Gene expression profiles of MM.1S cells after knockdown of HDAC3 or DNMT1

Previous study demonstrated that HDAC3 has a critical role in MM proliferation; however, the underlying mechanism has not yet been elucidated. We identify that HDAC3 inhibition targets DNMT1 through dual regulations. We demonstrate that knockdown of DNMT1 leads to apoptosis and significant growth inhibition in myeloma cells. HDAC3 inhibition by gene silencing or HDAC3 selective inhibitor BG45 downregulates an oncoprotein c-Myc through its acetylation. c-Myc directly regulates DNMT1 expression at its enhancer region. Furthermore, HDAC3 directly regulates the stability of DNMT1 protein through its acetylation. Pharmaceutical inhibition of HDAC3 and DNMT1 synergistically induce MM growth inhibition in in vitro and in vivo settings. The goal of this analysis is to identify genes whose expression changes after shRNA-mediated knockdown of HDAC3 or DNMT1 using the human U133 plus 2.0 Affymetrix GeneChip in myeloma cell line (MM.1S). Myeloma cell line (MM.1S) was transduced with either shRNAs targeting HDAC3 (duplicate hairpins), DNMT1 (duplicate hairpins) or luciferase (control) in duplicate. The gene expression profiles of HDAC3 or DNMT1 knockdown cells were compared with that of control cells. A total of 10 RNA samples (4 HDAC3 knockdown, 4 DNMT1 knockdown, and 2 control) were analyzed.