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Ezh2 loss propagates hypermethylation at T cell differentiation–regulating genes to promote leukemic transformation
Changshan Wang, … , Atsushi Iwama, Goro Sashida
Changshan Wang, … , Atsushi Iwama, Goro Sashida
Published August 6, 2018
Citation Information: J Clin Invest. 2018;128(9):3872-3886. https://doi.org/10.1172/JCI94645.
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Research Article Hematology Oncology

Ezh2 loss propagates hypermethylation at T cell differentiation–regulating genes to promote leukemic transformation

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Abstract

Early T cell precursor acute lymphoblastic leukemia (ETP-ALL) is a new pathological entity with poor outcomes in T cell ALL (T-ALL) that is characterized by a high incidence of loss-of-function mutations in polycomb repressive complex 2 (PRC2) genes. We generated a mouse model of ETP-ALL by deleting Ezh2, one of the PRC2 genes, in p53-null hematopoietic cells. The loss of Ezh2 in p53-null hematopoietic cells impeded the differentiation of ETPs and eventually induced ETP-ALL–like disease in mice, indicating that PRC2 functions as a bona fide tumor suppressor in ETPs. A large portion of PRC2 target genes acquired DNA hypermethylation of their promoters following reductions in H3K27me3 levels upon the loss of Ezh2, which included pivotal T cell differentiation–regulating genes. The reactivation of a set of regulators by a DNA-demethylating agent, but not the transduction of single regulator genes, effectively induced the differentiation of ETP-ALL cells. Thus, PRC2 protects key T cell developmental regulators from DNA hypermethylation in order to keep them primed for activation upon subsequent differentiation phases, while its insufficiency predisposes ETPs to leukemic transformation. These results revealed a previously unrecognized epigenetic switch in response to PRC2 dysfunction and provide the basis for specific rational epigenetic therapy for ETP-ALL with PRC2 insufficiency.

Authors

Changshan Wang, Motohiko Oshima, Daisuke Sato, Hirotaka Matsui, Sho Kubota, Kazumasa Aoyama, Yaeko Nakajima-Takagi, Shuhei Koide, Jun Matsubayashi, Makiko Mochizuki-Kashio, Takako Nakano-Yokomizo, Jie Bai, Toshitaka Nagao, Akinori Kanai, Atsushi Iwama, Goro Sashida

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Figure 5

Ezh2 loss led to the silencing of critical T cell lineage determinants.

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Ezh2 loss led to the silencing of critical T cell lineage determinants.
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(A) Scatter plots showing the relationship of the fold enrichment values (ChIP/input) of H3K27me3 (TSS ±2.0 kb of RefSeq genes) between WT, Ezh2Δ/Δ, p53Δ/Δ, and Ezh2Δ/Δp53Δ/Δ DN1 (CD44+CD25–Lin–) cells 2 months after the deletion of Ezh2 and/or p53. (B) GSEA plots for canonical PRC2 target genes comparing DN2 cells from WT mice to DN2 cells from Ezh2Δ/Δp53Δ/Δ mice at a predisease stage and 2 distinct Ezh2Δ/Δp53Δ/Δ ETP-ALL mice (nos. 13 and 19). Normalized enrichment score (NES), nominal P value, and FDR q values are indicated. (C) ChIP-seq view of H3K27me3 levels at the Cdkn2a locus in WT, Ezh2Δ/Δ, p53Δ/Δ, and Ezh2Δ/Δp53Δ/Δ DN1 cells (top), and a quantitative RT-PCR analysis of the expression of p16Ink4a and p19Arf in DN2 cells isolated from WT (n = 12), Ezh2Δ/Δ (n = 6), p53Δ/Δ (n = 6), and Ezh2Δ/Δp53Δ/Δ (n = 8) mice 3 months after transplantation and ETP-ALL mice (n = 8) (bottom). (D) ChIP-seq view of H3K27me3 levels at the Nr4a3 locus in WT, Ezh2Δ/Δ, p53Δ/Δ, and Ezh2Δ/Δp53Δ/Δ DN1 cells (top), and quantitative RT-PCR data of the expression of Nr4a3 in DN2 cells isolated from WT (n = 12), Ezh2Δ/Δ (n = 6), p53Δ/Δ (n = 6), and Ezh2Δ/Δp53Δ/Δ (n = 8) mice 3 months after transplantation and ETP-ALL mice (n = 8) (bottom) *P < 0.001. (E) GSEA plots for T cell differentiation regulators, which were upregulated at the transition from DN2 to DN3 stages (19), comparing the DN2 cells of 2 distinct Ezh2Δ/Δp53Δ/Δ ETP-ALL mice (nos. 13 and 19) with those of Ezh2Δ/Δp53Δ/Δ mice 3 months after transplantation. (F) Quantitative RT-PCR analysis of the expression of Runx1, Bcl11b, and Ptcra in DN2 cells isolated from WT (n = 12), Ezh2Δ/Δ (n = 6), p53Δ/Δ (n = 6), and Ezh2Δ/Δp53Δ/Δ (n = 8) mice 3 months after transplantation and Ezh2Δ/Δp53Δ/Δ ETP-ALL mice (n = 8). (G) Experimental schematic of the procedure to examine the T cell differentiation of Ezh2Δ/Δp53Δ/Δ leukemic cells. (H) Representative flow cytometric profiles of CD44 and CD25 expression in CD4–CD8–Lin–GFP+ transduced leukemic cells on day 9 of the culture (n = 3). Data are representative of 2 independent experiments. (I) Proportions of DN1, DN2, DN3, and DN4 cells in CD4–CD8–Lin–GFP+ transduced leukemic cells on day 9 of the control and RUNX1 cultures (n = 3). (J) GSEA plots for the gene expression signatures of HSCs comparing DN2 cells isolated from WT mice and 2 distinct Ezh2Δ/Δp53Δ/Δ ETP-ALL mice. (K) Quantitative RT-PCR analysis of the expression of Hlf and Hoxa10 in DN2 cells isolated from WT (n = 12) and Ezh2Δ/Δp53Δ/Δ (n = 8) mice 3 months after transplantation and Ezh2Δ/Δp53Δ/Δ ETP-ALL mice (n = 8). (C, D, F, and K) Data are shown as mean ± SEM. *P < 0.05; **P < 0.01; ***P < 0.001, Student’s t test (F [Runx1, Bcl11b]); Mann-Whitney U test (C, D, K, F [Ptcra]).

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