Ⅳ期结直肠癌患者淋巴结转移相关基因的研究

Study on the genes related to lymph node metastasis in patients with stageⅣcolorectal cancer

目的通过生物信息学方法探索影响Ⅳ期结直肠癌(colorectal cancer,CRC)患者淋巴结转移相关的核心基因,为进一步对转移相关的潜在机制的探索提供线索。方法本研究通过对GEO数据库进行检索,选择GSE63596的表达谱芯片进行后续研究。采用Agilent微阵列技术对所有15例患者的mRNA谱进行分析。差异分析采用LIMMA包进行运算,统计学过滤条件为:|Log2FC|>2,P<0.05。采用加权基因共表达网络分析(weighted gene co-expression network analysis,WGCNA)方法筛选出与CRC淋巴结转移相关的靶基因并构建预测模型。软件包glmnet,整合生存时间、生存状态和基因表达数据,利用LASSO回归分析,以获得最优模型。结果通过对GSE63596的表达谱芯片差异分析,提示有501个基因在淋巴结阳性的肿瘤中表达上调,另外有102个基因表达下调。通过R语言软件中cutreeDynamic和moduleEigengenes函数绘制聚类图,去除相似模块的影响,共得到15个模块,结果发现淋巴结阳性与drakgrey模块显著相关(cor=0.64,P=0.01),构建PPI网络后刷选出8个Hub基因。利用LASSO回归分析,以获得最优模型。设置Lambda值为0.0407,构建的模型公式为Riskscore=(0.1454)*DGAT1+(-0.0684)*GDPD3+(0.1404)*PDZK1IP1+(-0.1724)*PLA2G10。结论筛选出与CRC转移相关的4个基因,可为CRC发生、转移和治疗的研究提供参考。

Objective To explore the core genes related to lymph node metastasis in patients with stageⅣcolorectal cancer(CRC)by bioinformatics methods,so as to provide clues for further exploration of potential mechanisms related to metastasis.Methods In this study,the chip of GSE63596 expression spectrum was selected for follow-up study by searching the database GEO.The mRNA spectra of all 15 patients were analyzed by the technique of Agilent microarray technique.LIMMA package was employed to operate for variance analysis.The conditions of statistical filter were as follows:|Log2FC|>2,P<0.05.Weighted gene co-expression network analysis(WGCNA)was used to screen out the target genes associated with CRC lymph node metastasis and construct prediction models.The software package glmnet was adopted to integrate the survival time,survival status and gene expression data.And LASSO regression analysis was used to obtain the optimal model.Results The variance analysis of the chip of GSE63596 expression spectrum showed that 501 genes were up-regulated in positive lymph node tumors,and 102 genes were down-regulated.By using the cutree Dynamic and module Eigengenes functions in R language software,the cluster graph was drawn,in which after removing the influence of similar modules,a total of 15 modules were obtained.The results showed that the positivity of lymph nodes was significantly correlated with the drakgrey module(cor=0.64,P=0.01).Eight Hub genes were selected after the construction of PPI network.LASSO regression analysis was used to obtain the optimal model.The Lambda value was set as 0.0407 and the model formula was Riskscore=(0.1454)*DGAT1+(-0.0684)*GDPD3+(0.1404)*PDZK1IP1+(-0.1724)*PLA2G10.Conclusion Four genes related to CRC metastasis are screened out.They can provide reference for the research on the occurrence,metastasis and treatment of CRC.