Crosstalk between microRNA expression and DNA methylation drive the hormone-dependent phenotype of breast cancer

Abstract

BackgroundAbnormal DNA methylation is observed as an early event in breast carcinogenesis. However, how such alterations arise is still poorly understood. microRNAs (miRNAs) regulate gene expression at the post-transcriptional level and have been shown to play key roles in various biological processes. Here, we integrate miRNA expression and DNA methylation at CpGs to study how miRNAs may affect the breast cancer methylome and how DNA methylation may regulate miRNA expression. ResultsmiRNA expression and DNA methylation data from two breast cancer cohorts were subjected to genome-wide correlation analysis. Clustering of the miRNA expression-DNA methylation association pairs significant in both cohorts identified distinct clusters of miRNAs and CpGs. These clusters recapitulated important biological processes associated with breast cancer pathogenesis. Notably, two major clusters were related to immune or fibroblast infiltration, hence identifying miRNAs associated with cells of the tumor microenvironment, while another large cluster was related to estrogen receptor (ER) signaling. Studying the chromatin landscape surrounding the CpGs associated with the estrogen-signaling cluster, we found that miRNAs from this cluster are likely to be regulated through DNA methylation of enhancers bound by FOXA1, GATA2 and ER-alpha. Further, at the hub of the estrogen-cluster, we identified hsa-miR-29c-5p as negatively correlated with the mRNA and protein expression of the DNA methyltransferase DNMT3A, a key enzyme regulating DNA methylation. We found deregulation of hsa-miR-29c-5p already in pre-invasive breast lesions and postulate that hsa-miR-29c-5p may trigger early event abnormal DNA methylation in ER positive breast cancer. ConclusionsWe describe how miRNA expression and DNA methylation interact and associate with distinct breast cancer phenotypes.