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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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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: 22] [Impact Index Per Article: 5.5] [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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