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Piergentili R, Sechi S. Non-Coding RNAs of Mitochondrial Origin: Roles in Cell Division and Implications in Cancer. Int J Mol Sci 2024; 25:7498. [PMID: 39000605 PMCID: PMC11242419 DOI: 10.3390/ijms25137498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/01/2024] [Accepted: 07/05/2024] [Indexed: 07/16/2024] Open
Abstract
Non-coding RNAs (ncRNAs) are a heterogeneous group, in terms of structure and sequence length, consisting of RNA molecules that do not code for proteins. These ncRNAs have a central role in the regulation of gene expression and are virtually involved in every process analyzed, ensuring cellular homeostasis. Although, over the years, much research has focused on the characterization of non-coding transcripts of nuclear origin, improved bioinformatic tools and next-generation sequencing (NGS) platforms have allowed the identification of hundreds of ncRNAs transcribed from the mitochondrial genome (mt-ncRNA), including long non-coding RNA (lncRNA), circular RNA (circRNA), and microRNA (miR). Mt-ncRNAs have been described in diverse cellular processes such as mitochondrial proteome homeostasis and retrograde signaling; however, the function of the majority of mt-ncRNAs remains unknown. This review focuses on a subgroup of human mt-ncRNAs whose dysfunction is associated with both failures in cell cycle regulation, leading to defects in cell growth, cell proliferation, and apoptosis, and the development of tumor hallmarks, such as cell migration and metastasis formation, thus contributing to carcinogenesis and tumor development. Here we provide an overview of the mt-ncRNAs/cancer relationship that could help the future development of new biomedical applications in the field of oncology.
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Affiliation(s)
| | - Stefano Sechi
- Istituto di Biologia e Patologia Molecolari del Consiglio Nazionale delle Ricerche, Dipartimento di Biologia e Biotecnologie, Università Sapienza di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy;
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2
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Mably JD, Wang DZ. Long non-coding RNAs in cardiac hypertrophy and heart failure: functions, mechanisms and clinical prospects. Nat Rev Cardiol 2024; 21:326-345. [PMID: 37985696 PMCID: PMC11031336 DOI: 10.1038/s41569-023-00952-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/16/2023] [Indexed: 11/22/2023]
Abstract
The surge in reports describing non-coding RNAs (ncRNAs) has focused attention on their possible biological roles and effects on development and disease. ncRNAs have been touted as previously uncharacterized regulators of gene expression and cellular processes, possibly working to fine-tune these functions. The sheer number of ncRNAs identified has outpaced the capacity to characterize each molecule thoroughly and to reliably establish its clinical relevance; it has, nonetheless, created excitement about their potential as molecular targets for novel therapeutic approaches to treat human disease. In this Review, we focus on one category of ncRNAs - long non-coding RNAs - and their expression, functions and molecular mechanisms in cardiac hypertrophy and heart failure. We further discuss the prospects for this specific class of ncRNAs as novel targets for the diagnosis and treatment of these conditions.
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Affiliation(s)
- John D Mably
- Center for Regenerative Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
- USF Health Heart Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Da-Zhi Wang
- Center for Regenerative Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
- USF Health Heart Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
- Department of Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
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3
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Lu S, Zeng L, Mo G, Lei D, Li Y, Ou G, Wu H, Sun J, Rong C, He S, Zhong D, Ke Q, Zhang Q, Tan X, Cen H, Xie X, Liao C. Long non-coding RNA SNHG17 may function as a competitive endogenous RNA in diffuse large B-cell lymphoma progression by sponging miR-34a-5p. PLoS One 2023; 18:e0294729. [PMID: 37988356 PMCID: PMC10662735 DOI: 10.1371/journal.pone.0294729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 11/07/2023] [Indexed: 11/23/2023] Open
Abstract
We investigated the functional mechanism of long non-coding small nucleolar host gene 17 (SNHG17) in diffuse large B-cell lymphoma (DLBCL). lncRNAs related to the prognosis of patients with DLBCL were screened to analyze long non-coding small nucleolar host gene 17 (SNHG17) expression in DLBCL and normal tissues, and a nomogram established for predicting DLBCL prognosis. SNHG17 expression in B-cell lymphoma cells was detected using qPCR. The effects of SNHG17 with/without doxorubicin on the proliferation and apoptosis of DoHH2 and Daudi were detected. The effects of combined SNHG17 and doxorubicin were analyzed. The regulatory function of SNHG17 in DLBCL was investigated using a mouse tumor xenotransplantation model. RNA sequencing was used to analyze the signaling pathways involved in SNHG17 knockdown in B-cell lymphoma cell lines. The target relationships among SNHG17, microRNA, and downstream mRNA biomolecules were detected. A higher SNHG17 level predicted a lower survival rate. SNHG17 was highly expressed in DLBCL patient tissues and cell lines. We established a prognostic model containing SNHG17 expression, which could effectively predict the overall survival rate of DLBCL patients. SNHG17 knockdown inhibited the proliferation and induced the apoptosis of B-cell lymphoma cells, and the combination of SNHG17 and doxorubicin had a synergistic effect. SNHG17, miR-34a-5p, and ZESTE gene enhancer homolog 2 (EZH2) had common hypothetical binding sites, and the luciferase reporter assay verified that miR-34a-5p was the direct target of SNHG17, and EZH2 was the direct target of miR-34a-5p. The carcinogenic function of SNHG17 in the proliferation and apoptosis of DLBCL cells was partially reversed by a miR-34a-5p inhibitor. SNHG17 increases EZH2 levels by inhibiting miR-34a-5p. Our findings indicate SNHG17 as critical for promoting DLBCL progression by regulating the EZH2 signaling pathway and sponging miR-34a-5p. These findings provide a new prognostic marker and therapeutic target for the prognosis and treatment of DLBCL.
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Affiliation(s)
- Shengjuan Lu
- Department of Hematology/Oncology, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Lin Zeng
- Department of Hematology/Oncology, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Guojun Mo
- Department of Pharmacy, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
- Life Sciences Institute, Guangxi Medical University, Nanning, China
| | - Danqing Lei
- Life Sciences Institute, Guangxi Medical University, Nanning, China
| | - Yuanhong Li
- Department of Pharmacy, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Guodi Ou
- Pharmaceutical College, Guangxi Medical University, Nanning, China
| | - Hailian Wu
- Life Sciences Institute, Guangxi Medical University, Nanning, China
| | - Jie Sun
- Department of Hematology/Oncology, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Chao Rong
- Department of Hematology/Oncology, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Sha He
- Department of Hematology/Oncology, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Dani Zhong
- Department of Hematology/Oncology, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Qing Ke
- Department of Hematology/Oncology, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Qingmei Zhang
- Department of Histology and Embryology, School of Pre-clinical Medicine, Guangxi Medical University, Nanning, China
- Key Laboratory of Early Prevention and Treatment of Regional High Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, China
| | - Xiaohong Tan
- Department of Hematology/Oncology, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Hong Cen
- Department of Hematology/Oncology, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Xiaoxun Xie
- Department of Histology and Embryology, School of Pre-clinical Medicine, Guangxi Medical University, Nanning, China
- Key Laboratory of Early Prevention and Treatment of Regional High Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, China
| | - Chengcheng Liao
- Department of Hematology/Oncology, Guangxi Medical University Cancer Hospital, Nanning, China
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4
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Liu ZZ, Lin WJ, Feng Y, Huang CL, Yan YF, Guo WY, Zhang H, Lei Z, Lu QL, Liu P, Lin XM, Wu SD. Plasma lncRNA LIPCAR Expression Levels Associated with Neurological Impairment and Stroke Subtypes in Patients with Acute Cerebral Infarction: A Prospective Observational Study with a Control Group. Neurol Ther 2023; 12:1385-1398. [PMID: 37195410 PMCID: PMC10310665 DOI: 10.1007/s40120-023-00482-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 04/11/2023] [Indexed: 05/18/2023] Open
Abstract
INTRODUCTION This prospective observational study with a control group aimed to compare the plasma levels of long non-coding RNA (lncRNA) LIPCAR between patients with acute cerebral infarction (ACI) and healthy controls, and to assess the prognostic abilities of LIPCAR for adverse outcomes of patients with ACI at 1-year follow-up. METHODS Eighty patients with ACI, of whom 40 had large artery atherosclerosis (LAA) and 40 had cardioembolism (CE) and who were hospitalized at Xi'an No. 1 Hospital from July 2019 to June 2020, were selected as the case group. Age- and sex-matched non-stroke patients from the same hospital throughout the same time period were chosen as the control group. Real-time quantitative reverse transcription polymerase chain reaction was used to measure the levels of plasma lncRNA LIPCAR. The correlations of LIPCAR expression among the LAA, CE, and control groups were assessed using Spearman's correlation analysis. Curve fitting and multivariate logistic regression were used to analyze the LIPCAR levels and 1-year adverse outcomes of patients with ACI and its subtypes. RESULTS The expression of plasma LIPCAR in the case group was noticeably higher than that of the control group (2.42 ± 1.49 vs. 1.00 ± 0.47, p < 0.001). Patients with CE had considerably higher levels of LIPCAR expression than those with LAA. The National Institute of Health Stroke Scale score and modified Rankin scale score on admission were significantly positively correlated with LIPCAR expression in patients with CE and LAA. Furthermore, the correlation was stronger in patients with CE than in those with LAA, with correlation coefficients of 0.69 and 0.64, respectively. Curve fitting revealed a non-linear correlation between LIPCAR expression levels, 1-year recurrent stroke, all-cause mortalities, and poor prognoses, with a cut-off value of 2.2. CONCLUSION The expression level of lncRNA LIPCAR may play a potential role in the identification of neurological impairment and CE subtype in patients with ACI. Increased 1-year risk of adverse outcomes may be associated with high levels of LIPCAR expression.
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Affiliation(s)
- Zhong-Zhong Liu
- Department of Neurology, Xi'an No. 1 Hospital, The First Affiliated Hospital of Northwest University, Xi'an, 710002, China
- Xi'an Key Laboratory for Innovation and Translation of Neuroimmunological Diseases, Xi'an, 710002, China
- Department of Epidemiology and Biostatistics, School of Public Health of Xi'an Jiao Tong University Health Science Center, Xi'an, 7100061, China
| | - Wen-Juan Lin
- Xi'an No. 3 Hospital, School of Life Sciences and Medicine, Northwest University, Xi'an, 710021, China
| | - Yue Feng
- College of Life Science, Northwest University, Xi'an, 710069, China
| | - Cong-Li Huang
- Xi'an Key Laboratory for Innovation and Translation of Neuroimmunological Diseases, Xi'an, 710002, China
| | - Yin-Fang Yan
- Xi'an Key Laboratory for Innovation and Translation of Neuroimmunological Diseases, Xi'an, 710002, China
| | - Wei-Yan Guo
- Xi'an Key Laboratory for Innovation and Translation of Neuroimmunological Diseases, Xi'an, 710002, China
| | - Huan Zhang
- College of Life Science, Northwest University, Xi'an, 710069, China
| | - Zhen Lei
- College of Life Science, Northwest University, Xi'an, 710069, China
| | - Qing-Li Lu
- Department of Neurology, Xi'an No. 1 Hospital, The First Affiliated Hospital of Northwest University, Xi'an, 710002, China
- Xi'an Key Laboratory for Innovation and Translation of Neuroimmunological Diseases, Xi'an, 710002, China
| | - Pei Liu
- Department of Neurology, Xi'an No. 1 Hospital, The First Affiliated Hospital of Northwest University, Xi'an, 710002, China
- Xi'an Key Laboratory for Innovation and Translation of Neuroimmunological Diseases, Xi'an, 710002, China
| | - Xue-Mei Lin
- Department of Neurology, Xi'an No. 1 Hospital, The First Affiliated Hospital of Northwest University, Xi'an, 710002, China
- Xi'an Key Laboratory for Innovation and Translation of Neuroimmunological Diseases, Xi'an, 710002, China
| | - Song-di Wu
- Department of Neurology, Xi'an No. 1 Hospital, The First Affiliated Hospital of Northwest University, Xi'an, 710002, China.
- College of Life Science, Northwest University, Xi'an, 710069, China.
- Xi'an Key Laboratory for Innovation and Translation of Neuroimmunological Diseases, Xi'an, 710002, China.
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Barbalata T, Niculescu LS, Stancu CS, Pinet F, Sima AV. Elevated Levels of Circulating lncRNAs LIPCAR and MALAT1 Predict an Unfavorable Outcome in Acute Coronary Syndrome Patients. Int J Mol Sci 2023; 24:12076. [PMID: 37569451 PMCID: PMC10418585 DOI: 10.3390/ijms241512076] [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] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/04/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
Coronary artery disease (CAD) is a leading cause of mortality worldwide. In this study, we aimed to assess the potential of plasma long non-coding RNAs (lncRNAs) LIPCAR and MALAT1 and microRNAs (miRNAs) miR-142-3p and miR-155-5p to discriminate unstable CAD patients from stable ones. 23 stable angina (SA), 21 unstable angina (UA), and 50 ST-segment elevation myocardial infarction (STEMI) patients were enrolled; their plasma was collected. ncRNA plasma levels were evaluated using RT-qPCR. All measured ncRNA levels were significantly increased in UA patients' plasma compared to SA patients' plasma and in STEMI-with major adverse cardiovascular event (MACE) patients' plasma vs. STEMI-without MACE patients' plasma. ROC analysis showed that increased levels of LIPCAR and MALAT1 were associated with UA, and the prognostic model improved with the addition of miR-155-5p levels. The assessed lncRNAs discriminated between hyperglycemic (HG) and normoglycemic (NG) UA patients, and they were associated with MACE incidence in STEMI patients; this prediction was improved by the addition of miR-142-3p levels to the ROC multivariate model. We propose LIPCAR and MALAT1 as effective diagnostic markers for vulnerable CAD, their association with HG in UA patients, and as robust predictors for unfavorable evolution of STEMI patients.
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Affiliation(s)
- Teodora Barbalata
- Lipidomics Department, Institute of Cellular Biology and Pathology “Nicolae Simionescu” of the Romanian Academy, 8 Bogdan Petriceicu Hasdeu Street, 050568 Bucharest, Romania; (T.B.); (L.S.N.); (C.S.S.)
| | - Loredan S. Niculescu
- Lipidomics Department, Institute of Cellular Biology and Pathology “Nicolae Simionescu” of the Romanian Academy, 8 Bogdan Petriceicu Hasdeu Street, 050568 Bucharest, Romania; (T.B.); (L.S.N.); (C.S.S.)
| | - Camelia S. Stancu
- Lipidomics Department, Institute of Cellular Biology and Pathology “Nicolae Simionescu” of the Romanian Academy, 8 Bogdan Petriceicu Hasdeu Street, 050568 Bucharest, Romania; (T.B.); (L.S.N.); (C.S.S.)
| | - Florence Pinet
- U1167-RID-AGE-Facteurs de Risque et Déterminants Moléculaires des Maladies Liées au Vieillissement, Institut Pasteur de Lille, Université de Lille, INSERM, CHU Lille, F-59000 Lille, France;
| | - Anca V. Sima
- Lipidomics Department, Institute of Cellular Biology and Pathology “Nicolae Simionescu” of the Romanian Academy, 8 Bogdan Petriceicu Hasdeu Street, 050568 Bucharest, Romania; (T.B.); (L.S.N.); (C.S.S.)
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6
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LncRNA GACAT2 binds with protein PKM1/2 to regulate cell mitochondrial function and cementogenesis in an inflammatory environment. Bone Res 2022; 10:29. [PMID: 35296649 PMCID: PMC8927299 DOI: 10.1038/s41413-022-00197-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 10/31/2021] [Accepted: 12/21/2021] [Indexed: 12/17/2022] Open
Abstract
Periodontal ligament stem cells (PDLSCs) are a key cell type for restoring/regenerating lost/damaged periodontal tissues, including alveolar bone, periodontal ligament and root cementum, the latter of which is important for regaining tooth function. However, PDLSCs residing in an inflammatory environment generally exhibit compromised functions, as demonstrated by an impaired ability to differentiate into cementoblasts, which are responsible for regrowing the cementum. This study investigated the role of mitochondrial function and downstream long noncoding RNAs (lncRNAs) in regulating inflammation-induced changes in the cementogenesis of PDLSCs. We found that the inflammatory cytokine-induced impairment of the cementogenesis of PDLSCs was closely correlated with their mitochondrial function, and lncRNA microarray analysis and gain/loss-of-function studies identified GACAT2 as a regulator of the cellular events involved in inflammation-mediated mitochondrial function and cementogenesis. Subsequently, a comprehensive identification of RNA-binding proteins by mass spectrometry (ChIRP-MS) and parallel reaction monitoring (PRM) assays revealed that GACAT2 could directly bind to pyruvate kinase M1/2 (PKM1/2), a protein correlated with mitochondrial function. Further functional studies demonstrated that GACAT2 overexpression increased the cellular protein expression of PKM1/2, the PKM2 tetramer and phosphorylated PKM2, which led to enhanced pyruvate kinase (PK) activity and increased translocation of PKM2 into mitochondria. We then found that GACAT2 overexpression could reverse the damage to mitochondrial function and cementoblastic differentiation of PDLSCs induced by inflammation and that this effect could be abolished by PKM1/2 knockdown. Our data indicated that by binding to PKM1/2 proteins, the lncRNA GACAT2 plays a critical role in regulating mitochondrial function and cementogenesis in an inflammatory environment.
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7
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Han L, Yang L. Multidimensional Mechanistic Spectrum of Long Non-coding RNAs in Heart Development and Disease. Front Cardiovasc Med 2021; 8:728746. [PMID: 34604357 PMCID: PMC8483262 DOI: 10.3389/fcvm.2021.728746] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 08/16/2021] [Indexed: 12/24/2022] Open
Abstract
With the large-scale genome-wide sequencing, long non-coding RNAs (lncRNAs) have been found to compose of a large portion of the human transcriptome. Recent studies demonstrated the multidimensional functions of lncRNAs in heart development and disease. The subcellular localization of lncRNA is considered as a key factor that determines lncRNA function. Cytosolic lncRNAs mainly regulate mRNA stability, mRNA translation, miRNA processing and function, whereas nuclear lncRNAs epigenetically regulate chromatin remodeling, structure, and gene transcription. In this review, we summarize the molecular mechanisms of cytosolic and nuclear lncRNAs in heart development and disease separately, and emphasize the recent progress to dictate the crosstalk of cytosolic and nuclear lncRNAs in orchestrating the same biological process. Given the low evolutionary conservation of most lncRNAs, deeper understanding of human lncRNA will uncover a new layer of human regulatory mechanism underlying heart development and disease, and benefit the future clinical treatment for human heart disease.
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Affiliation(s)
- Lei Han
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Lei Yang
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States
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8
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Yan L, Zhang Y, Wang M, Wang L, Zhang W, Ge ZR. Circulating LIPCAR is a potential biomarker of heart failure in patients post-acute myocardial infarction. Exp Biol Med (Maywood) 2021; 246:2589-2594. [PMID: 34365838 DOI: 10.1177/15353702211036055] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In heart failure (HF) patients with reduced ejection fraction, LIPCAR, a long noncoding RNA is elevated and is associated with left ventricular remodeling and poor prognosis. We studied the role of LIPCAR in patients with HF post-acute myocardial infarction (AMI) to find biomarkers for early detection of HF. We conducted a study of 127 patients with AMI, of which 59 were patients with HF post-AMI. LIPCAR levels were higher in HF patients post-AMI than patients without HF, and LIPCAR had a high predictive value for diagnosis of HF, which was estimated by receiver operating characteristic curves (AUC: 0.985). The results indicate that LIPCAR may be a marker of early HF after AMI.
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Affiliation(s)
- Li Yan
- Department of Cardiology, Shanghai Gongli Hospital, The Second Military Medical University, Shanghai 200135, China
| | - Yu Zhang
- Department of Emergency Medicine, Shanghai Gongli Hospital, The Second Military Medical University, Shanghai 200135, China
| | - Mei Wang
- Department of Cardiology, Shanghai Gongli Hospital, The Second Military Medical University, Shanghai 200135, China.,The Graduate School, Ningxia Medical University, Yinchuan, Ningxia 750004, China
| | - Lu Wang
- Department of Cardiology, Shanghai Gongli Hospital, The Second Military Medical University, Shanghai 200135, China
| | - Wei Zhang
- Department of Cardiology, Shanghai Gongli Hospital, The Second Military Medical University, Shanghai 200135, China
| | - Zhi-Ru Ge
- Department of Cardiology, Shanghai Gongli Hospital, The Second Military Medical University, Shanghai 200135, China
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9
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Liang H, Liu J, Su S, Zhao Q. Mitochondrial noncoding RNAs: new wine in an old bottle. RNA Biol 2021; 18:2168-2182. [PMID: 34110970 DOI: 10.1080/15476286.2021.1935572] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Mitochondrial noncoding RNAs (mt-ncRNAs) include noncoding RNAs inside the mitochondria that are transcribed from the mitochondrial genome or nuclear genome, and noncoding RNAs transcribed from the mitochondrial genome that are transported to the cytosol or nucleus. Recent findings have revealed that mt-ncRNAs play important roles in not only mitochondrial functions, but also other cellular activities. This review proposes a classification of mt-ncRNAs and outlines the emerging understanding of mitochondrial circular RNAs (mt-circRNAs), mitochondrial microRNAs (mitomiRs), and mitochondrial long noncoding RNAs (mt-lncRNAs), with an emphasis on their identification and functions.
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Affiliation(s)
- Huixin Liang
- Department of Infectious Diseases, the Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Guangdong Provincial Key Laboratory of Liver Disease Research, the Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, China
| | - Jiayu Liu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
| | - Shicheng Su
- Department of Infectious Diseases, the Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Department of Immunology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
| | - Qiyi Zhao
- Department of Infectious Diseases, the Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Guangdong Provincial Key Laboratory of Liver Disease Research, the Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
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10
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Correia M, Bernardes de Jesus B, Nóbrega-Pereira S. Novel Insights Linking lncRNAs and Metabolism With Implications for Cardiac Regeneration. Front Physiol 2021; 12:586927. [PMID: 33776783 PMCID: PMC7987814 DOI: 10.3389/fphys.2021.586927] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 02/15/2021] [Indexed: 12/13/2022] Open
Abstract
Heart disease is the leading cause of mortality in developed countries. The associated pathology is typically characterized by the loss of cardiomyocytes that leads, eventually, to heart failure. Although conventional treatments exist, novel regenerative procedures are warranted for improving cardiac regeneration and patients well fare. Whereas following injury the capacity for regeneration of adult mammalian heart is limited, the neonatal heart is capable of substantial regeneration but this capacity is lost at postnatal stages. Interestingly, this is accompanied by a shift in the metabolic pathways and energetic fuels preferentially used by cardiomyocytes from embryonic glucose-driven anaerobic glycolysis to adult oxidation of substrates in the mitochondria. Apart from energetic sources, metabolites are emerging as key regulators of gene expression and epigenetic programs which could impact cardiac regeneration. Long non-coding RNAs (lncRNAs) are known master regulators of cellular and organismal carbohydrate and lipid metabolism and play multifaceted functions in the cardiovascular system. Still, our understanding of the metabolic determinants and pathways that can promote cardiac regeneration in the injured hearth remains limited. Here, we will discuss the emerging concepts that provide evidence for a molecular interplay between lncRNAs and metabolic signaling in cardiovascular function and whether exploiting this axis could provide ground for improved regenerative strategies in the heart.
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Affiliation(s)
- Magda Correia
- Department of Medical Sciences and Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal
| | - Bruno Bernardes de Jesus
- Department of Medical Sciences and Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal
| | - Sandrina Nóbrega-Pereira
- Department of Medical Sciences and Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal.,Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
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11
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Aillaud M, Schulte LN. Emerging Roles of Long Noncoding RNAs in the Cytoplasmic Milieu. Noncoding RNA 2020; 6:ncrna6040044. [PMID: 33182489 PMCID: PMC7711603 DOI: 10.3390/ncrna6040044] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/26/2020] [Accepted: 11/05/2020] [Indexed: 02/06/2023] Open
Abstract
While the important functions of long noncoding RNAs (lncRNAs) in nuclear organization are well documented, their orchestrating and architectural roles in the cytoplasmic environment have long been underestimated. However, recently developed fractionation and proximity labelling approaches have shown that a considerable proportion of cellular lncRNAs is exported into the cytoplasm and associates nonrandomly with proteins in the cytosol and organelles. The functions of these lncRNAs range from the control of translation and mitochondrial metabolism to the anchoring of cellular components on the cytoskeleton and regulation of protein degradation at the proteasome. In the present review, we provide an overview of the functions of lncRNAs in cytoplasmic structures and machineries und discuss their emerging roles in the coordination of the dense intracellular milieu. It is becoming apparent that further research into the functions of these lncRNAs will lead to an improved understanding of the spatiotemporal organization of cytoplasmic processes during homeostasis and disease.
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Affiliation(s)
- Michelle Aillaud
- Institute for Lung Research, Philipps University Marburg, 35043 Marburg, Germany;
| | - Leon N Schulte
- Institute for Lung Research, Philipps University Marburg, 35043 Marburg, Germany;
- German Center for Lung Research (DZL), 35392 Giessen, Germany
- Correspondence:
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12
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Wang Y, Sun X. The functions of LncRNA in the heart. Diabetes Res Clin Pract 2020; 168:108249. [PMID: 32531328 DOI: 10.1016/j.diabres.2020.108249] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/27/2020] [Accepted: 06/04/2020] [Indexed: 12/26/2022]
Abstract
Cardiovascular disease is a major cause of death and disability worldwide. Recently, increasing evidence has demonstrated that various lncRNAs play critical roles in the pathogenesis of cardiovascular diseases, including myocardial ischemia and reperfusion (I/R) injury. LncRNAs are transcripts longer than 200 nucleotides. They are considered a class of dynamic noncoding RNAs known to be involved in physiological and pathological conditions with regulatory and structural roles in numerous biological processes, including genomic imprinting, epigenetic regulation, cell proliferation, development, aging and apoptosis. They are emerging as potential key regulators of a variety of cardiovascular diseases. However, the roles of lncRNAs in the heart function remain largely unknown. The purpose of this review was to summarize the functions of lncRNAs in the heart and discuss the challenges and possible strategies of lncRNA research for cardiovascular disease.
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Affiliation(s)
- Yao Wang
- Shandong Institute of Endocrine and Metabolic Diseases, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Xianglan Sun
- Department of Geriatrics, Department of Geriatric Endocrinology, ShanDong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China.
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13
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Wang H, Song T, Zhao Y, Zhao J, Wang X, Fu X. Long non-coding RNA LICPAR regulates atrial fibrosis via TGF-β/Smad pathway in atrial fibrillation. Tissue Cell 2020; 67:101440. [PMID: 32971457 DOI: 10.1016/j.tice.2020.101440] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 09/04/2020] [Accepted: 09/08/2020] [Indexed: 01/11/2023]
Abstract
Long non-coding RNA predicting cardiac remodeling (lnc LIPCAR) was implicated in several human diseases, while its role in atrial fibrillation (AF) remained poorly understood. Our study aimed to discover the role of LICPAR played in AF. Samples of atrial muscle tissues from patients diagnosed with sinus rhythm (SR) and atrial fibrillation (AF) were collected, and human atrial fibroblasts were isolated and identified under immunofluorescence staining. After Angiotensin II (Ang II, as a activator of TGF-β) stimulation with LICPAR overexpression or knockdown, the viability and proliferation of atrial fibroblasts were respectively determined using cell counting kit-8 (CCK-8) assay and clone formation assay. Relative expressions of LICPAR, fibrosis- and transforming growth factor-β (TGF-β)/Smad2/3-pathway related proteins were measured using quantitative real-time polymerase chain reaction (qRT-PCR) and Western blot as needed. LICPAR and TGF-β1 were upregulated and were positively correlated in atrial muscle tissues from AF. Atrial fibroblasts were identified as Vimentin positive. Further analysis indicated that Ang II enhanced the levels of LIPCAR, Smad2/3 phosphorylation and α-smooth muscle actin (α-SMA). Also, upregulating LIPCAR further promoted the promotive effects of Ang II on levels of LIPCAR, Collagen I, Collagen II, α-SMA and Smad2/3 phosphorylation, cell viability and proliferation of atrial fibroblasts, whereas silencing LIPCAR resulted in opposite effects. LICPAR regulates atrial fibrosis via modulating TGF-β/Smad pathway, which provided a potential therapeutic method for AF in clinical practice in the future.
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Affiliation(s)
- Haiyan Wang
- Department of Cardiovascular Medicine, Second Hospital of HeBei Medical University, No. 215, Heping Road, Xinhua District, Shijiazhuang, 050000, China
| | - Tingting Song
- Department of Cardiovascular Medicine, Second Hospital of HeBei Medical University, No. 215, Heping Road, Xinhua District, Shijiazhuang, 050000, China
| | - Ying Zhao
- Department of Cardiovascular Medicine, Second Hospital of HeBei Medical University, No. 215, Heping Road, Xinhua District, Shijiazhuang, 050000, China
| | - Jiayu Zhao
- Department of Cardiovascular Medicine, Second Hospital of HeBei Medical University, No. 215, Heping Road, Xinhua District, Shijiazhuang, 050000, China
| | - Xun Wang
- Department of Cardiovascular Medicine, Second Hospital of HeBei Medical University, No. 215, Heping Road, Xinhua District, Shijiazhuang, 050000, China
| | - Xianghua Fu
- Department of Cardiovascular Medicine, Second Hospital of HeBei Medical University, No. 215, Heping Road, Xinhua District, Shijiazhuang, 050000, China.
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14
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Abstract
Currently, cardiovascular diseases continue to be the leading cause of death worldwide; therefore, atherosclerosis remains one of the most crucial public health problems. This chronic and complex disease is considered to be a result of aberrant lipid homeostasis and inflammation of the inner wall of arteries that leads to plaque development. In recent years, a specific class of non-coding RNAs that are characterised by transcript lengths longer than 200 nucleotides, called long non-coding RNAs (lncRNAs), has emerged. Moreover, a growing body of evidence indicates that deregulation of lncRNA expression may contribute to the development of many diseases. Despite continuous efforts in deciphering the molecular basis of atherosclerotic plaque (AP) formation, many aspects of this process remain elusive. Therefore, continuing efforts in this area should remain the highest priority in the coming years. Establishment of a standardised experimental pipeline and validation of lncRNAs as possible relevant biomarkers for cardiovascular disease would enable the translation of gathered findings into clinical practice.
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Affiliation(s)
- Weronika Kraczkowska
- Department of Biochemistry and Molecular Biology, Poznań University of Medical Science, 6 Święcickiego Street, 60-781, Poznan, Poland.
| | - Paweł Piotr Jagodziński
- Department of Biochemistry and Molecular Biology, Poznań University of Medical Science, 6 Święcickiego Street, 60-781, Poznan, Poland
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15
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Eldarov CM, Vangely IM, Vays VB, Sheval EV, Holtze S, Hildebrandt TB, Kolosova NG, Popkov VA, Plotnikov EY, Zorov DB, Bakeeva LE, Skulachev VP. Mitochondria in the Nuclei of Rat Myocardial Cells. Cells 2020; 9:E712. [PMID: 32183238 PMCID: PMC7140638 DOI: 10.3390/cells9030712] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 03/03/2020] [Accepted: 03/05/2020] [Indexed: 01/01/2023] Open
Abstract
Electron microscopic study of cardiomyocytes taken from healthy Wistar and OXYS rats and naked mole rats (Heterocephalus glaber) revealed mitochondria in nuclei that lacked part of the nuclear envelope. The direct interaction of mitochondria with nucleoplasm is shown. The statistical analysis of the occurrence of mitochondria in cardiomyocyte nuclei showed that the percentage of nuclei with mitochondria was roughly around 1%, and did not show age and species dependency. Confocal microscopy of normal rat cardiac myocytes revealed a branched mitochondrial network in the vicinity of nuclei with an organization different than that of interfibrillar mitochondria. This mitochondrial network was energetically functional because it carried the membrane potential that responded by oscillatory mode after photodynamic challenge. We suggest that the presence of functional mitochondria in the nucleus is not only a consequence of certain pathologies but rather represents a normal biological phenomenon involved in mitochondrial/nuclear interactions.
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Affiliation(s)
- Chupalav M Eldarov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Irina M Vangely
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Valeriya B Vays
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Eugene V Sheval
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Susanne Holtze
- Department of Reproduction Management, Leibniz-Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Thomas B Hildebrandt
- Department of Reproduction Management, Leibniz-Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Natalia G Kolosova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Vasily A Popkov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Egor Y Plotnikov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Dmitry B Zorov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Lora E Bakeeva
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Vladimir P Skulachev
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119992 Moscow, Russia
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16
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Gusic M, Prokisch H. ncRNAs: New Players in Mitochondrial Health and Disease? Front Genet 2020; 11:95. [PMID: 32180794 PMCID: PMC7059738 DOI: 10.3389/fgene.2020.00095] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 01/28/2020] [Indexed: 12/19/2022] Open
Abstract
The regulation of mitochondrial proteome is unique in that its components have origins in both mitochondria and nucleus. With the development of OMICS technologies, emerging evidence indicates an interaction between mitochondria and nucleus based not only on the proteins but also on the non-coding RNAs (ncRNAs). It is now accepted that large parts of the non‐coding genome are transcribed into various ncRNA species. Although their characterization has been a hot topic in recent years, the function of the majority remains unknown. Recently, ncRNA species microRNA (miRNA) and long-non coding RNAs (lncRNA) have been gaining attention as direct or indirect modulators of the mitochondrial proteome homeostasis. These ncRNA can impact mitochondria indirectly by affecting transcripts encoding for mitochondrial proteins in the cytoplasm. Furthermore, reports of mitochondria-localized miRNAs, termed mitomiRs, and lncRNAs directly regulating mitochondrial gene expression suggest the import of RNA to mitochondria, but also transcription from the mitochondrial genome. Interestingly, ncRNAs have been also shown to hide small open reading frames (sORFs) encoding for small functional peptides termed micropeptides, with several examples reported with a role in mitochondria. In this review, we provide a literature overview on ncRNAs and micropeptides found to be associated with mitochondrial biology in the context of both health and disease. Although reported, small study overlap and rare replications by other groups make the presence, transport, and role of ncRNA in mitochondria an attractive, but still challenging subject. Finally, we touch the topic of their potential as prognosis markers and therapeutic targets.
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Affiliation(s)
- Mirjana Gusic
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany.,Institute of Human Genetics, Technical University of Munich, Munich, Germany
| | - Holger Prokisch
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Human Genetics, Technical University of Munich, Munich, Germany
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17
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Wang X, Wang L, Ma Z, Liang W, Li J, Li Y, Gui Y, Ai S. Early expressed circulating long noncoding RNA CHAST is associated with cardiac contractile function in patients with acute myocardial infarction. Int J Cardiol 2019; 302:15-20. [PMID: 31924400 DOI: 10.1016/j.ijcard.2019.12.058] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 12/25/2019] [Accepted: 12/29/2019] [Indexed: 12/16/2022]
Abstract
BACKGROUND The mortality rate during the acute myocardial infarction (AMI) phase has substantially decreased, but post-AMI cardiac remodeling remains an important factor affecting patient prognosis. Several circulating long noncoding RNAs (lncRNAs) are reportedly involved in the chronic pathological process of cardiac function and remodeling in cardiovascular diseases. However, the potential roles of these circulating lncRNAs as biomarkers of cardiac function and remodeling during early-stage AMI remain unclear. METHODS Fifty-three patients with AMI and 90 controls without AMI were consecutively enrolled in this study. Clinical parameters and blood samples at different time points (i.e., 24 h and 3 days) were collected. RESULTS Compared with the controls, the circulating levels of cardiac hypertrophy-associated transcript (CHAST) significantly increased in AMI patients, and the CHAST levels obviously decreased at 3 days. In AMI patients, the expression levels of CHAST at 24 h were positively associated with cardiac contractile function and measured as left ventricular ejection fraction and left ventricular short-axis shortening rate (all P < 0.050). Multivariate regression analysis indicated that the expression level of CHAST at 24 h was an independent predictor of cardiac contractile function (standardized β = 0.319, P =0.034). When grouped according to the quartile values of the CHAST in the AMI population, patients with the highest quartiles of CHAST expression level showed better cardiac contractile function than all the other quartiles (all P < 0.050). CONCLUSION CHAST was an independent predictor of cardiac contractile function at early-stage AMI and may serve as a candidate biomarker for cardiac remodeling.
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Affiliation(s)
- Xuehui Wang
- Department of Cardiology, Heart Center, the First Affiliated Hospital of Xinxiang Medical University, Xinxiang Medical University, Weihui City 453100, China.
| | - Lei Wang
- Department of Cardiology, Xuchang Central Hospital, Xuchang City 461000, China
| | - Zhiyuan Ma
- Department of Cardiology, Heart Center, the First Affiliated Hospital of Xinxiang Medical University, Xinxiang Medical University, Weihui City 453100, China
| | - Wanqian Liang
- Department of Cardiology, Heart Center, the First Affiliated Hospital of Xinxiang Medical University, Xinxiang Medical University, Weihui City 453100, China
| | - Jianhua Li
- Department of Cardiology, Heart Center, the First Affiliated Hospital of Xinxiang Medical University, Xinxiang Medical University, Weihui City 453100, China
| | - Yan Li
- Department of Cardiology, Heart Center, the First Affiliated Hospital of Xinxiang Medical University, Xinxiang Medical University, Weihui City 453100, China
| | - Yingying Gui
- Department of Cardiology, Heart Center, the First Affiliated Hospital of Xinxiang Medical University, Xinxiang Medical University, Weihui City 453100, China
| | - Sizhi Ai
- Department of Cardiology, Heart Center, the First Affiliated Hospital of Xinxiang Medical University, Xinxiang Medical University, Weihui City 453100, China.
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18
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Kotrys AV, Szczesny RJ. Mitochondrial Gene Expression and Beyond-Novel Aspects of Cellular Physiology. Cells 2019; 9:cells9010017. [PMID: 31861673 PMCID: PMC7017415 DOI: 10.3390/cells9010017] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 12/15/2019] [Accepted: 12/17/2019] [Indexed: 02/06/2023] Open
Abstract
Mitochondria are peculiar organelles whose proper function depends on the crosstalk between two genomes, mitochondrial and nuclear. The human mitochondrial genome (mtDNA) encodes only 13 proteins; nevertheless, its proper expression is essential for cellular homeostasis, as mtDNA-encoded proteins are constituents of mitochondrial respiratory complexes. In addition, mtDNA expression results in the production of RNA molecules, which influence cell physiology once released from the mitochondria into the cytoplasm. As a result, dysfunctions of mtDNA expression may lead to pathologies in humans. Here, we review the mechanisms of mitochondrial gene expression with a focus on recent findings in the field. We summarize the complex turnover of mitochondrial transcripts and present an increasing body of evidence indicating new functions of mitochondrial transcripts. We discuss mitochondrial gene regulation in different cellular contexts, focusing on stress conditions. Finally, we highlight the importance of emerging aspects of mitochondrial gene regulation in human health and disease.
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19
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Zhao L, Liu Y, Zhang J, Liu Y, Qi Q. LncRNA SNHG14/miR-5590-3p/ZEB1 positive feedback loop promoted diffuse large B cell lymphoma progression and immune evasion through regulating PD-1/PD-L1 checkpoint. Cell Death Dis 2019; 10:731. [PMID: 31570691 PMCID: PMC6769008 DOI: 10.1038/s41419-019-1886-5] [Citation(s) in RCA: 137] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 08/12/2019] [Accepted: 08/20/2019] [Indexed: 12/22/2022]
Abstract
Diffuse large B cell lymphoma (DLBCL) is the commonest disorder derived from the B-lymphocytes. Inhibiting the immune checkpoint through naturalizing programmed death-1 (PD-1) and programmed death ligand 1 (PD-L1) is proved to be a successful therapeutic regime for lymphoma. Long non-coding RNAs (lncRNAs) are unceasingly reported to be promising biological targets for the cancer therapies. This study planned to explore the regulation of small nucleolar RNA host gene 14 (SNHG14) on DLBCL. SNHG14 level in DLBCL samples and cell lines was analyzed by GEPIA bioinformatics tool and RT-qPCR. Biological functions of SNHG14 in DLBCL were detected by CCK-8, colony formation, and transwell invasion assays. Molecular interaction was determined by RNA immunoprecipitation (RIP) and luciferase reporter assays. MiR-5590-3p-related pathway was identified through KEGG pathway analysis applying DAVID6.8 online bioinformatics tool. Effect of SNHG14 on CD8+ T cells was detected by flow cytometry. Results depicted that SNHG14 was upregulated in DLBCL and its depletion retarded proliferation, migration and epithelial-to-mesenchymal transition (EMT). Mechanistically, SNHG14 sponged miR-5590-3p to upregulate Zinc finger E-box binding homeobox 1 (ZEB1), and ZEB1 transcriptionally activated SNHG14 and PD-L1 to promote the immune evasion of DLBCL cells. In conclusion, we firstly showed that SNHG14/miR-5590-3p/ZEB1 positive feedback loop promoted diffuse large B cell lymphoma progression and immune evasion through regulating PD-1/PD-L1 checkpoint, indicating that targeting SNHG14 was a potential approach to improve the efficacy of immunotherapy in DLBCL.
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Affiliation(s)
- Lina Zhao
- Department of Hematology, The Tumor Hospital Affiliated to Harbin Medical University, Harbin, Heilongjiang, China.
| | - Ye Liu
- Department of Immunology Teaching and Research, Harbin Medical University, Harbin, China
| | - Jingbo Zhang
- Department of Hematology, The Tumor Hospital Affiliated to Harbin Medical University, Harbin, Heilongjiang, China
| | - Yan Liu
- Department of Hematology, The Tumor Hospital Affiliated to Harbin Medical University, Harbin, Heilongjiang, China
| | - Qi Qi
- Department of Hematology, The Tumor Hospital Affiliated to Harbin Medical University, Harbin, Heilongjiang, China
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20
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Pant T, Dhanasekaran A, Fang J, Bai X, Bosnjak ZJ, Liang M, Ge ZD. Current status and strategies of long noncoding RNA research for diabetic cardiomyopathy. BMC Cardiovasc Disord 2018; 18:197. [PMID: 30342478 PMCID: PMC6196023 DOI: 10.1186/s12872-018-0939-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 10/12/2018] [Indexed: 12/13/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are endogenous RNA transcripts longer than 200 nucleotides which regulate epigenetically the expression of genes but do not have protein-coding potential. They are emerging as potential key regulators of diabetes mellitus and a variety of cardiovascular diseases. Diabetic cardiomyopathy (DCM) refers to diabetes mellitus-elicited structural and functional abnormalities of the myocardium, beyond that caused by ischemia or hypertension. The purpose of this review was to summarize current status of lncRNA research for DCM and discuss the challenges and possible strategies of lncRNA research for DCM. A systemic search was performed using PubMed and Google Scholar databases. Major conference proceedings of diabetes mellitus and cardiovascular disease occurring between January, 2014 to August, 2018 were also searched to identify unpublished studies that may be potentially eligible. The pathogenesis of DCM involves elevated oxidative stress, myocardial inflammation, apoptosis, and autophagy due to metabolic disturbances. Thousands of lncRNAs are aberrantly regulated in DCM. Manipulating the expression of specific lncRNAs, such as H19, metastasis-associated lung adenocarcinoma transcript 1, and myocardial infarction-associated transcript, with genetic approaches regulates potently oxidative stress, myocardial inflammation, apoptosis, and autophagy and ameliorates DCM in experimental animals. The detail data regarding the regulation and function of individual lncRNAs in DCM are limited. However, lncRNAs have been considered as potential diagnostic and therapeutic targets for DCM. Overexpression of protective lncRNAs and knockdown of detrimental lncRNAs in the heart are crucial for defining the role and function of lncRNAs of interest in DCM, however, they are technically challenging due to the length, short life, and location of lncRNAs. Gene delivery vectors can provide exogenous sources of cardioprotective lncRNAs to ameliorate DCM, and CRISPR–Cas9 genome editing technology may be used to knockdown specific lncRNAs in DCM. In summary, current data indicate that LncRNAs are a vital regulator of DCM and act as the promising diagnostic and therapeutic targets for DCM.
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Affiliation(s)
- Tarun Pant
- Department of Medicine, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA.,Centre for Biotechnology, Anna University, Chennai, Tamil Nadu, India
| | | | - Juan Fang
- Department of Pediatrics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
| | - Xiaowen Bai
- Department of Cell Biology, Neurology & Anatomy, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA.,Department of Physiology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
| | - Zeljko J Bosnjak
- Department of Medicine, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA.,Department of Physiology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
| | - Mingyu Liang
- Department of Physiology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
| | - Zhi-Dong Ge
- Department of Ophthalmology, Stanford School of Medicine, 1651 Page Mill Road, Stanford, CA, 94304, USA.
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21
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Liu J, Jiang H, Zan J, Bao Y, Dong J, Xiong L, Nie L. Single-molecule long-read transcriptome profiling of Platysternon megacephalum mitochondrial genome with gene rearrangement and control region duplication. RNA Biol 2018; 15:1244-1249. [PMID: 30200821 DOI: 10.1080/15476286.2018.1521212] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
Platysternon megacephalum is the sole living representative of the poorly studied turtle lineage Platysternidae. Their mitochondrial genome has been subject to gene rearrangement and control region duplication, resulting in a unique mitochondrial gene order in vertebrates. In this study, we sequenced the first full-length turtle (P. megacephalum) liver transcriptome using single-molecule real-time sequencing to study the transcriptional mechanisms of its mitochondrial genome. ND5 and ND6 anti-sense (ND6AS) forms a single transcript with the same expression in the human mitochondrial genome, but here we demonstrated differential expression of the rearranged ND5 and ND6AS genes in P. megacephalum. And some polycistronic transcripts were also reported in this study. Notably, we detected some novel long non-coding RNAs with alternative polyadenylation from the duplicated control region, and a novel ND6AS transcript composed of a long non-coding sequence, ND6AS, and tRNA-GluAS. These results provide the first description of a mtDNA transcriptome with gene rearrangement and control region duplication. These findings further our understanding of the fundamental concepts of mitochondrial gene transcription and RNA processing, and provide a new insight into the mechanism of transcription regulation of the mitochondrial genome.
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Affiliation(s)
- Jianjun Liu
- a Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui , Life Science College of Anhui Normal University , Wuhu , Anhui , P.R. China
| | - Hui Jiang
- a Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui , Life Science College of Anhui Normal University , Wuhu , Anhui , P.R. China
| | - Jiawei Zan
- a Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui , Life Science College of Anhui Normal University , Wuhu , Anhui , P.R. China
| | - Yuantian Bao
- a Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui , Life Science College of Anhui Normal University , Wuhu , Anhui , P.R. China
| | - Jinxiu Dong
- a Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui , Life Science College of Anhui Normal University , Wuhu , Anhui , P.R. China
| | - Lei Xiong
- a Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui , Life Science College of Anhui Normal University , Wuhu , Anhui , P.R. China
| | - Liuwang Nie
- a Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui , Life Science College of Anhui Normal University , Wuhu , Anhui , P.R. China
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22
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Li M, Wang YF, Yang XC, Xu L, Li WM, Xia K, Zhang DP, Wu RN, Gan T. Circulating Long Noncoding RNA LIPCAR Acts as a Novel Biomarker in Patients with ST-Segment Elevation Myocardial Infarction. Med Sci Monit 2018; 24:5064-5070. [PMID: 30030914 PMCID: PMC6067052 DOI: 10.12659/msm.909348] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs) recently have been implicated in the pathological processes of cardiovascular diseases. In this study, LncRNADisease database and PubMed database were used to screen myocardial infraction (MI)-related lncRNAs and to investigate the diagnostic role of lncRNAs in ST-segment elevation myocardial infraction (STEMI). MATERIAL AND METHODS Forty-six patients with STEMI and 40 healthy controls were included in the study. Venous blood samples acquired at different time points and the expression levels of lncRNAs in plasma were measured by qRT-PCR. In addition, other blood samples were collected before and after percutaneous coronary intervention (PCI). Correlation analysis and receiver operating characteristic (ROC) curve were used to assess the diagnosis value of the markers. All included patients were followed up for 12±1 months. RESULTS Nine MI-related lncRNAs were selected from the database. The qRT-PCR results showed that the expression of hypoxia inducible factor 1A antisense RNA 2 (aHIF), member 1 opposite strand/antisense transcript 1 (KCNQ1OT1), and mitochondrial long noncoding RNA uc022bqs.1 (LIPCAR) were significantly increased in patients with STEMI compared to the control patients. The ROC curve showed that LIPCAR (AUC=0.782, 95% CI: 0.707-0.0.894) had better diagnostic accuracy. Moreover, correlation analysis indicated that LIPCAR were positively correlated with myocardial enzymes and negatively correlated with left ventricular ejection fraction. The level of LIPCAR in STEMI patients after PCI was lower (P<0.05). Multivariate regression analysis indicated that higher levels of LIPCAR were independent predictors of major adverse cardiovascular events in patients with STEMI (HR=5.93; 95% CI, 1.46-9.77; P=0.001). CONCLUSIONS Highly expressed LIPCAR in plasma may serve as a warning sign for the diagnosis of STEMI.
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Affiliation(s)
- Meng Li
- Heart Center, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China (mainland).,Department of Cardiology, Baotou Central Hospital, Baotou, Inner Mongolia, China (mainland)
| | - Yue-Feng Wang
- Heart Center, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China (mainland)
| | - Xin-Chun Yang
- Heart Center, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China (mainland)
| | - Li Xu
- Heart Center, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China (mainland)
| | - Wei-Ming Li
- Heart Center, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China (mainland)
| | - Kun Xia
- Heart Center, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China (mainland)
| | - Da-Peng Zhang
- Heart Center, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China (mainland)
| | - Ri-Na Wu
- Department of Cardiology, Baotou Central Hospital, Baotou, Inner Mongolia, China (mainland)
| | - Tian Gan
- Department of Radiology, Baogang Hospital, Baotou, Inner Mongolia, China (mainland)
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23
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Zhao S, Fang S, Liu Y, Li X, Liao S, Chen J, Liu J, Zhao L, Li H, Zhou W, Shen W, Dong X, Xiang R, Wang L, Zhao Y. The long non-coding RNA NONHSAG026900 predicts prognosis as a favorable biomarker in patients with diffuse large B-cell lymphoma. Oncotarget 2018; 8:34374-34386. [PMID: 28423735 PMCID: PMC5470975 DOI: 10.18632/oncotarget.16163] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 02/24/2017] [Indexed: 12/11/2022] Open
Abstract
Long non-coding RNAs are known to be involved in cancer progression, but their biological functions and prognostic values are still largely unexplored in diffuse large B-cell lymphoma. In this study, long non-coding RNAs expression was characterized in 1,403 samples including normal and diffuse large B-cell lymphoma by repurposing 7 microarray datasets. Compared with any stage of normal B cells, NONHSAG026900 expression was significantly decreased in tumor samples. And in germinal center B-cell subtype, the significantly higher expression of NONHSAG026900 indicated it was a favorable prognosis biomarker. Then the prognostic power of NONHSAG026900 was validated with another independent dataset and NONHSAG026900 improved the predictive power of International Prognostic Index as an independent factor. Moreover, functional prediction and validation demonstrated that NONHSAG026900 could inhibit cell cycle activity to restrain tumor proliferation. These findings identified NONHSAG026900 as a novel prognostic biomarker and offered a new therapeutic target for diffuse large B-cell lymphoma patients.
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Affiliation(s)
- Shuangtao Zhao
- Department of Radiation Oncology, National Cancer Center/Cancer Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Shuangsang Fang
- The Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Yanhua Liu
- The School of Medicine, Nankai University, Tianjin, China.,The Collaborative Innovation Center for Biotherapy, Nankai University, Tianjin, China.,The Tianjin Key Laboratory of Tumor Microenvironment and Neurovascular Regulation, Tianjin, China
| | - Xixi Li
- The School of Medicine, Nankai University, Tianjin, China.,Department of Pathology, Nankai University, Tianjin, China
| | - Shengyou Liao
- The Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Jinwen Chen
- The Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Jingjia Liu
- The Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Lianhe Zhao
- The Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Hui Li
- The Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Wei Zhou
- The School of Medicine, Nankai University, Tianjin, China.,The Collaborative Innovation Center for Biotherapy, Nankai University, Tianjin, China.,The Tianjin Key Laboratory of Tumor Microenvironment and Neurovascular Regulation, Tianjin, China
| | - Wenzhi Shen
- The School of Medicine, Nankai University, Tianjin, China.,The Collaborative Innovation Center for Biotherapy, Nankai University, Tianjin, China.,The Tianjin Key Laboratory of Tumor Microenvironment and Neurovascular Regulation, Tianjin, China
| | - Xiaoli Dong
- The School of Medicine, Nankai University, Tianjin, China.,The Collaborative Innovation Center for Biotherapy, Nankai University, Tianjin, China.,The Tianjin Key Laboratory of Tumor Microenvironment and Neurovascular Regulation, Tianjin, China
| | - Rong Xiang
- The School of Medicine, Nankai University, Tianjin, China.,The Collaborative Innovation Center for Biotherapy, Nankai University, Tianjin, China.,The Tianjin Key Laboratory of Tumor Microenvironment and Neurovascular Regulation, Tianjin, China
| | - Luhua Wang
- Department of Radiation Oncology, National Cancer Center/Cancer Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yi Zhao
- The Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
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24
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Li Y, Zhu Y, Li G, Xiao J. Noncoding RNAs in Cardiovascular Aging. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1086:37-53. [PMID: 30232751 DOI: 10.1007/978-981-13-1117-8_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
With a progressively growing elderly population, aging-associated cardiovascular diseases and other pathologies have brought great burden to the economy, society, and individuals. Therefore, identifying therapeutic targets and developing effective strategies to prevent from cardiovascular aging are highly needed. Accumulating evidences suggest that noncoding RNAs (ncRNAs) such as microRNAs and long noncoding RNAs (lncRNAs) play important roles in regulating gene expression, which contributes to many pathophysiological processes of cellular senescence, aging, and aging-related diseases in cardiovascular systems. Here we provided a general overview of ncRNAs as well as the underlying mechanisms involved in cardiovascular aging. Although the importance of ncRNAs in cardiovascular aging has been reported and commonly acknowledged, further studies are still necessary to elucidate the underlying molecular mechanisms.
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Affiliation(s)
- Yongqin Li
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, School of Life Science, Shanghai University, Shanghai, China
| | - Yujiao Zhu
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, School of Life Science, Shanghai University, Shanghai, China
| | - Guoping Li
- Cardiovascular Division of the Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Junjie Xiao
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, School of Life Science, Shanghai University, Shanghai, China.
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25
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Dong Y, Yoshitomi T, Hu JF, Cui J. Long noncoding RNAs coordinate functions between mitochondria and the nucleus. Epigenetics Chromatin 2017; 10:41. [PMID: 28835257 PMCID: PMC5569521 DOI: 10.1186/s13072-017-0149-x] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 08/17/2017] [Indexed: 11/23/2022] Open
Abstract
In animal cells, mitochondria are the primary powerhouses and metabolic factories. They also contain genomes and can produce mitochondrial-specific nucleic acids and proteins. To maintain homeostasis of the entire cell, an intense cross-talk between mitochondria and the nucleus, mediated by encoded noncoding RNAs (ncRNAs), as well as proteins, is required. Long ncRNAs (lncRNAs) contain characteristic structures, and they are involved in the regulation of almost every stage of gene expression, as well as being implicated in a variety of disease states, such as cancer. In the coordinated signaling system, several lncRNAs, transcribed in the nucleus but residing in mitochondria, play a key role in regulating mitochondrial functions or dynamics. For example, RMRP, a component of the mitochondrial RNase MRP, is important for mitochondrial DNA replication and RNA processing, and the steroid receptor RNA activator, SRA, is a key modulator of hormone signaling and is present in both the nucleus and mitochondria. Some RNA-binding proteins maybe play a role in the lncRNAs transport system, such as HuR, GRSF1, SHARP, SLIRP, PPR, and PNPASE. Furthermore, a series of nuclear DNA-encoded lncRNAs were implicated in mitochondria-mediated apoptosis, mitochondrial bioenergetics and biosynthesis, and glutamine metabolism. The mitochondrial genome can also encode a set of lncRNAs, and they are divided into three categories: (1) lncND5, lncND6, and lncCyt b RNA; (2) chimeric mitochondrial DNA-encoded lncRNAs; and (3) putative mitochondrial DNA-encoded lncRNAs. It has been reported that the mitochondrial DNA-encoded lncRNAs appear to operate in the nucleus. The molecular mechanisms underlying trafficking of the mitochondrial DNA-encoded lncRNAs to the nucleus in mammals are only now beginning to emerge. In conclusion, both nuclear- and mitochondrial DNA-encoded lncRNAs mediate an intense intercompartmental cross-talk, which opens a rich field for investigation of the mechanism underlying the intercompartmental coordination and the maintenance of whole cell homeostasis.
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Affiliation(s)
- Yaru Dong
- Department of Ophthalmology, The Second Hospital of Jilin University, 218 Ziqiang Street, Changchun, 130041, Jilin, China.,Stanford University Medical School, VA Palo Alto Health Care System, 3801 Miranda Avenue, Palo Alto, CA, 94304, USA
| | - Takeshi Yoshitomi
- Department of Ophthalmology, Akita University School of Medicine, 1-1-1 Hondo, Akita, 010-8543, Japan
| | - Ji-Fan Hu
- Stanford University Medical School, VA Palo Alto Health Care System, 3801 Miranda Avenue, Palo Alto, CA, 94304, USA. .,Stem Cell and Cancer Center, First Affiliated Hospital, Jilin University, Changchun, 130061, Jilin, China.
| | - Jizhe Cui
- Department of Ophthalmology, The Second Hospital of Jilin University, 218 Ziqiang Street, Changchun, 130041, Jilin, China.
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26
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Long Noncoding RNAs: From Clinical Genetics to Therapeutic Targets? J Am Coll Cardiol 2016; 67:1214-1226. [PMID: 26965544 DOI: 10.1016/j.jacc.2015.12.051] [Citation(s) in RCA: 344] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 11/26/2015] [Accepted: 12/14/2015] [Indexed: 12/13/2022]
Abstract
Recent studies suggest that the majority of the human genome is transcribed, but only about 2% accounts for protein-coding exons. Long noncoding RNAs (lncRNAs) constitute a heterogenic class of RNAs that includes, for example, intergenic lncRNAs, antisense transcripts, and enhancer RNAs. Moreover, alternative splicing can lead to the formation of circular RNAs. In support of putative functions, GWAS for cardiovascular diseases have shown predictive single-nucleotide polymorphisms in lncRNAs, such as the 9p21 susceptibility locus that encodes the lncRNA antisense noncoding RNA in the INK4 locus (ANRIL). Many lncRNAs are regulated during disease. For example, metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) and myocardial infarction-associated transcript (MIAT) were shown to affect endothelial cell functions and diabetic retinopathy, whereas lincRNA-p21 controls neointima formation. In the heart, several lncRNAs were shown to act as microRNA sponges and to control ischemia-reperfusion injury or act as epigenetic regulators. In this review, the authors summarize the current understanding of lncRNA functions and their role as biomarkers in cardiovascular diseases.
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27
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Tang J, Jiang R, Deng L, Zhang X, Wang K, Sun B. Circulation long non-coding RNAs act as biomarkers for predicting tumorigenesis and metastasis in hepatocellular carcinoma. Oncotarget 2015; 6:4505-15. [PMID: 25714016 PMCID: PMC4414207 DOI: 10.18632/oncotarget.2934] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Accepted: 12/16/2014] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND & AIMS Alpha Fetal Protein (AFP) was one of the traditional biomarker for diagnosis of Hepatocellular carcinoma (HCC) clinically, however, with the low specificity of AFP, the early diagnosis or the metastasis prediction of HCC is inferior. A new, minimally invasive and more specificity biomarker for the diagnosis or metastasis prediction of HCC are necessary. METHODS In this study, we applied an lncRNA microarray to screen the potential biomarker for HCC. The multi-stage validation and risk score formula detection was used for validation. RESULTS We discovered three lncRNA, RP11-160H22.5, XLOC_014172 and LOC149086, which were up-regulated in HCC comparing with the cancer-free controls with the merged area under curve (AUC) in training set and validation set of 0.999 and 0.896. Furthermore, XLOC_014172 and LOC149086 was confirmed highly increased in metastasis HCC patients with the merged AUC in training set and validation set of 0.900 and 0.934. Besides, most patients presented a decreased level of the three lncRNAs after operation, while the patients with secondary increased level might be associated with tumor hematogenous metastasis. CONCLUSIONS RP11-160H22.5, XLOC_014172 and LOC149086 might be the potential biomarker for the tumorigenesis prediction and XLOC_014172 and LOC149086 for metastasis prediction in the future.
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Affiliation(s)
- Junwei Tang
- Liver Transplantation Center of the First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, P.R.China.,Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu Province, P.R.China
| | - Runqiu Jiang
- Liver Transplantation Center of the First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, P.R.China.,Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu Province, P.R.China
| | - Lei Deng
- Liver Transplantation Center of the First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, P.R.China.,Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu Province, P.R.China
| | - Xudong Zhang
- Liver Transplantation Center of the First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, P.R.China.,Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu Province, P.R.China
| | - Ke Wang
- Liver Transplantation Center of the First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, P.R.China.,Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu Province, P.R.China
| | - Beicheng Sun
- Liver Transplantation Center of the First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, P.R.China.,Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu Province, P.R.China
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28
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Hjelm BE, Rollins B, Mamdani F, Lauterborn JC, Kirov G, Lynch G, Gall CM, Sequeira A, Vawter MP. Evidence of Mitochondrial Dysfunction within the Complex Genetic Etiology of Schizophrenia. MOLECULAR NEUROPSYCHIATRY 2015; 1:201-19. [PMID: 26550561 DOI: 10.1159/000441252] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 09/22/2015] [Indexed: 01/19/2023]
Abstract
Genetic evidence has supported the hypothesis that schizophrenia (SZ) is a polygenic disorder caused by the disruption in function of several or many genes. The most common and reproducible cellular phenotype associated with SZ is a reduction in dendritic spines within the neocortex, suggesting alterations in dendritic architecture may cause aberrant cortical circuitry and SZ symptoms. Here, we review evidence supporting a multifactorial model of mitochondrial dysfunction in SZ etiology and discuss how these multiple paths to mitochondrial dysfunction may contribute to dendritic spine loss and/or underdevelopment in some SZ subjects. The pathophysiological role of mitochondrial dysfunction in SZ is based upon genomic analyses of both the mitochondrial genome and nuclear genes involved in mitochondrial function. Previous studies and preliminary data suggest SZ is associated with specific alleles and haplogroups of the mitochondrial genome, and also correlates with a reduction in mitochondrial copy number and an increase in synonymous and nonsynonymous substitutions of mitochondrial DNA. Mitochondrial dysfunction has also been widely implicated in SZ by genome-wide association, exome sequencing, altered gene expression, proteomics, microscopy analyses, and induced pluripotent stem cell studies. Together, these data support the hypothesis that SZ is a polygenic disorder with an enrichment of mitochondrial targets.
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Affiliation(s)
- Brooke E Hjelm
- Departments of Psychiatry & Human Behavior, University of California, Irvine, Calif., USA
| | - Brandi Rollins
- Departments of Psychiatry & Human Behavior, University of California, Irvine, Calif., USA
| | - Firoza Mamdani
- Departments of Psychiatry & Human Behavior, University of California, Irvine, Calif., USA
| | - Julie C Lauterborn
- Departments of Anatomy & Neurobiology, University of California, Irvine, Calif., USA
| | - George Kirov
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Gary Lynch
- Departments of Psychiatry & Human Behavior, University of California, Irvine, Calif., USA; Departments of Anatomy & Neurobiology, University of California, Irvine, Calif., USA
| | - Christine M Gall
- Departments of Anatomy & Neurobiology, University of California, Irvine, Calif., USA; Departments of Neurobiology & Behavior, University of California, Irvine, Calif., USA
| | - Adolfo Sequeira
- Departments of Psychiatry & Human Behavior, University of California, Irvine, Calif., USA
| | - Marquis P Vawter
- Departments of Psychiatry & Human Behavior, University of California, Irvine, Calif., USA
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29
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Dietrich A, Wallet C, Iqbal RK, Gualberto JM, Lotfi F. Organellar non-coding RNAs: Emerging regulation mechanisms. Biochimie 2015; 117:48-62. [DOI: 10.1016/j.biochi.2015.06.027] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 06/29/2015] [Indexed: 02/06/2023]
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30
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Abstract
Transcriptional and epigenetic regulation is critical for proper heart development, cardiac homeostasis, and pathogenesis. Long noncoding RNAs have emerged as key components of the transcriptional regulatory pathways that govern cardiac development as well as stress response, signaling, and remodeling in cardiac pathologies. Within the past few years, studies have identified many long noncoding RNAs in the context of cardiovascular biology and have begun to reveal the key functions of these transcripts. In this review, we discuss the growing roles of long noncoding RNAs in different aspects of cardiovascular development as well as pathological responses during injury or disease. In addition, we discuss diverse mechanisms by which long noncoding RNAs orchestrate cardiac transcriptional programs. Finally, we explore the exciting potential of this novel class of transcripts as biomarkers and novel therapeutic targets for cardiovascular diseases.
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Affiliation(s)
- Gizem Rizki
- From the Department of Biology, Massachusetts Institute of Technology, Cambridge
| | - Laurie A Boyer
- From the Department of Biology, Massachusetts Institute of Technology, Cambridge.
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31
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Abstract
Heart failure is a major public health problem with an estimated prevalence of 1-2% in the adult population in developed countries. Despite some progress, the prognosis of heart failure is associated with high mortality. There is a need for prognostic markers for heart failure, such as circulating biomarkers, in order to better identify individual heart failure patients with high risk of early death, and to improve the selection of patients for invasive treatment with limited availability such as heart transplantation. Among the non coding RNA family, we investigated the potentiality of long non coding RNAs (lncRNA) as potential biomarkers in heart disease. We observed that the plasmatic levels of the lncRNA named LIPCAR may predict early mortality in patients with heart failure independently of the etiology and may improve clinical-decision making for a more personalized treatment of "high-risk" patients.
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Affiliation(s)
- Florence Pinet
- Inserm U1167, Institut Pasteur de Lille, université de Lille, CHRU de Lille, faculté de médecine, 1, rue du Professeur Calmette, 59019 Lille, France
| | - Christophe Bauters
- Inserm U1167, Institut Pasteur de Lille, université de Lille, CHRU de Lille, faculté de médecine, 1, rue du Professeur Calmette, 59019 Lille, France
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32
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Kim J, Kim KM, Noh JH, Yoon JH, Abdelmohsen K, Gorospe M. Long noncoding RNAs in diseases of aging. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:209-21. [PMID: 26141605 DOI: 10.1016/j.bbagrm.2015.06.013] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 06/13/2015] [Accepted: 06/24/2015] [Indexed: 12/22/2022]
Abstract
Aging is a process during which progressive deteriorating of cells, tissues, and organs over time lead to loss of function, disease, and death. Towards the goal of extending human health span, there is escalating interest in understanding the mechanisms that govern aging-associated pathologies. Adequate regulation of expression of coding and noncoding genes is critical for maintaining organism homeostasis and preventing disease processes. Long noncoding RNAs (lncRNAs) are increasingly recognized as key regulators of gene expression at all levels--transcriptional, post-transcriptional and post-translational. In this review, we discuss our emerging understanding of lncRNAs implicated in aging illnesses. We focus on diseases arising from age-driven impairment in energy metabolism (obesity, diabetes), the declining capacity to respond homeostatically to proliferative and damaging stimuli (cancer, immune dysfunction), and neurodegeneration. We identify the lncRNAs involved in these ailments and discuss the rising interest in lncRNAs as diagnostic and therapeutic targets to ameliorate age-associated pathologies and prolong health. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy1, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa.
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Affiliation(s)
- Jiyoung Kim
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Kyoung Mi Kim
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Ji Heon Noh
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Je-Hyun Yoon
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Kotb Abdelmohsen
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA.
| | - Myriam Gorospe
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA.
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33
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Abstract
In recent year, increasing evidence suggests that noncoding RNAs play important roles in the regulation of tissue homeostasis and pathophysiological conditions. Besides small noncoding RNAs (eg, microRNAs), >200-nucleotide long transcripts, namely long noncoding RNAs (lncRNAs), can interfere with gene expressions and signaling pathways at various stages. In the cardiovascular system, studies have detected and characterized the expression of lncRNAs under normal physiological condition and in disease states. Several lncRNAs are regulated during acute myocardial infarction (eg, Novlnc6) and heart failure (eg, Mhrt), whereas others control hypertrophy, mitochondrial function and apoptosis of cardiomyocytes. In the vascular system, the endothelial-expressed lncRNAs (eg, MALAT1 and Tie-1-AS) can regulate vessel growth and function, whereas the smooth-muscle-expressed lncRNA smooth muscle and endothelial cell-enriched migration/differentiation-associated long noncoding RNA was recently shown to control the contractile phenotype of smooth muscle cells. This review article summarizes the data on lncRNA expressions in mouse and human and highlights identified cardiovascular lncRNAs that might play a role in cardiovascular diseases. Although our understanding of lncRNAs is still in its infancy, these examples may provide helpful insights how lncRNAs interfere with cardiovascular diseases.
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Affiliation(s)
- Shizuka Uchida
- From the Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University Frankfurt, Frankfurt, Germany (S.U., S.D.); and German Center for Cardiovascular Research, Partner side Rhein-Main, Frankfurt, Germany (S.U., S.D.)
| | - Stefanie Dimmeler
- From the Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University Frankfurt, Frankfurt, Germany (S.U., S.D.); and German Center for Cardiovascular Research, Partner side Rhein-Main, Frankfurt, Germany (S.U., S.D.).
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34
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Noncoding RNAs in diabetes vascular complications. J Mol Cell Cardiol 2014; 89:42-50. [PMID: 25536178 DOI: 10.1016/j.yjmcc.2014.12.014] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 11/18/2014] [Accepted: 12/05/2014] [Indexed: 02/06/2023]
Abstract
Diabetes mellitus is the most common metabolic disorder and is recognised as a dominant health threat of our time. Diabetes induces a widespread damage of the macro- and microvasculature in different organs and tissues and disrupts the endogenous vascular repair mechanisms, thus causing diffuse and severe complications. Moreover, diabetic patients respond poorly to surgical interventions aiming to "revascularise" (i.e., to restore blood flow supply) the ischemic myocardium or lower limbs. The molecular causes underpinning diabetes vascular complications are still underappreciated and druggable molecular targets for therapeutic interventions have not yet clearly emerged. Moreover, diabetes itself and diabetes complications are often silent killers, requiring new prognostic, diagnostic and predictive biomarkers for use in the clinical practice. Noncoding RNA (ncRNAs) are emerging as new fundamental regulators of gene expression. The small microRNAs (miRNAs, miRs) have opened the field capturing the attention of basic and clinical scientists for their potential to become new therapeutic targets and clinical biomarkers. More recently, long ncRNAs (lncRNAs) have started to be actively investigated, leading to first exciting reports, which further suggest their important and yet largely unexplored contribution to vascular physiology and disease. This review introduces the different ncRNA types and focuses at the ncRNA roles in diabetes vascular complications. Furthermore, we discuss the potential value of ncRNAs as clinical biomarkers, and we examine the possibilities for therapeutic intervention targeting ncRNs in diabetes. This article is part of a Special Issue titled: Non-coding RNAs.
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35
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Yan B, Wang ZH, Liu JY, Tao ZF, Li XM, Qin J. Long noncoding RNAs: versatile players in biologcial processes and human disorders. Epigenomics 2014; 6:375-9. [PMID: 25333847 DOI: 10.2217/epi.14.29] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Biao Yan
- Eye Hospital, Nanjing Medical University, Nanjing, China
| | - Zhen-Hua Wang
- The Institute of Digital Ocean, College of InformationTechnology, Shanghai Ocean University, Shanghai, China
| | - Jing-Yu Liu
- Eye Hospital, Nanjing Medical University, Nanjing, China
| | - Zhi-Fu Tao
- Eye Hospital, Nanjing Medical University, Nanjing, China
| | - Xiu-Miao Li
- Eye Hospital, Nanjing Medical University, Nanjing, China
| | - Jiang Qin
- Eye Hospital, Nanjing Medical University, Nanjing, China
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