Supplementary Materials and Methods from Epigenetic Resensitization to Platinum in Ovarian Cancer

PDF file - 138K, Materials and Methods. Supplementary Table S1: Primers used for pyrosequencing Supplementary Table S2. DAVID Gene ontology (GO) enrichment analysis of differentially demethylated genes after decitabine in phase II PFS>6months vs. PFS<6months (biopsy, cut off beta>0.5; enrichment score>1.81) Supplementary Table 3. DAVID Gene ontology (GO) enrichment analysis of differentially hypermethylated genes before decitabine in phase II R (PFS>6months) vs. NR (PFS<6months) (biopsy, cut off beta>0.5; enrichment score>1.81) Figure legends: Supplementary Figure 1: LINE-1 demethylation in PBMC (A and B) and tumor biopsies (C) separated by group (PFS>6months or < 6months). Supplementary Figure 2: Full Heat Map shows all 842 unique hypermethylated genes for PFS > 6 months and 283 genes for PFS < 6 months. Methylation levels are color coded from green, β value =0, to red, β value =1. Supplementary Figure 3: Demethylation induced by decitabine in biopsy samples. (A) A map of enriched functional clusters for genes demethylated by decitabine in biopsy samples based on DAVID functional annotation clustering. The size of the bars and the circles represent the enrichment score and the gene count, respectively. Detailed information regarding lists of gene members of each cluster is provided in Supplementary Table S2. (B) The pathways enriched by unique demethylated genes in the 2 groups. Supplementary Figure 4: HOXA11 methylation levels (A) HOXA11 DNA methylation levels in patient biopsies measured by pyrosequencing on days 1 and 8. Bars/error bars represent mean +/- SD. (B) Treatment induced hypomethylation of HOXA11 in tumor biopsies in patients with PFS > 6 months vs. < 6 months (P < 0.01). Bars/error bars represent mean +/- SD. (C) Baseline methylation levels of HOXA11 in tumors or ascites correlate with PFS.