DNA methylation and hydroxymethylation results. (A) Global methylation and hydroxymethylation at baseline and after treatment (week 12). No significant changes were observed in either the patients with stable disease or the patients who demonstrated disease progression. (B) Volcano plots showing methylation changes in patients with stable disease (n = 5) and patients with disease progression (n = 3). Cytosine-phosphate-guanine sites (CpGs) with delta beta >5% and P values < .05 were considered significant. (C) Bar chart showing the proportion of differentially methylated CpGs in chromatin states from peripheral blood mononuclear cells reference in patients with stable disease (n = 5). Genomic association tester was used to determine whether the proportion of CpGs in each chromatin state showed significant enrichment. Only the hypomethylated CpGs showed significant enrichment in Enh, EnhBiv, and EnhG regions. (D) Correlation of methylation changes with hydroxymethylation changes in patients with stable disease (n = 5). CpGs with P values < .05 were plotted to demonstrate the impact on both 5 mC and 5 hydroxymethylcytosine at that site. The CpGs highlighted in red are the 935 hypomethylated CpGs identified in panel B. (E) Diseases and functions associated with hypomethylated CpGs in patients with stable disease. Data were analyzed using ingenuity pathway analysis. (F) Overlap of hypomethylated CpGs in patients with stable disease with publicly available K-562 TF binding data using ReMapEnrich. Enh, enhancer; EnhBiv, bivalent enhancer; EnhG, genic enhancer; PVal, P value.