Molecular Diagnostics

BJC Open article

British Journal of Cancer (2010) 102, 206–212. doi:10.1038/sj.bjc.6605468
Published online 8 December 2009

Gene set enrichment analysis provides insight into novel signalling pathways in breast cancer stem cells

M Murohashi1,6, K Hinohara1,6, M Kuroda2, T Isagawa3, S Tsuji3, S Kobayashi4, K Umezawa5, A Tojo4, H Aburatani3 and N Gotoh1

  1. 1Division of Systems Biomedical Technology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
  2. 2Department of Pathology, Tokyo Medical University, Tokyo, Japan
  3. 3Genome Science Division, Research Center of Advanced Science and Technology, University of Tokyo, Tokyo, Japan
  4. 4Division of Molecular Therapy, Institute of Medical Science, University of Tokyo, Tokyo, Japan
  5. 5Department of Applied Chemistry, Faculty of Science and Technology, Keio University, Yokohama, Japan

Correspondence: Dr N Gotoh, Division of Systems Biomedical Technology, Institute of Medical Science, University of Tokyo, Tokyo, Japan; E-mail:

6These authors contributed equally to this work.

Received 10 August 2009; Revised 26 October 2009; Accepted 9 November 2009
Advance online publication 8 December 2009





Tumour-initiating cells (TICs) or cancer stem cells can exist as a small population in malignant tissues. The signalling pathways activated in TICs that contribute to tumourigenesis are not fully understood.



Several breast cancer cell lines were sorted with CD24 and CD44, known markers for enrichment of breast cancer TICs. Tumourigenesis was analysed using sorted cells and total RNA was subjected to gene expression profiling and gene set enrichment analysis (GSEA).



We showed that several breast cancer cell lines have a small population of CD24/low/CD44+ cells in which TICs may be enriched, and confirmed the properties of TICs in a xenograft model. GSEA revealed that CD24/low/CD44+ cell populations are enriched for genes involved in transforming growth factor-β, tumour necrosis factor, and interferon response pathways. Moreover, we found the presence of nuclear factor-κB (NF-κB) activity in CD24/low/CD44+ cells, which was previously unrecognised. In addition, NF-κB inhibitor dehydroxymethylepoxyquinomicin (DHMEQ) prevented tumourigenesis of CD24/low/CD44+ cells in vivo.



Our findings suggest that signalling pathways identified using GSEA help to identify molecular targets and biomarkers for TIC-like cells.


tumour-initiating cells; NF-κB; CD24; CD44; gene expression profiling; DHMEQ



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