Fig. 1

Serial gene expression analysis in locally advanced breast cancer patients undergoing neoadjuvant chemotherapy (NAC). a Study schema. Gene expression analysis was performed on breast cancer tumors collected before treatment (T1), 24–96 hours after initiation of anthracycline-based NAC (T2) and at the time of surgery (TS). b Heat map showing results of supervised clustering analysis of expression profiles of tumors before treatment (T1) and 24–96 hours after initiation of NAC (T2). Rows indicate expression levels for each gene, and columns indicate individual samples. Blue indicates downregulation of gene expression, and red indicates upregulation of gene expression. The upper color bar indicates response to NAC as defined by residual cancer burden (RCB 0/I or RCB II/III). Bars on the left indicate assignment of genes to an ontology group (i.e., immune system– or proliferation-related genes). Her2 Human epidermal growth factor receptor 2, LumA luminal A, Lum B luminal B. c Subtype assignments of matched tumors at T1 and T2. Dark gray boxes running diagonally downward from top left indicate no change between two time points. d Heat map showing result of supervised clustering analysis of expression profiles of known nonresponding tumors at T1 and TS. The upper color bar indicates hormone receptor (HR) and HER2 status (blue = HR⁺HER2⁻; green = HR⁻HER2⁺; red = HR⁻HER2⁻; white = no data). The 10 most significant differentially expressed genes are indicated at the right of the heat map. Blue indicates downregulation of gene expression, and red indicates upregulation of gene expression. e Subtype assignments of matched tumors at T1 and TS. Dark gray boxes running diagonally downward from top left indicate no change between two time points