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Wang L, Ran L, Tian Y, Jin Y, Yi J, He X. Effect of thrombomodulin gene polymorphisms on venous thromboembolism: An analysis of evidence involving 6,629 patients. Vascular 2024; 32:374-384. [PMID: 36278273 DOI: 10.1177/17085381221135698] [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] [Indexed: 02/18/2024]
Abstract
BACKGROUD The association between thrombomodulin gene (THBD) c.1418 C>T polymorphisms and the risk of venous thromboembolism (VTE) is controversial. The purpose of this meta-analysis was to evaluate THBD c.1418 C>T polymorphisms and the risk of VTE. METHODS Computer searches were performed on the CNKI, Wanfang database, VIP database, PubMed, Embase, Web of Science, and Cochrane Library databases. The retrieval time limit was from the establishment of the database to June 2022. Case-control studies and cohort studies of THBD c.1418 C>T polymorphisms associated with VTE were included. The literature was screened according to inclusion and exclusion criteria, data extraction and literature quality evaluation. Meta-analysis was performed using STATA 14.0 software. RESULTS A total of 12 literature were included, including 2980 cases in the case group and 3649 cases in the control group. The meta-analysis results showed no significant association of the THBD c.1418 C> T polymorphisms with the occurrence of VTE (T vs C: OR = 1.17, 95%CI = 0.93-1.48; TT vs CT+CC: OR = 1.00, 95%CI = 0.75-1.33; TT+CT vs CC: OR = 1.22, 95%CI = 0.94-1.59). Subgroup analyses revealed an increased risk of VTE in Asian populations due to THBD c.1418 C>T polymorphisms (T vs C: OR = 1.48, 95%CI = 1.06-2.07; TT vs CT+CC: OR = 1.80, 95%CI = 1.13-2.85; TT+CT vs CC: OR = 1.58, 95%CI = 1.07-2.32). THBD c.1418 C>T polymorphisms increased the risk of DVT (T vs C: OR = 1.51, 95%CI = 1.24-1.85; TT vs CT+CC: OR = 1.85, 95%CI = 1.10-3.12; TT+CT vs CC: OR = 1.64, 95%CI = 1.28-2.11). THBD c.1418 C>T polymorphisms reduced the risk of VTE in non-Asian populations (TT vs CT+CC: OR = 0.66, 95%CI = 0.45-0.98). CONCLUSION THBD c.1418 C>T polymorphisms is associated with VTE in Asian population, which may be a factor in the occurrence of VTE in Asian population. THBD c.1418 C>T polymorphisms increases the risk of DVT. Given the limitations of this meta-analysis, the conclusions require being further supported by large-scale and high-quality studies.
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Affiliation(s)
- Lang Wang
- Nursing Department, Zhuzhou Central Hospital, Zhuzhou, China
| | - Luqin Ran
- Department of Oncology, Chongqing General Hospital, Chomgqing, China
| | - Yanzhen Tian
- Nursing Department, Zhuzhou Central Hospital, Zhuzhou, China
| | - Yunrui Jin
- Department of Oncology, Chongqing General Hospital, Chomgqing, China
| | - Jinhua Yi
- Operating Theater, Zhuzhou Central Hospital, Zhuzhou, China
| | - Xiaoyuan He
- Nursing Department, Zhuzhou Central Hospital, Zhuzhou, China
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2
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Le LTT, Nhu CXT. The Role of Long Non-Coding RNAs in Cardiovascular Diseases. Int J Mol Sci 2023; 24:13805. [PMID: 37762106 PMCID: PMC10531487 DOI: 10.3390/ijms241813805] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 08/04/2023] [Accepted: 08/11/2023] [Indexed: 09/29/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are non-coding RNA molecules longer than 200 nucleotides that regulate gene expression at the transcriptional, post-transcriptional, and translational levels. Abnormal expression of lncRNAs has been identified in many human diseases. Future improvements in diagnostic, prognostic, and therapeutic techniques will be facilitated by a deeper understanding of disease etiology. Cardiovascular diseases (CVDs) are the main cause of death globally. Cardiac development involves lncRNAs, and their abnormalities are linked to many CVDs. This review examines the relationship and function of lncRNA in a variety of CVDs, including atherosclerosis, myocardial infarction, myocardial hypertrophy, and heart failure. Therein, the potential utilization of lncRNAs in clinical diagnostic, prognostic, and therapeutic applications will also be discussed.
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Affiliation(s)
- Linh T. T. Le
- Biotechnology Department, Ho Chi Minh City Open University, Ho Chi Minh City 70000, Vietnam;
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3
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He S, Zhang S, Wang YJ, Gan XK, Chen JX, Zhou HX, Jia EZ. Long non-coding RNA in coronary artery disease: the role of PDXDC1-AS1 and SFI1-AS1. Funct Integr Genomics 2023; 23:219. [PMID: 37394483 DOI: 10.1007/s10142-023-01134-9] [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: 12/15/2022] [Revised: 06/08/2023] [Accepted: 06/09/2023] [Indexed: 07/04/2023]
Abstract
This study investigates the interaction between long non-coding RNAs (lncRNAs) and metabolic risk factors that contribute to coronary artery disease (CAD). A total transcriptome high throughput sequencing study was conducted on peripheral blood mononuclear cells from five patients with CAD and five healthy controls. Validation assay by qRT-PCR was conducted among 270 patients and 47 controls. Finally, to evaluate the lncRNAs' diagnostic value for CAD, the Spearman correlation test and receiver operating characteristic curve (ROC) analysis were utilized. Additionally, univariate and multivariate logistic regression along with crossover analyses were conducted to identify the interaction between lncRNA and environmental risk factors. A total of 2149 of 26,027 lncRNAs identified by RNA sequencing were differentially expressed in CAD patients compared to controls. Validation by qRT-PCR showed significantly different relative expression levels for lncRNAs PDXDC1-AS1, SFI1-AS1, RP13-143G15.3, DAPK1-IT1, PPIE-AS1, and RP11-362A1.1 between the two groups (all P<0.05). The area under the ROC values of PDXDC1-AS1 and SFI1-AS1 is 0.645 (sensitivity=0.443 and specificity=0.920) and 0.629 (sensitivity=0.571 and specificity=0.909), especially. Multivariate logistic regression analyses showed that lncRNAs PDXDC1-AS1 (OR=2.285, 95%CI=1.390-3.754, p=0.001) and SFI1-AS1 (OR=1.163, 95%CI=1.163-2.264, p=0.004) were protective factors against CAD. Under the additive model, cross-over analyses demonstrated significant interactions between lncRNAs PDXDC1-AS1 and smoking in relation to CAD risk (S=3.871, 95%CI=1.140-6.599). PDXDC1-AS1 and SFI1-AS1 were sensitive and specific biomarkers for CAD and exhibited synergistic effects with certain environmental factors. These results highlighted their potential use as CAD diagnostic biomarkers for future research.
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Affiliation(s)
- Shu He
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Nanjing Medical University, Guangzhou Road 300, Nanjing, 210029, Jiangsu Province, China
| | - Sheng Zhang
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Nanjing Medical University, Guangzhou Road 300, Nanjing, 210029, Jiangsu Province, China
| | - Yan-Jun Wang
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Nanjing Medical University, Guangzhou Road 300, Nanjing, 210029, Jiangsu Province, China
| | - Xiong-Kang Gan
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Nanjing Medical University, Guangzhou Road 300, Nanjing, 210029, Jiangsu Province, China
| | - Jia-Xin Chen
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Nanjing Medical University, Guangzhou Road 300, Nanjing, 210029, Jiangsu Province, China
| | - Han-Xiao Zhou
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Nanjing Medical University, Guangzhou Road 300, Nanjing, 210029, Jiangsu Province, China
| | - En-Zhi Jia
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Nanjing Medical University, Guangzhou Road 300, Nanjing, 210029, Jiangsu Province, China.
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4
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Ao X, Ding W, Li X, Xu Q, Chen X, Zhou X, Wang J, Liu Y. Non-coding RNAs regulating mitochondrial function in cardiovascular diseases. J Mol Med (Berl) 2023; 101:501-526. [PMID: 37014377 DOI: 10.1007/s00109-023-02305-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/14/2023] [Accepted: 03/13/2023] [Indexed: 04/05/2023]
Abstract
Cardiovascular disease (CVD) is the leading cause of disease-related death worldwide and a significant obstacle to improving patients' health and lives. Mitochondria are core organelles for the maintenance of myocardial tissue homeostasis, and their impairment and dysfunction are considered major contributors to the pathogenesis of various CVDs, such as hypertension, myocardial infarction, and heart failure. However, the exact roles of mitochondrial dysfunction involved in CVD pathogenesis remain not fully understood. Non-coding RNAs (ncRNAs), particularly microRNAs, long non-coding RNAs, and circular RNAs, have been shown to be crucial regulators in the initiation and development of CVDs. They can participate in CVD progression by impacting mitochondria and regulating mitochondrial function-related genes and signaling pathways. Some ncRNAs also exhibit great potential as diagnostic and/or prognostic biomarkers as well as therapeutic targets for CVD patients. In this review, we mainly focus on the underlying mechanisms of ncRNAs involved in the regulation of mitochondrial functions and their role in CVD progression. We also highlight their clinical implications as biomarkers for diagnosis and prognosis in CVD treatment. The information reviewed herein could be extremely beneficial to the development of ncRNA-based therapeutic strategies for CVD patients.
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Affiliation(s)
- Xiang Ao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao, 266021, China
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao, 266071, China
| | - Wei Ding
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266021, China
| | - Xiaoge Li
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao, 266071, China
| | - Qingling Xu
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao, 266071, China
| | - Xinhui Chen
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao, 266071, China
| | - Xuehao Zhou
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao, 266071, China
| | - Jianxun Wang
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao, 266071, China
| | - Ying Liu
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao, 266021, China.
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5
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Vanhaverbeke M, Attard R, Bartekova M, Ben-Aicha S, Brandenburger T, de Gonzalo-Calvo D, Emanueli C, Farrugia R, Grillari J, Hackl M, Kalocayova B, Martelli F, Scholz M, Wettinger SB, Devaux Y. Peripheral blood RNA biomarkers for cardiovascular disease from bench to bedside: a position paper from the EU-CardioRNA COST action CA17129. Cardiovasc Res 2022; 118:3183-3197. [PMID: 34648023 PMCID: PMC9799060 DOI: 10.1093/cvr/cvab327] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 10/06/2021] [Accepted: 10/12/2021] [Indexed: 01/25/2023] Open
Abstract
Despite significant advances in the diagnosis and treatment of cardiovascular diseases, recent calls have emphasized the unmet need to improve precision-based approaches in cardiovascular disease. Although some studies provide preliminary evidence of the diagnostic and prognostic potential of circulating coding and non-coding RNAs, the complex RNA biology and lack of standardization have hampered the translation of these markers into clinical practice. In this position paper of the CardioRNA COST action CA17129, we provide recommendations to standardize the RNA development process in order to catalyse efforts to investigate novel RNAs for clinical use. We list the unmet clinical needs in cardiovascular disease, such as the identification of high-risk patients with ischaemic heart disease or heart failure who require more intensive therapies. The advantages and pitfalls of the different sample types, including RNAs from plasma, extracellular vesicles, and whole blood, are discussed in the sample matrix, together with their respective analytical methods. The effect of patient demographics and highly prevalent comorbidities, such as metabolic disorders, on the expression of the candidate RNA is presented and should be reported in biomarker studies. We discuss the statistical and regulatory aspects to translate a candidate RNA from a research use only assay to an in-vitro diagnostic test for clinical use. Optimal planning of this development track is required, with input from the researcher, statistician, industry, and regulatory partners.
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Affiliation(s)
- Maarten Vanhaverbeke
- Department of Cardiovascular Medicine, University Hospitals Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Ritienne Attard
- Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida MSD 2080, Malta
| | - Monika Bartekova
- Institute for Heart Research, Centre of Experimental Medicine, Slovak Academy of Sciences, Dúbravská cesta 9, 84104 Bratislava, Slovakia
- Faculty of Medicine, Institute of Physiology, Comenius University, Sasinkova 2, 81372 Bratislava, Slovakia
| | - Soumaya Ben-Aicha
- Faculty of Medicine, Imperial College London, ICTEM Building, Du Cane Road, London W12 0NN, UK
| | - Timo Brandenburger
- Department of Anesthesiology, University Hospital Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - David de Gonzalo-Calvo
- Translational Research in Respiratory Medicine, IRBLleida, University Hospital Arnau de Vilanova and Santa Maria, Av. Alcalde Rovira Roure 80, 25198, Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Av. de Monforte de Lemos, 28029, Madrid, Spain
| | - Costanza Emanueli
- Faculty of Medicine, Imperial College London, ICTEM Building, Du Cane Road, London W12 0NN, UK
| | - Rosienne Farrugia
- Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida MSD 2080, Malta
| | - Johannes Grillari
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, AUVA Research Center, Donaueschingenstraße 13, 1200, Vienna, Austria
- Institute of Molecular Biotechnology, BOKU - University of Natural Resources and Life Sciences, Gregor-Mendel-Straße 33, 1180 Vienna, Austria
| | | | - Barbora Kalocayova
- Institute for Heart Research, Centre of Experimental Medicine, Slovak Academy of Sciences, Dúbravská cesta 9, 84104 Bratislava, Slovakia
| | - Fabio Martelli
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, Milan 20097, Italy
| | - Markus Scholz
- Institute of Medical Informatics, Statistics and Epidemiology, University of Leipzig, Haertelstrasse 16-18, 04107 Leipzig, Germany
| | - Stephanie Bezzina Wettinger
- Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida MSD 2080, Malta
| | - Yvan Devaux
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, 1A-B rue Edison, L-1445 Strassen, Luxembourg
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Guo Y, Jiang H, Wang J, Li P, Zeng X, Zhang T, Feng J, Nie R, Liu Y, Dong X, Hu Q. 5mC modification patterns provide novel direction for early acute myocardial infarction detection and personalized therapy. Front Cardiovasc Med 2022; 9:1053697. [PMID: 36620624 PMCID: PMC9816341 DOI: 10.3389/fcvm.2022.1053697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Background Most deaths from coronary artery disease (CAD) are due to acute myocardial infarction (AMI). There is an urgent need for early AMI detection, particularly in patients with stable CAD. 5-methylcytosine (5mC) regulatory genes have been demonstrated to involve in the progression and prognosis of cardiovascular diseases, while little research examined 5mC regulators in CAD to AMI progression. Method Two datasets (GSE59867 and GSE62646) were downloaded from Gene Expression Omnibus (GEO) database, and 21 m5C regulators were extracted from previous literature. Dysregulated 5mC regulators were screened out by "limma." The least absolute shrinkage and selection operator (LASSO) and support vector machine recursive feature elimination (SVM-RFE) algorithm were employed to identify hub 5mC regulators in CAD to AMI progression, and 43 clinical samples (Quantitative real-time PCR) were performed for expression validation. Then a logistic model was built to construct 5mC regulator signatures, and a series of bioinformatics algorithms were performed for model validation. Besides, 5mC-associated molecular clusters were studied via unsupervised clustering analysis, and correlation analysis between immunocyte and 5mC regulators in each cluster was conducted. Results Nine hub 5mC regulators were identified. A robust model was constructed, and its prominent classification accuracy was verified via ROC curve analysis (area under the curve [AUC] = 0.936 in the training cohort and AUC = 0.888 in the external validation cohort). Besides, the clinical effect of the model was validated by decision curve analysis. Then, 5mC modification clusters in AMI patients were identified, along with the immunocyte infiltration levels of each cluster. The correlation analysis found the strongest correlations were TET3-Mast cell in cluster-1 and TET3-MDSC in cluster-2. Conclusion Nine hub 5mC regulators (DNMT3B, MBD3, UHRF1, UHRF2, NTHL1, SMUG1, ZBTB33, TET1, and TET3) formed a diagnostic model, and concomitant results unraveled the critical impact of 5mC regulators, providing interesting epigenetics findings in AMI population vs. stable CAD.
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Affiliation(s)
- Yiqun Guo
- Department of Interventional Radiology and Vascular, Guangzhou Women and Children’s Medical Center, The Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Hua Jiang
- Department of Interventional Radiology and Vascular, Guangzhou Women and Children’s Medical Center, The Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jinlong Wang
- Department of Cardiology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, China
| | - Ping Li
- Department of Cardiology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, China
| | - Xiaoquan Zeng
- Department of Cardiology, Xinfeng County People’s Hospital, Shaoguan, Guangdong, China
| | - Tao Zhang
- Department of Cardiology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, China
| | - Jianyi Feng
- Department of Cardiology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, China
| | - Ruqiong Nie
- Department of Cardiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yulong Liu
- Department of Intervention and Vascular Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, China,*Correspondence: Yulong Liu,
| | - Xiaobian Dong
- Department of Cardiology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, China,Xiaobian Dong,
| | - Qingsong Hu
- Department of Cardiology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, China,Qingsong Hu,
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Li L, Xie W. LncRNA HDAC11-AS1 Suppresses Atherosclerosis by Inhibiting HDAC11-Mediated Adropin Histone Deacetylation. J Cardiovasc Transl Res 2022; 15:1256-1269. [PMID: 35505157 DOI: 10.1007/s12265-022-10248-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 03/31/2022] [Indexed: 12/16/2022]
Abstract
LncRNA HDAC11-AS1 (HDAC11-AS1) is the natural antisense transcript of HDAC11, a key enzyme for DNA histone deacetylation. We evaluated the role of HDAC11-AS1 in atherosclerosis. In this research, we found that HDAC11-AS1 ameliorated blood lipid levels and atherosclerosis in high fat-dieted apoE-/- mice by regulating HDAC11 negatively. The change in blood lipid levels is related to the expression of LPL, which is enhanced by HDAC11-AS1 through regulating adropin histone deacetylation in vitro and in vivo. In conclusion, HDAC11-AS1 plays an anti-atherogenic role through adropin to induce LPL expressions, thereby enhancing TG metabolism. The results are valuable for the further development of HDAC11-AS1 and its clinical applications. It provides a new clinical therapeutic target for cardiovascular disease treatment.
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Affiliation(s)
- Liang Li
- Department of Physiology, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Wei Xie
- Clinical Anatomy & Reproductive Medicine Application Institute, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China.
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Liu G, Hu X, Li Y, Long M. Circulating long non-coding RNA Coromarker expression correlated with inflammation, coronary artery stenosis, and plaque vulnerability in patients with coronary artery disease. J Clin Lab Anal 2022; 36:e24716. [PMID: 36164725 DOI: 10.1002/jcla.24716] [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: 07/28/2022] [Revised: 09/16/2022] [Accepted: 09/16/2022] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND The aim of the study was to assess the correlation between circulating long non-coding RNA (lncRNA) OTTHUMT00000387022 (named Coromarker) expression and disease severity, inflammatory cytokine levels, and plaque vulnerability in patients with coronary artery disease (CAD). METHODS A total of 134 participants who received coronary angiography were enrolled and classified them as CAD patients (N = 89) and controls (N = 45). Blood samples were obtained from all subjects. Quantitative polymerase chain reaction was used to evaluate Coromarker expression. The enzyme-linked immunosorbent test was used to measure inflammatory cytokines including high sensitivity C reactive protein (hsCRP), interleukin (IL)-1β (IL-1β), IL-6, NOD-like receptor protein 3 (NLRP3), and markers of coronary plaque stability including matrix metallopeptidase 9 (MMP-9) and soluble CD40 ligand (sCD40L). The severity of coronary stenosis was determined from the Gensini Score. RESULTS LncRNA Coromarker expression was elevated to a greater extent in CAD patients than in control subjects before and after adjustments for age/gender (both p < 0.001); it was an independent predictor of CAD risk (area under curve: 0.824, 95% CI: 0.732-0.915). Additionally, Coromarker expression was significantly associated with Gensini Score (r = 0.574, p < 0.001), hsCRP (r = 0.221, p = 0.015), IL-1β (r = 0.351, p < 0.001), IL-6 (r = 0.286, p < 0.01), and NLRP3 levels (r = 0.312, p < 0.001). Coromarker expression was found to be linked with MMP-9 (r = 0.260, p < 0.01) and sCD40L (r = 0.441, p < 0.001). CONCLUSION Circulating lncRNA Coromarker expression correlates with increased disease severity and inflammation as well as plaque vulnerability in patients with CAD.
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Affiliation(s)
- Gang Liu
- Department of Cardiology, The First Affiliated Hospital Sun Yat-Sen University, Guangzhou, China.,Key Laboratory on Assisted Circulation, Ministry of Health, Guangzhou, China
| | - Xun Hu
- Department of Cardiology, The First Affiliated Hospital Sun Yat-Sen University, Guangzhou, China.,Key Laboratory on Assisted Circulation, Ministry of Health, Guangzhou, China
| | - Yi Li
- Department of Cardiology, The First Affiliated Hospital Sun Yat-Sen University, Guangzhou, China.,Key Laboratory on Assisted Circulation, Ministry of Health, Guangzhou, China
| | - Ming Long
- Department of Cardiology, The First Affiliated Hospital Sun Yat-Sen University, Guangzhou, China.,Key Laboratory on Assisted Circulation, Ministry of Health, Guangzhou, China
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Scheurer T, Steffens J, Markert A, Du Marchie Sarvaas M, Roderburg C, Rink L, Tacke F, Luedde T, Kraus T, Baumann R. The human long noncoding RNAs CoroMarker, MALAT1, CDR1as, and LINC00460 in whole blood of individuals after controlled short-term exposure with ultrafine metal fume particles at workplace conditions, and in human macrophages in vitro. J Occup Med Toxicol 2022; 17:15. [PMID: 35915466 PMCID: PMC9344619 DOI: 10.1186/s12995-022-00356-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 07/12/2022] [Indexed: 11/24/2022] Open
Abstract
Background Short-term inhalation of occupationally relevant ultrafine zinc/copper (Zn/Cu) containing welding fumes has been shown to induce subclinical systemic inflammation, associated with an elevated risk for cardiovascular diseases. The involvement of noncoding RNAs (lncRNAs) in this setting is currently unknown. However, lncRNAs have been reported to fulfill essential roles in, e.g., cardiovascular diseases, inflammation, infectious diseases, and pollution-related lung disorders. Methods In this study, the specific lncRNAs levels of the 4 lncRNAs CoroMarker, MALAT1, CDR1as and LINC00460 were determined by RT-qPCR in THP-1 macrophages exposed to Zn/Cu metal fume suspensions for 1, 2, and 4 hours in vitro. Furthermore, 14 subjects were exposed to Zn/Cu containing welding fumes (at 2.5 mg/m3) for 6 hours. Before, 6, 10, and 29 hours after exposure start, whole blood cell lncRNAs levels were determined by RT-qPCR. Results In THP-1 macrophages, we observed a 2.3-fold increase of CDR1as at 1 h (Wilcoxon p = 0.03), a non-significant increase of CoroMarker at 1 h, and an increase of LINC00460 at 2 h (p = 0.03) and at 4 h (p = 0.06). In whole blood cells, we determined a non-significant upregulation of CDR1as at 6 h (p = 0.2), a significant downregulation of CoroMarker at 6 h (p = 0.04), and a significant upregulation of LINC00460 levels at 10 h (p = 0.04) and 29 h (p = 0.04). MALAT-1 remained unchanged in both settings. Conclusion The orientation of regulation of the lncRNAs is (except for CoroMarker) similar in the in vitro and in vivo experiments and in line with their described functions. Therefore, these results, e.g. the upregulation of the potential risk marker for cardiovascular diseases, CDR1as, contribute to understanding the underlying mechanisms of Zn/Cu-induced subclinical inflammation in metal workers.
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Affiliation(s)
- Theresa Scheurer
- Institute for Occupational, Social and Environmental Medicine, Medical Faculty, University Hospital RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany
| | - Jan Steffens
- Institute for Occupational, Social and Environmental Medicine, Medical Faculty, University Hospital RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany. .,Institute for Translational Medicine (ITM), Medical School Hamburg (MSH) - Am Kaiserkai 1, 20457, Hamburg, Germany.
| | - Agnieszka Markert
- Institute for Occupational, Social and Environmental Medicine, Medical Faculty, University Hospital RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany
| | - Miriam Du Marchie Sarvaas
- Institute for Occupational, Social and Environmental Medicine, Medical Faculty, University Hospital RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany
| | - Christoph Roderburg
- Department of Medicine III, Medical Faculty, University Hospital RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany.,Department of Hepatology and Gastroenterology, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany.,Clinic for Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Moorenstr. 5, 40225, Duesseldorf, Germany
| | - Lothar Rink
- Institute of Immunology, Medical Faculty, University Hospital RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany
| | - Frank Tacke
- Department of Medicine III, Medical Faculty, University Hospital RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany.,Department of Hepatology and Gastroenterology, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Tom Luedde
- Department of Medicine III, Medical Faculty, University Hospital RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany.,Clinic for Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Moorenstr. 5, 40225, Duesseldorf, Germany
| | - Thomas Kraus
- Institute for Occupational, Social and Environmental Medicine, Medical Faculty, University Hospital RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany
| | - Ralf Baumann
- Institute for Occupational, Social and Environmental Medicine, Medical Faculty, University Hospital RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany.,Institute for Translational Medicine (ITM), Medical School Hamburg (MSH) - Am Kaiserkai 1, 20457, Hamburg, Germany
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10
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Zhang T, Luo JY, Liu F, Zhang XH, Luo F, Yang YN, Li XM. Long noncoding RNA MALAT1 polymorphism predicts MACCEs in patients with myocardial infarction. BMC Cardiovasc Disord 2022; 22:152. [PMID: 35392816 PMCID: PMC8991554 DOI: 10.1186/s12872-022-02590-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 03/21/2022] [Indexed: 11/21/2022] Open
Abstract
Background Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) participates in the occurrence and development of cardiovascular and cerebrovascular diseases such as stroke and coronary heart disease by regulating inflammatory reactions, programmed cell death, and other pathological processes. Previous studies revealed that the MALAT1 gene polymorphism was associated with cardiac and cerebrovascular diseases. However, the prognostic role of the MALAT1 polymorphism in major adverse cardiac and cerebrovascular events (MACCEs) remains unknown. Therefore, this study intends to explore the association between the MALAT1 rs3200401 polymorphism and MACCEs. Method We enrolled 617 myocardial infarction (MI) patients and 1125 control participants who attended the First Affiliated Hospital of Xinjiang Medical University from January 2010 to 2018. SNPscan™ typing assays were used to detect the MALAT1 rs3200401 genotype. During the follow-up, MACCEs were recorded. Kaplan–Meier curves and univariate and multivariate Cox survival analyses were used to explore the correlation between MALAT1 gene polymorphisms and the occurrence of MACCEs. Results Among the total participants and MI patients, the frequencies of the T allele (total Participants 19.5% vs. 15.3%, P = 0.047, MI patients 20.7% vs. 14.1%, P = 0.014) and CT + TT genotypes (total Participants 37.4% vs. 28.1%, P = 0.013, MI patients 39.5% vs. 25.8%, P = 0.003) were significantly higher in subjects with MACCEs than in subjects without MACCEs. However, in control participants, the frequencies of the T allele (16.6% vs. 16.0%, P = 0.860) and CT + TT genotypes (31.4% vs. 29.3%, P = 0.760) were not higher in subjects with MACCEs than in subjects without MACCEs. In addition, among the total participants and MI patients, the Kaplan–Meier curve analysis indicated that the subjects with rs3200401 CT + TT genotypes had a higher incidence of MACCEs than CC genotype carriers (P = 0.015, P = 0.001). Nevertheless, similar results were not observed in the control participants (P = 0.790). Multivariate Cox regression indicated that compared with patients with the CC genotype, patients with CT + TT genotypes had a 1.554-fold increase in MACCE risk (hazard ratio: 1.554, 95% confidence interval: 1.060–2.277, P = 0.024). Conclusions The MALAT1 rs3200401 CT + TT genotypes could be a risk factor for MACCEs in MI patients, suggesting that the MALAT1 gene may become a biomarker for poor prognosis in MI patients.
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Affiliation(s)
- Tong Zhang
- Department of Cardiology, The First Affiliated Hospital of Xinjiang Medical University, 137 Liyushan South Road, Urumqi, 830054, Xinjiang, China
| | - Jun-Yi Luo
- Department of Cardiology, The First Affiliated Hospital of Xinjiang Medical University, 137 Liyushan South Road, Urumqi, 830054, Xinjiang, China
| | - Fen Liu
- Xinjiang Key Laboratory of Cardiovascular Disease Research, Urumqi, 830054, Xinjiang, China
| | - Xue-He Zhang
- Department of Cardiology, The First Affiliated Hospital of Xinjiang Medical University, 137 Liyushan South Road, Urumqi, 830054, Xinjiang, China
| | - Fan Luo
- Department of Cardiology, The First Affiliated Hospital of Xinjiang Medical University, 137 Liyushan South Road, Urumqi, 830054, Xinjiang, China
| | - Yi-Ning Yang
- Department of Cardiology, The First Affiliated Hospital of Xinjiang Medical University, 137 Liyushan South Road, Urumqi, 830054, Xinjiang, China. .,Xinjiang Key Laboratory of Cardiovascular Disease Research, Urumqi, 830054, Xinjiang, China. .,People's Hospital of Xinjiang Uygur Autonomous Region, 91 Tianchi Road, Urumqi, 830054, Xinjiang, China.
| | - Xiao-Mei Li
- Department of Cardiology, The First Affiliated Hospital of Xinjiang Medical University, 137 Liyushan South Road, Urumqi, 830054, Xinjiang, China. .,Xinjiang Key Laboratory of Cardiovascular Disease Research, Urumqi, 830054, Xinjiang, China.
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11
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The correlation of long non-coding RNAs IFNG-AS1 and ZEB2-AS1 with IFN-γ and ZEB-2 expression in PBMCs and clinical features of patients with coronary artery disease. Mol Biol Rep 2022; 49:3389-3399. [PMID: 35389131 DOI: 10.1007/s11033-022-07168-9] [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: 09/18/2021] [Accepted: 01/19/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND Aberrant expression of long non-coding RNAs (lncRNAs) can contribute to the pathogenesis of coronary artery disease (CAD). In this study, we aimed to evaluate the expression of lncRNA interferon γ-antisense 1 (IFNG-AS1), zinc finger E-box binding homeobox 2 antisense RNA 1 (ZEB2-AS1), and their direct target genes (IFN-γ and ZEB2, respectively) in peripheral blood mononuclear cell (PBMC) from CAD and healthy individuals. METHODS AND RESULTS We recruited 40 CAD patients and 40 healthy individuals. After doing some bioinformatics analyses, the expressions of IFNG-AS1/ ZEB2-AS1 lncRNAs and IFN-γ/ ZEB2 in PBMCs were measured using quantitative real-time PCR. The possible correlation between the putative lncRNAs and disease severity was also assessed. Receiver operating characteristic (ROC) curve analysis was used to evaluate the predictive role of lncRNAs as diagnostic biomarkers in CAD patients. The expressions of IFNG-AS1 lncRNA as well as IFN-γ and ZEB2 genes were significantly reduced in CAD patients compared to healthy subjects. In contrast, the expression of ZEB2-AS1 was up-regulated in these patients. Linear regression analysis unveiled that there is a positive correlation between the expression of IFNG-AS1 and IFN-γ, also similarly, ZEB2-AS1 and ZEB2 in PBMCs of subjects. Moreover, the expression of IFNG-AS1 and ZEB2-AS1 correlated with the Gensini score. The area under the ROC curves ranged from 0.633-0.742 for ZEB2-AS1/ZEB2 and IFNG-AS1/IFN-γ, respectively. CONCLUSIONS Our results indicated that the dysregulation of IFNG-AS1/IFN-γ and ZEB2-AS1/ZEB2 in PBMCs of CAD patients may be involved in CAD pathogenesis.
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12
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Du Y, Zhu Y, Liu Y, Liu J, Hu C, Sun Y, Zhang D, Lv S, Cheng Y, Han H, Zhang J, Zhao Y, Zhou Y. Expression profiles of long noncoding and messenger RNAs in epicardial adipose tissue derived from patients with coronary atherosclerosis. Curr Vasc Pharmacol 2022; 20:189-200. [PMID: 35049433 DOI: 10.2174/1570161120666220114095320] [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: 06/22/2021] [Revised: 08/21/2021] [Accepted: 12/02/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Given its close anatomical location to the heart and its endocrine properties, attention on epicardial adipose tissue (EAT) has increased. OBJECTIVE This study investigated the expression profiles of long noncoding RNAs (lncRNAs) and messenger RNAs (mRNAs) in EAT derived from patients with coronary artery disease (CAD). METHODS EAT samples from 8 CAD and 8 non-CAD patients were obtained during open-heart surgery. The expression of lncRNAs and mRNAs in each EAT sample was investigated using microarray analysis and further verified using reverse transcription-quantitative polymerase chain reaction. RESULTS Overall, 1,093 differentially expressed mRNAs and 2,282 differentially expressed lncRNAs were identified in EAT from CAD vs non-CAD patients. Analysis using Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes showed that these differentially expressed genes were mainly enriched in various inflammatory, immune, and metabolic processes. They were also involved in osteoclast differentiation, B cell receptor and adipocytokine signaling, and insulin resistance pathways. Additionally, lncRNA-mRNA and lncRNA-target pathway networks were built to identify potential core genes (e.g. Lnc-CCDC68-2:1, AC010148.1, NONHSAT104810) involved in atherosclerosis pathogenesis. CONCLUSION In summary, lncRNA and mRNA profiles in EAT were markedly different between CAD and non-CAD patients. Our study identifies several potential key genes and pathways that may participate in atherosclerosis development.
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Affiliation(s)
- Yu Du
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart Lung and Blood Vessel Disease, Beijing Key Laboratory of Precision Medicine of Coronary Atherosclerotic Disease, Clinical Center for Coronary Heart Disease, Capital Medical University, Beijing100029, China
| | - Yong Zhu
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart Lung and Blood Vessel Disease, Beijing Key Laboratory of Precision Medicine of Coronary Atherosclerotic Disease, Clinical Center for Coronary Heart Disease, Capital Medical University, Beijing100029, China
| | - Yan Liu
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart Lung and Blood Vessel Disease, Beijing Key Laboratory of Precision Medicine of Coronary Atherosclerotic Disease, Clinical Center for Coronary Heart Disease, Capital Medical University, Beijing100029, China
| | - Jinxing Liu
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart Lung and Blood Vessel Disease, Beijing Key Laboratory of Precision Medicine of Coronary Atherosclerotic Disease, Clinical Center for Coronary Heart Disease, Capital Medical University, Beijing100029, China
| | - Chengping Hu
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart Lung and Blood Vessel Disease, Beijing Key Laboratory of Precision Medicine of Coronary Atherosclerotic Disease, Clinical Center for Coronary Heart Disease, Capital Medical University, Beijing100029, China
| | - Yan Sun
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart Lung and Blood Vessel Disease, Beijing Key Laboratory of Precision Medicine of Coronary Atherosclerotic Disease, Clinical Center for Coronary Heart Disease, Capital Medical University, Beijing100029, China
| | - Dai Zhang
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart Lung and Blood Vessel Disease, Beijing Key Laboratory of Precision Medicine of Coronary Atherosclerotic Disease, Clinical Center for Coronary Heart Disease, Capital Medical University, Beijing100029, China
| | - Sai Lv
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart Lung and Blood Vessel Disease, Beijing Key Laboratory of Precision Medicine of Coronary Atherosclerotic Disease, Clinical Center for Coronary Heart Disease, Capital Medical University, Beijing100029, China
| | - Yujing Cheng
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart Lung and Blood Vessel Disease, Beijing Key Laboratory of Precision Medicine of Coronary Atherosclerotic Disease, Clinical Center for Coronary Heart Disease, Capital Medical University, Beijing100029, China
| | - Hongya Han
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart Lung and Blood Vessel Disease, Beijing Key Laboratory of Precision Medicine of Coronary Atherosclerotic Disease, Clinical Center for Coronary Heart Disease, Capital Medical University, Beijing100029, China
| | - Jianwei Zhang
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart Lung and Blood Vessel Disease, Beijing Key Laboratory of Precision Medicine of Coronary Atherosclerotic Disease, Clinical Center for Coronary Heart Disease, Capital Medical University, Beijing100029, China
| | - Yingxin Zhao
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart Lung and Blood Vessel Disease, Beijing Key Laboratory of Precision Medicine of Coronary Atherosclerotic Disease, Clinical Center for Coronary Heart Disease, Capital Medical University, Beijing100029, China
| | - Yujie Zhou
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart Lung and Blood Vessel Disease, Beijing Key Laboratory of Precision Medicine of Coronary Atherosclerotic Disease, Clinical Center for Coronary Heart Disease, Capital Medical University, Beijing100029, China
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Liu C, Liu L, Gao J, Wang J, Liu Y. Identification of Two Long Non-Coding RNAs AC010082.1 and AC011443.1 as Biomarkers of Coronary Heart Disease Based on Logistic Stepwise Regression Prediction Model. Front Genet 2021; 12:780431. [PMID: 34868268 PMCID: PMC8637336 DOI: 10.3389/fgene.2021.780431] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/01/2021] [Indexed: 12/23/2022] Open
Abstract
Coronary heart disease (CHD) is a global health concern with high morbidity and mortality rates. This study aimed to identify the possible long non-coding RNA (lncRNA) biomarkers of CHD. The lncRNA- and mRNA-related data of patients with CHD were downloaded from the Gene Expression Omnibus database (GSE113079). The limma package was used to identify differentially expressed lncRNAs and mRNAs (DElncRNAs and DEmRNAs, respectively). Then, miRcode, TargetScan, miRDB, and miRTarBase databases were used to form the competing endogenous RNA (ceRNA) network. Furthermore, SPSS Modeler 18.0 was used to construct a logistic stepwise regression prediction model for CHD diagnosis based on DElncRNAs. Of the microarray data, 70% was used as a training set and 30% as a test set. Moreover, a validation cohort including 30 patients with CHD and 30 healthy controls was used to verify the hub lncRNA expression through real-time reverse transcription-quantitative PCR (RT-qPCR). A total of 185 DElncRNAs (114 upregulated and 71 downregulated) and 382 DEmRNAs (162 upregulated and 220 downregulated) between CHD and healthy controls were identified from the microarray data. Furthermore, through bioinformatics prediction, a 38 lncRNA-21miRNA-40 mRNA ceRNA network was constructed. Next, by constructing a logistic stepwise regression prediction model for 38 DElncRNAs, we screened two hub lncRNAs AC010082.1 and AC011443.1 (p < 0.05). The sensitivity, specificity, and area under the curve were 98.41%, 100%, and 0.995, respectively, for the training set and 93.33%, 91.67%, and 0.983, respectively, for the test set. We further verified the significant upregulation of AC010082.1 (p < 0.01) and AC011443.1 (p < 0.05) in patients with CHD using RT-qPCR in the validation cohort. Our results suggest that lncRNA AC010082.1 and AC011443.1 are potential biomarkers of CHD. Their pathological mechanism in CHD requires further validation.
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Affiliation(s)
- Chao Liu
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China.,Graduate School, Beijing University of Chinese Medicine, Beijing, China
| | - Lanchun Liu
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China.,Graduate School, Beijing University of Chinese Medicine, Beijing, China
| | - Jialiang Gao
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jie Wang
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China.,Key Technology Laboratory of Cardiovascular Disease-Syndrome Combination, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yongmei Liu
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China.,Key Technology Laboratory of Cardiovascular Disease-Syndrome Combination, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
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14
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Wang S, Liu Y, Hu X, Zhang X, Xu L, Yang Y, Wu R, Wang E, Lv T. Identification of ceRNA (lncRNA-miRNA-mRNA) Regulatory Network in Myocardial Fibrosis After Acute Myocardial Infarction. Int J Gen Med 2021; 14:9977-9990. [PMID: 34984022 PMCID: PMC8702784 DOI: 10.2147/ijgm.s329391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 12/02/2021] [Indexed: 12/16/2022] Open
Abstract
Purpose Materials and Methods Results Conclusion
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Affiliation(s)
- Shuo Wang
- Department of Cardiovasology, Shijiazhuang People’s Hospital, Shijiazhuang, People’s Republic of China
| | - Yuying Liu
- Department of Cardiovasology, Shijiazhuang People’s Hospital, Shijiazhuang, People’s Republic of China
| | - Xitian Hu
- Department of Cardiovasology, Shijiazhuang People’s Hospital, Shijiazhuang, People’s Republic of China
- Correspondence: Xitian Hu Department of Cardiovasology, Shijiazhuang People’s Hospital, No. 9 Fangbei Road, Shijiazhuang, Hebei, 050000, People’s Republic of ChinaTel +86-17603119015 Email
| | - Xiaolei Zhang
- Department of Cardiovasology, Shijiazhuang People’s Hospital, Shijiazhuang, People’s Republic of China
| | - Lei Xu
- Department of Cardiovasology, Shijiazhuang People’s Hospital, Shijiazhuang, People’s Republic of China
| | - Yan Yang
- Department of Cardiovasology, Shijiazhuang People’s Hospital, Shijiazhuang, People’s Republic of China
| | - Rubing Wu
- Department of Cardiovasology, Shijiazhuang People’s Hospital, Shijiazhuang, People’s Republic of China
| | - Enmao Wang
- Department of Cardiovasology, Shijiazhuang People’s Hospital, Shijiazhuang, People’s Republic of China
| | - Tianjie Lv
- Department of Cardiovasology, Shijiazhuang People’s Hospital, Shijiazhuang, People’s Republic of China
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Alipoor B, Nikouei S, Rezaeinejad F, Malakooti-Dehkordi SN, Sabati Z, Ghasemi H. Long non-coding RNAs in metabolic disorders: pathogenetic relevance and potential biomarkers and therapeutic targets. J Endocrinol Invest 2021; 44:2015-2041. [PMID: 33792864 DOI: 10.1007/s40618-021-01559-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/22/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND It has been suggested that dysregulation of long non-coding RNAs (lncRNAs) could be associated with the incidence and development of metabolic disorders. AIM Accordingly, this narrative review described the molecular mechanisms of lncRNAs in the development of metabolic diseases including insulin resistance, diabetes, obesity, non-alcoholic fatty liver disease (NAFLD), cirrhosis, and coronary artery diseases (CAD). Furthermore, we investigated the up-to-date findings on the association of deregulated lncRNAs in the metabolic disorders, and potential use of lncRNAs as biomarkers and therapeutic targets. CONCLUSION LncRNAs/miRNA/regulatory proteins axis plays a crucial role in progression of metabolic disorders and may be used in development of therapeutic and diagnostic approaches.
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Affiliation(s)
- B Alipoor
- Department of Laboratory Sciences, Faculty of Paramedicine, Yasuj University of Medical Sciences, Yasuj, Iran
| | - S Nikouei
- Student Research Committee, Yasuj University of Medical Sciences, Yasuj, Iran
| | - F Rezaeinejad
- Department of Biochemistry, Faculty of Medicine, Yasuj University of Medical Sciences, Yasuj, Iran
| | | | - Z Sabati
- MSc student of Hematology, Student Research Committee, School of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - H Ghasemi
- Abadan Faculty of Medical Sciences, Abadan, Iran.
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Dysregulated Circulating Apoptosis- and Autophagy-Related lncRNAs as Diagnostic Markers in Coronary Artery Disease. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5517786. [PMID: 34513991 PMCID: PMC8426068 DOI: 10.1155/2021/5517786] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/03/2021] [Accepted: 08/16/2021] [Indexed: 12/24/2022]
Abstract
Objective Increasing evidence emphasizes the implications of dysregulated apoptosis and autophagy cellular processes in coronary artery disease (CAD). Herein, we aimed to explore apoptosis- and autophagy-related long noncoding RNAs (lncRNAs) in peripheral blood of CAD patients. Methods The mRNA and lncRNA expression profiles were retrieved from the Gene Expression Omnibus (GEO) database. With ∣fold change | >1.5 and adjusted p value < 0.05, differentially expressed apoptosis- and autophagy-related mRNAs were screened between CAD and healthy blood samples. Also, differentially expressed lncRNAs were identified for CAD. Using the psych package, apoptosis- and autophagy-related lncRNAs were defined with Spearson's correlation analysis. Receiver operating characteristic (ROC) curves were conducted for the assessment of the diagnosed efficacy of these apoptosis- and autophagy-related lncRNAs. Results Our results showed that 24 apoptosis- and autophagy-related mRNAs were abnormally expressed in CAD than normal controls. 12 circulating upregulated and 1 downregulated apoptosis- and autophagy-related lncRNAs were identified for CAD. The ROCs confirmed that AC004485.3 (AUC = 0.899), AC004920.3 (AUC = 0.93), AJ006998.2 (AUC = 0.776), H19 (AUC = 0.943), RP5-902P8.10 (AUC = 0.956), RP5-1114G22.2 (AUC = 0.883), RP11-247A12.1 (AUC = 0.885), RP11-288L9.4 (AUC = 0.928), RP11-344B5.2 (AUC = 0.858), RP11-452C8.1 (AUC = 0.929), RP11-565A3.1 (AUC = 0.893), and XXbac-B33L19.4 (AUC = 0.932) exhibited good performance in differentiating CAD from healthy controls. Conclusion Collectively, our findings proposed that circulating apoptosis- and autophagy-related lncRNAs could become underlying diagnostic markers for CAD in clinical practice.
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CAD increases the long noncoding RNA PUNISHER in small extracellular vesicles and regulates endothelial cell function via vesicular shuttling. MOLECULAR THERAPY-NUCLEIC ACIDS 2021; 25:388-405. [PMID: 34484864 PMCID: PMC8403722 DOI: 10.1016/j.omtn.2021.05.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 05/27/2021] [Indexed: 12/19/2022]
Abstract
Long noncoding RNAs (lncRNAs) have emerged as biomarkers and regulators of cardiovascular disease. However, the expression pattern of circulating extracellular vesicle (EV)-incorporated lncRNAs in patients with coronary artery disease (CAD) is still poorly investigated. A human lncRNA array revealed that certain EV-lncRNAs are significantly dysregulated in CAD patients. Circulating small EVs (sEVs) from patients with (n = 30) or without (n = 30) CAD were used to quantify PUNISHER (also known as AGAP2-antisense RNA 1 [AS1]), GAS5, MALAT1, and H19 RNA levels. PUNISHER (p = 0.002) and GAS5 (p = 0.02) were significantly increased in patients with CAD, compared to non-CAD patients. Fluorescent labeling and quantitative real-time PCR of sEVs demonstrated that functional PUNISHER was transported into the recipient cells. Mechanistically, the RNA-binding protein, heterogeneous nuclear ribonucleoprotein K (hnRNPK), interacts with PUNISHER, regulating its loading into sEVs. Knockdown of PUNISHER abrogated the EV-mediated effects on endothelial cell (EC) migration, proliferation, tube formation, and sprouting. Angiogenesis-related gene profiling showed that the expression of vascular endothelial growth factor A (VEGFA) RNA was significantly increased in EV recipient cells. Protein stability and RNA immunoprecipitation indicated that the PUNISHER-hnRNPK axis regulates the stability and binding of VEGFA mRNA to hnRNPK. Loss of PUNISHER in EVs abolished the EV-mediated promotion of VEGFA gene and protein expression. Intercellular transfer of EV-incorporated PUNISHER promotes a pro-angiogenic phenotype via a VEGFA-dependent mechanism.
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Krappinger JC, Bonstingl L, Pansy K, Sallinger K, Wreglesworth NI, Grinninger L, Deutsch A, El-Heliebi A, Kroneis T, Mcfarlane RJ, Sensen CW, Feichtinger J. Non-coding Natural Antisense Transcripts: Analysis and Application. J Biotechnol 2021; 340:75-101. [PMID: 34371054 DOI: 10.1016/j.jbiotec.2021.08.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 06/30/2021] [Accepted: 08/04/2021] [Indexed: 12/12/2022]
Abstract
Non-coding natural antisense transcripts (ncNATs) are regulatory RNA sequences that are transcribed in the opposite direction to protein-coding or non-coding transcripts. These transcripts are implicated in a broad variety of biological and pathological processes, including tumorigenesis and oncogenic progression. With this complex field still in its infancy, annotations, expression profiling and functional characterisations of ncNATs are far less comprehensive than those for protein-coding genes, pointing out substantial gaps in the analysis and characterisation of these regulatory transcripts. In this review, we discuss ncNATs from an analysis perspective, in particular regarding the use of high-throughput sequencing strategies, such as RNA-sequencing, and summarize the unique challenges of investigating the antisense transcriptome. Finally, we elaborate on their potential as biomarkers and future targets for treatment, focusing on cancer.
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Affiliation(s)
- Julian C Krappinger
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Christian Doppler Laboratory for innovative Pichia pastoris host and vector systems, Division of Cell Biology, Histology and Embryology, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria
| | - Lilli Bonstingl
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Center for Biomarker Research in Medicine, Stiftingtalstraße 5, 8010 Graz, Austria
| | - Katrin Pansy
- Division of Haematology, Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
| | - Katja Sallinger
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Center for Biomarker Research in Medicine, Stiftingtalstraße 5, 8010 Graz, Austria
| | - Nick I Wreglesworth
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, LL57 2UW Bangor, United Kingdom
| | - Lukas Grinninger
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Austrian Biotech University of Applied Sciences, Konrad Lorenz-Straße 10, 3430 Tulln an der Donau, Austria
| | - Alexander Deutsch
- Division of Haematology, Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria; BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
| | - Amin El-Heliebi
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Center for Biomarker Research in Medicine, Stiftingtalstraße 5, 8010 Graz, Austria
| | - Thomas Kroneis
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Center for Biomarker Research in Medicine, Stiftingtalstraße 5, 8010 Graz, Austria
| | - Ramsay J Mcfarlane
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, LL57 2UW Bangor, United Kingdom
| | - Christoph W Sensen
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria; Institute of Computational Biotechnology, Graz University of Technology, Petersgasse 14/V, 8010 Graz, Austria; HCEMM Kft., Római blvd. 21, 6723 Szeged, Hungary
| | - Julia Feichtinger
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Christian Doppler Laboratory for innovative Pichia pastoris host and vector systems, Division of Cell Biology, Histology and Embryology, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria.
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Zhang Q, Zheng Y, Ning M, Li T. KLRD1, FOSL2 and LILRB3 as potential biomarkers for plaques progression in acute myocardial infarction and stable coronary artery disease. BMC Cardiovasc Disord 2021; 21:344. [PMID: 34271875 PMCID: PMC8285847 DOI: 10.1186/s12872-021-01997-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/09/2021] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Myocardial infarction (MI) contributes to high mortality and morbidity and can also accelerate atherosclerosis, thus inducing recurrent event due to status changing of coronary artery walls or plaques. The research aimed to investigate the differentially expressed genes (DEGs), which may be potential therapeutic targets for plaques progression in stable coronary artery disease (CAD) and ST-elevated MI (STEMI). METHODS Two human datasets (GSE56885 and GSE59867) were analyzed by GEO2R and enrichment analysis was applied through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. To explore the seed genes, the protein-protein interaction (PPI) network was constructed and seed genes, as well as top30 ranking neighbours were screened out. To validate these findings, one human dataset GSE120521 was analyzed. Linear regression analysis and ROC curve were also performed to determine which seed genes above mentioned could be independent factors for plaques progression. Mice MI model and ELISA of seed genes were applied and ROC curve was also performed for in vivo validation. RESULTS 169 DEGs and 573 DEGs were screened out in GSE56885 and GSE59867, respectively. Utilizing GO and KEGG analysis, these DEGs mainly enriched in immune system response and cytokines interaction. PPI network analysis was carried out and 19 seed genes were screened out. To validate these findings, GSE120521 was analyzed and three genes were demonstrated to be targets for plaques progression and stable CAD progression, including KLRD1, FOSL2 and LILRB3. KLRD1 and LILRB3 were demonstrated to be high-expressed at 1d after MI compared to SHAM group and FOSL2 expression was low-expressed at 1d and 1w. To investigate the diagnostic abilities of seed genes, ROC analysis was applied and the AUCs of KLRD1, FOSL2 and LILRB3, were 0.771, 0.938 and 0.972, respectively. CONCLUSION This study provided the screened seed genes, KLRD1, FOSL2 and LILRB3, as credible molecular biomarkers for plaques status changing in CAD progression and MI recurrence. Other seed genes, such as FOS, SOCS3 and MCL1, may also be potential targets for treatment due to their special clinical value in cardiovascular diseases.
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Affiliation(s)
- Qiang Zhang
- Cardiology, The Third Central Clinical College of Tianjin Medical University, No. 83, Jintang Road, Hedong District, Tianjin, 300170, China
- Cardiology, Nankai University Affiliated Third Center Hospital, Tianjin, 300170, China
- Cardiology, The Third Central Hospital of Tianjin, 83 Jintang Road, Hedong District, Tianjin, 300170, China
| | - Yue Zheng
- Cardiology, The Third Central Clinical College of Tianjin Medical University, No. 83, Jintang Road, Hedong District, Tianjin, 300170, China
- School of Medicine, Nankai University, Tianjin, 300071, China
- Cardiology, Nankai University Affiliated Third Center Hospital, Tianjin, 300170, China
- Cardiology, The Third Central Hospital of Tianjin, 83 Jintang Road, Hedong District, Tianjin, 300170, China
- Tianjin Key Laboratory of Extracorporeal Life Support for Critical Diseases, Tianjin, China
| | - Meng Ning
- Cardiology, The Third Central Clinical College of Tianjin Medical University, No. 83, Jintang Road, Hedong District, Tianjin, 300170, China
- Cardiology, Nankai University Affiliated Third Center Hospital, Tianjin, 300170, China
- Cardiology, The Third Central Hospital of Tianjin, 83 Jintang Road, Hedong District, Tianjin, 300170, China
| | - Tong Li
- Cardiology, The Third Central Clinical College of Tianjin Medical University, No. 83, Jintang Road, Hedong District, Tianjin, 300170, China.
- Cardiology, Nankai University Affiliated Third Center Hospital, Tianjin, 300170, China.
- Cardiology, The Third Central Hospital of Tianjin, 83 Jintang Road, Hedong District, Tianjin, 300170, China.
- Tianjin Key Laboratory of Extracorporeal Life Support for Critical Diseases, Tianjin, China.
- Institute of Hepatobiliary Disease, Tianjin, China.
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Li P, Li Y, Chen L, Ma X, Yan X, Yan M, Qian B, Wang F, Xu J, Yin J, Xu G, Sun K. Long noncoding RNA uc003pxg.1 regulates endothelial cell proliferation and migration via miR‑25‑5p in coronary artery disease. Int J Mol Med 2021; 48:160. [PMID: 34212983 PMCID: PMC8262661 DOI: 10.3892/ijmm.2021.4993] [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: 01/19/2021] [Accepted: 05/21/2021] [Indexed: 12/13/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) have been reported to be associated with the progression of coronary artery disease (CAD). In our previous study, the levels of lncRNA uc003pxg.1 were upregulated in patients with CAD compared with those in control subjects. However, the role and underlying mechanism of the effects of uc003pxg.1 in CAD remain unknown. Therefore, the aim of the present study was to investigate the expression pattern and biological function of uc003pxg.1 in CAD. First, uc003pxg.1 expression levels were assessed in peripheral blood mononuclear cells isolated from patients with CAD by reverse transcription‑quantitative (RT‑q)PCR. The results demonstrated that the levels of uc003pxg.1 were significantly upregulated (~4.6‑fold) in samples from 80 patients with CAD compared with those in 80 healthy subjects. Subsequently, the present study demonstrated that small interfering RNA‑mediated uc003pxg.1 knockdown inhibited human umbilical vein endothelial cell (HUVEC) proliferation and migration, which was analyzed using the Cell Counting Kit‑8, cell cycle, EdU and Transwell assays. Additionally, the results of RT‑qPCR and western blot analyses revealed that uc003pxg.1 regulated the mRNA and protein levels of cyclin D1 and cyclin‑dependent kinase. Through high‑throughput sequencing and dual‑luciferase reporter assays, the present study demonstrated that microRNA (miR)‑25‑5p was a downstream target of uc003pxg.1. Further experiments verified that uc003pxg.1 regulated HUVEC proliferation and migration via miR‑25‑5p. The results of the present study may enhance the current understanding of the role of lncRNA uc003pxg.1 in CAD.
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Affiliation(s)
- Ping Li
- Department of Central Laboratory, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu 215008, P.R. China
| | - Yuan Li
- Department of Cardiology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu 215008, P.R. China
| | - Lu Chen
- Department of Cardiology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu 215008, P.R. China
| | - Xuexing Ma
- Department of Cardiology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu 215008, P.R. China
| | - Xinxin Yan
- Department of Central Laboratory, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu 215008, P.R. China
| | - Meina Yan
- Department of Central Laboratory, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu 215008, P.R. China
| | - Buyun Qian
- Department of Cardiology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu 215008, P.R. China
| | - Feng Wang
- Department of Central Laboratory, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu 215008, P.R. China
| | - Jingyi Xu
- Department of Central Laboratory, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu 215008, P.R. China
| | - Juan Yin
- Department of Central Laboratory, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu 215008, P.R. China
| | - Guidong Xu
- Department of Cardiology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu 215008, P.R. China
| | - Kangyun Sun
- Department of Cardiology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu 215008, P.R. China
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21
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Monocyte-to-albumin ratio as a novel predictor of long-term adverse outcomes in patients after percutaneous coronary intervention. Biosci Rep 2021; 41:229050. [PMID: 34137842 PMCID: PMC8243340 DOI: 10.1042/bsr20210154] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 06/02/2021] [Accepted: 06/15/2021] [Indexed: 12/15/2022] Open
Abstract
Background: Monocyte count and serum albumin (Alb) have been proven to be involved in the process of systemic inflammation. Therefore, we investigated the prognostic value of monocyte-to-albumin ratio (MAR) in patients who underwent percutaneous coronary intervention (PCI). Methods: We enrolled a total of 3561 patients in the present study from January 2013 to December 2017. They were divided into two groups according to MAR cut-off value (MAR < 0.014, n=2220; MAR ≥ 0.014, n=1119) as evaluated by receiver operating characteristic (ROC) curve. The average follow-up time was 37.59 ± 22.24 months. Results: The two groups differed significantly in the incidences of all-cause mortality (ACM; P<0.001), cardiac mortality (CM; P<0.001), major adverse cardiovascular events (MACEs; P=0.038), and major adverse cardiovascular and cerebrovascular events (MACCEs; P=0.037). Multivariate Cox regression analyses revealed MAR as an independent prognostic factor for ACM and CM. The incidence of ACM increased by 56.5% (hazard ratio [HR] = 1.565; 95% confidence interval [CI], 1.086–2.256; P=0.016) and that of CM increased by 76.3% (HR = 1.763; 95% CI, 1.106–2.810; P=0.017) in patients in the higher-MAR group. Kaplan–Meier survival analysis suggested that patients with higher MAR tended to have an increased accumulated risk of ACM (Log-rank P<0.001) and CM (Log-rank P<0.001). Conclusion: The findings of the present study suggested that MAR was a novel independent predictor of long-term mortality in patients who underwent PCI.
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22
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Ye WC, Huang SF, Hou LJ, Long HJ, Yin K, Hu CY, Zhao GJ. Potential Therapeutic Targeting of lncRNAs in Cholesterol Homeostasis. Front Cardiovasc Med 2021; 8:688546. [PMID: 34179148 PMCID: PMC8224755 DOI: 10.3389/fcvm.2021.688546] [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: 04/20/2021] [Accepted: 05/19/2021] [Indexed: 12/19/2022] Open
Abstract
Maintaining cholesterol homeostasis is essential for normal cellular and systemic functions. Long non-coding RNAs (lncRNAs) represent a mechanism to fine-tune numerous biological processes by controlling gene expression. LncRNAs have emerged as important regulators in cholesterol homeostasis. Dysregulation of lncRNAs expression is associated with lipid-related diseases, suggesting that manipulating the lncRNAs expression could be a promising therapeutic approach to ameliorate liver disease progression and cardiovascular disease (CVD). However, given the high-abundant lncRNAs and the poor genetic conservation between species, much work is required to elucidate the specific role of lncRNAs in regulating cholesterol homeostasis. In this review, we highlighted the latest advances in the pivotal role and mechanism of lncRNAs in regulating cholesterol homeostasis. These findings provide novel insights into the underlying mechanisms of lncRNAs in lipid-related diseases and may offer potential therapeutic targets for treating lipid-related diseases.
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Affiliation(s)
- Wen-Chu Ye
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, China
| | - Shi-Feng Huang
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, China
| | - Lian-Jie Hou
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, China
| | - Hai-Jiao Long
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, China.,Xiangya Hospital, Central South University, Changsha, China
| | - Kai Yin
- Guangxi Key Laboratory of Diabetic Systems Medicine, The Second Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
| | - Ching Yuan Hu
- Department of Human Nutrition, Food and Animal Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Guo-Jun Zhao
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, China
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23
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Ormseth MJ, Solus JF, Sheng Q, Chen SC, Ye F, Wu Q, Oeser AM, Allen R, Raggi P, Vickers KC, Stein CM. Plasma miRNAs improve the prediction of coronary atherosclerosis in patients with rheumatoid arthritis. Clin Rheumatol 2021; 40:2211-2219. [PMID: 33389220 PMCID: PMC8162679 DOI: 10.1007/s10067-020-05573-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/21/2020] [Accepted: 12/25/2020] [Indexed: 12/22/2022]
Abstract
OBJECTIVE MicroRNAs (miRNAs) regulate gene expression and are disease biomarkers. Rheumatoid arthritis (RA) patients have accelerated atherosclerosis leading to excess cardiovascular morbidity and mortality, but traditional risk factors for cardiovascular risk stratification are inadequate. In the general population, miRNAs improve cardiovascular risk estimation beyond traditional risk factors. Our objective was to develop a miRNA panel that predicts coronary atherosclerosis in RA patients. METHODS Plasma small RNA next-generation sequencing (NGS) was performed on 161 RA patients whose Agatston scores for coronary artery calcium were previously measured. Random forest analysis of plasma NGS miRNA expression was used to determine which miRNAs best differentiated between those patients with and without coronary artery calcium. Top predictive miRNAs were assayed by quantitative PCR (qPCR). Elastic net regression was used to develop the most parsimonious models with qPCR-measured miRNA concentrations and clinical variables (age, sex, ACC/AHA 10-year risk score, DAS28 score, and diabetes) separately to predict the presence of coronary artery calcium and high coronary artery calcium. C-statistics were used to assess performance model performance. RESULTS The top miRNAs which differentiated those with and without coronary atherosclerosis based on random forest analysis included let-7c-5p, miR-30e-5p, miR-30c-5p, miR-4446-3p, miR-126-5p, miR-3168, miR-425-5p, miR-126-3p, miR-30a-5p, and miR-125a-5p. For coronary artery calcium prediction, addition of all miRNAs except miR-126-3p to clinical factors improved the c-statistic modestly from 0.86 to 0.87. For high coronary artery calcium prediction, addition of all miRNAs except miR-30c-5p to clinical factors improved the c-statistic from 0.75 to 0.80. CONCLUSION A plasma miRNA panel improved the prediction of high coronary artery calcium beyond traditional risk factors and RA disease activity. Further evaluation of the miRNA panel for prediction of coronary events in RA is necessary. Key Point • A plasma microRNA panel including let-7c-5p, miR-30a-5p, miR-30e-5p, miR-125a-5p, miR-126-3p, miR-126-5p, miR-425-5p, miR-3168, and miR-4446-3p improved the prediction of high coronary artery calcium beyond clinical factors in patients with rheumatoid arthritis.
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Affiliation(s)
- Michelle J Ormseth
- Tennessee Valley Healthcare System, U.S. Department of Veterans Affairs, Nashville, TN, USA.
- Vanderbilt University Medical Center, 1161 21st Avenue South, T-3113 MCN, Nashville, TN, 37232-2681, USA.
| | - Joseph F Solus
- Vanderbilt University Medical Center, 1161 21st Avenue South, T-3113 MCN, Nashville, TN, 37232-2681, USA
| | - Quanhu Sheng
- Vanderbilt University Medical Center, 1161 21st Avenue South, T-3113 MCN, Nashville, TN, 37232-2681, USA
| | - Sheau-Chiann Chen
- Vanderbilt University Medical Center, 1161 21st Avenue South, T-3113 MCN, Nashville, TN, 37232-2681, USA
| | - Fei Ye
- Vanderbilt University Medical Center, 1161 21st Avenue South, T-3113 MCN, Nashville, TN, 37232-2681, USA
| | - Qiong Wu
- Vanderbilt University Medical Center, 1161 21st Avenue South, T-3113 MCN, Nashville, TN, 37232-2681, USA
| | - Annette M Oeser
- Vanderbilt University Medical Center, 1161 21st Avenue South, T-3113 MCN, Nashville, TN, 37232-2681, USA
| | - Ryan Allen
- Vanderbilt University Medical Center, 1161 21st Avenue South, T-3113 MCN, Nashville, TN, 37232-2681, USA
| | | | - Kasey C Vickers
- Vanderbilt University Medical Center, 1161 21st Avenue South, T-3113 MCN, Nashville, TN, 37232-2681, USA
| | - C Michael Stein
- Vanderbilt University Medical Center, 1161 21st Avenue South, T-3113 MCN, Nashville, TN, 37232-2681, USA
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24
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Wang W, Sun P, Han F, Wang C, Wang Y, Wang X, Cong L, Qu C. Transcriptome Sequencing Identifies Potential Biomarker for White Matter Lesions Diagnosis in the Hypertension Population. Neurochem Res 2021; 46:2079-2088. [PMID: 34037902 DOI: 10.1007/s11064-021-03346-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 04/21/2021] [Accepted: 05/12/2021] [Indexed: 11/29/2022]
Abstract
Hypertension is confirmed to be one of the major risk factors of leukoaraiosis (LA). However, the pathogenesis of LA is not completely understood and there is no reliable indicator for the early diagnosis of LA in the hypertensive population. This study was designed to explore the potential biomarker for LA diagnosis in patients with hypertension. And it serves as the basis for the further study of LA mechanism. In this study, This study included 110 subjects, including 50 in the LA group and 60 in the control group. First, we performed transcriptome sequencing and quantitative PCR (qPCR) in four samples from the LA group, and three from the control group (seven people) to identify relevant long non-coding RNAs (long ncRNAs or lncRNA). The 103 samples were used for qPCR validation of relevant lncRNAs and the results were consistent with the sequencing. In-depth bioinformatics analysis were performed on differentially expressed (DE) lncRNAs and mRNAs. Go-functional enrichment analysis was performed on DE mRNAs. Some DE mRNA were enriched to biological processes associated with LA, And some lncRNAs related to DE mRNAs were traceable through cis/trans analysis, suggesting that they might be regulated in some way. Additionally, potential biomarkers for LA diagnosis in the hypertension population were identified via RT-qPCR and receive operating characteristic curve (ROC) analysis of lncRNA. One lncRNA, AC020928.1, has been demonstrated to be potential biomarkers for LA diagnosis in the hypertension population. The results of the present study indicated that the lncRNA may have an important role in the pathogenesis of LA and may be a novel target for further research. As the relationship between lncRNAs and LA is just beginning to be unraveled, their specific mechanisms require further investigation.
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Affiliation(s)
- Wendi Wang
- Department of Neurology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, China
| | - Pei Sun
- Department of Neurology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250021, China
| | - Fengyue Han
- Department of Neurology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250021, China
| | - Chunjuan Wang
- Department of Neurology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250021, China
| | - Yongxiang Wang
- Department of Neurology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250021, China
| | - Xiang Wang
- Department of Neurology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250021, China
| | - Lin Cong
- Department of Neurology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250021, China
| | - Chuanqiang Qu
- Department of Neurology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250021, China.
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25
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Long Noncoding RNAs in Myocardial Ischemia-Reperfusion Injury. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:8889123. [PMID: 33884101 PMCID: PMC8041529 DOI: 10.1155/2021/8889123] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 11/17/2020] [Accepted: 03/23/2021] [Indexed: 12/19/2022]
Abstract
Following an acute myocardial infarction, reperfusion therapy is currently the most effective way to save the ischemic myocardium; however, restoring blood flow may lead to a myocardial ischemia-reperfusion injury (MIRI). Recent studies have confirmed that long-chain noncoding RNAs (LncRNAs) play important roles in the pathophysiology of MIRIs. These LncRNA-mediated roles include cardiomyocyte apoptosis, autophagy, necrosis, oxidative stress, inflammation, mitochondrial dysfunction, and calcium overload, which are regulated through the expression of target genes. Thus, LncRNAs may be used as clinical diagnostic markers and therapeutic targets to treat or prevent MIRI. This review evaluates the research on LncRNAs involved in MIRIs and provides new ideas for preventing and treating this type of injury.
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26
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Zheng PF, Chen LZ, Guan YZ, Liu P. Weighted gene co-expression network analysis identifies specific modules and hub genes related to coronary artery disease. Sci Rep 2021; 11:6711. [PMID: 33758323 PMCID: PMC7988178 DOI: 10.1038/s41598-021-86207-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 03/12/2021] [Indexed: 12/21/2022] Open
Abstract
This investigation seeks to dissect coronary artery disease molecular target candidates along with its underlying molecular mechanisms. Data on patients with CAD across three separate array data sets, GSE66360, GSE19339 and GSE97320 were extracted. The gene expression profiles were obtained by normalizing and removing the differences between the three data sets, and important modules linked to coronary heart disease were identified using weighted gene co-expression network analysis (WGCNA). Gene Ontology (GO) functional and Kyoto Encyclopedia of Genes and genomes (KEGG) pathway enrichment analyses were applied in order to identify statistically significant genetic modules with the Database for Annotation, Visualization and Integrated Discovery (DAVID) online tool (version 6.8; http://david.abcc.ncifcrf.gov ). The online STRING tool was used to construct a protein-protein interaction (PPI) network, followed by the use of Molecular Complex Detection (MCODE) plug-ins in Cytoscape software to identify hub genes. Two significant modules (green-yellow and magenta) were identified in the CAD samples. Genes in the magenta module were noted to be involved in inflammatory and immune-related pathways, based on GO and KEGG enrichment analyses. After the MCODE analysis, two different MCODE complexes were identified in the magenta module, and four hub genes (ITGAM, degree = 39; CAMP, degree = 37; TYROBP, degree = 28; ICAM1, degree = 18) were uncovered to be critical players in mediating CAD. Independent verification data as well as our RT-qPCR results were highly consistent with the above finding. ITGAM, CAMP, TYROBP and ICAM1 are potential targets in CAD. The underlying mechanism may be related to the transendothelial migration of leukocytes and the immune response.
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Affiliation(s)
- Peng-Fei Zheng
- Department of Cardiology, The Central Hospital of Shao Yang, 36 QianYuan lane, Shaoyang, 422000, Hunan, People's Republic of China.,Graduate School of Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, Guangxi, People's Republic of China
| | - Lu-Zhu Chen
- Department of Cardiology, The Central Hospital of Shao Yang, 36 QianYuan lane, Shaoyang, 422000, Hunan, People's Republic of China
| | - Yao-Zong Guan
- Graduate School of Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, Guangxi, People's Republic of China
| | - Peng Liu
- Department of Cardiology, The Central Hospital of Shao Yang, 36 QianYuan lane, Shaoyang, 422000, Hunan, People's Republic of China.
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Ghafouri-Fard S, Gholipour M, Taheri M. The Emerging Role of Long Non-coding RNAs and Circular RNAs in Coronary Artery Disease. Front Cardiovasc Med 2021; 8:632393. [PMID: 33708807 PMCID: PMC7940190 DOI: 10.3389/fcvm.2021.632393] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/15/2021] [Indexed: 12/21/2022] Open
Abstract
Coronary artery disease (CAD) is a common disorder caused by atherosclerotic processes in the coronary arteries. This condition results from abnormal interactions between numerous cell types in the artery walls. The main participating factors in this process are accumulation of lipid deposits, endothelial cell dysfunction, macrophage induction, and changes in smooth muscle cells. Several lines of evidence underscore participation of long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) in the pathogenesis of CAD. Several lncRNAs such as H19, ANRIL, MIAT, lnc-DC, IFNG-AS1, and LEF1-AS1 have been shown to be up-regulated in the biological materials obtained from CAD patients. On the other hand, Gas5, Chast, HULC, DICER1-AS1, and MEG3 have been down-regulated in CAD patients. Meanwhile, a number of circRNAs have been demonstrated to influence function of endothelial cells or vascular smooth muscle cells, thus contributing to the pathogenesis of CAD. In the current review, we summarize the function of lncRNAs and circRNAs in the development and progression of CAD.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Urogenital Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mahdi Gholipour
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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28
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LncRNAs Landscape in the patients of primary gout by microarray analysis. PLoS One 2021; 16:e0232918. [PMID: 33600466 PMCID: PMC7891695 DOI: 10.1371/journal.pone.0232918] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 01/30/2021] [Indexed: 02/05/2023] Open
Abstract
To determine the expression profile and clinical significance of long non-coding RNAs (lncRNAs) in peripheral blood mononuclear cells (PBMCs) of patients with primary gout and healthy control subjects. Human lncRNA microarrays were used to identify the differentially expressed lncRNAs and mRNAs in primary gout patients (n = 6) and healthy control subjects (n = 6). Bioinformatics analyses were performed to predict the roles of differently expressed lncRNAs and mRNAs. Quantitative real-time polymerase chain reaction (qRT-PCR) was performed to detect the expression levels of 8 lnRNAs in 64 primary gout patients and 32 healthy control subjects. Spearman’s correlation was used to analyze the correlation between these eight lncRNAs and the laboratory values of gout patients. A receiver operating characteristic (ROC) curve was constructed to evaluate the diagnostic value of the lncRNAs identified in gout. The microarray analysis identified 1479 differentially expressed lncRNAs (879 more highly expressed and 600 more lowly expressed), 862 differentially expressed mRNAs (390 more highly expressed and 472 more lowly expressed) in primary gout (fold change > 2, P < 0.05), respectively. The bioinformatic analysis indicated that the differentially expressed lncRNAs regulated the abnormally expressed mRNAs, which were involved in the pathogenesis of gout through several different pathways. The expression levels of TCONS_00004393 and ENST00000566457 were significantly increased in the acute gout flare group than those in the intercritical gout group or healthy subjects (P<0.01). Moreover, inflammation indicators were positive correlated with TCONS_00004393 and ENST00000566457 expression levels. The areas under the ROC curve of ENST00000566457 and NR-026756 were 0.868 and 0.948, respectively. Our results provide novel insight into the mechanisms of primary gout, and reveal that TCONS_00004393 and ENST00000566457 might be as candidate targets for the treatment of gout flare; ENST00000566457 and NR-026756 could effectively discriminate between the gout and the healthy control groups.
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Chen J, Dang J. LncRNA CASC11 was downregulated in coronary artery disease and inhibits transforming growth factor- β1. J Int Med Res 2021; 48:300060519889187. [PMID: 32223575 PMCID: PMC7133399 DOI: 10.1177/0300060519889187] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Objective To investigate the involvement of long non-coding RNA (lncRNA) Cancer Susceptibility 11 (CASC11) in patients with coronary artery disease (CAD). Methods This case–control study enrolled patients with CAD and age- and sex-matched healthy control subjects. The plasma levels of lncRNA CASC11 and transforming growth factor-beta 1 (TGF-β1) were measured. Diagnostic values of lncRNA CASC11 and TGF-β1 for CAD were determined using receiver operating characteristic curve analysis. Correlations between plasma levels of lncRNA CASC11 and TGF-β1 were analysed using linear regression. Results The study enrolled 82 patients with CAD and 82 healthy controls. Plasma levels of lncRNA CASC11 were downregulated in patients with CAD, while plasma TGF-β1 levels were upregulated in patients with CAD, compared with healthy controls. Plasma levels of lncRNA CASC11 and TGF-β1 distinguished patients with CAD from healthy controls and were inversely correlated in both groups. LncRNA CASC11 over-expression mediated the downregulation of TGF-β1 in human primary coronary artery endothelial cells, while TGF-β1 over-expression showed no significant effects on lncRNA CASC11 levels. An 8-year follow-up study showed that low lncRNA CASC11 levels were closely correlated with a higher mortality rate in patients with CAD. Conclusion LncRNA CASC11 is downregulated in CAD and inhibits TGF-β1.
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Affiliation(s)
- Junhua Chen
- Department of Cardiology, Xinjiang Armed Police Corps Hospital, Urumqi City, Xinjiang Province, China
| | - Jianli Dang
- Outpatient Department of the Health and Medical Centre of the People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi City, Xinjiang Province, China
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Su Y, Xu R, Zhang R, Qu Y, Zuo W, Ji Z, Geng H, Pan M, Ma G. N6-methyladenosine methyltransferase plays a role in hypoxic preconditioning partially through the interaction with lncRNA H19. Acta Biochim Biophys Sin (Shanghai) 2020; 52:1306-1315. [PMID: 33197240 DOI: 10.1093/abbs/gmaa130] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Indexed: 11/13/2022] Open
Abstract
N6-methyladenosine (m6A), a methylation in the N6 position of adenosine especially in the mRNA, exerts diverse physiological and pathological functions. However, the precise role of m6A methylation in hypoxic preconditioning (HPC) is still unknown. Here, we observed that HPC treatment protected H9c2 cells against H2O2-induced injury, upregulated the m6A level in the total RNA and the expression of methyltransferase like 3 (METTL3), methyltransferase like 14 (METTL14), and long noncoding RNA (lncRNA) H19. Either knockdown of METTL3 or METTL14 notably reversed the HPC-induced enhancement of cell viability, anti-apoptosis ability, and H19 expression. Methylated RNA immunoprecipitation (IP) indicated that knockdown of METTL3 or METTL14 decreased m6A level in the lncRNA H19. Gain-of-function assay demonstrated that H19 overexpression could partially rescue the decreased protection mediated by METTL3 or METTL14 knockdown in HPC-treated H9c2 cells. RNA binding protein immunoprecipitation (RIP) assay showed that METTL3 and METTL14 could directly bind with H19. Our study identified a novel pattern of posttranscriptional regulation in HPC treatment. Since METTL3, METTL14, and lncRNA H19 were involved in HPC protection, they could be considered as potential biomarkers and therapeutic targets in HPC-derived cardiac rehabilitation and therapeutic approaches.
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Affiliation(s)
- Yamin Su
- Department of Cardiology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, China
| | - Rongfeng Xu
- Department of Cardiology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, China
| | - Rui Zhang
- Department of Cardiology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, China
| | - Yangyang Qu
- Department of Cardiology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, China
| | - Wenjie Zuo
- Department of Cardiology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, China
| | - Zhenjun Ji
- Department of Cardiology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, China
| | - Haihua Geng
- Department of Cardiology, Affiliated Hospital of Nantong University, Nantong 226001, China
| | - Min Pan
- Department of Cardiology, Affiliated Hospital of Nantong University, Nantong 226001, China
| | - Genshan Ma
- Department of Cardiology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, China
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Xiao Y, Xiao Z, Feng X, Chen Z, Kuang L, Wang L. A novel computational model for predicting potential LncRNA-disease associations based on both direct and indirect features of LncRNA-disease pairs. BMC Bioinformatics 2020; 21:555. [PMID: 33267800 PMCID: PMC7709313 DOI: 10.1186/s12859-020-03906-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 11/25/2020] [Indexed: 12/25/2022] Open
Abstract
Background Accumulating evidence has demonstrated that long non-coding RNAs (lncRNAs) are closely associated with human diseases, and it is useful for the diagnosis and treatment of diseases to get the relationships between lncRNAs and diseases. Due to the high costs and time complexity of traditional bio-experiments, in recent years, more and more computational methods have been proposed by researchers to infer potential lncRNA-disease associations. However, there exist all kinds of limitations in these state-of-the-art prediction methods as well. Results In this manuscript, a novel computational model named FVTLDA is proposed to infer potential lncRNA-disease associations. In FVTLDA, its major novelty lies in the integration of direct and indirect features related to lncRNA-disease associations such as the feature vectors of lncRNA-disease pairs and their corresponding association probability fractions, which guarantees that FVTLDA can be utilized to predict diseases without known related-lncRNAs and lncRNAs without known related-diseases. Moreover, FVTLDA neither relies solely on known lncRNA-disease nor requires any negative samples, which guarantee that it can infer potential lncRNA-disease associations more equitably and effectively than traditional state-of-the-art prediction methods. Additionally, to avoid the limitations of single model prediction techniques, we combine FVTLDA with the Multiple Linear Regression (MLR) and the Artificial Neural Network (ANN) for data analysis respectively. Simulation experiment results show that FVTLDA with MLR can achieve reliable AUCs of 0.8909, 0.8936 and 0.8970 in 5-Fold Cross Validation (fivefold CV), 10-Fold Cross Validation (tenfold CV) and Leave-One-Out Cross Validation (LOOCV), separately, while FVTLDA with ANN can achieve reliable AUCs of 0.8766, 0.8830 and 0.8807 in fivefold CV, tenfold CV, and LOOCV respectively. Furthermore, in case studies of gastric cancer, leukemia and lung cancer, experiment results show that there are 8, 8 and 8 out of top 10 candidate lncRNAs predicted by FVTLDA with MLR, and 8, 7 and 8 out of top 10 candidate lncRNAs predicted by FVTLDA with ANN, having been verified by recent literature. Comparing with the representative prediction model of KATZLDA, comparison results illustrate that FVTLDA with MLR and FVTLDA with ANN can achieve the average case study contrast scores of 0.8429 and 0.8515 respectively, which are both notably higher than the average case study contrast score of 0.6375 achieved by KATZLDA. Conclusion The simulation results show that FVTLDA has good prediction performance, which is a good supplement to future bioinformatics research.
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Affiliation(s)
- Yubin Xiao
- College of Computer Engineering and Applied Mathematics, Changsha University, Changsha, 410001, People's Republic of China.,Key Laboratory of Hunan Province for Internet of Things and Information Security, Xiangtan University, Xiangtan, 411105, People's Republic of China
| | - Zheng Xiao
- Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Cancer Research Institute, University of South China, Hengyang, 421001, Hunan, People's Republic of China
| | - Xiang Feng
- College of Computer Engineering and Applied Mathematics, Changsha University, Changsha, 410001, People's Republic of China
| | - Zhiping Chen
- College of Computer Engineering and Applied Mathematics, Changsha University, Changsha, 410001, People's Republic of China
| | - Linai Kuang
- Key Laboratory of Hunan Province for Internet of Things and Information Security, Xiangtan University, Xiangtan, 411105, People's Republic of China
| | - Lei Wang
- College of Computer Engineering and Applied Mathematics, Changsha University, Changsha, 410001, People's Republic of China. .,Key Laboratory of Hunan Province for Internet of Things and Information Security, Xiangtan University, Xiangtan, 411105, People's Republic of China.
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Groeneweg KE, Au YW, Duijs JMGJ, Florijn BW, van Kooten C, de Fijter JW, Reinders MEJ, van Zonneveld AJ, Bijkerk R. Diabetic nephropathy alters circulating long noncoding RNA levels that normalize following simultaneous pancreas-kidney transplantation. Am J Transplant 2020; 20:3451-3461. [PMID: 32353171 PMCID: PMC7754299 DOI: 10.1111/ajt.15961] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 04/12/2020] [Accepted: 04/13/2020] [Indexed: 01/25/2023]
Abstract
Simultaneous pancreas-kidney transplantation (SPKT) replaces kidney function and restores endogenous insulin secretion in patients with diabetic nephropathy (DN). Here, we aimed to identify circulating long noncoding RNAs (lncRNAs) that are associated with DN and vascular injury in the context of SPKT. Based on a pilot study and a literature-based selection of vascular injury-related lncRNAs, we assessed 9 candidate lncRNAs in plasma samples of patients with diabetes mellitus with a kidney function >35 mL/min/1.73 m2 (DM; n = 12), DN (n = 14), SPKT (n = 35), healthy controls (n = 15), and renal transplant recipients (KTx; n = 13). DN patients were also studied longitudinally before and 1, 6, and 12 months after SPKT. Of 9 selected lncRNAs, we found MALAT1, LIPCAR, and LNC-EPHA6 to be higher in DN compared with healthy controls. SPKT caused MALAT1, LIPCAR, and LNC-EPHA6 to normalize to levels of healthy controls, which was confirmed in the longitudinal study. In addition, we observed a strong association between MALAT1, LNC-EPHA6, and LIPCAR and vascular injury marker soluble thrombomodulin and a subset of angiogenic microRNAs (miR-27a, miR-130b, miR-152, and miR-340). We conclude that specific circulating lncRNAs associate with DN-related vascular injury and normalize after SPKT, suggesting that lncRNAs may provide a promising novel monitoring strategy for vascular integrity in the context of SPKT.
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Affiliation(s)
- Koen E. Groeneweg
- Department of Internal Medicine (Nephrology)Einthoven Laboratory for Vascular and Regenerative MedicineLeiden University Medical CenterLeidenThe Netherlands
| | - Yu Wah Au
- Department of Internal Medicine (Nephrology)Einthoven Laboratory for Vascular and Regenerative MedicineLeiden University Medical CenterLeidenThe Netherlands
| | - Jacques M. G. J. Duijs
- Department of Internal Medicine (Nephrology)Einthoven Laboratory for Vascular and Regenerative MedicineLeiden University Medical CenterLeidenThe Netherlands
| | - Barend W. Florijn
- Department of Internal Medicine (Nephrology)Einthoven Laboratory for Vascular and Regenerative MedicineLeiden University Medical CenterLeidenThe Netherlands
| | - Cees van Kooten
- Department of Internal Medicine (Nephrology)Einthoven Laboratory for Vascular and Regenerative MedicineLeiden University Medical CenterLeidenThe Netherlands
| | - Johan W. de Fijter
- Department of Internal Medicine (Nephrology)Einthoven Laboratory for Vascular and Regenerative MedicineLeiden University Medical CenterLeidenThe Netherlands
| | - Marlies E. J. Reinders
- Department of Internal Medicine (Nephrology)Einthoven Laboratory for Vascular and Regenerative MedicineLeiden University Medical CenterLeidenThe Netherlands
| | - Anton Jan van Zonneveld
- Department of Internal Medicine (Nephrology)Einthoven Laboratory for Vascular and Regenerative MedicineLeiden University Medical CenterLeidenThe Netherlands
| | - Roel Bijkerk
- Department of Internal Medicine (Nephrology)Einthoven Laboratory for Vascular and Regenerative MedicineLeiden University Medical CenterLeidenThe Netherlands
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Lu S, Liang Q, Huang Y, Meng F, Liu J. Definition and review on a category of long non-coding RNA: Atherosclerosis-associated circulating lncRNA (ASCLncRNA). PeerJ 2020; 8:e10001. [PMID: 33240586 PMCID: PMC7666546 DOI: 10.7717/peerj.10001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 08/29/2020] [Indexed: 12/18/2022] Open
Abstract
Atherosclerosis (AS) is one of the most common cardiovascular system diseases which seriously affects public health in modern society. Finding potential biomarkers in the complicated pathological progression of AS is of great significance for the prevention and treatment of AS. Studies have shown that long noncoding RNAs (lncRNAs) can be widely involved in the regulation of many physiological processes, and have important roles in different stages of AS formation. LncRNAs can be secreted into the circulatory system through exosomes, microvesicles, and apoptotic bodies. Recently, increasing studies have been focused on the relationships between circulating lncRNAs and AS development. The lncRNAs in circulating blood are expected to be new non-invasive diagnostic markers for monitoring the progression of AS. We briefly reviewed the previously reported lncRNA transcripts which related to AS development and detectable in circulating blood, including ANRIL, SENCR, CoroMarker, LIPCAR, HIF1α-AS1, LncRNA H19, APPAT, KCNQ1OT1, LncPPARδ, LincRNA-p21, MALAT1, MIAT, and UCA1. Further researches and a definition of atherosclerosis-associated circulating lncRNA (ASCLncRNA) were also discussed.
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Affiliation(s)
- Shanshan Lu
- Department of Histology and Embryology, School of Basic Medical Science, Central South University, Changsha, Hunan Province, China
| | - Qin Liang
- Department of Histology and Embryology, School of Basic Medical Science, Central South University, Changsha, Hunan Province, China
| | - Yanqing Huang
- Department of Histology and Embryology, School of Basic Medical Science, Central South University, Changsha, Hunan Province, China
| | - Fanming Meng
- Department of Parasitology, School of Basic Medical Science, Central South University, Changsha, Hunan Province, China
| | - Junwen Liu
- Department of Histology and Embryology, School of Basic Medical Science, Central South University, Changsha, Hunan Province, China.,China-Africa Research Center of Infectious Diseases, School of Basic Medical Sciences, Central South University, Changsha, Hunan Province, China
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34
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Gast M, Rauch BH, Haghikia A, Nakagawa S, Haas J, Stroux A, Schmidt D, Schumann P, Weiss S, Jensen L, Kratzer A, Kraenkel N, Müller C, Börnigen D, Hirose T, Blankenberg S, Escher F, Kühl AA, Kuss AW, Meder B, Landmesser U, Zeller T, Poller W. Long noncoding RNA NEAT1 modulates immune cell functions and is suppressed in early onset myocardial infarction patients. Cardiovasc Res 2020; 115:1886-1906. [PMID: 30924864 DOI: 10.1093/cvr/cvz085] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 02/15/2019] [Accepted: 03/27/2019] [Indexed: 12/16/2022] Open
Abstract
AIMS Inflammation is a key driver of atherosclerosis and myocardial infarction (MI), and beyond proteins and microRNAs (miRs), long noncoding RNAs (lncRNAs) have been implicated in inflammation control. To obtain further information on the possible role of lncRNAs in the context of atherosclerosis, we obtained comprehensive transcriptome maps of circulating immune cells (peripheral blood mononuclear cells, PBMCs) of early onset MI patients. One lncRNA significantly suppressed in post-MI patients was further investigated in a murine knockout model. METHODS AND RESULTS Individual RNA-sequencing (RNA-seq) was conducted on PBMCs from 28 post-MI patients with a history of MI at age ≤50 years and stable disease ≥3 months before study participation, and from 31 healthy individuals without manifest cardiovascular disease or family history of MI as controls. RNA-seq revealed deregulated protein-coding transcripts and lncRNAs in post-MI PBMCs, among which nuclear enriched abundant transcript (NEAT1) was the most highly expressed lncRNA, and the only one significantly suppressed in patients. Multivariate statistical analysis of validation cohorts of 106 post-MI patients and 85 controls indicated that the PBMC NEAT1 levels were influenced (P = 0.001) by post-MI status independent of statin intake, left ventricular ejection fraction, low-density lipoprotein or high-density lipoprotein cholesterol, or age. We investigated NEAT1-/- mice as a model of NEAT1 deficiency to evaluate if NEAT1 depletion may directly and causally alter immune regulation. RNA-seq of NEAT1-/- splenocytes identified disturbed expression and regulation of chemokines/receptors, innate immunity genes, tumour necrosis factor (TNF) and caspases, and increased production of reactive oxygen species (ROS) under baseline conditions. NEAT1-/- spleen displayed anomalous Treg and TH cell differentiation. NEAT1-/- bone marrow-derived macrophages (BMDMs) displayed altered transcriptomes with disturbed chemokine/chemokine receptor expression, increased baseline phagocytosis (P < 0.0001), and attenuated proliferation (P = 0.0013). NEAT1-/- BMDMs responded to LPS with increased (P < 0.0001) ROS production and disturbed phagocytic activity (P = 0.0318). Monocyte-macrophage differentiation was deregulated in NEAT1-/- bone marrow and blood. NEAT1-/- mice displayed aortic wall CD68+ cell infiltration, and there was evidence of myocardial inflammation which could lead to severe and potentially life-threatening structural damage in some of these animals. CONCLUSION The study indicates distinctive alterations of lncRNA expression in post-MI patient PBMCs. Regarding the monocyte-enriched NEAT1 suppressed in post-MI patients, the data from NEAT1-/- mice identify NEAT1 as a novel lncRNA-type immunoregulator affecting monocyte-macrophage functions and T cell differentiation. NEAT1 is part of a molecular circuit also involving several chemokines and interleukins persistently deregulated post-MI. Individual profiling of this circuit may contribute to identify high-risk patients likely to benefit from immunomodulatory therapies. It also appears reasonable to look for new therapeutic targets within this circuit.
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Affiliation(s)
- Martina Gast
- Department of Cardiology, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Charite Centrum 11, Hindenburgdamm 30, Berlin, Germany
| | - Bernhard H Rauch
- Institute for Pharmacology, Universitätsmedizin Greifswald, Felix-Hausdorff-Strasse 3, Greifswald, Germany.,German Center for Cardiovascular Research (DZHK), Site Greifswald, Felix-Hausdorff-Strasse 3, Greifswald
| | - Arash Haghikia
- Department of Cardiology, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Charite Centrum 11, Hindenburgdamm 30, Berlin, Germany.,RNA Biology Laboratory, RIKEN Advanced Research Institute, Wako, Saitama, Japan
| | - Shinichi Nakagawa
- RNA Biology Laboratory, RIKEN Advanced Research Institute, Wako, Saitama, Japan.,Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12 jo, Nishi 6-chome, Kita-ku, Sapporo, Japan
| | - Jan Haas
- Department of Cardiology, Institute for Cardiomyopathies, University Hospital Heidelberg, Im Neuenheimer Feld 669, Heidelberg, Germany.,German Center for Cardiovascular Research (DZHK), Site Heidelberg, Im Neuenheimer Feld 669, Heidelberg, Germany
| | - Andrea Stroux
- Institute for Biometry and Clinical Epidemiology, Hindenburgdamm 30, Berlin, Germany
| | - David Schmidt
- Department of Cardiology, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Charite Centrum 11, Hindenburgdamm 30, Berlin, Germany
| | - Paul Schumann
- Department of Cardiology, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Charite Centrum 11, Hindenburgdamm 30, Berlin, Germany
| | - Stefan Weiss
- Interfaculty Institute for Genetics and Functional Genome Research, University of Greifswald, Felix-Hausdorff-Strasse 8, Greifswald, Germany
| | - Lars Jensen
- Interfaculty Institute for Genetics and Functional Genome Research, University of Greifswald, Felix-Hausdorff-Strasse 8, Greifswald, Germany
| | - Adelheid Kratzer
- Department of Cardiology, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Charite Centrum 11, Hindenburgdamm 30, Berlin, Germany
| | - Nicolle Kraenkel
- Department of Cardiology, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Charite Centrum 11, Hindenburgdamm 30, Berlin, Germany
| | - Christian Müller
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, Martinistrasse 52, Hamburg, Germany.,German Center for Cardiovascular Research (DZHK), Site Hamburg/Lübeck/Kiel, Martinistrasse 52, Hamburg, Germany
| | - Daniela Börnigen
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, Martinistrasse 52, Hamburg, Germany.,German Center for Cardiovascular Research (DZHK), Site Hamburg/Lübeck/Kiel, Martinistrasse 52, Hamburg, Germany
| | - Tetsuro Hirose
- Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
| | - Stefan Blankenberg
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, Martinistrasse 52, Hamburg, Germany.,German Center for Cardiovascular Research (DZHK), Site Hamburg/Lübeck/Kiel, Martinistrasse 52, Hamburg, Germany
| | - Felicitas Escher
- German Center for Cardiovascular Research (DZHK), Site Berlin, Hindenburgdamm 30, Berlin, Germany.,Institute of Cardiac Diagnostics and Therapy (IKDT), Hindenburgdamm 30, Berlin, Germany.,Department of Cardiology CVK, Hindenburgdamm 30, Berlin, Germany
| | - Anja A Kühl
- iPATH.Berlin-Core Unit Immunopathology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Andreas W Kuss
- Interfaculty Institute for Genetics and Functional Genome Research, University of Greifswald, Felix-Hausdorff-Strasse 8, Greifswald, Germany
| | - Benjamin Meder
- Department of Cardiology, Institute for Cardiomyopathies, University Hospital Heidelberg, Im Neuenheimer Feld 669, Heidelberg, Germany.,German Center for Cardiovascular Research (DZHK), Site Heidelberg, Im Neuenheimer Feld 669, Heidelberg, Germany.,Department of Genetics, Genome Technology Center, Stanford University Medical School, Stanford, CA, USA
| | - Ulf Landmesser
- Department of Cardiology, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Charite Centrum 11, Hindenburgdamm 30, Berlin, Germany.,German Center for Cardiovascular Research (DZHK), Site Berlin, Hindenburgdamm 30, Berlin, Germany.,Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Strasse 2, Berlin, Germany
| | - Tanja Zeller
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, Martinistrasse 52, Hamburg, Germany.,German Center for Cardiovascular Research (DZHK), Site Hamburg/Lübeck/Kiel, Martinistrasse 52, Hamburg, Germany
| | - Wolfgang Poller
- Department of Cardiology, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Charite Centrum 11, Hindenburgdamm 30, Berlin, Germany.,German Center for Cardiovascular Research (DZHK), Site Berlin, Hindenburgdamm 30, Berlin, Germany.,Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Hindenburgdamm 30, Berlin, Germany
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Zhao C, Lv Y, Duan Y, Li G, Zhang Z. Circulating Non-coding RNAs and Cardiovascular Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1229:357-367. [PMID: 32285424 DOI: 10.1007/978-981-15-1671-9_22] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The discovery of noncoding RNAs (ncRNAs) including short microRNAs, long ncRNAs and circular RNAs has broaden our knowledge about mammalian genomes and transcriptomes. A growing number of evidence on aberrantly regulated ncRNAs in cardiovascular diseases has indicated that ncRNAs are critical contributors to cardiovascular pathophysiology. Moreover, multiple recent studies have reported that ncRNAs can be detected in the bloodstream that differs between health subjects and diseased patients and some of them are remarkably stable. Although our knowledge about the origin and function of the circulating ncRNAs is still limited, these molecules have been regarded as promising noninvasive biomarker for risk stratification, diagnosis and prognosis of various cardiovascular diseases. In this chapter, we have described biological characteristics of circulating ncRNAs and discussed current trends and future prospects for the usage of circulating ncRNAs as biomarkers for common cardiovascular diseases.
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Affiliation(s)
- Chenglin Zhao
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, School of Life Science, Shanghai University, Shanghai, China
| | - Yicheng Lv
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, School of Life Science, Shanghai University, Shanghai, China
| | - Yi Duan
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, School of Life Science, Shanghai University, Shanghai, China
| | - Guoping Li
- Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Zhongrong Zhang
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, School of Life Science, Shanghai University, Shanghai, China.
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36
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Maguire EM, Xiao Q. Noncoding RNAs in vascular smooth muscle cell function and neointimal hyperplasia. FEBS J 2020; 287:5260-5283. [DOI: 10.1111/febs.15357] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 04/21/2020] [Accepted: 05/01/2020] [Indexed: 12/13/2022]
Affiliation(s)
- Eithne Margaret Maguire
- Centre for Clinical Pharmacology William Harvey Research Institute Barts and The London School of Medicine and Dentistry Queen Mary University of London UK
| | - Qingzhong Xiao
- Centre for Clinical Pharmacology William Harvey Research Institute Barts and The London School of Medicine and Dentistry Queen Mary University of London UK
- Key Laboratory of Cardiovascular Diseases at The Second Affiliated Hospital Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation School of Basic Medical Sciences Guangzhou Medical University China
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Construction and analysis for differentially expressed long non-coding RNAs and mRNAs in acute myocardial infarction. Sci Rep 2020; 10:6989. [PMID: 32332808 PMCID: PMC7181872 DOI: 10.1038/s41598-020-63840-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 04/06/2020] [Indexed: 12/18/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nucleotides. Some lncRNAs are related to acute myocardial infarction (AMI) and can serve as blood-based biomarkers for AMI detection. To identify whether new lncRNAs participate in AMI, the expression of lncRNAs and mRNAs was analysed by microarray analysis (Agilent human array) with the limma package in R in two series: five paired peripheral blood mononuclear cell (PBMC) samples and four paired plasma samples from different AMI patients. In PBMCs, a total of 2677 upregulated and 458 downregulated lncRNAs were significantly differentially expressed; additionally, 1168 mRNAs were upregulated and 1334 mRNAs were downregulated between the AMI patients and controls. In plasma, we found 41 upregulated and 51 downregulated lncRNAs that were differentially expressed, as well as 9 mRNAs that were upregulated and 9 mRNAs that were downregulated among the two groups. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed using the clusterProfiler package in R, and differentially expressed mRNAs were functionally annotated. The top differentially expressed mRNAs were associated with circadian rhythm, the NF-kB pathway, the p53 pathway and the metabolism pathway. We further performed target gene prediction and coexpression analysis and revealed the interrelationships among the significantly differentially expressed lncRNAs and mRNAs. The expression of four lncRNAs (uc002ddj.1, NR_047662, ENST00000581794.1 and ENST00000509938.1) was validated in the newly diagnosed AMI and control groups by quantitative real-time PCR (qRT-PCR). Our study demonstrated that the clustered expression of lncRNAs between PBMCs and plasma showed tremendous differences. The newly screened lncRNAs may play indispensable roles in the development of AMI, although their biological functions need to be further validated.
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Circulating Exosomal SOCS2-AS1 Acts as a Novel Biomarker in Predicting the Diagnosis of Coronary Artery Disease. BIOMED RESEARCH INTERNATIONAL 2020; 2020:9182091. [PMID: 32352013 PMCID: PMC7171639 DOI: 10.1155/2020/9182091] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 12/10/2019] [Accepted: 12/17/2019] [Indexed: 02/07/2023]
Abstract
Background and Aims Critical roles of circulating exosomal long noncoding RNAs (lncRNAs) have been implicated in multiple diseases. However, little is known about their roles in coronary artery disease (CAD). The aim of the present study was to investigate the relationships between circulating exosomal lncRNAs and CAD and identify the aberrantly expressed disease-related lncRNAs as biomarkers in diagnosing CAD. Methods The aberrantly expressed lncRNAs in plasma exosomes from CAD patients and controls were identified by microarray analysis and verified by quantitative real-time PCR (qRT-PCR). Then, the correlation between the expression level of candidate biomarker and clinic features in CAD patients, mild coronary artery stenosis (mCAS) patients, and controls was analyzed. Finally, we used the receiver operating characteristic (ROC) curve to examine the diagnosis value of candidate biomarkers. Results The downregulated SOCS2-AS1 was determined by microarray analysis and verified by qRT-PCR in plasma from CAD patients in contrast to controls. The SOCS2-AS1 expression level in plasma exosomes was negatively correlated with PLT and Lpa. Moreover, CAD patients with elevated levels of plasma exosome-encapsulated SOCS2-AS1 were susceptible to multicoronary artery lesions. Additionally, the area under ROC (AUC) of SOCS2-AS1 was 0.704 (95% CI = 0.607–0.801, P < 0.001) for diagnosis of CAD. Conclusions Plasma exosome-encapsulated SOCS2-AS1 was an independent protective factor against CAD and could be potentially used as a novel biomarker for the diagnosis of CAD.
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Li P, Yan X, Xu G, Pang Z, Weng J, Yin J, Li M, Yu L, Chen Q, Sun K. A novel plasma lncRNA ENST00000416361 is upregulated in coronary artery disease and is related to inflammation and lipid metabolism. Mol Med Rep 2020; 21:2375-2384. [PMID: 32323776 PMCID: PMC7185291 DOI: 10.3892/mmr.2020.11067] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 03/10/2020] [Indexed: 12/22/2022] Open
Abstract
Coronary artery disease (CAD) is a serious threat to human health and a major cause of mortality worldwide. Long noncoding RNAs (lncRNAs) affect the occurrence and development of CAD via the regulation of cell proliferation and apoptosis, inflammatory responses and lipid metabolism. Screening methods and therapeutic strategies for CAD have been extensively studied. The present study analyzed clinical indexes of 187 patients with CAD and 150 healthy subjects. The data showed significant differences in diabetes mellitus, hypertension, high-density lipoprotein level and smoking history between the CAD group and the control group. A series of differentially expressed lncRNAs were detected in the plasma samples of three patients with CAD by high-throughput sequencing. Reverse transcription-quantitative (RT-q)PCR data revealed that the expression level of the novel lncRNA ENST00000416361 was ~2.3-fold higher in the plasma of 50 patients with CAD compared with the 50 control subjects. Receiver operating characteristic (ROC) curves were generated, and the area under the ROC curve was 0.7902. Knockdown of ENST00000416361 in human umbilical vein endothelial cells markedly downregulated interleukin-6 and tumor necrosis factor-α levels. In addition, sterol regulatory element binding transcription factor (SREBP)1 and SREBP2 were upregulated in patients with CAD, and they were positively correlated with the expression of ENST00000416361. RT-qPCR further demonstrated that knockdown of ENST00000416361 led to the downregulation of SREBP1 and SREBP2. Overall, the novel lncRNA ENST00000416361 may be associated with CAD-induced inflammation and lipid metabolism, and it may serve as a potential biomarker for CAD.
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Affiliation(s)
- Ping Li
- Institute of Digestive Diseases and Nutrition, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, Jiangsu 215008, P.R. China
| | - Xinxin Yan
- Institute of Digestive Diseases and Nutrition, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, Jiangsu 215008, P.R. China
| | - Guidong Xu
- Department of Cardiology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, Jiangsu 215008, P.R. China
| | - Zhi Pang
- Institute of Digestive Diseases and Nutrition, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, Jiangsu 215008, P.R. China
| | - Jiayi Weng
- Department of Cardiology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, Jiangsu 215008, P.R. China
| | - Juan Yin
- Institute of Digestive Diseases and Nutrition, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, Jiangsu 215008, P.R. China
| | - Meifen Li
- Institute of Digestive Diseases and Nutrition, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, Jiangsu 215008, P.R. China
| | - Lan Yu
- Institute of Digestive Diseases and Nutrition, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, Jiangsu 215008, P.R. China
| | - Qian Chen
- Institute of Digestive Diseases and Nutrition, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, Jiangsu 215008, P.R. China
| | - Kangyun Sun
- Department of Cardiology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, Jiangsu 215008, P.R. China
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Yeh CF, Chang YCE, Lu CY, Hsuan CF, Chang WT, Yang KC. Expedition to the missing link: Long noncoding RNAs in cardiovascular diseases. J Biomed Sci 2020; 27:48. [PMID: 32241300 PMCID: PMC7114803 DOI: 10.1186/s12929-020-00647-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 03/27/2020] [Indexed: 12/31/2022] Open
Abstract
With the advances in deep sequencing-based transcriptome profiling technology, it is now known that human genome is transcribed more pervasively than previously thought. Up to 90% of the human DNA is transcribed, and a large proportion of the human genome is transcribed as long noncoding RNAs (lncRNAs), a heterogenous group of non-coding transcripts longer than 200 nucleotides. Emerging evidence suggests that lncRNAs are functional and contribute to the complex regulatory networks involved in cardiovascular development and diseases. In this article, we will review recent evidence on the roles of lncRNAs in the biological processes of cardiovascular development and disorders. The potential applications of lncRNAs as biomarkers and targets for therapeutics are also discussed.
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Affiliation(s)
- Chih-Fan Yeh
- Graduate Institute and Department of Pharmacology, National Taiwan University School of Medicine, No.1, Sec. 1, Ren-Ai Rd, 1150R, Taipei, Taiwan.,Division of Cardiology, Department of Internal Medicine, National Taiwan University Hospital, No.1, Sec. 1, Ren-Ai Rd, 1150R, Taipei, Taiwan
| | - Yu-Chen Eugene Chang
- Graduate Institute and Department of Pharmacology, National Taiwan University School of Medicine, No.1, Sec. 1, Ren-Ai Rd, 1150R, Taipei, Taiwan
| | - Cheng-Yuan Lu
- Graduate Institute and Department of Pharmacology, National Taiwan University School of Medicine, No.1, Sec. 1, Ren-Ai Rd, 1150R, Taipei, Taiwan
| | - Chin-Feng Hsuan
- Division of Cardiology, Department of Internal Medicine, E-Da Dachang Hospital, Kaohsiung, Taiwan.,Department of Medicine, I-Shou University School of Medicine, Kaohsiung, Taiwan
| | - Wei-Tien Chang
- Department of Emergency Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Kai-Chien Yang
- Graduate Institute and Department of Pharmacology, National Taiwan University School of Medicine, No.1, Sec. 1, Ren-Ai Rd, 1150R, Taipei, Taiwan. .,Division of Cardiology, Department of Internal Medicine, National Taiwan University Hospital, No.1, Sec. 1, Ren-Ai Rd, 1150R, Taipei, Taiwan.
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Gu Z, Shen HQ, Fu PH, Chen M. Screening of long non-coding RNAs markers in plasma of children with chronic gastritis. Chronic Dis Transl Med 2020; 6:62-68. [PMID: 32226936 PMCID: PMC7096328 DOI: 10.1016/j.cdtm.2020.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Indexed: 12/20/2022] Open
Abstract
Objective The study aimed to detect and analyze long non-coding RNAs (lncRNAs) in plasma of children diagnosed with chronic gastritis, and to explore its biological functions and involved signaling pathways. Methods The plasma samples were collected from six children that were diagnosed with chronic gastritis by physical examination, gastroscopy, and pathological examination and six healthy children. The plasma samples were assayed for determining the expression profiles of lncRNA based upon the gen chip detection. The specific expression of lcnRNA in plasma of children with chronic gastritis was analyzed and its biological functions were speculated. Results Five lncRNAs (RP11-697M17.1, RP11-388M20.9, AFAP1-AS1, BC062758, and XLOC001406) were significantly up-regulated, and five lncRNAs (UNQ697, BX571672.5, CYP4F35P, ANKRD20A5P, and AL832737) were observed to be significantly down-regulated. The lncRNAs RP11-697M17.1, and UNQ697 were detected with the highest up-regulation and down-regulation, respectively. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that the up-regulated lncRNAs were significantly enriched in 20 signaling pathways such as phosphoinositide-3-kinase–protein kinase B (PI3K-Akt) pathway, and the down-regulated lncRNAs target genes were significantly enriched in 20 signaling pathways such as the metabolic pathway. Conclusion The analysis of the lncRNA expression profiles in plasma of children with chronic gastritis revealed that the lncRNA RP11-697M17.1, and lncRNA UNQ697 may act as plasma markers for predicting chronic gastritis in children.
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Affiliation(s)
- Zhen Gu
- Department of Pediatrics, Shanghai Pudong New District Zhoupu Hospital, Shanghai 201318, China
| | - Hua-Qin Shen
- Department of Pediatrics, Shanghai Pudong New District Zhoupu Hospital, Shanghai 201318, China
| | - Pei-Hua Fu
- Department of Pediatrics, Shanghai Pudong New District Zhoupu Hospital, Shanghai 201318, China
| | - Mei Chen
- Department of Pediatrics, Shanghai Pudong New District Zhoupu Hospital, Shanghai 201318, China
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Abstract
Advances in molecular genetics have identified several species of RNA that fail to translate - hence the non-coding RNAs. The two major groups within this class of nucleic acids are microRNAs (miRNA) and long non-coding RNAs (lncRNA). There is growing body of evidence supporting the view that these molecules have regulatory effect on both DNA and RNA. The objective of this brief review is to explain the molecular genetic of these molecules, to summarize their potential as mediators of disease, and to highlight their value as diagnostic markers and as tools in disease management.
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Affiliation(s)
- P Waller
- Department of Biomedical Sciences, University of Kingston, London, UK
| | - A D Blann
- Institute of Biomedical Science, London, UK
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Cardona-Monzonís A, García-Giménez JL, Mena-Mollá S, Pareja-Galeano H, de la Guía-Galipienso F, Lippi G, Pallardó FV, Sanchis-Gomar F. Non-coding RNAs and Coronary Artery Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1229:273-285. [PMID: 32285418 DOI: 10.1007/978-981-15-1671-9_16] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Coronary artery disease (CAD) is the leading death cause worldwide. Non-coding RNA (ncRNA) are key regulators of genetic expression and thus can affect directly or indirectly the development and progression of different diseases. ncRNA can be classified in several types depending on the length or structure, as long non-coding RNA (lncRNA), microRNA (miRNA) and circularRNA (circRNA), among others. These types of RNA are present within cells or in circulation, and for this reason they have been used as biomarkers of different diseases, therefore revolutionizing precision medicine. Recent research studied the capability of circulating ncRNA to inform about CAD presence and predict the outcome of the disease. In this chapter we present a list of the miRNA, lncRNA and circRNA which are potential biomarkers of CAD.
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Affiliation(s)
- Alejandro Cardona-Monzonís
- Center for Biomedical Network Research-Instituto de Salud Carlos III. Department of Physiology, School of Medicine, University of Valencia and INCLIVA Biomedical Research Institute, Valencia, Spain
| | - José Luis García-Giménez
- Center for Biomedical Network Research-Instituto de Salud Carlos III. Department of Physiology, School of Medicine, University of Valencia and INCLIVA Biomedical Research Institute, Valencia, Spain
| | - Salvador Mena-Mollá
- Department of Physiology, School of Medicine, University of Valencia, Valencia, Spain
| | | | | | - Giuseppe Lippi
- Section of Clinical Biochemistry, University of Verona, Verona, Italy
| | - Federico V Pallardó
- Center for Biomedical Network Research-Instituto de Salud Carlos III. Department of Physiology, School of Medicine, University of Valencia and INCLIVA Biomedical Research Institute, Valencia, Spain
| | - Fabian Sanchis-Gomar
- Department of Physiology, Faculty of Medicine, University of Valencia and INCLIVA Biomedical Research Institute, Valencia, Spain.
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Mo X, Liu W, Yang Y, Imani S, Lu S, Dan G, Nie X, Yan J, Zhan R, Li X, Deng Y, Chen B, Cai Y. NCF2, MYO1F, S1PR4, and FCN1 as potential noninvasive diagnostic biomarkers in patients with obstructive coronary artery: A weighted gene co-expression network analysis. J Cell Biochem 2019; 120:18219-18235. [PMID: 31245869 PMCID: PMC6771964 DOI: 10.1002/jcb.29128] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 05/05/2019] [Accepted: 05/07/2019] [Indexed: 12/11/2022]
Abstract
This study aims to explore the predictive noninvasive biomarker for obstructive coronary artery disease (CAD). By using the data set GSE90074, weighted gene co-expression network analysis (WGCNA), and protein-protein interactive network, construction of differentially expressed genes in peripheral blood mononuclear cells was conducted to identify the most significant gene clusters associated with obstructive CAD. Univariate and multivariate stepwise logistic regression analyses and receiver operating characteristic analysis were used to predicate the diagnostic accuracy of biomarker candidates in the detection of obstructive CAD. Furthermore, functional prediction of candidate gene biomarkers was further confirmed in ST-segment elevation myocardial infarction (STEMI) patients or stable CAD patients by using the datasets of GSE62646 and GSE59867. We found that the blue module discriminated by WGCNA contained 13 hub-genes that could be independent risk factors for obstructive CAD (P < .05). Among these 13 hub-genes, a four-gene signature including neutrophil cytosol factor 2 (NCF2, P = .025), myosin-If (MYO1F, P = .001), sphingosine-1-phosphate receptor 4 (S1PR4, P = .015), and ficolin-1 (FCN1, P = .012) alone or combined with two risk factors (male sex and hyperlipidemia) may represent potential diagnostic biomarkers in obstructive CAD. Furthermore, the messenger RNA levels of NCF2, MYO1F, S1PR4, and FCN1 were higher in STEMI patients than that in stable CAD patients, although S1PR4 showed no statistical difference (P > .05). This four-gene signature could also act as a prognostic biomarker to discriminate STEMI patients from stable CAD patients. These findings suggest a four-gene signature (NCF2, MYO1F, S1PR4, and FCN1) alone or combined with two risk factors (male sex and hyperlipidemia) as a promising prognostic biomarker in the diagnosis of STEMI. Well-designed cohort studies should be implemented to warrant the diagnostic value of these genes in clinical purpose.
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Affiliation(s)
- Xian‐Gang Mo
- Department of GeriatricsThe Affiliated Hospital of Guizhou Medical UniversityGuiyangGuizhouChina
| | - Wei Liu
- Health Physical Examination CenterThe Affiliated Hospital of Qingdao UniversityQingdaoShandongChina
| | - Yao Yang
- Institute of Materia Medica, College of PharmacyArmy Medical University (Third Military Medical University)ChongqingChina
| | - Saber Imani
- Department of OncologyThe Affiliated Hospital of Southwest Medical UniversityLuzhouSichuanChina
| | - Shan Lu
- Institute of Materia Medica, College of PharmacyArmy Medical University (Third Military Medical University)ChongqingChina
| | - Guorong Dan
- Institute of Materia Medica, College of PharmacyArmy Medical University (Third Military Medical University)ChongqingChina
| | - Xuqiang Nie
- Institute of Materia Medica, College of PharmacyArmy Medical University (Third Military Medical University)ChongqingChina
| | - Jun Yan
- Center of Hepatobiliary Pancreatic DiseaseBeijing Tsinghua Changgung HospitalBeijingChina
| | - Rixing Zhan
- Institute of Burn Research, Southwest HospitalArmy Medical University (Third Military Medical University)ChongqingChina
| | - Xiaohui Li
- Institute of Materia Medica, College of PharmacyArmy Medical University (Third Military Medical University)ChongqingChina
| | - Youcai Deng
- Institute of Materia Medica, College of PharmacyArmy Medical University (Third Military Medical University)ChongqingChina
| | - Bingbo Chen
- Laboratory Animal CenterArmy Medical University (Third Military Medical University)ChongqingChina
| | - Yue Cai
- Department of Cardiology, Xijing HospitalFourth Military Medical UniversityXi'anShaanxiChina
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Expression profiles and potential functions of long non-coding RNA in stable angina pectoris patients from Uyghur population of China. Biosci Rep 2019; 39:BSR20190364. [PMID: 31413167 PMCID: PMC6722491 DOI: 10.1042/bsr20190364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 07/05/2019] [Accepted: 08/09/2019] [Indexed: 12/04/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are transcripts longer than 200 nt that are involved in cardiovascular diseases (CVDs). To determine whether lncRNAs are involved in stable angina pectoris (SAP), we analysed the expression profile of lncRNAs and mRNAs on a genome-wide scale in SAP of Uyghur population. Five pairs of SAP patients and healthy controls were screened by an Agilent microarray (human lncRNA + mRNA Array V4.0). Quantitative real-time polymerase chain reaction (qRT-PCR) was used to validate the lncRNA expression levels in 50 SAP and 50 controls. Data analyses were performed using R and Bioconductor. A total of 1871 up- and 231 down-regulated lncRNAs were identified to be differentially expressed in the peripheral blood mononuclear cells (PBMCs). Microarray analysis results identified the lncRNAs NR_037652.1, ENST00000607654.1, ENST00000589524.1 and uc004bhb.3, which were confirmed by qRT-PCR. Among screened lncRNAs, the annotation result of their co-expressed mRNAs showed that the most significantly related pathways were the NF-κB signalling pathway, apoptosis and the p53 signalling pathway, while the main significantly related diseases were the cholesterol, calcium and coronary disease. Our study indicated that clusters of lncRNAs were significantly differentially expressed between SAP patients and matched controls. These lncRNAs may play a significant role in SAP development and could serve as biomarkers and potential targets for the future treatment of SAP.
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Liao J, Wang J, Liu Y, Li J, Duan L. Transcriptome sequencing of lncRNA, miRNA, mRNA and interaction network constructing in coronary heart disease. BMC Med Genomics 2019; 12:124. [PMID: 31443660 PMCID: PMC6708182 DOI: 10.1186/s12920-019-0570-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 08/12/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Non-coding RNA has been shown to participate in numerous biological and pathological processes and has attracted increasing attention in recent years. Recent studies have demonstrated that long non-coding RNA and micro RNA can interact through various mechanisms to regulate mRNA. Yet the gene-gene interaction has not been investigated in coronary heart disease (CHD). METHODS High throughput sequencing were used to identify differentially expressed (DE) lncRNA, miRNA, and mRNA profiles between CHD and healthy control. Gene Oncology (GO), KEGG enrichment analysis were performed. Gene-gene interaction network were constructed and pivotal genes were screened out. Lentivirus-induced shRNA infection and qRT-PCR were performed to validated the gene-gene interactions. RESULTS A total of 62 lncRNAs, 332 miRNAs and 366 mRNAs were differentially expressed between CHD and healthy control. GO and KEGG analysis show that immune related molecular mechanisms and biological processes play a role in CHD. The gene-gene interaction network were constructed and visualized based on Pearson correlation coefficients and starBase database. 6 miRNAs in the network were significantly correlated to left ventricular ejection fraction, total choleterol and homocysteine. 2 lncRNAs (CTA-384D8.35 and CTB-114C7.4 (refseq entry LOC100128059)), 1 miRNA (miR-4497), and 1 mRNA (NR4A1) were the pivotal genes. Lentivirus-induced shRNA infection and qRT-PCR had validated the pivotal gene-gene interactions. CONCLUSIONS These results have shown the potential of lncRNA, miRNA, and mRNA as clinical biomarkers and in elucidating pathological mechanisms of CHD from a transcriptomic perspective.
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Affiliation(s)
- Jiangquan Liao
- Department of Cardiology, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- National Integrated Traditional and Western Medicine Center for Cardiovascular Disease, China-Japan Friendship Hospital, Beijing, China
| | - Jie Wang
- Department of Cardiology, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China.
| | - Yongmei Liu
- Department of Cardiology, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jun Li
- Department of Cardiology, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Lian Duan
- Department of Cardiology, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
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Finotti A, Fabbri E, Lampronti I, Gasparello J, Borgatti M, Gambari R. MicroRNAs and Long Non-coding RNAs in Genetic Diseases. Mol Diagn Ther 2019; 23:155-171. [PMID: 30610665 PMCID: PMC6469593 DOI: 10.1007/s40291-018-0380-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Since the discovery and classification of non-coding RNAs, their roles have gained great attention. In this respect, microRNAs and long non-coding RNAs have been firmly demonstrated to be linked to regulation of gene expression and onset of human diseases, including rare genetic diseases; therefore they are suitable targets for therapeutic intervention. This issue, in the context of rare genetic diseases, is being considered by an increasing number of research groups and is of key interest to the health community. In the case of rare genetic diseases, the possibility of developing personalized therapy in precision medicine has attracted the attention of researchers and clinicians involved in developing "orphan medicinal products" and proposing these to the European Medicines Agency (EMA) and to the Food and Drug Administration (FDA) Office of Orphan Products Development (OOPD) in the United States. The major focuses of these activities are the evaluation and development of products (drugs, biologics, devices, or medical foods) considered to be promising for diagnosis and/or treatment of rare diseases or conditions, including rare genetic diseases. In an increasing number of rare genetic diseases, analysis of microRNAs and long non-coding RNAs has been proven a promising strategy. These diseases include, but are not limited to, Duchenne muscular dystrophy, cystic fibrosis, Rett syndrome, and β-thalassemia. In conclusion, a large number of approaches based on targeting microRNAs and long non-coding RNAs are expected in the field of molecular diagnosis and therapy, with a facilitated technological transfer in the case of rare genetic diseases, in virtue of the existing regulation concerning these diseases.
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Affiliation(s)
- Alessia Finotti
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, University of Ferrara, Via Fossato di Mortara n.74, 44121, Ferrara, Italy
| | - Enrica Fabbri
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, University of Ferrara, Via Fossato di Mortara n.74, 44121, Ferrara, Italy
| | - Ilaria Lampronti
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, University of Ferrara, Via Fossato di Mortara n.74, 44121, Ferrara, Italy
| | - Jessica Gasparello
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, University of Ferrara, Via Fossato di Mortara n.74, 44121, Ferrara, Italy
| | - Monica Borgatti
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, University of Ferrara, Via Fossato di Mortara n.74, 44121, Ferrara, Italy
| | - Roberto Gambari
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, University of Ferrara, Via Fossato di Mortara n.74, 44121, Ferrara, Italy.
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Zhang Y, Zhang L, Wang Y, Ding H, Xue S, Qi H, Li P. MicroRNAs or Long Noncoding RNAs in Diagnosis and Prognosis of Coronary Artery Disease. Aging Dis 2019; 10:353-366. [PMID: 31011482 PMCID: PMC6457061 DOI: 10.14336/ad.2018.0617] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 06/17/2018] [Indexed: 12/14/2022] Open
Abstract
Coronary artery disease (CAD) is the result of atherosclerotic plaque development in the wall of the coronary arteries. The underlying mechanism involves atherosclerosis of the arteries of the heart which is a relatively complex process comprising several steps. In CAD, atherosclerosis induces functional and structural changes. The pathogenesis of CAD results from various changes in and interactions between multiple cell types in the artery walls; these changes mainly include endothelial cell (EC) dysfunction, vascular smooth muscle cell (SMC) alteration, lipid deposition and macrophage activation. Various blood markers associated with an increased risk for cardiovascular endpoints have been identified; however, few have yet been shown to have a diagnostic impact or important clinical implications that would affect patient management. Noncoding RNAs, especially microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), can be stable in plasma and other body fluids and could therefore serve as biomarkers for some diseases. Many studies have shown that some miRNAs and lncRNAs play key roles in heart and vascular development and in cardiac pathophysiology. Thus, we summarize here the latest research progress, focusing on the molecular mechanism of miRNAs and lncRNAs in CAD, with the intent of seeking new targets for the treatment of heart disease.
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Affiliation(s)
- Yuan Zhang
- Institute for Translational Medicine, Qingdao University, Deng Zhou Road 38, Qingdao 266021, China
| | - Lei Zhang
- Institute for Translational Medicine, Qingdao University, Deng Zhou Road 38, Qingdao 266021, China
| | - Yu Wang
- Institute for Translational Medicine, Qingdao University, Deng Zhou Road 38, Qingdao 266021, China
| | - Han Ding
- Institute for Translational Medicine, Qingdao University, Deng Zhou Road 38, Qingdao 266021, China
| | - Sheng Xue
- Institute for Translational Medicine, Qingdao University, Deng Zhou Road 38, Qingdao 266021, China
| | - Hongzhao Qi
- Institute for Translational Medicine, Qingdao University, Deng Zhou Road 38, Qingdao 266021, China
| | - Peifeng Li
- Institute for Translational Medicine, Qingdao University, Deng Zhou Road 38, Qingdao 266021, China
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Xu S, Kamato D, Little PJ, Nakagawa S, Pelisek J, Jin ZG. Targeting epigenetics and non-coding RNAs in atherosclerosis: from mechanisms to therapeutics. Pharmacol Ther 2019; 196:15-43. [PMID: 30439455 PMCID: PMC6450782 DOI: 10.1016/j.pharmthera.2018.11.003] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Atherosclerosis, the principal cause of cardiovascular death worldwide, is a pathological disease characterized by fibro-proliferation, chronic inflammation, lipid accumulation, and immune disorder in the vessel wall. As the atheromatous plaques develop into advanced stage, the vulnerable plaques are prone to rupture, which causes acute cardiovascular events, including ischemic stroke and myocardial infarction. Emerging evidence has suggested that atherosclerosis is also an epigenetic disease with the interplay of multiple epigenetic mechanisms. The epigenetic basis of atherosclerosis has transformed our knowledge of epigenetics from an important biological phenomenon to a burgeoning field in cardiovascular research. Here, we provide a systematic and up-to-date overview of the current knowledge of three distinct but interrelated epigenetic processes (including DNA methylation, histone methylation/acetylation, and non-coding RNAs), in atherosclerotic plaque development and instability. Mechanistic and conceptual advances in understanding the biological roles of various epigenetic modifiers in regulating gene expression and functions of endothelial cells (vascular homeostasis, leukocyte adhesion, endothelial-mesenchymal transition, angiogenesis, and mechanotransduction), smooth muscle cells (proliferation, migration, inflammation, hypertrophy, and phenotypic switch), and macrophages (differentiation, inflammation, foam cell formation, and polarization) are discussed. The inherently dynamic nature and reversibility of epigenetic regulation, enables the possibility of epigenetic therapy by targeting epigenetic "writers", "readers", and "erasers". Several Food Drug Administration-approved small-molecule epigenetic drugs show promise in pre-clinical studies for the treatment of atherosclerosis. Finally, we discuss potential therapeutic implications and challenges for future research involving cardiovascular epigenetics, with an aim to provide a translational perspective for identifying novel biomarkers of atherosclerosis, and transforming precision cardiovascular research and disease therapy in modern era of epigenetics.
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Affiliation(s)
- Suowen Xu
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA.
| | - Danielle Kamato
- School of Pharmacy, The University of Queensland, Wooloongabba, QLD 4102, Australia; Department of Pharmacy, Xinhua College of Sun Yat-sen University, Guangzhou 510520, China
| | - Peter J Little
- School of Pharmacy, The University of Queensland, Wooloongabba, QLD 4102, Australia; Department of Pharmacy, Xinhua College of Sun Yat-sen University, Guangzhou 510520, China
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12-jo Nishi 6-chome, Kita-ku, Sapporo 060-0812, Japan
| | - Jaroslav Pelisek
- Department of Vascular and Endovascular Surgery, Klinikum rechts der Isar der Technischen Universitaet Muenchen, Germany
| | - Zheng Gen Jin
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA.
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Xu J, Gu W, Ji K, Xu Z, Zhu H, Zheng W. Sequence analysis and structure prediction of ABHD16A and the roles of the ABHD family members in human disease. Open Biol 2019; 8:rsob.180017. [PMID: 29794032 PMCID: PMC5990648 DOI: 10.1098/rsob.180017] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 04/30/2018] [Indexed: 12/12/2022] Open
Abstract
Abhydrolase domain containing 16A (ABHD16A) is a member of the α/β hydrolase domain-containing (ABHD) protein family and is expressed in a variety of animal cells. Studies have shown that ABHD16A has acylglycerol lipase and phosphatidylserine lipase activities. Its gene location in the main histocompatibility complex (MHC) III gene cluster suggests that this protein may participate in the immunomodulation of the body. The results of studies investigating nearly 20 species of ABHDs reveal that the ABHD proteins are key factors in metabolic regulation and disease occurrence and development. In this paper, we summarize the related progress regarding the function of ABHD16A and other ABHD proteins. A prediction of the active sites and structural domains of ABHD16A and an analysis of the amino acid sites are included. Moreover, we analysed the amino acid sequences of the ABHD16A molecules in different species and provide an overview of the related functions and diseases associated with these proteins. The functions and diseases related to ABHD are systematically summarized and highlighted. Future research directions for studies investigating the functions and mechanisms of these proteins are also suggested. Further studies investigating the function of ABHD proteins may further confirm their positions as important determinants of lipid metabolism and related diseases.
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Affiliation(s)
- Jun Xu
- College of Life Sciences, Henan Agricultural University, 95 Wenhua Road, Zhengzhou 450002, People's Republic of China
| | - Weizhen Gu
- College of Life Sciences, Henan Agricultural University, 95 Wenhua Road, Zhengzhou 450002, People's Republic of China
| | - Kai Ji
- College of Life Sciences, Henan Agricultural University, 95 Wenhua Road, Zhengzhou 450002, People's Republic of China
| | - Zhao Xu
- College of Life Sciences, Henan Agricultural University, 95 Wenhua Road, Zhengzhou 450002, People's Republic of China
| | - Haihua Zhu
- College of Life Sciences, Henan Agricultural University, 95 Wenhua Road, Zhengzhou 450002, People's Republic of China.,Henan Business Research Institute Co. Ltd, Zhengzhou, He'nan, People's Republic of China
| | - Wenming Zheng
- College of Life Sciences, Henan Agricultural University, 95 Wenhua Road, Zhengzhou 450002, People's Republic of China
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