增生性瘢痕差异表达基因及小分子药物预测的生物信息学分析与验证  

Bioinformatics analysis and validation of differentially expressed genes and small molecule drug prediction in proliferative scar

作　　者：左俊 马少林[1] Zuo Jun;Ma Shaolin(Department of Plastic and Aesthetic Surgery,The First Affiliated Hospital of Xinjiang Medical University,Urumqi 830000,Xinjiang Uygur Autonomous Region,China)

机构地区：[1]新疆医科大学第一附属医院整形科,新疆维吾尔自治区乌鲁木齐市830000

出　　处：《中国组织工程研究》2024年第14期2166-2172,共7页Chinese Journal of Tissue Engineering Research

基　　金：国家自然科学基金地区科学基金项目(81760345),项目负责人:马少林;湖南省自然科学基金青年基金项目(2021JJ40487),项目负责人:左俊。

摘　　要：背景:增生性瘢痕是以成纤维细胞过度增殖、表皮增厚和角质层功能不良为特征的皮肤纤维化疾病,目前其具体发病机制仍不清楚。目的:基于生物信息学筛选增生性瘢痕相关数据集的核心(Hub)基因及重要信号通路,再用细胞实验加以验证,预测对其可能有治疗作用的小分子药物。方法:从基因表达综合数据库搜索增生性瘢痕相关的数据集,通过R软件筛选差异表达基因,对差异表达基因进行基因本体论和京都基因与基因组百科全书(Kyoto Encyclopedia of Genes and Gnomes,KEGG)富集分析,使用String在线平台构建差异表达基因的蛋白质相互作用网络,然后分别利用Cytoscape软件中的Cytohubba和MCODE插件筛选出蛋白质相互作用网络中的关键基因和核心模块,进一步将上述关键基因和构成核心模块的基因求交集得到Hub基因,通过荧光定量PCR验证Hub基因mRNA在人增生性瘢痕与正常皮肤表皮干细胞中的表达差异,并利用人类蛋白图谱中组织学数据验证Hub基因编码蛋白在2种组织中表达量和分布的差异,最后用connectivity map数据库预测针对增生性瘢痕的潜在作用药物。结果与结论:①筛选出的差异表达基因中上调基因102个、下调基因702个,基因本体论和KEGG分析结果显示,富集的信号通路及生物学过程主要涉及紧密连接、花生四烯酸代谢、细胞外基质受体交互、表皮发育和角质化等;②取交集得到8个Hub基因与调控胆固醇代谢的甲羟戊酸途径密切相关,分别是HMGCS1、DHCR7、MSMO1、FDPS、MVK、HMGCR、MVD和ACAT2;③荧光定量PCR结果显示,相比正常皮肤组,增生性瘢痕组HMGCS1、DHCR7、MSMO1、FDPS、HMGCR、MVD和ACAT2 mRNA的表达均显著下降(P<0.05),而MVK mRNA的表达无明显变化(P>0.05);④除MVK外,其余Hub基因编码蛋白在正常皮肤组织中表达水平均高于增生性瘢痕组织(P<0.05);⑤评分排列前10的候选药物包括蛋白激酶A抑制剂(H-89)�BACKGROUND:Hypertrophic scar is a skin fibrosis disease characterized by excessive proliferation of fibroblasts,epidermal thickening,and stratum corneum dysfunction.At present,the pathogenesis of Hypertrophic scar is still unclear.OBJECTIVE:To screen the core(Hub)genes and important signaling pathways in hypertrophic scar-related datasets based on bioinformatics,and then verify them by cell experiments to predict small molecule drugs that may have therapeutic effects on hypertrophic scar.METHODS:Datasets related to hypertrophic scar were searched from Gene Expression Omnibus(GEO)database,and differentially expressed genes were identified by R software analysis.Gene ontology and KEGG enrichment analyses were performed for differentially expressed genes.Protein-protein interaction network of differentially expressed genes was constructed using String online platform.Then,the key genes and core modules in the protein-protein interaction network were screened by Cytohubba and MCODE plugin-in Cytoscape software respectively,and the Hub genes were obtained by the intersection of the above key genes and the genes that formed the core module.Real-time fluorescent quantitative PCR was used to verify the difference in Hub gene mRNA expression between human hypertrophic scar and normal skin epidermal stem cells.The histological data from the Human Protein Atlas were used to verify the differences in the expression and distribution of Hub gene-encoded proteins in the two kinds of human tissues.Finally,the potential drugs for hypertrophic scar were predicted by the connectivity map database.RESULTS AND CONCLUSION:Among the identified differentially expressed genes,102 genes were up-regulated and 702 genes were down-regulated.Gene ontology and KEGG analysis showed that the enriched signaling pathways and biological processes were mainly involved in tight junction,arachidonic acid metabolism,extracellular matrix receptor interaction,epidermal development and keratinization.Eight Hub genes were found to be closely related to the

关 键 词：增生性瘢痕 生物信息学 成纤维细胞 表皮干细胞 角质化 脂质代谢 甲羟戊酸代谢途径 药物预测 

分 类 号：R459.9[医药卫生—治疗学] R318[医药卫生—临床医学] R619.6