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Zhang Q, Sun C, Liu X, Zhu C, Ma C, Feng R. Mechanism of immune infiltration in synovial tissue of osteoarthritis: a gene expression-based study. J Orthop Surg Res 2023; 18:58. [PMID: 36681837 PMCID: PMC9862811 DOI: 10.1186/s13018-023-03541-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 01/13/2023] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Osteoarthritis is a chronic degenerative joint disease, and increasing evidences suggest that the pathogenic mechanism involves immune system and inflammation. AIMS The aim of current study was to uncover hub genes linked to immune infiltration in osteoarthritis synovial tissue using comprehensive bioinformatics analysis and experimental confirmation. METHODS Multiple microarray datasets (GSE55457, GSE55235, GSE12021 and GSE1919) for osteoarthritis in Gene Expression Omnibus database were downloaded for analysis. Differentially expressed genes (DEGs) were identified using Limma package in R software, and immune infiltration was evaluated by CIBERSORT algorithm. Then weighted gene co-expression network analysis (WGCNA) was performed to uncover immune infiltration-associated gene modules. Protein-protein interaction (PPI) network was constructed to select the hub genes, and the tissue distribution of these genes was analyzed using BioGPS database. Finally, the expression pattern of these genes was confirmed by RT-qPCR using clinical samples. RESULTS Totally 181 DEGs between osteoarthritis and normal control were screened. Macrophages, mast cells, memory CD4 T cells and B cells accounted for the majority of immune cell composition in synovial tissue. Osteoarthritis synovial showed high abundance of infiltrating resting mast cells, B cells memory and plasma cells. WGCNA screened 93 DEGs related to osteoarthritis immune infiltration. These genes were involved in TNF signaling pathway, IL-17 signaling pathway, response to steroid hormone, glucocorticoid and corticosteroid. Ten hub genes including MYC, JUN, DUSP1, NFKBIA, VEGFA, ATF3, IL-6, PTGS2, IL1B and SOCS3 were selected by using PPI network. Among them, four genes (MYC, JUN, DUSP1 and NFKBIA) specifically expressed in immune system were identified and clinical samples revealed consistent change of these four genes in synovial tissue retrieved from patients with osteoarthritis. CONCLUSION A 4-gene-based diagnostic model was developed, which had well predictive performance in osteoarthritis. MYC, JUN, DUSP1 and NFKBIA might be biomarkers and potential therapeutic targets in osteoarthritis.
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Affiliation(s)
- Qingyu Zhang
- grid.460018.b0000 0004 1769 9639Department of Orthopedics, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No. 324, Road Jing Wu Wei Qi, Jinan, 250021 Shandong China
| | - Chao Sun
- grid.460018.b0000 0004 1769 9639Department of Orthopedics, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No. 324, Road Jing Wu Wei Qi, Jinan, 250021 Shandong China
| | - Xuchang Liu
- grid.460018.b0000 0004 1769 9639Department of Orthopedics, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No. 324, Road Jing Wu Wei Qi, Jinan, 250021 Shandong China
| | - Chao Zhu
- grid.460018.b0000 0004 1769 9639Department of Orthopedics, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No. 324, Road Jing Wu Wei Qi, Jinan, 250021 Shandong China
| | - Chuncheng Ma
- grid.460018.b0000 0004 1769 9639Department of Orthopedics, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No. 324, Road Jing Wu Wei Qi, Jinan, 250021 Shandong China
| | - Rongjie Feng
- grid.460018.b0000 0004 1769 9639Department of Orthopedics, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No. 324, Road Jing Wu Wei Qi, Jinan, 250021 Shandong China
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MicroRNAs (miRNAs) in Cardiovascular Complications of Rheumatoid Arthritis (RA): What Is New? Int J Mol Sci 2022; 23:ijms23095254. [PMID: 35563643 PMCID: PMC9101033 DOI: 10.3390/ijms23095254] [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: 04/18/2022] [Revised: 05/04/2022] [Accepted: 05/06/2022] [Indexed: 02/08/2023] Open
Abstract
Rheumatoid Arthritis (RA) is among the most prevalent and impactful rheumatologic chronic autoimmune diseases (AIDs) worldwide. Within a framework that recognizes both immunological activation and inflammatory pathways, the exact cause of RA remains unclear. It seems however, that RA is initiated by a combination between genetic susceptibility, and environmental triggers, which result in an auto-perpetuating process. The subsequently, systemic inflammation associated with RA is linked with a variety of extra-articular comorbidities, including cardiovascular disease (CVD), resulting in increased mortality and morbidity. Hitherto, vast evidence demonstrated the key role of non-coding RNAs such as microRNAs (miRNAs) in RA, and in RA-CVD related complications. In this descriptive review, we aim to highlight the specific role of miRNAs in autoimmune processes, explicitly on their regulatory roles in the pathogenesis of RA, and its CV consequences, their main role as novel biomarkers, and their possible role as therapeutic targets.
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Zhou J, He S, Wang B, Yang W, Zheng Y, Jiang S, Li D, Lin J. Construction and Bioinformatics Analysis of circRNA-miRNA-mRNA Network in Acute Myocardial Infarction. Front Genet 2022; 13:854993. [PMID: 35422846 PMCID: PMC9002054 DOI: 10.3389/fgene.2022.854993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/02/2022] [Indexed: 11/17/2022] Open
Abstract
Background: Acute myocardial infarction (AMI) is one of the main fatal diseases of cardiovascular diseases. Circular RNA (circRNA) is a non-coding RNA (ncRNA), which plays a role in cardiovascular disease as a competitive endogenous RNA (ceRNA). However, their role in AMI has not been fully clarified. This study aims to explore the mechanism of circRNA-related ceRNA network in AMI, and to identify the corresponding immune infiltration characteristics. Materials and Methods: The circRNA (GSE160717), miRNA (GSE24548), and mRNA (GSE60993) microarray datasets of AMI were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed circRNAs (DEcircRNAs), miRNAs (DEmiRNAs), and mRNAs (DEmRNAs) were identified by the “limma” package. After integrating the circRNA, miRNA and mRNA interaction, we constructed a circRNA-miRNA-mRNA network. The “clusterProfiler” package and String database were used for functional enrichment analysis and protein-protein interaction (PPI) analysis, respectively. After that, we constructed a circRNA-miRNA-hub gene network and validated the circRNAs and mRNAs using an independent dataset (GSE61144) as well as qRT-PCR. Finally, we used CIBERSORTx database to analyze the immune infiltration characteristics of AMI and the correlation between hub genes and immune cells. Results: Using the “limma” package of the R, 83 DEcircRNAs, 54 DEmiRNAs, and 754 DEmRNAs were identified in the microarray datasets of AMI. Among 83 DEcircRNAs, there are 55 exonic DEcircRNAs. Then, a circRNA-miRNA-mRNA network consists of 21 DEcircRNAs, 11 DEmiRNAs, and 106 DEmRNAs were predicted by the database. After that, 10 hub genes from the PPI network were identified. Then, a new circRNA-miRNA-hub gene network consists of 14 DEcircRNAs, 7 DEmiRNAs, and 9 DEmRNAs was constructed. After that, three key circRNAs (hsa_circ_0009018, hsa_circ_0030569 and hsa_circ_0031017) and three hub genes (BCL6, PTGS2 and PTEN) were identified from the network by qRT-PCR. Finally, immune infiltration analysis showed that hub genes were significantly positively correlated with up-regulated immune cells (neutrophils, macrophages and plasma cells) in AMI. Conclusion: Our study constructed a circRNA-related ceRNA networks in AMI, consists of hsa_circ_0031017/hsa-miR-142-5p/PTEN axis, hsa_circ_0030569/hsa-miR-545/PTGS2 axis and hsa_circ_0009018/hsa-miR-139-3p/BCL6 axis. These three hub genes were significantly positively correlated with up-regulated immune cells (neutrophils, macrophages and plasma cells) in AMI. It helps improve understanding of AMI mechanism and provides future potential therapeutic targets.
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Affiliation(s)
- Jin Zhou
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shaolin He
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Boyuan Wang
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wenling Yang
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuqi Zheng
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shijiu Jiang
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dazhu Li
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jibin Lin
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Shi X, Cao Y, Zhang X, Gu C, Liang F, Xue J, Ni HW, Wang Z, Li Y, Wang X, Cai Z, Hocher B, Shen LH, He B. Comprehensive Analysis of N6-Methyladenosine RNA Methylation Regulators Expression Identify Distinct Molecular Subtypes of Myocardial Infarction. Front Cell Dev Biol 2021; 9:756483. [PMID: 34778266 PMCID: PMC8578940 DOI: 10.3389/fcell.2021.756483] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 09/13/2021] [Indexed: 01/17/2023] Open
Abstract
Background: Myocardial infarction (MI) is one of the leading threats to human health. N6-methyladenosine (m6A) modification, as a pivotal regulator of messenger RNA stability, protein expression, and cellular processes, exhibits important roles in the development of cardiac remodeling and cardiomyocyte contractile function. Methods: The expression levels of m6A regulators were analyzed using the GSE5406 database. We analyzed genome-wide association study data and single-cell sequencing data to confirm the functional importance of m6A regulators in MI. Three molecular subtypes with different clinical characteristics were established to tailor treatment strategies for patients with MI. We applied pathway analysis and differentially expressed gene (DEG) analysis to study the changes in gene expression and identified four common DEGs. Furthermore, we constructed the protein–protein interaction network and confirmed several hub genes in three clusters of MI. To lucubrate the potential functions, we performed a ClueGO analysis of these hub networks. Results: In this study, we identified that the levels of FTO, YTHDF3, ZC3H13, and WTAP were dramatically differently expressed in MI tissues compared with controls. Bioinformatics analysis showed that DEGs in MI were significantly related to modulating calcium signaling and chemokine signaling, and m6A regulators were related to regulating glucose measurement and elevated blood glucose levels. Furthermore, genome-wide association study data analysis showed that WTAP single-nucleotide polymorphism was significantly related to the progression of MI. In addition, single-cell sequencing found that WTAP is widely expressed in the heart tissues. Moreover, we conducted consensus clustering for MI in view of the dysregulated m6A regulators’ expression in MI. According to the expression levels, we found MI patients could be clustered into three subtypes. Pathway analysis showed the DEGs among different clusters in MI were assigned to HIF-1, IL-17, MAPK, PI3K-Akt signaling pathways, etc. The module analysis detected several genes, including BAG2, BAG3, MMP2, etc. We also found that MI-related network was significantly related to positive and negative regulation of angiogenesis and response to heat. The hub networks in MI clusters were significantly related to antigen processing and ubiquitin-mediated proteolysis, RNA splicing, and stability, indicating that these processes may contribute to the development of MI. Conclusion: Collectively, our study could provide more information for understanding the roles of m6A in MI, which may provide a novel insight into identifying biomarkers for MI treatment and diagnosis.
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Affiliation(s)
- Xin Shi
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Yaochen Cao
- Department of Nephrology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Xiaobin Zhang
- Department of Cardiovascular Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Chang Gu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Feng Liang
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Jieyuan Xue
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Han-Wen Ni
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Zi Wang
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Yi Li
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xia Wang
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Zhaohua Cai
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Berthold Hocher
- 5th Department of Medicine (Nephrology, Hypertensiology, Endocrinology, Rheumatology), University Hospital Mannheim, University of Heidelberg, Mannheim, Germany
| | - Ling-Hong Shen
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Ben He
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
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Wang W, Wang Y, Zou J, Jia Y, Wang Y, Li J, Wang C, Sun J, Guo D, Wang F, Wu Z, Yang M, Wu L, Zhang X, Shi Y. The Mechanism Action of German Chamomile ( Matricaria recutita L.) in the Treatment of Eczema: Based on Dose-Effect Weight Coefficient Network Pharmacology. Front Pharmacol 2021; 12:706836. [PMID: 34658853 PMCID: PMC8515037 DOI: 10.3389/fphar.2021.706836] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 08/13/2021] [Indexed: 01/03/2023] Open
Abstract
To determine the active ingredients in German chamomile volatile oil and the mechanism of action in the treatment of eczema, this study used two parameters (ingredient content and oil–water partition coefficient) and established a new network pharmacology method based on the dose–effect weight coefficient. Through the new network pharmacology method, we found that German chamomile volatile oil regulated T-cell lymphatic subpopulations to inhibit the Th17 cell differentiation signaling pathway. This resulted in a reduction of interleukin 17 (IL-17), thereby inhibiting the activation of the nuclear factor kappa beta (NF-κB) and MAPK pathways, decreasing the secretion of the pro-inflammatory factors (tumor necrosis factor alpha (TNF-α) and interleukin 6 (IL-6)), and reducing inflammation. In this study, a new dose–effect relationship synergistic network pharmacology method was established to provide a new method for the screening of effective ingredients and pathways of drugs, and to provide a basis for the follow-up studies of German chamomile volatile oil in the treatment of eczema.
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Affiliation(s)
- Wenfei Wang
- Department of Pharmaceutics, College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Yichun Wang
- Department of Pharmaceutics, College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Junbo Zou
- Department of Pharmaceutics, College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, China.,Department of Pharmaceutics, The Key Laboratory of Basicand New Drug Research of Traditional Chinese Medicine, Shaaxi University of Chinese Medicine, Xianyang, China
| | - Yanzhuo Jia
- Department of Pharmaceutics, College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Yao Wang
- Department of Pharmaceutics, College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Jia Li
- Department of Pharmaceutics, College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Changli Wang
- Department of Pharmaceutics, College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, China.,Department of Pharmaceutics, The Key Laboratory of Basicand New Drug Research of Traditional Chinese Medicine, Shaaxi University of Chinese Medicine, Xianyang, China
| | - Jing Sun
- Department of Pharmaceutics, College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, China.,Department of Pharmaceutics, The Key Laboratory of Basicand New Drug Research of Traditional Chinese Medicine, Shaaxi University of Chinese Medicine, Xianyang, China
| | - Dongyan Guo
- Department of Pharmaceutics, College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, China.,Department of Pharmaceutics, The Key Laboratory of Basicand New Drug Research of Traditional Chinese Medicine, Shaaxi University of Chinese Medicine, Xianyang, China
| | - Fang Wang
- Department of Pharmaceutics, Key Laboratory of Modern Preparation of Traditional Chinese Medicine, Ministry of Education, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Zhenfeng Wu
- Department of Pharmaceutics, Key Laboratory of Modern Preparation of Traditional Chinese Medicine, Ministry of Education, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Ming Yang
- Department of Pharmaceutics, Key Laboratory of Modern Preparation of Traditional Chinese Medicine, Ministry of Education, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Lei Wu
- Henan Feinari Aromatic Biotechnology Co., Ltd, Zhumadian, China
| | - Xiaofei Zhang
- Department of Pharmaceutics, College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, China.,Department of Pharmaceutics, The Key Laboratory of Basicand New Drug Research of Traditional Chinese Medicine, Shaaxi University of Chinese Medicine, Xianyang, China.,Department of Pharmaceutics, Key Laboratory of Modern Preparation of Traditional Chinese Medicine, Ministry of Education, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Yajun Shi
- Department of Pharmaceutics, College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, China.,Department of Pharmaceutics, The Key Laboratory of Basicand New Drug Research of Traditional Chinese Medicine, Shaaxi University of Chinese Medicine, Xianyang, China
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