Challenges in Establishing Pure Lung Cancer Organoids Limit Their Utility for Personalized Medicine
Open accessAbstract
Clinical implementation of tumor organoids for personalized medicine requires that pure tumor organoids can be reliably established. Here, we present our experience with organoid cultures from >70 non-small cell lung cancer (NSCLC) samples. We systematically evaluate several methods to identify tumor purity of organoids established from intrapulmonary tumors. Eighty percent of organoids from intrapulmonary lesions have a normal copy number profile, suggesting overgrowth by normal airway organoids (AOs). This is further supported by the failure to detect mutations found in the original tumor in organoids. Histomorphology alone is insufficient to determine tumor purity, but when combined with p63 immunostaining, tumor and normal AOs can be distinguished. Taking into account overgrowth by normal AOs, the establishment rate of pure NSCLC organoids is 17%. Therefore, current methods are insufficient to establish pure NSCLC organoids from intrapulmonary lesions. We discourage their use unless steps are taken to prevent overgrowth by normal AOs.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
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?
Genetic drift can occur in organoids cultured for extended time, which can affect their reliability as models for functional and drug discovery studies.
“Overall, these studies showed that genetic drift can occur in organoids cultured for extended time, influencing their reliability as models for functional and drug discovery studies133.”
From Organoids (2022) · cites this paper as [133]
The 'Selection for Tumor Cells' section (page not available in our copy) says normal organoids may eventually dominate mixed cultures and that such cultures complicate interpretation of drug screens. This supports a concern about model reliability during culture, but the paper does not establish genetic drift in organoid cells after extended culture or its effect on functional studies. (LLM, conf=0.82)
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
NIH Image to ImageJ: 25 years of image analysis
Schneider, C. A., Rasband, W. S., & Eliceiri, K. W. (2012) · Nature Methods · doi:10.1038/nmeth.2089 · Cited by 64,638 · see citing works
An integrated encyclopedia of DNA elements in the human genome
The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072 · see citing works
Cerami, E., Gao, J., Dogrusoz, U., Gross, B. E., Sumer, S. O., Aksoy, B. A., Jacobsen, A., Byrne, C. J., Heuer, M. L., Larsson, E., et al. (2012) · Cancer Discovery · doi:10.1158/2159-8290.cd-12-0095 · Cited by 17,455 · see citing works
Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal
Gao, J., Aksoy, B. A., Dogrusoz, U., Dresdner, G., Gross, B., Sumer, S. O., Sun, Y., Jacobsen, A., Sinha, R., Larsson, E., et al. (2013) · Science Signaling · doi:10.1126/scisignal.2004088 · Cited by 15,160 · see citing works
Aligning sequence reads, clone sequences and assembly contigs with BWA-MEMPreprint
Li, H. (2013) · arXiv (Cornell University) · doi:10.48550/arxiv.1303.3997 · Cited by 9,540 · see citing works
Aligning sequence reads, clone sequences and assembly con*gs with BWA-MEMPreprint
Li, H. (2014) · arXiv (Cornell University) · doi:10.6084/m9.figshare.963153.v1 · Cited by 5,150 · see citing works
Prospective Derivation of a Living Organoid Biobank of Colorectal Cancer Patients
van de Wetering, M., Francies, H. E., Francis, J. M., Bounova, G., Iorio, F., Pronk, A., van Houdt, W., van Gorp, J., Taylor-Weiner, A., Kester, L., et al. (2015) · Cell · doi:10.1016/j.cell.2015.03.053 · Cited by 2,408 · see citing works
Self-citationPatient-derived organoids model treatment response of metastatic gastrointestinal cancers
Vlachogiannis, G., Hedayat, S., Vatsiou, A., Jamin, Y., Fernández-Mateos, J., Khan, K., Lampis, A., Eason, K., Huntingford, I., Burke, R., et al. (2018) · Science · doi:10.1126/science.aao2774 · Cited by 2,096 · see citing works
Drost, J., & Clevers, H. (2018) · Nature Reviews Cancer · doi:10.1038/s41568-018-0007-6 · Cited by 1,790 · see citing works
Self-citationOrganoid Cultures Derived from Patients with Advanced Prostate Cancer
Gao, D., Vela, I., Sboner, A., Iaquinta, P. J., Karthaus, W. R., Gopalan, A., Dowling, C., Wanjala, J. N., Undvall, E. A., Arora, V. K., et al. (2014) · Cell · doi:10.1016/j.cell.2014.08.016 · Cited by 1,559 · see citing works
Self-citationDistinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas
Cancer Genome Atlas Research Network, Campbell, J. D., Alexandrov, A., Kim, J., Wala, J., Berger, A. H., Pedamallu, C. S., Shukla, S. A., Guo, G., Brooks, A. N., et al. (2016) · Nature Genetics · doi:10.1038/ng.3564 · Cited by 1,200 · see citing works
Dijkstra, K. K., Cattaneo, C. M., Weeber, F., Chalabi, M., van de Haar, J., Fanchi, L. F., Slagter, M., van der Velden, D. L., Kaing, S., Kelderman, S., et al. (2018) · Cell · doi:10.1016/j.cell.2018.07.009 · Cited by 1,135 · see citing works
Self-citationPan-cancer whole-genome analyses of metastatic solid tumours
Priestley, P., Baber, J., Lolkema, M. P., Steeghs, N., de Bruijn, E., Shale, C., Duyvesteyn, K., Haidari, S., van Hoeck, A., Onstenk, W., et al. (2019) · Nature · doi:10.1038/s41586-019-1689-y · Cited by 1,106 · see citing works
Self-citationOrganoid Profiling Identifies Common Responders to Chemotherapy in Pancreatic Cancer
Tiriac, H., Belleau, P., Engle, D. D., Plenker, D., Deschênes, A., Somerville, T. D. D., Froeling, F. E. M., Burkhart, R. A., Denroche, R. E., Jang, G.-H., et al. (2018) · Cancer Discovery · doi:10.1158/2159-8290.cd-18-0349 · Cited by 1,092 · 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-citationBoeva, V., Popova, T. G., Kevin Bleakley, A., Chiche, P., Cappo, J., Schleiermacher, G., Janoueix‐Lerosey, I., Delattre, O., & Barillot, E. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr670 · Cited by 1,012 · see citing works
Fujii, M., Shimokawa, M., Date, S., Takano, A., Matano, M., Nanki, K., Ohta, Y., Toshimitsu, K., Nakazato, Y., Kawasaki, K., et al. (2016) · Cell Stem Cell · doi:10.1016/j.stem.2016.04.003 · Cited by 852 · see citing works
Ooft, S. N., Weeber, F., Dijkstra, K. K., McLean, C. M., Kaing, S., van Werkhoven, E., Schipper, L., Hoes, L., Vis, D. J., van de Haar, J., et al. (2019) · Science Translational Medicine · doi:10.1126/scitranslmed.aay2574 · Cited by 813 · see citing works
Self-citationPatient-derived lung cancer organoids as in vitro cancer models for therapeutic screening
Kim, M., Mun, H., Sung, C. O., Cho, E. J., Jeon, H.-J., Chun, S.-M., Jung, D. J., Shin, T. H., Jeong, G. S., Kim, D. K., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-11867-6 · Cited by 812 · 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-citation<i>Ex Vivo</i> Profiling of PD-1 Blockade Using Organotypic Tumor Spheroids
Jenkins, R. W., Aref, A. R., Lizotte, P. H., Ivanova, E., Stinson, S., Zhou, C. W., Bowden, M., Deng, J., Liu, H., Miao, D., et al. (2018) · Cancer Discovery · doi:10.1158/2159-8290.cd-17-0833 · Cited by 594 · see citing works
An evolutionary perspective on field cancerization
Curtius, K., Wright, N. A., & Graham, T. A. (2017) · Nature reviews. Cancer · doi:10.1038/nrc.2017.102 · Cited by 533 · 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
Self-citationWeeber, F., van de Wetering, M., Hoogstraat, M., Dijkstra, K. K., Krijgsman, O., Kuilman, T., Gadellaa-van Hooijdonk, C. G. M., van der Velden, D. L., Peeper, D. S., Cuppen, E. P. J. G., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1516689112 · Cited by 482 · see citing works
Self-citationDetection of Mycoplasma in cell cultures
Young, L., Sung, J., Stacey, G., & Masters, J. R. (2010) · Nature Protocols · doi:10.1038/nprot.2010.43 · Cited by 437 · see citing works
p63 In pulmonary epithelium, pulmonary squamous neoplasms, and other pulmonary tumors
Wang, B. Y., Gil, J., Kaufman, D. M., et al. (2002) · Human Pathology · doi:10.1053/hupa.2002.126878 · Cited by 180 · see citing works
Kim, M. J., Shin, H. C., Shin, K. C., & Ro, J. Y. (2012) · Annals of Diagnostic Pathology · doi:10.1016/j.anndiagpath.2012.07.006 · Cited by 80 · see citing works
Sugaya, M., Takenoyama, M., Osaki, T., et al. (2002) · CHEST Journal · doi:10.1378/chest.122.1.282 · Cited by 66 · see citing works
Exome sequencing identifies recurring FLT3 N676K mutations in core-binding factor leukemia
Opatz, S., Polzer, H., Herold, T., et al. (2013) · Blood · doi:10.1182/blood-2013-01-476473 · Cited by 55 · see citing works
Wallaschek, N., Niklas, C., Pompaiah, M., Wiegering, A., Germer, C., Kircher, S., Brändlein, S., Maurus, K., Rosenwald, A., Yan, H. H. N., et al. (2019) · Journal of Molecular Biology · doi:10.1016/j.jmb.2019.05.031 · Cited by 45 · see citing works
Establishment and characterization of primary lung cancer cell lines from Chinese population
Zheng, C., Sun, Y.-H., Ye, X.-L., Chen, H., & Ji, H.-B. (2011) · Acta Pharmacologica Sinica · doi:10.1038/aps.2010.214 · Cited by 41 · see citing works
Shalaby, A. A., Presneau, N., Idowu, B. D., THOMPSON, L. A., Briggs, T. W. R., Tirabosco, R., Diss, T. C., & Flanagan, A. M. (2009) · Modern Pathology · doi:10.1038/modpathol.2009.63 · Cited by 38 · see citing works
Padhye, A., Ungewiss, C., Fradette, J. J., Rodriguez, B. L., Albritton, J. L., Miller, J. S., & Gibbons, D. L. (2019) · Scientific Reports · doi:10.1038/s41598-019-41301-2 · Cited by 25 · see citing works
Gao, W., Mady, H. H., Melhem, M. F., et al. (2008) · Molecular Carcinogenesis · doi:10.1002/mc.20505 · Cited by 20 · see citing works
Flagged first, then by citations
Research works printed but not linked: 1
- Data and code availability Deposition of DNA sequencing data in publicly availably repositories is limited and regulated by the informed consent signed by patients participating in the study. Requests for sequencing and copy number data can be made by emailing the Institutional Review Board of the Netherlands Cancer Institute (IRB@nki.nl). Any other requests can be directed to the Lead author, Emile E. Voest (e.voest@nki.nl). EXPERIMENTAL MODEL AND SUBJECT DETAILS Patient tissue Tissue was obtained from NSCLC patients undergoing surgery or receiving a 18G core needle tumor biopsy. Tumor tissue and macroscopically inconspicuous normal lung tissue (distant from the tumor site) were obtained for organoid culture. Tumor and normal tissue from the same patient share the same prefix (e.g., ITO54-T and ITO54-H, respectively). Written informed consent was obtained from all patients, and the study was approved by the Medical Ethical Committee of the Netherlands Cancer Institute -Antoni van Leeuwenhoek hospital (study NL48824.031.14). Tissue was stored in Ad-DF+++ (Advanced DMEM/F12 (GIBCO), with 1% Ultraglut- amine I (GIBCO), 1% penicillin/streptomycin (GIBCO), 1% HEPES (GIBCO)) supplemented with 2% Primocin (Invivogen) at 4 C and processed for organoid culture within 24 hours. Organoids ITO22-T, ITO31-T1, ITO34-T, ITO41-T, ITO42-T, and ITO62-T have been described in Dijkstra et al., 2018 previously as (NSCLC-1 through NSCLC-6, respectively). Organoid establishment and culture Organoids were established and cultured as described in Sachs et al., 2019. Briefly, tumor or normal lung tissue was dissociated into small pieces using scalpels and digested for 30-60 minutes using 1.5 mg/mL collagenase II (Sigma-Aldrich), 2 mg/mL dispase type II (GIBCO), 10 mM Y-27632 (Sigma-Aldrich) and 1:500 Primocin in PBS. After digestion, cells were isolated by repeated resuspension and washed three times in PBS. Cells were plated in ice cold 10 mg/mL Geltrex (GIBCO) in 6-well culture plates. After letting Geltrex drops solidify for 15 minutes at 37 C, cells were overlaid with lung organoid medium, composed of Ad-DF+++ supplemented with 10% Noggin conditioned medium, 10% R-spondin-1 conditioned medium, 1x B27 supplement (GIBCO), 1.25
Cited by
Sorted by citations
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
Kim, S.-Y., Kim, S.-M., Lim, S., Lee, J. Y., Choi, S.-J., Yang, S.-D., Yun, M. R., Kim, C. G., Gu, S. R., Park, C., et al. (2021) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-20-5026 · Cited by 151 · see citing works
A pan-cancer organoid platform for precision medicine
Larsen, B. M., Kannan, M., Langer, L. F., Leibowitz, B. D., Bentaieb, A., Cancino, A., Dolgalev, I., Drummond, B. E., Dry, J. R., Ho, C.-S., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109429 · Cited by 105 · see citing works
- Authors
- Dijkstra, K. K., Monkhorst, K., Schipper, L. J., Hartemink, K. J., Smit, E. F., Kaing, S., de Groot, R., Wolkers, M. C., Clevers, H., Cuppen, E., & Voest, E. E.
- Affiliations
- The Netherlands Cancer Institute (NL)
- Amsterdam UMC Location University of Amsterdam (NL)
- University Medical Center Utrecht (NL)
- Corresponding author
- Voest, Emile E.
- ORCID
- Venue
- Cell Reports
- Publisher
- Elsevier BV
- Published
- 2020-05
- Volume
- 31
- Issue
- 5
- Pages
- 107588
- ISSN
- 2211-1247 (ISSN-L)
- OpenAlex
- W3022654777
- Cited by
- 254
- References
- 34
- Citations by year
- 2026: 29 · 2025: 48 · 2024: 55 · 2023: 44 · 2022: 30 · 2021: 42 · 2020: 6
- FWCI
- 11.02
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Cell Reports (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- KNAW research portal (Royal Academy of Art and Sciences (KNAW)) (publishedVersion, other-oa)
- Pure Amsterdam UMC (submittedVersion, cc-by-nc-nd)
- Data Archiving and Networked Services (DANS) (submittedVersion, other-oa)
- Data Archiving and Networked Services (DANS) (submittedVersion, cc-by-nc-nd)
- Leiden Repository (Leiden University) (submittedVersion, cc-by-nc-nd)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Utrecht University Repository (Utrecht University) (submittedVersion, other-oa)
- KNAW Research Portal (The Royal Netherlands Academy of Arts and Sciences) (submittedVersion, other-oa)
- Funders
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek
- KWF Kankerbestrijding
- Topics
- Health Sciences › Medicine › Oncology › Cancer Cells and Metastasis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Health Sciences › Medicine › Oncology › Lung Cancer Research Studies
- Keywords
- tumor organoids, non-small cell lung cancer, airway organoids, copy number profiling, personalized medicine, organoid culture
- MeSH terms
- Carcinoma, Non-Small-Cell Lung, Humans, Lung Neoplasms, Mutation, Organoids, Precision Medicine
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
