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Gravina T, Favero F, Rosano S, Parab S, Diaz Alcalde A, Bussolino F, Doronzo G, Corà D. Integrative Bioinformatics Analysis Reveals a Transcription Factor EB-Driven MicroRNA Regulatory Network in Endothelial Cells. Int J Mol Sci 2024; 25:7123. [PMID: 39000232 PMCID: PMC11241138 DOI: 10.3390/ijms25137123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 06/19/2024] [Accepted: 06/21/2024] [Indexed: 07/16/2024] Open
Abstract
Various human diseases are triggered by molecular alterations influencing the fine-tuned expression and activity of transcription factors, usually due to imbalances in targets including protein-coding genes and non-coding RNAs, such as microRNAs (miRNAs). The transcription factor EB (TFEB) modulates human cellular networks, overseeing lysosomal biogenesis and function, plasma-membrane trafficking, autophagic flux, and cell cycle progression. In endothelial cells (ECs), TFEB is essential for the maintenance of endothelial integrity and function, ensuring vascular health. However, the comprehensive regulatory network orchestrated by TFEB remains poorly understood. Here, we provide novel mechanistic insights into how TFEB regulates the transcriptional landscape in primary human umbilical vein ECs (HUVECs), using an integrated approach combining high-throughput experimental data with dedicated bioinformatics analysis. By analyzing HUVECs ectopically expressing TFEB using ChIP-seq and examining both polyadenylated mRNA and small RNA sequencing data from TFEB-silenced HUVECs, we have developed a bioinformatics pipeline mapping the different gene regulatory interactions driven by TFEB. We show that TFEB directly regulates multiple miRNAs, which in turn post-transcriptionally modulate a broad network of target genes, significantly expanding the repertoire of gene programs influenced by this transcription factor. These insights may have significant implications for vascular biology and the development of novel therapeutics for vascular disease.
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Affiliation(s)
- Teresa Gravina
- Department of Translational Medicine, University of Piemonte Orientale, 28100 Novara, Italy
- Center for Translational Research on Allergic and Autoimmune Diseases (CAAD), University of Piemonte Orientale, 28100 Novara, Italy
| | - Francesco Favero
- Department of Translational Medicine, University of Piemonte Orientale, 28100 Novara, Italy
- Center for Translational Research on Allergic and Autoimmune Diseases (CAAD), University of Piemonte Orientale, 28100 Novara, Italy
| | - Stefania Rosano
- Department of Oncology, University of Torino, 10124 Orbassano, Italy
- Candiolo Cancer Institute, IRCCS-FPO, 10060 Candiolo, Italy
| | - Sushant Parab
- Department of Oncology, University of Torino, 10124 Orbassano, Italy
- Candiolo Cancer Institute, IRCCS-FPO, 10060 Candiolo, Italy
| | - Alejandra Diaz Alcalde
- Department of Oncology, University of Torino, 10124 Orbassano, Italy
- Candiolo Cancer Institute, IRCCS-FPO, 10060 Candiolo, Italy
| | - Federico Bussolino
- Department of Oncology, University of Torino, 10124 Orbassano, Italy
- Candiolo Cancer Institute, IRCCS-FPO, 10060 Candiolo, Italy
| | - Gabriella Doronzo
- Department of Oncology, University of Torino, 10124 Orbassano, Italy
- Candiolo Cancer Institute, IRCCS-FPO, 10060 Candiolo, Italy
| | - Davide Corà
- Department of Translational Medicine, University of Piemonte Orientale, 28100 Novara, Italy
- Center for Translational Research on Allergic and Autoimmune Diseases (CAAD), University of Piemonte Orientale, 28100 Novara, Italy
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Tasopoulou KM, Karakasiliotis I, Argyriou C, Bampali M, Tsaroucha AK, Dovrolis N, Christaina E, Georgiadis GS. Next-Generation Sequencing of microRNAs in Small Abdominal Aortic Aneurysms: MiR-24 as a Biomarker. Ann Vasc Surg 2024; 99:366-379. [PMID: 37922957 DOI: 10.1016/j.avsg.2023.09.065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/28/2023] [Accepted: 09/02/2023] [Indexed: 11/07/2023]
Abstract
BACKGROUND Small abdominal aortic aneurysms (AAAs) are asymptomatic but can potentially lead to rupture if left undetected. To date, there is a lack of simple nonradiologic routine tests available for diagnosing AAAs. MicroRNAs (miRNAs) have been proven to be good-quality biomarkers in several diseases, including AAA. METHODS An attempt to identify a panel of circulating miRNAs with differential expression in AAAs via next-generation sequencing (NGS) was performed in serum samples: small AAAs (n = 3), large AAAs (n = 3), and controls (n = 3). For miR-24, validation with real-time polymerase chain reaction (PCR) was undertaken in a larger group (n = 80). RESULTS In the NGS study, 23 miRNAs were identified as differentially expressed (with statistical significance) in small AAAs in comparison with controls. Among them, miR-24 showed the largest upregulation with 23-fold change (log2FC 4.5, P = 0.024). For large AAAs compared with controls, and small AAAs compared with large AAAs, a panel of 33 and 131 miRNAs showed statistically significant differential expression, respectively. Based on the results of the NGS stage, a literature search was performed, and information regarding AAA pathogenesis, coronary artery disease, and peripheral arterial disease was documented where applicable: miR-24, miR-103, miR-193a, miR-486, miR-582, and miR-3663. Of these 6 miRNAs, miR-24 was chosen for further validation with real-time PCR. Additionally, in the NGS study analysis, 17 miRNAs were common between the small-large AAAs, small AAAs-controls, and large AAAs-controls comparisons: miR-7846, miR-3195, miR-486-2, miR-3194, miR-5589, miR-1538, miR-3178, miR-4771-1, miR-5695, miR-6504, miR-1908, miR-6823, miR-3159, miR-23a, miR-7853, miR-496, and miR-193a. Interestingly, in the validation stage with real-time PCR, miR-24 was found downregulated in small and large AAAs compared with controls (fold-changes: 0.27, P = 0.015 and 0.15, P = 0.005, respectively). No correlation was found between average Ct values, aneurysm diameter, and patients' age. CONCLUSIONS Our findings further highlight the importance of miR-24 as a potential biomarker as well as a therapeutic target for abdominal aneurysmal disease. Future research and validation of a panel of miRNAs for AAA would aid in diagnosis and discrimination between diseases with overlapping pathogeneses.
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Affiliation(s)
- Kalliopi-Maria Tasopoulou
- Department of Vascular Surgery, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece.
| | - Ioannis Karakasiliotis
- Laboratory of Biology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Christos Argyriou
- Department of Vascular Surgery, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece
| | - Maria Bampali
- Laboratory of Biology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Alexandra K Tsaroucha
- Department of Experimental Surgery, Democritus University of Thrace, Alexandroupolis, Greece
| | - Nikolas Dovrolis
- Laboratory of Biology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Eleni Christaina
- Department of Biostatistics, Democritus University of Thrace, Alexandroupolis, Greece
| | - George S Georgiadis
- Department of Vascular Surgery, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece
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Kotlyarov S. Identification of Important Genes Associated with the Development of Atherosclerosis. Curr Gene Ther 2024; 24:29-45. [PMID: 36999180 DOI: 10.2174/1566523223666230330091241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 12/06/2022] [Accepted: 01/26/2023] [Indexed: 04/01/2023]
Abstract
Atherosclerosis is one of the most important medical problems due to its prevalence and significant contribution to the structure of temporary and permanent disability and mortality. Atherosclerosis is a complex chain of events occurring in the vascular wall over many years. Disorders of lipid metabolism, inflammation, and impaired hemodynamics are important mechanisms of atherogenesis. A growing body of evidence strengthens the understanding of the role of genetic and epigenetic factors in individual predisposition and development of atherosclerosis and its clinical outcomes. In addition, hemodynamic changes, lipid metabolism abnormalities, and inflammation are closely related and have many overlapping links in regulation. A better study of these mechanisms may improve the quality of diagnosis and management of such patients.
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Affiliation(s)
- Stanislav Kotlyarov
- Department of Nursing, Ryazan State Medical University Named After Academician I.P. Pavlov, Russian Federation
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Tao Y, Li G, Yang Y, Wang Z, Wang S, Li X, Yu T, Fu X. Epigenomics in aortic dissection: From mechanism to therapeutics. Life Sci 2023; 335:122249. [PMID: 37940070 DOI: 10.1016/j.lfs.2023.122249] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/20/2023] [Accepted: 11/03/2023] [Indexed: 11/10/2023]
Abstract
Aortic dissection (AD) has an unfavorable prognosis. It requires early diagnosis, appropriate treatment strategies, and suspicion to recognize symptoms; thus, it is commonly described as an acute aortic emergency. The clinical manifestations of painless AD are complex and variable. However, there is no effective treatment to prevent the progression of AD. Therefore, study of the molecular targets and mechanisms of AD to enable prevention or early intervention is particularly important. Although multiple gene mutations have been proposed as linked to AD development, evidence that multiple epigenetic elements are strongly associated is steadily increasing. These epigenetic processes include DNA methylation, N6-methyladenosine, histone modification, non-histone posttranslational modification, and non-coding RNAs (ncRNAs). Among these processes, resveratrol targeting Sirtuin 1 (SIRT1), 5-azacytidine (5azaC) targeting DNA methyltransferase (DNMT), and vitamin C targeting ten-eleven translocation 2 (Tet2) showed unique advantages in improving AD and vascular dysfunction. Finally, we explored potential epigenetic drugs and diagnostic methods for AD, which might provide options for the future.
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Affiliation(s)
- Yan Tao
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, Qingdao 266000, People's Republic of China
| | - Gang Li
- Department of Vascular Surgery, Shandong Provincial Hospital affiliated to Shandong First Medical University, 324 Jingwu Road, Jinan, Shandong 250021, China; Department of Vascular Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, 324 Jingwu Road, Jinan, Shandong 250021, People's Republic of China
| | - Yanyan Yang
- Department of Immunology, Basic Medicine School, Qingdao University, No. 308 Ningxia Road, Qingdao 266071, People's Republic of China
| | - Zhibin Wang
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, Qingdao 266000, People's Republic of China
| | - Shizhong Wang
- The department of Cardiology surgery, The Affiliated Hospital of Qingdao University, Qingdao 266000, People's Republic of China
| | - Xiaolu Li
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, Qingdao 266000, People's Republic of China
| | - Tao Yu
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, Qingdao 266000, People's Republic of China; Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, No. 38 Dengzhou Road, Qingdao 266021, People's Republic of China.
| | - Xiuxiu Fu
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, Qingdao 266000, People's Republic of China.
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Zhang J, Xu M, Chen T, Zhou Y. Bioinformatics Analysis of Common Differential Genes of Viral Myocarditis and Dilated Cardiomyopathy: Screening for Potential Pharmacological Compounds. J Cardiovasc Dev Dis 2022; 9:jcdd9100353. [PMID: 36286305 PMCID: PMC9604690 DOI: 10.3390/jcdd9100353] [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: 09/14/2022] [Revised: 10/09/2022] [Accepted: 10/11/2022] [Indexed: 11/24/2022] Open
Abstract
(1) Background: The mechanism of viral myocarditis (VMC) progression to dilated cardiomyopathy (DCM) remains unclear. The aim of this study was to identify key genes in the progression of VMC to DCM, so as to find potential therapeutic drugs and provide insights for future research. (2) Methods: Differential expression analysis of GSE4172 and GSE17800 from the Gene Expression Omnibus (GEO) database was performed using GEO2R, which contained genome-wide analysis of myocardial biopsies from VMC and DCM, respectively. We used the Venn diagram analysis to screen the common differentially expressed genes (DEGs). GO functional enrichment analysis and KEGG pathway analysis were also performed. Then we conducted protein-protein interaction (PPI) networks using STRING and identified hub genes using Cytoscape. Finally, we used cMAP to screen out candidate compounds targeting these hub genes; (3) Results: In total, 2143 DEGs for VMC and 1365 DEGs for DCM were found. Then a total of 191 common DEGs were identified. Biological processes and pathway involved in these genes mainly include GABA-gated chloride ion channel activity and Rap1 signaling pathway. A total of 14 hub genes were identified. PPI network showed these hubs mainly enriched in regulation of WNT signaling pathway and GABA-gated chloride ion channel activity. Subgroup analysis of Severe VMC cohort revealed 10 hub genes which mainly clustered in GABA channel activity, extracellular matrix remodeling and sarcomere dysfunction. Using cMAP, we obtained top 10 potential medications, but only amlodipine is currently viable; (4) Conclusions: Our study finds the hub genes and reveals the important role of GABA-gated chloride ion channel, Rap1 signaling pathway, WNT signaling pathway, extracellular matrix remodeling and sarcomere dysfunction in the progression from VMC to DCM. Amlodipine is a potential viable drug in preventing the progression of VMC to DCM.
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Emerging Role of Non-Coding RNAs in Aortic Dissection. Biomolecules 2022; 12:biom12101336. [PMID: 36291545 PMCID: PMC9599213 DOI: 10.3390/biom12101336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 09/12/2022] [Accepted: 09/17/2022] [Indexed: 11/16/2022] Open
Abstract
Aortic dissection (AD) is a fatal cardiovascular acute disease with high incidence and mortality, and it seriously threatens patients’ lives and health. The pathogenesis of AD mainly includes vascular inflammation, extracellular matrix degradation, and phenotypic conversion as well as apoptosis of vascular smooth muscle cells (VSMCs); however, its detailed mechanisms are still not fully elucidated. Non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), are an emerging class of RNA molecules without protein-coding ability, and they play crucial roles in the progression of many diseases, including AD. A growing number of studies have shown that the dysregulation of ncRNAs contributes to the occurrence and development of AD by modulating the expression of specific target genes or the activity of related proteins. In addition, some ncRNAs exhibit great potential as promising biomarkers and therapeutic targets in AD treatment. In this review, we systematically summarize the recent findings on the underlying mechanism of ncRNA involved in AD regulation and highlight their clinical application as biomarkers and therapeutic targets in AD treatment. The information reviewed here will be of great benefit to the development of ncRNA-based therapeutic strategies for AD patients.
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Genetic and Epigenetic Regulation of Lipoxygenase Pathways and Reverse Cholesterol Transport in Atherogenesis. Genes (Basel) 2022; 13:genes13081474. [PMID: 36011386 PMCID: PMC9408222 DOI: 10.3390/genes13081474] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/12/2022] [Accepted: 08/16/2022] [Indexed: 11/16/2022] Open
Abstract
Atherosclerosis is one of the most important medical and social problems of modern society. Atherosclerosis causes a large number of hospitalizations, disability, and mortality. A considerable amount of evidence suggests that inflammation is one of the key links in the pathogenesis of atherosclerosis. Inflammation in the vascular wall has extensive cross-linkages with lipid metabolism, and lipid mediators act as a central link in the regulation of inflammation in the vascular wall. Data on the role of genetics and epigenetic factors in the development of atherosclerosis are of great interest. A growing body of evidence is strengthening the understanding of the significance of gene polymorphism, as well as gene expression dysregulation involved in cross-links between lipid metabolism and the innate immune system. A better understanding of the genetic basis and molecular mechanisms of disease pathogenesis is an important step towards solving the problems of its early diagnosis and treatment.
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Shao Y, Luo J, Ye L, Ran HY, Shi HM, Zhang C, Wu QC. Construction and Integrated Analysis of Competitive Endogenous Long Non-Coding RNA Network in Thoracic Aortic Dissection. Int J Gen Med 2021; 14:6863-6873. [PMID: 34703291 PMCID: PMC8528547 DOI: 10.2147/ijgm.s335082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 09/29/2021] [Indexed: 12/12/2022] Open
Abstract
Background Long non-coding RNAs (lncRNAs) can act as a competitive endogenous RNA (ceRNA) to regulate gene expression by sequestering the microRNA (miRNA). However, the lncRNA-miRNA-mRNA ceRNA network in thoracic aortic dissection (TAD) has been rarely documented. Methods Three Gene Expression Omnibus (GEO) datasets were used to detect differentially expressed mRNAs, miRNAs, and lncRNAs in TAD. Gene ontology and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted for the differentially expressed mRNAs. A protein–protein interaction network for differentially expressed mRNAs was also constructed, and hub genes were identified. We established a ceRNA network of TAD based on the differentially expressed miRNAs, mRNAs and lncRNAs, and verified our results using an independent dataset and quantitative real-time PCR (qRT-PCR). Results In TAD, 267 lncRNAs, 81 miRNAs, and 346 mRNAs were identified as differentially expressed. The established ceRNA network consisted of seven lncRNA nodes, three mRNA nodes, and three miRNA nodes, and the expression of miRNAs in TAD was opposite to that of lncRNAs and mRNAs. Subsequently, an independent GEO dataset and qRT-PCR were used to validate the expression of three mRNAs. In addition, the expression differences in SLC7A5, associated miRNA and lncRNA were verified. According to gene set enrichment analysis of SLC7A5, the most significant KEGG pathway was considerably enriched in spliceosome and pentose phosphate pathway. Conclusion We established a novel ceRNA regulatory network in TAD, which provides valuable information for further research in the molecular mechanisms of TAD.
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Affiliation(s)
- Yue Shao
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Jun Luo
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Liu Ye
- The First Branch, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Hao-Yu Ran
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Hao-Ming Shi
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Cheng Zhang
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Qing-Chen Wu
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
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