Molecular Biotechnology

, Volume 45, Issue 1, pp 39–48 | Cite as

Whole Genome Expression Profiling Reveals a Significant Role for the Cell Junction and Apoptosis Pathways in Breast Cancer Stem Cells



Side population (SP) cells in primary tumors and cell lines are a small cell population, but they are known to enrich cancer stem cells (CSCs). In this study, we isolated SP cells from the human breast cancer cell line MCF7 as a model for studying CSCs. Compared with non-SP cells, MCF7 SP cells had higher mammosphere-formation efficiency (MFE) in vitro and greater tumorigenicity in vivo, suggesting that MCF7 SP cells enrich CSCs. We first directly compared the gene expression profile of SP and non-SP cells from MCF7 cell line. Comparing the expression signature of SP to non-SP cells, we identified 753 differentially expressed genes (DEGs). Using Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, we identified multiple pathways that were aberrantly regulated in SP compared with non-SP cells. Several pathways, including cell junction and apoptosis, play important roles in breast CSC function. This study demonstrates that combining global gene expression analysis with detailed annotated pathway resources can enhance our understanding of the critical pathways that regulate breast CSCs.


Breast neoplasm Cancer stem cells Side population cells Microarray Gene regulatory networks 



The authors thank to ZhongXin Biotechnology (Shanghai, China) for the help of microarray analysis. This study was supported in part by the grant from National Natural Science Fund of China (30670798).


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© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  1. 1.Department of Radiotherapy, Xinhua HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
  2. 2.College of ChemistryNanjing UniversityNanjingChina
  3. 3.Department of Oncology, Renji HospitalShanghai Jiaotong University School of MedicineShanghaiChina

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