结直肠癌RNA结合蛋白相关长链非编码RNA预后模型的构建与应用
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四川省中医药管理局课题(2020JC0078,2020LC0145);川北医学院校级课题(CBY20-QA-Y13)


Construction and application of prognostic models for colorectal cancer based on RNA-binding proteins-related long non-coding RNAs
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    摘要:

    目的 构建RNA结合蛋白(RBP)相关长链非编码RNA(IncRNA)预后模型,为临床预测结直肠癌(CRC)患者的生存提供指导。方法 分析TCGA数据库中的398例结直肠癌组织标本及39例正常对照样本的数据,从EBICA网站(https://ebiac.uk/GOA/)获取RBP相关基因列表。应用R软件分析RBP相关基因的差异表达基因,GO富集分析对RBP相关基因的差异表达基因进行功能注释,采用相关性分析筛选与RBP基因相关的IncRNA。采用R软件caret程序包将筛选后的355例CRC样本按50%与50%的比例随机分为训练集及验证集。单因素Cox回归分析筛选与预后相关的RBP相关IncRNA,LASSO Cox回归分析方法用于确定最佳预后RBP相关IncRNA并构建预后模型。使用多因素Cox回归系数计算风险评分,分析低风险组和高风险组风险评分与CRC患者临床特征及总体生存时间的关系,并使用验证集进行验证。结合独立预后因素构建诺模图预测结直肠癌患者1、2、3年生存率,建议标准曲线进行验证。结果 RBP相关基因差异表达基因中,327个基因表达上调,166个基因表达下调。994个IncRNA被鉴定为RBP相关IncRNA(R2>0.4,P<0.001),其中29个IncRNA具有预后价值。3个RBP相关IncRNA(LINC02474,NKILA,ZEN1-AS1)与CRC患者的总体生存率显著相关,用于构建预后模型。高风险组和低风险组结直肠癌患者总体生存率存在明显差异(P<0.05),并且包含年龄、性别、分级、TNM分期和风险高低的诺模图可有效预测CRC患者的长期生存率。结论 LINC02474、NKILA、ZEN1-AS1这3个RBP相关IncRNA预后模型对CRC具有预后判断价值,在CRC的发病机制中可能发挥着重要作用。

    Abstract:

    Objective To construct a risk prediction models based on RNA-binding proteins(RBP)related long non-coding RNA (IncRNA),and provide guidance for clinical prediction of survival of patients with colorectal cancer(CRC).Methods Analysis of CRC data of 398 CRC tissue specimen and 39 normal control samples collected from the TCGA database was conducted, and the list of RBP-related genes were obtained from EBICA(https://ebiac.uk/GOA/). R software was applied to analyze the differentially expressed genes (DEGs) of RBP, Gene Ontology(GO)function analysis was carried out to perform functional annotation of RBP DEGs, and the IncRNA associated with RBP genes were screened by correlation analysis.355 CRC samples obtained by selection were randomly assigned to train dataset and validation dataset with a ration of 50%:50% using caret package in R. Univariate Coxregression analysis was adopted to screen prognostically significant RBPrelated IncRNA,LASSO Cox regression analysis was used to identify the optimal prognostic RBP-related IncRNA and construct the prognostic model. After the risk scores were calculated using Cox regression coefficient, the relationship between the risk score of low risk group and high risk group and clinicopathologic features as well as the overall survival (OS) was analyzed. Nomogram that combines the independent prognostic factors was constructed to predict CRC patients' 1year, 2years, and 3years OS probability and then was verified in the validation dataset.Results Among RBP DEGs, 327 genes were upregulated while 166 were downregulated. A total of 994 lncRNAs were identified as RBP-related lncRNAs (R2>0.4, P<0.001), of which 29 RBPrelated lncRNAs with prognostic value were obtained. Three out of those RBP-related lncRNAs (LINC02474,NKILA,ZEN1-AS1) were significantly associated with the CRC patients’ OS probability and used for the construction of prognostic model. Significant differences in OS probability were obtained between high-risk group and lowrisk group CRC patients. Additionally, a nomogram containing age,gender, stage,TNM system and risk could effectively predict longterm OS probability of CRC patients.Conclusion The 3 identified genes(LINC02474,NKILA,ZEN1-AS1)prognostic models has certain predictive value for the prognosis of CRC and play an essential role in the pathogenesis of CRC.

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  • 在线发布日期: 2022-01-12
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