应用生物信息学确定结直肠癌辐射抗性细胞的差异表达基因

Identification of genes for radiation resistance in colorectal cancer cells using bioinformatics analysis

目的 基于生物信息学的方法，筛选结直肠癌辐射抗性细胞中的差异表达基因，从分子水平上初步探讨与结直肠癌抗辐射相关的潜在基因。方法 从基因芯片公共数据库（GEO）中下载耐辐射的结直肠癌细胞基因表达谱数据（GSE43206），并利用R语言中的limma包进行差异基因筛选。对差异基因中的编码基因分别进行基因本体论（GO）富集分析、京都基因和基因组百科全书（KEGG）通路分析以及蛋白相互作用（PPI）分析，进一步筛选出PPI网络中的关键基因。通过实时荧光定量PCR实验确定5 Gy γ射线照射后人结肠癌HCT116细胞中关键基因的mRNA相对表达水平。采用Student t-test检验进行统计学分析，P〈0.05表示差异有统计学意义。结果 共筛选出101个差异基因，包含67个上调基因，34个下调基因。GO富集分析发现这些差异基因在细胞迁移、DNA复制等生物学过程中富集。KEGG通路分析证实这些差异基因主要富集在乏氧诱导因子1信号通路。通过构建PPI网络，筛选出NDRG1、PAG1、LRP1、PIM1、LDLR和PLAUR共6个与结直肠癌抗辐射相关的潜在基因。实时荧光定量PCR实验结果显示，与照射前比较，照射后人结肠癌HCT116细胞中NDRG1、PAG1、LRP1、PIM1、LDLR和NDRG1、PAG1、LRP1、PIM1、LDLR关键基因的mRNA表达量显著上升，差异均有统计学意义（t=49.981，P〈0.01；t=26.420、28.698、21.358、23.545，均P〈0.05；t=50.601，P〈0.01）。结论 利用生物信息学能够快速地筛选出与结直肠癌抗辐射相关的潜在基因，且潜在基因在结直肠癌HCT116细胞中差异表达。

Objective To preliminarily explore potential genes related to radiation resistance in colorectal cancer at the molecular level, we employed bioinformatics to screen different expression genes for radiation resistance in colorectal cancer cells. Methods The comparison between the gene expression levels of radiation resistance colorectal cancer cell lines and parental cell lines was downloaded from the Gene Expression Omnibus（GEO） database. The differentially expressed genes（DEGs） were screened by using the R Programming Language and were analyzed through Gene Ontology（GO） functional enrichment analysis and kyoto encyclopedia of genes and genomes（KEGG） pathway analysis and by using protein-protein interaction（PPI） networks. The hub genes were obtained on the basis of a PPI network. The mRNA relative expression level of the hub genes was verified via quantitative real-time polymerase chain reaction in HCT116 after radiation. The statistical significance of the results was analyzed via student t-test. Results A total of 101 DEGs were found in GSE43206, including 67 upregulated genes and 34 downregulated genes. The GO enrichment analysis suggested that these DEGs are enriched in biological processes, including cell migration and DNA replication. KEGG pathway analysis indicated that these DEGs were mainly enriched in the hypoxia inducible factor-1 signaling pathway. Six radiation resistance genes with high connectivity were identified on the basis of the PPI networks, including NDRG1, PAG1, LRP1, PIM1, LDLR, and PLAUR. Quantitative real-time polymerase chain reation verified that the expression levels of hub genes were markedly up-regulated in HCT116 after radiation, including NDRG1、PAG1、LRP1、PIM1、LDLR and PLAUR （t=49.981, P〈0.01; t=26.420, 28.698, 21.358, 23.545, all P〈0.05; t=50.601, P〈0.01）. Conclusions The use of bioinformatics enabled effectively screening radiation resistance genes in colorectal cancer, which can be used for further researches. The molecular biology experiments confirmed the differential expression of potential genes after irradiation in colorectal cancer cell HCT116.