1
|
Xiao F, Nguyen NUN, Wang P, Li S, Hsu CC, Thet S, Kimura W, Luo X, Lam NT, Menendez-Montes I, Elhelaly WM, Cardoso AC, Pereira AHM, Singh R, Sadayappan S, Kanchwala M, Xing C, Ladha FA, Hinson JT, Hajjar RJ, Hill JA, Sadek HA. Adducin Regulates Sarcomere Disassembly During Cardiomyocyte Mitosis. Circulation 2024; 150:791-805. [PMID: 38708635 DOI: 10.1161/circulationaha.122.059102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 03/29/2024] [Indexed: 05/07/2024]
Abstract
BACKGROUND Recent interest in understanding cardiomyocyte cell cycle has been driven by potential therapeutic applications in cardiomyopathy. However, despite recent advances, cardiomyocyte mitosis remains a poorly understood process. For example, it is unclear how sarcomeres are disassembled during mitosis to allow the abscission of daughter cardiomyocytes. METHODS Here, we use a proteomics screen to identify adducin, an actin capping protein previously not studied in cardiomyocytes, as a regulator of sarcomere disassembly. We generated many adeno-associated viruses and cardiomyocyte-specific genetic gain-of-function models to examine the role of adducin in neonatal and adult cardiomyocytes in vitro and in vivo. RESULTS We identify adducin as a regulator of sarcomere disassembly during mammalian cardiomyocyte mitosis. α/γ-adducins are selectively expressed in neonatal mitotic cardiomyocytes, and their levels decline precipitously thereafter. Cardiomyocyte-specific overexpression of various splice isoforms and phospho-isoforms of α-adducin in vitro and in vivo identified Thr445/Thr480 phosphorylation of a short isoform of α-adducin as a potent inducer of neonatal cardiomyocyte sarcomere disassembly. Concomitant overexpression of this α-adducin variant along with γ-adducin resulted in stabilization of the adducin complex and persistent sarcomere disassembly in adult mice, which is mediated by interaction with α-actinin. CONCLUSIONS These results highlight an important mechanism for coordinating cytoskeletal morphological changes during cardiomyocyte mitosis.
Collapse
Affiliation(s)
- Feng Xiao
- Department of Internal Medicine (Cardiology) (F.X., N.U.N.N., P.W., S.L., C.-C.H., S.T., W.K., X.L., N.T.L., I.M.-M., W.M.E., A.C.C., A.H.M.P., J.A.H., H.A.S.), University of Texas Southwestern Medical Center, Dallas
| | - Ngoc Uyen Nhi Nguyen
- Department of Internal Medicine (Cardiology) (F.X., N.U.N.N., P.W., S.L., C.-C.H., S.T., W.K., X.L., N.T.L., I.M.-M., W.M.E., A.C.C., A.H.M.P., J.A.H., H.A.S.), University of Texas Southwestern Medical Center, Dallas
| | - Ping Wang
- Department of Internal Medicine (Cardiology) (F.X., N.U.N.N., P.W., S.L., C.-C.H., S.T., W.K., X.L., N.T.L., I.M.-M., W.M.E., A.C.C., A.H.M.P., J.A.H., H.A.S.), University of Texas Southwestern Medical Center, Dallas
| | - Shujuan Li
- Department of Internal Medicine (Cardiology) (F.X., N.U.N.N., P.W., S.L., C.-C.H., S.T., W.K., X.L., N.T.L., I.M.-M., W.M.E., A.C.C., A.H.M.P., J.A.H., H.A.S.), University of Texas Southwestern Medical Center, Dallas
| | - Ching-Cheng Hsu
- Department of Internal Medicine (Cardiology) (F.X., N.U.N.N., P.W., S.L., C.-C.H., S.T., W.K., X.L., N.T.L., I.M.-M., W.M.E., A.C.C., A.H.M.P., J.A.H., H.A.S.), University of Texas Southwestern Medical Center, Dallas
| | - Suwannee Thet
- Department of Internal Medicine (Cardiology) (F.X., N.U.N.N., P.W., S.L., C.-C.H., S.T., W.K., X.L., N.T.L., I.M.-M., W.M.E., A.C.C., A.H.M.P., J.A.H., H.A.S.), University of Texas Southwestern Medical Center, Dallas
| | - Wataru Kimura
- Department of Internal Medicine (Cardiology) (F.X., N.U.N.N., P.W., S.L., C.-C.H., S.T., W.K., X.L., N.T.L., I.M.-M., W.M.E., A.C.C., A.H.M.P., J.A.H., H.A.S.), University of Texas Southwestern Medical Center, Dallas
- Life Science Center, Tsukuba Advanced Research Alliance, University of Tsukuba, Japan (W.K.)
| | - Xiang Luo
- Department of Internal Medicine (Cardiology) (F.X., N.U.N.N., P.W., S.L., C.-C.H., S.T., W.K., X.L., N.T.L., I.M.-M., W.M.E., A.C.C., A.H.M.P., J.A.H., H.A.S.), University of Texas Southwestern Medical Center, Dallas
| | - Nicholas T Lam
- Department of Internal Medicine (Cardiology) (F.X., N.U.N.N., P.W., S.L., C.-C.H., S.T., W.K., X.L., N.T.L., I.M.-M., W.M.E., A.C.C., A.H.M.P., J.A.H., H.A.S.), University of Texas Southwestern Medical Center, Dallas
| | - Ivan Menendez-Montes
- Department of Internal Medicine (Cardiology) (F.X., N.U.N.N., P.W., S.L., C.-C.H., S.T., W.K., X.L., N.T.L., I.M.-M., W.M.E., A.C.C., A.H.M.P., J.A.H., H.A.S.), University of Texas Southwestern Medical Center, Dallas
| | - Waleed M Elhelaly
- Department of Internal Medicine (Cardiology) (F.X., N.U.N.N., P.W., S.L., C.-C.H., S.T., W.K., X.L., N.T.L., I.M.-M., W.M.E., A.C.C., A.H.M.P., J.A.H., H.A.S.), University of Texas Southwestern Medical Center, Dallas
| | - Alisson Campos Cardoso
- Department of Internal Medicine (Cardiology) (F.X., N.U.N.N., P.W., S.L., C.-C.H., S.T., W.K., X.L., N.T.L., I.M.-M., W.M.E., A.C.C., A.H.M.P., J.A.H., H.A.S.), University of Texas Southwestern Medical Center, Dallas
- Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas (A.C.C., A.H.M.P.)
| | - Ana Helena Macedo Pereira
- Department of Internal Medicine (Cardiology) (F.X., N.U.N.N., P.W., S.L., C.-C.H., S.T., W.K., X.L., N.T.L., I.M.-M., W.M.E., A.C.C., A.H.M.P., J.A.H., H.A.S.), University of Texas Southwestern Medical Center, Dallas
- Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas (A.C.C., A.H.M.P.)
| | - Rohit Singh
- Center for Cardiovascular Research, Division of Cardiovascular Health and Disease, Department of Internal Medicine, University of Cincinnati College of Medicine, OH (R.S., S.S.)
- Amgen Research, Department of Cardiometabolic Disorders, Amgen, South San Francisco, CA (R.S.)
| | - Sakthivel Sadayappan
- Center for Cardiovascular Research, Division of Cardiovascular Health and Disease, Department of Internal Medicine, University of Cincinnati College of Medicine, OH (R.S., S.S.)
| | - Mohammed Kanchwala
- Eugene McDermott Center for Human Growth and Development (M.K., C.X.), University of Texas Southwestern Medical Center, Dallas
| | - Chao Xing
- Eugene McDermott Center for Human Growth and Development (M.K., C.X.), University of Texas Southwestern Medical Center, Dallas
- Lyda Hill Department of Bioinformatics (C.X.), University of Texas Southwestern Medical Center, Dallas
- O'Donnell School of Public Health (C.X.), University of Texas Southwestern Medical Center, Dallas
| | - Feria A Ladha
- University of Connecticut Health Center, Farmington (F.A.L., J.T.H.)
| | - J Travis Hinson
- Department of Internal Medicine (Cardiology) (F.X., N.U.N.N., P.W., S.L., C.-C.H., S.T., W.K., X.L., N.T.L., I.M.-M., W.M.E., A.C.C., A.H.M.P., J.A.H., H.A.S.), University of Texas Southwestern Medical Center, Dallas
- University of Connecticut Health Center, Farmington (F.A.L., J.T.H.)
- Jackson Laboratory for Genomic Medicine, Farmington, CT (J.T.H.)
| | - Roger J Hajjar
- Gene & Cell Therapy Institute, Mass General Brigham, Cambridge, MA (R.J.H.)
| | - Joseph A Hill
- Moss Heart Center (J.A.H.), University of Texas Southwestern Medical Center, Dallas
- Department of Molecular Biology (J.A.H., H.A.S.), University of Texas Southwestern Medical Center, Dallas
| | - Hesham A Sadek
- Department of Internal Medicine (Cardiology) (F.X., N.U.N.N., P.W., S.L., C.-C.H., S.T., W.K., X.L., N.T.L., I.M.-M., W.M.E., A.C.C., A.H.M.P., J.A.H., H.A.S.), University of Texas Southwestern Medical Center, Dallas
- Department of Molecular Biology (J.A.H., H.A.S.), University of Texas Southwestern Medical Center, Dallas
- Department of Biophysics (H.A.S.), University of Texas Southwestern Medical Center, Dallas
- Hamon Center for Regenerative Science and Medicine (H.A.S.), University of Texas Southwestern Medical Center, Dallas
- Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain (H.A.S.)
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
Ohiri JC, Dellefave‐Castillo L, Tomar G, Wilsbacher L, Choudhury L, Barefield DY, Fullenkamp D, Gacita AM, Monroe TO, Pesce L, Blancard M, Vaught L, George AL, Demonbreun AR, Puckelwartz MJ, McNally EM. Reduction of Filamin C Results in Altered Proteostasis, Cardiomyopathy, and Arrhythmias. J Am Heart Assoc 2024; 13:e030467. [PMID: 38761081 PMCID: PMC11179814 DOI: 10.1161/jaha.123.030467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 04/17/2024] [Indexed: 05/20/2024]
Abstract
BACKGROUND Many cardiomyopathy-associated FLNC pathogenic variants are heterozygous truncations, and FLNC pathogenic variants are associated with arrhythmias. Arrhythmia triggers in filaminopathy are incompletely understood. METHODS AND RESULTS We describe an individual with biallelic FLNC pathogenic variants, p.Arg650X and c.970-4A>G, with peripartum cardiomyopathy and ventricular arrhythmias. We also describe clinical findings in probands with FLNC variants including Val2715fs87X, Glu2458Serfs71X, Phe106Leu, and c.970-4A>G with hypertrophic and dilated cardiomyopathy, atrial fibrillation, and ventricular tachycardia. Induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) were generated. The FLNC truncation, Arg650X/c.970-4A>G, showed a marked reduction in filamin C protein consistent with biallelic loss of function mutations. To assess loss of filamin C, gene editing of a healthy control iPSC line was used to generate a homozygous FLNC disruption in the actin binding domain. Because filamin C has been linked to protein quality control, we assessed the necessity of filamin C in iPSC-CMs for response to the proteasome inhibitor bortezomib. After exposure to low-dose bortezomib, FLNC-null iPSC-CMs showed an increase in the chaperone proteins BAG3, HSP70 (heat shock protein 70), and HSPB8 (small heat shock protein B8) and in the autophagy marker LC3I/II. FLNC null iPSC-CMs had prolonged electric field potential, which was further prolonged in the presence of low-dose bortezomib. FLNC null engineered heart tissues had impaired function after low-dose bortezomib. CONCLUSIONS FLNC pathogenic variants associate with a predisposition to arrhythmias, which can be modeled in iPSC-CMs. Reduction of filamin C prolonged field potential, a surrogate for action potential, and with bortezomib-induced proteasome inhibition, reduced filamin C led to greater arrhythmia potential and impaired function.
Collapse
Affiliation(s)
- Joyce C. Ohiri
- Center for Genetic Medicine, Feinberg School of MedicineNorthwestern UniversityChicagoILUSA
| | | | - Garima Tomar
- Center for Genetic Medicine, Feinberg School of MedicineNorthwestern UniversityChicagoILUSA
| | - Lisa Wilsbacher
- Feinberg Cardiovascular and Renal Research Institute, Feinberg School of MedicineNorthwestern UniversityChicagoILUSA
| | - Lubna Choudhury
- Bluhm Cardiovascular InstituteNorthwestern MedicineChicagoILUSA
| | - David Y. Barefield
- Center for Genetic Medicine, Feinberg School of MedicineNorthwestern UniversityChicagoILUSA
- Cell and Molecular PhysiologyLoyola University Stritch School of MedicineMaywoodILUSA
| | - Dominic Fullenkamp
- Center for Genetic Medicine, Feinberg School of MedicineNorthwestern UniversityChicagoILUSA
| | - Anthony M. Gacita
- Center for Genetic Medicine, Feinberg School of MedicineNorthwestern UniversityChicagoILUSA
| | - Tanner O. Monroe
- Center for Genetic Medicine, Feinberg School of MedicineNorthwestern UniversityChicagoILUSA
| | - Lorenzo Pesce
- Center for Genetic Medicine, Feinberg School of MedicineNorthwestern UniversityChicagoILUSA
| | - Malorie Blancard
- Department of Pharmacology, Feinberg School of MedicineNorthwestern UniversityChicagoILUSA
| | - Lauren Vaught
- Center for Genetic Medicine, Feinberg School of MedicineNorthwestern UniversityChicagoILUSA
| | - Alfred L. George
- Department of Pharmacology, Feinberg School of MedicineNorthwestern UniversityChicagoILUSA
| | - Alexis R. Demonbreun
- Center for Genetic Medicine, Feinberg School of MedicineNorthwestern UniversityChicagoILUSA
- Department of Pharmacology, Feinberg School of MedicineNorthwestern UniversityChicagoILUSA
| | - Megan J. Puckelwartz
- Center for Genetic Medicine, Feinberg School of MedicineNorthwestern UniversityChicagoILUSA
- Department of Pharmacology, Feinberg School of MedicineNorthwestern UniversityChicagoILUSA
| | - Elizabeth M. McNally
- Center for Genetic Medicine, Feinberg School of MedicineNorthwestern UniversityChicagoILUSA
| |
Collapse
|
4
|
Visker JR, Brintz BJ, Kyriakopoulos CP, Hillas Y, Taleb I, Badolia R, Shankar TS, Amrute JM, Ling J, Hamouche R, Tseliou E, Navankasattusas S, Wever-Pinzon O, Ducker GS, Holland WL, Summers SA, Koenig SC, Hanff TC, Lavine KJ, Murali S, Bailey S, Alharethi R, Selzman CH, Shah P, Slaughter MS, Kanwar MK, Drakos SG. Integrating molecular and clinical variables to predict myocardial recovery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.16.589326. [PMID: 38659908 PMCID: PMC11042352 DOI: 10.1101/2024.04.16.589326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Mechanical unloading and circulatory support with left ventricular assist devices (LVADs) mediate significant myocardial improvement in a subset of advanced heart failure (HF) patients. The clinical and biological phenomena associated with cardiac recovery are under intensive investigation. Left ventricular (LV) apical tissue, alongside clinical data, were collected from HF patients at the time of LVAD implantation (n=208). RNA was isolated and mRNA transcripts were identified through RNA sequencing and confirmed with RT-qPCR. To our knowledge this is the first study to combine transcriptomic and clinical data to derive predictors of myocardial recovery. We used a bioinformatic approach to integrate 59 clinical variables and 22,373 mRNA transcripts at the time of LVAD implantation for the prediction of post-LVAD myocardial recovery defined as LV ejection fraction (LVEF) ≥40% and LV end-diastolic diameter (LVEDD) ≤5.9cm, as well as functional and structural LV improvement independently by using LVEF and LVEDD as continuous variables, respectively. To substantiate the predicted variables, we used a multi-model approach with logistic and linear regressions. Combining RNA and clinical data resulted in a gradient boosted model with 80 features achieving an AUC of 0.731±0.15 for predicting myocardial recovery. Variables associated with myocardial recovery from a clinical standpoint included HF duration, pre-LVAD LVEF, LVEDD, and HF pharmacologic therapy, and LRRN4CL (ligand binding and programmed cell death) from a biological standpoint. Our findings could have diagnostic, prognostic, and therapeutic implications for advanced HF patients, and inform the care of the broader HF population.
Collapse
|
5
|
Yu Y, Wang L, Hou W, Xue Y, Liu X, Li Y. Identification and validation of aging-related genes in heart failure based on multiple machine learning algorithms. Front Immunol 2024; 15:1367235. [PMID: 38686376 PMCID: PMC11056574 DOI: 10.3389/fimmu.2024.1367235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/03/2024] [Indexed: 05/02/2024] Open
Abstract
Background In the face of continued growth in the elderly population, the need to understand and combat age-related cardiac decline becomes even more urgent, requiring us to uncover new pathological and cardioprotective pathways. Methods We obtained the aging-related genes of heart failure through WGCNA and CellAge database. We elucidated the biological functions and signaling pathways involved in heart failure and aging through GO and KEGG enrichment analysis. We used three machine learning algorithms: LASSO, RF and SVM-RFE to further screen the aging-related genes of heart failure, and fitted and verified them through a variety of machine learning algorithms. We searched for drugs to treat age-related heart failure through the DSigDB database. Finally, We use CIBERSORT to complete immune infiltration analysis of aging samples. Results We obtained 57 up-regulated and 195 down-regulated aging-related genes in heart failure through WGCNA and CellAge databases. GO and KEGG enrichment analysis showed that aging-related genes are mainly involved in mechanisms such as Cellular senescence and Cell cycle. We further screened aging-related genes through machine learning and obtained 14 key genes. We verified the results on the test set and 2 external validation sets using 15 machine learning algorithm models and 207 combinations, and the highest accuracy was 0.911. Through screening of the DSigDB database, we believe that rimonabant and lovastatin have the potential to delay aging and protect the heart. The results of immune infiltration analysis showed that there were significant differences between Macrophages M2 and T cells CD8 in aging myocardium. Conclusion We identified aging signature genes and potential therapeutic drugs for heart failure through bioinformatics and multiple machine learning algorithms, providing new ideas for studying the mechanism and treatment of age-related cardiac decline.
Collapse
Affiliation(s)
- Yiding Yu
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Lin Wang
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Wangjun Hou
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yitao Xue
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Xiujuan Liu
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yan Li
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| |
Collapse
|
6
|
Tu D, Xu Q, Zuo X, Ma C. Uncovering hub genes and immunological characteristics for heart failure utilizing RRA, WGCNA and Machine learning. IJC HEART & VASCULATURE 2024; 51:101335. [PMID: 38371312 PMCID: PMC10869931 DOI: 10.1016/j.ijcha.2024.101335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 12/24/2023] [Accepted: 01/02/2024] [Indexed: 02/20/2024]
Abstract
Background Heart failure (HF) is a major public health issue with high mortality and morbidity. This study aimed to find potential diagnostic markers for HF by the combination of bioinformatics analysis and machine learning, as well as analyze the role of immune infiltration in the pathological process of HF. Methods The gene expression profiles of 124 HF patients and 135 nonfailing donors (NFDs) were obtained from six datasets in the NCBI Gene Expression Omnibus (GEO) public database. We applied robust rank aggregation (RRA) and weighted gene co-expression network analysis (WGCNA) method to identify critical genes in HF. To discover novel diagnostic markers in HF, three machine learning methods were employed, including best subset regression, regularization technique, and support vector machine-recursive feature elimination (SVM-RFE). Besides, immune infiltration was investigated in HF by single-sample gene set enrichment analysis (ssGSEA). Results Combining RRA with WGCNA method, we recognized 39 critical genes associated with HF. Through integrating three machine learning methods, FCN3 and SMOC2 were determined as novel diagnostic markers in HF. Differences in immune infiltration signature were also found between HF patients and NFDs. Moreover, we explored the potential associations between two diagnostic markers and immune response in the pathogenesis of HF. Conclusions In summary, FCN3 and SMOC2 can be used as diagnostic markers of HF, and immune infiltration plays an important role in the initiation and progression of HF.
Collapse
Affiliation(s)
- Dingyuan Tu
- Cardiovascular Research Institute and Department of Cardiology, General Hospital of Northern Theater Command, State Key Laboratory of Frigid Zone Cardiovascular Diseases (SKLFZCD), Shenyang, 110000 Liaoning, China
- Department of Cardiology, The 961st Hospital of Joint Logistic Support Force of PLA, 71 Youzheng Road, Qiqihar, 161000 Heilongjiang, China
| | - Qiang Xu
- Department of Cardiology, Navy 905 Hospital, Naval Medical University, 1328 Huashan Road, Changning District, Shanghai 200052, China
| | - Xiaoli Zuo
- Department of Cardiology, The 961st Hospital of Joint Logistic Support Force of PLA, 71 Youzheng Road, Qiqihar, 161000 Heilongjiang, China
| | - Chaoqun Ma
- Cardiovascular Research Institute and Department of Cardiology, General Hospital of Northern Theater Command, State Key Laboratory of Frigid Zone Cardiovascular Diseases (SKLFZCD), Shenyang, 110000 Liaoning, China
| |
Collapse
|
7
|
Tu D, Xu Q, Luan Y, Sun J, Zuo X, Ma C. Integrative analysis of bioinformatics and machine learning to identify cuprotosis-related biomarkers and immunological characteristics in heart failure. Front Cardiovasc Med 2024; 11:1349363. [PMID: 38562184 PMCID: PMC10982316 DOI: 10.3389/fcvm.2024.1349363] [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: 12/04/2023] [Accepted: 03/07/2024] [Indexed: 04/04/2024] Open
Abstract
Backgrounds Cuprotosis is a newly discovered programmed cell death by modulating tricarboxylic acid cycle. Emerging evidence showed that cuprotosis-related genes (CRGs) are implicated in the occurrence and progression of multiple diseases. However, the mechanism of cuprotosis in heart failure (HF) has not been investigated yet. Methods The HF microarray datasets GSE16499, GSE26887, GSE42955, GSE57338, GSE76701, and GSE79962 were downloaded from the Gene Expression Omnibus (GEO) database to identify differentially expressed CRGs between HF patients and nonfailing donors (NFDs). Four machine learning models were used to identify key CRGs features for HF diagnosis. The expression profiles of key CRGs were further validated in a merged GEO external validation dataset and human samples through quantitative reverse-transcription polymerase chain reaction (qRT-PCR). In addition, Gene Ontology (GO) function enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, and immune infiltration analysis were used to investigate potential biological functions of key CRGs. Results We discovered nine differentially expressed CRGs in heart tissues from HF patients and NFDs. With the aid of four machine learning algorithms, we identified three indicators of cuprotosis (DLAT, SLC31A1, and DLST) in HF, which showed good diagnostic properties. In addition, their differential expression between HF patients and NFDs was confirmed through qRT-PCR. Moreover, the results of enrichment analyses and immune infiltration exhibited that these diagnostic markers of CRGs were strongly correlated to energy metabolism and immune activity. Conclusions Our study discovered that cuprotosis was strongly related to the pathogenesis of HF, probably by regulating energy metabolism-associated and immune-associated signaling pathways.
Collapse
Affiliation(s)
- Dingyuan Tu
- Cardiovascular Research Institute and Department of Cardiology, General Hospital of Northern Theater Command, State Key Laboratory of Frigid Zone Cardiovascular Diseases (SKLFZCD), Shenyang, Liaoning, China
- Department of Cardiology, The 961st Hospital of PLA Joint Logistic Support Force, Qiqihar, Heilongjiang, China
| | - Qiang Xu
- Department of Cardiology, Changhai Hospital, Naval Medical University, Shanghai, China
- Department of Cardiology, Navy 905 Hospital, Naval Medical University, Shanghai, China
| | - Yanmin Luan
- Reproductive Medicine Center, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Jie Sun
- Hospital-Acquired Infection Control Department, Yantai Ludong Hospital, Yantai, Shandong, China
| | - Xiaoli Zuo
- Department of Cardiology, The 961st Hospital of PLA Joint Logistic Support Force, Qiqihar, Heilongjiang, China
| | - Chaoqun Ma
- Cardiovascular Research Institute and Department of Cardiology, General Hospital of Northern Theater Command, State Key Laboratory of Frigid Zone Cardiovascular Diseases (SKLFZCD), Shenyang, Liaoning, China
| |
Collapse
|
8
|
Cao J, Wei Z, Nie Y, Chen HZ. Therapeutic potential of alternative splicing in cardiovascular diseases. EBioMedicine 2024; 101:104995. [PMID: 38350330 PMCID: PMC10874720 DOI: 10.1016/j.ebiom.2024.104995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 01/19/2024] [Accepted: 01/21/2024] [Indexed: 02/15/2024] Open
Abstract
RNA splicing is an important RNA processing step required by multiexon protein-coding mRNAs and some noncoding RNAs. Precise RNA splicing is required for maintaining gene and cell function; however, mis-spliced RNA transcripts can lead to loss- or gain-of-function effects in human diseases. Mis-spliced RNAs induced by gene mutations or the dysregulation of splicing regulators may result in frameshifts, nonsense-mediated decay (NMD), or inclusion/exclusion of exons. Genetic animal models have characterised multiple splicing factors required for cardiac development or function. Moreover, sarcomeric and ion channel genes, which are closely associated with cardiovascular function and disease, are hotspots for AS. Here, we summarise splicing factors and their targets that are associated with cardiovascular diseases, introduce some therapies potentially related to pathological AS targets, and raise outstanding questions and future directions in this field.
Collapse
Affiliation(s)
- Jun Cao
- College of Chemistry and Life Science, Beijing University of Technology, Beijing, 100124, PR China; University of Texas Medical Branch at Galveston, TX, 77555, USA
| | - Ziyu Wei
- Department of Biochemistry & Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Yu Nie
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China.
| | - Hou-Zao Chen
- Department of Biochemistry & Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China; Medical Epigenetics Research Center, Chinese Academy of Medical Sciences, Beijing, China.
| |
Collapse
|
9
|
Cui Y, Zhang Z, Lv M, Duan Z, Liu W, Gao J, Xu R, Wan Q. Chromatin target of protein arginine methyltransferases alleviates cerebral ischemia/reperfusion-induced injury by regulating RNA alternative splicing. iScience 2024; 27:108688. [PMID: 38188517 PMCID: PMC10770728 DOI: 10.1016/j.isci.2023.108688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/01/2023] [Accepted: 12/05/2023] [Indexed: 01/09/2024] Open
Abstract
RNA splicing is a post-transcriptional event that regulates many physiological and pathological events. However, whether RNA splicing regulates cerebral I/R-induced brain injury remains largely unknown. In this study, we found that the chromatin target of Prmts (CHTOP) was highly expressed in neurons, and anti-inflammatory cytokine interleukin-10 (IL-10) upregulates its expression after ischemia. In addition, overexpression or knockdown of CHTOP alleviated or exacerbated neuronal death in both experimental stroke mice and cultured neurons. Mechanistically, RNA alternative splicing is altered early after oxygen and glucose deprivation/reoxygenation (OGD/R). CHTOP interacted with nuclear speckle-related proteins to regulate alternative mRNA splicing of neuronal survival-related genes after OGD/R. In addition, I/R injury-induced cytokines IL-10 regulate CHTOP-mediated RNA splicing to alleviate ischemic brain injury. Taken together, this study reveals the alteration of RNA splicing after OGD/R and identifies the IL-10-CHTOP-RNA splicing axis as a modulator of brain injury, which may be promising therapeutic targets for ischemic stroke.
Collapse
Affiliation(s)
- Yu Cui
- Institute of Neuroregeneration and Neurorehabilitation, Qingdao University, 308 Ningxia Road, Qingdao, Shandong 266071, China
- Qingdao Medical College, Qingdao University, Qingdao 266071, China
| | - Zhaolong Zhang
- Department of Interventional Radiology, The Affiliated Hospital of Qingdao University, 16 Jiangsu Road, Qingdao, Shandong 266000, China
| | - Mengfei Lv
- Institute of Neuroregeneration and Neurorehabilitation, Qingdao University, 308 Ningxia Road, Qingdao, Shandong 266071, China
- Qingdao Medical College, Qingdao University, Qingdao 266071, China
| | - Zhongying Duan
- Institute of Neuroregeneration and Neurorehabilitation, Qingdao University, 308 Ningxia Road, Qingdao, Shandong 266071, China
- Qingdao Medical College, Qingdao University, Qingdao 266071, China
| | - Wenhao Liu
- Department of Interventional Radiology, The Affiliated Hospital of Qingdao University, 16 Jiangsu Road, Qingdao, Shandong 266000, China
| | - Jingchen Gao
- Institute of Neuroregeneration and Neurorehabilitation, Qingdao University, 308 Ningxia Road, Qingdao, Shandong 266071, China
| | - Rui Xu
- Department of Interventional Radiology, The Affiliated Hospital of Qingdao University, 16 Jiangsu Road, Qingdao, Shandong 266000, China
| | - Qi Wan
- Institute of Neuroregeneration and Neurorehabilitation, Qingdao University, 308 Ningxia Road, Qingdao, Shandong 266071, China
- Qingdao Medical College, Qingdao University, Qingdao 266071, China
| |
Collapse
|
10
|
Tung LW, Groppa E, Soliman H, Lin B, Chang C, Cheung CW, Ritso M, Guo D, Rempel L, Sinha S, Eisner C, Brassard J, McNagny K, Biernaskie J, Rossi F. Spatiotemporal signaling underlies progressive vascular rarefaction in myocardial infarction. Nat Commun 2023; 14:8498. [PMID: 38129410 PMCID: PMC10739910 DOI: 10.1038/s41467-023-44227-6] [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: 08/04/2022] [Accepted: 12/05/2023] [Indexed: 12/23/2023] Open
Abstract
Therapeutic angiogenesis represents a promising avenue to revascularize the ischemic heart. Its limited success is partly due to our poor understanding of the cardiac stroma, specifically mural cells, and their response to ischemic injury. Here, we combine single-cell and positional transcriptomics to assess the behavior of mural cells within the healing heart. In response to myocardial infarction, mural cells adopt an altered state closely associated with the infarct and retain a distinct lineage from fibroblasts. This response is concurrent with vascular rarefaction and reduced vascular coverage by mural cells. Positional transcriptomics reveals that the infarcted heart is governed by regional-dependent and temporally regulated programs. While the remote zone acts as an important source of pro-angiogenic signals, the infarct zone is accentuated by chronic activation of anti-angiogenic, pro-fibrotic, and inflammatory cues. Together, our work unveils the spatiotemporal programs underlying cardiac repair and establishes an association between vascular deterioration and mural cell dysfunction.
Collapse
Affiliation(s)
- Lin Wei Tung
- School of Biomedical Engineering & Department of Medical Genetics, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Elena Groppa
- School of Biomedical Engineering & Department of Medical Genetics, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
- Borea Therapeutics, Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea, 265, 34136, Trieste, Italy
| | - Hesham Soliman
- School of Biomedical Engineering & Department of Medical Genetics, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
- Aspect Biosystems, 1781 W 75th Ave, Vancouver, BC, V6P 6P2, Canada
- Faculty of Pharmaceutical Sciences, Minia University, Minia, Egypt
| | - Bruce Lin
- School of Biomedical Engineering & Department of Medical Genetics, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Chihkai Chang
- School of Biomedical Engineering & Department of Medical Genetics, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Chun Wai Cheung
- School of Biomedical Engineering & Department of Medical Genetics, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Morten Ritso
- School of Biomedical Engineering & Department of Medical Genetics, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - David Guo
- School of Biomedical Engineering & Department of Medical Genetics, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Lucas Rempel
- School of Biomedical Engineering & Department of Medical Genetics, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Sarthak Sinha
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
- Department of Surgery, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Christine Eisner
- School of Biomedical Engineering & Department of Medical Genetics, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Julyanne Brassard
- School of Biomedical Engineering & Department of Medical Genetics, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Kelly McNagny
- School of Biomedical Engineering & Department of Medical Genetics, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Jeff Biernaskie
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
- Department of Surgery, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Fabio Rossi
- School of Biomedical Engineering & Department of Medical Genetics, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada.
| |
Collapse
|
11
|
Liu S, Yue S, Guo Y, Han JY, Wang H. Sorafenib induces cardiotoxicity through RBM20-mediated alternative splicing of sarcomeric and mitochondrial genes. Pharmacol Res 2023; 198:107017. [PMID: 38006979 DOI: 10.1016/j.phrs.2023.107017] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/12/2023] [Accepted: 11/22/2023] [Indexed: 11/27/2023]
Abstract
Sorafenib, a multi-targeted tyrosine kinase inhibitor, is a first-line treatment for advanced solid tumors, but it induces many adverse cardiovascular events, including myocardial infarction and heart failure. These cardiac defects can be mediated by alternative splicing of genes critical for heart function. Whether alternative splicing plays a role in sorafenib-induced cardiotoxicity remains unclear. Transcriptome of rat hearts or human cardiomyocytes treated with sorafenib was analyzed and validated to define alternatively spliced genes and their impact on cardiotoxicity. In rats, sorafenib caused severe cardiotoxicity with decreased left ventricular systolic pressure, elongated sarcomere, enlarged mitochondria and decreased ATP. This was associated with alternative splicing of hundreds of genes in the hearts, many of which were targets of a cardiac specific splicing factor, RBM20. Sorafenib inhibited RBM20 expression in both rat hearts and human cardiomyocytes. The splicing of RBM20's targets, SLC25A3 and FHOD3, was altered into fetal isoforms with decreased function. Upregulation of RBM20 during sorafenib treatment reversed the pathogenic splicing of SLC25A3 and FHOD3, and enhanced the phosphate transport into mitochondria by SLC25A3, ATP synthesis and cell survival.We envision this regulation may happen in many drug-induced cardiotoxicity, and represent a potential druggable pathway for mitigating sorafenib-induced cardiotoxicity.
Collapse
Affiliation(s)
- Songming Liu
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Shanshan Yue
- Department of Integration of Chinese and Western Medicine, School of Basic Medical Sciences, Peking University, Beijing 100191, China; Tasly Microcirculation Research Center, Peking University Health Science Center, Beijing 100191, China
| | - Yuxuan Guo
- Peking University Institute of Cardiovascular Sciences, Peking University Health Science Center, School of Basic Medical Sciences, Beijing 100191, China
| | - Jing-Yan Han
- Department of Integration of Chinese and Western Medicine, School of Basic Medical Sciences, Peking University, Beijing 100191, China; Tasly Microcirculation Research Center, Peking University Health Science Center, Beijing 100191, China.
| | - Huan Wang
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.
| |
Collapse
|
12
|
Schmeing S, Amrahova G, Bigler K, Chang JY, Openy J, Pal S, Posada L, Gasper R, 't Hart P. Rationally designed stapled peptides allosterically inhibit PTBP1-RNA-binding. Chem Sci 2023; 14:8269-8278. [PMID: 37564416 PMCID: PMC10411625 DOI: 10.1039/d3sc00985h] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 06/28/2023] [Indexed: 08/12/2023] Open
Abstract
The diverse role of the splicing factor PTBP1 in human cells has been widely studied and was found to be a driver for several diseases. PTBP1 binds RNA through its RNA-recognition motifs which lack obvious pockets for inhibition. A unique transient helix has been described to be part of its first RNA-recognition motif and to be important for RNA binding. In this study, we further confirmed the role of this helix and envisioned its dynamic nature as a unique opportunity to develop stapled peptide inhibitors of PTBP1. The peptides were found to be able to inhibit RNA binding via fluorescence polarization assays and directly occupy the helix binding site as observed by protein crystallography. These cell-permeable inhibitors were validated in cellulo to alter the regulation of alternative splicing events regulated by PTBP1. Our study demonstrates transient secondary structures of a protein can be mimicked by stapled peptides to inhibit allosteric mechanisms.
Collapse
Affiliation(s)
- Stefan Schmeing
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Gulshan Amrahova
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Katrin Bigler
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Jen-Yao Chang
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Joseph Openy
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Sunit Pal
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Laura Posada
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Raphael Gasper
- Crystallography and Biophysics Unit, Max-Planck-Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Peter 't Hart
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| |
Collapse
|
13
|
Friedman CE, Fayer S, Pendyala S, Chien WM, Loiben A, Tran L, Chao LS, Mckinstry A, Ahmed D, Karbassi E, Fenix AM, Murry CE, Starita LM, Fowler DM, Yang KC. CRaTER enrichment for on-target gene editing enables generation of variant libraries in hiPSCs. J Mol Cell Cardiol 2023; 179:60-71. [PMID: 37019277 PMCID: PMC10208587 DOI: 10.1016/j.yjmcc.2023.03.017] [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: 12/15/2022] [Revised: 03/14/2023] [Accepted: 03/29/2023] [Indexed: 04/07/2023]
Abstract
Standard transgenic cell line generation requires screening 100-1000s of colonies to isolate correctly edited cells. We describe CRISPRa On-Target Editing Retrieval (CRaTER) which enriches for cells with on-target knock-in of a cDNA-fluorescent reporter transgene by transient activation of the targeted locus followed by flow sorting to recover edited cells. We show CRaTER recovers rare cells with heterozygous, biallelic-editing of the transcriptionally-inactive MYH7 locus in human induced pluripotent stem cells (hiPSCs), enriching on average 25-fold compared to standard antibiotic selection. We leveraged CRaTER to enrich for heterozygous knock-in of a library of variants in MYH7, a gene in which missense mutations cause cardiomyopathies, and recovered hiPSCs with 113 different variants. We differentiated these hiPSCs to cardiomyocytes and show MHC-β fusion proteins can localize as expected. Additionally, single-cell contractility analyses revealed cardiomyocytes with a pathogenic, hypertrophic cardiomyopathy-associated MYH7 variant exhibit salient HCM physiology relative to isogenic controls. Thus, CRaTER substantially reduces screening required for isolation of gene-edited cells, enabling generation of functional transgenic cell lines at unprecedented scale.
Collapse
Affiliation(s)
- Clayton E Friedman
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Center for Cardiovascular Biology, University of Washington, Seattle, WA 98109, USA; Department of Medicine/Cardiology, University of Washington, Seattle, WA 98109, USA
| | - Shawn Fayer
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Sriram Pendyala
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Wei-Ming Chien
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Center for Cardiovascular Biology, University of Washington, Seattle, WA 98109, USA; Department of Medicine/Cardiology, University of Washington, Seattle, WA 98109, USA; Cardiology/Hospital Specialty Medicine, VA Puget Sound HCS, Seattle, WA 98108, USA
| | - Alexander Loiben
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Center for Cardiovascular Biology, University of Washington, Seattle, WA 98109, USA; Department of Medicine/Cardiology, University of Washington, Seattle, WA 98109, USA
| | - Linda Tran
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Center for Cardiovascular Biology, University of Washington, Seattle, WA 98109, USA; Department of Medicine/Cardiology, University of Washington, Seattle, WA 98109, USA
| | - Leslie S Chao
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Center for Cardiovascular Biology, University of Washington, Seattle, WA 98109, USA; Department of Medicine/Cardiology, University of Washington, Seattle, WA 98109, USA
| | - Ashley Mckinstry
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Center for Cardiovascular Biology, University of Washington, Seattle, WA 98109, USA; Department of Medicine/Cardiology, University of Washington, Seattle, WA 98109, USA
| | - Dania Ahmed
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Center for Cardiovascular Biology, University of Washington, Seattle, WA 98109, USA; Department of Medicine/Cardiology, University of Washington, Seattle, WA 98109, USA
| | - Elaheh Karbassi
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Center for Cardiovascular Biology, University of Washington, Seattle, WA 98109, USA; Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA 98109, USA
| | - Aidan M Fenix
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Center for Cardiovascular Biology, University of Washington, Seattle, WA 98109, USA; Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA 98109, USA
| | - Charles E Murry
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Center for Cardiovascular Biology, University of Washington, Seattle, WA 98109, USA; Department of Medicine/Cardiology, University of Washington, Seattle, WA 98109, USA; Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Lea M Starita
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Douglas M Fowler
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Kai-Chun Yang
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Center for Cardiovascular Biology, University of Washington, Seattle, WA 98109, USA; Department of Medicine/Cardiology, University of Washington, Seattle, WA 98109, USA; Cardiology/Hospital Specialty Medicine, VA Puget Sound HCS, Seattle, WA 98108, USA.
| |
Collapse
|
14
|
Gallinat A, Vilahur G, Padro T, Badimon L. Effects of Antioxidants in Fermented Beverages in Tissue Transcriptomics: Effect of Beer Intake on Myocardial Tissue after Oxidative Injury. Antioxidants (Basel) 2023; 12:antiox12051096. [PMID: 37237963 DOI: 10.3390/antiox12051096] [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: 04/06/2023] [Revised: 05/08/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
Fermented beverages, such as wine and beer, are rich in polyphenols that have been shown to have protective effects against oxidative stress. Oxidative stress plays a central role in the pathogenesis and progression of cardiovascular disease. However, the potential benefits of fermented beverages on cardiovascular health need to be fully investigated at a molecular level. In this study, we aimed at analyzing the effects of beer consumption in modulating the transcriptomic response of the heart to an oxidative stress challenge induced by myocardial ischemia (MI) in the presence of hypercholesterolemia in a pre-clinical swine model. Previous studies have shown that the same intervention induces organ protective benefits. We report a dose-dependent up-regulation of electron transport chain members and the down-regulation of spliceosome-associated genes linked to beer consumption. Additionally, low-dose beer consumption resulted in a down-regulation of genes associated with the immune response, that was not shown for moderate-dose beer consumption. These findings, observed in animals having demonstrated beneficial effects at the organ-level, indicate that the antioxidants in beer differentially affect the myocardial transcriptome in a dose-dependent manner.
Collapse
Affiliation(s)
- Alex Gallinat
- Cardiovascular Program-ICCC, IR-Hospital Santa Creu i Sant Pau, IIB-Sant Pau, IIBSANTPAU, 08041 Barcelona, Spain
| | - Gemma Vilahur
- Cardiovascular Program-ICCC, IR-Hospital Santa Creu i Sant Pau, IIB-Sant Pau, IIBSANTPAU, 08041 Barcelona, Spain
- Centro de Investigación Biomédica en Red Cardiovascular (CIBER-CV), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Teresa Padro
- Cardiovascular Program-ICCC, IR-Hospital Santa Creu i Sant Pau, IIB-Sant Pau, IIBSANTPAU, 08041 Barcelona, Spain
- Centro de Investigación Biomédica en Red Cardiovascular (CIBER-CV), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Lina Badimon
- Cardiovascular Program-ICCC, IR-Hospital Santa Creu i Sant Pau, IIB-Sant Pau, IIBSANTPAU, 08041 Barcelona, Spain
- Centro de Investigación Biomédica en Red Cardiovascular (CIBER-CV), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Cardiovascular Research Chair, Universitat Autònoma de Barcelona (UAB), 08193 Barcelona, Spain
| |
Collapse
|
15
|
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.
Collapse
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.
| |
Collapse
|
16
|
Sapashnik D, Newman R, Pietras CM, Zhou D, Devkota K, Qu F, Kofman L, Boudreau S, Fried I, Slonim DK. Cell-specific imputation of drug connectivity mapping with incomplete data. PLoS One 2023; 18:e0278289. [PMID: 36795645 PMCID: PMC9934325 DOI: 10.1371/journal.pone.0278289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 11/15/2022] [Indexed: 02/17/2023] Open
Abstract
Drug repositioning allows expedited discovery of new applications for existing compounds, but re-screening vast compound libraries is often prohibitively expensive. "Connectivity mapping" is a process that links drugs to diseases by identifying compounds whose impact on expression in a collection of cells reverses the disease's impact on expression in disease-relevant tissues. The LINCS project has expanded the universe of compounds and cells for which data are available, but even with this effort, many clinically useful combinations are missing. To evaluate the possibility of repurposing drugs despite missing data, we compared collaborative filtering using either neighborhood-based or SVD imputation methods to two naive approaches via cross-validation. Methods were evaluated for their ability to predict drug connectivity despite missing data. Predictions improved when cell type was taken into account. Neighborhood collaborative filtering was the most successful method, with the best improvements in non-immortalized primary cells. We also explored which classes of compounds are most and least reliant on cell type for accurate imputation. We conclude that even for cells in which drug responses have not been fully characterized, it is possible to identify unassayed drugs that reverse in those cells the expression signatures observed in disease.
Collapse
Affiliation(s)
- Diana Sapashnik
- Department of Computer Science, Tufts University, Medford, MA, United States of America
| | - Rebecca Newman
- Department of Computer Science, Tufts University, Medford, MA, United States of America
| | | | - Di Zhou
- Department of Computer Science, Tufts University, Medford, MA, United States of America
| | - Kapil Devkota
- Department of Computer Science, Tufts University, Medford, MA, United States of America
| | - Fangfang Qu
- Department of Computer Science, Tufts University, Medford, MA, United States of America
| | - Lior Kofman
- Department of Computer Science, Tufts University, Medford, MA, United States of America
| | - Sean Boudreau
- Department of Computer Science, Tufts University, Medford, MA, United States of America
| | - Inbar Fried
- Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, NC, United States of America
| | - Donna K. Slonim
- Department of Computer Science, Tufts University, Medford, MA, United States of America
- Department of Immunology, Tufts University School of Medicine, Boston, MA, United States of America
- * E-mail:
| |
Collapse
|
17
|
Ma C, Tu D, Xu Q, Wu Y, Song X, Guo Z, Zhao X. Identification of m 7G regulator-mediated RNA methylation modification patterns and related immune microenvironment regulation characteristics in heart failure. Clin Epigenetics 2023; 15:22. [PMID: 36782329 PMCID: PMC9926673 DOI: 10.1186/s13148-023-01439-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 02/05/2023] [Indexed: 02/15/2023] Open
Abstract
BACKGROUND N7-methylguanosine (m7G) modification has been reported to regulate RNA expression in multiple pathophysiological processes. However, little is known about its role and association with immune microenvironment in heart failure (HF). RESULTS One hundred twenty-four HF patients and 135 nonfailing donors (NFDs) from six microarray datasets in the gene expression omnibus (GEO) database were included to evaluate the expression profiles of m7G regulators. Results revealed that 14 m7G regulators were differentially expressed in heart tissues from HF patients and NFDs. Furthermore, a five-gene m7G regulator diagnostic signature, NUDT16, NUDT4, CYFIP1, LARP1, and DCP2, which can easily distinguish HF patients and NFDs, was established by cross-combination of three machine learning methods, including best subset regression, regularization techniques, and random forest algorithm. The diagnostic value of five-gene m7G regulator signature was further validated in human samples through quantitative reverse-transcription polymerase chain reaction (qRT-PCR). In addition, consensus clustering algorithms were used to categorize HF patients into distinct molecular subtypes. We identified two distinct m7G subtypes of HF with unique m7G modification pattern, functional enrichment, and immune characteristics. Additionally, two gene subgroups based on m7G subtype-related genes were further discovered. Single-sample gene-set enrichment analysis (ssGSEA) was utilized to assess the alterations of immune microenvironment. Finally, utilizing protein-protein interaction network and weighted gene co-expression network analysis (WGCNA), we identified UQCRC1, NDUFB6, and NDUFA13 as m7G methylation-associated hub genes with significant clinical relevance to cardiac functions. CONCLUSIONS Our study discovered for the first time that m7G RNA modification and immune microenvironment are closely correlated in HF development. A five-gene m7G regulator diagnostic signature for HF (NUDT16, NUDT4, CYFIP1, LARP1, and DCP2) and three m7G methylation-associated hub genes (UQCRC1, NDUFB6, and NDUFA13) were identified, providing new insights into the underlying mechanisms and effective treatments of HF.
Collapse
Affiliation(s)
- Chaoqun Ma
- Cardiovascular Research Institute and Department of Cardiology, General Hospital of Northern Theater Command, Shenyang, 110000, Liaoning, China
| | - Dingyuan Tu
- Cardiovascular Research Institute and Department of Cardiology, General Hospital of Northern Theater Command, Shenyang, 110000, Liaoning, China
- Department of Cardiology, Changhai Hospital, Naval Medical University, 168 Changhai Rd, Shanghai, 200433, China
| | - Qiang Xu
- Department of Cardiology, Navy 905 Hospital, Naval Medical University, Shanghai, 200052, China
| | - Yan Wu
- Department of Cardiology, Navy 905 Hospital, Naval Medical University, Shanghai, 200052, China
| | - Xiaowei Song
- Department of Cardiology, Changhai Hospital, Naval Medical University, 168 Changhai Rd, Shanghai, 200433, China.
| | - Zhifu Guo
- Department of Cardiology, Changhai Hospital, Naval Medical University, 168 Changhai Rd, Shanghai, 200433, China.
| | - Xianxian Zhao
- Department of Cardiology, Changhai Hospital, Naval Medical University, 168 Changhai Rd, Shanghai, 200433, China.
| |
Collapse
|
18
|
Rogalska ME, Vafiadaki E, Erpapazoglou Z, Haghighi K, Green L, Mantzoros CS, Hajjar RJ, Tranter M, Karakikes I, Kranias EG, Stillitano F, Kafasla P, Sanoudou D. Isoform changes of action potential regulators in the ventricles of arrhythmogenic phospholamban-R14del humanized mouse hearts. Metabolism 2023; 138:155344. [PMID: 36375644 DOI: 10.1016/j.metabol.2022.155344] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 10/30/2022] [Accepted: 11/01/2022] [Indexed: 11/13/2022]
Abstract
Arrhythmogenic cardiomyopathy (ACM) is characterized by life-threatening ventricular arrhythmias and sudden cardiac death and affects hundreds of thousands of patients worldwide. The deletion of Arginine 14 (p.R14del) in the phospholamban (PLN) gene has been implicated in the pathogenesis of ACM. PLN is a key regulator of sarcoplasmic reticulum (SR) Ca2+ cycling and cardiac contractility. Despite global gene and protein expression studies, the molecular mechanisms of PLN-R14del ACM pathogenesis remain unclear. Using a humanized PLN-R14del mouse model and human induced pluripotent stem cell derived cardiomyocytes (iPSC-CMs), we investigated the transcriptome-wide mRNA splicing changes associated with the R14del mutation. We identified >200 significant alternative splicing (AS) events and distinct AS profiles were observed in the right (RV) and left (LV) ventricles in PLN-R14del compared to WT mouse hearts. Enrichment analysis of the AS events showed that the most affected biological process was associated with "cardiac cell action potential", specifically in the RV. We found that splicing of 2 key genes, Trpm4 and Camk2d, which encode proteins regulating calcium homeostasis in the heart, were altered in PLN-R14del mouse hearts and human iPSC-CMs. Bioinformatical analysis pointed to the tissue-specific splicing factors Srrm4 and Nova1 as likely upstream regulators of the observed splicing changes in the PLN-R14del cardiomyocytes. Our findings suggest that aberrant splicing may affect Ca2+-homeostasis in the heart, contributing to the increased risk of arrythmogenesis in PLN-R14del ACM.
Collapse
Affiliation(s)
- Malgorzata E Rogalska
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
| | - Elizabeth Vafiadaki
- Molecular Biology Division, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Zoi Erpapazoglou
- Institute for Fundamental Biomedical Research, B.S.R.C. "Alexander Fleming", 16672 Athens, Greece
| | - Kobra Haghighi
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Lisa Green
- Department of Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Christos S Mantzoros
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA; Section of Endocrinology, Boston VA Healthcare System, Harvard Medical School, Boston, MA 02215, USA
| | | | - Michael Tranter
- Department of Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Ioannis Karakikes
- Department of Cardiothoracic Surgery and Cardiovascular Institute, Stanford University School of Medicine, 240 Pasteur Dr, Stanford, CA 94304, USA
| | - Evangelia G Kranias
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Francesca Stillitano
- Division Heart and Lung, Department of Cardiology, University Medical Center Utrecht, 3584, CX, Utrecht, the Netherlands
| | - Panagiota Kafasla
- Institute for Fundamental Biomedical Research, B.S.R.C. "Alexander Fleming", 16672 Athens, Greece
| | - Despina Sanoudou
- Molecular Biology Division, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece; Clinical Genomics and Pharmacogenomics Unit, 4(th) Department of Internal Medicine, Attikon Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; Center for New Biotechnologies and Precision Medicine, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece.
| |
Collapse
|
19
|
Reitz CJ, Rasouli M, Alibhai FJ, Khatua TN, Pyle WG, Martino TA. A brief morning rest period benefits cardiac repair in pressure overload hypertrophy and postmyocardial infarction. JCI Insight 2022; 7:164700. [PMID: 36256456 DOI: 10.1172/jci.insight.164700] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/12/2022] [Indexed: 12/15/2022] Open
Abstract
Rest has long been considered beneficial to patient healing; however, remarkably, there are no evidence-based experimental models determining how it benefits disease outcomes. Here, we created an experimental rest model in mice that briefly extends the morning rest period. We found in 2 major cardiovascular disease conditions (cardiac hypertrophy, myocardial infarction) that imposing a short, extended period of morning rest each day limited cardiac remodeling compared with controls. Mechanistically, rest mitigates autonomic-mediated hemodynamic stress on the cardiovascular system, relaxes myofilament contractility, and attenuates cardiac remodeling genes, consistent with the benefits on cardiac structure and function. These same rest-responsive gene pathways underlie the pathophysiology of many major human cardiovascular conditions, as demonstrated by interrogating open-source transcriptomic data; thus, patients with other conditions may also benefit from a morning rest period in a similar manner. Our findings implicate rest as a key driver of physiology, creating a potentially new field - as broad and important as diet, sleep, or exercise - and provide a strong rationale for investigation of rest-based therapy for major clinical diseases.
Collapse
|
20
|
Britto-Borges T, Ludt A, Boileau E, Gjerga E, Marini F, Dieterich C. Magnetique: an interactive web application to explore transcriptome signatures of heart failure. J Transl Med 2022; 20:513. [DOI: 10.1186/s12967-022-03694-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/05/2022] [Accepted: 10/06/2022] [Indexed: 11/09/2022] Open
Abstract
Abstract
Background
Despite a recent increase in the number of RNA-seq datasets investigating heart failure (HF), accessibility and usability remain critical issues for medical researchers. We address the need for an intuitive and interactive web application to explore the transcriptional signatures of heart failure with this work.
Methods
We reanalysed the Myocardial Applied Genomics Network RNA-seq dataset, one of the largest publicly available datasets of left ventricular RNA-seq samples from patients with dilated (DCM) or hypertrophic (HCM) cardiomyopathy, as well as unmatched non-failing hearts (NFD) from organ donors and patient characteristics that allowed us to model confounding factors. We analyse differential gene expression, associated pathway signatures and reconstruct signaling networks based on inferred transcription factor activities through integer linear programming. We additionally focus, for the first time, on differential RNA transcript isoform usage (DTU) changes and predict RNA-binding protein (RBP) to target transcript interactions using a Global test approach. We report results for all pairwise comparisons (DCM, HCM, NFD).
Results
Focusing on the DCM versus HCM contrast (DCMvsHCM), we identified 201 differentially expressed genes, some of which can be clearly associated with changes in ERK1 and ERK2 signaling. Interestingly, the signs of the predicted activity for these two kinases have been inferred to be opposite to each other: In the DCMvsHCM contrast, we predict ERK1 to be consistently less activated in DCM while ERK2 was more activated in DCM. In the DCMvsHCM contrast, we identified 149 differently used transcripts. One of the top candidates is the O-linked N-acetylglucosamine (GlcNAc) transferase (OGT), which catalyzes a common post-translational modification known for its role in heart arrhythmias and heart hypertrophy. Moreover, we reconstruct RBP – target interaction networks and showcase the examples of CPEB1, which is differentially expressed in the DCMvsHCM contrast.
Conclusion
Magnetique (https://shiny.dieterichlab.org/app/magnetique) is the first online application to provide an interactive view of the HF transcriptome at the RNA isoform level and to include transcription factor signaling and RBP:RNA interaction networks. The source code for both the analyses (https://github.com/dieterich-lab/magnetiqueCode2022) and the web application (https://github.com/AnnekathrinSilvia/magnetique) is available to the public. We hope that our application will help users to uncover the molecular basis of heart failure.
Collapse
|
21
|
Tu D, Ma C, Zeng Z, Xu Q, Guo Z, Song X, Zhao X. Identification of hub genes and transcription factor regulatory network for heart failure using RNA-seq data and robust rank aggregation analysis. Front Cardiovasc Med 2022; 9:916429. [PMID: 36386304 PMCID: PMC9649652 DOI: 10.3389/fcvm.2022.916429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 09/30/2022] [Indexed: 11/23/2022] Open
Abstract
Background Heart failure (HF) is the end stage of various cardiovascular diseases with a high mortality rate. Novel diagnostic and therapeutic biomarkers for HF are urgently required. Our research aims to identify HF-related hub genes and regulatory networks using bioinformatics and validation assays. Methods Using four RNA-seq datasets in the Gene Expression Omnibus (GEO) database, we screened differentially expressed genes (DEGs) of HF using Removal of Unwanted Variation from RNA-seq data (RUVSeq) and the robust rank aggregation (RRA) method. Then, hub genes were recognized using the STRING database and Cytoscape software with cytoHubba plug-in. Furthermore, reliable hub genes were validated by the GEO microarray datasets and quantitative reverse transcription polymerase chain reaction (qRT-PCR) using heart tissues from patients with HF and non-failing donors (NFDs). In addition, R packages “clusterProfiler” and “GSVA” were utilized for enrichment analysis. Moreover, the transcription factor (TF)–DEG regulatory network was constructed by Cytoscape and verified in a microarray dataset. Results A total of 201 robust DEGs were identified in patients with HF and NFDs. STRING and Cytoscape analysis recognized six hub genes, among which ASPN, COL1A1, and FMOD were confirmed as reliable hub genes through microarray datasets and qRT-PCR validation. Functional analysis showed that the DEGs and hub genes were enriched in T-cell-mediated immune response and myocardial glucose metabolism, which were closely associated with myocardial fibrosis. In addition, the TF–DEG regulatory network was constructed, and 13 significant TF–DEG pairs were finally identified. Conclusion Our study integrated different RNA-seq datasets using RUVSeq and the RRA method and identified ASPN, COL1A1, and FMOD as potential diagnostic biomarkers for HF. The results provide new insights into the underlying mechanisms and effective treatments of HF.
Collapse
Affiliation(s)
- Dingyuan Tu
- Department of Cardiology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Chaoqun Ma
- Department of Cardiology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - ZhenYu Zeng
- Department of Cardiology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Qiang Xu
- Department of Cardiology, Navy 905 Hospital, Naval Medical University, Shanghai, China
| | - Zhifu Guo
- Department of Cardiology, Changhai Hospital, Naval Medical University, Shanghai, China
- *Correspondence: Zhifu Guo,
| | - Xiaowei Song
- Department of Cardiology, Changhai Hospital, Naval Medical University, Shanghai, China
- Xiaowei Song,
| | - Xianxian Zhao
- Department of Cardiology, Changhai Hospital, Naval Medical University, Shanghai, China
- Xianxian Zhao,
| |
Collapse
|
22
|
Cardiovascular Involvement in Pediatric FLNC Variants: A Case Series of Fourteen Patients. J Cardiovasc Dev Dis 2022; 9:jcdd9100332. [PMID: 36286284 PMCID: PMC9604120 DOI: 10.3390/jcdd9100332] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 09/22/2022] [Indexed: 11/16/2022] Open
Abstract
Filamin C is a protein specifically expressed in myocytes and cardiomyocytes and is involved in several biological functions, including sarcomere contractile activity, signaling, cellular adhesion, and repair. FLNC variants are associated with different disorders ranging from striated muscle (myofibrillar distal or proximal) myopathy to cardiomyopathies (CMPs) (restrictive, hypertrophic, and dilated), or both. The outcome depends on functional consequences of the detected variants, which result either in FLNC haploinsufficiency or in an aberrant protein, the latter affecting sarcomere structure leading to protein aggregates. Cardiac manifestations of filaminopathies are most often described as adult onset CMPs and limited reports are available in children or on other cardiac spectrums (congenital heart defects-CHDs, or arrhythmias). Here we report on 13 variants in 14 children (2.8%) out of 500 pediatric patients with early-onset different cardiac features ranging from CMP to arrhythmias and CHDs. In one patient, we identified a deletion encompassing FLNC detected by microarray, which was overlooked by next generation sequencing. We established a potential genotype-phenotype correlation of the p.Ala1186Val variant in severe and early-onset restrictive cardiomyopathy (RCM) associated with a limb-girdle defect (two new patients in addition to the five reported in the literature). Moreover, in three patients (21%), we identified a relatively frequent finding of long QT syndrome (LQTS) associated with RCM (n = 2) and a hypertrabeculated left ventricle (n = 1). RCM and LQTS in children might represent a specific red flag for FLNC variants. Further studies are warranted in pediatric cohorts to delineate potential expanding phenotypes related to FLNC.
Collapse
|
23
|
Clavere NG, Alqallaf A, Rostron KA, Parnell A, Mitchell R, Patel K, Boateng SY. Inhibition of activin A receptor signalling attenuates age-related pathological cardiac remodelling. Dis Model Mech 2022; 15:275323. [PMID: 35380160 PMCID: PMC9118092 DOI: 10.1242/dmm.049424] [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: 12/17/2021] [Accepted: 03/16/2022] [Indexed: 11/20/2022] Open
Abstract
In the heart, ageing is associated with DNA damage, oxidative stress, fibrosis and activation of the activin signalling pathway, leading to cardiac dysfunction. The cardiac effects of activin signalling blockade in progeria are unknown. This study investigated the cardiac effects of progeria induced by attenuated levels of Ercc1, which is required for DNA excision and repair, and the impact of activin signalling blockade using a soluble activin receptor type IIB (sActRIIB). DNA damage and oxidative stress were significantly increased in Ercc1Δ/− hearts, but were reduced by sActRIIB treatment. sActRIIB treatment improved cardiac systolic function and induced cardiomyocyte hypertrophy in Ercc1Δ/− hearts. RNA-sequencing analysis showed that in Ercc1Δ/− hearts, there was an increase in pro-oxidant and a decrease in antioxidant gene expression, whereas sActRIIB treatment reversed this effect. Ercc1Δ/− hearts also expressed higher levels of anti-hypertrophic genes and decreased levels of pro-hypertrophic ones, which were also reversed by sActRIIB treatment. These results show for the first time that inhibition of activin A receptor signalling attenuates cardiac dysfunction, pathological tissue remodelling and gene expression in Ercc1-deficient mice and presents a potentially novel therapeutic target for heart diseases. Summary: Attenuated DNA repair is associated with pathological cardiac remodelling and gene expression. Much of this phenotype is attenuated by inhibition of the activin signalling pathway using soluble activin receptor treatment.
Collapse
Affiliation(s)
- Nicolas G Clavere
- Institute of Cardiovascular and Metabolic Research, School of Biological Sciences, Health and Life Sciences Building, University of Reading, Whiteknights, Reading RG6 6UB, UK
| | - Ali Alqallaf
- Institute of Cardiovascular and Metabolic Research, School of Biological Sciences, Health and Life Sciences Building, University of Reading, Whiteknights, Reading RG6 6UB, UK
| | - Kerry A Rostron
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College London, Commonwealth Building, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Andrew Parnell
- Institute of Cardiovascular and Metabolic Research, School of Biological Sciences, Health and Life Sciences Building, University of Reading, Whiteknights, Reading RG6 6UB, UK
| | - Robert Mitchell
- Institute of Cardiovascular and Metabolic Research, School of Biological Sciences, Health and Life Sciences Building, University of Reading, Whiteknights, Reading RG6 6UB, UK
| | - Ketan Patel
- Institute of Cardiovascular and Metabolic Research, School of Biological Sciences, Health and Life Sciences Building, University of Reading, Whiteknights, Reading RG6 6UB, UK
| | - Samuel Y Boateng
- Institute of Cardiovascular and Metabolic Research, School of Biological Sciences, Health and Life Sciences Building, University of Reading, Whiteknights, Reading RG6 6UB, UK
| |
Collapse
|
24
|
Robinson EL, Baker AH, Brittan M, McCracken I, Condorelli G, Emanueli C, Srivastava PK, Gaetano C, Thum T, Vanhaverbeke M, Angione C, Heymans S, Devaux Y, Pedrazzini T, Martelli F. Dissecting the transcriptome in cardiovascular disease. Cardiovasc Res 2022; 118:1004-1019. [PMID: 33757121 PMCID: PMC8930073 DOI: 10.1093/cvr/cvab117] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 03/22/2021] [Indexed: 12/12/2022] Open
Abstract
The human transcriptome comprises a complex network of coding and non-coding RNAs implicated in a myriad of biological functions. Non-coding RNAs exhibit highly organized spatial and temporal expression patterns and are emerging as critical regulators of differentiation, homeostasis, and pathological states, including in the cardiovascular system. This review defines the current knowledge gaps, unmet methodological needs, and describes the challenges in dissecting and understanding the role and regulation of the non-coding transcriptome in cardiovascular disease. These challenges include poor annotation of the non-coding genome, determination of the cellular distribution of transcripts, assessment of the role of RNA processing and identification of cell-type specific changes in cardiovascular physiology and disease. We highlight similarities and differences in the hurdles associated with the analysis of the non-coding and protein-coding transcriptomes. In addition, we discuss how the lack of consensus and absence of standardized methods affect reproducibility of data. These shortcomings should be defeated in order to make significant scientific progress and foster the development of clinically applicable non-coding RNA-based therapeutic strategies to lessen the burden of cardiovascular disease.
Collapse
Affiliation(s)
- Emma L Robinson
- Department of Cardiology, Cardiovascular Research Institute Maastricht (CARIM), Universiteitssingel 50, 6229 Maastricht University, Maastricht, The Netherlands
- The Division of Cardiology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Andrew H Baker
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Mairi Brittan
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Ian McCracken
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - G Condorelli
- Humanitas Research Hospital, Humanitas University, Via Manzoni 113, Rozzano, MI 20089, Italy
| | - C Emanueli
- Imperial College, National Heart and Lung Institute, Hammersmith campus, Du Cane Road, London W12 0NN, UK
| | - P K Srivastava
- Imperial College, National Heart and Lung Institute, Hammersmith campus, Du Cane Road, London W12 0NN, UK
| | - C Gaetano
- Laboratorio di Epigenetica, Istituti Clinici Scientifici Maugeri IRCCS, Via Maugeri 4, Pavia 27100, Italy
| | - T Thum
- Hannover Medical School, Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Carl-Neuberg-Straße 1 30625 Hannover, Germany
| | - M Vanhaverbeke
- UZ Gasthuisberg Campus, KU Leuven, Herestraat 49 3000 Leuven, Belgium
| | - C Angione
- Department of Computer Science and Information Systems, Teesside University, Middlesbrough, TS4 3BX, UK
| | - S Heymans
- Department of Cardiology, Cardiovascular Research Institute Maastricht (CARIM), Universiteitssingel 50, 6229 Maastricht University, Maastricht, The Netherlands
| | - Y Devaux
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, 1A-B, rue Thomas Edison, L-1445 Strassen, Luxembourg
| | - T Pedrazzini
- Experimental Cardiology Unit, Division of Cardiology, Department of Cardiovascular Medicine, University of Lausanne Medical School, 1011 Lausanne, Switzerland
| | - F Martelli
- Molecular Cardiology Laboratory, IRCCS-Policlinico San Donato, Piazza Edmondo Malan, 2, 20097 San Donato, Milan, Italy
| | | |
Collapse
|
25
|
Liang X, Bai Z, Wang F, Han Y, Sun H, Xiaokereti J, Zhang L, Zhou X, Lu Y, Tang B. Full-Length Transcriptome Sequencing: An Insight Into the Dog Model of Heart Failure. Front Cardiovasc Med 2021; 8:712797. [PMID: 34977163 PMCID: PMC8716442 DOI: 10.3389/fcvm.2021.712797] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 11/02/2021] [Indexed: 12/30/2022] Open
Abstract
Heart failure (HF) leads to a progressive increase in morbidity and mortality rates. This study aimed to explore the transcriptional landscape during HF and identify differentially expressed transcripts (DETs) and alternative splicing events associated with HF. We generated a dog model of HF (n = 3) using right ventricular pacemaker implantation. We performed full-length transcriptome sequencing (based on nanopore platform) on the myocardial tissues and analyzed the transcripts using differential expression analysis and functional annotation methods [Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses]. Additionally, we estimated the expression of the selected genes by quantitative real-time PCR (qRT-PCR) and detected the proportion of immune cells using flow cytometry. We found that increased B-type natriuretic peptide reduced ejection fraction, and apparent clinical signs were observed in the dog model of HF. We identified 67,458 transcripts using full-length transcriptome sequencing. A total of 785 DETs were obtained from the HF and control groups. These DETs were mainly enriched in the immune responses, especially Th1, Th2, and Th17 cell differentiation processes. Furthermore, flow cytometry results revealed that the proportion of Th1 and Th17 cells increased in patients with HF compared to controls, while the proportion of Th2 cells decreased. Differentially expressed genes in the HF and control groups associated with Th1, Th2, and Th17 cell differentiation were quantified using qRT-PCR. We also identified variable splicing events of sarcomere genes (e.g., MYBPC3, TNNT2, TTN, FLNC, and TTNI3). In addition, we detected 4,892 transcription factors and 406 lncRNAs associated with HF. Our analysis based on full-length transcript sequencing provided an analysis perspective in a dog model of HF, which is valuable for molecular research in an increasingly relevant large animal model of HF.
Collapse
Affiliation(s)
- Xiaoyan Liang
- Department of Pacing and Electrophysiology, The First Affiliated Hospital of Xinjiang Medical University, Ürümqi, China
- Xinjiang Key Laboratory of Cardiac Electrophysiology and Cardiac Remodeling, The First Affiliated Hospital of Xinjiang Medical University, Ürümqi, China
| | - Zechen Bai
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences (CAS), Shenzhen, China
| | - Feifei Wang
- Department of Pacing and Electrophysiology, The First Affiliated Hospital of Xinjiang Medical University, Ürümqi, China
- Xinjiang Key Laboratory of Cardiac Electrophysiology and Cardiac Remodeling, The First Affiliated Hospital of Xinjiang Medical University, Ürümqi, China
- Xinjiang First Aid Center, People's Hospital of Xinjiang Uygur Autonomous Region, Ürümqi, China
| | - Yafan Han
- Department of Pacing and Electrophysiology, The First Affiliated Hospital of Xinjiang Medical University, Ürümqi, China
- Xinjiang Key Laboratory of Cardiac Electrophysiology and Cardiac Remodeling, The First Affiliated Hospital of Xinjiang Medical University, Ürümqi, China
| | - Huaxin Sun
- Department of Pacing and Electrophysiology, The First Affiliated Hospital of Xinjiang Medical University, Ürümqi, China
- Xinjiang Key Laboratory of Cardiac Electrophysiology and Cardiac Remodeling, The First Affiliated Hospital of Xinjiang Medical University, Ürümqi, China
| | - Jiasuoer Xiaokereti
- Department of Pacing and Electrophysiology, The First Affiliated Hospital of Xinjiang Medical University, Ürümqi, China
- Xinjiang Key Laboratory of Cardiac Electrophysiology and Cardiac Remodeling, The First Affiliated Hospital of Xinjiang Medical University, Ürümqi, China
| | - Ling Zhang
- Xinjiang Key Laboratory of Cardiac Electrophysiology and Cardiac Remodeling, The First Affiliated Hospital of Xinjiang Medical University, Ürümqi, China
| | - Xianhui Zhou
- Department of Pacing and Electrophysiology, The First Affiliated Hospital of Xinjiang Medical University, Ürümqi, China
- Xinjiang Key Laboratory of Cardiac Electrophysiology and Cardiac Remodeling, The First Affiliated Hospital of Xinjiang Medical University, Ürümqi, China
| | - Yanmei Lu
- Department of Pacing and Electrophysiology, The First Affiliated Hospital of Xinjiang Medical University, Ürümqi, China
- Xinjiang Key Laboratory of Cardiac Electrophysiology and Cardiac Remodeling, The First Affiliated Hospital of Xinjiang Medical University, Ürümqi, China
- *Correspondence: Baopeng Tang
| | - Baopeng Tang
- Department of Pacing and Electrophysiology, The First Affiliated Hospital of Xinjiang Medical University, Ürümqi, China
- Xinjiang Key Laboratory of Cardiac Electrophysiology and Cardiac Remodeling, The First Affiliated Hospital of Xinjiang Medical University, Ürümqi, China
- Yanmei Lu
| |
Collapse
|
26
|
Montañés-Agudo P, Casini S, Aufiero S, Ernault AC, van der Made I, Pinto YM, Remme CA, Creemers EE. Inhibition of minor intron splicing reduces Na+ and Ca2+ channel expression and function in cardiomyocytes. J Cell Sci 2021; 135:273616. [PMID: 34859816 PMCID: PMC8767276 DOI: 10.1242/jcs.259191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 11/26/2021] [Indexed: 12/04/2022] Open
Abstract
Eukaryotic genomes contain a tiny subset of ‘minor class’ introns with unique sequence elements that require their own splicing machinery. These minor introns are present in certain gene families with specific functions, such as voltage-gated Na+ and voltage-gated Ca2+ channels. Removal of minor introns by the minor spliceosome has been proposed as a post-transcriptional regulatory layer, which remains unexplored in the heart. Here, we investigate whether the minor spliceosome regulates electrophysiological properties of cardiomyocytes by knocking down the essential minor spliceosome small nuclear snRNA component U6atac in neonatal rat ventricular myocytes. Loss of U6atac led to robust minor intron retention within Scn5a and Cacna1c, resulting in reduced protein levels of Nav1.5 and Cav1.2 channels. Functional consequences were studied through patch-clamp analysis, and revealed reduced Na+ and L-type Ca2+ currents after loss of U6atac. In conclusion, minor intron splicing modulates voltage-dependent ion channel expression and function in cardiomyocytes. This may be of particular relevance in situations in which minor splicing activity changes, such as in genetic diseases affecting minor spliceosome components, or in acquired diseases in which minor spliceosome components are dysregulated, such as heart failure. Summary: Knockdown of minor spliceosome component U6atac in cardiomyocytes reveals that expression of the Na+ channel Scn5a and the L-type Ca2+ channel Cacna1c critically depend on minor intron splicing.
Collapse
Affiliation(s)
- Pablo Montañés-Agudo
- Departments of Experimental Cardiology, Biostatistics and Bioinformatics, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| | - Simona Casini
- Departments of Experimental Cardiology, Biostatistics and Bioinformatics, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| | - Simona Aufiero
- Departments of Experimental Cardiology, Biostatistics and Bioinformatics, Amsterdam UMC, location AMC, Amsterdam, The Netherlands.,Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| | - Auriane C Ernault
- Departments of Experimental Cardiology, Biostatistics and Bioinformatics, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| | - Ingeborg van der Made
- Departments of Experimental Cardiology, Biostatistics and Bioinformatics, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| | - Yigal M Pinto
- Departments of Experimental Cardiology, Biostatistics and Bioinformatics, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| | - Carol Ann Remme
- Departments of Experimental Cardiology, Biostatistics and Bioinformatics, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| | - Esther E Creemers
- Departments of Experimental Cardiology, Biostatistics and Bioinformatics, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| |
Collapse
|
27
|
Fenix AM, Miyaoka Y, Bertero A, Blue SM, Spindler MJ, Tan KKB, Perez-Bermejo JA, Chan AH, Mayerl SJ, Nguyen TD, Russell CR, Lizarraga PP, Truong A, So PL, Kulkarni A, Chetal K, Sathe S, Sniadecki NJ, Yeo GW, Murry CE, Conklin BR, Salomonis N. Gain-of-function cardiomyopathic mutations in RBM20 rewire splicing regulation and re-distribute ribonucleoprotein granules within processing bodies. Nat Commun 2021; 12:6324. [PMID: 34732726 PMCID: PMC8566601 DOI: 10.1038/s41467-021-26623-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 09/22/2021] [Indexed: 12/16/2022] Open
Abstract
Mutations in the cardiac splicing factor RBM20 lead to malignant dilated cardiomyopathy (DCM). To understand the mechanism of RBM20-associated DCM, we engineered isogenic iPSCs with DCM-associated missense mutations in RBM20 as well as RBM20 knockout (KO) iPSCs. iPSC-derived engineered heart tissues made from these cell lines recapitulate contractile dysfunction of RBM20-associated DCM and reveal greater dysfunction with missense mutations than KO. Analysis of RBM20 RNA binding by eCLIP reveals a gain-of-function preference of mutant RBM20 for 3' UTR sequences that are shared with amyotrophic lateral sclerosis (ALS) and processing-body associated RNA binding proteins (FUS, DDX6). Deep RNA sequencing reveals that the RBM20 R636S mutant has unique gene, splicing, polyadenylation and circular RNA defects that differ from RBM20 KO. Super-resolution microscopy verifies that mutant RBM20 maintains very limited nuclear localization potential; rather, the mutant protein associates with cytoplasmic processing bodies (DDX6) under basal conditions, and with stress granules (G3BP1) following acute stress. Taken together, our results highlight a pathogenic mechanism in cardiac disease through splicing-dependent and -independent pathways.
Collapse
Affiliation(s)
- Aidan M Fenix
- Department of Laboratory Medicine and Pathology, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98195, USA
- Center for Cardiovascular Biology, University of Washington, 850 Republican Street, Brotman Building, Seattle, WA, 98109, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, WA, 98109, USA
| | - Yuichiro Miyaoka
- Regenerative Medicine Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan
- Gladstone Institutes, 1650 Owens St, San Francisco, CA, 94158, USA
| | - Alessandro Bertero
- Department of Laboratory Medicine and Pathology, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98195, USA
- Center for Cardiovascular Biology, University of Washington, 850 Republican Street, Brotman Building, Seattle, WA, 98109, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, WA, 98109, USA
| | - Steven M Blue
- Department of Cellular and Molecular Medicine, Stem Cell Program, and Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | | | - Kenneth K B Tan
- Gladstone Institutes, 1650 Owens St, San Francisco, CA, 94158, USA
| | | | - Amanda H Chan
- Gladstone Institutes, 1650 Owens St, San Francisco, CA, 94158, USA
| | - Steven J Mayerl
- Gladstone Institutes, 1650 Owens St, San Francisco, CA, 94158, USA
| | - Trieu D Nguyen
- Gladstone Institutes, 1650 Owens St, San Francisco, CA, 94158, USA
| | | | | | - Annie Truong
- Gladstone Institutes, 1650 Owens St, San Francisco, CA, 94158, USA
| | - Po-Lin So
- Gladstone Institutes, 1650 Owens St, San Francisco, CA, 94158, USA
| | - Aishwarya Kulkarni
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH, 45221, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Kashish Chetal
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Shashank Sathe
- Department of Cellular and Molecular Medicine, Stem Cell Program, and Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Nathan J Sniadecki
- Department of Laboratory Medicine and Pathology, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98195, USA
- Center for Cardiovascular Biology, University of Washington, 850 Republican Street, Brotman Building, Seattle, WA, 98109, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, WA, 98109, USA
- Department of Mechanical Engineering, University of Washington, 3720 15th Avenue NE, Seattle, WA, 98105, USA
- Department of Bioengineering, University of Washington, 3720 15th Avenue NE, Seattle, WA, 98105, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, Stem Cell Program, and Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Charles E Murry
- Department of Laboratory Medicine and Pathology, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98195, USA.
- Center for Cardiovascular Biology, University of Washington, 850 Republican Street, Brotman Building, Seattle, WA, 98109, USA.
- Institute for Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, WA, 98109, USA.
- Department of Bioengineering, University of Washington, 3720 15th Avenue NE, Seattle, WA, 98105, USA.
- Department of Medicine/Cardiology, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98195, USA.
- Sana Biotechnology, 188 E Blaine Street, Seattle, WA, 98102, USA.
| | - Bruce R Conklin
- Gladstone Institutes, 1650 Owens St, San Francisco, CA, 94158, USA.
- Department of Medicine, Cellular and Molecular Pharmacology, and Ophthalmology, University of California San Francisco, San Francisco, CA, 94158, USA.
| | - Nathan Salomonis
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, 45229, USA.
| |
Collapse
|
28
|
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.
Collapse
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
| |
Collapse
|
29
|
Yuan J, Wang JM, Li ZW, Zhang CS, Cheng B, Yang SH, Liu BT, Zhu LJ, Cai DJ, Yu SG. Full-length transcriptome analysis reveals the mechanism of acupuncture at PC6 improves cardiac function in myocardial ischemia model. Chin Med 2021; 16:55. [PMID: 34238326 PMCID: PMC8268520 DOI: 10.1186/s13020-021-00465-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 07/03/2021] [Indexed: 11/28/2022] Open
Abstract
Background The pathological process of myocardial ischemia (MI) is very complicated. Acupuncture at PC6 has been proved to be effective against MI injury, but the mechanism remains unclear. This study investigated the mechanism that underlies the effect of acupuncture on MI through full-length transcriptome. Methods Adult male C57/BL6 mice were randomly divided into control, MI, and PC6 groups. Mice in MI and PC6 group generated MI model by ligating the left anterior descending (LAD) coronary artery. The samples were collected 5 days after acupuncture treatment. Results The results showed that treatment by acupuncture improved cardiac function, decreased myocardial infraction area, and reduced the levels of cTnT and cTnI. Based on full-length transcriptome sequencing, 5083 differential expression genes (DEGs) and 324 DEGs were identified in the MI group and PC6 group, respectively. These genes regulated by acupuncture were mainly enriched in the inflammatory response pathway. Alternative splicing (AS) is a post-transcriptional action that contributes to the diversity of protein. In all samples, 8237 AS events associated with 1994 genes were found. Some differential AS-involved genes were enriched in the pathway related to heart disease. We also identified 602 new genes, 4 of which may the novel targets of acupuncture in MI. Conclusions Our findings suggest that the effect of acupuncture on MI may be based on the multi-level regulation of the transcriptome. Supplementary Information The online version contains supplementary material available at 10.1186/s13020-021-00465-8.
Collapse
Affiliation(s)
- Jing Yuan
- Acupuncture and Tuina School/Third Teaching Hospital, Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, Sichuan Province, China
| | - Jun-Meng Wang
- Acupuncture and Tuina School/Third Teaching Hospital, Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, Sichuan Province, China
| | - Zhi-Wei Li
- Acupuncture and Tuina School/Third Teaching Hospital, Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, Sichuan Province, China
| | - Cheng-Shun Zhang
- Acupuncture and Tuina School/Third Teaching Hospital, Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, Sichuan Province, China
| | - Bin Cheng
- Acupuncture and Tuina School/Third Teaching Hospital, Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, Sichuan Province, China
| | - Su-Hao Yang
- Acupuncture and Tuina School/Third Teaching Hospital, Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, Sichuan Province, China
| | - Bai-Tong Liu
- Acupuncture and Tuina School/Third Teaching Hospital, Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, Sichuan Province, China
| | - Li-Juan Zhu
- Acupuncture and Tuina School/Third Teaching Hospital, Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, Sichuan Province, China
| | - Ding-Jun Cai
- Acupuncture and Tuina School/Third Teaching Hospital, Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, Sichuan Province, China.
| | - Shu-Guang Yu
- Acupuncture and Tuina School/Third Teaching Hospital, Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, Sichuan Province, China.
| |
Collapse
|
30
|
Vancheri C, Morini E, Prandi FR, Alkhoury E, Celotto R, Romeo F, Novelli G, Amati F. Two RECK Splice Variants (Long and Short) Are Differentially Expressed in Patients with Stable and Unstable Coronary Artery Disease: A Pilot Study. Genes (Basel) 2021; 12:genes12060939. [PMID: 34205376 PMCID: PMC8234100 DOI: 10.3390/genes12060939] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/10/2021] [Accepted: 06/15/2021] [Indexed: 12/12/2022] Open
Abstract
Primary prevention is crucial for coronary heart disease (CAD) and the identification of new reliable biomarkers might help risk stratification or predict adverse coronary events. Alternative splicing (AS) is a less investigated genetic factors implicated in CAD etiology. We performed an RNA-seq study on PBMCs from CAD patients and control subjects (CTR) and observed 113 differentially regulated AS events (24 up and 89 downregulated) in 86 genes. The RECK (Reversion-inducing-cysteine-rich protein with Kazal motifs) gene was further analyzed in a larger case study (24 CTR subjects, 72 CAD and 32 AMI patients) for its Splicing-Index FC (FC = −2.64; p = 0.0217), the AS event involving an exon (exon 18), and its role in vascular inflammation and remodeling. We observed a significant downregulation of Long RECK splice variant (containing exon 18) in PBMCs of AMI compared to CTR subjects (FC = −3.3; p < 0.005). Interestingly, the Short RECK splice variant (lacking exon 18) was under-expressed in AMI compared to both CTR (FC = −4.5; p < 0.0001) and CAD patients (FC = −4.2; p < 0.0001). A ROC curve, constructed combining Long and Short RECK expression data, shows an AUC = 0.81 (p < 0.001) to distinguish AMI from stable CAD patients. A significant negative correlation between Long RECK and triglycerides in CTR group and a positive correlation in the AMI group was found. The combined evaluation of Long and Short RECK expression levels is a potential genomic biomarker for the discrimination of AMI from CAD patients. Our results underline the relevance of deeper studies on the expression of these two splice variants to elucidate their functional role in CAD development and progression.
Collapse
Affiliation(s)
- Chiara Vancheri
- Genetics Unit, Department of Biomedicine and Prevention, University of Rome “Tor Vergata”, 00133 Rome, Italy; (C.V.); (E.M.); (G.N.)
| | - Elena Morini
- Genetics Unit, Department of Biomedicine and Prevention, University of Rome “Tor Vergata”, 00133 Rome, Italy; (C.V.); (E.M.); (G.N.)
| | - Francesca Romana Prandi
- Unit of Cardiology, University Hospital “Tor Vergata”, 00133 Rome, Italy; (F.R.P.); (E.A.); (R.C.); (F.R.)
| | - Elie Alkhoury
- Unit of Cardiology, University Hospital “Tor Vergata”, 00133 Rome, Italy; (F.R.P.); (E.A.); (R.C.); (F.R.)
| | - Roberto Celotto
- Unit of Cardiology, University Hospital “Tor Vergata”, 00133 Rome, Italy; (F.R.P.); (E.A.); (R.C.); (F.R.)
| | - Francesco Romeo
- Unit of Cardiology, University Hospital “Tor Vergata”, 00133 Rome, Italy; (F.R.P.); (E.A.); (R.C.); (F.R.)
- Unicamillus International Medical University, 00131 Rome, Italy
| | - Giuseppe Novelli
- Genetics Unit, Department of Biomedicine and Prevention, University of Rome “Tor Vergata”, 00133 Rome, Italy; (C.V.); (E.M.); (G.N.)
- Medical Genetics Laboratories, Tor Vergata University Hospital, PTV, 00133 Rome, Italy
- Neuromed IRCCS Institute, 86077 Pozzilli, Italy
- School of Medicine, Reno University of Nevada, Reno, NV 1664, USA
| | - Francesca Amati
- Genetics Unit, Department of Biomedicine and Prevention, University of Rome “Tor Vergata”, 00133 Rome, Italy; (C.V.); (E.M.); (G.N.)
- Department for the Promotion of Human Science and Quality of Life, University San Raffaele, 00166 Rome, Italy
- Correspondence:
| |
Collapse
|
31
|
Ramirez Flores RO, Lanzer JD, Holland CH, Leuschner F, Most P, Schultz J, Levinson RT, Saez‐Rodriguez J. Consensus Transcriptional Landscape of Human End-Stage Heart Failure. J Am Heart Assoc 2021; 10:e019667. [PMID: 33787284 PMCID: PMC8174362 DOI: 10.1161/jaha.120.019667] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 02/18/2021] [Indexed: 12/13/2022]
Abstract
Background Transcriptomic studies have contributed to fundamental knowledge of myocardial remodeling in human heart failure (HF). However, the key HF genes reported are often inconsistent between studies, and systematic efforts to integrate evidence from multiple patient cohorts are lacking. Here, we aimed to provide a framework for comprehensive comparison and analysis of publicly available data sets resulting in an unbiased consensus transcriptional signature of human end-stage HF. Methods and Results We curated and uniformly processed 16 public transcriptomic studies of left ventricular samples from 263 healthy and 653 failing human hearts. First, we evaluated the degree of consistency between studies by using linear classifiers and overrepresentation analysis. Then, we meta-analyzed the deregulation of 14 041 genes to extract a consensus signature of HF. Finally, to functionally characterize this signature, we estimated the activities of 343 transcription factors, 14 signaling pathways, and 182 micro RNAs, as well as the enrichment of 5998 biological processes. Machine learning approaches revealed conserved disease patterns across all studies independent of technical differences. These consistent molecular changes were prioritized with a meta-analysis, functionally characterized and validated on external data. We provide all results in a free public resource (https://saezlab.shinyapps.io/reheat/) and exemplified usage by deciphering fetal gene reprogramming and tracing the potential myocardial origin of the plasma proteome markers in patients with HF. Conclusions Even though technical and sampling variability confound the identification of differentially expressed genes in individual studies, we demonstrated that coordinated molecular responses during end-stage HF are conserved. The presented resource is crucial to complement findings in independent studies and decipher fundamental changes in failing myocardium.
Collapse
Affiliation(s)
- Ricardo O. Ramirez Flores
- Faculty of Medicine, and Heidelberg University HospitalInstitute for Computational BiomedicineBioquantHeidelberg UniversityHeidelbergGermany
- Faculty of BiosciencesHeidelberg UniversityHeidelbergGermany
- Informatics for LifeHeidelbergGermany
| | - Jan D. Lanzer
- Faculty of Medicine, and Heidelberg University HospitalInstitute for Computational BiomedicineBioquantHeidelberg UniversityHeidelbergGermany
- Faculty of BiosciencesHeidelberg UniversityHeidelbergGermany
- Informatics for LifeHeidelbergGermany
- Department of General Internal Medicine and PsychosomaticsHeidelberg University HospitalHeidelbergGermany
| | - Christian H. Holland
- Faculty of Medicine, and Heidelberg University HospitalInstitute for Computational BiomedicineBioquantHeidelberg UniversityHeidelbergGermany
- Faculty of BiosciencesHeidelberg UniversityHeidelbergGermany
| | - Florian Leuschner
- Department of CardiologyMedical University HospitalHeidelbergGermany
- DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/MannheimHeidelbergGermany
| | - Patrick Most
- Department of CardiologyMedical University HospitalHeidelbergGermany
- DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/MannheimHeidelbergGermany
- Center for Translational MedicineJefferson UniversityPhiladelphiaPA
| | - Jobst‐Hendrik Schultz
- Department of General Internal Medicine and PsychosomaticsHeidelberg University HospitalHeidelbergGermany
| | - Rebecca T. Levinson
- Informatics for LifeHeidelbergGermany
- Department of General Internal Medicine and PsychosomaticsHeidelberg University HospitalHeidelbergGermany
| | - Julio Saez‐Rodriguez
- Faculty of Medicine, and Heidelberg University HospitalInstitute for Computational BiomedicineBioquantHeidelberg UniversityHeidelbergGermany
- Informatics for LifeHeidelbergGermany
- Faculty of MedicineJoint Research Centre for Computational Biomedicine (JRC‐COMBINE)RWTH Aachen UniversityAachenGermany
| |
Collapse
|
32
|
Auxerre-Plantié E, Nielsen T, Grunert M, Olejniczak O, Perrot A, Özcelik C, Harries D, Matinmehr F, Dos Remedios C, Mühlfeld C, Kraft T, Bodmer R, Vogler G, Sperling SR. Identification of MYOM2 as a candidate gene in hypertrophic cardiomyopathy and Tetralogy of Fallot, and its functional evaluation in the Drosophila heart. Dis Model Mech 2020; 13:dmm045377. [PMID: 33033063 PMCID: PMC7758640 DOI: 10.1242/dmm.045377] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 10/01/2020] [Indexed: 01/11/2023] Open
Abstract
The causal genetic underpinnings of congenital heart diseases, which are often complex and multigenic, are still far from understood. Moreover, there are also predominantly monogenic heart defects, such as cardiomyopathies, with known disease genes for the majority of cases. In this study, we identified mutations in myomesin 2 (MYOM2) in patients with Tetralogy of Fallot (TOF), the most common cyanotic heart malformation, as well as in patients with hypertrophic cardiomyopathy (HCM), who do not exhibit any mutations in the known disease genes. MYOM2 is a major component of the myofibrillar M-band of the sarcomere, and a hub gene within interactions of sarcomere genes. We show that patient-derived cardiomyocytes exhibit myofibrillar disarray and reduced passive force with increasing sarcomere lengths. Moreover, our comprehensive functional analyses in the Drosophila animal model reveal that the so far uncharacterized fly gene CG14964 [herein referred to as Drosophila myomesin and myosin binding protein (dMnM)] may be an ortholog of MYOM2, as well as other myosin binding proteins. Its partial loss of function or moderate cardiac knockdown results in cardiac dilation, whereas more severely reduced function causes a constricted phenotype and an increase in sarcomere myosin protein. Moreover, compound heterozygous combinations of CG14964 and the sarcomere gene Mhc (MYH6/7) exhibited synergistic genetic interactions. In summary, our results suggest that MYOM2 not only plays a critical role in maintaining robust heart function but may also be a candidate gene for heart diseases such as HCM and TOF, as it is clearly involved in the development of the heart.This article has an associated First Person interview with Emilie Auxerre-Plantié and Tanja Nielsen, joint first authors of the paper.
Collapse
Affiliation(s)
- Emilie Auxerre-Plantié
- Cardiovascular Genetics, Charité - Universitätsmedizin Berlin, 13125 Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Tanja Nielsen
- Cardiovascular Genetics, Charité - Universitätsmedizin Berlin, 13125 Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin, Germany
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany
| | - Marcel Grunert
- Cardiovascular Genetics, Charité - Universitätsmedizin Berlin, 13125 Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin, Germany
| | - Olga Olejniczak
- Cardiovascular Genetics, Charité - Universitätsmedizin Berlin, 13125 Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin, Germany
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany
| | - Andreas Perrot
- Cardiovascular Genetics, Charité - Universitätsmedizin Berlin, 13125 Berlin, Germany
- Experimental and Clinical Research Center, Charité - Universitätsmedizin Berlin, 13125 Berlin, Germany
| | - Cemil Özcelik
- Experimental and Clinical Research Center, Charité - Universitätsmedizin Berlin, 13125 Berlin, Germany
| | - Dennis Harries
- Medical School of Hannover, Institute of Molecular and Cell Physiology, 30625 Hannover, Germany
| | - Faramarz Matinmehr
- Medical School of Hannover, Institute of Molecular and Cell Physiology, 30625 Hannover, Germany
| | - Cristobal Dos Remedios
- Anatomy and Histology, School of Medical Sciences, Bosch Institute, University of Sydney, Camperdown, Sydney, New South Wales 2006, Australia
| | - Christian Mühlfeld
- Institute of Functional and Applied Anatomy, Hannover Medical School, 30625 Hannover, Germany
| | - Theresia Kraft
- Medical School of Hannover, Institute of Molecular and Cell Physiology, 30625 Hannover, Germany
| | - Rolf Bodmer
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Georg Vogler
- Cardiovascular Genetics, Charité - Universitätsmedizin Berlin, 13125 Berlin, Germany
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Silke R Sperling
- Cardiovascular Genetics, Charité - Universitätsmedizin Berlin, 13125 Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin, Germany
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany
| |
Collapse
|
33
|
Abstract
Gene expression is needed for the maintenance of heart function under normal conditions and in response to stress. Each cell type of the heart has a specific program controlling transcription. Different types of stress induce modifications of these programs and, if prolonged, can lead to altered cardiac phenotype and, eventually, to heart failure. The transcriptional status of a gene is regulated by the epigenome, a complex network of DNA and histone modifications. Until a few years ago, our understanding of the role of the epigenome in heart disease was limited to that played by histone deacetylation. But over the last decade, the consequences for the maintenance of homeostasis in the heart and for the development of cardiac hypertrophy of a number of other modifications, including DNA methylation and hydroxymethylation, histone methylation and acetylation, and changes in chromatin architecture, have become better understood. Indeed, it is now clear that many levels of regulation contribute to defining the epigenetic landscape required for correct cardiomyocyte function, and that their perturbation is responsible for cardiac hypertrophy and fibrosis. Here, we review these aspects and draw a picture of what epigenetic modification may imply at the therapeutic level for heart failure.
Collapse
Affiliation(s)
- Roberto Papait
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy; Humanitas Clinical Research Center-IRCCS, Rozzano, Italy; Humanitas University, Department of Biomedical Sciences, Pieve Emanuele, Italy; and National Research Council of Italy, Institute of Genetics and Biomedical Research, Milan Unit, Rozzano, Italy
| | - Simone Serio
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy; Humanitas Clinical Research Center-IRCCS, Rozzano, Italy; Humanitas University, Department of Biomedical Sciences, Pieve Emanuele, Italy; and National Research Council of Italy, Institute of Genetics and Biomedical Research, Milan Unit, Rozzano, Italy
| | - Gianluigi Condorelli
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy; Humanitas Clinical Research Center-IRCCS, Rozzano, Italy; Humanitas University, Department of Biomedical Sciences, Pieve Emanuele, Italy; and National Research Council of Italy, Institute of Genetics and Biomedical Research, Milan Unit, Rozzano, Italy
| |
Collapse
|
34
|
Dissecting the role of alternative splicing in the regulation of autophagy: a narrative review. JOURNAL OF BIO-X RESEARCH 2020. [DOI: 10.1097/jbr.0000000000000062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
|
35
|
Genetics of Anthracycline-Mediated Cardiotoxicity: Current Status and Challenges. CURRENT CARDIOVASCULAR RISK REPORTS 2020. [DOI: 10.1007/s12170-020-00647-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
36
|
Ho JWK. Biophysical Review's 'meet the editors series'-a profile of Joshua W. K. Ho. Biophys Rev 2020; 12:745-748. [PMID: 32725478 DOI: 10.1007/s12551-020-00744-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2020] [Indexed: 01/19/2023] Open
Abstract
It is my pleasure to write a few words to introduce myself to the readers of Biophysical Reviews as part of the 'meet the editors' series. A portrait of Dr. Joshua Ho.
Collapse
Affiliation(s)
- Joshua W K Ho
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong.
| |
Collapse
|
37
|
Jing L, Feng L, Zhou Z, Shi S, Deng R, Wang Z, Zhang Y, Ren Z, Liu Y. TNNT2 as a potential biomarker for the progression and prognosis of colorectal cancer. Oncol Rep 2020; 44:628-636. [PMID: 32627044 PMCID: PMC7336514 DOI: 10.3892/or.2020.7637] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 02/26/2020] [Indexed: 12/15/2022] Open
Abstract
Colorectal cancer (CRC) is the third most common cancer worldwide. At present, there are limited effective biomarkers of CRC. The present study aimed to identify potential signatures associated with the tumorigenesis and prognosis of CRC using publicly available databases, and further validate the identified biomarkers in CRC cell lines. Identification of differentially expressed mRNAs between CRC and paracancerous samples was conducted based on data from The Cancer Genome Atlas (TCGA; 471 tumor samples and 41 normal samples). Survival analysis was performed to explore the prognostic value of troponin 2 (TNNT2) in the TCGA training set, which was further validated in an external dataset, GSE17531. Functional enrichment analysis was conducted to determine the possible biological functions using GSEA 3.0. Reverse transcription-quantitative PCR (RT-qPCR) and western blotting were utilized to detect the mRNA and protein expression levels of TNNT2 between CRC and normal colorectal cells. Immunohistochemistry was performed to detect the protein expression of TNNT2 in CRC and normal tissues. TNNT2 was significantly upregulated in CRC samples compared with adjacent normal samples in the TCGA dataset. Increased expression of TNNT2 was associated with inferior prognosis in the TCGA training dataset and GSE17531 validation dataset. Functional enrichment analysis revealed that the ErbB signaling pathway and glycerophospholipid metabolism pathway were significantly activated in the TNNT2 high expression group. Overexpression of TNNT2 mRNA and TNNT2 protein in CRC tumor cells was confirmed by RT-qPCR and western blotting, respectively. Immunohistochemistry indicated increased protein expression levels of TNNT2 in CRC tissues in comparison with normal tissues. TNNT2 was associated with the tumorigenesis and prognosis of CRC, which may be useful for novel biomarker identification and targeted therapeutic strategy development.
Collapse
Affiliation(s)
- Li Jing
- Department of Medical Oncology, Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050011, P.R. China
| | - Li Feng
- Department of Medical Oncology, Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050011, P.R. China
| | - Zhiguo Zhou
- Department of Radiotherapy, Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050011, P.R. China
| | - Shuai Shi
- Hebei Medical University, Shijiazhuang, Hebei 050011, P.R. China
| | - Ruoying Deng
- Hebei Medical University, Shijiazhuang, Hebei 050011, P.R. China
| | - Zhicong Wang
- Hebei Medical University, Shijiazhuang, Hebei 050011, P.R. China
| | - Yi Zhang
- Hebei Medical University, Shijiazhuang, Hebei 050011, P.R. China
| | - Zhixue Ren
- The Seven People's Hospital of Hebei Province, Dingzhou, Hebei 073000, P.R. China
| | - Yibing Liu
- Department of Medical Oncology, Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050011, P.R. China
| |
Collapse
|
38
|
Jiang F, Fan H, Luo L, Li Y. An Integrative Transcriptome Analysis Reveals Consistently Dysregulated Long Noncoding RNAs and Their Transcriptional Regulation Relationships in Heart Failure. JOURNAL OF COMPUTATIONAL BIOLOGY : A JOURNAL OF COMPUTATIONAL MOLECULAR CELL BIOLOGY 2020; 27:958-964. [PMID: 31556694 DOI: 10.1089/cmb.2019.0246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Accumulating evidence suggests that long noncoding RNAs (lncRNAs) are emerging as important regulators involved in diseases, including heart failure (HF). In this study, we used microarray profiles to examine the transcriptome of lncRNAs in left ventricle samples derived from HF patients. We designed a custom pipeline to reannotate lncRNAs from microarray data and identified a set of consistently dysregulated lncRNAs in HF across the three independent cohorts. In total, 84 lncRNAs were found to be consistently dysregulated in at least two cohorts. By using a rank aggregation method, we integrated correlated protein-coding genes of the consistently dysregulated lncRNAs derived from HF samples and characterized their biological functions based on the correlated genes. The transcriptional regulation relationships of these lncRNAs ranged from 104 to 261, suggesting their important regulatory functions. Among the conserved lncRNAs, AC018647.1 and AC009113.1 showed significant dysregulation across all three cohorts. Our results showed that the two lncRNAs were involved in development-associated and cardiac cycle-associated functions.
Collapse
Affiliation(s)
- Fangping Jiang
- Department of Cardiovascular Medicine, 363 Hospital, Chengdu, China
| | - Hong Fan
- Department of Cardiovascular Medicine, 363 Hospital, Chengdu, China
| | - Lian Luo
- Department of Cardiovascular Medicine, 363 Hospital, Chengdu, China
| | - Yun Li
- Department of Cardiovascular Medicine, Chengdu Sixth People's Hospital, Chengdu, China
| |
Collapse
|
39
|
Wang H, Wang X, Xu L, Cao H. Identification of transcription factors MYC and C/EBPβ mediated regulatory networks in heart failure based on gene expression omnibus datasets. BMC Cardiovasc Disord 2020; 20:250. [PMID: 32460775 PMCID: PMC7251862 DOI: 10.1186/s12872-020-01527-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 05/13/2020] [Indexed: 11/29/2022] Open
Abstract
Background Heart failure is one of leading cause of death worldwide. However, the transcriptional profiling of heart failure is unclear. Moreover, the signaling pathways and transcription factors involving the heart failure development also are largely unknown. Using published Gene Expression Omnibus (GEO) datasets, in the present study, we aim to comprehensively analyze the differentially expressed genes in failing heart tissues, and identified the critical signaling pathways and transcription factors involving heart failure development. Methods The transcriptional profiling of heart failure was identified from previously published gene expression datasets deposited in GSE5406, GSE16499 and GSE68316. The enriched signaling pathways and transcription factors were analyzed using Database for Annotation, Visualization and Integrated Discovery (DAVID) website and gene set enrichment analysis (GSEA) assay. The transcriptional networks were created by Cytoscape. Results Compared with the normal heart tissues, 90 genes were particularly differentially expressed in failing heart tissues, and those genes were associated with multiple metabolism signaling pathways and insulin signaling pathway. Metabolism and insulin signaling pathway were both inactivated in failing heart tissues. Transcription factors MYC and C/EBPβ were both negatively associated with the expression profiling of failing heart tissues in GSEA assay. Moreover, compared with normal heart tissues, MYC and C/EBPβ were down regulated in failing heart tissues. Furthermore, MYC and C/EBPβ mediated downstream target genes were also decreased in failing heart tissues. MYC and C/EBPβ were positively correlated with each other. At last, we constructed MYC and C/EBPβ mediated regulatory networks in failing heart tissues, and identified the MYC and C/EBPβ target genes which had been reported involving the heart failure developmental progress. Conclusions Our results suggested that metabolism pathways and insulin signaling pathway, transcription factors MYC and C/EBPβ played critical roles in heart failure developmental progress.
Collapse
Affiliation(s)
- Haiwei Wang
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, FuZhou, 350001, FuJian, China
| | - Xinrui Wang
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, FuZhou, 350001, FuJian, China
| | - Liangpu Xu
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, FuZhou, 350001, FuJian, China
| | - Hua Cao
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, FuZhou, 350001, FuJian, China.
| |
Collapse
|
40
|
Fochi S, Lorenzi P, Galasso M, Stefani C, Trabetti E, Zipeto D, Romanelli MG. The Emerging Role of the RBM20 and PTBP1 Ribonucleoproteins in Heart Development and Cardiovascular Diseases. Genes (Basel) 2020; 11:genes11040402. [PMID: 32276354 PMCID: PMC7230170 DOI: 10.3390/genes11040402] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/04/2020] [Accepted: 04/06/2020] [Indexed: 12/17/2022] Open
Abstract
Alternative splicing is a regulatory mechanism essential for cell differentiation and tissue organization. More than 90% of human genes are regulated by alternative splicing events, which participate in cell fate determination. The general mechanisms of splicing events are well known, whereas only recently have deep-sequencing, high throughput analyses and animal models provided novel information on the network of functionally coordinated, tissue-specific, alternatively spliced exons. Heart development and cardiac tissue differentiation require thoroughly regulated splicing events. The ribonucleoprotein RBM20 is a key regulator of the alternative splicing events required for functional and structural heart properties, such as the expression of TTN isoforms. Recently, the polypyrimidine tract-binding protein PTBP1 has been demonstrated to participate with RBM20 in regulating splicing events. In this review, we summarize the updated knowledge relative to RBM20 and PTBP1 structure and molecular function; their role in alternative splicing mechanisms involved in the heart development and function; RBM20 mutations associated with idiopathic dilated cardiovascular disease (DCM); and the consequences of RBM20-altered expression or dysfunction. Furthermore, we discuss the possible application of targeting RBM20 in new approaches in heart therapies.
Collapse
|
41
|
Gao C, Wang Y. mRNA Metabolism in Cardiac Development and Disease: Life After Transcription. Physiol Rev 2020; 100:673-694. [PMID: 31751167 PMCID: PMC7327233 DOI: 10.1152/physrev.00007.2019] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 09/06/2019] [Accepted: 10/30/2019] [Indexed: 02/06/2023] Open
Abstract
The central dogma of molecular biology illustrates the importance of mRNAs as critical mediators between genetic information encoded at the DNA level and proteomes/metabolomes that determine the diverse functional outcome at the cellular and organ levels. Although the total number of protein-producing (coding) genes in the mammalian genome is ~20,000, it is evident that the intricate processes of cardiac development and the highly regulated physiological regulation in the normal heart, as well as the complex manifestation of pathological remodeling in a diseased heart, would require a much higher degree of complexity at the transcriptome level and beyond. Indeed, in addition to an extensive regulatory scheme implemented at the level of transcription, the complexity of transcript processing following transcription is dramatically increased. RNA processing includes post-transcriptional modification, alternative splicing, editing and transportation, ribosomal loading, and degradation. While transcriptional control of cardiac genes has been a major focus of investigation in recent decades, a great deal of progress has recently been made in our understanding of how post-transcriptional regulation of mRNA contributes to transcriptome complexity. In this review, we highlight some of the key molecular processes and major players in RNA maturation and post-transcriptional regulation. In addition, we provide an update to the recent progress made in the discovery of RNA processing regulators implicated in cardiac development and disease. While post-transcriptional modulation is a complex and challenging problem to study, recent technological advancements are paving the way for a new era of exciting discoveries and potential clinical translation in the context of cardiac biology and heart disease.
Collapse
Affiliation(s)
- Chen Gao
- Departments of Anesthesiology, Medicine, and Physiology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California
| | - Yibin Wang
- Departments of Anesthesiology, Medicine, and Physiology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California
| |
Collapse
|
42
|
Verdonschot JAJ, Vanhoutte EK, Claes GRF, Helderman-van den Enden ATJM, Hoeijmakers JGJ, Hellebrekers DMEI, de Haan A, Christiaans I, Lekanne Deprez RH, Boen HM, van Craenenbroeck EM, Loeys BL, Hoedemaekers YM, Marcelis C, Kempers M, Brusse E, van Waning JI, Baas AF, Dooijes D, Asselbergs FW, Barge-Schaapveld DQCM, Koopman P, van den Wijngaard A, Heymans SRB, Krapels IPC, Brunner HG. A mutation update for the FLNC gene in myopathies and cardiomyopathies. Hum Mutat 2020; 41:1091-1111. [PMID: 32112656 PMCID: PMC7318287 DOI: 10.1002/humu.24004] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/12/2020] [Accepted: 02/25/2020] [Indexed: 12/11/2022]
Abstract
Filamin C (FLNC) variants are associated with cardiac and muscular phenotypes. Originally, FLNC variants were described in myofibrillar myopathy (MFM) patients. Later, high‐throughput screening in cardiomyopathy cohorts determined a prominent role for FLNC in isolated hypertrophic and dilated cardiomyopathies (HCM and DCM). FLNC variants are now among the more prevalent causes of genetic DCM. FLNC‐associated DCM is associated with a malignant clinical course and a high risk of sudden cardiac death. The clinical spectrum of FLNC suggests different pathomechanisms related to variant types and their location in the gene. The appropriate functioning of FLNC is crucial for structural integrity and cell signaling of the sarcomere. The secondary protein structure of FLNC is critical to ensure this function. Truncating variants with subsequent haploinsufficiency are associated with DCM and cardiac arrhythmias. Interference with the dimerization and folding of the protein leads to aggregate formation detrimental for muscle function, as found in HCM and MFM. Variants associated with HCM are predominantly missense variants, which cluster in the ROD2 domain. This domain is important for binding to the sarcomere and to ensure appropriate cell signaling. We here review FLNC genotype–phenotype correlations based on available evidence.
Collapse
Affiliation(s)
- Job A J Verdonschot
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands.,Department of Cardiology, Cardiovascular Research Institute (CARIM), Maastricht University Medical Center, Maastricht, The Netherlands
| | - Els K Vanhoutte
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Godelieve R F Claes
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | | | | | - Debby M E I Hellebrekers
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Amber de Haan
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Imke Christiaans
- Department of Clinical Genetics, Amsterdam University Medical Center, Amsterdam, The Netherlands.,Department of Clinical Genetics, University Medical Centre Groningen, Groningen, The Netherlands
| | - Ronald H Lekanne Deprez
- Department of Clinical Genetics, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Hanne M Boen
- Department of Cardiology, Antwerp University Hospital, University of Antwerp, Antwerp, Belgium
| | | | - Bart L Loeys
- Department of Medical Genetics, Antwerp University Hospital, University of Antwerp, Antwerp, Belgium
| | - Yvonne M Hoedemaekers
- Department of Clinical Genetics, University Medical Centre Groningen, Groningen, The Netherlands.,Department of Clinical Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Carlo Marcelis
- Department of Clinical Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Marlies Kempers
- Department of Clinical Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Esther Brusse
- Department of Neurology, Erasmus MC University Medical Centre, Rotterdam, The Netherlands
| | - Jaap I van Waning
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands.,Department of Cardiology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Annette F Baas
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Dennis Dooijes
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Folkert W Asselbergs
- Department of Cardiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | | | - Arthur van den Wijngaard
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Stephane R B Heymans
- Department of Cardiology, Cardiovascular Research Institute (CARIM), Maastricht University Medical Center, Maastricht, The Netherlands.,Department of Cardiovascular Sciences, Centre for Molecular and Vascular Biology, KU Leuven, Leuven, Belgium.,The Netherlands Heart Institute, Utrecht, The Netherlands
| | - Ingrid P C Krapels
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Han G Brunner
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands.,Department of Clinical Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands.,Department of Genetics and Cell Biology, GROW Institute for Developmental Biology and Cancer, Maastricht University Medical Centre, Maastricht, The Netherlands
| |
Collapse
|
43
|
Liu C, Lim ST, Teo MHY, Tan MSY, Kulkarni MD, Qiu B, Li A, Lal S, Dos Remedios CG, Tan NS, Wahli W, Ferenczi MA, Song W, Hong W, Wang X. Collaborative Regulation of LRG1 by TGF-β1 and PPAR-β/δ Modulates Chronic Pressure Overload-Induced Cardiac Fibrosis. Circ Heart Fail 2019; 12:e005962. [PMID: 31830829 DOI: 10.1161/circheartfailure.119.005962] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
BACKGROUND Despite its established significance in fibrotic cardiac remodeling, clinical benefits of global inhibition of TGF (transforming growth factor)-β1 signaling remain controversial. LRG1 (leucine-rich-α2 glycoprotein 1) is known to regulate endothelial TGFβ signaling. This study evaluated the role of LRG1 in cardiac fibrosis and its transcriptional regulatory network in cardiac fibroblasts. METHODS Pressure overload-induced heart failure was established by transverse aortic constriction. Western blot, quantitative reverse transcription polymerase chain reaction, immunofluorescence, and immunohistochemistry were used to evaluate the expression level and pattern of interested targets or pathology during fibrotic cardiac remodeling. Cardiac function was assessed by pressure-volume loop analysis. RESULTS LRG1 expression was significantly suppressed in left ventricle of mice with transverse aortic constriction-induced fibrotic cardiac remodeling (mean difference, -0.00085 [95% CI, -0.0013 to -0.00043]; P=0.005) and of patients with end-stage ischemic-dilated cardiomyopathy (mean difference, 0.13 [95% CI, 0.012-0.25]; P=0.032). More profound cardiac fibrosis (mean difference, -0.014% [95% CI, -0.029% to -0.00012%]; P=0.048 for interstitial fibrosis; mean difference, -1.3 [95% CI, -2.5 to -0.2]; P=0.016 for perivascular fibrosis), worse cardiac dysfunction (mean difference, -2.5 ms [95% CI, -4.5 to -0.4 ms]; P=0.016 for Tau-g; mean difference, 13% [95% CI, 2%-24%]; P=0.016 for ejection fraction), and hyperactive TGFβ signaling in transverse aortic constriction-operated Lrg1-deficient mice (mean difference, -0.27 [95% CI, -0.47 to -0.07]; P<0.001), which could be reversed by cardiac-specific Lrg1 delivery mediated by adeno-associated virus 9. Mechanistically, LRG1 inhibits cardiac fibroblast activation by competing with TGFβ1 for receptor binding, while PPAR (peroxisome proliferator-activated receptor)-β/δ and TGFβ1 collaboratively regulate LRG1 expression via SMRT (silencing mediator for retinoid and thyroid hormone receptor). We further demonstrated functional interactions between LRG1 and PPARβ/δ in cardiac fibroblast activation. CONCLUSIONS Our results established a highly complex molecular network involving LRG1, TGFβ1, PPARβ/δ, and SMRT in regulating cardiac fibroblast activation and cardiac fibrosis. Targeting LRG1 or PPARβ/δ represents a promising strategy to control pathological cardiac remodeling in response to chronic pressure overload.
Collapse
Affiliation(s)
- Chenghao Liu
- Lee Kong Chian School of Medicine (C.L., S.T.L., M.H.Y.T., M.S.Y.T., M.D.K., N.S.T., W.W., M.A.F., W.S., X.W.), Nanyang Technological University Singapore
| | - Seok Ting Lim
- Lee Kong Chian School of Medicine (C.L., S.T.L., M.H.Y.T., M.S.Y.T., M.D.K., N.S.T., W.W., M.A.F., W.S., X.W.), Nanyang Technological University Singapore
| | - Melissa Hui Yen Teo
- Lee Kong Chian School of Medicine (C.L., S.T.L., M.H.Y.T., M.S.Y.T., M.D.K., N.S.T., W.W., M.A.F., W.S., X.W.), Nanyang Technological University Singapore
| | - Michelle Si Ying Tan
- Lee Kong Chian School of Medicine (C.L., S.T.L., M.H.Y.T., M.S.Y.T., M.D.K., N.S.T., W.W., M.A.F., W.S., X.W.), Nanyang Technological University Singapore
| | - Madhura Dattatraya Kulkarni
- Lee Kong Chian School of Medicine (C.L., S.T.L., M.H.Y.T., M.S.Y.T., M.D.K., N.S.T., W.W., M.A.F., W.S., X.W.), Nanyang Technological University Singapore
| | - Beiying Qiu
- Institute of Molecular and Cell Biology, Proteos, Agency for Science, Technology and Research, Singapore (B.Q., N.S.T., W.H., X.W.)
| | - Amy Li
- Anatomy and Histology, School of Medical Sciences, Bosch Institute, University of Sydney, Australia (A.L., S.L., C.G.d.R.)
| | - Sean Lal
- Anatomy and Histology, School of Medical Sciences, Bosch Institute, University of Sydney, Australia (A.L., S.L., C.G.d.R.)
| | - Cristobal G Dos Remedios
- Anatomy and Histology, School of Medical Sciences, Bosch Institute, University of Sydney, Australia (A.L., S.L., C.G.d.R.)
| | - Nguan Soon Tan
- Lee Kong Chian School of Medicine (C.L., S.T.L., M.H.Y.T., M.S.Y.T., M.D.K., N.S.T., W.W., M.A.F., W.S., X.W.), Nanyang Technological University Singapore.,School of Biological Sciences (N.S.T.), Nanyang Technological University Singapore.,Institute of Molecular and Cell Biology, Proteos, Agency for Science, Technology and Research, Singapore (B.Q., N.S.T., W.H., X.W.).,KK Research Centre, KK Women's and Children Hospital, Singapore (N.S.T.)
| | - Walter Wahli
- Lee Kong Chian School of Medicine (C.L., S.T.L., M.H.Y.T., M.S.Y.T., M.D.K., N.S.T., W.W., M.A.F., W.S., X.W.), Nanyang Technological University Singapore.,INRA ToxAlim, UMR1331, Chemin de Tournefeuille, Toulouse, France (W.W.).,Centre for Integrative Genomics, University of Lausanne, Le Genopode, Switzerland (W.W.)
| | - Michael Alan Ferenczi
- Lee Kong Chian School of Medicine (C.L., S.T.L., M.H.Y.T., M.S.Y.T., M.D.K., N.S.T., W.W., M.A.F., W.S., X.W.), Nanyang Technological University Singapore
| | - Weihua Song
- Lee Kong Chian School of Medicine (C.L., S.T.L., M.H.Y.T., M.S.Y.T., M.D.K., N.S.T., W.W., M.A.F., W.S., X.W.), Nanyang Technological University Singapore.,National Heart Centre Singapore (W.S.)
| | - Wanjin Hong
- Institute of Molecular and Cell Biology, Proteos, Agency for Science, Technology and Research, Singapore (B.Q., N.S.T., W.H., X.W.)
| | - Xiaomeng Wang
- Lee Kong Chian School of Medicine (C.L., S.T.L., M.H.Y.T., M.S.Y.T., M.D.K., N.S.T., W.W., M.A.F., W.S., X.W.), Nanyang Technological University Singapore.,Institute of Molecular and Cell Biology, Proteos, Agency for Science, Technology and Research, Singapore (B.Q., N.S.T., W.H., X.W.).,Institute of Ophthalmology, University College London, United Kingdom (X.W.).,Singapore Eye Research Institute, The Academia, Singapore (X.W.)
| |
Collapse
|
44
|
Dumont AA, Dumont L, Berthiaume J, Auger-Messier M. p38α MAPK proximity assay reveals a regulatory mechanism of alternative splicing in cardiomyocytes. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1866:118557. [PMID: 31505169 DOI: 10.1016/j.bbamcr.2019.118557] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 08/30/2019] [Accepted: 09/05/2019] [Indexed: 11/26/2022]
Abstract
The p38 mitogen-activated protein kinase (MAPK) signaling pathway is essential for normal heart function. However, p38 also contributes to heart failure pathogenesis by affecting cardiomyocytes contractility and survival. To unravel part of the complex role of p38 in cardiac function, we performed an APEX2-based proximity assay in cultured neonatal rat ventricular myocytes and identified the protein interaction networks (interactomes) of two highly expressed p38 isoforms in the heart. We found that p38α and p38γ have distinct interactomes in cardiomyocytes under both basal and osmotic stress-activated states. Interestingly, the activated p38α interactome contains many RNA-binding proteins implicated in splicing, including the serine/arginine-rich splicing factor 3 (SRSF3). Its interaction with the activated p38α was validated by co-immunoprecipitation. The cytoplasmic abundance and alternative splicing function of SRSF3 are also both modulated by the p38 signaling pathway. Our findings reveal a new function for p38 as a specific regulator of SRSF3 in cardiomyocytes.
Collapse
Affiliation(s)
- Audrey-Ann Dumont
- Département de Médecine, Service de Cardiologie, Centre de Recherche du CHUS, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Lauralyne Dumont
- Département de Médecine, Service de Cardiologie, Centre de Recherche du CHUS, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Jonathan Berthiaume
- Département de Médecine, Service de Cardiologie, Centre de Recherche du CHUS, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Mannix Auger-Messier
- Département de Médecine, Service de Cardiologie, Centre de Recherche du CHUS, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada.
| |
Collapse
|
45
|
Dorsch LM, Schuldt M, dos Remedios CG, Schinkel AFL, de Jong PL, Michels M, Kuster DWD, Brundel BJJM, van der Velden J. Protein Quality Control Activation and Microtubule Remodeling in Hypertrophic Cardiomyopathy. Cells 2019; 8:E741. [PMID: 31323898 PMCID: PMC6678711 DOI: 10.3390/cells8070741] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/11/2019] [Accepted: 07/17/2019] [Indexed: 12/14/2022] Open
Abstract
Hypertrophic cardiomyopathy (HCM) is the most common inherited cardiac disorder. It is mainly caused by mutations in genes encoding sarcomere proteins. Mutant forms of these highly abundant proteins likely stress the protein quality control (PQC) system of cardiomyocytes. The PQC system, together with a functional microtubule network, maintains proteostasis. We compared left ventricular (LV) tissue of nine donors (controls) with 38 sarcomere mutation-positive (HCMSMP) and 14 sarcomere mutation-negative (HCMSMN) patients to define HCM and mutation-specific changes in PQC. Mutations in HCMSMP result in poison polypeptides or reduced protein levels (haploinsufficiency, HI). The main findings were 1) several key PQC players were more abundant in HCM compared to controls, 2) after correction for sex and age, stabilizing heat shock protein (HSP)B1, and refolding, HSPD1 and HSPA2 were increased in HCMSMP compared to controls, 3) α-tubulin and acetylated α-tubulin levels were higher in HCM compared to controls, especially in HCMHI, 4) myosin-binding protein-C (cMyBP-C) levels were inversely correlated with α-tubulin, and 5) α-tubulin levels correlated with acetylated α-tubulin and HSPs. Overall, carrying a mutation affects PQC and α-tubulin acetylation. The haploinsufficiency of cMyBP-C may trigger HSPs and α-tubulin acetylation. Our study indicates that proliferation of the microtubular network may represent a novel pathomechanism in cMyBP-C haploinsufficiency-mediated HCM.
Collapse
Affiliation(s)
- Larissa M Dorsch
- Department of Physiology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam Cardiovascular Sciences, 1081 HV Amsterdam, The Netherlands.
| | - Maike Schuldt
- Department of Physiology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam Cardiovascular Sciences, 1081 HV Amsterdam, The Netherlands
| | - Cristobal G dos Remedios
- Sydney Heart Bank, Discipline of Anatomy, Bosch Institute, University of Sydney, Sydney 2006, Australia
| | - Arend F L Schinkel
- Department of Cardiology, Thoraxcenter, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Peter L de Jong
- Department of Cardiothoracic Surgery, Thoraxcenter, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Michelle Michels
- Department of Cardiology, Thoraxcenter, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Diederik W D Kuster
- Department of Physiology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam Cardiovascular Sciences, 1081 HV Amsterdam, The Netherlands
| | - Bianca J J M Brundel
- Department of Physiology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam Cardiovascular Sciences, 1081 HV Amsterdam, The Netherlands
| | - Jolanda van der Velden
- Department of Physiology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam Cardiovascular Sciences, 1081 HV Amsterdam, The Netherlands
- Netherlands Heart Institute, 3511 EP Utrecht, The Netherlands
| |
Collapse
|
46
|
Xiao J, Li F, Yang Q, Zeng X, Ke Z. Co‐expression analysis provides important module and pathways of human dilated cardiomyopathy. J Cell Physiol 2019; 235:494-503. [PMID: 31236962 DOI: 10.1002/jcp.28989] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 02/24/2019] [Accepted: 03/05/2019] [Indexed: 12/30/2022]
Affiliation(s)
- Junhui Xiao
- Department of Cardiology, Huadu District People's Hospital Southern Medical University Guangzhou China
| | - Fang Li
- Department of Cardiology, Huadu District People's Hospital Southern Medical University Guangzhou China
| | - Qianzhao Yang
- Department of Cardiology, Huadu District People's Hospital Southern Medical University Guangzhou China
| | | | - Zun‐Ping Ke
- Department of Cardiology, The Fifth People's Hospital of Shanghai Fudan University Shanghai China
| |
Collapse
|
47
|
Mirtschink P, Bischof C, Pham MD, Sharma R, Khadayate S, Rossi G, Fankhauser N, Traub S, Sossalla S, Hagag E, Berthonneche C, Sarre A, Stehr SN, Grote P, Pedrazzini T, Dimmeler S, Krek W, Krishnan J. Inhibition of the Hypoxia-Inducible Factor 1α-Induced Cardiospecific HERNA1 Enhance-Templated RNA Protects From Heart Disease. Circulation 2019; 139:2778-2792. [PMID: 30922078 PMCID: PMC6571183 DOI: 10.1161/circulationaha.118.036769] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Supplemental Digital Content is available in the text. Background: Enhancers are genomic regulatory elements conferring spatiotemporal and signal-dependent control of gene expression. Recent evidence suggests that enhancers can generate noncoding enhancer RNAs, but their (patho)biological functions remain largely elusive. Methods: We performed chromatin immunoprecipitation–coupled sequencing of histone marks combined with RNA sequencing of left ventricular biopsies from experimental and genetic mouse models of human cardiac hypertrophy to identify transcripts revealing enhancer localization, conservation with the human genome, and hypoxia-inducible factor 1α dependence. The most promising candidate, hypoxia-inducible enhancer RNA (HERNA)1, was further examined by investigating its capacity to modulate neighboring coding gene expression by binding to their gene promoters by using chromatin isolation by RNA purification and λN–BoxB tethering–based reporter assays. The role of HERNA1 and its neighboring genes for pathological stress–induced growth and contractile dysfunction, and the therapeutic potential of HERNA1 inhibition was studied in gapmer-mediated loss-of-function studies in vitro using human induced pluripotent stem cell–derived cardiomyocytes and various in vivo models of human pathological cardiac hypertrophy. Results: HERNA1 is robustly induced on pathological stress. Production of HERNA1 is initiated by direct hypoxia-inducible factor 1α binding to a hypoxia-response element in the histoneH3-lysine27acetylation marks–enriched promoter of the enhancer and confers hypoxia responsiveness to nearby genes including synaptotagmin XVII, a member of the family of membrane-trafficking and Ca2+-sensing proteins and SMG1, encoding a phosphatidylinositol 3-kinase–related kinase. Consequently, a substrate of SMG1, ATP-dependent RNA helicase upframeshift 1, is hyperphoshorylated in a HERNA1- and SMG1-dependent manner. In vitro and in vivo inactivation of SMG1 and SYT17 revealed overlapping and distinct roles in modulating cardiac hypertrophy. Finally, in vivo administration of antisense oligonucleotides targeting HERNA1 protected mice from stress-induced pathological hypertrophy. The inhibition of HERNA1 postdisease development reversed left ventricular growth and dysfunction, resulting in increased overall survival. Conclusions: HERNA1 is a novel heart-specific noncoding RNA with key regulatory functions in modulating the growth, metabolic, and contractile gene program in disease, and reveals a molecular target amenable to therapeutic exploitation.
Collapse
MESH Headings
- Animals
- Binding Sites
- Cardiomyopathy, Dilated/genetics
- Cardiomyopathy, Dilated/metabolism
- Cardiomyopathy, Dilated/pathology
- Cardiomyopathy, Dilated/prevention & control
- Cardiomyopathy, Hypertrophic/genetics
- Cardiomyopathy, Hypertrophic/metabolism
- Cardiomyopathy, Hypertrophic/pathology
- Cardiomyopathy, Hypertrophic/prevention & control
- Case-Control Studies
- Disease Models, Animal
- HEK293 Cells
- Humans
- Hypoxia-Inducible Factor 1, alpha Subunit/deficiency
- Hypoxia-Inducible Factor 1, alpha Subunit/genetics
- Hypoxia-Inducible Factor 1, alpha Subunit/metabolism
- Male
- Mice, Inbred C57BL
- Mice, Knockout
- Myocytes, Cardiac/metabolism
- Myocytes, Cardiac/pathology
- Oligonucleotides, Antisense/administration & dosage
- Promoter Regions, Genetic
- RNA, Untranslated/genetics
- RNA, Untranslated/metabolism
- Signal Transduction
- Von Hippel-Lindau Tumor Suppressor Protein/genetics
- Von Hippel-Lindau Tumor Suppressor Protein/metabolism
Collapse
Affiliation(s)
- Peter Mirtschink
- Institute of Molecular Health Sciences, ETH Zurich, Switzerland (P.M., G.R., N.F., S.T., W.K.)
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Dresden, Germany (P.M., E.H.)
| | - Corinne Bischof
- MRC Clinical Sciences Centre, Imperial College London, United Kingdom (C.B., S.K., J.K.)
- Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe-University Frankfurt, Germany (C.B., M.-D.P., R.S., P.G., S.D., J.K.)
| | - Minh-Duc Pham
- Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe-University Frankfurt, Germany (C.B., M.-D.P., R.S., P.G., S.D., J.K.)
| | - Rahul Sharma
- Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe-University Frankfurt, Germany (C.B., M.-D.P., R.S., P.G., S.D., J.K.)
| | - Sanjay Khadayate
- MRC Clinical Sciences Centre, Imperial College London, United Kingdom (C.B., S.K., J.K.)
| | - Geetha Rossi
- Institute of Molecular Health Sciences, ETH Zurich, Switzerland (P.M., G.R., N.F., S.T., W.K.)
| | - Niklaus Fankhauser
- Institute of Molecular Health Sciences, ETH Zurich, Switzerland (P.M., G.R., N.F., S.T., W.K.)
| | - Shuyang Traub
- Institute of Molecular Health Sciences, ETH Zurich, Switzerland (P.M., G.R., N.F., S.T., W.K.)
| | - Samuel Sossalla
- Department of Internal Medicine III: Cardiology and Angiology, University of Kiel, Germany (S.S.)
- Klinik für Kardiologie und Pneumologie, Georg-August-Universität Goettingen and DZHK (German Centre for Cardiovascular Research) (S.S.)
| | - Eman Hagag
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Dresden, Germany (P.M., E.H.)
| | - Corinne Berthonneche
- Cardiovascular Assessment Facility, University of Lausanne and CHUV, Switzerland (C.B., A.S.)
| | - Alexandre Sarre
- Cardiovascular Assessment Facility, University of Lausanne and CHUV, Switzerland (C.B., A.S.)
| | - Sebastian. N. Stehr
- Department of Anesthesiology and Intensive Care Medicine, University Hospital Schleswig-Holstein, and Department of Anesthesiology and Intensive Care Medicine, University Hospital Leipzig, Germany (S.N.S.)
| | - Phillip Grote
- Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe-University Frankfurt, Germany (C.B., M.-D.P., R.S., P.G., S.D., J.K.)
| | - Thierry Pedrazzini
- Department of Medicine, University of Lausanne Medical School, Switzerland (T.P.)
| | - Stefanie Dimmeler
- Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe-University Frankfurt, Germany (C.B., M.-D.P., R.S., P.G., S.D., J.K.)
| | - Wilhelm Krek
- Institute of Molecular Health Sciences, ETH Zurich, Switzerland (P.M., G.R., N.F., S.T., W.K.)
| | - Jaya Krishnan
- MRC Clinical Sciences Centre, Imperial College London, United Kingdom (C.B., S.K., J.K.)
- Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe-University Frankfurt, Germany (C.B., M.-D.P., R.S., P.G., S.D., J.K.)
| |
Collapse
|
48
|
Li A, Lal S, Dos Remedios CG. A step towards understanding the molecular nature of human heart failure: advances using the Sydney Heart Bank collection. Biophys Rev 2019; 11:241-244. [PMID: 30891671 DOI: 10.1007/s12551-019-00514-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 02/25/2019] [Indexed: 12/15/2022] Open
Affiliation(s)
- Amy Li
- The University of Sydney, Sydney, Australia
| | - Sean Lal
- The University of Sydney, Sydney, Australia
| | | |
Collapse
|
49
|
RNA binding protein 24 deletion disrupts global alternative splicing and causes dilated cardiomyopathy. Protein Cell 2018; 10:405-416. [PMID: 30267374 PMCID: PMC6538757 DOI: 10.1007/s13238-018-0578-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 08/24/2018] [Indexed: 01/08/2023] Open
Abstract
RNA splicing contributes to a broad spectrum of post-transcriptional gene regulation during normal development, as well as pathological manifestation of heart diseases. However, the functional role and regulation of splicing in heart failure remain poorly understood. RNA binding protein (RBP), a major component of the splicing machinery, is a critical factor in this process. RNA binding motif protein 24 (RBM24) is a tissue-specific RBP which is highly expressed in human and mouse heart. Previous studies demonstrated the functional role of RBM24 in the embryonic heart development. However, the role of RBM24 in postnatal heart development and heart disease has not been investigated. In this paper, using conditional RBM24 knockout mice, we demonstrated that ablation of RBM24 in postnatal heart led to rapidly progressive dilated cardiomyopathy (DCM), heart failure, and postnatal lethality. Global splicing profiling revealed that RBM24 regulated a network of genes related to cardiac function and diseases. Knockout of RBM24 resulted in misregulation of these splicing transitions which contributed to the subsequent development of cardiomyopathy. Notably, our analysis identified RBM24 as a splice factor that determined the splicing switch of a subset of genes in the sacomeric Z-disc complex, including Titin, the major disease gene of DCM and heart failure. Together, this study identifies regulation of RNA splicing by RBM24 as a potent player in remodeling of heart during postnatal development, and provides novel mechanistic insights to the pathogenesis of DCM.
Collapse
|
50
|
Yang X, Shi Y, Zhang L, Liu H, Shao Y, Zhang S. Overexpression of filamin c in chronic intermittent hypoxia-induced cardiomyocyte apoptosis is a potential cardioprotective target for obstructive sleep apnea. Sleep Breath 2018; 23:493-502. [PMID: 30194514 DOI: 10.1007/s11325-018-1712-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 08/04/2018] [Accepted: 08/22/2018] [Indexed: 12/17/2022]
Abstract
PURPOSE Chronic intermittent hypoxia (CIH) is key pathological mechanism of obstructive sleep apnea (OSA), which induced cardiac dysfunction. Filamin c (FLNC) is a muscle-restricted isoform and predominantly expressed in muscle tissue. In this study, we utilized a recently developed CIH rat model to mimic OSA, investigated the expression of FLNC in cardiomyocytes, and examined the correlations of FLNC with active caspase-3 to ascertain whether FLNC regulates the survival of cardiomyocytes. METHODS Forty Sprague-Dawley rats were randomly divided into normoxia and CIH groups. All rats were exposed either to normoxia or CIH 8 h daily for 6 weeks. Echocardiogram and HE staining were used to examine cardiac pathology, structure, and function. Body weight, heart weight, and blood gas values were recorded, respectively. The FLNC, Bax, Bcl-2, BNIP 3, and active caspase-3 proteins were detected by western blot; FLNC was examined by immunohistochemistry and immunofluorescence. Association of FLNC with cardiomyocyte apoptosis was detected by immunofluorescence. RESULTS CIH induced cardiac injuries and caused arterial blood gas disorder. FLNC significantly increased in CIH-induced cardiomyocytes than that in normoxia tissues. Pro-apoptotic BNIP 3 and Bax proteins were significantly increased in CIH, whereas anti-apoptotic member Bcl-2 was decreased. Active caspase-3, a universal marker of apoptosis, was significantly increased in CIH group. Co-localizations of FLNC and active caspase-3 were observed in CIH group. CONCLUSIONS These results suggested FLNC is implicated in the pathogenesis of CIH-induced cardiomyocyte apoptosis, and FLNC may serve as a novel cardioprotective target for OSA patients.
Collapse
Affiliation(s)
- Xuechao Yang
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Rd, Nanjing, 210029, Jiangsu, People's Republic of China
| | - Yang Shi
- Department of Cardiothoracic Surgery, Yancheng First People's Hospital, Yancheng, 224001, Jiangsu, People's Republic of China
| | - Linfei Zhang
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Rd, Nanjing, 210029, Jiangsu, People's Republic of China
| | - Huan Liu
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Rd, Nanjing, 210029, Jiangsu, People's Republic of China
| | - Yongfeng Shao
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Rd, Nanjing, 210029, Jiangsu, People's Republic of China
| | - Shijiang Zhang
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Rd, Nanjing, 210029, Jiangsu, People's Republic of China.
| |
Collapse
|