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Identifying regulators of aberrant stem cell and differentiation activity in colorectal cancer using a dual endogenous reporter system

Author

Listed:
  • Sandor Spisak

    (Dana-Farber Cancer Institute
    Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences)

  • David Chen

    (Dana-Farber Cancer Institute
    University of Toronto)

  • Pornlada Likasitwatanakul

    (Dana-Farber Cancer Institute
    Harvard Medical School
    Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University
    Faculty of Medicine Siriraj Hospital, Mahidol University)

  • Paul Doan

    (Dana-Farber Cancer Institute
    Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University)

  • Zhixin Li

    (Dana-Farber Cancer Institute
    Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University)

  • Pratyusha Bala

    (Dana-Farber Cancer Institute
    Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University)

  • Laura Vizkeleti

    (Faculty of Medicine, Semmelweis University)

  • Viktoria Tisza

    (Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences)

  • Pushpamali Silva

    (Dana-Farber Cancer Institute)

  • Marios Giannakis

    (Dana-Farber Cancer Institute
    Harvard Medical School
    Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University
    Gastrointestinal Cancer Center, Dana-Farber Cancer Institute)

  • Brian Wolpin

    (Dana-Farber Cancer Institute
    Harvard Medical School
    Gastrointestinal Cancer Center, Dana-Farber Cancer Institute)

  • Jun Qi

    (Dana-Farber Cancer Institute)

  • Nilay S. Sethi

    (Dana-Farber Cancer Institute
    Harvard Medical School
    Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University
    Gastrointestinal Cancer Center, Dana-Farber Cancer Institute)

Abstract

Aberrant stem cell-like activity and impaired differentiation are central to the development of colorectal cancer (CRC). To identify functional mediators of these key cellular programs, we engineer a dual endogenous reporter system by genome-editing the SOX9 and KRT20 loci of human CRC cell lines to express fluorescent reporters, broadcasting aberrant stem cell-like and differentiation activity, respectively. By applying a CRISPR screen targeting 78 epigenetic regulators with 542 sgRNAs to this platform, we identify factors that contribute to stem cell-like activity and differentiation in CRC. Perturbation single cell RNA sequencing (Perturb-seq) of validated hits nominate SMARCB1 of the BAF complex (also known as SWI/SNF) as a negative regulator of differentiation across an array of neoplastic colon models. SMARCB1 is a dependency and required for in vivo growth of human CRC models. These studies highlight the utility of biologically designed endogenous reporter platforms to uncover regulators with therapeutic potential.

Suggested Citation

  • Sandor Spisak & David Chen & Pornlada Likasitwatanakul & Paul Doan & Zhixin Li & Pratyusha Bala & Laura Vizkeleti & Viktoria Tisza & Pushpamali Silva & Marios Giannakis & Brian Wolpin & Jun Qi & Nilay, 2024. "Identifying regulators of aberrant stem cell and differentiation activity in colorectal cancer using a dual endogenous reporter system," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-46285-w
    DOI: 10.1038/s41467-024-46285-w
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