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LIU SS, GUO HY, ZHU J, MA JL, LIU SZ, HE KL, BIAN SY. Circulating circRNA expression profile and its potential role in late recurrence of paroxysmal atrial fibrillation post catheter ablation. J Geriatr Cardiol 2023; 20:788-800. [PMID: 38098469 PMCID: PMC10716615 DOI: 10.26599/1671-5411.2023.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Catheter-based pulmonary vein isolation (PVI) is an effective and well-established intervention for symptomatic paroxysmal atrial fibrillation (PAF). Nevertheless, late recurrences of atrial fibrillation (LRAF) occurring during 3 to 12 months are common, and the underlying mechanisms remain elusive. Circular RNAs (circRNAs) in atrial tissue have been linked to the pathophysiological mechanisms and progression of PAF in a few studies. However, their expression patterns in peripheral blood and regulatory function in LRAF are not clear. METHODS In the present study, the expression profile of circulating circRNAs in three paired nonvalvular PAF patients with or without LRAF was investigated by high-throughput sequencing and validated by quantitative real-time polymerase chain reaction (qRT-PCR). Bioinformatics analyses, including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and circRNA/miRNA regulatory network, were performed to predict the functions and potential regulatory roles of differentially expressed (DE) circRNAs. RESULTS A total of 12,834 circRNAs, comprising 5,491 down-regulated and 7,343 up-regulated circRNAs, were found to be DE in blood smaples from the two groups in peripheral blood between LRAF and non-recurrence control individuals. The most enriched GO categories in terms of molecular function, biological process, and cellular component features were catalytic activity, cellular metabolic process, and intracellular part, respectively. The KEGG enrichment study revealed that the most important metabolic process controlled by DE circRNAs is endocytosis. In the circRNA/microRNAs interaction network, four up-regulated circRNAs (hsa_circ_0002665, hsa_circ_0001953, hsa_circ_0003831, and hsa_circ_0040533) and one down-regulated circRNA (hsa_circ_0041103) were predicted to play potential regulatory roles in the pathogenesis of LRAF. CONCLUSIONS This investigation discovered the expression pattern of circulating circRNAs that is indicative of PAF late recurrence, which may serve as risk markers or therapeutic targets for LRAF after PVI.
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Affiliation(s)
- Shan-Shan LIU
- Department of Cardiology, the Second Medical Center, National Clinical Research Center of Geriatric Disease, Beijing Key Laboratory of Chronic Heart Failure Precision Medicine, Chinese PLA General Hospital, Beijing, China
| | - Hong-Yang GUO
- Department of Cardiology, the Six Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Jian ZHU
- Department of Cardiology, the Second Medical Center, National Clinical Research Center of Geriatric Disease, Beijing Key Laboratory of Chronic Heart Failure Precision Medicine, Chinese PLA General Hospital, Beijing, China
| | - Jin-Ling MA
- Department of Cardiology, the Second Medical Center, National Clinical Research Center of Geriatric Disease, Beijing Key Laboratory of Chronic Heart Failure Precision Medicine, Chinese PLA General Hospital, Beijing, China
| | - Sai-Zhe LIU
- Department of Cardiology, the Six Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Kun-Lun HE
- Medical Big Data Research Center, Medical Innovation Research Department, Beijing Key Laboratory of Chronic Heart Failure Precision Medicine, Chinese PLA General Hospital, Beijing, China
| | - Su-Yan BIAN
- Department of Cardiology, the Second Medical Center, National Clinical Research Center of Geriatric Disease, Beijing Key Laboratory of Chronic Heart Failure Precision Medicine, Chinese PLA General Hospital, Beijing, China
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Long non-coding RNA and circular RNA: new perspectives for molecular pathophysiology of atrial fibrillation. Mol Biol Rep 2023; 50:2835-2845. [PMID: 36596997 DOI: 10.1007/s11033-022-08216-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 12/15/2022] [Indexed: 01/05/2023]
Abstract
Many studies have demonstrated the association of atrial fibrillation (AF) with endogenous genetic regulatory mechanisms. These interactions could advance the understanding of the AF pathophysiological process, supporting the search for early biomarkers to improve diagnosis and disease monitoring. Among the endogenous genetic regulatory mechanisms, long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) have gained special attention, and studies have demonstrated their involvement in AF development and other AF-related diseases such as coronary artery disease and cardiomyopathy. This review describes the main experimental results reported by studies that analyzed the expression of lncRNAs and circRNAs in AF associated with miRNA or mRNA. The search was conducted in PubMed public database using the terms "lncRNA and atrial fibrillation" or "long ncRNA and atrial fibrillation" or "long non-coding RNA and atrial fibrillation" or "circular RNA and atrial fibrillation" or "circRNA and atrial fibrillation". There was no overlapping of lncRNA or circRNA among the studies, attributed to the different sample types, methods, species, and patient classification evaluated in these studies. Although the regulatory mechanisms in which these molecules are involved are not yet well understood, the studies analyzed show their importance in the pathophysiological process of AF, supporting the idea that lncRNAs and circRNAs are involved in miRNA or mRNA regulation in the molecular mechanism of this disease.
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Zhang L, Lou Q, Zhang W, Yang W, Li L, Zhao H, Kong Y, Li W. CircCAMTA1 facilitates atrial fibrosis by regulating the miR-214-3p/TGFBR1 axis in atrial fibrillation. J Mol Histol 2023; 54:55-65. [PMID: 36417034 DOI: 10.1007/s10735-022-10110-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 11/12/2022] [Indexed: 11/24/2022]
Abstract
Circular RNAs (circRNAs) have been shown to be associated with cardiac fibrosis. Atrial fibrosis is an important pathophysiological event in the progression of atrial fibrillation (AF). Although a novel circRNA calmodulin binding transcription activator 1 (circCAMTA1) has been reported to be related with the development of AF, the detailed molecular mechanisms remain largely unknown. In this study, we found that circCAMTA1 was upregulated in atrial muscle tissues of AF patients and angiotensin-II (Ang-II)-treated human atrial fibroblasts (HAFs). Moreover, circCAMTA1 expression was positively correlated with the expression of collagen (I and III) and α-SMA in atrial muscle tissues of AF patients. In vitro experiments, knockdown of circCAMTA1 significantly suppressed Ang-II-induced HAFs proliferation and reduced the expression of atrial fibrosis-associated genes, but overexpression of circCAMTA1 exhibited opposite results. In vivo experiments, circCAMTA1 knockdown ameliorated Ang-II-induced atrial fibrosis by reducing AF incidence, AF duration, and collagen synthesis. Functionally, circCAMTA1 facilitated Ang-II-induced atrial fibrosis in vitro and in vivo via downregulating the inhibitory effect of miR-214-3p on transforming growth factor β receptor 1 (TGFBR1) expression. In conclusions, circCAMTA1 knockdown alleviated atrial fibrosis through downregulating TGFBR1 expression intermediated by miR-214-3p in AF, suggesting circCAMTA1/miR-214-3p/TGFBR1 axis may be a novel therapeutic target for AF treatment in clinic.
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Affiliation(s)
- Li Zhang
- Department of Cardiology, The First Affiliated Hospital of Harbin Medical University, Youzheng Street No. 23, Nangang District, 150001, Harbin, Heilongjiang, China
| | - Qi Lou
- Department of Cardiology, The First Affiliated Hospital of Harbin Medical University, Youzheng Street No. 23, Nangang District, 150001, Harbin, Heilongjiang, China
| | - Wei Zhang
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Harbin Medical University, Youzheng Street No. 23, Nangang District, 150001, Harbin, Heilongjiang, China
| | - Wen Yang
- Department of Cardiology, The First Affiliated Hospital of Harbin Medical University, Youzheng Street No. 23, Nangang District, 150001, Harbin, Heilongjiang, China
| | - Luyifei Li
- Department of Cardiology, The First Affiliated Hospital of Harbin Medical University, Youzheng Street No. 23, Nangang District, 150001, Harbin, Heilongjiang, China
| | - Hongyan Zhao
- Department of Cardiology, The People's Hospital of Liaoning Province, Wenyi Road No. 33, Shenhe District, 110000, Shenyang, Liaoning, China
| | - Yihui Kong
- Department of Cardiology, The First Affiliated Hospital of Harbin Medical University, Youzheng Street No. 23, Nangang District, 150001, Harbin, Heilongjiang, China
| | - Weimin Li
- Department of Cardiology, The First Affiliated Hospital of Harbin Medical University, Youzheng Street No. 23, Nangang District, 150001, Harbin, Heilongjiang, China.
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da Silva RMFL, Borges LE. Neutrophil-Lymphocyte Ratio and Red Blood Cell Distribution Width in Patients with Atrial Fibrillation and Rheumatic Valve Disease. Curr Vasc Pharmacol 2023; 21:367-377. [PMID: 37493166 DOI: 10.2174/1570161121666230726123444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 05/24/2023] [Accepted: 06/22/2023] [Indexed: 07/27/2023]
Abstract
The lifetime risk of developing atrial fibrillation (AF) is 1 in 3 adults, resulting in a prevalence of 2-4%. Rheumatic heart disease (RHD) is a frequent aetiology of valvular heart disease in lowand middle-income countries. Between 21% and 80% of patients with mitral valve disease, especially with stenosis, may have AF. Both these conditions, AF and RHD, present a state of persistent inflammation. In turn, inflammation is a frequent cause of anisocytosis, which can be evidenced through the parameter RDW (red bold cell distribution width). Factors associated with increased RDW are also known as risk factors associated with a higher incidence of AF. RDW may have an independent role in the pathogenesis of AF and the increased propensity of both thromboembolic and bleeding events. Another marker involved in the incidence of AF is the neutrophil-lymphocyte ratio. This is also a marker of oxidative stress and inflammation and is associated with a higher rate of AF recurrence. This review will evaluate these biomarkers and their association with cardiovascular events in patients with AF and RHD. The hypotheses and current debates about the relationship of biomarkers with the severity of chronic valve dysfunction, with acute rheumatic carditis in the paediatric population, and with the presence of thrombus in the left atrium will be discussed.
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Affiliation(s)
- Rose Mary Ferreira Lisboa da Silva
- Department of Internal Medicine, Faculty of Medicine, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Postgraduate Program in Sciences Applied to Adult Health, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Lucas Espindula Borges
- Postgraduate Program in Sciences Applied to Adult Health, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Biocor Instituto, Belo Horizonte, Minas Gerais, Brazil
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Yuan C, Lu J, Chen Z, Zhou Q. Circ-GTF2I/miR-590-5p Axis Aggravates Myocardial Ischemia-Reperfusion Injury by Regulating Kelch Repeat and BTB Domain-Containing Protein 7. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2022; 2022:2327669. [PMID: 35668777 PMCID: PMC9166968 DOI: 10.1155/2022/2327669] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/27/2022] [Accepted: 05/03/2022] [Indexed: 11/26/2022]
Abstract
Purpose We investigated the effect of the circular RNA (circRNA) general transcription factor IIi (GTF2I) on myocardial ischemia (MI) deterioration and neonatal rat cardiomyocyte damage. Methods The cell experiment was performed by using neonatal rat cardiomyocytes. Moreover, a hypoxia/reoxygenation treatment model was established. Cell Counting Kit-8 assay was conducted, and EdU cell proliferation was detected. Cell apoptosis was detected via flow cytometry and quantitative RT-PCR (RT-qPCR). Binding detection was performed through a double-luciferase reporter assay. Interleukin-6 (IL-6), tumor necrosis factor-α (TNF-α), and lactate dehydrogenase (LDH) were detected via enzyme-linked immunosorbent assay (ELISA). Results Compared with that in the sham and control groups, circ-GTF2I expression in MIRI and the hypoxia/reoxygenation treatment model was significantly upregulated in vivo and in vitro. The knockdown of circ-GTF2I relieved neonatal rat cardiomyocyte damage and MI. Further detection through the double-luciferase reporter assay confirmed that the binding site of circ-GTF2I to miR-590-5p and miR-590-5p was Kelch repeat and BTB domain-containing protein 7 (KBTBD7). ELISA and RT-qPCR results showed that circ-GTF2I induced the abnormal expressions of IL-6 TNF-α, LDH, Bax, Bcl-2, and Cyt-c in MIRI and the hypoxia/reoxygenation treatment models by regulating miR-590-5p and the heart development transcription factor KBTBD7. Conclusions CircRNA circ-GTF2I aggravated MIRI and neonatal rat cardiomyocyte damage in vivo and in vitro by regulating miR-590-5p and the heart development transcription factor KBTBD7.
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Affiliation(s)
- Chunju Yuan
- Department of Cardiovascular Medicine, Zhongda Hospital Southeast University, Nanjing 210009, Jiangsu Province, China
| | - Jing Lu
- Department of Cardiovascular Medicine, Zhongda Hospital Southeast University, Nanjing 210009, Jiangsu Province, China
| | - Zhongpu Chen
- Department of Cardiovascular Medicine, Zhongda Hospital Southeast University, Nanjing 210009, Jiangsu Province, China
| | - Qianxing Zhou
- Department of Cardiovascular Medicine, Zhongda Hospital Southeast University, Nanjing 210009, Jiangsu Province, China
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6
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Wu F, Yang Q, Mi Y, Wang F, Cai K, Zhang Y, Wang Y, Wang X, Gui Y, Li Q. miR-29b-3p Inhibitor Alleviates Hypomethylation-Related Aberrations Through a Feedback Loop Between miR-29b-3p and DNA Methylation in Cardiomyocytes. Front Cell Dev Biol 2022; 10:788799. [PMID: 35478963 PMCID: PMC9035530 DOI: 10.3389/fcell.2022.788799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 03/18/2022] [Indexed: 11/17/2022] Open
Abstract
As a member of the miR-29 family, miR-29b regulates global DNA methylation through target DNA methyltransferases (DNMTs) and acts as both a target and a key effector in DNA methylation. In this study, we found that miR-29b-3p expression was inversely correlated with DNMT expression in the heart tissues of patients with congenital heart disease (CHD), but whether it interacts with DNMTs in cardiomyocytes remains unknown. Further results revealed a feedback loop between miR-29b-3p and DNMTs in cardiomyocytes. Moreover, miR-29b-3p inhibitor relieved the deformity of hypomethylated zebrafish and restored the DNA methylation patterns in cardiomyocytes, resulting in increased proliferation and renormalization of gene expression. These results suggest mutual regulation between miR-29b-3p and DNMTs in cardiomyocytes and support the epigenetic normalization of miRNA-based therapy in cardiomyocytes.
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Affiliation(s)
- Fang Wu
- Translational Medical Center for Development and Disease, Shanghai Key Laboratory of Birth Defect Prevention and Control, NHC Key Laboratory of Neonatal Diseases, Institute of Pediatrics, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
- Cardiovascular Center, NHC Key Laboratory of Neonatal Diseases, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
- Department of Neonatology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qian Yang
- Translational Medical Center for Development and Disease, Shanghai Key Laboratory of Birth Defect Prevention and Control, NHC Key Laboratory of Neonatal Diseases, Institute of Pediatrics, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
- Cardiovascular Center, NHC Key Laboratory of Neonatal Diseases, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Yaping Mi
- Cardiovascular Center, NHC Key Laboratory of Neonatal Diseases, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Feng Wang
- Translational Medical Center for Development and Disease, Shanghai Key Laboratory of Birth Defect Prevention and Control, NHC Key Laboratory of Neonatal Diseases, Institute of Pediatrics, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
- Cardiovascular Center, NHC Key Laboratory of Neonatal Diseases, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Ke Cai
- Cardiovascular Center, NHC Key Laboratory of Neonatal Diseases, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Yawen Zhang
- Translational Medical Center for Development and Disease, Shanghai Key Laboratory of Birth Defect Prevention and Control, NHC Key Laboratory of Neonatal Diseases, Institute of Pediatrics, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
- Cardiovascular Center, NHC Key Laboratory of Neonatal Diseases, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Youhua Wang
- Department of Cardiology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xu Wang
- Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Yonghao Gui
- Translational Medical Center for Development and Disease, Shanghai Key Laboratory of Birth Defect Prevention and Control, NHC Key Laboratory of Neonatal Diseases, Institute of Pediatrics, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
- Cardiovascular Center, NHC Key Laboratory of Neonatal Diseases, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
- *Correspondence: Qiang Li, ; Yonghao Gui,
| | - Qiang Li
- Translational Medical Center for Development and Disease, Shanghai Key Laboratory of Birth Defect Prevention and Control, NHC Key Laboratory of Neonatal Diseases, Institute of Pediatrics, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
- *Correspondence: Qiang Li, ; Yonghao Gui,
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7
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Yang ZY, Li PF, Li ZQ, Tang T, Liu W, Wang Y. Altered Expression of Transfer-RNA-Derived Small RNAs in Human With Rheumatic Heart Disease. Front Cardiovasc Med 2021; 8:716716. [PMID: 34926598 PMCID: PMC8671610 DOI: 10.3389/fcvm.2021.716716] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 11/08/2021] [Indexed: 11/30/2022] Open
Abstract
Rheumatic heart disease (RHD) remains a severe public health problem in developing countries. Atrial fibrillation (AF) is a medical complication of RHD. Although the understanding of disease pathogenesis has advanced in recent years, the key questions need to be addressed. Transfer RNA–derived small RNAs (tsRNAs) are a novel type of short non-coding RNAs with potential regulatory functions in various physiological and pathological processes. The present study used tsRNAs sequencing to investigate the relationship between RHD and atrial fibrillation (AF). Three paired cardiac papillary muscles were taken from six rheumatic RHD patients with AF (3 cases) or without AF (3 cases) from January 2016 to January 2017 in Xiangya Hospital, Central South University. A total of 219 precisely matched tsRNAs were identified, and 77 tsRNAs (fold change > 2.0 and P < 0.05) were differently changed. Three tsRNAs (AS-tDR-001269, AS-tDR-001363, AS-tDR-006049) were randomly selected and confirmed by qRT-PCR. The results of qRT-PCR were consistent with tsRNAs sequencing, suggesting the tsRNAs sequencing was reliable. Subsequently, we predicted the target mRNAs of the three tsRNAs. Moreover, we verified the functions of tsRNAs targeting mRNAs in vitro. Finally, bioinformatics analysis indicated that the target genes were abundant in regulation of transcription, DNA binding, intracellular. Most of the genes were predicted to interplay with cytokine-cytokine receptor by KEGG analysis. Our findings uncover the pathological process of AF in RHD through tsRNAs sequencing. This research provides a new perspective for future research on elucidating the mechanism of AF in RHD and offers potential new candidates for the treatment and diagnosis.
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Affiliation(s)
- Zhao-Yu Yang
- Department of Integrated Traditional Chinese and Western Medicine, Institute of Integrative Medicine, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Peng-Fei Li
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhi-Qing Li
- Hunan University of Chinese Medicine, Changsha, China
| | - Tao Tang
- Department of Integrated Traditional Chinese and Western Medicine, Institute of Integrative Medicine, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Wei Liu
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Cardiovascular Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Yang Wang
- Department of Integrated Traditional Chinese and Western Medicine, Institute of Integrative Medicine, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
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8
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Chen C, Chen Q, Cheng K, Zou T, Pang Y, Ling Y, Xu Y, Zhu W. Exosomes and Exosomal Non-coding RNAs Are Novel Promises for the Mechanism-Based Diagnosis and Treatments of Atrial Fibrillation. Front Cardiovasc Med 2021; 8:782451. [PMID: 34926627 PMCID: PMC8671698 DOI: 10.3389/fcvm.2021.782451] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 10/26/2021] [Indexed: 12/15/2022] Open
Abstract
Atrial fibrillation (AF) is the most common arrhythmia worldwide and has a significant impact on human health and substantial costs. Currently, there is a lack of accurate biomarkers for the diagnosis and prognosis of AF. Moreover, the long-term efficacy of the catheter ablation in the AF is unsatisfactory. Therefore, it is necessary to explore new biomarkers and treatment strategies for the mechanism-based AF. Exosomes are nano-sized biovesicles released by nearly all types of cells. Since the AF would be linked to the changes of the atrial cells and their microenvironment, and the AF would strictly influence the exosomal non-coding RNAs (exo-ncRNAs) expression, which makes them as attractive diagnostic and prognostic biomarkers for the AF. Simultaneously, the exo-ncRNAs have been found to play an important role in the mechanisms of the AF and have potential therapeutic prospects. Although the role of the exo-ncRNAs in the AF is being actively investigated, the evidence is still limited. Furthermore, there is a lack of consensus regarding the most appropriate approach for exosome isolation and characterization. In this article, we reviewed the new methodologies available for exosomes biogenesis, isolation, and characterization, and then discussed the mechanism of the AF and various levels and types of exosomes relevant to the AF, with the special emphasis on the exo-ncRNAs in the diagnosis, prognosis, and treatment of the mechanism-based AF.
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Affiliation(s)
| | | | | | | | | | | | | | - Wenqing Zhu
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai, China
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9
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Zhang L, Wang X, Huang C. A narrative review of non-coding RNAs in atrial fibrillation: potential therapeutic targets and molecular mechanisms. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1486. [PMID: 34734038 PMCID: PMC8506732 DOI: 10.21037/atm-21-4483] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/16/2021] [Indexed: 11/11/2022]
Abstract
Objective This review summarizes the advances in the study of ncRNAs and atrial remodeling mechanisms to explore potential therapeutic targets and strategies for AF. Background Atrial fibrillation (AF) is one of the most common arrhythmias, and its morbidity and mortality rates are gradually increasing. Non-coding ribonucleic acid RNAs (ncRNAs) are transcribed from the genome and do not have the ability to be translated into proteins. A growing body of evidence has shown ncRNAs are extensively involved in the pathophysiological processes underlying AF. However, the precise molecular mechanisms of these associations have not been fully elucidated. Atrial remodeling plays a key role in the occurrence and development of AF, and includes electrical remodeling, structural remodeling, and autonomic nerve remodeling. Research has shown that ncRNA expression is altered in the plasma and tissues of AF patients that mediate cardiac excitation and arrhythmia, and is closely related to atrial remodeling. Methods Literatures about ncRNAs and atrial fibrillation were extensively reviewed to discuss and analyze. Conclusions The biology of ncRNAs represents a relatively new field of research and is still in an emerging stage. Recent studies have laid a foundation for understanding the molecular mechanisms of AF, future studies aimed at identifying how ncRNAs act on atrial fibrillation to provide potentially promising therapeutic targets for the treatment of atrial fibrillation.
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Affiliation(s)
- Lan Zhang
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China.,Cardiovascular Research Institute, Wuhan University, Wuhan, China.,Hubei Key Laboratory of Cardiology, Wuhan, China
| | - Xi Wang
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China.,Cardiovascular Research Institute, Wuhan University, Wuhan, China.,Hubei Key Laboratory of Cardiology, Wuhan, China
| | - Congxin Huang
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China.,Cardiovascular Research Institute, Wuhan University, Wuhan, China.,Hubei Key Laboratory of Cardiology, Wuhan, China
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10
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Huang S, Deng Y, Xu J, Liu J, Liu L, Fan C. The Role of Exosomes and Their Cargos in the Mechanism, Diagnosis, and Treatment of Atrial Fibrillation. Front Cardiovasc Med 2021; 8:712828. [PMID: 34395566 PMCID: PMC8355361 DOI: 10.3389/fcvm.2021.712828] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 07/07/2021] [Indexed: 12/28/2022] Open
Abstract
Atrial fibrillation (AF) is the most common persistent arrhythmia, but the mechanism of AF has not been fully elucidated, and existing approaches to diagnosis and treatment face limitations. Recently, exosomes have attracted considerable interest in AF research due to their high stability, specificity and cell-targeting ability. The aim of this review is to summarize recent literature, analyze the advantages and limitations of exosomes, and to provide new ideas for their use in understanding the mechanism and improving the diagnosis and treatment of AF.
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Affiliation(s)
- Shengyuan Huang
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Yating Deng
- Xiangya Medical College of Central South University, Changsha, China
| | - Jiaqi Xu
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, China
| | - Jiachen Liu
- Xiangya Medical College of Central South University, Changsha, China
| | - Liming Liu
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Chengming Fan
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
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11
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Yang Q, Li F, He AT, Yang BB. Circular RNAs: Expression, localization, and therapeutic potentials. Mol Ther 2021; 29:1683-1702. [PMID: 33484969 PMCID: PMC8116570 DOI: 10.1016/j.ymthe.2021.01.018] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/15/2020] [Accepted: 01/13/2021] [Indexed: 12/14/2022] Open
Abstract
Circular RNAs (circRNAs) are RNAs with a unique circular structure that is generated from back-splicing processes. These circular molecules were discovered more than 40 years ago but failed to raise scientific interest until lately. Increasing studies have found that these circular RNAs might not just be byproducts of the splicing process but possess important regulatory functions through different cellular events. Most circular RNAs are currently being studied in the field of cancer, and many of them have been confirmed to be involved in the process of tumorigenesis. However, many circular RNAs are implicated in the developmental stages of diseases other than cancer. In this review, we focus on discussing the role of circular RNAs in non-cancer diseases, especially in cardiovascular diseases. Following the summary of the life cycle of circRNAs, we provide input on studying circRNA-protein interactions based on our experience, which modulate protein translocation. Furthermore, we outline the potential of circRNAs to be potent biomarkers, effective therapeutic targets, and potential treatments in cardiovascular diseases as well as other non-cancer fields.
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Affiliation(s)
- Qiwei Yang
- Sunnybrook Research Institute, Toronto, ON, Canada; Medical Research Center, Second Hospital of Jilin University, Changchun, China; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M4N 3M5, Canada
| | - Feiya Li
- Sunnybrook Research Institute, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M4N 3M5, Canada
| | - Alina T He
- Sunnybrook Research Institute, Toronto, ON, Canada
| | - Burton B Yang
- Sunnybrook Research Institute, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M4N 3M5, Canada.
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12
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miRNA-1183-targeted regulation of Bcl-2 contributes to the pathogenesis of rheumatic heart disease. Biosci Rep 2021; 40:226700. [PMID: 33073840 PMCID: PMC7607189 DOI: 10.1042/bsr20201573] [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: 05/20/2020] [Revised: 10/13/2020] [Accepted: 10/14/2020] [Indexed: 02/06/2023] Open
Abstract
To determine whether up-regulation of miR-1183 targeting the gene for anti-apoptotic factor, B-cell lymphoma 2 (BCL-2) contributes to apoptosis in patients with rheumatic heart disease (RHD). Peripheral blood samples were isolated for miR-1183 characterization. The function of miRNA-1183 in RHD using miRNA mimic on PBMCs and THP-1 cell models. The binding of miR-1183 and Bcl-2 gene was confirmed by luciferase activity test. We also measured expression levels of BCL-2 in heart valve tissue from patients with RHD using ELISA and immunohistochemistry. In silico analysis and reporter gene assays indicated that miR-1183 directly targets the mRNA encoding BCL-2. It is found that miR-1183 binds directly to the 3'UTR of the BCL-2 mRNA and down-regulates the mRNA and protein levels of BCL-2. Overexpression of miR-1183 in RHD patients and cell lines down-regulated BCL-2 expression and induced apoptosis. With the progression of the disease, the expression of BCL-2 in the heart valve tissue of patients with RHD decreased. MiRNA-1183 is up-regulated in RHD and induces cardiac myocyte apoptosis through direct targeting and suppression of BCL-2, both of which might play important roles in RHD pathogenesis. During the compensatory period of RHD, up-regulated miR-1183 destroyed the balance of apoptosis proteins (Bax and BAK) in Bcl-2 family, enhance the apoptosis cascade reaction and reduce the anti apoptosis effect. The significantly higher expression levels of miR-1183 appear to play distinct roles in RHD pathogenesis by regulation BCL-2, possibly affecting myocardial apoptosis and remodeling in the context of RHD.
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13
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Zhai X, Zhang Y, Xin S, Cao P, Lu J. Insights Into the Involvement of Circular RNAs in Autoimmune Diseases. Front Immunol 2021; 12:622316. [PMID: 33717126 PMCID: PMC7947908 DOI: 10.3389/fimmu.2021.622316] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 01/25/2021] [Indexed: 12/22/2022] Open
Abstract
Circular RNAs (circRNAs) are single-stranded, endogenous, non-coding RNA (ncRNA) molecules formed by the backsplicing of messenger RNA (mRNA) precursors and have covalently closed circular structures without 5′-end caps and 3′-end polyadenylation [poly(A)] tails. CircRNAs are characterized by abundant species, stable structures, conserved sequences, cell- or tissue-specific expression, and widespread and stable presence in many organisms. Therefore, circRNAs can be used as biomarkers for the prediction, diagnosis, and treatment of a variety of diseases. Autoimmune diseases (AIDs) are caused by defects in immune tolerance or abnormal immune regulation, which leads to damage to host organs. Due to the complexity of the pathophysiological processes of AIDs, clinical therapeutics have been suboptimal. The emergence of circRNAs sheds new light on the treatment of AIDs. In particular, circRNAs mainly participate in the occurrence and development of AIDs by sponging targets. This review systematically explains the formation, function, mechanism, and characteristics of circRNAs in the context of AIDs. With a deeper understanding of the pathophysiological functions of circRNAs in the pathogenesis of AIDs, circRNAs may become reasonable, accurate, and effective biomarkers for the diagnosis and treatment of AIDs in the future.
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Affiliation(s)
- Xingyu Zhai
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, China.,National Healthcare Commission Key Laboratory of Carcinogenesis, Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China.,China-Africa Research Center of Infectious Diseases, Central South University, Changsha, China
| | - Yunfei Zhang
- Center for Medical Experiments, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Shuyu Xin
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, China.,National Healthcare Commission Key Laboratory of Carcinogenesis, Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China
| | - Pengfei Cao
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, China
| | - Jianhong Lu
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, China.,National Healthcare Commission Key Laboratory of Carcinogenesis, Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China.,China-Africa Research Center of Infectious Diseases, Central South University, Changsha, China
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14
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Circular RNAs in Sudden Cardiac Death Related Diseases: Novel Biomarker for Clinical and Forensic Diagnosis. Molecules 2021; 26:molecules26041155. [PMID: 33670057 PMCID: PMC7926443 DOI: 10.3390/molecules26041155] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 11/17/2022] Open
Abstract
The prevention and diagnosis of sudden cardiac death (SCD) are among the most important keystones and challenges in clinical and forensic practice. However, the diagnostic value of the current biomarkers remains unresolved issues. Therefore, novel diagnostic biomarkers are urgently required to identify patients with early-stage cardiovascular diseases (CVD), and to assist in the postmortem diagnosis of SCD cases without typical cardiac damage. An increasing number of studies show that circular RNAs (circRNAs) have stable expressions in myocardial tissue, and their time- and tissue-specific expression levels might reflect the pathophysiological status of the heart, which makes them potential CVD biomarkers. In this article, we briefly introduced the biogenesis and functional characteristics of circRNAs. Moreover, we described the roles of circRNAs in multiple SCD-related diseases, including coronary artery disease (CAD), myocardial ischemia or infarction, arrhythmia, cardiomyopathy, and myocarditis, and discussed the application prospects and challenges of circRNAs as a novel biomarker in the clinical and forensic diagnosis of SCD.
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15
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Zhu X, Tang X, Chong H, Cao H, Fan F, Pan J, Wang D, Zhou Q. Expression Profiles of Circular RNA in Human Atrial Fibrillation With Valvular Heart Diseases. Front Cardiovasc Med 2020; 7:597932. [PMID: 33330659 PMCID: PMC7714832 DOI: 10.3389/fcvm.2020.597932] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 10/29/2020] [Indexed: 01/22/2023] Open
Abstract
Circular RNAs (circRNA) are involved in a variety of human heart diseases, however, circRNA expression profiles and circRNA-miRNA-mRNA regulatory network in human atrial fibrillation (AF) especially with valvular heart diseases (VHD) remain poorly understood. A high-throughput RNA sequencing was used to investigate the differentially expressed circRNAs in left atrial appendage from VHD patients with or without persistent AF. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed to predict the potential functions of the host genes of differentially expressed circRNA and their downstream targets. CircRNA-miRNA-mRNA regulatory network was constructed to identify mechanisms underlying circRNAs. qRT-PCR and sanger sequencing were further performed to validate the results. Compared with sinus rhythm (SR) patients, there were 3094 upregulated and 4472 downregulated circRNAs in AF patients respectively. The expression of 10 most differentially expressed circRNAs (circ 255-ITGA7, circ 418-KCNN2, circ 13913-MIB1, circ 44670-BARD1, circ 44782-LAMA2, circ 81906-RYR2, circ 35880-ANO5, circ 22249-TNNI3K, circ 3136-TNNI3K, circ 56186-TNNI3K) between SR and persistent AF patients were verified by qRT-PCR. In addition, specific back-splicing sites of these circRNAs was confirmed by sanger sequencing. GO and KEGG pathway analysis indicated that cAMP signal pathway and Wnt signal pathway might play important role in the development of AF in VHD patients, which might be affected by circRNAs. This study provided a preliminary landscape of circRNAs expression profiles which are involved in persistent AF due to VHD, and established the possibility for future related researches in this field.
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Affiliation(s)
- Xiyu Zhu
- Department of Cardio-Thoracic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Xinlong Tang
- Department of Cardio-Thoracic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Hoshun Chong
- Department of Cardio-Thoracic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Hailong Cao
- Department of Cardio-Thoracic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Fudong Fan
- Department of Cardio-Thoracic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Jun Pan
- Department of Cardio-Thoracic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Dongjin Wang
- Department of Cardio-Thoracic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Qing Zhou
- Department of Cardio-Thoracic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
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16
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Disease-Associated Circular RNAs: From Biology to Computational Identification. BIOMED RESEARCH INTERNATIONAL 2020; 2020:6798590. [PMID: 32908906 PMCID: PMC7450300 DOI: 10.1155/2020/6798590] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 07/10/2020] [Indexed: 02/07/2023]
Abstract
Circular RNAs (circRNAs) are endogenous RNAs with a covalently closed continuous loop, generated through various backsplicing events of pre-mRNA. An accumulating number of studies have shown that circRNAs are potential biomarkers for major human diseases such as cancer and Alzheimer's disease. Thus, identification and prediction of human disease-associated circRNAs are of significant importance. To this end, a computational analysis-assisted strategy is indispensable to detect, verify, and quantify circRNAs for downstream applications. In this review, we briefly introduce the biology of circRNAs, including the biogenesis, characteristics, and biological functions. In addition, we outline about 30 recent bioinformatic analysis tools that are publicly available for circRNA study. Principles for applying these computational strategies and considerations will be briefly discussed. Lastly, we give a complete survey on more than 20 key computational databases that are frequently used. To our knowledge, this is the most complete and updated summary on publicly available circRNA resources. In conclusion, this review summarizes key aspects of circRNA biology and outlines key computational strategies that will facilitate the genome-wide identification and prediction of circRNAs.
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17
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Li Z, Cheng Y, Wu F, Wu L, Cao H, Wang Q, Tang W. The emerging landscape of circular RNAs in immunity: breakthroughs and challenges. Biomark Res 2020; 8:25. [PMID: 32665846 PMCID: PMC7348111 DOI: 10.1186/s40364-020-00204-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 06/25/2020] [Indexed: 02/06/2023] Open
Abstract
Circular RNAs (circRNAs) are covalently linked RNAs that exhibit individual strand with a closed-loop framework compared with a conserving, steady and abundant linear counterpart. In recent years, as high-throughput sequencing advancement has been developing, functional circRNAs have been increasingly recognized, and more extensive analyses expounded their effect on different diseases. However, the study on the function of circRNAs in the immune system remains insufficient. This study discusses the basic principles of circRNAs regulation and the systems involved in physiology-related and pathology-related processes. The effect of circRNAs on immune regulation is elucidated. The ongoing development of circRNAs and basic immunology has multiplied their potential in treating diseases. Such perspective will summarize the status and effect of circRNAs on various immune cells in cancer, autoimmune diseases and infections. Moreover, this study will primarily expound the system of circRNAs in T lymphocytes, macrophages and other immune cells, which creates a novel perspective and lay a theoretical basis for treating diseases.
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Affiliation(s)
- Zhouxiao Li
- Department of Hand Surgery, Plastic Surgery and Aesthetic Surgery, Ludwig-Maximilians University, Munich, Germany
| | - Ye Cheng
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu China
| | - Fan Wu
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu China
| | - Liangliang Wu
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu China
| | - Hongyong Cao
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu China
| | - Qian Wang
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu China
| | - Weiwei Tang
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu China
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18
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Zhang C, Huo ST, Wu Z, Chen L, Wen C, Chen H, Du WW, Wu N, Guan D, Lian S, Yang BB. Rapid Development of Targeting circRNAs in Cardiovascular Diseases. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 21:568-576. [PMID: 32721877 PMCID: PMC7390851 DOI: 10.1016/j.omtn.2020.06.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/27/2020] [Accepted: 06/23/2020] [Indexed: 12/13/2022]
Abstract
Circular RNAs (circRNAs) are circularized, single-stranded RNAs that are covalently linked. With their abundance in tissues and developmental stage-specific expression, circRNAs participate in a variety of physiological and pathological processes. In this review, we discuss the development of circRNAs used as biomarkers and therapeutic targets for cardiovascular diseases (CVDs), focusing on recent discoveries and applications of exosomal circRNAs that highlight opportunities and challenges. Some studies have identified a spectrum of circRNAs that are differentially expressed in CVDs, while other studies further manipulated specific circRNA expression and showed an ameliorated pathogenic state such as ischemic injury, hypertrophy, and cardiac fibrosis. Studies and applications of circRNAs are being rapidly developed. We expect to see clinical use of circRNAs as biomarkers and targets for disease treatment in the near future.
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Affiliation(s)
- Chao Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Southern Medical University and Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Guangzhou 510000, Guangdong Province, China; Department of Laboratory Medicine, Nanhai Hospital, Southern Medical University, Foshan 510000, Guangdong Province, China; Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada.
| | - Si Tong Huo
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Zhiyong Wu
- College of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510000, Guangdong Province, China
| | - Lina Chen
- Basic Medical College, Xiangnan University, Chenzhou 523000, China
| | - Chang Wen
- Jiangxi Medical College, Nanchang University, Nanchang 330000, Nanchang, Jiangxi Province, China
| | - Honghao Chen
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Southern Medical University and Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Guangzhou 510000, Guangdong Province, China; Department of Laboratory Medicine, Nanhai Hospital, Southern Medical University, Foshan 510000, Guangdong Province, China
| | - William W Du
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Nan Wu
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Daogang Guan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Southern Medical University and Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Guangzhou 510000, Guangdong Province, China
| | - Sen Lian
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Southern Medical University and Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Guangzhou 510000, Guangdong Province, China.
| | - Burton B Yang
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A1, Canada.
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19
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Abstract
Circular RNAs (circRNAs) are a type of single-stranded RNA molecules that normally do not encode proteins. circRNAs are involved in many physiological processes as well as the pathogenesis of diseases. Cardiac fibrosis is increasingly recognized as a pathological force in advanced heart diseases. A growing number of studies have reported that the occurrence and development of cardiac fibrosis is closely associated with the regulation of circRNAs. This review summarizes the current understanding of circRNA biogenesis and function and will highlight the recent updates regarding the involvement of circRNAs in cardiac fibrosis, and their potential as emerging biomarkers and therapeutic targets.
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Affiliation(s)
- Fatemeh Yousefi
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, P.O. Box 14115-154, Tehran, Iran
| | - Bahram M Soltani
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, P.O. Box 14115-154, Tehran, Iran.
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20
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Integrative analysis reveals essential mRNA, long non-coding RNA (lncRNA), and circular RNA (circRNA) in paroxysmal and persistent atrial fibrillation patients. Anatol J Cardiol 2020; 25:414-428. [PMID: 34100729 DOI: 10.14744/anatoljcardiol.2020.57295] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
OBJECTIVE This study aimed to investigate the functions of mRNA, long non-coding RNA (lncRNA), and circular RNA (circRNA) in paroxysmal and persistent atrial fibrillation (AF) patients. METHODS A total of 9 left atrial appendage (LAA) tissues were collected from patients with AF (ParoAF patients = 3 and PersAF patients = 3) and donors (n=3). Genes and circRNAs were identified by per kilobase per million reads (RPKM) and number of circular reads/number of mapped reads/read length (SRPBM), respectively. Differentially expressed mRNAs (DE mRNAs), lncRNAs (DE lncRNAs), and circRNAs (DE circRNAs) were identified by | log2 (Fold Change) | ≥ 2 and p-value < 0.05. Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed. Protein-protein, mRNA-lncRNA, and circRNA-miRNA interaction networks were constructed. In addition, logistic analysis was conducted among AF and circRNAs. RESULTS A total of 285 (116 up-regulated and 169 down-regulated) and 275 (110 up-regulated and 165 down-regulated) DE mRNAs, 575 (276 up-regulated and 299 down-regulated) and 583 (330 up-regulated and 253 down-regulated) DE lncRNAs, and 83 (48 up-regulated and 35 down-regulated) and 99 (58 up-regulated and 41 down-regulated) circRNAs were detected in ParoAF and PersAF, respectively, as compared with control. MAPK signal pathway as well as voltage-dependent, L type, and alpha 1C subunit calcium channel (CACNA1C) might participate in AF occurrence by preventing atrial parasympathetic remodeling. Collagen type I alpha 1 (COL1A1) and COL1A2 mostly participated in the enriched GO and KEGG terms and connected with most of the DE mRNAs. The expression of chr10: 69902697|69948883 was a protective factor against PersAF after adjusting for age (p=0.022, 95% CI: 0.003-0.634). CONCLUSION We found that some mRNAs, lncRNAs, circRNAs, and pathways play essential roles in AF pathogenesis and development. Moreover, one protective factor against PersAF was detected.
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21
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Lei X, Fang Z. GBDTCDA: Predicting circRNA-disease Associations Based on Gradient Boosting Decision Tree with Multiple Biological Data Fusion. Int J Biol Sci 2019; 15:2911-2924. [PMID: 31853227 PMCID: PMC6909967 DOI: 10.7150/ijbs.33806] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 10/15/2019] [Indexed: 12/17/2022] Open
Abstract
Circular RNA (circRNA) is a closed-loop structural non-coding RNA molecule which plays a significant role during the gene regulation processes. There are many previous studies shown that circRNAs can be regarded as the sponges of miRNAs. Thus, circRNA is also a key point for disease diagnosing, treating and inferring. However, traditional experimental approaches to verify the associations between the circRNA and disease are time-consuming and money-consuming. There are few computational models to predict potential circRNA-disease associations, which become our motivation to propose a new computational model. In this study, we propose a machine learning based computational model named Gradient Boosting Decision Tree with multiple biological data to predict circRNA-disease associations (GBDTCDA). The known circRNA-disease associations' data are downloaded from cricR2Disease database (http://bioinfo.snnu.edu.cn/CircR2Disease/). The feature vector of each circRNA-disease association pair is composed of four parts, which are the statistics information of different biological networks, the graph theory information of different biological networks, circRNA-disease associations' network information and circRNA nucleotide sequence information, respectively. Therefore, we use those feature vectors to train the gradient boosting decision tree regression model. Then, the leave one out cross validation (LOOCV) is adopted to evaluate the performance of our computational model. As for predicting some common diseases related circRNAs, our method GBDTCDA also obtains the better results. The Area under the ROC Curve (AUC) values of Basal cell carcinoma, Non-small cell lung cancer and cervical cancer are 95.8%, 88.3% and 93.5%, respectively. For further illustrating the performance of GBDTCDA, a case study of breast cancer is also supplemented in this study. Thus, our proposed method GBDTCDA is a powerful tool to predict potential circRNA-disease associations based on experimental results and analyses.
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Affiliation(s)
- Xiujuan Lei
- School of Computer Science, Shaanxi Normal University, Xi'an 710119, China
| | - Zengqiang Fang
- School of Computer Science, Shaanxi Normal University, Xi'an 710119, China
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22
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Zhou Z, Sun B, Huang S, Zhao L. Roles of circular RNAs in immune regulation and autoimmune diseases. Cell Death Dis 2019; 10:503. [PMID: 31243263 PMCID: PMC6594938 DOI: 10.1038/s41419-019-1744-5] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 06/08/2019] [Accepted: 06/12/2019] [Indexed: 01/08/2023]
Abstract
Circular RNAs (circRNAs), as a novel class of endogenously expressed non-coding RNAs (ncRNAs), have a high stability and often present tissue-specific expression and evolutionary conservation. Emerging evidence has suggested that circRNAs play an essential role in complex human pathologies. Notably, circRNAs, important gene modulators in the immune system, are strongly associated with the occurrence and development of autoimmune diseases. Here, we focus on the roles of circRNAs in immune cells and immune regulation, highlighting their potential as biomarkers and biological functions in autoimmune diseases, such as systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), multiple sclerosis (MS), primary biliary cholangitis (PBC), and psoriasis, aiming at providing new insights into the diagnosis and therapy of these diseases.
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Affiliation(s)
- Zheng Zhou
- Department of Chinese Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000, China
| | - Bao Sun
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410000, China.,Hunan Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, Changsha, 410000, China
| | - Shiqiong Huang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410000, China.,Hunan Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, Changsha, 410000, China
| | - Lingling Zhao
- Department of Chinese Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000, China.
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