Fig. 3

Treatment with MS-275 modifies the proteome of mesenchymal-like MeT5A cells. Mesenchymal-like MeT5A cells were left untreated or treated for 72 hours with MS-275 (250 nM) (N = 2). Cells were lysed with RIPA buffer and quantified by Bradford assay. Total lysates were digested and separated in 8 fractions based on proteins’ hydrophobic properties. Separated fractions were analysed by label-free liquid chromatography-mass spectrometry (nLC-MS/MS). A Principal component analysis (PCA) of the LFQ intensities obtained in NT and MS-275 treated sample datasets. B Heat map of differentially expressed proteins in NT and MS-275 samples. LFQ intensities were expressed in z-score values (range of intensity z-score: ±2.4). Up-regulated and down-regulated proteins are expressed in red and green scales respectively. Hierarchical clustering was performed using Euclidean distance and average linkage using the Perseus software. C Volcano plots comparing NT (left panel) and MS-275 (right panel) upregulated proteins. Black curves represent the significance threshold at false discovery rate (FDR) of 0.05 and S0 of 0.1. D Gene Ontology enrichment analysis performed by Perseus software on differentially expressed proteins between NT and MS-275 datasets. GOCC: Gene ontology cellular components; GOMF: Gene ontology molecular functions (E) Table showing selected identified proteins belonging to specific Gene ontology biological processes (GOBP) shown in the right column