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Taking BETs on cardiomyocyte differentiation. NATURE CARDIOVASCULAR RESEARCH 2024; 3:265-266. [PMID: 39196116 DOI: 10.1038/s44161-024-00443-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/29/2024]
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Padmanabhan A, de Soysa TY, Pelonero A, Sapp V, Shah PP, Wang Q, Li L, Lee CY, Sadagopan N, Nishino T, Ye L, Yang R, Karnay A, Poleshko A, Bolar N, Linares-Saldana R, Ranade SS, Alexanian M, Morton SU, Jain M, Haldar SM, Srivastava D, Jain R. A genome-wide CRISPR screen identifies BRD4 as a regulator of cardiomyocyte differentiation. NATURE CARDIOVASCULAR RESEARCH 2024; 3:317-331. [PMID: 39196112 PMCID: PMC11361716 DOI: 10.1038/s44161-024-00431-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 01/19/2024] [Indexed: 08/29/2024]
Abstract
Human induced pluripotent stem cell (hiPSC) to cardiomyocyte (CM) differentiation has reshaped approaches to studying cardiac development and disease. In this study, we employed a genome-wide CRISPR screen in a hiPSC to CM differentiation system and reveal here that BRD4, a member of the bromodomain and extraterminal (BET) family, regulates CM differentiation. Chemical inhibition of BET proteins in mouse embryonic stem cell (mESC)-derived or hiPSC-derived cardiac progenitor cells (CPCs) results in decreased CM differentiation and persistence of cells expressing progenitor markers. In vivo, BRD4 deletion in second heart field (SHF) CPCs results in embryonic or early postnatal lethality, with mutants demonstrating myocardial hypoplasia and an increase in CPCs. Single-cell transcriptomics identified a subpopulation of SHF CPCs that is sensitive to BRD4 loss and associated with attenuated CM lineage-specific gene programs. These results highlight a previously unrecognized role for BRD4 in CM fate determination during development and a heterogenous requirement for BRD4 among SHF CPCs.
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Affiliation(s)
- Arun Padmanabhan
- Gladstone Institutes, San Francisco, CA, USA.
- Department of Medicine, University of California, San Francisco, School of Medicine, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | | | | | - Valerie Sapp
- Department of Medicine, University of California, San Diego, School of Medicine, San Diego, CA, USA
- Department of Pharmacology, University of California, San Diego, San Diego, CA, USA
| | - Parisha P Shah
- Cardiovascular Institute, Epigenetics Institute, and Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Qiaohong Wang
- Cardiovascular Institute, Epigenetics Institute, and Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Li Li
- Cardiovascular Institute, Epigenetics Institute, and Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Clara Youngna Lee
- Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, School of Medicine, San Francisco, CA, USA
| | - Nandhini Sadagopan
- Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, School of Medicine, San Francisco, CA, USA
| | | | - Lin Ye
- Gladstone Institutes, San Francisco, CA, USA
| | - Rachel Yang
- Cardiovascular Institute, Epigenetics Institute, and Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Ashley Karnay
- Cardiovascular Institute, Epigenetics Institute, and Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrey Poleshko
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Nikhita Bolar
- Cardiovascular Institute, Epigenetics Institute, and Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Ricardo Linares-Saldana
- Cardiovascular Institute, Epigenetics Institute, and Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Michael Alexanian
- Gladstone Institutes, San Francisco, CA, USA
- Department of Pediatrics, University of California, San Francisco, School of Medicine, San Francisco, CA, USA
| | - Sarah U Morton
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Mohit Jain
- Department of Medicine, University of California, San Diego, School of Medicine, San Diego, CA, USA
- Department of Pharmacology, University of California, San Diego, San Diego, CA, USA
| | - Saptarsi M Haldar
- Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, School of Medicine, San Francisco, CA, USA
- Amgen Research, Cardiometabolic Disorders, South San Francisco, CA, USA
| | - Deepak Srivastava
- Gladstone Institutes, San Francisco, CA, USA.
- Department of Pediatrics, University of California, San Francisco, School of Medicine, San Francisco, CA, USA.
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone Institutes, San Francisco, CA, USA.
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
| | - Rajan Jain
- Cardiovascular Institute, Epigenetics Institute, and Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA.
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Raghavan A, Pirruccello JP, Ellinor PT, Lindsay ME. Using Genomics to Identify Novel Therapeutic Targets for Aortic Disease. Arterioscler Thromb Vasc Biol 2024; 44:334-351. [PMID: 38095107 PMCID: PMC10843699 DOI: 10.1161/atvbaha.123.318771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 11/21/2023] [Indexed: 01/04/2024]
Abstract
Aortic disease, including dissection, aneurysm, and rupture, carries significant morbidity and mortality and is a notable cause of sudden cardiac death. Much of our knowledge regarding the genetic basis of aortic disease has relied on the study of individuals with Mendelian aortopathies and, until recently, the genetic determinants of population-level variance in aortic phenotypes remained unclear. However, the application of machine learning methodologies to large imaging datasets has enabled researchers to rapidly define aortic traits and mine dozens of novel genetic associations for phenotypes such as aortic diameter and distensibility. In this review, we highlight the emerging potential of genomics for identifying causal genes and candidate drug targets for aortic disease. We describe how deep learning technologies have accelerated the pace of genetic discovery in this field. We then provide a blueprint for translating genetic associations to biological insights, reviewing techniques for locus and cell type prioritization, high-throughput functional screening, and disease modeling using cellular and animal models of aortic disease.
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Affiliation(s)
- Avanthi Raghavan
- Cardiology Division, Massachusetts General Hospital, Boston, Massachusetts, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, USA
- Cardiovascular Disease Initiative, Broad Institute, Cambridge, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - James P. Pirruccello
- Division of Cardiology, University of California San Francisco, San Francisco, CA, USA
| | - Patrick T. Ellinor
- Cardiology Division, Massachusetts General Hospital, Boston, Massachusetts, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, USA
- Cardiovascular Disease Initiative, Broad Institute, Cambridge, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Mark E. Lindsay
- Cardiology Division, Massachusetts General Hospital, Boston, Massachusetts, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, USA
- Cardiovascular Disease Initiative, Broad Institute, Cambridge, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
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Eischer N, Arnold M, Mayer A. Emerging roles of BET proteins in transcription and co-transcriptional RNA processing. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1734. [PMID: 35491403 DOI: 10.1002/wrna.1734] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 04/06/2022] [Accepted: 04/09/2022] [Indexed: 01/31/2023]
Abstract
Transcription by RNA polymerase II (Pol II) gives rise to all nuclear protein-coding and a large set of non-coding RNAs, and is strictly regulated and coordinated with RNA processing. Bromodomain and extraterminal (BET) family proteins including BRD2, BRD3, and BRD4 have been implicated in the regulation of Pol II transcription in mammalian cells. However, only recent technological advances have allowed the analysis of direct functions of individual BET proteins with high precision in cells. These studies shed new light on the molecular mechanisms of transcription control by BET proteins challenging previous longstanding views. The most studied BET protein, BRD4, emerges as a master regulator of transcription elongation with roles also in coupling nascent transcription with RNA processing. In contrast, BRD2 is globally required for the formation of transcriptional boundaries to restrict enhancer activity to nearby genes. Although these recent findings suggest non-redundant functions of BRD4 and BRD2 in Pol II transcription, more research is needed for further clarification. Little is known about the roles of BRD3. Here, we illuminate experimental work that has initially linked BET proteins to Pol II transcription in mammalian cells, outline main methodological breakthroughs that have strongly advanced the understanding of BET protein functions, and discuss emerging roles of individual BET proteins in transcription and transcription-coupled RNA processing. Finally, we propose an updated model for the function of BRD4 in transcription and co-transcriptional RNA maturation. This article is categorized under: RNA Processing > 3' End Processing RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- Nicole Eischer
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Mirjam Arnold
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Andreas Mayer
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
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Abstract
Transcription elongation by RNA polymerase II (Pol II) has emerged as a regulatory hub in gene expression. A key control point occurs during early transcription elongation when Pol II pauses in the promoter-proximal region at the majority of genes in mammalian cells and at a large set of genes in Drosophila. An increasing number of trans-acting factors have been linked to promoter-proximal pausing. Some factors help to establish the pause, whereas others are required for the release of Pol II into productive elongation. A dysfunction of this elongation control point leads to aberrant gene expression and can contribute to disease development. The BET bromodomain protein BRD4 has been implicated in elongation control. However, only recently direct BRD4-specific functions in Pol II transcription elongation have been uncovered. This mainly became possible with technological advances that allow selective and rapid ablation of BRD4 in cells along with the availability of approaches that capture the immediate consequences on nascent transcription. This review sheds light on the experimental breakthroughs that led to the emerging view of BRD4 as a general regulator of transcription elongation.
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Affiliation(s)
- Elisabeth Altendorfer
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Yelizaveta Mochalova
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Andreas Mayer
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
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Padmanabhan A, Alexanian M, Linares-Saldana R, González-Terán B, Andreoletti G, Huang Y, Connolly AJ, Kim W, Hsu A, Duan Q, Winchester SAB, Felix F, Perez-Bermejo JA, Wang Q, Li L, Shah PP, Haldar SM, Jain R, Srivastava D. BRD4 (Bromodomain-Containing Protein 4) Interacts with GATA4 (GATA Binding Protein 4) to Govern Mitochondrial Homeostasis in Adult Cardiomyocytes. Circulation 2020; 142:2338-2355. [PMID: 33094644 DOI: 10.1161/circulationaha.120.047753] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND Gene regulatory networks control tissue homeostasis and disease progression in a cell type-specific manner. Ubiquitously expressed chromatin regulators modulate these networks, yet the mechanisms governing how tissue specificity of their function is achieved are poorly understood. BRD4 (bromodomain-containing protein 4), a member of the BET (bromo- and extraterminal domain) family of ubiquitously expressed acetyl-lysine reader proteins, plays a pivotal role as a coactivator of enhancer signaling across diverse tissue types in both health and disease and has been implicated as a pharmacological target in heart failure. However, the cell-specific role of BRD4 in adult cardiomyocytes remains unknown. METHODS We combined conditional mouse genetics, unbiased transcriptomic and epigenomic analyses, and classic molecular biology and biochemical approaches to understand the mechanism by which BRD4 in adult cardiomyocyte homeostasis. RESULTS Here, we show that cardiomyocyte-specific deletion of Brd4 in adult mice leads to acute deterioration of cardiac contractile function with mutant animals demonstrating a transcriptomic signature characterized by decreased expression of genes critical for mitochondrial energy production. Genome-wide occupancy data show that BRD4 enriches at many downregulated genes (including the master coactivators Ppargc1a, Ppargc1b, and their downstream targets) and preferentially colocalizes with GATA4 (GATA binding protein 4), a lineage-determining cardiac transcription factor not previously implicated in regulation of adult cardiac metabolism. BRD4 and GATA4 form an endogenous complex in cardiomyocytes and interact in a bromodomain-independent manner, revealing a new functional interaction partner for BRD4 that can direct its locus and tissue specificity. CONCLUSIONS These results highlight a novel role for a BRD4-GATA4 module in cooperative regulation of a cardiomyocyte-specific gene program governing bioenergetic homeostasis in the adult heart.
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Affiliation(s)
- Arun Padmanabhan
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA (A.P., M.A., B.G.-T., Y.H., A.H., Q.D., S.A.B.W., F.F., J.A.P.-B., S.M.H., D.S.).,Division of Cardiology, Department of Medicine (A.P., S.M.H.), University of California, San Francisco
| | - Michael Alexanian
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA (A.P., M.A., B.G.-T., Y.H., A.H., Q.D., S.A.B.W., F.F., J.A.P.-B., S.M.H., D.S.)
| | - Ricardo Linares-Saldana
- Institute of Regenerative Medicine, Penn Cardiovascular Institute, Departments of Medicine and Cell and Developmental Biology, Perelman School of Medicine, Philadelphia, PA (R.L.-S., W.K., Q.W., L.L., P.P.S., R.J.)
| | - Bárbara González-Terán
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA (A.P., M.A., B.G.-T., Y.H., A.H., Q.D., S.A.B.W., F.F., J.A.P.-B., S.M.H., D.S.)
| | - Gaia Andreoletti
- Bakar Computational Health Sciences Institute (G.A.), University of California, San Francisco
| | - Yu Huang
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA (A.P., M.A., B.G.-T., Y.H., A.H., Q.D., S.A.B.W., F.F., J.A.P.-B., S.M.H., D.S.)
| | - Andrew J Connolly
- Department of Pathology (A.J.C.), University of California, San Francisco
| | - Wonho Kim
- Institute of Regenerative Medicine, Penn Cardiovascular Institute, Departments of Medicine and Cell and Developmental Biology, Perelman School of Medicine, Philadelphia, PA (R.L.-S., W.K., Q.W., L.L., P.P.S., R.J.)
| | - Austin Hsu
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA (A.P., M.A., B.G.-T., Y.H., A.H., Q.D., S.A.B.W., F.F., J.A.P.-B., S.M.H., D.S.)
| | - Qiming Duan
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA (A.P., M.A., B.G.-T., Y.H., A.H., Q.D., S.A.B.W., F.F., J.A.P.-B., S.M.H., D.S.)
| | - Sarah A B Winchester
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA (A.P., M.A., B.G.-T., Y.H., A.H., Q.D., S.A.B.W., F.F., J.A.P.-B., S.M.H., D.S.)
| | - Franco Felix
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA (A.P., M.A., B.G.-T., Y.H., A.H., Q.D., S.A.B.W., F.F., J.A.P.-B., S.M.H., D.S.)
| | - Juan A Perez-Bermejo
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA (A.P., M.A., B.G.-T., Y.H., A.H., Q.D., S.A.B.W., F.F., J.A.P.-B., S.M.H., D.S.)
| | - Qiaohong Wang
- Institute of Regenerative Medicine, Penn Cardiovascular Institute, Departments of Medicine and Cell and Developmental Biology, Perelman School of Medicine, Philadelphia, PA (R.L.-S., W.K., Q.W., L.L., P.P.S., R.J.)
| | - Li Li
- Institute of Regenerative Medicine, Penn Cardiovascular Institute, Departments of Medicine and Cell and Developmental Biology, Perelman School of Medicine, Philadelphia, PA (R.L.-S., W.K., Q.W., L.L., P.P.S., R.J.)
| | - Parisha P Shah
- Institute of Regenerative Medicine, Penn Cardiovascular Institute, Departments of Medicine and Cell and Developmental Biology, Perelman School of Medicine, Philadelphia, PA (R.L.-S., W.K., Q.W., L.L., P.P.S., R.J.)
| | - Saptarsi M Haldar
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA (A.P., M.A., B.G.-T., Y.H., A.H., Q.D., S.A.B.W., F.F., J.A.P.-B., S.M.H., D.S.).,Division of Cardiology, Department of Medicine (A.P., S.M.H.), University of California, San Francisco
| | - Rajan Jain
- Institute of Regenerative Medicine, Penn Cardiovascular Institute, Departments of Medicine and Cell and Developmental Biology, Perelman School of Medicine, Philadelphia, PA (R.L.-S., W.K., Q.W., L.L., P.P.S., R.J.)
| | - Deepak Srivastava
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA (A.P., M.A., B.G.-T., Y.H., A.H., Q.D., S.A.B.W., F.F., J.A.P.-B., S.M.H., D.S.).,Department of Pediatrics (D.S.), University of California, San Francisco.,Department of Biochemistry and Biophysics (D.S.), University of California, San Francisco.,Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA (D.S.)
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Knollmann BC. Cardiac regulatory mechanisms: from cardiac mechanisms to novel therapeutic approaches. J Physiol 2020; 598:2815-2816. [PMID: 32666511 DOI: 10.1113/jp279641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 05/15/2020] [Indexed: 11/08/2022] Open
Affiliation(s)
- Björn C Knollmann
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Division of Clinical Pharmacology, Vanderbilt University School of Medicine, Nashville, TN, USA
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