Fig. 1.

Genetic selection and chemotherapy both enrich CSL subclones. (A) The proportion of each subclone with CSL vs. non-CSL populations in four patients. Cells were sorted via FACS using ALDEFLUOR and CD44 staining and DNA was isolated from each population, followed by low-coverage WGS to infer CNV and determine levels of subclonal CNVs. Heat maps for FACS mean values of ALDH, CD44 and CSL cells/Live upon chemotherapy treatment in cultured patient cells (B) and breast cancer cell lines (C) 3D organoids of patient cells and breast cancer cell lines were incubated with doxorubicin (0.1 µM), carboplatin (0.1 mM) and paclitaxel (1 µM) for 72 h, followed by ALDEFLUOR/CD44/DAPI staining and FACS to identify the FACS mean values of ALDH and CD44 in live populations and CSL cells/Live. The vehicle controls (DMSO treatment) were set as fold one. All the chemotherapy treatments were expressed as the fold change relative to the control. The mean values of triplicate tests were shown in the heat maps with color indicated as the legends for each treatment. Significance is marked with * for P<0.05, ** for P<0.01, *** for P<0.001.