Volume 10 Number 2 2026
Patient-derived organoids for cystic fibrosis drug discovery of biological validity and screening scalability
Umayyah Osman 1*
Integrative Biomedical Research 10 (2) 1-23 https://doi.org/10.25163/biomedical.10210961
Submitted: 04 September 2026 Revised: 22 October 2026 Accepted: 31 October 2026 Published: 02 November 2026
Cystic fibrosis remains a monogenic disease with a stubbornly heterogeneous therapeutic landscape. Small-molecule CFTR modulators now benefit most people carrying F508del, yet roughly one in ten patients — those with premature termination codons, ultra-rare missense alleles, or deep intronic splicing defects — derive little or no benefit, and even genotypically identical individuals respond unevenly. Patient-derived three-dimensional organoids have emerged as the preclinical system best positioned to close that gap. This review evaluates how far organoid-based high-throughput screening has actually come, separating what the evidence supports from what remains aspirational. We examine four questions in turn: whether organoids are biologically valid surrogates for the patient; whether the functional assays built on them measure what they claim to measure; whether those assays genuinely scale; and whether the platform can validate the nucleic acid and gene editing therapies now entering development. The forskolin-induced swelling assay anchors the field, and its concordance with sweat chloride, ppFEV1, and nasal potential difference is strong enough to have guided real prescribing decisions through initiatives such as HIT-CF. Miniaturization into 384-well formats, robotic liquid handling, and deep-learning image analysis — OrgaQuant, DETECTOR, OrgaSegment — have converted a laborious bench assay into a screening platform with acceptable statistical power. Opened-organoid monolayers resolve the geometric problem of an enclosed apical membrane, extending screening to ENaC, TMEM16A, and SLC6A14. Substantial obstacles persist, however: matrix variability, tissue-specific regulatory differences, cost, and the absence of a regulatory framework qualifying organoid response as a surrogate endpoint. We argue these are tractable engineering and governance problems rather than biological ones.
Keywords: cystic fibrosis; CFTR; patient-derived organoids; forskolin-induced swelling; high-throughput screening; theratyping; prime editing; deep learning
Ahmadi, S., Xia, S., Wu, Y. S., Di Paola, M., Laselva, O., Avolio, J., & Bear, C. E. (2017). Phenotypic profiling of CFTR modulators in patient-derived respiratory epithelia. npj Genomic Medicine, 2(1), 12.
Amatngalim, G. D., Rodenburg, L. W., Aalbers, B. L., Raeven, H. H., Aarts, E. M., Sarhane, D., Spelier, S., Lefferts, J. W., Silva, I. A. L., & Nijenhuis, W. (2022). Measuring cystic fibrosis drug responses in organoids derived from 2D differentiated nasal epithelia. Life Science Alliance, 5(12), e202101320.
Amistadi, S., Maule, G., Ciciani, M., Ensinck, M. M., De Keersmaecker, L., Ramalho, A. S., Guidone, D., Buccirossi, M., Galietta, L. J. V., Carlon, M. S., & Cereseto, A. (2023). Functional restoration of a CFTR splicing mutation through RNA delivery of CRISPR adenine base editor. Molecular Therapy, 31(5), 1647–1660.
Anzalone, A. V., Randolph, P. B., Davis, J. R., Sousa, A. A., Koblan, L. W., Levy, J. M., Chen, P. J., Wilson, C., Newby, G. A., Raguram, A., & Liu, D. R. (2019). Search-and-replace genome editing without double-strand breaks or donor DNA. Nature, 576(7785), 149–157.
Berical, A., Lee, R. E., Lu, J., Beermann, M. L., Le Suer, J. A., Mithal, A., Thomas, D., Ranallo, N., Peasley, M., Stuffer, A., & Hawkins, F. (2022). A multimodal iPSC platform for cystic fibrosis drug testing. Nature Communications, 13(1), 4270.
Berkers, G., van Mourik, P., Vonk, A. M., Kruisselbrink, E., Dekkers, J. F., de Winter-de Groot, K. M., Arets, H. G. M., Marck-van der Wilt, R. E. P., Dijkema, J. S., Vanderschuren, M. M., & Beekman, J. M. (2019). Rectal organoids enable personalized treatment of cystic fibrosis. Cell Reports, 26(7), 1701–1708.
Bierlaagh, M. C., Ramalho, A. S., Silva, I. A., Vonk, A. M., van den Bor, R. M., van Mourik, P., Pott, J., Suen, S. W. F., Boj, S. F., Vries, R. G. J., & Beekman, J. M. (2024). Repeatability and reproducibility of the forskolin-induced swelling (FIS) assay on intestinal organoids from people with cystic fibrosis. Journal of Cystic Fibrosis, 23(4), 693–702.
Boj, S. F., Vonk, A. M., Statia, M., Su, J., Vries, R. R. G., Beekman, J. M., & Clevers, H. (2017). Forskolin-induced swelling in intestinal organoids: An in vitro assay for assessing drug response in cystic fibrosis patients. Journal of Visualized Experiments, (120), e55159.
Boonekamp, K. E., & Boutros, M. (2026). Primer: Drug discovery and patient-derived organoids. Current Opinion in Systems Biology, 45, 100579.
Borten, M. A., Bajikar, S. S., Sasaki, N., Clevers, H., & Janes, K. A. (2018). Automated brightfield morphometry of 3D organoid populations by OrganoSeg. Scientific Reports, 8(1), 5319.
Brewington, J. J., Filbrandt, E. T., LaRosa, F. J., Ostmann, A. J., Strecker, L. M., Szczesniak, R. D., & Clancy, J. P. (2018). Detection of CFTR function and modulation in primary human nasal cell spheroids. Journal of Cystic Fibrosis, 17(1), 26–33.
Bulcaen, M., Kortleven, P., Liu, R. B., Maule, G., Dreano, E., Kelly, M., Ensinck, M. M., Thierie, S., Smits, M., Ciciani, M., Hatton, A., Chevalier, B., & Carlon, M. S. (2024). Prime editing functionally corrects cystic fibrosis-causing CFTR mutations in human organoids and airway epithelial cells. Cell Reports Medicine, 5(5), 101544.
Conti, J., Sorio, C., & Melotti, P. (2022). Organoid technology and its role for theratyping applications in cystic fibrosis. Children, 10(1), 4.
Cutting, G. R. (2015). Cystic fibrosis genetics: From molecular understanding to clinical application. Nature Reviews Genetics, 16(1), 45–56.
de Poel, E., Spelier, S., Hagemeijer, M. C., & Beekman, J. M. (2023). FDA-approved drug screening in patient-derived organoids demonstrates potential of drug repurposing for rare cystic fibrosis genotypes. Journal of Cystic Fibrosis, 22(3), 548–559.
de Poel, E., Spelier, S., Hagemeijer, M. C., van der Windt, I. S., van Hugten, C. F. J., van Beuningen, S. F. B., Rodenburg, R. N. P., & Beekman, J. M. (2022). Drug repurposing for cystic fibrosis: Identification of drugs that induce CFTR-independent fluid secretion in nasal organoids. International Journal of Molecular Sciences, 23(20), 12657.
de Winter-de Groot, K. M., Berkers, G., Marck-van der Wilt, R. E. P., van der Meer, R., Vonk, A., Dekkers, J. F., Geerdink, M., Michel, S., Kruisselbrink, E., Vries, R., & Beekman, J. M. (2019). Forskolin-induced swelling of intestinal organoids correlates with disease severity in adults with cystic fibrosis and homozygous F508del mutations. Journal of Cystic Fibrosis, 18(5), 614–619.
Dekkers, J. F., Berkers, G., Kruisselbrink, E., Vonk, A., de Jonge, H. R., Janssens, H. M., Bronsveld, I., van de Graaf, E. A., Nieuwenhuis, E. E. S., Houwen, R. H. J., & Beekman, J. M. (2016). Characterizing responses to CFTR-modulating drugs using rectal organoids derived from subjects with cystic fibrosis. Science Translational Medicine, 8(344), 344ra84.
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., & Beekman, J. M. (2013). A functional CFTR assay using primary cystic fibrosis intestinal organoids. Nature Medicine, 19(7), 939–945.
del Angel Zuvirie, C., van der Drift, L., Yan, K., Price, L. S., & Bange, H. (2022). Enabling RNA-based gene modification in high-throughput screenings using cystic fibrosis patient-derived organoids. Journal of Cystic Fibrosis, 21(Suppl. 1), S103–S104.
Demchenko, A., Balyasin, M., Nazarova, A., Grigorieva, O., Panchuk, I., Kondrateva, E., Tabakov, V., Schagina, O., Amelina, E., & Smirnikhina, S. (2025). Human induced lung organoids: A promising tool for cystic fibrosis drug screening. International Journal of Molecular Sciences, 26(1), 437.
Diosdi, A., Toth, T., Harmati, M., Istvan, G., Schrettner, B., Hapek, N., Kovacs, F., Kriston, A., Buzas, K., Pampaloni, F., Piccinini, F., & Horvath, P. (2025). HCS-3DX, a next-generation AI-driven automated 3D-oid high-content screening system. Nature Communications, 16(1), 8897.
Fawcett, L. K., Wakefield, C. E., Sivam, S., Middleton, P. G., Wark, P., Widger, J., Jaffe, A., & Waters, S. A. (2021). Avatar acceptability: Views from the Australian cystic fibrosis community on the use of personalised organoid technology to guide treatment decisions. ERJ Open Research, 7(1), 00448-2020.
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., & Clevers, H. (2020). CRISPR-based adenine base editing corrects cystic fibrosis mutations in intestinal organoids. Cell Stem Cell, 26(4), 503–510.
Guimbellot, J. S., Leach, J. M., Chaudhry, I. G., Quinney, N. L., Boyles, S. E., Chua, M., Aban, I., Jaspers, I., & Gentzsch, M. (2017). Nasospheroids permit measurements of CFTR-dependent fluid transport. JCI Insight, 2(21), e95734.
Hagemeijer, M. C., Vonk, A. M., Awatade, N. T., Silva, I. A., Tischer, C., Hilsenstein, V., Beekman, J. M., Amaral, M. D., & Botelho, H. M. (2020). An open-source high-content analysis workflow for CFTR function measurements using the forskolin-induced swelling assay. Bioinformatics, 36(24), 5686–5694.
Kassis, T., Hernandez-Gordillo, V., Langer, R., & Griffith, L. G. (2019). OrgaQuant: Human intestinal organoid localization and quantification using deep convolutional neural networks. Scientific Reports, 9(1), 12479.
Keating, D., Marigowda, G., Burr, L., Daines, C., Mall, M. A., McKone, E. F., Ramsey, B. W., Rowe, S. M., Taylor-Cousar, J. L., & Waltz, D. (2018). VX-445–tezacaftor–ivacaftor in patients with cystic fibrosis and one or two Phe508del alleles. New England Journal of Medicine, 379(17), 1612–1620.
Lefferts, J. W., Kroes, S., Smith, M. B., Niemöller, P. J., Nieuwenhuijze, N. D., Sonneveld van Kooten, H. N., van der Ent, C. K., Beekman, J. M., & van Beuningen, S. F. (2024). OrgaSegment: Deep-learning based organoid segmentation to quantify CFTR dependent fluid secretion. Communications Biology, 7(1), 319.
Lim, S. H., Aboualizadeh, F., Petschnigg, J., & Stagljar, I. (2021). Identification of FGL2 as a novel regulator of CFTR maturation and function using primary intestinal organoids. Molecular Systems Biology, 17(11), e10629.
Martin, U. (2015). Pluripotent stem cells for disease modeling and drug screening: New perspectives for treatment of cystic fibrosis? Molecular and Cellular Therapies, 3(1), 1–12.
McCauley, K. B., Hawkins, F., Serra, M., Thomas, D. C., Jacob, A., & Kotton, D. N. (2018). Efficient derivation of functional human airway epithelium from pluripotent stem cells via temporal regulation of Wnt signaling. Cell Stem Cell, 20(6), 844–857.
Ong, H. T., Karatas, E., Poquillon, T., Grenci, G., Furlan, A., Dilasser, F., & Virzì, A. (2025). Digitalized organoids: Integrated pipeline for high-speed 3D analysis of organoid structures using multilevel segmentation and cellular topology. Nature Methods, 22(7), 1343–1354.
Oren, Y. S., Irony-Tur Sinai, M., Golec, A., Barchad-Avitzur, O., Mutyam, V., Li, Y., Hong, J., Ozeri-Galai, E., Hatton, A., Leibson, C., & Kerem, E. (2021). Antisense oligonucleotide-based drug development for cystic fibrosis patients carrying the 3849+10 kb C-to-T splicing mutation. Journal of Cystic Fibrosis, 20(5), 865–875.
Pacheco, M. L., Silva, I. A. L., Railean, V., & Amaral, M. D. (2022). Novel cell models for cystic fibrosis drug development and personalized medicine. Journal of Personalized Medicine, 12(8), 1321.
Pachitariu, M., Rariden, M., & Stringer, C. (2025). Cellpose-SAM: Superhuman generalization for cellular segmentation. bioRxiv.
Pranke, I. M., Hatton, A., Simonin, J., Jais, J. P., Le Pimpec-Barthes, F., Carsin, A., Bonnette, P., Fayon, M., Stremler-Le Bel, N., Grenet, D., & Sermet-Gaudelus, I. (2017). Correction of CFTR function in nasal epithelial cells from cystic fibrosis patients predicts improvement of respiratory function by CFTR modulators. Scientific Reports, 7(1), 7375.
Ramalho, A. S., Furstova, E., Vonk, A. M., Ferrante, M., Verfaillie, C., Dupont, L., Boon, M., Proesmans, M., Beekman, J. M., Sarouk, I., & De Boeck, K. (2021). Correction of CFTR function in intestinal organoids to guide treatment of cystic fibrosis. European Respiratory Journal, 57(1), 1902426.
Ratjen, F., Bell, S. C., Rowe, S. M., Goss, C. H., Quittner, A. L., & Bush, A. (2015). Cystic fibrosis. Nature Reviews Disease Primers, 1, 15010.
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., & Clevers, H. (2009). Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche. Nature, 459(7244), 262–265.
Schwank, G., Koo, B. K., Sasselli, V., Dekkers, J. F., Heo, I., Demircan, T., Steiner, N., Lawrence, A. C., & Clevers, H. (2013). Functional repair of CFTR by CRISPR/Cas9 in intestinal stem cell organoids of cystic fibrosis patients. Cell Stem Cell, 13(6), 653–658.
Tsai, P. H., Yang, Y. P., Wang, C. H., Liang, K. H., Yeh, C. L., Huang, T. Y., Hwang, T. C., Lo, W. L., Lan, Y. T., Ching, L. J., Wang, M. L., Huo, T. L., Luo, Y. H., Chiou, S. H., & Chou, S. J. (2025). Multimodal single-cell transcriptomics with patient-specific iPSC-derived airway organoids as a drug screening approach for cystic fibrosis with nonsense mutations. Biomedicine & Pharmacotherapy, 191, 118476.
Vaidyanathan, S., Salahudeen, A. A., Sellers, Z. M., Bravo, D. T., Choi, S. S., Batish, A., Le, W., Baik, R., de la O, S., Kaushik, M. P., & Porteus, M. H. (2020). High-efficiency, selection-free gene repair in airway stem cells from cystic fibrosis patients rescues CFTR function in differentiated epithelia. Cell Stem Cell, 26(2), 161–171.
van Mourik, P., Beekman, J. M., & van der Ent, C. K. (2019). Intestinal organoids to model cystic fibrosis. European Respiratory Journal, 54(1), 1802379.
van Mourik, P., Michel, S., Vonk, A. M., Beekman, J. M., & van der Ent, C. K. (2020). Rationale and design of the HIT-CF organoid study: Stratifying cystic fibrosis patients based on intestinal organoid response to different CFTR-modulators. BMC Pulmonary Medicine, 20(1), 60.
Vonk, A. M., van Mourik, P., Ramalho, A. S., Silva, I. A. L., Statia, M., Kruisselbrink, E., Suen, S. W. F., Dekkers, J. F., Vleggaar, F. P., Houwen, R. H. J., & Beekman, J. M. (2020). Protocol for application, standardization and validation of the forskolin-induced swelling assay in cystic fibrosis human colon organoids. STAR Protocols, 1(1), 100019.
Xia, S. (2022). High-throughput screening assays for novel cystic fibrosis therapies [Doctoral dissertation, University of Toronto]. University of Toronto Research Repository.
Xia, S., Bozóky, Z., Laselva, O., Di Paola, M., Ahmadi, S., Jiang, J. X., ... & Bear, C. E. (2021). High-throughput functional analysis of CFTR and other apically localized channels in iPSC derived intestinal organoids. bioRxiv, 2021-07.
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