1、83现代检验医学杂志第 38 卷第 1 期2023 年 1 月J Mod Lab Med,Vol.38,No.1,Jan.2023基于 TCGA 数据库构建三阴性乳腺癌预后相关的 ceRNA 调控网络及分析肖姗姗1,2,李越1,周艳阳1,何谦1(1.西安交通大学第二附属医院检验科,西安 710004;2.空军军医大学唐都医院儿科,西安 710038)摘要:目的通过分析癌症基因组图谱(the cancer genome atlas,TCGA)数据库构建三阴性乳腺癌(triple negative breast cancer,TNBC)预后相关的竞争性内源性核糖核酸(competitive end
2、ogenous RNA,ceRNA)调控网络。方法从 TCGA 数据库中下载 TNBC lncRNA 表达 RNAseq 数据,对 TNBC 患者的 mRNA,miRNA 和 lncRNA 进行差异表达分析,并进一步行生存分析,得到与乳腺癌有明显差异表达同时也对生存有相关性的 mRNA,miRNA 和 lncRNA。同时构建 lncRNA-miRNA-mRNA 相关 ceRNA 调控网,再对生存相关 lncRNA 所相关的 mRNA 进一步功能富集和注释,并构建蛋白质互作网络最终用关键基因通过人类蛋白质图谱(the human protein atlas,HPA)数据库进行验证。结果在 TCG
3、A 中共找到 TNBC 差异表达 mRNA 2 331 个、差异 miRNA 100 个和差异 lncRNA 1 269 个。ceRNA 调控网中的 mRNA 在细胞黏附、唾液分泌和血小板活化、用于 IgA 产生的肠道免疫网络、补体和凝血级联反应等信号通路中明显富集。生存分析中,1 个差异 mRNA(NMUR1),1 个差异表达 miRNA(hsa-miR-6832-3p),2 个差异表达的 lncRNA(AC104809,LINC01297)的表达量均与 TNBC 患者的预后相关,差异具有统计学意义(P 0.05)。最后利用 HPA数据库对 NMUR1 蛋白水平和生存分析验证,NMUR1 的
4、高表达患者的总生存期显著高于 NMUR1 低表达组,差异有统计学意义(P 0.05)。结论成功构建了促进 TNBC 发生发展的 lncRNA-miRNA-mRNA 调控网络,筛选得到生存相关的差异 mRNA,miRNA 和 lncRNA 为 TNBC 发病机制的研究和诊疗生物标志物的探索提供参考依据。关键词:三阴性乳腺癌;癌症基因组图谱;竞争性内源性 RNA 调控网络中图分类号:R737.9;R730.43文献标识码:A文章编号:1671-7414(2023)01-083-07doi:10.3969/j.issn.1671-7414.2023.01.016Construction and An
5、alysis of ceRNA Regulatory Network Related to Prognosis of Triple Negative Breast Cancer Based on TCGA DatabaseXIAO Shan-shan1,2,LI Yue1,ZHOU Yan-yang1,HE Qian1(1.Department of Clinical Laboratory,the Second Affiliated Hospital of Xian Jiaotong University,Xian 710004,China;2.Department of Pediatrics
6、,Tangdu Hospital of Air Force Military Medical University,Xian 710038,China)Abstract:ObjectiveBy analyzing the cancer genome atlas(TCGA)database,a competitive endogenous RNA(ceRNA)regulatory network related to the prognosis of triple negative breast cancer(TNBC)was constructed.MethodsDownload TNBC l
7、ncRNA expression RNAseq data from the TCGA database,analyzed the differential expression of mRNA,miRNA and lncRNA in TNBC patients,and further conduct survival analysis to obtain mRNA,miRNA and lncRNA that have significant differential expression with breast cancer and were also relevant to survival
8、.At the same time,the lncRNA-miRNA-mRNA related ceRNA regulatory network was constructed,and then the mRNA related to survival related lncRNA was further enriched and annotated,and the protein interaction network was constructed.Finally,the key genes were verified by the human protein atlas(HPA)data
9、base.Results2 331 differentially expressed mRNA,100 differentially expressed miRNA and 1 269 differentially expressed lncRNA were found in TCGA in triple negative breast cancer.The mRNA in the ceRNA regulatory network was significantly enriched in signal pathways such as cell adhesion,salivary netwo
10、rk for IgA production,complement and coagulation cascade immune,platelet activation,intestinal in survival analysis,the expression of 1 differential mRNA(NMUR1),1 differential expression miRNA(hsa-miR-6832-3p),and 2 differential expression lncRNAs(AC104809,LINC01297)were all related to the prognosis
11、 of TNBC patients,and the difference was statistically significant(P 0.05).Finally,the analysis of NMUR1 protein level and survival using HPA database verified that the overall survival of patients with high NMUR1 expression was significantly higher than that of patients with low NMUR1 expression,an
12、d the difference was statistically 作者简介:肖姗姗(1989-),女,硕士研究生,主管检验技师,主要从事临床检验、免疫学研究,E-mail:。通讯作者:何谦(1971-),女,博士,主任技师,主要从事生化和分子生物学研究,E-mail:。84现代检验医学杂志第 38 卷第 1 期2023 年 1 月J Mod Lab Med,Vol.38,No.1,Jan.2023significant(P 0.05).ConclusionThe lncRNA-miRNA-mRNA regulatory network promoting the occurrence an
13、d development of TNBC has been successfully constructed,and the survival related differential mRNA,miRNA and lncRNA have been screened,providing a reference for the study of the pathogenesis of triple negative breast cancer and the exploration of biomarkers for diagnosis and treatment.Keywords:tripl
14、e negative breast cancer(TNBC);the cancer genome atlas(TCGA);competitive endogenous RNA(ceRNA)network乳腺癌发病率位列女性恶性肿瘤第一位,并且呈持续上升状态,严重影响女性的生命健康质量1,具有缺乏雌激素受体(estrogen receptor,ER)和 孕 激 素 受 体(progesterone receptor,PR),并 且不存在人表皮生长因子受体 2(human epidermal growth factor receptor 2,HER2)扩 增2特 征 的 三阴性乳腺癌(triple
15、 negative breast cancer,TNBC),是一种特殊亚型的乳腺癌,其发病率占所有乳腺癌的 20%3。它具有较高转移率、较高的增殖活性、较强的侵袭性、局部复发率高及远期预后较差的 特点4。随着研究深入,长链非编码 RNA(long non-coding RNA,lncRNA)在表观遗传修饰及基因转录和翻译中的调控作用受到重视5。近些年越来越多的报道表明lncRNA 的表达异常与肿瘤密切相关6。SALMENA 等7在 2011 年首次提出竞争性内源性RNA(competitive endogenous RNA,ceRNA)假说,lncRNA 作为 ceRNA 网络中重要靶点,通过
16、“分子海绵”作用于 miRNA,进而在翻译水平调控下游基因的表达。有报道称 lncRNA 浆细胞瘤多样异位基因 1(PVT1)在乳腺癌组织中的相对表达量显著高于癌旁正常组织8,是癌症相关基因的结合区。CHI 等9的研究结果表明 SNHG5 的下调抑制乳腺癌增殖,并通过海绵样 miR-154-5p 导致细胞周期停滞在 G1 期。这不仅为 TNBC 深入研究提供了新的思路,同时也为寻找肿瘤潜在的生物标志物及靶向治疗提供了新的思路。本研究拟利用公共数据库癌症基因组图谱(the Cancer Genome Atlas,TCGA)探究三阴性乳腺癌发生发展预后相关的异常基因表达谱,寻找预后相关 lncRNA,构建 ceRNA 竞争性网络及基因互作网络,以期对 TNBC 的个体化治疗提供理论依据。1材料和方法1.1资料来源从肿瘤基因组图谱 TCGA(http:/cancergenome.nih.gov/)中获取原发性乳腺癌组织TCGA-BRCA,miRNA,lncRNA readscount 数据和临床数据(时间截止 2022 年1月)。获得1 222 个样本的转录组 counts 数据,其中正常癌