Estrogen receptor beta impacts hormone-induced alternative mRNA splicing in breast cancer cells

Background: Estrogens play an important role in breast cancer (BC) development and progression; when the two isoforms of the estrogen receptor (ER alpha and ER beta) are co-expressed each of them mediate specific effects of these hormones in BC cells. ER beta has been suggested to exert an antagonist role toward the oncogenic activities of ER alpha, and for this reason it is considered an oncosuppressor. As clinical evidence regarding a prognostic role for this receptor subtype in hormone-responsive BC is still limited and conflicting, more knowledge is required on the biological functions of ER beta in cancer cells. We have previously described the ER beta and ER alpha interactomes from BC cells, identifying specific and distinct patterns of protein interactions for the two receptors. In particular, we identified factors involved in mRNA splicing and maturation as important components of both ER alpha and ER beta pathways. Guided by these findings, here we performed RNA sequencing to investigate in depth the differences in the early transcriptional events and RNA splicing patterns induced by estradiol in cells expressing ER alpha alone or ER alpha and ER beta. Results: Exon skipping was the most abundant splicing event in the post-transcriptional regulation by estradiol. We identified several splicing events induced by ER alpha alone and by ER alpha + ER beta, demonstrating for the first time that ER beta significantly affects estrogen-induced splicing in BC cells, as revealed by modification of a subset of ER alpha-dependent splicing by ER beta, as well as by the presence of splicing isoforms only in ER beta + cells. In particular, we observed that ER beta + BC cell lines exhibited around 2-fold more splicing events than the ER beta-cells. Interestingly, we identified putative direct targets of ER beta-mediated alternative splicing by correlating the genomic locations of ER beta and ER alpha binding sites with estradiol-induced differential splicing in the corresponding genes. Conclusions: Taken together, these results demonstrate that ER beta significantly affects estrogen-induced early transcription and mRNA splicing in hormone-responsive BC cells, providing novel information on the biological role of ER beta in these tumors.