Figure 3: Association between ESR1-enhancer methylation and breast cancer subtype. | Nature Communications

Figure 3: Association between ESR1-enhancer methylation and breast cancer subtype.

From: DNA methylation of oestrogen-regulated enhancers defines endocrine sensitivity in breast cancer

Figure 3

(a) A box plot showing the median methylation of all HM450 probes that overlap an enhancer region, an ESR1-binding site and demonstrate hypermethylation in endocrine-resistant versus parental MCF7 cells (n=801 probes), in normal breast tissue (green; n=97), luminal A (light blue; n=301), luminal B (dark blue; n=52) and ESR1-negative (red; n=105) breast cancer (data obtained from TCGA breast cancer cohort; *P<0.05, **P<<0.0001; Mann–Whitney U-test). (The whiskers of the box plot extend to the most extreme data point, which is no more than 1.5 × interquartile range from the box). (b) A heatmap showing the methylation profile of 801 ESR1-enhancer-specific HM450 probes that are more heavily methylated in endocrine-resistant versus parent MCF7 cells in normal breast tissue (green; n=97), luminal A (light blue; n=301), luminal B (dark blue; n=52) and ESR1-negative (red; n=105) breast cancer. Columns are patient samples and rows are HM450 probes. The level of methylation is represented by a colour scale—blue for low levels and red for high levels of methylation. (c) Box plots showing distribution of methylation β values in normal n=97 (green), luminal A (light blue; n=301), luminal B (dark blue; n=52) and ESR1-negative (red; n=105) breast cancer samples across HM450 probes overlapping the ESR1-binding site located within the DAXX enhancer (Chr6: 33288112-33288670; left panel) and the DAXX promoter region (1,000 bp upstream and 100 bp downstream of the transcription start site; Chr6: 33290693-33291793; right panel). (The whiskers of the box plots extend to the most extreme data point, which is no more than 1.5 × interquartile range from the box).

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