Neutrophils Derived from Ezh2 -/- Progenitor Cells Demonstrate Aberrant Erythroid Lineage Gene Expression

Introduction:

Ezh2 is the catalytic component of the polycomb repressive complex 2, which methylates lysine 27 of histone H3 (H3K27). Loss of function mutations in EZH2 are found in 6% of MDS patients and are independently associated with worse overall survival compared to patients with wildtype EZH2 (Bejar R. et al., 2011 and 2012). Our group has described that neutrophils derived from Ezh2^-/- mice have functional defects (Perez-Ladaga et al., 2013), including decreased phagocytosis, aberrant migration and overproduction of reactive oxygen species (ROS). To determine how loss of Ezh2 might contribute to these functional deficits, we performed gene expression profiling on immortalized myeloid cell lines capable of neutrophilic differentiation.

Methods:

Bone marrow from Ezh2 null (Ezh2^-/-) and littermate control mice (WT) were transduced with HOXB8 fused to the estrogen receptor ligand-binding domain to produce immortalized myeloid progenitor cells. Removal of estrogen from the media allows these cells differentiate into mature neutrophils (Wang G.G., 2006). RNA from progenitor and mature neutrophils (WT and Ezh2^-/-) was extracted each condition in duplicate and subjected to gene expression profile (Affymetrix). Transcriptome analysis was conducted with TAC software from Affymetrix and gene set comparisons between the different phenotypes were analyzed with Gene Set Enrichment Analysis (GSEA). Rescue by lentiviral re-introduction of Ezh2 into Ezh2^-/- cells is currently ongoing.

Results:

Estrogen withdrawal causes differentiation of WT and Ezh2^-/- lines into mature neutrophils after six days. Interestingly, WT neutrophils lose Ezh2 mRNA and protein expression as soon as three days after estrogen withdrawal. WT mature neutrophils lack Ezh2 and trimethyl-H3K27 (me3H3K27), showing similar amounts as Ezh2^-/- derived neutrophils.

Gene expression profiling of 65956 transcripts demonstrated that 1953 of them were differentially expressed between WT and Ezh2^-/- mature neutrophils. Nearly 65% of these genes were upregulated in Ezh2^-/- derived neutrophils when compared to WT. As Ezh2 levels in mature neutrophils are similar in both conditions, gene expression differences are likely due to EZH2 and me3H3K27 differences in the progenitor state.

Among the differentially expressed genes, the transcription factor GATA1 was found upregulated in Ezh2^-/- derived neutrophils, a result confirmed by qPCR. GATA1 regulates the expression of hundreds of genes and is essential for erythropoiesis. GATA1 target erythroid genes were also found upregulated in Ezh2^-/- derived neutrophils when compared to WT, while no significant differences in neutrophil gene expression were detected.

Similarly, GSEA analysis of Ezh2-/- vs. WT confirmed strong enrichment for erythroid associated expression programs. A Heme Metabolism Signature based on a panel of 182 genes showed a strong correlation with Ezh2^-/- derived neutrophils (Figure 1A).

GSEA was used to examine possible mechanisms behind the functional defects previously reported in Ezh2^-/- derived neutrophils such as overproduction of ROS and impaired migration. A gene set based on 192 genes encoding proteins involved in oxidative phosphorylation demonstrated a significant correlation between this pathway signature and Ezh2^-/- derived neutrophils (Figure 1B).On the other hand, GSEA showed a positive correlation between WT differentiated neutrophils and a panel of 115 genes involved in leukocyte transendothelial migration (Figure 1C).

Conclusion:

Our results show that HOXB8-ER immortalized myeloid progenitor cells are able to produce mature neutrophils even in absence of Ezh2. The loss of Ezh2 in myeloid progenitor cells is associated with the differential expression of 1953 genes in mature neutrophils, including the upregulation of genes involved in erythroid differentiation programs and oxidative phosphorylation, and the downregulation of genes involved in leukocyte migration. Ongoing rescue experiments re-introducing Ezh2 into Ezh2^-/- progenitor cells are being performed to determine if this restores normal neutrophil functions and silences the aberrant erythroid gene expression in Ezh2^-/- derived neutrophils. Our findings may help explain how Ezh2 loss causes neutrophil dysfunction and contributes to the adverse prognosis associated with EZH2 mutations in MDS patients.