Journal Article

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

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

2018

Overview

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. As the human body develops, countless cells change from one state into another. Two important cell states are known as epithelial and mesenchymal. Cells in the epithelial state tend to be tightly connected and form barriers, like skin cells. Mesenchymal state cells are loosely organized, move around more and make up connective tissues. Some cells alternate between these states via an epithelial-to-mesenchymal transition (EMT for short) and back again. Without this transition, certain organs would not develop and wounds would not heal. Yet, cancer cells also use this transition to spread to distant sites of the body. Such cancers are often the most aggressive, and therefore the most deadly. The epithelial-to-mesenchymal transition is dynamically regulated in a reversible manner. For example, the genes for some proteins might only be active in the epithelial state and further reinforce this state by turning on other ‘epithelial genes’. Alternatively, there might be differences in the processing of mRNA molecules – the intermediate molecules between DNA and protein – that result in the production of different proteins in epithelial and mesenchymal cells. Li, Choi et al. wanted to know which of the thousands of human genes can endow epithelial state cells with mesenchymal characteristics. A better understanding of the switch could help to prevent cancers undergoing an epithelial-to-mesenchymal transition. From a large-scale experiment in human breast cancer cells, Li, Choi et al. found that a group of proteins that bind and modify mRNA molecules are important for the epithelial-to-mesenchymal transition. Two proteins in particular promoted the transition, most likely by binding to the mRNA of a third protein called FLNB and removing a small piece of it. 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 also contain mesenchymal cells. Finding out which FLNB protein is made in a given cancer may provide an indication of its aggressiveness. Also, looking for drugs that can target the mRNA-binding proteins or FLNB may one day lead to new treatments for some of the most aggressive breast cancers.

• Publisher: eLife Science Publications, Ltd,eLife Sciences Publications, Ltd,eLife Sciences Publications Ltd
• Subject: Actin / alternative splicing / Alternative Splicing - genetics / Animals / basal-like breast cancer / Base Sequence / Binding proteins / Biochemistry / Breast cancer / Breast Neoplasms - genetics / Breast Neoplasms - pathology / Cancer Biology / Cancer cells / Cancer prevention / Cell Biology / Cell Line, Tumor / EMT / Epithelial-Mesenchymal Transition - genetics / Exons - genetics / Female / Filamins - genetics / Filamins - metabolism / FLNB / Gene expression / Gene Expression Regulation, Neoplastic / Genes / Genome, Human / Genomes / Genomics / Humans / Hyaluronan Receptors - metabolism / Mesenchymal Stem Cells - metabolism / Messenger RNA / Mice, Nude / Muscle proteins / Neoplasm Proteins - metabolism / Open Reading Frames - genetics / Protein binding / Protein Isoforms - genetics / Protein Isoforms - metabolism / Proteins / QKI / RBFOX1 / Reproducibility of Results / RNA / RNA, Messenger - genetics / RNA, Messenger - metabolism / RNA-Binding Proteins - metabolism / Skin / Stem cells / Transcription (Genetics) / Tumors