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生物信息学分析鉴定影响骨关节炎滑膜炎症的关键基因和通路。

Bioinformatics analysis to identify key genes and pathways influencing synovial inflammation in osteoarthritis.

机构信息

Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China.

Fujian Provincial Key Laboratory of Integrative Medicine on Geriatrics, Fuzhou, Fujian 350122, P.R. China.

出版信息

Mol Med Rep. 2018 Dec;18(6):5594-5602. doi: 10.3892/mmr.2018.9575. Epub 2018 Oct 23.


DOI:10.3892/mmr.2018.9575
PMID:30365099
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC6236257/
Abstract

Osteoarthritis (OA) is a chronic arthropathy that occurs in the middle‑aged and elderly population. The present study aimed to identify gene signature differences between synovial cells from OA synovial membrane with and without inflammation, and to explain the potential mechanisms involved. The differentially expressed genes (DEGs) between 12 synovial membrane with inflammation and 12 synovial membrane without inflammation from the dataset GSE46750 were identified using the Gene Expression Omnibus 2R. The DEGs were subjected to enrichment analysis, protein‑protein interaction (PPI) analysis and module analysis. The analysis results were compared with text‑mining results. A total of 174 DEGs were identified. Gene Ontology enrichment results demonstrated that functional molecules encoded by the DEGs primarily had extracellular location, molecular functions predominantly involving 'chemokine activity' and 'cytokine activity', and were associated with biological processes, including 'inflammatory response' and 'immune response'. The Kyoto Encyclopedia of Genes and Genomes results demonstrated that DEGS may function through pathways associated with 'rheumatoid arthritis', 'chemokine signaling pathway', 'complement and coagulation cascades', 'TNF signaling pathway', 'intestinal immune networks for IgA production', 'cytokine‑cytokine receptor interaction', 'allograft rejection', 'Toll‑like receptor signaling pathway' and 'antigen processing and presentation'. The top 10 hub genes [interleukin (IL)6, IL8, matrix metallopeptidase (MMP)9, colony stimulating factor 1 receptor, FOS proto‑oncogene, AP1 transcription factor subunit, insulin‑like growth factor 1, TYRO protein tyrosine kinase binding protein, MMP3, cluster of differentiation (CD)14 and CD163] and four gene modules were identified from the PPI network using Cytoscape. In addition, text‑mining was used to identify the commonly used drugs and their targets for the treatment of OA. It was initially verified whether the results of the present study were useful for the study of OA treatment targets and pathways. The present study provided insight for the molecular mechanisms of OA synovitis. The hub genes and associated pathways derived from analysis may be targets for OA treatment. IL8 and MMP9, which were validated by text‑mining, may be used as molecular targets for the OA treatment, while other hub genes require further validation.

摘要

骨关节炎(OA)是一种发生在中老年人中的慢性关节病。本研究旨在鉴定有炎症和无炎症的滑膜细胞之间滑膜组织的基因特征差异,并解释潜在的相关机制。通过基因表达综合数据库 2R 分析数据集 GSE46750 中 12 例炎症性滑膜膜和 12 例非炎症性滑膜膜之间的差异表达基因(DEGs)。对 DEGs 进行富集分析、蛋白-蛋白相互作用(PPI)分析和模块分析。并将分析结果与文本挖掘结果进行比较。共鉴定出 174 个 DEGs。基因本体论富集结果表明,DEGs 编码的功能分子主要位于细胞外位置,分子功能主要涉及“趋化因子活性”和“细胞因子活性”,并与“炎症反应”和“免疫反应”等生物过程相关。京都基因与基因组百科全书结果表明,DEGs 可能通过与“类风湿关节炎”、“趋化因子信号通路”、“补体和凝血级联”、“TNF 信号通路”、“IgA 产生的肠道免疫网络”、“细胞因子-细胞因子受体相互作用”、“同种异体移植排斥”、“Toll 样受体信号通路”和“抗原加工和呈递”相关的途径发挥作用。通过 Cytoscape 从 PPI 网络中鉴定出前 10 个枢纽基因[白细胞介素(IL)6、IL8、基质金属蛋白酶(MMP)9、集落刺激因子 1 受体、FOS 原癌基因、AP1 转录因子亚基、胰岛素样生长因子 1、TYRO 蛋白酪氨酸激酶结合蛋白、MMP3、分化群(CD)14 和 CD163]和 4 个基因模块。此外,还使用文本挖掘来识别治疗 OA 的常用药物及其靶点。最初验证了本研究的结果是否有助于 OA 治疗靶点和途径的研究。本研究为 OA 滑膜炎的分子机制提供了深入了解。分析得出的枢纽基因和相关途径可能是 OA 治疗的靶点。通过文本挖掘验证的 IL8 和 MMP9 可能作为 OA 治疗的分子靶点,而其他枢纽基因需要进一步验证。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5847/6236257/1847433c3752/MMR-18-06-5594-g05.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5847/6236257/f72fb30618eb/MMR-18-06-5594-g00.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5847/6236257/76c41a5cd4b4/MMR-18-06-5594-g01.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5847/6236257/332f9e877fb6/MMR-18-06-5594-g02.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5847/6236257/c28ce935af57/MMR-18-06-5594-g03.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5847/6236257/941c628801c8/MMR-18-06-5594-g04.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5847/6236257/1847433c3752/MMR-18-06-5594-g05.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5847/6236257/f72fb30618eb/MMR-18-06-5594-g00.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5847/6236257/76c41a5cd4b4/MMR-18-06-5594-g01.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5847/6236257/332f9e877fb6/MMR-18-06-5594-g02.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5847/6236257/c28ce935af57/MMR-18-06-5594-g03.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5847/6236257/941c628801c8/MMR-18-06-5594-g04.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5847/6236257/1847433c3752/MMR-18-06-5594-g05.jpg

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本文引用的文献

[1]
Therapeutics in Osteoarthritis Based on an Understanding of Its Molecular Pathogenesis.

Int J Mol Sci. 2018-2-27

[2]
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J Orthop Res. 2017-8

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