A Comprehensive Nuclear Receptor Network for Breast Cancer Cells

SummaryIn breast cancer, nuclear receptors (NRs) play a prominent role in governing gene expression, have prognostic utility, and are therapeutic targets. We built a regulatory map for 24 NRs, six chromatin state markers, and 14 breast-cancer-associated transcription factors (TFs) that are expressed in the breast cancer cell line MCF-7. The resulting network reveals a highly interconnected regulatory matrix where extensive crosstalk occurs among NRs and other breast -cancer-associated TFs. We show that large numbers of factors are coordinately bound to highly occupied target regions throughout the genome, and these regions are associated with active chromatin state and hormone-responsive gene expression. This network also provides a framework for stratifying and predicting patient outcomes, and we use it to show that the peroxisome proliferator-activated receptor delta binds to a set of genes also regulated by the retinoic acid receptors and whose expression is associated with poor prognosis in breast cancer.

Graphical AbstractFigure optionsDownload full-size imageDownload as PowerPoint slideHighlights► cis-regulatory map for 39 transcription factors in MCF-7 breast cancer cells ► Most factors are bound to highly occupied target (HOT) regions in the genome ► HOT regions are associated with active gene expression in breast cancer ► The regulatory network uncovers the interplay between nuclear receptors