摘要
目的:采用生物信息分析筛选三阴性乳腺癌脑转移相关差异性表达基因(differentially expressed genes,DEG),并探索影响预后的潜在作用机制.方法:在基因表达数据库(Gene Expression Omnibus,GEO)检索获得GSE76250(三阴性乳腺癌组织与正常乳腺组织)和GSE125989(三阴性乳腺癌脑转移病灶组织与三阴性乳腺癌原发灶组织)2个数据集,筛选DEG.采用GO(Gene Ontology)分析和KEGG(Kyoto Encyclopedia of Genes and Genomes)分析寻找潜在的三阴性乳腺癌脑转移相关基因.通过癌症基因组图谱(The Cancer Genome Atlas,TCGA)数据库中的临床组织样本,验证相关基因表达水平与乳腺癌预后间的关系,并使用KEGG的基因集进行基因富集分析,评估DEG可能参与的信号通路.结果:在GSE125989和GSE76250数据集中共筛选出52个DEG,蛋白质相互作用网络(protein-protein interaction,PPI)分析提示RAD51AP1为三阴性乳腺癌脑转移的重要相关基因.TCGA数据分析显示,相较于癌旁组织RAD51AP1在乳腺癌组织中高表达;不同分子分型中,基底样型中乳腺癌PAD51AP1高表达.以RAD51AP1在癌组织表达中位数[log2(TPM+1)=3.85],将乳腺癌患者分为高表达和低表达组,生存分析显示,高表达患者的中位生存期差于低表达者[3 873 d比3 945 d,P＜0.05,HR=1.40(1.01～1.94)].通过GO、KEGG、基因富集分析(gene set enrichment analysis,GSEA)发现,RAD51AP1在细胞周期、DNA复制、错配修复等信号通路中有富集明显.基于细胞周期和DNA损伤修复信号通路相关蛋白信息构建PPI,筛选与RAD51AP1直接相互作用的蛋白质,其中增殖细胞核抗原(proliferating cell nuclear antigen,PCNA)与RAD51AP1的相关性较强(R=0.715,P＜0.001).结论:RAD51AP1在三阴性乳腺癌及其脑转移组织中高表达,可能作为潜在的诊断三阴性乳腺癌及预后不良的生物标志物,且其异常表达介导乳腺癌脑转移进程可能与PCNA相关.
Abstract
Objective To screen differentially expressed genes(DEG)related to brain metastasis in triple negative breast cancer(TNBC)using bioinformatics analysis,and to explore the potential mechanism affecting the prognosis of TNBC patients.Methods Datasets including GSE76250(TNBC tissues and normal breast tissues)and GSE125989(TNBC brain metastases tissue and TNBC primary lesion tissue)were retrieved from Gene Expression Omnibus(GEO)database,and DEG was screened using Gene Ontology(GO)analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG)analy-sis to identify potential related genes contributing to brain metastasis in TNBC.The association between gene expression levels and breast cancer prognosis was verified by clinical tissue samples from The Cancer Genome Atlas(TCGA)database,and gene enrichment analysis was performed using the gene set of KEGG to assess the signaling pathways that involved in genes related to brain metastasis.Results A total of 52 DEGs were screened in GSE125989 and GSE76250 datasets.Pro-tein-protein interaction network(PPI)suggested that RAD51AP1 was an important gene related to brain metastasis in TNBC.Analysis of TCGA data showed that RAD51AP1 was significantly overexpressed in breast cancer tissues vs paracan-cerous tissues,and for different molecular subtypes of breast cancer,basal-like breast cancer had a higher level of RAD51AP1 than that in paracancerous tissues.Patients with breast cancer were divided into high expression and low ex-pression of RAD51AP1 group according to the median expression level of RAD51AP1 in cancer tissues[log2(TPM+1)=3.85].Survival analysis showed that the median survival of patients with high expression was lower than that of patients with low expression[median OS 3 873 days vs 3 945 days,P＜0.05,HR=1.40(1.01-1.94)].GO,KEGG and gene set enrichment analysis(GSEA)showed that signaling pathways,such as cell cycle,DNA replication and mismatch repair,were signifi-cantly enriched in RAD51AP1 highly expressed phenotypes.PPI was constructed based on cell cycle and DNA damage re-pair signaling pathway related protein information,and proteins that directly interacted with RAD51AP1 were screened.It re-vealed proliferating cell nuclear antigen(PCNA)was strongly correlated with RAD51AP1.Conclusions RAD51AP1 is highly expressed in TNBC and TNBC brain metastasis tissues,which may serve as a potential biomarker for diagnosis of TNBC and prediction of poor prognosis,and mechanism on RAD51AP1 mediating brain metastasis may be related to PCNA.
基金项目
上海交通大学医学转化交叉基金(ZH2018QNA54)
上海市科学技术委员会"科技创新行动计划"(22Y31900103)
国家科技期刊平台
NSTL
万方数据