Department of Rheumatology and Clinical Immunology, The First Affiliated Hospital of Xiamen University, Xiamen, China; Fuwai Central China Cardiovascular Hospital, Zhengzhou, China.
Department of Rheumatology and Clinical Immunology, The First Affiliated Hospital of Xiamen University, Xiamen, China.
Biochem Biophys Res Commun. 2019 Jan 8;508(2):392-397. doi: 10.1016/j.bbrc.2018.11.143. Epub 2018 Nov 28.
The purpose of this study is to provide a further theoretical basis for the role of Suberoyllanilide hyroxamic acid (SAHA) affect on Dendritic cells (DCs).
We first downloaded the GSE74306 microarray data, which was about the effect of SAHA act on DCs, from the Gene Expression Omnibus database. Then we analyzed the differential expression genes (DEGs) between SAHA-treated DCs and SAHA-untreated DCs by limma package of R software; The Database for Annotation, Visualization and Integrated Discovery was used to analyze the Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways for these DEGs. The protein protein interaction (PPI) network was constructed by using STRING database, Cytoscape 3.6.1 software was used to dispose the PPI network for visualization. Finally, we determine the Hub genes in the PPI network according by the degree centrality and betweenness centrality, which were calculated by the CentScaPe 2.2 plug-in of Cytoscape 3.6.1 software.
There were 551 DEGs between SAHA-treated DC cells and SAHA-untreated DC cells, including 357 upregulated genes and 194 downregulated genes. These DEGs genes were enriched in 115 Go terms (Biological Process, 51; Cellular Component, 35 and Molecular Function, 29) and a total of 16 pathways. Glutathione metabolic process, Glutathione metabolism pathway, Rheumatoid arthritis pathway and Systemic lupus erythematosus pathway were most significant function clusters. In the PPI network, Rad51, Src, and Eno2 were Hub genes.
The biological function and KEGG pathway enriched by DEGs may reveal the molecular mechanism of SAHA acting on DC cells. Its Hub genes, Src, Rad51 and Eno2, were expected to be new targets for SAHA therapeutic effects. However, it still need to be confirmed by the next more rigorous molecular biological experiments research.
本研究旨在为 Suberoylanilide hyroxamic acid（SAHA）对树突状细胞（DC）作用的影响提供进一步的理论依据。
我们首先从基因表达综合数据库中下载了关于 SAHA 作用于 DC 的 GSE74306 微阵列数据。然后，我们使用 R 软件的 limma 包分析了 SAHA 处理的 DC 与未经 SAHA 处理的 DC 之间的差异表达基因（DEGs）；使用数据库注释、可视化和综合发现（Database for Annotation, Visualization and Integrated Discovery）来分析这些 DEGs 的基因本体论（GO）和京都基因与基因组百科全书（KEGG）途径。使用 STRING 数据库构建蛋白质-蛋白质相互作用（PPI）网络，使用 Cytoscape 3.6.1 软件处理 PPI 网络进行可视化。最后，我们根据 CentScaPe 2.2 插件计算的度中心性和介数中心性，确定 PPI 网络中的枢纽基因。
SAHA 处理的 DC 细胞与未经 SAHA 处理的 DC 细胞之间存在 551 个 DEGs，包括 357 个上调基因和 194 个下调基因。这些 DEGs 基因富集于 115 个 GO 术语（生物过程 51 个，细胞成分 35 个，分子功能 29 个）和 16 条途径。谷胱甘肽代谢过程、谷胱甘肽代谢途径、类风湿关节炎途径和系统性红斑狼疮途径是最重要的功能簇。在 PPI 网络中，Rad51、Src 和 Eno2 是枢纽基因。
DEGs 富集的生物学功能和 KEGG 途径可能揭示了 SAHA 作用于 DC 细胞的分子机制。其枢纽基因 Src、Rad51 和 Eno2 有望成为 SAHA 治疗效果的新靶点。然而，这仍需要通过下一个更严格的分子生物学实验研究来证实。
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