Ezh2 Is Required for Developmental Stage-Specific Silencing of Oncofetal Genes in Hematopoietic Stem/Progenitor Cells

In contrast to adult bone marrow (BM) hematopoiesis, fetal liver (FL) hematopoiesis involves mainly erythropoiesis and myelopoiesis, with limited lymphopoiesis. Fetal hematopoietic stem cells (HSCs) are known to have greater repopulating capacity as compared with adult HSCs. Polycomb group (PcG) protein Ezh2 participates in gene silencing by catalyzing the trimethylation on H3K27 (H3K27me3). We previously reported that in transplantation assays, Ezh2-deficient FL hematopoietic cells have greater reconstitution capacity and establish significantly higher ratios of myeloid to lymphoid reconstitution relative to wild-type (WT). From these results, we hypothesized that adult BM hematopoietic cells repopulated with Ezh2-deficient FL cells partially retain the features of fetal hematopoietic cells as compared with WT.

To address this hypothesis, we transplanted Cre-ERT;Ezh2^fl/fl or WT FL hematopoietic cells and deleted Ezh2 (Ezh2 KO) via intraperitoneal administration of tamoxifen at 4 weeks after transplantation. At 3 months post-deletion of Ezh2, donor-derived lin^-Sca-1⁺c-Kit⁺ (LSK) HSC/MPP fraction were recovered and subjected to microarray analysis, together with LSK cells from WT E15.5 FL and adult BM. Within genes which showed higher expression in Ezh2 KO BM LSK cells compared with WT (453 genes: Ezh2 KO-gene), and higher in FL compared with adult BM LSK cells (1139 genes: FL-gene), 102 genes (23% of Ezh2 KO-gene and 9% of FL-specific gene) were overlapped (p-value < 1.0x10^-16).

Recently, Copley et al. (Nat Cell Biol, 2013) revealed that Lin28b is exclusively expressed in FL HSCs and the Lin28b/let7/Hmga2 axis plays a critical role in controlling developmental changes in HSC properties. As reported, we found that Lin28b was detected only in FL LSK cells, but of note, remarkably higher expression was observed in Ezh2 KO relative to WT LSK cells in adult BM. Lin28b is known to block the maturation of let-7 microRNAs, thereby up-regulates expression of let-7 target genes. Within 1648 putative let-7 miRNA target genes, 136 genes were highly expressed in FL LSK cells (FL-LSK let-7 target). Gene set enrichment analysis (GSEA) showed that FL-LSK let-7 target gene set was ectopically enriched in Ezh2 KO LSK and also GMP cells but not in WT cells in adult BM.

We next performed ChIP-seq analysis to evaluate the direct target of Ezh2 in adult BM, Lin28b promoter region appeared to be marked with PcG histone marks H3K27me3 and H2AK119Ub1 but not in FL. The levels of PcG histone marks were significantly low in Ezh2-deficient BM LSK cells and GMPs relative to WT. These findings indicate that Lin28 is directly regulated by PcG histone modifications in adult BM. Interestingly, Within FL-LSK let-7 target, 16 genes underwent H3K27me3 histone modifications in adult BM and several of them escaped gene silencing in the absence of Ezh2, including Igf2bp3, Hmga2, Jam3, Dcbld1 and Zfp354a., in the same way as Lin28b. These results demonstrated that a part of let-7 target genes are negatively regulated in BM not only by let-7 but also by PcG histone modifications in adult BM.

Recent analyses have revealed that inactivating somatic mutations in epigenetic regulator genes such as EZH2 or TET2 occur frequently in patients with myelodysplastic disorders. We previously reported that Ezh2 is largely dispensable for adult HSCs in contrast to fetal hematopoiesis but after a long latency, deletion of Ezh2 in adult hematopoietic cells induces myelodysplastic/myeloproliferative neoplasm (MDS/MPN)-like disorders characterized by myelodysplasia with higher repopulating capacity of HSCs. Furthermore, concurrent depletion of Ezh2 and Tet2 markedly accelerated the development of myelodysplastic syndrome (MDS) and MDS/MPN. Lin28b and its targets Igf2bp1 and Igf2bp3 are characterized as ‘oncofetal’ genes, which is highly expressed not only in early embryogenesis but also in various tumors. Corresponding to these findings, FL-LSK let-7 target genes were highly and more significantly enriched in Tet2^KD/KDEzh2^Δ/Δ(DKO) LSK and GMPs from MDS or MDS/MPN mice relative to Ezh2 KO in adult BM.

Taken together, Ezh2 is indispensable for the developmental stage-specific regulation of the Lin28b-let7 pathway, and Ezh2 deletion results in insufficient suppression of a subset of the oncofetal genes, which may contribute to the FL-like characteristics and the development of hematopoietic disorders.