformatics and Systems Cardiology, Department of Cardiology, Angiology, and Pneumology and Klaus Tschira Institute for Integrative Computational Cardiology, University of Heidelberg, Heidelberg, Germany
| | - Ellen Malovrh
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, University of Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Brandon Malone
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, University of Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
- Section of Bioinformatics and Systems Cardiology, Department of Cardiology, Angiology, and Pneumology and Klaus Tschira Institute for Integrative Computational Cardiology, University of Heidelberg, Heidelberg, Germany
| | - Agnieszka Gorska
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, University of Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Christoph Hofmann
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, University of Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Eshita Varma
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, University of Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Lonny Jürgensen
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, University of Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Verena Kamuf-Schenk
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, University of Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Janine Altmüller
- Cologne Center for Genomics, University Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Rewati Tappu
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, University of Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Martin Busch
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, University of Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Patrick Most
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, University of Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Hugo A Katus
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, University of Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Christoph Dieterich
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, University of Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
- Section of Bioinformatics and Systems Cardiology, Department of Cardiology, Angiology, and Pneumology and Klaus Tschira Institute for Integrative Computational Cardiology, University of Heidelberg, Heidelberg, Germany
| | - Mirko Völkers
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, University of Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
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12
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Haas J, Mester S, Lai A, Frese KS, Sedaghat-Hamedani F, Kayvanpour E, Rausch T, Nietsch R, Boeckel JN, Carstensen A, Völkers M, Dietrich C, Pils D, Amr A, Holzer DB, Martins Bordalo D, Oehler D, Weis T, Mereles D, Buss S, Riechert E, Wirsz E, Wuerstle M, Korbel JO, Keller A, Katus HA, Posch AE, Meder B. Genomic structural variations lead to dysregulation of important coding and non-coding RNA species in dilated cardiomyopathy. EMBO Mol Med 2019; 10:107-120. [PMID: 29138229 PMCID: PMC5760848 DOI: 10.15252/emmm.201707838] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The transcriptome needs to be tightly regulated by mechanisms that include transcription factors, enhancers, and repressors as well as non‐coding RNAs. Besides this dynamic regulation, a large part of phenotypic variability of eukaryotes is expressed through changes in gene transcription caused by genetic variation. In this study, we evaluate genome‐wide structural genomic variants (SVs) and their association with gene expression in the human heart. We detected 3,898 individual SVs affecting all classes of gene transcripts (e.g., mRNA, miRNA, lncRNA) and regulatory genomic regions (e.g., enhancer or TFBS). In a cohort of patients (n = 50) with dilated cardiomyopathy (DCM), 80,635 non‐protein‐coding elements of the genome are deleted or duplicated by SVs, containing 3,758 long non‐coding RNAs and 1,756 protein‐coding transcripts. 65.3% of the SV‐eQTLs do not harbor a significant SNV‐eQTL, and for the regions with both classes of association, we find similar effect sizes. In case of deleted protein‐coding exons, we find downregulation of the associated transcripts, duplication events, however, do not show significant changes over all events. In summary, we are first to describe the genomic variability associated with SVs in heart failure due to DCM and dissect their impact on the transcriptome. Overall, SVs explain up to 7.5% of the variation of cardiac gene expression, underlining the importance to study human myocardial gene expression in the context of the individual genome. This has immediate implications for studies on basic mechanisms of cardiac maladaptation, biomarkers, and (gene) therapeutic studies alike.
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Affiliation(s)
- Jan Haas
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Heidelberg, Germany
| | - Stefan Mester
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Heidelberg, Germany
| | - Alan Lai
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Heidelberg, Germany
| | - Karen S Frese
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Heidelberg, Germany
| | - Farbod Sedaghat-Hamedani
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Heidelberg, Germany
| | - Elham Kayvanpour
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Heidelberg, Germany
| | - Tobias Rausch
- EMBL (European Molecular Biology Laboratory), Heidelberg, Germany
| | - Rouven Nietsch
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany
| | - Jes-Niels Boeckel
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Heidelberg, Germany
| | - Avisha Carstensen
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany
| | - Mirko Völkers
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Heidelberg, Germany
| | - Carsten Dietrich
- Strategy and Innovation, Siemens Healthcare GmbH, Erlangen, Germany
| | - Dietmar Pils
- Siemens AG, Corporate Technology, Vienna, Austria.,Section for Clinical Biometrics, Center for Medical Statistics, Informatics, and Intelligent Systems (CeMSIIS), Medical University of Vienna, Vienna, Austria
| | - Ali Amr
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany
| | - Daniel B Holzer
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany
| | - Diana Martins Bordalo
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Heidelberg, Germany
| | - Daniel Oehler
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Heidelberg, Germany
| | - Tanja Weis
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Heidelberg, Germany
| | - Derliz Mereles
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Heidelberg, Germany
| | - Sebastian Buss
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany
| | - Eva Riechert
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Heidelberg, Germany
| | - Emil Wirsz
- Strategy and Innovation, Siemens Healthcare GmbH, Erlangen, Germany
| | | | - Jan O Korbel
- EMBL (European Molecular Biology Laboratory), Heidelberg, Germany
| | - Andreas Keller
- Department of Bioinformatics, University of Saarland, Saarbrücken, Germany
| | - Hugo A Katus
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Heidelberg, Germany
| | - Andreas E Posch
- Strategy and Innovation, Siemens Healthcare GmbH, Erlangen, Germany
| | - Benjamin Meder
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany .,DZHK (German Centre for Cardiovascular Research), Heidelberg, Germany
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13
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Riechert E, Doroudgar S, Ho TC, Malone B, Burghaus J, Katus HA, Dieterich C, Völkers M. Abstract 472: The mTOR-Dependent Translatome Adapts Early Changes in Gene Expression During Cardiac Growth. Circ Res 2017. [DOI: 10.1161/res.121.suppl_1.472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Introduction:
The mTOR kinase links nutrient and growth factor signaling to cell growth by controlling mRNA translation, but the role of translationally controlled networks during cardiac stress remains unknown. We hypothesized that activation of mTOR controls translation of networks of mRNAs, independent from transcription, to rapidly adapt gene expression to physiologic and pathologic stress. We tested this hypothesis by monitoring the transcriptome and the translatome after pharmacologic and genetic inhibition of mTOR in cardiac myocytes.
Methods and Results:
To define the mTOR-dependent translatome, we performed ribosome profiling after pharmacologic mTOR inhibition by Torin1. We found 166 decreased and 199 unchanged mRNAs that we used for further analysis. Among the decreased mRNAs, 17% have a known TOP or TOP like motif in the 5’UTR, explaining why mTOR inhibition selectively suppresses their translation. Gene ontology analyses of Torin1-suppressed mRNAs showed enrichment for genes involved in translation and metabolism.
P
roline
-r
ich
A
KT
s
ubstrate of
40
kDa (Pras40) inhibits mTORC1 activity.
In vivo,
mTOR inhibition by overexpression of Pras40 blocked pathologic growth, and improved cardiac function after transverse aortic constriction (TAC). Conversely, in a cardiomyocyte-specific Pras40 knock-out mouse, heart function was reduced and growth response attenuated after TAC surgery. Similarly, physiological heart growth was inhibited after Pras40 deletion. Mechanistically and in line with the pharmacologic results, global translation rates were decreased after Pras40 depletion. Mass-spectrometric analysis identified ribonucleoproteins, ribosomal proteins and chaperones as Pras40 interaction partners, suggesting a direct function in the protein synthesis and folding machinery downstream of mTOR. Monitoring the translatome
in vivo
after Pras40 depletion using a ribosome tagging approach, followed by ribosome profiling, identified the mTOR-dependent translatome.
Conclusions:
mTOR-dependent translational control might represent a crucial way of controlling gene expression during stress in the myocardium. Once elucidated, mTOR-based therapies could be a powerful approach to prevent worsening of cardiac function.
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