Notch, SUMOylation, and ESR-Mediated Signalling Are the Main Molecular Pathways Showing Significantly Different Epimutation Scores between Expressing or Not Oestrogen Receptor Breast Cancer in Three Public EWAS Datasets

Simple Summary The study compares two groups of breast cancer (BC) identified by estrogen receptor (ER) expression, using an epimutation score calculated from three public methylation datasets, based on the presence of epimutations and on the deviation amplitude of the methylation outlier value. Firstly, for each dataset, a pathway enrichment analysis was performed on the functional gene region with the highest epimutation score; then, the common pathways were found. A higher and significant epimutation score due to hypomethylation in ER-positive BC is present in the promoter region of the genes belonging to the estrogen receptor signaling (ERS) mediated pathway. This is consistent with an active pathway mediated by estrogen function in the group of ER-positive BC. A higher and significant epimutation score due to hypermethylation in ER-positive BC is present in the promoter region of the genes of the SUMOylation and Notch pathways which are associated with BC pathogenesis and play distinct roles in the two BC subgroups. We speculated that the altered methylation profile play a role in regulating pathways with specific functions in the two subgroups of BC. Abstract Oestrogen receptor expression in breast cancer (BC) cells is a marker of high cellular differentiation and allows the identification of two BC groups (ER-positive and ER-negative) that, although not completely homogeneous, differ in biological characteristics, clinical behaviour, and therapeutic options. The study, based on three publicly available EWAS (Epigenetic Wide Association Study) datasets, focuses on the comparison between these two groups of breast cancer using an epimutation score. The score is calculated not only based on the presence of the epimutation, but also on the deviation amplitude of the methylation outlier value. For each dataset, we performed a functional analysis based first on the functional gene region of each annotated gene (we aggregated the data per gene region TSS1500, TSS200, first-exon, and body-gene identified by the information from the Illumina Data Sheet), and then, we performed a pathway enrichment analysis through the REACTOME database based on the genes with the highest epimutation score. Thus, we blended our results and found common pathways for all three datasets. We found that a higher and significant epimutation score due to hypermethylation in ER-positive BC is present in the promoter region of the genes belonging to the SUMOylation pathway, the Notch pathway, the IFN-γ signalling pathway, and the deubiquitination protease pathway, while a higher and significant level of epimutation due to hypomethylation in ER-positive BC is present in the promoter region of the genes belonging to the ESR-mediated pathway. The presence of this state of promoter hypomethylation in the ESR-mediated signalling genes is consistent and coherent with an active signalling pathway mediated by oestrogen function in the group of ER-positive BC. The SUMOylation and Notch pathways are associated with BC pathogenesis and have been found to play distinct roles in the two BC subgroups. We speculated that the altered methylation profile may play a role in regulating signalling pathways with specific functions in the two subgroups of ER BC.