We identified clear transcriptional signatures of oncogenes associated with breast cancer progression such as the time-dependent increase in ALDOA, a gene that increases in vitro spheroid formation and increases abundance of cancer stem cells (Fig. 3D; Fig. S3D), and LAMB3, which mediates invasive and proliferative behaviours by the PI3K–AKT signalling pathway (Zhang et al., 2019), as well as the decrease in genes like MUC1, conversely, upon HER2 overexpression, the downregulation of which is linked to stem-like phenotype (Stingl, 2009). This evidence concerns the gene ERBB2 and breast cancer.