1
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Zorn P, Calvo Sánchez J, Alakhras T, Schreier B, Gekle M, Hüttelmaier S, Köhn M. Rbfox1 controls alternative splicing of focal adhesion genes in cardiac muscle cells. J Mol Cell Biol 2024; 16:mjae003. [PMID: 38253401 PMCID: PMC11216089 DOI: 10.1093/jmcb/mjae003] [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: 04/05/2023] [Revised: 11/30/2023] [Accepted: 01/19/2024] [Indexed: 01/24/2024] Open
Abstract
Alternative splicing is one of the major cellular processes that determine the tissue-specific expression of protein variants. However, it remains challenging to identify physiologically relevant and tissue-selective proteins that are generated by alternative splicing. Hence, we investigated the target spectrum of the splicing factor Rbfox1 in the cardiac muscle context in more detail. By using a combination of in silico target prediction and in-cell validation, we identified several focal adhesion proteins as alternative splicing targets of Rbfox1. We focused on the alternative splicing patterns of vinculin (metavinculin isoform) and paxillin (extended paxillin isoform) and identified both as potential Rbfox1 targets. Minigene analyses suggested that both isoforms are promoted by Rbfox1 due to binding in the introns. Focal adhesions play an important role in the cardiac muscle context, since they mainly influence cell shape, cytoskeletal organization, and cell-matrix association. Our data confirmed that depletion of Rbfox1 changed cardiomyoblast morphology, cytoskeletal organization, and multinuclearity after differentiation, which might be due to changes in alternative splicing of focal adhesion proteins. Hence, our results indicate that Rbfox1 promotes alternative splicing of focal adhesion genes in cardiac muscle cells, which might contribute to heart disease progression, where downregulation of Rbfox1 is frequently observed.
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Affiliation(s)
- Peter Zorn
- Junior Group ‘Non-coding RNAs and RBPs in Human Diseases’, Medical Faculty, University of Halle–Wittenberg, 06120 Halle (Saale), Germany
| | - Jaime Calvo Sánchez
- Junior Group ‘Non-coding RNAs and RBPs in Human Diseases’, Medical Faculty, University of Halle–Wittenberg, 06120 Halle (Saale), Germany
| | - Tala Alakhras
- Junior Group ‘Non-coding RNAs and RBPs in Human Diseases’, Medical Faculty, University of Halle–Wittenberg, 06120 Halle (Saale), Germany
| | - Barbara Schreier
- Julius Bernstein Institute of Physiology, Medical Faculty, University of Halle–Wittenberg, 06112 Halle (Saale), Germany
| | - Michael Gekle
- Julius Bernstein Institute of Physiology, Medical Faculty, University of Halle–Wittenberg, 06112 Halle (Saale), Germany
| | - Stefan Hüttelmaier
- Institute of Molecular Medicine, Medical Faculty, University of Halle–Wittenberg, 06120 Halle (Saale), Germany
| | - Marcel Köhn
- Junior Group ‘Non-coding RNAs and RBPs in Human Diseases’, Medical Faculty, University of Halle–Wittenberg, 06120 Halle (Saale), Germany
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2
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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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3
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Poore CP, Yang J, Wei S, Fhu CK, Bichler Z, Wang J, Soong TW, Liao P. Enhanced isradipine sensitivity in vascular smooth muscle cells due to hypoxia-induced Ca v1.2 splicing and RbFox1/Fox2 downregulation. FEBS J 2024. [PMID: 38794806 DOI: 10.1111/febs.17159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/15/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024]
Abstract
Calcium influx via the L-type voltage-gated Cav1.2 calcium channel in smooth muscle cells regulates vascular contraction. Calcium channel blockers (CCBs) are widely used to treat hypertension by inhibiting Cav1.2 channels. Using the vascular smooth muscle cell line, A7r5 and primary culture of cerebral vascular smooth muscle cells, we found that the expression and function of Cav1.2 channels are downregulated during hypoxia. Furthermore, hypoxia induces structural changes in Cav1.2 channels via alternative splicing. The expression of exon 9* is upregulated, whereas exon 33 is downregulated. Such structural alterations of Cav1.2 channels are caused by the decreased expression of RNA-binding proteins RNA-binding protein fox-1 homolog 1 and 2 (RbFox1 and RbFox2). Overexpression of RbFox1 and RbFox2 prevents hypoxia-induced exon 9* inclusion and exon 33 exclusion. Importantly, such structural alterations of the Cav1.2 channel partly contribute to the enhanced sensitivity of Cav1.2 to isradipine (a CCB) under hypoxia. Overexpression of RbFox1 and RbFox2 successfully reduces isradipine sensitivity in hypoxic smooth muscle cells. Our results suggest a new strategy to manage ischemic diseases such as stroke and myocardial infarction.
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Affiliation(s)
| | - Jialei Yang
- School of Public Health, Guangxi Medical University, Nanning, China
| | - Shunhui Wei
- Calcium Signaling Laboratory, National Neuroscience Institute, Singapore City, Singapore
| | - Chee Kong Fhu
- Calcium Signaling Laboratory, National Neuroscience Institute, Singapore City, Singapore
| | - Zoë Bichler
- Neurobehavioural Phenotyping Core, Center for Biometric Analysis, The Jackson Laboratory, Bar Harbor, ME, USA
| | - Juejin Wang
- Department of Physiology, Nanjing Medical University, Nanjing, China
| | - Tuck Wah Soong
- Department of Physiology, National University of Singapore, Singapore, Singapore
| | - Ping Liao
- Calcium Signaling Laboratory, National Neuroscience Institute, Singapore City, Singapore
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4
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Acharya P, Parkins S, Tranter M. RNA binding proteins as mediators of pathological cardiac remodeling. Front Cell Dev Biol 2024; 12:1368097. [PMID: 38818408 PMCID: PMC11137256 DOI: 10.3389/fcell.2024.1368097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 05/01/2024] [Indexed: 06/01/2024] Open
Abstract
RNA binding proteins (RBPs) play a central in the post-transcriptional regulation of gene expression, which can account for up to 50% of all variations in protein expression within a cell. Following their binding to target RNAs, RBPs most typically confer changes in gene expression through modulation of alternative spicing, RNA stabilization/degradation, or ribosome loading/translation rate. All of these post-transcriptional regulatory processes have been shown to play a functional role in pathological cardiac remodeling, and a growing body of evidence is beginning to identify the mechanistic contribution of individual RBPs and their cardiac RNA targets. This review highlights the mechanisms of RBP-dependent post-transcriptional gene regulation in cardiomyocytes and fibroblasts and our current understanding of how RNA binding proteins functionally contribute to pathological cardiac remodeling.
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Affiliation(s)
- Pooja Acharya
- Department of Molecular Medicine and Therapeutics, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Sharon Parkins
- Department of Molecular Medicine and Therapeutics, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Department of Internal Medicine, Division of Cardiovascular Health and Disease, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Michael Tranter
- Department of Molecular Medicine and Therapeutics, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, United States
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5
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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] [Grants] [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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6
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Kolpakov S, Yashkin A, Ukraintseva S, Yashin A, Akushevich I. Genome-Related Mechanisms Contributing to Differences in Alzheimer's Disease Incidence Between White and Black Older US Adults. J Racial Ethn Health Disparities 2024:10.1007/s40615-024-01907-3. [PMID: 38273182 DOI: 10.1007/s40615-024-01907-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 12/31/2023] [Accepted: 01/04/2024] [Indexed: 01/27/2024]
Abstract
In this manuscript, we leverage a modified GWAS algorithm adapted for use with multidimensional Cox models and data from the Health and Retirement Study to explore how genetic variation influences the size of the disparity in Alzheimer's disease (AD) incidence between older Black and White US adults. We identified four loci that were associated with higher AD incidence levels in older Black adults: (1) rs11077034 (hazard ratio (HR), 4.98) from the RBFOX1 gene; (2) rs7144494 (HR, 1.68) from the HISLA gene; (3) rs7660552 (HR, 3.07) from the SLC25A4 gene; and (4) rs12599485 (HR, 3.181) from the NIP30 gene. The RBFOX1, HISLA, SLC25A4, and NIP30 genes are known to be associated with AD (RBFOX1, NIP30) directly, and also influence the risk of AD risk-related morbidities such as hypertension (RBFOX1, SLC25A4), depression (SLC25A4), and certain cancers (HISLA, SLC25A4). A likely disparity-generating mechanism may lie in endocytosis and abnormal tissue growing mechanisms, depending on inherited gene mutations and the structure of proxies as well as gene-environment interactions with other risk factors such as lifestyle, education level, and access to adequate medical services.
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Affiliation(s)
- Stanislav Kolpakov
- Social Science Research Institute, Duke University, Durham, NC, 27710, USA.
| | - Arseniy Yashkin
- Social Science Research Institute, Duke University, Durham, NC, 27710, USA
| | | | - Anatoliy Yashin
- Social Science Research Institute, Duke University, Durham, NC, 27710, USA
| | - Igor Akushevich
- Social Science Research Institute, Duke University, Durham, NC, 27710, USA
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You Y, Wang W, Zhu W, Xu J. Identification of functional lncRNAs in atrial fibrillation based on RNA sequencing. BMC Cardiovasc Disord 2023; 23:539. [PMID: 37932671 PMCID: PMC10626701 DOI: 10.1186/s12872-023-03573-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 10/22/2023] [Indexed: 11/08/2023] Open
Abstract
BACKGROUND Atrial fibrillation (AF) is one of the most common arrhythmia contributing to serious conditions such as stroke and heart failure. Recent studies demonstrated that long noncoding RNAs (lncRNAs) were related to cardiovascular disease. However, the molecular mechanisms of AF are not fully clear. This study intended to discover lncRNAs that are differentially expressed in AF compared with controls and evaluate the potential functions of these lncRNAs. METHODS Ninety-seven patients (49 patients with AF and 48 patients without AF) were included in this study. Among these patients, leucocyte suspensions of 3 AF patients and 3 controls were sent for RNA-seq analysis to select differentially expressed lncRNA and mRNA. Different lncRNA expressions were validated in another samples (46 AF patients and 45 controls). Gene ontology (GO) enrichment analysis was conducted to annotate the function of selected mRNAs. Alternative splicing (AS) analysis was performed and a lncRNA-mRNA network was also constructed. The receiver operating characteristics (ROC) curve was used to evaluate diagnostic values. Logistic regression analysis was utilized to assess the risk or protective factor of AF. RESULTS A total of 223 mRNAs and 105 lncRNAs were detected in AF patients compared with controls. Total 4 lncRNAs (LINC01781, AC009509.2, AL662844.3, AL662844.4) associated with AF were picked out for validation in another samples by quantitative real-time PCR (qRT-PCR), detecting that upregulated AC009509.2 and downregulated LINC01781 in AF patients. Multivariate logistic regression analysis illustrated that left atrial diameter (OR 1.201; 95% CI 1.093-1.320; P=0.000) and AC009509.2 (OR 1.732; 95% CI 1.092-2.747; P=0.020) were related to AF respectively. ROC curve showed that AC009509.2, LINC01781 and left atrial diameter (LAD) were predictors of AF. For LINC01781, the area under the curve (AUC) was 0.654 (95% CI 0.541-0.767, P=0.0113). For AC009509.2, the AUC was 0.710 (95% CI 0.599-0.822, P=0.0005). Bioinformatic methods (GO enrichment, AS analysis and lncRNA-mRNA network construction) were performed to reveal the role of lncRNAs. CONCLUSIONS This study discussed differentially expressed lncRNA and their potential interaction with mRNA in AF. LncRNA AC009509.2 could be a new potential biomarker for AF prediction.
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Affiliation(s)
- Yangyang You
- Department of Cardiology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Wei Wang
- Department of Cardiology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Wenshu Zhu
- Department of Cardiology, Bengbu First People's Hospital, Bengbu, Anhui, 233000, China
| | - Jian Xu
- Department of Cardiology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China.
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8
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Huang J, Lee JZ, Rau CD, Pezhouman A, Yokota T, Miwa H, Feldman M, Kong TK, Yang Z, Tay WT, Pushkarsky I, Kim K, Parikh SS, Udani S, Soh BS, Gao C, Stiles L, Shirihai OS, Knollmann BC, Ardehali R, Di Carlo D, Wang Y. Regulation of Postnatal Cardiomyocyte Maturation by an RNA Splicing Regulator RBFox1. Circulation 2023; 148:1263-1266. [PMID: 37844148 PMCID: PMC10593507 DOI: 10.1161/circulationaha.122.061602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Affiliation(s)
- Jijun Huang
- Cardiovascular laboratory, Division of Molecular Medicine, Department of Anesthesiology and Perioperative Medicine
- Division of Endocrinology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles
| | - Josh Z. Lee
- Cardiovascular laboratory, Division of Molecular Medicine, Department of Anesthesiology and Perioperative Medicine
| | - Christoph D. Rau
- Cardiovascular laboratory, Division of Molecular Medicine, Department of Anesthesiology and Perioperative Medicine
- Department of Genetics and Computational Medicine, University of North Carolina, Chapel Hill, NC
| | - Arash Pezhouman
- Division of Cardiology, Department of Medicine, UCLA
- Section of Cardiology, Department of Internal Medicine, Baylor College of Medicine, Houston, Texas
| | - Tomohiro Yokota
- Cardiovascular laboratory, Division of Molecular Medicine, Department of Anesthesiology and Perioperative Medicine
- Division of Cardiology, Department of Medicine, UCLA
- Greater Los Angeles VA Healthcare System, Department of Medicine, Los Angeles, California, USA
| | - Hiromi Miwa
- Department of Bioengineering, Samueli School of Engineering, UCLA
| | | | - Tsz Kin Kong
- Cardiovascular laboratory, Division of Molecular Medicine, Department of Anesthesiology and Perioperative Medicine
| | - Ziyue Yang
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
| | - Woan Ting Tay
- Signature Research Program of Cardiovascular and Metabolic Diseases, Duke-NUS Medical School, Singapore
| | | | - Kyungsoo Kim
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN
| | - Shan S. Parikh
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN
| | - Shreya Udani
- Department of Bioengineering, Samueli School of Engineering, UCLA
| | - Boon Seng Soh
- Institute of Molecular and Cell Biology, The Agency for Science, Technology and Research (A*STAR), Singapore
| | - Chen Gao
- Cardiovascular laboratory, Division of Molecular Medicine, Department of Anesthesiology and Perioperative Medicine
- Department of Pharmacology and System Physiology, University of Cincinnati, Cincinnati, OH
| | - Linsey Stiles
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles
| | - Orian S. Shirihai
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles
| | - Bjorn C. Knollmann
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN
| | - Reza Ardehali
- Division of Cardiology, Department of Medicine, UCLA
- Section of Cardiology, Department of Internal Medicine, Baylor College of Medicine, Houston, Texas
| | - Dino Di Carlo
- Department of Bioengineering, Samueli School of Engineering, UCLA
| | - Yibin Wang
- Cardiovascular laboratory, Division of Molecular Medicine, Department of Anesthesiology and Perioperative Medicine
- Signature Research Program of Cardiovascular and Metabolic Diseases, Duke-NUS Medical School, Singapore
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9
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Boogerd CJ, Perini I, Kyriakopoulou E, Han SJ, La P, van der Swaan B, Berkhout JB, Versteeg D, Monshouwer-Kloots J, van Rooij E. Cardiomyocyte proliferation is suppressed by ARID1A-mediated YAP inhibition during cardiac maturation. Nat Commun 2023; 14:4716. [PMID: 37543677 PMCID: PMC10404286 DOI: 10.1038/s41467-023-40203-2] [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: 02/14/2022] [Accepted: 07/18/2023] [Indexed: 08/07/2023] Open
Abstract
The inability of adult human cardiomyocytes to proliferate is an obstacle to efficient cardiac regeneration after injury. Understanding the mechanisms that drive postnatal cardiomyocytes to switch to a non-regenerative state is therefore of great significance. Here we show that Arid1a, a subunit of the switching defective/sucrose non-fermenting (SWI/SNF) chromatin remodeling complex, suppresses postnatal cardiomyocyte proliferation while enhancing maturation. Genome-wide transcriptome and epigenome analyses revealed that Arid1a is required for the activation of a cardiomyocyte maturation gene program by promoting DNA access to transcription factors that drive cardiomyocyte maturation. Furthermore, we show that ARID1A directly binds and inhibits the proliferation-promoting transcriptional coactivators YAP and TAZ, indicating ARID1A sequesters YAP/TAZ from their DNA-binding partner TEAD. In ischemic heart disease, Arid1a expression is enhanced in cardiomyocytes of the border zone region. Inactivation of Arid1a after ischemic injury enhanced proliferation of border zone cardiomyocytes. Our study illuminates the pivotal role of Arid1a in cardiomyocyte maturation, and uncovers Arid1a as a crucial suppressor of cardiomyocyte proliferation.
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Affiliation(s)
- Cornelis J Boogerd
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, Netherlands.
| | - Ilaria Perini
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, Netherlands
| | - Eirini Kyriakopoulou
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, Netherlands
| | - Su Ji Han
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, Netherlands
| | - Phit La
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, Netherlands
| | - Britt van der Swaan
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, Netherlands
| | - Jari B Berkhout
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, Netherlands
| | - Danielle Versteeg
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, Netherlands
| | - Jantine Monshouwer-Kloots
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, Netherlands
| | - Eva van Rooij
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, Netherlands.
- Department of Cardiology, University Medical Center Utrecht, Utrecht, Netherlands.
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10
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Dai X, Lu X, Chekouo T. A Bayesian genomic selection approach incorporating prior feature ordering and population structures with application to coronary artery disease. Stat Methods Med Res 2023; 32:1616-1629. [PMID: 37376889 DOI: 10.1177/09622802231181231] [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: 06/29/2023]
Abstract
Coronary artery disease is one of the most common types of cardiovascular disease. Death from coronary heart disease is influenced by genetic factors in both women and men. In this article, we propose a novel Bayesian variable selection framework for the identification of important genetic variants associated with coronary artery disease disease status. Instead of treating each feature independently as in conventional Bayesian variable selection methods, we propose an innovative prior for the inclusion probabilities of genetic variants that accounts for their ordering structure. We assume that neighboring variants are more likely to be selected together as they tend to be highly correlated and have similar biological functions. Additionally, we propose to group participating subjects based on underlying population structure and fit separate regressions, so that the regression coefficients can better reflect different disease risks in different population groups. Our approach borrows strength across regression models through an innovative prior inspired by the Markov random fields. The proposed framework can improve variable selection and prediction performances as demonstrated in the simulation studies. We also apply the proposed framework to the CATHeterization GENetics data with binary Coronary artery disease disease status.
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Affiliation(s)
- Xiaotian Dai
- Department of Mathematics and Statistics, University of Calgary, Calgary, Canada
| | - Xuewen Lu
- Department of Mathematics and Statistics, University of Calgary, Calgary, Canada
| | - Thierry Chekouo
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA
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11
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Koslow M, Mondaca-Ruff D, Xu X. Transcriptome studies of inherited dilated cardiomyopathies. Mamm Genome 2023; 34:312-322. [PMID: 36749382 PMCID: PMC10426000 DOI: 10.1007/s00335-023-09978-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 01/16/2023] [Indexed: 02/08/2023]
Abstract
Dilated cardiomyopathy (DCM) is a group of heart muscle diseases that often lead to heart failure, with more than 50 causative genes have being linked to DCM. The heterogenous nature of the inherited DCMs suggest the need of precision medicine. Consistent with this emerging concept, transcriptome studies in human patients with DCM indicated distinct molecular signature for DCMs of different genetic etiology. To facilitate this line of research, we reviewed the status of transcriptome studies of inherited DCMs by focusing on three predominant DCM causative genes, TTN, LMNA, and BAG3. Besides studies in human patients, we summarized transcriptomic analysis of these inherited DCMs in a variety of model systems ranging from iPSCs to rodents and zebrafish. We concluded that the RNA-seq technology is a powerful genomic tool that has already led to the discovery of new modifying genes, signaling pathways, and related therapeutic avenues. We also pointed out that both temporal (different pathological stages) and spatial (different cell types) information need to be considered for future transcriptome studies. While an important bottle neck is the low throughput in experimentally testing differentially expressed genes, new technologies in efficient animal models such as zebrafish starts to be developed. It is anticipated that the RNA-seq technology will continue to uncover both unique and common pathological events, aiding the development of precision medicine for inherited DCMs.
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Affiliation(s)
- Matthew Koslow
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
- Department of Cardiovascular Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - David Mondaca-Ruff
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
- Department of Cardiovascular Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Xiaolei Xu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA.
- Department of Cardiovascular Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.
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12
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Mathew V, Mei A, Giwa H, Cheong A, Chander A, Zou A, Blanton RM, Kashpur O, Cui W, Slonim D, Mahmoud T, O'Tierney-Ginn P, Mager J, Draper I, Wallingford MC. hnRNPL expression dynamics in the embryo and placenta. Gene Expr Patterns 2023; 48:119319. [PMID: 37148985 PMCID: PMC10330435 DOI: 10.1016/j.gep.2023.119319] [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: 03/07/2022] [Revised: 03/13/2023] [Accepted: 04/04/2023] [Indexed: 05/08/2023]
Abstract
Heterogeneous nuclear ribonucleoprotein L (hnRNPL) is a conserved RNA binding protein (RBP) that plays an important role in the alternative splicing of gene transcripts, and thus in the generation of specific protein isoforms. Global deficiency in hnRNPL in mice results in preimplantation embryonic lethality at embryonic day (E) 3.5. To begin to understand the contribution of hnRNPL-regulated pathways in the normal development of the embryo and placenta, we determined hnRNPL expression profile and subcellular localization throughout development. Proteome and Western blot analyses were employed to determine hnRNPL abundance between E3.5 and E17.5. Histological analyses supported that the embryo and implantation site display distinct hnRNPL localization patterns. In the fully developed mouse placenta, nuclear hnRNPL was observed broadly in trophoblasts, whereas within the implantation site a discrete subset of cells showed hnRNPL outside the nucleus. In the first-trimester human placenta, hnRNPL was detected in the undifferentiated cytotrophoblasts, suggesting a role for this factor in trophoblast progenitors. Parallel in vitro studies utilizing Htr8 and Jeg3 cell lines confirmed expression of hnRNPL in cellular models of human trophoblasts. These studies [support] coordinated regulation of hnRNPL during the normal developmental program in the mammalian embryo and placenta.
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Affiliation(s)
- Vineetha Mathew
- Mother Infant Research Institute, Tufts Medical Center, 800 Washington St, Boston, MA, 02111, USA
| | - Ariel Mei
- Mother Infant Research Institute, Tufts Medical Center, 800 Washington St, Boston, MA, 02111, USA
| | - Hamida Giwa
- Mother Infant Research Institute, Tufts Medical Center, 800 Washington St, Boston, MA, 02111, USA
| | - Agnes Cheong
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, 01003, USA
| | - Ashmita Chander
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, 01003, USA
| | - Aaron Zou
- Molecular Cardiology Research Institute, Tufts Medical Center, 800 Washington St, Boston, MA, 02111, USA
| | - Robert M Blanton
- Molecular Cardiology Research Institute, Tufts Medical Center, 800 Washington St, Boston, MA, 02111, USA
| | - Olga Kashpur
- Mother Infant Research Institute, Tufts Medical Center, 800 Washington St, Boston, MA, 02111, USA
| | - Wei Cui
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, 01003, USA
| | - Donna Slonim
- Department of Computer Science, Tufts University, 177 College Avenue, Medford, MA, 02155, USA
| | - Taysir Mahmoud
- Mother Infant Research Institute, Tufts Medical Center, 800 Washington St, Boston, MA, 02111, USA
| | - Perrie O'Tierney-Ginn
- Mother Infant Research Institute, Tufts Medical Center, 800 Washington St, Boston, MA, 02111, USA
| | - Jesse Mager
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, 01003, USA
| | - Isabelle Draper
- Molecular Cardiology Research Institute, Tufts Medical Center, 800 Washington St, Boston, MA, 02111, USA.
| | - Mary C Wallingford
- Mother Infant Research Institute, Tufts Medical Center, 800 Washington St, Boston, MA, 02111, USA; Molecular Cardiology Research Institute, Tufts Medical Center, 800 Washington St, Boston, MA, 02111, USA.
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13
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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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14
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Svoboda LK, Wang K, Goodrich JM, Jones TR, Colacino JA, Peterson KE, Tellez-Rojo MM, Sartor MA, Dolinoy DC. Perinatal Lead Exposure Promotes Sex-Specific Epigenetic Programming of Disease-Relevant Pathways in Mouse Heart. TOXICS 2023; 11:85. [PMID: 36668811 PMCID: PMC9860846 DOI: 10.3390/toxics11010085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 12/21/2022] [Accepted: 12/25/2022] [Indexed: 06/17/2023]
Abstract
Environmental contaminants such as the metal lead (Pb) are associated with cardiovascular disease, but the underlying molecular mechanisms are poorly understood. In particular, little is known about how exposure to Pb during early development impacts the cardiac epigenome at any point across the life course and potential differences between sexes. In a mouse model of human-relevant perinatal exposures, we utilized RNA-seq and Enhanced Reduced Representation Bisulfite Sequencing (ERRBS) to investigate the effects of Pb exposure during gestation and lactation on gene expression and DNA methylation, respectively, in the hearts of male and female mice at weaning. For ERRBS, we identified differentially methylated CpGs (DMCs) or differentially methylated 1000 bp regions (DMRs) based on a minimum absolute change in methylation of 10% and an FDR < 0.05. For gene expression data, an FDR < 0.05 was considered significant. No individual genes met the FDR cutoff for gene expression; however, we found that Pb exposure leads to significant changes in the expression of gene pathways relevant to cardiovascular development and disease. We further found that Pb promotes sex-specific changes in DNA methylation at hundreds of gene loci (280 DMCs and 99 DMRs in males, 189 DMCs and 121 DMRs in females), and pathway analysis revealed that these CpGs and regions collectively function in embryonic development. In males, differential methylation also occurred at genes related to immune function and metabolism. We then investigated whether genes exhibiting differential methylation at weaning were also differentially methylated in hearts from a cohort of Pb-exposed mice at adulthood. We found that a single gene, Galnt2, showed differential methylation in both sexes and time points. In a human cohort investigating the influence of prenatal Pb exposure on the epigenome, we also observed an inverse association between first trimester Pb concentrations and adolescent blood leukocyte DNA methylation at a locus in GALNT2, suggesting that this gene may represent a biomarker of Pb exposure across species. Together, these data, across two time points in mice and in a human birth cohort study, collectively demonstrate that Pb exposure promotes sex-specific programming of the cardiac epigenome, and provide potential mechanistic insight into how Pb causes cardiovascular disease.
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Affiliation(s)
- Laurie K. Svoboda
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Kai Wang
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Jaclyn M. Goodrich
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Tamara R. Jones
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Justin A. Colacino
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Karen E. Peterson
- Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Martha M. Tellez-Rojo
- Center for Research on Nutrition and Health, National Institute of Public Health, Cuernavaca 62100, Mexico
| | - Maureen A. Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Dana C. Dolinoy
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
- Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
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15
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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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16
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Wang S, Ma J, Qiu H, Liu S, Zhang S, Liu H, Zhang P, Ge RL, Li G, Cui S. Plasma exosomal microRNA expression profiles in patients with high-altitude polycythemia. Blood Cells Mol Dis 2023; 98:102707. [DOI: 10.1016/j.bcmd.2022.102707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 10/19/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022]
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17
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He J, Lin H, Ding Y, Liu X, Xu K, Chen X, Shen W, Zhou S, Wang M, Xia J, He N. Genome-wide associated variants of subclinical atherosclerosis among young people with HIV and gene-environment interactions. J Transl Med 2022; 20:609. [PMID: 36539828 PMCID: PMC9764595 DOI: 10.1186/s12967-022-03817-6] [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: 10/20/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) have identified some variants associated with subclinical atherosclerosis (SCA) in general population but lacking sufficient validation. Besides traditional risk factors, whether and how would genetic variants associate with SCA among people with HIV (PWH) remains to be elucidated. METHOD A large original GWAS and gene-environment interaction analysis of SCA were conducted among Chinese PWH (n = 2850) and age/sex-matched HIV-negative controls (n = 5410). Subgroup analyses by age and functional annotations of variants were also performed. RESULTS Different from HIV-negative counterparts, host genome had a greater impact on young PWH rather than the elders: one genome-wide significant variant (rs77741796, P = 2.20 × 10-9) and eight suggestively significant variants (P < 1 × 10-6) were identified to be specifically associated with SCA among PWH younger than 45 years. Seven genomic loci and 15 genes were mapped to play a potential role on SCA among young PWH, which were enriched in the biological processes of atrial cardiac muscle cell membrane repolarization and molecular function of protein kinase A subunit binding. Furthermore, genome-wide interaction analyses revealed significant HIV-gene interactions overall as well as gene-environment interactions with alcohol consumption, tobacco use and obesity among PWH. The identified gene-environment interaction on SCA among PWH might be useful for discovering high-risk individuals for the prevention of SCA, particularly among those with tobacco use and alcohol consumption. CONCLUSION The present study provides new clues for the genetic contribution of SCA among young PWH and is the starting point of precision intervention targeting HIV-related atherosclerosis.
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Affiliation(s)
- Jiayu He
- grid.8547.e0000 0001 0125 2443Department of Epidemiology, School of Public Health, and Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China ,grid.8547.e0000 0001 0125 2443Yi-Wu Research Institute, Fudan University, Shanghai, China ,grid.8547.e0000 0001 0125 2443Shanghai Institute of Infectious Diseases and Biosecurity, Fudan University, Shanghai, China
| | - Haijiang Lin
- grid.8547.e0000 0001 0125 2443Department of Epidemiology, School of Public Health, and Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China ,Taizhou City Center for Disease Control and Prevention, Taizhou, Zhejiang China
| | - Yingying Ding
- grid.8547.e0000 0001 0125 2443Department of Epidemiology, School of Public Health, and Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China ,grid.8547.e0000 0001 0125 2443Yi-Wu Research Institute, Fudan University, Shanghai, China
| | - Xing Liu
- grid.8547.e0000 0001 0125 2443Department of Epidemiology, School of Public Health, and Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China ,grid.8547.e0000 0001 0125 2443Yi-Wu Research Institute, Fudan University, Shanghai, China
| | - Kelin Xu
- grid.8547.e0000 0001 0125 2443Department of Biostatistics, School of Public Health, Fudan University, Shanghai, China
| | - Xiaoxiao Chen
- grid.8547.e0000 0001 0125 2443Department of Epidemiology, School of Public Health, and Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China ,Taizhou City Center for Disease Control and Prevention, Taizhou, Zhejiang China
| | - Weiwei Shen
- Taizhou City Center for Disease Control and Prevention, Taizhou, Zhejiang China
| | - Sujuan Zhou
- grid.8547.e0000 0001 0125 2443Department of Epidemiology, School of Public Health, and Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China ,grid.8547.e0000 0001 0125 2443Yi-Wu Research Institute, Fudan University, Shanghai, China ,grid.8547.e0000 0001 0125 2443Shanghai Institute of Infectious Diseases and Biosecurity, Fudan University, Shanghai, China
| | - Miaochen Wang
- grid.8547.e0000 0001 0125 2443Department of Epidemiology, School of Public Health, and Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China ,grid.8547.e0000 0001 0125 2443Yi-Wu Research Institute, Fudan University, Shanghai, China
| | - Jingjing Xia
- grid.8547.e0000 0001 0125 2443Department of Epidemiology, School of Public Health, and Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China ,grid.8547.e0000 0001 0125 2443Yi-Wu Research Institute, Fudan University, Shanghai, China
| | - Na He
- grid.8547.e0000 0001 0125 2443Department of Epidemiology, School of Public Health, and Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China ,grid.8547.e0000 0001 0125 2443Yi-Wu Research Institute, Fudan University, Shanghai, China ,grid.8547.e0000 0001 0125 2443Shanghai Institute of Infectious Diseases and Biosecurity, Fudan University, Shanghai, China
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18
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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: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/27/2022] [Accepted: 11/01/2022] [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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19
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Holman AR, Chi NC. Fishing Out the Role of RBPMS2 in Cardiac Splicing. Circ Res 2022; 131:1001-1003. [PMID: 36454855 DOI: 10.1161/circresaha.122.321922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Affiliation(s)
- Alyssa R Holman
- Department of Medicine (A.R.H., N.C.C.).,Biomedical Sciences Graduate Program (A.R.H.), University of California, San Diego, La Jolla, CA
| | - Neil C Chi
- Department of Medicine (A.R.H., N.C.C.).,Institute of Genomic Medicine, School of Medicine (N.C.C.), University of California, San Diego, La Jolla, CA
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20
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Gao C, Gong J, Cao N, Wang Y, Steinberg SF. Lipid-independent activation of a muscle-specific PKCα splicing variant. Am J Physiol Heart Circ Physiol 2022; 323:H825-H832. [PMID: 36112502 PMCID: PMC9550568 DOI: 10.1152/ajpheart.00304.2022] [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: 06/21/2022] [Revised: 08/16/2022] [Accepted: 08/28/2022] [Indexed: 11/22/2022]
Abstract
Protein kinase C-α (PKCα) plays a major role in a diverse range of cellular processes. Studies to date have defined the regulatory controls and function of PKCα entirely based upon the previously annotated ubiquitously expressed prototypical isoform. From RNA-seq-based transcriptome analysis in murine heart, we identified a previously unannotated PKCα variant produced by alternative RNA splicing. This PKCα transcript variant, which we named PKCα-novel exon (PKCα-NE), contains an extra exon between exon 16 and exon 17, and is specifically detected in adult mouse cardiac and skeletal muscle, but not other tissues; it is also detected in human hearts. This transcript variant yields a PKCα isoform with additional 16 amino acids inserted in its COOH-terminal variable region. Although the canonical PKCα enzyme is a lipid-dependent kinase, in vitro kinase assays show that PKCα-NE displays a high level of basal lipid-independent catalytic activity. Our unbiased proteomic analysis identified a specific interaction between PKCα-NE and eukaryotic elongation factor-1α (eEF1A1). Studies in cardiomyocytes link PKCα-NE expression to an increase in eEF1A1 phosphorylation and elevated protein synthesis. In summary, we have identified a previously uncharacterized muscle-specific PKCα splicing variant, PKCα-NE, with distinct biochemical properties that plays a unique role in the control of the protein synthesis machinery in cardiomyocytes.NEW & NOTEWORTHY PKCα is an important signaling molecule extensively studied in many cellular processes. However, no isoforms have been reported for PKCα except one prototypic isoform. Alternative mRNA splicing of Prkca gene was detected for the first time in rodent and human cardiac tissue, which can produce a previously unknown PKCα-novel exon (NE) isoform. The biochemistry and molecular effects of PKCα-NE are markedly different from PKCα wild type, suggesting potential functional diversity of PKCα signaling in muscle.
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Affiliation(s)
- Chen Gao
- Department of Pharmacology and System Physiology, University of Cincinnati, Cincinnati, Ohio
| | - Jianli Gong
- The Department of Pharmacology, Columbia University College of Physicians and Surgeons, New York, New York
| | - Nancy Cao
- University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Yibin Wang
- Signature Research Program in Cardiovascular and Metabolic Diseases, Duke-NUS Medical School, Singapore
| | - Susan F Steinberg
- The Department of Pharmacology, Columbia University College of Physicians and Surgeons, New York, New York
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21
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Sikorski V, Vento A, Kankuri E. Emerging roles of the RNA modifications N6-methyladenosine and adenosine-to-inosine in cardiovascular diseases. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 29:426-461. [PMID: 35991314 PMCID: PMC9366019 DOI: 10.1016/j.omtn.2022.07.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Cardiovascular diseases lead the mortality and morbidity disease metrics worldwide. A multitude of chemical base modifications in ribonucleic acids (RNAs) have been linked with key events of cardiovascular diseases and metabolic disorders. Named either RNA epigenetics or epitranscriptomics, the post-transcriptional RNA modifications, their regulatory pathways, components, and downstream effects substantially contribute to the ways our genetic code is interpreted. Here we review the accumulated discoveries to date regarding the roles of the two most common epitranscriptomic modifications, N6-methyl-adenosine (m6A) and adenosine-to-inosine (A-to-I) editing, in cardiovascular disease.
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Affiliation(s)
- Vilbert Sikorski
- Department of Pharmacology, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
| | - Antti Vento
- Heart and Lung Center, Helsinki University Hospital, 00029 Helsinki, Finland
| | - Esko Kankuri
- Department of Pharmacology, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
- Corresponding author Esko Kankuri, M.D. Ph.D., Faculty of Medicine, Department of Pharmacology, PO Box 63 (Haartmaninkatu 8), FIN-00014 University of Helsinki, 00014 Helsinki, Finland.
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22
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Xu X, Zou R, Liu X, Su Q. Alternative splicing signatures of congenital heart disease and induced pluripotent stem cell-derived cardiomyocytes from congenital heart disease patients. Medicine (Baltimore) 2022; 101:e30123. [PMID: 35984151 PMCID: PMC9388029 DOI: 10.1097/md.0000000000030123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Congenital heart disease (CHD) is the most serious congenital defect in newborns with higher mortality. Alternative splicing (AS) plays an essential role in numerous heart diseases. However, our understanding of the link between mRNA splicing and CHD in humans is limited. Here, we try to investigate the genome-wide AS events in CHD using bioinformatics methods. We collected available RNA-seq datasets of CHD-induced pluripotent stem cell-cardiomyocytes (iPSC-CMs) (including single ventricle disease [SVD] and tetralogy of Fallot [TOF]) and non-CHD from the Gene Expression Omnibus database. Then, we unprecedentedly performed AS profiles in CHD-iPSC-CMs and non-CHD-iPSC-CMs. The rMAPS was used to generate RNA-maps for the analysis of RNA-binding proteins' (RBPs) binding sites. We used StringTie to identify and quantify the transcripts from aligned RNA-Seq reads. A quantification matrix was generated with respect to different groups by extracting the transcripts per million values from StringTie outputs. Then, this matrix was used for correlation analysis between the expression level of RBP and AS level. Finally, we validated our AS results using RNA-seq data from CHD and non-CHD patient tissue samples. We identified CHD-related AS events using CHD-iPSC-CMs and CHD samples from patients. The results showed that functional enrichment of abnormal AS in SVD and TOF was transcription factor-related. Using rMAPS, RNA-binding proteins which regulated these AS were also determined, and RBP-AS regulatory network was constructed. Overall, we identified abnormal AS in CHD-iPSC-CMs and CHD samples from patients. We predicted AS regulators in SVD and TOF, respectively. At last, we concluded that AS played a key role in the pathogenesis of CHD.
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Affiliation(s)
- Xiang Xu
- Department of Cardiology, The Second Affiliated Hospital of Kunming Medical University, Kunming City, China
| | - Renchao Zou
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Kunming Medical University, Kunming City, China
| | - Xiaoyong Liu
- Department of Cardiology, The Second Affiliated Hospital of Kunming Medical University, Kunming City, China
| | - Qianqian Su
- Department of Laboratory Animal Science, Kunming Medical University, Kunming City, China
- *Correspondence: Qianqian Su, Department of Laboratory Animal Science, Kunming Medical University, Kunming City, Yunnan Province, China (e-mail: )
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23
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Diminished Rbfox1 increases vascular constriction by dynamically regulating alternative splicing of CaV1.2 calcium channel in hypertension. Clin Sci (Lond) 2022; 136:803-817. [PMID: 35543237 DOI: 10.1042/cs20220226] [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: 04/05/2022] [Revised: 05/08/2022] [Accepted: 05/10/2022] [Indexed: 11/17/2022]
Abstract
Calcium influx from depolarized CaV1.2 calcium channels triggers the contraction of vascular smooth muscle cells (VSMCs), which is important for maintaining vascular myogenic tone and blood pressure. The function of CaV1.2 channel can be subtly modulated by alternative splicing (AS), and its aberrant splicing involves in the pathogenesis of multiple cardiovascular diseases. The RNA binding protein Rbfox1 is reported to regulate the AS events of CaV1.2 channel in the neuronal development, but its potential roles in vascular CaV1.2 channels and vasoconstriction remain undefined. Here, we detect Rbfox1 is expressed in rat vascular smooth muscles. Moreover, the protein level of Rbfox1 is dramatically decreased in the hypertensive small arteries from spontaneously hypertensive rats in comparison to normotensive ones from Wistar-Kyoto rats. In VSMCs, Rbfox1 could dynamically regulate the AS of CaV1.2 exons 9* and 33. By whole-cell patch clamp, we identify knockdown of Rbfox1 induces the hyperpolarization of CaV1.2 current-voltage relationship curve in VSMCs. Furthermore, siRNA-mediated knockdown of Rbfox1 increases the K+-induced constriction of rat mesenteric arteries. In summary, our results indicate Rbfox1 modulates vascular constriction by dynamically regulating CaV1.2 alternative exons 9* and 33. Therefore, our work elucidates the underlying mechanisms for CaV1.2 channels regulation and provides a potential therapeutic target for hypertension.
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24
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Malakootian M, Bagheri Moghaddam M, Kalayinia S, Farrashi M, Maleki M, Sadeghipour P, Amin A. Dilated cardiomyopathy caused by a pathogenic nucleotide variant in RBM20 in an Iranian family. BMC Med Genomics 2022; 15:106. [PMID: 35527250 PMCID: PMC9079971 DOI: 10.1186/s12920-022-01262-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 05/05/2022] [Indexed: 12/22/2022] Open
Abstract
Abstract
Introduction
Dilated cardiomyopathy (DCM) is characterized by the dilation and impaired contraction of 1 or both ventricles and can be caused by a variety of disorders. Up to 50% of idiopathic DCM cases have heritable familial diseases, and the clinical screening of family members is recommended. Identifying a genetic cause that can explain the DCM risk in the family can help with better screening planning and clinical decision-making. Whole-exome sequencing (WES) has aided significantly in the detection of causative genes in many genetically heterogeneous diseases. In the present study, we applied WES to identify the causative genetic variant in a family with heritable DCM.
Methods
WES was applied to identify genetic variants on a 26-year-old man as the proband of a family with DCM. Subsequently, Sanger sequencing was performed to confirm the variant in the patient and all the available affected and unaffected family members. The pathogenicity of the variant was evaluated through co-segregation analysis in the family and employment of in silico predictive software.
Results
WES demonstrated the missense pathogenic heterozygous nucleotide variant, c.1907G > A, (p.Arg636His, rs267607004, NM_0011343), in exon 9 of the RBM20 gene in the proband. The variant was co-segregated in all the affected family members in a heterozygous form and the unaffected family members. The in silico analysis confirmed the variant as pathogenic.
Conclusion
Pathogenic RBM20 nucleotide variants are associated with arrhythmogenic DCM. We believe that our report is the first to show an RBM20 variant in Iranian descent associated with DCM.
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25
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Gan P, Wang Z, Morales MG, Zhang Y, Bassel-Duby R, Liu N, Olson EN. RBPMS is an RNA-binding protein that mediates cardiomyocyte binucleation and cardiovascular development. Dev Cell 2022; 57:959-973.e7. [PMID: 35472321 PMCID: PMC9116735 DOI: 10.1016/j.devcel.2022.03.017] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 03/04/2022] [Accepted: 03/25/2022] [Indexed: 12/13/2022]
Abstract
Noncompaction cardiomyopathy is a common congenital cardiac disorder associated with abnormal ventricular cardiomyocyte trabeculation and impaired pump function. The genetic basis and underlying mechanisms of this disorder remain elusive. We show that the genetic deletion of RNA-binding protein with multiple splicing (Rbpms), an uncharacterized RNA-binding factor, causes perinatal lethality in mice due to congenital cardiovascular defects. The loss of Rbpms causes premature onset of cardiomyocyte binucleation and cell cycle arrest during development. Human iPSC-derived cardiomyocytes with RBPMS gene deletion have a similar blockade to cytokinesis. Sequencing analysis revealed that RBPMS plays a role in RNA splicing and influences RNAs involved in cytoskeletal signaling pathways. We found that RBPMS mediates the isoform switching of the heart-enriched LIM domain protein Pdlim5. The loss of Rbpms leads to an abnormal accumulation of Pdlim5-short isoforms, disrupting cardiomyocyte cytokinesis. Our findings connect premature cardiomyocyte binucleation to noncompaction cardiomyopathy and highlight the role of RBPMS in this process.
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Affiliation(s)
- Peiheng Gan
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zhaoning Wang
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA 92093, USA
| | - Maria Gabriela Morales
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yu Zhang
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Rhonda Bassel-Duby
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ning Liu
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Eric N Olson
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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26
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In heart failure reactivation of RNA-binding proteins is associated with the expression of 1,523 fetal-specific isoforms. PLoS Comput Biol 2022; 18:e1009918. [PMID: 35226669 PMCID: PMC8912908 DOI: 10.1371/journal.pcbi.1009918] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 03/10/2022] [Accepted: 02/10/2022] [Indexed: 01/03/2023] Open
Abstract
Reactivation of fetal-specific genes and isoforms occurs during heart failure. However, the underlying molecular mechanisms and the extent to which the fetal program switch occurs remains unclear. Limitations hindering transcriptome-wide analyses of alternative splicing differences (i.e. isoform switching) in cardiovascular system (CVS) tissues between fetal, healthy adult and heart failure have included both cellular heterogeneity across bulk RNA-seq samples and limited availability of fetal tissue for research. To overcome these limitations, we have deconvoluted the cellular compositions of 996 RNA-seq samples representing heart failure, healthy adult (heart and arteria), and fetal-like (iPSC-derived cardiovascular progenitor cells) CVS tissues. Comparison of the expression profiles revealed that reactivation of fetal-specific RNA-binding proteins (RBPs), and the accompanied re-expression of 1,523 fetal-specific isoforms, contribute to the transcriptome differences between heart failure and healthy adult heart. Of note, isoforms for 20 different RBPs were among those that reverted in heart failure to the fetal-like expression pattern. We determined that, compared with adult-specific isoforms, fetal-specific isoforms encode proteins that tend to have more functions, are more likely to harbor RBP binding sites, have canonical sequences at their splice sites, and contain typical upstream polypyrimidine tracts. Our study suggests that compared with healthy adult, fetal cardiac tissue requires stricter transcriptional regulation, and that during heart failure reversion to this stricter transcriptional regulation occurs. Furthermore, we provide a resource of cardiac developmental stage-specific and heart failure-associated genes and isoforms, which are largely unexplored and can be exploited to investigate novel therapeutics for heart failure. Heart failure is a chronic condition in which the heart does not pump enough blood. It has been shown that in heart failure, the adult heart reverts to a fetal-like metabolic state and oxygen consumption. Additionally, genes and isoforms that are expressed in the heart only during fetal development (i.e. not in the healthy adult heart) are turned on in heart failure. However, the underlying molecular mechanisms and the extent to which the switch to a fetal gene program occurs remains unclear. In this study, we initially characterized the differences between the fetal and adult heart transcriptomes (entire set of expressed genes and isoforms). We found that RNA binding proteins (RBPs), a family of genes that regulate multiple aspects of a transcript’s maturation, including transcription, splicing and post-transcriptional modifications, play a central role in the differences between fetal and adult heart tissues. We observed that many RBPs that are only expressed in the heart during fetal development become reactivated in heart failure, resulting in the expression of 1,523 fetal-specific isoforms. These findings suggest that reactivation of fetal-specific RBPs in heart failure drives a transcriptome-wide switch to expression of fetal-specific isoforms; and hence that RBPs could potentially serve as novel therapeutic targets.
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27
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Yu M, Tcheandjieu C, Georges A, Xiao K, Tejeda H, Dina C, Le Tourneau T, Fiterau M, Judy R, Tsao NL, Amgalan D, Munger CJ, Engreitz JM, Damrauer SM, Bouatia-Naji N, Priest JR. Computational estimates of annular diameter reveal genetic determinants of mitral valve function and disease. JCI Insight 2022; 7:146580. [PMID: 35132965 PMCID: PMC8855800 DOI: 10.1172/jci.insight.146580] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 12/21/2021] [Indexed: 11/17/2022] Open
Abstract
The fibrous annulus of the mitral valve plays an important role in valvular function and cardiac physiology, while normal variation in the size of cardiovascular anatomy may share a genetic link with common and rare disease. We derived automated estimates of mitral valve annular diameter in the 4-chamber view from 32,220 MRI images from the UK Biobank at ventricular systole and diastole as the basis for GWAS. Mitral annular dimensions corresponded to previously described anatomical norms, and GWAS inclusive of 4 population strata identified 10 loci, including possibly novel loci (GOSR2, ERBB4, MCTP2, MCPH1) and genes related to cardiac contractility (BAG3, TTN, RBFOX1). ATAC-Seq of primary mitral valve tissue localized multiple variants to regions of open chromatin in biologically relevant cell types and rs17608766 to an algorithmically predicted enhancer element in GOSR2. We observed strong genetic correlation with measures of contractility and mitral valve disease and clinical correlations with heart failure, cerebrovascular disease, and ventricular arrhythmias. Polygenic scoring of mitral valve annular diameter in systole was predictive of risk mitral valve prolapse across 4 cohorts. In summary, genetic and clinical studies of mitral valve annular diameter revealed genetic determinants of mitral valve biology, while highlighting clinical associations. Polygenic determinants of mitral valve annular diameter may represent an independent risk factor for mitral prolapse. Overall, computationally estimated phenotypes derived at scale from medical imaging represent an important substrate for genetic discovery and clinical risk prediction.
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Affiliation(s)
| | - Catherine Tcheandjieu
- Department of Pediatrics and.,Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Adrien Georges
- Paris Cardiovascular Research Center, INSERM, University of Paris, Paris, France
| | - Ke Xiao
- College of Information & Computer Sciences at University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | | | - Christian Dina
- University of Nantes, INSERM, CNRS, CHU Nantes, The Thorax Institute, Nantes, France
| | - Thierry Le Tourneau
- University of Nantes, INSERM, CNRS, CHU Nantes, The Thorax Institute, Nantes, France
| | - Madalina Fiterau
- College of Information & Computer Sciences at University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Renae Judy
- Department of Surgery, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Noah L Tsao
- Department of Surgery, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Dulguun Amgalan
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA.,Basic Science & Engineering Initiative & Betty Irene Moore Children's Heart Center, Lucile Packard Children's Hospital, Stanford, California, USA
| | - Chad J Munger
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA.,Basic Science & Engineering Initiative & Betty Irene Moore Children's Heart Center, Lucile Packard Children's Hospital, Stanford, California, USA
| | - Jesse M Engreitz
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA.,Basic Science & Engineering Initiative & Betty Irene Moore Children's Heart Center, Lucile Packard Children's Hospital, Stanford, California, USA
| | - Scott M Damrauer
- Department of Surgery, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Nabila Bouatia-Naji
- Paris Cardiovascular Research Center, INSERM, University of Paris, Paris, France
| | - James R Priest
- Department of Pediatrics and.,Chan-Zuckerberg Biohub, San Francisco, California, USA
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28
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Cornwell JD, McDermott JC. MEF2 in cardiac hypertrophy in response to hypertension. Trends Cardiovasc Med 2022; 33:204-212. [PMID: 35026393 DOI: 10.1016/j.tcm.2022.01.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/05/2022] [Accepted: 01/06/2022] [Indexed: 12/14/2022]
Abstract
Hypertension is a globally prevalent pathological condition and an underlying risk factor for the development of cardiac hypertrophy leading to heart failure. Myocyte enhancer factor 2 (Mef2) has been identified as one of the primary effectors of morphological changes in the hypertensive heart, as part of a complex network of molecular signaling controlling cardiac gene expression. Experimental chronic pressure-overload models that mimic hypertension in the mammalian heart lead to the activation of various pathological mechanisms that result in structural changes leading to debilitating cardiac hypertrophy and ultimately heart failure. The purpose here is to survey the literature implicating Mef2 in hypertension induced cardiac hypertrophy, towards illuminating points of interest for understanding and potentially treating heart failure.
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Affiliation(s)
- James D Cornwell
- Department of Biology, York University, Toronto, ON M3J 1P3, Canada
| | - John C McDermott
- Department of Biology, York University, Toronto, ON M3J 1P3, Canada; Muscle Health Research Centre (MHRC), York University, Toronto, ON M3J 1P3, Canada; Centre for Research in Biomolecular Interactions (CRBI), York University, Toronto, ON M3J 1P3, Canada.
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29
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Nikonova E, Mukherjee A, Kamble K, Barz C, Nongthomba U, Spletter ML. Rbfox1 is required for myofibril development and maintaining fiber type-specific isoform expression in Drosophila muscles. Life Sci Alliance 2022; 5:5/4/e202101342. [PMID: 34996845 PMCID: PMC8742874 DOI: 10.26508/lsa.202101342] [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: 12/16/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 11/24/2022] Open
Abstract
Protein isoform transitions confer muscle fibers with distinct properties and are regulated by differential transcription and alternative splicing. RNA-binding Fox protein 1 (Rbfox1) can affect both transcript levels and splicing, and is known to contribute to normal muscle development and physiology in vertebrates, although the detailed mechanisms remain obscure. In this study, we report that Rbfox1 contributes to the generation of adult muscle diversity in Drosophila Rbfox1 is differentially expressed among muscle fiber types, and RNAi knockdown causes a hypercontraction phenotype that leads to behavioral and eclosion defects. Misregulation of fiber type-specific gene and splice isoform expression, notably loss of an indirect flight muscle-specific isoform of Troponin-I that is critical for regulating myosin activity, leads to structural defects. We further show that Rbfox1 directly binds the 3'-UTR of target transcripts, regulates the expression level of myogenic transcription factors myocyte enhancer factor 2 and Salm, and both modulates expression of and genetically interacts with the CELF family RNA-binding protein Bruno1 (Bru1). Rbfox1 and Bru1 co-regulate fiber type-specific alternative splicing of structural genes, indicating that regulatory interactions between FOX and CELF family RNA-binding proteins are conserved in fly muscle. Rbfox1 thus affects muscle development by regulating fiber type-specific splicing and expression dynamics of identity genes and structural proteins.
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Affiliation(s)
- Elena Nikonova
- Department of Physiological Chemistry, Biomedical Center, Ludwig-Maximilians-Universität München, Martinsried-Planegg, Germany
| | - Amartya Mukherjee
- Department of Molecular Reproduction, Development and Genetics (MRDG), Indian Institute of Science, Bangalore, India
| | - Ketaki Kamble
- Department of Molecular Reproduction, Development and Genetics (MRDG), Indian Institute of Science, Bangalore, India
| | - Christiane Barz
- Muscle Dynamics Group, Max Planck Institute of Biochemistry, Martinsried-Planegg, Germany
| | - Upendra Nongthomba
- Department of Molecular Reproduction, Development and Genetics (MRDG), Indian Institute of Science, Bangalore, India
| | - Maria L Spletter
- Department of Physiological Chemistry, Biomedical Center, Ludwig-Maximilians-Universität München, Martinsried-Planegg, Germany
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30
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Meyer BJ. Mechanisms of sex determination and X-chromosome dosage compensation. Genetics 2022; 220:6498458. [PMID: 35100381 PMCID: PMC8825453 DOI: 10.1093/genetics/iyab197] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/25/2021] [Indexed: 12/03/2022] Open
Abstract
Abnormalities in chromosome number have the potential to disrupt the balance of gene expression and thereby decrease organismal fitness and viability. Such abnormalities occur in most solid tumors and also cause severe developmental defects and spontaneous abortions. In contrast to the imbalances in chromosome dose that cause pathologies, the difference in X-chromosome dose used to determine sexual fate across diverse species is well tolerated. Dosage compensation mechanisms have evolved in such species to balance X-chromosome gene expression between the sexes, allowing them to tolerate the difference in X-chromosome dose. This review analyzes the chromosome counting mechanism that tallies X-chromosome number to determine sex (XO male and XX hermaphrodite) in the nematode Caenorhabditis elegans and the associated dosage compensation mechanism that balances X-chromosome gene expression between the sexes. Dissecting the molecular mechanisms underlying X-chromosome counting has revealed how small quantitative differences in intracellular signals can be translated into dramatically different fates. Dissecting the process of X-chromosome dosage compensation has revealed the interplay between chromatin modification and chromosome structure in regulating gene expression over vast chromosomal territories.
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Affiliation(s)
- Barbara J Meyer
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720-3204, USA
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31
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Carnesecchi J, Boumpas P, van Nierop Y Sanchez P, Domsch K, Pinto HD, Borges Pinto P, Lohmann I. The Hox transcription factor Ultrabithorax binds RNA and regulates co-transcriptional splicing through an interplay with RNA polymerase II. Nucleic Acids Res 2021; 50:763-783. [PMID: 34931250 PMCID: PMC8789087 DOI: 10.1093/nar/gkab1250] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 12/01/2021] [Accepted: 12/07/2021] [Indexed: 11/13/2022] Open
Abstract
Transcription factors (TFs) play a pivotal role in cell fate decision by coordinating gene expression programs. Although most TFs act at the DNA layer, few TFs bind RNA and modulate splicing. Yet, the mechanistic cues underlying TFs activity in splicing remain elusive. Focusing on the Drosophila Hox TF Ultrabithorax (Ubx), our work shed light on a novel layer of Ubx function at the RNA level. Transcriptome and genome-wide binding profiles in embryonic mesoderm and Drosophila cells indicate that Ubx regulates mRNA expression and splicing to promote distinct outcomes in defined cellular contexts. Our results demonstrate a new RNA-binding ability of Ubx. We find that the N51 amino acid of the DNA-binding Homeodomain is non-essential for RNA interaction in vitro, but is required for RNA interaction in vivo and Ubx splicing activity. Moreover, mutation of the N51 amino acid weakens the interaction between Ubx and active RNA Polymerase II (Pol II). Our results reveal that Ubx regulates elongation-coupled splicing, which could be coordinated by a dynamic interplay with active Pol II on chromatin. Overall, our work uncovered a novel role of the Hox TFs at the mRNA regulatory layer. This could be an essential function for other classes of TFs to control cell diversity.
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Affiliation(s)
- Julie Carnesecchi
- Heidelberg University, Centre for Organismal Studies (COS) Heidelberg, Department of Developmental Biology, Heidelberg, Germany.,Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Panagiotis Boumpas
- Heidelberg University, Centre for Organismal Studies (COS) Heidelberg, Department of Developmental Biology, Heidelberg, Germany
| | - Patrick van Nierop Y Sanchez
- Heidelberg University, Centre for Organismal Studies (COS) Heidelberg, Department of Developmental Biology, Heidelberg, Germany
| | - Katrin Domsch
- Heidelberg University, Centre for Organismal Studies (COS) Heidelberg, Department of Developmental Biology, Heidelberg, Germany.,Friedrich-Alexander-University Erlangen-Nürnberg, Department Biology, Division of Developmental Biology, Erlangen, Germany
| | - Hugo Daniel Pinto
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Pedro Borges Pinto
- Heidelberg University, Centre for Organismal Studies (COS) Heidelberg, Department of Developmental Biology, Heidelberg, Germany.,Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Ingrid Lohmann
- Heidelberg University, Centre for Organismal Studies (COS) Heidelberg, Department of Developmental Biology, Heidelberg, Germany
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32
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Estrogenic hormones receptors in Alzheimer's disease. Mol Biol Rep 2021; 48:7517-7526. [PMID: 34657250 DOI: 10.1007/s11033-021-06792-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 09/15/2021] [Indexed: 02/06/2023]
Abstract
Estrogens are hormones that play a critical role during development and growth for the adequate functioning of the reproductive system of women, as well as for maintaining bones, metabolism, and cognition. During menopause, the levels of estrogens are decreased, altering their signaling mediated by their intracellular receptors such as estrogen receptor alpha and beta (ERα and ERβ), and G protein-coupled estrogen receptor (GPER). In the brain, the reduction of molecular pathways mediated by estrogenic receptors seems to favor the progression of Alzheimer's disease (AD) in postmenopausal women. In this review, we investigate the participation of estrogen receptors in AD in women during aging.
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33
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Alternative Splicing in Cardiovascular Disease-A Survey of Recent Findings. Genes (Basel) 2021; 12:genes12091457. [PMID: 34573439 PMCID: PMC8469243 DOI: 10.3390/genes12091457] [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: 08/04/2021] [Revised: 09/11/2021] [Accepted: 09/16/2021] [Indexed: 12/22/2022] Open
Abstract
Alternative splicing, a driver of posttranscriptional variance, differs from canonical splicing by arranging the introns and exons of an immature pre-mRNA transcript in a multitude of different ways. Although alternative splicing was discovered almost half a century ago, estimates of the proportion of genes that undergo alternative splicing have risen drastically over the last two decades. Deep sequencing methods and novel bioinformatic algorithms have led to new insights into the prevalence of spliced variants, tissue-specific splicing patterns and the significance of alternative splicing in development and disease. Thus far, the role of alternative splicing has been uncovered in areas ranging from heart development, the response to myocardial infarction to cardiac structural disease. Circular RNAs, a product of alternative back-splicing, were initially discovered in 1976, but landmark publications have only recently identified their regulatory role, tissue-specific expression, and transcriptomic abundance, spurring a renewed interest in the topic. The aim of this review is to provide a brief insight into some of the available findings on the role of alternative splicing in cardiovascular disease, with a focus on atherosclerosis, myocardial infarction, heart failure, dilated cardiomyopathy and circular RNAs in myocardial infarction.
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Larrasa-Alonso J, Villalba-Orero M, Martí-Gómez C, Ortiz-Sánchez P, López-Olañeta MM, Rey-Martín MA, Sánchez-Cabo F, McNicoll F, Müller-McNicoll M, García-Pavía P, Lara-Pezzi E. The SRSF4-GAS5-Glucocorticoid Receptor Axis Regulates Ventricular Hypertrophy. Circ Res 2021; 129:669-683. [PMID: 34333993 PMCID: PMC8409900 DOI: 10.1161/circresaha.120.318577] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Supplemental Digital Content is available in the text. RBPs (RNA-binding proteins) play critical roles in human biology and disease. Aberrant RBP expression affects various steps in RNA processing, altering the function of the target RNAs. The RBP SRSF4 (serine/arginine-rich splicing factor 4) has been linked to neuropathies and cancer. However, its role in the heart is completely unknown.
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Affiliation(s)
- Javier Larrasa-Alonso
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain (J.L.-A., M.V.-O., C.M.-G., P.O.S., M.M.L.-O., M.A.R.-M., F.S.C., E.L.-P.)
| | - María Villalba-Orero
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain (J.L.-A., M.V.-O., C.M.-G., P.O.S., M.M.L.-O., M.A.R.-M., F.S.C., E.L.-P.).,Centro de Investigación Biomédica en Red Cardiovascular (CIBERCV), Madrid, Spain (M.V.-O., P.G.-P., E.L.-P.)
| | - Carlos Martí-Gómez
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain (J.L.-A., M.V.-O., C.M.-G., P.O.S., M.M.L.-O., M.A.R.-M., F.S.C., E.L.-P.)
| | - Paula Ortiz-Sánchez
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain (J.L.-A., M.V.-O., C.M.-G., P.O.S., M.M.L.-O., M.A.R.-M., F.S.C., E.L.-P.)
| | - Marina M López-Olañeta
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain (J.L.-A., M.V.-O., C.M.-G., P.O.S., M.M.L.-O., M.A.R.-M., F.S.C., E.L.-P.)
| | - M Ascensión Rey-Martín
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain (J.L.-A., M.V.-O., C.M.-G., P.O.S., M.M.L.-O., M.A.R.-M., F.S.C., E.L.-P.)
| | - Fátima Sánchez-Cabo
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain (J.L.-A., M.V.-O., C.M.-G., P.O.S., M.M.L.-O., M.A.R.-M., F.S.C., E.L.-P.)
| | - François McNicoll
- Goethe University Frankfurt, Institute of Molecular Biosciences, Frankfurt/Main, Germany (F.M., M.M.-M.)
| | - Michaela Müller-McNicoll
- Goethe University Frankfurt, Institute of Molecular Biosciences, Frankfurt/Main, Germany (F.M., M.M.-M.)
| | - Pablo García-Pavía
- Centro de Investigación Biomédica en Red Cardiovascular (CIBERCV), Madrid, Spain (M.V.-O., P.G.-P., E.L.-P.).,Heart Failure and Inherited Cardiac Diseases Unit, Department of Cardiology, Hospital Universitario Puerta de Hierro, Madrid, Spain (P.G.-P.).,Facultad de Ciencias de la Salud, Universidad Francisco de Vitoria (UFV), Pozuelo de Alarcón, Madrid, Spain (P.G.-P.)
| | - Enrique Lara-Pezzi
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain (J.L.-A., M.V.-O., C.M.-G., P.O.S., M.M.L.-O., M.A.R.-M., F.S.C., E.L.-P.).,Centro de Investigación Biomédica en Red Cardiovascular (CIBERCV), Madrid, Spain (M.V.-O., P.G.-P., E.L.-P.)
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Dumont AA, Dumont L, Zhou D, Giguère H, Pileggi C, Harper ME, Blondin DP, Scott MS, Auger-Messier M. Cardiomyocyte-specific Srsf3 deletion reveals a mitochondrial regulatory role. FASEB J 2021; 35:e21544. [PMID: 33819356 DOI: 10.1096/fj.202002293rr] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 03/03/2021] [Accepted: 03/09/2021] [Indexed: 11/11/2022]
Abstract
Serine-rich splicing factor 3 (SRSF3) was recently reported as being necessary to preserve RNA stability via an mTOR mechanism in a cardiac mouse model in adulthood. Here, we demonstrate the link between Srsf3 and mitochondrial integrity in an embryonic cardiomyocyte-specific Srsf3 conditional knockout (cKO) mouse model. Fifteen-day-old Srsf3 cKO mice showed dramatically reduced (below 50%) survival and reduced the left ventricular systolic performance, and histological analysis of these hearts revealed a significant increase in cardiomyocyte size, confirming the severe remodeling induced by Srsf3 deletion. RNA-seq analysis of the hearts of 5-day-old Srsf3 cKO mice revealed early changes in expression levels and alternative splicing of several transcripts related to mitochondrial integrity and oxidative phosphorylation. Likewise, the levels of several protein complexes of the electron transport chain decreased, and mitochondrial complex I-driven respiration of permeabilized cardiac muscle fibers from the left ventricle was impaired. Furthermore, transmission electron microscopy analysis showed disordered mitochondrial length and cristae structure. Together with its indispensable role in the physiological maintenance of mouse hearts, these results highlight the previously unrecognized function of Srsf3 in regulating the mitochondrial integrity.
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Affiliation(s)
- Audrey-Ann Dumont
- Département de Médecine - Service de Cardiologie, Faculté de Médecine et des Sciences de la Santé, Centre de Recherche du CHUS, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Lauralyne Dumont
- Département de Médecine - Service de Cardiologie, Faculté de Médecine et des Sciences de la Santé, Centre de Recherche du CHUS, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Delong Zhou
- Département de microbiologie et d'infectiologie, Faculté de Médecine et des Sciences de la Santé, Centre de Recherche du CHUS, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Hugo Giguère
- Département de Médecine - Service de Cardiologie, Faculté de Médecine et des Sciences de la Santé, Centre de Recherche du CHUS, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Chantal Pileggi
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Mary-Ellen Harper
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Denis P Blondin
- Département de Médecine - Service de Cardiologie, Faculté de Médecine et des Sciences de la Santé, Centre de Recherche du CHUS, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Michelle S Scott
- Département de Biochimie et Génomique Fonctionnelle, Faculté de Médecine et des Sciences de la Santé, Centre de Recherche du CHUS, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Mannix Auger-Messier
- Département de Médecine - Service de Cardiologie, Faculté de Médecine et des Sciences de la Santé, Centre de Recherche du CHUS, Université de Sherbrooke, Sherbrooke, QC, Canada
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36
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Boeckel JN, Möbius-Winkler M, Müller M, Rebs S, Eger N, Schoppe L, Tappu R, Kokot KE, Kneuer JM, Gaul S, Bordalo DM, Lai A, Haas J, Ghanbari M, Drewe-Boss P, Liss M, Katus HA, Ohler U, Gotthardt M, Laufs U, Streckfuss-Bömeke K, Meder B. SLM2 Is A Novel Cardiac Splicing Factor Involved in Heart Failure due to Dilated Cardiomyopathy. GENOMICS PROTEOMICS & BIOINFORMATICS 2021; 20:129-146. [PMID: 34273561 PMCID: PMC9510876 DOI: 10.1016/j.gpb.2021.01.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/01/2021] [Indexed: 01/09/2023]
Abstract
Alternative mRNA splicing is a fundamental process to increase the versatility of the genome. In humans, cardiac mRNA splicing is involved in the pathophysiology of heart failure. Mutations in the splicing factor RNA binding motif protein 20 (RBM20) cause severe forms of cardiomyopathy. To identify novel cardiomyopathy-associated splicing factors, RNA-seq and tissue-enrichment analyses were performed, which identified up-regulated expression of Sam68-Like mammalian protein 2 (SLM2) in the left ventricle of dilated cardiomyopathy (DCM) patients. In the human heart, SLM2 binds to important transcripts of sarcomere constituents, such as those encoding myosin light chain 2 (MYL2), troponin I3 (TNNI3), troponin T2 (TNNT2), tropomyosin 1/2 (TPM1/2), and titin (TTN). Mechanistically, SLM2 mediates intron retention, prevents exon exclusion, and thereby mediates alternative splicing of the mRNA regions encoding the variable proline-, glutamate-, valine-, and lysine-rich (PEVK) domain and another part of the I-band region of titin. In summary, SLM2 is a novel cardiac splicing regulator with essential functions for maintaining cardiomyocyte integrity by binding to and processing the mRNAs of essential cardiac constituents such as titin.
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Affiliation(s)
- Jes-Niels Boeckel
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg 69120, Germany; Klinik und Poliklinik für Kardiologie, Universitätskrankenhaus Leipzig, Leipzig 04103, Germany
| | | | - Marion Müller
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg 69120, Germany; German Center for Cardiovascular Research (DZHK), Partner site Heidelberg, Heidelberg 69120, Germany; Clinic for General and Interventional Cardiology/ Angiology, Herz- und Diabeteszentrum NRW, Ruhr-Universität Bochum, Bad Oeynhausen 32545, Germany
| | - Sabine Rebs
- Department of Cardiology and Pneumology, University Hospital, Georg-August University Goettingen, Goettingen 37075, Germany; German Center for Cardiovascular Research (DZHK), Partner site Goettingen, Goettingen 37075, Germany
| | - Nicole Eger
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg 69120, Germany
| | - Laura Schoppe
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg 69120, Germany
| | - Rewati Tappu
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg 69120, Germany
| | - Karoline E Kokot
- Klinik und Poliklinik für Kardiologie, Universitätskrankenhaus Leipzig, Leipzig 04103, Germany
| | - Jasmin M Kneuer
- Klinik und Poliklinik für Kardiologie, Universitätskrankenhaus Leipzig, Leipzig 04103, Germany
| | - Susanne Gaul
- Klinik und Poliklinik für Kardiologie, Universitätskrankenhaus Leipzig, Leipzig 04103, Germany
| | - Diana M Bordalo
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg 69120, Germany; German Center for Cardiovascular Research (DZHK), Partner site Heidelberg, Heidelberg 69120, Germany
| | - Alan Lai
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg 69120, Germany; German Center for Cardiovascular Research (DZHK), Partner site Heidelberg, Heidelberg 69120, Germany
| | - Jan Haas
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg 69120, Germany; German Center for Cardiovascular Research (DZHK), Partner site Heidelberg, Heidelberg 69120, Germany
| | - Mahsa Ghanbari
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 10115, Germany; Institute of Biology, Humboldt Universität zu Berlin, Berlin 10099, Germany
| | - Philipp Drewe-Boss
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 10115, Germany; Institute of Biology, Humboldt Universität zu Berlin, Berlin 10099, Germany
| | - Martin Liss
- Neuromuscular and Cardiovascular Cell Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13092, Germany; German Center for Cardiovascular Research (DZHK), Partner site Berlin, Berlin 10117, Germany
| | - Hugo A Katus
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg 69120, Germany; German Center for Cardiovascular Research (DZHK), Partner site Heidelberg, Heidelberg 69120, Germany
| | - Uwe Ohler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 10115, Germany; Institute of Biology, Humboldt Universität zu Berlin, Berlin 10099, Germany
| | - Michael Gotthardt
- Neuromuscular and Cardiovascular Cell Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13092, Germany; German Center for Cardiovascular Research (DZHK), Partner site Berlin, Berlin 10117, Germany
| | - Ulrich Laufs
- Klinik und Poliklinik für Kardiologie, Universitätskrankenhaus Leipzig, Leipzig 04103, Germany
| | - Katrin Streckfuss-Bömeke
- Department of Cardiology and Pneumology, University Hospital, Georg-August University Goettingen, Goettingen 37075, Germany; German Center for Cardiovascular Research (DZHK), Partner site Goettingen, Goettingen 37075, Germany
| | - Benjamin Meder
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg 69120, Germany; German Center for Cardiovascular Research (DZHK), Partner site Heidelberg, Heidelberg 69120, Germany; Stanford Genome Technology Center, Department of Genetics, Stanford Medical School, Palo Alto, CA 94304, USA.
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37
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Qin J, Guo N, Tong J, Wang Z. Function of histone methylation and acetylation modifiers in cardiac hypertrophy. J Mol Cell Cardiol 2021; 159:120-129. [PMID: 34175302 DOI: 10.1016/j.yjmcc.2021.06.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 06/14/2021] [Accepted: 06/19/2021] [Indexed: 12/15/2022]
Abstract
Cardiac hypertrophy is an adaptive response of the heart to increased workload induced by various physiological or pathological stimuli. It is a common pathological process in multiple cardiovascular diseases, and it ultimately leads to heart failure. The development of cardiac hypertrophy is accompanied by gene expression reprogramming, a process that is largely dependent on epigenetic regulation. Histone modifications such as methylation and acetylation are dynamically regulated under cardiac stress. These consequently contribute to the pathogenesis of cardiac hypertrophy via compensatory or maladaptive transcriptome reprogramming. Histone methylation and acetylation modifiers play crucial roles in epigenetic remodeling during the pathogenesis of cardiac hypertrophy. Regulation of histone methylation and acetylation modifiers serves as a bridge between signal transduction and downstream gene reprogramming. Exploring the role of histone modifiers in cardiac hypertrophy provides novel therapeutic strategies to treat cardiac hypertrophy and heart failure. In this review, we summarize the recent advancements in functional histone methylation and acetylation modifiers in cardiac hypertrophy, with an emphasis on the underlying mechanisms and the therapeutic potential.
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Affiliation(s)
- Jian Qin
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Ningning Guo
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jingjing Tong
- School of Life Sciences, Central China Normal University, Wuhan, China
| | - Zhihua Wang
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China; Shenzhen Key Laboratory of Cardiovascular Disease, Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen, Shenzhen, China; State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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38
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Williams AL, Walton CB, Pinell B, Khadka VS, Dunn B, Lee K, Anagaran MCT, Avelar A, Shohet RV. Ischemic heart injury leads to HIF1-dependent differential splicing of CaMK2γ. Sci Rep 2021; 11:13116. [PMID: 34162925 PMCID: PMC8222303 DOI: 10.1038/s41598-021-92426-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 05/19/2021] [Indexed: 12/04/2022] Open
Abstract
Ischemic heart disease is a leading cause of heart failure and hypoxia inducible factor 1 (HIF1) is a key transcription factor in the response to hypoxic injury. Our lab has developed a mouse model in which a mutated, oxygen-stable form of HIF1α (HIF-PPN) can be inducibly expressed in cardiomyocytes. We observed rapid cardiac dilation and loss of contractility in these mice due to lower expression of excitation-contraction coupling genes and reduced calcium flux. As alternative splicing plays an underappreciated role in transcriptional regulation, we used RNA sequencing to search for splicing changes in calcium-handling genes of HIF-PPN hearts and compared them to previous sequencing data from a model of myocardial infarction (MI) to select for transcripts that are modified in a pathological setting. We found overlap between genes differentially expressed in HIF-PPN and post-MI mice (54/131 genes upregulated in HIF-PPN hearts at 1 day and/or 3 days post-MI, and 45/78 downregulated), as well as changes in alternative splicing. Interestingly, calcium/calmodulin dependent protein kinase II, gamma (CAMK2G) was alternatively spliced in both settings, with variant 1 (v1) substantially decreased compared to variants 2 (v2) and 3 (v3). These findings were also replicated in vitro when cells were transfected with HIF-PPN or exposed to hypoxia. Further analysis of CAMK2γ protein abundance revealed only v1 was detectable and substantially decreased up to 7 days post-MI. Rbfox1, a splicing factor of CAMK2G, was also decreased in HIF-PPN and post-MI hearts. Subcellular fractionation showed CAMK2γ v1 was found in the nuclear and cytoplasmic fractions, and abundance decreased in both fractions post-MI. Chromatin immunoprecipitation analysis of HIF1 in post-MI hearts also demonstrated direct HIF1 binding to CAMK2G. CaMK2 is a key transducer of calcium signals in both physiological and pathological settings. The predominantly expressed isoform in the heart, CaMK2δ, has been extensively studied in cardiac injury, but the specific role of CaMK2γ is not well defined. Our data suggest that loss of CaMK2γ after MI is HIF1-dependent and may play an important role in the heart's calcium signaling and transcriptional response to hypoxia.
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Affiliation(s)
- Allison Lesher Williams
- Center for Cardiovascular Research, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo St. BSB 311, Honolulu, HI, 96813, USA
| | - Chad B Walton
- Center for Cardiovascular Research, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo St. BSB 311, Honolulu, HI, 96813, USA
| | - Blake Pinell
- Center for Cardiovascular Research, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo St. BSB 311, Honolulu, HI, 96813, USA
| | - Vedbar S Khadka
- Bioinformatics Core, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, USA
| | - Brandyn Dunn
- Center for Cardiovascular Research, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo St. BSB 311, Honolulu, HI, 96813, USA
| | - Katie Lee
- Center for Cardiovascular Research, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo St. BSB 311, Honolulu, HI, 96813, USA
| | - M C Therese Anagaran
- Center for Cardiovascular Research, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo St. BSB 311, Honolulu, HI, 96813, USA
| | - Abigail Avelar
- Center for Cardiovascular Research, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo St. BSB 311, Honolulu, HI, 96813, USA
| | - Ralph V Shohet
- Center for Cardiovascular Research, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo St. BSB 311, Honolulu, HI, 96813, USA.
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39
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Baranowski BJ, Allen MD, Nyarko JN, Rector RS, Padilla J, Mousseau DD, Rau CD, Wang Y, Laughlin MH, Emter CA, MacPherson RE, Olver TD. Cerebrovascular insufficiency and amyloidogenic signaling in Ossabaw swine with cardiometabolic heart failure. JCI Insight 2021; 6:143141. [PMID: 34027891 PMCID: PMC8262360 DOI: 10.1172/jci.insight.143141] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 04/14/2021] [Indexed: 12/26/2022] Open
Abstract
Individuals with heart failure (HF) frequently present with comorbidities, including obesity, insulin resistance, hypertension, and dyslipidemia. Many patients with HF experience cardiogenic dementia, yet the pathophysiology of this disease remains poorly understood. Using a swine model of cardiometabolic HF (Western diet+aortic banding; WD-AB), we tested the hypothesis that WD-AB would promote a multidementia phenotype involving cerebrovascular dysfunction alongside evidence of Alzheimer’s disease (AD) pathology. The results provide evidence of cerebrovascular insufficiency coupled with neuroinflammation and amyloidosis in swine with experimental cardiometabolic HF. Although cardiac ejection fraction was normal, indices of arterial compliance and cerebral blood flow were reduced, and cerebrovascular regulation was impaired in the WD-AB group. Cerebrovascular dysfunction occurred concomitantly with increased MAPK signaling and amyloidogenic processing (i.e., increased APP, BACE1, CTF, and Aβ40 in the prefrontal cortex and hippocampus) in the WD-AB group. Transcriptomic profiles of the stellate ganglia revealed the WD-AB group displayed an enrichment of gene networks associated with MAPK/ERK signaling, AD, frontotemporal dementia, and a number of behavioral phenotypes implicated in cognitive impairment. These provide potentially novel evidence from a swine model that cerebrovascular and neuronal pathologies likely both contribute to the dementia profile in a setting of cardiometabolic HF.
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Affiliation(s)
- Bradley J Baranowski
- Department of Health Sciences and.,Centre for Neuroscience, Brock University, St. Catharines, Ontario, Canada
| | - Matti D Allen
- Department of Physical Medicine and Rehabilitation, School of Medicine, Faculty of Health Sciences, Queen's University, Kingston, Ontario, Canada
| | - Jennifer Nk Nyarko
- Department of Psychiatry, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - R Scott Rector
- Department of Nutrition and Exercise Physiology, University of Missouri, Columbia, Missouri, USA.,Research Service, Harry S. Truman Memorial Veterans' Hospital, Columbia, Missouri, USA
| | - Jaume Padilla
- Department of Nutrition and Exercise Physiology, University of Missouri, Columbia, Missouri, USA.,Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, USA
| | - Darrell D Mousseau
- Department of Psychiatry, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Christoph D Rau
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Yibin Wang
- Department of Anesthesiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - M Harold Laughlin
- Department of Biomedical Sciences, University of Missouri, Columbia, Missouri, USA
| | - Craig A Emter
- Department of Biomedical Sciences, University of Missouri, Columbia, Missouri, USA
| | - Rebecca Ek MacPherson
- Department of Health Sciences and.,Centre for Neuroscience, Brock University, St. Catharines, Ontario, Canada
| | - T Dylan Olver
- Department of Biomedical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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40
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Narumanchi S, Wang H, Perttunen S, Tikkanen I, Lakkisto P, Paavola J. Zebrafish Heart Failure Models. Front Cell Dev Biol 2021; 9:662583. [PMID: 34095129 PMCID: PMC8173159 DOI: 10.3389/fcell.2021.662583] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/06/2021] [Indexed: 01/02/2023] Open
Abstract
Heart failure causes significant morbidity and mortality worldwide. The understanding of heart failure pathomechanisms and options for treatment remain incomplete. Zebrafish has proven useful for modeling human heart diseases due to similarity of zebrafish and mammalian hearts, fast easily tractable development, and readily available genetic methods. Embryonic cardiac development is rapid and cardiac function is easy to observe and quantify. Reverse genetics, by using morpholinos and CRISPR-Cas9 to modulate gene function, make zebrafish a primary animal model for in vivo studies of candidate genes. Zebrafish are able to effectively regenerate their hearts following injury. However, less attention has been given to using zebrafish models to increase understanding of heart failure and cardiac remodeling, including cardiac hypertrophy and hyperplasia. Here we discuss using zebrafish to study heart failure and cardiac remodeling, and review zebrafish genetic, drug-induced and other heart failure models, discussing the advantages and weaknesses of using zebrafish to model human heart disease. Using zebrafish models will lead to insights on the pathomechanisms of heart failure, with the aim to ultimately provide novel therapies for the prevention and treatment of heart failure.
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Affiliation(s)
- Suneeta Narumanchi
- Unit of Cardiovascular Research, Minerva Foundation Institute for Medical Research, Biomedicum Helsinki, Helsinki, Finland
| | - Hong Wang
- Unit of Cardiovascular Research, Minerva Foundation Institute for Medical Research, Biomedicum Helsinki, Helsinki, Finland
| | - Sanni Perttunen
- Unit of Cardiovascular Research, Minerva Foundation Institute for Medical Research, Biomedicum Helsinki, Helsinki, Finland
| | - Ilkka Tikkanen
- Unit of Cardiovascular Research, Minerva Foundation Institute for Medical Research, Biomedicum Helsinki, Helsinki, Finland.,Abdominal Center Nephrology, University of Helsinki, Helsinki University Hospital, Helsinki, Finland
| | - Päivi Lakkisto
- Unit of Cardiovascular Research, Minerva Foundation Institute for Medical Research, Biomedicum Helsinki, Helsinki, Finland.,Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki University Hospital, Helsinki, Finland
| | - Jere Paavola
- Unit of Cardiovascular Research, Minerva Foundation Institute for Medical Research, Biomedicum Helsinki, Helsinki, Finland
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Riechert E, Kmietczyk V, Stein F, Schwarzl T, Sekaran T, Jürgensen L, Kamuf-Schenk V, Varma E, Hofmann C, Rettel M, Gür K, Ölschläger J, Kühl F, Martin J, Ramirez-Pedraza M, Fernandez M, Doroudgar S, Méndez R, Katus HA, Hentze MW, Völkers M. Identification of dynamic RNA-binding proteins uncovers a Cpeb4-controlled regulatory cascade during pathological cell growth of cardiomyocytes. Cell Rep 2021; 35:109100. [PMID: 33979607 DOI: 10.1016/j.celrep.2021.109100] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 02/03/2021] [Accepted: 04/16/2021] [Indexed: 11/18/2022] Open
Abstract
RNA-binding proteins (RBPs) control critical aspects of cardiomyocyte function, but the repertoire of active RBPs in cardiomyocytes during the growth response is largely unknown. We define RBPs in healthy and diseased cardiomyocytes at a system-wide level by RNA interactome capture. This identifies 67 cardiomyocyte-specific RBPs, including several contractile proteins. Furthermore, we identify the cytoplasmic polyadenylation element-binding protein 4 (Cpeb4) as a dynamic RBP, regulating cardiac growth both in vitro and in vivo. We identify mRNAs bound to and regulated by Cpeb4 in cardiomyocytes. Cpeb4 regulates cardiac remodeling by differential expression of transcription factors. Among Cpeb4 target mRNAs, two zinc finger transcription factors (Zeb1 and Zbtb20) are discovered. We show that Cpeb4 regulates the expression of these mRNAs and that Cpeb4 depletion increases their expression. Thus, Cpeb4 emerges as a critical regulator of cardiomyocyte function by differential binding to specific mRNAs in response to pathological growth stimulation.
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Affiliation(s)
- Eva Riechert
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany; DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Germany
| | - Vivien Kmietczyk
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany; DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Germany
| | - Frank Stein
- Proteomics Core Facility, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Thomas Schwarzl
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Thileepan Sekaran
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Lonny Jürgensen
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany; DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Germany
| | - Verena Kamuf-Schenk
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany; DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Germany
| | - Eshita Varma
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany; DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Germany
| | - Christoph Hofmann
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany; DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Germany
| | - Mandy Rettel
- Proteomics Core Facility, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Kira Gür
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany; DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Germany
| | - Julie Ölschläger
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany; DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Germany
| | - Friederike Kühl
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany; DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Germany
| | - Judit Martin
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | | | | | - Shirin Doroudgar
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany; DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Germany
| | - Raúl Méndez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain; Institució Catalana de Recerca I Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Hugo A Katus
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany; DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Germany
| | - Matthias W Hentze
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Mirko Völkers
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany; DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Germany.
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42
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Duran J, Nickel L, Estrada M, Backs J, van den Hoogenhof MMG. CaMKIIδ Splice Variants in the Healthy and Diseased Heart. Front Cell Dev Biol 2021; 9:644630. [PMID: 33777949 PMCID: PMC7991079 DOI: 10.3389/fcell.2021.644630] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/22/2021] [Indexed: 01/16/2023] Open
Abstract
RNA splicing has been recognized in recent years as a pivotal player in heart development and disease. The Ca2+/calmodulin dependent protein kinase II delta (CaMKIIδ) is a multifunctional Ser/Thr kinase family and generates at least 11 different splice variants through alternative splicing. This enzyme, which belongs to the CaMKII family, is the predominant family member in the heart and functions as a messenger toward adaptive or detrimental signaling in cardiomyocytes. Classically, the nuclear CaMKIIδB and cytoplasmic CaMKIIδC splice variants are described as mediators of arrhythmias, contractile function, Ca2+ handling, and gene transcription. Recent findings also put CaMKIIδA and CaMKIIδ9 as cardinal players in the global CaMKII response in the heart. In this review, we discuss and summarize the new insights into CaMKIIδ splice variants and their (proposed) functions, as well as CaMKII-engineered mouse phenotypes and cardiac dysfunction related to CaMKIIδ missplicing. We also discuss RNA splicing factors affecting CaMKII splicing. Finally, we discuss the translational perspective derived from these insights and future directions on CaMKIIδ splicing research in the healthy and diseased heart.
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Affiliation(s)
- Javier Duran
- Institute of Experimental Cardiology, Heidelberg University, Heidelberg, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Lennart Nickel
- Institute of Experimental Cardiology, Heidelberg University, Heidelberg, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Manuel Estrada
- Faculty of Medicine, Institute of Biomedical Sciences, University of Chile, Santiago, Chile
| | - Johannes Backs
- Institute of Experimental Cardiology, Heidelberg University, Heidelberg, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Maarten M G van den Hoogenhof
- Institute of Experimental Cardiology, Heidelberg University, Heidelberg, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
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Kelly SC, Rau CD, Ouyang A, Thorne PK, Olver TD, Edwards JC, Domeier TL, Padilla J, Grisanti LA, Fleenor BS, Wang Y, Rector RS, Emter CA. The right ventricular transcriptome signature in Ossabaw swine with cardiometabolic heart failure: implications for the coronary vasculature. Physiol Genomics 2021; 53:99-115. [PMID: 33491589 PMCID: PMC7988741 DOI: 10.1152/physiolgenomics.00093.2020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 01/14/2021] [Accepted: 01/19/2021] [Indexed: 11/22/2022] Open
Abstract
Heart failure (HF) patients with deteriorating right ventricular (RV) structure and function have a nearly twofold increased risk of death compared with those without. Despite the well-established clinical risk, few studies have examined the molecular signature associated with this HF condition. The purpose of this study was to integrate morphological, molecular, and functional data with the transcriptome data set in the RV of a preclinical model of cardiometabolic HF. Ossabaw swine were fed either normal diet without surgery (lean control, n = 5) or Western diet and aortic-banding (WD-AB; n = 4). Postmortem RV weight was increased and positively correlated with lung weight in the WD-AB group compared with CON. Total RNA-seq was performed and gene expression profiles were compared and analyzed using principal component analysis, weighted gene co-expression network analysis, module enrichment analysis, and ingenuity pathway analysis. Gene networks specifically associated with RV hypertrophic remodeling identified a hub gene in MAPK8 (or JNK1) that was associated with the selective induction of the extracellular matrix (ECM) component fibronectin. JNK1 and fibronectin protein were increased in the right coronary artery (RCA) of WD-AB animals and associated with a decrease in matrix metalloproteinase 14 protein, which specifically degrades fibronectin. RCA fibronectin content was correlated with increased vascular stiffness evident as a decreased elastin elastic modulus in WD-AB animals. In conclusion, this study establishes a molecular and transcriptome signature in the RV using Ossabaw swine with cardiometabolic HF. This signature was associated with altered ECM regulation and increased vascular stiffness in the RCA, with selective dysregulation of fibronectin.
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Affiliation(s)
- Shannon C Kelly
- Department of Biomedical Sciences, University of Missouri, Columbia, Missouri
| | - Christoph D Rau
- Department of Computational Medicine and Genetics, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - An Ouyang
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Pamela K Thorne
- Department of Biomedical Sciences, University of Missouri, Columbia, Missouri
| | - T Dylan Olver
- Department of Biomedical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Jenna C Edwards
- Department of Biomedical Sciences, University of Missouri, Columbia, Missouri
| | - Timothy L Domeier
- Department of Medical Pharmacology and Physiology, University of Missouri, Columbia, Missouri
| | - Jaume Padilla
- Department of Nutrition and Exercise Physiology, University of Missouri, Columbia, Missouri
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri
| | - Laurel A Grisanti
- Department of Biomedical Sciences, University of Missouri, Columbia, Missouri
| | - Bradley S Fleenor
- Human Performance Laboratory, School of Kinesiology, Ball State University, Muncie, Indiana
| | - Yibin Wang
- David Geffen School of Medicine, University of California, Los Angeles, California
| | - R Scott Rector
- Department of Nutrition and Exercise Physiology, University of Missouri, Columbia, Missouri
- Department of Medicine-Gastroenterology and Hepatology, University of Missouri, Columbia, Missouri
- Research Service, Harry S. Truman Memorial VA Hospital, University of Missouri, Columbia, Missouri
| | - Craig A Emter
- Department of Biomedical Sciences, University of Missouri, Columbia, Missouri
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44
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Di Giorgio E, Wang L, Xiong Y, Akimova T, Christensen LM, Han R, Samanta A, Trevisanut M, Bhatti TR, Beier UH, Hancock WW. MEF2D sustains activation of effector Foxp3+ Tregs during transplant survival and anticancer immunity. J Clin Invest 2021; 130:6242-6260. [PMID: 32790649 DOI: 10.1172/jci135486] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 08/06/2020] [Indexed: 12/11/2022] Open
Abstract
The transcription factor MEF2D is important in the regulation of differentiation and adaptive responses in many cell types. We found that among T cells, MEF2D gained new functions in Foxp3+ T regulatory (Treg) cells due to its interactions with the transcription factor Foxp3 and its release from canonical partners, like histone/protein deacetylases. Though not necessary for the generation and maintenance of Tregs, MEF2D was required for the expression of IL-10, CTLA4, and Icos, and for the acquisition of an effector Treg phenotype. At these loci, MEF2D acted both synergistically and additively to Foxp3, and downstream of Blimp1. Mice with the conditional deletion in Tregs of the gene encoding MEF2D were unable to maintain long-term allograft survival despite costimulation blockade, had enhanced antitumor immunity in syngeneic models, but displayed only minor evidence of autoimmunity when maintained under normal conditions. The role played by MEF2D in sustaining effector Foxp3+ Treg functions without abrogating their basal actions suggests its suitability for drug discovery efforts in cancer therapy.
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Affiliation(s)
- Eros Di Giorgio
- Division of Transplant Immunology, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Department of Medicine, Università degli Studi di Udine, Udine, Italy
| | - Liqing Wang
- Division of Transplant Immunology, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Yan Xiong
- Division of Transplant Immunology, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Institute of Hepatobiliary Diseases of Wuhan University, Transplant Centre of Wuhan University, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Tatiana Akimova
- Division of Transplant Immunology, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Lanette M Christensen
- Division of Transplant Immunology, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Rongxiang Han
- Division of Transplant Immunology, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Arabinda Samanta
- Division of Transplant Immunology, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Matteo Trevisanut
- Division of Transplant Immunology, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Department of Medicine, Università degli Studi di Udine, Udine, Italy
| | - Tricia R Bhatti
- Division of Anatomical Pathology, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ulf H Beier
- Division of Nephrology, Department of Pediatrics, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Wayne W Hancock
- Division of Transplant Immunology, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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45
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Sex-Specific Alterations in Cardiac DNA Methylation in Adult Mice by Perinatal Lead Exposure. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18020577. [PMID: 33445541 PMCID: PMC7826866 DOI: 10.3390/ijerph18020577] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 12/27/2020] [Accepted: 01/04/2021] [Indexed: 12/27/2022]
Abstract
Environmental factors play an important role in the etiology of cardiovascular diseases. Cardiovascular diseases exhibit marked sexual dimorphism; however, the sex-specific effects of environmental exposures on cardiac health are incompletely understood. Perinatal and adult exposures to the metal lead (Pb) are linked to several adverse cardiovascular outcomes, but the sex-specific effects of this toxicant on the heart have received little attention. Perinatal environmental exposures can lead to disease through disruption of the normal epigenetic programming that occurs during early development. Using a mouse model of human-relevant perinatal environmental exposure, we investigated the effects of exposure to Pb during gestation and lactation on DNA methylation in the hearts of adult offspring mice (n = 6 per sex). Two weeks prior to mating, dams were assigned to control or Pb acetate (32 ppm) water, and exposure continued until offspring were weaned at three weeks of age. Enhanced reduced-representation bisulfite sequencing was used to measure DNA methylation in the hearts of offspring at five months of age. Although Pb exposure stopped at three weeks of age, we discovered hundreds of differentially methylated cytosines (DMCs) and regions (DMRs) in males and females at five months of age. DMCs/DMRs and their associated genes were sex-specific, with a small, but statistically significant subset overlapping between sexes. Pathway analysis revealed altered methylation of genes important for cardiac and other tissue development in males, and histone demethylation in females. Together, these data demonstrate that perinatal exposure to Pb induces sex-specific changes in cardiac DNA methylation that are present long after cessation of exposure, and highlight the importance of considering sex in environmental epigenetics and mechanistic toxicology studies.
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Chen X, Liu Y, Xu C, Ba L, Liu Z, Li X, Huang J, Simpson E, Gao H, Cao D, Sheng W, Qi H, Ji H, Sanderson M, Cai CL, Li X, Yang L, Na J, Yamamura K, Liu Y, Huang G, Shou W, Sun N. QKI is a critical pre-mRNA alternative splicing regulator of cardiac myofibrillogenesis and contractile function. Nat Commun 2021; 12:89. [PMID: 33397958 PMCID: PMC7782589 DOI: 10.1038/s41467-020-20327-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 11/27/2020] [Indexed: 01/29/2023] Open
Abstract
The RNA-binding protein QKI belongs to the hnRNP K-homology domain protein family, a well-known regulator of pre-mRNA alternative splicing and is associated with several neurodevelopmental disorders. Qki is found highly expressed in developing and adult hearts. By employing the human embryonic stem cell (hESC) to cardiomyocyte differentiation system and generating QKI-deficient hESCs (hESCs-QKIdel) using CRISPR/Cas9 gene editing technology, we analyze the physiological role of QKI in cardiomyocyte differentiation, maturation, and contractile function. hESCs-QKIdel largely maintain normal pluripotency and normal differentiation potential for the generation of early cardiogenic progenitors, but they fail to transition into functional cardiomyocytes. In this work, by using a series of transcriptomic, cell and biochemical analyses, and the Qki-deficient mouse model, we demonstrate that QKI is indispensable to cardiac sarcomerogenesis and cardiac function through its regulation of alternative splicing in genes involved in Z-disc formation and contractile physiology, suggesting that QKI is associated with the pathogenesis of certain forms of cardiomyopathies.
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Affiliation(s)
- Xinyun Chen
- grid.8547.e0000 0001 0125 2443Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China ,grid.411333.70000 0004 0407 2968Shanghai Key Laboratory of Birth Defects, Children’s Hospital of Fudan University, Shanghai, China ,grid.257413.60000 0001 2287 3919Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN USA
| | - Ying Liu
- grid.257413.60000 0001 2287 3919Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN USA
| | - Chen Xu
- grid.8547.e0000 0001 0125 2443Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China ,grid.257413.60000 0001 2287 3919Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN USA
| | - Lina Ba
- grid.257413.60000 0001 2287 3919Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN USA
| | - Zhuo Liu
- grid.257413.60000 0001 2287 3919Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN USA
| | - Xiuya Li
- grid.8547.e0000 0001 0125 2443Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Jie Huang
- grid.8547.e0000 0001 0125 2443Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Ed Simpson
- grid.257413.60000 0001 2287 3919Department of Bioinformatics, Indiana University School of Medicine, Indianapolis, IN USA
| | - Hongyu Gao
- grid.257413.60000 0001 2287 3919Department of Bioinformatics, Indiana University School of Medicine, Indianapolis, IN USA
| | - Dayan Cao
- Institute of Materia Medica and Center of Translational Medicine, College of Pharmacy, Army Medical University, Chongqing, China
| | - Wei Sheng
- grid.411333.70000 0004 0407 2968Shanghai Key Laboratory of Birth Defects, Children’s Hospital of Fudan University, Shanghai, China ,grid.257413.60000 0001 2287 3919Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN USA
| | - Hanping Qi
- grid.257413.60000 0001 2287 3919Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN USA
| | - Hongrui Ji
- grid.257413.60000 0001 2287 3919Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN USA
| | - Maria Sanderson
- grid.257413.60000 0001 2287 3919Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN USA
| | - Chen-Leng Cai
- grid.257413.60000 0001 2287 3919Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN USA
| | - Xiaohui Li
- Institute of Materia Medica and Center of Translational Medicine, College of Pharmacy, Army Medical University, Chongqing, China
| | - Lei Yang
- grid.257413.60000 0001 2287 3919Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN USA
| | - Jie Na
- grid.12527.330000 0001 0662 3178Center for Stem Cell Biology and Regenerative Medicine, School of Medicine, Tsinghua University, Beijing, China
| | - Kenichi Yamamura
- Institute of Resource Development and Analysis, Kumanoto University, Kumanoto, Japan
| | - Yunlong Liu
- grid.257413.60000 0001 2287 3919Department of Bioinformatics, Indiana University School of Medicine, Indianapolis, IN USA
| | - Guoying Huang
- grid.411333.70000 0004 0407 2968Shanghai Key Laboratory of Birth Defects, Children’s Hospital of Fudan University, Shanghai, China
| | - Weinian Shou
- grid.257413.60000 0001 2287 3919Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN USA
| | - Ning Sun
- grid.8547.e0000 0001 0125 2443Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China ,grid.411333.70000 0004 0407 2968Shanghai Key Laboratory of Birth Defects, Children’s Hospital of Fudan University, Shanghai, China
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Qian Y, Li L, Sun Z, Liu J, Yuan W, Wang Z. A multi-omics view of the complex mechanism of vascular calcification. Biomed Pharmacother 2021; 135:111192. [PMID: 33401220 DOI: 10.1016/j.biopha.2020.111192] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 12/19/2020] [Accepted: 12/26/2020] [Indexed: 02/07/2023] Open
Abstract
Vascular calcification is a high incidence and high risk disease with increasing morbidity and high mortality, which is considered the consequence of smooth muscle cell transdifferentiation initiating the mechanism of accumulation of hydroxyl calcium phosphate. Vascular calcification is also thought to be strongly associated with poor outcomes in diabetes and chronic kidney disease. Numerous studies have been accomplished; however, the specific mechanism of the disease remains unclear. Development of the genome project enhanced the understanding of life science and has entered the post-genomic era resulting in a variety of omics techniques used in studies and a large amount of available data; thus, a new perspective on data analysis has been revealed. Omics has a broader perspective and is thus advantageous over a single pathway analysis in the study of complex vascular calcification mechanisms. This paper reviews in detail various omics studies including genomics, proteomics, transcriptomics, metabolomics and multiple group studies on vascular calcification. Advances and deficiencies in the use of omics to study vascular calcification are presented in a comprehensive view. We also review the methodology of the omics studies and omics data analysis and processing. In addition, the methodology and data processing presented here can be applied to other areas. An omics landscape perspective across the boundaries between genomics, transcriptomics, proteomics and metabolomics is used to examine the mechanisms of vascular calcification. The perspective combined with various technologies also provides a direction for the subsequent exploration of clinical significance.
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Affiliation(s)
- Yongjiang Qian
- Department of Cardiology, Affiliated Hospital of Jiangsu University, 212000, Zhenjiang, China
| | - Lihua Li
- Department of Pathology, Affiliated Hospital of Jiangsu University, 212000, Zhenjiang, China
| | - Zhen Sun
- Department of Cardiology, Affiliated Hospital of Jiangsu University, 212000, Zhenjiang, China
| | - Jia Liu
- Department of Cardiology, Affiliated Hospital of Jiangsu University, 212000, Zhenjiang, China
| | - Wei Yuan
- Department of Cardiology, Affiliated Hospital of Jiangsu University, 212000, Zhenjiang, China
| | - Zhongqun Wang
- Department of Cardiology, Affiliated Hospital of Jiangsu University, 212000, Zhenjiang, China.
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Farboud B, Novak CS, Nicoll M, Quiogue A, Meyer BJ. Dose-dependent action of the RNA binding protein FOX-1 to relay X-chromosome number and determine C. elegans sex. eLife 2020; 9:62963. [PMID: 33372658 PMCID: PMC7787662 DOI: 10.7554/elife.62963] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 12/23/2020] [Indexed: 12/25/2022] Open
Abstract
We demonstrate how RNA binding protein FOX-1 functions as a dose-dependent X-signal element to communicate X-chromosome number and thereby determine nematode sex. FOX-1, an RNA recognition motif protein, triggers hermaphrodite development in XX embryos by causing non-productive alternative pre-mRNA splicing of xol-1, the master sex-determination switch gene that triggers male development in XO embryos. RNA binding experiments together with genome editing demonstrate that FOX-1 binds to multiple GCAUG and GCACG motifs in a xol-1 intron, causing intron retention or partial exon deletion, thereby eliminating male-determining XOL-1 protein. Transforming all motifs to GCAUG or GCACG permits accurate alternative splicing, demonstrating efficacy of both motifs. Mutating subsets of both motifs partially alleviates non-productive splicing. Mutating all motifs blocks it, as does transforming them to low-affinity GCUUG motifs. Combining multiple high-affinity binding sites with the twofold change in FOX-1 concentration between XX and XO embryos achieves dose-sensitivity in splicing regulation to determine sex.
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Affiliation(s)
- Behnom Farboud
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, United States.,Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, United States
| | - Catherine S Novak
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, United States.,Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, United States
| | - Monique Nicoll
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, United States.,Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, United States
| | - Alyssa Quiogue
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, United States.,Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, United States
| | - Barbara J Meyer
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, United States.,Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, United States
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Heterozygous loss of Rbm24 in the adult mouse heart increases sarcomere slack length but does not affect function. Sci Rep 2020; 10:7687. [PMID: 32376900 PMCID: PMC7203132 DOI: 10.1038/s41598-020-64667-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 04/20/2020] [Indexed: 12/19/2022] Open
Abstract
RNA-binding proteins are key regulators of post-transcriptional processes such as alternative splicing and mRNA stabilization. Rbm24 acts as a regulator of alternative splicing in heart and skeletal muscle, and is essential for sarcomere assembly. Homozygous inactivation of Rbm24 in mice disrupts cardiac development and results in embryonic lethality around E12.5. In the present study, we generated somatic Rbm24 knockout (KO) mice and investigated the effects of reduced levels of Rbm24 in the adult heart. Due to the embryonic lethality of Rbm24 KO mice, we examined cardiac structure and function in adult Rbm24 heterozygotes (HETs). Rbm24 protein expression was 40% downregulated in HET hearts compared to WT hearts. Force measurements on isolated membrane-permeabilized myocytes showed increased sarcomere slack length and lower myofilament passive stiffness in adult Rbm24 HET compared to wildtype cardiomyocytes. As a result of the differences in sarcomere slack length, the relations between force development and sarcomere length differed between WT and Rbm24 HET hearts. No differences in sarcomere structure and titin isoform composition were observed. Likewise, in vivo cardiac function and myocardial structure was unaltered in Rbm24 HET mice compared to WT, at baseline and upon pressure overload after transverse aortic constriction. In conclusion, we generated a somatic Rbm24 KO model and recapitulated the previously reported embryonic phenotype. In adult Rbm24 HET cardiomyocytes we observed increased sarcomere slack length, but no difference in sarcomere structure and cardiac function.
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Abstract
Maturation is the last phase of heart development that prepares the organ for strong, efficient, and persistent pumping throughout the mammal's lifespan. This process is characterized by structural, gene expression, metabolic, and functional specializations in cardiomyocytes as the heart transits from fetal to adult states. Cardiomyocyte maturation gained increased attention recently due to the maturation defects in pluripotent stem cell-derived cardiomyocyte, its antagonistic effect on myocardial regeneration, and its potential contribution to cardiac disease. Here, we review the major hallmarks of ventricular cardiomyocyte maturation and summarize key regulatory mechanisms that promote and coordinate these cellular events. With advances in the technical platforms used for cardiomyocyte maturation research, we expect significant progress in the future that will deepen our understanding of this process and lead to better maturation of pluripotent stem cell-derived cardiomyocyte and novel therapeutic strategies for heart disease.
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Affiliation(s)
- Yuxuan Guo
- Department of Cardiology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - William Pu
- Department of Cardiology, Boston Children’s Hospital, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
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