Luminal long non-coding RNAs regulated by estrogen receptor alpha in a ligand-independent manner show functional roles in breast cancer

// Valentina Miano 1, 2 , Giulio Ferrero 1, 2, 3 , Stefania Reineri 1, 2, 4 , Livia Caizzi 1, 6 , Laura Annaratone 5 , Laura Ricci 1, 2 , Santina Cutrupi 1, 2 , Isabella Castellano 5 , Francesca Cordero 1, 3 , Michele De Bortoli 1, 2 1 Center for Molecular Systems Biology, University of Turin, Turin, Italy 2 Department of Clinical and Biological Sciences, University of Turin, Turin, Italy 3 Department of Computer Science, University of Turin, Turin, Italy 4 Bioindustry Park Silvano Fumero, Turin, Italy 5 Department of Medical Sciences, University of Turin, Turin, Italy 6 Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany Correspondence to: Michele De Bortoli, e-mail: michele.debortoli@unito.it Keywords: lncRNA, breast cancer, estrogen receptor, data integration, DSCAM-AS1 Received: August 05, 2015 Accepted: November 16, 2015 Published: November 28, 2015 ABSTRACT Estrogen Receptor alpha (ERα) activation by estrogenic hormones induces luminal breast cancer cell proliferation. However, ERα plays also important hormone-independent functions to maintain breast tumor cells epithelial phenotype. We reported previously by RNA-Seq that in MCF-7 cells in absence of hormones ERα down-regulation changes the expression of several genes linked to cellular development, representing a specific subset of estrogen-induced genes. Here, we report regulation of long non-coding RNAs from the same experimental settings. A list of 133 Apo-ERα-Regulated lncRNAs (AER-lncRNAs) was identified and extensively characterized using published data from cancer cell lines and tumor tissues, or experiments on MCF-7 cells. For several features, we ran validation using cell cultures or fresh tumor biopsies. AER-lncRNAs represent a specific subset, only marginally overlapping estrogen-induced transcripts, whose expression is largely restricted to luminal cells and which is able to perfectly classify breast tumor subtypes. The most abundant AER-lncRNA, DSCAM-AS1, is expressed in ERα+ breast carcinoma, but not in pre-neoplastic lesions, and correlates inversely with EMT markers. Down-regulation of DSCAM-AS1 recapitulated, in part, the effect of silencing ERα, i.e. growth arrest and induction of EMT markers. In conclusion, we report an ERα-dependent lncRNA set representing a novel luminal signature in breast cancer cells.