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Jia K, Cheng H, Ma W, Zhuang L, Li H, Li Z, Wang Z, Sun H, Cui Y, Zhang H, Xie H, Yi L, Chen Z, Sano M, Fukuda K, Lu L, Pu J, Zhang Y, Gao L, Zhang R, Yan X. RNA Helicase DDX5 Maintains Cardiac Function by Regulating CamkIIδ Alternative Splicing. Circulation 2024; 150:1121-1139. [PMID: 39056171 DOI: 10.1161/circulationaha.123.064774] [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: 03/15/2023] [Accepted: 06/19/2024] [Indexed: 07/28/2024]
Abstract
BACKGROUND Heart failure (HF) is a leading cause of morbidity and mortality worldwide. RNA-binding proteins are identified as regulators of cardiac disease; DDX5 (dead-box helicase 5) is a master regulator of many RNA processes, although its function in heart physiology remains unclear. METHODS We assessed DDX5 expression in human failing hearts and a mouse HF model. To study the function of DDX5 in heart, we engineered cardiomyocyte-specific Ddx5 knockout mice. We overexpressed DDX5 in cardiomyocytes using adeno-associated virus serotype 9 and performed transverse aortic constriction to establish the murine HF model. The mechanisms underlined were subsequently investigated using immunoprecipitation-mass spectrometry, RNA-sequencing, alternative splicing analysis, and RNA immunoprecipitation sequencing. RESULTS We screened transcriptome databases of murine HF and human dilated cardiomyopathy samples and found that DDX5 was significantly downregulated in both. Cardiomyocyte-specific deletion of Ddx5 resulted in HF with reduced cardiac function, an enlarged heart chamber, and increased fibrosis in mice. DDX5 overexpression improved cardiac function and protected against adverse cardiac remodeling in mice with transverse aortic constriction-induced HF. Furthermore, proteomics revealed that DDX5 is involved in RNA splicing in cardiomyocytes. We found that DDX5 regulated the aberrant splicing of Ca2+/calmodulin-dependent protein kinase IIδ (CamkIIδ), thus preventing the production of CaMKIIδA, which phosphorylates L-type calcium channel by serine residues of Cacna1c, leading to impaired Ca2+ homeostasis. In line with this, we found increased intracellular Ca2+ transients and increased sarcoplasmic reticulum Ca2+ content in DDX5-depleted cardiomyocytes. Using adeno-associated virus serotype 9 knockdown of CaMKIIδA partially rescued the cardiac dysfunction and HF in Ddx5 knockout mice. CONCLUSIONS These findings reveal a role for DDX5 in maintaining calcium homeostasis and cardiac function by regulating alternative splicing in cardiomyocytes, identifying the DDX5 as a potential target for therapeutic intervention in HF.
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Affiliation(s)
- Kangni Jia
- Department of Cardiovascular Medicine, Ruijin Hospital (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.L., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
- Institute of Cardiovascular Diseases (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.C., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
| | - Haomai Cheng
- Department of Cardiovascular Medicine, Ruijin Hospital (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.L., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
- Institute of Cardiovascular Diseases (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.C., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
| | - Wenqi Ma
- Department of Cardiovascular Medicine, Ruijin Hospital (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.L., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
- Institute of Cardiovascular Diseases (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.C., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
| | - Lingfang Zhuang
- Department of Cardiovascular Medicine, Ruijin Hospital (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.L., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
- Institute of Cardiovascular Diseases (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.C., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
| | - Hao Li
- Translational Medical Center for Stem Cell Therapy & Institutes for Regenerative Medicine, Shanghai East Hospital, Tongji University School of Medicine, China (H.L., L.G.)
| | - Zhigang Li
- Department of Cardiovascular Medicine, Ruijin Hospital (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.L., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
- Institute of Cardiovascular Diseases (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.C., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
| | - Ziyang Wang
- Department of Cardiovascular Medicine, Ruijin Hospital (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.L., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
- Institute of Cardiovascular Diseases (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.C., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
| | - Hang Sun
- Department of Cardiovascular Medicine, Ruijin Hospital (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.L., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
- Institute of Cardiovascular Diseases (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.C., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
| | - Yuke Cui
- Institute of Cardiovascular Diseases (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.C., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
| | - Hang Zhang
- Institute of Cardiovascular Diseases (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.C., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
| | - Hongyang Xie
- Department of Cardiovascular Medicine, Ruijin Hospital (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.L., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
- Institute of Cardiovascular Diseases (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.C., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
| | - Lei Yi
- Department of Cardiovascular Medicine, Ruijin Hospital (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.L., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
- Institute of Cardiovascular Diseases (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.C., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
| | - Zhiyong Chen
- Department of Cardiovascular Medicine, Ruijin Hospital (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.L., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
- Institute of Cardiovascular Diseases (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.C., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
| | - Motoaki Sano
- Department of Cardiology, Keio University School of Medicine, Tokyo, Japan (M.S., K.F.)
| | - Keiichi Fukuda
- Department of Cardiology, Keio University School of Medicine, Tokyo, Japan (M.S., K.F.)
| | - Lin Lu
- Department of Cardiovascular Medicine, Ruijin Hospital (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.L., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
| | - Jun Pu
- Department of Cardiology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital (J.P.), School of Medicine, Shanghai Jiao Tong University, China
| | - Yan Zhang
- State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, Peking University, Beijing, China (Y.Z.)
| | - Ling Gao
- Translational Medical Center for Stem Cell Therapy & Institutes for Regenerative Medicine, Shanghai East Hospital, Tongji University School of Medicine, China (H.L., L.G.)
| | - Ruiyan Zhang
- Department of Cardiovascular Medicine, Ruijin Hospital (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.L., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
- Institute of Cardiovascular Diseases (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.C., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
| | - Xiaoxiang Yan
- Department of Cardiovascular Medicine, Ruijin Hospital (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.L., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
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Sharp JA, Sparago E, Thomas R, Alimenti K, Wang W, Blower MD. Role of the SAF-A SAP domain in X inactivation, transcription, splicing, and cell proliferation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.09.612041. [PMID: 39314300 PMCID: PMC11419091 DOI: 10.1101/2024.09.09.612041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
SAF-A is conserved throughout vertebrates and has emerged as an important factor regulating a multitude of nuclear functions, including lncRNA localization, gene expression, and splicing. SAF-A has several functional domains, including an N-terminal SAP domain that binds directly to DNA. Phosphorylation of SAP domain serines S14 and S26 are important for SAF-A localization and function during mitosis, however whether these serines are involved in interphase functions of SAF-A is not known. In this study we tested for the role of the SAP domain, and SAP domain serines S14 and S26 in X chromosome inactivation, protein dynamics, gene expression, splicing, and cell proliferation. Here we show that the SAP domain serines S14 and S26 are required to maintain XIST RNA localization and polycomb-dependent histone modifications on the inactive X chromosome in female cells. In addition, we present evidence that an Xi localization signal resides in the SAP domain. We found that that the SAP domain is not required to maintain gene expression and plays only a minor role in mRNA splicing. In contrast, the SAF-A SAP domain, in particular serines S14 and S26, are required for normal protein dynamics, and to maintain normal cell proliferation. We propose a model whereby dynamic phosphorylation of SAF-A serines S14 and S26 mediates rapid turnover of SAF-A interactions with DNA during interphase.
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Affiliation(s)
- Judith A Sharp
- Department of Biochemistry and Cell Biology, Chobanian and Avedisian School of Medicine, Boston University, 72 E. Concord St, K112, Boston, MA 02118
| | - Emily Sparago
- Department of Biochemistry and Cell Biology, Chobanian and Avedisian School of Medicine, Boston University, 72 E. Concord St, K112, Boston, MA 02118
| | - Rachael Thomas
- Department of Biochemistry and Cell Biology, Chobanian and Avedisian School of Medicine, Boston University, 72 E. Concord St, K112, Boston, MA 02118
| | - Kaitlyn Alimenti
- Department of Biochemistry and Cell Biology, Chobanian and Avedisian School of Medicine, Boston University, 72 E. Concord St, K112, Boston, MA 02118
| | - Wei Wang
- Department of Biochemistry and Cell Biology, Chobanian and Avedisian School of Medicine, Boston University, 72 E. Concord St, K112, Boston, MA 02118
| | - Michael D Blower
- Department of Biochemistry and Cell Biology, Chobanian and Avedisian School of Medicine, Boston University, 72 E. Concord St, K112, Boston, MA 02118
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3
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Giménez-Escamilla I, Pérez-Carrillo L, González-Torrent I, Delgado-Arija M, Benedicto C, Portolés M, Tarazón E, Roselló-Lletí E. Transcriptomic Alterations in Spliceosome Components in Advanced Heart Failure: Status of Cardiac-Specific Alternative Splicing Factors. Int J Mol Sci 2024; 25:9590. [PMID: 39273537 PMCID: PMC11395552 DOI: 10.3390/ijms25179590] [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: 08/02/2024] [Revised: 08/29/2024] [Accepted: 09/03/2024] [Indexed: 09/15/2024] Open
Abstract
Heart failure (HF) is associated with global changes in gene expression. Alternative mRNA splicing (AS) is a key regulatory mechanism underlying these changes. However, the whole status of molecules involved in the splicing process in human HF is unknown. Therefore, we analysed the spliceosome transcriptome in cardiac tissue (n = 36) from control subjects and HF patients (with ischaemic (ICM) and dilated (DCM) cardiomyopathies) using RNA-seq. We found greater deregulation of spliceosome machinery in ICM. Specifically, we showed widespread upregulation of the E and C complex components, highlighting an increase in SNRPD2 (FC = 1.35, p < 0.05) and DHX35 (FC = 1.34, p < 0.001) mRNA levels. In contrast, we observed generalised downregulation of the A complex and cardiac-specific AS factors, such as the multifunctional protein PCBP2 (FC = -1.29, p < 0.001) and the RNA binding proteins QKI (FC = -1.35, p < 0.01). In addition, we found a relationship between SNPRD2 (an E complex component) and the left ventricular mass index in ICM patients (r = 0.779; p < 0.01). On the other hand, we observed the specific underexpression of DDX46 (FC = -1.29), RBM17 (FC = -1.33), SDE2 (FC = -1.35) and RBFOX1 (FC = -1.33), p < 0.05, in DCM patients. Therefore, these aetiology-related alterations may indicate the differential involvement of the splicing process in the development of ICM and DCM.
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Affiliation(s)
- Isaac Giménez-Escamilla
- Clinical and Translational Research in Cardiology Unit, Health Research Institute Hospital La Fe (IIS La Fe), Avd. Fernando Abril Martorell 106, 46026 Valencia, Spain
- Center for Biomedical Research Network on Cardiovascular Diseases (CIBERCV), Avd. Monforte de Lemos 3-5, 28029 Madrid, Spain
| | - Lorena Pérez-Carrillo
- Clinical and Translational Research in Cardiology Unit, Health Research Institute Hospital La Fe (IIS La Fe), Avd. Fernando Abril Martorell 106, 46026 Valencia, Spain
- Center for Biomedical Research Network on Cardiovascular Diseases (CIBERCV), Avd. Monforte de Lemos 3-5, 28029 Madrid, Spain
| | - Irene González-Torrent
- Clinical and Translational Research in Cardiology Unit, Health Research Institute Hospital La Fe (IIS La Fe), Avd. Fernando Abril Martorell 106, 46026 Valencia, Spain
| | - Marta Delgado-Arija
- Clinical and Translational Research in Cardiology Unit, Health Research Institute Hospital La Fe (IIS La Fe), Avd. Fernando Abril Martorell 106, 46026 Valencia, Spain
- Center for Biomedical Research Network on Cardiovascular Diseases (CIBERCV), Avd. Monforte de Lemos 3-5, 28029 Madrid, Spain
| | - Carlota Benedicto
- Clinical and Translational Research in Cardiology Unit, Health Research Institute Hospital La Fe (IIS La Fe), Avd. Fernando Abril Martorell 106, 46026 Valencia, Spain
| | - Manuel Portolés
- Clinical and Translational Research in Cardiology Unit, Health Research Institute Hospital La Fe (IIS La Fe), Avd. Fernando Abril Martorell 106, 46026 Valencia, Spain
- Center for Biomedical Research Network on Cardiovascular Diseases (CIBERCV), Avd. Monforte de Lemos 3-5, 28029 Madrid, Spain
| | - Estefanía Tarazón
- Clinical and Translational Research in Cardiology Unit, Health Research Institute Hospital La Fe (IIS La Fe), Avd. Fernando Abril Martorell 106, 46026 Valencia, Spain
- Center for Biomedical Research Network on Cardiovascular Diseases (CIBERCV), Avd. Monforte de Lemos 3-5, 28029 Madrid, Spain
| | - Esther Roselló-Lletí
- Clinical and Translational Research in Cardiology Unit, Health Research Institute Hospital La Fe (IIS La Fe), Avd. Fernando Abril Martorell 106, 46026 Valencia, Spain
- Center for Biomedical Research Network on Cardiovascular Diseases (CIBERCV), Avd. Monforte de Lemos 3-5, 28029 Madrid, Spain
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4
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Mokin YI, Povarova OI, Antifeeva IA, Artemov AV, Uversky VN, Turoverov KK, Kuznetsova IM, Fonin AV. Bioinformatics Analysis of Actin Interactome: Characterization of the Nuclear and Cytoplasmic Actin-Binding Proteins. Protein J 2024; 43:675-682. [PMID: 38824467 DOI: 10.1007/s10930-024-10207-y] [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] [Accepted: 05/09/2024] [Indexed: 06/03/2024]
Abstract
Actin is present in the cytoplasm and nucleus of every eukaryotic cell. In the cytoplasm, framework and motor functions of actin are associated with its ability to polymerize to form F-actin. In the nucleus, globular actin plays a significant functional role. For a globular protein, actin has a uniquely large number of proteins with which it interacts. Bioinformatics analysis of the actin interactome showed that only a part of actin-binding proteins are both cytoplasmic and nuclear. There are proteins that interact only with cytoplasmic, or only with nuclear actin. The first pool includes proteins associated with the formation, regulation, and functioning of the actin cytoskeleton predominate, while nuclear actin-binding proteins are involved in the majority of key nuclear processes, from regulation of transcription to DNA damage response. Bioinformatics analysis of the structure of actin-binding proteins showed that these are mainly intrinsically disordered proteins, many of which are part of membrane-less organelles. Interestingly, although the number of intrinsically disordered actin-binding proteins in the nucleus is greater than in the cytoplasm, the drivers for the formation of the membrane-less organelles in the cytoplasm are significantly (four times) greater than in the nucleus.
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Affiliation(s)
- Yakov I Mokin
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russian Federation
| | - Olga I Povarova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russian Federation
| | - Iuliia A Antifeeva
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russian Federation
| | - Alexey V Artemov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russian Federation
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, USF Health Byrd Alzheimer's Research Institute, University of South Florida, 12901 Bruce B. Downs Blvd., MDC07, Tampa, FL, 33612, USA.
| | - Konstantin K Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russian Federation
| | - Irina M Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russian Federation.
| | - Alexander V Fonin
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russian Federation.
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Jiang J, Wu H, Ji Y, Han K, Tang JM, Hu S, Lei W. Development and disease-specific regulation of RNA splicing in cardiovascular system. Front Cell Dev Biol 2024; 12:1423553. [PMID: 39045460 PMCID: PMC11263117 DOI: 10.3389/fcell.2024.1423553] [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: 04/26/2024] [Accepted: 06/17/2024] [Indexed: 07/25/2024] Open
Abstract
Alternative splicing is a complex gene regulatory process that distinguishes itself from canonical splicing by rearranging the introns and exons of an immature pre-mRNA transcript. This process plays a vital role in enhancing transcriptomic and proteomic diversity from the genome. Alternative splicing has emerged as a pivotal mechanism governing complex biological processes during both heart development and the development of cardiovascular diseases. Multiple alternative splicing factors are involved in a synergistic or antagonistic manner in the regulation of important genes in relevant physiological processes. Notably, circular RNAs have only recently garnered attention for their tissue-specific expression patterns and regulatory functions. This resurgence of interest has prompted a reevaluation of the topic. Here, we provide an overview of our current understanding of alternative splicing mechanisms and the regulatory roles of alternative splicing factors in cardiovascular development and pathological process of different cardiovascular diseases, including cardiomyopathy, myocardial infarction, heart failure and atherosclerosis.
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Affiliation(s)
- Jinxiu Jiang
- Department of Cardiovascular Surgery of the First Affiliated Hospital and Institute for Cardiovascular Science, State Key Laboratory of Radiation Medicine and Protection, Suzhou Medical College, Soochow University, Suzhou, China
| | - Hongchun Wu
- Department of Cardiovascular Surgery of the First Affiliated Hospital and Institute for Cardiovascular Science, State Key Laboratory of Radiation Medicine and Protection, Suzhou Medical College, Soochow University, Suzhou, China
| | - Yabo Ji
- Department of Cardiovascular Surgery of the First Affiliated Hospital and Institute for Cardiovascular Science, State Key Laboratory of Radiation Medicine and Protection, Suzhou Medical College, Soochow University, Suzhou, China
| | - Kunjun Han
- Department of Cardiovascular Surgery of the First Affiliated Hospital and Institute for Cardiovascular Science, State Key Laboratory of Radiation Medicine and Protection, Suzhou Medical College, Soochow University, Suzhou, China
| | - Jun-Ming Tang
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
| | - Shijun Hu
- Department of Cardiovascular Surgery of the First Affiliated Hospital and Institute for Cardiovascular Science, State Key Laboratory of Radiation Medicine and Protection, Suzhou Medical College, Soochow University, Suzhou, China
| | - Wei Lei
- Department of Cardiovascular Surgery of the First Affiliated Hospital and Institute for Cardiovascular Science, State Key Laboratory of Radiation Medicine and Protection, Suzhou Medical College, Soochow University, Suzhou, China
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Lee EJ, Charles JF, Sinha I, Neppl RL. Loss of HNRNPU in Skeletal Muscle Increases Intramuscular Infiltration of Ly6C Positive Cells, leading to Muscle Atrophy through Activation of NF-κB Signaling. Adv Biol (Weinh) 2024; 8:e2400152. [PMID: 38797891 DOI: 10.1002/adbi.202400152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/10/2024] [Indexed: 05/29/2024]
Abstract
Heterogeneous nuclear ribonucleoprotein U (hnRNPU) is known to play multiple biological roles by regulating transcriptional expression, RNA splicing, RNA stability, and chromatin structure in a tissue-dependent manner. The role of hnRNPU in skeletal muscle development and maintenance has not been previously evaluated. In this study, skeletal muscle specific hnRNPU knock out mice is utilized and evaluated skeletal muscle mass and immune cell infiltration through development. By 4 weeks, muscle-specific hnRNPU knockout mice revealed Ly6C+ monocyte infiltration into skeletal muscle, which preceded muscle atrophy. Canonical NF-kB signaling is activated in a myofiber-autonomous manner with hnRNPU repression. Inducible hnRNPU skeletal muscle knockout mice further demonstrated that deletion of hnRNPU in adulthood is sufficient to cause muscle atrophy, suggesting that hnRNPU's role in muscle maintenance is not during development alone. Treatment with salirasib, to inhibit proliferation of immune cells, prevents muscle atrophy in muscle-specific hnRNPU knock out mice, indicating that immune cell infiltration plays causal role in muscle atrophy of hnRNPU knock out mice. Overall, the findings suggest that loss of hnRNPU triggers muscle inflammation and activates NF-κB signaling in a cell-autonomous manner, culminating in muscle atrophy.
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Affiliation(s)
- Eun-Joo Lee
- Department of Orthopedic Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Julia F Charles
- Department of Orthopedic Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Division of Rheumatology, Inflammation and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Indranil Sinha
- Division of Plastic and reconstructive Surgery, Department of Surgery, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Ronald L Neppl
- Department of Orthopedic Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
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7
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Zhang D, Li L, Li M, Cao X. Biological functions and clinic significance of SAF‑A (Review). Biomed Rep 2024; 20:88. [PMID: 38665420 PMCID: PMC11040223 DOI: 10.3892/br.2024.1776] [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: 12/27/2023] [Accepted: 03/28/2024] [Indexed: 04/28/2024] Open
Abstract
As one member of the heterogeneous ribonucleoprotein (hnRNP) family, scaffold attachment factor A (SAF-A) or hnRNP U, is an abundant nuclear protein. With RNA and DNA binding activities, SAF-A has multiple functions. The present review focused on the biological structure and different roles of SAF-A and SAF-A-related diseases. It was found that SAF-A maintains the higher-order chromatin organization via RNA and DNA, and regulates transcription at the initiation and elongation stages. In addition to regulating pre-mRNA splicing, mRNA transportation and stabilization, SAF-A participates in double-strand breaks and mitosis repair. Therefore, the aberrant expression and mutation of SAF-A results in tumors and impaired neurodevelopment. Moreover, SAF-A may play a role in the anti-virus system. In conclusion, due to its essential biological functions, SAF-A may be a valuable clinical prediction factor or therapeutic target. Since the role of SAF-A in tumors and viral infections may be controversial, more animal experiments and clinical assays are needed.
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Affiliation(s)
- Daiquan Zhang
- Department of Traditional Chinese Medicine, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Li Li
- Immune Mechanism and Therapy of Major Diseases of Luzhou Key Laboratory, School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Mengni Li
- Department of Pediatrics, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan 610072, P.R. China
| | - Xinmei Cao
- Immune Mechanism and Therapy of Major Diseases of Luzhou Key Laboratory, School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
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8
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Wen Y, Zhou S, Gui Y, Li Z, Yin L, Xu W, Feng S, Ma X, Gan S, Xiong M, Dong J, Cheng K, Wang X, Yuan S. hnRNPU is required for spermatogonial stem cell pool establishment in mice. Cell Rep 2024; 43:114113. [PMID: 38625792 DOI: 10.1016/j.celrep.2024.114113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 01/28/2024] [Accepted: 03/29/2024] [Indexed: 04/18/2024] Open
Abstract
The continuous regeneration of spermatogonial stem cells (SSCs) underpins spermatogenesis and lifelong male fertility, but the developmental origins of the SSC pool remain unclear. Here, we document that hnRNPU is essential for establishing the SSC pool. In male mice, conditional loss of hnRNPU in prospermatogonia (ProSG) arrests spermatogenesis and results in sterility. hnRNPU-deficient ProSG fails to differentiate and migrate to the basement membrane to establish SSC pool in infancy. Moreover, hnRNPU deletion leads to the accumulation of ProSG and disrupts the process of T1-ProSG to T2-ProSG transition. Single-cell transcriptional analyses reveal that germ cells are in a mitotically quiescent state and lose their unique identity upon hnRNPU depletion. We further show that hnRNPU could bind to Vrk1, Slx4, and Dazl transcripts that have been identified to suffer aberrant alternative splicing in hnRNPU-deficient testes. These observations offer important insights into SSC pool establishment and may have translational implications for male fertility.
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Affiliation(s)
- Yujiao Wen
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Shumin Zhou
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yiqian Gui
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zeqing Li
- School of Nuclear Technology and Chemistry & Biology, Hubei University of Science and Technology, Xianning 437100, China
| | - Lisha Yin
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Wenchao Xu
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Shenglei Feng
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Laboratory of Animal Center, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xixiang Ma
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Laboratory of Animal Center, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Shiming Gan
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Mengneng Xiong
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Juan Dong
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Keren Cheng
- Center for Reproductive Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu 322000, China
| | - Xiaoli Wang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Shuiqiao Yuan
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Laboratory of Animal Center, Huazhong University of Science and Technology, Wuhan 430030, China; Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen 518057, China.
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9
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Cao J, Wei Z, Nie Y, Chen HZ. Therapeutic potential of alternative splicing in cardiovascular diseases. EBioMedicine 2024; 101:104995. [PMID: 38350330 PMCID: PMC10874720 DOI: 10.1016/j.ebiom.2024.104995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 01/19/2024] [Accepted: 01/21/2024] [Indexed: 02/15/2024] Open
Abstract
RNA splicing is an important RNA processing step required by multiexon protein-coding mRNAs and some noncoding RNAs. Precise RNA splicing is required for maintaining gene and cell function; however, mis-spliced RNA transcripts can lead to loss- or gain-of-function effects in human diseases. Mis-spliced RNAs induced by gene mutations or the dysregulation of splicing regulators may result in frameshifts, nonsense-mediated decay (NMD), or inclusion/exclusion of exons. Genetic animal models have characterised multiple splicing factors required for cardiac development or function. Moreover, sarcomeric and ion channel genes, which are closely associated with cardiovascular function and disease, are hotspots for AS. Here, we summarise splicing factors and their targets that are associated with cardiovascular diseases, introduce some therapies potentially related to pathological AS targets, and raise outstanding questions and future directions in this field.
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Affiliation(s)
- Jun Cao
- College of Chemistry and Life Science, Beijing University of Technology, Beijing, 100124, PR China; University of Texas Medical Branch at Galveston, TX, 77555, USA
| | - Ziyu Wei
- Department of Biochemistry & Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Yu Nie
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China.
| | - Hou-Zao Chen
- Department of Biochemistry & Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China; Medical Epigenetics Research Center, Chinese Academy of Medical Sciences, Beijing, China.
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10
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Dong YY, Wang MY, Jing JJ, Wu YJ, Li H, Yuan Y, Sun LP. Alternative Splicing Factor Heterogeneous Nuclear Ribonucleoprotein U as a Promising Biomarker for Gastric Cancer Risk and Prognosis with Tumor-Promoting Properties. THE AMERICAN JOURNAL OF PATHOLOGY 2024; 194:13-29. [PMID: 37923250 DOI: 10.1016/j.ajpath.2023.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/22/2023] [Accepted: 10/02/2023] [Indexed: 11/07/2023]
Abstract
Gastric cancer (GC) is a major global health concern with poor outcomes. Heterogeneous nuclear ribonucleoprotein U (HNRNPU) is a multifunctional protein that participates in pre-mRNA packaging, alternative splicing regulation, and chromatin remodeling. Its potential role in GC remains unclear. In this study, the expression characteristics of HNRNPU were analyzed by The Cancer Genome Atlas data, Gene Expression Omnibus data, and then further identified by real-time quantitative PCR and immunohistochemistry using tissue specimens. From superficial gastritis, atrophic gastritis, and hyperplasia to GC, the in situ expression of HNRNPU protein gradually increased, and the areas under the curve for diagnosis of GC and its precancerous lesions were 0.911 and 0.847, respectively. A nomogram integrating HNRNPU expression, lymph node metastasis, and other prognostic indicators exhibited an area under the curve of 0.785 for predicting survival risk. Knockdown of HNRNPU significantly inhibited GC cell proliferation, migration, and invasion and promoted apoptosis in vitro. In addition, RNA-sequencing analysis showed that HNRNPU could affect alternative splicing events in GC cells, with functional enrichment analysis revealing that HNRNPU may exert malignant biological function in GC progression through alternative splicing regulation. In summary, the increased expression of HNRNPU was significantly associated with the development of GC, with a good performance in diagnosing and predicting the prognostic risk of GC. Functionally, HNRNPU may play an oncogenic role in GC by regulating alternative splicing.
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Affiliation(s)
- Ying-Ying Dong
- Tumor Etiology and Screening Department of Cancer Institute and Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, China; Key Laboratory of Gastrointestinal Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, China
| | - Meng-Ya Wang
- Tumor Etiology and Screening Department of Cancer Institute and Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, China; Department of Radiotherapy, Zhumadian Central Hospital, Zhumadian, China
| | - Jing-Jing Jing
- Tumor Etiology and Screening Department of Cancer Institute and Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, China; Key Laboratory of Gastrointestinal Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, China
| | - Yi-Jun Wu
- Tumor Etiology and Screening Department of Cancer Institute and Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, China; Key Laboratory of Gastrointestinal Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, China
| | - Hao Li
- Department of Clinical Laboratory, The First Hospital of China Medical University, Shenyang, China
| | - Yuan Yuan
- Tumor Etiology and Screening Department of Cancer Institute and Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, China; Key Laboratory of Gastrointestinal Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, China.
| | - Li-Ping Sun
- Tumor Etiology and Screening Department of Cancer Institute and Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, China; Key Laboratory of Gastrointestinal Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, China.
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11
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Mastropasqua F, Oksanen M, Soldini C, Alatar S, Arora A, Ballarino R, Molinari M, Agostini F, Poulet A, Watts M, Rabkina I, Becker M, Li D, Anderlid BM, Isaksson J, Lundin Remnelius K, Moslem M, Jacob Y, Falk A, Crosetto N, Bienko M, Santini E, Borgkvist A, Bölte S, Tammimies K. Deficiency of the Heterogeneous Nuclear Ribonucleoprotein U locus leads to delayed hindbrain neurogenesis. Biol Open 2023; 12:bio060113. [PMID: 37815090 PMCID: PMC10581386 DOI: 10.1242/bio.060113] [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: 08/25/2023] [Accepted: 09/04/2023] [Indexed: 10/11/2023] Open
Abstract
Genetic variants affecting Heterogeneous Nuclear Ribonucleoprotein U (HNRNPU) have been identified in several neurodevelopmental disorders (NDDs). HNRNPU is widely expressed in the human brain and shows the highest postnatal expression in the cerebellum. Recent studies have investigated the role of HNRNPU in cerebral cortical development, but the effects of HNRNPU deficiency on cerebellar development remain unknown. Here, we describe the molecular and cellular outcomes of HNRNPU locus deficiency during in vitro neural differentiation of patient-derived and isogenic neuroepithelial stem cells with a hindbrain profile. We demonstrate that HNRNPU deficiency leads to chromatin remodeling of A/B compartments, and transcriptional rewiring, partly by impacting exon inclusion during mRNA processing. Genomic regions affected by the chromatin restructuring and host genes of exon usage differences show a strong enrichment for genes implicated in epilepsies, intellectual disability, and autism. Lastly, we show that at the cellular level HNRNPU downregulation leads to an increased fraction of neural progenitors in the maturing neuronal population. We conclude that the HNRNPU locus is involved in delayed commitment of neural progenitors to differentiate in cell types with hindbrain profile.
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Affiliation(s)
- Francesca Mastropasqua
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institute, Region Stockholm, 17164 Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, 17164 Stockholm, Sweden
| | - Marika Oksanen
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institute, Region Stockholm, 17164 Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, 17164 Stockholm, Sweden
| | - Cristina Soldini
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institute, Region Stockholm, 17164 Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, 17164 Stockholm, Sweden
| | - Shemim Alatar
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institute, Region Stockholm, 17164 Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, 17164 Stockholm, Sweden
| | - Abishek Arora
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institute, Region Stockholm, 17164 Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, 17164 Stockholm, Sweden
| | - Roberto Ballarino
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17164 Stockholm, Sweden
- Science for Life Laboratory, Tomtebodavägen 23A, 17165 Solna, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17165 Stockholm, Sweden
| | - Maya Molinari
- Department of Neuroscience, Karolinska Institutet, 17176 Solna, Sweden
| | - Federico Agostini
- Science for Life Laboratory, Tomtebodavägen 23A, 17165 Solna, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17165 Stockholm, Sweden
| | - Axel Poulet
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Michelle Watts
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institute, Region Stockholm, 17164 Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, 17164 Stockholm, Sweden
| | - Ielyzaveta Rabkina
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institute, Region Stockholm, 17164 Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, 17164 Stockholm, Sweden
| | - Martin Becker
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institute, Region Stockholm, 17164 Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, 17164 Stockholm, Sweden
| | - Danyang Li
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institute, Region Stockholm, 17164 Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, 17164 Stockholm, Sweden
| | - Britt-Marie Anderlid
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 17177 Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, 17164 Stockholm, Sweden
| | - Johan Isaksson
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institute, Region Stockholm, 17164 Stockholm, Sweden
- Department of Medical Sciences, Child and Adolescent Psychiatry Unit, Uppsala University, 75309 Uppsala, Sweden
| | - Karl Lundin Remnelius
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institute, Region Stockholm, 17164 Stockholm, Sweden
| | - Mohsen Moslem
- Department of Neuroscience, Karolinska Institutet, 17176 Solna, Sweden
| | - Yannick Jacob
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Anna Falk
- Department of Neuroscience, Karolinska Institutet, 17176 Solna, Sweden
- Lund Stem Cell Center, Lund University, 22100 Lund, Sweden
| | - Nicola Crosetto
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17164 Stockholm, Sweden
- Science for Life Laboratory, Tomtebodavägen 23A, 17165 Solna, Sweden
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
| | - Magda Bienko
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17164 Stockholm, Sweden
- Science for Life Laboratory, Tomtebodavägen 23A, 17165 Solna, Sweden
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
| | - Emanuela Santini
- Department of Neuroscience, Karolinska Institutet, 17176 Solna, Sweden
| | - Anders Borgkvist
- Department of Neuroscience, Karolinska Institutet, 17176 Solna, Sweden
| | - Sven Bölte
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institute, Region Stockholm, 17164 Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, 17164 Stockholm, Sweden
- Curtin Autism Research Group, Curtin School of Allied Health, Curtin University, 6845 Perth, Western Australia
- Child and Adolescent Psychiatry, Stockholm Health Care Services, Region Stockholm, 10431 Stockholm, Sweden
| | - Kristiina Tammimies
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institute, Region Stockholm, 17164 Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, 17164 Stockholm, Sweden
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12
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Sapir T, Reiner O. HNRNPU's multi-tasking is essential for proper cortical development. Bioessays 2023; 45:e2300039. [PMID: 37439444 DOI: 10.1002/bies.202300039] [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: 02/26/2023] [Revised: 05/27/2023] [Accepted: 06/12/2023] [Indexed: 07/14/2023]
Abstract
Heterogeneous nuclear ribonucleoprotein U (HNRNPU) is a nuclear protein that plays a crucial role in various biological functions, such as RNA splicing and chromatin organization. HNRNPU/scaffold attachment factor A (SAF-A) activities are essential for regulating gene expression, DNA replication, genome integrity, and mitotic fidelity. These functions are critical to ensure the robustness of developmental processes, particularly those involved in shaping the human brain. As a result, HNRNPU is associated with various neurodevelopmental disorders (HNRNPU-related neurodevelopmental disorder, HNRNPU-NDD) characterized by developmental delay and intellectual disability. Our research demonstrates that the loss of HNRNPU function results in the death of both neural progenitor cells and post-mitotic neurons, with a higher sensitivity observed in the former. We reported that HNRNPU truncation leads to the dysregulation of gene expression and alternative splicing of genes that converge on several signaling pathways, some of which are likely to be involved in the pathology of HNRNPU-related NDD.
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Affiliation(s)
- Tamar Sapir
- Weizmann Institute of Science, Molecular Genetics and Molecular Neuroscience, Rehovot, Central, Israel
| | - Orly Reiner
- Weizmann Institute of Science, Molecular Genetics and Molecular Neuroscience, Rehovot, Central, Israel
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13
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Lim YH, Yoon G, Ryu Y, Jeong D, Song J, Kim YS, Ahn Y, Kook H, Kim YK. Human lncRNA SUGCT-AS1 Regulates the Proinflammatory Response of Macrophage. Int J Mol Sci 2023; 24:13315. [PMID: 37686120 PMCID: PMC10487982 DOI: 10.3390/ijms241713315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/20/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
Macrophages are the major primary immune cells that mediate the inflammatory response. In this process, long non-coding RNAs (lncRNAs) play an important, yet largely unknown role. Therefore, utilizing several publicly available RNA sequencing datasets, we predicted and selected lncRNAs that are differentially expressed in M1 or M2 macrophages and involved in the inflammatory response. We identified SUGCT-AS1, which is a human macrophage-specific lncRNA whose expression is increased upon M1 macrophage stimulation. Conditioned media of SUGCT-AS1-depleted M1 macrophages induced an inflammatory phenotype of vascular smooth muscle cells, which included increased expression of inflammatory genes (IL1B and IL6), decreased contractile marker proteins (ACTA2 and SM22α), and increased cell migration. Depletion of SUGCT-AS1 promoted the expression and secretion of proinflammatory cytokines, such as TNF, IL1B, and IL6, in M1 macrophages, and transcriptomic analysis showed that SUGCT-AS1 has functions related to inflammatory responses and cytokines. Furthermore, we found that SUGCT-AS1 directly binds to hnRNPU and regulates its nuclear-cytoplasmic translocation. This translocation of hnRNPU altered the proportion of the MALT1 isoforms by regulating the alternative splicing of MALT1, a mediator of NF-κB signaling. Overall, our findings suggest that lncRNAs can be used for future studies on macrophage regulation. Moreover, they establish the SUGCT-AS1/hnRNPU/MALT1 axis, which is a novel inflammatory regulatory mechanism in macrophages.
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Affiliation(s)
- Yeong-Hwan Lim
- Basic Research Laboratory for Vascular Remodeling, Chonnam National University Medical School, Hwasun 58128, Republic of Korea
- Department of Biochemistry, Chonnam National University Medical School, Hwasun 58128, Republic of Korea
- BioMedical Sciences Graduate Program (BMSGP), Chonnam National University, Hwasun 58128, Republic of Korea
| | - Gwangho Yoon
- Division of Brain Disease Research, Department for Chronic Disease Convergence Research, Korea National Institute of Health, Cheongju 28159, Republic of Korea
| | - Yeongseo Ryu
- Department of Biochemistry, Chonnam National University Medical School, Hwasun 58128, Republic of Korea
- BioMedical Sciences Graduate Program (BMSGP), Chonnam National University, Hwasun 58128, Republic of Korea
| | - Dahee Jeong
- Department of Biochemistry, Chonnam National University Medical School, Hwasun 58128, Republic of Korea
- BioMedical Sciences Graduate Program (BMSGP), Chonnam National University, Hwasun 58128, Republic of Korea
| | - Juhyun Song
- BioMedical Sciences Graduate Program (BMSGP), Chonnam National University, Hwasun 58128, Republic of Korea
- Department of Anatomy, Chonnam National University Medical School, Hwasun 58128, Republic of Korea
| | - Yong Sook Kim
- Basic Research Laboratory for Vascular Remodeling, Chonnam National University Medical School, Hwasun 58128, Republic of Korea
- Cell Regeneration Research Center, Chonnam National University Hospital, Gwangju 61469, Republic of Korea
- Biomedical Research Institute, Chonnam National University Hospital, Gwangju 61469, Republic of Korea
| | - Youngkeun Ahn
- Basic Research Laboratory for Vascular Remodeling, Chonnam National University Medical School, Hwasun 58128, Republic of Korea
- Cell Regeneration Research Center, Chonnam National University Hospital, Gwangju 61469, Republic of Korea
- Department of Cardiology, Chonnam National University Medical School, Gwangju 61469, Republic of Korea
| | - Hyun Kook
- Basic Research Laboratory for Vascular Remodeling, Chonnam National University Medical School, Hwasun 58128, Republic of Korea
- BioMedical Sciences Graduate Program (BMSGP), Chonnam National University, Hwasun 58128, Republic of Korea
- Department of Pharmacology, Chonnam National University Medical School, Hwasun 58128, Republic of Korea
| | - Young-Kook Kim
- Basic Research Laboratory for Vascular Remodeling, Chonnam National University Medical School, Hwasun 58128, Republic of Korea
- Department of Biochemistry, Chonnam National University Medical School, Hwasun 58128, Republic of Korea
- BioMedical Sciences Graduate Program (BMSGP), Chonnam National University, Hwasun 58128, Republic of Korea
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14
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Shi DL. RNA-Binding Proteins as Critical Post-Transcriptional Regulators of Cardiac Regeneration. Int J Mol Sci 2023; 24:12004. [PMID: 37569379 PMCID: PMC10418649 DOI: 10.3390/ijms241512004] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
Myocardial injury causes death to cardiomyocytes and leads to heart failure. The adult mammalian heart has very limited regenerative capacity. However, the heart from early postnatal mammals and from adult lower vertebrates can fully regenerate after apical resection or myocardial infarction. Thus, it is of particular interest to decipher the mechanism underlying cardiac regeneration that preserves heart structure and function. RNA-binding proteins, as key regulators of post-transcriptional gene expression to coordinate cell differentiation and maintain tissue homeostasis, display dynamic expression in fetal and adult hearts. Accumulating evidence has demonstrated their importance for the survival and proliferation of cardiomyocytes following neonatal and postnatal cardiac injury. Functional studies suggest that RNA-binding proteins relay damage-stimulated cell extrinsic or intrinsic signals to regulate heart regenerative capacity by reprogramming multiple molecular and cellular processes, such as global protein synthesis, metabolic changes, hypertrophic growth, and cellular plasticity. Since manipulating the activity of RNA-binding proteins can improve the formation of new cardiomyocytes and extend the window of the cardiac regenerative capacity in mammals, they are potential targets of therapeutic interventions for cardiovascular disease. This review discusses our evolving understanding of RNA-binding proteins in regulating cardiac repair and regeneration, with the aim to identify important open questions that merit further investigations.
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Affiliation(s)
- De-Li Shi
- Department of Medical Research, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524001, China
- Laboratory of Developmental Biology (CNRS-UMR7622), Institute de Biologie Paris-Seine (IBPS), Sorbonne University, 75005 Paris, France
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15
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Montañés-Agudo P, Pinto YM, Creemers EE. Splicing factors in the heart: Uncovering shared and unique targets. J Mol Cell Cardiol 2023; 179:72-79. [PMID: 37059416 DOI: 10.1016/j.yjmcc.2023.04.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/29/2023] [Accepted: 04/09/2023] [Indexed: 04/16/2023]
Abstract
Alternative splicing generates specialized protein isoforms that allow the heart to adapt during development and disease. The recent discovery that mutations in the splicing factor RNA-binding protein 20 (RBM20) cause a severe form of familial dilated cardiomyopathy has sparked a great interest in alternative splicing in the field of cardiology. Since then, identification of splicing factors controlling alternative splicing in the heart has grown at a rapid pace. Despite the intriguing observation that a certain overlap exists between the targets of some splicing factors, an integrated and systematic analysis of their splicing networks is missing. Here, we compared the splicing networks of individual splicing factors by re-analyzing original RNA-sequencing data from eight previously published mouse models, in which a single splicing factor has been genetically deleted (i.e. HNRNPU, MBNL1/2, QKI, RBM20, RBM24, RBPMS, SRSF3, SRSF4). We show that key splicing events in Camk2d, Ryr2, Tpm1, Tpm2 and Pdlim5 require the combined action of the majority of these splicing factors. Additionally, we identified common targets and pathways among splicing factors, with the largest overlap between the splicing networks of MBNL, QKI and RBM24. We also re-analyzed a large-scale RNA-sequencing study on hearts of 128 heart failure patients. Here, we observed that MBNL1, QKI and RBM24 expression varied greatly. This variation in expression correlated with differential splicing of their downstream targets as found in mice, suggesting that aberrant splicing by MBNL1, QKI and RBM24 might contribute to the disease mechanism in heart failure.
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Affiliation(s)
- Pablo Montañés-Agudo
- Experimental Cardiology, Room K2-112, Amsterdam UMC Location University of Amsterdam, Meibergdreef 15, Amsterdam 1105AZ, the Netherlands.
| | - Yigal M Pinto
- Experimental Cardiology, Room K2-104, Amsterdam UMC, location University of Amsterdam, Meibergdreef 15, Amsterdam 1105AZ, the Netherlands.
| | - Esther E Creemers
- Experimental Cardiology, Room K2-104-2, Amsterdam UMC, Location University of Amsterdam, Meibergdreef 15, Amsterdam 1105AZ, the Netherlands.
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16
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Aslan GS, Jaé N, Manavski Y, Fouani Y, Shumliakivska M, Kettenhausen L, Kirchhof L, Günther S, Fischer A, Luxán G, Dimmeler S. Malat1 deficiency prevents neonatal heart regeneration by inducing cardiomyocyte binucleation. JCI Insight 2023; 8:162124. [PMID: 36883566 PMCID: PMC10077484 DOI: 10.1172/jci.insight.162124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 02/01/2023] [Indexed: 03/09/2023] Open
Abstract
The adult mammalian heart has limited regenerative capacity, while the neonatal heart fully regenerates during the first week of life. Postnatal regeneration is mainly driven by proliferation of preexisting cardiomyocytes and supported by proregenerative macrophages and angiogenesis. Although the process of regeneration has been well studied in the neonatal mouse, the molecular mechanisms that define the switch between regenerative and nonregenerative cardiomyocytes are not well understood. Here, using in vivo and in vitro approaches, we identified the lncRNA Malat1 as a key player in postnatal cardiac regeneration. Malat1 deletion prevented heart regeneration in mice after myocardial infarction on postnatal day 3 associated with a decline in cardiomyocyte proliferation and reparative angiogenesis. Interestingly, Malat1 deficiency increased cardiomyocyte binucleation even in the absence of cardiac injury. Cardiomyocyte-specific deletion of Malat1 was sufficient to block regeneration, supporting a critical role of Malat1 in regulating cardiomyocyte proliferation and binucleation, a landmark of mature nonregenerative cardiomyocytes. In vitro, Malat1 deficiency induced binucleation and the expression of a maturation gene program. Finally, the loss of hnRNP U, an interaction partner of Malat1, induced similar features in vitro, suggesting that Malat1 regulates cardiomyocyte proliferation and binucleation by hnRNP U to control the regenerative window in the heart.
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Affiliation(s)
- Galip S Aslan
- Institute of Cardiovascular Regeneration, Center of Molecular Medicine, and.,Faculty of Biological Sciences, Goethe University, Frankfurt, Germany.,German Center for Cardiovascular Research DZHK, Berlin, Germany, partner site Frankfurt Rhine-Main, Germany.,Cardiopulmonary Institute, Goethe University, Frankfurt, Germany
| | - Nicolas Jaé
- Institute of Cardiovascular Regeneration, Center of Molecular Medicine, and.,German Center for Cardiovascular Research DZHK, Berlin, Germany, partner site Frankfurt Rhine-Main, Germany
| | - Yosif Manavski
- Institute of Cardiovascular Regeneration, Center of Molecular Medicine, and.,German Center for Cardiovascular Research DZHK, Berlin, Germany, partner site Frankfurt Rhine-Main, Germany.,Cardiopulmonary Institute, Goethe University, Frankfurt, Germany
| | - Youssef Fouani
- Institute of Cardiovascular Regeneration, Center of Molecular Medicine, and.,Faculty of Biological Sciences, Goethe University, Frankfurt, Germany.,German Center for Cardiovascular Research DZHK, Berlin, Germany, partner site Frankfurt Rhine-Main, Germany
| | - Mariana Shumliakivska
- Institute of Cardiovascular Regeneration, Center of Molecular Medicine, and.,German Center for Cardiovascular Research DZHK, Berlin, Germany, partner site Frankfurt Rhine-Main, Germany.,Cardiopulmonary Institute, Goethe University, Frankfurt, Germany
| | - Lisa Kettenhausen
- Institute of Cardiovascular Regeneration, Center of Molecular Medicine, and.,Cardiopulmonary Institute, Goethe University, Frankfurt, Germany
| | - Luisa Kirchhof
- Institute of Cardiovascular Regeneration, Center of Molecular Medicine, and.,Faculty of Biological Sciences, Goethe University, Frankfurt, Germany.,German Center for Cardiovascular Research DZHK, Berlin, Germany, partner site Frankfurt Rhine-Main, Germany
| | - Stefan Günther
- German Center for Cardiovascular Research DZHK, Berlin, Germany, partner site Frankfurt Rhine-Main, Germany.,Cardiopulmonary Institute, Goethe University, Frankfurt, Germany.,Max Planck Institute for Heart and Lung Research, Bioinformatics and Deep Sequencing Platform, Bad Nauheim, Germany
| | - Ariane Fischer
- Institute of Cardiovascular Regeneration, Center of Molecular Medicine, and
| | - Guillermo Luxán
- Institute of Cardiovascular Regeneration, Center of Molecular Medicine, and.,German Center for Cardiovascular Research DZHK, Berlin, Germany, partner site Frankfurt Rhine-Main, Germany.,Cardiopulmonary Institute, Goethe University, Frankfurt, Germany
| | - Stefanie Dimmeler
- Institute of Cardiovascular Regeneration, Center of Molecular Medicine, and.,Faculty of Biological Sciences, Goethe University, Frankfurt, Germany.,German Center for Cardiovascular Research DZHK, Berlin, Germany, partner site Frankfurt Rhine-Main, Germany.,Cardiopulmonary Institute, Goethe University, Frankfurt, Germany
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17
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Ressler AK, Sampaio GL, Dugger SA, Sapir T, Krizay D, Boland MJ, Reiner O, Goldstein DB. Evidence of shared transcriptomic dysregulation of HNRNPU-related disorder between human organoids and embryonic mice. iScience 2023; 26:105797. [PMID: 36594023 PMCID: PMC9804147 DOI: 10.1016/j.isci.2022.105797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 08/16/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
Generating effective therapies for neurodevelopmental disorders has remained elusive. An emerging drug discovery approach for neurodevelopmental disorders is to characterize transcriptome-wide dysregulation in an appropriate model system and screen therapeutics based on their capacity to restore functionally relevant expression patterns. We characterized transcriptomic dysregulation in a human model of HNRNPU-related disorder to explore the potential of such a paradigm. We identified widespread dysregulation in functionally relevant pathways and then compared dysregulation in a human model to transcriptomic differences in embryonic and perinatal mice to determine whether dysregulation in an in vitro human model is partially replicated in an in vivo model of HNRNPU-related disorder. Strikingly, we find enrichment of co-dysregulation between 45-day-old human organoids and embryonic, but not perinatal, mice from distinct models of HNRNPU-related disorder. Thus, hnRNPU deficient human organoids may only be suitable to model transcriptional dysregulation in certain cell types within a specific developmental time window.
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Affiliation(s)
- Andrew K. Ressler
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Gabriela L.A. Sampaio
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Sarah A. Dugger
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Tamar Sapir
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Daniel Krizay
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Michael J. Boland
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Neurology, Columbia University, New York, NY 10032, USA
| | - Orly Reiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- Incumbent of the Berstein-Mason Professorial Chair of Neurochemistry, Head of M. Judith Ruth Institute of Preclinical Brain Research, Weizmann Institute of Science, Rehovot, Israel
| | - David B. Goldstein
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
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18
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Ahmed RE, Tokuyama T, Anzai T, Chanthra N, Uosaki H. Sarcomere maturation: function acquisition, molecular mechanism, and interplay with other organelles. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210325. [PMID: 36189811 PMCID: PMC9527934 DOI: 10.1098/rstb.2021.0325] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 06/15/2022] [Indexed: 12/31/2022] Open
Abstract
During postnatal cardiac development, cardiomyocytes mature and turn into adult ones. Hence, all cellular properties, including morphology, structure, physiology and metabolism, are changed. One of the most important aspects is the contractile apparatus, of which the minimum unit is known as a sarcomere. Sarcomere maturation is evident by enhanced sarcomere alignment, ultrastructural organization and myofibrillar isoform switching. Any maturation process failure may result in cardiomyopathy. Sarcomere function is intricately related to other organelles, and the growing evidence suggests reciprocal regulation of sarcomere and mitochondria on their maturation. Herein, we summarize the molecular mechanism that regulates sarcomere maturation and the interplay between sarcomere and other organelles in cardiomyocyte maturation. This article is part of the theme issue 'The cardiomyocyte: new revelations on the interplay between architecture and function in growth, health, and disease'.
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Affiliation(s)
- Razan E. Ahmed
- Division of Regenerative Medicine, Center for Molecular Medicine, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi 329-0498, Japan
| | - Takeshi Tokuyama
- Division of Regenerative Medicine, Center for Molecular Medicine, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi 329-0498, Japan
| | - Tatsuya Anzai
- Division of Regenerative Medicine, Center for Molecular Medicine, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi 329-0498, Japan
- Department of Pediatrics, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi 329-0498, Japan
| | - Nawin Chanthra
- Division of Regenerative Medicine, Center for Molecular Medicine, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi 329-0498, Japan
| | - Hideki Uosaki
- Division of Regenerative Medicine, Center for Molecular Medicine, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi 329-0498, Japan
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19
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Isaac R, Vinik Y, Mikl M, Nadav-Eliyahu S, Shatz-Azoulay H, Yaakobi A, DeForest N, Majithia AR, Webster NJ, Shav-Tal Y, Elhanany E, Zick Y. A seven-transmembrane protein-TM7SF3, resides in nuclear speckles and regulates alternative splicing. iScience 2022; 25:105270. [PMID: 36304109 PMCID: PMC9593240 DOI: 10.1016/j.isci.2022.105270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 06/08/2022] [Accepted: 09/26/2022] [Indexed: 11/17/2022] Open
Abstract
The seven-transmembrane superfamily member 3 protein (TM7SF3) is a p53-regulated homeostatic factor that attenuates cellular stress and the unfolded protein response. Here we show that TM7SF3 localizes to nuclear speckles; eukaryotic nuclear bodies enriched in splicing factors. This unexpected location for a trans -membranal protein enables formation of stable complexes between TM7SF3 and pre-mRNA splicing factors including DHX15, LARP7, HNRNPU, RBM14, and HNRNPK. Indeed, TM7SF3 regulates alternative splicing of >330 genes, mainly at the 3'end of introns by directly modulating the activity of splicing factors such as HNRNPK. These effects are observed both in cell lines and primary human pancreatic islets. Accordingly, silencing of TM7SF3 results in differential expression of 1465 genes (about 7% of the human genome); with 844 and 621 genes being up- or down-regulated, respectively. Our findings implicate TM7SF3, as a resident protein of nuclear speckles and suggest a role for seven-transmembrane proteins as regulators of alternative splicing.
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Affiliation(s)
- Roi Isaac
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
- Department of Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Yaron Vinik
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Martin Mikl
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
- Department of Biology, University of Haifa, Haifa, Israel
| | - Shani Nadav-Eliyahu
- The Mina & Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Hadas Shatz-Azoulay
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Adi Yaakobi
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Natalie DeForest
- Department of Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA 92093, USA
| | - Amit R. Majithia
- Department of Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Nicholas J.G. Webster
- Department of Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- VA San Diego Healthcare System, San Diego, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Yaron Shav-Tal
- The Mina & Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Eytan Elhanany
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yehiel Zick
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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20
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Xiao J, Wang WX. Patterns and Crucial Regulation of Alternative Splicing During Early Development in Zebrafish. J Mol Biol 2022; 434:167821. [PMID: 36087778 DOI: 10.1016/j.jmb.2022.167821] [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: 04/29/2022] [Revised: 08/30/2022] [Accepted: 08/30/2022] [Indexed: 10/31/2022]
Abstract
Many vertebrate genes generate multiple transcript variants that may encode functionally distinct protein isoforms, but the transcriptomes of various developmental stages are poorly defined. Identifying the transcriptome and its regulation during the normal developmental process is the key to deciphering the developmental stage-specific functions of genes. Here we presented a systematic assessment of the temporal alternative splicing (AS) events during the critical development stages to capture the dynamic gene expression changes and AS in zebrafish. An unexpected transcriptome complexity generated by AS was observed during zebrafish development. The patterns of AS events varied substantially among developmental stages despite the similarities in the total proportion of AS genes. We further found that AS afforded substantial functional diversification of genes through the generation of stage-specific AS events from broadly protein-coding genes as an essential developmental regulatory mechanism. Skipped exon (SE) showed the strongest signals among developmental AS (devAS), suggesting that devAS events generated by SE may be necessary for the normal development of zebrafish. Most developmental genes regulated by AS mechanisms were not modulated in terms of their overall expression levels, indicating that AS shaped the transcriptome independently from transcriptional regulation during development. 128-cell stage was a critical stage for gene transcription during embryonic development. Splicing factors as an essential developmental regulator underwent AS in the potential autoregulatory feedback loop and expressed multiple isoforms. Thus, zebrafish development was shaped by an interplay of programs controlling gene expression levels and AS. Overall, we provided a global view of developmental patterns of AS during zebrafish development and revealed that AS transitions were the crucial regulatory component of zebrafish embryonic development.
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Affiliation(s)
- Jie Xiao
- School of Energy and Environment and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong, China; Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China
| | - Wen-Xiong Wang
- School of Energy and Environment and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong, China; Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China.
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21
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de Avila JG, Redondo CS, Alviz-Amador A. Bioinformatic Analysis of Plus Gene Expression Related to Progression from Leukoplakia to Oral Squamous Cell Carcinoma. Asian Pac J Cancer Prev 2022; 23:3833-3842. [PMID: 36444596 PMCID: PMC9930946 DOI: 10.31557/apjcp.2022.23.11.3833] [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: 06/14/2022] [Indexed: 11/30/2022] Open
Abstract
INTRODUCTION Leukoplakia is one of the most frequently found lesions in the oral cavity, with a probability of 17 to 24% of becoming malignant cells in a period of 30 years. OBJECTIVE To identify differentially expressed gene profiles of leukoplakia and its progression to oral squamous cell carcinoma, essential for the discovery of new biomarkers to predict and prevent the presence of diseases in the oral cavity. METHODS Initially, gene profiles of GSE85514 and GSE160042 from the Gene Expression Omnibus database were used. Differentially expressed genes were identified using GEO2R. The CLUEGO plugin in Cytoscape was used for DEG functionality and enrichment analysis. Finally, a protein-protein interaction (PPI) network was constructed using Cytoscape from data collected online from the STRING server. RESULTS According to the MCC algorithm, the 10 most found gene sequences were HNRNPU, SMC1A, PAFAH1B1, EHMT1, SPTBN4, OLFM1, NCAM1, SF3B3, FGF2, and UBE2I; with HNRNPU, SMC1A, and PAFAH1B1 being the most representative of the modules. CONCLUSIONS We were able to describe the gene sequences that promote the progression from leukoplakia to oral squamous cell carcinoma. Within these genes, the HNRNPU, SMC1A, and PAFAH1B1 constitute the main promising therapeutic targets to counteract the progression of oral cancer, they could also be important biomarkers for the diagnosis and classification of the disease.
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Affiliation(s)
- Jaime Guzman de Avila
- Department of Oral Medicine, School of Dentistry, University of Cartagena Cartagena, Colombia.
| | | | - Antistio Alviz-Amador
- Pharmacology and Therapeutic Group, Faculty of Pharmaceutical Sciences, University of Cartagena, Health Science Campus, Colombia. ,For Correspondence:
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22
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Sapir T, Kshirsagar A, Gorelik A, Olender T, Porat Z, Scheffer IE, Goldstein DB, Devinsky O, Reiner O. Heterogeneous nuclear ribonucleoprotein U (HNRNPU) safeguards the developing mouse cortex. Nat Commun 2022; 13:4209. [PMID: 35864088 PMCID: PMC9304408 DOI: 10.1038/s41467-022-31752-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 06/30/2022] [Indexed: 11/20/2022] Open
Abstract
HNRNPU encodes the heterogeneous nuclear ribonucleoprotein U, which participates in RNA splicing and chromatin organization. Microdeletions in the 1q44 locus encompassing HNRNPU and other genes and point mutations in HNRNPU cause brain disorders, including early-onset seizures and severe intellectual disability. We aimed to understand HNRNPU’s roles in the developing brain. Our work revealed that HNRNPU loss of function leads to rapid cell death of both postmitotic neurons and neural progenitors, with an apparent higher sensitivity of the latter. Further, expression and alternative splicing of multiple genes involved in cell survival, cell motility, and synapse formation are affected following Hnrnpu’s conditional truncation. Finally, we identified pharmaceutical and genetic agents that can partially reverse the loss of cortical structures in Hnrnpu mutated embryonic brains, ameliorate radial neuronal migration defects and rescue cultured neural progenitors’ cell death. HNRNPU is an RNA splicing protein associated with brain disorders such as early onset seizures. Here they show that HNRNPU functions to maintain neural progenitors and their progeny by regulating splicing of key neuronal genes.
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Affiliation(s)
- Tamar Sapir
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Aditya Kshirsagar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Anna Gorelik
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Tsviya Olender
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ziv Porat
- Flow Cytometry Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Ingrid E Scheffer
- The University of Melbourne, Austin Health and Royal Children's Hospital, Florey and Murdoch Children's Research Institutes, Melbourne, VIC, Australia
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | | | - Orly Reiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
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23
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Song Y, Ren X, Gao F, Li F, Zhou J, Chen J, Zhang Y. LINC01588 regulates WWP2-mediated cardiomyocyte injury by interacting with HNRNPL. ENVIRONMENTAL TOXICOLOGY 2022; 37:1629-1641. [PMID: 35258167 DOI: 10.1002/tox.23512] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 01/25/2022] [Accepted: 02/19/2022] [Indexed: 06/14/2023]
Abstract
Cardiomyocyte dysfunction and apoptosis induced by ischemia-hypoxia are common features of many acute and chronic heart diseases. WW domain-containing E3 ubiquitin ligase (WWP2) has been identified as an important regulator in pathogenesis of some health-threatening diseases. Although a couple of recent reports prompted the potential role of WWP2 in heart dysfunction, however, its exact role and how its expression was regulated in ischemic-hypoxic cardiomyocytes are still elusive. Here, we found that WWP2 protein level was induced in anoxia/reoxygenation (A/R) treated cardiomyocytes in a time-dependent manner, accompanied by synchronous expression of LINC01588 and HNRNPL. Knockdown of LINC01588 increased cardiomyocyte apoptosis, the level of oxidative stress, and expression of pro-inflammatory cytokine genes, down-regulated the expression of WWP2 and promoted expression of SEPT4 gene that contributed to cardiomyocyte dysfunction and was a target gene of WWP2. LINC01588 overexpression improved the functions of A/R treated cardiomyocytes, up-regulated WWP2 and reduced SEPT4 expression. In the mechanism exploration, we found that LINC01588 could directly bind with HNRNPL protein that could interact with WWP2, suggesting that WWP2 was involved in the regulation of LINC01588 in A/R treated cardiomyocytes. Moreover, WWP2 inhibition declined the protective role of LINC01588 in cardiomyocyte dysfunction induced by A/R. Finally, we demonstrated that LINC01588 overexpression improved acute myocardial infarction in mice in vivo. In conclusion, LINC01588 improved A/R-induced cardiomyocyte dysfunction by interacting with HNRNPL and promoting WWP2-mediated degradation of SEPT4.
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Affiliation(s)
- Yanbin Song
- Department of Cardiovasology, Yan'an University Affiliated Hospital, China
- Heart and Brain Laboratory, Yan'an University Affiliated Hospital, China
| | - Xiaoyue Ren
- Department of Oncology, Yan'an University Affiliated Hospital, China
| | - Feng Gao
- Department of Cardiovasology, Yan'an University Affiliated Hospital, China
- Heart and Brain Laboratory, Yan'an University Affiliated Hospital, China
| | - Fei Li
- Department of Cardiovasology, Yan'an University Affiliated Hospital, China
- Heart and Brain Laboratory, Yan'an University Affiliated Hospital, China
| | - Jing Zhou
- Department of Cardiovasology, Yan'an University Affiliated Hospital, China
- Heart and Brain Laboratory, Yan'an University Affiliated Hospital, China
| | - Junmin Chen
- Department of Cardiovasology, Yan'an University Affiliated Hospital, China
- Heart and Brain Laboratory, Yan'an University Affiliated Hospital, China
| | - Yunqing Zhang
- Department of Pathology, Yan'an University Affiliated Hospital, China
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24
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Sarkar A, Panati K, Narala VR. Code inside the codon: The role of synonymous mutations in regulating splicing machinery and its impact on disease. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2022; 790:108444. [PMID: 36307006 DOI: 10.1016/j.mrrev.2022.108444] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 10/10/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022]
Abstract
In eukaryotes, precise pre-mRNA processing, including alternative splicing, is essential to carry out the intricate protein translation process. Both point mutations (that alter the translated protein sequence) and synonymous mutations (that do not alter the translated protein sequence) are capable of affecting the splicing process. Synonymous mutations are known to affect gene expression via altering mRNA stability, mRNA secondary structure, splicing processes, and translational kinetics. In higher eukaryotes, precise splicing is regulated by three weakly conserved cis-elements, 5' and 3' splice sites and the branch site. Many other cis-acting elements (exonic/intronic splicing enhancers and silencers) and trans-acting splicing factors (serine and arginine-rich proteins and heterogeneous nuclear ribonucleoproteins) have also been found to enhance or suppress the splicing process. The appearance of synonymous mutations in cis-acting elements can alter the splicing process by changing the binding pattern of splicing factors to exonic splicing enhancers or silencer motifs. This results in exon skipping, intron retention, and various other forms of alternative splicing, eventually leading to the emergence of a wide range of diseases. The focus of this review is to elucidate the role of synonymous mutations and their impact on abnormal splicing mechanisms. Further, this study highlights the function of synonymous mutation in mediating abnormal splicing in cancer and development of X-linked, and autosomal inherited diseases.
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Affiliation(s)
- Avik Sarkar
- Department of Zoology, Vidyasagar University, Midnapore, West Bengal 721102, India
| | - Kalpana Panati
- Department of Biotechnology, Government College for Men, Kadapa 516004, India
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25
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Zhang H, Kou X, Xiao D, Yu Z. Long non-coding RNA lincRNA-erythroid prosurvival attenuates inflammation by enhancing myosin heavy chain 6 stability through recruitment of heterogeneous nuclear ribonucleoprotein L in myocardial infarction. Bioengineered 2022; 13:14426-14437. [PMID: 36694458 PMCID: PMC9995127 DOI: 10.1080/21655979.2022.2086376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Myocardial infarction (MI), a prevalent cardiac disorder with high mortality, leads to severe heart injury associated with inflammation and cardiomyocyte apoptosis. Long non-coding RNAs have been widely found to participate in the progression of MI. Here, we aimed to explore the impact of lincRNA-erythroid prosurvival (EPS) on MI-induced inflammation and cardiomyocyte apoptosis. Significantly, lincRNA-EPS was lowly expressed in MI mice and in oxygen and glucose deprivation (OGD)-treated HL-1 cells. Echocardiography analysis revealed that lincRNA-EPS overexpression increased left ventricular ejection fraction and left ventricular fraction shortening, and decreased left ventricular internal diameter at end systole and left ventricular internal diameter at end diastole in a mouse model. In our study, the expression levels of interleukin-6, tumor necrosis factor-alpha, interleukin-1β, and interleukin-18 were upregulated in the MI mice and OGD-treated HL-1 cells, while lincRNA-EPS overexpression reversed these phenotypes. Meanwhile, lincRNA-EPS reduced MI-induced cardiomyocyte apoptosis in vivo and in vitro. Mechanically, lincRNA-EPS interacted with myosin heavy chain 6 (MYH6) and heterogeneous nuclear ribonucleoprotein L (HNRNPL), and the depletion of lincRNA-EPS and HNRNPL inhibited MYH6 mRNA stability in HL-1 cells. HNRNPL knockdown blocked lincRNA-EPS overexpression-induced MYH6 expression in the system. The depletion of MYH6 and HNRNPL could rescue lincRNA-EPS overexpression-reduced inflammation and apoptosis in HL-1 cells. Thus, we conclude that lincRNA-EPS attenuates inflammation and apoptosis in MI-induced myocardial injury by maintaining MYH6 stability through the recruitment of HNRNPL.
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Affiliation(s)
- Huizhen Zhang
- Department of Cardiology, the First People's Hospital of Jinan, Jinan, P.R. China
| | - Xuejun Kou
- Department of Cardiology, Shandong Provincial Third Hospital, Jinan, P.R. China
| | - Dong Xiao
- Department of Medicine, Jinan Hospital, Jinan, P.R. China
| | - Zhangjian Yu
- Department of Emergency, Jinan Central Hospital, Jinan, P.R. China
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26
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Wang H, Liu H, Zhao X, Chen X. Heterogeneous nuclear ribonucleoprotein U-actin complex derived from extracellular vesicles facilitates proliferation and migration of human coronary artery endothelial cells by promoting RNA polymerase II transcription. Bioengineered 2022; 13:11469-11486. [PMID: 35535400 PMCID: PMC9276035 DOI: 10.1080/21655979.2022.2066754] [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] [Indexed: 12/02/2022] Open
Abstract
Coronary artery disease (CAD) represents a fatal public threat. The involvement of extracellular vesicles (EVs) in CAD has been documented. This study explored the regulation of embryonic stem cells (ESCs)-derived EVs-hnRNPU-actin complex in human coronary artery endothelial cell (HCAEC) growth. Firstly, in vitro HCAEC hypoxia models were established. EVs were extracted from ESCs by ultracentrifugation. HCAECs were treated with EVs and si-VEGF for 24 h under hypoxia, followed by assessment of cell proliferation, apoptosis, migration, and tube formation. Uptake of EVs by HCAECs was testified. Additionally, hnRNPU, VEGF, and RNA Pol II levels were determined using Western blotting and CHIP assays. Interaction between hnRNPU and actin was evaluated by Co-immunoprecipitation assay. HCAEC viability and proliferation were lowered, apoptosis was enhanced, wound fusion was decreased, and the number of tubular capillary structures was reduced under hypoxia, whereas ESC-EVs treatment counteracted these effects. Moreover, EVs transferred hnRNPU into HCAECs. EVs-hnRNPU-actin complex increased RNA Pol II level on the VEGF gene promoter and promoted VEGF expression in HCAECs. Inhibition of hnRNPU or VEGF both annulled the promotion of EVs on HCAEC growth. Collectively, ESC-EVs-hnRNPU-actin increased RNA Pol II phosphorylation and VEGF expression, thus promoting HCAEC growth.
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Affiliation(s)
- Han Wang
- Department of Cardiovascular, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Hengdao Liu
- Department of Cardiovascular, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Xi Zhao
- Department of Cardiovascular, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Xiaowei Chen
- Department of Cardiovascular, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
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27
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Connolly C, Takahashi S, Miura H, Hiratani I, Gilbert N, Donaldson AD, Hiraga SI. SAF-A promotes origin licensing and replication fork progression to ensure robust DNA replication. J Cell Sci 2022; 135:jcs258991. [PMID: 34888666 DOI: 10.1242/jcs.258991] [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: 06/02/2021] [Accepted: 12/02/2021] [Indexed: 11/20/2022] Open
Abstract
The organisation of chromatin is closely intertwined with biological activities of chromosome domains, including transcription and DNA replication status. Scaffold-attachment factor A (SAF-A), also known as heterogeneous nuclear ribonucleoprotein U (HNRNPU), contributes to the formation of open chromatin structure. Here, we demonstrate that SAF-A promotes the normal progression of DNA replication and enables resumption of replication after inhibition. We report that cells depleted of SAF-A show reduced origin licensing in G1 phase and, consequently, reduced origin activation frequency in S phase. Replication forks also progress less consistently in cells depleted of SAF-A, contributing to reduced DNA synthesis rate. Single-cell replication timing analysis revealed two distinct effects of SAF-A depletion: first, the boundaries between early- and late-replicating domains become more blurred; and second, SAF-A depletion causes replication timing changes that tend to bring regions of discordant domain compartmentalisation and replication timing into concordance. Associated with these defects, SAF-A-depleted cells show elevated formation of phosphorylated histone H2AX (γ-H2AX) and tend to enter quiescence. Overall, we find that SAF-A protein promotes robust DNA replication to ensure continuing cell proliferation.
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Affiliation(s)
- Caitlin Connolly
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Saori Takahashi
- RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
| | - Hisashi Miura
- RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
| | - Ichiro Hiratani
- RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
| | - Nick Gilbert
- MRC Human Genetics Unit, The University of Edinburgh, Crewe Rd, Edinburgh EH4 2XU, UK
| | - Anne D Donaldson
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Shin-Ichiro Hiraga
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
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28
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Genome-Wide DNA Methylation Signatures Predict the Early Asymptomatic Doxorubicin-Induced Cardiotoxicity in Breast Cancer. Cancers (Basel) 2021; 13:cancers13246291. [PMID: 34944912 PMCID: PMC8699582 DOI: 10.3390/cancers13246291] [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: 10/01/2021] [Revised: 12/07/2021] [Accepted: 12/08/2021] [Indexed: 11/17/2022] Open
Abstract
Chemotherapy with doxorubicin (DOX) may cause unpredictable cardiotoxicity. This study aimed to determine whether the methylation signature of peripheral blood mononuclear cells (PBMCs) prior to and after the first cycle of DOX-based chemotherapy could predict the risk of cardiotoxicity in breast cancer patients. Cardiotoxicity was defined as a decrease in left ventricular ejection fraction (LVEF) by >10%. DNA methylation of PBMCs from 9 patients with abnormal LVEF and 10 patients with normal LVEF were examined using Infinium HumanMethylation450 BeadChip. We have identified 14,883 differentially methylated CpGs at baseline and 18,718 CpGs after the first cycle of chemotherapy, which significantly correlated with LVEF status. Significant differentially methylated regions (DMRs) were found in the promoter and the gene body of SLFN12, IRF6 and RNF39 in patients with abnormal LVEF. The pathway analysis found enrichment for regulation of transcription, mRNA splicing, pathways in cancer and ErbB2/4 signaling. The preliminary results from this study showed that the DNA methylation profile of PBMCs may predict the risk of DOX-induced cardiotoxicity prior to chemotherapy. Further studies with larger cohorts of patients are needed to confirm these findings.
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29
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Wen Y, Ma X, Wang X, Wang F, Dong J, Wu Y, Lv C, Liu K, Zhang Y, Zhang Z, Yuan S. hnRNPU in Sertoli cells cooperates with WT1 and is essential for testicular development by modulating transcriptional factors Sox8/9. Am J Cancer Res 2021; 11:10030-10046. [PMID: 34815802 PMCID: PMC8581416 DOI: 10.7150/thno.66819] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 10/12/2021] [Indexed: 12/25/2022] Open
Abstract
Background: Sertoli cells are essential regulators of testicular fate in the differentiating gonad; however, its role and underlying molecular mechanism of regulating testicular development in prepubertal testes are poorly understood. Although several critical regulatory factors of Sertoli cell development and function have been identified, identifying extrinsic factors that regulate gonocyte proliferation and migration processes during neonatal testis development remains largely unknown. Methods: We used the Sertoli cell-specific conditional knockout strategy (Cre/Loxp) in mice and molecular biological analyses (Luciferase assay, ChIP-qPCR, RNA-Seq, etc.) in vitro and in vivo to study the physiological roles of hnRNPU in Sertoli cells on regulating testicular development in prepubertal testes. Results: We identified a co-transcription factor, hnRNPU, which is highly expressed in mouse and human Sertoli cells and required for neonatal Sertoli cell and pre-pubertal testicular development. Conditional knockout of hnRNPU in murine Sertoli cells leads to severe testicular atrophy and male sterility, characterized by rapid depletion of both Sertoli cells and germ cells and failure of spermatogonia proliferation and migration during pre-pubertal testicular development. At molecular levels, we found that hnRNPU interacts with two Sertoli cell markers WT1 and SOX9, and enhances the expression of two transcriptional factors, Sox8 and Sox9, in Sertoli cells by directly binding to their promoter regions. Further RNA-Seq and bioinformatics analyses revealed the transcriptome-wide of key genes essential for Sertoli cell and germ cell fate control, such as biological adhesion, proliferation and migration, were deregulated in Sertoli cell-specific hnRNPU mutant testes. Conclusion: Our findings demonstrate an essential role of hnRNPU in Sertoli cells for prepubertal testicular development and testis microenvironment maintenance and define a new insight for our understanding of male infertility therapy.
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30
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Marenda M, Lazarova E, Gilbert N. The role of SAF-A/hnRNP U in regulating chromatin structure. Curr Opin Genet Dev 2021; 72:38-44. [PMID: 34823151 DOI: 10.1016/j.gde.2021.10.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/15/2021] [Accepted: 10/27/2021] [Indexed: 01/01/2023]
Abstract
Scaffold attachment factor A (SAF-A) or hnRNP U is a nuclear RNA-binding protein with a well-documented role in processing newly transcribed RNA. Recent studies also indicate that SAF-A can oligomerise in an ATP-dependent manner and interact with RNA to form a dynamic nuclear mesh. This mesh is thought to regulate nuclear and chromatin architecture, yet a mechanistic understanding is lacking. Here, we review developments in the field to understand how the SAF-A/RNA mesh affects chromatin organisation in interphase and mitosis. As SAF-A has an intrinsically disordered domain we discuss how the chromatin mesh is related to nuclear phase-separated condensates, which in other situations have been shown to regulate transcription and cell functions. Finally, we infer possible links between diseases emerging from SAF-A mutations and its role in chromatin organisation and regulation.
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Affiliation(s)
- Mattia Marenda
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Elena Lazarova
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Nick Gilbert
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK.
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31
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Proteomic Analysis of Exosomes during Cardiogenic Differentiation of Human Pluripotent Stem Cells. Cells 2021; 10:cells10102622. [PMID: 34685602 PMCID: PMC8533815 DOI: 10.3390/cells10102622] [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: 09/10/2021] [Revised: 09/23/2021] [Accepted: 09/28/2021] [Indexed: 11/26/2022] Open
Abstract
Efforts to direct the specification of human pluripotent stem cells (hPSCs) to therapeutically important somatic cell types have focused on identifying proper combinations of soluble cues. Yet, whether exosomes, which mediate intercellular communication, play a role in the differentiation remains unexplored. We took a first step toward addressing this question by subjecting hPSCs to stage-wise specification toward cardiomyocytes (CMs) in scalable stirred-suspension cultures and collecting exosomes. Samples underwent liquid chromatography (LC)/mass spectrometry (MS) and subsequent proteomic analysis revealed over 300 unique proteins from four differentiation stages including proteins such as PPP2CA, AFM, MYH9, MYH10, TRA2B, CTNNA1, EHD1, ACTC1, LDHB, and GPC4, which are linked to cardiogenic commitment. There was a significant correlation of the protein composition of exosomes with the hPSC line and stage of commitment. Differentiating hPSCs treated with exosomes from hPSC-derived CMs displayed improved efficiency of CM formation compared to cells without exogenously added vesicles. Collectively, these results demonstrate that exosomes from hPSCs induced along the CM lineage contain proteins linked to the specification process with modulating effects and open avenues for enhancing the biomanufacturing of stem cell products for cardiac diseases.
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32
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Sanderson MR, Fahlman RP, Wevrick R. The N-terminal domain of the Schaaf-Yang syndrome protein MAGEL2 likely has a role in RNA metabolism. J Biol Chem 2021; 297:100959. [PMID: 34265304 PMCID: PMC8350409 DOI: 10.1016/j.jbc.2021.100959] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 06/22/2021] [Accepted: 07/11/2021] [Indexed: 02/08/2023] Open
Abstract
MAGEL2 encodes the L2 member of the melanoma-associated antigen gene (MAGE) protein family, truncating mutations of which can cause Schaaf-Yang syndrome, an autism spectrum disorder. MAGEL2 is also inactivated in Prader-Willi syndrome, which overlaps clinically and mechanistically with Schaaf-Yang syndrome. Studies to date have only investigated the C-terminal portion of the MAGEL2 protein, containing the MAGE homology domain that interacts with RING-E3 ubiquitin ligases and deubiquitinases to form protein complexes that modify protein ubiquitination. In contrast, the N-terminal portion of the MAGEL2 protein has never been studied. Here, we find that MAGEL2 has a low-complexity intrinsically disordered N-terminus rich in Pro-Xn-Gly motifs that is predicted to mediate liquid-liquid phase separation to form biomolecular condensates. We used proximity-dependent biotin identification (BioID) and liquid chromatography-tandem mass spectrometry to identify MAGEL2-proximal proteins, then clustered these proteins into functional networks. We determined that coding mutations analogous to disruptive mutations in other MAGE proteins alter these networks in biologically relevant ways. Proteins identified as proximal to the N-terminal portion of MAGEL2 are primarily involved in mRNA metabolic processes and include three mRNA N 6-methyladenosine (m6A)-binding YTHDF proteins and two RNA interference-mediating TNRC6 proteins. We found that YTHDF2 coimmunoprecipitates with MAGEL2, and coexpression of MAGEL2 reduces the nuclear accumulation of YTHDF2 after heat shock. We suggest that the N-terminal region of MAGEL2 may have a role in RNA metabolism and in particular the regulation of mRNAs modified by m6A methylation. These results provide mechanistic insight into pathogenic MAGEL2 mutations associated with Schaaf-Yang syndrome and related disorders.
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Affiliation(s)
- Matthea R Sanderson
- Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Richard P Fahlman
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada; Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
| | - Rachel Wevrick
- Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada.
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33
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Nguyen LXT, Zhang B, Hoang DH, Zhao D, Wang H, Wu H, Su YL, Dong H, Rodriguez-Rodriguez S, Armstrong B, Ghoda LY, Perrotti D, Pichiorri F, Chen J, Li L, Kortylewski M, Rockne RC, Kuo YH, Khaled S, Carlesso N, Marcucci G. Cytoplasmic DROSHA and non-canonical mechanisms of MiR-155 biogenesis in FLT3-ITD acute myeloid leukemia. Leukemia 2021; 35:2285-2298. [PMID: 33589748 PMCID: PMC8973317 DOI: 10.1038/s41375-021-01166-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/07/2021] [Accepted: 01/26/2021] [Indexed: 01/29/2023]
Abstract
We report here on a novel pro-leukemogenic role of FMS-like tyrosine kinase 3-internal tandem duplication (FLT3-ITD) that interferes with microRNAs (miRNAs) biogenesis in acute myeloid leukemia (AML) blasts. We showed that FLT3-ITD interferes with the canonical biogenesis of intron-hosted miRNAs such as miR-126, by phosphorylating SPRED1 protein and inhibiting the "gatekeeper" Exportin 5 (XPO5)/RAN-GTP complex that regulates the nucleus-to-cytoplasm transport of pre-miRNAs for completion of maturation into mature miRNAs. Of note, despite the blockage of "canonical" miRNA biogenesis, miR-155 remains upregulated in FLT3-ITD+ AML blasts, suggesting activation of alternative mechanisms of miRNA biogenesis that circumvent the XPO5/RAN-GTP blockage. MiR-155, a BIC-155 long noncoding (lnc) RNA-hosted oncogenic miRNA, has previously been implicated in FLT3-ITD+ AML blast hyperproliferation. We showed that FLT3-ITD upregulates miR-155 by inhibiting DDX3X, a protein implicated in the splicing of lncRNAs, via p-AKT. Inhibition of DDX3X increases unspliced BIC-155 that is then shuttled by NXF1 from the nucleus to the cytoplasm, where it is processed into mature miR-155 by cytoplasmic DROSHA, thereby bypassing the XPO5/RAN-GTP blockage via "non-canonical" mechanisms of miRNA biogenesis.
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Affiliation(s)
- Le Xuan Truong Nguyen
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, CA, USA.
| | - Bin Zhang
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Dinh Hoa Hoang
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Dandan Zhao
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Huafeng Wang
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Herman Wu
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Yu-Lin Su
- Department of Immuno-Oncology, City of Hope Medical Center, Duarte, CA, USA
| | - Haojie Dong
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Sonia Rodriguez-Rodriguez
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Brian Armstrong
- Light Microscopy Core, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Lucy Y Ghoda
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Danilo Perrotti
- Department of Medicine, Biochemistry and Molecular Biology and the Marlene and Greenebaum Comprehensive Cancer Center, University of Maryland, Baltimore, MD, USA
| | - Flavia Pichiorri
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Jianjun Chen
- Department of System Biology, City of Hope Medical Center, Duarte, CA, USA
| | - Ling Li
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Marcin Kortylewski
- Department of Immuno-Oncology, City of Hope Medical Center, Duarte, CA, USA
| | - Russell C Rockne
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Ya-Huei Kuo
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Samer Khaled
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Nadia Carlesso
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Guido Marcucci
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, CA, USA.
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34
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Dumont AA, Dumont L, Zhou D, Giguère H, Pileggi C, Harper ME, Blondin DP, Scott MS, Auger-Messier M. Cardiomyocyte-specific Srsf3 deletion reveals a mitochondrial regulatory role. FASEB J 2021; 35:e21544. [PMID: 33819356 DOI: 10.1096/fj.202002293rr] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 03/03/2021] [Accepted: 03/09/2021] [Indexed: 11/11/2022]
Abstract
Serine-rich splicing factor 3 (SRSF3) was recently reported as being necessary to preserve RNA stability via an mTOR mechanism in a cardiac mouse model in adulthood. Here, we demonstrate the link between Srsf3 and mitochondrial integrity in an embryonic cardiomyocyte-specific Srsf3 conditional knockout (cKO) mouse model. Fifteen-day-old Srsf3 cKO mice showed dramatically reduced (below 50%) survival and reduced the left ventricular systolic performance, and histological analysis of these hearts revealed a significant increase in cardiomyocyte size, confirming the severe remodeling induced by Srsf3 deletion. RNA-seq analysis of the hearts of 5-day-old Srsf3 cKO mice revealed early changes in expression levels and alternative splicing of several transcripts related to mitochondrial integrity and oxidative phosphorylation. Likewise, the levels of several protein complexes of the electron transport chain decreased, and mitochondrial complex I-driven respiration of permeabilized cardiac muscle fibers from the left ventricle was impaired. Furthermore, transmission electron microscopy analysis showed disordered mitochondrial length and cristae structure. Together with its indispensable role in the physiological maintenance of mouse hearts, these results highlight the previously unrecognized function of Srsf3 in regulating the mitochondrial integrity.
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Affiliation(s)
- Audrey-Ann Dumont
- Département de Médecine - Service de Cardiologie, Faculté de Médecine et des Sciences de la Santé, Centre de Recherche du CHUS, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Lauralyne Dumont
- Département de Médecine - Service de Cardiologie, Faculté de Médecine et des Sciences de la Santé, Centre de Recherche du CHUS, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Delong Zhou
- Département de microbiologie et d'infectiologie, Faculté de Médecine et des Sciences de la Santé, Centre de Recherche du CHUS, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Hugo Giguère
- Département de Médecine - Service de Cardiologie, Faculté de Médecine et des Sciences de la Santé, Centre de Recherche du CHUS, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Chantal Pileggi
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Mary-Ellen Harper
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Denis P Blondin
- Département de Médecine - Service de Cardiologie, Faculté de Médecine et des Sciences de la Santé, Centre de Recherche du CHUS, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Michelle S Scott
- Département de Biochimie et Génomique Fonctionnelle, Faculté de Médecine et des Sciences de la Santé, Centre de Recherche du CHUS, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Mannix Auger-Messier
- Département de Médecine - Service de Cardiologie, Faculté de Médecine et des Sciences de la Santé, Centre de Recherche du CHUS, Université de Sherbrooke, Sherbrooke, QC, Canada
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35
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Huang Y, Qiao Y, Zhao Y, Li Y, Yuan J, Zhou J, Sun H, Wang H. Large scale RNA-binding proteins/LncRNAs interaction analysis to uncover lncRNA nuclear localization mechanisms. Brief Bioinform 2021; 22:6287336. [PMID: 34056657 DOI: 10.1093/bib/bbab195] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 04/28/2021] [Accepted: 04/29/2021] [Indexed: 12/25/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are key regulators of major biological processes and their functional modes are dictated by their subcellular localization. Relative nuclear enrichment of lncRNAs compared to mRNAs is a prevalent phenomenon but the molecular mechanisms governing their nuclear retention in cells remain largely unknown. Here in this study, we harness the recently released eCLIP data for a large number of RNA-binding proteins (RBPs) in K562 and HepG2 cells and utilize multiple bioinformatics methods to comprehensively survey the roles of RBPs in lncRNA nuclear retention. We identify an array of splicing RBPs that bind to nuclear-enriched lincRNAs (large intergenic non-coding RNAs) thus may act as trans-factors regulating their nuclear retention. Further analyses reveal that these RBPs may bind with distinct core motifs, flanking sequence compositions, or secondary structures to drive lincRNA nuclear retention. Moreover, network analyses uncover potential co-regulatory RBP clusters and the physical interaction between HNRNPU and SAFB2 proteins in K562 cells is further experimentally verified. Altogether, our analyses reveal previously unknown factors and mechanisms that govern lincRNA nuclear localization in cells.
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Affiliation(s)
- Yile Huang
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Yulong Qiao
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Yu Zhao
- Department of Orthaepedics and Traumatology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Yuying Li
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Jie Yuan
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Jiajian Zhou
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Hao Sun
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Huating Wang
- Department of Orthaepedics and Traumatology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
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36
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Lee EJ, Neppl RL. Influence of Age on Skeletal Muscle Hypertrophy and Atrophy Signaling: Established Paradigms and Unexpected Links. Genes (Basel) 2021; 12:genes12050688. [PMID: 34063658 PMCID: PMC8147613 DOI: 10.3390/genes12050688] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 12/16/2022] Open
Abstract
Skeletal muscle atrophy in an inevitable occurrence with advancing age, and a consequence of disease including cancer. Muscle atrophy in the elderly is managed by a regimen of resistance exercise and increased protein intake. Understanding the signaling that regulates muscle mass may identify potential therapeutic targets for the prevention and reversal of muscle atrophy in metabolic and neuromuscular diseases. This review covers the major anabolic and catabolic pathways that regulate skeletal muscle mass, with a focus on recent progress and potential new players.
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37
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Song Z, Zhang Y, Yang C, Yi Z, Li F, Xue J, Yang X, Li B. De novo frameshift variants of HNRNPU in patients with early infantile epileptic encephalopathy: Two case reports and literature review. Int J Dev Neurosci 2021; 81:663-668. [PMID: 33914968 DOI: 10.1002/jdn.10115] [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: 01/14/2021] [Revised: 04/19/2021] [Accepted: 04/21/2021] [Indexed: 11/06/2022] Open
Abstract
Variants in HNRNPU have been reported in patients with epileptic encephalopathy, early infantile 54 (OMIM 602,869). We hereby describe two children from different families with autosomal dominance early-onset epileptic encephalopathy and summarize the genotype and phenotype of reported individuals. Whole-exome sequencing analysis was applied to the patients. De novo frameshift variants in the HNRNPU, c.143_149del7 (p.G48Afs*11) and c.1282delC(p.G429Afs*53) were identified. This is the first time to report Chinese patients with early infantile epileptic encephalopathy caused by HNRNPU variants, and so far, these variants have not been reported in population gene database. This study expands our knowledge of HNRNPU variants and emphasizes the importance of early gene diagnosis.
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Affiliation(s)
- Zhenfeng Song
- Department of Pediatrics, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Department of Pediatric Neurology and Endocrinology, the Affiliated Hospital of Qingdao University, Qingdao, China
| | - Ying Zhang
- Department of Pediatric Neurology and Endocrinology, the Affiliated Hospital of Qingdao University, Qingdao, China
| | - Chengqing Yang
- Department of Pediatric Neurology and Endocrinology, the Affiliated Hospital of Qingdao University, Qingdao, China
| | - Zhi Yi
- Department of Pediatric Neurology and Endocrinology, the Affiliated Hospital of Qingdao University, Qingdao, China
| | - Fei Li
- Department of Pediatric Neurology and Endocrinology, the Affiliated Hospital of Qingdao University, Qingdao, China
| | - Jiao Xue
- Department of Pediatric Neurology and Endocrinology, the Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xiaofan Yang
- Department of Pediatrics, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Baomin Li
- Department of Pediatrics, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
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New Insights into Cellular Functions of Nuclear Actin. BIOLOGY 2021; 10:biology10040304. [PMID: 33916969 PMCID: PMC8067577 DOI: 10.3390/biology10040304] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/30/2021] [Accepted: 04/01/2021] [Indexed: 12/12/2022]
Abstract
Simple Summary It is well known that actin forms a cytoplasmic network of microfilaments, the part of the cytoskeleton, in the cytoplasm of eukaryotic cells. The presence of nuclear actin was elusive for a very long time. Now, there is a very strong evidence that actin plays many important roles in the nucleus. Here, we discuss the recently discovered functions of the nuclear actin pool. Actin does not have nuclear localization signal (NLS), so its import to the nucleus is facilitated by the NLS-containing proteins. Nuclear actin plays a role in the maintenance of the nuclear structure and the nuclear envelope breakdown. It is also involved in chromatin remodeling, and chromatin and nucleosome movement necessary for DNA recombination, repair, and the initiation of transcription. It also binds RNA polymerases, promoting transcription. Because of the multifaceted role of nuclear actin, the future challenge will be to further define its functions in various cellular processes and diseases. Abstract Actin is one of the most abundant proteins in eukaryotic cells. There are different pools of nuclear actin often undetectable by conventional staining and commercial antibodies used to identify cytoplasmic actin. With the development of more sophisticated imaging and analytical techniques, it became clear that nuclear actin plays a crucial role in shaping the chromatin, genomic, and epigenetic landscape, transcriptional regulation, and DNA repair. This multifaceted role of nuclear actin is not only important for the function of the individual cell but also for the establishment of cell fate, and tissue and organ differentiation during development. Moreover, the changes in the nuclear, chromatin, and genomic architecture are preamble to various diseases. Here, we discuss some of the newly described functions of nuclear actin.
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39
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Sharp JA, Perea-Resa C, Wang W, Blower MD. Cell division requires RNA eviction from condensing chromosomes. J Cell Biol 2021; 219:211450. [PMID: 33053167 PMCID: PMC7549315 DOI: 10.1083/jcb.201910148] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 08/21/2020] [Accepted: 08/31/2020] [Indexed: 12/28/2022] Open
Abstract
During mitosis, the genome is transformed from a decondensed, transcriptionally active state to a highly condensed, transcriptionally inactive state. Mitotic chromosome reorganization is marked by the general attenuation of transcription on chromosome arms, yet how the cell regulates nuclear and chromatin-associated RNAs after chromosome condensation and nuclear envelope breakdown is unknown. SAF-A/hnRNPU is an abundant nuclear protein with RNA-to-DNA tethering activity, coordinated by two spatially distinct nucleic acid–binding domains. Here we show that RNA is evicted from prophase chromosomes through Aurora-B–dependent phosphorylation of the SAF-A DNA-binding domain; failure to execute this pathway leads to accumulation of SAF-A–RNA complexes on mitotic chromosomes, defects in metaphase chromosome alignment, and elevated rates of chromosome missegregation in anaphase. This work reveals a role for Aurora-B in removing chromatin-associated RNAs during prophase and demonstrates that Aurora-B–dependent relocalization of SAF-A during cell division contributes to the fidelity of chromosome segregation.
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Affiliation(s)
- Judith A Sharp
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA.,Department of Genetics, Harvard Medical School, Boston, MA
| | - Carlos Perea-Resa
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA.,Department of Genetics, Harvard Medical School, Boston, MA
| | - Wei Wang
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA.,Department of Genetics, Harvard Medical School, Boston, MA
| | - Michael D Blower
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA.,Department of Genetics, Harvard Medical School, Boston, MA
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40
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Puvvula PK, Moon AM. Novel Cell-Penetrating Peptides Derived From Scaffold-Attachment- Factor A Inhibits Cancer Cell Proliferation and Survival. Front Oncol 2021; 11:621825. [PMID: 33859938 PMCID: PMC8042391 DOI: 10.3389/fonc.2021.621825] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 02/18/2021] [Indexed: 12/12/2022] Open
Abstract
Scaffold-attachment-factor A (SAFA) has important roles in many normal and pathologic cellular processes but the scope of its function in cancer cells is unknown. Here, we report dominant-negative activity of novel peptides derived from the SAP and RGG-domains of SAFA and their effects on proliferation, survival and the epigenetic landscape in a range of cancer cell types. The RGG-derived peptide dysregulates SAFA binding and regulation of alternatively spliced targets and decreases levels of key spliceosome proteins in a cell-type specific manner. In contrast, the SAP-derived peptide reduces active histone marks, promotes chromatin compaction, and activates the DNA damage response and cell death in a subset of cancer cell types. Our findings reveal an unprecedented function of SAFA-derived peptides in regulating diverse SAFA molecular functions as a tumor suppressive mechanism and demonstrate the potential therapeutic utility of SAFA-peptides in a wide range of cancer cells.
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Affiliation(s)
- Pavan Kumar Puvvula
- Department of Molecular and Functional Genomics, Weis Center for Research, Geisinger Clinic, Danville, PA, United States
| | - Anne M Moon
- Department of Molecular and Functional Genomics, Weis Center for Research, Geisinger Clinic, Danville, PA, United States.,Department of Human Genetics, University of Utah, Salt Lake City, UT, United States.,The Mindich Child Health and Development Institute, Hess Center for Science and Medicine at Mount Sinai, New York, NY, United States
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41
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Sex-Specific Alterations in Cardiac DNA Methylation in Adult Mice by Perinatal Lead Exposure. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18020577. [PMID: 33445541 PMCID: PMC7826866 DOI: 10.3390/ijerph18020577] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 12/27/2020] [Accepted: 01/04/2021] [Indexed: 12/27/2022]
Abstract
Environmental factors play an important role in the etiology of cardiovascular diseases. Cardiovascular diseases exhibit marked sexual dimorphism; however, the sex-specific effects of environmental exposures on cardiac health are incompletely understood. Perinatal and adult exposures to the metal lead (Pb) are linked to several adverse cardiovascular outcomes, but the sex-specific effects of this toxicant on the heart have received little attention. Perinatal environmental exposures can lead to disease through disruption of the normal epigenetic programming that occurs during early development. Using a mouse model of human-relevant perinatal environmental exposure, we investigated the effects of exposure to Pb during gestation and lactation on DNA methylation in the hearts of adult offspring mice (n = 6 per sex). Two weeks prior to mating, dams were assigned to control or Pb acetate (32 ppm) water, and exposure continued until offspring were weaned at three weeks of age. Enhanced reduced-representation bisulfite sequencing was used to measure DNA methylation in the hearts of offspring at five months of age. Although Pb exposure stopped at three weeks of age, we discovered hundreds of differentially methylated cytosines (DMCs) and regions (DMRs) in males and females at five months of age. DMCs/DMRs and their associated genes were sex-specific, with a small, but statistically significant subset overlapping between sexes. Pathway analysis revealed altered methylation of genes important for cardiac and other tissue development in males, and histone demethylation in females. Together, these data demonstrate that perinatal exposure to Pb induces sex-specific changes in cardiac DNA methylation that are present long after cessation of exposure, and highlight the importance of considering sex in environmental epigenetics and mechanistic toxicology studies.
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Spagnoli C, Rizzi S, Salerno GG, Frattini D, Koskenvuo J, Fusco C. Pharmacological Treatment of Severe Breathing Abnormalities in a Case of HNRNPU Epileptic Encephalopathy. Mol Syndromol 2021; 12:101-105. [PMID: 34012379 DOI: 10.1159/000512566] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 10/26/2020] [Indexed: 11/19/2022] Open
Abstract
Abnormal breathing patterns are a typical feature of Rett and Pitt-Hopkins syndrome and their variants. Their treatment can be challenging, with a risk of long-term detrimental consequences. Early infantile epileptic encephalopathy (EIEE) type 54 is a rare epileptic encephalopathy caused by pathogenic variants in the heterogeneous nuclear ribonucleoprotein U (HNRNPU) gene. Only one case has been described in the literature with episodes of hyperventilation and apnea, but treatment was not discussed. We describe the clinical and genetic features and treatment strategies in a case of EIEE type 54 and severely abnormal breathing pattern. A novel and likely pathogenic c.2277dup, p.(Pro760Serfs*5) variant in the HNRNPU gene was found in a male patient with severe episodes of hyperventilation and apnea, leading to syncope. Combination therapy with acetazolamide, alprazolam and aripiprazole led to significant clinical improvement. Although HNRNPU has not been implicated in breathing control, pathogenic variants in this gene can be associated with the development of abnormal breathing patterns reminiscent of Rett and Pitt-Hopkins syndrome. Its function as a gene expression regulator and its interaction with transcription factors offers a potential pathogenetic link between these 3 disorders. Based on our experience, treatment strategies can be similar to those already applied for patients with Pitt-Hopkins and Rett syndrome.
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Affiliation(s)
- Carlotta Spagnoli
- Child Neurology Unit, Department of Pediatrics, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Susanna Rizzi
- Child Neurology Unit, Department of Pediatrics, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Grazia Gabriella Salerno
- Child Neurology Unit, Department of Pediatrics, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Daniele Frattini
- Child Neurology Unit, Department of Pediatrics, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | | | - Carlo Fusco
- Child Neurology Unit, Department of Pediatrics, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy.,Pediatric Neurophysiology Laboratory, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
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43
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Wang W, Frankel WN. Overlaps, gaps, and complexities of mouse models of Developmental and Epileptic Encephalopathy. Neurobiol Dis 2021; 148:105220. [PMID: 33301879 PMCID: PMC8547712 DOI: 10.1016/j.nbd.2020.105220] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/17/2020] [Accepted: 12/04/2020] [Indexed: 11/28/2022] Open
Abstract
Mouse models have made innumerable contributions to understanding the genetic basis of neurological disease and pathogenic mechanisms and to therapy development. Here we consider the current state of mouse genetic models of Developmental and Epileptic Encephalopathy (DEE), representing a set of rare but devastating and largely intractable childhood epilepsies. By examining the range of mouse lines available in this rapidly moving field and by detailing both expected and unusual features in representative examples, we highlight lessons learned in an effort to maximize the full potential of this powerful resource for preclinical studies.
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Affiliation(s)
- Wanqi Wang
- Department of Genetics & Development, Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, United States of America.
| | - Wayne N Frankel
- Department of Genetics & Development, Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, United States of America.
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44
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Liu B, Li X, Zhao C, Wang Y, Lv M, Shi X, Han C, Pandey P, Qian C, Guo C, Zhang Y. Proteomic Analysis of Atrial Appendages Revealed the Pathophysiological Changes of Atrial Fibrillation. Front Physiol 2020; 11:573433. [PMID: 33041871 PMCID: PMC7526521 DOI: 10.3389/fphys.2020.573433] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 08/13/2020] [Indexed: 11/18/2022] Open
Abstract
Atrial fibrillation (AF), known as the most common arrhythmia in the developed world, affects 1.5–2.0% of the population. Numerous basic studies have been carried out to identify the roles of electric and structural remodeling in the pathophysiological changes of AF, but more explorations are required to further understand the mechanisms of AF development. Proteomics enables researchers to identify protein alterations responsible for the pathological developing progresses of diseases. Compared to the genome, the proteome is closely related to the disease phenotype and can better manifest the progression of diseases. In this study, AF patients proteomically analyzed to identify possible mechanisms. Totally 20 patients undergoing cardiac surgery (10 with paroxysmal AF and 10 with persistent AF) and 10 healthy subjects were recruited. The differentially expressed proteins identified here included AKR1A1, LYZ, H2AFY, DDAH1, FGA, FGB, LAMB1, LAMC1, MYL2, MYBPC3, MYL5, MYH10, HNRNPU, DKK3, COPS7A, YWHAQ, and PAICS. These proteins were mainly involved in the development of structural remodeling. The differently expressed proteins may provide a new perspective for the pathological process of AF, and may enable useful targets for drug interference. Nevertheless, more research in terms of multi-omics is required to investigate possible implicated molecular pathways of AF development.
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Affiliation(s)
- Ban Liu
- Department of Cardiology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiang Li
- Department of Cardiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Medical University, Chongqing, China
| | - Cuimei Zhao
- Department of Cardiology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yuliang Wang
- Department of Immunology, School of Basic Medical Science, Nanjing Medical University, Nanjing, China
| | - Mengwei Lv
- Shanghai East Hospital of Clinical Medical College, Nanjing Medical University, Shanghai, China.,Department of Cardiovascular Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xin Shi
- Department of Pediatric Cardiology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Chunyan Han
- Department of Cardiology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Pratik Pandey
- Department of Cardiology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chunhua Qian
- Department of Endocrinology and Metabolism, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Changfa Guo
- Department of Cardiovascular Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yangyang Zhang
- Department of Cardiovascular Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
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45
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Zietzer A, Hosen MR, Wang H, Goody PR, Sylvester M, Latz E, Nickenig G, Werner N, Jansen F. The RNA-binding protein hnRNPU regulates the sorting of microRNA-30c-5p into large extracellular vesicles. J Extracell Vesicles 2020; 9:1786967. [PMID: 32944175 PMCID: PMC7480565 DOI: 10.1080/20013078.2020.1786967] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The transfer of microRNAs (miRs) via extracellular vesicles (EVs) is a functionally relevant mechanism of intercellular communication that regulates both organ homoeostasis and disease development. Little is known about the packaging of miRs into EVs. Previous studies have shown that certain miRs are exported by RNA-binding proteins into small EVs, while for other miRs and for large EVs, in general, the export mechanisms remain unclear. Therefore, a proteomic analysis of endothelial cell-derived large EVs was performed, which revealed that heterogeneous nuclear ribonucleoprotein U (hnRNPU) is abundantly present in EVs. EVs were characterized by electron microscopy, immunoblotting and nanoparticle tracking analysis. Taqman microRNA array and single qPCR experiments identified specific miR patterns to be exported into EVs in an hnRNPU-dependent way. The specific role of hnRNPU for vesicular miR-sorting was confirmed independently by gain- and loss-of-function experiments. In our study, miR-30c-5p was the miR whose export was most significantly regulated by hnRNPU. Mechanistically, in silico binding analysis showed that the export of miRs into EVs depends on the binding efficiency of the respective miRs to hnRNPU. Among the exported miRs, a significant enrichment of the sequence motif AAMRUGCU was detected as a potential sorting signal. Experimentally, binding of miR-30c-5p to hnRNPU was confirmed independently by RNA-immunoprecipitation, electrophoretic mobility shift assay and reciprocally by miR-pulldown. Nuclear binding of miR-30c-5p to hnRNPU and subsequent stabilization was associated with a lower cytoplasmatic abundance and consequently reduced availability for vesicular export. hnRNPU-dependent miR-30c-5p export reduced cellular migration as well as pro-angiogenic gene expression in EV-recipient cells. In summary, hnRNPU retains miR-30c-5p and other miRs and thereby prevents their export into large EVs. The data presented provide a novel and functionally relevant mechanism of vesicular miR export.
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Affiliation(s)
- Andreas Zietzer
- Heart Center Bonn, Medical Department II, University Hospital Bonn, Venusberg-Campus 1, Bonn, Germany
| | - Mohammed Rabiul Hosen
- Heart Center Bonn, Medical Department II, University Hospital Bonn, Venusberg-Campus 1, Bonn, Germany
| | - Han Wang
- Heart Center Bonn, Medical Department II, University Hospital Bonn, Venusberg-Campus 1, Bonn, Germany
| | - Philip Roger Goody
- Heart Center Bonn, Medical Department II, University Hospital Bonn, Venusberg-Campus 1, Bonn, Germany
| | - Marc Sylvester
- Core Facility Mass Spectrometry, Institute of Biochemistry and Molecular Biology,Medical Faculty, University of Bonn, Bonn, Germany
| | - Eicke Latz
- Institute of Innate Immunity, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Georg Nickenig
- Heart Center Bonn, Medical Department II, University Hospital Bonn, Venusberg-Campus 1, Bonn, Germany
| | - Nikos Werner
- Heart Center Bonn, Medical Department II, University Hospital Bonn, Venusberg-Campus 1, Bonn, Germany.,Internal Medicine III, Krankenhaus Der Barmherzigen Brüder Trier, Trier, Germany
| | - Felix Jansen
- Heart Center Bonn, Medical Department II, University Hospital Bonn, Venusberg-Campus 1, Bonn, Germany
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46
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Bagchi D, Mason BD, Baldino K, Li B, Lee EJ, Zhang Y, Chu LK, El Raheb S, Sinha I, Neppl RL. Adult-Onset Myopathy with Constitutive Activation of Akt following the Loss of hnRNP-U. iScience 2020; 23:101319. [PMID: 32659719 PMCID: PMC7358745 DOI: 10.1016/j.isci.2020.101319] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/30/2020] [Accepted: 06/24/2020] [Indexed: 01/03/2023] Open
Abstract
Skeletal muscle has the remarkable ability to modulate its mass in response to changes in nutritional input, functional utilization, systemic disease, and age. This is achieved by the coordination of transcriptional and post-transcriptional networks and the signaling cascades balancing anabolic and catabolic processes with energy and nutrient availability. The extent to which alternative splicing regulates these signaling networks is uncertain. Here we investigate the role of the RNA-binding protein hnRNP-U on the expression and splicing of genes and the signaling processes regulating skeletal muscle hypertrophic growth. Muscle-specific Hnrnpu knockout (mKO) mice develop an adult-onset myopathy characterized by the selective atrophy of glycolytic muscle, the constitutive activation of Akt, increases in cellular and metabolic stress gene expression, and changes in the expression and splicing of metabolic and signal transduction genes. These findings link Hnrnpu with the balance between anabolic signaling, cellular and metabolic stress, and physiological growth. Hnrnpu mKO mice develop adult-onset myopathy with selective glycolytic muscle atrophy Akt is constitutively active in the atrophied muscles of Hnrnpu mKO mice Hnrnpu mutants show altered gene expression and alternative splicing patterns Induction of genes associated with cellular and metabolic stress
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Affiliation(s)
- Debalina Bagchi
- Department of Orthopaedic Surgery, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA
| | - Benjamin D Mason
- Department of Orthopaedic Surgery, Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, USA
| | - Kodilichi Baldino
- Division of Plastic Surgery, Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA
| | - Bin Li
- Division of Plastic Surgery, Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA
| | - Eun-Joo Lee
- Department of Orthopaedic Surgery, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA
| | - Yuteng Zhang
- Division of Plastic Surgery, Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA
| | - Linh Khanh Chu
- Department of Orthopaedic Surgery, Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, USA
| | - Sherif El Raheb
- Department of Orthopaedic Surgery, Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, USA
| | - Indranil Sinha
- Division of Plastic Surgery, Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA
| | - Ronald L Neppl
- Department of Orthopaedic Surgery, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA.
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47
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Laaref AM, Manchon L, Bareche Y, Lapasset L, Tazi J. The core spliceosomal factor U2AF1 controls cell-fate determination via the modulation of transcriptional networks. RNA Biol 2020; 17:857-871. [PMID: 32150510 PMCID: PMC7549707 DOI: 10.1080/15476286.2020.1733800] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 02/10/2020] [Indexed: 12/16/2022] Open
Abstract
Alternative splicing (AS) plays a central role during cell-fate determination. However, how the core spliceosomal factors (CSFs) are involved in this process is poorly understood. Here, we report the down-regulation of the U2AF1 CSF during stem cell differentiation. To investigate its function in stemness and differentiation, we downregulated U2AF1 in human induced pluripotent stem cells (hiPSCs), using an inducible-shRNA system, to the level found in differentiated ectodermal, mesodermal and endodermal cells. RNA sequencing and computational analysis reveal that U2AF1 down-regulation modulates the expression of development-regulating genes and regulates transcriptional networks involved in cell-fate determination. Furthermore, U2AF1 down-regulation induces a switch in the AS of transcription factors (TFs) required to establish specific cell lineages, and favours the splicing of a differentiated cell-specific isoform of DNMT3B. Our results showed that the differential expression of the core spliceosomal factor U2AF1, between stem cells and the precursors of the three germ layers regulates a cell-type-specific alternative splicing programme and a transcriptional network involved in cell-fate determination via the modulation of gene expression and alternative splicing of transcription regulators.
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Affiliation(s)
| | | | - Yacine Bareche
- IGMM, CNRS, University of Montpellier, Montpellier, France
- Breast Cancer Translational Research Laboratory, J. C. Heuson, Institut Jules Bordet, Université Libre De Bruxelles, Brussels, Belgium
| | - Laure Lapasset
- IGMM, CNRS, University of Montpellier, Montpellier, France
- VP research, CNRS, University of Montpellier, Montpellier, France
| | - Jamal Tazi
- IGMM, CNRS, University of Montpellier, Montpellier, France
- Lead Contact
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48
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Yugami M, Okano H, Nakanishi A, Yano M. Analysis of the nucleocytoplasmic shuttling RNA-binding protein HNRNPU using optimized HITS-CLIP method. PLoS One 2020; 15:e0231450. [PMID: 32302342 PMCID: PMC7164624 DOI: 10.1371/journal.pone.0231450] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 03/24/2020] [Indexed: 01/08/2023] Open
Abstract
RNA-binding proteins (RBPs) control many types of post-transcriptional regulation, including mRNA splicing, mRNA stability, and translational efficiency, by directly binding to their target RNAs and their mutation and dysfunction are often associated with several human neurological diseases and tumorigenesis. Crosslinking immunoprecipitation (CLIP), coupled with high-throughput sequencing (HITS-CLIP), is a powerful technique for investigating the molecular mechanisms underlying disease pathogenesis by comprehensive identification of RBP target sequences at the transcriptome level. However, HITS-CLIP protocol is still required for some optimization due to experimental complication, low efficiency and time-consuming, whose library has to be generated from very small amounts of RNAs. Here we improved a more efficient, rapid, and reproducible CLIP method by optimizing BrdU-CLIP. Our protocol produced a 10-fold greater yield of pre-amplified CLIP library, which resulted in a low duplicate rate of CLIP-tag reads because the number of PCR cycles required for library amplification was reduced. Variance of the yields was also reduced, and the experimental period was shortened by 2 days. Using this, we validated IL-6 expression by a nuclear RBP, HNRNPU, which directly binds the 3’-UTR of IL-6 mRNA in HeLa cells. Importantly, this interaction was only observed in the cytoplasmic fraction, suggesting a role of cytoplasmic HNRNPU in mRNA stability control. This optimized method enables us to accurately identify target genes and provides a snapshot of the protein-RNA interactions of nucleocytoplasmic shuttling RBPs.
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Affiliation(s)
- Masato Yugami
- Takeda Pharmaceutical Company, Ltd, Osaka, Japan
- * E-mail: (MYu); (MYa)
| | - Hideyuki Okano
- Department of Physiology, School of Medicine, Keio University, Minato, Japan
| | | | - Masato Yano
- Department of Physiology, School of Medicine, Keio University, Minato, Japan
- Division of Neurobiology and Anatomy, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
- * E-mail: (MYu); (MYa)
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A tumor-specific modulation of heterogeneous ribonucleoprotein A0 promotes excessive mitosis and growth in colorectal cancer cells. Cell Death Dis 2020; 11:245. [PMID: 32303675 PMCID: PMC7165183 DOI: 10.1038/s41419-020-2439-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 12/10/2019] [Accepted: 12/10/2019] [Indexed: 11/11/2022]
Abstract
RNA regulation mediating RNA-binding proteins (RBPs) have been shown to be related to the maintenance of homeostasis as well as cancer progression. However, the tumor-associated functions as well as the detailed mechanisms underlying the anti-tumor effects of most RBPs have yet to be explored. We herein report that the phosphorylated heterogeneous ribonucleoprotein (hnRNP) A0 promotes mitosis through the RAS-associated protein 3 GTPase-activating protein catalytic subunit 1 (RAB3GAP1)-Zeste white 10 interactor (ZWINT1) cascade. The downregulation assay of 20 representative hnRNPs, a major family of RNA-binding proteins, in colorectal cancer cells revealed that hnRNPA0 is a strong regulator of cancer cell growth. The tumor promotive function of hnRNPA0 was confirmed in gastrointestinal cancer cells, including pancreatic, esophageal, and gastric cancer cells, but not in non-cancerous cells. Flow cytometry and Western blotting analyses revealed that hnRNPA0 inhibited the apoptosis through the maintenance of G2/M phase promotion in colorectal cancer cells. A comprehensive analysis of mRNAs regulated by hnRNP A0 and immunostaining revealed that mitotic events were regulated by the hnRNPA0-RAB3GAP1 mRNA-mediated ZWINT-1 stabilization in colorectal cancer cells, but not in non-tumorous cells. The interaction of hnRNP A0 with mRNAs was dramatically changed by the deactivation of its phosphorylation site in cancer cells, but not in non-tumorous cells. Therefore, the tumor-specific biological functions characterized by the abnormal phosphorylation of RBPs are considered to be an attractive target for tumor treatment.
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Abstract
Maturation is the last phase of heart development that prepares the organ for strong, efficient, and persistent pumping throughout the mammal's lifespan. This process is characterized by structural, gene expression, metabolic, and functional specializations in cardiomyocytes as the heart transits from fetal to adult states. Cardiomyocyte maturation gained increased attention recently due to the maturation defects in pluripotent stem cell-derived cardiomyocyte, its antagonistic effect on myocardial regeneration, and its potential contribution to cardiac disease. Here, we review the major hallmarks of ventricular cardiomyocyte maturation and summarize key regulatory mechanisms that promote and coordinate these cellular events. With advances in the technical platforms used for cardiomyocyte maturation research, we expect significant progress in the future that will deepen our understanding of this process and lead to better maturation of pluripotent stem cell-derived cardiomyocyte and novel therapeutic strategies for heart disease.
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Affiliation(s)
- Yuxuan Guo
- Department of Cardiology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - William Pu
- Department of Cardiology, Boston Children’s Hospital, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
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