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Mariappan V, Srinivasan R, Pratheesh R, Jujjuvarapu MR, Pillai AB. Predictive biomarkers for the early detection and management of heart failure. Heart Fail Rev 2024; 29:331-353. [PMID: 37702877 DOI: 10.1007/s10741-023-10347-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/04/2023] [Indexed: 09/14/2023]
Abstract
Cardiovascular disease (CVD) is a serious public health concern whose incidence has been on a rise and is projected by the World Health Organization to be the leading global cause of mortality by 2030. Heart failure (HF) is a complicated syndrome resulting from various CVDs of heterogeneous etiologies and exhibits varying pathophysiology, including activation of inflammatory signaling cascade, apoptosis, fibrotic pathway, and neuro-humoral system, thereby leading to compromised cardiac function. During this process, several biomolecules involved in the onset and progression of HF are released into circulation. These circulating biomolecules could serve as unique biomarkers for the detection of subclinical changes and can be utilized for monitoring disease severity. Hence, it is imperative to identify these biomarkers to devise an early predictive strategy to stop the deterioration of cardiac function caused by these complex cellular events. Furthermore, measurement of multiple biomarkers allows clinicians to divide HF patients into sub-groups for treatment and management based on early health outcomes. The present article provides a comprehensive overview of current omics platform available for discovering biomarkers for HF management. Some of the existing and novel biomarkers for the early detection of HF with special reference to endothelial biology are also discussed.
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Affiliation(s)
- Vignesh Mariappan
- Mahatma Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth (Deemed to be University), Puducherry, 607402, India
| | - Rajesh Srinivasan
- Mahatma Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth (Deemed to be University), Puducherry, 607402, India
| | - Ravindran Pratheesh
- Department of Neurosurgery, Mahatma Gandhi Medical College and Research Institute (MGMCRI), Sri Balaji Vidyapeeth (Deemed to be University), Puducherry, 607402, India
| | - Muraliswar Rao Jujjuvarapu
- Radiodiagnosis and Imageology, Aware Gleneagles Global Hospital, LB Nagar, Hyderabad, Telangana, 500035, India
| | - Agieshkumar Balakrishna Pillai
- Mahatma Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth (Deemed to be University), Puducherry, 607402, India.
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2
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Peng W, Xie Y, Xia J, Qi H, Liu K, Li B, Zhang F, Wen F, Zhang L. Integrated analysis of the lncRNA-associated competing endogenous RNA network in salt sensitivity of blood pressure. Heliyon 2023; 9:e22466. [PMID: 38125519 PMCID: PMC10731005 DOI: 10.1016/j.heliyon.2023.e22466] [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: 07/16/2023] [Revised: 11/12/2023] [Accepted: 11/13/2023] [Indexed: 12/23/2023] Open
Abstract
Accumulating evidence showed that competing endogenous RNA (ceRNA) mechanism plays a pivotal role in salt sensitivity of blood pressure (SSBP). We constructed a ceRNA network based on SSBP-related differently expressed lncRNAs (2), mRNAs (73) and miRNAs (18). Bioinformatic analyses were utilized to analyze network and found network genes participate in biological pathways related to SSBP pathogenesis such as regulation of nitric oxide biosynthetic process (GO:0045,428) and cellular response to cytokine stimulus (GO:0071,345). Fourteen candidate ceRNA pathways were selected from network to perform qRT-PCR validation and found nine RNAs (KCNQ1OT1, SLC8A1-AS1, IL1B, BCL2L11, KCNJ15, CX3CR1, KLF2, hsa-miR-362-5p and hsa-miR-423-5p) differently expressed between salt-sensitive (SS) and salt-resistant (SR) groups (P < 0.05). Four ceRNA pathways were further validated by luciferase reporter assay and found KCNQ1OT1→hsa-miR-362-5p/hsa-miR-423-5p→IL1B pathways may influence the pathogenic mechanism of SS. Our findings suggested the ceRNA pathway and network may affect SS occurrence mainly through endothelial dysfunction and inflammatory activation.
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Affiliation(s)
- Wenjuan Peng
- Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University, And Beijing Municipal Key Laboratory of Clinical Epidemiology, Beijing 100069, China
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China
| | - Yunyi Xie
- Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University, And Beijing Municipal Key Laboratory of Clinical Epidemiology, Beijing 100069, China
| | - Juan Xia
- Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University, And Beijing Municipal Key Laboratory of Clinical Epidemiology, Beijing 100069, China
| | - Han Qi
- Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University, And Beijing Municipal Key Laboratory of Clinical Epidemiology, Beijing 100069, China
| | - Kuo Liu
- Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University, And Beijing Municipal Key Laboratory of Clinical Epidemiology, Beijing 100069, China
| | - Bingxiao Li
- Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University, And Beijing Municipal Key Laboratory of Clinical Epidemiology, Beijing 100069, China
| | - Fengxu Zhang
- Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University, And Beijing Municipal Key Laboratory of Clinical Epidemiology, Beijing 100069, China
| | - Fuyuan Wen
- Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University, And Beijing Municipal Key Laboratory of Clinical Epidemiology, Beijing 100069, China
| | - Ling Zhang
- Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University, And Beijing Municipal Key Laboratory of Clinical Epidemiology, Beijing 100069, China
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Aderinto N, Abdulbasit MO, Olatunji G, Edun M, Aboderin G. The promise of RNA-based therapeutics in revolutionizing heart failure management - a narrative review of current evidence. Ann Med Surg (Lond) 2023; 85:4442-4453. [PMID: 37663746 PMCID: PMC10473317 DOI: 10.1097/ms9.0000000000001118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 07/18/2023] [Indexed: 09/05/2023] Open
Abstract
This review elucidates the potential of RNA-based therapeutics to revolutionize heart failure (HF) management. Through a comprehensive analysis of relevant studies, this review reveals the promising prospects of these novel interventions in personalized treatment strategies, targeted modulation of specific molecular pathways, and the attainment of synergistic effects via combination therapies. Moreover, the regenerative capacity of RNA-based therapeutics for cardiac repair and the inherent advantages associated with noninvasive routes of administration are explored. Additionally, the studies accentuate the significance of diligent monitoring of disease progression and treatment response, ensuring safety and considering long-term outcomes. While ongoing research endeavours and technological advancements persist in addressing extant challenges and limitations, the transformative potential of RNA-based therapeutics in HF management offers a beacon of hope for enhanced patient outcomes.
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Affiliation(s)
- Nicholas Aderinto
- Department of Medicine and Surgery, Ladoke Akintola University of Technology, Ogbomoso, Oyo State
| | - Muili O. Abdulbasit
- Department of Medicine and Surgery, Ladoke Akintola University of Technology, Ogbomoso, Oyo State
| | - Gbolahan Olatunji
- Department of Medicine and Surgery, University of Ilorin, Ilorin, Kwara State, Nigeria
| | - Mariam Edun
- Department of Medicine and Surgery, University of Ilorin, Ilorin, Kwara State, Nigeria
| | - Gbolahan Aboderin
- Department of Medicine and Surgery, Ladoke Akintola University of Technology, Ogbomoso, Oyo State
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SNPs in 3'UTR miRNA Target Sequences Associated with Individual Drug Susceptibility. Int J Mol Sci 2022; 23:ijms232213725. [PMID: 36430200 PMCID: PMC9692299 DOI: 10.3390/ijms232213725] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/04/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022] Open
Abstract
The complementary interaction of microRNAs (miRNAs) with their binding sites in the 3'untranslated regions (3'UTRs) of target gene mRNAs represses translation, playing a leading role in gene expression control. MiRNA recognition elements (MREs) in the 3'UTRs of genes often contain single nucleotide polymorphisms (SNPs), which can change the binding affinity for target miRNAs leading to dysregulated gene expression. Accumulated data suggest that these SNPs can be associated with various human pathologies (cancer, diabetes, neuropsychiatric disorders, and cardiovascular diseases) by disturbing the interaction of miRNAs with their MREs located in mRNA 3'UTRs. Numerous data show the role of SNPs in 3'UTR MREs in individual drug susceptibility and drug resistance mechanisms. In this review, we brief the data on such SNPs focusing on the most rigorously proven cases. Some SNPs belong to conventional genes from the drug-metabolizing system (in particular, the genes coding for cytochromes P450 (CYP 450), phase II enzymes (SULT1A1 and UGT1A), and ABCB3 transporter and their expression regulators (PXR and GATA4)). Other examples of SNPs are related to the genes involved in DNA repair, RNA editing, and specific drug metabolisms. We discuss the gene-by-gene studies and genome-wide approaches utilized or potentially utilizable to detect the MRE SNPs associated with individual response to drugs.
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Role of Different Types of miRNAs in Some Cardiovascular Diseases and Therapy-Based miRNA Strategies: A Mini Review. BIOMED RESEARCH INTERNATIONAL 2022; 2022:2738119. [PMID: 36187500 PMCID: PMC9519277 DOI: 10.1155/2022/2738119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 08/26/2022] [Accepted: 08/27/2022] [Indexed: 11/17/2022]
Abstract
The role of microRNAs (miRNAs) in the pathogenesis of cardiovascular disease has been extensively studied. miRNAs have been highlighted as an important physiological regulator for activities like cardiac protection. miRNAs are present in the circulation, and they have been investigated as physiological markers, especially in the condition of heart failure. However, there is less compelling verification that miRNAs can outperform traditional biomarkers. However, clinical evidence is still required. In this review article, we explored the feasibility of miRNAs as diagnostic biomarkers for heart failure in a systematic study. Searching in the PubMed database to identify miRNA molecules that are differentially expressed between groups of patients with heart failure or heart disease and controls, throughout the investigation, we discovered no significant overlap in differentially expressed miRNAs. Only four miRNAs (“miR-126,” “miR-150-5p,” “hsa-miR-233,” and “miR-423-5p”) were differentially expressed. Results from our review show that there is not enough evidence to support the use of miRNAs as biomarkers in clinical settings.
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lncRNA ADAMTS9-AS1/circFN1 Competitively Binds to miR-206 to Elevate the Expression of ACTB, Thus Inducing Hypertrophic Cardiomyopathy. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:1450610. [PMID: 35401927 PMCID: PMC8989615 DOI: 10.1155/2022/1450610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 11/25/2021] [Accepted: 12/03/2021] [Indexed: 11/17/2022]
Abstract
Hypertrophic cardiomyopathy (HCM) is a genetic cardiac disease and can result in substantial disability. The current study explored the potentials of long noncoding RNA- (lncRNA-) circular RNA- (circRNA-) microRNA- (miRNA-) messenger RNA (mRNA) networks in HCM. Firstly, HCM-related microarray data were procured from the GEO database, with differentially expressed genes (DEGs) obtained. HCM-related target genes were retrieved in combination with GeneCards and CTD databases, and candidate target genes were subsequently obtained by intersection screening. Further, an interaction network diagram of candidate target genes was constructed using the STRING database, and the hub genes in the network were determined according to the core degree. The “ClusterProfiler” package of the R software was adopted for GO and KEGG analyses of candidate target genes, to analyze the potential molecular pathways in HCM. Next, upstream miRNA, lncRNA, and circRNA of ACTB were predicted with RNAInter, mirDIP, TargetScan, DIANA-LncBase, and StarBase databases, followed by construction of lncRNA/circRNA-miRNA-mRNA coexpression networks. ACTB, miR-206, circFN1, and ADAMTS9-AS1 expression in peripheral blood samples from HCM patients and normal healthy controls were detected using RT-qPCR. Moreover, rat cardiomyocyte cell lines H9c2 and HEK293 cells were selected for in vitro verification of competitive endogenous RNA (ceRNA) regulation mechanism. A total of 15 candidate target genes related to HCM were screened using the online databases. Further protein-protein interaction analysis identified ACTB as the hub gene for HCM. The targeted binding relationship between miR-206, miR-145-5p, miR-1-3p, and ACTB was found. Furthermore, ADAMTS9-AS1 and circFN1 were discovered as the upstream genes of miR-206. Moreover, ADAMTS9-AS1, circFN1, and ACTB were found to be poorly expressed, and miR-206 was highly expressed in HCM. In vitro experimentation further confirmed that ADAMTS9-AS1 and circFN1 could competitively bind to miR-206, thereby augmenting ACTB expression. Taken all, ADAMTS9-AS1/circFN1-miR-206-ACTB regulatory network may involve in HCM occurrence, providing a novel theoretical basis for in-depth understanding of mechanism of HCM.
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Chen F, Li G, Wu C, Wang L, Ko CN, Ma DL, Leung CH. Interference Reduction Biosensing Strategy for Highly Sensitive microRNA Detection. Anal Chem 2022; 94:4513-4521. [PMID: 35234447 DOI: 10.1021/acs.analchem.2c00138] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
MicroRNAs are potential biomarkers for human cancers and other diseases due to their roles as post-transcriptional regulators for gene expression. However, the detection of miRNAs by conventional methods such as RT-qPCR, in situ hybridization, northern blot-based platforms, and next-generation sequencing is complicated by short length, low abundance, high sequence homology, and susceptibility to degradation of miRNAs. In this study, we developed a nicking endonuclease-mediated interference reduction rolling circle amplification (NEM-IR-RCA) strategy for the ultrasensitive and highly specific detection of miRNA-21. This method exploits the advantages of the optical properties of long-lived iridium(III) probes, in conjunction with time-resolved emission spectroscopy (TRES) and exponential rolling circle amplification (E-RCA). Under the NEM-IR-RCA-based signal enhancement processes, the limit of detection of miRNA-21 was down to 0.0095 fM with a linear range from 0.05 to 100 fM, which is comparable with the conventional RT-qPCR. Unlike RT-qPCR, the strategy was performed at a lower and constant temperature without heating/cooling cycles and reverse transcription. The strategy could clearly discriminate between matched and mismatched targets, demonstrating high specificity. Moreover, the potential application of this method was demonstrated in cancer cells and mouse serum samples, showing good agreement with RT-qPCR results. Apart from miRNA-21 detection, this platform could be also adapted for detecting other miRNAs, such as let-7a and miRNA-22, indicating its excellent potential for biomedical research and clinical diagnostics.
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Affiliation(s)
- Feng Chen
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau SAR 999078, China
| | - Guodong Li
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau SAR 999078, China.,Zhuhai UM Science and Technology Research Institute, Zhuhai 519031, China
| | - Chun Wu
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR 999077, China
| | - Ling Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau SAR 999078, China
| | - Chung-Nga Ko
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR 999077, China
| | - Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR 999077, China
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau SAR 999078, China.,Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Taipa, Macao SAR 999078, China.,Zhuhai UM Science and Technology Research Institute, Zhuhai 519031, China
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8
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Regulatory network of miRNA, lncRNA, transcription factor and target immune response genes in bovine mastitis. Sci Rep 2021; 11:21899. [PMID: 34753991 PMCID: PMC8578396 DOI: 10.1038/s41598-021-01280-9] [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: 06/04/2021] [Accepted: 10/25/2021] [Indexed: 12/03/2022] Open
Abstract
Pre- and post-transcriptional modifications of gene expression are emerging as foci of disease studies, with some studies revealing the importance of non-coding transcripts, like long non-coding RNAs (lncRNAs) and microRNAs (miRNAs). We hypothesize that transcription factors (TFs), lncRNAs and miRNAs modulate immune response in bovine mastitis and could potentially serve as disease biomarkers and/or drug targets. With computational analyses, we identified candidate genes potentially regulated by miRNAs and lncRNAs base pair complementation and thermodynamic stability of binding regions. Remarkably, we found six miRNAs, two being bta-miR-223 and bta-miR-24-3p, to bind to several targets. LncRNAs NONBTAT027932.1 and XR_003029725.1, were identified to target several genes. Functional and pathway analyses revealed lipopolysaccharide-mediated signaling pathway, regulation of chemokine (C-X-C motif) ligand 2 production and regulation of IL-23 production among others. The overarching interactome deserves further in vitro/in vivo explication for specific molecular regulatory mechanisms during bovine mastitis immune response and could lay the foundation for development of disease markers and therapeutic intervention.
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Chair SY, Chan JYW, Waye MMY, Liu T, Law BMH, Chien WT. Exploration of Potential Genetic Biomarkers for Heart Failure: A Systematic Review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18115904. [PMID: 34072866 PMCID: PMC8198957 DOI: 10.3390/ijerph18115904] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/12/2022]
Abstract
Patients with heart failure (HF) often present with signs and symptoms that are often nonspecific and with a wide differential diagnosis, making diagnosis and prognosis of HF by clinical presentation alone challenging. Our knowledge on genetic diversity is rapidly evolving with high-throughput DNA sequencing technology, which makes a great potential for genetic biomarker development. The present review attempts to provide a comprehensive review on the modification of major genetic components in HF patients and to explore the potential application of these components as clinical biomarkers in the diagnosis and in monitoring the progress of HF. The literature search was conducted using six databases, resulting in the inclusion of eighteen studies in the review. The findings of these studies were summarized narratively. An appraisal of the reporting quality of the included studies was conducted using a twelve-item checklist adapted from the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) checklist. The findings showed that changes in genetic components in patients with HF compared to healthy controls could be noninvasive diagnostic or prognostic tools for HF with higher specificity and sensitivity in comparison with the traditional biomarkers. This review provided evidence for the potential of developing genetic biomarkers of HF.
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Affiliation(s)
- Sek-Ying Chair
- The Nethersole School of Nursing, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; (S.-Y.C.); (M.-M.-Y.W.); (T.L.); (B.-M.-H.L.); (W.-T.C.)
- Asia-Pacific Genomic and Genetic Nursing Centre, The Nethersole School of Nursing, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Judy-Yuet-Wa Chan
- The Nethersole School of Nursing, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; (S.-Y.C.); (M.-M.-Y.W.); (T.L.); (B.-M.-H.L.); (W.-T.C.)
- Correspondence:
| | - Mary-Miu-Yee Waye
- The Nethersole School of Nursing, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; (S.-Y.C.); (M.-M.-Y.W.); (T.L.); (B.-M.-H.L.); (W.-T.C.)
- The Croucher Laboratory for Human Genomics, The Nethersole School of Nursing, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Ting Liu
- The Nethersole School of Nursing, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; (S.-Y.C.); (M.-M.-Y.W.); (T.L.); (B.-M.-H.L.); (W.-T.C.)
| | - Bernard-Man-Hin Law
- The Nethersole School of Nursing, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; (S.-Y.C.); (M.-M.-Y.W.); (T.L.); (B.-M.-H.L.); (W.-T.C.)
| | - Wai-Tong Chien
- The Nethersole School of Nursing, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; (S.-Y.C.); (M.-M.-Y.W.); (T.L.); (B.-M.-H.L.); (W.-T.C.)
- Asia-Pacific Genomic and Genetic Nursing Centre, The Nethersole School of Nursing, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
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Qi Y, Wang X, Li W, Chen D, Meng H, An S. Pseudogenes in Cardiovascular Disease. Front Mol Biosci 2021; 7:622540. [PMID: 33644114 PMCID: PMC7902774 DOI: 10.3389/fmolb.2020.622540] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 12/07/2020] [Indexed: 11/23/2022] Open
Abstract
Cardiovascular disease is the main disease that affects human life span. In recent years, the disease has been increasingly addressed at the molecular levels, for example, pseudogenes are now known to be involved in the pathogenesis and development of cardiovascular diseases. Pseudogenes are non-coding homologs of protein-coding genes and were once called “junk gene.” Since they are highly homologous to their functional parental genes, it is somewhat difficult to distinguish them. With the development of sequencing technology and bioinformatics, pseudogenes have become readily identifiable. Recent studies indicate that pseudogenes are closely related to cardiovascular diseases. This review provides an overview of pseudogenes and their roles in the pathogenesis of cardiovascular diseases. This new knowledge adds to our understanding of cardiovascular disease at the molecular level and will help develop new biomarkers and therapeutic approaches designed to prevent and treat the disease.
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Affiliation(s)
- Yanyan Qi
- Department of Cardiology, Anesthesiology and Emergency Medicine, Henan Province People's Hospital and People's Hospital of Zhengzhou University, Zhengzhou, China
| | - Xi Wang
- Department of Cardiology, People's Hospital of Zhengzhou University, Zhengzhou, China
| | - Wenbo Li
- Department of Cardiology, Henan Province People's Hospital and People's Hospital of Zhengzhou University, Zhengzhou, China
| | - Dongchang Chen
- Department of Cardiology, Henan Province People's Hospital and People's Hospital of Zhengzhou University, Zhengzhou, China
| | - Hua Meng
- Department of Cardiology, Henan Province People's Hospital and People's Hospital of Zhengzhou University, Zhengzhou, China
| | - Songtao An
- Department of Cardiology, Henan Province People's Hospital and People's Hospital of Zhengzhou University, Zhengzhou, China
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Fan Y, Arbab AAI, Zhang H, Yang Y, Lu X, Han Z, Yang Z. MicroRNA-193a-5p Regulates the Synthesis of Polyunsaturated Fatty Acids by Targeting Fatty Acid Desaturase 1 ( FADS1) in Bovine Mammary Epithelial Cells. Biomolecules 2021; 11:biom11020157. [PMID: 33504005 PMCID: PMC7911131 DOI: 10.3390/biom11020157] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/12/2021] [Accepted: 01/20/2021] [Indexed: 12/13/2022] Open
Abstract
Cardiovascular diseases (CVDs) are seriously threatening to human life and health. Polyunsaturated fatty acids (PUFAs) are known for their role in preventing CVDs. It is beneficial to population health to promote the content of PUFAs in bovine milk. In recent years, limited research based on molecular mechanisms has focused on this field. The biological roles of numerous microRNAs (miRNAs) remain unknown. In this study, a promising and negatively correlated pair of the miRNA (miRNA-193a-5p) and a fatty acid desaturase 1 (FADS1) gene are identified and screened to explore whether they are potential factors of PUFAs’ synthesis in bovine milk. The targeted relationship between miRNA-193a-5p and FADS1 in bovine mammary epithelial cells (BMECs) is demonstrated by dual luciferase reporter assays. qRT-PCR and western blot assays indicate that both the expression of mRNA and the protein FADS1 show a negative correlation with miRNA-193a-5p expression in BMECs. Also, miR-193a-5p expression is positively correlated with the expression of genes associated with milk fatty acid metabolism, including ELOVL fatty acid elongase 6 (ELOVL6) and diacylglycerol O-acyltransferase 2 (DGAT2). The expression of fatty acid desaturase 2 (FADS2) is negatively correlated with miR-193a-5p expression in BMECs. The contents of triglycerides (TAG), eicosapentaenoic acid (EPA), docosapentaenoic acid (DPA) and docosahexaenoic acid (DHA) have a significant positive correlation with the expression of FADS1 and a significant negative correlation with the expression of miR-193a-5p in BMECs. For the first time, this study confirms that miRNA-193a-5p regulates PUFAs metabolism in BMECs by targeting FADS1, indicating that miRNA-193a-5p and FADS1 are underlying factors that improve PUFAs content in bovine milk.
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Affiliation(s)
- Yongliang Fan
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.F.); (A.A.I.A.); (H.Z.); (X.L.); (Z.H.)
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Abdelaziz Adam Idriss Arbab
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.F.); (A.A.I.A.); (H.Z.); (X.L.); (Z.H.)
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Huimin Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.F.); (A.A.I.A.); (H.Z.); (X.L.); (Z.H.)
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Yi Yang
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China;
| | - Xubin Lu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.F.); (A.A.I.A.); (H.Z.); (X.L.); (Z.H.)
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Ziyin Han
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.F.); (A.A.I.A.); (H.Z.); (X.L.); (Z.H.)
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Zhangping Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.F.); (A.A.I.A.); (H.Z.); (X.L.); (Z.H.)
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
- Correspondence: ; Tel.: +86-0514-8797-9269
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12
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Identification of Functional Genes in Pterygium Based on Bioinformatics Analysis. BIOMED RESEARCH INTERNATIONAL 2020; 2020:2383516. [PMID: 33299863 PMCID: PMC7704136 DOI: 10.1155/2020/2383516] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 10/12/2020] [Accepted: 10/24/2020] [Indexed: 12/24/2022]
Abstract
Purpose The competing endogenous RNA (ceRNA) network regulatory has been investigated in the occurrence and development of many diseases. This research aimed at identifying the key RNAs of ceRNA network in pterygium and exploring the underlying molecular mechanism. Methods Differentially expressed long noncoding RNAs (lncRNAs), microRNAs (miRNAs), and mRNAs were obtained from the Gene Expression Omnibus (GEO) database and analyzed with the R programming language. LncRNA and miRNA expressions were extracted and pooled by the GEO database and compared with those in published literature. The lncRNA-miRNA-mRNA network was constructed of selected lncRNAs, miRNAs, and mRNAs. Metascape was used to perform Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses on mRNAs of the ceRNA network and to perform Protein-Protein Interaction (PPI) Network analysis on the String website to find candidate hub genes. The Comparative Toxicogenomic Database (CTD) was used to find hub genes closely related to pterygium. The differential expressions of hub genes were verified using the reverse transcription-real-time fluorescent quantitative PCR (RT-qPCR). Result There were 8 lncRNAs, 12 miRNAs, and 94 mRNAs filtered to construct the primary ceRNA network. A key lncRNA LIN00472 ranking the top 1 node degree was selected to reconstruct the LIN00472 network. The GO and KEGG pathway enrichment showed the mRNAs in ceRNA networks mainly involved in homophilic cell adhesion via plasma membrane adhesion molecules, developmental growth, regulation of neuron projection development, cell maturation, synapse assembly, central nervous system neuron differentiation, and PID FOXM1 PATHWAY. According to the Protein-Protein Interaction Network (PPI) analysis on mRNAs in LINC00472 network, 10 candidate hub genes were identified according to node degree ranking. Using the CTD database, we identified 8 hub genes closely related to pterygium; RT-qPCR verified 6 of them were highly expressed in pterygium. Conclusion Our research found LINC00472 might regulate 8 hub miRNAs (miR-29b-3p, miR-183-5p, miR-138-5p, miR-211-5p, miR-221-3p, miR-218-5p, miR-642a-5p, miR-5000-3p) and 6 hub genes (CDH2, MYC, CCNB1, RELN, ERBB4, RB1) in the ceRNA network through mainly PID FOXM1 PATHWAY and play an important role in the development of pterygium.
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Peterlin A, Počivavšek K, Petrovič D, Peterlin B. The Role of microRNAs in Heart Failure: A Systematic Review. Front Cardiovasc Med 2020; 7:161. [PMID: 33195446 PMCID: PMC7593250 DOI: 10.3389/fcvm.2020.00161] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 07/31/2020] [Indexed: 12/31/2022] Open
Abstract
MicroRNAs are highly investigated for their role in the pathogenesis of cardiovascular diseases. Nevertheless, evidence for clinical implementation is still lacking. In our systematic review, we evaluated the potential of microRNAs as pathophysiological and diagnostic biomarkers of heart failure. We identified 72 differentially expressed microRNA molecules among groups of heart failure patients and control groups by searching the PubMed database. We did not identify a substantial overlap of differentially expressed microRNAs among different studies; only five microRNAs (miR-1228, miR-122, miR-423-5p, miR-142-3p, and exosomal miR-92b-5p) were differentially expressed in more than one included study. Gene set enrichment analysis, based on the gene targets of microRNAs presented in the included studies, showed that gene targets of differentially expressed microRNAs were enriched in the MAPK, TGFβ, PI3K-Akt, and IL-2 signaling pathways, as well as apoptosis pathway, p53 activity regulation, and angiogenesis pathway. Results of our systematic review show that there is currently insufficient support for the use of any of the presented microRNAs as pathophysiological or prognostic biomarkers in the clinical setting.
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Affiliation(s)
- Ana Peterlin
- Faculty of Medicine, Institute of Histology and Embryology, University of Ljubljana, Ljubljana, Slovenia
| | - Karolina Počivavšek
- Department of Cardiovascular Surgery, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Danijel Petrovič
- Faculty of Medicine, Institute of Histology and Embryology, University of Ljubljana, Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
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Peng W, Cao H, Liu K, Guo C, Sun Y, Qi H, Liu Z, Xie Y, Liu X, Li B, Zhang L. Identification of lncRNA-NR_104160 as a biomarker and construction of a lncRNA-related ceRNA network for essential hypertension. Am J Transl Res 2020; 12:6060-6075. [PMID: 33194014 PMCID: PMC7653565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 06/03/2020] [Indexed: 06/11/2023]
Abstract
OBJECTIVES To identify long noncoding RNAs (lncRNAs) and construct a competing endogenous RNA (ceRNA) network for essential hypertension. METHODS An RNA microarray and two-step quantitative real-time PCR were applied to identify differentially expressed RNAs (DE-RNAs), and a luciferase assay was performed to explore the binding relationship between RNAs. A generalized linear model and logistic regression model were used to analyze the associations between different RNAs and of RNAs with hypertension. Receiver operating characteristic curve analysis was executed to evaluate the diagnostic performance. Bioinformatics analysis was applied for network construction. RESULTS In total, 439 DE-RNAs (387 lncRNAs and 52 mRNAs) were identified in the microarray, and 71 'lncRNA-miRNA-mRNA' loops formed the ceRNA network. The first validation confirmed that five RNAs (NR_104160, lnc-GPR63-8:1, lnc-HPRT1-9:1, ID1 and RSL24D1) were significantly upregulated in hypertensives (P < 0.05). NR_104160 was significantly associated with hypertension (OR = 2.863, 95% CI: 1.143-7.172; P = 0.025) after adjusting for confounding factors. NR_104160 was included in the hypertension diagnostic model, with an area under the curve of 0.852 (95% CI: 0.761-0.944). In the second validation, NR_104160 showed a constant significant difference (P = 0.001). An elevated expression level of NR_104160 was associated with the expression of ID1 (β = 0.2235, P = 0.005). Luciferase assays showed hsa-miR-101-3p stimulation significantly inhibited the reporter gene activation ability of the NR_104160 wild-type plasmid (P < 0.001). CONCLUSIONS Our study constructed a ceRNA network to provide hypotheses regarding the mechanism of hypertension development. lncRNA-NR_104160 was identified as a hub element that participates in hypertension transcriptional regulation and as a potential biomarker.
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Affiliation(s)
- Wenjuan Peng
- Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University, Beijing Municipal Key Laboratory of Clinical EpidemiologyBeijing 100069, People’s Republic of China
| | - Han Cao
- Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University, Beijing Municipal Key Laboratory of Clinical EpidemiologyBeijing 100069, People’s Republic of China
| | - Kuo Liu
- Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University, Beijing Municipal Key Laboratory of Clinical EpidemiologyBeijing 100069, People’s Republic of China
| | - Chunyue Guo
- Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University, Beijing Municipal Key Laboratory of Clinical EpidemiologyBeijing 100069, People’s Republic of China
| | - Yanyan Sun
- Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University, Beijing Municipal Key Laboratory of Clinical EpidemiologyBeijing 100069, People’s Republic of China
| | - Han Qi
- The National Clinical Research Center for Mental Disorders and Beijing Key Laboratory of Mental Disorders and The Advanced Innovation Center for Human Brain Protection, Beijing Anding Hospital, School of Mental Health, Capital Medical UniversityBeijing 100088, People’s Republic of China
| | - Zheng Liu
- Science Department, Peking University People’s HospitalBeijing 100044, People’s Republic of China
| | - Yunyi Xie
- Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University, Beijing Municipal Key Laboratory of Clinical EpidemiologyBeijing 100069, People’s Republic of China
| | - Xiaohui Liu
- Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University, Beijing Municipal Key Laboratory of Clinical EpidemiologyBeijing 100069, People’s Republic of China
| | - Bingxiao Li
- Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University, Beijing Municipal Key Laboratory of Clinical EpidemiologyBeijing 100069, People’s Republic of China
| | - Ling Zhang
- Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University, Beijing Municipal Key Laboratory of Clinical EpidemiologyBeijing 100069, People’s Republic of China
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Non-Coding RNA Databases in Cardiovascular Research. Noncoding RNA 2020; 6:ncrna6030035. [PMID: 32887511 PMCID: PMC7549374 DOI: 10.3390/ncrna6030035] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 08/28/2020] [Accepted: 09/01/2020] [Indexed: 12/11/2022] Open
Abstract
Cardiovascular diseases (CVDs) are of multifactorial origin and can be attributed to several genetic and environmental components. CVDs are the leading cause of mortality worldwide and they primarily damage the heart and the vascular system. Non-coding RNA (ncRNA) refers to functional RNA molecules, which have been transcribed into DNA but do not further get translated into proteins. Recent transcriptomic studies have identified the presence of thousands of ncRNA molecules across species. In humans, less than 2% of the total genome represents the protein-coding genes. While the role of many ncRNAs is yet to be ascertained, some long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) have been associated with disease progression, serving as useful diagnostic and prognostic biomarkers. A plethora of data repositories specialized in ncRNAs have been developed over the years using publicly available high-throughput data from next-generation sequencing and other approaches, that cover various facets of ncRNA research like basic and functional annotation, expressional profile, structural and molecular changes, and interaction with other biomolecules. Here, we provide a compendium of the current ncRNA databases relevant to cardiovascular research.
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Gholizadeh N, Emami Razavi A, Mohammadpour H, Tavakol F, Sheykhbahaei N. Association of MAPK and its regulatory miRNAs (603, 4301, 8485, and 4731) with the malignant transformation of oral lichen planus. Mol Biol Rep 2019; 47:1223-1232. [PMID: 31828562 DOI: 10.1007/s11033-019-05223-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 12/04/2019] [Indexed: 12/19/2022]
Abstract
Oral lichen planus (OLP) is a potentially malignant oral lesion that may transform into oral squamous cell carcinoma (OSCC). The purpose of this study was to assess the level of expression of MAPK/ERK1/2 gene, and microRNA (miR)-603, 4301, 8485, and 4731 in the MAPK signaling pathway in OLP and OSCC lesions. This case-control study evaluated 26 OSCC, 20 OLP and 20 healthy control tissue specimens. After RNA extraction, the respective miRNA and MAPK/ERK1/2 mRNA levels were assessed by quantitative reverse transcription polymerase chain reaction (RT-PCR). Significant upregulation of MAPK/ERK1/2 gene was noted in the OLP and OSCC specimens compared with healthy controls (p < 0.001). The expression level of miR-4731 was significantly lower in the OLP and OSCC specimens than in the healthy specimens (p < 0.001). The expression of MiR-603 was the lowest in OLP, followed by OSCC and then the control group (p < 0.001). No significant difference was found in miR-4801 levels between OSCC and OLP specimens compared with healthy controls (p = 0.43 and p = 0.86, respectively). In addition, a non-significant decrease in miR-8485 levels was noted in the OSCC and OLP specimens compared with healthy controls (p = 0.98 and p = 0.61, respectively). A significant decrease in level of miR-603 was noted in OLP compared with OSCC group (p < 0.001). The miR-4801 and miR-8485 expression levels were directly correlated with MAPK/ERK1/2 mRNA expression (p = 0.01). Higher expression level of MAPK/ERK1/2, miR-603, miR-4801, and miR-4731, and lower expression level of miR-8485 were correlated with significantly lower overall survival rate in OSCC patients. The increased expression of MAPK/ERK1/2 and decreased expression of miR-603 and miR-4731 are associated with greater risk of OLP malignant transformation and poor histopathological characteristics of OSCC.
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Affiliation(s)
- Narges Gholizadeh
- Department of Oral & Maxillofacial Medicine, School of Dentistry, Tehran University of Medical Science, Tehran, Iran
| | - Amirnader Emami Razavi
- Iran National Tumor Bank, Cancer Biology Research Center, Cancer Institute of Iran, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Fatemeh Tavakol
- Department of Oral & Maxillofacial Medicine, School of Dentistry, Tehran University of Medical Science, Tehran, Iran
| | - Nafiseh Sheykhbahaei
- Department of Oral & Maxillofacial Medicine, School of Dentistry, Tehran University of Medical Science, Tehran, Iran.
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