Fig. 6 |. Mechanistic evaluation of GSK3685032 and DAC in AML.

a, Changes in 5-methylcytosine (day 4, n = 2 biologically independent experiments) following treatment of MV4–11 cells. Dotted line represents the maximal average hypomethylation achieved by DAC or GSK3685032. b, Heatmap of log₂ fold-change values for differentially expressed genes (n = 8,363 genes) in MV4–11 cells treated with GSK3685032 or DAC (3.2–10,000 nM, day 4, RNA-seq). c, Venn diagram showing the overlap of up- and down-regulated genes (day 4, MV4–11, RNA-seq). d, Up- and down-regulated gene expression changes (RNA-seq, FDR < 0.05, log₂ fold change > 1 or < −1) in MV4–11 cells following treatment (400 nM) over time. e, Genome browser tracks of MV4–11 alignments separated by plus strand (scale, 0–50) and minus strand (scale, 0–2,600) for the human endogenous retroviral (ERV) element located within chr6:67,880,000–67,890,000 (subfamily H (HERVH), ERV1 family) demonstrating double-stranded transcripts. MV4–11 cells were treated with GSK3685032 (3.2–10,000 nM, day 4, RNA-seq). f, Dose-dependent (3.2–10,000 nM) differential hERV expression (n = 394 hERV families, log₂ fold-change) in MV4–11 treated cells (day 4, RNA-seq). Box bounds show the 25th to 75th percentiles with the center at 50%, and whiskers show the 5th to 95th percentiles. g, Methylation beta values (Infinium Methylation EPIC, vehicle, day 4, MV4–11) for probes that fall at promoters with average beta value ≥0.8 (1,500 bp ± TSS, n = 13,185 probes), within an annotated hERV (n = 16,958 probes) or at promoters of combined Hallmark IFN-α and -γ genes from MsigDB (n = 205 probes). Box bounds show the 25th to 75th percentiles with the center at 50%, whiskers show the 5th to 95th percentiles and outliers are plotted as individual circles. h, Dose-dependent fold-change in hERV expression (RNA-seq, n = 394 hERV families) and methylation for all probes (n = 16,958 probes) on the Infinium Methylation EPIC array contained within an hERV (day 4, MV4–11). i, Time course of the average log₂ fold-change in expression (RNA-seq) in MV4–11 cells treated with 400 nM GSK3685032 or DAC for genes with promotor beta values ≥0.8 (n = 12,352 genes), hERVs (n = 364 families) or IFN gene set (n = 219 genes).