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

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.

A Regulatory Axis between Epithelial Splicing Regulatory Proteins and Estrogen Receptor α Modulates the Alternative Transcriptome of Luminal Breast Cancer

“…The direct ERα regulation of these gene expression was provided by RNA-Seq and ChIP-Seq data analysis in MCF-7 and primary tumors. This is further supported by the correlation analysis performed in primary tumor data and by the strong ESRP1 and ESRP2 downregulation upon ERα silencing in hormone-deprived MCF-7 [21]. Whereas a clear ERα chromatin binding is observed at the ESRP2 promoter and first intron in both cell lines and primary BCs, the binding at ESRP1 promoter was not observed in our hormone-deprived MCF-7.…”

“…Since apoERα regulates ESRP1 and ESRP2 expression, the overlap of ESRP1/2-modulated ASEs with those observed upon apoERα silencing in MCF-7 cells was evaluated [ 21 ]. The overlap revealed 64 commonly dysregulated events: 50 ES (78%), 5 MXE (7.80%), 4 A5′SS (6.25%), 2 A3′SS (3.13%), and 3 (4.68%) RI events ( Supplementary Materials Figure S9a and Table S8a ).…”

“…We further demonstrated that these interactions occur in endocrine-resistant cells and regulate the expression of genes relevant to BC progression [ 19 , 20 ]. More recently, we showed that a high proportion of apoERα-regulated genes and isoforms are composed of RBPs, most of which (75%) were lost upon ERα depletion, including ESRP1 and ESRP2 [ 21 ].…”

Pharmacological inhibition of bromodomain and extra-terminal proteins induces NRF-2-mediated inhibition of SARS-CoV-2 replication and is subject to viral antagonism

“…Detection of these enrichments, independent of SARS-CoV-2 infection, argues for a dominant role of JQ-1 treatment on transcription modulation via the CNC-bZIP and NFY TF families. Secondly, motifs annotated to a superfamily of steroid-induced nuclear receptor (NR) TFs, whose signalling drives cellular RNA splicing processes (Auboeuf et al, 2004; Elhasnaoui et al, 2021), were also enriched in JQ-1-treated groups irrespective of the infection status (Sup. Table 1B-C).…”

Functional Relationships between Long Non-Coding RNAs and Estrogen Receptor Alpha: A New Frontier in Hormone-Responsive Breast Cancer Management

“…The unliganded receptors also bind to multiple chromatin sites, thus ensuring the constitutive expression of several coding and non-coding RNAs [ 14 , 15 ] to promote cell development and epithelial phenotype maintenance. Among the ERα estrogen-independent functions, RNA processing activity was observed [ 16 ]; this activity was also shared by ligand-activated receptors [ 17 ], suggesting a new landscape that might be studied and exploited for novel potential therapeutic target identification.…”