Epigenetic Regulation and Therapeutic Targeting in Myeloma

Genetic alterations of epigenetic regulators that alter the repressive trimethylation of lysine 27 on histone H3 (H3K27me3) are a recurrent feature in cancer. The histone demethylase UTX/KDM6A Is mutated in ~5% of multiple myeloma (MM) at diagnosis and is commonly absent in MM cell lines, derived from patients with advanced disease. KDM6A forms a complex containing H3K4 specific methyltransferases KMT2D and KMT2C, the histone acetyltransferase CBP/p300 and SWI/SNF chromatin-remodelers. Collectively the complex adds activation marks on histones and removes the gene repression associated H3K37me mark at enhancers. Removal of KDM6A from MM cells using CRISPR and re-expression of KDM6A in deficient cells showed that KDM6A has tumor suppressor function and regulates genes involved in cell adhesion. ChIP-studies showed that loss of KDM6A lead to decreased H3K27 acetylation and increased H3K27me at specific loci, but at other loci changes in H3K27Ac are the major effect of changes in KDM6A expression. KDM6A loss shifts the balance of gene expression to repression and KDM6A null cells had heightened sensitivity to EZH2 inhibitors. H3K27me/Ac chromatin modifications are also deregulated in MM associated with t(4;14) and overexpression of the NSD2/MMSET histone methyltransferase. NSD2 overexpression leads to a ~10-fold genome wide increase in histone 3 lysine 36 dimethylation (H3K36me2), a chromatin mark associated with gene activation and similar loss of H3K27me3. As a result, many genes are aberrantly activated and NSD2 aberrant stimulates cell growth in part through activation of c-myc. However, some loci are repressed in the presence of high NSD2 due to redistribution of EZH2. These genes may also be important for pathogenesis and growth since NSD2 high cells also show increased sensitivity to EZH2 inhibitors. Nevertheless, the global loss of H3K27me3 makes the chromatin structure of NSD2 overexpressing MM cells more "open" and these cells demonstrated increased DNA damage in response to genotoxic agents. At the same time NSD2 overexpression increased increases DNA repair processes making cells relatively resistant to chemotherapy, potentially explaining the poor prognosis of such patients. A point mutation in NSD2, E1099K is found in some MM patients, the commonly utilized MM.1 model cell line and in up to 15% of cases of relapsed childhood acute lymphocytic leukemia (ALL). This mutation increases the activity of the enzyme and also globally increases H3K36me2 and decreases H3K27me3. Removal of the mutant allele from ALL cells lines reverses of histone methylation patterns, deceased growth, altered cellular adhesion and increased susceptibility to therapy. RNA-seq analysis showed that similar to the UTX mutation, NSD2 mutation activated a program of cell adhesion, motility and signaling. Furthermore in in ALL, the activity of mutant NSD2 blocks glucocorticoid induced expression of pro-apoptotic genes, promoting tumor relapse. In summary deregulation of histone methylation patterns in MM plays an important role in disease pathogenesis and progression. Rebalancing histone modifications using appropriate inhibitors represent a potential therapeutic strategy.