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

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.

Non-coding RNAs: long non-coding RNAs and microRNAs in endocrine-related cancers

“…In contrast, HOTAIR was not among the 20 lncRNAs identified as upregulated and 9 downregulated by "apo-ERα" (non-ligand-occupied ERα) in a bioinformatic analysis of BCa cell lines and tumor tissues with experimental follow-up in MCF-7 cells (Miano et al 2016). That study identified DSCAM-AS1 as the most apo-ERα upregulated lncRNA and its expression was higher in luminal A and B breast tumors compared to normal breast, HER2+, or basal-like tumors.…”

“…This review is not comprehensive with respect to lncRNAs in endocrine-related cancers, but summarizes representative lncRNAs that are bestcharacterized ( Table 2 and described below). Examples of recent reviews of lncRNAs include roles in: female reproductive cancers (Ong, et al 2017), BCa (Malih, et al 2015;Miano, et al 2016;Niknafs, et al 2016;Venkatesh et al 2015;Warburton and Boone 2017), prostate cancer (PCa) (Alahari, et al 2016;, and thyroid cancer (Murugan, et al 2017).…”

“…Knockdown of DSCAM-AS1 stimulated an increase in epithelial-to-mesenchymal (EMT) markers in MCF-7 cells. DSCAM-AS1 was also upregulated in prostate and lung tumors (Miano et al 2016). A bioinformatics interrogation of 947 breast tumor RNA-seq libraries identified gene sets positively correlated with DSCAM-AS1 expression as significantly associated with clinical signatures of cancer aggression, tamoxifen resistance, higher grade, stage and metastasis (Niknafs et al 2016).…”

Portraying breast cancers with long noncoding RNAs

“…By RNA-seq in breast cancer cell lines, two recent studies identified lncRNAs regulated by the ER in the presence or absence of an estrogen agonist ( 43 , 44 ). However, we found only two lncRNAs (DSCAM-AS1 and RP11-161M6.2) that overlap with our ER-related signature and also between these two studies themselves, suggesting differential mechanism between cell lines and tissues and/or specificities related to the method/platform used.…”

Insights from Global Analyses of Long Noncoding RNAs in Breast Cancer

“…Overexpression of DCCAM-AS1 promoted growth in the absence of estrogen indicating a possible role in tumor progression and tamoxifen resistance [82]. DDCAM-AS1 was found by another group to be the most abundant lncRNA of 133 that are regulated by ligand-independent ERα activity, further suggesting a role in tamoxifen resistance [83]. …”