基于加权基因共表达网络分析方法筛选并鉴定结直肠癌的驱动基因

Screening and identification of driving genes for colorectal cancer based on weighted gene coexpression network analysis method

目的基于加权基因共表达网络分析(WGCNA)方法筛选并鉴定结直肠癌(CRC)的驱动基因,探讨核心驱动基因在CRC发生发展、诊断和治疗中的作用。方法通过NCBI基因表达综合数据库(GEO)收集CRC相关的数据,数据集为GSE21510,芯片平台为GPL570;使用GEO2R工具对差异基因进行分析,根据P值和基因表达fold-change对差异基因进行排序,选择前2000个样本进行进一步分析。使用WGCNA算法进行模块构建,分析模块与临床特征的相关性,鉴定出与临床表型高度相关的模块,提取与临床性状相关性最高的模块内基因,将基因导入Cytoscape,分析核心基因,选择核心基因CYTH1进一步研究。基于Oncomine数据库分析CYTH1在结直肠癌组织与对照结直肠组织中的差异表达。取对数生长期LOVO、SW620、HCT116、SW480、RKO、CaCo2和NCM460细胞,应用实时荧光定量-聚合酶链式反应(RT-qPCR)法检测CYTH1在各种细胞中的表达;取对数生长期HCT116和SW480细胞,转染CYTH1基因干扰片段,采用细胞计数试剂盒-8法检测细胞增殖情况,Transwell实验检测细胞迁移能力。结果WGCNA结果显示,turquoise模块与CRC临床转移特征有相关性。分析turquoise模块的权重基因,使用Cytoscape软件将turquoise模块的权重基因构建共表达网络图,筛选出核心基因CYTH1。基于Oncomine数据库检索结果,与正常结直肠组织相比,CRC组织中CYTH1 mRNA表达水平下调约75%。RT-qPCR检测结果显示,LOVO、SW620、HCT116、SW480、RKO和CaCo2细胞中CYTH1相对表达量显著低于NCM460(t=31.080、21.262、51.963、3.093、114.344、216.340,P<0.001)。干预1、2、3、4 d,si-NC-HCT116细胞与si-CYTH1-HCT116细胞增殖率比较差异无统计学意义(t=0.321、-0.474、-0.711、1.011,P>0.05),si-NC-SW480细胞与si-CYTH1-SW480细胞增殖率比较差异无统计学意义(t=0.148、-0.254、0.040、0.157,P>0.05)。培养24 h后,si-CYTH1-HCT116细胞迁移数显著高于si-NC-HCT116细胞(t=-17.318,P<0.001);si-CYTH1-SW480细胞迁移数显著高于si-NC-SW480细胞(t=-7.876,P<0.001)。结论CYTH1在CRC组织和细胞中表达下调,可抑制CRC细胞的迁移能力,在CRC中发挥抑癌作用,其有可能成为CRC有效的治疗靶点。

Objective To screen and identify the driving genes in colorectal cancer(CRC)based on weighted gene co-expression network analysis(WGCNA)method,and explore the effect of core driving genes in the occurrence,development,diagnosis and treatment of CRC.Methods The data of CRC were collected through the NCBI gene expression omnibu(GEO)database,the data set was GSE21510,and the chip platform was GPL570.The differential genes was analyzed by GEO2R tool.The differential genes were sequenced according to P value and gene expression fold-change,and the first 2000 samples were selected for further analysis.The modules was constructed by the WGCNA algorithm,the correlation between the modules and clinical characteristics was analyzed,and the modules highly correlated with clinical phenotypes was identified,the genes within the module that were most correlated with clinical traits was extracted,the genes was imported into Cytoscape,the core genes was analyzed,and the core gene CYTH1 was selected for further research.The differential expression of CYTH1 in CRC and control colorectal tissues was analyzed based on Oncomine database.The LOVO,SW620,HCT116,SW480,RKO,CaCo2 and NCM460 cells at logarithmic growth phase were collected,and the expression of CYTH1 in these cells was detected by real-time fluorescence quantification-polymerase chain reaction(RT-qPCR).The HCT116 and SW480 cells at logarithmic growth phase were transfected with the CYTH1 gene interference fragment,and the cell proliferation was detected by cell counting kit-8 assay,the migration of the cells were detected by Transwell assay.Results The results of WGCNA showed that the turquoise module was correlated with the characteristics of CRC clinical metastasis.The weight genes of the turquoise module were analyzed,the co-expression network diagram of the weight genes in the turquoise module was constructed by Cytoscape software,and the core gene CYTH1 was screened out.Based on the retrieval results from the Oncomine database,the expression level of CYTH1 mRNA in CRC tissues was down-regulated by about 75%compared with that in normal colorectal tissues.The results of RT-qPCR showed that the relative expression level of CYTH1 in LOVO,SW620,HCT116,SW480,RKO and CaCo2 cells was significantly lower than that in NCM460(t=31.080,21.262,51.963,3.093,114.344,216.340;P<0.001).At 1,2,3 and 4 days of intervention,there was no significant difference in the proliferation rate between si-NC-HCT116 cells and si-CYTH1-HCT116 cells(t=0.321,-0.474,-0.711,1.011;P>0.05);and there was no significant difference in the proliferation rate between si-NC-SW480 cells and si-CYTH1-SW480 cells(t=0.148,-0.254,0.040,0.157;P>0.05).At 24 hours of culture,the migration number of si-CYTH1-HCT116 cells was significantly higher than that of si-NC-HCT116 cells(t=-17.318,P<0.001);and the migration number of si-CYTH1-SW480 cells was significantly higher than that of si-NC-SW480 cells(t=-7.876,P<0.001).Conclusion CYTH1 is downregulated in CRC tissues and cells,which can inhibit the migration ability of CRC cells and play an inhibitory role in CRC,and it may become an effective therapeutic target for CRC.