1. Cancer Biology
  2. Cell Biology
Download icon

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

  1. Ji Li
  2. Peter S Choi
  3. Christine L Chaffer
  4. Katherine Labella
  5. Justin H Hwang
  6. Andrew O Giacomelli
  7. Jong Wook Kim
  8. Nina Ilic
  9. John G Doench
  10. Seav Huong Ly
  11. Chao Dai
  12. Kimberly Hagel
  13. Andrew L Hong
  14. Ole Gjoerup
  15. Shom Goel
  16. Jennifer Y Ge
  17. David E Root
  18. Jean J Zhao
  19. Angela N Brooks
  20. Robert A Weinberg
  21. William C Hahn  Is a corresponding author
  1. Dana-Farber Cancer Institute, United States
  2. Whitehead Institute for Biomedical Research, United States
  3. Broad Institute, United States
  4. Dana-Farber Cancer Institue, United States
  5. Harvard Medical School, United States
  6. University of California, Santa Cruz, United States
Research Article
  • Cited 28
  • Views 4,195
  • Annotations
Cite this article as: eLife 2018;7:e37184 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.

Data availability

Both the RNA-seq data and the CLIP-seq data are deposited at NCBI Gene Expression Omnibus (accession number GSE98210).

The following data sets were generated

Article and author information

Author details

  1. Ji Li

    Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Peter S Choi

    Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Christine L Chaffer

    Whitehead Institute for Biomedical Research, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Katherine Labella

    Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Justin H Hwang

    Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Andrew O Giacomelli

    Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2109-0458
  7. Jong Wook Kim

    Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Nina Ilic

    Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. John G Doench

    Broad Institute, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  10. Seav Huong Ly

    Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
  11. Chao Dai

    Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
  12. Kimberly Hagel

    Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
  13. Andrew L Hong

    Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0374-1667
  14. Ole Gjoerup

    Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
  15. Shom Goel

    Broad Institute, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  16. Jennifer Y Ge

    Department of Medical Oncology, Dana-Farber Cancer Institue, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
  17. David E Root

    Broad Institute, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  18. Jean J Zhao

    Department of Cancer Biology, Harvard Medical School, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
  19. Angela N Brooks

    University of California, Santa Cruz, Santa Cruz, United States
    Competing interests
    The authors declare that no competing interests exist.
  20. Robert A Weinberg

    Whitehead Institute for Biomedical Research, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  21. William C Hahn

    Department of Medical Oncology, Dana-Farber Cancer Institue, Cambridge, United States
    For correspondence
    william_hahn@dfci.harvard.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2840-9791

Funding

National Cancer Institute (R01 CA130988)

  • William C Hahn

National Cancer Institute (U01 CA176058)

  • William C Hahn

Susan G. Komen (PDF14300517)

  • Ji Li

Terri Brodeur Breast Cancer Foundation grant

  • Ji Li

National Cancer Institute (K99 CA208028)

  • Peter S Choi

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Animal experimentation: This study with use of animals was performed in accordance to the protocol (04-101) approved by Dana-Farber Cancer Institute (DFCI)'s Institutional Animal Care and Use Committee (IACUC). The animals were handled according to the Guide for the Care and Use of Laboratory Animals of the National Institute of Health.

Reviewing Editor

  1. Douglas L Black, University of California, Los Angeles, United States

Publication history

  1. Received: April 1, 2018
  2. Accepted: July 24, 2018
  3. Accepted Manuscript published: July 30, 2018 (version 1)
  4. Version of Record published: August 21, 2018 (version 2)

Copyright

© 2018, Li et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 4,195
    Page views
  • 715
    Downloads
  • 28
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Download citations (links to download the citations from this article in formats compatible with various reference manager tools)

Open citations (links to open the citations from this article in various online reference manager services)

Further reading

    1. Cancer Biology
    Polona Safaric Tepes et al.
    Research Article Updated

    Despite current advancements in research and therapeutics, lung cancer remains the leading cause of cancer-related mortality worldwide. This is mainly due to the resistance that patients develop against chemotherapeutic agents over the course of treatment. In the context of non-small cell lung cancers (NSCLC) harboring EGFR-oncogenic mutations, augmented levels of AXL and GAS6 have been found to drive resistance to EGFR tyrosine kinase inhibitors such as Erlotinib and Osimertinib in certain tumors with mesenchymal-like features. By studying the ontogeny of AXL-positive cells, we have identified a novel non-genetic mechanism of drug resistance based on cell-state transition. We demonstrate that AXL-positive cells are already present as a subpopulation of cancer cells in Erlotinib-naïve tumors and tumor-derived cell lines and that the expression of AXL is regulated through a stochastic mechanism centered on the epigenetic regulation of miR-335. The existence of a cell-intrinsic program through which AXL-positive/Erlotinib-resistant cells emerge infers the need of treating tumors harboring EGFR-oncogenic mutations upfront with combinatorial treatments targeting both AXL-negative and AXL-positive cancer cells.

    1. Cancer Biology
    Nicolai J Toft et al.
    Research Article Updated

    Breast cancer heterogeneity in histology and molecular subtype influences metabolic and proliferative activity and hence the acid load on cancer cells. We hypothesized that acid-base transporters and intracellular pH (pHi) dynamics contribute inter-individual variability in breast cancer aggressiveness and prognosis. We show that Na+,HCO3 cotransport and Na+/H+ exchange dominate cellular net acid extrusion in human breast carcinomas. Na+/H+ exchange elevates pHi preferentially in estrogen receptor-negative breast carcinomas, whereas Na+,HCO3 cotransport raises pHi more in invasive lobular than ductal breast carcinomas and in higher malignancy grade breast cancer. HER2-positive breast carcinomas have elevated protein expression of Na+/H+ exchanger NHE1/SLC9A1 and Na+,HCO3 cotransporter NBCn1/SLC4A7. Increased dependency on Na+,HCO3 cotransport associates with severe breast cancer: enlarged CO2/HCO3-dependent rises in pHi predict accelerated cell proliferation, whereas enhanced CO2/HCO3-dependent net acid extrusion, elevated NBCn1 protein expression, and reduced NHE1 protein expression predict lymph node metastasis. Accordingly, we observe reduced survival for patients suffering from luminal A or basal-like/triple-negative breast cancer with high SLC4A7 and/or low SLC9A1 mRNA expression. We conclude that the molecular mechanisms of acid-base regulation depend on clinicopathological characteristics of breast cancer patients. NBCn1 expression and dependency on Na+,HCO3 cotransport for pHi regulation, measured in biopsies of human primary breast carcinomas, independently predict proliferative activity, lymph node metastasis, and patient survival.