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Sweat ME, Cao Y, Zhang X, Burnicka-Turek O, Perez-Cervantes C, Arulsamy K, Lu F, Keating EM, Akerberg BN, Ma Q, Wakimoto H, Gorham JM, Hill LD, Kyoung Song M, Trembley MA, Wang P, Gianeselli M, Prondzynski M, Bortolin RH, Bezzerides VJ, Chen K, Seidman JG, Seidman CE, Moskowitz IP, Pu WT. Tbx5 maintains atrial identity in post-natal cardiomyocytes by regulating an atrial-specific enhancer network. NATURE CARDIOVASCULAR RESEARCH 2023; 2:881-898. [PMID: 38344303 PMCID: PMC10854392 DOI: 10.1038/s44161-023-00334-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 08/21/2023] [Indexed: 02/15/2024]
Abstract
Understanding how the atrial and ventricular heart chambers maintain distinct identities is a prerequisite for treating chamber-specific diseases. Here, we selectively knocked out (KO) the transcription factor Tbx5 in the atrial working myocardium to evaluate its requirement for atrial identity. Atrial Tbx5 inactivation downregulated atrial cardiomyocyte (aCM) selective gene expression. Using concurrent single nucleus transcriptome and open chromatin profiling, genomic accessibility differences were identified between control and Tbx5 KO aCMs, revealing that 69% of the control-enriched ATAC regions were bound by TBX5. Genes associated with these regions were downregulated in KO aCMs, suggesting they function as TBX5-dependent enhancers. Comparing enhancer chromatin looping using H3K27ac HiChIP identified 510 chromatin loops sensitive to TBX5 dosage, and 74.8% of control-enriched loops contained anchors in control-enriched ATAC regions. Together, these data demonstrate TBX5 maintains the atrial gene expression program by binding to and preserving the tissue-specific chromatin architecture of atrial enhancers.
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Affiliation(s)
- Mason E. Sweat
- Department of Cardiology, Boston Children’s Hospital, 300 Longwood Ave, Boston, MA 02115
| | - Yangpo Cao
- Department of Cardiology, Boston Children’s Hospital, 300 Longwood Ave, Boston, MA 02115
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Xiaoran Zhang
- Department of Cardiology, Boston Children’s Hospital, 300 Longwood Ave, Boston, MA 02115
| | - Ozanna Burnicka-Turek
- Department of Pediatrics, Pathology, and Human Genetics, The University of Chicago, Chicago, IL
| | - Carlos Perez-Cervantes
- Department of Pediatrics, Pathology, and Human Genetics, The University of Chicago, Chicago, IL
| | - Kulandai Arulsamy
- Department of Cardiology, Boston Children’s Hospital, 300 Longwood Ave, Boston, MA 02115
| | - Fujian Lu
- Department of Cardiology, Boston Children’s Hospital, 300 Longwood Ave, Boston, MA 02115
| | - Erin M. Keating
- Department of Cardiology, Boston Children’s Hospital, 300 Longwood Ave, Boston, MA 02115
| | - Brynn N. Akerberg
- Department of Cardiology, Boston Children’s Hospital, 300 Longwood Ave, Boston, MA 02115
| | - Qing Ma
- Department of Cardiology, Boston Children’s Hospital, 300 Longwood Ave, Boston, MA 02115
| | - Hiroko Wakimoto
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Joshua M. Gorham
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Lauren D. Hill
- Department of Cardiology, Boston Children’s Hospital, 300 Longwood Ave, Boston, MA 02115
| | - Mi Kyoung Song
- Department of Cardiology, Boston Children’s Hospital, 300 Longwood Ave, Boston, MA 02115
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Korea
| | - Michael A. Trembley
- Department of Cardiology, Boston Children’s Hospital, 300 Longwood Ave, Boston, MA 02115
| | - Peizhe Wang
- Department of Cardiology, Boston Children’s Hospital, 300 Longwood Ave, Boston, MA 02115
| | - Matteo Gianeselli
- Department of Cardiology, Boston Children’s Hospital, 300 Longwood Ave, Boston, MA 02115
| | | | - Raul H. Bortolin
- Department of Cardiology, Boston Children’s Hospital, 300 Longwood Ave, Boston, MA 02115
| | | | - Kaifu Chen
- Department of Cardiology, Boston Children’s Hospital, 300 Longwood Ave, Boston, MA 02115
| | - Jonathan G. Seidman
- Department of Pediatrics, Pathology, and Human Genetics, The University of Chicago, Chicago, IL
| | - Christine E. Seidman
- Department of Pediatrics, Pathology, and Human Genetics, The University of Chicago, Chicago, IL
| | - Ivan P. Moskowitz
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - William T. Pu
- Department of Cardiology, Boston Children’s Hospital, 300 Longwood Ave, Boston, MA 02115
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Huiskes FG, Creemers EE, Brundel BJJM. Dissecting the Molecular Mechanisms Driving Electropathology in Atrial Fibrillation: Deployment of RNA Sequencing and Transcriptomic Analyses. Cells 2023; 12:2242. [PMID: 37759465 PMCID: PMC10526291 DOI: 10.3390/cells12182242] [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: 07/15/2023] [Revised: 08/30/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Despite many efforts to treat atrial fibrillation (AF), the most common progressive and age-related cardiac tachyarrhythmia in the Western world, the efficacy is still suboptimal. A plausible reason for this is that current treatments are not directed at underlying molecular root causes that drive electrical conduction disorders and AF (i.e., electropathology). Insights into AF-induced transcriptomic alterations may aid in a deeper understanding of electropathology. Specifically, RNA sequencing (RNA-seq) facilitates transcriptomic analyses and discovery of differences in gene expression profiles between patient groups. In the last decade, various RNA-seq studies have been conducted in atrial tissue samples of patients with AF versus controls in sinus rhythm. Identified differentially expressed molecular pathways so far include pathways related to mechanotransduction, ECM remodeling, ion channel signaling, and structural tissue organization through developmental and inflammatory signaling pathways. In this review, we provide an overview of the available human AF RNA-seq studies and highlight the molecular pathways identified. Additionally, a comparison is made between human RNA-seq findings with findings from experimental AF model systems and we discuss contrasting findings. Finally, we elaborate on new exciting RNA-seq approaches, including single-nucleotide variants, spatial transcriptomics and profiling of different populations of total RNA, small RNA and long non-coding RNA.
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Affiliation(s)
- Fabries G. Huiskes
- Department of Physiology, Amsterdam UMC, Location Vrije Universiteit, VUmc, Amsterdam Cardiovascular Sciences, Heart Failure and Arrhythmias, 1081 HZ, Amsterdam, The Netherlands;
- Department of Experimental Cardiology, Amsterdam UMC, Location AMC, Amsterdam Cardiovascular Sciences, Heart Failure and Arrhythmias, 1105 AZ Amsterdam, The Netherlands;
| | - Esther E. Creemers
- Department of Experimental Cardiology, Amsterdam UMC, Location AMC, Amsterdam Cardiovascular Sciences, Heart Failure and Arrhythmias, 1105 AZ Amsterdam, The Netherlands;
| | - Bianca J. J. M. Brundel
- Department of Physiology, Amsterdam UMC, Location Vrije Universiteit, VUmc, Amsterdam Cardiovascular Sciences, Heart Failure and Arrhythmias, 1081 HZ, Amsterdam, The Netherlands;
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Sweat ME, Cao Y, Zhang X, Burnicka-Turek O, Perez-Cervantes C, Akerberg BN, Ma Q, Wakimoto H, Gorham JM, Song MK, Trembley MA, Wang P, Lu F, Gianeselli M, Prondzynski M, Bortolin RH, Seidman JG, Seidman CE, Moskowitz IP, Pu WT. Tbx5 maintains atrial identity by regulating an atrial enhancer network. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.21.537535. [PMID: 37131696 PMCID: PMC10153240 DOI: 10.1101/2023.04.21.537535] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Understanding how the atrial and ventricular chambers of the heart maintain their distinct identity is a prerequisite for treating chamber-specific diseases. Here, we selectively inactivated the transcription factor Tbx5 in the atrial working myocardium of the neonatal mouse heart to show that it is required to maintain atrial identity. Atrial Tbx5 inactivation downregulated highly chamber specific genes such as Myl7 and Nppa , and conversely, increased the expression of ventricular identity genes including Myl2 . Using combined single nucleus transcriptome and open chromatin profiling, we assessed genomic accessibility changes underlying the altered atrial identity expression program, identifying 1846 genomic loci with greater accessibility in control atrial cardiomyocytes compared to KO aCMs. 69% of the control-enriched ATAC regions were bound by TBX5, demonstrating a role for TBX5 in maintaining atrial genomic accessibility. These regions were associated with genes that had higher expression in control aCMs compared to KO aCMs, suggesting they act as TBX5-dependent enhancers. We tested this hypothesis by analyzing enhancer chromatin looping using HiChIP and found 510 chromatin loops that were sensitive to TBX5 dosage. Of the loops enriched in control aCMs, 73.7% contained anchors in control-enriched ATAC regions. Together, these data demonstrate a genomic role for TBX5 in maintaining the atrial gene expression program by binding to atrial enhancers and preserving tissue-specific chromatin architecture of atrial enhancers.
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Li J, Liu W, Peng F, Cao X, Xie X, Peng C. The multifaceted biology of lncR-Meg3 in cardio-cerebrovascular diseases. Front Genet 2023; 14:1132884. [PMID: 36968595 PMCID: PMC10036404 DOI: 10.3389/fgene.2023.1132884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 02/28/2023] [Indexed: 03/12/2023] Open
Abstract
Cardio-cerebrovascular disease, related to high mortality and morbidity worldwide, is a type of cardiovascular or cerebrovascular dysfunction involved in various processes. Therefore, it is imperative to conduct additional research into the pathogenesis and new therapeutic targets of cardiovascular and cerebrovascular disorders. Long non-coding RNAs (lncRNAs) have multiple functions and are involved in nearly all cellular biological processes, including translation, transcription, signal transduction, and cell cycle control. LncR-Meg3 is one of them and is becoming increasingly popular. By binding proteins or directly or competitively binding miRNAs, LncR-Meg3 is involved in apoptosis, inflammation, oxidative stress, endoplasmic reticulum stress, epithelial-mesenchymal transition, and other processes. Recent research has shown that LncR-Meg3 is associated with acute myocardial infarction and can be used to diagnose this condition. This article examines the current state of knowledge regarding the expression and regulatory function of LncR-Meg3 in relation to cardiovascular and cerebrovascular diseases. The abnormal expression of LncR-Meg3 can influence neuronal cell death, inflammation, apoptosis, smooth muscle cell proliferation, etc., thereby aggravating or promoting the disease. In addition, we review the bioactive components that target lncR-Meg3 and propose some potential delivery vectors. A comprehensive and in-depth analysis of LncR-Meg3’s role in cardiovascular disease suggests that targeting LncR-Meg3 may be an alternative therapy in the near future, providing new options for slowing the progression of cardiovascular disease.
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Affiliation(s)
- Jing Li
- Key Laboratory of Southwestern Chinese Medicine Resources, Key Laboratory of standardization of Chinese herbal medicine of MOE, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Wenxiu Liu
- Key Laboratory of Southwestern Chinese Medicine Resources, Key Laboratory of standardization of Chinese herbal medicine of MOE, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Fu Peng
- Key Laboratory of Southwestern Chinese Medicine Resources, Key Laboratory of standardization of Chinese herbal medicine of MOE, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Department of Pharmacology, Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, China
- *Correspondence: Fu Peng, ; Xiaofang Xie, ; Cheng Peng,
| | - Xiaoyu Cao
- Key Laboratory of Southwestern Chinese Medicine Resources, Key Laboratory of standardization of Chinese herbal medicine of MOE, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xiaofang Xie
- Key Laboratory of Southwestern Chinese Medicine Resources, Key Laboratory of standardization of Chinese herbal medicine of MOE, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- *Correspondence: Fu Peng, ; Xiaofang Xie, ; Cheng Peng,
| | - Cheng Peng
- Key Laboratory of Southwestern Chinese Medicine Resources, Key Laboratory of standardization of Chinese herbal medicine of MOE, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- *Correspondence: Fu Peng, ; Xiaofang Xie, ; Cheng Peng,
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5
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Soda T, Brunetti V, Berra-Romani R, Moccia F. The Emerging Role of N-Methyl-D-Aspartate (NMDA) Receptors in the Cardiovascular System: Physiological Implications, Pathological Consequences, and Therapeutic Perspectives. Int J Mol Sci 2023; 24:ijms24043914. [PMID: 36835323 PMCID: PMC9965111 DOI: 10.3390/ijms24043914] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023] Open
Abstract
N-methyl-D-aspartate receptors (NMDARs) are ligand-gated ion channels that are activated by the neurotransmitter glutamate, mediate the slow component of excitatory neurotransmission in the central nervous system (CNS), and induce long-term changes in synaptic plasticity. NMDARs are non-selective cation channels that allow the influx of extracellular Na+ and Ca2+ and control cellular activity via both membrane depolarization and an increase in intracellular Ca2+ concentration. The distribution, structure, and role of neuronal NMDARs have been extensively investigated and it is now known that they also regulate crucial functions in the non-neuronal cellular component of the CNS, i.e., astrocytes and cerebrovascular endothelial cells. In addition, NMDARs are expressed in multiple peripheral organs, including heart and systemic and pulmonary circulations. Herein, we survey the most recent information available regarding the distribution and function of NMDARs within the cardiovascular system. We describe the involvement of NMDARs in the modulation of heart rate and cardiac rhythm, in the regulation of arterial blood pressure, in the regulation of cerebral blood flow, and in the blood-brain barrier (BBB) permeability. In parallel, we describe how enhanced NMDAR activity could promote ventricular arrhythmias, heart failure, pulmonary artery hypertension (PAH), and BBB dysfunction. Targeting NMDARs could represent an unexpected pharmacological strategy to reduce the growing burden of several life-threatening cardiovascular disorders.
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Affiliation(s)
- Teresa Soda
- Department of Health Sciences, University of Magna Graecia, 88100 Catanzaro, Italy
| | - Valentina Brunetti
- Laboratory of General Physiology, Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Roberto Berra-Romani
- Department of Biomedicine, School of Medicine, Benemérita Universidad Autónoma de Puebla, Puebla 72410, Mexico
| | - Francesco Moccia
- Laboratory of General Physiology, Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy
- Correspondence: ; Tel.: +39-0382-987613
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6
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Zeemering S, Isaacs A, Winters J, Maesen B, Bidar E, Dimopoulou C, Guasch E, Batlle M, Haase D, Hatem SN, Kara M, Kääb S, Mont L, Sinner MF, Wakili R, Maessen J, Crijns HJGM, Fabritz L, Kirchhof P, Stoll M, Schotten U. Atrial fibrillation in the presence and absence of heart failure enhances expression of genes involved in cardiomyocyte structure, conduction properties, fibrosis, inflammation, and endothelial dysfunction. Heart Rhythm 2022; 19:2115-2124. [PMID: 36007727 DOI: 10.1016/j.hrthm.2022.08.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 07/29/2022] [Accepted: 08/16/2022] [Indexed: 12/14/2022]
Abstract
BACKGROUND Little is known about genome-wide changes in the atrial transcriptome as a cause or consequence of atrial fibrillation (AF), and the effect of its common and clinically relevant comorbidity-heart failure (HF). OBJECTIVE The purpose of this study was to explore candidate disease processes for AF by investigating gene expression changes in atrial tissue samples from patients with and without AF, stratified by HF. METHODS RNA sequencing was performed in right and left atrial appendage tissue in 195 patients undergoing open heart surgery from centers participating in the CATCH-ME consortium (no history of AF, n = 91; paroxysmal AF, n = 53; persistent/permanent AF, n = 51). Analyses were stratified into patients with/without HF (n = 75/120) and adjusted for age, sex, atrial side, and a combination of clinical characteristics. RESULTS We identified 35 genes associated with persistent AF compared to patients without a history of AF, both in the presence or absence of HF (false discovery rate <0.05). These were mostly novel associations, including 13 long noncoding RNAs. Genes were involved in regulation of cardiomyocyte structure, conduction properties, fibrosis, inflammation, and endothelial dysfunction. Gene set enrichment analysis identified mainly inflammatory gene sets to be enriched in AF patients without HF, and gene sets involved in cellular respiration in AF patients with HF. CONCLUSION Analysis of atrial gene expression profiles identified numerous novel genes associated with persistent AF, in the presence or absence of HF. Interestingly, no consistent transcriptional changes were associated with paroxysmal AF, suggesting that AF-induced changes in gene expression predominate other changes.
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Affiliation(s)
- Stef Zeemering
- Department of Physiology, Cardiovascular Research Institute Maastricht, University Maastricht, Maastricht, the Netherlands
| | - Aaron Isaacs
- Department of Physiology, Cardiovascular Research Institute Maastricht, University Maastricht, Maastricht, the Netherlands; Maastricht Centre for Systems Biology, Maastricht University, Maastricht, the Netherlands
| | - Joris Winters
- Department of Physiology, Cardiovascular Research Institute Maastricht, University Maastricht, Maastricht, the Netherlands
| | - Bart Maesen
- Department of Cardiothoracic Surgery, Maastricht University Medical Centre, University Maastricht, Maastricht, the Netherlands
| | - Elham Bidar
- Department of Cardiothoracic Surgery, Maastricht University Medical Centre, University Maastricht, Maastricht, the Netherlands
| | | | - Eduard Guasch
- Cardiovascular Institute, Hospital Clinic Barcelona, Barcelona, Spain; Institut d'Investigacions Biomèdiques August Pi I Sunyer, Barcelona, Spain; CIBERCV, Madrid, Spain
| | - Montserrat Batlle
- Institut d'Investigacions Biomèdiques August Pi I Sunyer, Barcelona, Spain; CIBERCV, Madrid, Spain
| | | | - Stéphane N Hatem
- INSERM UMRS1166, Institute of CardioMetabolism and Nutrition, Sorbonne Université, Paris, France; Institut de Cardiologie, Hôpital Pitié-Salpêtrière, Paris, France
| | - Mansour Kara
- Institut de Cardiologie, Hôpital Pitié-Salpêtrière, Paris, France
| | - Stefan Kääb
- Department of Medicine I, University Hospital, Munich, Germany; German Centre for Cardiovascular Research, partner site Munich Heart, Munich, Germany
| | - Lluis Mont
- European Society of Cardiology, Sophia Antipolis, France; Cardiovascular Institute, Hospital Clinic Barcelona, Barcelona, Spain; Institut d'Investigacions Biomèdiques August Pi I Sunyer, Barcelona, Spain; CIBERCV, Madrid, Spain
| | - Moritz F Sinner
- Department of Medicine I, University Hospital, Munich, Germany; German Centre for Cardiovascular Research, partner site Munich Heart, Munich, Germany
| | - Reza Wakili
- German Centre for Cardiovascular Research, partner site Munich Heart, Munich, Germany; Department of Cardiology and Vascular Medicine, West German Heart and Vascular Center Essen, Essen, Germany
| | - Jos Maessen
- Maastricht Centre for Systems Biology, Maastricht University, Maastricht, the Netherlands
| | - Harry J G M Crijns
- Institute of Cardiovascular Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Larissa Fabritz
- Department of Cardiology, Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, the Netherlands; Department of Cardiology, UHB and SWBH NHS Trusts, Birmingham, United Kingdom
| | - Paulus Kirchhof
- INSERM UMRS1166, Institute of CardioMetabolism and Nutrition, Sorbonne Université, Paris, France; Institute of Cardiovascular Sciences, University of Birmingham, Birmingham, United Kingdom; University Heart and Vascular Center UKE Hamburg, Hamburg, Germany; German Center for Cardiovascular Research, partner site Hamburg/Kiel/Lübeck, Germany
| | - Monika Stoll
- Maastricht Centre for Systems Biology, Maastricht University, Maastricht, the Netherlands; Institute of Human Genetics, University of Muenster, Muenster, Germany
| | - Ulrich Schotten
- Department of Physiology, Cardiovascular Research Institute Maastricht, University Maastricht, Maastricht, the Netherlands; INSERM UMRS1166, Institute of CardioMetabolism and Nutrition, Sorbonne Université, Paris, France.
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