Connecting signaling and metabolic pathways in EGF receptor-mediated oncogenesis of glioblastoma
Fig 4
Comparative proteome analysis between the GBM cell lines U87MG (EGFRwt) and U87MGvIII (EGFRvIII).
Protein identification and quantification were done by nano-HPLC Q-TOF MS/MS and peptide searches using the SwissProt databank for human proteins. Quantitation of the protein expressions was label-free by calculating the emPAI values for each protein. (A) Venn diagram for the statistics of proteins identified in U87MG and U87MGvIII. In three independent biological replicates of the proteome analysis for each cell line 907 proteins were identified, 528 common, 243 only for U87MG and 136 only for U87MGvIII cells. Of the shared proteins, 458 were equivalently and 70 differentially expressed. (B) Distribution of equivalently and differentially expressed proteins. Of the 449 differentially expressed proteins 243 were only present in U87MG and 136 in only U87MGvIII and 70 were present in both but in differential expression (down right). In total 268 were up-regulated and 181 down-regulated in U87MGvIII compared to U87MG. (C-D) Pathway over-representation analysis. Panels C and D plot the enriched pathways for proteins exclusively overexpressed in U87MGvIII (EGFRvIII) and U87MG (EGFRwt), respectively. One thirty four out of 136 and 235 out of 243 proteins overexpressed in U87MGvIII (EGFRvIII) and U87MG (EGFRwt) were mapped onto pathways. (E-F) Panels E and F plot enriched pathways of commonly up-regulated and down-regulated proteins between U87MGvIII and U87MG. Fourty five out of 45 and 24 out of 25 proteins commonly overexpressed in U87MGvIII (EGFRvIII) and U87MG (EGFRwt) were mapped onto pathways.