RNA-Seq探索基底型乳腺癌干细胞差异表达基因

Screening differentially expressed genes in basal breast cancer stem cells by RNA-Seq

基底型乳腺癌许多特性与肿瘤干细胞十分相似,为筛选出基底型乳腺癌的关键靶点,从乳腺癌干细胞入手,采用乳腺癌干细胞标志物CD44^+ CD24^(-/low)流式分选HCC1937和SUM149PT乳腺癌细胞系的干细胞及非干细胞,利用高通量转录组测序筛选干细胞和非干细胞差异表达的基因,并对其进行相关生物信息学分析,最后随机选取部分差异表达基因进行qRT-PCR验证。结果表明筛选出的关键差异表达基因共134个,其中39个基因在干细胞中上调,95个基因下调。从生物过程、细胞组分、分子功能3方面GO功能分类表明,差异基因富集最显著的条目分别是胞外基质组成、胞外区、过氧化物酶活性,KEGG富集发现差异表达基因最显著富集的通路是肿瘤相关通路,qRT-PCR结果表明差异表达基因在干细胞中的表达趋势与转录组测序结果一致。通过对肿瘤干细胞全转录组水平进行研究,筛选其关键差异表达基因,为揭示肿瘤干细胞的分子机制以及基底型乳腺癌的靶向治疗奠定了理论基础。

The key targets of basal tumors were identified from cancer stem cells,given their many shared features with this oncogenic cell nich. The stem cell marker CD44~＋ CD24^（-/low）was used to sort cancer stem cells and non-stem cells from HCC1937 and SUM149 PT cell lines by flow cytometry. RNA-Seq was performed to identify the differentially expressed genes among different cell subsets,then qRT-PCR was used to validate the results of RNA-Seq. The results showed that there were 134 key differentially expressed genes between cancer stem and non stem cells,including 39 up-regulated and 95 down-regulated ones. Gene Ontology analysis indicated that the most enriched biological process,cellularcomponent,molecular functions were extracellular matrix organization,extracellular region and peroxidase activity,respectively. Moreover,the pathway most enriched for differentially expressed genes was cancer＇,and qRT-PCR results were correlated with the RNA-Seq.