A functional genetic toolbox for human tissue-derived organoids
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Abstract
Human organoid systems recapitulate key features of organs offering platforms for modelling developmental biology and disease. Tissue-derived organoids have been widely used to study the impact of extrinsic niche factors on stem cells. However, they are rarely used to study endogenous gene function due to the lack of efficient gene manipulation tools. Previously, we established a human foetal lung organoid system (Nikolić et al., 2017). Here, using this organoid system as an example, we have systematically developed and optimised a complete genetic toolbox for use in tissue-derived organoids. This includes ‘Organoid Easytag’, our efficient workflow for targeting all types of gene loci through CRISPR-mediated homologous recombination followed by flow cytometry for enriching correctly targeted cells. Our toolbox also incorporates conditional gene knockdown or overexpression using tightly inducible CRISPR interference and CRISPR activation which is the first efficient application of these techniques to tissue-derived organoids. These tools will facilitate gene perturbation studies in tissue-derived organoids facilitating human disease modelling and providing a functional counterpart to many ongoing descriptive studies, such as the Human Cell Atlas Project.
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Some CRISPR methods have been tested on a small scale but have not yet been fully adopted for large-scale screens in tissue-derived organoids.
“While some of these methods have been tested on a small scale35,36, they have not yet been fully adopted for large-scale screens in tissue-derived organoids.”
From Large-scale CRISPR screening in primary human 3D gastric organoids enables comprehensive dissection of gene-drug interactions (2025) · cites this paper as [35]
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- Authors
- Sun, D., Evans, L., Perrone, F., Sokleva, V., Lim, K., Rezakhani, S., Lutolf, M., Zilbauer, M., & Rawlins, E. L.
- Affiliations
- University of Cambridge (GB)
- University College London (GB)
- École Polytechnique Fédérale de Lausanne (CH)
- École Polytechnique Fédérale de Lausanne (EPFL)
- Corresponding author
- Rawlins, Emma L
- Venue
- eLife
- Publisher
- eLife Sciences Publications, Ltd
- Published
- 2021-10-06
- Volume
- 10
- ISSN
- 2050-084X (ISSN-L)
- PMC
- PMC8553336
- OpenAlex
- W3203843972
- Cited by
- 71
- References
- 37
- Citations by year
- 2026: 7 · 2025: 20 · 2024: 7 · 2023: 13 · 2022: 20 · 2021: 3 · 2020: 1
- FWCI
- 3.37
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- eLife (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Infoscience (Ecole Polytechnique Fédérale de Lausanne) (submittedVersion, cc-by-nc-nd)
- Apollo (University of Cambridge) (submittedVersion, cc-by)
- Apollo (cc-by)
- Apollo
- Funders
- Medical Research Council (MR/P009581/1, New Investigator Research Grant MR/T001917/1)
- Wellcome Trust (PhD Studentship 109146/Z/15/Z, Core Support for Gurdon Institute 203144/Z/16/Z, PhD studentship 102175/B/13/Z)
- Alzheimers Research UK Stem Cell Research Centre
- National Research Foundation of Korea (2018R1A6A3A03012122)
- Cancer Research UK (Core Support for Gurdon Institute C6946/A24843)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Pluripotent Stem Cells Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Keywords
- gene targeting, conditional gene knockdown, CRISPR interference, CRISPR activation, gene perturbation, disease modeling, Human Cell Atlas
- MeSH terms
- Humans, Lung, Organoids, Gene Targeting, Gene Knockdown Techniques, CRISPR-Cas Systems
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