1
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Li Q, Liu Y, Li B, Zheng C, Yu B, Niu K, Qiao Y. Bioinformatics analysis of oxidative stress genes in the pathogenesis of ulcerative colitis based on a competing endogenous RNA regulatory network. PeerJ 2024; 12:e17213. [PMID: 39161963 PMCID: PMC11332386 DOI: 10.7717/peerj.17213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 03/19/2024] [Indexed: 08/21/2024] Open
Abstract
Background Ulcerative colitis (UC) is a common chronic disease associated with inflammation and oxidative stress. This study aimed to construct a long noncoding RNA (lncRNA)-microRNA (miRNA)-messenger RNA (mRNA) network based on bioinformatics analysis and to explore oxidative stress-related genes underlying the pathogenesis of UC. Methods The GSE75214, GSE48959, and GSE114603 datasets were downloaded from the Gene Expression Omnibus database. Following differentially expressed (DE) analysis, the regulatory relationships among these DERNAs were identified through miRDB, miRTarBase, and TargetScan; then, the lncRNA-miRNA-mRNA network was established. The Molecular Signatures Database (MSigDB) was used to search oxidative stress-related genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed for functional annotation and enrichment analyses. Based on the drug gene interaction database DGIdb, drugs that interact with oxidative stress-associated genes were explored. A dextran sulfate sodium (DSS)-induced UC mouse model was used for experimental validation. Results A total of 30 DE-lncRNAs, 3 DE-miRNAs, and 19 DE-mRNAs were used to construct a lncRNA-miRNA-mRNA network. By comparing these 19 DE-mRNAs with oxidative stress-related genes in MSigDB, three oxidative stress-related genes (CAV1, SLC7A11, and SLC7A5) were found in the 19 DEM sets, which were all negatively associated with miR-194. GO and KEGG analyses showed that CAV1, SLC7A11, and SLC7A5 were associated with immune inflammation and steroid hormone synthesis. In animal experiments, the results showed that dexamethasone, a well-known glucocorticoid drug, could significantly decrease the expression of CAV1, SLC7A11, and SLC7A5 as well as improve UC histology, restore antioxidant activities, inhibit inflammation, and decrease myeloperoxidase activity. Conclusion SLC7A5 was identified as a representative gene associated with glucocorticoid therapy resistance and thus may be a new therapeutic target for the treatment of UC in the clinic.
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MESH Headings
- Animals
- Humans
- Mice
- Colitis, Ulcerative/genetics
- Colitis, Ulcerative/metabolism
- Colitis, Ulcerative/chemically induced
- Computational Biology
- Databases, Genetic
- Dextran Sulfate/toxicity
- Disease Models, Animal
- Gene Expression Profiling
- Gene Regulatory Networks/drug effects
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Oxidative Stress/genetics
- Oxidative Stress/drug effects
- RNA, Competitive Endogenous/genetics
- RNA, Competitive Endogenous/metabolism
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
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Affiliation(s)
- Qifang Li
- Department of Traditional Chinese Medicine, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Yuan Liu
- College of Integrated Chinese and Western Medicine, Jining Medical University, Jining, Shandong, China
| | - Bingbing Li
- College of Integrated Chinese and Western Medicine, Jining Medical University, Jining, Shandong, China
| | - Canlei Zheng
- College of Integrated Chinese and Western Medicine, Jining Medical University, Jining, Shandong, China
| | - Bin Yu
- College of Integrated Chinese and Western Medicine, Jining Medical University, Jining, Shandong, China
| | - Kai Niu
- College of Integrated Chinese and Western Medicine, Jining Medical University, Jining, Shandong, China
| | - Yi Qiao
- School of Public Health, Jining Medical University, Jining, Shandong, China
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2
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Gao Y, Wu C, Huang J, Huang Z, Jin Z, Guo S, Tao X, Lu S, Zhang J, Zhang F, Zhai Y, Shi R, Ye P, Wu J. A new strategy to identify ADAM12 and PDGFRB as a novel prognostic biomarker for matrine regulates gastric cancer via high throughput chip mining and computational verification. Comput Biol Med 2023; 166:107562. [PMID: 37847945 DOI: 10.1016/j.compbiomed.2023.107562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/26/2023] [Accepted: 10/10/2023] [Indexed: 10/19/2023]
Abstract
BACKGROUND Gastric cancer is a life-threatening disease that poses a serious risk to human health. Although there are numerous molecular targets for gastric cancer in clinical practice, they often exhibit low specificity and sensitivity. Consequently, this can result in a low early diagnosis rate, delayed treatment, and poor prognosis for patients with gastric cancer. Hence, it remains crucial to identify more precise diagnostic markers for this disease. METHODS This study utilized ceRNA chips and bioinformatics methods to investigate the key genes and mechanisms involved in matrine intervention in gastric cancer cells. RESULTS ADAM12 and PDGFRB are the key genes that are down-regulated after matrine intervention in gastric cancer cells. By conducting bioinformatics analysis, two ceRNA regulatory axes were identified, which are associated with the prognosis of gastric cancer. These axes are lncRNA DGCR5/hsa-miR-206/ADAM12 and circRNA ITGA3/hsa-miR-24-3p/PDGFRB. CONCLUSION The low expression of ADAM12 may weaken the digestion of extracellular matrix (ECM) molecules, which can result in the invasion and metastasis of tumor cells. This occurs without the catalysis of ECM proteases, thereby impacting the invasion and metastasis of gastric cancer cells. Additionally, the analysis of immune infiltration suggests that ADAM12 and PDGFRB may influence changes in the tumor immune microenvironment, thereby affecting the occurrence and development of gastric cancer. This study contributes to a deeper understanding of the role of the matrine-related ceRNA network in gastric cancer, providing a reference for clinical diagnosis and treatment. It holds significant importance in discovering new drug treatment targets.
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Affiliation(s)
- Yifei Gao
- Department of Clinical Pharmacology of Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Chao Wu
- Department of Clinical Pharmacology of Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Jiaqi Huang
- Department of Clinical Pharmacology of Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Zhihong Huang
- Department of Clinical Pharmacology of Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Zhengsen Jin
- Department of Clinical Pharmacology of Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Siyu Guo
- Department of Clinical Pharmacology of Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Xiaoyu Tao
- Department of Clinical Pharmacology of Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Shan Lu
- Department of Clinical Pharmacology of Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Jingyuan Zhang
- Department of Clinical Pharmacology of Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Fanqin Zhang
- Department of Clinical Pharmacology of Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Yiyan Zhai
- Department of Clinical Pharmacology of Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Rui Shi
- Department of Clinical Pharmacology of Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Peizhi Ye
- National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Jiarui Wu
- Department of Clinical Pharmacology of Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China.
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Zhang Y, Wang X, Ding Z, Lin N, Zhang Y. Enhanced efficacy with reduced toxicity of tripterygium glycoside tablet by compatibility with total glucosides of paeony for rheumatoid arthritis therapy. Biomed Pharmacother 2023; 166:115417. [PMID: 37666179 DOI: 10.1016/j.biopha.2023.115417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/29/2023] [Accepted: 08/29/2023] [Indexed: 09/06/2023] Open
Abstract
BACKGROUND AND AIMS Drug-induced liver injury remains a critical issue to hinder clinical application of Tripterygium Glycosides Tablets (TGTs) for rheumatoid arthritis (RA) therapy. Combination of TGTs with Total Glucosides of Peony (TGP) may be the most common therapeutic strategy for enhancing TGTs' efficacy and reducing its toxicity. Herein, we aimed to investigate the efficacy-enhancing and toxicity-reducing properties and mechanisms of TGT-TGP combination. METHODS Both TGT-induced acute and chronic liver injury animal models were established. ELISA, transmission electron microscopy, immunohistochemistry, western blot and quantitative PCR were performed to determine the efficacy, toxicity and regulatory mechanisms of TGT-TGP combination. RESULTS The compatibility of TGP significantly reduced the abnormal serum ALT and AST levels, and improved liver histopathological changes in both acute and chronic DILI animal models induced by TGTs, with the most effective dosage of TGP-M (medium-dose TGP, 450 mg/kg). Additionally, TGP and TGT synergistically alleviated joint swelling and improved the elevation of serum inflammatory factors, in line with the positive changes in joint histopathological features of collagen induced arthritis mice, with the same effective dosage of TGP-M following 5 weeks' drug combination treatment. Mechanically, TGT significantly increased the number of autophagosomes and the expression of LC3II protein while reducing p62 protein expression in the liver tissues, which were significantly reversed by the compatibility with TGP, similar to the findings based on the inflamed joint tissues. CONCLUSIONS These findings suggest an enhanced efficacy with reduced toxicity of TGT by the compatibility with TGP for RA therapy, possibly through regulating various autophagy-related proteins.
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Affiliation(s)
- Yi Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Xiaoyue Wang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Zihe Ding
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Na Lin
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Yanqiong Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
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4
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Wang X, Zhang Y, Ding Z, Du L, Zhang Y, Yan S, Lin N. Cross-talk between the RAS-ERK and mTOR signalings-associated autophagy contributes to tripterygium glycosides tablet-induced liver injury. Biomed Pharmacother 2023; 160:114325. [PMID: 36738501 DOI: 10.1016/j.biopha.2023.114325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/19/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND AND AIMS Drug-induced liver injury (DILI) remains a critical issue and a hindrance to clinical application of Tripterygium Glycosides Tablet (TGT) despite its favorable therapeutic efficacy in rheumatoid arthritis. Herein, we aimed to elucidate the molecular mechanisms underlying TGT-induced hepatotoxicity. METHODS Chemical profiling of TGT was identified by UPLC-Q/TOF-MS/MS and its putative targets were predicted based on chemical structure similarity calculation. Following "DILI-related gene-TGT putative target" interaction network construction, a list of key network targets was screened according to nodes' topological importance and functional relevance. Both in vivo and in vitro experiments were performed to determine drug hepatotoxicity and the underlying mechanisms. RESULT A total of 49 chemical components and 914 putative targets of TGTs were identified. Network calculation and functional modularization screened RAS-ERK and mTOR signalings-associated autophagy to be one of the candidate targets of TGT-induced hepatotoxicity. Experimentally, TGT significantly activated RAS-ERK axis, elevated the number of autophagosomes and the expression of LC3II protein, but reduced the expression of p62 protein and suppressed mTOR phosphorylation in the liver tissues of TGT-induced acute liver injury mice and chronic liver injury mice in vivo and AML12 cells in vitro. Moreover, TGT and mL-098 (an activator of RAS) co-treatment reduced AML12 cell viability via regulating autophagy and TGT-induced liver injury-related indicators more dramatically than TGT treatment alone, whereas Salirasib (an inhibitor of RAS) had an opposite effect. CONCLUSION RAS-ERK-mTOR cross-talk may play a crucial role in TGT-induced hepatocyte autophagy, offering a promising target for developing novel therapeutics to combat TGT-induced hepatotoxicity.
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Affiliation(s)
- Xiaoyue Wang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Yi Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Zihe Ding
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Lijing Du
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yanqiong Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Shikai Yan
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Na Lin
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
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5
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Yang J, Li Z, Wang L, Yun X, Zeng Y, Ng JP, Lo H, Wang Y, Zhang K, Law BYK, Wong VKW. The role of non-coding RNAs (miRNA and lncRNA) in the clinical management of rheumatoid arthritis. Pharmacol Res 2022; 186:106549. [DOI: 10.1016/j.phrs.2022.106549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 11/04/2022] [Accepted: 11/06/2022] [Indexed: 11/09/2022]
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6
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Zhao H, Li L, Zhao N, Lu A, Lu C, He X. The effect of long non-coding RNAs in joint destruction of rheumatoid arthritis. Front Cell Dev Biol 2022; 10:1011371. [PMID: 36263019 PMCID: PMC9574091 DOI: 10.3389/fcell.2022.1011371] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 09/12/2022] [Indexed: 11/18/2022] Open
Abstract
Rheumatoid arthritis (RA) is a systemic autoimmune disease accompanied with joint destruction. Serious joint destruction will eventually lead to disability and the decline of life quality in RA patients. At present, the therapeutic effect of drugs to alleviate joint destruction in RA is limited. Recently, accumulating evidences have shown that long non-coding RNAs (lncRNAs) play an important role in the pathogenesis of joint diseases. Therefore, this paper reviews the expression change and the action mechanism of lncRNAs in joint destruction of RA in recent years. A more comprehensive understanding of the role of lncRNAs in joint destruction will help the treatment of RA.
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Affiliation(s)
- Hanxiao Zhao
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Li Li
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ning Zhao
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Aiping Lu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
- Shanghai GuangHua Hospital of Integrated Traditional Chinese and Western Medicine, Institute of Arthritis Research, Shanghai Academy of Chinese Medical Sciences, Shanghai, China
- *Correspondence: Aiping Lu, ; Cheng Lu, ; Xiaojuan He,
| | - Cheng Lu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
- *Correspondence: Aiping Lu, ; Cheng Lu, ; Xiaojuan He,
| | - Xiaojuan He
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
- *Correspondence: Aiping Lu, ; Cheng Lu, ; Xiaojuan He,
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7
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Dong L, Zhang R, Huang Q, Shen Y, Li H, Yu S, Wu Q. Construction, bioinformatics analysis, and validation of competitive endogenous RNA networks in ulcerative colitis. Front Genet 2022; 13:951243. [PMID: 36061211 PMCID: PMC9428148 DOI: 10.3389/fgene.2022.951243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 07/06/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Ulcerative colitis (UC) is a common chronic disease of the digestive system. Recently, competitive endogenous RNAs (ceRNAs) have been increasingly used to reveal key mechanisms for the pathogenesis and treatment of UC. However, the role of ceRNA in UC pathogenesis has not been fully clarified. This study aimed to explore the mechanism of the lncRNA-miRNA-mRNA ceRNA network in UC and identify potential biomarkers and therapeutic targets. Materials and Methods: An integrative analysis of mRNA, microRNA (miRNA), and long non-coding RNA (lncRNA) files downloaded from the Gene Expression Omnibus (GEO) was performed. Differentially expressed mRNA (DE-mRNAs), miRNA (DE-miRNAs), and lncRNA (DE-lncRNAs) were investigated between the normal and UC groups by the limma package. A weighted correlation network analysis (WGCNA) was used to identify the relative model for constructing the ceRNA network, and, concurrently, miRWalk and DIANA-LncBase databases were used for target prediction. Consecutively, the Gene Ontology (GO), Kyoto encyclopedia of genes and genomes (KEGG) pathway, and Reactome pathway enrichment analyses, protein-protein interaction (PPI) network, Cytohubba, and ClueGO were performed to identify hub genes. Additionally, we examined the immune infiltration characteristics of UC and the correlation between hub genes and immune cells using the immuCellAI database. Finally, the expression of potential biomarkers of ceRNA was validated via qRT-PCR in an experimental UC model induced by dextran sulfate sodium (DSS). Result: The ceRNA network was constructed by combining four mRNAs, two miRNAs, and two lncRNAs, and the receiver operating characteristic (ROC) analysis showed that two mRNAs (CTLA4 and STAT1) had high diagnostic accuracy (area under the curve [AUC] > 0.9). Furthermore, CTLA4 up-regulation was positively correlated with the infiltration of immune cells. Finally, as a result of this DSS-induced experimental UC model, CTLA4, MIAT, and several associate genes expression were consistent with the results of previous bioinformatics analysis, which proved our hypothesis. Conclusion: The investigation of the ceRNA network in this study could provide insight into UC pathogenesis. CTLA4, which has immune-related properties, can be a potential biomarker in UC, and MIAT/miR-422a/CTLA4 ceRNA networks may play important roles in UC.
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Affiliation(s)
- Longcong Dong
- Acupuncture and Tuina College, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Ruibin Zhang
- Acupuncture and Tuina College, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Qin Huang
- Acupuncture and Tuina College, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yuan Shen
- Acupuncture and Tuina College, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Hongying Li
- Acupuncture and Tuina College, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Shuguang Yu
- Acupuncture and Tuina College, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Qiaofeng Wu
- Acupuncture and Tuina College, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Acupuncture and Chronobiology Key Laboratory of Sichuan Province, Chengdu, China
- *Correspondence: Qiaofeng Wu,
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8
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Huang Z, Kuang N. Construction of a ceRNA Network Related to Rheumatoid Arthritis. Genes (Basel) 2022; 13:genes13040647. [PMID: 35456453 PMCID: PMC9031934 DOI: 10.3390/genes13040647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/03/2022] [Accepted: 04/05/2022] [Indexed: 01/27/2023] Open
Abstract
(1) Background: Rheumatoid arthritis (RA) is a common systemic autoimmune disease affecting many people and has an unclear and complicated physiological mechanism. The competing endogenous RNA (ceRNA) network plays an essential role in the development and occurrence of various human physiological processes. This study aimed to construct a ceRNA network related to RA. (2) Methods: We explored the GEO database for peripheral blood mononuclear cell (PBMC) samples and then analyzed the RNA of 52 samples (without treatment) to obtain lncRNAs (DELs), miRNAs (DEMs), and mRNAs (DEGs), which can be differentially expressed with statistical significance in the progression of RA. Next, a ceRNA network was constructed, based on the DELs, DEMs, and DEGs. At the same time, the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analysis were used to validate the possible function of the ceRNA network. (3) Results: Through our analysis, 389 DELs, 247 DEMs, and 1081 DEGs were screened. After this, a ceRNA network was constructed for further statistical comparisons, including 16 lncRNAs, 1 miRNA, and 15 mRNAs. According to the GO and KEGG analysis, the ceRNA network was mainly enriched in the mTOR pathway, the dopaminergic system, and the Wnt signaling pathway. (4) Conclusions: The novel ceRNA network related to RA that we constructed offers novel insights into and targets for the underlying molecular mechanisms of the mTOR pathway, the dopaminergic system, and the Wnt signaling pathway (both classic and nonclassic pathways) that affect the level of the genetic regulator, which might offer novel ways to treat RA.
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Affiliation(s)
- Zhanya Huang
- Queen Mary School, Nanchang University, Nanchang 330006, China;
- Department of Immunology, Medical College of Nanchang University, Nanchang 330006, China
| | - Nanzhen Kuang
- Department of Immunology, Medical College of Nanchang University, Nanchang 330006, China
- Correspondence:
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Wang F, Zhang H, Qiu G, Li Z, Wang Y. The LINC00452/miR-204/CHST4 Axis Regulating Thymic Tregs Might Be Involved in the Progression of Thymoma-Associated Myasthenia Gravis. Front Neurol 2022; 13:828970. [PMID: 35432149 PMCID: PMC9005856 DOI: 10.3389/fneur.2022.828970] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/14/2022] [Indexed: 11/24/2022] Open
Abstract
Background Myasthenia gravis (MG) is an autoimmune disease that mainly affects neuromuscular junctions and is usually associated with immune disorders in the thymoma. The competitive endogenous RNA (ceRNA) hypothesis has been demonstrated to be an intrinsic mechanism regulating the development of several autoimmune diseases; however, the mechanism where the ceRNA network regulates immune cells in patients with thymoma-associated MG (TAMG) has rarely been explored. Methods RNA-seq data and clinical information of 124 patients with thymoma were obtained from The Cancer Genome Atlas (TCGA) database. The patients were divided into two groups according to whether they were diagnosed with MG. We applied the propensity score matching method to reduce the incidence of baseline confounders. We then constructed a ceRNA network with differentially expressed RNAs between the groups based on four public databases. The expression of genes of interest was validated by qPCR. Moreover, we predicted the immune cells that infiltrated the thymoma and then analyzed the association between immune cells and RNA in the ceRNA network. To further determine the function of the mRNAs associated with immune cells in patients with TAMG, we performed gene set enrichment analysis in thymoma patients with MG. Results After matching, 94 patients were included in the following analysis. A total of 847 mRNAs, 409 lncRNAs, and 45 miRNAs were differentially expressed between the groups. The ceRNA network, including 18 lncRNAs, four miRNAs, and 13 mRNAs, was then constructed. We then confirmed that CHST4 and LINC00452, miR-204-3p and miR-204-5p were differentially expressed between patients with TAMG and thymoma patients without MG (NMG) by qPCR. Moreover, we found that the percentage of predicted regulatory T (Treg) cells was significantly decreased in patients with TAMG. Further analysis indicated that the LINC00452/miR-204/CHST4 axis might regulate thymic regulatory T cells (Tregs) in the progression of MG. Conclusions In this research, we constructed a ceRNA network involved in the progression of TAMG, discovered that thymic Tregs were significantly decreased in patients with TAMG, and assumed that the LINC00452/miR-204/CHST4 axis may regulate thymic Tregs in the development of TAMG. These findings may deepen our understanding of the roles of the ceRNA network in regulating TAMG and highlight the function of CHST4 in recruiting peripheral T cells in the progression of TAMG.
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Affiliation(s)
- Fuqiang Wang
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Hanlu Zhang
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Guanghao Qiu
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Zhiyang Li
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Yun Wang
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
- *Correspondence: Yun Wang
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10
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Wen JT, Liu J, Wan L, Xin L, Guo JC, Sun YQ, Wang X, Wang J. Triptolide inhibits cell growth and inflammatory response of fibroblast-like synoviocytes by modulating hsa-circ-0003353/microRNA-31-5p/CDK1 axis in rheumatoid arthritis. Int Immunopharmacol 2022; 106:108616. [PMID: 35203042 DOI: 10.1016/j.intimp.2022.108616] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/24/2022] [Accepted: 02/06/2022] [Indexed: 11/15/2022]
Abstract
Triptolide (TPL) is an active component derived from Tripterygium wilfordii Hook F (TwHF) with therapeutic potential for rheumatoid arthritis (RA). However, the underlying mechanism of TPL is remains under-studied. Competing endogenous RNA (ceRNA) networks may participate in the response to TPL in RA. Herein, we sought to identify a TPL response-related ceRNA axis. A circular RNA (circRNA)-microRNA (miRNA)-mRNA ceRNA axis associated with the TPL response was constructed according to our previous study. Modulatory mechanisms of the ceRNA axis were ascertained through a series of experimentations. The clinical relevance of the ceRNA axis was also determined using computational models. Here, we found that TPL had excellent clinical effect on RA and promising therapeutic efficacy in experimental animals. The ceRNA axis of hsa-circ-0003353 (circ0003353), miR-31-5p, and CDK1 was identified as a candidate biomarker for the response of RA patients to TPL. TPL inhibited the viability, proliferation, and cell cycle entry of RA-fibroblast-like synoviocytes (FLSs), as well as the production of cytokines. Overexpression of circ0003353 abolished the inhibitory effects of TPL on RA-FLSs. Mechanistically, circ0003353 sponged miR-31-5p that inversely targeted CDK1 and manipulated the p21/Cyclin B axis. Additionally, consecutive rescue experiments indicated that the inhibitory impacts of TPL on RA-FLSs were dependent on the circ0003353/miR-31-5p/CDK1 axis. Molecular docking was also applied to predict the specific binding sites and binding capacity of TPL to related targets. In conclusion, the present study demonstrated that TPL repressed the cell growth and inflammatory response of RA-FLSs by mediating the expression of the circ0003353/miR-31-5p/CDK1 axis. This novel ceRNA axis may serve as a biomarker for screening RA patients who respond to TPL treatment, which holds potential applications in the diagnosis and therapy of RA.
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Affiliation(s)
- Jian-Ting Wen
- Department of Rheumatology and Immunology, First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui 230031, China; Institute of Rheumatology, Anhui Academy of Chinese Medicine, Hefei, Anhui 230012, China; Key Laboratory of Xin'an Medicine of the Ministry of Education, Anhui University of Chinese Medicine, Hefei, Anhui 230038, China.
| | - Jian Liu
- Department of Rheumatology and Immunology, First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui 230031, China; Institute of Rheumatology, Anhui Academy of Chinese Medicine, Hefei, Anhui 230012, China; Anhui Province Key Laboratory of Modern Chinese Medicine Department of Internal Medicine Application Foundation Research and Development, Hefei, Anhui 230031, China.
| | - Lei Wan
- Department of Rheumatology and Immunology, First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui 230031, China; Institute of Rheumatology, Anhui Academy of Chinese Medicine, Hefei, Anhui 230012, China; Anhui Province Key Laboratory of Modern Chinese Medicine Department of Internal Medicine Application Foundation Research and Development, Hefei, Anhui 230031, China.
| | - Ling Xin
- Department of Rheumatology and Immunology, First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui 230031, China; Anhui Province Key Laboratory of Modern Chinese Medicine Department of Internal Medicine Application Foundation Research and Development, Hefei, Anhui 230031, China.
| | - Jin-Chen Guo
- Key Laboratory of Xin'an Medicine of the Ministry of Education, Anhui University of Chinese Medicine, Hefei, Anhui 230038, China; Anhui University of Chinese Medicine, Hefei, Anhui 230038, China.
| | - Yan-Qiu Sun
- Department of Rheumatology and Immunology, First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui 230031, China; Anhui Province Key Laboratory of Modern Chinese Medicine Department of Internal Medicine Application Foundation Research and Development, Hefei, Anhui 230031, China.
| | - Xin Wang
- Department of Rheumatology and Immunology, First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui 230031, China; Anhui Province Key Laboratory of Modern Chinese Medicine Department of Internal Medicine Application Foundation Research and Development, Hefei, Anhui 230031, China.
| | - Jie Wang
- Department of Rheumatology and Immunology, First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui 230031, China; Anhui Province Key Laboratory of Modern Chinese Medicine Department of Internal Medicine Application Foundation Research and Development, Hefei, Anhui 230031, China.
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Ma Z, Liu Y, Li C, Zhang Y, Lin N. Repurposing a clinically approved prescription Colquhounia root tablet to treat diabetic kidney disease via suppressing PI3K/AKT/NF-kB activation. Chin Med 2022; 17:2. [PMID: 34980163 PMCID: PMC8725443 DOI: 10.1186/s13020-021-00563-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/25/2021] [Indexed: 11/17/2022] Open
Abstract
Background Growing clinical evidences show the potentials of Colquhounia root tablet (CRT) in alleviating diabetic kidney disease (DKD). However, its pharmacological properties and underlying mechanisms remain unclear. Methods ‘Drug target-Disease gene’ interaction network was constructed and the candidate network targets were screened through evaluating node genes' topological importance. Then, a DKD rat model induced by high-fat diet/streptozotocin was established and used to determine pharmacological effects and network regulatory mechanisms of CRT against DKD, which were also verified using HK2 cell model induced by high glucose. Results The candidate network targets of CRT against DKD were involved into various type II diabetes-related and nephropathy-related pathways. Due to the topological importance of the candidate network targets and the important role of the imbalance between immunity and inflammation in the pathogenesis of DKD, PI3K/AKT/NF-кB signaling-mediated immune-modulatory and anti-inflammatory actions of CRT were selected to be experimentally verified. On the basis of high-fat diet (HFD) / streptozotocin (STZ)-induced DKD rat model, CRT effectively reduced the elevated level of blood glucose, decreased the accumulation of renal lipid, suppressed inflammation and the generation of ECM proteins, and ameliorated kidney function and the renal histopathology through inhibiting the activation of PI3K, AKT and NF-кB proteins, reducing the nuclear accumulation of NF-кB protein and the serum levels of downstream cytokines, which were in line with the in vitro findings. Conclusions Our data suggest that CRT may be the promising candidate drug for treating DKD via reversing the imbalance of immune-inflammation system mediated by the PI3K/AKT/NF-кB/IL-1β/TNF-α signaling. Supplementary Information The online version contains supplementary material available at 10.1186/s13020-021-00563-7.
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Affiliation(s)
- Zhaochen Ma
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16, Nanxiaojie, Dongzhimennei, Beijing, 100700, China
| | - Yudong Liu
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16, Nanxiaojie, Dongzhimennei, Beijing, 100700, China
| | - Congchong Li
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16, Nanxiaojie, Dongzhimennei, Beijing, 100700, China
| | - Yanqiong Zhang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16, Nanxiaojie, Dongzhimennei, Beijing, 100700, China.
| | - Na Lin
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16, Nanxiaojie, Dongzhimennei, Beijing, 100700, China.
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Li J, Liu D, Wu K, Chen Q, Lei J. Circ_0003972 Promotes the Proliferation and Inflammation of Fibroblast-like Synovial Cells in Rheumatoid Arthritis through Regulation of the miR-654-5p/FZD4 Axis. Immunol Invest 2021; 51:1437-1451. [PMID: 34325604 DOI: 10.1080/08820139.2021.1958837] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND Circular RNAs (circRNAs) have been shown to play an important role in rheumatoid arthritis (RA) progression. This study aims to explore the role and mechanism of circ_0003972 in RA progression. METHODS Quantitative real-time PCR was used to determine gene expression. The proliferation and apoptosis of human RA fibroblast-like synovial (HFLS-RA) cells were measured using cell counting kit 8 assay, EdU staining and flow cytometry. Western blot analysis was performed to measure protein expression, and ELISA assay was used to examine the concentrations of inflammation factors. The interaction between miR-654-5p and circ_0003972 or FZD4 was confirmed by dual-luciferase reporter assay and RIP assay. RESULTS Circ_0003972 was highly expressed in RA patients and HFLS-RA cells. Circ_0003972 knockdown inhibited the proliferation, inflammation, while promoted the apoptosis of TNFα-induced HFLS-RA cells. MiR-654-5p was downregulated in RA patients and HFLS-RA cells, and it could be sponged by circ_0003972. MiR-654-5p inhibitor reversed the effect of circ_0003972 silencing on the proliferation, inflammation, and apoptosis of TNFα-induced HFLS-RA cells. Frizzled-4 (FZD4) could be targeted by miR-654-5p, and its expression was positively regulated by circ_0003972. Furthermore, FZD4 overexpression also reversed the effects of miR-654-5p on proliferation, inflammation and apoptosis in TNFα-induced HFLS-RA cells. CONCLUSION Our data suggested that circ_0003972 might promote the proliferation and inflammation of HFLS-RA cells to accelerate RA progression via regulating miR-654-5p/FZD4.
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Affiliation(s)
- Juan Li
- Department of Rheumatology and Immunology, Xi'an No.5 Hospital, Xi'an City, China
| | - Dan Liu
- Department of Rheumatology and Immunology, Xi'an No.5 Hospital, Xi'an City, China.,Core Research Laboratory, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Kunyi Wu
- Core Research Laboratory, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Qun Chen
- Institute of Endemic Diseases, Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission of the People's Republic of China, Xi'an Jiaotong University Health Science Center, Xi'an, P.R. China
| | - Jianhong Lei
- Department of Rheumatology and Immunology, Xi'an No.5 Hospital, Xi'an City, China
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Zhang Y, Mao X, Li W, Chen W, Wang X, Ma Z, Lin N. Tripterygium wilfordii: An inspiring resource for rheumatoid arthritis treatment. Med Res Rev 2020; 41:1337-1374. [PMID: 33296090 DOI: 10.1002/med.21762] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/02/2020] [Accepted: 11/22/2020] [Indexed: 12/22/2022]
Abstract
Tripterygium wilfordii Hook F (TwHF)-based therapy is among the most efficient and crucial therapeutics for the treatment of rheumatoid arthritis (RA), which indicates that TwHF is a potential source of novel anti-RA drugs. However, accumulating studies have observed that TwHF-based therapy induces multi-organ toxicity, which prevents the wide use of this herb in clinical practice, although several recent studies have attempted to reduce the toxicity of TwHF. Notably, our research group developed a "Clinical Practice Guideline for Tripterygium Glycosides/Tripterygium wilfordii Tablets in the Treatment of Rheumatoid Arthritis" (No. T/CACM 1337-2020) approved by the China Association of Chinese Medicine to standardize the clinical application of TwHF-based therapy and thus avoid adverse effects. Although great strides have been made toward the characterization of TwHF-based therapy and revealing its underlying pharmacological and toxicological mechanisms, several crucial gaps in knowledge remain as potential barriers to enhance its therapeutic effects on the premise of safety assurance. This review offers a global view of TwHF, ranging from its chemical constituents, quality control, clinical observations, and underlying pharmacological mechanisms to toxic manifestations and mechanisms. We focus on the important and emerging aspects of this field and highlight the major challenges and strategies for using novel techniques and approaches to gain new insights into unresolved questions. We hope that this review will improve the understanding of TwHF application and draw increasing interdisciplinary attention from clinicians that practice both Chinese and Western medicine, basic researchers, and computer scientists.
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Affiliation(s)
- Yanqiong Zhang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xia Mao
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Weijie Li
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Wenjia Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xiaoyue Wang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Zhaochen Ma
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Na Lin
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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