Identifying Gene Signatures Associated with Cancer Stem Cells and Drug Resistance from Triple Negative Breast Cancer Cells after Gene Targeting Treatment

Over 90% of breast cancer death is due to metastatic disease; however, the metastatic behavior of aggressive breast cancer is still not well understood. Accumulating evidence support the idea that initiation, maintenance and metastasis of tumors are through cancer stem cells (or tumor initiating cells). In this study, we focused on the representative MDA-MB-231 cells of the highly aggressive triple negative breast cancer subtype. We obtained and re-analyzed three previously published datasets on MDA-MB-231 cells after treatment targeting the expression ofGATA3, Pin1, or LSD1. Two distinct computational algorithms (dChip and GEO2R) were employed to cross-compare the resulting gene expression profiles. We identified a common gene signature consists of eight genes among the three datasets. Three of the eight genes, i.e., ABCC3, AGR2, and PTGES, were highly correlated with the properties of breast cancer stem cells and drug resistance. Thus, they are predicted as potential genemarkers of breast cancer stem cells and may serve as novel therapeutic targets to combat poor prognostic breast cancers.