The CD44(hi) compartment in human breast cancer is enriched in tumor-initiating 
cells; however, the functional heterogeneity within this subpopulation remains 
poorly defined. We used a triple-negative breast cancer cell line with a known 
bilineage phenotype to isolate and clone CD44(hi) single cells that exhibited 
mesenchymal/basal B and luminal/basal A features, respectively. Herein, we 
demonstrate in this and other triple-negative breast cancer cell lines that, 
rather than CD44(hi)/CD24(-) mesenchymal-like basal B cells, the 
CD44(hi)/CD24(lo) epithelioid basal A cells retained classic cancer stem cell 
features, such as tumor-initiating capacity in vivo, mammosphere formation and 
resistance to standard chemotherapy. These results complement previous findings 
using oncogene-transformed normal mammary cells showing that only cell clones 
with a mesenchymal phenotype exhibit cancer stem cell features. Further, we 
performed comparative quantitative proteomic and gene array analyses of these 
cells and identified potential novel markers of breast cancer cells with 
tumor-initiating features, such as lipolysis-stimulated lipoprotein receptor 
(LSR), RAB25, S100A14 and mucin 1 (MUC1), as well as a novel 31-gene signature 
capable of predicting distant metastasis in cohorts of estrogen 
receptor-negative human breast cancers. These findings strongly favor functional 
heterogeneity in the breast cancer cell compartment and hold promise for further 
refinements of prognostic marker profiling. Our work confirms that, in addition 
to cancer stem cells with mesenchymal-like morphology, those tumor-initiating 
cells with epithelial-like morphology should also be the focus of drug 
development.