The Estrogen Receptor α Signaling Pathway Controls Alternative Splicing in the Absence of Ligands in Breast Cancer Cells

SIMPLE SUMMARY: Aberrant alternative splicing is now considered a hallmark of cancer, including breast cancer. This results in the production of novel tumor-specific splice RNA variants, and the activation of biological processes such as epithelial-to-mesenchymal transition, leading to more aggressive phenotypes. The purpose of this study was to explore the role of estrogen receptor α in regulating the expression of RNA-binding proteins in luminal breast cancer cells and to determine the effects of its downregulation at the isoform level by exploring changes in isoform usage and alternative splicing. The findings of this study unravel a novel layer of gene regulation mediated by estrogen receptor α, which is fundamental for breast cancer cell growth as well as epithelial-to-mesenchymal transition. Finally, we foresee that this novel feature should be considered when studying the functional roles of estrogen receptor α in the onset and progression of breast cancer. ABSTRACT: Background: The transcriptional activity of estrogen receptor α (ERα) in breast cancer (BC) is extensively characterized. Our group has previously shown that ERα controls the expression of a number of genes in its unliganded form (apoERα), among which a large group of RNA-binding proteins (RBPs) encode genes, suggesting its role in the control of co- and post-transcriptional events. Methods: apoERα-mediated RNA processing events were characterized by the analysis of transcript usage and alternative splicing changes in an RNA-sequencing dataset from MCF-7 cells after siRNA-induced ERα downregulation. Results: ApoERα depletion induced an expression change of 681 RBPs, including 84 splicing factors involved in translation, ribonucleoprotein complex assembly, and 3′end processing. ApoERα depletion results in 758 isoform switching events with effects on 3′end length and the splicing of alternative cassette exons. The functional enrichment of these events shows that post-transcriptional regulation is part of the mechanisms by which apoERα controls epithelial-to-mesenchymal transition and BC cell proliferation. In primary BCs, the inclusion levels of the experimentally identified alternatively spliced exons are associated with overall and disease-free survival. Conclusion: Our data supports the role of apoERα in maintaining the luminal phenotype of BC cells by extensively regulating gene expression at the alternative splicing level.