Fig. 4

Comparison of protein profiles from BC-PDMs and corresponding primary tumor tissue. N = 20 matched BC-PDM and PTT-pairs were analyzed. (A) X–Y plot of correlated protein means of BC-PDMs and PTT. Protein signals of measured BC-PDM-PTT samples were correlated using Pearson correlation. DigiWest AFI protein signals were averaged for BC-PDMs/ PTT and log₂ transformed. Each dot represents one protein. Pearson r = 0.856; ***p < 0.001. (B) Overall signaling pathway activity in BC-PDMs resembled that of primary BC tumors. Proteins were sorted by pathway affiliation. Shown are AFI protein signals, averaged for BC-PDMs/PTT and log₂ transformed. Mann–Whitney test; p values as indicated. (C-D) Differently expressed proteins of matched BC-PDMs-PTT samples. Volcano plot shows proteins with significantly decreased or increased expression in BC-PDMs (red) with an adjusted FDR p-value (-log10 (q)) > 1.3 and a log₂ fold change >|1|; multiple t-test with Welch correction; Benjamini, Krieger, and Yekutieli FDR. Exact values are shown in (D). (E) Heatmap of unclustered pearson correlation coefficients (r) shows moderate correlation of AFI protein signals over BC-PDMs and matched PTT samples. (F) Pearson correlation coefficients (r) displayed as scatter plot with a median correlation of r = 0.44. Data are mean with SEM. AFI: averaged fluorescent intensities