Genome-Scale CRISPR Screening in Human Intestinal Organoids Identifies Drivers of TGF-β Resistance

Till Ringel, Nina Frey, Femke Ringnalda, Sharan Janjuha, Sarah Cherkaoui, Stefan Butz, Sumana Srivatsa, Martin Pirkl, Giancarlo Russo, Lukas Villiger, Gerhard Rogler, Hans Clevers, Niko Beerenwinkel, Nicola Zamboni, Tuncay Baubec, Gerald Schwank

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Abstract

Forward genetic screens with genome-wide CRISPR libraries are powerful tools for resolving cellular circuits and signaling pathways. Applying this technology to organoids, however, has been hampered by technical limitations. Here we report improved accuracy and robustness for pooled-library CRISPR screens by capturing sgRNA integrations in single organoids, substantially reducing required cell numbers for genome-scale screening. We applied our approach to wild-type and APC mutant human intestinal organoids to identify genes involved in resistance to TGF-β-mediated growth restriction, a key process during colorectal cancer progression, and validated hits including multiple subunits of the tumor-suppressive SWI/SNF chromatin remodeling complex. Mutations within these genes require concurrent inactivation of APC to promote TGF-β resistance and attenuate TGF-β target gene transcription. Our approach can be applied to a variety of assays and organoid types to facilitate biological discovery in primary 3D tissue models.

Original languageEnglish
Pages (from-to)431-440.e8
JournalCell Stem Cell
Volume26
Issue number3
DOIs
Publication statusPublished - 05 Mar 2020

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    Ringel, T., Frey, N., Ringnalda, F., Janjuha, S., Cherkaoui, S., Butz, S., Srivatsa, S., Pirkl, M., Russo, G., Villiger, L., Rogler, G., Clevers, H., Beerenwinkel, N., Zamboni, N., Baubec, T., & Schwank, G. (2020). Genome-Scale CRISPR Screening in Human Intestinal Organoids Identifies Drivers of TGF-β Resistance. Cell Stem Cell, 26(3), 431-440.e8. https://doi.org/10.1016/j.stem.2020.02.007