E2F1 and epigenetic modifiers orchestrate breast cancer progression by regulating oxygen-dependent ESRP1 expression

Cheemala Ashok,Sanjeev Shukla,Subhashis Natua,Atul Samaiya,Jharna Mishra,Neha Ahuja

doi:10.1038/s41389-021-00347-6

Abstract

Epithelial splicing regulatory protein 1 (ESRP1) is an RNA binding protein that governs the alternative splicing events related to epithelial phenotypes. ESRP1 contributes significantly at different stages of cancer progression. ESRP1 expression is substantially elevated in carcinoma in situ compared to the normal epithelium, whereas it is drastically ablated in cancer cells within hypoxic niches, which promotes epithelial to mesenchymal transition (EMT). Although a considerable body of research sought to understand the EMT-associated ESRP1 downregulation, the regulatory mechanisms underlying ESRP1 upregulation in primary tumors remained largely uncharted. This study seeks to unveil the regulatory mechanisms that spatiotemporally fine-tune the ESRP1 expression during breast carcinogenesis. Our results reveal that an elevated expression of transcription factor E2F1 and increased CpG hydroxymethylation of the E2F1 binding motif conjointly induce ESRP1 expression in breast carcinoma. However, E2F1 fails to upregulate ESRP1 despite its abundance in oxygen-deprived breast cancer cells. Mechanistically, impelled by the hypoxia-driven reduction of tet methylcytosine dioxygenase 3 (TET3) activity, CpG sites across the E2F1 binding motif lose the hydroxymethylation marks while gaining the de novo methyltransferase-elicited methylation marks. These two oxygen-sensitive epigenetic events work in concert to repel E2F1 from the ESRP1 promoter, thereby diminishing ESRP1 expression under hypoxia. Furthermore, E2F1 skews the cancer spliceome by upregulating splicing factor SRSF7 in hypoxic breast cancer cells. Our findings provide previously unreported mechanistic insights into the plastic nature of ESRP1 expression and insinuate important implications in therapeutics targeting breast cancer progression.

Highlights

Despite the enormous progress made in the realm of screening, diagnosis, and therapeutic strategies engaged in cancer management, breast cancer remains a major health concern and currently represents a top biomedical research priority
Transcription factor E2F1 is essential for Epithelial splicing regulatory protein 1 (ESRP1) mediated breast carcinogenesis A series of recent studies have established an elevated ESRP1 level as a key determinant of tumorigenesis in several cancers, such as colorectal cancer, ovarian cancer, and head and neck cancer
ESRP1, a member of the RBM family of RNA-binding proteins (RBPs), was initially identified as epithelium-specific splicing regulators in a genome-wide high-throughput cDNA screen aimed at finding the key regulators of FGFR2 splicing in epithelial cells [22]

Summary

Introduction

Despite the enormous progress made in the realm of screening, diagnosis, and therapeutic strategies engaged in cancer management, breast cancer remains a major health concern and currently represents a top biomedical research priority. The complex process of breast cancer initiation and progression is associated with a dysregulation in many gene regulatory networks at the transcriptional, post-transcriptional, and epigenetic levels. RNA-binding proteins (RBPs), which govern the post-transcriptional events, including alternative pre-mRNA splicing, polyadenylation, mRNA stability, mRNA localization, and translation, are emerging as critical regulators of several processes in breast carcinogenesis [1,2,3]. The heterogeneous nuclear ribonucleoprotein M (hnRNPM) promotes epithelial-mesenchymal transition (EMT) and metastasis in breast cancer by promoting the biased expression of CD44 standard isoform (CD44s) [7]. HnRNP A2 increases breast cancer cell invasion by promoting the expression of a specific isoform of TP53INP2 [8]. RNA binding protein FOX2 ( known as RBM9) drives mesenchymal-specific splicing to regulate EMT [9, 10]

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Conclusion