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Aghagolzadeh P, Plaisance I, Bernasconi R, Treibel TA, Pulido Quetglas C, Wyss T, Wigger L, Nemir M, Sarre A, Chouvardas P, Johnson R, González A, Pedrazzini T. Assessment of the Cardiac Noncoding Transcriptome by Single-Cell RNA Sequencing Identifies FIXER, a Conserved Profibrogenic Long Noncoding RNA. Circulation 2023; 148:778-797. [PMID: 37427428 DOI: 10.1161/circulationaha.122.062601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 06/02/2023] [Indexed: 07/11/2023]
Abstract
BACKGROUND Cardiac fibroblasts have crucial roles in the heart. In particular, fibroblasts differentiate into myofibroblasts in the damaged myocardium, contributing to scar formation and interstitial fibrosis. Fibrosis is associated with heart dysfunction and failure. Myofibroblasts therefore represent attractive therapeutic targets. However, the lack of myofibroblast-specific markers has precluded the development of targeted therapies. In this context, most of the noncoding genome is transcribed into long noncoding RNAs (lncRNAs). A number of lncRNAs have pivotal functions in the cardiovascular system. lncRNAs are globally more cell-specific than protein-coding genes, supporting their importance as key determinants of cell identity. METHODS In this study, we evaluated the value of the lncRNA transcriptome in very deep single-cell RNA sequencing. We profiled the lncRNA transcriptome in cardiac nonmyocyte cells after infarction and probed heterogeneity in the fibroblast and myofibroblast populations. In addition, we searched for subpopulation-specific markers that can constitute novel targets in therapy for heart disease. RESULTS We demonstrated that cardiac cell identity can be defined by the sole expression of lncRNAs in single-cell experiments. In this analysis, we identified lncRNAs enriched in relevant myofibroblast subpopulations. Selecting 1 candidate we named FIXER (fibrogenic LOX-locus enhancer RNA), we showed that its silencing limits fibrosis and improves heart function after infarction. Mechanitically, FIXER interacts with CBX4, an E3 SUMO protein ligase and transcription factor, guiding CBX4 to the promoter of the transcription factor RUNX1 to control its expression and, consequently, the expression of a fibrogenic gene program.. FIXER is conserved in humans, supporting its translational value. CONCLUSIONS Our results demonstrated that lncRNA expression is sufficient to identify the various cell types composing the mammalian heart. Focusing on cardiac fibroblasts and their derivatives, we identified lncRNAs uniquely expressed in myofibroblasts. In particular, the lncRNA FIXER represents a novel therapeutic target for cardiac fibrosis.
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Affiliation(s)
- Parisa Aghagolzadeh
- Experimental Cardiology Unit, Division of Cardiology, Department of Cardiovascular Medicine, University of Lausanne Medical School, Switzerland (P.A., I.P., R.B., M.N., T.P.)
| | - Isabelle Plaisance
- Experimental Cardiology Unit, Division of Cardiology, Department of Cardiovascular Medicine, University of Lausanne Medical School, Switzerland (P.A., I.P., R.B., M.N., T.P.)
| | - Riccardo Bernasconi
- Experimental Cardiology Unit, Division of Cardiology, Department of Cardiovascular Medicine, University of Lausanne Medical School, Switzerland (P.A., I.P., R.B., M.N., T.P.)
| | - Thomas A Treibel
- Institute of Cardiovascular Sciences, University College London, United Kingdom (T.A.T.)
| | - Carlos Pulido Quetglas
- Department for BioMedical Research, University of Bern, Switzerland (C.P.Q., P.C., R.J.)
| | - Tania Wyss
- Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Epalinges, Switzerland (T.W.)
- Swiss Institute of Bioinformatics, Lausanne, Switzerland (T.W., L.W.)
| | - Leonore Wigger
- Swiss Institute of Bioinformatics, Lausanne, Switzerland (T.W., L.W.)
| | - Mohamed Nemir
- Experimental Cardiology Unit, Division of Cardiology, Department of Cardiovascular Medicine, University of Lausanne Medical School, Switzerland (P.A., I.P., R.B., M.N., T.P.)
| | - Alexandre Sarre
- Cardiovascular Assessment Facility, University of Lausanne, Switzerland (A.S.)
| | - Panagiotis Chouvardas
- Department for BioMedical Research, University of Bern, Switzerland (C.P.Q., P.C., R.J.)
| | - Rory Johnson
- Department for BioMedical Research, University of Bern, Switzerland (C.P.Q., P.C., R.J.)
| | - Arantxa González
- Program of Cardiovascular Diseases, CIMA Universidad de Navarra and IdiSNA, Pamplona, Spain (A.G.)
- CIBERCV, Madrid, Spain (A.G.)
| | - Thierry Pedrazzini
- Experimental Cardiology Unit, Division of Cardiology, Department of Cardiovascular Medicine, University of Lausanne Medical School, Switzerland (P.A., I.P., R.B., M.N., T.P.)
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2
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Petrone I, dos Santos EC, Binato R, Abdelhay E. Epigenetic Alterations in DCIS Progression: What Can lncRNAs Teach Us? Int J Mol Sci 2023; 24:8733. [PMID: 37240077 PMCID: PMC10218364 DOI: 10.3390/ijms24108733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/07/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
Some transcripts that are not translated into proteins can be encoded by the mammalian genome. Long noncoding RNAs (lncRNAs) are noncoding RNAs that can function as decoys, scaffolds, and enhancer RNAs and can regulate other molecules, including microRNAs. Therefore, it is essential that we obtain a better understanding of the regulatory mechanisms of lncRNAs. In cancer, lncRNAs function through several mechanisms, including important biological pathways, and the abnormal expression of lncRNAs contributes to breast cancer (BC) initiation and progression. BC is the most common type of cancer among women worldwide and has a high mortality rate. Genetic and epigenetic alterations that can be regulated by lncRNAs may be related to early events of BC progression. Ductal carcinoma in situ (DCIS) is a noninvasive BC that is considered an important preinvasive BC early event because it can progress to invasive BC. Therefore, the identification of predictive biomarkers of DCIS-invasive BC progression has become increasingly important in an attempt to optimize the treatment and quality of life of patients. In this context, this review will address the current knowledge about the role of lncRNAs in DCIS and their potential contribution to the progression of DCIS to invasive BC.
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Affiliation(s)
- Igor Petrone
- Stem Cell Laboratory, Center for Bone Marrow Transplants, Brazilian National Cancer Institute—INCA, Rio de Janeiro 20230-240, Brazil; (I.P.); (E.C.d.S.); (R.B.)
- Stricto Sensu Graduate Program in Oncology, Brazilian National Cancer Institute—INCA, Rio de Janeiro 20230-240, Brazil
| | - Everton Cruz dos Santos
- Stem Cell Laboratory, Center for Bone Marrow Transplants, Brazilian National Cancer Institute—INCA, Rio de Janeiro 20230-240, Brazil; (I.P.); (E.C.d.S.); (R.B.)
- Stricto Sensu Graduate Program in Oncology, Brazilian National Cancer Institute—INCA, Rio de Janeiro 20230-240, Brazil
| | - Renata Binato
- Stem Cell Laboratory, Center for Bone Marrow Transplants, Brazilian National Cancer Institute—INCA, Rio de Janeiro 20230-240, Brazil; (I.P.); (E.C.d.S.); (R.B.)
- Stricto Sensu Graduate Program in Oncology, Brazilian National Cancer Institute—INCA, Rio de Janeiro 20230-240, Brazil
| | - Eliana Abdelhay
- Stem Cell Laboratory, Center for Bone Marrow Transplants, Brazilian National Cancer Institute—INCA, Rio de Janeiro 20230-240, Brazil; (I.P.); (E.C.d.S.); (R.B.)
- Stricto Sensu Graduate Program in Oncology, Brazilian National Cancer Institute—INCA, Rio de Janeiro 20230-240, Brazil
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3
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Zhao H, Zhang S, Yin X, Zhang C, Wang L, Liu K, Xu H, Liu W, Bo L, Lin S, Feng K, Lin L, Fei M, Ning S, Wang L. Identifying enhancer-driven subtype-specific prognostic markers in breast cancer based on multi-omics data. Front Immunol 2022; 13:990143. [PMID: 36304471 PMCID: PMC9592759 DOI: 10.3389/fimmu.2022.990143] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 09/27/2022] [Indexed: 11/22/2022] Open
Abstract
Breast cancer is a cancer of high complexity and heterogeneity, with differences in prognosis and survival among patients of different subtypes. Copy number variations (CNVs) within enhancers are crucial drivers of tumorigenesis by influencing expression of their targets. In this study, we performed an integrative approach to identify CNA-driven enhancers and their effect on expression of target genes in four breast cancer subtypes by integrating expression data, copy number data and H3K27ac data. We identified 672, 555, 531, 361 CNA-driven enhancer-gene pairs and 280, 189, 113 and 98 CNA-driven enhancer-lncRNA pairs in the Basal-like, Her2, LumA and LumB subtypes, respectively. We then reconstructed a CNV-driven enhancer-lncRNA-mRNA regulatory network in each subtype. Functional analysis showed CNA-driven enhancers play an important role in the progression of breast cancer subtypes by influencing P53 signaling pathway, PPAR signaling pathway, systemic lupus erythematosus and MAPK signaling pathway in the Basal-like, Her2, LumA and LumB subtypes, respectively. We characterized the potentially prognostic value of target genes of CNV-driven enhancer and lncRNA-mRNA pairs in the subtype-specific network. We identified MUM1 and AC016876.1 as prognostic biomarkers in LumA and Basal-like subtypes, respectively. Higher expression of MUM1 with an amplified enhancer exhibited poorer prognosis in LumA patients. Lower expression of AC016876.1 with a deleted enhancer exhibited poorer survival outcomes of Basal-like patients. We also identified enhancer-related lncRNA-mRNA pairs as prognostic biomarkers, including AC012313.2-MUM1 in the LumA, AC026471.4-PLK5 in the LumB, AC027307.2-OAZ1 in the Basal-like and AC022431.1-HCN2 in the Her2 subtypes. Finally, our results highlighted target genes of CNA-driven enhancers and enhancer-related lncRNA-mRNA pairs could act as prognostic markers and potential therapeutic targets in breast cancer subtypes.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Li Wang
- *Correspondence: Li Wang, ; Shangwei Ning,
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4
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Wang Y, Zhang C, Wang Y, Liu X, Zhang Z. Enhancer RNA (eRNA) in Human Diseases. Int J Mol Sci 2022; 23:11582. [PMID: 36232885 PMCID: PMC9569849 DOI: 10.3390/ijms231911582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 09/22/2022] [Accepted: 09/24/2022] [Indexed: 11/16/2022] Open
Abstract
Enhancer RNAs (eRNAs), a class of non-coding RNAs (ncRNAs) transcribed from enhancer regions, serve as a type of critical regulatory element in gene expression. There is increasing evidence demonstrating that the aberrant expression of eRNAs can be broadly detected in various human diseases. Some studies also revealed the potential clinical utility of eRNAs in these diseases. In this review, we summarized the recent studies regarding the pathological mechanisms of eRNAs as well as their potential utility across human diseases, including cancers, neurodegenerative disorders, cardiovascular diseases and metabolic diseases. It could help us to understand how eRNAs are engaged in the processes of diseases and to obtain better insight of eRNAs in diagnosis, prognosis or therapy. The studies we reviewed here indicate the enormous therapeutic potency of eRNAs across human diseases.
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Affiliation(s)
- Yunzhe Wang
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Chenyang Zhang
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Yuxiang Wang
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Xiuping Liu
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Zhao Zhang
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
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5
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García-Padilla C, Dueñas Á, García-López V, Aránega A, Franco D, Garcia-Martínez V, López-Sánchez C. Molecular Mechanisms of lncRNAs in the Dependent Regulation of Cancer and Their Potential Therapeutic Use. Int J Mol Sci 2022; 23:764. [PMID: 35054945 PMCID: PMC8776057 DOI: 10.3390/ijms23020764] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 12/31/2021] [Accepted: 01/08/2022] [Indexed: 12/16/2022] Open
Abstract
Deep whole genome and transcriptome sequencing have highlighted the importance of an emerging class of non-coding RNA longer than 200 nucleotides (i.e., long non-coding RNAs (lncRNAs)) that are involved in multiple cellular processes such as cell differentiation, embryonic development, and tissue homeostasis. Cancer is a prime example derived from a loss of homeostasis, primarily caused by genetic alterations both in the genomic and epigenetic landscape, which results in deregulation of the gene networks. Deregulation of the expression of many lncRNAs in samples, tissues or patients has been pointed out as a molecular regulator in carcinogenesis, with them acting as oncogenes or tumor suppressor genes. Herein, we summarize the distinct molecular regulatory mechanisms described in literature in which lncRNAs modulate carcinogenesis, emphasizing epigenetic and genetic alterations in particular. Furthermore, we also reviewed the current strategies used to block lncRNA oncogenic functions and their usefulness as potential therapeutic targets in several carcinomas.
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Affiliation(s)
- Carlos García-Padilla
- Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (Á.D.); (A.A.); (D.F.)
- Department of Human Anatomy and Embryology, University of Extremadura, 06006 Badajoz, Spain; (V.G.-L.); (V.G.-M.)
- Institute of Molecular Pathology Biomarkers, University of Extremadura, 06006 Badajoz, Spain
| | - Ángel Dueñas
- Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (Á.D.); (A.A.); (D.F.)
- Department of Human Anatomy and Embryology, University of Extremadura, 06006 Badajoz, Spain; (V.G.-L.); (V.G.-M.)
- Institute of Molecular Pathology Biomarkers, University of Extremadura, 06006 Badajoz, Spain
| | - Virginio García-López
- Department of Human Anatomy and Embryology, University of Extremadura, 06006 Badajoz, Spain; (V.G.-L.); (V.G.-M.)
- Institute of Molecular Pathology Biomarkers, University of Extremadura, 06006 Badajoz, Spain
| | - Amelia Aránega
- Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (Á.D.); (A.A.); (D.F.)
- Fundación Medina, 18016 Granada, Spain
| | - Diego Franco
- Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (Á.D.); (A.A.); (D.F.)
- Fundación Medina, 18016 Granada, Spain
| | - Virginio Garcia-Martínez
- Department of Human Anatomy and Embryology, University of Extremadura, 06006 Badajoz, Spain; (V.G.-L.); (V.G.-M.)
- Institute of Molecular Pathology Biomarkers, University of Extremadura, 06006 Badajoz, Spain
| | - Carmen López-Sánchez
- Department of Human Anatomy and Embryology, University of Extremadura, 06006 Badajoz, Spain; (V.G.-L.); (V.G.-M.)
- Institute of Molecular Pathology Biomarkers, University of Extremadura, 06006 Badajoz, Spain
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6
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Wang W, Yang N, Yang YH, Wen R, Liu CF, Zhang TN. Non-Coding RNAs: Master Regulators of Inflammasomes in Inflammatory Diseases. J Inflamm Res 2021; 14:5023-5050. [PMID: 34616171 PMCID: PMC8490125 DOI: 10.2147/jir.s332840] [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: 08/05/2021] [Accepted: 09/21/2021] [Indexed: 12/11/2022] Open
Abstract
Emerging data indicates that non-coding RNAs (ncRNAs) represent more than just “junk sequences” of the genome and have been found to be involved in multiple diseases by regulating various biological process, including the activation of inflammasomes. As an important aspect of innate immunity, inflammasomes are large immune multiprotein complexes that tightly regulate the production of pro-inflammatory cytokines and mediate pyroptosis; the activation of the inflammasomes is a vital biological process in inflammatory diseases. Recent studies have emphasized the function of ncRNAs in the fine control of inflammasomes activation either by directly targeting components of the inflammasomes or by controlling the activity of various factors that control the activation of inflammasomes; consequently, ncRNAs may represent potential therapeutic targets for inflammatory diseases. Understanding the precise role of ncRNAs in controlling the activation of inflammasomes will help us to design targeted therapies for multiple inflammatory diseases. In this review, we summarize the regulatory role and therapeutic potential of ncRNAs in the activation of inflammasomes by focusing on a range of inflammatory diseases, including microbial infection, sterile inflammatory diseases, and fibrosis-related diseases. Our goal is to provide new ideas and perspectives for future research.
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Affiliation(s)
- Wei Wang
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, People's Republic of China
| | - Ni Yang
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, People's Republic of China
| | - Yu-Hang Yang
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, People's Republic of China
| | - Ri Wen
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, People's Republic of China
| | - Chun-Feng Liu
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, People's Republic of China
| | - Tie-Ning Zhang
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, People's Republic of China
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7
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Li X, Pan X, Zhou H, Wang P, Gao Y, Shang S, Guo S, Sun J, Xiong Z, Ning S, Zhi H, Li X. Comprehensive characterization genetic regulation and chromatin landscape of enhancer-associated long non-coding RNAs and their implication in human cancer. Brief Bioinform 2021; 23:6375264. [PMID: 34581409 DOI: 10.1093/bib/bbab401] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/19/2021] [Accepted: 09/02/2021] [Indexed: 02/06/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) that emanate from enhancer regions (defined as enhancer-associated lncRNAs, or elncRNAs) are emerging as critical regulators in disease progression. However, their biological characteristics and clinical relevance have not been fully portrayed. Here, based on the traditional expression quantitative loci (eQTL) and our optimized residual eQTL method, we comprehensively described the genetic effect on elncRNA expression in more than 300 lymphoblastoid cell lines. Meanwhile, a chromatin atlas of elncRNAs relative to the genetic regulation state was depicted. By applying the maximum likelihood estimate method, we successfully identified causal elncRNAs for protein-coding gene expression reprogramming and showed their associated single nucleotide polymorphisms (SNPs) favor binding of transcription factors. Further epigenome analysis revealed two immune-associated elncRNAs AL662844.4 and LINC01215 possess high levels of H3K27ac and H3K4me1 in human cancer. Besides, pan-cancer analysis of 3D genome, transcriptome, and regulatome data showed they potentially regulate tumor-immune cell interaction through affecting MHC class I genes and CD47, respectively. Moreover, our study showed there exist associations between elncRNA and patient survival. Finally, we made a user-friendly web interface available for exploring the regulatory relationship of SNP-elncRNA-protein-coding gene triplets (http://bio-bigdata.hrbmu.edu.cn/elncVarReg). Our study provides critical mechanistic insights for elncRNA function and illustrates their implications in human cancer.
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Affiliation(s)
- Xin Li
- College of Bioinformatics Science and Technology, Harbin Medical University, China
| | - Xu Pan
- College of Bioinformatics Science and Technology, Harbin Medical University, China
| | - Hanxiao Zhou
- College of Bioinformatics Science and Technology, Harbin Medical University, China
| | - Peng Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, China
| | - Yue Gao
- College of Bioinformatics Science and Technology, Harbin Medical University, China
| | - Shipeng Shang
- College of Bioinformatics Science and Technology, Harbin Medical University, China
| | - Shuang Guo
- College of Bioinformatics Science and Technology, Harbin Medical University, China
| | - Jie Sun
- College of Bioinformatics Science and Technology, Harbin Medical University, China
| | - Zhiying Xiong
- College of Bioinformatics Science and Technology, Harbin Medical University, China
| | - Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, China
| | - Hui Zhi
- College of Bioinformatics Science and Technology, Harbin Medical University, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, China
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8
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Kay M, Soltani BM, Nemir M, Aghagolzadeh P, Pezzuto I, Chouvardas P, Ruberto F, Movahedi F, Ansari H, Baharvand H, Pedrazzini T. The conserved long noncoding RNA CARMA regulates cardiomyocyte differentiation. Cardiovasc Res 2021; 118:2339-2353. [PMID: 34459880 DOI: 10.1093/cvr/cvab281] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 08/26/2021] [Indexed: 12/13/2022] Open
Abstract
AIMS Production of functional cardiomyocytes from pluripotent stem cells requires tight control of the differentiation process. Long noncoding RNAs (lncRNAs) exert critical regulatory function in cell specification during development. In this study, we designed an integrated approach to identify lncRNAs implicated in cardiogenesis in differentiating human embryonic stem cells (ESCs). METHODS AND RESULTS We identified CARMA (CARdiomyocyte Maturation-Associated lncRNA), a conserved lncRNA controlling cardiomyocyte differentiation and maturation in human ESCs. CARMA is located adjacent to MIR-1-1HG, the host gene for two cardiogenic miRNAs: MIR1-1 and MIR-133a2, and transcribed in an antisense orientation. The expression of CARMA and the miRNAs is negatively correlated, and CARMA knockdown increases MIR1-1 and MIR-133a2 expression. In addition, CARMA possesses MIR-133a2 binding sites, suggesting the lncRNA could be also a target of miRNA action. Upon CARMA downregulation, MIR-133a2 target protein-coding genes are coordinately downregulated. Among those, we found RBPJ, the gene encoding the effector of the NOTCH pathway. NOTCH has been shown to control a binary cell fate decision between the mesoderm and the neuroectoderm lineages, and NOTCH inhibition leads to enhanced cardiomyocyte differentiation at the expense of neuroectodermal derivatives. Interestingly, two lncRNAs, linc1230 and linc1335, which are known repressors of neuroectodermal specification, were found upregulated upon Notch1 silencing in ESCs. Forced expression of either linc1230 or linc1335 improved ESC-derived cardiomyocyte production. These two lncRNAs were also found upregulated following CARMA knockdown in ESCs. CONCLUSIONS Altogether, these data suggest the existence of a network, implicating three newly identified lncRNAs, the two myomirs MIR1-1 and MIR-133a2 and the NOTCH signaling pathway, for the coordinated regulation of cardiogenic differentiation in ESCs. TRANSLATIONAL PERSPECTIVE Cardiac dysfunction and heart failure develop secondary to a massive loss of cardiomyocytes in the damaged myocardium. Several avenues have been evaluated to promote regeneration following injury. Cell therapy for heart disease envisages the production of functional cardiomyocytes from differentiating pluripotent stem cells prior transfer into the injured heart muscle. Here, we report the functional characterization of CARMA, a lncRNA implicated in cardiogenesis. CARMA knockdown in differentiating human embryonic stem cells (ESCs) promotes cardiogenic commitment and cardiomyocyte differentiation. CARMA represents therefore a novel target for improving human ESC-derived cardiomyocyte production, and cell-based regenerative strategies for heart disease.
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Affiliation(s)
- Maryam Kay
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.,Experimental Cardiology Unit, Divison of Cardiology, Department of Cardiovascular Medicine, University of Lausanne Medical School, Lausanne, Switzerland
| | - Bahram M Soltani
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mohamed Nemir
- Experimental Cardiology Unit, Divison of Cardiology, Department of Cardiovascular Medicine, University of Lausanne Medical School, Lausanne, Switzerland
| | - Parisa Aghagolzadeh
- Experimental Cardiology Unit, Divison of Cardiology, Department of Cardiovascular Medicine, University of Lausanne Medical School, Lausanne, Switzerland
| | - Iole Pezzuto
- Experimental Cardiology Unit, Divison of Cardiology, Department of Cardiovascular Medicine, University of Lausanne Medical School, Lausanne, Switzerland
| | | | - Francesco Ruberto
- Experimental Cardiology Unit, Divison of Cardiology, Department of Cardiovascular Medicine, University of Lausanne Medical School, Lausanne, Switzerland
| | - Fatemeh Movahedi
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, Tehran, Iran
| | - Hassan Ansari
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, Tehran, Iran
| | - Hossein Baharvand
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, Tehran, Iran
| | - Thierry Pedrazzini
- Experimental Cardiology Unit, Divison of Cardiology, Department of Cardiovascular Medicine, University of Lausanne Medical School, Lausanne, Switzerland
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9
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Bär C, Chatterjee S, Falcão Pires I, Rodrigues P, Sluijter JPG, Boon RA, Nevado RM, Andrés V, Sansonetti M, de Windt L, Ciccarelli M, Hamdani N, Heymans S, Figuinha Videira R, Tocchetti CG, Giacca M, Zacchigna S, Engelhardt S, Dimmeler S, Madonna R, Thum T. Non-coding RNAs: update on mechanisms and therapeutic targets from the ESC Working Groups of Myocardial Function and Cellular Biology of the Heart. Cardiovasc Res 2021; 116:1805-1819. [PMID: 32638021 DOI: 10.1093/cvr/cvaa195] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/15/2020] [Accepted: 06/30/2020] [Indexed: 02/06/2023] Open
Abstract
Vast parts of mammalian genomes are actively transcribed, predominantly giving rise to non-coding RNA (ncRNA) transcripts including microRNAs, long ncRNAs, and circular RNAs among others. Contrary to previous opinions that most of these RNAs are non-functional molecules, they are now recognized as critical regulators of many physiological and pathological processes including those of the cardiovascular system. The discovery of functional ncRNAs has opened up new research avenues aiming at understanding ncRNA-related disease mechanisms as well as exploiting them as novel therapeutics in cardiovascular therapy. In this review, we give an update on the current progress in ncRNA research, particularly focusing on cardiovascular physiological and disease processes, which are under current investigation at the ESC Working Groups of Myocardial Function and Cellular Biology of the Heart. This includes a range of topics such as extracellular vesicle-mediated communication, neurohormonal regulation, inflammation, cardiac remodelling, cardio-oncology as well as cardiac development and regeneration, collectively highlighting the wide-spread involvement and importance of ncRNAs in the cardiovascular system.
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Affiliation(s)
- Christian Bär
- Institute for Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Hannover, Germany.,REBIRTH Center for Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany
| | - Shambhabi Chatterjee
- Institute for Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Hannover, Germany.,REBIRTH Center for Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany
| | - Inês Falcão Pires
- Cardiovascular Research and Development Center, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Patrícia Rodrigues
- Cardiovascular Research and Development Center, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Joost P G Sluijter
- Experimental Cardiology Laboratory, UMC Utrecht Regenerative Medicine Center, University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
| | - Reinier A Boon
- Department of Physiology, Amsterdam Cardiovascular Sciences (ACS), Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands.,Institute for Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University, Frankfurt am Main, Germany.,Partner site Rhein/Main, German Center for Cardiovascular Research (DZHK), Frankfurt am Main, Germany
| | - Rosa M Nevado
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Spain
| | - Vicente Andrés
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Spain
| | - Marida Sansonetti
- Institute for Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Hannover, Germany.,REBIRTH Center for Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany.,Department of Molecular Genetics, Faculty of Science and Engineering, Maastricht University, Maastricht, The Netherlands.,Department of Cardiology, CARIM School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Leon de Windt
- Department of Molecular Genetics, Faculty of Science and Engineering, Maastricht University, Maastricht, The Netherlands.,Department of Cardiology, CARIM School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Michele Ciccarelli
- Department of Medicine, Surgery and Dentistry, University of Salerno, Italy
| | - Nazha Hamdani
- Department of Molecular and Experimental Cardiology, Ruhr University Bochum, Bochum, Germany.,Department of Cardiology, St. Josef-Hospital, Ruhr University Bochum, Bochum, Germany
| | - Stephane Heymans
- Department of Cardiology, Maastricht University Medical Centre, University Hospital Maastricht, The Netherlands.,Center for Heart Failure Research, Cardiovascular Research Institute Maastricht (CARIM), University Hospital Maastricht, The Netherlands
| | - Raquel Figuinha Videira
- Cardiovascular Research and Development Center, Faculty of Medicine, University of Porto, Porto, Portugal.,Department of Molecular Genetics, Faculty of Science and Engineering, Maastricht University, Maastricht, The Netherlands.,Department of Cardiology, CARIM School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Carlo G Tocchetti
- Department of Translational Medical Sciences and Interdepartmental Center of Clinical and Translational Research (CIRCET), Federico II University, Naples, Italy
| | - Mauro Giacca
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy.,School of Cardiovascular Medicine & Sciences, King's College London, London, UK.,Department of Medicine, Surgery and Health Sciences, University of Trieste, Italy
| | - Serena Zacchigna
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy.,Department of Medicine, Surgery and Health Sciences, University of Trieste, Italy
| | - Stefan Engelhardt
- Institute of Pharmacology and Toxicology, Technische Universität München, Biedersteiner Str. 29, Munich 80802, Germany.,DZHK (German Center for Cardiovascular Research), Partner site Munich Heart Alliance, Biedersteiner Str. 29, Munich 80802, Germany
| | - Stefanie Dimmeler
- Institute for Cardiovascular Regeneration, Goethe University, Germany.,German Center for Cardiovascular Research (DZHK), Frankfurt, Germany.,Cardio-Pulmonary Institute (CPI), Frankfurt, Germany
| | - Rosalinda Madonna
- Institute of Cardiology, University of Pisa, Pisa, Italy.,Department of Internal Medicine, University of Texas Medical School, Houston, TX, USA
| | - Thomas Thum
- Institute for Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Hannover, Germany.,REBIRTH Center for Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany
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10
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Yousefi L, Osquee HO, Ghotaslou R, Rezaee MA, Pirzadeh T, Sadeghi J, Hemmati F, Yousefi B, Moaddab SY, Yousefi M, Shirmohammadi M, Somi MH, Ganbarov K, Kafil HS. Dysregulation of lncRNA in Helicobacter pylori-Infected Gastric Cancer Cells. BIOMED RESEARCH INTERNATIONAL 2021; 2021:6911734. [PMID: 34337048 PMCID: PMC8286195 DOI: 10.1155/2021/6911734] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/25/2021] [Accepted: 06/30/2021] [Indexed: 12/31/2022]
Abstract
Helicobacter pylori (H. pylori) infection is the most common cause of gastric cancer (GC). This microorganism is genetically diverse; GC is caused by several genetic deregulations in addition to environmental factors and bacterial virulence factors. lncRNAs (long noncoding RNAs) are significant biological macromolecules in GC, have specific functions in diseases, and could be therapeutic targets. Altered lncRNAs can lead to the abnormal expression of adjacent protein-coding genes, which may be important in cancer development. Their mechanisms have not been well understood, so we are going to investigate the risk of GC in a population with both high lncRNA and H. pylori infection.
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Affiliation(s)
- Leila Yousefi
- Student Research Committee, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hamid Owaysee Osquee
- Pharmaceutical Nanotechnology Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Reza Ghotaslou
- Pharmaceutical Nanotechnology Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Tahereh Pirzadeh
- Immunology Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Javid Sadeghi
- Immunology Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Fatemeh Hemmati
- Student Research Committee, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Bahman Yousefi
- Stem Cell Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Seyyed Yaghoub Moaddab
- Liver and Gastrointestinal Diseases Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mehdi Yousefi
- Stem Cell Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Masoud Shirmohammadi
- Liver and Gastrointestinal Diseases Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Hossein Somi
- Liver and Gastrointestinal Diseases Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Hossein Samadi Kafil
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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11
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Braga L, Ali H, Secco I, Giacca M. Non-coding RNA therapeutics for cardiac regeneration. Cardiovasc Res 2021; 117:674-693. [PMID: 32215566 PMCID: PMC7898953 DOI: 10.1093/cvr/cvaa071] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 03/02/2020] [Accepted: 03/20/2020] [Indexed: 12/19/2022] Open
Abstract
A growing body of evidence indicates that cardiac regeneration after myocardial infarction can be achieved by stimulating the endogenous capacity of cardiomyocytes (CMs) to replicate. This process is controlled, both positively and negatively, by a large set of non-coding RNAs (ncRNAs). Some of the microRNAs (miRNAs) that can stimulate CM proliferation is expressed in embryonic stem cells and is required to maintain pluripotency (e.g. the miR-302∼367 cluster). Others also govern the proliferation of different cell types, including cancer cells (e.g. the miR-17∼92 cluster). Additional miRNAs were discovered through systematic screenings (e.g. miR-199a-3p and miR-590-3p). Several miRNAs instead suppress CM proliferation and are involved in the withdrawal of CMs from the cell cycle after birth (e.g. the let-7 and miR-15 families). Similar regulatory roles on CM proliferation are also exerted by a few long ncRNAs. This body of information has obvious therapeutic implications, as miRNAs with activator function or short antisense oligonucleotides against inhibitory miRNAs or lncRNAs can be administered to stimulate cardiac regeneration. Expression of miRNAs can be achieved by gene therapy using adeno-associated vectors, which transduce CMs with high efficiency. More effective and safer for therapeutic purposes, small nucleic acid therapeutics can be obtained as chemically modified, synthetic molecules, which can be administered through lipofection or inclusion in lipid or polymer nanoparticles for efficient cardiac delivery. The notion that it is possible to reprogramme CMs into a regenerative state and that this property can be enhanced by ncRNA therapeutics remains exciting, however extensive experimentation in large mammals and rigorous assessment of safety are required to advance towards clinical application.
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Affiliation(s)
- Luca Braga
- British Heart Foundation Centre of Research Excellence, School of Cardiovascular Medicine & Sciences, King’s College London, The James Black Centre, 125 Coldharbour Lane, London SE5 9NU, UK
| | - Hashim Ali
- British Heart Foundation Centre of Research Excellence, School of Cardiovascular Medicine & Sciences, King’s College London, The James Black Centre, 125 Coldharbour Lane, London SE5 9NU, UK
| | - Ilaria Secco
- British Heart Foundation Centre of Research Excellence, School of Cardiovascular Medicine & Sciences, King’s College London, The James Black Centre, 125 Coldharbour Lane, London SE5 9NU, UK
| | - Mauro Giacca
- British Heart Foundation Centre of Research Excellence, School of Cardiovascular Medicine & Sciences, King’s College London, The James Black Centre, 125 Coldharbour Lane, London SE5 9NU, UK
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
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12
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Alexanian M, Ounzain S. Long Noncoding RNAs in Cardiac Development. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a037374. [PMID: 31932317 DOI: 10.1101/cshperspect.a037374] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The exquisite transcriptional control of developmental gene programs is critical for hardwiring the complex expression patterns that govern cell-fate determination and differentiation during heart development. During the past several years, studies have illuminated our understanding of a complex noncoding transcriptional landscape, primarily associated with long noncoding RNAs (lncRNAs), that is implicated in these developmental processes and has begun to reveal key functions of these transcripts. In this review, we discuss the expanding roles for lncRNAs in the earliest points of cardiac development and through differentiation and maturation of multiple cell types within the adult heart. We go on to outline the diverse mechanisms by which cardiovascular lncRNAs orchestrate these transcriptional programs, explore the challenges linked to the study of lncRNAs in developmental phenotypes, and summarize the implications for these molecules in human cardiovascular disorders.
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Affiliation(s)
| | - Samir Ounzain
- HAYA Therapeutics SA, Lausanne, Vaud 1066, Switzerland
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13
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Bektik E, Cowan DB, Wang DZ. Long Non-Coding RNAs in Atrial Fibrillation: Pluripotent Stem Cell-Derived Cardiomyocytes as a Model System. Int J Mol Sci 2020; 21:ijms21155424. [PMID: 32751460 PMCID: PMC7432754 DOI: 10.3390/ijms21155424] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 12/19/2022] Open
Abstract
Atrial fibrillation (AF) is a type of sustained arrhythmia in humans often characterized by devastating alterations to the cardiac conduction system as well as the structure of the atria. AF can lead to decreased cardiac function, heart failure, and other complications. Long non-coding RNAs (lncRNAs) have been shown to play important roles in the cardiovascular system, including AF; however, a large group of lncRNAs is not conserved between mouse and human. Furthermore, AF has complex networks showing variations in mechanisms in different species, making it challenging to utilize conventional animal models to investigate the functional roles and potential therapeutic benefits of lncRNAs for AF. Fortunately, pluripotent stem cell (PSC)-derived cardiomyocytes (CMs) offer a reliable platform to study lncRNA functions in AF because of certain electrophysiological and molecular similarities with native human CMs. In this review, we first summarize the broad aspects of lncRNAs in various heart disease settings, then focus on their potential roles in AF development and pathophysiology. We also discuss current uses of PSCs in AF research and describe how these studies could be developed into novel therapeutics for AF and other cardiovascular diseases.
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Affiliation(s)
- Emre Bektik
- Department of Cardiology, Boston Children’s Hospital, Harvard Medical School, 300 Longwood, Boston, MA 02115, USA; (E.B.); (D.B.C.)
| | - Douglas B. Cowan
- Department of Cardiology, Boston Children’s Hospital, Harvard Medical School, 300 Longwood, Boston, MA 02115, USA; (E.B.); (D.B.C.)
| | - Da-Zhi Wang
- Department of Cardiology, Boston Children’s Hospital, Harvard Medical School, 300 Longwood, Boston, MA 02115, USA; (E.B.); (D.B.C.)
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
- Correspondence:
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14
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Exploring the Role of Non-Coding RNAs in the Pathophysiology of Systemic Lupus Erythematosus. Biomolecules 2020; 10:biom10060937. [PMID: 32580306 PMCID: PMC7356926 DOI: 10.3390/biom10060937] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/04/2020] [Accepted: 06/10/2020] [Indexed: 12/11/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is a chronic immune-related disorder designated by a lack of tolerance to self-antigens and the over-secretion of autoantibodies against several cellular compartments. Although the exact pathophysiology of SLE has not been clarified yet, this disorder has a strong genetic component based on the results of familial aggregation and twin studies. Variation in the expression of non-coding RNAs has been shown to influence both susceptibility to SLE and the clinical course of this disorder. Several long non-coding RNAs (lncRNAs) such as GAS5, MALAT1 and NEAT1 are dysregulated in SLE patients. Moreover, genetic variants within lncRNAs such as SLEAR and linc00513 have been associated with risk of this disorder. The dysregulation of a number of lncRNAs in the peripheral blood of SLE patients has potentiated them as biomarkers for diagnosis, disease activity and therapeutic response. MicroRNAs (miRNAs) have also been shown to affect apoptosis and the function of immune cells. Taken together, there is a compelling rationale for the better understanding of the involvement of these two classes of non-coding RNAs in the pathogenesis of SLE. Clarification of the function of these transcripts has the potential to elucidate the molecular pathophysiology of SLE and provide new opportunities for the development of targeted therapies for this disorder.
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15
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Paracrine Mechanisms of Mesenchymal Stromal Cells in Angiogenesis. Stem Cells Int 2020; 2020:4356359. [PMID: 32215017 PMCID: PMC7085399 DOI: 10.1155/2020/4356359] [Citation(s) in RCA: 131] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 02/05/2020] [Indexed: 12/11/2022] Open
Abstract
The role of the mesenchymal stromal cell- (MSC-) derived secretome is becoming increasingly intriguing from a clinical perspective due to its ability to stimulate endogenous tissue repair processes as well as its effective regulation of the immune system, mimicking the therapeutic effects produced by the MSCs. The secretome is a composite product secreted by MSC in vitro (in conditioned medium) and in vivo (in the extracellular milieu), consisting of a protein soluble fraction (mostly growth factors and cytokines) and a vesicular component, extracellular vesicles (EVs), which transfer proteins, lipids, and genetic material. MSC-derived secretome differs based on the tissue from which the MSCs are isolated and under specific conditions (e.g., preconditioning or priming) suggesting that clinical applications should be tailored by choosing the tissue of origin and a priming regimen to specifically correct a given pathology. MSC-derived secretome mediates beneficial angiogenic effects in a variety of tissue injury-related diseases. This supports the current effort to develop cell-free therapeutic products that bring both clinical benefits (reduced immunogenicity, persistence in vivo, and no genotoxicity associated with long-term cell cultures) and manufacturing advantages (reduced costs, availability of large quantities of off-the-shelf products, and lower regulatory burden). In the present review, we aim to give a comprehensive picture of the numerous components of the secretome produced by MSCs derived from the most common tissue sources for clinical use (e.g., AT, BM, and CB). We focus on the factors involved in the complex regulation of angiogenic processes.
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16
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Tong L, Qiu Y, Wang H, Qu Y, Zhao Y, Lin L, Wang Y, Xu W, Zhao W, He H, Zhao G, Zhang MH, Yang D, Ge X, Zhong Z. Expression Profile and Function Analysis of Long Non-coding RNAs in the Infection of Coxsackievirus B3. Virol Sin 2019; 34:618-630. [PMID: 31388922 DOI: 10.1007/s12250-019-00152-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 06/17/2019] [Indexed: 02/07/2023] Open
Abstract
The roles of lncRNAs in the infection of enteroviruses have been barely demonstrated. In this study, we used coxsackievirus B3 (CVB3), a typical enterovirus, as a model to investigate the expression profiles and functional roles of lncRNAs in enterovirus infection. We profiled lncRNAs and mRNA expression in CVB3-infected HeLa cells by lncRNA-mRNA integrated microarrays. As a result, 700 differentially expressed lncRNAs (431 up-regulated and 269 down-regulated) and 665 differentially expressed mRNAs (299 up-regulated and 366 down-regulated) were identified in CVB3 infection. Then we performed lncRNA-mRNA integrated pathway analysis to identify potential functional impacts of the differentially expressed mRNAs, in which lncRNA-mRNA correlation network was built. According to lncRNA-mRNA correlation, we found that XLOC-001188, an lncRNA down-regulated in CVB3 infection, was negatively correlated with NFAT5 mRNA, an anti-CVB3 gene reported previously. This interaction was supported by qPCR detection following siRNA-mediated knockdown of XLOC-001188, which showed an increase of NFAT5 mRNA and a reduction of CVB3 genomic RNA. In addition, we observed that four most significantly altered lncRNAs, SNHG11, RP11-145F16.2, RP11-1023L17.1 and RP11-1021N1.2 share several common correlated genes critical for CVB3 infection, such as BRE and IRF2BP1. In all, our studies reveal the alteration of lncRNA expression in CVB3 infection and its potential influence on CVB3 replication, providing useful information for future studies of enterovirus infection.
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Affiliation(s)
- Lei Tong
- Department of Microbiology, Harbin Medical University, Harbin, 150081, China
| | - Ye Qiu
- College of Biology, Hunan University, Changsha, 410012, China
| | - Hui Wang
- Department of Microbiology, Harbin Medical University, Harbin, 150081, China
| | - Yunyue Qu
- Department of Microbiology, Harbin Medical University, Harbin, 150081, China
| | - Yuanbo Zhao
- College of Biology, Hunan University, Changsha, 410012, China
| | - Lexun Lin
- Department of Microbiology, Harbin Medical University, Harbin, 150081, China
| | - Yan Wang
- Department of Cell Biology, Harbin Medical University, Harbin, 150081, China
| | - Weizhen Xu
- Department of Microbiology, Harbin Medical University, Harbin, 150081, China
| | - Wenran Zhao
- Department of Cell Biology, Harbin Medical University, Harbin, 150081, China
| | - Hongyan He
- College of Biology, Hunan University, Changsha, 410012, China
| | - Guangze Zhao
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6Z 1Y6, Canada
| | - Mary H Zhang
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6Z 1Y6, Canada
| | - Decheng Yang
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6Z 1Y6, Canada
| | - Xingyi Ge
- College of Biology, Hunan University, Changsha, 410012, China.
| | - Zhaohua Zhong
- Department of Microbiology, Harbin Medical University, Harbin, 150081, China.
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17
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Kong Y, Lu Z, Liu P, Liu Y, Wang F, Liang EY, Hou FF, Liang M. Long Noncoding RNA: Genomics and Relevance to Physiology. Compr Physiol 2019; 9:933-946. [PMID: 31187897 DOI: 10.1002/cphy.c180032] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The mammalian cell expresses thousands of long noncoding RNAs (lncRNAs) that are longer than 200 nucleotides but do not encode any protein. lncRNAs can change the expression of protein-coding genes through both cis and trans mechanisms, including imprinting and other types of transcriptional regulation, and posttranscriptional regulation including serving as molecular sponges. Deep sequencing, coupled with analysis of sequence characteristics, is the primary method used to identify lncRNAs. Physiological roles of specific lncRNAs can be examined using genetic targeting or knockdown with modified oligonucleotides. Identification of nucleic acids or proteins with which an lncRNA interacts is essential for understanding the molecular mechanism underlying its physiological role. lncRNAs have been reported to contribute to the regulation of physiological functions and disease development in several organ systems, including the cardiovascular, renal, muscular, endocrine, digestive, nervous, respiratory, and reproductive systems. The physiological role of the majority of lncRNAs, many of which are species and tissue specific, remains to be determined. © 2019 American Physiological Society. Compr Physiol 9:933-946, 2019.
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Affiliation(s)
- Yiwei Kong
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Department of Nephrology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Zeyuan Lu
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Department of Nephrology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Pengyuan Liu
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Sir Run Run Shaw Hospital, Institute of Translational Medicine, Zhejiang University, Zhejiang, China
| | - Yong Liu
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Feng Wang
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Department of Nephrology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Eugene Y Liang
- Center for Advancing Population Science, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Fan Fan Hou
- National Clinical Research Center for Kidney Disease, State Key Laboratory of Organ Failure Research, Guangzhou Regenerative Medicine and Health - Guangdong Laboratory, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Mingyu Liang
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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18
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Abstract
PURPOSE OF REVIEW Human genome is pervasively transcribed, producing coding and noncoding RNAs. Recent studies have revealed the roles of a class of noncoding RNAs, the long noncoding RNAs (lncRNAs), in heart failure and other cardiovascular diseases. This review provides a brief summary of recent findings on lncRNA function. RECENT FINDINGS Recent studies have documented the roles of lncRNAs in cardiac regeneration, conduction, hypertrophy/dysfunction, and endothelial function. LncRNAs perform these functions through acting as competing RNA (by binding and sequestering MicroRNAs) or acting as guides to protein targeting. A few lncRNAs also encode small peptides (e.g., Dwarf Open Reading Frame RNA) and in the context of heart regulate cardiac calcium homeostasis. SUMMARY Noncoding RNA provides a versatile mechanism of gene regulation and thereby present as novel targets for intervention in various cardiovascular disease. Future studies aimed at defining the context-dependent lncRNA mechanisms will be required to advance our understanding and relish the goal of RNA therapeutics.
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Affiliation(s)
- Priyatansh Gurha
- Center for Cardiovascular Genetics, Institute of Molecular Medicine and Department of Medicine, University of Texas Health Sciences Center at Houston, and Texas Heart Institute, Houston, TX 77030., Tel: +1 713-500-2335,
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19
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20
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Locatelli P, Giménez CS, Vega MU, Crottogini A, Belaich MN. Targeting the Cardiomyocyte Cell Cycle for Heart Regeneration. Curr Drug Targets 2018; 20:241-254. [DOI: 10.2174/1389450119666180801122551] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 07/27/2018] [Accepted: 07/31/2018] [Indexed: 02/07/2023]
Abstract
Adult mammalian cardiomyocytes (CMs) exhibit limited proliferative capacity, as cell cycle
activity leads to an increase in DNA content, but mitosis and cytokinesis are infrequent. This
makes the heart highly inefficient in replacing with neoformed cardiomyocytes lost contractile cells as
occurs in diseases such as myocardial infarction and dilated cardiomyopathy. Regenerative therapies
based on the implant of stem cells of diverse origin do not warrant engraftment and electromechanical
connection of the new cells with the resident ones, a fundamental condition to restore the physiology
of the cardiac syncytium. Consequently, there is a growing interest in identifying factors playing relevant
roles in the regulation of the CM cell cycle to be targeted in order to induce the resident cardiomyocytes
to divide into daughter cells and thus achieve myocardial regeneration with preservation of
physiologic syncytial performance.
Despite the scientific progress achieved over the last decades, many questions remain unanswered, including
how cardiomyocyte proliferation is regulated during heart development in gestation and neonatal
life. This can reveal unknown cell cycle regulation mechanisms and molecules that may be manipulated
to achieve cardiac self-regeneration.
We hereby revise updated data on CM cell cycle regulation, participating molecules and pathways recently
linked with the cell cycle, as well as experimental therapies involving them.
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Affiliation(s)
- Paola Locatelli
- Laboratorio de Regeneracion Cardiovascular, Instituto de Medicina Traslacional, Trasplante y Bioingenieria (IMETTYB), Consejo Nacional de Investigaciones Científicas y Tecnicas (CONICET) - Universidad Favaloro, Solis 453, Buenos Aires, Argentina
| | - Carlos Sebastián Giménez
- Laboratorio de Regeneracion Cardiovascular, Instituto de Medicina Traslacional, Trasplante y Bioingenieria (IMETTYB), Consejo Nacional de Investigaciones Científicas y Tecnicas (CONICET) - Universidad Favaloro, Solis 453, Buenos Aires, Argentina
| | - Martín Uranga Vega
- Laboratorio de Regeneracion Cardiovascular, Instituto de Medicina Traslacional, Trasplante y Bioingenieria (IMETTYB), Consejo Nacional de Investigaciones Científicas y Tecnicas (CONICET) - Universidad Favaloro, Solis 453, Buenos Aires, Argentina
| | - Alberto Crottogini
- Laboratorio de Regeneracion Cardiovascular, Instituto de Medicina Traslacional, Trasplante y Bioingenieria (IMETTYB), Consejo Nacional de Investigaciones Científicas y Tecnicas (CONICET) - Universidad Favaloro, Solis 453, Buenos Aires, Argentina
| | - Mariano Nicolás Belaich
- Laboratorio de Ingenieria Genetica y Biologia Celular y Molecular, Consejo Nacional de Investigaciones Científicas y Tecnicas (CONICET) - Universidad Nacional de Quilmes (UNQ), Roque Saenz Pena 352, Bernal, Buenos Aires, Argentina
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21
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Hurtado Del Pozo C, Garreta E, Izpisúa Belmonte JC, Montserrat N. Modeling epigenetic modifications in renal development and disease with organoids and genome editing. Dis Model Mech 2018; 11:dmm035048. [PMID: 30459215 PMCID: PMC6262817 DOI: 10.1242/dmm.035048] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Understanding epigenetic mechanisms is crucial to our comprehension of gene regulation in development and disease. In the past decades, different studies have shown the role of epigenetic modifications and modifiers in renal disease, especially during its progression towards chronic and end-stage renal disease. Thus, the identification of genetic variation associated with chronic kidney disease has resulted in better clinical management of patients. Despite the importance of these findings, the translation of genotype-phenotype data into gene-based medicine in chronic kidney disease populations still lacks faithful cellular or animal models that recapitulate the key aspects of the human kidney. The latest advances in the field of stem cells have shown that it is possible to emulate kidney development and function with organoids derived from human pluripotent stem cells. These have successfully recapitulated not only kidney differentiation, but also the specific phenotypical traits related to kidney function. The combination of this methodology with CRISPR/Cas9 genome editing has already helped researchers to model different genetic kidney disorders. Nowadays, CRISPR/Cas9-based approaches also allow epigenetic modifications, and thus represent an unprecedented tool for the screening of genetic variants, epigenetic modifications or even changes in chromatin structure that are altered in renal disease. In this Review, we discuss these technical advances in kidney modeling, and offer an overview of the role of epigenetic regulation in kidney development and disease.
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Affiliation(s)
- Carmen Hurtado Del Pozo
- Pluripotency for organ regeneration. Institute for Bioengineering of Catalonia (IBEC), the Barcelona Institute of Technology (BIST), 08028 Barcelona, Spain
| | - Elena Garreta
- Pluripotency for organ regeneration. Institute for Bioengineering of Catalonia (IBEC), the Barcelona Institute of Technology (BIST), 08028 Barcelona, Spain
| | | | - Nuria Montserrat
- Pluripotency for organ regeneration. Institute for Bioengineering of Catalonia (IBEC), the Barcelona Institute of Technology (BIST), 08028 Barcelona, Spain
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22
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Zhao C, Shen Q. Overexpression of small ubiquitin‑like modifier 2 ameliorates high glucose‑induced reductions in cardiomyocyte proliferation via the transforming growth factor‑β/Smad pathway. Mol Med Rep 2018; 18:4877-4885. [PMID: 30280191 PMCID: PMC6236294 DOI: 10.3892/mmr.2018.9522] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 12/12/2017] [Indexed: 12/16/2022] Open
Abstract
Hyperglycemia may induce diabetic cardiomyopathy (DC). In the current study, the mechanism underlying the alleviation of high glucose (HG)-induced impairments in the proliferation of H9c2 embryo cardiomyocyte proliferation by small ubiquitin-like modifier 2 (SUMO2) overexpression was investigated. H9c2 cell morphology was identified as classical long shuttle type by optical microscopy. The viability of HG-injured H9c2 cells was evaluated by a Cell Counting Kit-8 assay and the results indicated that viability was inhibited in a dose-dependent (5.6, 10, 20 and 30 mmol/l) and time-dependent (6, 12 and 24 h) manner. H9c2 cells treated with 20 mmol/l HG for 24 h were selected for subsequent experiments due to the extent of injury caused at a low density. Flow cytometry was conducted to confirm cell cycle arrest between G1/S phases and apoptosis promotion in HG-injured H9c2 cells, and the subsequent alleviating effect of SUMO2 overexpression on these HG-induced effects. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and western blot analysis were performed to detect mRNA and protein expression levels of cell cycle-and apoptosis-associated factors. The results indicated that the expression ofthe cell cycle-associated factors CyclinA2 and C-Myc was upregulated, and cyclin-dependent kinase inhibitor 1a was downregulated. The expression of the apoptosis-associated factor Bcl-2 was upregulated, while Bcl-2-associated X and caspase-3 expression was downregulated, by SUMO2 overexpression. Furthermore, the effect of SUMO2 overexpression on the transforming growth factor (TGF)-β/Smad pathway was also determined using RT-qPCR and western blot analysis. The results indicated the mRNA and protein levels of TGF-β1 and Smad3 in HG-injured H9c2 cells were significantly decreased following SUMO2 overexpression. Thus, the results demonstrated that overexpression of SUMO2 may alleviate H9c2 cardiomyocyte cell cycle arrest and apoptosis promotion induced by HG via regulation of cell cycle- and apoptosis-associated factors, as well as inhibition of the TGF-β/Smad pathway. These results may therefore provide a novel strategy for the protection of cardiomyocytes and may aid the diagnosis and prognosis of patients with DC.
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Affiliation(s)
- Chen Zhao
- Department of Geriatric, Shanghai Tongren Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200336, P.R. China
| | - Qile Shen
- Department of Geriatric, Shanghai Tongren Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200336, P.R. China
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23
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Ballarino M, Cipriano A, Tita R, Santini T, Desideri F, Morlando M, Colantoni A, Carrieri C, Nicoletti C, Musarò A, Carroll DO, Bozzoni I. Deficiency in the nuclear long noncoding RNA Charme causes myogenic defects and heart remodeling in mice. EMBO J 2018; 37:embj.201899697. [PMID: 30177572 PMCID: PMC6138438 DOI: 10.15252/embj.201899697] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 07/17/2018] [Accepted: 07/21/2018] [Indexed: 01/03/2023] Open
Abstract
Myogenesis is a highly regulated process that involves the conversion of progenitor cells into multinucleated myofibers. Besides proteins and miRNAs, long noncoding RNAs (lncRNAs) have been shown to participate in myogenic regulatory circuitries. Here, we characterize a murine chromatin‐associated muscle‐specific lncRNA, Charme, which contributes to the robustness of the myogenic program in vitro and in vivo. In myocytes, Charme depletion triggers the disassembly of a specific chromosomal domain and the downregulation of myogenic genes contained therein. Notably, several Charme‐sensitive genes are associated with human cardiomyopathies and Charme depletion in mice results in a peculiar cardiac remodeling phenotype with changes in size, structure, and shape of the heart. Moreover, the existence of an orthologous transcript in human, regulating the same subset of target genes, suggests an important and evolutionarily conserved function for Charme. Altogether, these data describe a new example of a chromatin‐associated lncRNA regulating the robustness of skeletal and cardiac myogenesis.
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Affiliation(s)
- Monica Ballarino
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Andrea Cipriano
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Rossella Tita
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Tiziana Santini
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
| | - Fabio Desideri
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Mariangela Morlando
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Alessio Colantoni
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Claudia Carrieri
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Carmine Nicoletti
- DAHFMO-Unit of Histology and Medical Embryology, Sapienza University of Rome, Rome, Italy
| | - Antonio Musarò
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy.,DAHFMO-Unit of Histology and Medical Embryology, Sapienza University of Rome, Rome, Italy
| | - Dònal O' Carroll
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Irene Bozzoni
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy .,Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy.,Institute Pasteur Fondazione Cenci-Bolognetti, Sapienza University of Rome, Rome, Italy.,Institute of Molecular Biology and Pathology, CNR, Sapienza University of Rome, Rome, Italy
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24
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Gao Y, Li S, Zhang Z, Yu X, Zheng J. The Role of Long Non-coding RNAs in the Pathogenesis of RA, SLE, and SS. Front Med (Lausanne) 2018; 5:193. [PMID: 30018955 PMCID: PMC6038710 DOI: 10.3389/fmed.2018.00193] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 06/11/2018] [Indexed: 12/13/2022] Open
Abstract
Rheumatoid diseases are a group of systemic autoimmune diseases which affect multiple organs with largely unknown etiology. In the past decade, long non-coding RNAs (lncRNAs) have emerged as important regulators of biological processes and contribute deeply to immune cell development and immune responses. Substantial evidences have been accumulated showing that LncRNAs involved in the pathogenesis of the rheumatoid diseases, including rheumatoid arthritis (RA), systemic lupus erythematosus (SLE) and Sjögren's syndrome (SS). In this review, we summarize literature combined with bioinformatics methods to analyze the unique and common lncRNAs patterns in rheumatoid diseases and try to reveal the important function of lncRNAs in RA, SLE and SS.
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Affiliation(s)
- Yunzhen Gao
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, XinXiang, China
| | - Shasha Li
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, XinXiang, China
| | - Zhongjian Zhang
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, XinXiang, China
| | - Xinhua Yu
- Priority Area Asthma and Allergy, Research Center Borstel, Airway Research Center North, Members of the German Center for Lung Research, Borstel, Germany
| | - Junfeng Zheng
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, XinXiang, China
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25
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Tang P, Ma S, Dong M, Wang J, Chai S, Liu T, Li J. Effect of interleukin-6 on myocardial regeneration in mice after cardiac injury. Biomed Pharmacother 2018; 106:303-308. [PMID: 29966974 DOI: 10.1016/j.biopha.2018.06.090] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 06/14/2018] [Indexed: 10/28/2022] Open
Abstract
Our aim was to investigate the role of interleukin-6 (IL-6) in myocardial regeneration from mice after cardiac injury. The newborn mice were divided into the following 4 groups (16 in each group): sham group, model group, IL-6-/- group (IL-6 knockout) and IL-6 group (IL-6 overexpression). Electrocardiography was performed on all mice and found higher LVEDD, LVESD and IVST and lower LVEF and LVFS in the IL-6 group compared with the sham group. Using HE staining, severe myocardial injury combined with infarction and fibrosis were observed in the IL-6-/- group, while the damaged myocardial tissue was repaired to some extent in the IL-6 group. The expression of IL-6 in the IL-6 group were significantly up-regulated. BrdU immunofluorescence found that the IL-6-/- group had the least number of BrdU positive cells, while the IL-6 group had more BrdU positive cells than the model group and the IL-6-/- group. Expressions of IL-6, cyclinD1 and Bcl-2 in the IL-6 group were up-regulated compared with other groups. In conclusion, IL-6 overexpression could enhance cardiomyocyte proliferation and relevant protein expression in mice myocardium, thus promoting cardiac regeneration.
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Affiliation(s)
- Peizhe Tang
- Department of Cardiovascular Surgery, Liaocheng People's Hospital, Liaocheng, Shandong Province, China.
| | - Shengjun Ma
- Department of Cardiovascular Surgery, Liaocheng People's Hospital, Liaocheng, Shandong Province, China
| | - Mingfeng Dong
- Department of Cardiovascular Surgery, Liaocheng People's Hospital, Liaocheng, Shandong Province, China
| | - Jiantang Wang
- Department of Cardiovascular Surgery, Liaocheng People's Hospital, Liaocheng, Shandong Province, China
| | - Shoudong Chai
- Department of Cardiovascular Surgery, Liaocheng People's Hospital, Liaocheng, Shandong Province, China
| | - Tao Liu
- Department of Cardiovascular Surgery, Liaocheng People's Hospital, Liaocheng, Shandong Province, China
| | - Jindong Li
- Department of Cardiovascular Surgery, Liaocheng People's Hospital, Liaocheng, Shandong Province, China
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26
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Bei Y, Tao L, Cretoiu D, Cretoiu SM, Xiao J. MicroRNAs Mediate Beneficial Effects of Exercise in Heart. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1000:261-280. [PMID: 29098626 DOI: 10.1007/978-981-10-4304-8_15] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
MicroRNAs (miRNAs, miRs), a group of small non-coding RNAs, repress gene expressions at posttranscriptional level in most cases and are involved in cardiovascular physiology and disease pathogenesis. Increasing evidence has proved that miRNAs are potential regulators of exercise induced cardiac growth and mediate the benefits of exercise in a variety of cardiovascular diseases. In this chapter, we will review the regulatory effects of miRNAs in cardiac adaptations to exercise, and summarize their cardioprotective effects against myocardial infarction, ischemia/reperfusion injury, heart failure, diabetic cardiomyopathy, atherosclerosis, hypertension, and pulmonary hypertension. Also, we will introduce circulating miRNAs in response to acute and chronic exercise. Therefore, miRNAs may serve as novel therapeutic targets and potential biomarkers for cardiovascular diseases.
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Affiliation(s)
- Yihua Bei
- Cardiac Regeneration and Ageing Lab, School of Life Science, Shanghai University, Shanghai, 200444, China
| | - Lichan Tao
- Department of Cardiology, The Third Affiliated Hospital of Soochow University, Changzhou, 213003, China
| | - Dragos Cretoiu
- Victor Babes National Institute of Pathology, Bucharest, 050096, Romania.,Division of Cellular and Molecular Biology and Histology, Carol Davila University of Medicine and Pharmacy, Bucharest, 050474, Romania
| | - Sanda Maria Cretoiu
- Victor Babes National Institute of Pathology, Bucharest, 050096, Romania.,Division of Cellular and Molecular Biology and Histology, Carol Davila University of Medicine and Pharmacy, Bucharest, 050474, Romania
| | - Junjie Xiao
- Cardiac Regeneration and Ageing Lab, School of Life Science, Shanghai University, Shanghai, 200444, China.
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27
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Micheletti R, Plaisance I, Abraham BJ, Sarre A, Ting CC, Alexanian M, Maric D, Maison D, Nemir M, Young RA, Schroen B, González A, Ounzain S, Pedrazzini T. The long noncoding RNA Wisper controls cardiac fibrosis and remodeling. Sci Transl Med 2018. [PMID: 28637928 DOI: 10.1126/scitranslmed.aai9118] [Citation(s) in RCA: 214] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Long noncoding RNAs (lncRNAs) are emerging as powerful regulators of cardiac development and disease. However, our understanding of the importance of these molecules in cardiac fibrosis is limited. Using an integrated genomic screen, we identified Wisper (Wisp2 super-enhancer-associated RNA) as a cardiac fibroblast-enriched lncRNA that regulates cardiac fibrosis after injury. Wisper expression was correlated with cardiac fibrosis both in a murine model of myocardial infarction (MI) and in heart tissue from human patients suffering from aortic stenosis. Loss-of-function approaches in vitro using modified antisense oligonucleotides (ASOs) demonstrated that Wisper is a specific regulator of cardiac fibroblast proliferation, migration, and survival. Accordingly, ASO-mediated silencing of Wisper in vivo attenuated MI-induced fibrosis and cardiac dysfunction. Functionally, Wisper regulates cardiac fibroblast gene expression programs critical for cell identity, extracellular matrix deposition, proliferation, and survival. In addition, its association with TIA1-related protein allows it to control the expression of a profibrotic form of lysyl hydroxylase 2, implicated in collagen cross-linking and stabilization of the matrix. Together, our findings identify Wisper as a cardiac fibroblast-enriched super-enhancer-associated lncRNA that represents an attractive therapeutic target to reduce the pathological development of cardiac fibrosis in response to MI and prevent adverse remodeling in the damaged heart.
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Affiliation(s)
- Rudi Micheletti
- Experimental Cardiology Unit, Department of Cardiovascular Medicine, University of Lausanne Medical School, Lausanne, Switzerland
| | - Isabelle Plaisance
- Experimental Cardiology Unit, Department of Cardiovascular Medicine, University of Lausanne Medical School, Lausanne, Switzerland
| | - Brian J Abraham
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Alexandre Sarre
- Cardiovascular Assessment Facility, University of Lausanne, Lausanne, Switzerland
| | - Ching-Chia Ting
- Experimental Cardiology Unit, Department of Cardiovascular Medicine, University of Lausanne Medical School, Lausanne, Switzerland
| | - Michael Alexanian
- Experimental Cardiology Unit, Department of Cardiovascular Medicine, University of Lausanne Medical School, Lausanne, Switzerland
| | - Daniel Maric
- Experimental Cardiology Unit, Department of Cardiovascular Medicine, University of Lausanne Medical School, Lausanne, Switzerland
| | - Damien Maison
- Experimental Cardiology Unit, Department of Cardiovascular Medicine, University of Lausanne Medical School, Lausanne, Switzerland
| | - Mohamed Nemir
- Experimental Cardiology Unit, Department of Cardiovascular Medicine, University of Lausanne Medical School, Lausanne, Switzerland
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Blanche Schroen
- Center for Heart Failure Research, Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, Netherlands
| | - Arantxa González
- Centre for Applied Medical Research, University of Navarra, Pamplona, Spain.,National Institute of Health Carlos III, Madrid, Spain
| | - Samir Ounzain
- Experimental Cardiology Unit, Department of Cardiovascular Medicine, University of Lausanne Medical School, Lausanne, Switzerland.
| | - Thierry Pedrazzini
- Experimental Cardiology Unit, Department of Cardiovascular Medicine, University of Lausanne Medical School, Lausanne, Switzerland.
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28
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García-Padilla C, Aránega A, Franco D. The role of long non-coding RNAs in cardiac development and disease. AIMS GENETICS 2018; 5:124-140. [PMID: 31435517 PMCID: PMC6698576 DOI: 10.3934/genet.2018.2.124] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 03/15/2018] [Indexed: 12/12/2022]
Abstract
Cells display a set of RNA molecules at one time point, reflecting thus the cellular transcriptional steady state, configuring therefore its transcriptome. It is basically composed of two different classes of RNA molecules; protein-coding RNAs (cRNAs) and protein non-coding RNAs (ncRNAs). Sequencing of the human genome and subsequently the ENCODE project identified that more than 80% of the genome is transcribed in some type of RNA. Importantly, only 3% of these transcripts correspond to protein-coding RNAs, pointing that ncRNAs are as important or even more as cRNAs. ncRNAs have pivotal roles in development, differentiation and disease. Non-coding RNAs can be classified into two distinct classes according to their length; i.e., small (<200 nt) and long (>200 nt) noncoding RNAs. The structure, biogenesis and functional roles of small non-coding RNA have been widely studied, particularly for microRNAs (miRNAs). In contrast to microRNAs, our current understanding of long non-coding RNAs (lncRNAs) is limited. In this manuscript, we provide state-of-the art review of the functional roles of long non-coding RNAs during cardiac development as well as an overview of the emerging role of these ncRNAs in distinct cardiac diseases.
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Affiliation(s)
| | | | - Diego Franco
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaén, Jaén, Spain
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29
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Cipriano A, Ballarino M. The Ever-Evolving Concept of the Gene: The Use of RNA/Protein Experimental Techniques to Understand Genome Functions. Front Mol Biosci 2018; 5:20. [PMID: 29560353 PMCID: PMC5845540 DOI: 10.3389/fmolb.2018.00020] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 02/20/2018] [Indexed: 12/12/2022] Open
Abstract
The completion of the human genome sequence together with advances in sequencing technologies have shifted the paradigm of the genome, as composed of discrete and hereditable coding entities, and have shown the abundance of functional noncoding DNA. This part of the genome, previously dismissed as “junk” DNA, increases proportionally with organismal complexity and contributes to gene regulation beyond the boundaries of known protein-coding genes. Different classes of functionally relevant nonprotein-coding RNAs are transcribed from noncoding DNA sequences. Among them are the long noncoding RNAs (lncRNAs), which are thought to participate in the basal regulation of protein-coding genes at both transcriptional and post-transcriptional levels. Although knowledge of this field is still limited, the ability of lncRNAs to localize in different cellular compartments, to fold into specific secondary structures and to interact with different molecules (RNA or proteins) endows them with multiple regulatory mechanisms. It is becoming evident that lncRNAs may play a crucial role in most biological processes such as the control of development, differentiation and cell growth. This review places the evolution of the concept of the gene in its historical context, from Darwin's hypothetical mechanism of heredity to the post-genomic era. We discuss how the original idea of protein-coding genes as unique determinants of phenotypic traits has been reconsidered in light of the existence of noncoding RNAs. We summarize the technological developments which have been made in the genome-wide identification and study of lncRNAs and emphasize the methodologies that have aided our understanding of the complexity of lncRNA-protein interactions in recent years.
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Affiliation(s)
- Andrea Cipriano
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Monica Ballarino
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy
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30
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Chen YM, Li H, Fan Y, Zhang QJ, Li X, Wu LJ, Chen ZJ, Zhu C, Qian LM. Identification of differentially expressed lncRNAs involved in transient regeneration of the neonatal C57BL/6J mouse heart by next-generation high-throughput RNA sequencing. Oncotarget 2018; 8:28052-28062. [PMID: 28427208 PMCID: PMC5438630 DOI: 10.18632/oncotarget.15887] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 02/20/2017] [Indexed: 02/01/2023] Open
Abstract
Previous studies have shown that mammalian cardiac tissue has a regenerative capacity. Remarkably, neonatal mice can regenerate their cardiac tissue for up to 6 days after birth, but this capacity is lost by day 7. In this study, we aimed to explore the expression pattern of long noncoding RNA (lncRNA) during this period and examine the mechanisms underlying this process. We found that 685 lncRNAs and 1833 mRNAs were differentially expressed at P1 and P7 by the next-generation high-throughput RNA sequencing. The coding genes associated with differentially expressed lncRNAs were mainly involved in metabolic processes and cell proliferation, and also were potentially associated with several key regeneration signalling pathways, including PI3K-Akt, MAPK, Hippo and Wnt. In addition, we identified some correlated targets of highly-dysregulated lncRNAs such as Igfbp3, Trnp1, Itgb6, and Pim3 by the coding-noncoding gene co-expression network. These data may offer a reference resource for further investigation about the mechanisms by which lncRNAs regulate cardiac regeneration.
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Affiliation(s)
- Yu-Mei Chen
- Department of Emergency, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Hua Li
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, P. R. China
| | - Yi Fan
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, P. R. China
| | - Qi-Jun Zhang
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, P. R. China
| | - Xing Li
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, P. R. China
| | - Li-Jie Wu
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, P. R. China
| | - Zi-Jie Chen
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, P. R. China
| | - Chun Zhu
- Department of Pediatrics, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing, Jiangsu 210004, P. R. China
| | - Ling-Mei Qian
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, P. R. China
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31
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A transcribed enhancer dictates mesendoderm specification in pluripotency. Nat Commun 2017; 8:1806. [PMID: 29180618 PMCID: PMC5703900 DOI: 10.1038/s41467-017-01804-w] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 10/16/2017] [Indexed: 12/31/2022] Open
Abstract
Enhancers and long noncoding RNAs (lncRNAs) are key determinants of lineage specification during development. Here, we evaluate remodeling of the enhancer landscape and modulation of the lncRNA transcriptome during mesendoderm specification. We sort mesendodermal progenitors from differentiating embryonic stem cells (ESCs) according to Eomes expression, and find that enhancer usage is coordinated with mesendoderm-specific expression of key lineage-determining transcription factors. Many of these enhancers are associated with the expression of lncRNAs. Examination of ESC-specific enhancers interacting in three-dimensional space with mesendoderm-specifying transcription factor loci identifies MesEndoderm Transcriptional Enhancer Organizing Region (Meteor). Genetic and epigenetic manipulation of the Meteor enhancer reveal its indispensable role during mesendoderm specification and subsequent cardiogenic differentiation via transcription-independent and -dependent mechanisms. Interestingly, Meteor-deleted ESCs are epigenetically redirected towards neuroectodermal lineages. Loci, topologically associating a transcribed enhancer and its cognate protein coding gene, appear to represent therefore a class of genomic elements controlling developmental competence in pluripotency. Long noncoding RNAs (lncRNAs) are key regulators of lineage specification during development. Here, the authors investigate remodeling of enhancers and regulation of the lncRNA transcriptome during mesendoderm specification, and identify a pluripotent stage-specific transcribed enhancer controlling adoption of the mesendodermal cell fate.
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32
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Sommese L, Zullo A, Schiano C, Mancini FP, Napoli C. Possible Muscle Repair in the Human Cardiovascular System. Stem Cell Rev Rep 2017; 13:170-191. [PMID: 28058671 DOI: 10.1007/s12015-016-9711-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The regenerative potential of tissues and organs could promote survival, extended lifespan and healthy life in multicellular organisms. Niches of adult stemness are widely distributed and lead to the anatomical and functional regeneration of the damaged organ. Conversely, muscular regeneration in mammals, and humans in particular, is very limited and not a single piece of muscle can fully regrow after a severe injury. Therefore, muscle repair after myocardial infarction is still a chimera. Recently, it has been recognized that epigenetics could play a role in tissue regrowth since it guarantees the maintenance of cellular identity in differentiated cells and, therefore, the stability of organs and tissues. The removal of these locks can shift a specific cell identity back to the stem-like one. Given the gradual loss of tissue renewal potential in the course of evolution, in the last few years many different attempts to retrieve such potential by means of cell therapy approaches have been performed in experimental models. Here we review pathways and mechanisms involved in the in vivo repair of cardiovascular muscle tissues in humans. Moreover, we address the ongoing research on mammalian cardiac muscle repair based on adult stem cell transplantation and pro-regenerative factor delivery. This latter issue, involving genetic manipulations of adult cells, paves the way for developing possible therapeutic strategies in the field of cardiovascular muscle repair.
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Affiliation(s)
- Linda Sommese
- Department of Internal and Specialty Medicine, U.O.C. Clinical Immunology, Immunohematology, Transfusion Medicine and Transplant Immunology, Regional Reference Laboratory of Transplant Immunology, Azienda Ospedaliera Universitaria, Università degli Studi della Campania "Luigi Vanvitelli", Piazza Miraglia 2, 80138, Naples, Italy.
| | - Alberto Zullo
- Department of Sciences and Technologies, University of Sannio, Benevento, Italy.,CEINGE Advanced Biotechnologies, s.c.ar.l, Naples, Italy
| | | | - Francesco P Mancini
- Department of Sciences and Technologies, University of Sannio, Benevento, Italy
| | - Claudio Napoli
- Department of Internal and Specialty Medicine, U.O.C. Clinical Immunology, Immunohematology, Transfusion Medicine and Transplant Immunology, Regional Reference Laboratory of Transplant Immunology, Azienda Ospedaliera Universitaria, Università degli Studi della Campania "Luigi Vanvitelli", Piazza Miraglia 2, 80138, Naples, Italy.,IRCCS Foundation SDN, Naples, Italy
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33
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Fatima F, Ekstrom K, Nazarenko I, Maugeri M, Valadi H, Hill AF, Camussi G, Nawaz M. Non-coding RNAs in Mesenchymal Stem Cell-Derived Extracellular Vesicles: Deciphering Regulatory Roles in Stem Cell Potency, Inflammatory Resolve, and Tissue Regeneration. Front Genet 2017; 8:161. [PMID: 29123544 PMCID: PMC5662888 DOI: 10.3389/fgene.2017.00161] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 10/12/2017] [Indexed: 12/20/2022] Open
Abstract
Extracellular vesicles (EVs) are heterogeneous populations of nano- and micro-sized vesicles secreted by various cell types. There is mounting evidence that EVs have widespread roles in transporting proteins, lipids, and nucleic acids between cells and serve as mediators of intercellular communication. EVs secreted from stem cells could function as paracrine factors, and appear to mimic and recapitulate several features of their secreting cells. EV-mediated transport of regulatory RNAs provides a novel source of trans-regulation between cells. As such, stem cells have evolved unique forms of paracrine mechanisms for recapitulating their potencies with specialized functions by transporting non-coding RNAs (ncRNAs) via EVs. This includes the dissemination of stem cell-derived EV-ncRNAs and their regulatory effects elicited in differentiation, self-renewal, pluripotency, and the induction of reparative programs. Here, we summarize and discuss the therapeutic effects of mesenchymal stem cell-derived EV-ncRNAs in the induction of intrinsic regenerative programs elicited through regulating several mechanisms. Among them, most noticeable are the EV-mediated enrichment of ncRNAs at the injury sites contributing the regulation of matrix remodeling, epithelial mesenchymal transitions, and attraction of fibroblasts. Additionally, we emphasize EV-mediated transmission of anti-inflammatory RNAs from stem cells to injury site that potentially orchestrate the resolution of the inflammatory responses and immune alleviation to better facilitate healing processes. Collectively, this knowledge indicates a high value and potential of EV-mediated RNA-based therapeutic approaches in regenerative medicine.
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Affiliation(s)
- Farah Fatima
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Pathology and Forensic Medicine, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Karin Ekstrom
- Department of Biomaterials, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Irina Nazarenko
- Faculty of Medicine, Institute for Infection Prevention and Hospital Epidemiology, Medical Centre, University of Freiburg, Freiburg, Germany
| | - Marco Maugeri
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Hadi Valadi
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Andrew F Hill
- Department of Biochemistry and Genetics, La Trobe Institute of Molecular Science, La Trobe University, Bundoora, VIC, Australia
| | - Giovanni Camussi
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Torino, Italy
| | - Muhammad Nawaz
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Pathology and Forensic Medicine, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
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Sattler S, Fairchild P, Watt FM, Rosenthal N, Harding SE. The adaptive immune response to cardiac injury-the true roadblock to effective regenerative therapies? NPJ Regen Med 2017; 2:19. [PMID: 29302355 PMCID: PMC5677967 DOI: 10.1038/s41536-017-0022-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Revised: 05/17/2017] [Accepted: 05/17/2017] [Indexed: 02/06/2023] Open
Abstract
The regenerative capacity of adult human tissues and organs is limited, but recent developments have seen the advent of promising new technologies for regenerative therapy. The human heart is of particular interest for regenerative medicine, as cardiac tissue damage is repaired by the formation of rigid scar tissue, which causes inevitable structural changes and progressive functional decline leading to heart failure. Cardiac regenerative medicine aims to prevent scar formation or replace existing scars to halt or reverse adverse remodeling and therapeutic approaches include the use of biomaterials, gene therapies, delivery of growth factors, and (stem) cell therapies. Regenerative therapies, however, face significant obstacles in a hostile microenvironment. While the early immune response to a myocardial infarct is essential to ensure tissue integrity and to avoid fatal cardiac rupture, excessive activation of endogenous repair mechanisms may lead to ongoing inflammation, fibrosis, and sustained autoimmune-mediated tissue damage. Anti-cardiac autoreactivity of the adaptive immune system has been suggested to be involved in structural remodeling, functional decline, and the development of heart failure. It is, therefore, crucial to first understand the endogenous response to cardiac tissue damage and how to restore immune tolerance to cardiac tissue, before additional regenerative therapies can achieve their full potential.
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Affiliation(s)
- Susanne Sattler
- National Heart and Lung Institute, Imperial College London, London, W12 0NN UK
| | - Paul Fairchild
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE UK
| | - Fiona M Watt
- Centre for Stem Cells & Regenerative Medicine, King's College London, London, SE1 9RT UK
| | - Nadia Rosenthal
- National Heart and Lung Institute, Imperial College London, London, W12 0NN UK.,The Jackson Laboratory, Bar Harbor, ME 04609 USA
| | - Sian E Harding
- National Heart and Lung Institute, Imperial College London, London, W12 0NN UK
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35
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Garreta E, Prado P, Izpisua Belmonte JC, Montserrat N. Non-coding microRNAs for cardiac regeneration: Exploring novel alternatives to induce heart healing. Noncoding RNA Res 2017; 2:93-99. [PMID: 30159426 PMCID: PMC6096419 DOI: 10.1016/j.ncrna.2017.05.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 05/15/2017] [Accepted: 05/15/2017] [Indexed: 01/06/2023] Open
Abstract
In recent years, different studies have revealed that adult mammalian cardiomyocytes have the capacity to self-renew under homeostatic conditions and after myocardial injury. Interestingly, data from animal models capable of regeneration, such as the adult zebrafish and neonatal mice, have identified different non-coding RNAs (ncRNAs) as functional RNA molecules driving cardiac regeneration and repair. In this review, we summarize the current knowledge of the roles that a specific subset of ncRNAs, namely microRNAs (miRNA), plays in these animal models. We also emphasize the importance of characterizing and manipulating miRNAs as a novel approach to awaken the dormant regenerative potential of the adult mammalian heart by the administration of miRNA mimics or inhibitors. Overall, the use of these strategies alone or in combination with current cardiac therapies may represent new avenues to pursue for cardiac regeneration.
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Affiliation(s)
- Elena Garreta
- Pluripotent Stem Cells and Activation of Endogenous Tissue Programs for Organ Regeneration, Institute for Bioengineering of Catalonia (IBEC), Barcelona, Spain
| | - Patricia Prado
- Pluripotent Stem Cells and Activation of Endogenous Tissue Programs for Organ Regeneration, Institute for Bioengineering of Catalonia (IBEC), Barcelona, Spain
| | | | - Nuria Montserrat
- Pluripotent Stem Cells and Activation of Endogenous Tissue Programs for Organ Regeneration, Institute for Bioengineering of Catalonia (IBEC), Barcelona, Spain
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Viereck J, Thum T. Circulating Noncoding RNAs as Biomarkers of Cardiovascular Disease and Injury. Circ Res 2017; 120:381-399. [PMID: 28104771 DOI: 10.1161/circresaha.116.308434] [Citation(s) in RCA: 284] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 11/26/2016] [Accepted: 12/06/2016] [Indexed: 12/12/2022]
Abstract
The discovery of thousands of noncoding RNAs (ncRNAs) has expanded our view on mammalian genomes and transcriptomes, as well as their organization and regulation. Accumulating evidence on aberrantly regulated ncRNAs, including short microRNAs, long ncRNAs and circular RNAs, across various heart diseases indicates that ncRNAs are critical contributors to cardiovascular pathophysiology. In addition, ncRNAs are released into the circulation where they are present in concentration levels that differ between healthy subjects and diseased patients. Although little is known about the origin and function of such circulating ncRNAs, these molecules are increasingly recognized as noninvasive and readily accessible biomarker for risk stratification, diagnosis and prognosis of cardiac injury, and multiple forms of cardiovascular disease. In this review, we summarize recent findings on biological characteristics of circulating ncRNAs and highlight their value as potential biomarker in selected pathologies of cardiovascular disease.
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Affiliation(s)
- Janika Viereck
- From the Institute of Molecular and Translational Therapeutic Strategies, IFB-Tx (J.V., T.T.), and Excellence Cluster REBIRTH (T.T.), Hannover Medical School, Germany; and National Heart and Lung Institute, Imperial College London, United Kingdom (T.T.)
| | - Thomas Thum
- From the Institute of Molecular and Translational Therapeutic Strategies, IFB-Tx (J.V., T.T.), and Excellence Cluster REBIRTH (T.T.), Hannover Medical School, Germany; and National Heart and Lung Institute, Imperial College London, United Kingdom (T.T.).
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37
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Liu Y, Zheng L, Wang Q, Hu YW. Emerging roles and mechanisms of long noncoding RNAs in atherosclerosis. Int J Cardiol 2016; 228:570-582. [PMID: 27875736 DOI: 10.1016/j.ijcard.2016.11.182] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 11/06/2016] [Indexed: 12/17/2022]
Abstract
Atherosclerosis is the most common cause of heart attacks, strokes, and peripheral vascular disease. Atherosclerosis is predicted to be the primary cause of death in the world by 2020. Increasing evidence suggests that long non-protein-coding RNAs (lncRNAs) are important for the regulation of tissue homeostasis and pathophysiological conditions. Although knowledge about lncRNAs in atherosclerosis and other cardiovascular diseases is sparse, lncRNAs are clinically interesting because of their diagnostic and therapeutic value. This review summarizes knowledge about lncRNAs through their actions, related research methods and effects on atherosclerosis to provide helpful insights about how lncRNAs work and control atherosclerosis process and how lncRNA-related strategies could benefit human beings.
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Affiliation(s)
- Yao Liu
- The Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Lei Zheng
- The Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Qian Wang
- The Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Yan-Wei Hu
- The Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China.
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Plaisance I, Perruchoud S, Fernandez-Tenorio M, Gonzales C, Ounzain S, Ruchat P, Nemir M, Niggli E, Pedrazzini T. Cardiomyocyte Lineage Specification in Adult Human Cardiac Precursor Cells Via Modulation of Enhancer-Associated Long Noncoding RNA Expression. JACC Basic Transl Sci 2016; 1:472-493. [PMID: 29707678 PMCID: PMC5916868 DOI: 10.1016/j.jacbts.2016.06.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Human CPCs produce predominantly smooth muscle cells. CPCs can be redirected to the cardiomyocyte fate by transient activation followed by inhibition of NOTCH signaling. Inhibition of NOTCH signaling during differentiation represses MIR-143/145 expression and blocks smooth muscle differentiation. Expression of the microRNAs is under control of CARMEN, a long noncoding RNA associated with an enhancer located in the MIR-143/145 locus and target of NOTCH signaling. The CARMEN/MIR-145/143 locus represents a promising therapeutic target to favor production of cardiomyocytes in cell replacement therapies.
The mechanisms controlling differentiation in adult cardiac precursor cells (CPCs) are still largely unknown. In this study, CPCs isolated from the human heart were found to produce predominantly smooth muscle cells but could be redirected to the cardiomyocyte fate by transient activation followed by inhibition of NOTCH signaling. NOTCH inhibition repressed MIR-143/145 expression, and blocked smooth muscle differentiation. Expression of the microRNAs is under control of CARMEN, a long noncoding RNA associated with an enhancer located in the MIR-143/145 locus and target of NOTCH signaling. The CARMEN/MIR-145/143 axis represents, therefore, a promising target to favor production of cardiomyocytes in cell replacement therapies.
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Affiliation(s)
- Isabelle Plaisance
- Experimental Cardiology Unit, Department of Medicine, University of Lausanne Medical School, Lausanne, Switzerland
| | - Stéphanie Perruchoud
- Experimental Cardiology Unit, Department of Medicine, University of Lausanne Medical School, Lausanne, Switzerland
| | | | - Christine Gonzales
- Experimental Cardiology Unit, Department of Medicine, University of Lausanne Medical School, Lausanne, Switzerland
| | - Samir Ounzain
- Experimental Cardiology Unit, Department of Medicine, University of Lausanne Medical School, Lausanne, Switzerland
| | - Patrick Ruchat
- Department of Cardiovascular Surgery, University of Lausanne Medical School, Lausanne, Switzerland
| | - Mohamed Nemir
- Experimental Cardiology Unit, Department of Medicine, University of Lausanne Medical School, Lausanne, Switzerland
| | - Ernst Niggli
- Department of Physiology, University of Bern, Bern, Switzerland
| | - Thierry Pedrazzini
- Experimental Cardiology Unit, Department of Medicine, University of Lausanne Medical School, Lausanne, Switzerland
- Reprint requests and correspondence: Dr. Thierry Pedrazzini, Experimental Cardiology Unit, Department of Medicine, University of Lausanne Medical School, CH-1011 Lausanne, Switzerland.
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Kashkin KN, Sverdlov ED. Properties, functions, and therapeutic prospects of enhancer RNAs. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2016. [DOI: 10.1134/s1068162016050083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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40
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Ounzain S, Pedrazzini T. Long non-coding RNAs in heart failure: a promising future with much to learn. ANNALS OF TRANSLATIONAL MEDICINE 2016; 4:298. [PMID: 27569219 DOI: 10.21037/atm.2016.07.13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Samir Ounzain
- Experimental Cardiology Unit, Department of Medicine, University of Lausanne Medical School, Lausanne, Switzerland
| | - Thierry Pedrazzini
- Experimental Cardiology Unit, Department of Medicine, University of Lausanne Medical School, Lausanne, Switzerland
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41
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Simandi Z, Horvath A, Nagy P, Nagy L. Prediction and Validation of Gene Regulatory Elements Activated During Retinoic Acid Induced Embryonic Stem Cell Differentiation. J Vis Exp 2016. [PMID: 27403939 DOI: 10.3791/53978] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Embryonic development is a multistep process involving activation and repression of many genes. Enhancer elements in the genome are known to contribute to tissue and cell-type specific regulation of gene expression during the cellular differentiation. Thus, their identification and further investigation is important in order to understand how cell fate is determined. Integration of gene expression data (e.g., microarray or RNA-seq) and results of chromatin immunoprecipitation (ChIP)-based genome-wide studies (ChIP-seq) allows large-scale identification of these regulatory regions. However, functional validation of cell-type specific enhancers requires further in vitro and in vivo experimental procedures. Here we describe how active enhancers can be identified and validated experimentally. This protocol provides a step-by-step workflow that includes: 1) identification of regulatory regions by ChIP-seq data analysis, 2) cloning and experimental validation of putative regulatory potential of the identified genomic sequences in a reporter assay, and 3) determination of enhancer activity in vivo by measuring enhancer RNA transcript level. The presented protocol is detailed enough to help anyone to set up this workflow in the lab. Importantly, the protocol can be easily adapted to and used in any cellular model system.
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Affiliation(s)
- Zoltan Simandi
- Sanford-Burnham-Prebys Medical Discovery Institute at Lake Nona
| | - Attila Horvath
- Department of Biochemistry and Molecular Biology, Research Center for Molecular Medicine, Medical and Health Science Center, University of Debrecen
| | - Peter Nagy
- Sanford-Burnham-Prebys Medical Discovery Institute at Lake Nona
| | - Laszlo Nagy
- Sanford-Burnham-Prebys Medical Discovery Institute at Lake Nona; Department of Biochemistry and Molecular Biology, Research Center for Molecular Medicine, Medical and Health Science Center, University of Debrecen; MTA-DE "Lendulet" Immunogenomics Research Group, University of Debrecen;
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42
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Chu H, Kohane DS, Langer R. RNA therapeutics - The potential treatment for myocardial infarction. Regen Ther 2016; 4:83-91. [PMID: 31245491 PMCID: PMC6581817 DOI: 10.1016/j.reth.2016.03.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 03/05/2016] [Accepted: 03/05/2016] [Indexed: 01/19/2023] Open
Abstract
RNA therapeutics mainly control gene expression at the transcript level. In contrast to conventional gene therapy which solely increases production of a protein, delivered RNAs can enhance, reduce or abolish synthesis of a particular protein, which control its relevant activities in a more diverse fashion. Thus, they hold promise to treat many human diseases including myocardial infarction (MI). MI is a serious health burden that causes substantial morbidity and mortality. An unmet clinical need for treating MI is the recovery of cardiac function, which requires regeneration of the functional tissues including the vasculature, nerves, and myocardium. Several classes of RNA therapeutics have been investigated in preclinical MI models, and the results have demonstrated their benefits and encourage their future development. In this review, we summarize the common RNA therapeutic approaches and highlight their application in MI therapy.
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Affiliation(s)
- Hunghao Chu
- Laboratory for Biomaterials and Drug Delivery, Department of Anesthesiology, Division of Critical Care Medicine, Children's Hospital Boston, Harvard Medical School, Boston, MA 02115, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Daniel S. Kohane
- Laboratory for Biomaterials and Drug Delivery, Department of Anesthesiology, Division of Critical Care Medicine, Children's Hospital Boston, Harvard Medical School, Boston, MA 02115, United States
| | - Robert Langer
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
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43
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Hou J, Zhou C, Long H, Zheng S, Guo T, Wu Q, Wu H, Zhong T, Wang T. Long noncoding RNAs: Novel molecules in cardiovascular biology, disease and regeneration. Exp Mol Pathol 2016; 100:493-501. [PMID: 27180105 DOI: 10.1016/j.yexmp.2016.05.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Revised: 04/19/2016] [Accepted: 05/10/2016] [Indexed: 12/22/2022]
Abstract
Remarkable breakthroughs made in genomic technologies have facilitated the discovery of thousands of novel transcripts that do not template protein synthesis. Numerous RNAs termed as long noncoding RNAs (lncRNAs) generated from this pervasive transcription function vividly in gene regulatory networks and a variety of biological and cellular processes. Here, we make a brief description of the known and putative functions of lncRNAs in cardiovascular biology and disease. The association between lncRNAs and stem cells mediated cardiomyocytes differentiation and neovascularization is discussed then. It will provide a new clue for further studies on these novel molecules in cardiovascular disease and bring bright prospects for their future applications in cardiac regenerative medicine.
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Affiliation(s)
- Jingying Hou
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, The Sun Yat-sen Memorial Hospital of Sun Yat-sen University, 107 Yanjiang Xi Road, Guangzhou, Guangdong 510120, China; Department of Emergency, The Sun Yat-sen Memorial Hospital of Sun Yat-sen University, 107 Yanjiang Xi Road, Guangzhou, Guangdong, China
| | - Changqing Zhou
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, The Sun Yat-sen Memorial Hospital of Sun Yat-sen University, 107 Yanjiang Xi Road, Guangzhou, Guangdong 510120, China; Department of Emergency, The Sun Yat-sen Memorial Hospital of Sun Yat-sen University, 107 Yanjiang Xi Road, Guangzhou, Guangdong, China
| | - Huibao Long
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, The Sun Yat-sen Memorial Hospital of Sun Yat-sen University, 107 Yanjiang Xi Road, Guangzhou, Guangdong 510120, China; Department of Emergency, The Sun Yat-sen Memorial Hospital of Sun Yat-sen University, 107 Yanjiang Xi Road, Guangzhou, Guangdong, China
| | - Shaoxin Zheng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, The Sun Yat-sen Memorial Hospital of Sun Yat-sen University, 107 Yanjiang Xi Road, Guangzhou, Guangdong 510120, China; Guangdong Province Key Laboratory of Arrhythmia and Electrophysiology, 107 Yanjiang Xi Road, Guangzhou, Guangdong, China
| | - Tianzhu Guo
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, The Sun Yat-sen Memorial Hospital of Sun Yat-sen University, 107 Yanjiang Xi Road, Guangzhou, Guangdong 510120, China; Department of Emergency, The Sun Yat-sen Memorial Hospital of Sun Yat-sen University, 107 Yanjiang Xi Road, Guangzhou, Guangdong, China
| | - Quanhua Wu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, The Sun Yat-sen Memorial Hospital of Sun Yat-sen University, 107 Yanjiang Xi Road, Guangzhou, Guangdong 510120, China; Department of Emergency, The Sun Yat-sen Memorial Hospital of Sun Yat-sen University, 107 Yanjiang Xi Road, Guangzhou, Guangdong, China
| | - Hao Wu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, The Sun Yat-sen Memorial Hospital of Sun Yat-sen University, 107 Yanjiang Xi Road, Guangzhou, Guangdong 510120, China; Department of Emergency, The Sun Yat-sen Memorial Hospital of Sun Yat-sen University, 107 Yanjiang Xi Road, Guangzhou, Guangdong, China
| | - Tingting Zhong
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, The Sun Yat-sen Memorial Hospital of Sun Yat-sen University, 107 Yanjiang Xi Road, Guangzhou, Guangdong 510120, China; Department of Emergency, The Sun Yat-sen Memorial Hospital of Sun Yat-sen University, 107 Yanjiang Xi Road, Guangzhou, Guangdong, China
| | - Tong Wang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, The Sun Yat-sen Memorial Hospital of Sun Yat-sen University, 107 Yanjiang Xi Road, Guangzhou, Guangdong 510120, China; Guangdong Province Key Laboratory of Arrhythmia and Electrophysiology, 107 Yanjiang Xi Road, Guangzhou, Guangdong, China; Department of Emergency, The Sun Yat-sen Memorial Hospital of Sun Yat-sen University, 107 Yanjiang Xi Road, Guangzhou, Guangdong, China.
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Qu Q, Fang F, Wu B, Hu Y, Chen M, Deng Z, Ma D, Chen T, Hao Y, Ge Y. Potential Role of Long Non-Coding RNA in Osteogenic Differentiation of Human Periodontal Ligament Stem Cells. J Periodontol 2016; 87:e127-37. [PMID: 26991483 DOI: 10.1902/jop.2016.150592] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) are emerging as important regulators of eukaryotic gene expression and have been shown to regulate various modular components of development and differentiation. However, the roles of lncRNAs in the regulation of osteogenic differentiation of human periodontal ligament stem cells (hPDLSCs) remain poorly understood. METHODS Expression patterns of lncRNA and messenger RNA (mRNA) during osteogenic differentiation were profiled using microarray analysis. Quantitative reverse transcription polymerase chain reaction was performed to validate the microarray data. Biologic functions of candidates were revealed by: 1) cluster analysis; 2) gene ontology (GO); and 3) pathway analysis. Coding-non-coding gene coexpression (CNC) networks were constructed to investigate potential regulatory roles of lncRNAs and osteogenesis-related mRNAs. RESULTS After osteoinduction, 3,557 mRNAs and 2,171 lncRNAs were differentially expressed, of which 994 lncRNAs were upregulated and 1,177 were downregulated (fold change >2.0 or <-2.0; P <0.05). Cluster analysis showed that lncRNAs and mRNAs from the experimental and control groups belonged to different clusters. GO analysis demonstrated that: 1) cellular process; 2) biologic regulation; and 3) regulation of biologic process were the most significant groups related to induction. Pathway analysis indicated that 83 pathways corresponded to differentially expressed mRNAs, including: 1) mitogen-activated protein kinase; 2) vascular endothelial growth factor; and 3) transforming growth factor-β signaling pathways. CNC network analysis indicated that 393 lncRNAs were closely related to osteogenesis-related mRNAs. CONCLUSIONS Expression profiles of lncRNAs and mRNAs were significantly altered during osteogenic differentiation of hPDLSCs. This result suggests that lncRNAs may play crucial roles in this process and could regulate mRNA expression.
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Affiliation(s)
- Qian Qu
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Fuchun Fang
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Buling Wu
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yanwei Hu
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University
| | - Ming Chen
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zilong Deng
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Dandan Ma
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ting Chen
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yilin Hao
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yihong Ge
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
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Fang Y, Fullwood MJ. Roles, Functions, and Mechanisms of Long Non-coding RNAs in Cancer. GENOMICS PROTEOMICS & BIOINFORMATICS 2016; 14:42-54. [PMID: 26883671 PMCID: PMC4792843 DOI: 10.1016/j.gpb.2015.09.006] [Citation(s) in RCA: 720] [Impact Index Per Article: 90.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 08/31/2015] [Accepted: 09/17/2015] [Indexed: 12/28/2022]
Abstract
Long non-coding RNAs (lncRNAs) play important roles in cancer. They are involved in chromatin remodeling, as well as transcriptional and post-transcriptional regulation, through a variety of chromatin-based mechanisms and via cross-talk with other RNA species. lncRNAs can function as decoys, scaffolds, and enhancer RNAs. This review summarizes the characteristics of lncRNAs, including their roles, functions, and working mechanisms, describes methods for identifying and annotating lncRNAs, and discusses future opportunities for lncRNA-based therapies using antisense oligonucleotides.
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Affiliation(s)
- Yiwen Fang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Melissa J Fullwood
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore; Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore; Yale-NUS Liberal Arts College, Singapore 138527, Singapore.
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Ounzain S, Pedrazzini T. Super-enhancer lncs to cardiovascular development and disease. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1863:1953-60. [PMID: 26620798 DOI: 10.1016/j.bbamcr.2015.11.026] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 11/20/2015] [Accepted: 11/23/2015] [Indexed: 01/12/2023]
Abstract
Cardiac development, function and pathological remodelling in response to stress depend on the dynamic control of tissue specific gene expression by distant acting transcriptional enhancers. Recently, super-enhancers (SEs), also known as stretch or large enhancer clusters, are emerging as sentinel regulators within the gene regulatory networks that underpin cellular functions. It is becoming increasingly evident that long noncoding RNAs (lncRNAs) associated with these sequences play fundamental roles for enhancer activity and the regulation of the gene programs hardwired by them. Here, we review this emerging landscape, focusing on the roles of SEs and their derived lncRNAs in cardiovascular development and disease. We propose that exploration of this genomic landscape could provide novel therapeutic targets and approaches for the amelioration of cardiovascular disease. Ultimately we envisage a future of ncRNA therapeutics targeting the SE landscape to alleviate cardiovascular disease. This article is part of a Special Issue entitled: Cardiomyocyte Biology: Integration of Developmental and Environmental Cues in the Heart edited by Marcus Schaub and Hughes Abriel.
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Affiliation(s)
- Samir Ounzain
- Experimental Cardiology Unit, Department of Medicine, University of Lausanne Medical School, Switzerland.
| | - Thierry Pedrazzini
- Experimental Cardiology Unit, Department of Medicine, University of Lausanne Medical School, Switzerland.
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47
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Breckwoldt K, Weinberger F, Eschenhagen T. Heart regeneration. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1863:1749-59. [PMID: 26597703 DOI: 10.1016/j.bbamcr.2015.11.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 11/06/2015] [Accepted: 11/12/2015] [Indexed: 01/14/2023]
Abstract
Regenerating an injured heart holds great promise for millions of patients suffering from heart diseases. Since the human heart has very limited regenerative capacity, this is a challenging task. Numerous strategies aiming to improve heart function have been developed. In this review we focus on approaches intending to replace damaged heart muscle by new cardiomyocytes. Different strategies for the production of cardiomyocytes from human embryonic stem cells or human induced pluripotent stem cells, by direct reprogramming and induction of cardiomyocyte proliferation are discussed regarding their therapeutic potential and respective advantages and disadvantages. Furthermore, different methods for the transplantation of pluripotent stem cell-derived cardiomyocytes are described and their clinical perspectives are discussed. This article is part of a Special Issue entitled: Cardiomyocyte Biology: Integration of Developmental and Environmental Cues in the Heart edited by Marcus Schaub and Hughes Abriel.
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Affiliation(s)
- Kaja Breckwoldt
- Department of Experimental Pharmacology and Toxicology, Cardiovascular Research Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Germany
| | - Florian Weinberger
- Center for Cardiovascular Biology, University of Washington, Seattle, WA 98109, USA
| | - Thomas Eschenhagen
- Department of Experimental Pharmacology and Toxicology, Cardiovascular Research Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Germany.
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48
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Ounzain S, Burdet F, Ibberson M, Pedrazzini T. Discovery and functional characterization of cardiovascular long noncoding RNAs. J Mol Cell Cardiol 2015; 89:17-26. [PMID: 26408097 DOI: 10.1016/j.yjmcc.2015.09.013] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 09/15/2015] [Accepted: 09/19/2015] [Indexed: 02/04/2023]
Abstract
Recent advances in sequencing and genomic technologies have resulted in the discovery of thousands of previously unannotated long noncoding RNAs (lncRNAs). However, their function in the cardiovascular system remains elusive. Here we review and discuss considerations for cardiovascular lncRNA discovery, annotation and functional characterization. Although we primarily focus on the heart, the proposed pipeline should foster functional and mechanistic exploration of these transcripts in various cardiovascular pathologies. Moreover, these insights could ultimately lead to novel therapeutic approaches targeting lncRNAs for the amelioration of cardiovascular diseases including heart failure.
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Affiliation(s)
- Samir Ounzain
- Experimental Cardiology Unit, Department of Medicine, University of Lausanne Medical School, Lausanne, Switzerland.
| | - Frédéric Burdet
- Vital-IT, Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Mark Ibberson
- Vital-IT, Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Thierry Pedrazzini
- Experimental Cardiology Unit, Department of Medicine, University of Lausanne Medical School, Lausanne, Switzerland.
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49
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Jeyabal P, Thandavarayan RA, Babu SS, Krishnamurthy P. Enhancer-associated long noncoding RNAs: A novel frontier with new perception in cardiac regeneration. Trends Cardiovasc Med 2015; 25:603-5. [PMID: 25812420 DOI: 10.1016/j.tcm.2015.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 02/18/2015] [Indexed: 11/16/2022]
Affiliation(s)
- Prince Jeyabal
- Department of Cardiovascular Sciences, Centre for Cardiovascular Regeneration, Houston Methodist Research Institute, Houston, TX
| | - Rajarajan A Thandavarayan
- Department of Cardiovascular Sciences, Centre for Cardiovascular Regeneration, Houston Methodist Research Institute, Houston, TX
| | - Sahana Suresh Babu
- Department of Cardiovascular Sciences, Centre for Cardiovascular Regeneration, Houston Methodist Research Institute, Houston, TX
| | - Prasanna Krishnamurthy
- Department of Cardiovascular Sciences, Centre for Cardiovascular Regeneration, Houston Methodist Research Institute, Houston, TX.
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