Fig. 4

DNA methylation differences among BCBM subtypes. a Hierarchical cluster analysis using Euclidean distance for the DNAm level of 409 regions significantly differentially methylated (one-way ANOVA; FDR-corrected q-value < 0.0005; Supplementary Data 7) among the three breast cancer molecular subtypes (n = 24 BCBM specimens). This analysis revealed three distinct clusters of genomic regions. CL1 includes regions specifically methylated in HR+/HER2− BCBM, CL2 includes regions methylated in both, HR+/HER2− BCBM and HER2+ BCBM, and CL3 includes regions specifically methylated in HR−/HER2− BCBM. b Two-dimensional projection depicting the DCA for differentially methylated regions (n = 409) and BCBM specimens (n = 24) with known IHC profile. This plot shows the spatial overlapping of genomic regions with relative importance for each BCBM molecular subtype. c PCA including 24 BCBM specimens with known molecular subtypes and four BCBM with missing IHC information using 126 genomic regions with classification potential. The unconfirmed specimens were assigned to two different clusters. BCBM-10 and BCBM-23 overlapped with HR+/HER2− BCBM and BCBM-20 and BCBM-31 overlapped with HER2+ BCBM. d IHC evaluation in a CLIA-certified Pathology Department for ER, PgR, and HER2 expression (scale bar, 100 µm). The results confirm the DNAm-based prediction for the expression of HR and HER2. e Magnetic resonance imaging showing two patients with synchronous (case 1) BCBM lesions (BCBM-03 and BCBM-04) and asynchronous (case 2) BCBM lesions (BCBM-05 and BCBM-19). f Phylogenetic tree generated using the Euclidian metric distance for BCBM according to DNAm profile of the 126 genomic regions