Abstract: 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 SUM149PT 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, cellular_component, 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. 

Key words: basal breast cancer, CSCs(Cancer stem cells), CD44+CD24-/low, RNA-Seq