摘要
目的采用生物信息学方法识别绝经后骨质疏松症中免疫反应相关的基因,并探讨其作用机制和筛选靶向中药活性成分。方法在基因表达数据库(GEO)中检索“postmenopausal osteoporosis”,下载基因数据集GSE230665,通过R软件中的“limma”数据包获取差异表达基因,使用David工具对差异基因进行基因本体(GO)功能富集分析并筛选出免疫反应相关的关键基因,然后对关键基因进行GO功能富集分析和京都基因与基因组百科全书(KEGG)通路富集分析。采用STRING平台和Cystoscope软件建立蛋白相互作用(PPI)网络,用MCODE和CytoNCA插件识别重要基因簇模块和核心基因。在CTD数据库搜索“postmenopausal osteoporosis”对核心基因进一步筛选并搜索靶向核心基因的中药活性成分,并在PubChem数据库中搜索中药活性成分的3D结构,Autodock4软件进行分子对接,以及探索核心基因与绝经后骨质疏松症的相互作用。结果在绝经后骨质疏松症中筛选出43个关键基因,GO富集分析显示主要参与涉及正向调节炎症反应、白细胞介素(IL)-12的产生、肿瘤坏死因子的产生、细胞迁移和趋化作用等;KEGG通路主要涉及趋化因子信号通路、磷脂酰肌醇3-激酶/蛋白激酶B(PI3K/Akt)信号通路、肿瘤坏死因子(TNF)信号通路、核因子-κB(NF-κB)信号通路等。鉴定出9个核心基因依次为IL-10、B2M、IL-17A、CXCR4、TLR4、CCR5、NOTCH1、TLR2、SMAD3。通过验证,在绝经后骨质疏松症患者中核心基因的表达均上调。核心基因对应的中药活性成分为雌二醇、白藜芦醇、槲皮素、姜黄素、双酚A和木黄酮等,这些中药活性成分可能通过抑制免疫反应来修复绝经后骨质疏松症。结论利用生物信息学筛选出与免疫反应相关的核心基因(IL-10、B2M、IL-17A、CXCR4、TLR4、CCR5、NOTCH1、TLR2、SMAD3)以及其受靶向调控的主要中药活性成分(雌二醇、白藜芦醇、槲皮素、姜黄素、双酚
Objective To identify genes related to immune response in postmenopausal osteoporosis by bioinformatics,and to investigate the mechanism of their action and screen the active ingredients of targeted traditional Chinese medicines.Methods Search for“postmenopausal osteoporosis”in the gene expression database(GEO),download the gene dataset GSE230665,and obtain the differentially expressed genes through the“limma”packet in R software.David tool was used to perform GO functional enrichment analysis for differential genes and screen out key genes related to immune response,and then GO functional enrichment analysis and KEGG pathway enrichment analysis were performed for key genes.STRING platform and Cystoscope software were used to establish protein interaction(PPI)network,and MCODE and CytoNCA plug-ins were used to identify important gene cluster modules and core genes.Search for“postmenopausal osteoporosis”in CTD database to further screen core genes and search for TCM active ingredients targeting core genes,search for 3D structure of TCM active ingredients in PubChem database,and perform molecular docking with Autodock 4 software.And explore the interaction between core genes and postmenopausal osteoporosis.Results 43 Key genes were selected in postmenopausal osteoporosis,and GO enrichment analysis showed that they were mainly involved in the positive regulation of inflammatory response,the production of IL-12,tumor necrosis factor,cell migration and chemotaxis.KEGG pathway mainly involves chemokine signaling pathway,PI3K/Akt signaling pathway,TNF signaling pathway,NF-κB signaling pathway,etc.9 Core genes were identified as IL-10,B2M,IL-17A,CXCR4,TLR4,CCR5,NOTCH1,TLR2,and SMAD3.It was verified that the expression of core genes was up-regulated in postmenopausal osteoporosis patients.Estradiol,resveratrol,quercetin,curcumin,bisphenol A,and lignans showed high interaction indices with the core genes,and the active ingredients of these herbal medicines may repair postmenopausal osteoporosis by suppressing
作者
王刚
董舶昶
康伯源
徐西林
WANG Gang;DONG Bochang;KANG Boyuan;XU Xilin(Heilongjiang University of Traditional Chinese Medicine,Harbin 150006,China;The Third Hospital Affiliated to Heilongjiang University of Traditional Chinese Medicine,Harbin 150006,China)
出处
《现代药物与临床》
CAS
2024年第4期839-847,共9页
Drugs & Clinic
基金
国家中医药管理局青年岐黄学者支持项目(国中医药人教发[2020]7号)
黑龙江省重点研发计划(GZ20210136)
黑龙江省中医药科研项目(ZHY2023-099)。
