Fig. 2

Proteomic and transcriptomic characterization of MB-R/S models. A PCA displaying distribution of MB-S/R samples from DAOY (■, n = 5) and HD-MB03 (●, n = 3) cell lines, and HuTuP33 (▲, n = 3) primary cells based on label-free MS-based protein expression data. B Heatmap reporting normalized protein abundancy of differentially expressed proteins (DEP, p < 0.05, n = 268 by t test) between MB-S and MB-R samples as in A; FC: fold change. C Pathway enrichment analysis (within the Gene Ontology (GO) terms) of DEP clustered into four distinct networks identified through STRING protein–protein interaction analysis (see also Additional file 1: Fig. S3C). Proteins significantly contributing to the reported GO enrichments are highlighted by colored dots. Cluster 1 (shades of blue): n = 86, Cluster 2 (shades of green): n = 85, Cluster 3 (shades of yellow): n = 51 and Cluster 4 (shades of red): n = 39 (Supplementary Table S1). D PCA displaying distribution of MB-S/R samples from DAOY (■, n = 4) and HD-MB03 (●, n = 4) cell lines, and HuTuP33 (▲, n = 4) primary cells based on Clariom S™ arrays-based whole transcriptome data. E Enrichment map summarizing GSEA results performed in the Hallmarks, C2cp, and C5bp MsigDB gene set collections (q < 0.1 and p < 0.05); NES: Normalized Enrichment Score. F Chord plot highlighting a high concordance between the enriched cellular processes/pathways identified through proteomic and transcriptomic analyses