Targeting molecular mechanisms for epigenetic silencing in multiple myeloma : Implications for biology and precision medicine

Abstract: Multiple myeloma (MM) is a heterogeneous haematological cancer where malignant plasma cells clonally expand within the bone marrow. The transcriptional repressor PRC2 and its catalytic subunit EZH2 play a major role in MM, as PRC2 re-targeting results in a MM-specific gene silencing profile. In paper I, we explored the metabolic response to EZH2 inhibition (EZH2i). A global loss of H3K27me3 was found in all EZH2i-treated MM cell lines. EZH2i-sensitive cell lines acquired a unique metabolic signature, following the upregulation of a cluster of miRNAs which target methionine cycling-associated genes and are silenced by H3K27me3. These miRNAs were not upregulated in resistant cell lines, due to additional DNA methylation-mediated silencing.Therefore, in paper II we sought to evaluate the combinatorial effect of DNA demethylation agents and EZH2 inhibitors. Here, we provided a comprehensive map of the reconfiguration of the epigenome in primary MM samples. Furthermore, we demonstrated a direct protein-protein interaction between DNMT1 and EZH2 and showed that co-inhibition of these enzymes has an enhanced effect in synergistically activating genes regulating apoptosis and cell cycling. PRC2 lacks sequence specificity but contains a lncRNA binding pocket. In paper III, we hypothesized that PRC2 targeting to specific genomic regions could be mediated by lncRNAs in the context of MM. Coupling RIP- and RNA-seq, we identified a physical interaction between the lncRNA PVT1 and EZH2, as well as 270 genes potentially targeted by the EZH2-PVT1 axis. In addition, we found that independent inhibition of EZH2 and PVT1 resulted in the upregulation of the tumour suppressor genes ZBTB7C, RNF144A and CCDC136, suggesting a functional interdependency between these two epigenetic regulators. In paper IV we investigated the effects of dual G9a/DNMT inhibition in MM cells, resulting in suppressed expression of MM-associated oncogenes and increased tumour cell death. By coupling ChIP-seq, DNA methylation arrays and RNA-seq, we identified a group of genes silenced by G9a and/or DNMTs that when activated, blocked MM proliferative potential by activating genes with tumour suppressor function. In summary, this thesis highlights the strong interconnection between the dysregulation of epigenetic/metabolic regulatory mechanisms and MM pathogenesis, providing insights into how these mechanisms can be targeted to promote anti-MM effects.