依据铁死亡相关长链非编码RNA特征对结肠癌患者进行预后分析

Analysis of prognosis for colon cancer patients based on the characteristics of ferroptosis-related long non-coding RNA

目的探讨应用基于铁死亡相关长链非编码RNA(lncRNA)构建的预后模型预测结肠癌患者预后的价值。方法从FerrDb数据库下载铁死亡相关基因,从癌症基因组图谱(TCGA)数据库下载建库至2021年11月结肠癌患者RNA测序基因数据和临床数据。应用R3.6.3软件对从TCGA数据库获取的结肠癌基因表达数据与FerrDb数据库铁死亡相关基因进行分析,获取结肠癌与正常组织差异表达的铁死亡相关基因;应用R3.6.3软件计算结肠癌铁死亡相关基因和lncRNA之间表达的相关性,确定结肠癌铁死亡相关lncRNA。筛选出与生存相关的差异表达铁死亡相关lncRNA,将其纳入多因素Cox比例风险模型,构建结肠癌预后模型;根据lncRNA表达量,通过预后模型计算结肠癌患者预后的风险评分。根据中位风险评分,将从TCGA数据库收集的临床病例分为高风险组和低风险组,各223例,对两组进行Kaplan-Meier生存分析。应用受试者工作特征(ROC)曲线分析应用预后模型风险评分及临床特征预测所有患者生存的效果。应用GSEA 4.1.0软件对高风险组和低风险组lncRNA进行基因集富集分析(GSEA),采用R3.6.3软件的ggpubr程序包对高风险组和低风险组间差异表达lncRNA进行免疫细胞及免疫功能的单样本基因集富集分析(ssGSEA)。结果依据数据库获取的铁死亡相关基因和差异表达基因的交集获得了65个差异表达的铁死亡相关基因,分析最终纳入24个结肠癌预后相关lncRNA,基于这些lncRNA构建了预后模型。Kaplan-Meier生存分析显示低风险组的生存优于高风险组(P<0.001);ROC曲线分析显示,应用预后模型风险评分预测所有患者1、2、3年生存的曲线下面积(AUC)均>0.750,风险评分预测所有患者1年生存的AUC大于年龄、性别、美国综合癌症网络(NCCN)临床分期、T分期、N分期、M分期。GSEA结果显示,高风险组和低风险组差异表达lncRNA集中在肿瘤和免疫相关通路;ssGSEA结果显示,高风险组和低风险组间T细胞、巨噬细胞、肥大细胞、中性粒细胞、免疫刺激、人白细胞抗原(HLA)及Ⅰ型、Ⅱ型干扰素反应方面均存在差异(均P<0.05),其中免疫检查位点的CD200、TNFRSF14表达量差异明显(均P<0.01)。结论铁死亡相关lncRNA可能在结肠癌的肿瘤免疫中发挥重要作用,其可用于结肠癌患者的预后分析。

Objective To explore the value of prognostic model based on ferroptosis-related long non-coding RNA(lncRNA)in predicting the prognosis of patients with colon cancer.Methods Ferroptosis-related genes were downloaded from FerrDb database,and the RNA sequencing gene data and clinical data of colon cancer patients from the establishment of the database to November 2021 were downloaded from the Cancer Genome Atlas(TCGA)database.Through R3.6.3 software,the colon cancer gene expression data obtained from TCGA database and ferroptosis-related genes obtained from FerreDb database were analyzed to obtain differentially expressed ferroptosis-related genes in colon cancer and normal tissues.The expression correlation between ferroptosis-related genes and lncRNA in colon cancer was calculated by using R3.6.3 software to determine ferroptosis-related lncRNA in colon cancer.The survival-related differentially expressed ferroptosis-related lncRNA was screened and included in the multivariate Cox proportional hazards model to construct a colon cancer prognosis model;and the risk score of colon cancer patients was calculated by the prognostic model according to the lncRNA expression.According to the median risk score,the clinical cases collected from TCGA database were divided into high-risk group and low-risk group with 223 cases in each group.Kaplan-Meier survival analysis was performed for the two groups.The receiver operating characteristic(ROC)curve was used to analyze the effect of prognostic model risk score and clinical characteristics on predicting the survival of all patients.GSEA 4.1.0 software was used for gene set enrichment analysis(GSEA)of lncRNA in high-risk and low-risk groups,and ggpubr package of R3.6.3 software was used for single sample GSEA(ssGSEA)of immune cells and immune function of differentially expressed lncRNA between high-risk and low-risk groups.Results According to the intersection of ferroptosis-related genes and differentially expressed genes obtained from databases,65 differentially expressed ferroptosis-related genes were obtained,and 24 lncRNA related to the prognosis of colon cancer were analyzed,and then prognostic model was constructed based on lncRNA.Kaplan-Meier survival analysis showed that the survival of low-risk group was better than that of high-risk group(P<0.001);ROC curve analysis showed that the area under the curve(AUC)of 1-,2-,3-year survival predicted by the prognostic model risk score was more than 0.75,and the AUC of 1-year survival predicted by the risk score for all patients was greater than age,gender,the National Comprehensive Cancer Network(NCCN),T staging,N staging and M staging.GSEA showed that differentially expressed lncRNA in high-risk and low-risk groups concentrated in tumor and immune-related pathways;ssGSEA showed that there were differences in T cells,macrophages,mast cells,neutrophils,immune stimulation,human leukocyte antigen,typeⅠand typeⅡinterferon response between high-risk group and low-risk group(all P<0.05),and the expression levels of CD200 and TNFRSF14 at the immune checkpoint were significantly different(both P<0.01).Conclusions Ferroptosis-related lncRNA may play an important role in tumor immunity of colon cancer,and it can be used for the prognosis analysis of patients with colon cancer.