1
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Boretto M, Geurts MH, Gandhi S, Ma Z, Staliarova N, Celotti M, Lim S, He GW, Millen R, Driehuis E, Begthel H, Smabers L, Roodhart J, van Es J, Wu W, Clevers H. Epidermal growth factor receptor (EGFR) is a target of the tumor-suppressor E3 ligase FBXW7. Proc Natl Acad Sci U S A 2024; 121:e2309902121. [PMID: 38483988 PMCID: PMC10962967 DOI: 10.1073/pnas.2309902121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 01/08/2024] [Indexed: 03/19/2024] Open
Abstract
FBXW7 is an E3 ubiquitin ligase that targets proteins for proteasome-mediated degradation and is mutated in various cancer types. Here, we use CRISPR base editors to introduce different FBXW7 hotspot mutations in human colon organoids. Functionally, FBXW7 mutation reduces EGF dependency of organoid growth by ~10,000-fold. Combined transcriptomic and proteomic analyses revealed increased EGFR protein stability in FBXW7 mutants. Two distinct phosphodegron motifs reside in the cytoplasmic tail of EGFR. Mutations in these phosphodegron motifs occur in human cancer. CRISPR-mediated disruption of the phosphodegron motif at T693 reduced EGFR degradation and EGF growth factor dependency. FBXW7 mutant organoids showed reduced sensitivity to EGFR-MAPK inhibitors. These observations were further strengthened in CRC-derived organoid lines and validated in a cohort of patients treated with panitumumab. Our data imply that FBXW7 mutations reduce EGF dependency by disabling EGFR turnover.
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Affiliation(s)
- Matteo Boretto
- Organoid group, Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, 3584CTUtrecht, the Netherlands
| | - Maarten H. Geurts
- Organoid group, Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, 3584CTUtrecht, the Netherlands
| | - Shashank Gandhi
- Organoid group, Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, 3584CTUtrecht, the Netherlands
- Department of Molecular and Cellular Biology, Miller Institute for Basic Research in Science, University of California, Berkeley, CA94720
| | - Ziliang Ma
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore138648, Singapore
- Department of Pharmacy, National University of Singapore, Singapore117543, Singapore
- Department of Biomolecular Mass Spectrometry and Proteomics, Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CHUtrecht, the Netherlands
| | - Nadzeya Staliarova
- Department of Biomolecular Mass Spectrometry and Proteomics, Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CHUtrecht, the Netherlands
| | - Martina Celotti
- Organoid group, Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, 3584CTUtrecht, the Netherlands
| | - Sangho Lim
- Organoid group, Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, 3584CTUtrecht, the Netherlands
| | - Gui-Wei He
- Organoid group, Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, 3584CTUtrecht, the Netherlands
| | - Rosemary Millen
- Organoid group, Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, 3584CTUtrecht, the Netherlands
| | - Else Driehuis
- Organoid group, Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, 3584CTUtrecht, the Netherlands
| | - Harry Begthel
- Organoid group, Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, 3584CTUtrecht, the Netherlands
| | - Lidwien Smabers
- Department of Medical Oncology, University Medical Center Utrecht, 3584 CXUtrecht, the Netherlands
| | - Jeanine Roodhart
- Department of Medical Oncology, University Medical Center Utrecht, 3584 CXUtrecht, the Netherlands
| | - Johan van Es
- Organoid group, Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, 3584CTUtrecht, the Netherlands
| | - Wei Wu
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore138648, Singapore
- Department of Pharmacy, National University of Singapore, Singapore117543, Singapore
- Department of Biomolecular Mass Spectrometry and Proteomics, Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CHUtrecht, the Netherlands
| | - Hans Clevers
- Organoid group, Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, 3584CTUtrecht, the Netherlands
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2
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Hendriks D, Brouwers JF, Hamer K, Geurts MH, Luciana L, Massalini S, López-Iglesias C, Peters PJ, Rodríguez-Colman MJ, Chuva de Sousa Lopes S, Artegiani B, Clevers H. Engineered human hepatocyte organoids enable CRISPR-based target discovery and drug screening for steatosis. Nat Biotechnol 2023; 41:1567-1581. [PMID: 36823355 PMCID: PMC10635827 DOI: 10.1038/s41587-023-01680-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 01/19/2023] [Indexed: 02/25/2023]
Abstract
The lack of registered drugs for nonalcoholic fatty liver disease (NAFLD) is partly due to the paucity of human-relevant models for target discovery and compound screening. Here we use human fetal hepatocyte organoids to model the first stage of NAFLD, steatosis, representing three different triggers: free fatty acid loading, interindividual genetic variability (PNPLA3 I148M) and monogenic lipid disorders (APOB and MTTP mutations). Screening of drug candidates revealed compounds effective at resolving steatosis. Mechanistic evaluation of effective drugs uncovered repression of de novo lipogenesis as the convergent molecular pathway. We present FatTracer, a CRISPR screening platform to identify steatosis modulators and putative targets using APOB-/- and MTTP-/- organoids. From a screen targeting 35 genes implicated in lipid metabolism and/or NAFLD risk, FADS2 (fatty acid desaturase 2) emerged as an important determinant of hepatic steatosis. Enhancement of FADS2 expression increases polyunsaturated fatty acid abundancy which, in turn, reduces de novo lipogenesis. These organoid models facilitate study of steatosis etiology and drug targets.
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Affiliation(s)
- Delilah Hendriks
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, Utrecht, The Netherlands.
- Oncode Institute, Utrecht, The Netherlands.
| | - Jos F Brouwers
- Research Group Analysis Techniques in the Life Sciences, School of Life Sciences and Technology, Avans University of Applied Sciences, Breda, The Netherlands
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Karien Hamer
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Maarten H Geurts
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Léa Luciana
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Simone Massalini
- The Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Carmen López-Iglesias
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, The Netherlands
| | - Peter J Peters
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, The Netherlands
| | - Maria J Rodríguez-Colman
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Benedetta Artegiani
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, Utrecht, The Netherlands.
- The Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands.
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, Utrecht, The Netherlands.
- Oncode Institute, Utrecht, The Netherlands.
- The Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands.
- University Medical Center Utrecht, Utrecht, The Netherlands.
- Pharma, Research and Early Development of F. Hoffmann-La Roche Ltd, Basel, Switzerland.
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3
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Tiroille V, Krug A, Bokobza E, Kahi M, Bulcaen M, Ensinck MM, Geurts MH, Hendriks D, Vermeulen F, Larbret F, Gutierrez-Guerrero A, Chen Y, Van Zundert I, Rocha S, Rios AC, Medaer L, Gijsbers R, Mangeot PE, Clevers H, Carlon MS, Bost F, Verhoeyen E. Nanoblades allow high-level genome editing in murine and human organoids. Mol Ther Nucleic Acids 2023; 33:57-74. [PMID: 37435135 PMCID: PMC10331042 DOI: 10.1016/j.omtn.2023.06.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 06/04/2023] [Indexed: 07/13/2023]
Abstract
Genome engineering has become more accessible thanks to the CRISPR-Cas9 gene-editing system. However, using this technology in synthetic organs called "organoids" is still very inefficient. This is due to the delivery methods for the CRISPR-Cas9 machinery, which include electroporation of CRISPR-Cas9 DNA, mRNA, or ribonucleoproteins containing the Cas9-gRNA complex. However, these procedures are quite toxic for the organoids. Here, we describe the use of the "nanoblade (NB)" technology, which outperformed by far gene-editing levels achieved to date for murine- and human tissue-derived organoids. We reached up to 75% of reporter gene knockout in organoids after treatment with NBs. Indeed, high-level NB-mediated knockout for the androgen receptor encoding gene and the cystic fibrosis transmembrane conductance regulator gene was achieved with single gRNA or dual gRNA containing NBs in murine prostate and colon organoids. Likewise, NBs achieved 20%-50% gene editing in human organoids. Most importantly, in contrast to other gene-editing methods, this was obtained without toxicity for the organoids. Only 4 weeks are required to obtain stable gene knockout in organoids and NBs simplify and allow rapid genome editing in organoids with little to no side effects including unwanted insertion/deletions in off-target sites thanks to transient Cas9/RNP expression.
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Affiliation(s)
- Victor Tiroille
- Université Côte d’Azur, INSERM, C3M, 06204 Nice, France
- Equipe labélisée Ligue National Contre le Cancer, Basel, Switzerland
| | - Adrien Krug
- Université Côte d’Azur, INSERM, C3M, 06204 Nice, France
| | - Emma Bokobza
- Université Côte d’Azur, INSERM, C3M, 06204 Nice, France
- Equipe labélisée Ligue National Contre le Cancer, Basel, Switzerland
| | - Michel Kahi
- Université Côte d’Azur, INSERM, C3M, 06204 Nice, France
- Equipe labélisée Ligue National Contre le Cancer, Basel, Switzerland
| | - Mattijs Bulcaen
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, Faculty of Medicine, KU Leuven, Leuven, Belgium
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Marjolein M. Ensinck
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, Faculty of Medicine, KU Leuven, Leuven, Belgium
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Maarten H. Geurts
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Hubrecht Institute, Utrecht, the Netherlands
| | - Delilah Hendriks
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Hubrecht Institute, Utrecht, the Netherlands
| | | | | | - Alejandra Gutierrez-Guerrero
- CIRI – International Center for Infectiology Research, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Université Lyon, F-69007 Lyon, France
| | - Yu Chen
- Human Oncology and Pathogenesis Program, Department of Medicine, Memorial Sloan; Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Indra Van Zundert
- Synthetic Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, the Netherlands
| | - Susana Rocha
- Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Anne C. Rios
- Oncode Institute, Hubrecht Institute, Utrecht, the Netherlands
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Louise Medaer
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, Faculty of Medicine, KU Leuven, Leuven, Belgium
| | - Rik Gijsbers
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, Faculty of Medicine, KU Leuven, Leuven, Belgium
| | - Philippe E. Mangeot
- CIRI – International Center for Infectiology Research, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Université Lyon, F-69007 Lyon, France
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Hubrecht Institute, Utrecht, the Netherlands
| | - Marianne S. Carlon
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, Faculty of Medicine, KU Leuven, Leuven, Belgium
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Frédéric Bost
- Université Côte d’Azur, INSERM, C3M, 06204 Nice, France
- Equipe labélisée Ligue National Contre le Cancer, Basel, Switzerland
| | - Els Verhoeyen
- Université Côte d’Azur, INSERM, C3M, 06204 Nice, France
- CIRI – International Center for Infectiology Research, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Université Lyon, F-69007 Lyon, France
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4
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Mykytyn AZ, Breugem TI, Geurts MH, Beumer J, Schipper D, van Acker R, van den Doel PB, van Royen ME, Zhang J, Clevers H, Haagmans BL, Lamers MM. SARS-CoV-2 Omicron entry is type II transmembrane serine protease-mediated in human airway and intestinal organoid models. J Virol 2023; 97:e0085123. [PMID: 37555660 PMCID: PMC10506477 DOI: 10.1128/jvi.00851-23] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 06/24/2023] [Indexed: 08/10/2023] Open
Abstract
SARS-CoV-2 can enter cells after its spike protein is cleaved by either type II transmembrane serine proteases (TTSPs), like TMPRSS2, or cathepsins. It is now widely accepted that the Omicron variant uses TMPRSS2 less efficiently and instead enters cells via cathepsins, but these findings have yet to be verified in more relevant cell models. Although we could confirm efficient cathepsin-mediated entry for Omicron in a monkey kidney cell line, experiments with protease inhibitors showed that Omicron (BA.1 and XBB1.5) did not use cathepsins for entry into human airway organoids and instead utilized TTSPs. Likewise, CRISPR-edited intestinal organoids showed that entry of Omicron BA.1 relied on the expression of the serine protease TMPRSS2 but not cathepsin L or B. Together, these data force us to rethink the concept that Omicron has adapted to cathepsin-mediated entry and indicate that TTSP inhibitors should not be dismissed as prophylactic or therapeutic antiviral strategy against SARS-CoV-2. IMPORTANCE Coronavirus entry relies on host proteases that activate the viral fusion protein, spike. These proteases determine the viral entry route, tropism, host range, and can be attractive drug targets. Whereas earlier studies using cell lines suggested that the Omicron variant of SARS-CoV-2 has changed its protease usage, from cell surface type II transmembrane serine proteases (TTSPs) to endosomal cathepsins, we report that this is not the case in human airway and intestinal organoid models, suggesting that host TTSP inhibition is still a viable prophylactic or therapeutic antiviral strategy against current SARS-CoV-2 variants and highlighting the importance of relevant human in vitro cell models.
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Affiliation(s)
- Anna Z. Mykytyn
- Viroscience Department, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Tim I. Breugem
- Viroscience Department, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Maarten H. Geurts
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Amsterdam, the Netherlands
| | - Joep Beumer
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Amsterdam, the Netherlands
| | - Debby Schipper
- Viroscience Department, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Romy van Acker
- Viroscience Department, Erasmus Medical Center, Rotterdam, the Netherlands
| | | | - Martin E. van Royen
- Department of Pathology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Jingshu Zhang
- Viroscience Department, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Hans Clevers
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Amsterdam, the Netherlands
| | - Bart L. Haagmans
- Viroscience Department, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Mart M. Lamers
- Viroscience Department, Erasmus Medical Center, Rotterdam, the Netherlands
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
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5
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Geurts MH, Gandhi S, Boretto MG, Akkerman N, Derks LLM, van Son G, Celotti M, Harshuk-Shabso S, Peci F, Begthel H, Hendriks D, Schürmann P, Andersson-Rolf A, Chuva de Sousa Lopes SM, van Es JH, van Boxtel R, Clevers H. One-step generation of tumor models by base editor multiplexing in adult stem cell-derived organoids. Nat Commun 2023; 14:4998. [PMID: 37591832 PMCID: PMC10435570 DOI: 10.1038/s41467-023-40701-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 08/07/2023] [Indexed: 08/19/2023] Open
Abstract
Optimization of CRISPR/Cas9-mediated genome engineering has resulted in base editors that hold promise for mutation repair and disease modeling. Here, we demonstrate the application of base editors for the generation of complex tumor models in human ASC-derived organoids. First we show efficacy of cytosine and adenine base editors in modeling CTNNB1 hot-spot mutations in hepatocyte organoids. Next, we use C > T base editors to insert nonsense mutations in PTEN in endometrial organoids and demonstrate tumorigenicity even in the heterozygous state. Moreover, drug sensitivity assays on organoids harboring either PTEN or PTEN and PIK3CA mutations reveal the mechanism underlying the initial stages of endometrial tumorigenesis. To further increase the scope of base editing we combine SpCas9 and SaCas9 for simultaneous C > T and A > G editing at individual target sites. Finally, we show that base editor multiplexing allow modeling of colorectal tumorigenesis in a single step by simultaneously transfecting sgRNAs targeting five cancer genes.
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Affiliation(s)
- Maarten H Geurts
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Utrecht, the Netherlands.
- Oncode Institute, 3521AL, Utrecht, the Netherlands.
- Princess Maxima Center for Pediatric Oncology, 3584 CS, Utrecht, the Netherlands.
| | - Shashank Gandhi
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Utrecht, the Netherlands
- Miller Institute for Basic Research in Science, University of California, Berkeley, CA, 94720, USA
| | - Matteo G Boretto
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Utrecht, the Netherlands
- Oncode Institute, 3521AL, Utrecht, the Netherlands
| | - Ninouk Akkerman
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Utrecht, the Netherlands
- Oncode Institute, 3521AL, Utrecht, the Netherlands
| | - Lucca L M Derks
- Oncode Institute, 3521AL, Utrecht, the Netherlands
- Princess Maxima Center for Pediatric Oncology, 3584 CS, Utrecht, the Netherlands
| | - Gijs van Son
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Utrecht, the Netherlands
- Oncode Institute, 3521AL, Utrecht, the Netherlands
- Princess Maxima Center for Pediatric Oncology, 3584 CS, Utrecht, the Netherlands
| | - Martina Celotti
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Utrecht, the Netherlands
- Oncode Institute, 3521AL, Utrecht, the Netherlands
| | - Sarina Harshuk-Shabso
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Utrecht, the Netherlands
- Oncode Institute, 3521AL, Utrecht, the Netherlands
| | - Flavia Peci
- Oncode Institute, 3521AL, Utrecht, the Netherlands
- Princess Maxima Center for Pediatric Oncology, 3584 CS, Utrecht, the Netherlands
| | - Harry Begthel
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Utrecht, the Netherlands
- Oncode Institute, 3521AL, Utrecht, the Netherlands
| | - Delilah Hendriks
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Utrecht, the Netherlands
- Oncode Institute, 3521AL, Utrecht, the Netherlands
- Princess Maxima Center for Pediatric Oncology, 3584 CS, Utrecht, the Netherlands
| | - Paul Schürmann
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Utrecht, the Netherlands
- Oncode Institute, 3521AL, Utrecht, the Netherlands
| | - Amanda Andersson-Rolf
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Utrecht, the Netherlands
- Oncode Institute, 3521AL, Utrecht, the Netherlands
| | | | - Johan H van Es
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Utrecht, the Netherlands
- Oncode Institute, 3521AL, Utrecht, the Netherlands
| | - Ruben van Boxtel
- Oncode Institute, 3521AL, Utrecht, the Netherlands
- Princess Maxima Center for Pediatric Oncology, 3584 CS, Utrecht, the Netherlands
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Utrecht, the Netherlands.
- Oncode Institute, 3521AL, Utrecht, the Netherlands.
- Pharma Research Early Development, Basel, Switzerland.
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6
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Millen R, De Kort WWB, Koomen M, van Son GJF, Gobits R, Penning de Vries B, Begthel H, Zandvliet M, Doornaert P, Raaijmakers CPJ, Geurts MH, Elias SG, van Es RJJ, de Bree R, Devriese LA, Willems SM, Kranenburg O, Driehuis E, Clevers H. Patient-derived head and neck cancer organoids allow treatment stratification and serve as a tool for biomarker validation and identification. Med 2023; 4:290-310.e12. [PMID: 37178682 DOI: 10.1016/j.medj.2023.04.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/20/2023] [Accepted: 04/12/2023] [Indexed: 05/15/2023]
Abstract
BACKGROUND Organoids are in vitro three-dimensional structures that can be grown from patient tissue. Head and neck cancer (HNC) is a collective term used for multiple tumor types including squamous cell carcinomas and salivary gland adenocarcinomas. METHODS Organoids were established from HNC patient tumor tissue and characterized using immunohistochemistry and DNA sequencing. Organoids were exposed to chemo- and radiotherapy and a panel of targeted agents. Organoid response was correlated with patient clinical response. CRISPR-Cas9-based gene editing of organoids was applied for biomarker validation. FINDINGS A HNC biobank consisting of 110 models, including 65 tumor models, was generated. Organoids retained DNA alterations found in HNC. Comparison of organoid and patient response to radiotherapy (primary [n = 6] and adjuvant [n = 15]) indicated potential for guiding treatment options in the adjuvant setting. In organoids, the radio-sensitizing potential of cisplatin and carboplatin could be validated. However, cetuximab conveyed radioprotection in most models. HNC-targeted treatments were tested on 31 models, indicating possible novel treatment options with the potential for treatment stratification in the future. Activating PIK3CA mutations did not predict alpelisib response in organoids. Protein arginine methyltransferase 5 (PRMT5) inhibitors were identified as a potential treatment option for cyclin-dependent kinase inhibitor 2A (CDKN2A) null HNC. CONCLUSIONS Organoids hold potential as a diagnostic tool in personalized medicine for HNC. In vitro organoid response to radiotherapy (RT) showed a trend that mimics clinical response, indicating the predictive potential of patient-derived organoids. Moreover, organoids could be used for biomarker discovery and validation. FUNDING This work was funded by Oncode PoC 2018-P0003.
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Affiliation(s)
- Rosemary Millen
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), Utrecht, the Netherlands.
| | - Willem W B De Kort
- Department of Oral and Maxillofacial Surgery, University Medical Center Utrecht, Utrecht, the Netherlands; Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Mandy Koomen
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), Utrecht, the Netherlands
| | - Gijs J F van Son
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), Utrecht, the Netherlands; Princess Maxima Center, Utrecht, the Netherlands
| | - Roán Gobits
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), Utrecht, the Netherlands
| | - Bas Penning de Vries
- Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Harry Begthel
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), Utrecht, the Netherlands
| | - Maurice Zandvliet
- Department of Clinical Sciences - Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Patricia Doornaert
- Department of Radiotherapy, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Maarten H Geurts
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), Utrecht, the Netherlands
| | - Sjoerd G Elias
- Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Robert J J van Es
- Department of Oral and Maxillofacial Surgery, University Medical Center Utrecht, Utrecht, the Netherlands; Department of Head and Neck Surgical Oncology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Remco de Bree
- Department of Head and Neck Surgical Oncology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Lot A Devriese
- Department of Medical Oncology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Stefan M Willems
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands; Department of Pathology, University Medical Center Groningen, Groningen, the Netherlands
| | - Onno Kranenburg
- Utrecht Platform for Organoid Technology (U-PORT), Utrecht Medical Center Utrecht, Utrecht, the Netherlands
| | - Else Driehuis
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), Utrecht, the Netherlands.
| | - Hans Clevers
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), Utrecht, the Netherlands.
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7
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Bannier-Hélaouët M, Geurts MH, Korving J, Begthel H, Clevers H. Establishment, Maintenance, Differentiation, Genetic Manipulation, and Transplantation of Mouse and Human Lacrimal Gland Organoids. J Vis Exp 2023. [PMID: 36804367 DOI: 10.3791/65040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The lacrimal gland is an essential organ for ocular surface homeostasis. By producing the aqueous part of the tear film, it protects the eye from desiccation stress and external insults. Little is known about lacrimal gland (patho)physiology because of the lack of adequate in vitro models. Organoid technology has proven itself as a useful experimental platform for multiple organs. Here, we share a protocol to establish and maintain mouse and human lacrimal gland organoids starting from lacrimal gland biopsies. By modifying the culture conditions, we enhance lacrimal gland organoid functionality. Organoid functionality can be probed through a "crying" assay, which involves exposing the lacrimal gland organoids to selected neurotransmitters to trigger tear release in their lumen. We explain how to image and quantify this phenomenon. To investigate the role of genes of interest in lacrimal gland homeostasis, these can be genetically modified. We thoroughly describe how to genetically modify lacrimal gland organoids using base editors-from guide RNA design to organoid clone genotyping. Lastly, we show how to probe the regenerative potential of human lacrimal gland organoids by orthotopic implantation in the mouse. Together, this comprehensive toolset provides resources to use mouse and human lacrimal gland organoids to study lacrimal gland (patho)physiology.
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Affiliation(s)
- Marie Bannier-Hélaouët
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Center Utrecht; Oncode Institute, Hubrecht Institute
| | - Maarten H Geurts
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Center Utrecht; Oncode Institute, Hubrecht Institute
| | - Jeroen Korving
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Center Utrecht
| | - Harry Begthel
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Center Utrecht
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Center Utrecht; Oncode Institute, Hubrecht Institute;
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8
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Dekkers JF, Alieva M, Cleven A, Keramati F, Wezenaar AKL, van Vliet EJ, Puschhof J, Brazda P, Johanna I, Meringa AD, Rebel HG, Buchholz MB, Barrera Román M, Zeeman AL, de Blank S, Fasci D, Geurts MH, Cornel AM, Driehuis E, Millen R, Straetemans T, Nicolasen MJT, Aarts-Riemens T, Ariese HCR, Johnson HR, van Ineveld RL, Karaiskaki F, Kopper O, Bar-Ephraim YE, Kretzschmar K, Eggermont AMM, Nierkens S, Wehrens EJ, Stunnenberg HG, Clevers H, Kuball J, Sebestyen Z, Rios AC. Uncovering the mode of action of engineered T cells in patient cancer organoids. Nat Biotechnol 2023; 41:60-69. [PMID: 35879361 PMCID: PMC9849137 DOI: 10.1038/s41587-022-01397-w] [Citation(s) in RCA: 45] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 06/14/2022] [Indexed: 01/22/2023]
Abstract
Extending the success of cellular immunotherapies against blood cancers to the realm of solid tumors will require improved in vitro models that reveal therapeutic modes of action at the molecular level. Here we describe a system, called BEHAV3D, developed to study the dynamic interactions of immune cells and patient cancer organoids by means of imaging and transcriptomics. We apply BEHAV3D to live-track >150,000 engineered T cells cultured with patient-derived, solid-tumor organoids, identifying a 'super engager' behavioral cluster comprising T cells with potent serial killing capacity. Among other T cell concepts we also study cancer metabolome-sensing engineered T cells (TEGs) and detect behavior-specific gene signatures that include a group of 27 genes with no previously described T cell function that are expressed by super engager killer TEGs. We further show that type I interferon can prime resistant organoids for TEG-mediated killing. BEHAV3D is a promising tool for the characterization of behavioral-phenotypic heterogeneity of cellular immunotherapies and may support the optimization of personalized solid-tumor-targeting cell therapies.
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Affiliation(s)
- Johanna F Dekkers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Utrecht, the Netherlands
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Maria Alieva
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Astrid Cleven
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Farid Keramati
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Amber K L Wezenaar
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Esmée J van Vliet
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Jens Puschhof
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
- Microbiome and Cancer Division, German Cancer Research Center, Heidelberg, Germany
| | - Peter Brazda
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Inez Johanna
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Angelo D Meringa
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Heggert G Rebel
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Maj-Britt Buchholz
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Mario Barrera Román
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Amber L Zeeman
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Sam de Blank
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Domenico Fasci
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Maarten H Geurts
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Annelisa M Cornel
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Else Driehuis
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Rosemary Millen
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Trudy Straetemans
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- Department of Hematology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Mara J T Nicolasen
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Tineke Aarts-Riemens
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Hendrikus C R Ariese
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Hannah R Johnson
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Ravian L van Ineveld
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Froso Karaiskaki
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Oded Kopper
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Yotam E Bar-Ephraim
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Kai Kretzschmar
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
- Mildred Scheel Early Career Center for Cancer Research Würzburg, University Hospital Würzburg, MSNZ/IZKF, Wurzburg, Germany
| | - Alexander M M Eggermont
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- University Medical Center Utrecht, Utrecht, the Netherlands
- Comprehensive Cancer Center München, Munich, Germany
| | - Stefan Nierkens
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Ellen J Wehrens
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | | | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Utrecht, the Netherlands
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
- Pharma, Research and Early Development, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Jürgen Kuball
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- Department of Hematology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Zsolt Sebestyen
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Anne C Rios
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.
- Oncode Institute, Utrecht, the Netherlands.
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9
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Wang Z, Boretto M, Millen R, Natesh N, Reckzeh ES, Hsu C, Negrete M, Yao H, Quayle W, Heaton BE, Harding AT, Bose S, Driehuis E, Beumer J, Rivera GO, van Ineveld RL, Gex D, DeVilla J, Wang D, Puschhof J, Geurts MH, Yeung A, Hamele C, Smith A, Bankaitis E, Xiang K, Ding S, Nelson D, Delubac D, Rios A, Abi-Hachem R, Jang D, Goldstein BJ, Glass C, Heaton NS, Hsu D, Clevers H, Shen X. Rapid tissue prototyping with micro-organospheres. Stem Cell Reports 2022; 17:1959-1975. [PMID: 35985334 PMCID: PMC9481922 DOI: 10.1016/j.stemcr.2022.07.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/22/2022] [Accepted: 07/23/2022] [Indexed: 12/22/2022] Open
Abstract
In vitro tissue models hold great promise for modeling diseases and drug responses. Here, we used emulsion microfluidics to form micro-organospheres (MOSs), which are droplet-encapsulated miniature three-dimensional (3D) tissue models that can be established rapidly from patient tissues or cells. MOSs retain key biological features and responses to chemo-, targeted, and radiation therapies compared with organoids. The small size and large surface-to-volume ratio of MOSs enable various applications including quantitative assessment of nutrient dependence, pathogen-host interaction for anti-viral drug screening, and a rapid potency assay for chimeric antigen receptor (CAR)-T therapy. An automated MOS imaging pipeline combined with machine learning overcomes plating variation, distinguishes tumorspheres from stroma, differentiates cytostatic versus cytotoxic drug effects, and captures resistant clones and heterogeneity in drug response. This pipeline is capable of robust assessments of drug response at individual-tumorsphere resolution and provides a rapid and high-throughput therapeutic profiling platform for precision medicine.
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Affiliation(s)
- Zhaohui Wang
- Woo Center for Big Data and Precision Health, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Matteo Boretto
- Oncode, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center (UMC) Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Rosemary Millen
- Oncode, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center (UMC) Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Naveen Natesh
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Elena S Reckzeh
- Oncode, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center (UMC) Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Carolyn Hsu
- College of Arts and Sciences, University of Chapel Hill, Chapel Hill, NC, USA
| | - Marcos Negrete
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Haipei Yao
- Biology Department, Trinity School of Arts and Sciences, Duke University, Durham, NC, USA
| | | | - Brook E Heaton
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, USA
| | - Alfred T Harding
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, USA
| | - Shree Bose
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Else Driehuis
- Oncode, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center (UMC) Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Joep Beumer
- Oncode, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center (UMC) Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Grecia O Rivera
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Ravian L van Ineveld
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 Utrecht, the Netherlands; Cancer Genomics Netherlands, Oncode Institute, 3584 Utrecht, the Netherlands
| | | | | | - Daisong Wang
- Oncode, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center (UMC) Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Jens Puschhof
- Oncode, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center (UMC) Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands; Microbiome and Cancer Division, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Maarten H Geurts
- Oncode, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center (UMC) Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Athena Yeung
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Cait Hamele
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, USA
| | | | | | - Kun Xiang
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Shengli Ding
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA; Xilis, Inc., Durham, NC, USA
| | | | | | - Anne Rios
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 Utrecht, the Netherlands
| | - Ralph Abi-Hachem
- Department of Head and Neck Surgery and Communication Sciences, School of Medicine, Duke University, Durham, NC, USA
| | - David Jang
- Department of Head and Neck Surgery and Communication Sciences, School of Medicine, Duke University, Durham, NC, USA
| | - Bradley J Goldstein
- Department of Head and Neck Surgery and Communication Sciences, School of Medicine, Duke University, Durham, NC, USA
| | - Carolyn Glass
- Department of Pathology, School of Medicine, Duke University, Durham, NC, USA
| | - Nicholas S Heaton
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, USA
| | - David Hsu
- Division of Medical Oncology, Duke Cancer Institute, Duke University, Durham, NC, USA.
| | - Hans Clevers
- Oncode, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center (UMC) Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands; Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 Utrecht, the Netherlands.
| | - Xiling Shen
- Woo Center for Big Data and Precision Health, Pratt School of Engineering, Duke University, Durham, NC, USA; Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA; Terasaki Institute, Los Angeles, CA, USA.
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10
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van der Vaart J, Böttinger L, Geurts MH, van de Wetering WJ, Knoops K, Sachs N, Begthel H, Korving J, Lopez‐Iglesias C, Peters PJ, Eitan K, Gileles‐Hillel A, Clevers H. Modelling of primary ciliary dyskinesia using patient-derived airway organoids. EMBO Rep 2021; 22:e52058. [PMID: 34693619 PMCID: PMC8647008 DOI: 10.15252/embr.202052058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 09/19/2021] [Accepted: 09/21/2021] [Indexed: 01/08/2023] Open
Abstract
Patient-derived human organoids can be used to model a variety of diseases. Recently, we described conditions for long-term expansion of human airway organoids (AOs) directly from healthy individuals and patients. Here, we first optimize differentiation of AOs towards ciliated cells. After differentiation of the AOs towards ciliated cells, these can be studied for weeks. When returned to expansion conditions, the organoids readily resume their growth. We apply this condition to AOs established from nasal inferior turbinate brush samples of patients suffering from primary ciliary dyskinesia (PCD), a pulmonary disease caused by dysfunction of the motile cilia in the airways. Patient-specific differences in ciliary beating are observed and are in agreement with the patients' genetic mutations. More detailed organoid ciliary phenotypes can thus be documented in addition to the standard diagnostic procedure. Additionally, using genetic editing tools, we show that a patient-specific mutation can be repaired. This study demonstrates the utility of organoid technology for investigating hereditary airway diseases such as PCD.
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Affiliation(s)
- Jelte van der Vaart
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW)University Medical Centre UtrechtUtrechtThe Netherlands
- Oncode InstituteHubrecht InstituteUtrechtThe Netherlands
| | - Lena Böttinger
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW)University Medical Centre UtrechtUtrechtThe Netherlands
| | - Maarten H Geurts
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW)University Medical Centre UtrechtUtrechtThe Netherlands
- Oncode InstituteHubrecht InstituteUtrechtThe Netherlands
| | | | - Kèvin Knoops
- The Maastricht Multimodal Molecular Imaging InstituteMaastricht UniversityMaastrichtThe Netherlands
| | - Norman Sachs
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW)University Medical Centre UtrechtUtrechtThe Netherlands
- Present address:
Vertex IncSan DiegoCAUSA
| | - Harry Begthel
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW)University Medical Centre UtrechtUtrechtThe Netherlands
- Oncode InstituteHubrecht InstituteUtrechtThe Netherlands
| | - Jeroen Korving
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW)University Medical Centre UtrechtUtrechtThe Netherlands
- Oncode InstituteHubrecht InstituteUtrechtThe Netherlands
| | - Carmen Lopez‐Iglesias
- The Maastricht Multimodal Molecular Imaging InstituteMaastricht UniversityMaastrichtThe Netherlands
| | - Peter J Peters
- The Maastricht Multimodal Molecular Imaging InstituteMaastricht UniversityMaastrichtThe Netherlands
| | - Kerem Eitan
- Division of Cell Biology, Immunology and Cancer ResearchHebrew University‐Hadassah Medical SchoolJerusalemIsrael
| | - Alex Gileles‐Hillel
- Division of Cell Biology, Immunology and Cancer ResearchHebrew University‐Hadassah Medical SchoolJerusalemIsrael
- Department of Paediatrics, Paediatric Pulmonology and SleepHadassah Hebrew University Medical CentreJerusalemIsrael
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW)University Medical Centre UtrechtUtrechtThe Netherlands
- Oncode InstituteHubrecht InstituteUtrechtThe Netherlands
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11
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Geurts MH, de Poel E, Pleguezuelos-Manzano C, Oka R, Carrillo L, Andersson-Rolf A, Boretto M, Brunsveld JE, van Boxtel R, Beekman JM, Clevers H. Evaluating CRISPR-based prime editing for cancer modeling and CFTR repair in organoids. Life Sci Alliance 2021; 4:e202000940. [PMID: 34373320 PMCID: PMC8356249 DOI: 10.26508/lsa.202000940] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 07/13/2021] [Accepted: 07/16/2021] [Indexed: 12/14/2022] Open
Abstract
Prime editing is a recently reported genome editing tool using a nickase-cas9 fused to a reverse transcriptase that directly synthesizes the desired edit at the target site. Here, we explore the use of prime editing in human organoids. Common TP53 mutations can be correctly modeled in human adult stem cell-derived colonic organoids with efficiencies up to 25% and up to 97% in hepatocyte organoids. Next, we functionally repaired the cystic fibrosis CFTR-F508del mutation and compared prime editing to CRISPR/Cas9-mediated homology-directed repair and adenine base editing on the CFTR-R785* mutation. Whole-genome sequencing of prime editing-repaired organoids revealed no detectable off-target effects. Despite encountering varying editing efficiencies and undesired mutations at the target site, these results underline the broad applicability of prime editing for modeling oncogenic mutations and showcase the potential clinical application of this technique, pending further optimization.
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Affiliation(s)
- Maarten H Geurts
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Hubrecht Institute, Utrecht, the Netherlands
| | - Eyleen de Poel
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, the Netherlands
- Regenerative Medicine Utrecht, University Medical Center, Utrecht University, Utrecht, the Netherlands
| | - Cayetano Pleguezuelos-Manzano
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Hubrecht Institute, Utrecht, the Netherlands
| | - Rurika Oka
- Oncode Institute,Princes Maxima Center, Utrecht, The Netherlands
| | - Léo Carrillo
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Hubrecht Institute, Utrecht, the Netherlands
| | - Amanda Andersson-Rolf
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Hubrecht Institute, Utrecht, the Netherlands
| | - Matteo Boretto
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Hubrecht Institute, Utrecht, the Netherlands
| | - Jesse E Brunsveld
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, the Netherlands
- Regenerative Medicine Utrecht, University Medical Center, Utrecht University, Utrecht, the Netherlands
| | - Ruben van Boxtel
- Oncode Institute,Princes Maxima Center, Utrecht, The Netherlands
| | - Jeffrey M Beekman
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, the Netherlands
- Regenerative Medicine Utrecht, University Medical Center, Utrecht University, Utrecht, the Netherlands
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Hubrecht Institute, Utrecht, the Netherlands
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12
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Geurts MH, van der Vaart J, Beumer J, Clevers H. The Organoid Platform: Promises and Challenges as Tools in the Fight against COVID-19. Stem Cell Reports 2021; 16:412-418. [PMID: 33691146 PMCID: PMC7940129 DOI: 10.1016/j.stemcr.2020.11.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 12/13/2022] Open
Abstract
Many pathogenic viruses that affect man display species specificity, limiting the use of animal models. Studying viral biology and identifying potential treatments therefore benefits from the development of in vitro cell systems that closely mimic human physiology. In the current COVID-19 pandemic, rapid scientific insights are of the utmost importance to limit its impact on public health and society. Organoids are emerging as versatile tools to progress the understanding of SARS-CoV-2 biology and to aid in the quest for novel treatments.
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Affiliation(s)
- Maarten H Geurts
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Jelte van der Vaart
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Joep Beumer
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands.
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands.
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13
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Dekkers JF, Whittle JR, Vaillant F, Chen HR, Dawson C, Liu K, Geurts MH, Herold MJ, Clevers H, Lindeman GJ, Visvader JE. Modeling Breast Cancer Using CRISPR-Cas9-Mediated Engineering of Human Breast Organoids. J Natl Cancer Inst 2021; 112:540-544. [PMID: 31589320 DOI: 10.1093/jnci/djz196] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 09/04/2019] [Accepted: 09/20/2019] [Indexed: 12/14/2022] Open
Abstract
Breast cancer is characterized by histological and functional heterogeneity, posing a clinical challenge for patient treatment. Emerging evidence suggests that the distinct subtypes reflect the repertoire of genetic alterations and the target cell. However, the precise initiating events that predispose normal epithelium to neoplasia are poorly understood. Here, we demonstrate that breast epithelial organoids can be generated from human reduction mammoplasties (12 out of 12 donors), thus creating a tool to study the clonal evolution of breast cancer. To recapitulate de novo oncogenesis, we exploited clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 for targeted knockout of four breast cancer-associated tumor suppressor genes (P53, PTEN, RB1, NF1) in mammary progenitor cells from six donors. Mutant organoids gained long-term culturing capacity and formed estrogen-receptor positive luminal tumors on transplantation into mice for one out of six P53/PTEN/RB1-mutated and three out of six P53/PTEN/RB1/NF1-mutated lines. These organoids responded to endocrine therapy or chemotherapy, supporting the potential utility of this model to enhance our understanding of the molecular events that culminate in specific subtypes of breast cancer.
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Affiliation(s)
- Johanna F Dekkers
- ACRF Cancer Biology and Stem Cells Division.,The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology
| | - James R Whittle
- ACRF Cancer Biology and Stem Cells Division.,The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology.,Department of Medicine (GHL), The University of Melbourne, Parkville, VIC, Australia; Department of Medical Oncology, The Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - François Vaillant
- ACRF Cancer Biology and Stem Cells Division.,The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology
| | - Huei-Rong Chen
- ACRF Cancer Biology and Stem Cells Division.,The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology
| | - Caleb Dawson
- ACRF Cancer Biology and Stem Cells Division.,The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology
| | - Kevin Liu
- ACRF Cancer Biology and Stem Cells Division.,The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology
| | - Maarten H Geurts
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) University Medical Center Utrecht, Utrecht, the Netherlands.,Department of Cancer Research, Oncode Institute, Hubrecht Institute-KNAW Utrecht, Utrecht, the Netherlands
| | - Marco J Herold
- Blood Cells and Blood Cancer Division.,The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) University Medical Center Utrecht, Utrecht, the Netherlands.,Department of Cancer Research, Oncode Institute, Hubrecht Institute-KNAW Utrecht, Utrecht, the Netherlands.,Cancer Genomics Center, Utrecht, the Netherlands
| | - Geoffrey J Lindeman
- ACRF Cancer Biology and Stem Cells Division.,Department of Medicine (GHL), The University of Melbourne, Parkville, VIC, Australia; Department of Medical Oncology, The Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Jane E Visvader
- ACRF Cancer Biology and Stem Cells Division.,The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology
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14
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Miao Y, Ha A, de Lau W, Yuki K, Santos AJM, You C, Geurts MH, Puschhof J, Pleguezuelos-Manzano C, Peng WC, Senlice R, Piani C, Buikema JW, Gbenedio OM, Vallon M, Yuan J, de Haan S, Hemrika W, Rösch K, Dang LT, Baker D, Ott M, Depeille P, Wu SM, Drost J, Nusse R, Roose JP, Piehler J, Boj SF, Janda CY, Clevers H, Kuo CJ, Garcia KC. Next-Generation Surrogate Wnts Support Organoid Growth and Deconvolute Frizzled Pleiotropy In Vivo. Cell Stem Cell 2020; 27:840-851.e6. [PMID: 32818433 DOI: 10.1016/j.stem.2020.07.020] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 05/02/2020] [Accepted: 07/29/2020] [Indexed: 12/15/2022]
Abstract
Modulation of Wnt signaling has untapped potential in regenerative medicine due to its essential functions in stem cell homeostasis. However, Wnt lipidation and Wnt-Frizzled (Fzd) cross-reactivity have hindered translational Wnt applications. Here, we designed and engineered water-soluble, Fzd subtype-specific "next-generation surrogate" (NGS) Wnts that hetero-dimerize Fzd and Lrp6. NGS Wnt supports long-term expansion of multiple different types of organoids, including kidney, colon, hepatocyte, ovarian, and breast. NGS Wnts are superior to Wnt3a conditioned media in organoid expansion and single-cell organoid outgrowth. Administration of Fzd subtype-specific NGS Wnt in vivo reveals that adult intestinal crypt proliferation can be promoted by agonism of Fzd5 and/or Fzd8 receptors, while a broad spectrum of Fzd receptors can induce liver zonation. Thus, NGS Wnts offer a unified organoid expansion protocol and a laboratory "tool kit" for dissecting the functions of Fzd subtypes in stem cell biology.
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Affiliation(s)
- Yi Miao
- Department of Molecular and Cellular Physiology, Department of Structural Biology, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Andrew Ha
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Wim de Lau
- Oncode Institute, Hubrecht Institute, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Kanako Yuki
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - António J M Santos
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Changjiang You
- Division of Biophysics, Department of Biology, University of Osnabrück, 49076 Osnabrück, Germany
| | - Maarten H Geurts
- Oncode Institute, Hubrecht Institute, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Jens Puschhof
- Oncode Institute, Hubrecht Institute, University Medical Centre Utrecht, Utrecht, the Netherlands
| | | | - Weng Chuan Peng
- Howard Hughes Medical Institute, Department of Developmental Biology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Ramazan Senlice
- Foundation Hubrecht Organoid Technology (HUB), Utrecht, the Netherlands
| | - Carol Piani
- Foundation Hubrecht Organoid Technology (HUB), Utrecht, the Netherlands
| | - Jan W Buikema
- Department of Cardiology, University Medical Center Utrecht & Utrecht Regenerative Medicine Center, Utrecht University, 3508 GA Utrecht, the Netherlands
| | | | - Mario Vallon
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jenny Yuan
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sanne de Haan
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Wieger Hemrika
- U-Protein Express BV, Yalelaan 62, 3584 CM Utrecht, the Netherlands
| | - Kathrin Rösch
- Gladstone Institutes and Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Luke T Dang
- Department of Biochemistry, Institute for Protein Design and Howard Hughes Medical Institute, University of Washington, Seattle, WA 98105, USA
| | - David Baker
- Department of Biochemistry, Institute for Protein Design and Howard Hughes Medical Institute, University of Washington, Seattle, WA 98105, USA
| | - Melanie Ott
- Gladstone Institutes and Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Philippe Depeille
- Department of Cardiology, University Medical Center Utrecht & Utrecht Regenerative Medicine Center, Utrecht University, 3508 GA Utrecht, the Netherlands
| | - Sean M Wu
- Division of Cardiovascular Medicine, Department of Medicine, Cardiovascular Institute and Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jarno Drost
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Roeland Nusse
- Howard Hughes Medical Institute, Department of Developmental Biology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jeroen P Roose
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA
| | - Jacob Piehler
- Division of Biophysics, Department of Biology, University of Osnabrück, 49076 Osnabrück, Germany
| | - Sylvia F Boj
- Foundation Hubrecht Organoid Technology (HUB), Utrecht, the Netherlands
| | - Claudia Y Janda
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Hans Clevers
- Oncode Institute, Hubrecht Institute, University Medical Centre Utrecht, Utrecht, the Netherlands; Oncode Institute, Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Calvin J Kuo
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Department of Structural Biology, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
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15
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Beumer J, Puschhof J, Bauzá-Martinez J, Martínez-Silgado A, Elmentaite R, James KR, Ross A, Hendriks D, Artegiani B, Busslinger GA, Ponsioen B, Andersson-Rolf A, Saftien A, Boot C, Kretzschmar K, Geurts MH, Bar-Ephraim YE, Pleguezuelos-Manzano C, Post Y, Begthel H, van der Linden F, Lopez-Iglesias C, van de Wetering WJ, van der Linden R, Peters PJ, Heck AJR, Goedhart J, Snippert H, Zilbauer M, Teichmann SA, Wu W, Clevers H. High-Resolution mRNA and Secretome Atlas of Human Enteroendocrine Cells. Cell 2020; 182:1062-1064. [PMID: 32822568 DOI: 10.1016/j.cell.2020.08.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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16
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Beumer J, Puschhof J, Bauzá-Martinez J, Martínez-Silgado A, Elmentaite R, James KR, Ross A, Hendriks D, Artegiani B, Busslinger GA, Ponsioen B, Andersson-Rolf A, Saftien A, Boot C, Kretzschmar K, Geurts MH, Bar-Ephraim YE, Pleguezuelos-Manzano C, Post Y, Begthel H, van der Linden F, Lopez-Iglesias C, van de Wetering WJ, van der Linden R, Peters PJ, Heck AJR, Goedhart J, Snippert H, Zilbauer M, Teichmann SA, Wu W, Clevers H. High-Resolution mRNA and Secretome Atlas of Human Enteroendocrine Cells. Cell 2020; 181:1291-1306.e19. [PMID: 32407674 DOI: 10.1016/j.cell.2020.04.036] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 03/10/2020] [Accepted: 04/21/2020] [Indexed: 12/11/2022]
Abstract
Enteroendocrine cells (EECs) sense intestinal content and release hormones to regulate gastrointestinal activity, systemic metabolism, and food intake. Little is known about the molecular make-up of human EEC subtypes and the regulated secretion of individual hormones. Here, we describe an organoid-based platform for functional studies of human EECs. EEC formation is induced in vitro by transient expression of NEUROG3. A set of gut organoids was engineered in which the major hormones are fluorescently tagged. A single-cell mRNA atlas was generated for the different EEC subtypes, and their secreted products were recorded by mass-spectrometry. We note key differences to murine EECs, including hormones, sensory receptors, and transcription factors. Notably, several hormone-like molecules were identified. Inter-EEC communication is exemplified by secretin-induced GLP-1 secretion. Indeed, individual EEC subtypes carry receptors for various EEC hormones. This study provides a rich resource to study human EEC development and function.
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Affiliation(s)
- Joep Beumer
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Jens Puschhof
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Julia Bauzá-Martinez
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Adriana Martínez-Silgado
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Rasa Elmentaite
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Kylie R James
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Alexander Ross
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK; Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Delilah Hendriks
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Benedetta Artegiani
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Georg A Busslinger
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Bas Ponsioen
- Oncode Institute, Center for Molecular Medicine, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Amanda Andersson-Rolf
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Aurelia Saftien
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Charelle Boot
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Kai Kretzschmar
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Maarten H Geurts
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Yotam E Bar-Ephraim
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Cayetano Pleguezuelos-Manzano
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Yorick Post
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Harry Begthel
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Franka van der Linden
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Amsterdam, the Netherlands
| | - Carmen Lopez-Iglesias
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, 6229 ER Maastricht, the Netherlands
| | - Willine J van de Wetering
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, 6229 ER Maastricht, the Netherlands
| | - Reinier van der Linden
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Peter J Peters
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, 6229 ER Maastricht, the Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Joachim Goedhart
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Amsterdam, the Netherlands
| | - Hugo Snippert
- Oncode Institute, Center for Molecular Medicine, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Matthias Zilbauer
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK; Theory of Condensed Matter, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge CB3 0HE, UK; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Wei Wu
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands; The Princess Maxima Center for Pediatric Oncology, 3584 CS Utrecht, the Netherlands.
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17
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Geurts MH, de Poel E, Amatngalim GD, Oka R, Meijers FM, Kruisselbrink E, van Mourik P, Berkers G, de Winter-de Groot KM, Michel S, Muilwijk D, Aalbers BL, Mullenders J, Boj SF, Suen SWF, Brunsveld JE, Janssens HM, Mall MA, Graeber SY, van Boxtel R, van der Ent CK, Beekman JM, Clevers H. CRISPR-Based Adenine Editors Correct Nonsense Mutations in a Cystic Fibrosis Organoid Biobank. Cell Stem Cell 2020; 26:503-510.e7. [PMID: 32084388 DOI: 10.1016/j.stem.2020.01.019] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 12/11/2019] [Accepted: 01/27/2020] [Indexed: 02/06/2023]
Abstract
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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Affiliation(s)
- Maarten H Geurts
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Eyleen de Poel
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, the Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT Utrecht, the Netherlands
| | - Gimano D Amatngalim
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, the Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT Utrecht, the Netherlands
| | - Rurika Oka
- Princess Maxima Center, 3584 CS Utrecht, the Netherlands; Oncode Institute, Princess Maxima Center, 3584 CS Utrecht, the Netherlands
| | - Fleur M Meijers
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, the Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT Utrecht, the Netherlands
| | - Evelien Kruisselbrink
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, the Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT Utrecht, the Netherlands
| | - Peter van Mourik
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, the Netherlands
| | - Gitte Berkers
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, the Netherlands
| | - Karin M de Winter-de Groot
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, the Netherlands
| | - Sabine Michel
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, the Netherlands
| | - Danya Muilwijk
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, the Netherlands
| | - Bente L Aalbers
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, the Netherlands
| | | | - Sylvia F Boj
- Hubrecht Organoid Technology, 3584 CM, Utrecht, the Netherlands
| | - Sylvia W F Suen
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, the Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT Utrecht, the Netherlands
| | - Jesse E Brunsveld
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, the Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT Utrecht, the Netherlands
| | - Hettie M Janssens
- Department of Pediatrics, division of Respiratory Medicine and Allergology, ErasmusMC-Sophia Children's Hospital, University Hospital Rotterdam, 3015 GD Rotterdam, the Netherlands
| | - Marcus A Mall
- Department of Pediatric Pulmonology, Immunology and Critical Care Medicine, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany; Berlin Institute of Health (BIH), 10178 Berlin, Germany
| | - Simon Y Graeber
- Department of Pediatric Pulmonology, Immunology and Critical Care Medicine, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany; Berlin Institute of Health (BIH), 10178 Berlin, Germany
| | - Ruben van Boxtel
- Princess Maxima Center, 3584 CS Utrecht, the Netherlands; Oncode Institute, Princess Maxima Center, 3584 CS Utrecht, the Netherlands
| | - Cornelis K van der Ent
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, the Netherlands
| | - Jeffrey M Beekman
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, the Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT Utrecht, the Netherlands.
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands.
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18
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Pleguezuelos-Manzano C, Puschhof J, Rosendahl Huber A, van Hoeck A, Wood HM, Nomburg J, Gurjao C, Manders F, Dalmasso G, Stege PB, Paganelli FL, Geurts MH, Beumer J, Mizutani T, Miao Y, van der Linden R, van der Elst S, Garcia KC, Top J, Willems RJL, Giannakis M, Bonnet R, Quirke P, Meyerson M, Cuppen E, van Boxtel R, Clevers H. Mutational signature in colorectal cancer caused by genotoxic pks + E. coli. Nature 2020; 580:269-273. [PMID: 32106218 PMCID: PMC8142898 DOI: 10.1038/s41586-020-2080-8] [Citation(s) in RCA: 522] [Impact Index Per Article: 130.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 02/17/2020] [Indexed: 02/06/2023]
Abstract
Various species of the intestinal microbiota have been associated with the development of colorectal cancer1,2, but it has not been demonstrated that bacteria have a direct role in the occurrence of oncogenic mutations. Escherichia coli can carry the pathogenicity island pks, which encodes a set of enzymes that synthesize colibactin3. This compound is believed to alkylate DNA on adenine residues4,5 and induces double-strand breaks in cultured cells3. Here we expose human intestinal organoids to genotoxic pks+ E. coli by repeated luminal injection over five months. Whole-genome sequencing of clonal organoids before and after this exposure revealed a distinct mutational signature that was absent from organoids injected with isogenic pks-mutant bacteria. The same mutational signature was detected in a subset of 5,876 human cancer genomes from two independent cohorts, predominantly in colorectal cancer. Our study describes a distinct mutational signature in colorectal cancer and implies that the underlying mutational process results directly from past exposure to bacteria carrying the colibactin-producing pks pathogenicity island.
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Affiliation(s)
- Cayetano Pleguezuelos-Manzano
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Jens Puschhof
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Axel Rosendahl Huber
- Oncode Institute, Utrecht, The Netherlands
- The Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Arne van Hoeck
- Oncode Institute, Utrecht, The Netherlands
- Center for Molecular Medicine, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Henry M Wood
- Pathology and Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Jason Nomburg
- Graduate Program in Virology, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Carino Gurjao
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Freek Manders
- Oncode Institute, Utrecht, The Netherlands
- The Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Guillaume Dalmasso
- University Clermont Auvergne, Inserm U1071, INRA USC2018, M2iSH, Clermont-Ferrand, France
| | - Paul B Stege
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Fernanda L Paganelli
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Maarten H Geurts
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Joep Beumer
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Utrecht, The Netherlands
| | - Tomohiro Mizutani
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Yi Miao
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Reinier van der Linden
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Utrecht, The Netherlands
| | - Stefan van der Elst
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Utrecht, The Netherlands
| | - K Christopher Garcia
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Janetta Top
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rob J L Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marios Giannakis
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Richard Bonnet
- University Clermont Auvergne, Inserm U1071, INRA USC2018, M2iSH, Clermont-Ferrand, France
- Department of Bacteriology, University Hospital of Clermont-Ferrand, Clermont-Ferrand, France
| | - Phil Quirke
- Pathology and Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Edwin Cuppen
- Oncode Institute, Utrecht, The Netherlands
- Center for Molecular Medicine, University Medical Centre Utrecht, Utrecht, The Netherlands
- Hartwig Medical Foundation, Amsterdam, The Netherlands
- CPCT Consortium, Rotterdam, The Netherlands
| | - Ruben van Boxtel
- Oncode Institute, Utrecht, The Netherlands.
- The Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Utrecht, The Netherlands.
- Oncode Institute, Utrecht, The Netherlands.
- The Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.
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19
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Hu JH, Miller SM, Geurts MH, Tang W, Chen L, Sun N, Zeina CM, Gao X, Rees HA, Lin Z, Liu DR. Evolved Cas9 variants with broad PAM compatibility and high DNA specificity. Nature 2018; 556:57-63. [PMID: 29512652 PMCID: PMC5951633 DOI: 10.1038/nature26155] [Citation(s) in RCA: 962] [Impact Index Per Article: 160.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 02/21/2018] [Indexed: 12/18/2022]
Abstract
A key limitation to the use of CRISPR-Cas9 proteins for genome editing and other applications is the requirement that a protospacer adjacent motif (PAM) be present at the target site. For the most commonly used Cas9 from Streptococcus pyogenes (SpCas9), this PAM requirement is NGG. No natural or engineered Cas9 variants shown to function efficiently in mammalian cells offer a PAM less restrictive than NGG. Here we used phage-assisted continuous evolution (PACE) to evolve an expanded PAM SpCas9 variant (xCas9) that can recognize a broad range of PAM sequences including NG, GAA, and GAT. The PAM compatibility of xCas9 is the broadest reported to date among Cas9s active in mammalian cells, and supports applications in human cells including targeted transcriptional activation, nuclease-mediated gene disruption, and both cytidine and adenine base editing. Remarkably, despite its broadened PAM compatibility, xCas9 has much greater DNA specificity than SpCas9, with substantially lower genome-wide off-target activity at all NGG target sites tested, as well as minimal off-target activity when targeting genomic sites with non-NGG PAMs. These findings expand the DNA targeting scope of CRISPR systems and establish that there is no necessary trade-off between Cas9 editing efficiency, PAM compatibility, and DNA specificity.
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Affiliation(s)
- Johnny H Hu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Shannon M Miller
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Maarten H Geurts
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Weixin Tang
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Liwei Chen
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Ning Sun
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Christina M Zeina
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Xue Gao
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Holly A Rees
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Zhi Lin
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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