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Völkers M, Preiss T, Hentze MW. RNA-binding proteins in cardiovascular biology and disease: the beat goes on. Nat Rev Cardiol 2024; 21:361-378. [PMID: 38163813 DOI: 10.1038/s41569-023-00958-z] [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: 11/06/2023] [Indexed: 01/03/2024]
Abstract
Cardiac development and function are becoming increasingly well understood from different angles, including signalling, transcriptional and epigenetic mechanisms. By contrast, the importance of the post-transcriptional landscape of cardiac biology largely remains to be uncovered, building on the foundation of a few existing paradigms. The discovery during the past decade of hundreds of additional RNA-binding proteins in mammalian cells and organs, including the heart, is expected to accelerate progress and has raised intriguing possibilities for better understanding the intricacies of cardiac development, metabolism and adaptive alterations. In this Review, we discuss the progress and new concepts on RNA-binding proteins and RNA biology and appraise them in the context of common cardiovascular clinical conditions, from cell and organ-wide perspectives. We also discuss how a better understanding of cardiac RNA-binding proteins can fill crucial knowledge gaps in cardiology and might pave the way to developing better treatments to reduce cardiovascular morbidity and mortality.
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Affiliation(s)
- Mirko Völkers
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Heidelberg and Mannheim, Germany
| | - Thomas Preiss
- Shine-Dalgarno Centre for RNA Innovation, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
- Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia
| | - Matthias W Hentze
- European Molecular Biology Laboratory, Heidelberg, Germany.
- Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany.
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Montañés-Agudo P, van der Made I, Aufiero S, Tijsen AJ, Pinto YM, Creemers EE. Quaking regulates circular RNA production in cardiomyocytes. J Cell Sci 2023; 136:jcs261120. [PMID: 37272356 PMCID: PMC10323251 DOI: 10.1242/jcs.261120] [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: 03/01/2023] [Accepted: 05/25/2023] [Indexed: 06/06/2023] Open
Abstract
Circular RNAs (circRNAs) are a class of non-coding RNA molecules that are gaining increasing attention for their roles in various pathophysiological processes. The RNA-binding protein quaking (QKI) has been identified as a regulator of circRNA formation. In this study, we investigate the role of QKI in the formation of circRNAs in the heart by performing RNA-sequencing on Qki-knockout mice. Loss of QKI resulted in the differential expression of 17% of the circRNAs in adult mouse hearts. Interestingly, the majority of the QKI-regulated circRNAs (58%) were derived from genes undergoing QKI-dependent splicing, indicating a relationship between back-splicing and linear splicing. We compared these QKI-dependent circRNAs with those regulated by RBM20, another cardiac splicing factor essential for circRNA formation. We found that QKI and RBM20 regulate the formation of a distinct, but partially overlapping set of circRNAs in the heart. Strikingly, many shared circRNAs were derived from the Ttn gene, and they were regulated in an opposite manner. Our findings indicate that QKI not only regulates alternative splicing in the heart but also the formation of circRNAs.
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Affiliation(s)
- Pablo Montañés-Agudo
- Department of Experimental Cardiology, Amsterdam Cardiovascular Sciences, Amsterdam UMC location University of Amsterdam, 1105AZ, Amsterdam, The Netherlands
| | - Ingeborg van der Made
- Department of Experimental Cardiology, Amsterdam Cardiovascular Sciences, Amsterdam UMC location University of Amsterdam, 1105AZ, Amsterdam, The Netherlands
| | - Simona Aufiero
- Department of Experimental Cardiology, Amsterdam Cardiovascular Sciences, Amsterdam UMC location University of Amsterdam, 1105AZ, Amsterdam, The Netherlands
| | - Anke J. Tijsen
- Department of Experimental Cardiology, Amsterdam Cardiovascular Sciences, Amsterdam UMC location University of Amsterdam, 1105AZ, Amsterdam, The Netherlands
| | - Yigal M. Pinto
- Department of Experimental Cardiology, Amsterdam Cardiovascular Sciences, Amsterdam UMC location University of Amsterdam, 1105AZ, Amsterdam, The Netherlands
| | - Esther E. Creemers
- Department of Experimental Cardiology, Amsterdam Cardiovascular Sciences, Amsterdam UMC location University of Amsterdam, 1105AZ, Amsterdam, The Netherlands
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Olthof AM, White AK, Kanadia RN. The emerging significance of splicing in vertebrate development. Development 2022; 149:dev200373. [PMID: 36178052 PMCID: PMC9641660 DOI: 10.1242/dev.200373] [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] [Indexed: 01/19/2023]
Abstract
Splicing is a crucial regulatory node of gene expression that has been leveraged to expand the proteome from a limited number of genes. Indeed, the vast increase in intron number that accompanied vertebrate emergence might have aided the evolution of developmental and organismal complexity. Here, we review how animal models for core spliceosome components have provided insights into the role of splicing in vertebrate development, with a specific focus on neuronal, neural crest and skeletal development. To this end, we also discuss relevant spliceosomopathies, which are developmental disorders linked to mutations in spliceosome subunits. Finally, we discuss potential mechanisms that could underlie the tissue-specific phenotypes often observed upon spliceosome inhibition and identify gaps in our knowledge that, we hope, will inspire further research.
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Affiliation(s)
- Anouk M. Olthof
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen 2200, Denmark
| | - Alisa K. White
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA
| | - Rahul N. Kanadia
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
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Liu N, Bowen CM, Shoja MM, Castro de Pereira KL, Dongur LP, Saad A, Russell WK, Broderick TC, Fair JH, Fagg WS. Comparative Analysis of Co-Cultured Amniotic Cell-Conditioned Media with Cell-Free Amniotic Fluid Reveals Differential Effects on Epithelial–Mesenchymal Transition and Myofibroblast Activation. Biomedicines 2022; 10:biomedicines10092189. [PMID: 36140291 PMCID: PMC9495976 DOI: 10.3390/biomedicines10092189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 11/16/2022] Open
Abstract
Myofibroblast activation is a cellular response elicited by a variety of physiological or pathological insults whereby cells initiate a coordinated response intended to eradicate the insult and then revert back to a basal state. However, an underlying theme in various disease states is persistent myofibroblast activation that fails to resolve. Based on multiple observations, we hypothesized that the secreted factors harvested from co-culturing amniotic stem cells might mimic the anti-inflammatory state that cell-free amniotic fluid (AF) elicits. We optimized an amnion epithelial and amniotic fluid cell co-culture system, and tested this hypothesis in the context of myofibroblast activation. However, we discovered that co-cultured amniotic cell conditioned media (coACCM) and AF have opposing effects on myofibroblast activation: coACCM activates the epithelial–mesenchymal transition (EMT) and stimulates gene expression patterns associated with myofibroblast activation, while AF does the opposite. Intriguingly, extracellular vesicles (EVs) purified from AF are necessary and sufficient to activate EMT and inflammatory gene expression patterns, while the EV-depleted AF potently represses these responses. In summary, these data indicate that coACCM stimulates myofibroblast activation, while AF represses it. We interpret these findings to suggest that coACCM, AF, and fractionated AF represent unique biologics that elicit different cellular responses that are correlated with a wide variety of pathological states, and therefore could have broad utility in the clinic and the lab.
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Affiliation(s)
- Naiyou Liu
- Division of Transplant, Department of Surgery, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Charles M. Bowen
- Division of Transplant, Department of Surgery, University of Texas Medical Branch, Galveston, TX 77555, USA
- John Sealy School of Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Mohammadali M. Shoja
- Division of Transplant, Department of Surgery, University of Texas Medical Branch, Galveston, TX 77555, USA
| | | | - Laxmi Priya Dongur
- Division of Transplant, Department of Surgery, University of Texas Medical Branch, Galveston, TX 77555, USA
- John Sealy School of Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Antonio Saad
- Department of Obstetrics and Gynecology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - William K. Russell
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Thomas Christopher Broderick
- Merakris Therapeutics, RTP Frontier, Research Triangle Park, NC 27709, USA
- Golden LEAF Biomanufacturing Training and Education Center, North Carolina State University, Raleigh, NC 27606, USA
| | - Jeffrey H. Fair
- Division of Transplant, Department of Surgery, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - William Samuel Fagg
- Division of Transplant, Department of Surgery, University of Texas Medical Branch, Galveston, TX 77555, USA
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Merakris Therapeutics, RTP Frontier, Research Triangle Park, NC 27709, USA
- Correspondence: ; Tel.: +1-(409)-772-2412; Fax: +1-(409)-747-7364
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