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Li H, Sun C, Luo B, Zhan C, Li W, Deng L, Kang K, Gou D. Exploring the Spectrum of Long Non-Coding RNA CARMN in Physiological and Pathological Contexts. Biomolecules 2024; 14:954. [PMID: 39199342 PMCID: PMC11353180 DOI: 10.3390/biom14080954] [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: 06/28/2024] [Revised: 07/27/2024] [Accepted: 08/02/2024] [Indexed: 09/01/2024] Open
Abstract
Cardiac mesoderm enhancer-associated non-coding RNA (CARMN), an evolutionarily conserved long non-coding RNA (lncRNA), serves as the host gene for the miR143/145 cluster. It plays a crucial role in cardiovascular cell differentiation and the maintenance of vascular smooth muscle cell (VSMC) homeostasis, which are vital for normal physiological processes. Specifically, CARMN is associated with the pathological progression of cardiovascular diseases such as atherosclerosis, abdominal aortic aneurysm, and chronic heart failure. Moreover, it acts as a tumor suppressor in various cancers, including hepatocellular carcinoma, bladder cancer, and breast cancer, highlighting its potential as a beneficial biomarker and therapeutic target. This review provides a detailed examination of the roles of CARMN, its evolutionary conservation, expression patterns, and regulatory mechanisms. It also outlines its significant implications in the diagnosis, prognosis, and treatment of these diseases, underscoring the need for further translational research to exploit its clinical potential.
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Affiliation(s)
- Hui Li
- Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518060, China; (H.L.); (C.S.); (B.L.); (C.Z.); (W.L.)
| | - Chuannan Sun
- Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518060, China; (H.L.); (C.S.); (B.L.); (C.Z.); (W.L.)
| | - Bin Luo
- Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518060, China; (H.L.); (C.S.); (B.L.); (C.Z.); (W.L.)
| | - Chuzhi Zhan
- Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518060, China; (H.L.); (C.S.); (B.L.); (C.Z.); (W.L.)
| | - Weitao Li
- Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518060, China; (H.L.); (C.S.); (B.L.); (C.Z.); (W.L.)
| | - Lu Deng
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Vascular Disease Research Center, College of Life Sciences and Oceanography, Guangdong Provincial Key Laboratory of Regional Immunity and Disease, Carson International Cancer Center, School of Medicine, Shenzhen University, Shenzhen 518060, China;
| | - Kang Kang
- Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518060, China; (H.L.); (C.S.); (B.L.); (C.Z.); (W.L.)
| | - Deming Gou
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Vascular Disease Research Center, College of Life Sciences and Oceanography, Guangdong Provincial Key Laboratory of Regional Immunity and Disease, Carson International Cancer Center, School of Medicine, Shenzhen University, Shenzhen 518060, China;
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Liu N, Jiang X, Zhang G, Long S, Li J, Jiang M, Jia G, Sun R, Zhang L, Zhang Y. LncRNA CARMN m6A demethylation by ALKBH5 inhibits mutant p53-driven tumour progression through miR-5683/FGF2. Clin Transl Med 2024; 14:e1777. [PMID: 39039912 PMCID: PMC11263751 DOI: 10.1002/ctm2.1777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 06/25/2024] [Accepted: 07/09/2024] [Indexed: 07/24/2024] Open
Abstract
N-methyladenosine (m6A) represents a prevalent RNA modification observed in colorectal cancer. Despite its abundance, the biological implications of m6A methylation on the lncRNA CARMN remain elusive in colorectal cancer, especially for mutant p53 gain-of-function. Here, we elucidate that CARMN exhibits diminished expression levels in colorectal cancer patients with mutant p53, attributed to its rich m6A methylation, which promotes cancer proliferation, invasion and metastasis in vitro and in vivo. Further investigation illustrates that ALKBH5 acts as a direct demethylase of CARMN, targeting 477 methylation sites, thereby preserving CARMN expression. However, the interaction of mutant p53 with the ALKBH5 promoter impedes its transcription, enhancing m6A methylation levels on CARMN. Subsequently, YTHDF2/YTHDF3 recognise and degrade m6A-modified CARMN. Concurrently, overexpressing CARMN significantly suppressed colorectal cancer progression in vitro and in vivo. Additionally, miR-5683 was identified as a direct downstream target of lncRNA CARMN, exerting an antitumour effect by cooperatively downregulating FGF2 expression. Our findings revealed the regulator and functional mechanism of CARMN in colorectal cancer with mutant p53, potentially offering insights into demethylation-based strategies for cancer diagnosis and therapy. The m6A methylation of CARMN that is prime for mutant p53 gain-of-function-induced malignant progression of colorectal cancer, identifying a promising approach for cancer therapy.
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Affiliation(s)
- Nannan Liu
- School of Biomedical SciencesHunan UniversityChangshaChina
| | - Xinxiu Jiang
- School of Biomedical SciencesHunan UniversityChangshaChina
| | - Ge Zhang
- Department of Laboratory MedicineThe Third Xiangya HospitalCentral South UniversityChangshaChina
- Department of GastroenterologyThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Shuaiyu Long
- Hebei Provincial Mental Health CenterHebei Key Laboratory of Major Mental and Behavioral DisordersThe Sixth Clinical Medical College of Hebei UniversityBaodingHebeiChina
| | - Jiehan Li
- Department of GastroenterologyThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Meimei Jiang
- School of Biomedical SciencesHunan UniversityChangshaChina
| | - Guiyun Jia
- School of Biomedical SciencesHunan UniversityChangshaChina
| | - Renyuan Sun
- Department of GastroenterologyThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Lingling Zhang
- Department of Laboratory MedicineThe Third Xiangya HospitalCentral South UniversityChangshaChina
| | - Yingjie Zhang
- School of Biomedical SciencesHunan UniversityChangshaChina
- Department of GastroenterologyHuadong Hospital, Shanghai Medical College, Fudan UniversityShanghaiP.R. China
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Brown SD, Klimi E, Bakker WAM, Beqqali A, Baker AH. Non-coding RNAs to treat vascular smooth muscle cell dysfunction. Br J Pharmacol 2024. [PMID: 38773733 DOI: 10.1111/bph.16409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 02/19/2024] [Accepted: 03/14/2024] [Indexed: 05/24/2024] Open
Abstract
Vascular smooth muscle cell (vSMC) dysfunction is a critical contributor to cardiovascular diseases, including atherosclerosis, restenosis and vein graft failure. Recent advances have unveiled a fascinating range of non-coding RNAs (ncRNAs) that play a pivotal role in regulating vSMC function. This review aims to provide an in-depth analysis of the mechanisms underlying vSMC dysfunction and the therapeutic potential of various ncRNAs in mitigating this dysfunction, either preventing or reversing it. We explore the intricate interplay of microRNAs, long-non-coding RNAs and circular RNAs, shedding light on their roles in regulating key signalling pathways associated with vSMC dysfunction. We also discuss the prospects and challenges associated with developing ncRNA-based therapies for this prevalent type of cardiovascular pathology.
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Affiliation(s)
- Simon D Brown
- BHF Centre for Cardiovascular Science, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Eftychia Klimi
- BHF Centre for Cardiovascular Science, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | | | - Abdelaziz Beqqali
- BHF Centre for Cardiovascular Science, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Andrew H Baker
- BHF Centre for Cardiovascular Science, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Centre, Maastricht, The Netherlands
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Liu S, Zhou H, Han D, Song H, Li Y, He S, Du Y, Wang K, Huang X, Li X, Huang Z. LncRNA CARMN inhibits abdominal aortic aneurysm formation and vascular smooth muscle cell phenotypic transformation by interacting with SRF. Cell Mol Life Sci 2024; 81:175. [PMID: 38597937 PMCID: PMC11006735 DOI: 10.1007/s00018-024-05193-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 04/11/2024]
Abstract
Phenotypic transformation of vascular smooth muscle cells (VSMCs) plays a crucial role in abdominal aortic aneurysm (AAA) formation. CARMN, a highly conserved, VSMC-enriched long noncoding RNA (lncRNA), is integral in orchestrating various vascular pathologies by modulating the phenotypic dynamics of VSMCs. The influence of CARMN on AAA formation, particularly its mechanisms, remains enigmatic. Our research, employing single-cell and bulk RNA sequencing, has uncovered a significant suppression of CARMN in AAA specimens, which correlates strongly with the contractile function of VSMCs. This reduced expression of CARMN was consistent in both 7- and 14-day porcine pancreatic elastase (PPE)-induced mouse models of AAA and in human clinical cases. Functional analyses disclosed that the diminution of CARMN exacerbated PPE-precipitated AAA formation, whereas its augmentation conferred protection against such formation. Mechanistically, we found CARMN's capacity to bind with SRF, thereby amplifying its role in driving the transcription of VSMC marker genes. In addition, our findings indicate an enhancement in CAMRN transcription, facilitated by the binding of NRF2 to its promoter region. Our study indicated that CARMN plays a protective role in preventing AAA formation and restrains the phenotypic transformation of VSMC through its interaction with SRF. Additionally, we observed that the expression of CARMN is augmented by NRF2 binding to its promoter region. These findings suggest the potential of CARMN as a viable therapeutic target in the treatment of AAA.
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Affiliation(s)
- Shenrong Liu
- Department of Cardiology, The Key Laboratory of Advanced Interdisciplinary Studies Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Haobin Zhou
- Department of Cardiology, The Key Laboratory of Advanced Interdisciplinary Studies Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Dunzheng Han
- Department of Cardiology, The Key Laboratory of Advanced Interdisciplinary Studies Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Haoyu Song
- Wards of Cadres, Zhuhai People's Hospital (Zhuhai Hospital Affiliated With Jinan University), Zhuhai, 519000, China
| | - Yuanqing Li
- Department of Cardiology, The Key Laboratory of Advanced Interdisciplinary Studies Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Shangfei He
- Department of Cardiology, The Key Laboratory of Advanced Interdisciplinary Studies Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Yipeng Du
- Department of Cardiology, The Key Laboratory of Advanced Interdisciplinary Studies Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Kai Wang
- Department of Cardiovascular Surgery, The Key Laboratory of Advanced Interdisciplinary Studies Center, The First Affiliated Hospital of Guangzhou Medical University, Guangdong, 510120, China
| | - Xingfu Huang
- Department of Cardiology, Nanfang Hospital, Southern Medical University, Guangzhou, 510400, Guangdong, China
| | - Xin Li
- Department of Emergency Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510400, Guangdong, China.
| | - Zheng Huang
- Department of Cardiology, The Key Laboratory of Advanced Interdisciplinary Studies Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China.
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Nemeth K, Bayraktar R, Ferracin M, Calin GA. Non-coding RNAs in disease: from mechanisms to therapeutics. Nat Rev Genet 2024; 25:211-232. [PMID: 37968332 DOI: 10.1038/s41576-023-00662-1] [Citation(s) in RCA: 71] [Impact Index Per Article: 71.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2023] [Indexed: 11/17/2023]
Abstract
Non-coding RNAs (ncRNAs) are a heterogeneous group of transcripts that, by definition, are not translated into proteins. Since their discovery, ncRNAs have emerged as important regulators of multiple biological functions across a range of cell types and tissues, and their dysregulation has been implicated in disease. Notably, much research has focused on the link between microRNAs (miRNAs) and human cancers, although other ncRNAs, such as long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs), are also emerging as relevant contributors to human disease. In this Review, we summarize our current understanding of the roles of miRNAs, lncRNAs and circRNAs in cancer and other major human diseases, notably cardiovascular, neurological and infectious diseases. Further, we discuss the potential use of ncRNAs as biomarkers of disease and as therapeutic targets.
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Affiliation(s)
- Kinga Nemeth
- Translational Molecular Pathology Department, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Recep Bayraktar
- Translational Molecular Pathology Department, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Manuela Ferracin
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy.
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy.
| | - George A Calin
- Translational Molecular Pathology Department, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- The RNA Interference and Non-coding RNA Center, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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Ramos TAR, Urquiza-Zurich S, Kim SY, Gillette TG, Hill JA, Lavandero S, do Rêgo TG, Maracaja-Coutinho V. Single-cell transcriptional landscape of long non-coding RNAs orchestrating mouse heart development. Cell Death Dis 2023; 14:841. [PMID: 38110334 PMCID: PMC10728149 DOI: 10.1038/s41419-023-06296-9] [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: 12/28/2022] [Revised: 10/18/2023] [Accepted: 11/13/2023] [Indexed: 12/20/2023]
Abstract
Long non-coding RNAs (lncRNAs) comprise the most representative transcriptional units of the mammalian genome. They are associated with organ development linked with the emergence of cardiovascular diseases. We used bioinformatic approaches, machine learning algorithms, systems biology analyses, and statistical techniques to define co-expression modules linked to heart development and cardiovascular diseases. We also uncovered differentially expressed transcripts in subpopulations of cardiomyocytes. Finally, from this work, we were able to identify eight cardiac cell-types; several new coding, lncRNA, and pcRNA markers; two cardiomyocyte subpopulations at four different time points (ventricle E9.5, left ventricle E11.5, right ventricle E14.5 and left atrium P0) that harbored co-expressed gene modules enriched in mitochondrial, heart development and cardiovascular diseases. Our results evidence the role of particular lncRNAs in heart development and highlight the usage of co-expression modular approaches in the cell-type functional definition.
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Grants
- R01 HL155765 NHLBI NIH HHS
- R01 HL126012 NHLBI NIH HHS
- R01 HL147933 NHLBI NIH HHS
- R01 HL128215 NHLBI NIH HHS
- R01 HL120732 NHLBI NIH HHS
- Agencia Nacional de Investigacion y Desarrollo (ANID, Chile), FONDAP 15130011 (SL), FONDECYT 1200490 (SL)
- the NIH: HL-120732 (JAH), HL-128215 (JAH), HL-126012 (JAH), HL-147933, (JAH), HL-155765 (JAH), 14SFRN20510023 (JAH), 14SFRN20670003 (JAH), Leducq grant number 11CVD04 (JAH), Cancer Prevention and Research Institute of Texas grant RP110486P3 (JAH)
- Agencia Nacional de Investigacion y Desarrollo (ANID, Chile), FONDAP 15130011 (VMC) and FONDECYT 1211731 (VMC).
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Affiliation(s)
- Thaís A R Ramos
- Advanced Center for Chronic Diseases (ACCDiS), Faculty of Chemical & Pharmaceutical Sciences & Faculty of Medicine, Universidad de Chile, Santiago, Chile
- Programa de Pós-Graduação em Bioinformática, Bioinformatics Multidisciplinary Environment (BioME), Instituto Metrópole Digital, Universidade Federal do Rio Grande do Norte, João Pessoa, Brazil
- Departamento de Informática, Centro de Informática, Universidade Federal da Paraíba, João Pessoa, Brazil
| | - Sebastián Urquiza-Zurich
- Advanced Center for Chronic Diseases (ACCDiS), Faculty of Chemical & Pharmaceutical Sciences & Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Soo Young Kim
- Division of Cardiology, Department of Internal Medicine, University of Texas Southwestern Medical Center Dallas, Dallas, TX, USA
| | - Thomas G Gillette
- Division of Cardiology, Department of Internal Medicine, University of Texas Southwestern Medical Center Dallas, Dallas, TX, USA
| | - Joseph A Hill
- Division of Cardiology, Department of Internal Medicine, University of Texas Southwestern Medical Center Dallas, Dallas, TX, USA
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sergio Lavandero
- Advanced Center for Chronic Diseases (ACCDiS), Faculty of Chemical & Pharmaceutical Sciences & Faculty of Medicine, Universidad de Chile, Santiago, Chile.
- Corporación Centro de Estudios Científicos de las Enfermedades Crónicas (CECEC), Santiago, Chile.
| | - Thaís G do Rêgo
- Programa de Pós-Graduação em Bioinformática, Bioinformatics Multidisciplinary Environment (BioME), Instituto Metrópole Digital, Universidade Federal do Rio Grande do Norte, João Pessoa, Brazil.
- Departamento de Informática, Centro de Informática, Universidade Federal da Paraíba, João Pessoa, Brazil.
| | - Vinicius Maracaja-Coutinho
- Advanced Center for Chronic Diseases (ACCDiS), Faculty of Chemical & Pharmaceutical Sciences & Faculty of Medicine, Universidad de Chile, Santiago, Chile.
- Programa de Pós-Graduação em Bioinformática, Bioinformatics Multidisciplinary Environment (BioME), Instituto Metrópole Digital, Universidade Federal do Rio Grande do Norte, João Pessoa, Brazil.
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Panagopoulos I, Andersen K, Brunetti M, Gorunova L, Kostolomov I, Kildal W, Hognestad HR, Lobmaier I, Micci F, Heim S. Pathogenetic Dichotomy in Angioleiomyoma. Cancer Genomics Proteomics 2023; 20:556-566. [PMID: 37889065 PMCID: PMC10614064 DOI: 10.21873/cgp.20405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/22/2023] [Accepted: 07/24/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND/AIM Angioleiomyoma is a benign tumor, occurs at any age, and arises most frequently in the lower extremities. Genetic information on angioleiomyomas is restricted to six reported abnormal karyotypes, losses in chromosome 22 and gains in Xq found by comparative genomic hybridization, and mutation analysis of notch receptor 2 (NOTCH2), NOTCH3, platelet-derived growth factor receptor beta (PDGFRB), and mediator complex subunit 12 (MED12) in a few tumors. Herein, we report the genetic findings in another three angioleiomyomas. MATERIALS AND METHODS The tumors were examined using G-banding and karyotyping, RNA sequencing, reverse transcription-polymerase chain reaction, Sanger sequencing, and expression analysis. RESULTS The first tumor carried a t(4;5)(p12;q32) translocation resulting in fusion of the cardiac mesoderm enhancer-associated non-coding RNA (CARMN in 5q32) with the TXK tyrosine kinase gene (TXK in 4p12) leading to overexpression of TXK. To our knowledge, this is the first time that a recurrent chromosome translocation and its resulting fusion gene have been described in angioleiomyomas. The second tumor carried a four-way translocation, t(X;3;4;16)(q22;p11;q11;p13) which fused the myosin heavy chain 11 gene (MYH11 in 16p13) with intergenic sequences from Xq22 that mapped a few kilobase pairs distal to the insulin receptor substrate 4 gene (IRS4), resulting in enhanced IRS4 expression. The third angioleiomyoma carried another rearrangement of chromosome band Xq22, t(X;9)(q22;q32), as the sole cytogenetic aberration, but no material was available for further molecular investigation. CONCLUSION Our data, together with previously reported abnormal karyotypes in angioleiomyomas, show the presence of two recurrent genetic pathways in this tumor type: The first is characterized by presence of the translocation t(4;5)(p12;q32), which generates a CARMN::TXK chimera. The second is recurrent rearrangement of Xq22 resulting in overexpression of IRS4.
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Affiliation(s)
- Ioannis Panagopoulos
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway;
| | - Kristin Andersen
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Marta Brunetti
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Ludmila Gorunova
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Ilyá Kostolomov
- Section for Applied Informatics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Wanja Kildal
- Section for Interphase Genetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | | | | | - Francesca Micci
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Sverre Heim
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
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Kałafut J, Czerwonka A, Czapla K, Przybyszewska-Podstawka A, Hermanowicz JM, Rivero-Müller A, Borkiewicz L. Regulation of Notch1 Signalling by Long Non-Coding RNAs in Cancers and Other Health Disorders. Int J Mol Sci 2023; 24:12579. [PMID: 37628760 PMCID: PMC10454443 DOI: 10.3390/ijms241612579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 07/30/2023] [Accepted: 08/05/2023] [Indexed: 08/27/2023] Open
Abstract
Notch1 signalling plays a multifaceted role in tissue development and homeostasis. Currently, due to the pivotal role of Notch1 signalling, the relationship between NOTCH1 expression and the development of health disorders is being intensively studied. Nevertheless, Notch1 signalling is not only controlled at the transcriptional level but also by a variety of post-translational events. First is the ligand-dependent mechanical activation of NOTCH receptors and then the intracellular crosstalk with other signalling molecules-among those are long non-coding RNAs (lncRNAs). In this review, we provide a detailed overview of the specific role of lncRNAs in the modulation of Notch1 signalling, from expression to activity, and their connection with the development of health disorders, especially cancers.
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Affiliation(s)
- Joanna Kałafut
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Aleje Raławickie 1, 20-059 Lublin, Poland; (J.K.); (A.C.); (K.C.); (A.P.-P.)
| | - Arkadiusz Czerwonka
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Aleje Raławickie 1, 20-059 Lublin, Poland; (J.K.); (A.C.); (K.C.); (A.P.-P.)
| | - Karolina Czapla
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Aleje Raławickie 1, 20-059 Lublin, Poland; (J.K.); (A.C.); (K.C.); (A.P.-P.)
| | - Alicja Przybyszewska-Podstawka
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Aleje Raławickie 1, 20-059 Lublin, Poland; (J.K.); (A.C.); (K.C.); (A.P.-P.)
| | - Justyna Magdalena Hermanowicz
- Department of Pharmacodynamics, Medical University of Bialystok, Mickiewicza 2C, 15-222 Bialystok, Poland;
- Department of Clinical Pharmacy, Medical University of Bialystok, Waszyngtona 15, 15-274 Bialystok, Poland
| | - Adolfo Rivero-Müller
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Aleje Raławickie 1, 20-059 Lublin, Poland; (J.K.); (A.C.); (K.C.); (A.P.-P.)
| | - Lidia Borkiewicz
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Aleje Raławickie 1, 20-059 Lublin, Poland; (J.K.); (A.C.); (K.C.); (A.P.-P.)
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He X, Dong K, Shen J, Hu G, Mintz JD, Atawia RT, Zhao J, Chen X, Caldwell RW, Xiang M, Stepp DW, Fulton DJ, Zhou J. The Long Noncoding RNA Cardiac Mesoderm Enhancer-Associated Noncoding RNA (Carmn) Is a Critical Regulator of Gastrointestinal Smooth Muscle Contractile Function and Motility. Gastroenterology 2023; 165:71-87. [PMID: 37030336 PMCID: PMC10330198 DOI: 10.1053/j.gastro.2023.03.229] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 03/15/2023] [Accepted: 03/20/2023] [Indexed: 04/10/2023]
Abstract
BACKGROUND & AIMS Visceral smooth muscle cells (SMCs) are an integral component of the gastrointestinal (GI) tract that regulate GI motility. SMC contraction is regulated by posttranslational signaling and the state of differentiation. Impaired SMC contraction is associated with significant morbidity and mortality, but the mechanisms regulating SMC-specific contractile gene expression, including the role of long noncoding RNAs (lncRNAs), remain largely unexplored. Herein, we reveal a critical role of Carmn (cardiac mesoderm enhancer-associated noncoding RNA), an SMC-specific lncRNA, in regulating visceral SMC phenotype and contractility of the GI tract. METHODS Genotype-Tissue Expression and publicly available single-cell RNA sequencing (scRNA-seq) data sets from embryonic, adult human, and mouse GI tissues were interrogated to identify SMC-specific lncRNAs. The functional role of Carmn was investigated using novel green fluorescent protein (GFP) knock-in (KI) reporter/knock-out (KO) mice. Bulk RNA-seq and single nucleus RNA sequencing (snRNA-seq) of colonic muscularis were used to investigate underlying mechanisms. RESULTS Unbiased in silico analyses and GFP expression patterns in Carmn GFP KI mice revealed that Carmn is highly expressed in GI SMCs in humans and mice. Premature lethality was observed in global Carmn KO and inducible SMC-specific KO mice due to GI pseudo-obstruction and severe distension of the GI tract, with dysmotility in cecum and colon segments. Histology, GI transit, and muscle myography analysis revealed severe dilation, significantly delayed GI transit, and impaired GI contractility in Carmn KO vs control mice. Bulk RNA-seq of GI muscularis revealed that loss of Carmn promotes SMC phenotypic switching, as evidenced by up-regulation of extracellular matrix genes and down-regulation of SMC contractile genes, including Mylk, a key regulator of SMC contraction. snRNA-seq further revealed SMC Carmn KO not only compromised myogenic motility by reducing contractile gene expression but also impaired neurogenic motility by disrupting cell-cell connectivity in the colonic muscularis. These findings may have translational significance, because silencing CARMN in human colonic SMCs significantly attenuated contractile gene expression, including MYLK, and decreased SMC contractility. Luciferase reporter assays showed that CARMN enhances the transactivation activity of the master regulator of SMC contractile phenotype, myocardin, thereby maintaining the GI SMC myogenic program. CONCLUSIONS Our data suggest that Carmn is indispensable for maintaining GI SMC contractile function in mice and that loss of function of CARMN may contribute to human visceral myopathy. To our knowledge this is the first study showing an essential role of lncRNA in the regulation of visceral SMC phenotype.
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Affiliation(s)
- Xiangqin He
- Department of Pharmacology & Toxicology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Kunzhe Dong
- Department of Pharmacology & Toxicology, Medical College of Georgia, Augusta University, Augusta, Georgia; Immunology Center of Georgia, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Jian Shen
- Department of Pharmacology & Toxicology, Medical College of Georgia, Augusta University, Augusta, Georgia; Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Guoqing Hu
- Department of Pharmacology & Toxicology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - James D Mintz
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Reem T Atawia
- Department of Pharmacology & Toxicology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Juanjuan Zhao
- Department of Pharmacology & Toxicology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Xiuxu Chen
- Department of Pathology and Laboratory Medicine, Loyola University Health System, Maywood, Illinois
| | - Robert W Caldwell
- Department of Pharmacology & Toxicology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Meixiang Xiang
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - David W Stepp
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, Georgia; Department of Physiology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - David J Fulton
- Department of Pharmacology & Toxicology, Medical College of Georgia, Augusta University, Augusta, Georgia; Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Jiliang Zhou
- Department of Pharmacology & Toxicology, Medical College of Georgia, Augusta University, Augusta, Georgia.
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10
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Plaisance I, Chouvardas P, Sun Y, Nemir M, Aghagolzadeh P, Aminfar F, Shen S, Shim WJ, Rochais F, Johnson R, Palpant N, Pedrazzini T. A transposable element into the human long noncoding RNA CARMEN is a switch for cardiac precursor cell specification. Cardiovasc Res 2023; 119:1361-1376. [PMID: 36537036 PMCID: PMC10262180 DOI: 10.1093/cvr/cvac191] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 10/20/2022] [Accepted: 11/04/2022] [Indexed: 03/25/2024] Open
Abstract
AIMS The major cardiac cell types composing the adult heart arise from common multipotent precursor cells. Cardiac lineage decisions are guided by extrinsic and cell-autonomous factors, including recently discovered long noncoding RNAs (lncRNAs). The human lncRNA CARMEN, which is known to dictate specification toward the cardiomyocyte (CM) and the smooth muscle cell (SMC) fates, generates a diversity of alternatively spliced isoforms. METHODS AND RESULTS The CARMEN locus can be manipulated to direct human primary cardiac precursor cells (CPCs) into specific cardiovascular fates. Investigating CARMEN isoform usage in differentiating CPCs represents therefore a unique opportunity to uncover isoform-specific functions in lncRNAs. Here, we identify one CARMEN isoform, CARMEN-201, to be crucial for SMC commitment. CARMEN-201 activity is encoded within an alternatively spliced exon containing a MIRc short interspersed nuclear element. This element binds the transcriptional repressor REST (RE1 Silencing Transcription Factor), targets it to cardiogenic loci, including ISL1, IRX1, IRX5, and SFRP1, and thereby blocks the CM gene program. In turn, genes regulating SMC differentiation are induced. CONCLUSIONS These data show how a critical physiological switch is wired by alternative splicing and functional transposable elements in a long noncoding RNA. They further demonstrated the crucial importance of the lncRNA isoform CARMEN-201 in SMC specification during heart development.
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Affiliation(s)
- Isabelle Plaisance
- Experimental Cardiology Unit, Division of Cardiology, University of Lausanne Medical School, Lausanne, Switzerland
| | | | - Yuliangzi Sun
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Mohamed Nemir
- Experimental Cardiology Unit, Division of Cardiology, University of Lausanne Medical School, Lausanne, Switzerland
| | - Parisa Aghagolzadeh
- Experimental Cardiology Unit, Division of Cardiology, University of Lausanne Medical School, Lausanne, Switzerland
| | - Farhang Aminfar
- Experimental Cardiology Unit, Division of Cardiology, University of Lausanne Medical School, Lausanne, Switzerland
| | - Sophie Shen
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Woo Jun Shim
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Francesca Rochais
- Aix Marseille University, Marseille Medical Genetics, INSERM, U1251, Marseille, France
| | - Rory Johnson
- Department of Medical Oncology, Inselspital, University of Bern, Bern, Switzerland
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Nathan Palpant
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Thierry Pedrazzini
- Experimental Cardiology Unit, Division of Cardiology, University of Lausanne Medical School, Lausanne, Switzerland
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11
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Vazgiourakis VM, Zervou MI, Papageorgiou L, Chaniotis D, Spandidos DA, Vlachakis D, Eliopoulos E, Goulielmos GN. Association of endometriosis with cardiovascular disease: Genetic aspects (Review). Int J Mol Med 2023; 51:29. [PMID: 36799179 PMCID: PMC9943539 DOI: 10.3892/ijmm.2023.5232] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 02/07/2023] [Indexed: 02/17/2023] Open
Abstract
Cardiovascular disease (CVD) comprises a broad spectrum of pathological conditions that affect the heart or blood vessels, including sequelae that arise from damaged vasculature in other organs of the body, such as the brain, kidneys or eyes. Atherosclerosis is a chronic inflammatory disease of the arterial intima and is the primary cause of coronary artery disease, peripheral vascular disease, heart attack, stroke and renal pathology. It represents a leading cause of mortality worldwide and the loss of human productivity that is marked by an altered immune response. Endometriosis is a heritable, heterogeneous, common gynecological condition influenced by multiple genetic, epigenetic and environmental factors, affecting up to 10% of the female population of childbearing age, causing pain and infertility; it is characterized by the ectopic growth of endometrial tissue outside the uterine cavity. Of note, epidemiological data obtained thus far have suggested a link between endometriosis and the risk of developing CVD. The similarities observed in specific molecular and cellular pathways of endometriosis and CVD may be partially explained by a shared genetic background. The present review presents and discusses the shared genetic factors which have been reported to be associated with the development of both disorders.
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Affiliation(s)
- Vassilios M. Vazgiourakis
- Intensive Care Unit, University Hospital of Larissa, University of Thessaly, Faculty of Medicine, 41110 Larissa, Greece
| | - Maria I. Zervou
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine, School of Medicine, University of Crete, 71403 Heraklion, Greece,Correspondence to: Dr Maria I. Zervou, Section of Molecular Pathology and Human Genetics, Department of Internal Medicine, School of Medicine, University of Crete, University Campus of Voutes, 71403 Heraklion, Greece, E-mail:
| | - Louis Papageorgiou
- Department of Biomedical Sciences, School of Health and Care Sciences, University of West Attica, 12243 Athens, Greece,Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Dimitrios Chaniotis
- Department of Biomedical Sciences, School of Health and Care Sciences, University of West Attica, 12243 Athens, Greece
| | - Demetrios A. Spandidos
- Laboratory of Clinical Virology, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Dimitrios Vlachakis
- Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Elias Eliopoulos
- Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - George N. Goulielmos
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine, School of Medicine, University of Crete, 71403 Heraklion, Greece,Department of Internal Medicine, University Hospital of Heraklion, 71500 Heraklion, Greece
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12
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Nemir M, Kay M, Maison D, Berthonneche C, Sarre A, Plaisance I, Pedrazzini T. Inhibition of the NOTCH1 Pathway in the Stressed Heart Limits Fibrosis and Promotes Recruitment of Non-Myocyte Cells into the Cardiomyocyte Fate. J Cardiovasc Dev Dis 2022; 9:jcdd9040111. [PMID: 35448087 PMCID: PMC9024539 DOI: 10.3390/jcdd9040111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 04/04/2022] [Accepted: 04/06/2022] [Indexed: 12/10/2022] Open
Abstract
Cardiac pathologies lead to an acute or gradual loss of cardiomyocytes. Because of the limited regenerative capacity of the mammalian heart, cardiomyocytes are only replaced by fibrotic tissue. Excessive fibrosis contributes to the deterioration of cardiac function and the transition to heart failure, which is the leading cause of morbidity and mortality worldwide. Currently, no treatments can promote replenishment of the injured heart with newly formed cardiomyocytes. In this context, regenerative strategies explore the possibility to promote recovery through induction of cardiomyocyte production from pre-existing cardiomyocytes. On the other hand, cardiac non-myocyte cells can be directly reprogrammed into induced cardiac precursor cells and cardiomyocytes, suggesting that these cells could be exploited to produce cardiomyocytes in vivo. Here, we provide evidence that the sequential activation and inhibition of the NOTCH1 signaling pathway in the stressed heart decreases fibrosis and improves cardiac function in the stressed heart. This is accompanied by the emergence of new cardiomyocytes from non-myocyte origin. Overall, our data show how a developmental pathway such as the NOTCH pathway can be manipulated to provide therapeutic benefit in the damaged heart.
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Affiliation(s)
- Mohamed Nemir
- Experimental Cardiology Unit, Division of Cardiology, Department of Cardiovascular Medicine, University of Lausanne Medical School, 1011 Lausanne, Switzerland; (M.N.); (M.K.); (D.M.); (I.P.)
| | - Maryam Kay
- Experimental Cardiology Unit, Division of Cardiology, Department of Cardiovascular Medicine, University of Lausanne Medical School, 1011 Lausanne, Switzerland; (M.N.); (M.K.); (D.M.); (I.P.)
| | - Damien Maison
- Experimental Cardiology Unit, Division of Cardiology, Department of Cardiovascular Medicine, University of Lausanne Medical School, 1011 Lausanne, Switzerland; (M.N.); (M.K.); (D.M.); (I.P.)
| | - Corinne Berthonneche
- Cardiovascular Assessment Facility, University of Lausanne, 1011 Lausanne, Switzerland; (C.B.); (A.S.)
| | - Alexandre Sarre
- Cardiovascular Assessment Facility, University of Lausanne, 1011 Lausanne, Switzerland; (C.B.); (A.S.)
| | - Isabelle Plaisance
- Experimental Cardiology Unit, Division of Cardiology, Department of Cardiovascular Medicine, University of Lausanne Medical School, 1011 Lausanne, Switzerland; (M.N.); (M.K.); (D.M.); (I.P.)
| | - Thierry Pedrazzini
- Experimental Cardiology Unit, Division of Cardiology, Department of Cardiovascular Medicine, University of Lausanne Medical School, 1011 Lausanne, Switzerland; (M.N.); (M.K.); (D.M.); (I.P.)
- Correspondence: ; Tel.: +41-21-314-0765
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13
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Gu W, Jiang X, Wang W, Mujagond P, Liu J, Mai Z, Tang H, li S, Xiao H, Zhao J. Super-Enhancer-Associated Long Non-Coding RNA LINC01485 Promotes Osteogenic Differentiation of Human Bone Marrow Mesenchymal Stem Cells by Regulating MiR-619-5p/RUNX2 Axis. Front Endocrinol (Lausanne) 2022; 13:846154. [PMID: 35663324 PMCID: PMC9161675 DOI: 10.3389/fendo.2022.846154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 04/05/2022] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVE To investigate the mechanisms of super-enhancer-associated LINC01485/miR-619-5p/RUNX2 signaling axis involvement in osteogenic differentiation of human bone marrow mesenchymal stem cells (hBMSCs). METHODS Osteogenic differentiation of hBMSCs was induced in vitro. The expression levels of LINC01485 and miR-619-5p during osteogenesis were measured using quantitative real-time polymerase chain reaction (qRT-PCR). Osteogenic differentiation was examined by qRT-PCR, western blot, alkaline phosphatase (ALP) staining, ALP activity measurement, and Alizarin Red S (ARS) staining assays. Thereafter, the effects of LINC01485 and miR-619-5p on osteogenic differentiation of hBMSCs were evaluated by performing loss- and gain-of-function experiments. Subsequently, a fluorescence in situ hybridization (FISH) assay was employed to determine the cellular localization of LINC01485. Bioinformatics analysis, RNA antisense purification (RAP) assay, and dual-luciferase reporter assays were conducted to analyze the interactions of LINC01485, miR-619-5p, and RUNX2. Rescue experiments were performed to further delineate the role of the competitive endogenous RNA (ceRNA) signaling axis consisting of LINC01485/miR-619-5p/RUNX2 in osteogenic differentiation of hBMSCs. RESULTS The expression of LINC01485 was up-regulated during osteogenic differentiation of hBMSCs. The overexpression of LINC01485 promoted osteogenic differentiation of hBMSCs by up-regulating the expression of osteogenesis-related genes [e.g., runt-related transcription factor 2 (RUNX2), osterix (OSX), collagen type 1 alpha 1 (COL1A1), osteocalcin (OCN), and osteopontin (OPN)], and increasing the activity of ALP. ALP staining and ARS staining were also found to be increased upon overexpression of LINC01485. The opposing results were obtained upon LINC01485 interference in hBMSCs. miR-619-5p was found to inhibit osteogenic differentiation. FISH assay displayed that LINC01485 was mainly localized in the cytoplasm. RAP assay results showed that LINC01485 bound to miR-619-5p, and dual-luciferase reporter assay verified that LINC01485 bound to miR-619-5p, while miR-619-5p and RUNX2 bound to each other. Rescue experiments illustrated that LINC01485 could promote osteogenesis by increasing RUNX2 expression by sponging miR-619-5p. CONCLUSION LINC01485 could influence RUNX2 expression by acting as a ceRNA of miR-619-5p, thereby promoting osteogenic differentiation of hBMSCs. The LINC01485/miR-619-5p/RUNX2 axis might comprise a novel target in the bone tissue engineering field.
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Affiliation(s)
- Wenli Gu
- Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Xiao Jiang
- Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Wei Wang
- Stomatological Hospital, Southern Medical University, Guangzhou, China
| | | | - Jingpeng Liu
- Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Zhaoyi Mai
- Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Hai Tang
- Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Simin li
- Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Hui Xiao
- Stomatological Hospital, Southern Medical University, Guangzhou, China
- *Correspondence: Hui Xiao, ; Jianjiang Zhao,
| | - Jianjiang Zhao
- Shenzhen Stomatological Hospital, Southern Medical University, Shenzhen, China
- *Correspondence: Hui Xiao, ; Jianjiang Zhao,
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14
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Dong K, Shen J, He X, Hu G, Wang L, Osman I, Bunting KM, Dixon-Melvin R, Zheng Z, Xin H, Xiang M, Vazdarjanova A, Fulton DJR, Zhou J. CARMN Is an Evolutionarily Conserved Smooth Muscle Cell-Specific LncRNA That Maintains Contractile Phenotype by Binding Myocardin. Circulation 2021; 144:1856-1875. [PMID: 34694145 PMCID: PMC8726016 DOI: 10.1161/circulationaha.121.055949] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Vascular homeostasis is maintained by the differentiated phenotype of vascular smooth muscle cells (VSMCs). The landscape of protein coding genes comprising the transcriptome of differentiated VSMCs has been intensively investigated but many gaps remain including the emerging roles of noncoding genes. METHODS We reanalyzed large-scale, publicly available bulk and single-cell RNA sequencing datasets from multiple tissues and cell types to identify VSMC-enriched long noncoding RNAs. The in vivo expression pattern of a novel smooth muscle cell (SMC)-expressed long noncoding RNA, Carmn (cardiac mesoderm enhancer-associated noncoding RNA), was investigated using a novel Carmn green fluorescent protein knock-in reporter mouse model. Bioinformatics and quantitative real-time polymerase chain reaction analysis were used to assess CARMN expression changes during VSMC phenotypic modulation in human and murine vascular disease models. In vitro, functional assays were performed by knocking down CARMN with antisense oligonucleotides and overexpressing Carmn by adenovirus in human coronary artery SMCs. Carotid artery injury was performed in SMC-specific Carmn knockout mice to assess neointima formation and the therapeutic potential of reversing CARMN loss was tested in a rat carotid artery balloon injury model. The molecular mechanisms underlying CARMN function were investigated using RNA pull-down, RNA immunoprecipitation, and luciferase reporter assays. RESULTS We identified CARMN, which was initially annotated as the host gene of the MIR143/145 cluster and recently reported to play a role in cardiac differentiation, as a highly abundant and conserved, SMC-specific long noncoding RNA. Analysis of the Carmn GFP knock-in mouse model confirmed that Carmn is transiently expressed in embryonic cardiomyocytes and thereafter becomes restricted to SMCs. We also found that Carmn is transcribed independently of Mir143/145. CARMN expression is dramatically decreased by vascular disease in humans and murine models and regulates the contractile phenotype of VSMCs in vitro. In vivo, SMC-specific deletion of Carmn significantly exacerbated, whereas overexpression of Carmn markedly attenuated, injury-induced neointima formation in mouse and rat, respectively. Mechanistically, we found that Carmn physically binds to the key transcriptional cofactor myocardin, facilitating its activity and thereby maintaining the contractile phenotype of VSMCs. CONCLUSIONS CARMN is an evolutionarily conserved SMC-specific long noncoding RNA with a previously unappreciated role in maintaining the contractile phenotype of VSMCs and is the first noncoding RNA discovered to interact with myocardin.
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Affiliation(s)
- Kunzhe Dong
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, Georgia, 30912, USA
| | - Jian Shen
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, Georgia, 30912, USA
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, 310009, China
| | - Xiangqin He
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, Georgia, 30912, USA
| | - Guoqing Hu
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, Georgia, 30912, USA
| | - Liang Wang
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, Georgia, 30912, USA
- Department of Cardiology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, China
| | - Islam Osman
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, Georgia, 30912, USA
| | - Kristopher M. Bunting
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, Georgia, 30912, USA
| | - Rachael Dixon-Melvin
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, Georgia, 30912, USA
| | - Zeqi Zheng
- Department of Cardiology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, China
| | - Hongbo Xin
- The National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational Medicine, Nanchang University, Nanchang, Jiangxi, 330031, China
- School of Life Sciences, Nanchang University, Nanchang, Jiangxi, 330031, China
| | - Meixiang Xiang
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, 310009, China
| | - Almira Vazdarjanova
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, Georgia, 30912, USA
| | - David J. R. Fulton
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, Georgia, 30912, USA
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, Georgia, 30912, USA
| | - Jiliang Zhou
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, Georgia, 30912, USA
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15
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Cable J, Heard E, Hirose T, Prasanth KV, Chen LL, Henninger JE, Quinodoz SA, Spector DL, Diermeier SD, Porman AM, Kumar D, Feinberg MW, Shen X, Unfried JP, Johnson R, Chen CK, Wilusz JE, Lempradl A, McGeary SE, Wahba L, Pyle AM, Hargrove AE, Simon MD, Marcia M, Przanowska RK, Chang HY, Jaffrey SR, Contreras LM, Chen Q, Shi J, Mendell JT, He L, Song E, Rinn JL, Lalwani MK, Kalem MC, Chuong EB, Maquat LE, Liu X. Noncoding RNAs: biology and applications-a Keystone Symposia report. Ann N Y Acad Sci 2021; 1506:118-141. [PMID: 34791665 PMCID: PMC9808899 DOI: 10.1111/nyas.14713] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 10/06/2021] [Indexed: 01/07/2023]
Abstract
The human transcriptome contains many types of noncoding RNAs, which rival the number of protein-coding species. From long noncoding RNAs (lncRNAs) that are over 200 nucleotides long to piwi-interacting RNAs (piRNAs) of only 20 nucleotides, noncoding RNAs play important roles in regulating transcription, epigenetic modifications, translation, and cell signaling. Roles for noncoding RNAs in disease mechanisms are also being uncovered, and several species have been identified as potential drug targets. On May 11-14, 2021, the Keystone eSymposium "Noncoding RNAs: Biology and Applications" brought together researchers working in RNA biology, structure, and technologies to accelerate both the understanding of RNA basic biology and the translation of those findings into clinical applications.
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Affiliation(s)
| | - Edith Heard
- European Molecular Biology Laboratory (EMBL), Heidelberg, Heidelberg, Germany
- Collège de France, Paris, France
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
- Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
| | - Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of the Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- School of Life Sciences, Hangzhou Institute for Advanced Study, University of the Chinese Academy of Sciences, Hangzhou, China
| | | | - Sofia A Quinodoz
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey
| | - David L Spector
- Cold Spring Harbor Laboratory, Cold Spring Harbor and Genetics Program, Stony Brook University, Stony Brook, New York
| | - Sarah D Diermeier
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Allison M Porman
- Biochemistry and Molecular Genetics Department, University of Colorado, Anschutz Medical Campus, Aurora, Colorado
| | - Dhiraj Kumar
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Mark W Feinberg
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Xiaohua Shen
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, China
| | - Juan Pablo Unfried
- Center for Applied Medical Research (CIMA), Department of Gene Therapy and Regulation of Gene Expression, Universidad de Navarra (UNAV), Pamplona, Spain
| | - Rory Johnson
- Department of Medical Oncology, Inselspital, Bern University Hospital; and Department for BioMedical Research University of Bern, Bern, Switzerland
- School of Biology and Environmental Science and Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Chun-Kan Chen
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Jeremy E Wilusz
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Adelheid Lempradl
- Department of Metabolism and Nutritional Programming, Van Andel Research Institute, Grand Rapids, Michigan
| | - Sean E McGeary
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts
- Howard Hughes Medical Institute and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Lamia Wahba
- Department of Genetics, Stanford University School of Medicine, Stanford, California
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Anna Marie Pyle
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut
- Connecticut and Howard Hughes Medical Institute, Chevy Chase, Maryland
| | | | - Matthew D Simon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut
| | - Marco Marcia
- European Molecular Biology Laboratory (EMBL) Grenoble, Grenoble, France
| | - Róża K Przanowska
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California
- Howard Hughes Medical Institute, Stanford University, Stanford, California
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Medical College of Cornell University, New York, New York
| | - Lydia M Contreras
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas
| | - Qi Chen
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, California
| | - Junchao Shi
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, California
| | - Joshua T Mendell
- Department of Molecular Biology, Harold C. Simmons Comprehensive Cancer Center, Hamon Center for Regenerative Science and Medicine; and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Lin He
- Division of Cellular and Developmental Biology, Molecular and Cell Biology Department, University of California at Berkeley, Berkeley, California
| | - Erwei Song
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center and Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Bioland Laboratory; Program of Molecular Medicine, Zhongshan School of Medicine, Sun Yat-sen University; and Fountain-Valley Institute for Life Sciences, Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences Guangzhou, Guangzhou, China
| | - John L Rinn
- Department of Biochemistry, BioFrontiers Institute, and Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, Colorado
| | - Mukesh Kumar Lalwani
- Queens Medical Research Institute, BHF Centre for Cardiovascular Sciences, University of Edinburgh, Scotland, United Kingdom
| | - Murat Can Kalem
- Department of Microbiology and Immunology, Witebsky Center for Microbial Pathogenesis and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, SUNY, Buffalo, New York
| | - Edward B Chuong
- Department of Molecular, Cellular, and Developmental Biology and BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry and Center for RNA Biology, University of Rochester, Rochester, New York
| | - Xuhang Liu
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, New York
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16
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Thankam FG, Agrawal DK. Single Cell Genomics Identifies Unique Cardioprotective Phenotype of Stem Cells derived from Epicardial Adipose Tissue under Ischemia. Stem Cell Rev Rep 2021; 18:294-335. [PMID: 34661829 DOI: 10.1007/s12015-021-10273-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2021] [Indexed: 12/21/2022]
Abstract
The conventional management strategies of myocardial infarction (MI) are effective to sustain life; however, myocardial regeneration has not been achieved owing to the inherently poor regenerative capacity of the native myocardium. Stem cell-based therapies are promising; however, lineage specificity and undesired differentiation profile are challenging. Herein, we focused on the epicardial fat (EF) as an ideal source for mesenchymal stem cells (MSCs) owing to the proximity and same microvasculature with cardiac muscle. Unfortunately, the epicardial adipose tissue derived stem cells (EATDS) remain understudied regarding their phenotype heterogeneity and cardiac regeneration potential. As EF closely reflects the cardiac pathology during ischemia, the present study aims to determine the EATDS subpopulations under simulated ischemic and reperfused conditions employing single cell RNA sequencing (scRNAseq). EATDS were isolated from three hyperlipidemic Yucatan microswine and were divided into Control, Ischemia (ISC), and Ischemia/reperfusion (ISC/R). The scRNAseq analysis was performed using 10 genomics platform which revealed 18 unique cell clusters suggesting the existence of heterogeneous phenotypes. The upregulated genes were taken into consideration and subsequent functional assessment revealed the cardioprotective phenotypes with diverse mechanisms including epigenetic regulation (Cluster 1), myocardial homeostasis (Cluster 1), cell integrity and cell cycle (Clusters 2 and 3), prevention of fibroblast differentiation (Cluster 4), differentiation to myocardial lineage (Cluster 6), anti-inflammatory responses (Clusters 5, 8, and 11), prevention of ER-stress (Cluster 9), and increasing the energy metabolism (Cluster 10). These unique phenotypes of heterogeneous EATDS population open significant translational opportunities for myocardial regeneration and cardiac management.
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Affiliation(s)
- Finosh G Thankam
- Department of Translational Research, Western University of Health Sciences, 309 E. Second Street, Pomona, CA, 91766-1854, USA.
| | - Devendra K Agrawal
- Department of Translational Research, Western University of Health Sciences, 309 E. Second Street, Pomona, CA, 91766-1854, USA
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17
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Vacante F, Rodor J, Lalwani MK, Mahmoud AD, Bennett M, De Pace AL, Miller E, Van Kuijk K, de Bruijn J, Gijbels M, Williams TC, Clark MB, Scanlon JP, Doran AC, Montgomery R, Newby DE, Giacca M, O'Carroll D, Hadoke PWF, Denby L, Sluimer JC, Baker AH. CARMN Loss Regulates Smooth Muscle Cells and Accelerates Atherosclerosis in Mice. Circ Res 2021; 128:1258-1275. [PMID: 33622045 DOI: 10.1161/circresaha.120.318688] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Francesca Vacante
- Queens Medical Research Institute, BHF Centre for Cardiovascular Sciences (F.V., J.R., M.K.L., A.D.M., M.B., E.M., J.P.S., D.E.N., P.W.F.H., L.D., J.C.S., A.H.B.), University of Edinburgh, Scotland
| | - Julie Rodor
- Queens Medical Research Institute, BHF Centre for Cardiovascular Sciences (F.V., J.R., M.K.L., A.D.M., M.B., E.M., J.P.S., D.E.N., P.W.F.H., L.D., J.C.S., A.H.B.), University of Edinburgh, Scotland
| | - Mukesh K Lalwani
- Queens Medical Research Institute, BHF Centre for Cardiovascular Sciences (F.V., J.R., M.K.L., A.D.M., M.B., E.M., J.P.S., D.E.N., P.W.F.H., L.D., J.C.S., A.H.B.), University of Edinburgh, Scotland
| | - Amira D Mahmoud
- Queens Medical Research Institute, BHF Centre for Cardiovascular Sciences (F.V., J.R., M.K.L., A.D.M., M.B., E.M., J.P.S., D.E.N., P.W.F.H., L.D., J.C.S., A.H.B.), University of Edinburgh, Scotland
| | - Matthew Bennett
- Queens Medical Research Institute, BHF Centre for Cardiovascular Sciences (F.V., J.R., M.K.L., A.D.M., M.B., E.M., J.P.S., D.E.N., P.W.F.H., L.D., J.C.S., A.H.B.), University of Edinburgh, Scotland
| | - Azzurra L De Pace
- Institute for Regeneration and Repair, Centre for Regenerative Medicine (A.D.P., D.O.), University of Edinburgh, Scotland
| | - Eileen Miller
- Queens Medical Research Institute, BHF Centre for Cardiovascular Sciences (F.V., J.R., M.K.L., A.D.M., M.B., E.M., J.P.S., D.E.N., P.W.F.H., L.D., J.C.S., A.H.B.), University of Edinburgh, Scotland
| | - Kim Van Kuijk
- Pathology, Maastricht Medical Center, the Netherlands (K.V.K., J.d., J.C.S., A.H.B.)
| | - Jenny de Bruijn
- Pathology, Maastricht Medical Center, the Netherlands (K.V.K., J.d., J.C.S., A.H.B.)
| | - Marion Gijbels
- Pathology CARIM, Cardiovascular Research Institute Maastricht, GROW-School for Oncology and Developmental Biology, Maastricht University, the Netherlands (M. Gijbels)
| | - Thomas C Williams
- Insitute of Genetics and Molecular Medicine (T.C.W.), University of Edinburgh, Scotland
| | - Michael B Clark
- Centre for Stem Cell Systems, Department of Anatomy and Neuroscience, The University of Melbourne, Australia (M.B.C.)
| | - Jessica P Scanlon
- Queens Medical Research Institute, BHF Centre for Cardiovascular Sciences (F.V., J.R., M.K.L., A.D.M., M.B., E.M., J.P.S., D.E.N., P.W.F.H., L.D., J.C.S., A.H.B.), University of Edinburgh, Scotland
| | - Amanda C Doran
- Medicine, Vanderbilt University Medical Center, Nashville, Tennessee (A.C.D)
| | | | - David E Newby
- Queens Medical Research Institute, BHF Centre for Cardiovascular Sciences (F.V., J.R., M.K.L., A.D.M., M.B., E.M., J.P.S., D.E.N., P.W.F.H., L.D., J.C.S., A.H.B.), University of Edinburgh, Scotland
| | - Mauro Giacca
- Medical Biochemistry, Experimental Vascular Biology, Amsterdam UMC, University of Amsterdam, the Netherlands (M. Gijbels).,King's College London, England (M. Giacca)
| | - Dónal O'Carroll
- Institute for Regeneration and Repair, Centre for Regenerative Medicine (A.D.P., D.O.), University of Edinburgh, Scotland
| | - Patrick W F Hadoke
- Queens Medical Research Institute, BHF Centre for Cardiovascular Sciences (F.V., J.R., M.K.L., A.D.M., M.B., E.M., J.P.S., D.E.N., P.W.F.H., L.D., J.C.S., A.H.B.), University of Edinburgh, Scotland
| | - Laura Denby
- Queens Medical Research Institute, BHF Centre for Cardiovascular Sciences (F.V., J.R., M.K.L., A.D.M., M.B., E.M., J.P.S., D.E.N., P.W.F.H., L.D., J.C.S., A.H.B.), University of Edinburgh, Scotland
| | - Judith C Sluimer
- Queens Medical Research Institute, BHF Centre for Cardiovascular Sciences (F.V., J.R., M.K.L., A.D.M., M.B., E.M., J.P.S., D.E.N., P.W.F.H., L.D., J.C.S., A.H.B.), University of Edinburgh, Scotland.,Pathology, Maastricht Medical Center, the Netherlands (K.V.K., J.d., J.C.S., A.H.B.)
| | - Andrew H Baker
- Queens Medical Research Institute, BHF Centre for Cardiovascular Sciences (F.V., J.R., M.K.L., A.D.M., M.B., E.M., J.P.S., D.E.N., P.W.F.H., L.D., J.C.S., A.H.B.), University of Edinburgh, Scotland.,Pathology, Maastricht Medical Center, the Netherlands (K.V.K., J.d., J.C.S., A.H.B.)
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18
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Ono K, Horie T, Baba O, Kimura M, Tsuji S, Rodriguez RR, Miyagawa S, Kimura T. Functional non-coding RNAs in vascular diseases. FEBS J 2020; 288:6315-6330. [PMID: 33340430 PMCID: PMC9292203 DOI: 10.1111/febs.15678] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 11/01/2020] [Accepted: 12/17/2020] [Indexed: 12/14/2022]
Abstract
Recently, advances in genomic technology such as RNA sequencing and genome‐wide profiling have enabled the identification of considerable numbers of non‐coding RNAs (ncRNAs). MicroRNAs have been studied for decades, leading to the identification of those with disease‐causing and/or protective effects in vascular disease. Although other ncRNAs such as long ncRNAs have not been fully described yet, recent studies have indicated their important functions in the development of vascular diseases. Here, we summarize the current understanding of the mechanisms and functions of ncRNAs, focusing on microRNAs, circular RNAs and long ncRNAs in vascular diseases.
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Affiliation(s)
- Koh Ono
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Japan
| | - Takahiro Horie
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Japan
| | - Osamu Baba
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Japan
| | - Masahiro Kimura
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Japan
| | - Shuhei Tsuji
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Japan
| | | | - Sawa Miyagawa
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Japan
| | - Takeshi Kimura
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Japan
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19
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Lim YH, Ryu J, Kook H, Kim YK. Identification of Long Noncoding RNAs Involved in Differentiation and Survival of Vascular Smooth Muscle Cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 22:209-221. [PMID: 33230428 PMCID: PMC7515970 DOI: 10.1016/j.omtn.2020.08.032] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 08/25/2020] [Indexed: 02/07/2023]
Abstract
Long noncoding RNAs (lncRNAs) have recently been implicated in many pathophysiological cardiovascular processes, including vascular remodeling and atherosclerosis. However, the functional role of lncRNAs in the differentiation, proliferation, and apoptosis of vascular smooth muscle cells (VSMCs) is largely unknown. In this study, differentially expressed lncRNAs in synthetic and contractile human VSMCs were screened using RNA sequencing. Among the seven selected lncRNAs, the expression of MSC-AS1, MBNL1-AS1, and GAS6-AS2 was upregulated, whereas the expression of NR2F1-AS1, FUT8-AS1, FOXC2-AS1, and CTD-2207P18.2 was reduced upon VSMC differentiation. We focused on the NR2F1-AS1 and FOXC2-AS1 lncRNAs and showed that their knockdown significantly reduced the expression of smooth muscle contractile marker genes (ACTA2, CNN1, and TAGLN). Furthermore, FOXC2-AS1 was found to regulate cell proliferation and apoptosis through Akt/mTOR signaling, and affect Notch signaling, which is a key regulator of the contractile phenotype of VSMCs. Taken together, we identified novel lncRNAs involved in VSMC proliferation and differentiation and FOXC2-AS1 as a multifunctional regulator for vascular homeostasis and associated diseases.
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Affiliation(s)
- Yeong-Hwan Lim
- Basic Research Laboratory for Vascular Remodeling Research Laboratory, Chonnam National University Medical School, Jeollanam-do, Republic of Korea.,Department of Biochemistry, Chonnam National University Medical School, Jeollanam-do, Republic of Korea.,Department of Biomedical Sciences, Center for Creative Biomedical Scientists at Chonnam National University, Jeollanam-do, Republic of Korea
| | - Juhee Ryu
- Basic Research Laboratory for Vascular Remodeling Research Laboratory, Chonnam National University Medical School, Jeollanam-do, Republic of Korea.,Department of Biomedical Sciences, Center for Creative Biomedical Scientists at Chonnam National University, Jeollanam-do, Republic of Korea.,Department of Pharmacology, Chonnam National University Medical School, Jeollanam-do, Republic of Korea
| | - Hyun Kook
- Basic Research Laboratory for Vascular Remodeling Research Laboratory, Chonnam National University Medical School, Jeollanam-do, Republic of Korea.,Department of Biomedical Sciences, Center for Creative Biomedical Scientists at Chonnam National University, Jeollanam-do, Republic of Korea.,Department of Pharmacology, Chonnam National University Medical School, Jeollanam-do, Republic of Korea
| | - Young-Kook Kim
- Basic Research Laboratory for Vascular Remodeling Research Laboratory, Chonnam National University Medical School, Jeollanam-do, Republic of Korea.,Department of Biochemistry, Chonnam National University Medical School, Jeollanam-do, Republic of Korea.,Department of Biomedical Sciences, Center for Creative Biomedical Scientists at Chonnam National University, Jeollanam-do, Republic of Korea
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20
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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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21
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Inhibition of the long non-coding RNA NEAT1 protects cardiomyocytes from hypoxia in vitro via decreased pri-miRNA processing. Cell Death Dis 2020; 11:677. [PMID: 32826883 PMCID: PMC7442835 DOI: 10.1038/s41419-020-02854-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 07/30/2020] [Accepted: 07/30/2020] [Indexed: 02/06/2023]
Abstract
While restoration of coronary blood flow to the ischemic heart is the most effective strategy for reducing infarct size, reperfusion injury represents a significant limiting factor on clinical outcomes in myocardial infarction patients. Ischemic preconditioning (IPC) has been shown to inhibit reperfusion injury and represents an attractive model for studying cardioprotective signal transduction pathways. Long non-coding RNAs (lncRNAs) are a structurally and functionally heterogenous class of RNA transcripts with unknown roles in IPC-induced cardioprotection. Through microarray-based expression profiling of 31,423 lncRNAs in cardiac tissue from IPC mice, we identified the nuclear transcript Neat1 to be rapidly and robustly decreased in response to IPC. siRNA-mediated knock down of Neat1 reduced apoptosis and necrosis in murine cardiomyocytes (CM) and human iPS-derived CMs in response to prolonged hypoxia and hypoxia-reoxygenation, assessed with Annexin V/propidium iodide-staining, a Caspase 3/7 activity assay, LDH release, and western blot for cleaved Caspase 3. Mechanistically, Neat1 was shown to regulate processing of pro-apoptotic microRNA-22 (miR-22) in murine and human CM nuclei using a luciferase reporter assay. Hypoxia-induced downregulation of Neat1 was shown to result in accumulation of unprocessed pri-miRNA and decreased availability of biologically active miRNA, including miR-22. Addition of exogenous synthetic miR-22 reversed the protective effect of Neat1 knock down in human iPS-CM. In conclusion, we have identified the nuclear lncRNA Neat1 as part of a conserved oxygen-sensitive feedback mechanism by regulation of miRNA processing and a potential target in cardioprotection.
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22
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Pidíkova P, Reis R, Herichova I. miRNA Clusters with Down-Regulated Expression in Human Colorectal Cancer and Their Regulation. Int J Mol Sci 2020; 21:E4633. [PMID: 32610706 PMCID: PMC7369991 DOI: 10.3390/ijms21134633] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/24/2020] [Accepted: 06/27/2020] [Indexed: 02/07/2023] Open
Abstract
Regulation of microRNA (miRNA) expression has been extensively studied with respect to colorectal cancer (CRC), since CRC is one of the leading causes of cancer mortality worldwide. Transcriptional control of miRNAs creating clusters can be, to some extent, estimated from cluster position on a chromosome. Levels of miRNAs are also controlled by miRNAs "sponging" by long non-coding RNAs (ncRNAs). Both types of miRNA regulation strongly influence their function. We focused on clusters of miRNAs found to be down-regulated in CRC, containing miR-1, let-7, miR-15, miR-16, miR-99, miR-100, miR-125, miR-133, miR-143, miR-145, miR-192, miR-194, miR-195, miR-206, miR-215, miR-302, miR-367 and miR-497 and analysed their genome position, regulation and functions. Only evidence provided with the use of CRC in vivo and/or in vitro models was taken into consideration. Comprehensive research revealed that down-regulated miRNA clusters in CRC are mostly located in a gene intron and, in a majority of cases, miRNA clusters possess cluster-specific transcriptional regulation. For all selected clusters, regulation mediated by long ncRNA was experimentally demonstrated in CRC, at least in one cluster member. Oncostatic functions were predominantly linked with the reviewed miRNAs, and their high expression was usually associated with better survival. These findings implicate the potential of down-regulated clusters in CRC to become promising multi-targets for therapeutic manipulation.
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Affiliation(s)
- Paulína Pidíkova
- Department of Animal Physiology and Ethology, Faculty of Natural Sciences, Comenius University in Bratislava, 842 15 Bratislava, Slovakia;
| | - Richard Reis
- First Surgery Department, University Hospital, Comenius University in Bratislava, 811 07 Bratislava, Slovakia;
| | - Iveta Herichova
- Department of Animal Physiology and Ethology, Faculty of Natural Sciences, Comenius University in Bratislava, 842 15 Bratislava, Slovakia;
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23
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Interaction of Long Noncoding RNAs and Notch Signaling: Implications for Tissue Homeostasis Loss. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1227:107-129. [PMID: 32072502 DOI: 10.1007/978-3-030-36422-9_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The Notch signaling is a crucial pathway involved in cellular development, progression, and differentiation. Deregulation of Notch signaling pathway commonly impacts tissue homeostasis, being highly associated with proliferative disorders. The long noncoding RNAs (lncRNAs), which are transcripts with more than 200 nucleotides that do not code for proteins, were already described as Notch signaling pathway-interacting molecules. Many of them act as important transcriptional and posttranscriptional regulators, affecting gene expression and targeting other regulatory molecules, such as miRNAs. Due to their strong impact on function and gene expression of Notch-related molecules, lncRNAs influence susceptibility to cancer and other diseases, and can be regarded as potential biomarkers and therapeutic targets. Along this chapter, we summarize the cross talk between the Notch signaling pathway and their most important modulating lncRNAs, as well as the pathological consequences of these interactions, in different tissues.
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24
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García-Padilla C, Domínguez JN, Aránega AE, Franco D. Differential chamber-specific expression and regulation of long non-coding RNAs during cardiac development. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2019; 1862:194435. [PMID: 31678627 DOI: 10.1016/j.bbagrm.2019.194435] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 09/26/2019] [Accepted: 09/27/2019] [Indexed: 12/12/2022]
Abstract
Cardiovascular development is governed by a complex interplay between inducting signals such as Bmps and Fgfs leading to activation of cardiac specific transcription factors such as Nkx2.5, Mef2c and Srf that orchestrate the initial steps of cardiogenesis. Over the last decade we have witnessed the discovery of novel layers of gene regulation, i.e. post-transcriptional regulation exerted by non-coding RNAs. The function role of small non coding RNAs has been widely demonstrated, e.g. miR-1 knockout display several cardiovascular abnormalities during embryogenesis. More recently long non-coding RNAs have been also reported to modulate gene expression and function in the developing heart, as exemplified by the embryonic lethal phenotypes of Fendrr and Braveheart knock out mice, respectively. In this study, we investigated the differential expression profile during cardiogenesis of previously reported lncRNAs in heart development. Our data revealed that Braveheart, Fendrr, Carmen display a preferential adult expression while Miat, Alien, H19 preferentially display chamber-specific expression at embryonic stages. We also demonstrated that these lncRNAs are differentially regulated by Nkx2.5, Srf and Mef2c, Pitx2 > Wnt > miRNA signaling pathway and angiotensin II and thyroid hormone administration. Importantly isoform-specific expression and distinct nuclear vs cytoplasmic localization of Braveheart, Carmen and Fendrr during chamber morphogenesis is observed, suggesting distinct functional roles of these lncRNAs in atrial and ventricular chambers. Furthermore, we demonstrate by in situ hybridization a dynamic epicardial, myocardial and endocardial expression of H19 during cardiac development. Overall our data support novel roles of these lncRNAs in different temporal and tissue-restricted fashion during cardiogenesis.
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Affiliation(s)
- Carlos García-Padilla
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaen, Jaen, Spain
| | - Jorge N Domínguez
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaen, Jaen, Spain
| | - Amelia E Aránega
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaen, Jaen, Spain
| | - Diego Franco
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaen, Jaen, Spain.
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25
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Aquila G, Kostina A, Vieceli Dalla Sega F, Shlyakhto E, Kostareva A, Marracino L, Ferrari R, Rizzo P, Malaschicheva A. The Notch pathway: a novel therapeutic target for cardiovascular diseases? Expert Opin Ther Targets 2019; 23:695-710. [PMID: 31304807 DOI: 10.1080/14728222.2019.1641198] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Introduction: The Notch pathway is involved in determining cell fate during development and postnatally in continuously renewing tissues, such as the endothelium, the epithelium, and in the stem cells pool. The dysregulation of the Notch pathway is one of the causes of limited response, or resistance, to available cancer treatments and novel therapeutic strategies based on Notch inhibition are being investigated in preclinical and clinical studies in oncology. A large body of evidence now shows that the dysregulation of the Notch pathway is also involved in the pathophysiology of cardiovascular diseases (CVDs). Areas covered: This review discusses the molecular mechanisms involving Notch which underlie heart failure, aortic valve calcification, and aortic aneurysm. Expert opinion: Despite the existence of preventive, pharmacological and surgical interventions approaches, CVDs are the first causes of mortality worldwide. The Notch pathway is becoming increasingly recognized as being involved in heart failure, aortic aneurysm and aortic valve calcification, which are among the most common global causes of mortality due to CVDs. As already shown in cancer, the dissection of the biological processes and molecular mechanisms involving Notch should pave the way for new strategies to prevent and cure these diseases.
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Affiliation(s)
- Giorgio Aquila
- Department of Medical Sciences, University of Ferrara , Ferrara , Italy
| | - Aleksandra Kostina
- Laboratory of Molecular Cardiology, Almazov National Medical Research Centre , St-Petersburg , Russia.,Laboratory of Regenerative Biomedicine, Institute of Cytology, Russian Academy of Sciences , St-Petersburg , Russia
| | | | - Eugeniy Shlyakhto
- Laboratory of Molecular Cardiology, Almazov National Medical Research Centre , St-Petersburg , Russia
| | - Anna Kostareva
- Laboratory of Molecular Cardiology, Almazov National Medical Research Centre , St-Petersburg , Russia
| | - Luisa Marracino
- Department of Morphology, Surgery and Experimental Medicine and Laboratory for Technologies of Advanced Therapies (LTTA), University of Ferrara , Ferrara , Italy
| | - Roberto Ferrari
- Department of Medical Sciences, University of Ferrara , Ferrara , Italy.,Maria Cecilia Hospital, GVM Care & Research , Cotignola , Italy
| | - Paola Rizzo
- Maria Cecilia Hospital, GVM Care & Research , Cotignola , Italy.,Department of Morphology, Surgery and Experimental Medicine and Laboratory for Technologies of Advanced Therapies (LTTA), University of Ferrara , Ferrara , Italy
| | - Anna Malaschicheva
- Laboratory of Molecular Cardiology, Almazov National Medical Research Centre , St-Petersburg , Russia.,Laboratory of Regenerative Biomedicine, Institute of Cytology, Russian Academy of Sciences , St-Petersburg , Russia.,Department of Embryology, Faculty of Biology, Saint-Petersburg State University , St. Petersburg , Russia
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26
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27
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Ehrlich KC, Lacey M, Ehrlich M. Tissue-specific epigenetics of atherosclerosis-related ANGPT and ANGPTL genes. Epigenomics 2019; 11:169-186. [PMID: 30688091 PMCID: PMC6371847 DOI: 10.2217/epi-2018-0150] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Aim: To understand tissue-specific regulation of angiopoietin/angiopoietin-like (ANGPT/ANGPTL) genes (especially the five genes embedded in introns of host genes) and their association with atherosclerosis. Methods: Transcription and epigenomic databases from various normal tissues were examined in the vicinity of ANGPT1, ANGPT2, ANGPTL1, ANGPTL2, ANGPTL3, ANGPTL4 and ANGPTL8. Results: We identified tissue-specific enhancer chromatin regions that are likely to regulate transcription of ANGPT/ANGPTL genes and were intragenic, intergenic or host gene-linked. In addition, we found atherosclerosis-linked differentially methylated regions associated with ANGPT2 and with sequences encoding miR-145, a microRNA that targets ANGPT2 mRNA in cancers. Conclusion: Our findings implicate enhancers as major contributors to tissue-specific expression of ANGPT/ANGPTL genes, which play critical roles in angiogenesis, atherosclerosis, cancer, and inflammatory and metabolic diseases.
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Affiliation(s)
- Kenneth C Ehrlich
- Center for Bioinformatics & Genomics, Tulane University Health Sciences Center, New Orleans, LA 70112, USA
| | - Michelle Lacey
- Department of Mathematics, Tulane University, New Orleans, LA 70118, USA.,Tulane Cancer Center, Tulane University Health Sciences Center, New Orleans, LA 70112, USA
| | - Melanie Ehrlich
- Center for Bioinformatics & Genomics, Tulane University Health Sciences Center, New Orleans, LA 70112, USA.,Tulane Cancer Center, Tulane University Health Sciences Center, New Orleans, LA 70112, USA.,Hayward Genetics Center Tulane University Health Sciences Center, New Orleans, LA 70112, USA
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28
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Vacante F, Denby L, Sluimer JC, Baker AH. The function of miR-143, miR-145 and the MiR-143 host gene in cardiovascular development and disease. Vascul Pharmacol 2019; 112:24-30. [PMID: 30502421 PMCID: PMC6395947 DOI: 10.1016/j.vph.2018.11.006] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 11/22/2018] [Accepted: 11/22/2018] [Indexed: 02/09/2023]
Abstract
Noncoding RNAs (long noncoding RNAs and small RNAs) are emerging as critical modulators of phenotypic changes associated with physiological and pathological contexts in a variety of cardiovascular diseases (CVDs). Although it has been well established that hereditable genetic alterations and exposure to risk factors are crucial in the development of CVDs, other critical regulators of cell function impact on disease processes. Here we discuss noncoding RNAs have only recently been identified as key players involved in the progression of disease. In particular, we discuss micro RNA (miR)-143/145 since they represent one of the most characterised microRNA clusters regulating smooth muscle cell (SMC) differentiation and phenotypic switch in response to vascular injury and remodelling. MiR143HG is a well conserved long noncoding RNA (lncRNA), which is the host gene for miR-143/145 and recently implicated in cardiac specification during heart development. Although the lncRNA-miRNA interactions have not been completely characterised, their crosstalk is now beginning to emerge and likely requires further research focus. In this review we give an overview of the biology of the genomic axis that is miR-143/145 and MiR143HG, focusing on their important functional role(s) in the cardiovascular system.
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Affiliation(s)
- Francesca Vacante
- Centre for Cardiovascular Science, The Queen's Medical Research Institute, Edinburgh EH16 4TJ, UK
| | - Laura Denby
- Centre for Cardiovascular Science, The Queen's Medical Research Institute, Edinburgh EH16 4TJ, UK
| | - Judith C Sluimer
- Centre for Cardiovascular Science, The Queen's Medical Research Institute, Edinburgh EH16 4TJ, UK; Maastricht University Medical Centre, Dept. of Pathology, Maastricht 6229 HX, The Netherlands
| | - Andrew H Baker
- Centre for Cardiovascular Science, The Queen's Medical Research Institute, Edinburgh EH16 4TJ, UK.
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29
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Abstract
SIGNIFICANCE The concepts of junk DNA and transcriptional noise are long gone as the existence of noncoding RNAs (ncRNAs) has been tested extensively in recent years. Given that the epigenetic status of cells affects many biological processes, how ncRNAs mechanistically contribute to these processes is of great interest. Recent Advances: Recent studies show that various ncRNAs interact with epigenetic and/or transcription factors to modulate the epigenetic status of cells directly and/or indirectly. There exists growing interest in the field of cardiovascular research to understand the roles of ncRNAs. Due to the large number of ncRNAs in the mammalian genome, only a handful of ncRNAs have been functionally elucidated, which makes it difficult to understand how ncRNAs interact with protein-coding genes and their encoded proteins. CRITICAL ISSUES Although the canonical function of microRNAs (miRNAs) to inhibit the translation of protein-coding genes is well established, the number of functionally annotated long noncoding RNAs (lncRNAs) is still small, which is especially true in the heart. FUTURE DIRECTIONS Future studies must connect the epigenetic controls of various cellular phenomena by incorporating both miRNAs and lncRNAs. Antioxid. Redox Signal. 29, 832-845.
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Affiliation(s)
- Shizuka Uchida
- 1 Cardiovascular Innovation Institute, University of Louisville , Louisville, Kentucky
| | - Roberto Bolli
- 1 Cardiovascular Innovation Institute, University of Louisville , Louisville, Kentucky.,2 Institute of Molecular Cardiology, University of Louisville , Louisville, Kentucky
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30
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Puttini S, Plaisance I, Barile L, Cervio E, Milano G, Marcato P, Pedrazzini T, Vassalli G. ALDH1A3 Is the Key Isoform That Contributes to Aldehyde Dehydrogenase Activity and Affects in Vitro Proliferation in Cardiac Atrial Appendage Progenitor Cells. Front Cardiovasc Med 2018; 5:90. [PMID: 30087899 PMCID: PMC6066537 DOI: 10.3389/fcvm.2018.00090] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 06/25/2018] [Indexed: 12/23/2022] Open
Abstract
High aldehyde dehydrogenase (ALDHhi) activity has been reported in normal and cancer stem cells. We and others have shown previously that human ALDHhi cardiac atrial appendage cells are enriched with stem/progenitor cells. The role of ALDH in these cells is poorly understood but it may come down to the specific ALDH isoform(s) expressed. This study aimed to compare ALDHhi and ALDHlo atrial cells and to identify the isoform(s) that contribute to ALDH activity, and their functional role. Methods and Results: Cells were isolated from atrial appendage specimens from patients with ischemic and/or valvular heart disease undergoing heart surgery. ALDHhi activity assessed with the Aldefluor reagent coincided with primitive surface marker expression (CD34+). Depending on their ALDH activity, RT-PCR analysis of ALDHhi and ALDHlo cells demonstrated a differential pattern of pluripotency genes (Oct 4, Nanog) and genes for more established cardiac lineages (Nkx2.5, Tbx5, Mef2c, GATA4). ALDHhi cells, but not ALDHlo cells, formed clones and were culture-expanded. When cultured under cardiac differentiation conditions, ALDHhi cells gave rise to a higher number of cardiomyocytes compared with ALDHlo cells. Among 19 ALDH isoforms known in human, ALDH1A3 was most highly expressed in ALDHhi atrial cells. Knocking down ALDH1A3, but not ALDH1A1, ALDH1A2, ALDH2, ALDH4A1, or ALDH8A1 using siRNA decreased ALDH activity and cell proliferation in ALDHhi cells. Conversely, overexpressing ALDH1A3 with a retroviral vector increased proliferation in ALDHlo cells. Conclusions: ALDH1A3 is the key isoform responsible for ALDH activity in ALDHhi atrial appendage cells, which have a propensity to differentiate into cardiomyocytes. ALDH1A3 affects in vitro proliferation of these cells.
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Affiliation(s)
- Stefania Puttini
- Cardiovascular Department, CHUV University Hospital, Lausanne, Switzerland
| | - Isabelle Plaisance
- Cardiovascular Department, CHUV University Hospital, Lausanne, Switzerland
| | - Lucio Barile
- Cardiocentro Ticino Foundation and Swiss Institute for Regenerative Medicine, Lugano, Switzerland
| | - Elisabetta Cervio
- Cardiocentro Ticino Foundation and Swiss Institute for Regenerative Medicine, Lugano, Switzerland
| | - Giuseppina Milano
- Cardiovascular Department, CHUV University Hospital, Lausanne, Switzerland.,Cardiocentro Ticino Foundation and Swiss Institute for Regenerative Medicine, Lugano, Switzerland
| | - Paola Marcato
- Departments of Pathology, Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
| | - Thierry Pedrazzini
- Cardiovascular Department, CHUV University Hospital, Lausanne, Switzerland
| | - Giuseppe Vassalli
- Cardiovascular Department, CHUV University Hospital, Lausanne, Switzerland.,Cardiocentro Ticino Foundation and Swiss Institute for Regenerative Medicine, Lugano, Switzerland
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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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