Fig. 4: Downregulation of ERBB2 and mTOR signaling in cases with pCR.

a Effect of anti-ERBB2 treatment on ERBB2 RNA, protein, and phosphoprotein levels for each patient with on-treatment data. p-values were calculated by paired Wilcoxon signed rank tests for on-treatment vs. pre-treatment ERBB2 expression for each group. The pCR vs. non-pCR p-values are derived from Wilcoxon rank sum tests comparing log2 fold changes of on-treatment to pre-treatment levels from pCR patients to those from non-pCR patients. For patients with multiple cores, the mean expression value was used. n = 3 for all non-pCR; n = 6 for pCR RNA or n = 7 for pCR protein and phosphoprotein. Boxplots are centered on the median and show first and third quartiles for each group. Asterisk indicates patient BCN1369 that didn’t receive Pertuzumab. b Scatter plot showing differential regulation of individual phosphosites before and after treatment in pCR and in non-pCR cases. Shown are the on-treatment vs. pre-treatment log2 fold changes in non-pCR (y-axis) vs. the log2 changes in pCR samples (x-axis) for phosphosites with p-value < 0.05 by limma analysis of differential expression in either group (n = 7 for pCR; n = 2 for non-pCR). Blue and green circles indicate phosphosites in pCR and non-pCR, respectively that show significant differential regulation in either group alone. Purple circles indicate significantly regulated phosphosites in both sets of patients. The orange diamond outlines highlight phosphosites on proteins in the KEGG ErbB signaling pathway (hsa04012). The transparency of each point reflects its significance after BH-adjustment (adjusted p < 0.05 is solid, and more transparent points have higher adjusted p-values). c PTM-SEA was applied to the signed -Log10 p-values from limma differential expression analysis of on- vs. pre-treatment phosphosite levels from pCR (upper panel) and non-pCR (lower panel) cases. The volcano plots show the Normalized Enrichment Scores (NES) for kinase signatures. Brown circles indicate signatures with significant FDR ( < 0.05).