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Yu X, Liu H, Chang N, Fu W, Guo Z, Wang Y. Circular RNAs: New players involved in the regulation of cognition and cognitive diseases. Front Neurosci 2023; 17:1097878. [PMID: 36816112 PMCID: PMC9932922 DOI: 10.3389/fnins.2023.1097878] [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: 11/14/2022] [Accepted: 01/16/2023] [Indexed: 02/05/2023] Open
Abstract
Circular RNAs (circRNAs), a type of covalently closed endogenous single-stranded RNA, have been regarded as the byproducts of the aberrant splicing of genes without any biological functions. Recently, with the development of high-throughput sequencing and bioinformatics, thousands of circRNAs and their differential biological functions have been identified. Except for the great advances in identifying circRNA roles in tumor progression, diagnosis, and treatment, accumulated evidence shows that circRNAs are enriched in the brain, especially in the synapse, and dynamically change with the development or aging of organisms. Because of the specific roles of synapses in higher-order cognitive functions, circRNAs may not only participate in cognitive functions in normal physiological conditions but also lead to cognition-related diseases after abnormal regulation of their expression or location. Thus, in this review, we summarized the progress of studies looking at the role of circRNA in cognitive function, as well as their involvement in the occurrence, development, prognosis, and treatment of cognitive-related diseases, including autism, depression, and Alzheimer's diseases.
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Affiliation(s)
- Xiaohan Yu
- School of Clinical and Basic Medical Sciences, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Haoyu Liu
- School of Clinical and Basic Medical Sciences, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Ning Chang
- School of Clinical and Basic Medical Sciences, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Weijia Fu
- School of Clinical and Basic Medical Sciences, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Zhiwen Guo
- School of Clinical and Basic Medical Sciences, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Yue Wang
- School of Clinical and Basic Medical Sciences, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China,Medical Science and Technology Innovation Center, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China,*Correspondence: Yue Wang,
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2
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Wu D, Chen T, Zhao X, Huang D, Huang J, Huang Y, Huang Q, Liang Z, Chen C, Chen M, Li D, Wu B, Li L. HIF1α-SP1 interaction disrupts the circ-0001875/miR-31-5p/SP1 regulatory loop under a hypoxic microenvironment and promotes non-small cell lung cancer progression. J Exp Clin Cancer Res 2022; 41:156. [PMID: 35473752 PMCID: PMC9044860 DOI: 10.1186/s13046-022-02336-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/18/2022] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Circular RNAs (circRNAs) play an important role in the progression of non-small cell lung cancer (NSCLC), especially under tumor hypoxia. However, the precise functions and underlying mechanisms of dysregulated circRNAs in NSCLC are largely unknown. METHODS High-throughput RNA sequencing was performed to identify significantly expressed circRNAs in NSCLC tissues. The functions of circ-0001875 in NSCLC cells were investigated in vitro and in vivo. The regulatory relationships of circ-0001875, miR-31-5p and SP1 were examined by dual luciferase reporter assays and rescue experiments. The signal pathway of epithelial-to-mesenchymal transition and the formation of filopodia were analyzed by western blot and immunofluorescence staining. The binding of SP1 to Alu elements was evaluated by RNA immunoprecipitation, and the HIF1α and SP1 interaction was detected by co-immunoprecipitation. RESULTS We identified the novel Has_circ_0001875 as a significantly upregulated circRNA in NSCLC tissues and cell lines. circ-0001875 promoted the proliferation and metastasis of NSCLC both in vitro and in vivo, and induced NSCLC cells to extend filopodia. Mechanistically, circ-0001875 sponged miR-31-5p to regulate SP1, influencing epithelial-to-mesenchymal transition via the TGFβ/Smad2 signal pathway. SP1 negatively regulated circ-0001875 formation through an AluSq-dependent feedback loop, which was disrupted by competitive binding of HIF1α to SP1 under hypoxia condition. The circ-0001875/miR-31-5p/SP1 axis was associated with the clinical features and prognosis of NSCLC patients. CONCLUSIONS Our results revealed that the circ-0001875/miR-31-5p/SP1 axis and the complex regulatory loops influence NSCLC progression. These findings provide new insights into the regulation of circRNA formation under tumor hypoxia.
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Affiliation(s)
- Dong Wu
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Tingting Chen
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Xuanna Zhao
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Dan Huang
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Jiawei Huang
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Yujie Huang
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Qiu Huang
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Zhu Liang
- Department of Cardiothoracic Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524000, China
| | - Chunyuan Chen
- Department of Cardiothoracic Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524000, China
| | - Min Chen
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Dongming Li
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China.
| | - Bin Wu
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China.
| | - Lixia Li
- Cancer Hospital, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524000, China.
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3
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Yu W, Gu Q, Wu D, Zhang W, Li G, Lin L, Lowe JM, Hu S, Li TW, Zhou Z, Miao MZ, Gong Y, Zhao Y, Lu E. Identification of potentially functional circRNAs and prediction of circRNA-miRNA-mRNA regulatory network in periodontitis: Bridging the gap between bioinformatics and clinical needs. J Periodontal Res 2022; 57:594-614. [PMID: 35388494 PMCID: PMC9325354 DOI: 10.1111/jre.12989] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 03/19/2022] [Accepted: 03/23/2022] [Indexed: 02/06/2023]
Abstract
Background and Objective Periodontitis is a multifactorial chronic inflammatory disease that can lead to the irreversible destruction of dental support tissues. As an epigenetic factor, the expression of circRNA is tissue‐dependent and disease‐dependent. This study aimed to identify novel periodontitis‐associated circRNAs and predict relevant circRNA‐periodontitis regulatory network by using recently developed bioinformatic tools and integrating sequencing profiling with clinical information for getting a better and more thorough image of periodontitis pathogenesis, from gene to clinic. Material and Methods High‐throughput sequencing and RT‐qPCR were conducted to identify differentially expressed circRNAs in gingival tissues from periodontitis patients. The relationship between upregulated circRNAs expression and probing depth (PD) was performed using Spearman's correlation analysis. Bioinformatic analyses including GO analysis, circRNA‐disease association prediction, and circRNA‐miRNA‐mRNA network prediction were performed to clarify potential regulatory functions of identified circRNAs in periodontitis. A receiver‐operating characteristic (ROC) curve was established to assess the diagnostic significance of identified circRNAs. Results High‐throughput sequencing identified 70 differentially expressed circRNAs (68 upregulated and 2 downregulated circRNAs) in human periodontitis (fold change >2.0 and p < .05). The top five upregulated circRNAs were validated by RT‐qPCR that had strong associations with multiple human diseases, including periodontitis. The upregulation of circRNAs were positively correlated with PD (R = .40–.69, p < .05, moderate). A circRNA‐miRNA‐mRNA network with the top five upregulated circRNAs, differentially expressed mRNAs, and overlapped predicted miRNAs indicated potential roles of circRNAs in immune response, cell apoptosis, migration, adhesion, and reaction to oxidative stress. The ROC curve showed that circRNAs had potential value in periodontitis diagnosis (AUC = 0.7321–0.8667, p < .05). Conclusion CircRNA‐disease associations were predicted by online bioinformatic tools. Positive correlation between upregulated circRNAs, circPTP4A2, chr22:23101560‐23135351+, circARHGEF28, circBARD1 and circRASA2, and PD suggested function of circRNAs in periodontitis. Network prediction further focused on downstream targets regulated by circRNAs during periodontitis pathogenesis.
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Affiliation(s)
- Weijun Yu
- Department of Stomatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
| | - Qisheng Gu
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China.,Department of Immunology, Bio Sorbonne Paris Cité, University of Paris, Paris, France
| | - Di Wu
- Division of Oral and Craniofacial Biomedicine, University of North Carolina Adams School of Dentistry, Chapel Hill, North Carolina, USA.,Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Weiqi Zhang
- Department of Stomatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Gang Li
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Lu Lin
- Department of Stomatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jared M Lowe
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Shucheng Hu
- Department of Stomatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Tia Wenjun Li
- Division of Oral and Craniofacial Biomedicine, University of North Carolina Adams School of Dentistry, Chapel Hill, North Carolina, USA.,Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Zhen Zhou
- Center for Biomedical Image Computing and Analytics, Department of Radiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Michael Z Miao
- Division of Oral and Craniofacial Biomedicine, University of North Carolina Adams School of Dentistry, Chapel Hill, North Carolina, USA
| | - Yuhua Gong
- Department of Stomatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yifei Zhao
- Department of Stomatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Eryi Lu
- Department of Stomatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
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Ma X, Wang X, Ma X, Zhang X, Gong X, Sun R, Wong SH, Chan MTV, Wu WKK. An update on the roles of circular RNAs in spinal cord injury. Mol Neurobiol 2022; 59:2620-2628. [PMID: 35112318 DOI: 10.1007/s12035-021-02721-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/24/2021] [Indexed: 10/19/2022]
Abstract
Spinal cord injury (SCI) is a disabling condition for which therapeutic options are limited. Increasing number of microarray and next-generation sequencing studies have demonstrated that SCI coincides with altered expression of circular RNAs (circRNAs) in the damaged tissue. Emerging functional evidence further pinpointed specific differentially expressed circRNAs (e.g., circ-HIPK3, cicRNA.7079, circRNA_01477, circRNA-2960, and circ_0001723) for their effects on cellular processes relevant to SCI repair and regeneration, including neuronal apoptosis, astrocyte activation, and neuroinflammation, via sponging SCI-related microRNAs. Although circRNAs and their target microRNAs appear to be good candidates for therapeutic exploitation in SCI, further investigation into the efficient delivery of these regulatory molecules in a cell-type specific manner is a pre-requisite for translating these basic discoveries into clinical benefits.
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Affiliation(s)
- Xuezhen Ma
- Department Oncology of Qingdao Hospital Central, Central Qingdao Hospital, Qingdao, Shandong, China
| | - Xuesong Wang
- Department Spinal of Qingdao Hospital Central, Qingdao Hospital Central, Qingdao, Shandong, China.
| | - Xuexiao Ma
- Department Spinal of affiliated, Hospital of Qingdao University, Qingdao, Shandong, China
| | - Xiugong Zhang
- Department Spinal of Qingdao Hospital Central, Qingdao Hospital Central, Qingdao, Shandong, China
| | - Xiaojin Gong
- Department Spinal of Qingdao Hospital Central, Qingdao Hospital Central, Qingdao, Shandong, China
| | - Ruifu Sun
- Department Spinal of Qingdao Hospital Central, Qingdao Hospital Central, Qingdao, Shandong, China
| | - Sunny H Wong
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- State Key Laboratory of Digestive Disease and LKS Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Matthew T V Chan
- Department of Anaesthesia and Intensive Care and Peter Hung Pain Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - William Ka Kei Wu
- State Key Laboratory of Digestive Disease and LKS Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Department of Anaesthesia and Intensive Care and Peter Hung Pain Research Institute, The Chinese University of Hong Kong, Hong Kong, China
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5
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Guo C, Mi J, Li H, Su P, Nie H. Dysregulated circular RNAs as novel biomarkers in esophageal squamous cell carcinoma: a meta-analysis. Cancer Med 2021; 10:7895-7908. [PMID: 34704390 PMCID: PMC8607254 DOI: 10.1002/cam4.3703] [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: 05/10/2020] [Accepted: 10/18/2020] [Indexed: 01/10/2023] Open
Abstract
Introduction Circular RNAs (circRNAs) play critical roles in tumorigenesis, but their clinical efficacy in esophageal squamous cell carcinoma (ESCC) still retains controversial. This meta‐analysis aims at evaluating the associations between circRNA expressions and clinicopathologic features as well as the diagnostic and prognostic values of circRNAs in ESCC. Materials & Methods PubMed, EMBASE, and other online databases were systematically searched to collect studies on circRNAs and clinicopathological features, diagnostic, and/or prognostic assessments of ESCC. The quality of included studies was evaluated using the Quality Assessment of Diagnostic Accuracy Studies 2 (QUADAS‐2) and Newcastle‐Ottawa Scale (NOS) scales. The included studies were quantitatively weighted and merged, and diagnostic indicators, hazard ratios (HRs) and the corresponding 95% confidence intervals (CIs) were calculated. P values were merged by Fisher᾽s method. Sources of heterogeneity were traced using subgroup, sensitivity, and meta‐regression analyses. Results As a result, 12 studies were included, representing 769 ESCC patients. The meta‐analysis showed that abnormal expressions of circRNAs were associated to TNM stage as well as lymph node and distant metastases in ESCC cases. CircRNA was used to distinguish ESCC patients from healthy controls, and the merged sensitivity, specificity, and the area under the curve (AUC) of ESCC were 0.78 (95% CI: 0.74–0.81), 0.79 (95% CI: 0.75–0.83), and 0.86, respectively. The survival analysis showed that upregulated oncogenic circRNA levels in ESCC tissues was associated with the shorter overall survival (OS) of the patients (univariate analysis: HR = 2.25, 95% CI: 1.71–2.95, p = 0.000, I2 = 0.0%; multivariate analysis: HR = 2.50, 95% CI: 1.61–3.89, p = 0.000, I2 = 0.0%), while the OS of ESCC patients presenting overexpressions of tumor‐suppressive circRNAs was significantly ameliorated (HR = 0.29, 95% CI: 0.20–0.42, p = 0.000, I2 = 0.0%). The subgroup analyses based on circRNA biofunctions, sample size, and reference gene also revealed robust results. Conclusion CircRNAs can be used as promising molecular biomarkers for the early diagnosis and prognosis monitoring of ESCC.
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Affiliation(s)
- Chengcheng Guo
- Department of Pathology, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, China
| | - Jianqiang Mi
- Department of Pathology, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, China
| | - Haike Li
- Faculty of Basic Medicine, Henan Vocational College of Tuina, Luoyang, China
| | - Panke Su
- Department of Pathology, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, China
| | - He Nie
- Department of Nuclear Medicine, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, China
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6
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Mahjoubin-Tehran M, Rezaei S, Jalili A, Sahebkar A, Aghaee-Bakhtiari SH. A comprehensive review of online resources for microRNA-diseases associations: the state of the art. Brief Bioinform 2021; 23:6376589. [PMID: 34571538 DOI: 10.1093/bib/bbab381] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/07/2021] [Accepted: 08/24/2021] [Indexed: 12/16/2022] Open
Abstract
MicroRNAs (miRNAs) as small 19- to 24-nucleotide noncoding RNAs regulate several mRNA targets and signaling pathways. Therefore, miRNAs are considered key regulators in cellular pathways as well as various pathologies. There is substantial interest in the relationship between disease and miRNAs, which made that one of the important research topics. Interestingly, miRNAs emerged as an attractive approach for clinical application, not only as biomarkers for diagnosis and prognosis or in the prediction of therapy response but also as therapeutic tools. For these purposes, the identification of crucial miRNAs in disease is very important. Databases provided valuable experimental and computational miRNAs-disease information in an accessible and comprehensive manner, such as miRNA target genes, miRNA related in signaling pathways and miRNA involvement in various diseases. In this review, we summarized miRNAs-disease databases in two main categories based on the general or specific diseases. In these databases, researchers could search diseases to identify critical miRNAs and developed that for clinical applications. In another way, by searching particular miRNAs, they could recognize in which disease these miRNAs would be dysregulated. Despite the significant development that has been done in these databases, there are still some limitations, such as not being updated and not providing uniform and detailed information that should be resolved in future databases. This survey can be helpful as a comprehensive reference for choosing a suitable database by researchers and as a guideline for comparing the features and limitations of the database by developer or designer. Short abstract We summarized miRNAs-disease databases that researchers could search disease to identify critical miRNAs and developed that for clinical applications. This survey can help choose a suitable database for researchers.
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Affiliation(s)
- Maryam Mahjoubin-Tehran
- Bioinformatics Research Group, Mashhad University of Medical Sciences, Mashhad, Iran and Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Samaneh Rezaei
- Bioinformatics Research Group, Mashhad University of Medical Sciences, Mashhad, Iran and Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amin Jalili
- Bioinformatics Research Group, Mashhad University of Medical Sciences, Mashhad, Iran and Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amirhossein Sahebkar
- Bioinformatics Research Group, Mashhad University of Medical Sciences, Mashhad, Iran and Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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7
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Yaghoubi N, Avval FZ, Khazaei M, Sahebkar A, Aghaee-Bakhtiari SH. High Diagnostic and Prognostic Value of miRNAs Compared with the Carcinoembryonic Antigen as a Traditional Tumor Marker. Anticancer Agents Med Chem 2021; 22:206-214. [PMID: 34102990 DOI: 10.2174/1871520621666210608094908] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 03/30/2021] [Accepted: 04/12/2021] [Indexed: 11/22/2022]
Abstract
A significant challenge in cancer detection and treatment is early diagnosis and accurate prognosis of the disease that enables effective therapies and interventions to improve the patient's condition. Up to now, many parts of research have tended to focus on the carcinoembryonic antigen (CEA) to detect cancers and estimate the survival rates of patients with multiple cancer types, including colorectal, breast, non-small cell lung, and pancreas cancer. Limited sensitivity and specificity of this traditional tumor marker make it an inappropriate biomarker to diagnose cancer, especially in the early stages, while several lines of research have introduced miRNAs as reliable indicators of tumor initiation, development, and therapy response. Indeed, miRNAs have unique properties that provide considerable benefits, such as discriminating benign diseases from malignancies, prediction of cancer possibility and progress, checking sensitivity to treatment, and initial detection of tumors. This review summarizes the relationships between miRNAs and CEA, the diagnostic significance of CEA in combination with miRNAs, and the distinct advantages of miRNAs over CEA as tumor biomarkers. Advancement in our current understanding of miRNAs is essential to discover new and effective biomarkers for diagnostic, prognostic, and therapeutic goals of cancer patients.
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Affiliation(s)
- Neda Yaghoubi
- Department of Clinical Biochemistry, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Farnaz Zahedi Avval
- Department of Clinical Biochemistry, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Majid Khazaei
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amirhossein Sahebkar
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
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Siddika T, Heinemann IU. Bringing MicroRNAs to Light: Methods for MicroRNA Quantification and Visualization in Live Cells. Front Bioeng Biotechnol 2021; 8:619583. [PMID: 33537295 PMCID: PMC7848212 DOI: 10.3389/fbioe.2020.619583] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/15/2020] [Indexed: 12/12/2022] Open
Abstract
MiRNAs are small non-coding RNAs that interact with their target mRNAs for posttranscriptional gene regulation. Finely controlled miRNA biogenesis, target recognition and degradation indicate that maintaining miRNA homeostasis is essential for regulating cell proliferation, growth, differentiation and apoptosis. Increasingly, miRNAs have been recognized as a potential biomarker for disease diagnosis. MiRNAs can be found in blood, plasma, and tissues, and miRNA expression and activity differ in developmental stages, tissues and in response to external stimuli. MiRNA transcripts are matured from pri-miRNA over pre-miRNA to mature miRNA, a process that includes multiple steps and enzymes. Many tools are available to identify and quantify specific miRNAs, ranging from measuring total miRNA, specific miRNA activity, miRNA arrays and miRNA localization. The various miRNA assays differ in accuracy, cost, efficiency and convenience of monitoring miRNA dynamics. To acknowledge the significance and increasing research interest in miRNAs, we summarize the traditional as well as novel methods of miRNA quantification with strengths and limitations of various techniques in biochemical and medical research.
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Affiliation(s)
| | - Ilka U. Heinemann
- Department of Biochemistry, The University of Western Ontario, London, ON, Canada
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9
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Zucko D, Boris-Lawrie K. Circular RNAs Are Regulators of Diverse Animal Transcriptomes: One Health Perspective. Front Genet 2020; 11:999. [PMID: 33193584 PMCID: PMC7531264 DOI: 10.3389/fgene.2020.00999] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 08/06/2020] [Indexed: 12/13/2022] Open
Abstract
Derived from linear (parental) precursor mRNA, circRNA are recycled exons and introns whose ends are ligated. By titrating microRNAs and RNA binding proteins, circRNA interconnect networks of competing endogenous RNAs. Without altering chromosomal DNA, circRNA regulates skeletal muscle development and proliferation, lactation, ovulation, brain development, and responses to infections and metabolic stress. This review integrates emerging knowledge of circRNA activity coming from genome-wide characterizations in many clades of animals. circRNA research addresses one of the main pillars of the One Health vision – to improve the health and productivity of food animals and generate translational knowledge in animal species.
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Affiliation(s)
- Dora Zucko
- Department of Veterinary and Biomedical Sciences, Veterinary Medicine Graduate Program, University of Minnesota Twin Cities, Saint Paul, MN, United States
| | - Kathleen Boris-Lawrie
- Department of Veterinary and Biomedical Sciences, Veterinary Medicine Graduate Program, University of Minnesota Twin Cities, Saint Paul, MN, United States
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10
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Disease-Associated Circular RNAs: From Biology to Computational Identification. BIOMED RESEARCH INTERNATIONAL 2020; 2020:6798590. [PMID: 32908906 PMCID: PMC7450300 DOI: 10.1155/2020/6798590] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 07/10/2020] [Indexed: 02/07/2023]
Abstract
Circular RNAs (circRNAs) are endogenous RNAs with a covalently closed continuous loop, generated through various backsplicing events of pre-mRNA. An accumulating number of studies have shown that circRNAs are potential biomarkers for major human diseases such as cancer and Alzheimer's disease. Thus, identification and prediction of human disease-associated circRNAs are of significant importance. To this end, a computational analysis-assisted strategy is indispensable to detect, verify, and quantify circRNAs for downstream applications. In this review, we briefly introduce the biology of circRNAs, including the biogenesis, characteristics, and biological functions. In addition, we outline about 30 recent bioinformatic analysis tools that are publicly available for circRNA study. Principles for applying these computational strategies and considerations will be briefly discussed. Lastly, we give a complete survey on more than 20 key computational databases that are frequently used. To our knowledge, this is the most complete and updated summary on publicly available circRNA resources. In conclusion, this review summarizes key aspects of circRNA biology and outlines key computational strategies that will facilitate the genome-wide identification and prediction of circRNAs.
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Lim TB, Lavenniah A, Foo RSY. Circles in the heart and cardiovascular system. Cardiovasc Res 2020; 116:269-278. [PMID: 31552406 DOI: 10.1093/cvr/cvz227] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 08/19/2019] [Indexed: 12/16/2022] Open
Abstract
The combination of next-generation sequencing, advanced bioinformatics analysis, and molecular research has now established circular RNAs (circRNAs) as a heterogeneous group of non-coding RNA that is widely and abundantly expressed. CircRNAs are single-stranded RNA, covalently backspliced to form closed circular loops. Different models of back-splicing have been proposed, and mechanisms for circRNA function include sequestering microRNAs, direct interaction with proteins, regulation of transcription, and translation. Exploring the role of circRNAs in different disease settings, and understanding how they contribute to disease progression promises to provide valuable insight into potential novel therapeutic approaches. Here, we review the growing number of published research on circRNAs in the heart and cardiovascular system and summarize the circRNAs that have been implicated in disease.
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Affiliation(s)
- Tingsen Benson Lim
- Cardiovascular Research Institute, National University Health Systems, MD6 Centre for Translational Medicine, 14 Medical Drive, Singapore 117599, Singapore.,Genome Institute of Singapore, Genome, 60 Biopolis Street, Singapore 138672, Singapore
| | - Annadoray Lavenniah
- Cardiovascular Research Institute, National University Health Systems, MD6 Centre for Translational Medicine, 14 Medical Drive, Singapore 117599, Singapore.,Genome Institute of Singapore, Genome, 60 Biopolis Street, Singapore 138672, Singapore
| | - Roger Sik-Yin Foo
- Cardiovascular Research Institute, National University Health Systems, MD6 Centre for Translational Medicine, 14 Medical Drive, Singapore 117599, Singapore.,Genome Institute of Singapore, Genome, 60 Biopolis Street, Singapore 138672, Singapore
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Yu Y, Han S, Li M, Song Y, Qi F. Circ_0004913 sponges miR-1290 and regulates FOXC1 to inhibit the proliferation of hepatocellular carcinoma. Cancer Cell Int 2020. [DOI: 10.1186/s12935-020-01521-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Abstract
Background
Circular RNA (circRNA), an novel type of non-coding RNA, could interact with miRNA and protein molecules to regulate the occurrence and progression of hepatocellular carcinoma (HCC). However, little is known about the pathogenesis of circ_0004913 in HCC.
Materials
Through the GEO (Gene Expression Omnibus database) to find dysfunctional circRNAs in HCC, and circ_0004913 was selected as the research object. Quantitative reverse transcription PCR (qRT-PCR) was used to detect the expression level of circ_0067934 in HCC tissues and cells. CCK-8, Edu and flow cytometry assays were used to determine the malignant behavior of transfected HCC cells. Mechanistically, RNA immunoprecipitation and dual-luciferase reporter gene assay were performed to explore the relation between circ_0067934, miR-1290 and FOXC1 (Forkhead box C1) in HCC.
Results
The expression of circ_0004913 was down-regulated in HCC tissues and cell lines, while the overexpression of circ_0004913 attenuates the malignant behavior of HCC cells. Bioinformatics predicted that circ_0004913 interacts with miR-1290, which targeted FOXC1 mRNA. In fact, miR-1290 promoted the malignant behavior of HCC cells, while FOXC1 had the opposite effect. In addition, circ_0004913 overexpression enhanced FOXC1 expression by reducing miR-1290 expression, thereby inhibiting the proliferation of HCC cells.
Conclusions
Circ_0004913 / miR-1290 / FOXC1 regulatory axis could inhibit the progress of HCC. Our findings may provide potential new targets for the diagnosis and treatment of HCC.
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Tran AM, Chalbatani GM, Berland L, Cruz De Los Santos M, Raj P, Jalali SA, Gharagouzloo E, Ivan C, Dragomir MP, Calin GA. A New World of Biomarkers and Therapeutics for Female Reproductive System and Breast Cancers: Circular RNAs. Front Cell Dev Biol 2020; 8:50. [PMID: 32211400 PMCID: PMC7075436 DOI: 10.3389/fcell.2020.00050] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 01/20/2020] [Indexed: 12/12/2022] Open
Abstract
As one of the most recently (re)discovered types of non-coding RNAs (ncRNA), circular RNAs (circRNAs) differentiate from other ncRNAs by a specific biogenesis, high stability, and distinct functions. The biogenesis of circRNAs can be categorized into three mechanisms that permit the back-splicing reaction: exon-skipping, pairing of neighboring introns, and dimerization of RNA-binding proteins. Regarding their stability, circRNAs have no free ends, specific to linear RNA molecules, prompting a longer half-life and resistance to exonuclease-mediated activity by RNase R, bypassing the common RNA turnover process. Regarding their functions, circular transcripts can be categorized into four broad roles: miRNA sponging, protein binding, regulation of transcription, and coding for proteins and peptides. Female reproductive system (including mainly ovarian, corpus, and cervix uteri cancers) and breast cancers are the primary causes of death in women worldwide, accounting for over 1,212,772 deaths in 2018. We consider that a better understanding of the molecular pathophysiology through the study of coding and non-coding RNA regulators could improve the diagnosis and therapeutics of these cancers. Developments in the field of circRNA in regard to breast or gynecological cancers are recent, with most circRNA-related discoveries having been made in the last 2 years. Therefore, in this review we summarize the newly detected roles of circRNAs in female reproductive system (cervical cancer, ovarian cancer, and endometrial cancer) and breast cancers. We argue that circRNAs can become essential elements of the diagnostic and therapeutic tools for female reproductive system cancers in the future.
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Affiliation(s)
- Anh M Tran
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Ghanbar Mahmoodi Chalbatani
- Cancer Research Center, Cancer Institute of Iran, Tehran University of Medical Sciences, Tehran, Iran.,Department of Medical Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Lea Berland
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Mireia Cruz De Los Santos
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Priyank Raj
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Seyed Amir Jalali
- Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Elahe Gharagouzloo
- Cancer Research Center, Cancer Institute of Iran, Tehran University of Medical Sciences, Tehran, Iran.,Department of Medical Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Cristina Ivan
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States.,Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Mihnea P Dragomir
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States.,Department of Surgery, Fundeni Clinical Hospital, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - George A Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States.,Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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Rezaei S, Mahjoubin Tehran M, Sahebkar A, Jalili A, Aghaee‐Bakhtiari SH. Androgen receptor‐related micro RNAs in prostate cancer and their role in antiandrogen drug resistance. J Cell Physiol 2019; 235:3222-3234. [DOI: 10.1002/jcp.29275] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 09/27/2019] [Indexed: 12/24/2022]
Affiliation(s)
- Samaneh Rezaei
- Department of Medical Biotechnology, Faculty of Medicine Mashhad University of Medical Sciences Mashhad Iran
| | - Maryam Mahjoubin Tehran
- Department of Medical Biotechnology, Faculty of Medicine Mashhad University of Medical Sciences Mashhad Iran
| | - Amirhossein Sahebkar
- Department of Medical Biotechnology, Faculty of Medicine Mashhad University of Medical Sciences Mashhad Iran
- Biotechnology Research Center, Pharmaceutical Technology Institute Mashhad University of Medical Sciences Mashhad Iran
- Neurogenic Inflammation Research Center Mashhad University of Medical Sciences Mashhad Iran
| | - Amin Jalili
- Department of Medical Biotechnology, Faculty of Medicine Mashhad University of Medical Sciences Mashhad Iran
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Greco S, Cardinali B, Falcone G, Martelli F. Circular RNAs in Muscle Function and Disease. Int J Mol Sci 2018; 19:ijms19113454. [PMID: 30400273 PMCID: PMC6274904 DOI: 10.3390/ijms19113454] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 10/30/2018] [Accepted: 10/31/2018] [Indexed: 12/11/2022] Open
Abstract
Circular RNAs (circRNAs) are a class of RNA produced during pre-mRNA splicing that are emerging as new members of the gene regulatory network. In addition to being spliced in a linear fashion, exons of pre-mRNAs can be circularized by use of the 3' acceptor splice site of upstream exons, leading to the formation of circular RNA species. In this way, genetic information can be re-organized, increasing gene expression potential. Expression of circRNAs is developmentally regulated, tissue and cell-type specific, and shared across eukaryotes. The importance of circRNAs in gene regulation is now beginning to be recognized and some putative functions have been assigned to them, such as the sequestration of microRNAs or proteins, the modulation of transcription, the interference with splicing, and translation of small proteins. In accordance with an important role in normal cell biology, circRNA deregulation has been reported to be associated with diseases. Recent evidence demonstrated that circRNAs are highly expressed in striated muscle tissue, both skeletal and cardiac, that is also one of the body tissue showing the highest levels of alternative splicing. Moreover, initial studies revealed altered circRNA expression in diseases involving striated muscle, suggesting important functions of these molecules in the pathogenetic mechanisms of both heart and skeletal muscle diseases. The recent findings in this field will be described and discussed.
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Affiliation(s)
- Simona Greco
- Molecular Cardiology Laboratory, IRCCS-Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy.
| | - Beatrice Cardinali
- Institute of Cell Biology and Neurobiology, National Research Council, Monterotondo, 00015 Rome, Italy.
| | - Germana Falcone
- Institute of Cell Biology and Neurobiology, National Research Council, Monterotondo, 00015 Rome, Italy.
| | - Fabio Martelli
- Molecular Cardiology Laboratory, IRCCS-Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy.
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