A novel molecular marker of breast cancer stem cells identified by cell-SELEX method. 
Breast cancer stem cells (CSCs) are thought to initiate mammary tumors and render them resistant to anti-cancer therapies.  However, there are currently no ideal biomarkers to identify this minority population in breast cancer.  To find out the oligonucleotides with high specificity and affinity for mammosphere cells using a high capacity ssDNA library.  We used the cell-SELEX (systematic evolution of ligands by exponential enrichment process) method.  MCF-7 cells were cultured in serum-free media to form mammosphere cells as enriched stem cells, and were used as the positive target cells.  The normal breast epithelial MCF-10A and MCF-7sal cells, which are MCF-7 cells treated with Salinomycin, were used as the negative target cells.  We collected the ssDNA pools that were bound to positive target cells, and could not bind negative target cells.  After 13 rounds of selection, we isolated the MS03 aptamer with high specificity and affinity for mammosphere cells.  When compared with CD44(+)/CD24(-/low) cells, MS03(+) cells did not show any significant difference in sphere formation ability in vitro.  In addition, 63.3% of MS03 aptamer-selected cells exhibited the CD44(+)/CD24(-/low) phenotype.  Because the MS03 aptamer is synthesized easily and non-immunogenic, it is much more flexible than CD44/CD24 as a breast CSC biomarker.  The MS03 aptamer may become a promising molecular probe during diagnostic and therapeutic applications in breast cancer.