Estrogen receptor β target gene expression reveals novel repressive functions in aggressive breast cancer [RNA-Seq]

Inflammatory breast cancer (IBC) is a highly metastatic breast carcinoma with high frequency of estrogen receptor a (ERα) negativity and limited treatment options. We previously explored the second ER subtype, (ERβ) and reported correlation of its tumor expression with reduced metastasis in patients and in preclinical models of the disease. We initially associated the anti-metastatic function of the receptor with the inhibition of actin-based cell migration and the associated Rho GTPase signaling in IBC cells. We have now followed an integrated genomics approach to fully delineate the signaling underlying the anti-metastatic effects of ERβ. Through mapping binding sites in IBC cells that express endogenous and transfected ERβ in the presence of an agonist and interrogating this information with altered expression of protein coding mRNAs and miRNAs we have defined the interaction of a biologically active receptor with the cancer genome that controls metastatic signals. We reveal key regulatory chromatin binding sites and motifs and identify direct target genes and miRNAs and the associated biological functions. Our new findings implicate the regulation of metabolic pathways and signaling in development and tumor microenvironment in anti-metastatic activity of ERβ. Through a rigorous analysis of target genes in clinical datasets we also associate downstream factors with patient outcomes reporting new molecules with targeting potential and strengthening the relevance of ERβ signaling for the metastatic process in breast cancer. Our findings thus offer an opportunity to validate the tumor repressive role of ERβ through a better understanding of its mechanism of action.