An alternative splicing switch in FLNB promotes the mesenchymal cell state in human breast cancer.

Ji Li,Seav Huong Ly,Jong Wook Kim,Katherine Labella,Jennifer Y Ge,Ole Gjoerup,Shom Goel,Chao Dai,Justin Hwang ,Nina Ilić ,Peter S Choi ,John G Doench ,Angela N Brooks ,Robert A Weinberg ,Andrew L Hong ,David E Root ,Andrew O Giacomelli ,Christine L Chaffer ,Kimberly R Hagel ,Jean J Zhao ,William C Hahn

doi:10.7554/elife.37184

Abstract

Alternative splicing of mRNA precursors represents a key gene expression regulatory step and permits the generation of distinct protein products with diverse functions. In a genome-scale expression screen for inducers of the epithelial-to-mesenchymal transition (EMT), we found a striking enrichment of RNA-binding proteins. We validated that QKI and RBFOX1 were necessary and sufficient to induce an intermediate mesenchymal cell state and increased tumorigenicity. Using RNA-seq and eCLIP analysis, we found that QKI and RBFOX1 coordinately regulated the splicing and function of the actin-binding protein FLNB, which plays a causal role in the regulation of EMT. Specifically, the skipping of FLNB exon 30 induced EMT by releasing the FOXC1 transcription factor. Moreover, skipping of FLNB exon 30 is strongly associated with EMT gene signatures in basal-like breast cancer patient samples. These observations identify a specific dysregulation of splicing, which regulates tumor cell plasticity and is frequently observed in human cancer.

Highlights

Alternative splicing (AS) of mRNA precursors is a fundamental biological process that provides a reversible mechanism to modulate the expression of related but distinct proteins in response to internal and external stimuli (Chen and Manley, 2009)
We found that QKI-binding sites were highly enriched for the RBFOX-binding motif, UGCAUG (Figure 4B,C) and overall, there was a substantial degree of overlap between QKI and RBFOX1 eCLIP-binding peaks (p
Among all the common targets of QKI and RBFOX1, we found that CD44 (IC:0.857, p value:

Summary

Introduction

Alternative splicing (AS) of mRNA precursors is a fundamental biological process that provides a reversible mechanism to modulate the expression of related but distinct proteins in response to internal and external stimuli (Chen and Manley, 2009). FLNB normally works to prevent the epithelial-to-mesenchymal transition, but the smaller protein encoded by the shorter mRNA promoted the transition by turning on ‘mesenchymal genes’ This switching between different FLNB proteins happens in some of the more aggressive breast cancers, which contain mesenchymal cells. Exon skipping in KIF13A and CTTN (Braeutigam et al, 2014; Venables et al, 2013; Yang et al, 2016) and in circular RNA formation (Conn et al, 2015) It remains unclear whether the upregulation of any specific RBPs is sufficient or required for the induction of mesenchymal state transitions or is merely one of many downstream manifestations of the EMT. We have undertaken a comprehensive approach to identify genes that regulate the EMT in breast cancer and found that genes whose protein products participate in AS regulate the transition to mesenchymal- and stem-like cell states

Results

Discussion

Materials and methods