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Qijiao W, Tao Z, Haimei L, Guomin L, Li S. Identifying circRNA-associated-ceRNA networks in juvenile spondyloarthropathies patients. Pediatr Rheumatol Online J 2023; 21:75. [PMID: 37507775 PMCID: PMC10386608 DOI: 10.1186/s12969-023-00855-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 07/02/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND Juvenile spondyloarthropathies (JSpA) are defined as a heterogeneous group of diseases that start before the age of 16. The study aimed to identify key genes and pathways that are influenced by circRNAs and to screen potential therapeutic agents for JSpA. The study involved the analysis of circRNA expression profiles, identification of circRNA-miRNA-mRNA regulatory networks, and functional annotation of differentially expressed genes. The results of the study may have provided insights into the molecular mechanisms underlying JSpA and potential therapeutic targets for this disease. METHODS In this study, sequencing data of circRNA, miRNA, and mRNA were obtained from the GEO datasets. The data were then analyzed to identify candidates for constructing a circRNA-miRNA-mRNA network based on circRNA-miRNA interactions and miRNA-mRNA interactions. Functional enrichments of genes were performed using the DAVID database. A PPI network was constructed using the STRING database and visualized using Cytoscape software. The MCODE plugin app was used to explore hub genes in the PPI network. The expression changes in immune cells were assessed using the online CIBERSORT algorithm to obtain the proportion of various types of immune cells. Finally, the Connectivity Map L1000 platform was used to identify potential agents for JSpA treatment. Overall, this study aimed to provide a comprehensive understanding of the molecular mechanisms underlying JSpA and to identify potential therapeutic agents for this disease. RESULTS A total of 225 differentially expressed circRNAs (DEcircRNAs), 23 differentially expressed miRNAs (DEmiRNAs) and 1324 differentially expressed mRNAs (DEmRNAs) were identified. We integrated 5 overlapped circRNAs, 7 miRNAs and 299 target mRNAs into a circRNA-miRNA-mRNA network. We next identified 10 hub genes based on the PPI network. KEGG pathway analysis revealed that the DEGs were mainly associated with JAK-STAT signal pathway. We found that neutrophils accounted for the majority of all enriched cells. In addition, we discovered several chemicals as potential treatment options for JSpA. CONCLUSIONS Through this bioinformatics analysis, we suggest a regulatory role for circRNAs in the pathogenesis and treatment of JSpA from the view of a competitive endogenous RNA (ceRNA) network.
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Affiliation(s)
- Wei Qijiao
- Department of Rheumatology, Children's Hospital of Fudan University, Shanghai, China
| | - Zhang Tao
- Department of Rheumatology, Children's Hospital of Fudan University, Shanghai, China
| | - Liu Haimei
- Department of Rheumatology, Children's Hospital of Fudan University, Shanghai, China
| | - Li Guomin
- Department of Rheumatology, Children's Hospital of Fudan University, Shanghai, China
| | - Sun Li
- Department of Rheumatology, Children's Hospital of Fudan University, Shanghai, China.
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Zhang C, Gao R, Zhou R, Chen H, Liu C, Zhu T, Chen C. The emerging power and promise of non-coding RNAs in chronic pain. Front Mol Neurosci 2022; 15:1037929. [PMID: 36407760 PMCID: PMC9668864 DOI: 10.3389/fnmol.2022.1037929] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 10/07/2022] [Indexed: 08/26/2023] Open
Abstract
Chronic pain (CP) is an unpleasant sensory and emotional experience associated with, or resembling that associated with, actual or potential tissue damage lasting longer than 3 months. CP is the main reason why people seek medical care and exerts an enormous economic burden. Genome-wide expression analysis has revealed that diverse essential genetic elements are altered in CP patients. Although many possible mechanisms of CP have been revealed, we are still unable to meet all the analgesic needs of patients. In recent years, non-coding RNAs (ncRNAs) have been shown to play essential roles in peripheral neuropathy and axon regeneration, which is associated with CP occurrence and development. Multiple key ncRNAs have been identified in animal models of CP, such as microRNA-30c-5p, ciRS-7, and lncRNA MRAK009713. This review highlights different kinds of ncRNAs in the regulation of CP, which provides a more comprehensive understanding of the pathogenesis of the disease. It mainly focuses on the contributions of miRNAs, circRNAs, and lncRNAs to CP, specifically peripheral neuropathic pain (NP), diabetic NP, central NP associated with spinal cord injury, complex regional pain syndrome, inflammatory pain, and cancer-induced pain. In addition, we summarize some potential ncRNAs as novel biomarkers for CP and its complications. With an in-depth understanding of the mechanism of CP, ncRNAs may provide novel insight into CP and could become new therapeutic targets in the future.
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Affiliation(s)
- Changteng Zhang
- Department of Anesthesiology and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and The Research Units of West China (2018RU012), Chinese Academy of Medical Sciences, Chengdu, China
- Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital, Sichuan University, Chengdu, China
| | - Rui Gao
- Department of Anesthesiology and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and The Research Units of West China (2018RU012), Chinese Academy of Medical Sciences, Chengdu, China
- Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital, Sichuan University, Chengdu, China
| | - Ruihao Zhou
- Department of Anesthesiology and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and The Research Units of West China (2018RU012), Chinese Academy of Medical Sciences, Chengdu, China
- Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital, Sichuan University, Chengdu, China
| | - Hai Chen
- Department of Respiratory and Critical Care Medicine, West China Medical School/West China Hospital, Sichuan University, Chengdu, China
- Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Changliang Liu
- Department of Anesthesiology and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and The Research Units of West China (2018RU012), Chinese Academy of Medical Sciences, Chengdu, China
- Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital, Sichuan University, Chengdu, China
| | - Tao Zhu
- Department of Anesthesiology and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and The Research Units of West China (2018RU012), Chinese Academy of Medical Sciences, Chengdu, China
- Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital, Sichuan University, Chengdu, China
| | - Chan Chen
- Department of Anesthesiology and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and The Research Units of West China (2018RU012), Chinese Academy of Medical Sciences, Chengdu, China
- Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital, Sichuan University, Chengdu, China
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Practical Significance of Biomarkers in Axial Spondyloarthritis: Updates on Diagnosis, Disease Activity, and Prognosis. Int J Mol Sci 2022; 23:ijms231911561. [PMID: 36232862 PMCID: PMC9570274 DOI: 10.3390/ijms231911561] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/20/2022] [Accepted: 09/22/2022] [Indexed: 11/26/2022] Open
Abstract
Axial spondyloarthritis (axSpA) is a chronic inflammatory disease that can lead to ankylosis by secondary ossification of inflammatory lesions, with progressive disability and a significant impact on quality of life. It is also a risk factor for the occurrence of comorbidities, especially cardiovascular diseases (CVDs), mood disorders, osteoporosis, and malignancies. Early diagnosis and treatment are needed to prevent or decrease functional decline and to improve the patient's prognosis. In respect of axSpA, there is an unmet need for biomarkers that can help to diagnose the disease, define disease activity and prognosis, and establish personalized treatment approaches. The aim of this review was to summarize the available information regarding the most promising biomarkers for axSpA. We classified and identified six core categories of biomarkers: (i) systemic markers of inflammation; (ii) molecules involved in bone homeostasis; (iii) HLA-B27 and newer genetic biomarkers; (iv) antibody-based biomarkers; (v) microbiome biomarkers; and (vi) miscellaneous biomarkers. Unfortunately, despite efforts to validate new biomarkers, few of them are used in clinical practice; however, we believe that these studies provide useful data that could aid in better disease management.
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Yang Q, Li Y, Wang Y, Qiao X, Liu T, Wang H, Shen H. The circRNA circSIAE Inhibits Replication of Coxsackie Virus B3 by Targeting miR-331-3p and Thousand and One Amino-Acid Kinase 2. Front Cell Infect Microbiol 2022; 11:779919. [PMID: 35141166 PMCID: PMC8820919 DOI: 10.3389/fcimb.2021.779919] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 12/21/2021] [Indexed: 01/15/2023] Open
Abstract
Coxsackie virus B3 (CVB3), an enterovirus, is the main pathogen causing viral myocarditis, pericarditis, hepatitis and other inflammation-related diseases. Non-coding RNAs with a closed loop molecular structure, called circular RNAs (circRNAs), have been shown to be involved in multiple virus-related processes, but roles and mechanisms in CVB3 infection have not been systematically studied. In this study, when HeLa cells were infected with CVB3, the expression of hsa_circ_0000367 (circSIAE) was significantly decreased as demonstrated by real-time quantitative PCR assays. We found that circSIAE downregulated the expression of miR-331-3p through direct binding and inhibited the replication of CVB3 in HeLa and 293T cells. The analysis of signals downstream of miR-331-3p suggested that miR-331-3p promotes CVB3 replication, viral plaque formation and fluorescent virus cell production through interactions with the gene coding for thousand and one amino-acid kinase 2 (TAOK2). In conclusion, this study found that circSIAE can target TAOK2 through sponge adsorption of miR-331-3p to inhibit the replication and proliferation of CVB3 virus, providing an early molecular target for the diagnosis of CVB3 infection.
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Affiliation(s)
- Qingru Yang
- Medical College, Jiangsu University, Zhenjiang, China
- Clinical Laboratory, Jiangyin Municipal Center for Disease Control and Prevention, Jiangyin, China
| | - Yuhan Li
- Medical College, Jiangsu University, Zhenjiang, China
| | - Yan Wang
- Medical College, Jiangsu University, Zhenjiang, China
| | - Xiaorong Qiao
- Medical College, Jiangsu University, Zhenjiang, China
| | - Tingjun Liu
- Medical College, Jiangsu University, Zhenjiang, China
| | - Hua Wang
- Medical College, Jiangsu University, Zhenjiang, China
- *Correspondence: Hua Wang, ; Hongxing Shen,
| | - Hongxing Shen
- Medical College, Jiangsu University, Zhenjiang, China
- *Correspondence: Hua Wang, ; Hongxing Shen,
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Sharma AR, Bhattacharya M, Bhakta S, Saha A, Lee SS, Chakraborty C. Recent research progress on circular RNAs: Biogenesis, properties, functions, and therapeutic potential. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 25:355-371. [PMID: 34484862 PMCID: PMC8399087 DOI: 10.1016/j.omtn.2021.05.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Circular RNAs (circRNAs), an emerging family member of RNAs, have gained importance in research due to their new functional roles in cellular physiology and disease progression. circRNAs are usually available in a wide range of cells and have shown tissue-specific expression as well as developmental specific expression. circRNAs are characterized by structural stability, conservation, and high abundance in the cell. In this review, we discuss the different models of biogenesis. The properties of circRNAs such as localization, structure and conserved pattern, stability, and expression specificity are also been illustrated. Furthermore, we discuss the biological functions of circRNAs such as microRNA (miRNA) sponging, cell cycle regulation, cell-to-cell communication, transcription regulation, translational regulation, disease diagnosis, and therapeutic potential. Finally, we discuss the recent research progress and future perspective of circRNAs. This review provides an understanding of potential diagnostic markers and the therapeutic potential of circRNAs, which are emerging daily.
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Affiliation(s)
- Ashish Ranjan Sharma
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si 24252, Gangwon-do, Republic of Korea
| | - Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore 756020, Odisha, India
| | - Swarnav Bhakta
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Barasat-Barrackpore Road, Jagannathpur, Kolkata, West Bengal 700126, India
| | - Abinit Saha
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Barasat-Barrackpore Road, Jagannathpur, Kolkata, West Bengal 700126, India
| | - Sang-Soo Lee
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si 24252, Gangwon-do, Republic of Korea
| | - Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Barasat-Barrackpore Road, Jagannathpur, Kolkata, West Bengal 700126, India
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