Genome-Scale CRISPR Screening in Human Intestinal Organoids Identifies Drivers of TGF-β Resistance
Open accessAbstract
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.
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CRISPR cutting screens in 3D organoids have been implemented to explore factors such as growth factor dependency for cell growth, identify potential cancer-driving forces, and uncover key genetic events in cell differentiation.
“Even more exciting is the implementation of CRISPR cutting screens in 3D organoids to explore factors such as growth factor dependency for cell growth14–16, identifying potential cancer-driving forces17–19, and uncovering key genetic events in cell differentiation20–22.”
From Large-scale CRISPR screening in primary human 3D gastric organoids enables comprehensive dissection of gene-drug interactions (2025) · cites this paper as [15]
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- Authors
- 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.
- Affiliations
- University of Zurich (CH)
- ETH Zurich (CH)
- University Hospital Zurich (CH)
- Royal Netherlands Academy of Arts and Sciences (NL)
- Corresponding author
- Schwank, Gerald
- ORCID
- Venue
- Cell Stem Cell
- Publisher
- Elsevier BV
- Published
- 2020-03
- Volume
- 26
- Issue
- 3
- Pages
- 431-440.e8
- ISSN
- 1875-9777 (ISSN-L)
- 1934-5909
- OpenAlex
- W3009694030
- Cited by
- 202
- References
- 11
- Citations by year
- 2026: 24 · 2025: 41 · 2024: 36 · 2023: 23 · 2022: 31 · 2021: 33 · 2020: 13
- FWCI
- 8.19
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell stem cell (publishedVersion)
- PubMed (publishedVersion)
- KNAW Research Portal (The Royal Netherlands Academy of Arts and Sciences) (publishedVersion)
- Zurich Open Repository and Archive (University of Zurich) (acceptedVersion, cc-by-nc-nd)
- Utrecht University Repository (Utrecht University) (submittedVersion, other-oa)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- Zurich Open Repository and Archive (University of Zurich) (submittedVersion, cc-by-nc-nd)
- Zurich Open Repository and Archive (University of Zurich)
- Funders
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › TGF-β signaling in diseases
- Keywords
- CRISPR screen, intestinal organoids, TGF-beta resistance, colorectal cancer progression, APC mutation, SWI/SNF complex, growth restriction, forward genetic screen, 3D tissue models
- MeSH terms
- Genetic Testing, Humans, Intestines, Organoids, Transforming Growth Factor beta, Clustered Regularly Interspaced Short Palindromic Repeats
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