Comparative transcriptome and proteome analysis of Ha-ras and B-raf mutated mouse liver tumors.

Mouse liver tumors frequently harbor activating mutations in the Ha-ras protooncogene. In addition, mutations are also found in the B-raf gene leading to constitutive activation of the B-Raf kinase. In two previous studies, we have investigated by microarray analysis the effect of the mutations on the mRNA expression patterns of the respective tumors. In the present study, we analyzed proteome changes in Ha-ras and B-raf mutated liver tumors by 2-D gel-electrophoretic separation of proteins followed by their identification by mass spectrometry. In total, 104 significantly altered protein spots were identified in Ha-ras mutated tumors and 111 in B-raf mutated tumors when compared to the corresponding normal liver tissue. The changes in protein expression patterns were highly correlated between Ha-ras and B-raf mutated tumors, and in the majority of the cases, both tumor types showed the respective alteration. Most of the tumor-specific changes in protein expression were reflected by similar changes in their mRNAs except for some up-regulated proteins without accompanying changes in mRNA levels. Interestingly, Ha-ras but not B-raf mutated tumors showed high levels of the phosphorylated (activated) form of the Ras/Raf/MEK effector kinase ERK which was, however, not associated with any detectable difference in the transcriptome or protein setup of the tumors.