HDAC3 Maintains DNMT1 through Dual Mechanisms in Multiple Myeloma

Histone deacetylases (HDACs) represent novel therapeutic targets for the treatment of multiple myeloma (MM). Although non-selective HDAC inhibitors demonstrate remarkable anti-MM activity, they also are associated with side effects. To avoid these adverse events without reducing anti-MM efficacy, we have been developing isoform- or class-selective HDAC inhibitors. Specifically, we showed that HDAC3 plays an important role in MM cell proliferation (Minami J, et al, Leukemia. 2014), and here delineate the mechanism whereby HDAC3 inhibition abrogates MM cell growth.

We first carried out gene expression profiling before and after knocking down of HDAC3 in MM.1S cells. Among significantly downregulated genes (adjusted P values < 0.001, log fold change > 1.0), we selected DNA methyltranseferase 1 (DNMT1) for further studies. Downregulation of DNMT1 by HDAC3 knockdown was first confirmed by quantitative real time PCR (Q-PCR) and immunoblotting in both MM.1S and RPMI 8226 cells. HDAC3 selective inhibitor BG45 also downregulated DNMT1 expression. Importantly, knockdown of DNMT1triggers apoptosis in MM cells, suggesting that DNMT1 downregulation plays, at least in part, a role in HDAC3 inhibitor-induced MM cell growth inhibition.

Previous studies show that HDAC inhibitors downregulate c-Myc expression (Hideshima T, et al. Blood Cancer J. 2015), and we confirmed that c-Myc was downregulated by genetic downregulation and pharmacological inhibition of HDAC3 by HDAC3 shRNA and BG45, respectively. Moreover, treatment of MM.1S cells with BG45 markedly increased c-Myc acetylation. Importantly, c-Myc was significantly degraded after treatment of MM.1S with HDAC3 inhibitor BG45 in the presence of cycloheximide (CHX), indicating that downregulation of c-Myc by HDAC3 inhibition is due to loss of protein stability. To determine whether DNMT1 expression is regulated by c-Myc, we next analyzed ChIP-Seq data in MM.1S cells (GSE36354) and found that c-Myc binds to DNMT1 promoter region. We confirmed downregulation of DNMT1 after knockdown of MYC in MM.1S and RPMI 8226 cells by Q-PCR and immunoblotting. These results suggest that HDAC3 inhibition downregulates DNMT1 through downregulation of c-Myc.

A recent study reported that acetylation of DNMT1 leads to its ubiquitination, resulting in degradation of DNMT1 (Cheng J, et al. Nat Commun. 2015). We showed that treatment of MM.1S cells with BG45 in the presence of CHX triggered hyperacetylation of DNMT1, followed by its degradation. We further confirmed this association of acetylation and ubiquitination of DNMT1 protein using a dequbiquitination assay in 293T cells. As expected, HDAC3 blocked DNMT1 ubiquitination. Taken together, these results suggest that HDAC3 inhibition modulates DNMT1 via both c-Myc and by acetylation and thereby altering protein stability.

Finally, Azacytidine (AZA) is used as a DNMT1 inhibitor in the treatment of acute myeloid leukemia and myelodysplastic syndrome. We therefore examined combination treatment of MM cells with BG45 combined with AZA. Importantly, this combination triggered synergistic downregulation of DNMT1 and growth inhibition through apoptosis in both MM cell lines and patient MM cells. Efficacy of combination treatment was confirmed in a murine xenograft MM model, evidenced by both tumor growth inhibition and prolonged overall host survival.

Our results therefore provide the rationale for combination treatment with HDAC3 inhibitor and DNMT1 inhibitor to improve patient outcome in MM.