An integrated analysis of the coordinated dysregulation of microRNAs and their targets in pre-invasive breast cancer

microRNAs (miRNAs) are short noncoding RNAs that act predominantly as negative regulators of post-transcriptional gene expression. miRNAs may play a causal role in cancer, including breast cancer. However, at what stage of breast cancer development miRNAs become dysregulated is unknown. It is established that changes in DNA and messenger RNA (mRNA) are present at the pre-invasive stage and these resemble changes at the invasive stage. However, it is unknown if this is also true for miRNAs. Additionally, the role miRNAs may play in regulating these mRNA changes is unknown. We hypothesized that differences in miRNA expression will exist in early breast cancer, these will be associated with mRNA expression and DNA changes, and together these will help to elucidate important steps early in breast tumor genesis.;Using micro-dissected breast epithelium from a set of primary patient tissue samples, we obtained data on miRNA expression, mRNA expression and DNA copy number. Using an integrative approach, we demonstrate that: a distinct miRNA expression signature exists in normal breast epithelium; miRNA expression is dysregulated in pre-invasive breast cancer; miRNA and mRNA targets are coordinately dysregulated; and miRNA modulation elicits changes in candidate target gene expression. We explored a potential mechanism of miRNA mis-expression: their localization at areas of DNA copy number variation. Several miRNA loci are consistently lost or gained, and these changes correlated to expression changes. Finally, we used SNP data to evaluate polymorphic target sites (poly-miRTS) that can alter miRNA binding sites in putative mRNA targets.;These results provide a miRNA profile of histologically normal breast epithelium and of pre-invasive breast carcinoma and demonstrate that: altered miRNA expression can modulate gene expression changes, characterizing the pre-invasive stage of breast cancer; miRNA expression dysregulation can be due to DNA copy number changes; and the presence of poly-miRTS could alter miRNA-mediated gene repression. Together, these findings support the use of integrative approaches that combine multi-level data, and utilize a variety of analysis methods, in order to understand a complex disease. Furthermore, this information can be utilized to devise clinical and therapeutic applications, using miRNAs as diagnostic and prognostic indicators of early breast disease.