基于多数据库分析转移性黑色素瘤和乳腺癌脑转移的关键调控基因及其生物学特征

Analysis of key regulatory genes and their biological features in metastatic melanoma and breast cancer brain metastasis:exploring new directions in tumor brain metastasis through multi-database approach

目的通过生物信息数据库的挖掘,探究转移性黑色素瘤和乳腺癌脑转移的关键调控基因、生物学特征和通路。方法使用基因表达综合(GEO)数据库中转移性黑色素瘤和乳腺癌脑转移的样本数据集GSE8401、GSE46517和GSE12237进行差异基因筛选,设定P<0.05及logFC>2具有统计学意义,找出差异基因(DEGs)。进一步对DEGs进行基因本体论(Gene Ontology)分析和DAVID数据库通路分析,使用String数据库制作DEGs的蛋白质相互作用(PPI)网络并利用Cytoscape可视化,使用分子复合物检测(MCODE)插件用于筛选Cytoscape中PPI网络的显著交互模块,使用cytoHubba插件对网络进一步分析,采用六种算法来选择枢纽基因,最后使用GeneMARIA数据库构建了枢纽基因和具有共同生物学功能的基因的共表达网络。结果最终得到158个DEGs(P<0.05,logFC>2),其中45个基因显著下调,113个显著上调。筛选所得的DEGs主要GO富集为:(1)生物过程(BP):DEGs主要富集在RNA剪接的调控,通过剪接体调控mRNA的剪接,DNA重组的正调控,双链断裂修复的正调控。(2)细胞成分(CC):DEGs主要集中在核小体,焦点黏附,细胞-基质结合点,核染色体,原始溶酶体,嗜酸性颗粒体。(3)分子功能(MF):DEGs主要集中在DNA转录因子结合和RNA聚合酶Ⅱ特异性DNA结合转录因子结合上。通过string数据库,获得初步的DEGs的PPI网络(度截止=2,节点分数截止=0.2,k核心=2,最大深度=100),得到158个蛋白质节点和196条连线。通过Cytoscape筛选获得显著的交互模块,模块1的MCODE得分为4.8,而其seed基因为UBE2V1。筛选出核心DEGs 5个,分别为UBE2N、UBE2V2、RBX1、UBE2B和RXRA。结论泛素化途径和核调控的细胞死亡和代谢在转移性黑色素瘤和乳腺癌脑转移中发挥重要作用。

Objective Through the mining of bioinformatics databases,this study aimed to explore the key regulatory genes,biological characteristics,and pathways involved in the brain metastasis of metastatic melanoma and breast cancer.Methods Differential gene screening was performed using sample datasets(GSE8401,GSE46517,and GSE12237)from the GEO database for metastatic melanoma and breast cancer brain metastasis.The identified differentially expressed genes(DEGs)were further analyzed using Gene Ontology and pathway analysis in the DAVID database.Protein-protein interaction(PPI)networks of the DEGs were constructed using the String database and visualized using Cytoscape.The significant interacting modules of the PPI network were selected using the molecular complex detection(MCODE)plugin.Network analysis was conducted using the cytoHubba plugin to identify hub genes based on six algorithms:MNC,MCC,EPC,Degree,Closeness,and Radiality.Finally,a co-expression network of hub genes and functionally related genes was constructed using the GeneMARIA database.Results A total of 158 DEGs were identified(P<0.05,logFC>2),including 45 significantly downregulated genes and 113 significantly upregulated genes.The enriched Gene Ontology categories of the selected DEGs were mainly associated with:(1)biological processes(BP):regulation of RNA splicing,mRNA splicing via spliceosome,positive regulation of DNA recombination,and positive regulation of double-strand break repair;(2)cellular components(CC):nucleolus,focal adhesion,cell-matrix junction,nuclear chromosome,primary lysosome,and eosinophilic granule;and(3)molecular functions(MF):DNA-binding transcription factor activity and RNA polymeraseⅡ-specific DNA-binding transcription factor activity.Using the String database,a preliminary PPI network of DEGs was obtained,consisting of 158 protein nodes and 196 edges(degree cutoff=2,node score cutoff=0.2,k-core=2,maximum depth=100).Significant interaction modules were identified through Cytoscape,with module 1 having an MCODE score of 4.8,and its seed gene being UBE2V1.Five core DEGs were selected:UBE2N,UBE2V2,RBX1,UBE2B,and RXRA.Conclusion The ubiquitination pathway and nuclear regulation of cell death and metabolism play important roles in the brain metastasis of metastatic melanoma and breast cancer.