CRISPR-Based Adenine Editors Correct Nonsense Mutations in a Cystic Fibrosis Organoid Biobank
Open accessAbstract
Adenine base editing (ABE) enables enzymatic conversion from A-T into G-C base pairs. ABE holds promise for clinical application, as it does not depend on the introduction of double-strand breaks, contrary to conventional CRISPR/Cas9-mediated genome engineering. Here, we describe a cystic fibrosis (CF) intestinal organoid biobank, representing 664 patients, of which ~20% can theoretically be repaired by ABE. We apply SpCas9-ABE (PAM recognition sequence: NGG) and xCas9-ABE (PAM recognition sequence: NGN) on four selected CF organoid samples. Genetic and functional repair was obtained in all four cases, while whole-genome sequencing (WGS) of corrected lines of two patients did not detect off-target mutations. These observations exemplify the value of large, patient-derived organoid biobanks representing hereditary disease and indicate that ABE may be safely applied in human cells.
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ABEs have been used in Cystic Fibrosis patient-derived organoids to functionally repair mutations in CFTR without genome-wide off-targets.
“We have previously described the use of ABEs in Cystic Fibrosis patient-derived organoids to functionally repair mutations in CFTR without genome-wide off-targets31.”
From One-step generation of tumor models by base editor multiplexing in adult stem cell-derived organoids (2023) · cites this paper as [31]
The Summary reports genetic and functional repair in four patient-derived CF organoid samples. It says whole-genome sequencing of corrected lines from two patients detected no off-target mutations; the Results and Discussion likewise say no genome-wide off-target effects could be detected. The claim omits that testing was limited to those lines and presents non-detection as an unqualified absence of off-targets. (LLM, conf=0.85)
Experimental — accuracy not yet measuredBase editors have been applied before in organoids to model and repair diseases, and this study significantly extends their application by demonstrating opportunities in multiplexing CBEs and ABEs, Cas9 homologs, and evolved Cas9 variants.
“While base editors have been applied before in organoids to model36 and repair31 diseases, we significantly extend their application by demonstrating the opportunities that reside in multiplexing CBE’s and ABE’s, as well as Cas9 homologs and evolved Cas9 variants.”
From One-step generation of tumor models by base editor multiplexing in adult stem cell-derived organoids (2023) · cites this paper as [31]
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- Authors
- Geurts, M. H., de Poel, E., Amatngalim, G. D., Oka, R., Meijers, F. M., Kruisselbrink, E., van Mourik, P., Berkers, G., de Winter-de Groot, K. M., Michel, S., Muilwijk, D., Aalbers, B. L., Mullenders, J., Boj, S. F., Suen, S. W. F., Brunsveld, J. E., Janssens, H. M., Mall, M. A., Graeber, S. Y., van Boxtel, R., van der Ent, C. K., Beekman, J. M., & Clevers, H.
- Affiliations
- Royal Netherlands Academy of Arts and Sciences (NL)
- Utrecht University (NL)
- Oncode Institute (NL)
- Erasmus MC (NL)
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin (DE)
- Corresponding author
- Beekman, Jeffrey M.
- Clevers, Hans
- ORCID
- Venue
- Cell Stem Cell
- Publisher
- Elsevier BV
- Published
- 2020-04
- Volume
- 26
- Issue
- 4
- Pages
- 503-510.e7
- ISSN
- 1875-9777 (ISSN-L)
- 1934-5909
- OpenAlex
- W3007694991
- Cited by
- 222
- References
- 46
- Citations by year
- 2026: 19 · 2025: 33 · 2024: 31 · 2023: 37 · 2022: 33 · 2021: 44 · 2020: 25
- FWCI
- 11.37
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell stem cell (publishedVersion)
- PubMed (publishedVersion)
- EUR Research Repository (Erasmus University Rotterdam) (publishedVersion)
- EUR Research Repository (Erasmus University Rotterdam) (submittedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- Utrecht University Repository (Utrecht University) (submittedVersion, other-oa)
- KNAW Research Portal (The Royal Netherlands Academy of Arts and Sciences) (submittedVersion)
- Funders
- Cancer Research UK (C6307/A29058)
- Charité – Universitätsmedizin Berlin
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek (737.016.009)
- Berlin Institute of Health
- Nederlandse Cystic Fibrosis Stichting
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Health Sciences › Medicine › Pulmonary and Respiratory Medicine › Cystic Fibrosis Research Advances
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
- Keywords
- adenine base editing, cystic fibrosis, nonsense mutation, intestinal organoids, organoid biobank, gene correction, off-target mutations, genetic disorders, patient-derived cells
- MeSH terms
- Gene Editing, CRISPR-Associated Protein 9, Adenine, Cystic Fibrosis, Humans, Organoids, Biological Specimen Banks, Codon, Nonsense, Clustered Regularly Interspaced Short Palindromic Repeats, CRISPR-Cas Systems
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