Impact of combinatorial dysfunctions of Tet2 and Ezh2 on the epigenome in the pathogenesis of myelodysplastic syndrome

Abstract

Somatic inactivating mutations in epigenetic regulators are frequently found in combination in myelodysplastic syndrome (MDS). However, the mechanisms by which combinatory mutations in epigenetic regulators promote the development of MDS remain unknown. Here we performed epigenomic profiling of hematopoietic progenitors in MDS mice hypomorphic for Tet2 following the loss of the polycomb-group gene Ezh2 (Tet2Ezh2). Aberrant DNA methylation propagated in a sequential manner from a Tet2-insufficient state to advanced MDS with deletion of Ezh2. Hyper-differentially methylated regions (hyper-DMRs) in Tet2Ezh2 MDS hematopoietic stem/progenitor cells were largely distinct from those in each single mutant and correlated with transcriptional repression. Although Tet2 hypomorph was responsible for enhancer hypermethylation, the loss of Ezh2 induced hyper-DMRs that were enriched for CpG islands of polycomb targets. Notably, Ezh2 targets largely lost the H3K27me3 mark while acquiring a significantly higher level of DNA methylation than Ezh1 targets that retained the mark. These findings indicate that Ezh2 targets are the major targets of the epigenetic switch in MDS with Ezh2 insufficiency. Our results provide a detailed trail for the epigenetic drift in a well-defined MDS model and demonstrate that the combined dysfunction of epigenetic regulators cooperatively remodels the epigenome in the pathogenesis of MDS.

The Augmented R-Loop Is a Unifying Mechanism for Myelodysplastic Syndromes Induced by High-Risk Splicing Factor Mutations

“…Thus, the precise mechanism(s) for U2AF35 mutation-induced events in both promoter and non-promoter regions remain(s) elusive. In any case, given the elucidated roles of both SRSF2 and U2AF35 in transcription, it is also worth noting that EZH2 is a well-established transcription factor and that TET2, a key enzyme involved in DNA demethylation (Hasegawa et al, 2017), may modify the chromatin to affect transcription. This has led to the speculation that MDS may be a disease of both splicing and transcription and that multiple mechanisms may cooperate with one another to account for complex biological consequences (Cimmino et al, 2017; Dvinge et al, 2016).…”

“…Interestingly, multiple mutations in genes involved in the DNA demethylation pathway have also been found to co-evolve with splicing factor mutations, such as those in TET2 and IDH1/2 (Makishima et al, 2017). These mutations may cause transcriptional repression because of increased DNA methylation in promoter-associated CpG islands (Hasegawa et al, 2017), synergizing with mutations in splicing factors to exacerbate transcription.…”

Multifaceted role of the polycomb-group gene EZH2 in hematological malignancies

“…2c) [37,54]. Decitabine, a hypomethylating agent, attenuated DNA hypermethylation followed by derepression of target genes expression to some extent, and attenuated the proliferative capacity of MDS cells [54]. These results clearly indicate that alternative epigenetic machineries contribute to the development of MDS in the setting of EZH2 insufficiency.…”

“…Gata2, Gata3, and Nr4a2) and multiple developmental pathway genes (Fig. 2c) [37,54]. Decitabine, a hypomethylating agent, attenuated DNA hypermethylation followed by derepression of target genes expression to some extent, and attenuated the proliferative capacity of MDS cells [54].…”

Deregulated Polycomb functions in myeloproliferative neoplasms

“…Because of the bimodal pathogenic functions of EZH2 as an oncogene and a tumor suppressor gene, pharmacological inhibition of EZH2 and both EZH1 and EZH2 has being tested extensively in pre-clinical and clinical studies in solid tumors, B-cell lymphoma, and AML [45]. An Ezh2 insufficiency aberrantly activates expression of certain oncogenes because of reduced levels of H3K27me3, but Ezh1-PRC2 partly compensates for Ezh2 loss in the maintenance of transcriptional repression of Ezh2 target genes [46]. In good agreement with these findings, AML cells are efficiently eradicated by the deletion of both Ezh1 and Ezh2 and treatment with EZH1/2 dual-inhibitors [47,48], which indicates that Ezh1 is essential for the self-renewal capacity of leukemic stem cells in Ezh2-deficient conditions.…”