Hormonal Risk Factors for Breast Cancer and DNA Methylation

Epigenetic modifications influence gene expression and have been implicated in the development of breast cancer. Few studies have evaluated breast cancer risk factors in relation to DNA methylation. We examined known reproductive and hormonal risk factors for breast cancer and epigenome-wide methylation patterns. Participants included 612 women enrolled in the Sister Study prospective cohort who did not have breast cancer. DNA methylation profiling was performed using an Illumina array at the NIH Center for Inherited Disease (CIDR) on DNA extracted from whole blood. Methylation data was obtained at single CpG site resolution for 27,578 CpG sites covering >14,000 genes across 23 chromosomes. Statistical analyses were performed using normalized methylation residuals from a linear model adjusting for age and experimental variables. Controlling for a false discovery rate of 5% (q < 0.05), 1,452 methylation sites (1,220 in CpG islands) were differentially methylated in postmenopausal women compared to premenopausal women. Average methylation was increased at 1,040 sites and decreased at 412 sites. Gene ontology (GO) analysis suggested enrichment of several biological pathways including lobular involution. Among parous women, only 2 sites (1 CpG island) were differentially methylated among women with older versus younger ages at first birth. A single CpG site demonstrated lower average methylation values among long-term users of postmenopausal hormones compared to short-term users. No further statistically significant differences in methylation patterns (q < 0.05) were observed according to age at menarche, parity, breastfeeding history, or postmenopausal hormone use. These data support the menopausal transition as an influential period for epigenetic modifications; few associations between DNA methylation and other classical reproductive and hormonal breast cancer risk factors were observed.