Introduction: Histone deacetylase (HDAC) inhibitors are a novel class of drugs with demonstrated activity in hematological malignancies. Vorinostat and romidepsin are FDA approved for treatment of cutaneous T-cell lymphoma and inhibit HDACs1, 2, 3 and 6 or HDAC1, 2 and 3, respectively. It is unknown which HDACs are most important for the survival of hematological tumors, however a targeted approach using HDAC-selective inhibitors could improve efficacy and reduce toxicity in the clinic. Here we utilised RNAi technology and an HDAC-specific inhibitor to investigate whether depletion/inhibition of individual or multiple HDACs could phenocopy the effects of pan-HDACi in B-cell lymphoma and acute myeloid leukemia (AML). Methods: HDACs were individually knocked down in murine Eμ-Myc (HDACs1, 2, 3, 6) and AML (MLL-AF9+NrasG12D; HDACs 1-11) cells using constitutive (pLMS/pLMN) or Tetracycline-inducible (pTRMPVIN) vectors in vitro and in vivo. Eµ-Myc cells were treated with HDAC3-specific inhibitor RGFP966. Cell proliferation, apoptosis, cell cycle, protein expression and gene knockdown were assessed by FACS, western blot and qRT-PCR. Global gene expression was assessed using RNAseq technology.

Results: Loss of HDACs1, 2 or 6 had no long term effects on cell growth, while Eμ-Myc and AML cells depleted of HDAC3 were reproducibly lost from culture in vitro and in vivo. This phenotype was not prevented by Bcl-2 over-expression, caspase inhibition or knockout of p21 in Eμ-Myc but appeared dependent on Trp53 expression, including specific mutants of Trp53. HDAC3 knockdown altered the transcription of <0.05% genes in Eμ-Myc cells. Importantly, HDAC3-specific inhibitor RGFP966 reduced the growth rate of Eμ-Myc cells at low micromolar concentrations (0.5-1µM) while inducing apoptosis above 2µM, also partially dependent on Trp53 status. Conclusions: Our results have revealed exquisite sensitivities of murine B cell lymphoma and AML cells to depletion of HDAC3 in vitro and in vivo. This strongly suggests that HDAC3-specific inhibitors could prove useful for the treatment of various hematological malignancies. Further work investigating the molecular events underpinning the loss of proliferation induced by HDAC3 knockdown/inhibition and the effects of depleting multiple HDACs are currently underway. Ultimately, we aim to use this technology to discover efficacious HDACi with the best toxicity profile for the treatment of hematological malignancies.

Citation Format: Geoffrey M. Matthews, Leonie Cluse, Eric Wang, Mareike Roth, Chris Vakoc, Wenyan Miao, James Rusche, Johannes Zuber, Ricky W. Johnstone. RNAi-mediated depletion of histone deacetylases highlights the potential for isoform-specific inhibitors in B-cell lymphoma and acute myeloid leukemia. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5533. doi:10.1158/1538-7445.AM2014-5533