基于生物信息学构建膀胱尿路上皮癌的ceRNA网络以及关键mRNA与免疫功能分析
Construction of ceRNA Network and Analysis of Key mRNA and Immune Function for Bladder Urothelial Carcinoma Based on Bioinformatics
邵波 1汪进 2万水 2吴开秀 3田申 2杜沂宸 4陈丹霞 4马园园5
作者信息
- 1. 安徽中医药大学附属芜湖市中医医院专业学位硕士研究生培养基地,安徽芜湖 241003
- 2. 安徽中医药高等专科学校附属医院/芜湖市中医医院泌尿外科,安徽芜湖 241001
- 3. 昆明医科大学海源学院,昆明 650106
- 4. 安徽中医药高等专科学校附属医院/芜湖市中医医院皮肤科,安徽芜湖 241001
- 5. 安徽中医药高等专科学校附属医院/芜湖市中医医院肛肠科,安徽芜湖 241001
- 折叠
摘要
目的 构建膀胱尿路上皮癌(bladder urothelial carcinoma,BLCA)具有预后价值的内源竞争性核糖核酸(competing endogenous RNA,ceRNA)调控网络,分析关键信使RNA(messenger RNA,mRNA)与免疫功能的关系.方法 UCSC Xena数据库下载 404 例BLCA患者和 28 例正常人的mRNA表达数据,通过差异分析筛选关键mRNA.ENCORI数据库中查找与关键mRNA结合的微小核糖核酸(micro RNA,miRNA)以及与miRNA结合的长链非编码核糖核酸(long non-coding RNA,LncRNA).TCGA数据库下载miRNA和LncRNA的表达数据,对关键mRNA与所有miRNA以及miRNA与所有LncRNA进行共表达分析,筛选出关键的miRNA和LncRNA.根据关键mRNA,miRNA和LncRNA在肿瘤患者和正常人之间表达量的差异进行生存分析,最后构建了ceRNA调控网络.借助TIMER 2.0 数据库,分析关键mRNA与免疫细胞、免疫检查点(CD274,PDCD1,CTLA4)以及免疫细胞标记基因(immunomarker genes,IG)的相关性.结果 筛选出关键mRNA*共 22 个,其中差异显著性最高的是脯氨酸 3-羟化酶 4(proline 3-hydroxylase 4,P3H4).在BLCA中,P3H4 表达高,在高表达组患者的生存时间较短.以关键mRNA为中心环节,共筛选出 33 个miRNA和 14 个LncRNA.经过共表达分析和生存分析后,筛选出具有预后价值的关键miRNA和关键LncRNA分别为hsa-miR-151a-3p和MIR100HG.上述分析结果差异具有统计学意义(均P＜0.05).综合以上结果,构建了包含 1 个mRNA,1 个miRNA和 1 个LncRNA的ceRNA调控网络.免疫分析首次在BLCA肿瘤微环境中发现了与P3H4表达量呈显著正相关的双阳性T细胞.此外还有3种免疫细胞(肿瘤相关性中性粒细胞、肿瘤相关巨噬细胞、树突状细胞)、3 个免疫检查点(CD274,PDCD1,CTLA4)以及 15 个IG与P3H4 相关度显著,这些差异具有统计学意义(均P＜0.01).结论 该研究有助于揭示BLCA的进展机制,构建的ceRNA网络及免疫分析,可为BLCA患者的诊断、治疗、预测提供新的生物学靶点和方向.
Abstract
Objective To construct a regulatory network of competing endogenous RNA(ceRNA)with prognostic value for bladder urothelial carcinoma(BLCA),and analyze the relationship between key messenger RNA(mRNA)and immune function.Methods The UCSC Xena database was used to download mRNA expression data from 404 BLCA patients and 28 normal individuals and key mRNAs were screened by differential analysis.ENCORI database was utilized to search microRNAs(miRNAs)that bind to key mRNAs and all long non-coding RNAs(LncRNAs)that bind to miRNAs.The expression data of miRNA and LncRNA were downloaded from TCGA database,co-expression analysis was performed to identify key mRNA with all miRNAs and miRNA with all LncRNAs,and thus key miRNAs and LncRNAs were screened out.Survival analysis was conducted based on the differences in expression levels of these key mRNAs,miRNAs,and LncRNAs between tumor patients and normal individuals,and finally a ceRNA regulatory network was constructed.The correlation between key mRNAs and immune cells,immune checkpoints(CD274,PDCD1 and CTLA4),and immune cell marker genes(IG)was analyzed using the TIMER 2.0 database.Results A total of 22 key mRNAs were screened,with the most significant difference being proline 3-hydroxylase 4(P3H4).The expression of P3H4 in patients with BLCA was high,and survival time was shorter in patients with high expression.A sum of 33 miRNAs and 14 LncRNAs were screened using the key mRNAs as the central link.Through co-expression analysis and survival analysis,hsa-miR-151a-3p and MIR100 HG were identified as the key miRNA and key LncRNA with prognostic value.The differences in the above analysis results were statistically significant(all P＜0.05).Based on these findings,a ceRNA regulatory network consisting of 1 mRNA,1 miRNA,and 1 LncRNA was constructed.Immunoassay firstly revealed a significant positive correlation between double positive T cells and P3H4 expression in the tumor microenvironment of BLCA.Moreover,there were 3 types of immune cells(tumor-associated neutrophils,and tumor-associated macrophages,dendritic cells),3 immune checkpoints(CD274,PDCD1,CTLA4),and 15 IGs with significant correlation with P3H4.These differences were statistically significant(all P＜0.01).Conclusion This study could help to reveal the progression mechanism of BLCA.The constructed ceRNA network and immune analysis can offer new insights into potential biological targets and immunotherapy directions for the diagnosis,treatment,and prediction of BLCA patients.
关键词
膀胱尿路上皮癌/信使核糖核酸/内源竞争性RNA/免疫功能Key words
bladder urothelial carcinoma/messenger RNA/competing endogenous RNA/immune function引用本文复制引用
基金项目
安徽省高等学校科学研究项目(2022AH052642)
芜湖市科技成果转化项目(2021cg07)
芜湖市科技成果转化项目(2022cg37)
出版年
2024
国家科技期刊平台
NSTL
维普
万方数据