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. 2015 Oct 15;126(16):1930-9.
doi: 10.1182/blood-2015-06-649087. Epub 2015 Aug 28.

EHMT1 and EHMT2 Inhibition Induces Fetal Hemoglobin Expression

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Free PMC article

EHMT1 and EHMT2 Inhibition Induces Fetal Hemoglobin Expression

Aline Renneville et al. Blood. .
Free PMC article

Abstract

Fetal hemoglobin (HbF, α2γ2) induction is a well-validated strategy for sickle cell disease (SCD) treatment. Using a small-molecule screen, we found that UNC0638, a selective inhibitor of EHMT1 and EHMT2 histone methyltransferases, induces γ-globin expression. EHMT1/2 catalyze mono- and dimethylation of lysine 9 on histone 3 (H3K9), raising the possibility that H3K9Me2, a repressive chromatin mark, plays a role in silencing γ-globin expression. In primary human adult erythroid cells, UNC0638 and EHMT1 or EHMT2 short hairpin RNA-mediated knockdown significantly increased γ-globin expression, HbF synthesis, and the percentage of cells expressing HbF. At effective concentrations, UNC0638 did not alter cell morphology, proliferation, or erythroid differentiation of primary human CD34(+) hematopoietic stem and progenitor cells in culture ex vivo. In murine erythroleukemia cells, UNC0638 and Ehmt2 CRISPR/Cas9-mediated knockout both led to a marked increase in expression of embryonic β-globin genes Hbb-εy and Hbb-βh1. In primary human adult erythroblasts, chromatin immunoprecipitation followed by sequencing analysis revealed that UNC0638 treatment leads to genome-wide depletion in H3K9Me2 and a concomitant increase in the activating mark H3K9Ac, which was especially pronounced at the γ-globin gene region. In RNA-sequencing analysis of erythroblasts, γ-globin genes were among the most significantly upregulated genes by UNC0638. Further increase in γ-globin expression in primary human adult erythroid cells was achieved by combining EHMT1/2 inhibition with the histone deacetylase inhibitor entinostat or hypomethylating agent decitabine. Our data provide genetic and pharmacologic evidence that EHMT1 and EHMT2 are epigenetic regulators involved in γ-globin repression and represent a novel therapeutic target for SCD.

Figures

Figure 1
Figure 1
UNC0638 increases human γ-globin and HbF expression and mouse embryonic β-globin gene expression in a dose-dependent manner. (A) Fold change in HBA1/2, HBB, and HBG1/2 mRNA levels relative to GAPDH in primary adult human erythroid cells at day 14 of erythroid differentiation and after 10 days of UNC0638 treatment (mean ± standard deviation [SD], n = 5-6 biological replicates). (B) Relative expression of γ-globin genes in primary adult human erythroid cells at day 14 of erythroid differentiation and after 10 days of UNC0638 treatment (mean ± SD, n = 5-6 biological replicates). (C) HbF levels assessed by HPLC in primary adult human erythroid cells at day 14 of erythroid differentiation (mean ± SD, n = 4-8 biological replicates). (D) Representative HPLC chromatograms showing HbF abundance. (E) Flow cytometry analysis for F-cells: representative histograms showing the percentage of adult human erythroid cells expressing HbF and the fluorescence intensity relative to the cell number at day 14 of erythroid differentiation (mean ± SD, n = 3-4 biological replicates). ***P < .001. (F) Relative expression levels of the mouse embryonic globin genes Hbb-εy and Hbb-βh1 in MEL cells after 48 hours of UNC0638 treatment and in Ehmt2 knockout MEL cells (mean ± SD, n = 3 biological replicates). *P < .05. Cl., clone.
Figure 2
Figure 2
EHMT1 or EHMT2 knockdown increases γ-globin gene expression and HbF synthesis in primary adult human erythroid cells. (A) Validation of shRNA-mediated knockdown of EHMT1 or EHMT2 in primary adult human erythroid cells by qRT-PCR at day 14 of erythroid differentiation (mean ± SD, n = 5-6 biological replicates). (B) Validation of shRNA-mediated knockdown of EHMT1 or EHMT2 by western blot analysis in primary adult human erythroid cells at day 9 of erythroid differentiation and after 4 days of puromycin selection. shRNA-mediated knockdown of EHMT1 or EHMT2 increases γ-globin mRNA levels (mean ± SD, n = 5-6 biological replicates) (C) and HbF levels assessed by HPLC in primary adult human erythroid cells at day 14 of erythroid differentiation (mean ± SD, n = 4-6 biological replicates) (D). (E) Representative HPLC chromatograms showing HbF abundance. (F) Flow cytometry analysis for F cells: representative histograms showing the percentage of adult human erythroid cells expressing HbF and the fluorescence intensity relative to the cell number at day 14 of erythroid differentiation (mean ± SD, n = 3-5 biological replicates). **P < .01; ***P < .001.
Figure 3
Figure 3
Effect of UNC0638 treatment on cell morphology, proliferation, and differentiation of primary adult human erythroid cells in culture. (A) Representative images of the morphology of primary adult human erythroid cells differentiated ex vivo in the presence of 0.25 μM UNC0638 or the vehicle control. Bar represents 10 μm. (B) Cell proliferation assessed by trypan blue staining in the presence of 3 doses of UNC0638 or the vehicle control (mean ± SD, n = 3 biological replicates). (C) Cell Titer Glo curves for a wide range of UNC0638 concentrations and for 3 different treatment duration (mean ± SD, n = 5-6 biological replicates). (D) Flow cytometry analysis of cell-surface differentiation marker expression at day 15 of erythroid differentiation (mean ± SD, n = 3-4 biological replicates). *P < .05; **P < .01.
Figure 4
Figure 4
H3K9Me2 levels decrease during erythroid differentiation and are further decreased by EHMT1/2 pharmacologic inhibition or knockdown in primary adult human erythroid cells. (A) EHMT1 and EHMT2 mRNA expression in human CD34+ cells from adult or umbilical CB. Results show the mean value ± SD of 2 different donors for adult CD34+ and 2 pools of 10 cords for CB CD34+. (B) Western blot analysis showing EHMT1, EHMT2, and lamin B1 (loading control) in primary adult human cells during erythroid differentiation ex vivo. (C) Representative flow plots of H3K9Me2 level according to the cell number and the size during erythroid differentiation ex vivo. (D) Representative histogram showing the fluorescence intensity for H3K9Me2 relative to the cell number in erythroid cells differentiated in the presence of 0.25 μM UNC0638 or the vehicle control for 7 days. (E) Dot plots showing the median fluorescence intensity (MFI) for H3K9Me2 after 7 days of treatment according to the UNC0638 concentration (mean ± SD, n = 8 biological replicates). (F) Dot plots showing the MFI for H3K9Me2 in EHMT1 or EHMT2 knockdown cells (mean ± SD, n = 5-8 biological replicates). ***P < .001.
Figure 5
Figure 5
Effects of UNC0638 on H3K9Me2 and H3K9Ac chromatin occupancy at the β-globin locus and gene expression in primary human erythroblasts. (A) Integrative genome viewer screenshot at the β-globin locus in erythroblasts derived from umbilical CB or adult CD34+ cells that were differentiated in the presence of 0.25 μM UNC0638 or the vehicle control. ChIP-seq analysis was performed at day 11 of erythroid differentiation and after 7 days of treatment. H3K9Me2 or H3K9Ac reads are normalized to H3 reads for Mint-ChIP internal normalization, as indicated by the values on the y-axis. The tracks represent the pool of 3 biological replicates. (B) Corresponding histograms representing the normalized number of reads in the indicated region of the β-globin locus for both histone marks. H3K9Me2 or H3K9Ac reads are normalized to H3 reads for Mint-ChIP internal normalization (mean ± SD, n = 3 biological replicates). *P < .05; **P < .01; ***P < .001, relative to untreated adult erythroblasts. (C) Volcano plot illustrating changes in gene expression induced by UNC0638. RNA-seq analysis was performed in primary adult human erythroid cells at day 11 of erythroid differentiation and after 7 days of treatment with 0.25 μM UNC0638 or the vehicle control. The plot represents statistical significance vs the fold change in gene expression between the 2 conditions. Results from 3 biological replicates are shown. FDR, false discovery rate.
Figure 6
Figure 6
Combination of EHMT1/2 pharmacologic inhibition or knockdown with entinostat or decitabine shows additive effects on γ-globin gene induction in primary adult human erythroid cells. (A) Histograms showing the relative percentage of γ-globin genes expression according to the concentration of drug(s). qRT-PCR analysis was performed at day 14 of erythroid differentiation, after treatment with UNC0638 only, entinostat (MS-275) only, or UNC0638 + MS-275 for 7 days (from day 7 to day 14) (mean ± SD, n = 5 biological replicates). ***P < .001. (B) Histograms showing the relative percentage of γ-globin genes expression according to the concentration of drug(s). qRT-PCR analysis was performed at day 14 of erythroid differentiation, after treatment with UNC0638 only (from day 7 to day 14), decitabine (DAC) only (from day 11 to day 14), or UNC0638 + DAC (from day 7 to day 14 for UNC0638 and from day 11 to day 14 for DAC) (mean ± SD, n = 5 biological replicates). **P < .01; ***P < .001. (C) Histograms showing the relative percentage of γ-globin genes expression in knockdown cells, in the presence of 0.5 μM MS-275 or the vehicle control for 3 days (from day 11 to day 14). qRT-PCR analysis was performed at day 14 of erythroid differentiation (mean ± SD, n = 4-6 biological replicates). One-way ANOVA, P < .001. (D) Histograms showing the relative percentage of γ-globin genes expression in knockdown cells, in the presence of 0.5 μM DAC or the vehicle control for 3 days (from day 11 to day 14). qRT-PCR analysis was performed at day 14 of erythroid differentiation (mean ± SD, n = 4-6 biological replicates). One-way ANOVA, P < .001.

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