Loss of EZH2 and Aberrant DNA Methylation Account for PKC412 Drug Resistance in the FLT3-ITD Positive Acute Myeloid Leukemia (AML) Cell Line MV4-11,

Abstract 3468

The development of drug resistance is a common feature in AML that occurs towards classical cytotoxic drugs as well as novel kinase inhibitors. Mutations in primary drug targets explain a significant fraction of acquired drug resistance but the mechanisms of resistance still remain unknown in most patients. About 20–30% of all AML patients possess the mutant FLT3-ITD leading to a constitutive activation of the FLT3 kinase. Flt3-mutations can be targeted by treatment with tyrosine kinase inhibitors. Resistance to these kinase inhibitors is an increasing phenomenon whose mechanisms are not entirely understood today. As epigenetic mechanisms are shown to play an important role in leukemia pathogenesis they are also likely to influence drug resistance. To elucidate the potential role of epigenetic mechanisms in the development of drug resistance towards kinase inhibitors we used a PKC412 partially resistant clone (MV4-11R) of the AML cell line MV4-11, which harbors a homozygous FLT3 internal tandem duplication (ITD) mutation.

An initial screening for histone modifying enzymes revealed a downregulation of EZH2 on mRNA as well as protein level compared with the parental cell line. The reduction of EZH2, a H3K27 methyltransferase, in MV4-11R is furthermore correlating with globally diminished H3K27me3 levels. ChIP-Seq experiments using H3K27me3 antibody revealed differences in histone 3 K27 methylation at specific promoter sites between the parental and resistant MV4-11. To test for an increased drug resistance due to reduced EZH2 protein levels lentiviral knock-down of EZH2 was performed in the MV4-11 parental cell line and three individual knock-down cell clones were investigated for their drug resistance potential. These knock downs all showed elevated IC₅₀ values as well as resistance towards the apoptosis-inducing effects of PKC412 compared with the scrambled shRNA cells. Furthermore, EZH2 protein levels of 5 FLT3-ITD-positive AML patient samples were determined by Western Blot, samples were treated with PKC412 for 3 days and cell survival was assayed. Using this approach higher EZH2 levels in patients could also be associated with a higher sensitivity to PKC412 pointing to a putative role of EZH2 in the development of PKC412 resistance in vivo.

As EZH2 has been shown to interact with DNMTs in the context of the Polycomb Repressive Complex 2 and 3 (Viré et al., Nature 2006), we analyzed whether parental and resistant MV4-11 differ in their DNA methylation pattern. To identify hyper-/hypomethylated genes in MV4-11R, we applied the Illumina 27k Methylation BeadChip approach as well as Reduced Representation Bisulfite Sequencing (RRBS) for a genome wide CpG methylation analysis. In particular genes associated with apoptosis pathways and signal transduction were hypermethylated in MV4-11R cells compared to the parental cell line. Based on the observation of DNA methylation changes between the parental cell line and MV4-11R, treatment with the demethylating agent 2-deoxy-5-azacytidine (Aza dC) was conducted to investigate recovery of drug sensitivity. Incubation with 250 nM Aza dC for 5 days could restore the sensitivity of MV4-11R towards PKC412 as shown in proliferation and apoptosis assays. Using the Affymetrix Human Gene 1.0 ST Array platform we identified 110 genes whose expression was reactivated after treatment of MV4-11R with Aza dC, predominantly genes playing a role in signal transduction, apoptosis pathways and cell cycle. A cell cycle analysis of the MV4-11 and MV4-11R cells indeed showed that the resistant cell line is cycling less than the parental one, which possibly also favors the resistance development towards PKC412.

Summarized, our data show that a loss of EZH2 accompanied by DNA methylation changes lead to PKC412 resistance in a FLT3-ITD AML cell line model possibly reflecting a way of acquisition of drug resistance in patients.