Comprehensive transcriptomic analysis of molecularly targeted drugs in cancer for target pathway evaluation.
Bottom Line: These results confirmed that the gene signatures of these drugs reflected their modes of action.Of note, inhibitors of oncogenic kinase pathways formed a large unique cluster, showing that these agents affect a shared molecular pathway distinct from classical antitumor agents and other classes of agents.The gene expression analysis was also valuable in uncovering unexpected target pathways of some anticancer agents.
Affiliation: Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan.Show MeSH
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Mentions: As described above, the anticancer drugs were basically clustered in a target pathway-dependent manner. However, we also found several agents that were clustered in unexpected positions. As shown in Figure1, CDK4 inhibitor, AG1024 (IGF1R inhibitor), and FH535 (β-catenin/TCF inhibitor) unexpectedly showed similar gene expression signatures with the ER stress inducers. Amrubicin is an anthracycline drug that is supposed to target DNA topoisomerase II.24 However, the agent was not clustered together with other topoisomerase II inhibitors but instead with the proteasome inhibitors (Fig.1). These data suggest potential novel modes of action for these agents. Among these drugs with unexpected gene signatures, we focused on vismodegib, a Hedgehog pathway inhibitor,25 because our clustering analysis suggested its possible similarity with the oncogenic kinase inhibitors (Fig.1). To validate whether vismodegib could affect kinase signaling pathways, we examined its effect on the phosphorylation of components in the MEK/ERK and AKT/mTOR pathways. As shown in Figure4, vismodegib clearly suppressed the phosphorylation of p70S6K, a molecule downstream of mTOR, in HT-29 cells as well as in PC3 cells in which the AKT/mTOR pathways are strongly activated. As a positive control, we also observed inhibition of p70S6K phosphorylation by temsirolimus, a clinically used mTOR inhibitor. In contrast, ERK and AKT phosphorylation was not significantly affected by vismodegib treatment, although we observed a marginal inhibition of ERK phosphorylation in PC3 cells (Fig.4). These data indicated that our gene signature analysis successfully revealed a novel action of vismodegib on the mTOR pathway.
Affiliation: Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan.