DNA Methylation and Breast Cancer Risk: An Epigenome-Wide Study of Normal Breast Tissue and Blood

SIMPLE SUMMARY: As known breast cancer risk factors do not accurately predict the risk of developing breast cancer, breast cancer screening is still based solely on age. At the interface between environmental exposures and gene expression, DNA methylation patterns are potential biomarkers for assessing breast cancer risk, thus allowing for implementation of personalized screening and risk-reducing strategies. We used a comprehensive high-throughput DNA methylation assay in an unprecedented study design of normal breast epithelial tissue to detect methylation changes that are causally related to breast cancer occurrence and replicated our analyses in two independent datasets of normal breast tissue and blood. We identified several methylation differences in cancer-related genes, some of which overlapped between normal breast tissue and blood and were reported in previous studies. Our findings warrant further investigation on novel biomarkers for identifying women that will benefit the most from breast cancer screening. ABSTRACT: Differential DNA methylation is a potential marker of breast cancer risk. Few studies have investigated DNA methylation changes in normal breast tissue and were largely confounded by cancer field effects. To detect methylation changes in normal breast epithelium that are causally associated with breast cancer occurrence, we used a nested case–control study design based on a prospective cohort of patients diagnosed with a primary invasive hormone receptor-positive breast cancer. Twenty patients diagnosed with a contralateral breast cancer (CBC) were matched (1:1) with 20 patients who did not develop a CBC on relevant risk factors. Differentially methylated Cytosine-phosphate-Guanines (CpGs) and regions in normal breast epithelium were identified using an epigenome-wide DNA methylation assay and robust linear regressions. Analyses were replicated in two independent sets of normal breast tissue and blood. We identified 7315 CpGs (FDR < 0.05), 52 passing strict Bonferroni correction (p < 1.22 × 10(−7)) and 43 mapping to known genes involved in metabolic diseases with significant enrichment (p < 0.01) of pathways involving fatty acids metabolic processes. Four differentially methylated genes were detected in both site-specific and regions analyses (LHX2, TFAP2B, JAKMIP1, SEPT9), and three genes overlapped all three datasets (POM121L2, KCNQ1, CLEC4C). Once validated, the seven differentially methylated genes distinguishing women who developed and who did not develop a sporadic breast cancer could be used to enhance breast cancer risk-stratification, and allow implementation of targeted screening and preventive strategies that would ultimately improve breast cancer prognosis.