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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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2
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Verma SK, Kuyumcu-Martinez MN. RNA binding proteins in cardiovascular development and disease. Curr Top Dev Biol 2024; 156:51-119. [PMID: 38556427 DOI: 10.1016/bs.ctdb.2024.01.007] [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] [Indexed: 04/02/2024]
Abstract
Congenital heart disease (CHD) is the most common birth defect affecting>1.35 million newborn babies worldwide. CHD can lead to prenatal, neonatal, postnatal lethality or life-long cardiac complications. RNA binding protein (RBP) mutations or variants are emerging as contributors to CHDs. RBPs are wizards of gene regulation and are major contributors to mRNA and protein landscape. However, not much is known about RBPs in the developing heart and their contributions to CHD. In this chapter, we will discuss our current knowledge about specific RBPs implicated in CHDs. We are in an exciting era to study RBPs using the currently available and highly successful RNA-based therapies and methodologies. Understanding how RBPs shape the developing heart will unveil their contributions to CHD. Identifying their target RNAs in the embryonic heart will ultimately lead to RNA-based treatments for congenital heart disease.
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Affiliation(s)
- Sunil K Verma
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine Charlottesville, VA, United States.
| | - Muge N Kuyumcu-Martinez
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine Charlottesville, VA, United States; Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, United States; University of Virginia Cancer Center, Charlottesville, VA, United States.
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3
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Cao J, Wei Z, Nie Y, Chen HZ. Therapeutic potential of alternative splicing in cardiovascular diseases. EBioMedicine 2024; 101:104995. [PMID: 38350330 PMCID: PMC10874720 DOI: 10.1016/j.ebiom.2024.104995] [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: 09/24/2023] [Revised: 01/19/2024] [Accepted: 01/21/2024] [Indexed: 02/15/2024] Open
Abstract
RNA splicing is an important RNA processing step required by multiexon protein-coding mRNAs and some noncoding RNAs. Precise RNA splicing is required for maintaining gene and cell function; however, mis-spliced RNA transcripts can lead to loss- or gain-of-function effects in human diseases. Mis-spliced RNAs induced by gene mutations or the dysregulation of splicing regulators may result in frameshifts, nonsense-mediated decay (NMD), or inclusion/exclusion of exons. Genetic animal models have characterised multiple splicing factors required for cardiac development or function. Moreover, sarcomeric and ion channel genes, which are closely associated with cardiovascular function and disease, are hotspots for AS. Here, we summarise splicing factors and their targets that are associated with cardiovascular diseases, introduce some therapies potentially related to pathological AS targets, and raise outstanding questions and future directions in this field.
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Affiliation(s)
- Jun Cao
- College of Chemistry and Life Science, Beijing University of Technology, Beijing, 100124, PR China; University of Texas Medical Branch at Galveston, TX, 77555, USA
| | - Ziyu Wei
- Department of Biochemistry & Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Yu Nie
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China.
| | - Hou-Zao Chen
- Department of Biochemistry & Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China; Medical Epigenetics Research Center, Chinese Academy of Medical Sciences, Beijing, China.
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4
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Monziani A, Ulitsky I. Noncoding snoRNA host genes are a distinct subclass of long noncoding RNAs. Trends Genet 2023; 39:908-923. [PMID: 37783604 DOI: 10.1016/j.tig.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/04/2023] [Accepted: 09/07/2023] [Indexed: 10/04/2023]
Abstract
Mammalian genomes are pervasively transcribed into different noncoding (nc)RNA classes, each one with its own hallmarks and exceptions. Some of them are nested into each other, such as host genes for small nucleolar RNAs (snoRNAs), which were long believed to simply act as molecular containers strictly facilitating snoRNA biogenesis. However, recent findings show that noncoding snoRNA host genes (ncSNHGs) display features different from those of 'regular' long ncRNAs (lncRNAs) and, more importantly, they can exert independent and unrelated functions to those of the encoded snoRNAs. Here, we review and summarize past and recent evidence that ncSNHGs form a defined subclass among the plethora of lncRNAs, and discuss future research that can further elucidate their biological relevance.
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Affiliation(s)
- Alan Monziani
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel; Department of Molecular Neuroscience, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Igor Ulitsky
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel; Department of Molecular Neuroscience, Weizmann Institute of Science, 7610001 Rehovot, Israel.
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Moss ND, Wells KL, Theis A, Kim YK, Spigelman AF, Liu X, MacDonald PE, Sussel L. Modulation of insulin secretion by RBFOX2-mediated alternative splicing. Nat Commun 2023; 14:7732. [PMID: 38007492 PMCID: PMC10676425 DOI: 10.1038/s41467-023-43605-4] [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: 01/31/2023] [Accepted: 11/15/2023] [Indexed: 11/27/2023] Open
Abstract
Insulin secretion is a tightly regulated process that is vital for maintaining blood glucose homeostasis. Although the molecular components of insulin granule trafficking and secretion are well established, how they are regulated to rapidly fine-tune secretion in response to changing environmental conditions is not well characterized. Recent studies have determined that dysregulation of RNA-binding proteins (RBPs) and aberrant mRNA splicing occurs at the onset of diabetes. We demonstrate that the RBP, RBFOX2, is a critical regulator of insulin secretion through the alternative splicing of genes required for insulin granule docking and exocytosis. Conditional mutation of Rbfox2 in the mouse pancreas results in decreased insulin secretion and impaired blood glucose homeostasis. Consistent with defects in secretion, we observe reduced insulin granule docking and corresponding splicing defects in the SNARE complex components. These findings identify an additional mechanism for modulating insulin secretion in both healthy and dysfunctional pancreatic β cells.
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Affiliation(s)
- Nicole D Moss
- Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Kristen L Wells
- Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Alexandra Theis
- Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Yong-Kyung Kim
- Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Aliya F Spigelman
- Department of Pharmacology and Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - Xiong Liu
- Department of Pharmacology and Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - Patrick E MacDonald
- Department of Pharmacology and Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - Lori Sussel
- Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
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Li P, Qin D, Chen T, Hou W, Song X, Yin S, Song M, Fernando WCHA, Chen X, Sun Y, Wang J. Dysregulated Rbfox2 produces aberrant splicing of Ca V1.2 calcium channel in diabetes-induced cardiac hypertrophy. Cardiovasc Diabetol 2023; 22:168. [PMID: 37415128 PMCID: PMC10324275 DOI: 10.1186/s12933-023-01894-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 06/19/2023] [Indexed: 07/08/2023] Open
Abstract
BACKGROUND L-type Ca2+ channel CaV1.2 is essential for cardiomyocyte excitation, contraction and gene transcription in the heart, and abnormal functions of cardiac CaV1.2 channels are presented in diabetic cardiomyopathy. However, the underlying mechanisms are largely unclear. The functions of CaV1.2 channels are subtly modulated by splicing factor-mediated alternative splicing (AS), but whether and how CaV1.2 channels are alternatively spliced in diabetic heart remains unknown. METHODS Diabetic rat models were established by using high-fat diet in combination with low dose streptozotocin. Cardiac function and morphology were assessed by echocardiography and HE staining, respectively. Isolated neonatal rat ventricular myocytes (NRVMs) were used as a cell-based model. Cardiac CaV1.2 channel functions were measured by whole-cell patch clamp, and intracellular Ca2+ concentration was monitored by using Fluo-4 AM. RESULTS We find that diabetic rats develop diastolic dysfunction and cardiac hypertrophy accompanied by an increased CaV1.2 channel with alternative exon 9* (CaV1.2E9*), but unchanged that with alternative exon 8/8a or exon 33. The splicing factor Rbfox2 expression is also increased in diabetic heart, presumably because of dominate-negative (DN) isoform. Unexpectedly, high glucose cannot induce the aberrant expressions of CaV1.2 exon 9* and Rbfox2. But glycated serum (GS), the mimic of advanced glycation end-products (AGEs), upregulates CaV1.2E9* channels proportion and downregulates Rbfox2 expression in NRVMs. By whole-cell patch clamp, we find GS application hyperpolarizes the current-voltage curve and window currents of cardiac CaV1.2 channels. Moreover, GS treatment raises K+-triggered intracellular Ca2+ concentration ([Ca2+]i), enlarges cell surface area of NRVMs and induces hypertrophic genes transcription. Consistently, siRNA-mediated knockdown of Rbfox2 in NRVMs upregulates CaV1.2E9* channel, shifts CaV1.2 window currents to hyperpolarization, increases [Ca2+]i and induces cardiomyocyte hypertrophy. CONCLUSIONS AGEs, not glucose, dysregulates Rbfox2 which thereby increases CaV1.2E9* channels and hyperpolarizes channel window currents. These make the channels open at greater negative potentials and lead to increased [Ca2+]i in cardiomyocytes, and finally induce cardiomyocyte hypertrophy in diabetes. Our work elucidates the underlying mechanisms for CaV1.2 channel regulation in diabetic heart, and targeting Rbfox2 to reset the aberrantly spliced CaV1.2 channel might be a promising therapeutic approach in diabetes-induced cardiac hypertrophy.
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Affiliation(s)
- Pengpeng Li
- Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
- Department of Physiology, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
| | - Dongxia Qin
- Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
- Department of Physiology, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
| | - Tiange Chen
- Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
- Department of Physiology, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
| | - Wei Hou
- Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
- Department of Physiology, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
| | - Xinyu Song
- Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
- Department of Physiology, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
| | - Shumin Yin
- Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
- Department of Physiology, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
| | - Miaomiao Song
- Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
- Department of Physiology, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
| | - W C Hewith A Fernando
- Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
- Department of Physiology, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
| | - Xiaojie Chen
- Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
- Department of Physiology, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
| | - Yu Sun
- Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, China.
- Department of Physiology, Nanjing Medical University, Nanjing, Jiangsu, 211166, China.
| | - Juejin Wang
- Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, China.
- Department of Physiology, Nanjing Medical University, Nanjing, Jiangsu, 211166, China.
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Lu YW, Liang Z, Guo H, Fernandes T, Espinoza-Lewis RA, Wang T, Li K, Li X, Singh GB, Wang Y, Cowan D, Mably JD, Philpott CC, Chen H, Wang DZ. PCBP1 regulates alternative splicing of AARS2 in congenital cardiomyopathy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.18.540420. [PMID: 37293078 PMCID: PMC10245752 DOI: 10.1101/2023.05.18.540420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Alanyl-transfer RNA synthetase 2 (AARS2) is a nuclear encoded mitochondrial tRNA synthetase that is responsible for charging of tRNA-Ala with alanine during mitochondrial translation. Homozygous or compound heterozygous mutations in the Aars2 gene, including those affecting its splicing, are linked to infantile cardiomyopathy in humans. However, how Aars2 regulates heart development, and the underlying molecular mechanism of heart disease remains unknown. Here, we found that poly(rC) binding protein 1 (PCBP1) interacts with the Aars2 transcript to mediate its alternative splicing and is critical for the expression and function of Aars2. Cardiomyocyte-specific deletion of Pcbp1 in mice resulted in defects in heart development that are reminiscent of human congenital cardiac defects, including noncompaction cardiomyopathy and a disruption of the cardiomyocyte maturation trajectory. Loss of Pcbp1 led to an aberrant alternative splicing and a premature termination of Aars2 in cardiomyocytes. Additionally, Aars2 mutant mice with exon-16 skipping recapitulated heart developmental defects observed in Pcbp1 mutant mice. Mechanistically, we found dysregulated gene and protein expression of the oxidative phosphorylation pathway in both Pcbp1 and Aars2 mutant hearts; these date provide further evidence that the infantile hypertrophic cardiomyopathy associated with the disorder oxidative phosphorylation defect type 8 (COXPD8) is mediated by Aars2. Our study therefore identifies Pcbp1 and Aars2 as critical regulators of heart development and provides important molecular insights into the role of disruptions in metabolism on congenital heart defects.
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8
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Parker LE, Kurzlechner LM, Landstrom AP. Induced Pluripotent Stem Cell-Based Modeling of Single-Ventricle Congenital Heart Diseases. Curr Cardiol Rep 2023; 25:295-305. [PMID: 36930454 PMCID: PMC10726018 DOI: 10.1007/s11886-023-01852-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/16/2023] [Indexed: 03/18/2023]
Abstract
PURPOSE OF REVIEW Congenital heart disease includes a wide variety of structural cardiac defects, the most severe of which are single ventricle defects (SVD). These patients suffer from significant morbidity and mortality; however, our understanding of the developmental etiology of these conditions is limited. Model organisms offer a window into normal and abnormal cardiogenesis yet often fail to recapitulate complex congenital heart defects seen in patients. The use of induced pluripotent stem cells (iPSCs) derived from patients with single-ventricle defects opens the door to studying SVD in patient-derived cardiomyocytes (iPSC-CMs) in a variety of different contexts, including organoids and chamber-specific cardiomyocytes. As the genetic and cellular causes of SVD are not well defined, patient-derived iPSC-CMs hold promise for uncovering mechanisms of disease development and serve as a platform for testing therapies. The purpose of this review is to highlight recent advances in iPSC-based models of SVD. RECENT FINDINGS Recent advances in patient-derived iPSC-CM differentiation, as well as the development of both chamber-specific and non-myocyte cardiac cell types, make it possible to model the complex genetic and molecular architecture involved in SVD development. Moreover, iPSC models have become increasingly complex with the generation of 3D organoids and engineered cardiac tissues which open the door to new mechanistic insight into SVD development. Finally, iPSC-CMs have been used in proof-of-concept studies that the molecular underpinnings of SVD may be targetable for future therapies. While each platform has its advantages and disadvantages, the use of patient-derived iPSC-CMs offers a window into patient-specific cardiogenesis and SVD development. Advancement in stem-cell based modeling of SVD promises to revolutionize our understanding of the developmental etiology of SVD and provides a tool for developing and testing new therapies.
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Affiliation(s)
- Lauren E Parker
- Department of Pediatrics, Division of Cardiology, Duke University School of Medicine, Durham, NC, USA
| | - Leonie M Kurzlechner
- Department of Pediatrics, Division of Cardiology, Duke University School of Medicine, Durham, NC, USA
| | - Andrew P Landstrom
- Department of Pediatrics, Division of Cardiology, Duke University School of Medicine, Durham, NC, USA.
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA.
- Duke University Medical Center, Box 2652, Durham, NC, 27710, USA.
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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: 0] [Impact Index Per Article: 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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Mehta Z, Touma M. Post-Transcriptional Modification by Alternative Splicing and Pathogenic Splicing Variants in Cardiovascular Development and Congenital Heart Defects. Int J Mol Sci 2023; 24:ijms24021555. [PMID: 36675070 PMCID: PMC9862068 DOI: 10.3390/ijms24021555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/08/2023] [Accepted: 01/09/2023] [Indexed: 01/15/2023] Open
Abstract
Advancements in genomics, bioinformatics, and genome editing have uncovered new dimensions in gene regulation. Post-transcriptional modifications by the alternative splicing of mRNA transcripts are critical regulatory mechanisms of mammalian gene expression. In the heart, there is an expanding interest in elucidating the role of alternative splicing in transcriptome regulation. Substantial efforts were directed toward investigating this process in heart development and failure. However, few studies shed light on alternative splicing products and their dysregulation in congenital heart defects (CHDs). While elegant reports showed the crucial roles of RNA binding proteins (RBPs) in orchestrating splicing transitions during heart development and failure, the impact of RBPs dysregulation or genetic variation on CHDs has not been fully addressed. Herein, we review the current understanding of alternative splicing and RBPs' roles in heart development and CHDs. Wediscuss the impact of perinatal splicing transition and its dysregulation in CHDs. We further summarize the discoveries made of causal splicing variants in key transcription factors that are implicated in CHDs. An improved understanding of the roles of alternative splicing in heart development and CHDs may potentially inform novel preventive and therapeutic advancements for newborn infants with CHDs.
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Affiliation(s)
- Zubin Mehta
- Neonatal/Congenital Heart Laboratory, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Children’s Discovery and Innovation Institute, Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Stem Cell Research Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Marlin Touma
- Neonatal/Congenital Heart Laboratory, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Children’s Discovery and Innovation Institute, Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Stem Cell Research Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Correspondence:
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Suppression of RBFox2 by Multiple MiRNAs in Pressure Overload-Induced Heart Failure. Int J Mol Sci 2023; 24:ijms24021283. [PMID: 36674797 PMCID: PMC9867119 DOI: 10.3390/ijms24021283] [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: 11/28/2022] [Revised: 12/25/2022] [Accepted: 01/06/2023] [Indexed: 01/11/2023] Open
Abstract
Heart failure is the final stage of various cardiovascular diseases and seriously threatens human health. Increasing mediators have been found to be involved in the pathogenesis of heart failure, including the RNA binding protein RBFox2. It participates in multiple aspects of the regulation of cardiac function and plays a critical role in the process of heart failure. However, how RBFox2 itself is regulated remains unclear. Here, we dissected transcriptomic signatures, including mRNAs and miRNAs, in a mouse model of heart failure after TAC surgery. A global analysis showed that an asymmetric alternation in gene expression and a large-scale upregulation of miRNAs occurred in heart failure. An association analysis revealed that the latter not only contributed to the degradation of numerous mRNA transcripts, but also suppressed the translation of key proteins such as RBFox2. With the aid of Ago2 CLIP-seq data, luciferase assays verified that RBFox2 was targeted by multiple miRNAs, including Let-7, miR-16, and miR-200b, which were significantly upregulated in heart failure. The overexpression of these miRNAs suppressed the RBFox2 protein and its downstream effects in cardiomyocytes, which was evidenced by the suppressed alternative splicing of the Enah gene and impaired E-C coupling via the repression of the Jph2 protein. The inhibition of Let-7, the most abundant miRNA family targeting RBFox2, could restore the RBFox2 protein as well as its downstream effects in dysfunctional cardiomyocytes induced by ISO treatment. In all, these findings revealed the molecular mechanism leading to RBFox2 depression in heart failure, and provided an approach to rescue RBFox2 through miRNA inhibition for the treatment of heart failure.
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12
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Jia Y, Chen J, Zhong J, He X, Zeng L, Wang Y, Li J, Xia S, Ye E, Zhao J, Ke B, Li C. Novel rare mutation in a conserved site of PTPRB causes human hypoplastic left heart syndrome. Clin Genet 2023; 103:79-86. [PMID: 36148623 DOI: 10.1111/cge.14234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 12/14/2022]
Abstract
Hypoplastic left heart syndrome (HLHS) is a rare but fatal birth defect in which the left side of the heart is underdeveloped. HLHS accounts for 2% to 4% of congenital heart anomalies. Whole genome sequencing (WGS) was conducted for a family trio consisting of a proband and his parents. A homozygous rare variant was detected in the PTPRB (Protein Tyrosine Phosphatase Receptor Type B) gene of the proband by functional annotation and co-segregation analysis. Sanger sequencing was used to confirm genotypes of the variant. The in silico prediction tools, including Mutation Taster, SpliceAI, and CADD, were used to predict the impact of the mutation. The allele frequencies across populations were compared based on multiple databases, including "1000 genomes" and "gnomAD". We used two vectors (pcMINI and pcDNA3.1) to generate a minigene construct to validate the mutational effect at the transcriptional level. Family-based WGS analyses showed that only a homozygous splice acceptor variant (NC_000012.12: g.70636068T>G, NM_001109754.4: c.56-2A>C, NG_029940.2: g.6373A>C) at the exon-intron border of PTPRB gene associates with HLHS. This variant is also within the region with the enhancer activity based on UCSC genome annotation. Genotyping and Sanger sequencing revealed that the proband's parents are heterozygous for this variant. Evolutionary conservation analysis revealed that the site (NC_000012.12: g.70636068) is extremely conserved across species, supporting the evolutionary functional constraints of the ancestral wild type (T). In silico tools universally predicted a deleterious or disease-causing impact of the mutation from T to G. The mutation was not found in the 1000 genomes and gnomAD databases, which indicates that this mutation is very rare in most human populations. A splicing assay indicated that the mutated minigene caused aberrant splicing of mRNA, in which a 3 bp missing in the second exon resulted in the deletion of one amino acid (NP_001103224.1:p.Glu19del) compared to the normal protein of PRPTB (also the VE-PTP). Structure prediction revealed that the deletion occurred within the C-region of the signal peptide of VE-PTP, suggesting signal peptide-related defects as a potential mechanism for the HLHS cellular pathogeny. We report a rare homozygous variant with splicing error in PTPRB associated with HLHS. Previous model species studies revealed conserved functions of PTPRB in cardiovascular and heart development in mice and zebrafish. Our study is the first report to show the association between PTPRB and HLHS in humans.
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Affiliation(s)
- Yangying Jia
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Jianhai Chen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Jie Zhong
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Xuefei He
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Li Zeng
- The Department of Pediatric Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Yanmin Wang
- Chinese Institute for Brain Research, Beijing, China
| | - Jiakun Li
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China.,Department of Urology, Institute of Urology, West China Hospital of Sichuan University, Chengdu, China
| | - Shengqian Xia
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, USA
| | - Erdengqieqieke Ye
- Department of Prenatal Diagnosis, Reproductive Medicine Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Jing Zhao
- Department of Prenatal Diagnosis, Reproductive Medicine Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Bin Ke
- Department of Neurology, Laboratory of Neurodegenerative Disorders, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Chunyu Li
- Department of Neurology, Laboratory of Neurodegenerative Disorders, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
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Akerberg AA, Trembley M, Butty V, Schwertner A, Zhao L, Beerens M, Liu X, Mahamdeh M, Yuan S, Boyer L, MacRae C, Nguyen C, Pu WT, Burns CE, Burns CG. RBPMS2 Is a Myocardial-Enriched Splicing Regulator Required for Cardiac Function. Circ Res 2022; 131:980-1000. [PMID: 36367103 PMCID: PMC9770155 DOI: 10.1161/circresaha.122.321728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND RBPs (RNA-binding proteins) perform indispensable functions in the post-transcriptional regulation of gene expression. Numerous RBPs have been implicated in cardiac development or physiology based on gene knockout studies and the identification of pathogenic RBP gene mutations in monogenic heart disorders. The discovery and characterization of additional RBPs performing indispensable functions in the heart will advance basic and translational cardiovascular research. METHODS We performed a differential expression screen in zebrafish embryos to identify genes enriched in nkx2.5-positive cardiomyocytes or cardiopharyngeal progenitors compared to nkx2.5-negative cells from the same embryos. We investigated the myocardial-enriched gene RNA-binding protein with multiple splicing (variants) 2 [RBPMS2)] by generating and characterizing rbpms2 knockout zebrafish and human cardiomyocytes derived from RBPMS2-deficient induced pluripotent stem cells. RESULTS We identified 1848 genes enriched in the nkx2.5-positive population. Among the most highly enriched genes, most with well-established functions in the heart, we discovered the ohnologs rbpms2a and rbpms2b, which encode an evolutionarily conserved RBP. Rbpms2 localizes selectively to cardiomyocytes during zebrafish heart development and strong cardiomyocyte expression persists into adulthood. Rbpms2-deficient embryos suffer from early cardiac dysfunction characterized by reduced ejection fraction. The functional deficit is accompanied by myofibril disarray, altered calcium handling, and differential alternative splicing events in mutant cardiomyocytes. These phenotypes are also observed in RBPMS2-deficient human cardiomyocytes, indicative of conserved molecular and cellular function. RNA-sequencing and comparative analysis of genes mis-spliced in RBPMS2-deficient zebrafish and human cardiomyocytes uncovered a conserved network of 29 ortholog pairs that require RBPMS2 for alternative splicing regulation, including RBFOX2, SLC8A1, and MYBPC3. CONCLUSIONS Our study identifies RBPMS2 as a conserved regulator of alternative splicing, myofibrillar organization, and calcium handling in zebrafish and human cardiomyocytes.
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Affiliation(s)
- Alexander A. Akerberg
- Division of Basic and Translational Cardiovascular Research, Department of Cardiology, Boston Children’s Hospital, Boston‚ MA (A.A.A., M.T., X.L., W.T.P., C.E.B., C.G.B.).,Cardiovascular Research Center, Massachusetts General Hospital, Charlestown‚ MA (A.A.A., A.S., L.Z., M.M., S.Y., C.N., C.E.B., C.G.B.).,Harvard Medical School, Boston, MA (A.A.A., M.T., A.S., L.Z., M.B., X.L., M.M., S.Y., C.M., C.N., W.T.P., C.E.B., C.G.B.)
| | - Michael Trembley
- Division of Basic and Translational Cardiovascular Research, Department of Cardiology, Boston Children’s Hospital, Boston‚ MA (A.A.A., M.T., X.L., W.T.P., C.E.B., C.G.B.).,Harvard Medical School, Boston, MA (A.A.A., M.T., A.S., L.Z., M.B., X.L., M.M., S.Y., C.M., C.N., W.T.P., C.E.B., C.G.B.)
| | - Vincent Butty
- BioMicroCenter, Department of Biology (V.B.), Massachusetts Institute of Technology, Cambridge‚ MA.,Department of Biology (V.B., L.B.), Massachusetts Institute of Technology, Cambridge‚ MA
| | - Asya Schwertner
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown‚ MA (A.A.A., A.S., L.Z., M.M., S.Y., C.N., C.E.B., C.G.B.).,Harvard Medical School, Boston, MA (A.A.A., M.T., A.S., L.Z., M.B., X.L., M.M., S.Y., C.M., C.N., W.T.P., C.E.B., C.G.B.)
| | - Long Zhao
- Harvard Medical School, Boston, MA (A.A.A., M.T., A.S., L.Z., M.B., X.L., M.M., S.Y., C.M., C.N., W.T.P., C.E.B., C.G.B.)
| | - Manu Beerens
- Harvard Medical School, Boston, MA (A.A.A., M.T., A.S., L.Z., M.B., X.L., M.M., S.Y., C.M., C.N., W.T.P., C.E.B., C.G.B.).,Division of Cardiovascular Medicine, Brigham and Women’s Hospital, Boston, MA (M.B., C.M.)
| | - Xujie Liu
- Division of Basic and Translational Cardiovascular Research, Department of Cardiology, Boston Children’s Hospital, Boston‚ MA (A.A.A., M.T., X.L., W.T.P., C.E.B., C.G.B.).,Harvard Medical School, Boston, MA (A.A.A., M.T., A.S., L.Z., M.B., X.L., M.M., S.Y., C.M., C.N., W.T.P., C.E.B., C.G.B.)
| | - Mohammed Mahamdeh
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown‚ MA (A.A.A., A.S., L.Z., M.M., S.Y., C.N., C.E.B., C.G.B.).,Harvard Medical School, Boston, MA (A.A.A., M.T., A.S., L.Z., M.B., X.L., M.M., S.Y., C.M., C.N., W.T.P., C.E.B., C.G.B.)
| | - Shiaulou Yuan
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown‚ MA (A.A.A., A.S., L.Z., M.M., S.Y., C.N., C.E.B., C.G.B.).,Harvard Medical School, Boston, MA (A.A.A., M.T., A.S., L.Z., M.B., X.L., M.M., S.Y., C.M., C.N., W.T.P., C.E.B., C.G.B.)
| | - Laurie Boyer
- Department of Biology (V.B., L.B.), Massachusetts Institute of Technology, Cambridge‚ MA.,Department of Biological Engineering (L.B.), Massachusetts Institute of Technology, Cambridge‚ MA
| | - Calum MacRae
- Harvard Medical School, Boston, MA (A.A.A., M.T., A.S., L.Z., M.B., X.L., M.M., S.Y., C.M., C.N., W.T.P., C.E.B., C.G.B.).,Division of Cardiovascular Medicine, Brigham and Women’s Hospital, Boston, MA (M.B., C.M.)
| | - Christopher Nguyen
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown‚ MA (A.A.A., A.S., L.Z., M.M., S.Y., C.N., C.E.B., C.G.B.).,Harvard Medical School, Boston, MA (A.A.A., M.T., A.S., L.Z., M.B., X.L., M.M., S.Y., C.M., C.N., W.T.P., C.E.B., C.G.B.).,Cardiovascular Innovation Research Center, Heart Vascular & Thoracic Institute, Cleveland Clinic‚ Cleveland‚ OH (C.N.)
| | - William T. Pu
- Division of Basic and Translational Cardiovascular Research, Department of Cardiology, Boston Children’s Hospital, Boston‚ MA (A.A.A., M.T., X.L., W.T.P., C.E.B., C.G.B.).,Harvard Medical School, Boston, MA (A.A.A., M.T., A.S., L.Z., M.B., X.L., M.M., S.Y., C.M., C.N., W.T.P., C.E.B., C.G.B.).,Harvard Stem Cell Institute, Cambridge, MA (W.T.P., C.E.B.)
| | - Caroline E. Burns
- Division of Basic and Translational Cardiovascular Research, Department of Cardiology, Boston Children’s Hospital, Boston‚ MA (A.A.A., M.T., X.L., W.T.P., C.E.B., C.G.B.).,Cardiovascular Research Center, Massachusetts General Hospital, Charlestown‚ MA (A.A.A., A.S., L.Z., M.M., S.Y., C.N., C.E.B., C.G.B.).,Harvard Medical School, Boston, MA (A.A.A., M.T., A.S., L.Z., M.B., X.L., M.M., S.Y., C.M., C.N., W.T.P., C.E.B., C.G.B.).,Harvard Stem Cell Institute, Cambridge, MA (W.T.P., C.E.B.)
| | - C. Geoffrey Burns
- Division of Basic and Translational Cardiovascular Research, Department of Cardiology, Boston Children’s Hospital, Boston‚ MA (A.A.A., M.T., X.L., W.T.P., C.E.B., C.G.B.).,Cardiovascular Research Center, Massachusetts General Hospital, Charlestown‚ MA (A.A.A., A.S., L.Z., M.M., S.Y., C.N., C.E.B., C.G.B.).,Harvard Medical School, Boston, MA (A.A.A., M.T., A.S., L.Z., M.B., X.L., M.M., S.Y., C.M., C.N., W.T.P., C.E.B., C.G.B.)
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14
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Zhang S, Yang X, Jiang M, Ma L, Hu J, Zhang HH. Post-transcriptional control by RNA-binding proteins in diabetes and its related complications. Front Physiol 2022; 13:953880. [PMID: 36277184 PMCID: PMC9582753 DOI: 10.3389/fphys.2022.953880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 09/20/2022] [Indexed: 11/25/2022] Open
Abstract
Diabetes mellitus (DM) is a fast-growing chronic metabolic disorder that leads to significant health, social, and economic problems worldwide. Chronic hyperglycemia caused by DM leads to multiple devastating complications, including macrovascular complications and microvascular complications, such as diabetic cardiovascular disease, diabetic nephropathy, diabetic neuropathy, and diabetic retinopathy. Numerous studies provide growing evidence that aberrant expression of and mutations in RNA-binding proteins (RBPs) genes are linked to the pathogenesis of diabetes and associated complications. RBPs are involved in RNA processing and metabolism by directing a variety of post-transcriptional events, such as alternative splicing, stability, localization, and translation, all of which have a significant impact on RNA fate, altering their function. Here, we purposed to summarize the current progression and underlying regulatory mechanisms of RBPs in the progression of diabetes and its complications. We expected that this review will open the door for RBPs and their RNA networks as novel therapeutic targets for diabetes and its related complications.
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Affiliation(s)
- Shiyu Zhang
- Department of Endocrinology, The Second Affiliated Hospital, Soochow University, Suzhou, China
| | - Xiaohua Yang
- The Affiliated Haian Hospital of Nantong University, Nantong, China
| | - Miao Jiang
- Department of Endocrinology, The Second Affiliated Hospital, Soochow University, Suzhou, China
| | - Lianhua Ma
- Department of Endocrinology, The Second Affiliated Hospital, Soochow University, Suzhou, China
| | - Ji Hu
- Department of Endocrinology, The Second Affiliated Hospital, Soochow University, Suzhou, China,*Correspondence: Ji Hu, ; Hong-Hong Zhang,
| | - Hong-Hong Zhang
- Department of Endocrinology, The Second Affiliated Hospital, Soochow University, Suzhou, China,*Correspondence: Ji Hu, ; Hong-Hong Zhang,
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15
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Intrinsic myocardial defects underlie an Rbfox-deficient zebrafish model of hypoplastic left heart syndrome. Nat Commun 2022; 13:5877. [PMID: 36198703 PMCID: PMC9534849 DOI: 10.1038/s41467-022-32982-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 08/18/2022] [Indexed: 02/03/2023] Open
Abstract
Hypoplastic left heart syndrome (HLHS) is characterized by underdevelopment of left sided structures including the ventricle, valves, and aorta. Prevailing paradigm suggests that HLHS is a multigenic disease of co-occurring phenotypes. Here, we report that zebrafish lacking two orthologs of the RNA binding protein RBFOX2, a gene linked to HLHS in humans, display cardiovascular defects overlapping those in HLHS patients including ventricular, valve, and aortic deficiencies. In contrast to current models, we demonstrate that these structural deficits arise secondary to impaired pump function as these phenotypes are rescued when Rbfox is specifically expressed in the myocardium. Mechanistically, we find diminished expression and alternative splicing of sarcomere and mitochondrial components that compromise sarcomere assembly and mitochondrial respiration, respectively. Injection of human RBFOX2 mRNA restores cardiovascular development in rbfox mutant zebrafish, while HLHS-linked RBFOX2 variants fail to rescue. This work supports an emerging paradigm for HLHS pathogenesis that centers on myocardial intrinsic defects.
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van den Bosch QCC, Nguyen JQN, Brands T, van den Bosch TPP, Verdijk RM, Paridaens D, Naus NC, de Klein A, Kiliç E, Brosens E. FOXD1 Is a Transcription Factor Important for Uveal Melanocyte Development and Associated with High-Risk Uveal Melanoma. Cancers (Basel) 2022; 14:cancers14153668. [PMID: 35954332 PMCID: PMC9367502 DOI: 10.3390/cancers14153668] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/12/2022] [Accepted: 07/22/2022] [Indexed: 11/27/2022] Open
Abstract
Simple Summary Despite successful treatment of primary uveal melanoma (UM), metastases still occur in approximately 50% of the patients. Unfortunately, little is known about the mechanism behind metastasized UM. By reanalyzing publicly available single-cell RNA sequencing data of embryonic zebrafish larvae and validating the results with UM data, we have identified five transcription regulators of interest: ELL2, KDM5B, REXO4, RBFOX2 and FOXD1. The most significant finding is FOXD1, which is nearly exclusively expressed in high-risk UM and is associated with poor survival. FOXD1 is a novel gene which could be involved in the metastatic capability of UM. Elucidating its function and role in metastatic UM could help to understand and develop treatment for UM. Abstract Uveal melanoma (UM) is a deadly ocular malignancy, originating from uveal melanocytes. Although much is known regarding prognostication in UM, the exact mechanism of metastasis is mostly unknown. Metastatic tumor cells are known to express a more stem-like RNA profile which is seen often in cell-specific embryonic development to induce tumor progression. Here, we identified novel transcription regulators by reanalyzing publicly available single cell RNA sequencing experiments. We identified five transcription regulators of interest: ELL2, KDM5B, REXO4, RBFOX2 and FOXD1. Our most significant finding is FOXD1, as this gene is nearly exclusively expressed in high-risk UM and its expression is associated with a poor prognosis. Even within the BAP1-mutated UM, the expression of FOXD1 is correlated with poor survival. FOXD1 is a novel factor which could potentially be involved in the metastatic capacity of high-risk UM. Elucidating the function of FOXD1 in UM could provide insight into the malignant transformation of uveal melanocytes, especially in high-risk UM.
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Affiliation(s)
- Quincy C. C. van den Bosch
- Department of Ophthalmology, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (Q.C.C.v.d.B.); (J.Q.N.N.); (T.B.); (N.C.N.)
- Department of Clinical Genetics, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands;
| | - Josephine Q. N. Nguyen
- Department of Ophthalmology, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (Q.C.C.v.d.B.); (J.Q.N.N.); (T.B.); (N.C.N.)
- Department of Clinical Genetics, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands;
| | - Tom Brands
- Department of Ophthalmology, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (Q.C.C.v.d.B.); (J.Q.N.N.); (T.B.); (N.C.N.)
- Department of Clinical Genetics, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands;
| | - Thierry P. P. van den Bosch
- Department of Pathology, Section Ophthalmic Pathology, Erasmus MC Cancer Institute, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (T.P.P.v.d.B.); (R.M.V.)
| | - Robert M. Verdijk
- Department of Pathology, Section Ophthalmic Pathology, Erasmus MC Cancer Institute, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (T.P.P.v.d.B.); (R.M.V.)
- Department of Pathology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Dion Paridaens
- The Rotterdam Eye Hospital, 3011 BH Rotterdam, The Netherlands;
| | - Nicole C. Naus
- Department of Ophthalmology, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (Q.C.C.v.d.B.); (J.Q.N.N.); (T.B.); (N.C.N.)
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands;
| | - Emine Kiliç
- Department of Ophthalmology, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (Q.C.C.v.d.B.); (J.Q.N.N.); (T.B.); (N.C.N.)
- Correspondence: (E.K.); (E.B.); Tel.: +31-107030683 (E.B.)
| | - Erwin Brosens
- Department of Clinical Genetics, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands;
- Correspondence: (E.K.); (E.B.); Tel.: +31-107030683 (E.B.)
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