Functional Repair of CFTR by CRISPR/Cas9 in Intestinal Stem Cell Organoids of Cystic Fibrosis Patients
Open accessAbstract
Single murine and human intestinal stem cells can be expanded in culture over long time periods as genetically and phenotypically stable epithelial organoids. Increased cAMP levels induce rapid swelling of such organoids by opening the cystic fibrosis transmembrane conductor receptor (CFTR). This response is lost in organoids derived from cystic fibrosis (CF) patients. Here we use the CRISPR/Cas9 genome editing system to correct the CFTR locus by homologous recombination in cultured intestinal stem cells of CF patients. The corrected allele is expressed and fully functional as measured in clonally expanded organoids. This study provides proof of concept for gene correction by homologous recombination in primary adult stem cells derived from patients with a single-gene hereditary defect.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Organoids derived from intestinal epithelial cells of pediatric IBD patients had IBD-specific DNA methylation signatures despite retaining similar morphologies.
“For instance, organoids derived from intestinal epithelial cells of pediatric IBD patients had IBD-specific DNA methylation signatures despite retaining similar morphologies195.”
From Organoids (2022) · cites this paper as [195]
The CRISPR-nuclease SpCas9 was harnessed to correct the ΔF508 mutation by homology-directed repair (HDR).
“The CRISPR-nuclease SpCas9 was harnessed to correct the ΔF508 mutation by homology-directed repair (HDR)22.”
From Allele specific repair of splicing mutations in cystic fibrosis through AsCas12a genome editing (2019) · cites this paper as [22]
Several groups have demonstrated in vitro correction of genetic disease genes including CFTR, Crygc and DMD in organoids or mouse zygotes.
“Several groups have also demonstrated in vitro correction of genetic disease genes including CFTR (cystic fibrosis)9, Crygc (cataracts)10 and DMD (Duchenne muscular dystrophy)11 in organoids or mouse zygotes.”
From Therapeutic genome editing by combined viral and non-viral delivery of CRISPR system components in vivo (2016) · cites this paper as [9]
CRISPR-Cas9 genome editing has been applied to correct disease-causing mutations in mouse zygotes and human cell lines for cataract and cystic fibrosis.
“CRISPR-Cas9 genome editing has been applied to correct disease-causing mutations in mouse zygotes and human cell lines for cataract5 and cystic fibrosis6”
From Genome editing with Cas9 in adult mice corrects a disease mutation and phenotype (2014) · cites this paper as [6]
In human intestinal stem cells from cystic fibrosis patients, CFTR was rectified by homologous recombination during CRISPR-Cas9 genome editing while pluripotency was retained.
“In human intestinal stem cells collected from patients with cystic fibrosis, the culprit gene cystic fibrosis transmembrane conductance regulator was rectified by homologous recombination during CRISPR-Cas9 genome editing while the pluripotency was retained as demonstrated by formations of organ-like expansions in cell culture.33”
From CRISPR-Cas9: a new and promising player in gene therapy (2015) · cites this paper as [33]
Cites
A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity
Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A., & Charpentier, E. (2012) · Science · doi:10.1126/science.1225829 · Cited by 17,116 · see citing works
Multiplex Genome Engineering Using CRISPR/Cas Systems
Cong, L., Ran, F. A., Cox, D., Lin, S., Barretto, R., Habib, N., Hsu, P. D., Wu, X., Jiang, W., Marraffini, L. A., et al. (2013) · Science · doi:10.1126/science.1231143 · Cited by 15,339 · see citing works
Identification of the Cystic Fibrosis Gene: Cloning and Characterization of Complementary DNA
Riordan, J. R., Rommens, J. M., Kerem, B.-S., Alon, N., Rozmahel, R., Grzelczak, Z., Zielenski, J., Lok, S., Plavsic, N., Chou, J.-L., et al. (1989) · Science · doi:10.1126/science.2475911 · Cited by 7,418 · see citing works
Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche
Sato, T., Vries, R. G., Snippert, H. J., van de Wetering, M., Barker, N., Stange, D. E., van Es, J. H., Abo, A., Kujala, P., Peters, P. J., et al. (2009) · Nature · doi:10.1038/nature07935 · Cited by 7,204 · see citing works
Self-citationDNA targeting specificity of RNA-guided Cas9 nucleases
Hsu, P. D., Scott, D. A., Weinstein, J. A., Ran, F. A., Konermann, S., Agarwala, V., Li, Y., Fine, E. J., Wu, X., Shalem, O., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2647 · Cited by 4,741 · see citing works
Ratjen, A. K. W. F. A. (2006) · Cited by 4,406 · see citing works
Identification of the Cystic Fibrosis Gene: Genetic Analysis
Kerem, B.-S., Rommens, J. M., Buchanan, J. A., Markiewicz, D., Cox, T. K., Chakravarti, A., Buchwald, M., & Tsui, L.-C. (1989) · Science · doi:10.1126/science.2570460 · Cited by 4,142 · see citing works
Sato, T., Stange, D. E., Ferrante, M., Vries, R. G. J., van Es, J. H., van den Brink, S., van Houdt, W. J., Pronk, A., van Gorp, J., Siersema, P. D., et al. (2011) · Gastroenterology · doi:10.1053/j.gastro.2011.07.050 · Cited by 3,753 · see citing works
Self-citationWang, H., Yang, H., Shivalila, C. S., Dawlaty, M. M., Cheng, A. W., Zhang, F., & Jaenisch, R. (2013) · Cell · doi:10.1016/j.cell.2013.04.025 · Cited by 3,495 · see citing works
Identification of the Cystic Fibrosis Gene: Chromosome Walking and Jumping
Rommens, J. M., Iannuzzi, M. C., Kerem, B.-S., Drumm, M. L., Melmer, G., Dean, M. C., Rozmahel, R. F., Cole, J. L., Kennedy, D., Hidaka, N., et al. (1989) · Science · doi:10.1126/science.2772657 · Cited by 3,238 · see citing works
Efficient genome editing in zebrafish using a CRISPR-Cas system
Hwang, W. Y., Fu, Y., Reyon, D., Maeder, M. L., Tsai, S. Q., Sander, J. D., Peterson, R. T., Yeh, J.-R. J., & Joung, J. K. (2013) · Nature Biotechnology · doi:10.1038/nbt.2501 · Cited by 2,937 · see citing works
Site-directed mutagenesis by gene targeting in mouse embryo-derived stem cells
Thomas, K. R., & Capecchi, M. R. (1987) · Cell · doi:10.1016/0092-8674(87)90646-5 · Cited by 2,355 · see citing works
RNA-programmed genome editing in human cells
Jinek, M., East, A., Cheng, A., Lin, S., Ma, E., & Doudna, J. (2013) · eLife · doi:10.7554/elife.00471 · Cited by 2,098 · see citing works
Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease
Cho, S. W., Kim, S., Kim, J. M., & Kim, J.-S. (2013) · Nature Biotechnology · doi:10.1038/nbt.2507 · Cited by 1,863 · see citing works
Cheng, S. H., Gregory, R. J., Marshall, J., Paul, S., Souza, D. W., White, G. A., O’Riordan, C. R., & Smith, A. E. (1990) · Cell · doi:10.1016/0092-8674(90)90148-8 · Cited by 1,792 · see citing works
Mali, P., Aach, J., Stranges, P. B., Esvelt, K. M., Moosburner, M., Kosuri, S., Yang, L., & Church, G. M. (2013) · Nature Biotechnology · doi:10.1038/nbt.2675 · Cited by 1,752 · cited 4× · see citing works
“Recently, several groups have demonstrated the use of the CRISPR/Cas9 system for genome engineering in various species (Chang et al., 2013; Cho et al., 2013; Cong et al., 2013; Friedland et al., 2013; Hou et al., 2013; Hwang et al., 2013; Jinek et al., 2013; Li et al., 2013; Mali et al., 2013; Nekrasov et al., 2013; S…”
BackgroundResultInfluentialHighly efficient endogenous human gene correction using designed zinc-finger nucleases
Urnov, F. D., Miller, J. C., Lee, Y.-L., Beausejour, C. M., Rock, J. M., Augustus, S., Jamieson, A. C., Porteus, M. H., Gregory, P. D., & Holmes, M. C. (2005) · Nature · doi:10.1038/nature03556 · Cited by 1,642 · see citing works
In vitro expansion of single Lgr5+ liver stem cells induced by Wnt-driven regeneration
Huch, M., Dorrell, C., Boj, S. F., van Es, J. H., Li, V. S. W., van de Wetering, M., Sato, T., Hamer, K., Sasaki, N., Finegold, M. J., et al. (2013) · Nature · doi:10.1038/nature11826 · Cited by 1,555 · see citing works
Self-citationLgr5+ve Stem Cells Drive Self-Renewal in the Stomach and Build Long-Lived Gastric Units In Vitro
Barker, N., Huch, M., Kujala, P., van de Wetering, M., Snippert, H. J., van Es, J. H., Sato, T., Stange, D. E., Begthel, H., van den Born, M., et al. (2010) · Cell Stem Cell · doi:10.1016/j.stem.2009.11.013 · Cited by 1,547 · see citing works
Self-citationLi, J., Norville, J. E., Aach, J., McCormack, M., Zhang, D., Bush, J., Church, G. M., & Sheen, J. (2013) · Nature Biotechnology · doi:10.1038/nbt.2654 · Cited by 1,499 · see citing works
Pattanayak, V., Lin, S., Guilinger, J. P., Ma, E., Doudna, J. A., & Liu, D. R. (2013) · Nature Biotechnology · doi:10.1038/nbt.2673 · Cited by 1,487 · cited 1× · see citing works
“It has been reported that sgRNAs can potentially tolerate mismatches in the 20 bp protospacer target sequence, which can lead to the generation of undesirable ‘‘off-target’’ indels (Hsu et al., 2013; Mali et al., 2013; Pattanayak et al., 2013).”
BackgroundLgr5 homologues associate with Wnt receptors and mediate R-spondin signalling
de Lau, W., Barker, N., Low, T. Y., Koo, B., Li, V. S. W., Teunissen, H., Kujala, P., Haegebarth, A., Peters, P. J., van de Wetering, M., et al. (2011) · Nature · doi:10.1038/nature10337 · Cited by 1,267 · see citing works
Self-citationTargeted mutagenesis in the model plant Nicotiana benthamiana using Cas9 RNA-guided endonuclease
Nekrasov, V., Staskawicz, B. J., Weigel, D., Jones, J. D. G., & Kamoun, S. (2013) · Nature Biotechnology · doi:10.1038/nbt.2655 · Cited by 1,123 · see citing works
A functional CFTR assay using primary cystic fibrosis intestinal organoids
Dekkers, J. F., Wiegerinck, C. L., de Jonge, H. R., Bronsveld, I., Janssens, H. M., de Winter-de Groot, K. M., Brandsma, A. M., de Jong, N. W. M., Bijvelds, M. J. C., Scholte, B. J., et al. (2013) · Nature Medicine · doi:10.1038/nm.3201 · Cited by 999 · see citing works
Self-citationTumour suppressor RNF43 is a stem-cell E3 ligase that induces endocytosis of Wnt receptors
Koo, B., Spit, M., Jordens, I., Low, T. Y., Stange, D. E., van de Wetering, M., van Es, J. H., Mohammed, S., Heck, A. J. R., Maurice, M. M., et al. (2012) · Nature · doi:10.1038/nature11308 · Cited by 991 · see citing works
Self-citationZNRF3 promotes Wnt receptor turnover in an R-spondin-sensitive manner
Hao, H.-X., Xie, Y., Zhang, Y., Charlat, O., Oster, E., Avello, M., Lei, H., Mickanin, C., Liu, D., Ruffner, H., et al. (2012) · Nature · doi:10.1038/nature11019 · Cited by 962 · see citing works
Ratjen, F. A., & Döring, G. (2003) · The Lancet · doi:10.1016/s0140-6736(03)12567-6 · Cited by 905 · see citing works
Heritable genome editing in C. elegans via a CRISPR-Cas9 system
Friedland, A. E., Tzur, Y. B., Esvelt, K. M., Colaiácovo, M. P., Church, G. M., & Calarco, J. A. (2013) · Nature Methods · doi:10.1038/nmeth.2532 · Cited by 899 · see citing works
Carmon, K. S., Gong, X. W., Lin, Q., Thomas, A., & Liu, Q. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1106083108 · Cited by 857 · see citing works
Enhancing Gene Targeting with Designed Zinc Finger Nucleases
Bibikova, M. V., Beumer, K. J., Trautman, J. K., & Carroll, D. (2003) · Science · doi:10.1126/science.1079512 · Cited by 824 · see citing works
Genome editing with RNA-guided Cas9 nuclease in Zebrafish embryos
Chang, N., Sun, C., Gao, L., Zhu, D., Xu, X., Zhu, X., Xiong, J., & Xi, J. (2013) · Cell Research · doi:10.1038/cr.2013.45 · Cited by 819 · see citing works
Functional engraftment of colon epithelium expanded in vitro from a single adult Lgr5+ stem cell
Yui, S., Nakamura, T., Sato, T., Nemoto, Y., Mizutani, T., Zheng, X., Ichinose, S., Nagaishi, T., Okamoto, R., Tsuchiya, K., et al. (2012) · Nature Medicine · doi:10.1038/nm.2695 · Cited by 805 · see citing works
Self-citationUnlimited in vitro expansion of adult bi-potent pancreas progenitors through the Lgr5/R-spondin axis
Huch, M., Bonfanti, P., Boj, S., Sato, T., Loomans, C. J. M., van de Wetering, M., Sojoodi, M., Li, V. S. W., Schuijers, J., Gračanin, A., et al. (2013) · EMBO Journal · doi:10.1038/emboj.2013.204 · Cited by 710 · see citing works
Self-citationIsolation and in vitro expansion of human colonic stem cells
Jung, P., Sato, T., Merlos-Suárez, A., Barriga, F. M., Iglesias, M., Rossell, D., Auer, H., Gallardo, M., Blasco, M. A., Sancho, E., et al. (2011) · Nature Medicine · doi:10.1038/nm.2470 · Cited by 709 · see citing works
Self-citationHou, Z., Zhang, Y., Propson, N. E., Howden, S. E., Chu, L.-F., Sontheimer, E. J., & Thomson, J. A. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1313587110 · Cited by 681 · see citing works
Gene targeting using zinc finger nucleases
Porteus, M. H., & Carroll, D. (2005) · Nature Biotechnology · doi:10.1038/nbt1125 · Cited by 641 · see citing works
Generation of gene-modified mice via Cas9/RNA-mediated gene targeting
Shen, B., Zhang, J., Wu, H., Wang, J., Ma, K., Li, Z., Zhang, X., Zhang, P., & Huang, X. (2013) · Cell Research · doi:10.1038/cr.2013.46 · Cited by 556 · see citing works
Chromosomal deletions and inversions mediated by TALENs and CRISPR/Cas in zebrafish
Xiao, A., Wang, Z., Hu, Y., Wu, Y., Luo, Z., Yang, Z., Zu, Y., Li, W., Huang, P., Tong, X., et al. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt464 · Cited by 388 · see citing works
Highly Efficient Genome Modifications Mediated by CRISPR/Cas9 in Drosophila
Yu, Z., Ren, M., Wang, Z., Zhang, B., Rong, Y. S., Jiao, R., & Gao, G. (2013) · Genetics · doi:10.1534/genetics.113.153825 · Cited by 339 · see citing works
DNA double-strand break repair by homologous recombination
Dudáš, A., & Chovanec, M. (2003) · Mutation Research/Reviews in Mutation Research · doi:10.1016/j.mrrev.2003.07.001 · Cited by 268 · see citing works
DNA Double-Strand Break Repair by Homologous Recombination
van den Bosch, M., Lohman, P. H. M., & Pastink, A. (2002) · Biological Chemistry · doi:10.1515/bc.2002.095 · Cited by 169 · see citing works
Thiagarajah, J. R., Song, Y., Haggie, P. M., & Verkman, A. S. (2004) · The FASEB Journal · doi:10.1096/fj.03-1248fje · Cited by 107 · see citing works
Generation of BAC Transgenic Epithelial Organoids
Schwank, G., Andersson-Rolf, A., Koo, B., Sasaki, N., & Clevers, H. C. (2013) · PLoS ONE · doi:10.1371/journal.pone.0076871 · Cited by 98 · see citing works
Self-citationLgr5 + liver stem cells, hepatic organoids and regenerative medicine
Huch, M., Boj, S. F., & Clevers, H. C. (2013) · Regenerative Medicine · doi:10.2217/rme.13.39 · Cited by 88 · see citing works
Self-citationNon-homologous end joining as a mechanism of DNA repair
Barnes, D. E. (2001) · Current Biology · doi:10.1016/s0960-9822(01)00279-2 · Cited by 64 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
The new frontier of genome engineering with CRISPR-Cas9
Doudna, J. A., & Charpentier, E. (2014) · Science · doi:10.1126/science.1258096 · Cited by 7,062 · see citing works
Development and Applications of CRISPR-Cas9 for Genome Engineering
Hsu, P. D., Lander, E. S., & Zhang, F. (2014) · Cell · doi:10.1016/j.cell.2014.05.010 · Cited by 5,762 · see citing works
Modeling Development and Disease with Organoids
Clevers, H. (2016) · Cell · doi:10.1016/j.cell.2016.05.082 · Cited by 3,196 · see citing works
Self-citationHuman organoids: model systems for human biology and medicine
Kim, J., Koo, B.-K., & Knoblich, J. A. (2020) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-020-0259-3 · Cited by 2,187 · see citing works
Self-citationDrost, J., & Clevers, H. (2018) · Nature Reviews Cancer · doi:10.1038/s41568-018-0007-6 · Cited by 1,790 · see citing works
Self-citationLong-Term Culture of Genome-Stable Bipotent Stem Cells from Adult Human Liver
Huch, M., Gehart, H., van Boxtel, R., Hamer, K., Blokzijl, F., Verstegen, M. M. A., Ellis, E., van Wenum, M., Fuchs, S. A., de Ligt, J., et al. (2015) · Cell · doi:10.1016/j.cell.2014.11.050 · Cited by 1,619 · see citing works
Self-citationProgress and potential in organoid research
Rossi, G., Manfrin, A., & Lutolf, M. P. (2018) · Nature Reviews Genetics · doi:10.1038/s41576-018-0051-9 · Cited by 1,182 · see citing works
Therapeutic genome editing: prospects and challenges
Cox, D. B. T., Platt, R. J., & Zhang, F. (2015) · Nature Medicine · doi:10.1038/nm.3793 · Cited by 1,336 · see citing works
Delivering CRISPR: a review of the challenges and approaches
Lino, C. A., Harper, J. C., Carney, J. P., & Timlin, J. A. (2018) · Drug Delivery · doi:10.1080/10717544.2018.1474964 · Cited by 1,185 · see citing works
Hofer, M., & Lutolf, M. P. (2021) · Nature Reviews Materials · doi:10.1038/s41578-021-00279-y · Cited by 1,184 · see citing works
A guide to genome engineering with programmable nucleases
Kim, S., & Kim, J. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3686 · Cited by 1,162 · see citing works
CRISPR/Cas9 in Genome Editing and Beyond
Wang, H., Russa, M. F. L., & Qi, L. S. (2016) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-060815-014607 · Cited by 1,165 · see citing works
Modeling colorectal cancer using CRISPR-Cas9–mediated engineering of human intestinal organoids
Matano, M., Date, S., Shimokawa, M., Takano, A., Fujii, M., Ohta, Y., Watanabe, T., Kanai, T., & Sato, T. (2015) · Nature Medicine · doi:10.1038/nm.3802 · Cited by 1,135 · see citing works
Sequential cancer mutations in cultured human intestinal stem cells
Drost, J., van Jaarsveld, R. H., Ponsioen, B., Zimberlin, C., van Boxtel, R., Buijs, A., Sachs, N., Overmeer, R. M., Offerhaus, G. J., Begthel, H., et al. (2015) · Nature · doi:10.1038/nature14415 · Cited by 1,067 · see citing works
Self-citationLong‐term expanding human airway organoids for disease modeling
Sachs, N., Papaspyropoulos, A., Zomer‐van Ommen, D. D., Heo, I., Böttinger, L., Klay, D., Weeber, F., Huelsz‐Prince, G., Iakobachvili, N., Amatngalim, G. D., et al. (2019) · The EMBO Journal · doi:10.15252/embj.2018100300 · Cited by 1,082 · see citing works
Self-citationCRISPR-Based Technologies for the Manipulation of Eukaryotic Genomes
Komor, A. C., Badran, A. H., & Liu, D. R. (2016) · Cell · doi:10.1016/j.cell.2016.10.044 · Cited by 1,011 · see citing works
Tales from the crypt: new insights into intestinal stem cells
Gehart, H., & Clevers, H. C. (2018) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-018-0081-y · Cited by 984 · see citing works
Self-citationGenome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells
Wu, X., Scott, D. A., Kriz, A. J., Chiu, A. C., Hsu, P. D., Dadon, D. B., Cheng, A. W., Trevino, A. E., Konermann, S., Chen, S., et al. (2014) · Nature Biotechnology · doi:10.1038/nbt.2889 · Cited by 944 · see citing works
Zhao, Z., Chen, X., Dowbaj, A. M., Sljukic, A., Bratlie, K., Lin, L., Fong, E. L. S., Balachander, G. M., Chen, Z., Soragni, A., et al. (2022) · Nature Reviews Methods Primers · doi:10.1038/s43586-022-00174-y · Cited by 1,001 · see citing works
“Cystic fibrosis organoids have also been used to investigate gene therapy interventions and are able to rescue the effect of CFTR mutations in intestinal organoids using CRISPR–Cas9 (ref.(195)).”
BackgroundApplications of CRISPR technologies in research and beyond
Barrangou, R., & Doudna, J. A. (2016) · Nature Biotechnology · doi:10.1038/nbt.3659 · Cited by 1,005 · see citing works
Cystic fibrosis genetics: from molecular understanding to clinical application
Cutting, G. R. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3849 · Cited by 969 · see citing works
Genome editing with Cas9 in adult mice corrects a disease mutation and phenotype
Yin, H., Xue, W., Chen, S., Bogorad, R. L., Benedetti, E., Grompe, M., Koteliansky, V., Sharp, P. A., Jacks, T., & Anderson, D. G. (2014) · Nature Biotechnology · doi:10.1038/nbt.2884 · Cited by 951 · see citing works
Yin, H., Song, C.-Q., Dorkin, J. R., Zhu, L. J., Li, Y., Wu, Q., Park, A., Yang, J., Suresh, S., Bizhanova, A., et al. (2016) · Nature Biotechnology · doi:10.1038/nbt.3471 · Cited by 876 · see citing works
Disease modeling in stem cell-derived 3D organoid systems
Dutta, D., Heo, I., & Clevers, H. (2017) · Trends in Molecular Medicine · doi:10.1016/j.molmed.2017.02.007 · Cited by 838 · see citing works
Self-citationBroutier, L., Andersson-Rolf, A., Hindley, C. J., Boj, S. F., Clevers, H., Koo, B.-K., & Huch, M. (2016) · Nature Protocols · doi:10.1038/nprot.2016.097 · Cited by 834 · see citing works
Self-citationEngineering Stem Cell Organoids
Yin, X., Mead, B. E., Safaee, H., Langer, R., Karp, J. M., & Levy, O. (2016) · Cell Stem Cell · doi:10.1016/j.stem.2015.12.005 · Cited by 866 · see citing works
A distinct role for Lgr5+ stem cells in primary and metastatic colon cancer
Melo, F. D. S. E., Kurtova, A. V., Harnoss, J. M., Kljavin, N. M., Hoeck, J. D., Hung, J., Anderson, J. E., Storm, E. E., Modrusan, Z. D., Koeppen, H., et al. (2017) · Nature · doi:10.1038/nature21713 · Cited by 782 · see citing works
Prevention of muscular dystrophy in mice by CRISPR/Cas9–mediated editing of germline DNA
Long, C., McAnally, J. R., Shelton, J. M., Mireault, A. A., Bassel-Duby, R., & Olson, E. N. (2014) · Science · doi:10.1126/science.1254445 · Cited by 720 · see citing works
Identification of Multipotent Luminal Progenitor Cells in Human Prostate Organoid Cultures
Karthaus, W. R., Iaquinta, P. J., Drost, J., Gracanin, A., van Boxtel, R., Wongvipat, J., Dowling, C., Gao, D., Begthel, H., Sachs, N., et al. (2014) · Cell · doi:10.1016/j.cell.2014.08.017 · Cited by 720 · see citing works
Self-citationCRISPR/Cas9 therapeutics: progress and prospects
Li, T., Yang, Y., Qi, H., Cui, W., Zhang, L., Fu, X., He, X., Liu, M., Li, P., & Yu, T. (2023) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-023-01309-7 · Cited by 770 · see citing works
Genome-editing Technologies for Gene and Cell Therapy
Maeder, M. L., & Gersbach, C. A. (2016) · Molecular Therapy · doi:10.1038/mt.2016.10 · Cited by 722 · see citing works
Organoid culture systems for prostate epithelial and cancer tissue
Drost, J., Karthaus, W. R., Gao, D., Driehuis, E., Sawyers, C. L., Chen, Y., & Clevers, H. C. (2016) · Nature Protocols · doi:10.1038/nprot.2016.006 · Cited by 694 · see citing works
Self-citationYAP/TAZ-Dependent Reprogramming of Colonic Epithelium Links ECM Remodeling to Tissue Regeneration
Yui, S., Azzolin, L., Maimets, M., Pedersen, M. T., Fordham, R. P., Hansen, S. L., Larsen, H. L., Guiu, J., Alves, M. R. P., Rundsten, C. F., et al. (2017) · Cell stem cell · doi:10.1016/j.stem.2017.11.001 · Cited by 678 · see citing works
Three-dimensional organotypic culture: experimental models of mammalian biology and disease
Shamir, E. R., & Ewald, A. J. (2014) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3873 · Cited by 719 · see citing works
Pluripotent stem cells in disease modelling and drug discovery
Avior, Y., Sagi, I., & Benvenisty, N. (2016) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2015.27 · Cited by 592 · see citing works
Delivery technologies for genome editing
Yin, H., Kauffman, K. J., & Anderson, D. G. (2017) · Nature Reviews Drug Discovery · doi:10.1038/nrd.2016.280 · Cited by 597 · see citing works
Wei, T., Cheng, Q., Min, Y.-L., Olson, E. N., & Siegwart, D. J. (2020) · Nature Communications · doi:10.1038/s41467-020-17029-3 · Cited by 603 · see citing works
Direct cytosolic delivery of CRISPR/Cas9-ribonucleoprotein for efficient gene editing
Mout, R., Ray, M., Yesilbag Tonga, G., Lee, Y.-W., Tay, T., Sasaki, K., & Rotello, V. M. (2017) · ACS Nano · doi:10.1021/acsnano.6b07600 · Cited by 579 · see citing works
The CRISPR-Cas immune system: Biology, mechanisms and applications
Rath, D., Amlinger, L., Rath, A., & Lundgren, M. (2015) · Biochimie · doi:10.1016/j.biochi.2015.03.025 · Cited by 565 · see citing works
Corrò, C., Novellasdemunt, L., & Li, V. S. W. (2020) · American Journal of Physiology-Cell Physiology · doi:10.1152/ajpcell.00120.2020 · Cited by 561 · see citing works
Wang, H.-X., Li, M., Lee, C. M., Chakraborty, S., Kim, H.-W., Bao, G., & Leong, K. W. (2017) · Chemical Reviews · doi:10.1021/acs.chemrev.6b00799 · Cited by 560 · see citing works
Modeling mouse and human development using organoid cultures
Huch, M., & Koo, B. (2015) · Development · doi:10.1242/dev.118570 · Cited by 543 · see citing works
Self-citationExpanding the genetic editing tool kit: ZFNs, TALENs, and CRISPR-Cas9
Gupta, R. M., & Musunuru, K. (2014) · Journal of Clinical Investigation · doi:10.1172/jci72992 · Cited by 545 · see citing works
Induced Pluripotent Stem Cells Meet Genome Editing
Hockemeyer, D., & Jaenisch, R. (2016) · Cell Stem Cell · doi:10.1016/j.stem.2016.04.013 · Cited by 499 · see citing works
“Combining the cellular versatility of iPSC differentiation with the ease of CRISPR/Cas9-mediated genome editing proved to be a very powerful experimental approach and by now genome editing in hPSCs has become a standard tool in stem cell research and human disease modeling (Johnson and Hockemeyer, 2015; Matano et al.,…”
BackgroundVisualization of a short-range Wnt gradient in the intestinal stem-cell niche
Farin, H. F., Jordens, I., Mosa, M. H., Basak, O., Korving, J., Tauriello, D. V. F., de Punder, K., Angers, S., Peters, P. J., Maurice, M. M., et al. (2016) · Nature · doi:10.1038/nature16937 · Cited by 525 · see citing works
Self-citationHuman Organoids: Tools for Understanding Biology and Treating Diseases
Schutgens, F., & Clevers, H. C. (2019) · Annual Review of Pathology Mechanisms of Disease · doi:10.1146/annurev-pathmechdis-012419-032611 · Cited by 506 · see citing works
Self-citationGiobbe, G. G., Crowley, C., Luni, C., Campinoti, S., Khedr, M., Kretzschmar, K., De Santis, M. M., Zambaiti, E., Michielin, F., Meran, L., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-13605-4 · Cited by 500 · see citing works
Self-citationMutations and mechanisms of WNT pathway tumour suppressors in cancer
Bugter, J. M., Fenderico, N., & Maurice, M. M. (2021) · Nature Reviews Cancer · doi:10.1038/s41568-020-00307-z · Cited by 466 · see citing works
CRISPR-Cas: biology, mechanisms and relevance
Hille, F., & Charpentier, E. (2016) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2015.0496 · Cited by 503 · see citing works
Human organoids in basic research and clinical applications
Tang, X., Wu, S., Wang, D., Chu, C., Hong, Y., Tao, M., Hu, H., Xu, M., Guo, X., & Liu, Y. (2022) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-022-01024-9 · Cited by 424 · see citing works
Tumor Organoids as a Pre-clinical Cancer Model for Drug Discovery
Weeber, F., Ooft, S., Dijkstra, K. K., & Voest, E. E. (2017) · Cell chemical biology · doi:10.1016/j.chembiol.2017.06.012 · Cited by 486 · see citing works
Organoids: Modeling Development and the Stem Cell Niche in a Dish
Kretzschmar, K., & Clevers, H. C. (2016) · Developmental Cell · doi:10.1016/j.devcel.2016.08.014 · Cited by 480 · see citing works
Self-citationEfficient Gene Disruption in Diverse Strains of Toxoplasma gondii Using CRISPR/CAS9
Shen, B., Brown, K. M., Lee, T. D., & Sibley, L. D. (2014) · mBio · doi:10.1128/mbio.01114-14 · Cited by 453 · see citing works
The Intestinal Barrier and Current Techniques for the Assessment of Gut Permeability
Schoultz, I., & Keita, Å. V. (2020) · Cells · doi:10.3390/cells9081909 · Cited by 479 · see citing works
Ousterout, D. G., Kabadi, A. M., Thakore, P. I., Majoros, W. H., Reddy, T. E., & Gersbach, C. A. (2015) · Nature Communications · doi:10.1038/ncomms7244 · Cited by 470 · see citing works
Mechanism and Applications of CRISPR/Cas-9-Mediated Genome Editing
Mengstie, M. A., & Wondimu, B. Z. (2021) · Biologics · doi:10.2147/btt.s326422 · Cited by 478 · see citing works
Progress in therapies for cystic fibrosis
Boeck, K. D., & Amaral, M. D. (2016) · The Lancet Respiratory Medicine · doi:10.1016/s2213-2600(16)00023-0 · Cited by 453 · see citing works
The hope and the hype of organoid research
Huch, M., Knoblich, J. A., Lutolf, M. P., & Martinez-Arias, A. (2017) · Development · doi:10.1242/dev.150201 · Cited by 409 · see citing works
Rapid modelling of cooperating genetic events in cancer through somatic genome editing
Rivera, F. J. S., Papagiannakopoulos, T. Y., Romero, R., Tammela, T., Bauer, M. R., Bhutkar, A. J., Joshi, N. S., Subbaraj, L., Bronson, R. T., Xue, W., et al. (2014) · Nature · doi:10.1038/nature13906 · Cited by 404 · see citing works
Towards organoid culture without Matrigel
Kozlowski, M. T., Crook, C. J., & Ku, H. T. (2021) · Communications Biology · doi:10.1038/s42003-021-02910-8 · Cited by 409 · see citing works
Xu, Y., & Li, Z. (2020) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2020.08.031 · Cited by 424 · see citing works
Saxena, K., Blutt, S. E., Ettayebi, K., Zeng, X.-L., Broughman, J. R., Crawford, S. E., Karandikar, U. C., Sastri, N. P., Conner, M. E., Opekun, A. R., et al. (2016) · Journal of Virology · doi:10.1128/jvi.01930-15 · Cited by 375 · see citing works
Disease modelling in human organoids
Lancaster, M. A., & Huch, M. (2019) · Disease Models & Mechanisms · doi:10.1242/dmm.039347 · Cited by 379 · see citing works
Efficient genetic engineering of human intestinal organoids using electroporation
Fujii, M., Matano, M., Nanki, K., & Sato, T. (2015) · Nature Protocols · doi:10.1038/nprot.2015.088 · Cited by 364 · see citing works
Target specificity of the CRISPR‐Cas9 system
Wu, X., Kriz, A. J., & Sharp, P. A. (2014) · Quantitative Biology · doi:10.1007/s40484-014-0030-x · Cited by 373 · see citing works
Organoids — Preclinical Models of Human Disease
Li, M., & Belmonte, J. C. I. (2019) · New England Journal of Medicine · doi:10.1056/nejmra1806175 · Cited by 360 · see citing works
Single luminal epithelial progenitors can generate prostate organoids in culture
Chua, C. W., Shibata, M., Lei, M., Toivanen, R., Barlow, L. J., Bergren, S. K., Badani, K. K., McKiernan, J. M., Benson, M. C., Hibshoosh, H. H., et al. (2014) · Nature Cell Biology · doi:10.1038/ncb3047 · Cited by 352 · see citing works
Tak, Y. G., & Farnham, P. (2015) · Epigenetics & Chromatin · doi:10.1186/s13072-015-0050-4 · Cited by 342 · see citing works
In vivo genome editing and organoid transplantation models of colorectal cancer and metastasis
Roper, J., Tammela, T., Cetinbas, N. M., Akkad, A., Roghanian, A., Rickelt, S., Almeqdadi, M., Wu, K., Oberli, M. A., Rivera, F. J. S., et al. (2017) · Nature Biotechnology · doi:10.1038/nbt.3836 · Cited by 345 · see citing works
Canver, M. C., Bauer, D. E., Dass, A., Yien, Y. Y., Chung, J., Masuda, T., Maeda, T., Paw, B. H., & Orkin, S. H. (2014) · Journal of Biological Chemistry · doi:10.1074/jbc.m114.564625 · Cited by 342 · see citing works
Smith, C., Gore, A., Yan, W., Abalde-Atristain, L., Li, Z., He, C., Wang, Y., Brodsky, R. A., Zhang, K., Cheng, L., et al. (2014) · Cell stem cell · doi:10.1016/j.stem.2014.06.011 · Cited by 342 · see citing works
Human tissues in a dish: The research and ethical implications of organoid technology
Bredenoord, A. L., Clevers, H., & Knoblich, J. A. (2017) · Science · doi:10.1126/science.aaf9414 · Cited by 334 · see citing works
Self-citationDivergent Routes toward Wnt and R-spondin Niche Independency during Human Gastric Carcinogenesis
Nanki, K., Toshimitsu, K., Takano, A., Fujii, M., Shimokawa, M., Ohta, Y., Matano, M., Seino, T., Nishikori, S., Ishikawa, K., et al. (2018) · Cell · doi:10.1016/j.cell.2018.07.027 · Cited by 335 · see citing works
Self-citationHeichler, C., Koop, K., Schmied, A., Geppert, C. I., Schmid, B., Wirtz, S. J., Thoma, O., Kramer, V., Waldner, M. J., Büttner, C., et al. (2019) · Gut · doi:10.1136/gutjnl-2019-319200 · Cited by 330 · see citing works
CRISPR/Cas9 for cancer research and therapy
Zhan, T., Rindtorff, N., Betge, J., Ebert, M., & Boutros, M. (2018) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2018.04.001 · Cited by 333 · see citing works
Functional Gene Correction for Cystic Fibrosis in Lung Epithelial Cells Generated from Patient iPSCs
Firth, A. L., Menon, T., Parker, G. S., Qualls, S. J., Lewis, B. M., Ke, E., Dargitz, C., Wright, R., Khanna, A., Gage, F. H., et al. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.07.062 · Cited by 327 · see citing works
Ong, T., & Ramsey, B. W. (2023) · JAMA · doi:10.1001/jama.2023.8120 · Cited by 327 · see citing works
Current Biomedical Applications of 3D Printing and Additive Manufacturing
Ahangar, P., Cooke, M. E., Weber, M. H., & Rosenzweig, D. H. (2019) · Applied Sciences · doi:10.3390/app9081713 · Cited by 315 · see citing works
Artegiani, B., Hendriks, D. F. G., Beumer, J., Kok, R. N. U., Zheng, X., Joore, I. P., Lopes, S. M. C. D. S., van Zon, J. S., Tans, S. J., & Clevers, H. C. (2020) · Nature Cell Biology · doi:10.1038/s41556-020-0472-5 · Cited by 302 · see citing works
Self-citationPost-translational Regulation of Cas9 during G1 Enhances Homology-Directed Repair
Gutschner, T., Hämmerle, M., Genovese, G., Draetta, G. F., & Chin, L. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.01.019 · Cited by 296 · see citing works
CRISPR Ethics: Moral Considerations for Applications of a Powerful Tool
Brokowski, C., & Adli, M. (2018) · Journal of Molecular Biology · doi:10.1016/j.jmb.2018.05.044 · Cited by 320 · see citing works
Zachos, N., Kovbasnjuk, O., Foulke-Abel, J. D., In, J. G., Blutt, S., de Jonge, H. D., Estes, M., & Donowitz, M. (2015) · Journal of Biological Chemistry · doi:10.1074/jbc.r114.635995 · Cited by 261 · see citing works
Recent Advances in CRISPR/Cas9 Delivery Strategies
Yip, B. H. (2020) · Biomolecules · doi:10.3390/biom10060839 · Cited by 303 · see citing works
CRISPR-Cas9: A Preclinical and Clinical Perspective for the Treatment of Human Diseases
Sharma, G., Sharma, A. R., Bhattacharya, M., Lee, S., & Chakraborty, C. (2020) · Molecular Therapy · doi:10.1016/j.ymthe.2020.09.028 · Cited by 295 · see citing works
Growth of Epithelial Organoids in a Defined Hydrogel
Broguiere, N., Isenmann, L., Hirt, C., Ringel, T., Placzek, S., Cavalli, E., Ringnalda, F., Villiger, L., Züllig, R., Lehmann, R., et al. (2018) · Advanced Materials · doi:10.1002/adma.201801621 · Cited by 282 · see citing works
Self-citationTALEN and CRISPR/Cas Genome Editing Systems: Tools of Discovery
Nemudryi, A. A., Valetdinova, K. R., Medvedev, S. P., & Zakian, S. M. (2014) · Acta Naturae · doi:10.32607/20758251-2014-6-3-19-40 · Cited by 284 · see citing works
Lgr5-expressing chief cells drive epithelial regeneration and cancer in the oxyntic stomach
Leushacke, M., Tan, S. H., Wong, A. M. L., Yada, S., Hajamohideen, A., Tan, L. T., Goh, J., Wong, E. S. P., Denil, S. L. I. J., Murakami, K., et al. (2017) · Nature Cell Biology · doi:10.1038/ncb3541 · Cited by 276 · see citing works
Personalized Cancer Medicine: An Organoid Approach
Es, H. A., Montazeri, L., Aref, A. R., Vosough, M., & Baharvand, H. (2018) · Trends in biotechnology · doi:10.1016/j.tibtech.2017.12.005 · Cited by 277 · see citing works
Machine Learning in Genomic Medicine: A Review of Computational Problems and Data Sets
Leung, M. K. K., Delong, A., Alipanahi, B., & Frey, B. J. (2015) · Proceedings of the IEEE · doi:10.1109/jproc.2015.2494198 · Cited by 276 · see citing works
Organoids: The current status and biomedical applications
Yang, S., Hu, H., Kung, H., Zou, R.-Q., Dai, Y.-S., Hu, Y.-F., Wang, T., Lv, T., Yu, J., & Li, F. (2023) · MedComm · doi:10.1002/mco2.274 · Cited by 282 · see citing works
Genome modification by CRISPR /Cas9
Ma, Y., Zhang, L., & Huang, X. (2014) · FEBS Journal · doi:10.1111/febs.13110 · Cited by 279 · see citing works
CRISPR/Cas9‐mediated genome engineering: An adeno‐associated viral (AAV) vector toolbox
Senís, E., Fatouros, C., Große, S., Wiedtke, E., Niopek, D., Mueller, A., Börner, K., & Grimm, D. (2014) · Biotechnology Journal · doi:10.1002/biot.201400046 · Cited by 262 · see citing works
Fumagalli, A., Drost, J., Suijkerbuijk, S. J. E., van Boxtel, R., de Ligt, J., Offerhaus, G. J. A., Begthel, H., Beerling, E., Tan, E. H., Sansom, O. J., et al. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1701219114 · Cited by 259 · see citing works
Self-citationEstablishment and Culture of Human Intestinal Organoids Derived from Adult Stem Cells
Pleguezuelos‐Manzano, C., Puschhof, J., van den Brink, S., Geurts, V., Beumer, J., & Clevers, H. C. (2020) · Current Protocols in Immunology · doi:10.1002/cpim.106 · Cited by 256 · see citing works
Self-citationCFTR: cystic fibrosis and beyond
Mall, M. A., & Hartl, D. (2014) · European Respiratory Journal · doi:10.1183/09031936.00228013 · Cited by 257 · see citing works
Advances in therapeutic CRISPR/Cas9 genome editing
Savić, N., & Schwank, G. (2016) · Translational Research · doi:10.1016/j.trsl.2015.09.008 · Cited by 257 · see citing works
Self-citationCheroni, C., Caporale, N., & Testa, G. (2020) · Molecular Autism · doi:10.1186/s13229-020-00370-1 · Cited by 268 · see citing works
Cystic fibrosis: current therapeutic targets and future approaches
Rafeeq, M. M., & Murad, H. A. S. (2017) · Journal of Translational Medicine · doi:10.1186/s12967-017-1193-9 · Cited by 254 · see citing works
Marinko, J. T., Huang, H., Penn, W. D., Capra, J. A., Schlebach, J. P., & Sanders, C. R. (2019) · Chemical Reviews · doi:10.1021/acs.chemrev.8b00532 · Cited by 249 · see citing works
Prostaglandin E2 promotes intestinal repair through an adaptive cellular response of the epithelium
Miyoshi, H., VanDussen, K. L., Malvin, N. P., Ryu, H., Wang, Y., Sonnek, N. M., Lai, C., & Stappenbeck, T. S. (2016) · The EMBO Journal · doi:10.15252/embj.201694660 · Cited by 244 · see citing works
- Authors
- Schwank, G., Koo, B.-K., Sasselli, V., Dekkers, J. F., Heo, I., Demircan, T., Sasaki, N., Boymans, S., Cuppen, E., van der Ent, C. K., Nieuwenhuis, E. E. S., Beekman, J. M., & Clevers, H.
- Affiliations
- University Medical Center Utrecht (NL)
- Wilhelmina Children's Hospital (NL)
- Hubrecht Institute for Developmental Biology and Stem Cell Research (NL)
- Corresponding author
- Clevers, Hans
- ORCID
- Venue
- Cell Stem Cell
- Publisher
- Elsevier BV
- Published
- 2013-12
- Volume
- 13
- Issue
- 6
- Pages
- 653-658
- ISSN
- 1875-9777 (ISSN-L)
- 1934-5909
- OpenAlex
- W1986316308
- Cited by
- 1,424
- References
- 45
- Citations by year
- 2026: 64 · 2025: 74 · 2024: 92 · 2023: 78 · 2022: 105 · 2021: 152 · 2020: 137 · 2019: 120 · 2018: 118 · 2017: 148 · 2016: 150 · 2015: 110 · 2014: 72 · 2013: 3
- FWCI
- 50.06
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell stem cell (publishedVersion)
- PubMed (publishedVersion)
- KNAW research portal (Royal Academy of Art and Sciences (KNAW)) (publishedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- Funders
- Wellcome Trust (079249, 097922/C/11/Z)
- 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 › Genetics › Virus-based gene therapy research
- Keywords
- cystic fibrosis, CFTR, CRISPR/Cas9 genome editing, homologous recombination, gene correction, cAMP signaling, adult stem cells
- MeSH terms
- Adult, Animals, Base Sequence, Cystic Fibrosis, Humans, Intestines, Molecular Sequence Data, Organoids, Stem Cells, Genetic Therapy, RNA Editing, Cystic Fibrosis Transmembrane Conductance Regulator, Mice, Adult Stem Cells, Clustered Regularly Interspaced Short Palindromic Repeats, CRISPR-Associated Proteins
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
