肌层浸润性膀胱癌亚型的生物信息学分析

目的通过生物信息学分析研究两种膀胱癌亚型(基底样膀胱癌和管腔型膀胱癌)之间不同的分子调控机制和分子特性,为更准确地区分膀胱癌亚型和探索潜在的治疗靶点提供帮助。方法利用稳健的多芯片平均算法将由22个基底样膀胱癌和132管腔型膀胱癌样本组成的数据集进行标准化,并选择其中前1000个具有最高标准差的基因进行两种亚型的差异表达基因分析。将得到的差异表达基因进行GO功能注释和KEGG通路富集分析。此外,选择前100个差异表达基因构建蛋白质互作网络。结果得到基底样和管腔型膀胱癌差异表达基因共742,其中基底样亚型上调的基因405个,下调的基因337个。GO富集分析显示差异表达基因显著富集在细胞外区基质、趋化性、炎症等功能上,KEGG通路富集显示差异表达基因显著富集在细胞外基质受体相互作用的通路上。构建的蛋白质互作网络显示重要的hub蛋白质为LNX1、MSN和PPARG。结论本研究得到的基底样和管腔型膀胱癌亚型分子机制的区别主要体现在细胞外区域的分子作用机制、细胞趋化性和炎症反应等,基因LNX1、MSN和PPARG为区别两种膀胱癌亚型的特征基因。

Bioinformatics analysis of the muscle-invasive bladder cancer subtypes

Objective In order to improve the accuracy in distinguishing subtypes of bladder cancer and to explore its potential therapeutic targets,we identify differences between two kinds of bladder cancer subtypes ( basal-like and luminal ) in molecular mechanism and molecular characteristics based on the bioinformatics analysis. Methods In this study,the RMA ( robust multichip averaging) was applied to normalize the mRNA profile which included 22 samples from basal-like subtype and 132 from luminal subtype,and the differential expression analysis of genes with top 1000 highest standard deviation was performed. Then,the Gene Ontology and KEGG pathway enrichment analysis of differentially expressed genes was performed. In addition, the protein-protein interactions networks analysis for the top 100 most significant differentially expressed genes was performed. Results A total of 742 differentially expressed genes distinguishing basal-like and luminal subtypes were found,of which 405 were up-regulated and 337 genes were down-regulated in basal-like subtype. GO enrichment analysis showed that differentially expressed genes were significantly enriched in the extracellular matrix, chemotaxis and inflammatory response. KEGG pathway enrichment analysis showed that the differentially expressed genes were significantly enriched in the pathway of extracellular matrix receptor interaction. The hub proteins we founded in protein-protein interactionnetworks were LNX1, MSN and PPARG. Conclusions In this study, the mainly difference of molecular mechanism between basal-like and luminal subtypes are alteration in extracellular matrix region,cell chemotaxis and inflammatory response. Genes such as LNX1,MSN and PPARG were forecast to play important roles in the classification of bladder carcinoma subtypes.