A methyl-deviator epigenotype of estrogen-receptor-positive breast carcinoma is associated with malignant biology

We broadly profiled DNA methylation in breast cancers (n=351) and benign parenchyma (n=47) for correspondence with disease phenotype using formalin-fixed paraffin-embedded (FFPE) diagnostic surgical pathology specimens. Exploratory analysis revealed a distinctive primary invasive carcinoma subclass featuring extreme global methylation deviation. Subsequently we tested the correlation between methylation remodeling pervasiveness and malignant biology. A methyl deviation index (MDI) was calculated for each lesion relative to terminal ductal-lobular unit (TDLU) baseline, and group comparisons revealed that high-grade, short-survival ER+ cancers manifest significantly higher MDI than low-grade, long-survival ER+ cancers. In contrast, ER- cancers display significantly lower MDI, revealing a striking epigenomic distinction between cancer hormone receptor subtypes. Kaplan-Meier survival curves of MDI-based risk classes showed significant divergence between low- and high-risk groups. MDI showed superior prognostic performance to crude methylation levels, and MDI retained prognostic significance (p<0.01) in Cox multivariate analysis including clinical stage and pathologic grade. Most MDI targets individually are significant markers of ER+ cancer survival. Lymphoid and mesenchymal indices were not substantially different between ER+ and ER- groups, and do not explain MDI dichotomy. However, mesenchymal index was associated with ER+ cancer survival, and high lymphoid indices with medullary carcinoma. Finally, comparison between metastases and primaries suggests methylation patterns are established early and maintained through disease progression for both ER+ and ER- tumors. Bisulfite-converted DNA from 397 lesions were analyzed with the Illumina GoldenGate Methylation Cancer Panel I array.