Figure 6
AzaC reverses a specific signature of aberrant promoter DNA methylation and associated gene silencing in AML. (a) Clusters of upregulated genes with similar differential methylation signatures [27]. Orange highlight regions, 75% upregulated. (b) Differential methylation up and downstream of TSS (0 bp). Y-axis, differential methylation, -1 to 1, complete hypomethylation and hypermethylation, respectively. Fold change (log2) gene expression is indicated (>0 = upregulated by AzaC) (Black to red, extent of upregulation). (c) Average differential methylation in AML3 -/+AzaC, over 246 genes identified by the gene list tool. (d) Average fraction methylation (Y-axis) around TSS of 246 genes in AzaC-untreated AML3. (e) Average plot of differential methylation, HSPC, and AML3 cells, over 336 genes identified by the gene list tool. (f) Overlap between 246 genes differentially methylated between AzaC-treated and untreated AML3 ((AML3_AzaC_WIMSi_246), Additional file 5: Dataset 3) and 336 genes differentially methylated between HSPC and AML3 ((Split WIMSi_336), Additional file 5: Dataset 4) (2.18-fold enrichment over random (P < 1 × 10-37), Additional file 5: Dataset 5)). (g) Overlap between 246 genes differentially methylated between AzaC-treated and untreated AML3 (AML3_AzaC_WIMSi_246) and genes downregulated in expression in AML3 cells compared to both HSPC data sets (NIH and UNSW) and significantly regulated by AzaC in AML3) (Additional file 5: Dataset 6, HSPC_AML Expr both Down_259). Eighty-four gene overlap represents a 1.5-fold enrichment over random (P < 3 × 10-6) (Additional file 5: Dataset 7). (h) Overlap between 246 genes differentially methylated between AzaC-treated and untreated AML3 (AML3_AzaC_WIMSi_246) and genes upregulated in expression in AML3 cells compared to both HSPC data sets (NIH and UNSW) and significantly regulated by AzaC in AML3 (HSPC_AML Expr both Up_410) (Additional file 5: Dataset 8). Fifty-six gene overlap represents a 1.57-fold depletion over random (P <1 × 10-6) (Additional file 5: Dataset 9). (i) Fraction of 246 genes differentially methylated between AzaC-treated and untreated AML3 (AML3_AzaC_WIMSi_246) with indicated gene expression in AML3 and HSPC cells (NIH or UNSW datasets).