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RNA splicing is a key mediator of tumour cell plasticity and a therapeutic vulnerability in colorectal cancer

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  • Adam E. Hall

    (The University of Edinburgh, Western General Hospital Campus
    The University of Edinburgh, Western General Hospital)

  • Sebastian Öther-Gee Pohl

    (The University of Edinburgh, Western General Hospital Campus
    The University of Edinburgh, Western General Hospital)

  • Patrizia Cammareri

    (The University of Edinburgh, Western General Hospital Campus
    The University of Edinburgh, Western General Hospital)

  • Stuart Aitken

    (The University of Edinburgh, Western General Hospital Campus
    The University of Edinburgh, Western General Hospital)

  • Nicholas T. Younger

    (University of Edinburgh)

  • Michela Raponi

    (The University of Edinburgh, Western General Hospital Campus
    The University of Edinburgh, Western General Hospital
    Garscube Estate)

  • Caroline V. Billard

    (The University of Edinburgh, Western General Hospital Campus
    The University of Edinburgh, Western General Hospital)

  • Alfonso Bolado Carrancio

    (The University of Edinburgh, Western General Hospital Campus
    The University of Edinburgh, Western General Hospital)

  • Aslihan Bastem

    (The University of Edinburgh, Western General Hospital Campus
    The University of Edinburgh, Western General Hospital)

  • Paz Freile

    (The University of Edinburgh, Western General Hospital Campus
    The University of Edinburgh, Western General Hospital)

  • Fiona Haward

    (The University of Edinburgh, Western General Hospital Campus
    The University of Edinburgh, Western General Hospital
    University of Dundee)

  • Ian R. Adams

    (The University of Edinburgh, Western General Hospital Campus
    The University of Edinburgh, Western General Hospital)

  • Javier F. Caceres

    (The University of Edinburgh, Western General Hospital Campus
    The University of Edinburgh, Western General Hospital)

  • Paula Preyzner

    (The University of Edinburgh, Western General Hospital Campus
    The University of Edinburgh, Western General Hospital)

  • Alex Kriegsheim

    (The University of Edinburgh, Western General Hospital Campus
    The University of Edinburgh, Western General Hospital)

  • Malcolm G. Dunlop

    (The University of Edinburgh, Western General Hospital Campus
    The University of Edinburgh, Western General Hospital)

  • Farhat V. Din

    (The University of Edinburgh, Western General Hospital Campus
    The University of Edinburgh, Western General Hospital)

  • Kevin B. Myant

    (The University of Edinburgh, Western General Hospital Campus
    The University of Edinburgh, Western General Hospital)

Abstract

Tumour cell plasticity is a major barrier to the efficacy of targeted cancer therapies but the mechanisms that mediate it are poorly understood. Here, we identify dysregulated RNA splicing as a key driver of tumour cell dedifferentiation in colorectal cancer (CRC). We find that Apc-deficient CRC cells have dysregulated RNA splicing machinery and exhibit global rewiring of RNA splicing. We show that the splicing factor SRSF1 controls the plasticity of tumour cells by controlling Kras splicing and is required for CRC invasion in a mouse model of carcinogenesis. SRSF1 expression maintains stemness in human CRC organoids and correlates with cancer stem cell marker expression in human tumours. Crucially, partial genetic downregulation of Srsf1 does not detrimentally affect normal tissue homeostasis, demonstrating that tumour cell plasticity can be differentially targeted. Thus, our findings link dysregulation of the RNA splicing machinery and control of tumour cell plasticity.

Suggested Citation

  • Adam E. Hall & Sebastian Öther-Gee Pohl & Patrizia Cammareri & Stuart Aitken & Nicholas T. Younger & Michela Raponi & Caroline V. Billard & Alfonso Bolado Carrancio & Aslihan Bastem & Paz Freile & Fio, 2022. "RNA splicing is a key mediator of tumour cell plasticity and a therapeutic vulnerability in colorectal cancer," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
  • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-30489-z
    DOI: 10.1038/s41467-022-30489-z
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    1. Adam L. Haber & Moshe Biton & Noga Rogel & Rebecca H. Herbst & Karthik Shekhar & Christopher Smillie & Grace Burgin & Toni M. Delorey & Michael R. Howitt & Yarden Katz & Itay Tirosh & Semir Beyaz & Da, 2017. "A single-cell survey of the small intestinal epithelium," Nature, Nature, vol. 551(7680), pages 333-339, November.
    2. Cheryl M. Koh & Marco Bezzi & Diana H. P. Low & Wei Xia Ang & Shun Xie Teo & Florence P. H. Gay & Muthafar Al-Haddawi & Soo Yong Tan & Motomi Osato & Arianna Sabò & Bruno Amati & Keng Boon Wee & Ernes, 2015. "MYC regulates the core pre-mRNA splicing machinery as an essential step in lymphomagenesis," Nature, Nature, vol. 523(7558), pages 96-100, July.
    3. Julia Joung & Jesse M. Engreitz & Silvana Konermann & Omar O. Abudayyeh & Vanessa K. Verdine & Francois Aguet & Jonathan S. Gootenberg & Neville E. Sanjana & Jason B. Wright & Charles P. Fulco & Yuen-, 2017. "Erratum: Genome-scale activation screen identifies a lncRNA locus regulating a gene neighbourhood," Nature, Nature, vol. 549(7672), pages 418-418, September.
    4. Hua Tian & Brian Biehs & Søren Warming & Kevin G. Leong & Linda Rangell & Ophir D. Klein & Frederic J. de Sauvage, 2011. "A reserve stem cell population in small intestine renders Lgr5-positive cells dispensable," Nature, Nature, vol. 478(7368), pages 255-259, October.
    5. Mariko Shimokawa & Yuki Ohta & Shingo Nishikori & Mami Matano & Ai Takano & Masayuki Fujii & Shoichi Date & Shinya Sugimoto & Takanori Kanai & Toshiro Sato, 2017. "Visualization and targeting of LGR5+ human colon cancer stem cells," Nature, Nature, vol. 545(7653), pages 187-192, May.
    6. Nick Barker & Johan H. van Es & Jeroen Kuipers & Pekka Kujala & Maaike van den Born & Miranda Cozijnsen & Andrea Haegebarth & Jeroen Korving & Harry Begthel & Peter J. Peters & Hans Clevers, 2007. "Identification of stem cells in small intestine and colon by marker gene Lgr5," Nature, Nature, vol. 449(7165), pages 1003-1007, October.
    7. Victoria Gudiño & Sebastian Öther-Gee Pohl & Caroline V. Billard & Patrizia Cammareri & Alfonso Bolado & Stuart Aitken & David Stevenson & Adam E. Hall & Mark Agostino & John Cassidy & Colin Nixon & A, 2021. "RAC1B modulates intestinal tumourigenesis via modulation of WNT and EGFR signalling pathways," Nature Communications, Nature, vol. 12(1), pages 1-17, December.
    8. Julia Joung & Jesse M. Engreitz & Silvana Konermann & Omar O. Abudayyeh & Vanessa K. Verdine & Francois Aguet & Jonathan S. Gootenberg & Neville E. Sanjana & Jason B. Wright & Charles P. Fulco & Yuen-, 2017. "Genome-scale activation screen identifies a lncRNA locus regulating a gene neighbourhood," Nature, Nature, vol. 548(7667), pages 343-346, August.
    9. Felipe de Sousa e Melo & Antonina V. Kurtova & Jonathan M. Harnoss & Noelyn Kljavin & Joerg D. Hoeck & Jeffrey Hung & Jeffrey Eastham Anderson & Elaine E. Storm & Zora Modrusan & Hartmut Koeppen & Ger, 2017. "A distinct role for Lgr5+ stem cells in primary and metastatic colon cancer," Nature, Nature, vol. 543(7647), pages 676-680, March.
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