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Cui M, Bezprozvannaya S, Hao T, Elnwasany A, Szweda LI, Liu N, Bassel-Duby R, Olson EN. Transcription factor NFYa controls cardiomyocyte metabolism and proliferation during mouse fetal heart development. Dev Cell 2023; 58:2867-2880.e7. [PMID: 37972593 PMCID: PMC11000264 DOI: 10.1016/j.devcel.2023.10.012] [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: 05/31/2023] [Revised: 08/22/2023] [Accepted: 10/24/2023] [Indexed: 11/19/2023]
Abstract
Cardiomyocytes are highly metabolic cells responsible for generating the contractile force in the heart. During fetal development and regeneration, these cells actively divide but lose their proliferative activity in adulthood. The mechanisms that coordinate their metabolism and proliferation are not fully understood. Here, we study the role of the transcription factor NFYa in developing mouse hearts. Loss of NFYa alters cardiomyocyte composition, causing a decrease in immature regenerative cells and an increase in trabecular and mature cardiomyocytes, as identified by spatial and single-cell transcriptome analyses. NFYa-deleted cardiomyocytes exhibited reduced proliferation and impaired mitochondrial metabolism, leading to cardiac growth defects and embryonic death. NFYa, interacting with cofactor SP2, activates genes linking metabolism and proliferation at the transcription level. Our study identifies a nodal role of NFYa in regulating prenatal cardiac growth and a previously unrecognized transcriptional control mechanism of heart metabolism, highlighting the importance of mitochondrial metabolism during heart development and regeneration.
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Affiliation(s)
- Miao Cui
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Ave, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
| | - Svetlana Bezprozvannaya
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine and Sen. Paul D. Wellstone Muscular Dystrophy Specialized Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Tian Hao
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Ave, Boston, MA 02115, USA
| | - Abdallah Elnwasany
- Division of Cardiology, Department of Internal Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Luke I Szweda
- Division of Cardiology, Department of Internal Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Ning Liu
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine and Sen. Paul D. Wellstone Muscular Dystrophy Specialized Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Rhonda Bassel-Duby
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine and Sen. Paul D. Wellstone Muscular Dystrophy Specialized Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Eric N Olson
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine and Sen. Paul D. Wellstone Muscular Dystrophy Specialized Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA.
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2
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Liu S, Yue S, Guo Y, Han JY, Wang H. Sorafenib induces cardiotoxicity through RBM20-mediated alternative splicing of sarcomeric and mitochondrial genes. Pharmacol Res 2023; 198:107017. [PMID: 38006979 DOI: 10.1016/j.phrs.2023.107017] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/12/2023] [Accepted: 11/22/2023] [Indexed: 11/27/2023]
Abstract
Sorafenib, a multi-targeted tyrosine kinase inhibitor, is a first-line treatment for advanced solid tumors, but it induces many adverse cardiovascular events, including myocardial infarction and heart failure. These cardiac defects can be mediated by alternative splicing of genes critical for heart function. Whether alternative splicing plays a role in sorafenib-induced cardiotoxicity remains unclear. Transcriptome of rat hearts or human cardiomyocytes treated with sorafenib was analyzed and validated to define alternatively spliced genes and their impact on cardiotoxicity. In rats, sorafenib caused severe cardiotoxicity with decreased left ventricular systolic pressure, elongated sarcomere, enlarged mitochondria and decreased ATP. This was associated with alternative splicing of hundreds of genes in the hearts, many of which were targets of a cardiac specific splicing factor, RBM20. Sorafenib inhibited RBM20 expression in both rat hearts and human cardiomyocytes. The splicing of RBM20's targets, SLC25A3 and FHOD3, was altered into fetal isoforms with decreased function. Upregulation of RBM20 during sorafenib treatment reversed the pathogenic splicing of SLC25A3 and FHOD3, and enhanced the phosphate transport into mitochondria by SLC25A3, ATP synthesis and cell survival.We envision this regulation may happen in many drug-induced cardiotoxicity, and represent a potential druggable pathway for mitigating sorafenib-induced cardiotoxicity.
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Affiliation(s)
- Songming Liu
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Shanshan Yue
- Department of Integration of Chinese and Western Medicine, School of Basic Medical Sciences, Peking University, Beijing 100191, China; Tasly Microcirculation Research Center, Peking University Health Science Center, Beijing 100191, China
| | - Yuxuan Guo
- Peking University Institute of Cardiovascular Sciences, Peking University Health Science Center, School of Basic Medical Sciences, Beijing 100191, China
| | - Jing-Yan Han
- Department of Integration of Chinese and Western Medicine, School of Basic Medical Sciences, Peking University, Beijing 100191, China; Tasly Microcirculation Research Center, Peking University Health Science Center, Beijing 100191, China.
| | - Huan Wang
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.
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3
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Montañés-Agudo P, Pinto YM, Creemers EE. Splicing factors in the heart: Uncovering shared and unique targets. J Mol Cell Cardiol 2023; 179:72-79. [PMID: 37059416 DOI: 10.1016/j.yjmcc.2023.04.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/29/2023] [Accepted: 04/09/2023] [Indexed: 04/16/2023]
Abstract
Alternative splicing generates specialized protein isoforms that allow the heart to adapt during development and disease. The recent discovery that mutations in the splicing factor RNA-binding protein 20 (RBM20) cause a severe form of familial dilated cardiomyopathy has sparked a great interest in alternative splicing in the field of cardiology. Since then, identification of splicing factors controlling alternative splicing in the heart has grown at a rapid pace. Despite the intriguing observation that a certain overlap exists between the targets of some splicing factors, an integrated and systematic analysis of their splicing networks is missing. Here, we compared the splicing networks of individual splicing factors by re-analyzing original RNA-sequencing data from eight previously published mouse models, in which a single splicing factor has been genetically deleted (i.e. HNRNPU, MBNL1/2, QKI, RBM20, RBM24, RBPMS, SRSF3, SRSF4). We show that key splicing events in Camk2d, Ryr2, Tpm1, Tpm2 and Pdlim5 require the combined action of the majority of these splicing factors. Additionally, we identified common targets and pathways among splicing factors, with the largest overlap between the splicing networks of MBNL, QKI and RBM24. We also re-analyzed a large-scale RNA-sequencing study on hearts of 128 heart failure patients. Here, we observed that MBNL1, QKI and RBM24 expression varied greatly. This variation in expression correlated with differential splicing of their downstream targets as found in mice, suggesting that aberrant splicing by MBNL1, QKI and RBM24 might contribute to the disease mechanism in heart failure.
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Affiliation(s)
- Pablo Montañés-Agudo
- Experimental Cardiology, Room K2-112, Amsterdam UMC Location University of Amsterdam, Meibergdreef 15, Amsterdam 1105AZ, the Netherlands.
| | - Yigal M Pinto
- Experimental Cardiology, Room K2-104, Amsterdam UMC, location University of Amsterdam, Meibergdreef 15, Amsterdam 1105AZ, the Netherlands.
| | - Esther E Creemers
- Experimental Cardiology, Room K2-104-2, Amsterdam UMC, Location University of Amsterdam, Meibergdreef 15, Amsterdam 1105AZ, the Netherlands.
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4
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Hinkle ER, Wiedner HJ, Torres EV, Jackson M, Black AJ, Blue RE, Harris SE, Guzman BB, Gentile GM, Lee EY, Tsai YH, Parker J, Dominguez D, Giudice J. Alternative splicing regulation of membrane trafficking genes during myogenesis. RNA (NEW YORK, N.Y.) 2022; 28:523-540. [PMID: 35082143 PMCID: PMC8925968 DOI: 10.1261/rna.078993.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/17/2021] [Indexed: 06/14/2023]
Abstract
Alternative splicing transitions occur during organ development, and, in numerous diseases, splicing programs revert to fetal isoform expression. We previously found that extensive splicing changes occur during postnatal mouse heart development in genes encoding proteins involved in vesicle-mediated trafficking. However, the regulatory mechanisms of this splicing-trafficking network are unknown. Here, we found that membrane trafficking genes are alternatively spliced in a tissue-specific manner, with striated muscles exhibiting the highest levels of alternative exon inclusion. Treatment of differentiated muscle cells with chromatin-modifying drugs altered exon inclusion in muscle cells. Examination of several RNA-binding proteins revealed that the poly-pyrimidine tract binding protein 1 (PTBP1) and quaking regulate splicing of trafficking genes during myogenesis, and that removal of PTBP1 motifs prevented PTBP1 from binding its RNA target. These findings enhance our understanding of developmental splicing regulation of membrane trafficking proteins which might have implications for muscle disease pathogenesis.
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Affiliation(s)
- Emma R Hinkle
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Curriculum in Genetics and Molecular Biology (GMB), The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Hannah J Wiedner
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Curriculum in Genetics and Molecular Biology (GMB), The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Eduardo V Torres
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Micaela Jackson
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Adam J Black
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - R Eric Blue
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Sarah E Harris
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Bryan B Guzman
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Gabrielle M Gentile
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Curriculum in Genetics and Molecular Biology (GMB), The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Eunice Y Lee
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Yi-Hsuan Tsai
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Joel Parker
- Curriculum in Genetics and Molecular Biology (GMB), The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Daniel Dominguez
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Jimena Giudice
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Curriculum in Genetics and Molecular Biology (GMB), The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- McAllister Heart Institute, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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5
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Robinson EL, Baker AH, Brittan M, McCracken I, Condorelli G, Emanueli C, Srivastava PK, Gaetano C, Thum T, Vanhaverbeke M, Angione C, Heymans S, Devaux Y, Pedrazzini T, Martelli F. Dissecting the transcriptome in cardiovascular disease. Cardiovasc Res 2022; 118:1004-1019. [PMID: 33757121 PMCID: PMC8930073 DOI: 10.1093/cvr/cvab117] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 03/22/2021] [Indexed: 12/12/2022] Open
Abstract
The human transcriptome comprises a complex network of coding and non-coding RNAs implicated in a myriad of biological functions. Non-coding RNAs exhibit highly organized spatial and temporal expression patterns and are emerging as critical regulators of differentiation, homeostasis, and pathological states, including in the cardiovascular system. This review defines the current knowledge gaps, unmet methodological needs, and describes the challenges in dissecting and understanding the role and regulation of the non-coding transcriptome in cardiovascular disease. These challenges include poor annotation of the non-coding genome, determination of the cellular distribution of transcripts, assessment of the role of RNA processing and identification of cell-type specific changes in cardiovascular physiology and disease. We highlight similarities and differences in the hurdles associated with the analysis of the non-coding and protein-coding transcriptomes. In addition, we discuss how the lack of consensus and absence of standardized methods affect reproducibility of data. These shortcomings should be defeated in order to make significant scientific progress and foster the development of clinically applicable non-coding RNA-based therapeutic strategies to lessen the burden of cardiovascular disease.
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Affiliation(s)
- Emma L Robinson
- Department of Cardiology, Cardiovascular Research Institute Maastricht (CARIM), Universiteitssingel 50, 6229 Maastricht University, Maastricht, The Netherlands
- The Division of Cardiology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Andrew H Baker
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Mairi Brittan
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Ian McCracken
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - G Condorelli
- Humanitas Research Hospital, Humanitas University, Via Manzoni 113, Rozzano, MI 20089, Italy
| | - C Emanueli
- Imperial College, National Heart and Lung Institute, Hammersmith campus, Du Cane Road, London W12 0NN, UK
| | - P K Srivastava
- Imperial College, National Heart and Lung Institute, Hammersmith campus, Du Cane Road, London W12 0NN, UK
| | - C Gaetano
- Laboratorio di Epigenetica, Istituti Clinici Scientifici Maugeri IRCCS, Via Maugeri 4, Pavia 27100, Italy
| | - T Thum
- Hannover Medical School, Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Carl-Neuberg-Straße 1 30625 Hannover, Germany
| | - M Vanhaverbeke
- UZ Gasthuisberg Campus, KU Leuven, Herestraat 49 3000 Leuven, Belgium
| | - C Angione
- Department of Computer Science and Information Systems, Teesside University, Middlesbrough, TS4 3BX, UK
| | - S Heymans
- Department of Cardiology, Cardiovascular Research Institute Maastricht (CARIM), Universiteitssingel 50, 6229 Maastricht University, Maastricht, The Netherlands
| | - Y Devaux
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, 1A-B, rue Thomas Edison, L-1445 Strassen, Luxembourg
| | - T Pedrazzini
- Experimental Cardiology Unit, Division of Cardiology, Department of Cardiovascular Medicine, University of Lausanne Medical School, 1011 Lausanne, Switzerland
| | - F Martelli
- Molecular Cardiology Laboratory, IRCCS-Policlinico San Donato, Piazza Edmondo Malan, 2, 20097 San Donato, Milan, Italy
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6
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Lemay SE, Awada C, Shimauchi T, Wu WH, Bonnet S, Provencher S, Boucherat O. Fetal Gene Reactivation in Pulmonary Arterial Hypertension: GOOD, BAD, or BOTH? Cells 2021; 10:1473. [PMID: 34208388 PMCID: PMC8231250 DOI: 10.3390/cells10061473] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/04/2021] [Accepted: 06/09/2021] [Indexed: 12/15/2022] Open
Abstract
Pulmonary arterial hypertension is a debilitating chronic disorder marked by the progressive obliteration of the pre-capillary arterioles. This imposes a pressure overload on the right ventricle (RV) pushing the latter to undergo structural and mechanical adaptations that inexorably culminate in RV failure and death. Thanks to the advances in molecular biology, it has been proposed that some aspects of the RV and pulmonary vascular remodeling processes are orchestrated by a subversion of developmental regulatory mechanisms with an upregulation of a suite of genes responsible for the embryo's early growth and normally repressed in adults. In this review, we present relevant background regarding the close relationship between overactivation of fetal genes and cardiopulmonary remodeling, exploring whether the reawakening of developmental factors plays a causative role or constitutes a protective mechanism in the setting of PAH.
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Affiliation(s)
- Sarah-Eve Lemay
- Pulmonary Hypertension Research Group, Centre de Recherche de l’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec, QC G1V 4G5, Canada; (S.-E.L.); (C.A.); (T.S.); (W.-H.W.); (S.B.); (S.P.)
| | - Charifa Awada
- Pulmonary Hypertension Research Group, Centre de Recherche de l’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec, QC G1V 4G5, Canada; (S.-E.L.); (C.A.); (T.S.); (W.-H.W.); (S.B.); (S.P.)
| | - Tsukasa Shimauchi
- Pulmonary Hypertension Research Group, Centre de Recherche de l’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec, QC G1V 4G5, Canada; (S.-E.L.); (C.A.); (T.S.); (W.-H.W.); (S.B.); (S.P.)
| | - Wen-Hui Wu
- Pulmonary Hypertension Research Group, Centre de Recherche de l’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec, QC G1V 4G5, Canada; (S.-E.L.); (C.A.); (T.S.); (W.-H.W.); (S.B.); (S.P.)
- Department of Cardio-Pulmonary Circulation, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
| | - Sébastien Bonnet
- Pulmonary Hypertension Research Group, Centre de Recherche de l’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec, QC G1V 4G5, Canada; (S.-E.L.); (C.A.); (T.S.); (W.-H.W.); (S.B.); (S.P.)
| | - Steeve Provencher
- Pulmonary Hypertension Research Group, Centre de Recherche de l’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec, QC G1V 4G5, Canada; (S.-E.L.); (C.A.); (T.S.); (W.-H.W.); (S.B.); (S.P.)
| | - Olivier Boucherat
- Pulmonary Hypertension Research Group, Centre de Recherche de l’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec, QC G1V 4G5, Canada; (S.-E.L.); (C.A.); (T.S.); (W.-H.W.); (S.B.); (S.P.)
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7
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Inácio JM, von Gilsa Lopes J, Silva AM, Cristo F, Marques S, Futschik ME, Belo JA. DAND5 Inactivation Enhances Cardiac Differentiation in Mouse Embryonic Stem Cells. Front Cell Dev Biol 2021; 9:629430. [PMID: 33928078 PMCID: PMC8078107 DOI: 10.3389/fcell.2021.629430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 03/18/2021] [Indexed: 11/13/2022] Open
Abstract
Deciphering the clues of a regenerative mechanism for the mammalian adult heart would save millions of lives in the near future. Heart failure due to cardiomyocyte loss is still one of the significant health burdens worldwide. Here, we show the potential of a single molecule, DAND5, in mouse pluripotent stem cell-derived cardiomyocytes specification and proliferation. Dand5 loss-of-function generated the double of cardiac beating foci compared to the wild-type cells. The early formation of cardiac progenitor cells and the increased proliferative capacity of Dand5 KO mESC-derived cardiomyocytes contribute to the observed higher number of derived cardiac cells. Transcriptional profiling sequencing and quantitative RT-PCR assays showed an upregulation of early cardiac gene networks governing cardiomyocyte differentiation, cell cycling, and cardiac regenerative pathways but reduced levels of genes involved in cardiomyocyte maturation. These findings prompt DAND5 as a key driver for the generation and expansion of pluripotent stem cell-derived cardiomyocytes systems with further clinical application purposes.
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Affiliation(s)
- José Manuel Inácio
- iNOVA4Health, CEDOC, NOVA Medical School, NMS, Universidade Nova de Lisboa, Lisbon, Portugal
| | - João von Gilsa Lopes
- iNOVA4Health, CEDOC, NOVA Medical School, NMS, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Ana Mafalda Silva
- iNOVA4Health, CEDOC, NOVA Medical School, NMS, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Fernando Cristo
- iNOVA4Health, CEDOC, NOVA Medical School, NMS, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Sara Marques
- iNOVA4Health, CEDOC, NOVA Medical School, NMS, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Matthias E Futschik
- Faculty of Medicine, School of Public Health, Imperial College London, Medical School, St. Mary's Hospital, London, United Kingdom
| | - José António Belo
- iNOVA4Health, CEDOC, NOVA Medical School, NMS, Universidade Nova de Lisboa, Lisbon, Portugal
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8
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Li J, Lee JK, Miwa K, Kuramoto Y, Masuyama K, Yasutake H, Tomoyama S, Nakanishi H, Sakata Y. Scaffold-Mediated Developmental Effects on Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes Are Preserved After External Support Removal. Front Cell Dev Biol 2021; 9:591754. [PMID: 33659246 PMCID: PMC7917244 DOI: 10.3389/fcell.2021.591754] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 01/27/2021] [Indexed: 12/29/2022] Open
Abstract
Human induced pluripotent stem (hiPS) cells have been used as a cell source for regenerative therapy and disease modeling. The purity of hiPS-cardiomyocytes (hiPS-CMs) has markedly improved with advancements in cell culture and differentiation protocols. However, the morphological features and molecular properties of the relatively immature cells are still unclear, which has hampered their clinical application. The aim of the present study was to investigate the extent to which topographic substrates actively influence hiPS-CMs. hiPS-CMs were seeded on randomized oriented fiber substrate (random), anisotropic aligned fiber substrate (align), and flat non-scaffold substrate (flat). After culturing for one week, the hiPS-CMs on the aligned patterns showed more mature-like properties, including elongated rod shape, shorter duration of action potential, accelerated conduction velocity, and elevated cardiac gene expression. Subsequently, to determine whether this development was irreversible or was altered after withdrawal of the structural support, the hiPS-CMs were harvested from the three different patterns and reseeded on the non-scaffold (flat) pattern. After culturing for one more week, the improvements in morphological and functional properties diminished, although hiPS-CMs pre-cultured on the aligned pattern retained the molecular features of development, which were even more significant as compared to that observed during the pre-culture stage. Our results suggested that the anisotropic fiber substrate can induce the formation of geometrical mimic-oriented heart tissue in a short time. Although the morphological and electrophysiological properties of hiPS-CMs obtained via facilitated maturation somehow rely on the existence of an exterior scaffold, the molecular developmental features were preserved even in the absence of the external support, which might persist throughout hiPS-CM development.
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Affiliation(s)
- Jun Li
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Jong-Kook Lee
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Japan.,Department of Cardiovascular Regenerative Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Keiko Miwa
- Department of Cardiovascular Regenerative Medicine, Osaka University Graduate School of Medicine, Suita, Japan.,Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Japan
| | - Yuki Kuramoto
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Kiyoshi Masuyama
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Hideki Yasutake
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Satoki Tomoyama
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Hiroyuki Nakanishi
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yasushi Sakata
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Japan
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9
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Desideri F, Cipriano A, Petrezselyova S, Buonaiuto G, Santini T, Kasparek P, Prochazka J, Janson G, Paiardini A, Calicchio A, Colantoni A, Sedlacek R, Bozzoni I, Ballarino M. Intronic Determinants Coordinate Charme lncRNA Nuclear Activity through the Interaction with MATR3 and PTBP1. Cell Rep 2020; 33:108548. [PMID: 33357424 PMCID: PMC7773549 DOI: 10.1016/j.celrep.2020.108548] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 10/27/2020] [Accepted: 12/02/2020] [Indexed: 12/19/2022] Open
Abstract
Chromatin architect of muscle expression (Charme) is a muscle-restricted long noncoding RNA (lncRNA) that plays an important role in myogenesis. Earlier evidence indicates that the nuclear Charme isoform, named pCharme, acts on the chromatin by assisting the formation of chromatin domains where myogenic transcription occurs. By combining RNA antisense purification (RAP) with mass spectrometry and loss-of-function analyses, we have now identified the proteins that assist these chromatin activities. These proteins—which include a sub-set of splicing regulators, principally PTBP1 and the multifunctional RNA/DNA binding protein MATR3—bind to sequences located within the alternatively spliced intron-1 to form nuclear aggregates. Consistent with the functional importance of pCharme interactome in vivo, a targeted deletion of the intron-1 by a CRISPR-Cas9 approach in mouse causes the release of pCharme from the chromatin and results in cardiac defects similar to what was observed upon knockout of the full-length transcript. pCharme is the chromatin-retained isoform of the muscle-specific Charme lncRNA Intronic signals coordinate the association of pCharme with MATR3 and PTBP1 The particle assembly prompts pCharme intron-1 chromatin retention Deletion of the intron-1 by CRISPR-Cas9 leads to heart defects in mouse
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Affiliation(s)
- Fabio Desideri
- Department of Biology and Biotechnology "Charles Darwin," Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Andrea Cipriano
- Department of Biology and Biotechnology "Charles Darwin," Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Silvia Petrezselyova
- Czech Centre of Phenogenomics and Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Giulia Buonaiuto
- Department of Biology and Biotechnology "Charles Darwin," Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Tiziana Santini
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
| | - Petr Kasparek
- Czech Centre of Phenogenomics and Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Jan Prochazka
- Czech Centre of Phenogenomics and Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Giacomo Janson
- Department of Biochemical Sciences "A. Rossi Fanelli," Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Alessandro Paiardini
- Department of Biochemical Sciences "A. Rossi Fanelli," Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Alessandro Calicchio
- Department of Biology and Biotechnology "Charles Darwin," Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Alessio Colantoni
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
| | - Radislav Sedlacek
- Czech Centre of Phenogenomics and Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Irene Bozzoni
- Department of Biology and Biotechnology "Charles Darwin," Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy; Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy.
| | - Monica Ballarino
- Department of Biology and Biotechnology "Charles Darwin," Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy.
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10
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Zhang H, Brown RD, Stenmark KR, Hu CJ. RNA-Binding Proteins in Pulmonary Hypertension. Int J Mol Sci 2020; 21:ijms21113757. [PMID: 32466553 PMCID: PMC7312837 DOI: 10.3390/ijms21113757] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/20/2020] [Accepted: 05/21/2020] [Indexed: 12/21/2022] Open
Abstract
Pulmonary hypertension (PH) is a life-threatening disease characterized by significant vascular remodeling and aberrant expression of genes involved in inflammation, apoptosis resistance, proliferation, and metabolism. Effective therapeutic strategies are limited, as mechanisms underlying PH pathophysiology, especially abnormal expression of genes, remain unclear. Most PH studies on gene expression have focused on gene transcription. However, post-transcriptional alterations have been shown to play a critical role in inflammation and metabolic changes in diseases such as cancer and systemic cardiovascular diseases. In these diseases, RNA-binding proteins (RBPs) have been recognized as important regulators of aberrant gene expression via post-transcriptional regulation; however, their role in PH is less clear. Identifying RBPs in PH is of great importance to better understand PH pathophysiology and to identify new targets for PH treatment. In this manuscript, we review the current knowledge on the role of dysregulated RBPs in abnormal mRNA gene expression as well as aberrant non-coding RNA processing and expression (e.g., miRNAs) in PH.
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Affiliation(s)
- Hui Zhang
- Cardiovascular Pulmonary Research Laboratories, Departments of Pediatrics and Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (H.Z.); (R.D.B.); (K.R.S.)
| | - R. Dale Brown
- Cardiovascular Pulmonary Research Laboratories, Departments of Pediatrics and Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (H.Z.); (R.D.B.); (K.R.S.)
| | - Kurt R. Stenmark
- Cardiovascular Pulmonary Research Laboratories, Departments of Pediatrics and Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (H.Z.); (R.D.B.); (K.R.S.)
| | - Cheng-Jun Hu
- Cardiovascular Pulmonary Research Laboratories, Departments of Pediatrics and Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (H.Z.); (R.D.B.); (K.R.S.)
- Department of Craniofacial Biology School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Correspondence: ; Tel.: +1-303-724-4576; Fax: +1-303-724-4580
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11
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Cui M, Wang Z, Chen K, Shah AM, Tan W, Duan L, Sanchez-Ortiz E, Li H, Xu L, Liu N, Bassel-Duby R, Olson EN. Dynamic Transcriptional Responses to Injury of Regenerative and Non-regenerative Cardiomyocytes Revealed by Single-Nucleus RNA Sequencing. Dev Cell 2020; 53:102-116.e8. [PMID: 32220304 DOI: 10.1016/j.devcel.2020.02.019] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 01/07/2020] [Accepted: 02/25/2020] [Indexed: 12/22/2022]
Abstract
The adult mammalian heart is incapable of regeneration following injury. In contrast, the neonatal mouse heart can efficiently regenerate during the first week of life. The molecular mechanisms that mediate the regenerative response and its blockade in later life are not understood. Here, by single-nucleus RNA sequencing, we map the dynamic transcriptional landscape of five distinct cardiomyocyte populations in healthy, injured, and regenerating mouse hearts. We identify immature cardiomyocytes that enter the cell cycle following injury and disappear as the heart loses the ability to regenerate. These proliferative neonatal cardiomyocytes display a unique transcriptional program dependent on nuclear transcription factor Y subunit alpha (NFYa) and nuclear factor erythroid 2-like 1 (NFE2L1) transcription factors, which exert proliferative and protective functions, respectively. Cardiac overexpression of these two factors conferred protection against ischemic injury in mature mouse hearts that were otherwise non-regenerative. These findings advance our understanding of the cellular basis of neonatal heart regeneration and reveal a transcriptional landscape for heart repair following injury.
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Affiliation(s)
- Miao Cui
- Department of Molecular Biology, The Hamon Center for Regenerative Science and Medicine and Sen. Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Zhaoning Wang
- Department of Molecular Biology, The Hamon Center for Regenerative Science and Medicine and Sen. Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Kenian Chen
- Quantitative Biomedical Research Center, Department of Population & Data Sciences and Department of Pediatrics, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Akansha M Shah
- Department of Molecular Biology, The Hamon Center for Regenerative Science and Medicine and Sen. Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Wei Tan
- Department of Molecular Biology, The Hamon Center for Regenerative Science and Medicine and Sen. Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Lauren Duan
- Department of Molecular Biology, The Hamon Center for Regenerative Science and Medicine and Sen. Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Efrain Sanchez-Ortiz
- Department of Molecular Biology, The Hamon Center for Regenerative Science and Medicine and Sen. Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Hui Li
- Department of Molecular Biology, The Hamon Center for Regenerative Science and Medicine and Sen. Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Lin Xu
- Quantitative Biomedical Research Center, Department of Population & Data Sciences and Department of Pediatrics, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Ning Liu
- Department of Molecular Biology, The Hamon Center for Regenerative Science and Medicine and Sen. Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Rhonda Bassel-Duby
- Department of Molecular Biology, The Hamon Center for Regenerative Science and Medicine and Sen. Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Eric N Olson
- Department of Molecular Biology, The Hamon Center for Regenerative Science and Medicine and Sen. Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA.
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12
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Long-term functional and structural preservation of precision-cut human myocardium under continuous electromechanical stimulation in vitro. Nat Commun 2019; 10:117. [PMID: 30631059 PMCID: PMC6328583 DOI: 10.1038/s41467-018-08003-1] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 12/10/2018] [Indexed: 12/26/2022] Open
Abstract
In vitro models incorporating the complexity and function of adult human tissues are highly desired for translational research. Whilst vital slices of human myocardium approach these demands, their rapid degeneration in tissue culture precludes long-term experimentation. Here, we report preservation of structure and performance of human myocardium under conditions of physiological preload, compliance, and continuous excitation. In biomimetic culture, tissue slices prepared from explanted failing human hearts attain a stable state of contractility that can be monitored for up to 4 months or 2000000 beats in vitro. Cultured myocardium undergoes particular alterations in biomechanics, structure, and mRNA expression. The suitability of the model for drug safety evaluation is exemplified by repeated assessment of refractory period that permits sensitive analysis of repolarization impairment induced by the multimodal hERG-inhibitor pentamidine. Biomimetic tissue culture will provide new opportunities to study drug targets, gene functions, and cellular plasticity in adult human myocardium. Myocardial tissue undergoes steady functional decline when cultured in vitro. Here, the authors report a protocol for culture of human cardiac slices that allows maintenance of contractility for up to four months, and show that the model is suitable for evaluation of drug safety, as exemplified for drugs interfering with cardiomyocyte repolarization.
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13
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Cui M, Wang Z, Bassel-Duby R, Olson EN. Genetic and epigenetic regulation of cardiomyocytes in development, regeneration and disease. Development 2018; 145:145/24/dev171983. [PMID: 30573475 DOI: 10.1242/dev.171983] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Embryonic and postnatal life depend on the uninterrupted function of cardiac muscle cells. These cells, termed cardiomyocytes, display many fascinating behaviors, including complex morphogenic movements, interactions with other cell types of the heart, persistent contractility and quiescence after birth. Each of these behaviors depends on complex interactions between both cardiac-restricted and widely expressed transcription factors, as well as on epigenetic modifications. Here, we review recent advances in our understanding of the genetic and epigenetic control of cardiomyocyte differentiation and proliferation during heart development, regeneration and disease. We focus on those regulators that are required for both heart development and disease, and highlight the regenerative principles that might be manipulated to restore function to the injured adult heart.
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Affiliation(s)
- Miao Cui
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, and Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Zhaoning Wang
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, and Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Rhonda Bassel-Duby
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, and Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Eric N Olson
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, and Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
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14
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Abstract
Alternative splicing is an important mechanism used by the cell to generate greater transcriptomic and proteomic diversity from the genome. In the heart, alternative splicing is increasingly being recognised as an important layer of post-transcriptional gene regulation. Driven by rapidly evolving technologies in next-generation sequencing, alternative splicing has emerged as a crucial process governing complex biological processes during cardiac development and disease. The recent identification of several cardiac splice factors, such as RNA-binding motif protein 20 and 24, not only provided important insight into the mechanisms underlying alternative splicing but also revealed how these splicing factors impact functional properties of the heart. Here, we review our current knowledge of alternative splicing in the heart, with a particular focus on the factors controlling cardiac alternative splicing and their role in cardiomyopathies and subsequent heart failure.
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15
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LOX-1 and Its Splice Variants: A New Challenge for Atherosclerosis and Cancer-Targeted Therapies. Int J Mol Sci 2017; 18:ijms18020290. [PMID: 28146073 PMCID: PMC5343826 DOI: 10.3390/ijms18020290] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 01/15/2017] [Accepted: 01/23/2017] [Indexed: 12/13/2022] Open
Abstract
Alternative splicing (AS) is a process in which precursor messenger RNA (pre-mRNA) splicing sites are differentially selected to diversify the protein isoform population. Changes in AS patterns have an essential role in normal development, differentiation and response to physiological stimuli. It is documented that AS can generate both “risk” and “protective” splice variants that can contribute to the pathogenesis of several diseases including atherosclerosis. The main endothelial receptor for oxidized low-density lipoprotein (ox-LDLs) is LOX-1 receptor protein encoded by the OLR1 gene. When OLR1 undergoes AS events, it generates three variants: OLR1, OLR1D4 and LOXIN. The latter lacks exon 5 and two-thirds of the functional domain. Literature data demonstrate a protective role of LOXIN in pathologies correlated with LOX-1 overexpression such as atherosclerosis and tumors. In this review, we summarize recent developments in understanding of OLR1 AS while also highlighting data warranting further investigation of this process as a novel therapeutic target.
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16
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Neonatal cardiac dysfunction and transcriptome changes caused by the absence of Celf1. Sci Rep 2016; 6:35550. [PMID: 27759042 PMCID: PMC5069560 DOI: 10.1038/srep35550] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 09/30/2016] [Indexed: 01/26/2023] Open
Abstract
The RNA binding protein Celf1 regulates alternative splicing in the nucleus and mRNA stability and translation in the cytoplasm. Celf1 is strongly down-regulated during mouse postnatal heart development. Its re-induction in adults induced severe heart failure and reversion to fetal splicing and gene expression patterns. However, the impact of Celf1 depletion on cardiac transcriptional and posttranscriptional dynamics in neonates has not been addressed. We found that homozygous Celf1 knock-out neonates exhibited cardiac dysfunction not observed in older homozygous animals, although homozygous mice are smaller than wild type littermates throughout development. RNA-sequencing of mRNA from homozygous neonatal hearts identified a network of cell cycle genes significantly up-regulated and down-regulation of ion transport and circadian genes. Cell cycle genes are enriched for Celf1 binding sites supporting a regulatory role in mRNA stability of these transcripts. We also identified a cardiac splicing network coordinated by Celf1 depletion. Target events contain multiple Celf1 binding sites and enrichment in GU-rich motifs. Identification of direct Celf1 targets will advance our knowledge in the mechanisms behind developmental networks regulated by Celf1 and diseases where Celf1 is mis-regulated.
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17
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Genome-wide analysis of alternative splicing during human heart development. Sci Rep 2016; 6:35520. [PMID: 27752099 PMCID: PMC5067579 DOI: 10.1038/srep35520] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 09/27/2016] [Indexed: 12/16/2022] Open
Abstract
Alternative splicing (AS) drives determinative changes during mouse heart development. Recent high-throughput technological advancements have facilitated genome-wide AS, while its analysis in human foetal heart transition to the adult stage has not been reported. Here, we present a high-resolution global analysis of AS transitions between human foetal and adult hearts. RNA-sequencing data showed extensive AS transitions occurred between human foetal and adult hearts, and AS events occurred more frequently in protein-coding genes than in long non-coding RNA (lncRNA). A significant difference of AS patterns was found between foetal and adult hearts. The predicted difference in AS events was further confirmed using quantitative reverse transcription-polymerase chain reaction analysis of human heart samples. Functional foetal-specific AS event analysis showed enrichment associated with cell proliferation-related pathways including cell cycle, whereas adult-specific AS events were associated with protein synthesis. Furthermore, 42.6% of foetal-specific AS events showed significant changes in gene expression levels between foetal and adult hearts. Genes exhibiting both foetal-specific AS and differential expression were highly enriched in cell cycle-associated functions. In conclusion, we provided a genome-wide profiling of AS transitions between foetal and adult hearts and proposed that AS transitions and deferential gene expression may play determinative roles in human heart development.
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18
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Raghow R. An 'Omics' Perspective on Cardiomyopathies and Heart Failure. Trends Mol Med 2016; 22:813-827. [PMID: 27499035 DOI: 10.1016/j.molmed.2016.07.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 07/15/2016] [Accepted: 07/15/2016] [Indexed: 12/27/2022]
Abstract
Pathological enlargement of the heart, represented by hypertrophic cardiomyopathy (HCM) and dilated cardiomyopathy (DCM), occurs in response to many genetic and non-genetic factors. The clinical course of cardiac hypertrophy is remarkably variable, ranging from lifelong absence of symptoms to rapidly declining heart function and sudden cardiac death (SCD). Unbiased omics studies have begun to provide a glimpse into the molecular framework underpinning altered mechanotransduction, mitochondrial energetics, oxidative stress, and extracellular matrix in the heart undergoing physiological and pathological hypertrophy. Omics analyses indicate that post-transcriptional regulation of gene expression plays an overriding role in the normal and diseased heart. Studies to date highlight a need for more effective bioinformatics to better integrate patient omics data with their comprehensive clinical histories.
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Affiliation(s)
- Rajendra Raghow
- Department of Pharmacology, College of Medicine, The University of Tennessee Health Science Center and the VA Medical Center, Memphis, TN 38104, USA.
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19
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Pasipoularides A. Calcific Aortic Valve Disease: Part 2-Morphomechanical Abnormalities, Gene Reexpression, and Gender Effects on Ventricular Hypertrophy and Its Reversibility. J Cardiovasc Transl Res 2016; 9:374-99. [PMID: 27184804 PMCID: PMC4992466 DOI: 10.1007/s12265-016-9695-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 05/03/2016] [Indexed: 02/07/2023]
Abstract
In part 1, we considered cytomolecular mechanisms underlying calcific aortic valve disease (CAVD), hemodynamics, and adaptive feedbacks controlling pathological left ventricular hypertrophy provoked by ensuing aortic valvular stenosis (AVS). In part 2, we survey diverse signal transduction pathways that precede cellular/molecular mechanisms controlling hypertrophic gene expression by activation of specific transcription factors that induce sarcomere replication in-parallel. Such signaling pathways represent potential targets for therapeutic intervention and prevention of decompensation/failure. Hypertrophy provoking signals, in the form of dynamic stresses and ligand/effector molecules that bind to specific receptors to initiate the hypertrophy, are transcribed across the sarcolemma by several second messengers. They comprise intricate feedback mechanisms involving gene network cascades, specific signaling molecules encompassing G protein-coupled receptors and mechanotransducers, and myocardial stresses. Future multidisciplinary studies will characterize the adaptive/maladaptive nature of the AVS-induced hypertrophy, its gender- and individual patient-dependent peculiarities, and its response to surgical/medical interventions. They will herald more effective, precision medicine treatments.
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Affiliation(s)
- Ares Pasipoularides
- Duke University School of Medicine, Durham, NC, USA.
- Duke/NSF Research Center for Emerging Cardiovascular Technologies, Duke University, Durham, NC, 27710, USA.
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20
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Abstract
RNA splicing represents a post-transcriptional mechanism to generate multiple functional RNAs or proteins from a single transcript. The evolution of RNA splicing is a prime example of the Darwinian function follows form concept. A mutation that leads to a new mRNA (form) that encodes for a new functional protein (function) is likely to be retained, and this way, the genome has gradually evolved to encode for genes with multiple isoforms, thereby creating an enormously diverse transcriptome. Advances in technologies to characterize RNA populations have led to a better understanding of RNA processing in health and disease. In the heart, alternative splicing is increasingly being recognized as an important layer of post-transcriptional gene regulation. Moreover, the recent identification of several cardiac splice factors, such as RNA-binding motif protein 20 and SF3B1, not only provided important insight into the mechanisms underlying alternative splicing but also revealed how these splicing factors impact functional properties of the heart. Here, we review our current knowledge of alternative splicing in the heart, with a particular focus on the major and minor spliceosome, the factors controlling RNA splicing, and the role of alternative splicing in cardiac development and disease.
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Affiliation(s)
- Maarten M.G. van den Hoogenhof
- From the Department of Experimental Cardiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Yigal M. Pinto
- From the Department of Experimental Cardiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Esther E. Creemers
- From the Department of Experimental Cardiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
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21
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Ladd AN. New Insights Into the Role of RNA-Binding Proteins in the Regulation of Heart Development. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 324:125-85. [PMID: 27017008 DOI: 10.1016/bs.ircmb.2015.12.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The regulation of gene expression during development takes place both at the transcriptional and posttranscriptional levels. RNA-binding proteins (RBPs) regulate pre-mRNA processing, mRNA localization, stability, and translation. Many RBPs are expressed in the heart and have been implicated in heart development, function, or disease. This chapter will review the current knowledge about RBPs in the developing heart, focusing on those that regulate posttranscriptional gene expression. The involvement of RBPs at each stage of heart development will be considered in turn, including the establishment of specific cardiac cell types and formation of the primitive heart tube, cardiac morphogenesis, and postnatal maturation and aging. The contributions of RBPs to cardiac birth defects and heart disease will also be considered in these contexts. Finally, the interplay between RBPs and other regulatory factors in the developing heart, such as transcription factors and miRNAs, will be discussed.
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Affiliation(s)
- A N Ladd
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States of America.
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22
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Dixon DM, Choi J, El-Ghazali A, Park SY, Roos KP, Jordan MC, Fishbein MC, Comai L, Reddy S. Loss of muscleblind-like 1 results in cardiac pathology and persistence of embryonic splice isoforms. Sci Rep 2015; 5:9042. [PMID: 25761764 PMCID: PMC4356957 DOI: 10.1038/srep09042] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 02/02/2015] [Indexed: 01/05/2023] Open
Abstract
Cardiac dysfunction is a prominent cause of mortality in myotonic dystrophy I (DM1), a disease where expanded CUG repeats bind and disable the muscleblind-like family of splice regulators. Deletion of muscleblind-like 1 (Mbnl1ΔE2/ΔE2) in 129 sv mice results in QRS, QTc widening, bundle block and STc narrowing at 2–4 months of age. With time, cardiac function deteriorates further and at 6 months, decreased R wave amplitudes, sinus node dysfunction, cardiac hypertrophy, interstitial fibrosis, multi-focal myocardial fiber death and calcification manifest. Sudden death, where no end point illness is overt, is observed at a median age of 6.5 and 4.8 months in ~67% and ~86% of male and female Mbnl1ΔE2/ΔE2 mice, respectively. Mbnl1 depletion results in the persistence of embryonic splice isoforms in a network of cardiac RNAs, some of which have been previously implicated in DM1, regulating sodium and calcium currents, Scn5a, Junctin, Junctate, Atp2a1, Atp11a, Cacna1s, Ryr2, intra and inter cellular transport, Clta, Stx2, Tjp1, cell survival, Capn3, Sirt2, Csda, sarcomere and cytoskeleton organization and function, Trim55, Mapt, Pdlim3, Pdlim5, Sorbs1, Sorbs2, Fhod1, Spag9 and structural components of the sarcomere, Myom1, Tnnt2, Zasp. Thus this study supports a key role for Mbnl1 loss in the initiation of DM1 cardiac disease.
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Affiliation(s)
- Donald M Dixon
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA
| | - Jongkyu Choi
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA
| | - Ayea El-Ghazali
- 1] Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA [2] Department of Microbiology and Immunology, University of Southern California, Los Angeles, CA 90033, USA
| | - Sun Young Park
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA
| | - Kenneth P Roos
- Department of Physiology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Maria C Jordan
- Department of Physiology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Michael C Fishbein
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Lucio Comai
- Department of Microbiology and Immunology, University of Southern California, Los Angeles, CA 90033, USA
| | - Sita Reddy
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA
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23
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Weeland CJ, van den Hoogenhof MM, Beqqali A, Creemers EE. Insights into alternative splicing of sarcomeric genes in the heart. J Mol Cell Cardiol 2015; 81:107-13. [PMID: 25683494 DOI: 10.1016/j.yjmcc.2015.02.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 01/15/2015] [Accepted: 02/05/2015] [Indexed: 12/14/2022]
Abstract
Driven by rapidly evolving technologies in next-generation sequencing, alternative splicing has emerged as a crucial layer in gene expression, greatly expanding protein diversity and governing complex biological processes in the cardiomyocyte. At the core of cardiac contraction, the physical properties of the sarcomere are carefully orchestrated through alternative splicing to fit the varying demands on the heart. By the recent discovery of RBM20 and RBM24, two major heart and skeletal muscle-restricted splicing factors, it became evident that alternative splicing events in the heart occur in regulated networks rather than in isolated events. Analysis of knockout mice of these splice factors has shed light on the importance of these fundamental processes in the heart. In this review, we discuss recent advances in our understanding of the role and regulation of alternative splicing in the developing and diseased heart, specifically within the sarcomere. Through various examples (titin, myomesin, troponin T, tropomyosin and LDB3) we illustrate how alternative splicing regulates the functional properties of the sarcomere. Finally, we evaluate opportunities and obstacles to modulate alternative splicing in therapeutic approaches for cardiac disease.
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Affiliation(s)
- Cornelis J Weeland
- Experimental Cardiology, Academic Medical Center, Meibergdreef 15, 1105AZ Amsterdam, The Netherlands
| | | | - Abdelaziz Beqqali
- Experimental Cardiology, Academic Medical Center, Meibergdreef 15, 1105AZ Amsterdam, The Netherlands
| | - Esther E Creemers
- Experimental Cardiology, Academic Medical Center, Meibergdreef 15, 1105AZ Amsterdam, The Netherlands.
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24
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Alternative splicing regulates vesicular trafficking genes in cardiomyocytes during postnatal heart development. Nat Commun 2014; 5:3603. [PMID: 24752171 PMCID: PMC4018662 DOI: 10.1038/ncomms4603] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 03/10/2014] [Indexed: 12/22/2022] Open
Abstract
During postnatal development the heart undergoes a rapid and dramatic transition to adult function through transcriptional and post-transcriptional mechanisms, including alternative splicing (AS). Here we perform deep RNA-sequencing on RNA from cardiomyocytes and cardiac fibroblasts to conduct a high-resolution analysis of transcriptome changes during postnatal mouse heart development. We reveal extensive changes in gene expression and AS that occur primarily between postnatal days 1 and 28. Cardiomyocytes and cardiac fibroblasts show reciprocal regulation of gene expression reflecting differences in proliferative capacity, cell adhesion functions, and mitochondrial metabolism. We further demonstrate that AS plays a role in vesicular trafficking and membrane organization, These AS transitions are enriched among targets of two RNA-binding proteins, Celf1 and Mbnl1, which undergo developmentally regulated changes in expression. Vesicular trafficking genes affected by AS during normal development (when Celf1 is down-regulated) show a reversion to neonatal splicing patterns after Celf1 re-expression in adults. Short-term Celf1 induction in adult animals results in disrupted transverse tubule organization and calcium handling. These results identify potential roles for AS in multiple aspects of postnatal heart maturation, including vesicular trafficking and intracellular membrane dynamics.
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Oosterlinck W, Herijgers P. Cardiomyocyte changes in the metabolic syndrome and implications for endogeneous protective strategies. Expert Rev Cardiovasc Ther 2014; 12:331-43. [DOI: 10.1586/14779072.2014.893825] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Kim T, Kim JO, Oh JG, Hong SE, Kim DH. Pressure-overload cardiac hypertrophy is associated with distinct alternative splicing due to altered expression of splicing factors. Mol Cells 2014; 37:81-7. [PMID: 24552714 PMCID: PMC3907004 DOI: 10.14348/molcells.2014.2337] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 11/18/2013] [Indexed: 01/05/2023] Open
Abstract
Chronic pressure-overload cardiac hypertrophy is associated with an increased risk of morbidity/mortality, largely due to maladaptive remodeling and dilatation that progresses to dilated cardiomyopathy. Alternative splicing is an important biological mechanism that generates proteomic complexity and diversity. The recent development of next-generation RNA sequencing has improved our understanding of the qualitative signatures associated with alternative splicing in various biological conditions. However, the role of alternative splicing in cardiac hypertrophy is yet unknown. The present study employed RNA-Seq and a bioinformatic approach to detect the RNA splicing regulatory elements involved in alternative splicing during pressure-overload cardiac hypertrophy. We found GC-rich exonic motifs that regulate intron retention in 5' UTRs and AT-rich exonic motifs that are involved in exclusion of the AT-rich elements that cause mRNA instability in 3' UTRs. We also identified motifs in the intronic regions involved in exon exclusion and inclusion, which predicted splicing factors that bind to these motifs. We found, through Western blotting, that the expression levels of three splicing factors, ESRP1, PTB and SF2/ASF, were significantly altered during cardiac hypertrophy. Collectively, the present results suggest that chronic pressure-overload hypertrophy is closely associated with distinct alternative splicing due to altered expression of splicing factors.
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Affiliation(s)
- Taeyong Kim
- School of Life Sciences and Systems Biology Research Center, Gwangju Institute of Science and Technology, Gwangju 500-712,
Korea
| | - Jin Ock Kim
- School of Life Sciences and Systems Biology Research Center, Gwangju Institute of Science and Technology, Gwangju 500-712,
Korea
| | | | - Seong-Eui Hong
- School of Life Sciences and Systems Biology Research Center, Gwangju Institute of Science and Technology, Gwangju 500-712,
Korea
| | - Do Han Kim
- School of Life Sciences and Systems Biology Research Center, Gwangju Institute of Science and Technology, Gwangju 500-712,
Korea
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Affiliation(s)
- Chen Gao
- Departments of Anesthesiology, Physiology and Medicine, Molecular Biology Institute, David Geffen School of Medicine at University of California at Los Angeles
| | - Yibin Wang
- Departments of Anesthesiology, Physiology and Medicine, Molecular Biology Institute, David Geffen School of Medicine at University of California at Los Angeles
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Giudice J, Cooper TA. RNA-binding proteins in heart development. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 825:389-429. [PMID: 25201112 DOI: 10.1007/978-1-4939-1221-6_11] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
RNA-binding proteins (RBPs) are key players of posttranscriptional regulation occurring during normal tissue development. All tissues examined thus far have revealed the importance of RBPs in the regulation of complex networks involved in organ morphogenesis, maturation, and function. They are responsible for controlling tissue-specific gene expression by regulating alternative splicing, mRNA stability, translation, and poly-adenylation. The heart is the first organ form during embryonic development and is also the first to acquire functionality. Numerous remodeling processes take place during late cardiac development since fetal heart first adapts to birth and then undergoes a transition to adult functionality. This physiological remodeling involves transcriptional and posttranscriptional networks that are regulated by RBPs. Disruption of the normal regulatory networks has been shown to cause cardiomyopathy in humans and animal models. Here we review the complexity of late heart development and the current information regarding how RBPs control aspects of postnatal heart development. We also review how activities of RBPs are modulated adding complexity to the regulation of developmental networks.
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Affiliation(s)
- Jimena Giudice
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, 77030, USA,
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Blech-Hermoni Y, Ladd AN. RNA binding proteins in the regulation of heart development. Int J Biochem Cell Biol 2013; 45:2467-78. [PMID: 23973289 DOI: 10.1016/j.biocel.2013.08.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 08/09/2013] [Accepted: 08/13/2013] [Indexed: 11/28/2022]
Abstract
In vivo, RNA molecules are constantly accompanied by RNA binding proteins (RBPs), which are intimately involved in every step of RNA biology, including transcription, editing, splicing, transport and localization, stability, and translation. RBPs therefore have opportunities to shape gene expression at multiple levels. This capacity is particularly important during development, when dynamic chemical and physical changes give rise to complex organs and tissues. This review discusses RBPs in the context of heart development. Since the targets and functions of most RBPs--in the heart and at large--are not fully understood, this review focuses on the expression and roles of RBPs that have been implicated in specific stages of heart development or developmental pathology. RBPs are involved in nearly every stage of cardiogenesis, including the formation, morphogenesis, and maturation of the heart. A fuller understanding of the roles and substrates of these proteins could ultimately provide attractive targets for the design of therapies for congenital heart defects, cardiovascular disease, or cardiac tissue repair.
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Affiliation(s)
- Yotam Blech-Hermoni
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Program in Cell Biology, Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
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Swist S, Linke WA. Untangling regulatory networks to spot drivers and modulators of cardiac disease. J Mol Cell Cardiol 2013; 63:1-3. [PMID: 23859767 DOI: 10.1016/j.yjmcc.2013.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Revised: 07/05/2013] [Accepted: 07/07/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Sandra Swist
- Dept. of Cardiovascular Physiology, Ruhr University Bochum, MA 3/56, D-44780 Bochum, Germany
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