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Caporali A, Anwar M, Devaux Y, Katare R, Martelli F, Srivastava PK, Pedrazzini T, Emanueli C. Non-coding RNAs as therapeutic targets and biomarkers in ischaemic heart disease. Nat Rev Cardiol 2024; 21:556-573. [PMID: 38499868 DOI: 10.1038/s41569-024-01001-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/19/2024] [Indexed: 03/20/2024]
Abstract
The adult heart is a complex, multicellular organ that is subjected to a series of regulatory stimuli and circuits and has poor reparative potential. Despite progress in our understanding of disease mechanisms and in the quality of health care, ischaemic heart disease remains the leading cause of death globally, owing to adverse cardiac remodelling, leading to ischaemic cardiomyopathy and heart failure. Therapeutic targets are urgently required for the protection and repair of the ischaemic heart. Moreover, personalized clinical biomarkers are necessary for clinical diagnosis, medical management and to inform the individual response to treatment. Non-coding RNAs (ncRNAs) deeply influence cardiovascular functions and contribute to communication between cells in the cardiac microenvironment and between the heart and other organs. As such, ncRNAs are candidates for translation into clinical practice. However, ncRNA biology has not yet been completely deciphered, given that classes and modes of action have emerged only in the past 5 years. In this Review, we discuss the latest discoveries from basic research on ncRNAs and highlight both the clinical value and the challenges underscoring the translation of these molecules as biomarkers and therapeutic regulators of the processes contributing to the initiation, progression and potentially the prevention or resolution of ischaemic heart disease and heart failure.
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Affiliation(s)
- Andrea Caporali
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, UK
| | - Maryam Anwar
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Yvan Devaux
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, Luxembourg, Luxemburg
| | - Rajesh Katare
- Department of Physiology, HeartOtago, University of Otago, Dunedin, New Zealand
| | - Fabio Martelli
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, Milan, Italy
| | | | - Thierry Pedrazzini
- Experimental Cardiology Unit, Division of Cardiology, Department of Cardiovascular Medicine, University of Lausanne Medical School, Lausanne, Switzerland
- School of Cardiovascular and Metabolic Medicine & Sciences, King's College London, London, UK
- British Heart Foundation Centre of Research Excellence, King's College London, London, UK
| | - Costanza Emanueli
- National Heart and Lung Institute, Imperial College London, London, UK.
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2
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Li L, Xia X, Yang T, Sun Y, Liu X, Xu W, Lu M, Cui D, Wu Y. RNA methylation: A potential therapeutic target in autoimmune disease. Int Rev Immunol 2024; 43:160-177. [PMID: 37975549 DOI: 10.1080/08830185.2023.2280544] [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: 01/19/2023] [Accepted: 11/02/2023] [Indexed: 11/19/2023]
Abstract
Autoimmune diseases such as rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), and inflammatory bowel disease (IBD) are caused by the body's immune response to autoantigens. The pathogenesis of autoimmune diseases is unclear. Numerous studies have demonstrated that RNA methylation plays a key role in disease progression, which is essential for post-transcriptional regulation and has gradually become a broad regulatory mechanism that controls gene expression in various physiological processes, including RNA nuclear output, translation, splicing, and noncoding RNA processing. Here, we outline the writers, erasers, and readers of RNA methylation, including N6-methyladenosine (m6A), 2'-O-methylation (Nm), 2'-O-dimethyladenosine (m6Am), N1-methyladenosine (m1A), 5-methylcytidine (m5C) and N7-methylguanosine (m7G). As the role of RNA methylation modifications in the immune system and diseases is explained, the potential treatment value of these modifications has also been demonstrated. This review reports the relationship between RNA methylation and autoimmune diseases, highlighting the need for future research into the therapeutic potential of RNA modifications.
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Affiliation(s)
- Lele Li
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Xiaoping Xia
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Tian Yang
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Yuchao Sun
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Xueke Liu
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Wei Xu
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Mei Lu
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Dawei Cui
- The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yingping Wu
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Jinhua, China
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Benak D, Holzerova K, Hrdlicka J, Kolar F, Olsen M, Karelson M, Hlavackova M. Epitranscriptomic regulation in fasting hearts: implications for cardiac health. RNA Biol 2024; 21:1-14. [PMID: 38326277 PMCID: PMC10854364 DOI: 10.1080/15476286.2024.2307732] [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] [Accepted: 01/16/2024] [Indexed: 02/09/2024] Open
Abstract
Cardiac tolerance to ischaemia can be increased by dietary interventions such as fasting, which is associated with significant changes in myocardial gene expression. Among the possible mechanisms of how gene expression may be altered are epigenetic modifications of RNA - epitranscriptomics. N6-methyladenosine (m6A) and N6,2'-O-dimethyladenosine (m6Am) are two of the most prevalent modifications in mRNA. These methylations are reversible and regulated by proteins called writers, erasers, readers, and m6A-repelled proteins. We analysed 33 of these epitranscriptomic regulators in rat hearts after cardioprotective 3-day fasting using RT-qPCR, Western blot, and targeted proteomic analysis. We found that the most of these regulators were changed on mRNA or protein levels in fasting hearts, including up-regulation of both demethylases - FTO and ALKBH5. In accordance, decreased methylation (m6A+m6Am) levels were detected in cardiac total RNA after fasting. We also identified altered methylation levels in Nox4 and Hdac1 transcripts, both of which play a role in the cytoprotective action of ketone bodies produced during fasting. Furthermore, we investigated the impact of inhibiting demethylases ALKBH5 and FTO in adult rat primary cardiomyocytes (AVCMs). Our findings indicate that inhibiting these demethylases reduced the hypoxic tolerance of AVCMs isolated from fasting rats. This study showed that the complex epitranscriptomic machinery around m6A and m6Am modifications is regulated in the fasting hearts and might play an important role in cardiac adaptation to fasting, a well-known cardioprotective intervention.
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Affiliation(s)
- Daniel Benak
- Laboratory of Developmental Cardiology, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
- Department of Physiology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Kristyna Holzerova
- Laboratory of Developmental Cardiology, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jaroslav Hrdlicka
- Laboratory of Developmental Cardiology, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Frantisek Kolar
- Laboratory of Developmental Cardiology, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Mark Olsen
- Department of Pharmaceutical Sciences, College of Pharmacy-Glendale, Midwestern University, Glendale, Arizona, USA
| | - Mati Karelson
- Institute of Chemistry, University of Tartu, Tartu, Estonia
| | - Marketa Hlavackova
- Laboratory of Developmental Cardiology, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
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Kunovac A, Hathaway QA, Thapa D, Durr AJ, Taylor AD, Rizwan S, Sharif D, Valentine SJ, Hollander JM. N 6-methyladenosine (M 6A) in fetal offspring modifies mitochondrial gene expression following gestational nano-TiO 2 inhalation exposure. Nanotoxicology 2023; 17:651-668. [PMID: 38180356 PMCID: PMC10988778 DOI: 10.1080/17435390.2023.2293144] [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: 07/26/2023] [Accepted: 12/06/2023] [Indexed: 01/06/2024]
Abstract
N6-methyladenosine (m6A) is the most prominent epitranscriptomic modification to RNA in eukaryotes, but it's role in adaptive changes within the gestational environment are poorly understood. We propose that gestational exposure to nano titanium dioxide (TiO2) contributes to cardiac m6A methylation in fetal offspring and influences mitochondrial gene expression. 10-week-old pregnant female FVB/NJ wild-type mice underwent 6 nonconsecutive days of whole-body inhalation exposure beginning on gestational day (GD) 5. Mice were exposed to filtered room air or nano-TiO2 with a target aerosol mass concentration of 12 mg/m3. At GD 15 mice were humanely killed and cardiac RNA and mitochondrial proteins extracted. Immunoprecipitation with m6A antibodies was performed followed by sequencing of immunoprecipitant (m6A) and input (mRNA) on the Illumina NextSeq 2000. Protein extraction, preparation, and LC-MS/MS were used for mitochondrial protein quantification. There were no differences in maternal or fetal pup weights, number of pups, or pup heart weights between exposure and control groups. Transcriptomic sequencing revealed 3648 differentially expressed mRNA in nano-TiO2 exposed mice (Padj ≤ 0.05). Transcripts involved in mitochondrial bioenergetics were significantly downregulated (83 of 85 genes). 921 transcripts revealed significant m6A methylation sites (Padj ≤ 0.10). 311 of the 921 mRNA were identified to have both 1) significantly altered expression and 2) differentially methylated sites. Mitochondrial proteomics revealed decreased expression of ATP Synthase subunits in the exposed group (P ≤ 0.05). The lack of m6A modifications to mitochondrial transcripts suggests a mechanism for decreased transcript stability and reduced protein expression due to gestational nano-TiO2 inhalation exposure.
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Affiliation(s)
- Amina Kunovac
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, WV, USA
- Mitochondria, Metabolism & Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, WV, USA
- Center for Inhalation Toxicology (iTOX), West Virginia University School of Medicine, Morgantown, WV, USA
| | - Quincy A. Hathaway
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, WV, USA
- Department of Medical Education, West Virginia University School of Medicine, Morgantown, WV, USA
| | - Dharendra Thapa
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, WV, USA
- Mitochondria, Metabolism & Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, WV, USA
| | - Andrya J. Durr
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, WV, USA
- Mitochondria, Metabolism & Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, WV, USA
| | - Andrew D. Taylor
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, WV, USA
- Mitochondria, Metabolism & Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, WV, USA
| | - Saira Rizwan
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, WV, USA
- Mitochondria, Metabolism & Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, WV, USA
| | - Daud Sharif
- Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | | | - John M. Hollander
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, WV, USA
- Mitochondria, Metabolism & Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, WV, USA
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Benak D, Kolar F, Zhang L, Devaux Y, Hlavackova M. RNA modification m 6Am: the role in cardiac biology. Epigenetics 2023; 18:2218771. [PMID: 37331009 DOI: 10.1080/15592294.2023.2218771] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 05/19/2023] [Accepted: 05/23/2023] [Indexed: 06/20/2023] Open
Abstract
Epitranscriptomic modifications have recently emerged into the spotlight of researchers due to their vast regulatory effects on gene expression and thereby cellular physiology and pathophysiology. N6,2'-O-dimethyladenosine (m6Am) is one of the most prevalent chemical marks on RNA and is dynamically regulated by writers (PCIF1, METTL4) and erasers (FTO). The presence or absence of m6Am in RNA affects mRNA stability, regulates transcription, and modulates pre-mRNA splicing. Nevertheless, its functions in the heart are poorly known. This review summarizes the current knowledge and gaps about m6Am modification and its regulators in cardiac biology. It also points out technical challenges and lists the currently available techniques to measure m6Am. A better understanding of epitranscriptomic modifications is needed to improve our knowledge of the molecular regulations in the heart which may lead to novel cardioprotective strategies.
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Affiliation(s)
- Daniel Benak
- Laboratory of Developmental Cardiology, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
- Department of Physiology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Frantisek Kolar
- Laboratory of Developmental Cardiology, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Lu Zhang
- Bioinformatics Platform, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Yvan Devaux
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Marketa Hlavackova
- Laboratory of Developmental Cardiology, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
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Krejčí J, Arcidiacono OA, Čegan R, Radaszkiewicz K, Pacherník J, Pirk J, Pešl M, Fila P, Bártová E. Cell Differentiation and Aging Lead To Up-Regulation of FTO, While the ALKBH5 Protein Level Was Stable During Aging but Up-Regulated During in vitro-Induced Cardiomyogenesis. Physiol Res 2023; 72:425-444. [PMID: 37795886 PMCID: PMC10634569 DOI: 10.33549/physiolres.935078] [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: 02/07/2023] [Accepted: 05/25/2023] [Indexed: 01/05/2024] Open
Abstract
FTO and ALKBH5 proteins are essential erasers of N6-adenosine methylation in RNA. We studied how levels of FTO and ALKBH5 proteins changed during mouse embryonic development, aging, cardiomyogenesis, and neuroectodermal differentiation. We observed that aging in male and female mice was associated with FTO up-regulation in mouse hearts, brains, lungs, and kidneys, while the ALKBH5 level remained stable. FTO and ALKBH5 proteins were up-regulated during experimentally induced cardiomyogenesis, but the level of ALKBH5 protein was not changed when neuroectodermal differentiation was induced. HDAC1 depletion in mouse ES cells caused FTO down-regulation. In these cells, mRNA, carrying information from genes that regulate histone signature, RNA processing, and cell differentiation, was characterized by a reduced level of N6-adenosine methylation in specific gene loci, primarily regulating cell differentiation into neuroectoderm. Together, when we compared both RNA demethylating proteins, the FTO protein level undergoes the most significant changes during cell differentiation and aging. Thus, we conclude that during aging and neuronal differentiation, m6A RNA demethylation is likely regulated by the FTO protein but not via the function of ALKBH5.
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Affiliation(s)
- J Krejčí
- Department of Cell Biology and Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic.
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Wang J, Wang L, Tian X, Luo L. N 6-methyladenosine reader YTHDF1 regulates the proliferation and migration of airway smooth muscle cells through m 6A/cyclin D1 in asthma. PeerJ 2023; 11:e14951. [PMID: 36992945 PMCID: PMC10042154 DOI: 10.7717/peerj.14951] [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: 09/19/2022] [Accepted: 02/03/2023] [Indexed: 03/31/2023] Open
Abstract
Asthma is a chronic inflammatory respiratory disease, which is involved in multiple pathologic molecular mechanisms and presents a huge challenge to clinic nursing. Emerging evidence suggests that N6-methyladenosine (m6A) plays critical roles in respiratory system disease. Thus, present work tried to investigate the functions of m6A reader YTHDF 1 in asthma. The results indicated that YTHDF1 significantly upregulated in platelet-derived growth factor (PDGF) induced airway smooth muscle cells (ASMCs). Functionally, overexpression of YTHDF1 promoted the proliferation and migration of ASMCs, while YTHDF1 knockdown repressed the proliferation and migration. Mechanistically, there was a m6A modification site on cyclin D1 RNA (CCND1 genome) and YTHDF1 combined with cyclin D1 mRNA, thereby enhancing its mRNA stability via m6A-dependent manner. Collectively, these findings reveal a novel axis of YTHDF1/m6A/cyclin D1 in asthma's airway remodeling, which may provide novel therapeutic strategy for asthma.
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Affiliation(s)
- Juan Wang
- Department of Nursing, Fenyang Colleage of Shanxi Medical University, Fenyang, China
| | - Lei Wang
- College of Nursing, Shanxi Medical University, Taiyuan, China
| | - Xingfeng Tian
- Department of Student Affairs, Fenyang Colleage of Shanxi Medical University, Fenyang, China
| | - Lingping Luo
- Department of Nursing, Fenyang Colleage of Shanxi Medical University, Fenyang, China
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Jusic A, Stellos K, Ferreira L, Baker AH, Devaux Y. (Epi)transcriptomics in cardiovascular and neurological complications of COVID-19. JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY PLUS 2022; 1:100013. [PMID: 36164464 PMCID: PMC9330360 DOI: 10.1016/j.jmccpl.2022.100013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/14/2022] [Accepted: 07/15/2022] [Indexed: 06/16/2023]
Abstract
Although systemic inflammation and pulmonary complications increase the mortality rate in COVID-19, a broad spectrum of cardiovascular and neurological complications can also contribute to significant morbidity and mortality. The molecular mechanisms underlying cardiovascular and neurological complications during and after SARS-CoV-2 infection are incompletely understood. Recently reported perturbations of the epitranscriptome of COVID-19 patients indicate that mechanisms including those derived from RNA modifications and non-coding RNAs may play a contributing role in the pathogenesis of COVID-19. In this review paper, we gathered recently published studies investigating (epi)transcriptomic fluctuations upon SARS-CoV-2 infection, focusing on the brain-heart axis since neurological and cardiovascular events and their sequelae are of utmost prevalence and importance in this disease.
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Affiliation(s)
- Amela Jusic
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg
- Department of Biology, Faculty of Natural Sciences and Mathematics, University of Tuzla, 75000 Tuzla, Bosnia and Herzegovina
| | - Konstantinos Stellos
- Department of Cardiovascular Research, European Centre for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- German Centre for Cardiovascular Research (Deutsches Zentrum für Herz-Kreislauf-Forschung, DZHK), Heidelberg/Mannheim Partner Site, Mannheim, Germany
- Department of Cardiology, University Hospital Mannheim, Mannheim, Germany
- Biosciences Institute, Vascular Biology and Medicine Theme, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Lino Ferreira
- CNC-Center for Neurosciences and Cell Biology, CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Portugal
- Faculty of Medicine, University Coimbra, 3000-548 Coimbra, Portugal
| | - Andrew H. Baker
- Centre for Cardiovascular Science, University of Edinburgh, Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
- CARIM Institute, University of Maastricht, Universiteitssingel 50, 6200 MD Maastricht, the Netherlands
| | - Yvan Devaux
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg
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Regulation of N6-Methyladenosine after Myocardial Infarction. Cells 2022; 11:cells11152271. [PMID: 35892568 PMCID: PMC9329994 DOI: 10.3390/cells11152271] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 07/19/2022] [Accepted: 07/19/2022] [Indexed: 12/10/2022] Open
Abstract
Development of heart failure (HF) after myocardial infarction (MI) is responsible for premature death. Complex cellular and molecular mechanisms are involved in this process. A number of studies have linked the epitranscriptomic RNA modification N6-methyladenosine (m6A) with HF, but it remains unknown how m6A affects the risk of developing HF after MI. We addressed the regulation of m6A and its demethylase fat mass and obesity-associated (FTO) after MI and their association with HF. Using liquid chromatography coupled to mass spectrometry, we observed an increase of m6A content in the infarcted area of rat hearts subjected to coronary ligation and a decrease in blood. FTO expression measured by quantitative PCR was downregulated in the infarcted hearts. In whole blood samples collected at the time of reperfusion in MI patients, m6A content was lower in patients who developed HF as attested by a 4-month ejection fraction (EF) of ≤40% as compared to patients who did not develop HF (EF > 50%). M6A content was higher in females. These results show that m6A measured in blood is associated with HF development after MI and motivate further investigation of the potential role of m6A as a novel epitranscriptomics biomarker and therapeutic target of HF.
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