肝癌自噬相关LncRNA预后预测模型的构建

Construction of prognostic model of autophagy-related LncRNA in hepatocellular carcinoma

目的构建并验证自噬相关长链非编码RNA(long non-coding RNA,LncRNA)在肝癌患者中的预后相关预测模型。方法获取癌症基因组图谱(the Cancer Genome Atlas,TCGA)数据库中374例肝癌患者的转录组数据中的mRNA表达谱、LncRNA表达谱和临床特征。从mRNA表达谱中提取自噬相关基因(来自Human Autophagy Database)表达量,与LncRNA表达谱进行相关性分析筛选,得到与自噬相关基因高度相关的LncRNA。将上述自噬相关LncRNA在374例肝癌组织和50例癌旁组织中的表达量进行差异表达分析和单因素分析筛选,得到差异表达且与肝癌预后显著相关的自噬LncRNA,将其纳入Cox比例风险模型筛选和建立肝癌患者预后预测模型,根据预测模型计算风险指数(riskscore)并将患者分为高风险组和低风险组,进行Kaplan-Meier生存分析、Cox回归分析和受试者工作特征曲线(receiver operating characteristic curve,ROC)评价该模型的预后评估价值。基因集富集分析(gene set enrichment analysis,GSEA)得到高低风险患者基因富集的信号通路。结果筛选得到582个自噬LncRNA(r≥0.6,P<0.001),其中有23个差异表达并与肝癌预后显著相关的自噬LncRNA,构建了由MKLN1-AS、AC012360.3、AC145207.5、AL513320.1、AC099850.3和AL049840.2共6个LncRNA组成的预后预测模型。KM生存分析得到高风险组生存时间明显低于低风险组(中位生存时间为6.937、2.323年,P<0.001),Cox回归分析得到高风险组患者生存时间明显低于低风险组(HR=3.773,95%CI:2.252~6.322,P<0.001),风险值1、2、3、4、5、6年生存的ROC曲线下面积分别为0.760、0.729、0.731、0.722、0.696和0.685。GSEA分析得到高风险组基因主要富集在细胞周期、细胞自噬、肿瘤、泛素介导的蛋白水解作用、RNA降解等。结论由MKLN1-AS、AC012360.3、AC145207.5、AL513320.1、AC099850.3和AL049840.2共6个LncRNA组成的预后预测模型可用于肝癌患者预后预测,期待能够指导临床治疗。

Objective To construct and verify a model for predicting the prognosis of liver cancer patients with autophagy-related long non-coding RNA(LncRNA)expression.Methods LncRNA expression spectrum,mRNA expression spectrum and clinical characteristics of 374 patients with liver cancer were obtained from the Cancer Genome Atlas(TCGA)Database.The expression levels of autophagy-related genes(from the Human Autophagy Database)were extracted from the mRNA expression profile,and the LncRNA was screened to obtain the highly relevant autophagy-related genes by correlation analysis with the LncRNA expression profile.Differential expression analysis and single factor analysis were conducted between the expressions of the above established autophagy-related LncRNA in 374 cancer tissues and 50 normal tissues to screen autophagy LncRNAs which were differentially expressed and was associated with a significant liver cancer prognosis.The above screened LncRNA were included in the risk of Cox proportional model selection and the prognosis of patients with liver cancer predictionmodel was established.The risk index(risk score)was calculated according to the forecast model and patients could be divided into high-risk and low-risk groups.Kaplan-Meier survival analysis,Cox regression analysis and receiver operating characteristic curve(ROC)were conducted to evaluate the prognostic value of the model.Gene set enrichment analysis(GSEA)was carried out to analyze the signal pathway of gene enrichment in patients with a high or a low risk.Results We screened 582 autophagy LncRNAs(R≥0.6,P<0.001)to obtain 23 LncRNAs which were differentially expressed and associated with a significant liver cancer prognosis.A prognostic model consisting of 6 LncRNAs,namely,MKLN1-AS,AC012360.3,AC145207.5,AL513320.1,AC099850.3 and AL049840.2 were constructed.KM survival analysis showed that the survival time of the high-risk group was significantly lower than that of the low-risk group(median survival time:6.937 years and 2.323 years,P<0.001).Cox regression analysis showed that the survival time of patients in the high-risk group was significantly lower than that in the low-risk group(HR=3.773,95%CI:2.252-6.322,P<0.001);the area under the time dependent ROC curve for 1,2,3,4,5 and 6-year overall survival was 0.760,0.729,0.731,0.722,0.696 and 0.685.GSEA analysis showed that the genes in the high-risk group were mainly concentrated in cell cycle,autophagy,tumor,ubiquitin-mediated proteolysis,and RNA degradation.Conclusion The prognostic model composed of MKLN1-AS,AC012360.3,AC145207.5,AL513320.1,AC099850.3 and AL049840.2 can be used to predict the prognosis of liver cancer patients,which is expected to guide clinical treatment.