A Systems Approach to Understand the Molecular Synergy of Combined mTOR/Histone Deacetylase (HDAC) Inhibition in the Treatment of Cancer

Abstract

The clinical necessity of combining molecularly targeted agents to effectively treat cancer is clear. At the molecular level, the limitations of single-target inhibition due to the complexity and redundancy of oncogenic signaling networks has been well demonstrated. High-throughput chemical and functional genomic approaches have identified potential combinations with synergistic effects on tumor cell viability and proliferation. Yet, elucidation of how these combinations cooperate in the context of highly complex oncogenic networks remains challenging. A multifaceted approach at the cellular and organismal level was taken to evaluate the synergistic activity of combining mTOR and HDAC inhibitors. Promising evidence of activity and synergy was observed in high-throughput matrix dose-response screening of large human cancer cell line libraries, in vivo testing in a genetically-engineered mouse (GEM) model, traditional xenografts, and in ex vivo treated patient samples. In a GEM myeloma model, a conservative mTORi/HDACi treatment regimen significantly improved overall survival compared to vehicle or single agents, with median survival increased by 3 months. We then developed a network-driven approach to identify synergistic activity of the combination at the molecular level on critical oncogenic regulators. Co-expression analysis of cells treated individually and in combination identified a distinct network of cooperatively targeted genes. We evaluated the cooperative network for differential expression between normal and malignant cells, as well as for correlation with survival in a large patient dataset. 37 cooperatively affected genes were both differentially expressed in MM and predictive of survival (p