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There is increasing evidence that recurrent metastatic breast cancer arises in part due to the presence of long-lived, slow-cycling, and drug-resistant stem cells. Adult stem cells, known as side population (SP) cells, whose phenotype has been demonstrated to be due to the expression of ABCG2, are known to be resistant to a number of structurally unrelated compounds. In the present study we have observed that while both oestrogen-responsive and non-oestrogen-responsive breast cancer cell lines contain SP, exhibit multidrug resistance and express elevated levels of ABCG2, the non-oestrogen-responsive more highly metastatic MDA-MB-231 SP cells exhibit higher levels of mitoxantrone resistance than the other cell populations examined. These SP cells would therefore have a higher survival capacity when exposed to many currently utilised therapeutic regimes. Importantly, we have shown there is a statistically significant relationship between the presence of these SP cells in fine needle aspirates associated with ER-negative palpable breast lesions, and that these cells are more frequently associated with triple-negative breast tumours. Novel treatments directed against SP cells should be sought to offer patients better treatment strategies in these triple-negative tumours that fail to respond to conventional targeted therapy. Further analysis of this small population of potentially important cells is warranted.