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Arrieta A, Chapski DJ, Reese A, Kimball TH, Song K, Rosa-Garrido M, Vondriska TM. Circadian Control of Histone Turnover During Cardiac Development and Growth. J Biol Chem 2024:107434. [PMID: 38830405 DOI: 10.1016/j.jbc.2024.107434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 04/30/2024] [Accepted: 05/21/2024] [Indexed: 06/05/2024] Open
Abstract
During postnatal cardiac hypertrophy, cardiomyocytes undergo mitotic exit, relying on DNA replication-independent mechanisms of histone turnover to maintain chromatin organization and gene transcription. In other tissues, circadian oscillations in nucleosome occupancy influence clock-controlled gene expression, suggesting a role for the circadian clock in temporal control of histone turnover and coordinated cardiomyocyte gene expression. To elucidate roles for the master circadian transcription factor, Bmal1, in histone turnover, chromatin organization, and myocyte-specific gene expression and cell growth in the neonatal period. Bmal1 knockdown in neonatal rat ventricular myocytes (NRVM) decreased myocyte size, total cellular protein synthesis, and transcription of the fetal hypertrophic gene Nppb following treatment with serum or the α-adrenergic agonist phenylephrine (PE). Depletion of Bmal1 decreased expression of clock-controlled genes Per2 and Tcap, as well as Sik1, a Bmal1 target upregulated in adult versus embryonic hearts. Bmal1 knockdown impaired Per2 and Sik1 promoter accessibility as measured by MNase-qPCR and impaired histone turnover as measured by metabolic labeling of acid-soluble chromatin fractions. Sik1 knockdown in turn decreased myocyte size, while simultaneously inhibiting Nppb transcription and activating Per2 transcription. Linking these changes to chromatin remodeling, depletion of the replication-independent histone variant H3.3a inhibited myocyte hypertrophy and prevented PE-induced changes in clock-controlled gene transcription. Bmal1 is required for neonatal myocyte growth, replication-independent histone turnover, and chromatin organization at the Sik1 promoter. Sik1 represents a novel clock-controlled gene that coordinates myocyte growth with hypertrophic and clock-controlled gene transcription. Replication-independent histone turnover is required for transcriptional remodeling of clock-controlled genes in cardiac myocytes in response to growth stimuli.
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Affiliation(s)
- Adrian Arrieta
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine at UCLA
| | - Douglas J Chapski
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine at UCLA
| | - Anna Reese
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine at UCLA
| | - Todd H Kimball
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine at UCLA
| | - Kunhua Song
- Internal Medicine, Heart Institute, Center for Regenerative Medicine, University of South Florida
| | - Manuel Rosa-Garrido
- Department of Biomedical Engineering, School of Medicine and School of Engineering, University of Alabama at Birmingham
| | - Thomas M Vondriska
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine at UCLA; Department of Medicine, Division of Cardiology, David Geffen School of Medicine at UCLA; Department of Physiology, David Geffen School of Medicine at UCLA.
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2
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Hu S, Chapski DJ, Gehred ND, Kimball TH, Gromova T, Flores A, Rowat AC, Chen J, Packard RRS, Olszewski E, Davis J, Rau CD, McKinsey TA, Rosa-Garrido M, Vondriska TM. Histone H1.0 couples cellular mechanical behaviors to chromatin structure. NATURE CARDIOVASCULAR RESEARCH 2024; 3:441-459. [PMID: 38765203 PMCID: PMC11101354 DOI: 10.1038/s44161-024-00460-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 03/06/2024] [Indexed: 05/21/2024]
Abstract
Tuning of genome structure and function is accomplished by chromatin-binding proteins, which determine the transcriptome and phenotype of the cell. Here we investigate how communication between extracellular stress and chromatin structure may regulate cellular mechanical behaviors. We demonstrate that histone H1.0, which compacts nucleosomes into higher-order chromatin fibers, controls genome organization and cellular stress response. We show that histone H1.0 has privileged expression in fibroblasts across tissue types and that its expression is necessary and sufficient to induce myofibroblast activation. Depletion of histone H1.0 prevents cytokine-induced fibroblast contraction, proliferation and migration via inhibition of a transcriptome comprising extracellular matrix, cytoskeletal and contractile genes, through a process that involves locus-specific H3K27 acetylation. Transient depletion of histone H1.0 in vivo prevents fibrosis in cardiac muscle. These findings identify an unexpected role of linker histones to orchestrate cellular mechanical behaviors, directly coupling force generation, nuclear organization and gene transcription.
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Affiliation(s)
- Shuaishuai Hu
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA USA
| | - Douglas J. Chapski
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA USA
| | - Natalie D. Gehred
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA USA
| | - Todd H. Kimball
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA USA
| | - Tatiana Gromova
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA USA
| | - Angelina Flores
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA USA
| | - Amy C. Rowat
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA USA
| | - Junjie Chen
- Department of Medicine, Division of Cardiology, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA USA
| | - René R. Sevag Packard
- Department of Medicine, Division of Cardiology, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA USA
- Department of Physiology, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA USA
| | - Emily Olszewski
- Department of Bioengineering, University of Washington, Seattle, WA USA
| | - Jennifer Davis
- Department of Bioengineering, University of Washington, Seattle, WA USA
| | - Christoph D. Rau
- Department of Genetics and McAllister Heart Institute, University of North Carolina, Chapel Hill, NC USA
| | - Timothy A. McKinsey
- Department of Medicine, Division of Cardiology and Consortium for Fibrosis Research & Translation, University of Colorado Anschutz Medical Campus, Aurora, CO USA
| | - Manuel Rosa-Garrido
- Department of Biomedical Engineering, School of Medicine and School of Engineering, University of Alabama at Birmingham, Birmingham, AL USA
| | - Thomas M. Vondriska
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA USA
- Department of Medicine, Division of Cardiology, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA USA
- Department of Physiology, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA USA
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Nie Y, Song C, Huang H, Mao S, Ding K, Tang H. Chromatin modifiers in human disease: from functional roles to regulatory mechanisms. MOLECULAR BIOMEDICINE 2024; 5:12. [PMID: 38584203 PMCID: PMC10999406 DOI: 10.1186/s43556-024-00175-1] [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: 11/07/2023] [Accepted: 02/21/2024] [Indexed: 04/09/2024] Open
Abstract
The field of transcriptional regulation has revealed the vital role of chromatin modifiers in human diseases from the beginning of functional exploration to the process of participating in many types of disease regulatory mechanisms. Chromatin modifiers are a class of enzymes that can catalyze the chemical conversion of pyrimidine residues or amino acid residues, including histone modifiers, DNA methyltransferases, and chromatin remodeling complexes. Chromatin modifiers assist in the formation of transcriptional regulatory circuits between transcription factors, enhancers, and promoters by regulating chromatin accessibility and the ability of transcription factors to acquire DNA. This is achieved by recruiting associated proteins and RNA polymerases. They modify the physical contact between cis-regulatory factor elements, transcription factors, and chromatin DNA to influence transcriptional regulatory processes. Then, abnormal chromatin perturbations can impair the homeostasis of organs, tissues, and cells, leading to diseases. The review offers a comprehensive elucidation on the function and regulatory mechanism of chromatin modifiers, thereby highlighting their indispensability in the development of diseases. Furthermore, this underscores the potential of chromatin modifiers as biomarkers, which may enable early disease diagnosis. With the aid of this paper, a deeper understanding of the role of chromatin modifiers in the pathogenesis of diseases can be gained, which could help in devising effective diagnostic and therapeutic interventions.
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Affiliation(s)
- Yali Nie
- Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Clinical Research Center for Myocardial Injury in Hunan Province, Hengyang, Hunan, 421001, China
| | - Chao Song
- Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Hong Huang
- Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Clinical Research Center for Myocardial Injury in Hunan Province, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Shuqing Mao
- Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Clinical Research Center for Myocardial Injury in Hunan Province, Hengyang, Hunan, 421001, China
| | - Kai Ding
- The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Clinical Research Center for Myocardial Injury in Hunan Province, Hengyang, Hunan, 421001, China
| | - Huifang Tang
- Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases, University of South China, Hengyang, Hunan, 421001, China.
- The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.
- Clinical Research Center for Myocardial Injury in Hunan Province, Hengyang, Hunan, 421001, China.
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.
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Bridges J, Ramirez-Guerrero JA, Rosa-Garrido M. Gender-specific genetic and epigenetic signatures in cardiovascular disease. Front Cardiovasc Med 2024; 11:1355980. [PMID: 38529333 PMCID: PMC10962446 DOI: 10.3389/fcvm.2024.1355980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 02/13/2024] [Indexed: 03/27/2024] Open
Abstract
Cardiac sex differences represent a pertinent focus in pursuit of the long-awaited goal of personalized medicine. Despite evident disparities in the onset and progression of cardiac pathology between sexes, historical oversight has led to the neglect of gender-specific considerations in the treatment of patients. This oversight is attributed to a predominant focus on male samples and a lack of sex-based segregation in patient studies. Recognizing these sex differences is not only relevant to the treatment of cisgender individuals; it also holds paramount importance in addressing the healthcare needs of transgender patients, a demographic that is increasingly prominent in contemporary society. In response to these challenges, various agencies, including the National Institutes of Health, have actively directed their efforts toward advancing our comprehension of this phenomenon. Epigenetics has proven to play a crucial role in understanding sex differences in both healthy and disease states within the heart. This review presents a comprehensive overview of the physiological distinctions between males and females during the development of various cardiac pathologies, specifically focusing on unraveling the genetic and epigenetic mechanisms at play. Current findings related to distinct sex-chromosome compositions, the emergence of gender-biased genetic variations, and variations in hormonal profiles between sexes are highlighted. Additionally, the roles of DNA methylation, histone marks, and chromatin structure in mediating pathological sex differences are explored. To inspire further investigation into this crucial subject, we have conducted global analyses of various epigenetic features, leveraging data previously generated by the ENCODE project.
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Affiliation(s)
| | | | - Manuel Rosa-Garrido
- Department of Biomedical Engineering, School of Medicine, School of Engineering, University of Alabama at Birmingham, Birmingham, AL, United States
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Pane R, Laib L, Formoso K, Détrait M, Sainte-Marie Y, Bourgailh F, Ruffenach N, Faugeras H, Simon I, Lhuillier E, Lezoualc'h F, Conte C. Macromolecular Complex Including MLL3, Carabin and Calcineurin Regulates Cardiac Remodeling. Circ Res 2024; 134:100-113. [PMID: 38084599 DOI: 10.1161/circresaha.123.323458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 11/27/2023] [Indexed: 01/06/2024]
Abstract
BACKGROUND Cardiac hypertrophy is an intermediate stage in the development of heart failure. The structural and functional processes occurring in cardiac hypertrophy include extensive gene reprogramming, which is dependent on epigenetic regulation and chromatin remodeling. However, the chromatin remodelers and their regulatory functions involved in the pathogenesis of cardiac hypertrophy are not well characterized. METHODS Protein interaction was determined by immunoprecipitation assay in primary cardiomyocytes and mouse cardiac samples subjected or not to transverse aortic constriction for 1 week. Chromatin immunoprecipitation and DNA sequencing (ChIP-seq) experiments were performed on the chromatin of adult mouse cardiomyocytes. RESULTS We report that the calcium-activated protein phosphatase CaN (calcineurin), its endogenous inhibitory protein carabin, the STK24 (STE20-like protein kinase 3), and the histone monomethyltransferase, MLL3 (mixed lineage leukemia 3) form altogether a macromolecular complex at the chromatin of cardiomyocytes. Under basal conditions, carabin prevents CaN activation while the serine/threonine kinase STK24 maintains MLL3 inactive via phosphorylation. After 1 week of transverse aortic constriction, both carabin and STK24 are released from the CaN-MLL3 complex leading to the activation of CaN, dephosphorylation of MLL3, and in turn, histone H3 lysine 4 monomethylation. Selective cardiac MLL3 knockdown mitigates hypertrophy, and chromatin immunoprecipitation and DNA sequencing analysis demonstrates that MLL3 is de novo recruited at the transcriptional start site of genes implicated in cardiomyopathy in stress conditions. We also show that CaN and MLL3 colocalize at chromatin and that CaN activates MLL3 histone methyl transferase activity at distal intergenic regions under hypertrophic conditions. CONCLUSIONS Our study reveals an unsuspected epigenetic mechanism of CaN that directly regulates MLL3 histone methyl transferase activity to promote cardiac remodeling.
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Affiliation(s)
- Roberto Pane
- Institut des Maladies Métaboliques et Cardiovasculaires, Inserm, Université de Toulouse III-Paul Sabatier, France (R.P., L.L., K.F., M.D.., Y.S.-M., F.B., N.R., H.F., I.S., E.L., F.L., C.C.)
| | - Loubna Laib
- Institut des Maladies Métaboliques et Cardiovasculaires, Inserm, Université de Toulouse III-Paul Sabatier, France (R.P., L.L., K.F., M.D.., Y.S.-M., F.B., N.R., H.F., I.S., E.L., F.L., C.C.)
| | - Karina Formoso
- Institut des Maladies Métaboliques et Cardiovasculaires, Inserm, Université de Toulouse III-Paul Sabatier, France (R.P., L.L., K.F., M.D.., Y.S.-M., F.B., N.R., H.F., I.S., E.L., F.L., C.C.)
| | - Maximin Détrait
- Institut des Maladies Métaboliques et Cardiovasculaires, Inserm, Université de Toulouse III-Paul Sabatier, France (R.P., L.L., K.F., M.D.., Y.S.-M., F.B., N.R., H.F., I.S., E.L., F.L., C.C.)
| | - Yannis Sainte-Marie
- Institut des Maladies Métaboliques et Cardiovasculaires, Inserm, Université de Toulouse III-Paul Sabatier, France (R.P., L.L., K.F., M.D.., Y.S.-M., F.B., N.R., H.F., I.S., E.L., F.L., C.C.)
| | - Florence Bourgailh
- Institut des Maladies Métaboliques et Cardiovasculaires, Inserm, Université de Toulouse III-Paul Sabatier, France (R.P., L.L., K.F., M.D.., Y.S.-M., F.B., N.R., H.F., I.S., E.L., F.L., C.C.)
| | - Nolan Ruffenach
- Institut des Maladies Métaboliques et Cardiovasculaires, Inserm, Université de Toulouse III-Paul Sabatier, France (R.P., L.L., K.F., M.D.., Y.S.-M., F.B., N.R., H.F., I.S., E.L., F.L., C.C.)
| | - Hanamée Faugeras
- Institut des Maladies Métaboliques et Cardiovasculaires, Inserm, Université de Toulouse III-Paul Sabatier, France (R.P., L.L., K.F., M.D.., Y.S.-M., F.B., N.R., H.F., I.S., E.L., F.L., C.C.)
| | - Ilias Simon
- Institut des Maladies Métaboliques et Cardiovasculaires, Inserm, Université de Toulouse III-Paul Sabatier, France (R.P., L.L., K.F., M.D.., Y.S.-M., F.B., N.R., H.F., I.S., E.L., F.L., C.C.)
| | - Emeline Lhuillier
- Institut des Maladies Métaboliques et Cardiovasculaires, Inserm, Université de Toulouse III-Paul Sabatier, France (R.P., L.L., K.F., M.D.., Y.S.-M., F.B., N.R., H.F., I.S., E.L., F.L., C.C.)
- GeT-Sante, Plateforme Genome et Transcriptome, GenoToul, Toulouse, France (E.L.)
| | - Frank Lezoualc'h
- Institut des Maladies Métaboliques et Cardiovasculaires, Inserm, Université de Toulouse III-Paul Sabatier, France (R.P., L.L., K.F., M.D.., Y.S.-M., F.B., N.R., H.F., I.S., E.L., F.L., C.C.)
| | - Caroline Conte
- Institut des Maladies Métaboliques et Cardiovasculaires, Inserm, Université de Toulouse III-Paul Sabatier, France (R.P., L.L., K.F., M.D.., Y.S.-M., F.B., N.R., H.F., I.S., E.L., F.L., C.C.)
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Shi J, Yang C, Zhang J, Zhao K, Li P, Kong C, Wu X, Sun H, Zheng R, Sun W, Chen L, Kong X. NAT10 Is Involved in Cardiac Remodeling Through ac4C-Mediated Transcriptomic Regulation. Circ Res 2023; 133:989-1002. [PMID: 37955115 DOI: 10.1161/circresaha.122.322244] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 10/30/2023] [Indexed: 11/14/2023]
Abstract
BACKGROUND Heart failure, characterized by cardiac remodeling, is associated with abnormal epigenetic processes and aberrant gene expression. Here, we aimed to elucidate the effects and mechanisms of NAT10 (N-acetyltransferase 10)-mediated N4-acetylcytidine (ac4C) acetylation during cardiac remodeling. METHODS NAT10 and ac4C expression were detected in both human and mouse subjects with cardiac remodeling through multiple assays. Subsequently, acetylated RNA immunoprecipitation and sequencing, thiol-linked alkylation for the metabolic sequencing of RNA (SLAM-seq), and ribosome sequencing (Ribo-seq) were employed to elucidate the role of ac4C-modified posttranscriptional regulation in cardiac remodeling. Additionally, functional experiments involving the overexpression or knockdown of NAT10 were conducted in mice models challenged with Ang II (angiotensin II) and transverse aortic constriction. RESULTS NAT10 expression and RNA ac4C levels were increased in in vitro and in vivo cardiac remodeling models, as well as in patients with cardiac hypertrophy. Silencing and inhibiting NAT10 attenuated Ang II-induced cardiomyocyte hypertrophy and cardiofibroblast activation. Next-generation sequencing revealed ac4C changes in both mice and humans with cardiac hypertrophy were associated with changes in global mRNA abundance, stability, and translation efficiency. Mechanistically, NAT10 could enhance the stability and translation efficiency of CD47 and ROCK2 transcripts by upregulating their mRNA ac4C modification, thereby resulting in an increase in their protein expression during cardiac remodeling. Furthermore, the administration of Remodelin, a NAT10 inhibitor, has been shown to prevent cardiac functional impairments in mice subjected to transverse aortic constriction by suppressing cardiac fibrosis, hypertrophy, and inflammatory responses, while also regulating the expression levels of CD47 and ROCK2 (Rho associated coiled-coil containing protein kinase 2). CONCLUSIONS Therefore, our data suggest that modulating epitranscriptomic processes, such as ac4C acetylation through NAT10, may be a promising therapeutic target against cardiac remodeling.
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Affiliation(s)
- Jing Shi
- Department of Cardiology (J.S., K.Z., J.Z., P.L., X.W., W.S., X.K.), The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, China
| | - Chuanxi Yang
- Department of Cardiology, Yangpu Hospital, Tongji University School of Medicine, Shanghai, China (C.Y.)
| | - Jing Zhang
- Department of Cardiology (J.S., K.Z., J.Z., P.L., X.W., W.S., X.K.), The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, China
| | - Kun Zhao
- Department of Cardiology (J.S., K.Z., J.Z., P.L., X.W., W.S., X.K.), The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, China
| | - Peng Li
- Department of Cardiology (J.S., K.Z., J.Z., P.L., X.W., W.S., X.K.), The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, China
| | - Chuiyu Kong
- Department of Cardio-Thoracic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing University, Jiangsu, China (C.K.)
| | - Xiaoguang Wu
- Department of Cardiology (J.S., K.Z., J.Z., P.L., X.W., W.S., X.K.), The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, China
| | - Haoliang Sun
- Department of Cardiovascular Surgery (H.S., R.Z.), The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, China
| | - Rui Zheng
- Department of Cardiovascular Surgery (H.S., R.Z.), The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, China
| | - Wei Sun
- Department of Cardiology (J.S., K.Z., J.Z., P.L., X.W., W.S., X.K.), The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, China
| | - Lianmin Chen
- Changzhou Medical Center of the Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University and Department of Cardiology of the First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China (L.C.)
| | - Xiangqing Kong
- Department of Cardiology (J.S., K.Z., J.Z., P.L., X.W., W.S., X.K.), The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, China
- Cardiovascular Research Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China (X.K.)
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7
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Arrieta A, Chapski DJ, Reese A, Kimball T, Song K, Rosa-Garrido M, Vondriska TM. Circadian Control of Histone Turnover During Cardiac Development and Growth. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.14.567086. [PMID: 38014083 PMCID: PMC10680691 DOI: 10.1101/2023.11.14.567086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Rationale: During postnatal cardiac hypertrophy, cardiomyocytes undergo mitotic exit, relying on DNA replication-independent mechanisms of histone turnover to maintain chromatin organization and gene transcription. In other tissues, circadian oscillations in nucleosome occupancy influence clock-controlled gene expression, suggesting an unrecognized role for the circadian clock in temporal control of histone turnover and coordinate cardiomyocyte gene expression. Objective: To elucidate roles for the master circadian transcription factor, Bmal1, in histone turnover, chromatin organization, and myocyte-specific gene expression and cell growth in the neonatal period. Methods and Results: Bmal1 knockdown in neonatal rat ventricular myocytes (NRVM) decreased myocyte size, total cellular protein, and transcription of the fetal hypertrophic gene Nppb following treatment with increasing serum concentrations or the α-adrenergic agonist phenylephrine (PE). Bmal1 knockdown decreased expression of clock-controlled genes Per2 and Tcap, and salt-inducible kinase 1 (Sik1) which was identified via gene ontology analysis of Bmal1 targets upregulated in adult versus embryonic hearts. Epigenomic analyses revealed co-localized chromatin accessibility and Bmal1 localization in the Sik1 promoter. Bmal1 knockdown impaired Per2 and Sik1 promoter accessibility as measured by MNase-qPCR and impaired histone turnover indicated by metabolic labeling of acid-soluble chromatin fractions and immunoblots of total and chromatin-associated core histones. Sik1 knockdown basally increased myocyte size, while simultaneously impairing and driving Nppb and Per2 transcription, respectively. Conclusions: Bmal1 is required for neonatal myocyte growth, replication-independent histone turnover, and chromatin organization at the Sik1 promoter. Sik1 represents a novel clock-controlled gene that coordinates myocyte growth with hypertrophic and clock-controlled gene transcription.
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Wołowiec A, Wołowiec Ł, Grześk G, Jaśniak A, Osiak J, Husejko J, Kozakiewicz M. The Role of Selected Epigenetic Pathways in Cardiovascular Diseases as a Potential Therapeutic Target. Int J Mol Sci 2023; 24:13723. [PMID: 37762023 PMCID: PMC10531432 DOI: 10.3390/ijms241813723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/03/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
Epigenetics is a rapidly developing science that has gained a lot of interest in recent years due to the correlation between characteristic epigenetic marks and cardiovascular diseases (CVDs). Epigenetic modifications contribute to a change in gene expression while maintaining the DNA sequence. The analysis of these modifications provides a thorough insight into the cardiovascular system from its development to its further functioning. Epigenetics is strongly influenced by environmental factors, including known cardiovascular risk factors such as smoking, obesity, and low physical activity. Similarly, conditions affecting the local microenvironment of cells, such as chronic inflammation, worsen the prognosis in cardiovascular diseases and additionally induce further epigenetic modifications leading to the consolidation of unfavorable cardiovascular changes. A deeper understanding of epigenetics may provide an answer to the continuing strong clinical impact of cardiovascular diseases by improving diagnostic capabilities, personalized medical approaches and the development of targeted therapeutic interventions. The aim of the study was to present selected epigenetic pathways, their significance in cardiovascular diseases, and their potential as a therapeutic target in specific medical conditions.
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Affiliation(s)
- Anna Wołowiec
- Department of Geriatrics, Division of Biochemistry and Biogerontology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 87-100 Torun, Poland
| | - Łukasz Wołowiec
- Department of Cardiology and Clinical Pharmacology, Faculty of Health Sciences, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 87-100 Torun, Poland
| | - Grzegorz Grześk
- Department of Cardiology and Clinical Pharmacology, Faculty of Health Sciences, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 87-100 Torun, Poland
| | - Albert Jaśniak
- Department of Cardiology and Clinical Pharmacology, Faculty of Health Sciences, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 87-100 Torun, Poland
| | - Joanna Osiak
- Department of Cardiology and Clinical Pharmacology, Faculty of Health Sciences, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 87-100 Torun, Poland
| | - Jakub Husejko
- Department of Cardiology and Clinical Pharmacology, Faculty of Health Sciences, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 87-100 Torun, Poland
| | - Mariusz Kozakiewicz
- Department of Geriatrics, Division of Biochemistry and Biogerontology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 87-100 Torun, Poland
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9
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Sopic M, Robinson EL, Emanueli C, Srivastava P, Angione C, Gaetano C, Condorelli G, Martelli F, Pedrazzini T, Devaux Y. Integration of epigenetic regulatory mechanisms in heart failure. Basic Res Cardiol 2023; 118:16. [PMID: 37140699 PMCID: PMC10158703 DOI: 10.1007/s00395-023-00986-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/27/2023] [Accepted: 04/10/2023] [Indexed: 05/05/2023]
Abstract
The number of "omics" approaches is continuously growing. Among others, epigenetics has appeared as an attractive area of investigation by the cardiovascular research community, notably considering its association with disease development. Complex diseases such as cardiovascular diseases have to be tackled using methods integrating different omics levels, so called "multi-omics" approaches. These approaches combine and co-analyze different levels of disease regulation. In this review, we present and discuss the role of epigenetic mechanisms in regulating gene expression and provide an integrated view of how these mechanisms are interlinked and regulate the development of cardiac disease, with a particular attention to heart failure. We focus on DNA, histone, and RNA modifications, and discuss the current methods and tools used for data integration and analysis. Enhancing the knowledge of these regulatory mechanisms may lead to novel therapeutic approaches and biomarkers for precision healthcare and improved clinical outcomes.
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Affiliation(s)
- Miron Sopic
- Department of Medical Biochemistry, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
| | - Emma L Robinson
- Division of Cardiology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Costanza Emanueli
- National Heart & Lung Institute, Imperial College London, London, UK
| | | | - Claudio Angione
- School of Computing, Engineering & Digital Technologies, Teesside University, Tees Valley, Middlesbrough, TS1 3BA, UK
- Centre for Digital Innovation, Teesside University, Campus Heart, Tees Valley, Middlesbrough, TS1 3BX, UK
- National Horizons Centre, Darlington, DL1 1HG, UK
| | - Carlo Gaetano
- Laboratorio di Epigenetica, Istituti Clinici Scientifici Maugeri IRCCS, Via Maugeri 10, 27100, Pavia, Italy
| | - Gianluigi Condorelli
- IRCCS-Humanitas Research Hospital, Via Manzoni 56, 20089, Rozzano, MI, Italy
- Institute of Genetic and Biomedical Research, National Research Council of Italy, Arnold-Heller-Str.3, 24105, Milan, Italy
| | - Fabio Martelli
- Molecular Cardiology Laboratory, IRCCS-Policlinico San Donato, Via Morandi 30, San Donato Milanese, 20097, Milan, Italy
| | - Thierry Pedrazzini
- Experimental Cardiology Unit, Division of Cardiology, Department of Cardiovascular Medicine, University of Lausanne Medical School, 1011, Lausanne, Switzerland
| | - Yvan Devaux
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, L-1445, Strassen, Luxembourg.
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10
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Gromova T, Gehred ND, Vondriska TM. Single-cell transcriptomes in the heart: when every epigenome counts. Cardiovasc Res 2023; 119:64-78. [PMID: 35325060 DOI: 10.1093/cvr/cvac040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 02/03/2022] [Accepted: 02/14/2022] [Indexed: 11/13/2022] Open
Abstract
The response of an organ to stimuli emerges from the actions of individual cells. Recent cardiac single-cell RNA-sequencing studies of development, injury, and reprogramming have uncovered heterogeneous populations even among previously well-defined cell types, raising questions about what level of experimental resolution corresponds to disease-relevant, tissue-level phenotypes. In this review, we explore the biological meaning behind this cellular heterogeneity by undertaking an exhaustive analysis of single-cell transcriptomics in the heart (including a comprehensive, annotated compendium of studies published to date) and evaluating new models for the cardiac function that have emerged from these studies (including discussion and schematics that depict new hypotheses in the field). We evaluate the evidence to support the biological actions of newly identified cell populations and debate questions related to the role of cell-to-cell variability in development and disease. Finally, we present emerging epigenomic approaches that, when combined with single-cell RNA-sequencing, can resolve basic mechanisms of gene regulation and variability in cell phenotype.
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Affiliation(s)
- Tatiana Gromova
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Medicine/Cardiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Natalie D Gehred
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Medicine/Cardiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Thomas M Vondriska
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Medicine/Cardiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
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11
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Kraus L, Beavens B. The Current Therapeutic Role of Chromatin Remodeling for the Prognosis and Treatment of Heart Failure. Biomedicines 2023; 11:biomedicines11020579. [PMID: 36831115 PMCID: PMC9953583 DOI: 10.3390/biomedicines11020579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
Cardiovascular diseases are a major cause of death globally, with no cure to date. Many interventions have been studied and suggested, of which epigenetics and chromatin remodeling have been the most promising. Over the last decade, major advancements have been made in the field of chromatin remodeling, particularly for the treatment of heart failure, because of innovations in bioinformatics and gene therapy. Specifically, understanding changes to the chromatin architecture have been shown to alter cardiac disease progression via variations in genomic sequencing, targeting cardiac genes, using RNA molecules, and utilizing chromatin remodeler complexes. By understanding these chromatin remodeling mechanisms in an injured heart, treatments for heart failure have been suggested through individualized pharmaceutical interventions as well as biomarkers for major disease states. By understanding the current roles of chromatin remodeling in heart failure, a potential therapeutic approach may be discovered in the future.
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12
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Kervella M, Jahier M, Meli AC, Muchir A. Genome organization in cardiomyocytes expressing mutated A-type lamins. Front Cell Dev Biol 2022; 10:1030950. [PMID: 36274847 PMCID: PMC9585167 DOI: 10.3389/fcell.2022.1030950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 09/26/2022] [Indexed: 11/13/2022] Open
Abstract
Cardiomyopathy is a myocardial disorder, in which the heart muscle is structurally and functionally abnormal, often leading to heart failure. Dilated cardiomyopathy is characterized by a compromised left ventricular function and contributes significantly to the heart failure epidemic, which represents a staggering clinical and public health problem worldwide. Gene mutations have been identified in 35% of patients with dilated cardiomyopathy. Pathogenic variants in LMNA, encoding nuclear A-type lamins, are one of the major causative causes of dilated cardiomyopathy (i.e. CardioLaminopathy). A-type lamins are type V intermediate filament proteins, which are the main components of the nuclear lamina. The nuclear lamina is connected to the cytoskeleton on one side, and to the chromatin on the other side. Among the models proposed to explain how CardioLaminopathy arises, the “chromatin model” posits an effect of mutated A-type lamins on the 3D genome organization and thus on the transcription activity of tissue-specific genes. Chromatin contacts with the nuclear lamina via specific genomic regions called lamina-associated domains lamina-associated domains. These LADs play a role in the chromatin organization and gene expression regulation. This review focuses on the identification of LADs and chromatin remodeling in cardiac muscle cells expressing mutated A-type lamins and discusses the methods and relevance of these findings in disease.
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Affiliation(s)
- Marie Kervella
- PhyMedExp, University of Montpellier, INSERM, CNRS, Montpellier, France
| | - Maureen Jahier
- Sorbonne Université, INSERM U974, Institute of Myology, Center of Research in Myology, Paris, France
| | - Albano C. Meli
- PhyMedExp, University of Montpellier, INSERM, CNRS, Montpellier, France
| | - Antoine Muchir
- Sorbonne Université, INSERM U974, Institute of Myology, Center of Research in Myology, Paris, France
- *Correspondence: Antoine Muchir,
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13
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Chen J, Zhu AJ, Packard RRS, Vondriska TM, Chapski DJ. genomeSidekick: A user-friendly epigenomics data analysis tool. FRONTIERS IN BIOINFORMATICS 2022; 2:831025. [PMID: 36304311 PMCID: PMC9580848 DOI: 10.3389/fbinf.2022.831025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 06/28/2022] [Indexed: 11/24/2022] Open
Abstract
Recent advances in epigenomics measurements have resulted in a preponderance of genomic sequencing datasets that require focused analyses to discover mechanisms governing biological processes. In addition, multiple epigenomics experiments are typically performed within the same study, thereby increasing the complexity and difficulty of making meaningful inferences from large datasets. One gap in the sequencing data analysis pipeline is the availability of tools to efficiently browse genomic data for scientists that do not have bioinformatics training. To bridge this gap, we developed genomeSidekick, a graphical user interface written in R that allows researchers to perform bespoke analyses on their transcriptomic and chromatin accessibility or chromatin immunoprecipitation data without the need for command line tools. Importantly, genomeSidekick outputs lists of up- and downregulated genes or chromatin features with differential accessibility or occupancy; visualizes omics data using interactive volcano plots; performs Gene Ontology analyses locally; and queries PubMed for selected gene candidates for further evaluation. Outputs can be saved using the user interface and the code underlying genomeSidekick can be edited for custom analyses. In summary, genomeSidekick brings wet lab scientists and bioinformaticians into a shared fluency with the end goal of driving mechanistic discovery.
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Affiliation(s)
- Junjie Chen
- Division of Cardiology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Ashley J. Zhu
- Department of Anesthesiology and Perioperative Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - René R. S. Packard
- Division of Cardiology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Ronald Reagan UCLA Medical Center, Los Angeles, CA, United States
- Veterans Affairs West Los Angeles Medical Center, Los Angeles, CA, United States
| | - Thomas M. Vondriska
- Division of Cardiology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Anesthesiology and Perioperative Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Douglas J. Chapski
- Department of Anesthesiology and Perioperative Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- *Correspondence: Douglas J. Chapski,
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14
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Cao Y, Vergnes L, Wang YC, Pan C, Chella Krishnan K, Moore TM, Rosa-Garrido M, Kimball TH, Zhou Z, Charugundla S, Rau CD, Seldin MM, Wang J, Wang Y, Vondriska TM, Reue K, Lusis AJ. Sex differences in heart mitochondria regulate diastolic dysfunction. Nat Commun 2022; 13:3850. [PMID: 35787630 PMCID: PMC9253085 DOI: 10.1038/s41467-022-31544-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 06/15/2022] [Indexed: 01/10/2023] Open
Abstract
Heart failure with preserved ejection fraction (HFpEF) exhibits a sex bias, being more common in women than men, and we hypothesize that mitochondrial sex differences might underlie this bias. As part of genetic studies of heart failure in mice, we observe that heart mitochondrial DNA levels and function tend to be reduced in females as compared to males. We also observe that expression of genes encoding mitochondrial proteins are higher in males than females in human cohorts. We test our hypothesis in a panel of genetically diverse inbred strains of mice, termed the Hybrid Mouse Diversity Panel (HMDP). Indeed, we find that mitochondrial gene expression is highly correlated with diastolic function, a key trait in HFpEF. Consistent with this, studies of a "two-hit" mouse model of HFpEF confirm that mitochondrial function differs between sexes and is strongly associated with a number of HFpEF traits. By integrating data from human heart failure and the mouse HMDP cohort, we identify the mitochondrial gene Acsl6 as a genetic determinant of diastolic function. We validate its role in HFpEF using adenoviral over-expression in the heart. We conclude that sex differences in mitochondrial function underlie, in part, the sex bias in diastolic function.
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Affiliation(s)
- Yang Cao
- Division of Cardiology, Department of Medicine, University of California, Los Angeles, CA, USA
| | - Laurent Vergnes
- Metabolism Theme, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90024, USA
| | - Yu-Chen Wang
- Division of Cardiology, Department of Medicine, University of California, Los Angeles, CA, USA
| | - Calvin Pan
- Division of Cardiology, Department of Medicine, University of California, Los Angeles, CA, USA
| | - Karthickeyan Chella Krishnan
- Division of Cardiology, Department of Medicine, University of California, Los Angeles, CA, USA
- Department of Pharmacology and Physiology, University of Cincinnati College of Medicine, Cincinnati, USA
| | - Timothy M Moore
- Division of Cardiology, Department of Medicine, University of California, Los Angeles, CA, USA
| | - Manuel Rosa-Garrido
- Department of Biomedical Engineering, School of Medicine and School of Engineering, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Todd H Kimball
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Zhiqiang Zhou
- Division of Cardiology, Department of Medicine, University of California, Los Angeles, CA, USA
| | - Sarada Charugundla
- Division of Cardiology, Department of Medicine, University of California, Los Angeles, CA, USA
| | - Christoph D Rau
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Marcus M Seldin
- Division of Cardiology, Department of Medicine, University of California, Los Angeles, CA, USA
| | - Jessica Wang
- Division of Cardiology, Department of Medicine, University of California, Los Angeles, CA, USA
| | - Yibin Wang
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Department of Physiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Thomas M Vondriska
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Department of Physiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Karen Reue
- Metabolism Theme, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90024, USA
- Molecular Biology Institute at UCLA, Los Angeles, CA, 90095, USA
| | - Aldons J Lusis
- Division of Cardiology, Department of Medicine, University of California, Los Angeles, CA, USA.
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90024, USA.
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, USA.
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15
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Zhang H, Pei L, Ouyang Z, Wang H, Chen X, Jiang K, Huang S, Jiang R, Xiang Y, Wei K. AP-1 activation mediates postnatal cardiomyocyte maturation. Cardiovasc Res 2022; 119:536-550. [PMID: 35640820 DOI: 10.1093/cvr/cvac088] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 05/05/2022] [Accepted: 05/12/2022] [Indexed: 11/13/2022] Open
Abstract
AIMS Postnatal maturation of mammalian cardiomyocytes proceeds rapidly after birth, with most of the myocytes exiting cell cycle, becoming binucleated, and adopting oxidative phosphorylation as the primary metabolic route. The triggers and transcriptional programs regulating cardiomyocyte maturation have not been fully understood yet. We performed single cell RNA-Seq in postnatal rat hearts in order to identify the important factors for this process. METHODS AND RESULTS Single cell RNA-Seq profiling was performed of postnatal day 1 and day 7 rat hearts, and we found that members of the AP-1 transcription factors showed a transient upregulation in the maturing cardiomyocytes, suggesting their functional involvement in the process. Activating members of the AP-1 family by palmitate or adrenergic stimulation inhibited cardiomyocyte cytokinesis and promoted cardiomyocyte maturation. In contrast, knocking down AP-1 members Atf3 and Jun promoted cardiomyocyte cytokinesis, reduced polyploidy and inhibited maturation. Mechanistically, RNA-Seq results and rescue experiments indicated that AP-1 members activate the expression of fatty acid metabolic genes to promote cardiomyocyte maturation. Finally, intraperitoneal injection of AP-1 inhibitor T-5224 in neonatal mice inhibits cardiomyocyte maturation in vivo. CONCLUSION Our results are the first evidence implicating AP-1 transcription factors in postnatal cardiomyocyte maturation both in vitro and in vivo, which expand our understanding of the molecular mechanism of cardiomyocyte maturation, and may lead to novel therapies to treat congenital heart diseases. TRANSLATIONAL PERSPECTIVE Postnatal cardiomyocyte maturation is a crucial process of cardiac development that determines fitness of the adult heart, and can be affected by multiple congenital heart diseases which lead to adult heart conditions. Our finding that AP-1 transcription factors transiently activated by multiple cues such as fatty acid and adrenergic signal promote cardiomyocyte maturation provided novel targets for therapeutic intervention, which may be applied during the narrow time window of postnatal cardiomyocyte maturation to treat congenital heart diseases and limit their impact on the adult heart.
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Affiliation(s)
- Hongjie Zhang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, P.R. China
| | - Lijuan Pei
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, P.R. China
| | - Zhaohui Ouyang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, P.R. China
| | - Haocun Wang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, P.R. China
| | - Xin Chen
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Kai Jiang
- Shanghai East Hospital, Key Laboratory of Arrhythmias of the Ministry of Education of China, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Shiqi Huang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, P.R. China
| | - Rui Jiang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, P.R. China
| | - Yaozu Xiang
- Shanghai East Hospital, Key Laboratory of Arrhythmias of the Ministry of Education of China, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Ke Wei
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, P.R. China
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16
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Hu S, Vondriska TM. How Chromatin Stiffens Fibroblasts. CURRENT OPINION IN PHYSIOLOGY 2022; 26. [DOI: 10.1016/j.cophys.2022.100537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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17
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Integrative analysis reveals multiple modes of LXR transcriptional regulation in liver. Proc Natl Acad Sci U S A 2022; 119:2122683119. [PMID: 35145035 PMCID: PMC8851562 DOI: 10.1073/pnas.2122683119] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/05/2022] [Indexed: 02/08/2023] Open
Abstract
The nuclear receptors liver X receptor (LXR) α and β play crucial roles in hepatic metabolism. Many genes induced in response to pharmacologic LXR agonism have been defined; however, the transcriptional consequences of loss of LXR binding to its genomic targets are less well characterized. Here, we addressed how deletion of both LXRα and LXRβ from mouse liver (LXR double knockout [DKO]) affects the transcriptional regulatory landscape by integrating changes in LXR binding, chromatin accessibility, and gene expression. Many genes involved in fatty acid metabolism showed reduced expression and chromatin accessibility at their intergenic and intronic regions in LXRDKO livers. Genes that were up-regulated with LXR deletion had increased chromatin accessibility at their promoter regions and were enriched for functions not linked to lipid metabolism. Loss of LXR binding in liver reduced the activity of a broad set of hepatic transcription factors, inferred through changes in motif accessibility. By contrast, accessibility at promoter nuclear factor Y (NF-Y) motifs was increased in the absence of LXR. Unexpectedly, we also defined a small set of LXR targets for direct ligand-dependent repression. These genes have LXR-binding sites but showed increased expression in LXRDKO liver and reduced expression in response to the LXR agonist. In summary, the binding of LXRs to the hepatic genome has broad effects on the transcriptional landscape that extend beyond its canonical function as an activator of lipid metabolic genes.
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18
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Pezhouman A, Nguyen NB, Sercel AJ, Nguyen TL, Daraei A, Sabri S, Chapski DJ, Zheng M, Patananan AN, Ernst J, Plath K, Vondriska TM, Teitell MA, Ardehali R. Transcriptional, Electrophysiological, and Metabolic Characterizations of hESC-Derived First and Second Heart Fields Demonstrate a Potential Role of TBX5 in Cardiomyocyte Maturation. Front Cell Dev Biol 2021; 9:787684. [PMID: 34988079 PMCID: PMC8722677 DOI: 10.3389/fcell.2021.787684] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 11/25/2021] [Indexed: 12/03/2022] Open
Abstract
Background: Human embryonic stem cell-derived cardiomyocytes (hESC-CMs) can be used as a source for cell delivery to remuscularize the heart after myocardial infarction. Despite their therapeutic potential, the emergence of ventricular arrhythmias has limited their application. We previously developed a double reporter hESC line to isolate first heart field (FHF: TBX5+NKX2-5+) and second heart field (SHF: TBX5-NKX2-5+) CMs. Herein, we explore the role of TBX5 and its effects on underlying gene regulatory networks driving phenotypical and functional differences between these two populations. Methods: We used a combination of tools and techniques for rapid and unsupervised profiling of FHF and SHF populations at the transcriptional, translational, and functional level including single cell RNA (scRNA) and bulk RNA sequencing, atomic force and quantitative phase microscopy, respirometry, and electrophysiology. Results: Gene ontology analysis revealed three biological processes attributed to TBX5 expression: sarcomeric structure, oxidative phosphorylation, and calcium ion handling. Interestingly, migratory pathways were enriched in SHF population. SHF-like CMs display less sarcomeric organization compared to FHF-like CMs, despite prolonged in vitro culture. Atomic force and quantitative phase microscopy showed increased cellular stiffness and decreased mass distribution over time in FHF compared to SHF populations, respectively. Electrophysiological studies showed longer plateau in action potentials recorded from FHF-like CMs, consistent with their increased expression of calcium handling genes. Interestingly, both populations showed nearly identical respiratory profiles with the only significant functional difference being higher ATP generation-linked oxygen consumption rate in FHF-like CMs. Our findings suggest that FHF-like CMs display more mature features given their enhanced sarcomeric alignment, calcium handling, and decreased migratory characteristics. Finally, pseudotime analyses revealed a closer association of the FHF population to human fetal CMs along the developmental trajectory. Conclusion: Our studies reveal that distinguishing FHF and SHF populations based on TBX5 expression leads to a significant impact on their downstream functional properties. FHF CMs display more mature characteristics such as enhanced sarcomeric organization and improved calcium handling, with closer positioning along the differentiation trajectory to human fetal hearts. These data suggest that the FHF CMs may be a more suitable candidate for cardiac regeneration.
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Affiliation(s)
- Arash Pezhouman
- Division of Cardiology, Department of Internal Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Eli and Edythe Broad Stem Cell Research Center, University of California, Los Angeles, Los Angeles, CA, United States
| | - Ngoc B. Nguyen
- Division of Cardiology, Department of Internal Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Eli and Edythe Broad Stem Cell Research Center, University of California, Los Angeles, Los Angeles, CA, United States
- Molecular, Cellular and Integrative Physiology Graduate Program, University of California, Los Angeles, Los Angeles, CA, United States
| | - Alexander J. Sercel
- Molecular Biology Interdepartmental Doctoral Program, University of California, Los Angeles, Los Angeles, CA, United States
| | - Thang L. Nguyen
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, United States
| | - Ali Daraei
- Division of Cardiology, Department of Internal Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Shan Sabri
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, United States
| | - Douglas J. Chapski
- Department of Anesthesiology and Perioperative Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Melton Zheng
- Division of Cardiology, Department of Internal Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Alexander N. Patananan
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, United States
| | - Jason Ernst
- Eli and Edythe Broad Stem Cell Research Center, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, United States
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, United States
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Kathrin Plath
- Eli and Edythe Broad Stem Cell Research Center, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, United States
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Thomas M. Vondriska
- Department of Anesthesiology and Perioperative Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Physiology, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Michael A. Teitell
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, United States
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, United States
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Pediatrics, University of California, Los Angeles, Los Angeles, CA, United States
| | - Reza Ardehali
- Division of Cardiology, Department of Internal Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Eli and Edythe Broad Stem Cell Research Center, University of California, Los Angeles, Los Angeles, CA, United States
- Molecular, Cellular and Integrative Physiology Graduate Program, University of California, Los Angeles, Los Angeles, CA, United States
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, United States
- *Correspondence: Reza Ardehali,
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