基于生物信息学分析的结肠腺癌预后微小RNA的鉴定与预后预测模型构建
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1.中南大学湘雅医学院附属株洲医院 病理科,湖南 株洲 412007;2.中南大学基础医学院 病理学系,湖南 长沙 410013

作者简介:

向瑶,中南大学湘雅医学院附属株洲医院住院医师,主要从事消化系统肿瘤方面的研究。

基金项目:

湖南省株洲市科技局创新型城市建设专项社会化出资基金资助项目[株科办(2022)1号];湖南省株洲市科技指导性计划基金资助项目[株科发(2019)57号]。


Identification of prognostic microRNAs in colorectal adenocarcinoma and prognostic prediction model construction based on bioinformatics analysis
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1.Department of Pathology, Zhuzhou Hospital Affiliated to Xiangya Medical College of Central South University, Zhuzhou, Hunan 412007, China;2.Department of Pathology, School of Basic Medical Sciences, Central South University, Changsha 410013, China

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    摘要:

    背景与目的 结肠腺癌(COAD)是癌症相关死亡的主要原因之一,准确预测COAD患者预后,评估COAD生存风险因素尤为重要。微小RNA(miRNA)通过靶向下游mRNA广泛参与肿瘤生物学行为调控,已成为具有应用研究前景的标志物。本研究旨在通过生物信息学方法鉴定COAD预后miRNA并构建预后预测模型,为COAD预后判断和制订个体化治疗方案提供参考。方法 从TCGA数据库中下载COAD患者的临床信息以及miRNA-seq数据,获取差异的miRNA。利用单变量和多变量Cox比例风险回归模型获得关键预后miRNA,用多因素Cox回归模型构建风险评分计算公式。利用Kaplan-Meier方法分析高、低风险评分患者的生存状态;ROC曲线评估风险评分的敏感度及特异度,并且从样本中随机抽取50%的病例做内部验证。采用预后风险模型列线图模型确定COAD患者临床病理参数及风险评分。使用Targetscan及miRDB数据库对预后miRNA模型进行靶基因预测以及利用String数据库进行蛋白与蛋白互作网络分析。结果 差异表达分析获得320个miRNA,其中167个上调,153个下调。利用单变量和多变量Cox比例风险回归对差异的miRNA进行分析,发现miR-503-5p、miR-335-3p、miR-185-5p、miR-4436b-5p、miR-125b-2-3p为COAD患者关键预后miRNA。结合风险评分的生存分析结果显示,高风险评分患者预后明显差于低风险评分患者(P=0.005 6),在随机抽取的内部验证组中也得到验证(P=0.014)。1、3、5年风险评分模型ROC曲线下面积(AUC)分别为0.666、0.724、0.707,内部验证组分别为0.681、0.699、0.703。Cox回归分析显示,建立用于预测COAD患者预后预测列线图的一致系数为0.836。单因素和多因素Cox分析显示,在建模组及内部验证组中风险评分是COAD的独立预后因素(均P<0.01)。miRNA靶基因预测获得87个靶基因。蛋白与蛋白互作网络分析获得10个蛋白质互作的关键基因。结论 所建立COAD预后miRNA模型以及基于年龄、AJCC分期、T分期、放化疗以及风险评分等因素构建的列线图将较准确地预测COAD的风险,对鉴定高或低风险患者、精准预测预后及评估患者生存风险提供理论基础。

    Abstract:

    Background and Aims Colorectal adenocarcinoma (COAD) is one of the major causes of cancer-related mortality, and accurate prediction of prognosis and assessment of survival risk factors in COAD patients are particularly important. MicroRNAs (miRNAs) extensively participate in regulating tumor biology by targeting downstream mRNA and have become promising biomarkers for application research. This study aims to identify prognostic miRNAs for COAD through bioinformatics methods and to construct a prognostic prediction model, providing references for COAD prognosis determination and individualized treatment planning.Methods Clinical information and miRNA-seq data of COAD patients were downloaded from the TCGA database to obtain differentially expressed miRNAs. Key prognostic miRNAs were obtained through univariate and multivariate Cox proportional hazard regression models, and a risk score calculation formula was constructed using the multivariate Cox regression model. The Kaplan-Meier method was used to analyze the survival status of high- and low-risk patients, and the sensitivity and specificity of the risk score were evaluated using ROC curves. Internal validation was performed by randomly selecting 50% of cases from the sample. The prognostic risk nomogram model was used to determine the clinical and pathological parameters and risk scores of COAD patients using a column diagram model. The Targetscan and miRDB databases were used to predict target genes of the prognostic miRNA model, and the String database was used to analyze protein-protein interactions.Results Differential expression analysis identified 320 miRNAs, among which 167 were upregulated and 153 were downregulated. Univariate and multivariate Cox proportional hazards regression analysis of the differentially expressed miRNAs revealed miR-503-5p, miR-335-3p, miR-185-5p, miR-4436b-5p, and miR-125b-2-3p as key prognostic miRNAs for COAD patients. The survival analysis results, combined with risk score, showed that patients with high-risk scores had significantly worse prognosis than those with low-risk scores (P=0.005 6), which was also validated in a randomly selected internal validation group (P=0.014). The area under the ROC curve of the 1-, 3-, and 5-year risk scoring models were 0.666, 0.724, and 0.707, respectively, while the values for the internal validation group were 0.681, 0.699, and 0.703, respectively. Cox regression analysis showed that the consistency coefficient for the predictive nomogram of COAD was 0.836. Univariate and multivariate Cox analysis showed that the risk score was an independent prognostic factor for COAD in the modeling group and the internal validation group (both P<0.01). The miRNA target gene prediction revealed 87 target genes, while the protein-protein interaction network analysis identified 10 key genes involved in protein interactions.Conclusion The COAD prognostic miRNA model and the nomogram constructed based on factors such as age, AJCC stage, T stage, radiotherapy and chemotherapy, and risk score can accurately predict the risk of COAD, providing a theoretical basis for identifying high or low-risk patients, accurately predicting prognosis, and assessing patient survival risk.

    表 1 多因素Cox回归模型与COAD患者OS时间相关的miRNATable 1 Multivariate Cox regression model of miRNAs related to the OS time of COAD patients
    图1 差异表达的miRNAs A :热图(癌和癌旁组织中差异表达的miRNA);B:火山图(红点为上调的miRNAs;蓝点为下调的miRNAs;黑点为无差异miRNAs)Fig.1 Differentially expressed miRNAs A: Heat map (miRNAs differentially expressed in cancer and adjacent tissues); B: Volcano plot (red dots representing upregulated miRNAs; blue dots representing downregulated miRNAs; black dots representing miRNAs with no significant difference)
    图2 Lasso回归分析 A:Lasso筛选变量动态过程图;B:交叉验证过程参数λ的筛选过程Fig.2 Lasso regression analysis A: Dynamic process diagram of Lasso variable selection; B: Selection process of cross-validation process parameter λ
    图3 高风险评分与低风险评分COAD患者预后风险模型 A:高风险(红色)和低风险(蓝色)患者风险评分分布、生存状态(蓝色表示存活患者;红色代表死亡患者)及miRNA表达的热图(红色代表免疫基因高表达;黑色代表免疫基因低表达);B:高风险评分与低风险评分患者生存曲线(黄色代表高风险评分患者;蓝色代表低风险评分患者);C:miRNA预后模型时间依赖性ROC曲线显示患者1、3、5年OS时间的AUCFig.3 Prognostic risk model high-risk and low-risk score COAD patients A: Distribution of risk scores (red representing high-risk patients, blue representing low-risk patients), survival status (blue representing surviving patients, and red representing deceased patients), and heatmap of miRNA expression (red representing high expression of immune genes, black represents low expression of immune genes); B: Survival curves for high-risk and low-risk score patients (yellow representing high-risk score patients, blue representing low-risk score patients); C: Time-dependent ROC curve of the miRNA prognostic model showing the AUC values for 1-, 3-, and 5-year OS
    图4 内部验证高风险评分与低风险评分COAD患者预后风险模型 A:高风险(红色)和低风险(蓝色)患者风险评分分布、生存状态(蓝色表示存活患者;红色代表死亡患者)及miRNA表达的热图(红色代表免疫基因高表达;黑色代表免疫基因低表达);B:高风险评分与低风险评分患者生存曲线(黄色代表高风险评分患者;蓝色代表低风险评分患者);C:miRNA预后模型时间依赖性ROC曲线显示患者1、3、5年OS时间的AUCFig.4 Internal validation of the prognostic risk model for high-risk and low-risk COAD patients A: Distribution of risk scores (red representing high-risk patients, blue representing low-risk patients), survival status (blue representing surviving patients, and red representing deceased patients), and heatmap of miRNA expression (red representing high expression of immune genes, black represents low expression of immune genes); B: Survival curves for high-risk and low-risk score patients (yellow representing high-risk score patients, blue representing low-risk score patients); C: Time-dependent ROC curve of the miRNA prognostic model showing the AUC values for 1-, 3-, and 5-year OS
    图5 COAD患者OS时间列线图Fig.5 Nomogram of OS time in COAD patients
    图6 miRNA模型的PPI网络图Fig.6 PPI network diagram of miRNAs model
    表 2 COAD患者OS的单因素和多因素Cox回归分析Table 2 Univariate and multivariate Cox regression analysis of OS in COAD patients
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向瑶,王俊普,周伟弘,任建强,幸雯雯,陈栋良,黄美园.基于生物信息学分析的结肠腺癌预后微小RNA的鉴定与预后预测模型构建[J].中国普通外科杂志,2023,32(4):557-565.
DOI:10.7659/j. issn.1005-6947.2023.04.010

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  • 收稿日期:2021-09-29
  • 最后修改日期:2022-04-21
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  • 在线发布日期: 2023-04-28