Molecular analysis of combined mTOR/HDAC inhibition in multiple myeloma

The molecular pathogenesis of many cancer types, including multiple myeloma (MM), involves alterations in the PI3K/AKT/mTOR (mTOR) and cyclin/CDK/Rb (CDK/Rb) pathways, often through activation of the mTOR pathway and epigenetic silencing of tumor suppressors in the CDK/Rb pathway. Previous studies have identified HDAC and mTOR inhibitors as effective in combating these molecular alterations in the CDK/mTOR pathways, respectively. Evaluating molecular synergy of combinations is challenging, yet identification of cooperatively responding, biologically-relevant targets is potentially useful for defining patient subsets for which the combination would be active. Previous work took an integrated, systems-level approach to distill the core synergistic consequence of combining MS-275 (Class I HDACi) with rapamycin (mTORi). Transcriptional co-expression analysis of multiple myeloma (MM) cells treated individually and in combination was used to define the contribution of each drug to an overall response network. Five highly connected transcriptional modules were identified, of which one distinct module of 126 genes was cooperatively affected by both drugs. Of the cooperatively affected genes, 37 were found to be differentially expressed in MM and predictive of survival (p<0.01). The pharmacodynamic response of the signature to the drug combination was examined by Western Blot and NanoString in a large number of MM cell lines before and after treatment. Ingenuity transcription factor enrichment testing identified MYC as one of the regulators of the synergistic transcriptional response. Inducible MYC cell lines have shown diminished protein, but not mRNA, expression in response to the drug combination. Likewise, MYC is required for combination sensitivity and for the synergistic response of the gene signature to combined mTOR/HDAC inhibition. This analysis identified an alternative route to MYC inhibition and a systems-level approach for defining the molecular underpinnings of drug combinations which can be applied to many disease states.