PRC2 inhibition derepresses transcription of Polycomb target genes downregulated in AML-HSPCs. (A) Volcano plot displaying differentially expressed genes identified using DESeq2 in AML- (red) and control- (blue) HSPCs, following 72 hours of treatment with 2 μM UNC1999 (left) or 2 μM UNC1999 + 1 μM AZA (right) compared with treatment with DMSO (n = 3). Dashed lines denote cutoffs for the significance threshold (FDR = 0.05, horizontal; |log2(fold change)| = 1, vertical). (B) GSEA plots comparing gene expression profiles between differentiated AML-HSPCs treated with UNC1999 or DMSO for 72 hours. (C) Dot plots displaying NES scores from GSEA using ranked gene expression changes in AML-HSPCs treated with UNC1999, UNC1999 + AZA, or in untreated vs control-HSPCs. Gene sets tested include genes upregulated following treatment, as well as genes marked by H3K27me3 and H3K4me3 (bivalent) (D) Venn diagrams showing the overlap of upregulated genes in AML-HSPCs treated with UNC1999 (left) or UNC1999 + AZA (right) compared with those treated with DMSO. (E) Heat map showing row-wise z scores of log2(CPM) expression values of 154 upregulated genes in AML-HSPCs treated with 2 μM UNC1999 or 2 μM UNC1999 + 1 μM AZA that overlap with genes downregulated in DMSO-treated control-HSPCs. ∗∗∗P ≤ .001. CPM, counts per million; FDR, false discovery rate; NES, normalized enrichment score.
