1
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Alieva M, Barrera Román M, de Blank S, Petcu D, Zeeman AL, Dautzenberg NMM, Cornel AM, van de Ven C, Pieters R, den Boer ML, Nierkens S, Calkoen FGJ, Clevers H, Kuball J, Sebestyén Z, Wehrens EJ, Dekkers JF, Rios AC. BEHAV3D: a 3D live imaging platform for comprehensive analysis of engineered T cell behavior and tumor response. Nat Protoc 2024:10.1038/s41596-024-00972-6. [PMID: 38504137 DOI: 10.1038/s41596-024-00972-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 01/04/2024] [Indexed: 03/21/2024]
Abstract
Modeling immuno-oncology by using patient-derived material and immune cell co-cultures can advance our understanding of immune cell tumor targeting in a patient-specific manner, offering leads to improve cellular immunotherapy. However, fully exploiting these living cultures requires analysis of the dynamic cellular features modeled, for which protocols are currently limited. Here, we describe the application of BEHAV3D, a platform that implements multi-color live 3D imaging and computational tools for: (i) analyzing tumor death dynamics at both single-organoid or cell and population levels, (ii) classifying T cell behavior and (iii) producing data-informed 3D images and videos for visual inspection and further insight into obtained results. Together, this enables a refined assessment of how solid and liquid tumors respond to cellular immunotherapy, critically capturing both inter- and intratumoral heterogeneity in treatment response. In addition, BEHAV3D uncovers T cell behavior involved in tumor targeting, offering insight into their mode of action. Our pipeline thereby has strong implications for comparing, prioritizing and improving immunotherapy products by highlighting the behavioral differences between individual tumor donors, distinct T cell therapy concepts or subpopulations. The protocol describes critical wet lab steps, including co-culture preparations and fast 3D imaging with live cell dyes, a segmentation-based image processing tool to track individual organoids, tumor and immune cells and an analytical pipeline for behavioral profiling. This 1-week protocol, accessible to users with basic cell culture, imaging and programming expertise, can easily be adapted to any type of co-culture to visualize and exploit cell behavior, having far-reaching implications for the immuno-oncology field and beyond.
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Affiliation(s)
- Maria Alieva
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.
- Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM), CSIC-UAM, Madrid, Spain.
| | - Mario Barrera Román
- 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
| | - Diana Petcu
- 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
| | | | - Annelisa M Cornel
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Center for Translational Immunology, University Medical Centre (UMC) Utrecht, Utrecht, the Netherlands
| | - Cesca van de Ven
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Rob Pieters
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Monique L den Boer
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Stefan Nierkens
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Center for Translational Immunology, University Medical Centre (UMC) Utrecht, Utrecht, the Netherlands
| | - Friso G J Calkoen
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Hans Clevers
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Utrecht, the Netherlands
- Pharma, Research and Early Development (pRED), F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Jürgen Kuball
- Center for Translational Immunology, University Medical Centre (UMC) Utrecht, Utrecht, the Netherlands
- Department of Hematology, UMC Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Zsolt Sebestyén
- Center for Translational Immunology, University Medical Centre (UMC) Utrecht, Utrecht, the Netherlands
| | - Ellen J Wehrens
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Johanna F Dekkers
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Anne C Rios
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.
- Oncode Institute, Utrecht, the Netherlands.
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2
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Vennin C, Cattaneo CM, Bosch L, Vegna S, Ma X, Damstra HGJ, Martinovic M, Tsouri E, Ilic M, Azarang L, van Weering JRT, Pulver E, Zeeman AL, Schelfhorst T, Lohuis JO, Rios AC, Dekkers JF, Akkari L, Menezes R, Medema R, Baglio SR, Akhmanova A, Linn SC, Lemeer S, Pegtel DM, Voest EE, van Rheenen J. Taxanes trigger cancer cell killing in vivo by inducing non-canonical T cell cytotoxicity. Cancer Cell 2023; 41:1170-1185.e12. [PMID: 37311414 DOI: 10.1016/j.ccell.2023.05.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 02/28/2023] [Accepted: 05/11/2023] [Indexed: 06/15/2023]
Abstract
Although treatment with taxanes does not always lead to clinical benefit, all patients are at risk of their detrimental side effects such as peripheral neuropathy. Understanding the in vivo mode of action of taxanes can help design improved treatment regimens. Here, we demonstrate that in vivo, taxanes directly trigger T cells to selectively kill cancer cells in a non-canonical, T cell receptor-independent manner. Mechanistically, taxanes induce T cells to release cytotoxic extracellular vesicles, which lead to apoptosis specifically in tumor cells while leaving healthy epithelial cells intact. We exploit these findings to develop an effective therapeutic approach, based on transfer of T cells pre-treated with taxanes ex vivo, thereby avoiding toxicity of systemic treatment. Our study reveals a different in vivo mode of action of one of the most commonly used chemotherapies, and opens avenues to harness T cell-dependent anti-tumor effects of taxanes while avoiding systemic toxicity.
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Affiliation(s)
- Claire Vennin
- Division of Molecular Pathology, the Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066CX Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands
| | - Chiara M Cattaneo
- Oncode Institute, Amsterdam, the Netherlands; Department of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066CX Amsterdam, the Netherlands
| | - Leontien Bosch
- Department of Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081HV Amsterdam, the Netherlands
| | - Serena Vegna
- Oncode Institute, Amsterdam, the Netherlands; Division of Tumor Biology and Immunology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Xuhui Ma
- Oncode Institute, Amsterdam, the Netherlands; Department of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066CX Amsterdam, the Netherlands
| | - Hugo G J Damstra
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, 3584CT Utrecht, the Netherlands
| | - Moreno Martinovic
- Division of Gene Regulation, the Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066CX Amsterdam, the Netherlands
| | - Efi Tsouri
- Oncode Institute, Amsterdam, the Netherlands; Division of Tumor Biology and Immunology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Mila Ilic
- Oncode Institute, Amsterdam, the Netherlands; Division of Cell Biology, the Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066CX Amsterdam, the Netherlands
| | - Leyla Azarang
- Biostatistics Centre & Department of Psychosocial Research and Epidemiology, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Jan R T van Weering
- Department of Human Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam UMC, 1105AZ Amsterdam, the Netherlands
| | - Emilia Pulver
- Division of Molecular Pathology, the Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066CX Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands
| | - Amber L Zeeman
- Oncode Institute, Amsterdam, the Netherlands; Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Centre (UMC), 3584CT Utrecht, the Netherlands; Princess Maxima Center for Pediatric Oncology, 3584CT Utrecht, the Netherlands
| | - Tim Schelfhorst
- Division of Molecular Pathology, the Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066CX Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands
| | - Jeroen O Lohuis
- Division of Molecular Pathology, the Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066CX Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands
| | - Anne C Rios
- Oncode Institute, Amsterdam, the Netherlands; Princess Maxima Center for Pediatric Oncology, 3584CT Utrecht, the Netherlands
| | - Johanna F Dekkers
- Oncode Institute, Amsterdam, the Netherlands; Princess Maxima Center for Pediatric Oncology, 3584CT Utrecht, the Netherlands
| | - Leila Akkari
- Oncode Institute, Amsterdam, the Netherlands; Division of Tumor Biology and Immunology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Renee Menezes
- Biostatistics Centre & Department of Psychosocial Research and Epidemiology, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Rene Medema
- Oncode Institute, Amsterdam, the Netherlands; Division of Cell Biology, the Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066CX Amsterdam, the Netherlands
| | - Serena R Baglio
- Department of Pathology, Cancer Center Amsterdam, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Anna Akhmanova
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, 3584CT Utrecht, the Netherlands
| | - Sabine C Linn
- Divisions of Molecular Pathology and of Medical Oncology, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Department of Pathology, University Medical Center, 1081HV Utrecht, the Netherlands
| | - Simone Lemeer
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584CT Utrecht, the Netherlands; Netherlands Proteomics Center, 3584CT Utrecht, the Netherlands
| | - Dirk M Pegtel
- Department of Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081HV Amsterdam, the Netherlands
| | - Emile E Voest
- Oncode Institute, Amsterdam, the Netherlands; Department of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066CX Amsterdam, the Netherlands
| | - Jacco van Rheenen
- Division of Molecular Pathology, the Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066CX Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands.
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3
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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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4
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Heitink L, Whittle JR, Vaillant F, Capaldo BD, Dekkers JF, Dawson CA, Milevskiy MJG, Surgenor E, Tsai M, Chen H, Christie M, Chen Y, Smyth GK, Herold MJ, Strasser A, Lindeman GJ, Visvader JE. In vivo genome-editing screen identifies tumor suppressor genes that cooperate with Trp53 loss during mammary tumorigenesis. Mol Oncol 2022; 16:1119-1131. [PMID: 35000262 PMCID: PMC8895454 DOI: 10.1002/1878-0261.13179] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 09/23/2021] [Revised: 11/07/2021] [Accepted: 01/07/2022] [Indexed: 11/20/2022] Open
Abstract
Breast cancer is a heterogeneous disease that comprises multiple histological and molecular subtypes. To gain insight into mutations that drive breast tumorigenesis, we describe a pipeline for the identification and validation of tumor suppressor genes. Based on an in vivo genome‐wide CRISPR/Cas9 screen in Trp53+/– heterozygous mice, we identified tumor suppressor genes that included the scaffold protein Axin1, the protein kinase A regulatory subunit gene Prkar1a, as well as the proof‐of‐concept genes Pten, Nf1, and Trp53 itself. Ex vivo editing of primary mammary epithelial organoids was performed to further interrogate the roles of Axin1 and Prkar1a. Increased proliferation and profound changes in mammary organoid morphology were observed for Axin1/Trp53 and Prkar1a/Trp53 double mutants compared to Pten/Trp53 double mutants. Furthermore, direct in vivo genome editing via intraductal injection of lentiviruses engineered to express dual short‐guide RNAs revealed that mutagenesis of Trp53 and either Prkar1a, Axin1, or Pten markedly accelerated tumor development compared to Trp53‐only mutants. This proof‐of‐principle study highlights the application of in vivo CRISPR/Cas9 editing for uncovering cooperativity between defects in tumor suppressor genes that elicit mammary tumorigenesis.
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Affiliation(s)
- Luuk Heitink
- ACRF Cancer Biology and Stem Cells DivisionThe Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
- Department of Medical BiologyThe University of MelbourneParkvilleAustralia
| | - James R. Whittle
- ACRF Cancer Biology and Stem Cells DivisionThe Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
- Department of Medical BiologyThe University of MelbourneParkvilleAustralia
- Department of Medical OncologyPeter MacCallum Cancer CentreMelbourneAustralia
| | - François Vaillant
- ACRF Cancer Biology and Stem Cells DivisionThe Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
- Department of Medical BiologyThe University of MelbourneParkvilleAustralia
| | - Bianca D. Capaldo
- ACRF Cancer Biology and Stem Cells DivisionThe Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
- Department of Medical BiologyThe University of MelbourneParkvilleAustralia
| | - Johanna F. Dekkers
- ACRF Cancer Biology and Stem Cells DivisionThe Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands
| | - Caleb A. Dawson
- ACRF Cancer Biology and Stem Cells DivisionThe Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
- Department of Medical BiologyThe University of MelbourneParkvilleAustralia
- Immunology DivisionThe Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
| | - Michael J. G. Milevskiy
- ACRF Cancer Biology and Stem Cells DivisionThe Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
- Department of Medical BiologyThe University of MelbourneParkvilleAustralia
| | - Elliot Surgenor
- ACRF Cancer Biology and Stem Cells DivisionThe Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
| | - Minhsuang Tsai
- ACRF Cancer Biology and Stem Cells DivisionThe Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
| | - Huei‐Rong Chen
- ACRF Cancer Biology and Stem Cells DivisionThe Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
| | - Michael Christie
- Personalised Oncology DivisionThe Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
- Department of PathologyThe Royal Melbourne HospitalParkvilleAustralia
| | - Yunshun Chen
- Department of Medical BiologyThe University of MelbourneParkvilleAustralia
- Bioinformatics DivisionThe Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
| | - Gordon K. Smyth
- Bioinformatics DivisionThe Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
- School of Mathematics and StatisticsThe University of MelbourneParkvilleAustralia
| | - Marco J. Herold
- Department of Medical BiologyThe University of MelbourneParkvilleAustralia
- Blood Cells and Blood Cancer DivisionThe Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
| | - Andreas Strasser
- Department of Medical BiologyThe University of MelbourneParkvilleAustralia
- Blood Cells and Blood Cancer DivisionThe Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
| | - Geoffrey J. Lindeman
- ACRF Cancer Biology and Stem Cells DivisionThe Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
- Department of Medical BiologyThe University of MelbourneParkvilleAustralia
- Department of Medical OncologyPeter MacCallum Cancer CentreMelbourneAustralia
| | - Jane E. Visvader
- ACRF Cancer Biology and Stem Cells DivisionThe Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
- Department of Medical BiologyThe University of MelbourneParkvilleAustralia
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5
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van Ineveld RL, Kleinnijenhuis M, Alieva M, de Blank S, Barrera Roman M, van Vliet EJ, Martínez Mir C, Johnson HR, Bos FL, Heukers R, Chuva de Sousa Lopes SM, Drost J, Dekkers JF, Wehrens EJ, Rios AC. Revealing the spatio-phenotypic patterning of cells in healthy and tumor tissues with mLSR-3D and STAPL-3D. Nat Biotechnol 2021; 39:1239-1245. [PMID: 34083793 PMCID: PMC7611791 DOI: 10.1038/s41587-021-00926-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 04/16/2021] [Indexed: 12/12/2022]
Abstract
Despite advances in three-dimensional (3D) imaging, it remains challenging to profile all the cells within a large 3D tissue, including the morphology and organization of the many cell types present. Here, we introduce eight-color, multispectral, large-scale single-cell resolution 3D (mLSR-3D) imaging and image analysis software for the parallelized, deep learning-based segmentation of large numbers of single cells in tissues, called segmentation analysis by parallelization of 3D datasets (STAPL-3D). Applying the method to pediatric Wilms tumor, we extract molecular, spatial and morphological features of millions of cells and reconstruct the tumor’s spatio-phenotypic patterning. In situ population profiling and pseudotime ordering reveals a highly disorganized spatial pattern in Wilms tumor compared to healthy fetal kidney, yet cellular profiles closely resembling human fetal kidney cells could be observed. In addition, we identify previously unreported tumor-specific populations, uniquely characterized by their spatial embedding or morphological attributes. Our results demonstrate the use of combining mLSR-3D and STAPL-3D to generate a comprehensive cellular map of human tumors.
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Affiliation(s)
- Ravian L van Ineveld
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Cancer Genomics Netherlands, Oncode Institute, Utrecht, the Netherlands
| | - Michiel Kleinnijenhuis
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Cancer Genomics Netherlands, Oncode Institute, Utrecht, the Netherlands
| | - Maria Alieva
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Cancer Genomics Netherlands, Oncode Institute, Utrecht, the Netherlands
| | - Sam de Blank
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Cancer Genomics Netherlands, Oncode Institute, Utrecht, the Netherlands
| | - Mario Barrera Roman
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Cancer Genomics Netherlands, Oncode Institute, Utrecht, the Netherlands
| | - Esmée J van Vliet
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Cancer Genomics Netherlands, Oncode Institute, Utrecht, the Netherlands
| | - Clara Martínez Mir
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Cancer Genomics Netherlands, Oncode Institute, Utrecht, the Netherlands
| | - Hannah R Johnson
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Cancer Genomics Netherlands, Oncode Institute, Utrecht, the Netherlands
| | - Frank L Bos
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Cancer Genomics Netherlands, Oncode Institute, Utrecht, the Netherlands
| | | | | | - Jarno Drost
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Cancer Genomics Netherlands, Oncode Institute, Utrecht, the Netherlands
| | - Johanna F Dekkers
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Cancer Genomics Netherlands, Oncode Institute, Utrecht, the Netherlands
| | - Ellen J Wehrens
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Cancer Genomics Netherlands, Oncode Institute, Utrecht, the Netherlands
| | - Anne C Rios
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands. .,Cancer Genomics Netherlands, Oncode Institute, Utrecht, the Netherlands.
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6
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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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7
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Abstract
Organoid technology, in vitro 3D culturing of miniature tissue, has opened a new experimental window for cellular processes that govern organ development and function as well as disease. Fluorescence microscopy has played a major role in characterizing their cellular composition in detail and demonstrating their similarity to the tissue they originate from. In this article, we present a comprehensive protocol for high-resolution 3D imaging of whole organoids upon immunofluorescent labeling. This method is widely applicable for imaging of organoids differing in origin, size and shape. Thus far we have applied the method to airway, colon, kidney, and liver organoids derived from healthy human tissue, as well as human breast tumor organoids and mouse mammary gland organoids. We use an optical clearing agent, FUnGI, which enables the acquisition of whole 3D organoids with the opportunity for single-cell quantification of markers. This three-day protocol from organoid harvesting to image analysis is optimized for 3D imaging using confocal microscopy.
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Affiliation(s)
- Ravian L van Ineveld
- Princess Máxima Center for Pediatric Oncology; Department of Cancer Research, Oncode Institute, Hubrecht Institute-KNAW Utrecht; Cancer Genomics Center (CGC)
| | - Hendrikus C R Ariese
- Princess Máxima Center for Pediatric Oncology; Department of Cancer Research, Oncode Institute, Hubrecht Institute-KNAW Utrecht; Cancer Genomics Center (CGC)
| | - Ellen J Wehrens
- Princess Máxima Center for Pediatric Oncology; Department of Cancer Research, Oncode Institute, Hubrecht Institute-KNAW Utrecht; Cancer Genomics Center (CGC)
| | - Johanna F Dekkers
- Princess Máxima Center for Pediatric Oncology; Department of Cancer Research, Oncode Institute, Hubrecht Institute-KNAW Utrecht; Cancer Genomics Center (CGC); Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center (UMC) Utrecht
| | - Anne C Rios
- Princess Máxima Center for Pediatric Oncology; Department of Cancer Research, Oncode Institute, Hubrecht Institute-KNAW Utrecht; Cancer Genomics Center (CGC);
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8
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Vonk AM, van Mourik P, Ramalho AS, Silva IAL, Statia M, Kruisselbrink E, Suen SWF, Dekkers JF, Vleggaar FP, Houwen RHJ, Mullenders J, Boj SF, Vries R, Amaral MD, de Boeck K, van der Ent CK, Beekman JM. Protocol for Application, Standardization and Validation of the Forskolin-Induced Swelling Assay in Cystic Fibrosis Human Colon Organoids. STAR Protoc 2020; 1:100019. [PMID: 33111074 PMCID: PMC7580120 DOI: 10.1016/j.xpro.2020.100019] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
This protocol describes the isolation, handling, culture of, and experiments with human colon stem cell organoids in the context of cystic fibrosis (CF). In human colon organoids, the function of cystic fibrosis transmembrane conductance regulator (CFTR) protein and its rescue by CFTR modulators can be quantified using the forskolin-induced swelling assay. Implementation procedures and validation experiments are described for six CF human colon organoid lines, and representative CFTR genotypes are tested for basal CFTR function and response to CFTR-modulating drugs. For complete details on the use and execution of this protocol, please refer to Dekkers et al (2016) and Berkers and van Mourik (2019). Rectal biopsies are used to efficiently establish human colon organoid cultures Human colon organoids can be cultured and biobanked for prolonged periods Human colon organoids can be used to measure function of the CFTR protein using FIS Reference CF organoid lines are available for validation of the FIS assay
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Affiliation(s)
- Annelotte M Vonk
- Dept. of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.,Regenerative Medicine Utrecht, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Peter van Mourik
- Dept. of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.,Regenerative Medicine Utrecht, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Anabela S Ramalho
- Katholieke Universiteit Leuven, Dept. of Development and Regeneration, Leuven, Belgium
| | - Iris A L Silva
- University of Lisboa, Faculty of Sciences, BioISI- Biosystems & Integrative Sciences Institute, Lisboa, Portugal
| | - Marvin Statia
- Hubrecht Organoid Technology (HUB), Utrecht, the Netherlands
| | - Evelien Kruisselbrink
- Dept. of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.,Regenerative Medicine Utrecht, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Sylvia W F Suen
- Dept. of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.,Regenerative Medicine Utrecht, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | | | - Frank P Vleggaar
- Gastroenterology and Hepatology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Roderick H J Houwen
- Dept. of Pediatric Gastroenterology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Sylvia F Boj
- Hubrecht Organoid Technology (HUB), Utrecht, the Netherlands
| | - Robert Vries
- Hubrecht Organoid Technology (HUB), Utrecht, the Netherlands
| | - Margarida D Amaral
- University of Lisboa, Faculty of Sciences, BioISI- Biosystems & Integrative Sciences Institute, Lisboa, Portugal
| | - Kris de Boeck
- Katholieke Universiteit Leuven, Dept. of Development and Regeneration, Leuven, Belgium
| | - Cornelis K van der Ent
- Dept. of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Jeffrey M Beekman
- Dept. of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.,Regenerative Medicine Utrecht, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
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9
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Whittle JR, Vaillant F, Surgenor E, Policheni AN, Giner G, Capaldo BD, Chen HR, Liu HK, Dekkers JF, Sachs N, Clevers H, Fellowes A, Green T, Xu H, Fox SB, Herold MJ, Smyth GK, Gray DHD, Visvader JE, Lindeman GJ. Dual Targeting of CDK4/6 and BCL2 Pathways Augments Tumor Response in Estrogen Receptor-Positive Breast Cancer. Clin Cancer Res 2020; 26:4120-4134. [PMID: 32245900 DOI: 10.1158/1078-0432.ccr-19-1872] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [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: 02/20/2020] [Accepted: 03/31/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE Although cyclin-dependent kinase 4 and 6 (CDK4/6) inhibitors significantly extend tumor response in patients with metastatic estrogen receptor-positive (ER+) breast cancer, relapse is almost inevitable. This may, in part, reflect the failure of CDK4/6 inhibitors to induce apoptotic cell death. We therefore evaluated combination therapy with ABT-199 (venetoclax), a potent and selective BCL2 inhibitor. EXPERIMENTAL DESIGN BCL2 family member expression was assessed following treatment with endocrine therapy and the CDK4/6 inhibitor palbociclib. Functional assays were used to determine the impact of adding ABT-199 to fulvestrant and palbociclib in ER+ breast cancer cell lines, patient-derived organoid (PDO), and patient-derived xenograft (PDX) models. A syngeneic ER+ mouse mammary tumor model was used to study the effect of combination therapy on the immune system. RESULTS Triple therapy was well tolerated and produced a superior and more durable tumor response compared with single or doublet therapy. This was associated with marked apoptosis, including of senescent cells, indicative of senolysis. Unexpectedly, ABT-199 resulted in Rb dephosphorylation and reduced G1-S cyclins, most notably at high doses, thereby intensifying the fulvestrant/palbociclib-induced cell-cycle arrest. Interestingly, a CRISPR/Cas9 screen suggested that ABT-199 could mitigate loss of Rb (and potentially other mechanisms of acquired resistance) to palbociclib. ABT-199 did not abrogate the favorable immunomodulatory effects of palbociclib in a syngeneic ER+ mammary tumor model and extended tumor response when combined with anti-PD1 therapy. CONCLUSIONS This study illustrates the potential for targeting BCL2 in combination with CDK4/6 inhibitors and supports investigation of combination therapy in ER+ breast cancer.
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Affiliation(s)
- James R Whittle
- Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Oncology, The Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - François Vaillant
- Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Elliot Surgenor
- Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Antonia N Policheni
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia.,Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Göknur Giner
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia.,Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Bianca D Capaldo
- Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Huei-Rong Chen
- Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - He K Liu
- Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Johanna F Dekkers
- Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Centre (UMC), Utrecht, the Netherlands.,Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Norman Sachs
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Centre (UMC), Utrecht, the Netherlands
| | - Hans Clevers
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Centre (UMC), Utrecht, the Netherlands.,Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Andrew Fellowes
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Thomas Green
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Huiling Xu
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Stephen B Fox
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Marco J Herold
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia.,Blood Cells and Blood Cancer Division, The Walter and Eliza Institute of Medical Research, Parkville, Victoria, Australia
| | - Gordon K Smyth
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,School of Mathematics and Statistics, The University of Melbourne, Parkville, Victoria, Australia
| | - Daniel H D Gray
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia.,Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Jane E Visvader
- Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Geoffrey J Lindeman
- Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia. .,Department of Medical Oncology, The Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Department of Medicine, The University of Melbourne, Parkville, Victoria, Australia
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10
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Dekkers JF, Alieva M, Wellens LM, Ariese HCR, Jamieson PR, Vonk AM, Amatngalim GD, Hu H, Oost KC, Snippert HJG, Beekman JM, Wehrens EJ, Visvader JE, Clevers H, Rios AC. High-resolution 3D imaging of fixed and cleared organoids. Nat Protoc 2019; 14:1756-1771. [PMID: 31053799 DOI: 10.1038/s41596-019-0160-8] [Citation(s) in RCA: 246] [Impact Index Per Article: 49.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 03/04/2019] [Indexed: 12/15/2022]
Abstract
In vitro 3D organoid systems have revolutionized the modeling of organ development and diseases in a dish. Fluorescence microscopy has contributed to the characterization of the cellular composition of organoids and demonstrated organoids' phenotypic resemblance to their original tissues. Here, we provide a detailed protocol for performing high-resolution 3D imaging of entire organoids harboring fluorescence reporters and upon immunolabeling. This method is applicable to a wide range of organoids of differing origins and of various sizes and shapes. We have successfully used it on human airway, colon, kidney, liver and breast tumor organoids, as well as on mouse mammary gland organoids. It includes a simple clearing method utilizing a homemade fructose-glycerol clearing agent that captures 3D organoids in full and enables marker quantification on a cell-by-cell basis. Sample preparation has been optimized for 3D imaging by confocal, super-resolution confocal, multiphoton and light-sheet microscopy. From organoid harvest to image analysis, the protocol takes 3 d.
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Affiliation(s)
- Johanna F Dekkers
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center (UMC) Utrecht, Utrecht, the Netherlands.,Department of Cancer Research, Oncode Institute, Hubrecht Institute-KNAW Utrecht, Utrecht, the Netherlands.,Cancer Genomics Center (CGC), Utrecht, the Netherlands
| | - Maria Alieva
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Department of Cancer Research, Oncode Institute, Hubrecht Institute-KNAW Utrecht, Utrecht, the Netherlands.,Cancer Genomics Center (CGC), Utrecht, the Netherlands
| | - Lianne M Wellens
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Department of Cancer Research, Oncode Institute, Hubrecht Institute-KNAW Utrecht, Utrecht, the Netherlands.,Cancer Genomics Center (CGC), Utrecht, the Netherlands
| | - Hendrikus C R Ariese
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Department of Cancer Research, Oncode Institute, Hubrecht Institute-KNAW Utrecht, Utrecht, the Netherlands.,Cancer Genomics Center (CGC), Utrecht, the Netherlands
| | - Paul R Jamieson
- Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Annelotte M Vonk
- Regenerative Medicine Center Utrecht, University Medical Center, Utrecht University, Utrecht, the Netherlands.,Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, the Netherlands
| | - Gimano D Amatngalim
- Regenerative Medicine Center Utrecht, University Medical Center, Utrecht University, Utrecht, the Netherlands.,Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, the Netherlands
| | - Huili Hu
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center (UMC) Utrecht, Utrecht, the Netherlands.,Department of Cancer Research, Oncode Institute, Hubrecht Institute-KNAW Utrecht, Utrecht, the Netherlands.,Cancer Genomics Center (CGC), Utrecht, the Netherlands
| | - Koen C Oost
- Department of Cancer Research, Oncode Institute, Hubrecht Institute-KNAW Utrecht, Utrecht, the Netherlands.,Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Hugo J G Snippert
- Department of Cancer Research, Oncode Institute, Hubrecht Institute-KNAW Utrecht, Utrecht, the Netherlands.,Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Jeffrey M Beekman
- Regenerative Medicine Center Utrecht, University Medical Center, Utrecht University, Utrecht, the Netherlands.,Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, the Netherlands
| | - Ellen J Wehrens
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Department of Cancer Research, Oncode Institute, Hubrecht Institute-KNAW Utrecht, Utrecht, the Netherlands.,Cancer Genomics Center (CGC), Utrecht, the Netherlands
| | - Jane E Visvader
- Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Hans Clevers
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center (UMC) Utrecht, Utrecht, the Netherlands.,Department of Cancer Research, Oncode Institute, Hubrecht Institute-KNAW Utrecht, Utrecht, the Netherlands.,Cancer Genomics Center (CGC), Utrecht, the Netherlands
| | - Anne C Rios
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands. .,Department of Cancer Research, Oncode Institute, Hubrecht Institute-KNAW Utrecht, Utrecht, the Netherlands. .,Cancer Genomics Center (CGC), Utrecht, the Netherlands.
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11
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Sachs N, Papaspyropoulos A, Zomer-van Ommen DD, Heo I, Böttinger L, Klay D, Weeber F, Huelsz-Prince G, Iakobachvili N, Amatngalim GD, de Ligt J, van Hoeck A, Proost N, Viveen MC, Lyubimova A, Teeven L, Derakhshan S, Korving J, Begthel H, Dekkers JF, Kumawat K, Ramos E, van Oosterhout MF, Offerhaus GJ, Wiener DJ, Olimpio EP, Dijkstra KK, Smit EF, van der Linden M, Jaksani S, van de Ven M, Jonkers J, Rios AC, Voest EE, van Moorsel CH, van der Ent CK, Cuppen E, van Oudenaarden A, Coenjaerts FE, Meyaard L, Bont LJ, Peters PJ, Tans SJ, van Zon JS, Boj SF, Vries RG, Beekman JM, Clevers H. Long-term expanding human airway organoids for disease modeling. EMBO J 2019; 38:embj.2018100300. [PMID: 30643021 PMCID: PMC6376275 DOI: 10.15252/embj.2018100300] [Citation(s) in RCA: 522] [Impact Index Per Article: 104.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 12/07/2018] [Accepted: 12/07/2018] [Indexed: 12/30/2022] Open
Abstract
Organoids are self-organizing 3D structures grown from stem cells that recapitulate essential aspects of organ structure and function. Here, we describe a method to establish long-term-expanding human airway organoids from broncho-alveolar resections or lavage material. The pseudostratified airway organoids consist of basal cells, functional multi-ciliated cells, mucus-producing secretory cells, and CC10-secreting club cells. Airway organoids derived from cystic fibrosis (CF) patients allow assessment of CFTR function in an organoid swelling assay. Organoids established from lung cancer resections and metastasis biopsies retain tumor histopathology as well as cancer gene mutations and are amenable to drug screening. Respiratory syncytial virus (RSV) infection recapitulates central disease features, dramatically increases organoid cell motility via the non-structural viral NS2 protein, and preferentially recruits neutrophils upon co-culturing. We conclude that human airway organoids represent versatile models for the in vitro study of hereditary, malignant, and infectious pulmonary disease.
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Affiliation(s)
- Norman Sachs
- Oncode Institute, Hubrecht Institute-KNAW and UMC Utrecht, Utrecht, The Netherlands
| | | | | | - Inha Heo
- Oncode Institute, Hubrecht Institute-KNAW and UMC Utrecht, Utrecht, The Netherlands
| | - Lena Böttinger
- Oncode Institute, Hubrecht Institute-KNAW and UMC Utrecht, Utrecht, The Netherlands
| | - Dymph Klay
- St. Antonius Hospital Nieuwegein, Nieuwegein, The Netherlands
| | - Fleur Weeber
- The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | | | | | | | | | - Natalie Proost
- Mouse Clinic for Cancer and Aging (MCCA) Preclinical Intervention Unit, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Anna Lyubimova
- Oncode Institute, Hubrecht Institute-KNAW and UMC Utrecht, Utrecht, The Netherlands
| | - Luc Teeven
- Oncode Institute, Hubrecht Institute-KNAW and UMC Utrecht, Utrecht, The Netherlands
| | - Sepideh Derakhshan
- Wilhelmina Children's Hospital and UMC Utrecht, Utrecht, The Netherlands
| | - Jeroen Korving
- Oncode Institute, Hubrecht Institute-KNAW and UMC Utrecht, Utrecht, The Netherlands
| | - Harry Begthel
- Oncode Institute, Hubrecht Institute-KNAW and UMC Utrecht, Utrecht, The Netherlands
| | - Johanna F Dekkers
- Oncode Institute, Hubrecht Institute-KNAW and UMC Utrecht, Utrecht, The Netherlands
| | - Kuldeep Kumawat
- Wilhelmina Children's Hospital and UMC Utrecht, Utrecht, The Netherlands
| | - Emilio Ramos
- Hubrecht Organoid Technology, Utrecht, The Netherlands
| | | | | | - Dominique J Wiener
- Oncode Institute, Hubrecht Institute-KNAW and UMC Utrecht, Utrecht, The Netherlands
| | | | | | - Egbert F Smit
- The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | | | - Marieke van de Ven
- Mouse Clinic for Cancer and Aging (MCCA) Preclinical Intervention Unit, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jos Jonkers
- Mouse Clinic for Cancer and Aging (MCCA) Preclinical Intervention Unit, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Anne C Rios
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Emile E Voest
- The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | | | | | | | | | - Linde Meyaard
- Wilhelmina Children's Hospital and UMC Utrecht, Utrecht, The Netherlands
| | - Louis J Bont
- Wilhelmina Children's Hospital and UMC Utrecht, Utrecht, The Netherlands
| | | | | | | | - Sylvia F Boj
- Hubrecht Organoid Technology, Utrecht, The Netherlands
| | | | - Jeffrey M Beekman
- Wilhelmina Children's Hospital and UMC Utrecht, Utrecht, The Netherlands
| | - Hans Clevers
- Oncode Institute, Hubrecht Institute-KNAW and UMC Utrecht, Utrecht, The Netherlands .,Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
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12
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de Winter-de Groot KM, Janssens HM, van Uum RT, Dekkers JF, Berkers G, Vonk A, Kruisselbrink E, Oppelaar H, Vries R, Clevers H, Houwen RH, Escher JC, Elias SG, de Jonge HR, de Rijke YB, Tiddens HA, van der Ent CK, Beekman JM. Stratifying infants with cystic fibrosis for disease severity using intestinal organoid swelling as a biomarker of CFTR function. Eur Respir J 2018; 52:13993003.02529-2017. [DOI: 10.1183/13993003.02529-2017] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 07/20/2018] [Indexed: 12/18/2022]
Abstract
Forskolin-induced swelling (FIS) of intestinal organoids from individuals with cystic fibrosis (CF) measures function of the cystic fibrosis transmembrane conductance regulator (CFTR), the protein mutated in CF.We investigated whether FIS corresponds with clinical outcome parameters and biomarkers of CFTR function in 34 infants diagnosed with CF. Relationships with FIS were studied for indicators of pulmonary and gastrointestinal disease.Children with low FIS had higher levels of immunoreactive trypsinogen (p=0.030) and pancreatitis-associated protein (p=0.039), more often had pancreatic insufficiency (p<0.001), had more abnormalities on chest computed tomography (p=0.049), and had lower z-scores for maximal expiratory flow at functional residual capacity (p=0.033) when compared to children with high FIS values. FIS significantly correlated with sweat chloride concentration (SCC) and intestinal current measurement (ICM) (r= −0.82 and r=0.70, respectively; both p<0.001). Individual assessment of SCC, ICM and FIS suggested that FIS can help to classify individual disease severity.Thus, stratification by FIS identified subgroups that differed in pulmonary and gastrointestinal outcome parameters. FIS of intestinal organoids correlated well with established CFTR-dependent biomarkers such as SCC and ICM, and performed adequately at group and individual level in this proof-of-concept study.
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13
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Michalak EM, Milevskiy MJG, Joyce RM, Dekkers JF, Jamieson PR, Pal B, Dawson CA, Hu Y, Orkin SH, Alexander WS, Lindeman GJ, Smyth GK, Visvader JE. Canonical PRC2 function is essential for mammary gland development and affects chromatin compaction in mammary organoids. PLoS Biol 2018; 16:e2004986. [PMID: 30080881 PMCID: PMC6095611 DOI: 10.1371/journal.pbio.2004986] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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: 12/01/2017] [Revised: 08/16/2018] [Accepted: 07/25/2018] [Indexed: 12/14/2022] Open
Abstract
Distinct transcriptional states are maintained through organization of chromatin, resulting from the sum of numerous repressive and active histone modifications, into tightly packaged heterochromatin versus more accessible euchromatin. Polycomb repressive complex 2 (PRC2) is the main mammalian complex responsible for histone 3 lysine 27 trimethylation (H3K27me3) and is integral to chromatin organization. Using in vitro and in vivo studies, we show that deletion of Suz12, a core component of all PRC2 complexes, results in loss of H3K27me3 and H3K27 dimethylation (H3K27me2), completely blocks normal mammary gland development, and profoundly curtails progenitor activity in 3D organoid cultures. Through the application of mammary organoids to bypass the severe phenotype associated with Suz12 loss in vivo, we have explored gene expression and chromatin structure in wild-type and Suz12-deleted basal-derived organoids. Analysis of organoids led to the identification of lineage-specific changes in gene expression and chromatin structure, inferring cell type-specific PRC2-mediated gene silencing of the chromatin state. These expression changes were accompanied by cell cycle arrest but not lineage infidelity. Together, these data indicate that canonical PRC2 function is essential for development of the mammary gland through the repression of alternate transcription programs and maintenance of chromatin states.
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Affiliation(s)
- Ewa M. Michalak
- ACRF Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Michael J. G. Milevskiy
- ACRF Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Rachel M. Joyce
- ACRF Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Johanna F. Dekkers
- ACRF Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Paul R. Jamieson
- ACRF Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Bhupinder Pal
- ACRF Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Caleb A. Dawson
- ACRF Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Yifang Hu
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Stuart H. Orkin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Warren S. Alexander
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
- Cancer and Haematology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Geoffrey J. Lindeman
- ACRF Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medicine, University of Melbourne, Parkville, Victoria, Australia
- Familial Cancer Centre, Royal Melbourne Hospital and Peter MacCallum Cancer Centre, Parkville, Victoria, Australia
| | - Gordon K. Smyth
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- School of Mathematics and Statistics, The University of Melbourne, Parkville, Victoria, Australia
| | - Jane E. Visvader
- ACRF Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
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14
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Dekkers JF, Berkers G, Kruisselbrink E, Vonk A, de Jonge HR, Janssens HM, Bronsveld I, van de Graaf EA, Nieuwenhuis EES, Houwen RHJ, Vleggaar FP, Escher JC, de Rijke YB, Majoor CJ, Heijerman HGM, de Winter-de Groot KM, Clevers H, van der Ent CK, Beekman JM. Characterizing responses to CFTR-modulating drugs using rectal organoids derived from subjects with cystic fibrosis. Sci Transl Med 2017; 8:344ra84. [PMID: 27334259 DOI: 10.1126/scitranslmed.aad8278] [Citation(s) in RCA: 368] [Impact Index Per Article: 52.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 06/04/2016] [Indexed: 12/15/2022]
Abstract
Identifying subjects with cystic fibrosis (CF) who may benefit from cystic fibrosis transmembrane conductance regulator (CFTR)-modulating drugs is time-consuming, costly, and especially challenging for individuals with rare uncharacterized CFTR mutations. We studied CFTR function and responses to two drugs-the prototypical CFTR potentiator VX-770 (ivacaftor/KALYDECO) and the CFTR corrector VX-809 (lumacaftor)-in organoid cultures derived from the rectal epithelia of subjects with CF, who expressed a broad range of CFTR mutations. We observed that CFTR residual function and responses to drug therapy depended on both the CFTR mutation and the genetic background of the subjects. In vitro drug responses in rectal organoids positively correlated with published outcome data from clinical trials with VX-809 and VX-770, allowing us to predict from preclinical data the potential for CF patients carrying rare CFTR mutations to respond to drug therapy. We demonstrated proof of principle by selecting two subjects expressing an uncharacterized rare CFTR genotype (G1249R/F508del) who showed clinical responses to treatment with ivacaftor and one subject (F508del/R347P) who showed a limited response to drug therapy both in vitro and in vivo. These data suggest that in vitro measurements of CFTR function in patient-derived rectal organoids may be useful for identifying subjects who would benefit from CFTR-correcting treatment, independent of their CFTR mutation.
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Affiliation(s)
- Johanna F Dekkers
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, 3584 EA Utrecht, Netherlands. Laboratory of Translational Immunology, Wilhelmina Children's Hospital, University Medical Center Utrecht, 3584 EA Utrecht, Netherlands
| | - Gitte Berkers
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, 3584 EA Utrecht, Netherlands
| | - Evelien Kruisselbrink
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, 3584 EA Utrecht, Netherlands. Laboratory of Translational Immunology, Wilhelmina Children's Hospital, University Medical Center Utrecht, 3584 EA Utrecht, Netherlands
| | - Annelotte Vonk
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, 3584 EA Utrecht, Netherlands. Laboratory of Translational Immunology, Wilhelmina Children's Hospital, University Medical Center Utrecht, 3584 EA Utrecht, Netherlands
| | - Hugo R de Jonge
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center, 3015 CE Rotterdam, Netherlands
| | - Hettie M Janssens
- Department of Pediatric Pulmonology, Erasmus University Medical Center/Sophia Children's Hospital, 3015 CN Rotterdam, Netherlands
| | - Inez Bronsveld
- Department of Pulmonology, University Medical Center Utrecht, 3584 CX Utrecht, Netherlands
| | - Eduard A van de Graaf
- Department of Pulmonology, University Medical Center Utrecht, 3584 CX Utrecht, Netherlands
| | - Edward E S Nieuwenhuis
- Department of Pediatric Gastroenterology, Wilhelmina Children's Hospital, University Medical Center Utrecht, 3584 EA Utrecht, Netherlands
| | - Roderick H J Houwen
- Department of Pediatric Gastroenterology, Wilhelmina Children's Hospital, University Medical Center Utrecht, 3584 EA Utrecht, Netherlands
| | - Frank P Vleggaar
- Department of Gastroenterology and Hepatology, University Medical Center Utrecht, 3584 CX Utrecht, Netherlands
| | - Johanna C Escher
- Department of Pediatric Gastroenterology, Erasmus University Medical Center/Sophia Children's Hospital, 3015 CN Rotterdam, Netherlands
| | - Yolanda B de Rijke
- Department of Clinical Chemistry, Erasmus University Medical Center/Sophia Children's Hospital, 3015 CN Rotterdam, Netherlands
| | - Christof J Majoor
- Department of Respiratory Medicine, Academic Medical Center, 1105 AZ Amsterdam, Netherlands
| | - Harry G M Heijerman
- Department of Pulmonology and Cystic Fibrosis, Haga Teaching Hospital, 2545 CH The Hague, Netherlands
| | - Karin M de Winter-de Groot
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, 3584 EA Utrecht, Netherlands
| | - Hans Clevers
- Hubrecht Institute for Developmental Biology and Stem Cell Research and University Medical Center Utrecht, 3584 CT Utrecht, Netherlands
| | - Cornelis K van der Ent
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, 3584 EA Utrecht, Netherlands
| | - Jeffrey M Beekman
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, 3584 EA Utrecht, Netherlands. Laboratory of Translational Immunology, Wilhelmina Children's Hospital, University Medical Center Utrecht, 3584 EA Utrecht, Netherlands. Regenerative Medicine Center Utrecht, University Medical Center Utrecht, 3584 CX Utrecht, Netherlands.
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15
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Alton EWFW, Beekman JM, Boyd AC, Brand J, Carlon MS, Connolly MM, Chan M, Conlon S, Davidson HE, Davies JC, Davies LA, Dekkers JF, Doherty A, Gea-Sorli S, Gill DR, Griesenbach U, Hasegawa M, Higgins TE, Hironaka T, Hyndman L, McLachlan G, Inoue M, Hyde SC, Innes JA, Maher TM, Moran C, Meng C, Paul-Smith MC, Pringle IA, Pytel KM, Rodriguez-Martinez A, Schmidt AC, Stevenson BJ, Sumner-Jones SG, Toshner R, Tsugumine S, Wasowicz MW, Zhu J. Preparation for a first-in-man lentivirus trial in patients with cystic fibrosis. Thorax 2016; 72:137-147. [PMID: 27852956 PMCID: PMC5284333 DOI: 10.1136/thoraxjnl-2016-208406] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 06/21/2016] [Accepted: 06/28/2016] [Indexed: 01/03/2023]
Abstract
We have recently shown that non-viral gene therapy can stabilise the decline of lung function in patients with cystic fibrosis (CF). However, the effect was modest, and more potent gene transfer agents are still required. Fuson protein (F)/Hemagglutinin/Neuraminidase protein (HN)-pseudotyped lentiviral vectors are more efficient for lung gene transfer than non-viral vectors in preclinical models. In preparation for a first-in-man CF trial using the lentiviral vector, we have undertaken key translational preclinical studies. Regulatory-compliant vectors carrying a range of promoter/enhancer elements were assessed in mice and human air–liquid interface (ALI) cultures to select the lead candidate; cystic fibrosis transmembrane conductance receptor (CFTR) expression and function were assessed in CF models using this lead candidate vector. Toxicity was assessed and ‘benchmarked’ against the leading non-viral formulation recently used in a Phase IIb clinical trial. Integration site profiles were mapped and transduction efficiency determined to inform clinical trial dose-ranging. The impact of pre-existing and acquired immunity against the vector and vector stability in several clinically relevant delivery devices was assessed. A hybrid promoter hybrid cytosine guanine dinucleotide (CpG)- free CMV enhancer/elongation factor 1 alpha promoter (hCEF) consisting of the elongation factor 1α promoter and the cytomegalovirus enhancer was most efficacious in both murine lungs and human ALI cultures (both at least 2-log orders above background). The efficacy (at least 14% of airway cells transduced), toxicity and integration site profile supports further progression towards clinical trial and pre-existing and acquired immune responses do not interfere with vector efficacy. The lead rSIV.F/HN candidate expresses functional CFTR and the vector retains 90–100% transduction efficiency in clinically relevant delivery devices. The data support the progression of the F/HN-pseudotyped lentiviral vector into a first-in-man CF trial in 2017.
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Affiliation(s)
- Eric W F W Alton
- Department of Gene Therapy, National Heart and Lung Institute, Imperial College London, London, UK.,UK Cystic Fibrosis Gene Therapy Consortium, Oxford, UK
| | - Jeffery M Beekman
- Department of Pediatric Pulmonology, Laboratory of Translational Immunology, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands
| | - A Christopher Boyd
- Centre for Genomic and Experimental Medicine, IGMM, University of Edinburgh, Edinburgh, UK.,UK Cystic Fibrosis Gene Therapy Consortium, Oxford, UK
| | - June Brand
- Centre for Genomic and Experimental Medicine, IGMM, University of Edinburgh, Edinburgh, UK.,Lung Pathology Unit, Department of Airway Disease Infection, NHLI, Imperial College London, London, UK
| | - Marianne S Carlon
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Brussels, Belgium
| | - Mary M Connolly
- UK Cystic Fibrosis Gene Therapy Consortium, Oxford, UK.,Gene Medicine Research Group, NDCLS, John Radcliffe Hospital, Oxford, UK
| | - Mario Chan
- Department of Gene Therapy, National Heart and Lung Institute, Imperial College London, London, UK.,UK Cystic Fibrosis Gene Therapy Consortium, Oxford, UK
| | - Sinead Conlon
- Department of Gene Therapy, National Heart and Lung Institute, Imperial College London, London, UK.,UK Cystic Fibrosis Gene Therapy Consortium, Oxford, UK
| | - Heather E Davidson
- UK Cystic Fibrosis Gene Therapy Consortium, Oxford, UK.,Centre for Genomic and Experimental Medicine, IGMM, University of Edinburgh, Edinburgh, UK
| | - Jane C Davies
- Department of Gene Therapy, National Heart and Lung Institute, Imperial College London, London, UK.,UK Cystic Fibrosis Gene Therapy Consortium, Oxford, UK
| | - Lee A Davies
- UK Cystic Fibrosis Gene Therapy Consortium, Oxford, UK.,Gene Medicine Research Group, NDCLS, John Radcliffe Hospital, Oxford, UK
| | - Johanna F Dekkers
- Department of Pediatric Pulmonology, Laboratory of Translational Immunology, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands
| | - Ann Doherty
- UK Cystic Fibrosis Gene Therapy Consortium, Oxford, UK.,Centre for Genomic and Experimental Medicine, IGMM, University of Edinburgh, Edinburgh, UK
| | - Sabrina Gea-Sorli
- Department of Gene Therapy, National Heart and Lung Institute, Imperial College London, London, UK.,UK Cystic Fibrosis Gene Therapy Consortium, Oxford, UK
| | - Deborah R Gill
- UK Cystic Fibrosis Gene Therapy Consortium, Oxford, UK.,Gene Medicine Research Group, NDCLS, John Radcliffe Hospital, Oxford, UK
| | - Uta Griesenbach
- Department of Gene Therapy, National Heart and Lung Institute, Imperial College London, London, UK.,UK Cystic Fibrosis Gene Therapy Consortium, Oxford, UK
| | | | - Tracy E Higgins
- Department of Gene Therapy, National Heart and Lung Institute, Imperial College London, London, UK.,UK Cystic Fibrosis Gene Therapy Consortium, Oxford, UK
| | | | - Laura Hyndman
- UK Cystic Fibrosis Gene Therapy Consortium, Oxford, UK.,Centre for Genomic and Experimental Medicine, IGMM, University of Edinburgh, Edinburgh, UK
| | - Gerry McLachlan
- UK Cystic Fibrosis Gene Therapy Consortium, Oxford, UK.,Roslin Institute & R(D)SVS, University of Edinburgh, Midlothian, UK
| | - Makoto Inoue
- ID Pharme Co. Ltd. (DNAVEC Center), Tsukuba, Japan
| | - Stephen C Hyde
- UK Cystic Fibrosis Gene Therapy Consortium, Oxford, UK.,Gene Medicine Research Group, NDCLS, John Radcliffe Hospital, Oxford, UK
| | - J Alastair Innes
- UK Cystic Fibrosis Gene Therapy Consortium, Oxford, UK.,Centre for Genomic and Experimental Medicine, IGMM, University of Edinburgh, Edinburgh, UK
| | - Toby M Maher
- Fibrosis Research Group, Inflammation, Repair & Development Section, National Heart and Lung Institute, Sir Alexander Fleming Building, Imperial College, London, UK
| | - Caroline Moran
- Department of Gene Therapy, National Heart and Lung Institute, Imperial College London, London, UK.,UK Cystic Fibrosis Gene Therapy Consortium, Oxford, UK
| | - Cuixiang Meng
- Department of Gene Therapy, National Heart and Lung Institute, Imperial College London, London, UK.,UK Cystic Fibrosis Gene Therapy Consortium, Oxford, UK
| | - Michael C Paul-Smith
- Department of Gene Therapy, National Heart and Lung Institute, Imperial College London, London, UK.,UK Cystic Fibrosis Gene Therapy Consortium, Oxford, UK
| | - Ian A Pringle
- UK Cystic Fibrosis Gene Therapy Consortium, Oxford, UK.,Gene Medicine Research Group, NDCLS, John Radcliffe Hospital, Oxford, UK
| | - Kamila M Pytel
- Department of Gene Therapy, National Heart and Lung Institute, Imperial College London, London, UK.,UK Cystic Fibrosis Gene Therapy Consortium, Oxford, UK
| | - Andrea Rodriguez-Martinez
- Department of Gene Therapy, National Heart and Lung Institute, Imperial College London, London, UK.,UK Cystic Fibrosis Gene Therapy Consortium, Oxford, UK
| | | | - Barbara J Stevenson
- UK Cystic Fibrosis Gene Therapy Consortium, Oxford, UK.,Centre for Genomic and Experimental Medicine, IGMM, University of Edinburgh, Edinburgh, UK
| | - Stephanie G Sumner-Jones
- UK Cystic Fibrosis Gene Therapy Consortium, Oxford, UK.,Gene Medicine Research Group, NDCLS, John Radcliffe Hospital, Oxford, UK
| | - Richard Toshner
- Fibrosis Research Group, Inflammation, Repair & Development Section, National Heart and Lung Institute, Sir Alexander Fleming Building, Imperial College, London, UK
| | | | - Marguerite W Wasowicz
- Department of Gene Therapy, National Heart and Lung Institute, Imperial College London, London, UK.,UK Cystic Fibrosis Gene Therapy Consortium, Oxford, UK
| | - Jie Zhu
- Lung Pathology Unit, Department of Airway Disease Infection, NHLI, Imperial College London, London, UK
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16
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Vijftigschild LAW, Berkers G, Dekkers JF, Zomer-van Ommen DD, Matthes E, Kruisselbrink E, Vonk A, Hensen CE, Heida-Michel S, Geerdink M, Janssens HM, van de Graaf EA, Bronsveld I, de Winter-de Groot KM, Majoor CJ, Heijerman HGM, de Jonge HR, Hanrahan JW, van der Ent CK, Beekman JM. β2-Adrenergic receptor agonists activate CFTR in intestinal organoids and subjects with cystic fibrosis. Eur Respir J 2016; 48:768-79. [PMID: 27471203 DOI: 10.1183/13993003.01661-2015] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 05/11/2016] [Indexed: 01/12/2023]
Abstract
We hypothesized that people with cystic fibrosis (CF) who express CFTR (cystic fibrosis transmembrane conductance regulator) gene mutations associated with residual function may benefit from G-protein coupled receptor (GPCR)-targeting drugs that can activate and enhance CFTR function.We used intestinal organoids to screen a GPCR-modulating compound library and identified β2-adrenergic receptor agonists as the most potent inducers of CFTR function.β2-Agonist-induced organoid swelling correlated with the CFTR genotype, and could be induced in homozygous CFTR-F508del organoids and highly differentiated primary CF airway epithelial cells after rescue of CFTR trafficking by small molecules. The in vivo response to treatment with an oral or inhaled β2-agonist (salbutamol) in CF patients with residual CFTR function was evaluated in a pilot study. 10 subjects with a R117H or A455E mutation were included and showed changes in the nasal potential difference measurement after treatment with oral salbutamol, including a significant improvement of the baseline potential difference of the nasal mucosa (+6.35 mV, p<0.05), suggesting that this treatment might be effective in vivo Furthermore, plasma that was collected after oral salbutamol treatment induced CFTR activation when administered ex vivo to organoids.This proof-of-concept study suggests that organoids can be used to identify drugs that activate CFTR function in vivo and to select route of administration.
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Affiliation(s)
- Lodewijk A W Vijftigschild
- Dept of Pediatric Pulmonology, University Medical Center, Utrecht, The Netherlands Laboratory of Translational Immunology, University Medical Center, Utrecht, The Netherlands These two authors contributed equally to this work
| | - Gitte Berkers
- Dept of Pediatric Pulmonology, University Medical Center, Utrecht, The Netherlands These two authors contributed equally to this work
| | - Johanna F Dekkers
- Dept of Pediatric Pulmonology, University Medical Center, Utrecht, The Netherlands Laboratory of Translational Immunology, University Medical Center, Utrecht, The Netherlands These two authors contributed equally to this work
| | - Domenique D Zomer-van Ommen
- Dept of Pediatric Pulmonology, University Medical Center, Utrecht, The Netherlands Laboratory of Translational Immunology, University Medical Center, Utrecht, The Netherlands These two authors contributed equally to this work
| | - Elizabeth Matthes
- CF Translational Research Centre, Dept of Physiology, McGill University, Montréal, QC, Canada
| | - Evelien Kruisselbrink
- Dept of Pediatric Pulmonology, University Medical Center, Utrecht, The Netherlands Laboratory of Translational Immunology, University Medical Center, Utrecht, The Netherlands
| | - Annelotte Vonk
- Dept of Pediatric Pulmonology, University Medical Center, Utrecht, The Netherlands Laboratory of Translational Immunology, University Medical Center, Utrecht, The Netherlands
| | - Chantal E Hensen
- Dept of Pediatric Pulmonology, University Medical Center, Utrecht, The Netherlands
| | - Sabine Heida-Michel
- Dept of Pediatric Pulmonology, University Medical Center, Utrecht, The Netherlands
| | - Margot Geerdink
- Dept of Pediatric Pulmonology, University Medical Center, Utrecht, The Netherlands
| | - Hettie M Janssens
- Dept of Pediatric Pulmonology, Erasmus Medical Center/Sophia Children's Hospital, Rotterdam, The Netherlands
| | | | - Inez Bronsveld
- Dept of Pulmonology, University Medical Center, Utrecht, The Netherlands
| | | | - Christof J Majoor
- Dept of Respiratory Medicine, Academic Medical Center, Amsterdam, The Netherlands
| | - Harry G M Heijerman
- Dept of Pulmonology and Cystic Fibrosis, Haga Teaching Hospital, The Hague, The Netherlands
| | - Hugo R de Jonge
- Dept of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - John W Hanrahan
- CF Translational Research Centre, Dept of Physiology, McGill University, Montréal, QC, Canada
| | | | - Jeffrey M Beekman
- Dept of Pediatric Pulmonology, University Medical Center, Utrecht, The Netherlands Regenerative Medicine Center Utrecht, University Medical Center, Utrecht, The Netherlands
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17
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Vidović D, Carlon MS, da Cunha MF, Dekkers JF, Hollenhorst MI, Bijvelds MJC, Ramalho AS, Van den Haute C, Ferrante M, Baekelandt V, Janssens HM, De Boeck K, Sermet-Gaudelus I, de Jonge HR, Gijsbers R, Beekman JM, Edelman A, Debyser Z. rAAV-CFTRΔR Rescues the Cystic Fibrosis Phenotype in Human Intestinal Organoids and Cystic Fibrosis Mice. Am J Respir Crit Care Med 2016; 193:288-98. [PMID: 26509335 DOI: 10.1164/rccm.201505-0914oc] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RATIONALE Gene therapy holds promise for a curative mutation-independent treatment applicable to all patients with cystic fibrosis (CF). The various viral vector-based clinical trials conducted in the past have demonstrated safety and tolerance of different vectors, but none have led to a clear and persistent clinical benefit. Recent clinical breakthroughs in recombinant adeno-associated viral vector (rAAV)-based gene therapy encouraged us to reexplore an rAAV approach for CF. OBJECTIVES We evaluated the preclinical potential of rAAV gene therapy for CF to restore chloride and fluid secretion in two complementary models: intestinal organoids derived from subjects with CF and a CF mouse model, an important milestone toward the development of a clinical rAAV candidate for CF gene therapy. METHODS We engineered an rAAV vector containing a truncated CF transmembrane conductance regulator (CFTRΔR) combined with a short promoter (CMV173) to ensure optimal gene expression. A rescue in chloride and fluid secretion after rAAV-CFTRΔR treatment was assessed by forskolin-induced swelling in CF transmembrane conductance regulator (CFTR)-deficient organoids and by nasal potential differences in ΔF508 mice. MEASUREMENTS AND MAIN RESULTS rAAV-CFTRΔR transduction of human CFTR-deficient organoids resulted in forskolin-induced swelling, indicating a restoration of CFTR function. Nasal potential differences demonstrated a clear response to low chloride and forskolin perfusion in most rAAV-CFTRΔR-treated CF mice. CONCLUSIONS Our study provides robust evidence that rAAV-mediated gene transfer of a truncated CFTR functionally rescues the CF phenotype across the nasal mucosa of CF mice and in patient-derived organoids. These results underscore the clinical potential of rAAV-CFTRΔR in offering a cure for all patients with CF in the future.
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Affiliation(s)
| | | | - Mélanie F da Cunha
- 2 INSERM U1151, University Paris Descartes, Faculté de Médecine Necker Enfants-Malades, Paris, France
| | - Johanna F Dekkers
- 3 Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, and.,4 Laboratory of Translational Immunology, University Medical Center, Utrecht, the Netherlands
| | - Monika I Hollenhorst
- 2 INSERM U1151, University Paris Descartes, Faculté de Médecine Necker Enfants-Malades, Paris, France
| | - Marcel J C Bijvelds
- 5 Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | | | | | - Marc Ferrante
- 9 Translational Research in Gastrointestinal Disorders, KU Leuven, Flanders, Belgium
| | | | - Hettie M Janssens
- 10 Department of Pediatric Pulmonology, Erasmus University Medical Centre/Sophia Children's Hospital, Rotterdam, the Netherlands; and
| | | | - Isabelle Sermet-Gaudelus
- 2 INSERM U1151, University Paris Descartes, Faculté de Médecine Necker Enfants-Malades, Paris, France
| | - Hugo R de Jonge
- 5 Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Rik Gijsbers
- 1 Molecular Virology and Gene Therapy.,8 Leuven Viral Vector Core, and
| | - Jeffrey M Beekman
- 3 Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, and.,4 Laboratory of Translational Immunology, University Medical Center, Utrecht, the Netherlands
| | - Aleksander Edelman
- 2 INSERM U1151, University Paris Descartes, Faculté de Médecine Necker Enfants-Malades, Paris, France
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18
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Dekkers JF, Van Mourik P, Vonk AM, Kruisselbrink E, Berkers G, de Winter-de Groot KM, Janssens HM, Bronsveld I, van der Ent CK, de Jonge HR, Beekman JM. Potentiator synergy in rectal organoids carrying S1251N, G551D, or F508del CFTR mutations. J Cyst Fibros 2016; 15:568-78. [PMID: 27160424 DOI: 10.1016/j.jcf.2016.04.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [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: 12/09/2015] [Revised: 03/21/2016] [Accepted: 04/18/2016] [Indexed: 12/16/2022]
Abstract
The potentiator VX-770 (ivacaftor/KALYDECO™) targets defective gating of CFTR and has been approved for treatment of cystic fibrosis (CF) subjects carrying G551D, S1251N or one of 8 other mutations. Still, the current potentiator treatment does not normalize CFTR-dependent biomarkers, indicating the need for development of more effective potentiator strategies. We have recently pioneered a functional CFTR assay in primary rectal organoids and used this model to characterize interactions between VX-770, genistein and curcumin, the latter 2 being natural food components with established CFTR potentiation capacities. Results indicated that all possible combinations of VX-770, genistein and curcumin synergistically repaired CFTR-dependent forskolin-induced swelling of organoids with CFTR-S1251N or CFTR-G551D, even under suboptimal CFTR activation and compounds concentrations, conditions that may predominate in vivo. Genistein and curcumin also enhanced forskolin-induced swelling of F508del homozygous organoids that were treated with VX-770 and the prototypical CFTR corrector VX-809. These results indicate that VX-770, genistein and curcumin in double or triple combinations can synergize in restoring CFTR-dependent fluid secretion in primary CF cells and support the use of multiple potentiators for treatment of CF.
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Affiliation(s)
- Johanna F Dekkers
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands; Laboratory of Translational Immunology, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands
| | - Peter Van Mourik
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands; Laboratory of Translational Immunology, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands
| | - Annelotte M Vonk
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands; Laboratory of Translational Immunology, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands
| | - Evelien Kruisselbrink
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands; Laboratory of Translational Immunology, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands
| | - Gitte Berkers
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands
| | - Karin M de Winter-de Groot
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands
| | - Hettie M Janssens
- Department of Pediatric Pulmonology, Erasmus University Medical Centre/Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Inez Bronsveld
- Department of Pulmonology, University Medical Centre, Utrecht, The Netherlands
| | - Cornelis K van der Ent
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands
| | - Hugo R de Jonge
- Department of Gastroenterology and Hepatology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Jeffrey M Beekman
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands; Laboratory of Translational Immunology, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands
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Griesenbach U, Alton EWF, Beekman JM, Boyd CA, Davies JC, Davies LA, Dekkers JF, Gill DR, Hasegawa M, Higgins TE, Hironaka T, Inoue M, Hyde SC, Innes AJ, Pringle IA, Pytel KM, Sumner-Jones SG, Tsugumine S, Wasowicz MW. 534. Preparation for a First-in-Man Lentivirus Trial in Cystic Fibrosis Patients. Mol Ther 2016. [DOI: 10.1016/s1525-0016(16)33343-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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20
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Dekkers JF, Gogorza Gondra RA, Kruisselbrink E, Vonk AM, Janssens HM, de Winter-de Groot KM, van der Ent CK, Beekman JM. Optimal correction of distinct CFTR folding mutants in rectal cystic fibrosis organoids. Eur Respir J 2016; 48:451-8. [PMID: 27103391 DOI: 10.1183/13993003.01192-2015] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 03/07/2016] [Indexed: 11/05/2022]
Abstract
Small-molecule therapies that restore defects in cystic fibrosis transmembrane conductance regulator (CFTR) gating (potentiators) or trafficking (correctors) are being developed for cystic fibrosis (CF) in a mutation-specific fashion. Options for pharmacological correction of CFTR-p.Phe508del (F508del) are being extensively studied but correction of other trafficking mutants that may also benefit from corrector treatment remains largely unknown.We studied correction of the folding mutants CFTR-p.Phe508del, -p.Ala455Glu (A455E) and -p.Asn1303Lys (N1303K) by VX-809 and 18 other correctors (C1-C18) using a functional CFTR assay in human intestinal CF organoids.Function of both CFTR-p.Phe508del and -p.Ala455Glu was enhanced by a variety of correctors but no residual or corrector-induced activity was associated with CFTR-p.Asn1303Lys. Importantly, VX-809-induced correction was most dominant for CFTR-p.Phe508del, while correction of CFTR-p.Ala455Glu was highest by a subgroup of compounds called bithiazoles (C4, C13, C14 and C17) and C5.These data support the development of mutation-specific correctors for optimal treatment of different CFTR trafficking mutants, and identify C5 and bithiazoles as the most promising compounds for correction of CFTR-p.Ala455Glu.
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Affiliation(s)
- Johanna F Dekkers
- Dept of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands Laboratory of Translational Immunology, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands
| | - Ricardo A Gogorza Gondra
- Dept of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands Laboratory of Translational Immunology, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands
| | - Evelien Kruisselbrink
- Dept of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands Laboratory of Translational Immunology, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands
| | - Annelotte M Vonk
- Dept of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands Laboratory of Translational Immunology, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands
| | - Hettie M Janssens
- Dept of Pediatric Pulmonology, Sophia Children's Hospital/Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Karin M de Winter-de Groot
- Dept of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands
| | - Cornelis K van der Ent
- Dept of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands
| | - Jeffrey M Beekman
- Dept of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands Laboratory of Translational Immunology, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands
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21
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Jamieson PR, Dekkers JF, Rios AC, Fu NY, Lindeman GJ, Visvader JE. Derivation of a robust mouse mammary organoid system for studying tissue dynamics. Development 2016; 144:1065-1071. [DOI: 10.1242/dev.145045] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 11/30/2016] [Indexed: 12/17/2022]
Abstract
Advances in stem cell research have enabled the generation of mini-organs or organoids that recapitulate phenotypic traits of the original biological specimen. Although organoids have been demonstrated for multiple organ systems, there are more limited options for studying mouse mammary gland formation in vitro. Here we have built upon previously described culture assays to define culture conditions that enable the efficient generation of clonal organoid structures from single-sorted basal mammary epithelial cells (MECs). Analysis of Confetti-reporter mice revealed the formation of uni-coloured structures and thus the clonal nature of these organoids. High resolution 3D imaging demonstrated that basal cell-derived, complex organoids comprised an inner compartment of polarized luminal cells with milk-producing capacity and an outer network of elongated myoepithelial cells. Conversely, structures generated from luminal MECs rarely contained basal/myoepithelial cells. Moreover, flow cytometry and 3D microscopy of organoids generated from lineage-specific reporter mice established the bipotent capacity of basal cells and the restricted potential of luminal cells. In summary, we describe optimized in vitro conditions for the efficient generation of mouse mammary organoids that recapitulate features of mammary tissue architecture and function, and can be applied to understand tissue dynamics and cell-fate decisions.
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Affiliation(s)
- Paul R. Jamieson
- Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Johanna F. Dekkers
- Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Anne C. Rios
- Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Nai Yang Fu
- Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Geoffrey J. Lindeman
- Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Familial Cancer Centre and Department of Medical Oncology, The Royal Melbourne Hospital, Parkville, VIC 3050, Australia
- Department of Medicine, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Jane E. Visvader
- Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
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22
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Griesenbach U, Alton EWFW, Beekman JM, Boyd AC, Chan M, Davies JC, Davies LA, Davidson HE, Dekkers JF, Gea-Sorli S, Gill DR, Hasegawa M, Higgins T, Hyndman L, McLachlan G, Inoue M, Hyde SC, Moran C, Meng C, Paul-Smith MC, Pringle IA, Pytel KM, Rodriguez-Martinez A, Stevenson BJ, Tsugumine S. S56 Moving lentiviral-based gene therapy into a first-in-man CF trial. Thorax 2015. [DOI: 10.1136/thoraxjnl-2015-207770.62] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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23
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Yin Y, Bijvelds M, Dang W, Xu L, van der Eijk AA, Knipping K, Tuysuz N, Dekkers JF, Wang Y, de Jonge J, Sprengers D, van der Laan LJW, Beekman JM, Ten Berge D, Metselaar HJ, de Jonge H, Koopmans MPG, Peppelenbosch MP, Pan Q. Modeling rotavirus infection and antiviral therapy using primary intestinal organoids. Antiviral Res 2015; 123:120-31. [PMID: 26408355 DOI: 10.1016/j.antiviral.2015.09.010] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [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: 06/19/2015] [Revised: 09/18/2015] [Accepted: 09/19/2015] [Indexed: 01/06/2023]
Abstract
Despite the introduction of oral vaccines, rotavirus still kills over 450,000 children under five years of age annually. The absence of specific treatment prompts research aiming at further understanding of pathogenesis and the development of effective antiviral therapy, which in turn requires advanced experimental models. Given the intrinsic limitations of the classical rotavirus models using immortalized cell lines infected with laboratory-adapted strains in two dimensional cultures, our study aimed to model infection and antiviral therapy of both experimental and patient-derived rotavirus strains using three dimensional cultures of primary intestinal organoids. Intestinal epithelial organoids were successfully cultured from mouse or human gut tissues. These organoids recapitulate essential features of the in vivo tissue architecture, and are susceptible to rotavirus. Human organoids are more permissive to rotavirus infection, displaying an over 10,000-fold increase in genomic RNA following 24h of viral replication. Furthermore, infected organoids are capable of producing infectious rotavirus particles. Treatment of interferon-alpha or ribavirin inhibited viral replication in organoids of both species. Importantly, human organoids efficiently support the infection of patient-derived rotavirus strains and can be potentially harnessed for personalized evaluation of the efficacy of antiviral medications. Therefore, organoids provide a robust model system for studying rotavirus-host interactions and assessing antiviral medications.
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Affiliation(s)
- Yuebang Yin
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Marcel Bijvelds
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Wen Dang
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Lei Xu
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | | | | | - Nesrin Tuysuz
- Department of Cell Biology, Erasmus MC Stem Cell Institute, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Johanna F Dekkers
- Department of Pediatric Pulmonology/Laboratory of Translational Immunology, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands
| | - Yijin Wang
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Jeroen de Jonge
- Department of Surgery, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Dave Sprengers
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Luc J W van der Laan
- Department of Surgery, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Jeffrey M Beekman
- Department of Pediatric Pulmonology/Laboratory of Translational Immunology, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands
| | - Derk Ten Berge
- Department of Cell Biology, Erasmus MC Stem Cell Institute, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Herold J Metselaar
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Hugo de Jonge
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Marion P G Koopmans
- Department of Viroscience, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Maikel P Peppelenbosch
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Qiuwei Pan
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands.
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24
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Roth DM, Hutt DM, Tong J, Bouchecareilh M, Wang N, Seeley T, Dekkers JF, Beekman JM, Garza D, Drew L, Masliah E, Morimoto RI, Balch WE. Modulation of the maladaptive stress response to manage diseases of protein folding. PLoS Biol 2014; 12:e1001998. [PMID: 25406061 PMCID: PMC4236052 DOI: 10.1371/journal.pbio.1001998] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [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: 03/31/2014] [Accepted: 10/07/2014] [Indexed: 12/31/2022] Open
Abstract
Diseases of protein folding arise because of the inability of an altered peptide sequence to properly engage protein homeostasis components that direct protein folding and function. To identify global principles of misfolding disease pathology we examined the impact of the local folding environment in alpha-1-antitrypsin deficiency (AATD), Niemann-Pick type C1 disease (NPC1), Alzheimer's disease (AD), and cystic fibrosis (CF). Using distinct models, including patient-derived cell lines and primary epithelium, mouse brain tissue, and Caenorhabditis elegans, we found that chronic expression of misfolded proteins not only triggers the sustained activation of the heat shock response (HSR) pathway, but that this sustained activation is maladaptive. In diseased cells, maladaptation alters protein structure-function relationships, impacts protein folding in the cytosol, and further exacerbates the disease state. We show that down-regulation of this maladaptive stress response (MSR), through silencing of HSF1, the master regulator of the HSR, restores cellular protein folding and improves the disease phenotype. We propose that restoration of a more physiological proteostatic environment will strongly impact the management and progression of loss-of-function and gain-of-toxic-function phenotypes common in human disease.
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Affiliation(s)
- Daniela Martino Roth
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Darren M. Hutt
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Jiansong Tong
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Marion Bouchecareilh
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Ning Wang
- Department of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, Illinois, United States of America
| | - Theo Seeley
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Johanna F. Dekkers
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands
- Laboratory of Translational Immunology, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands
| | - Jeffrey M. Beekman
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands
- Laboratory of Translational Immunology, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands
| | - Dan Garza
- Proteostasis Therapeutics Inc., Cambridge, Massachusetts, United States of America
| | - Lawrence Drew
- Proteostasis Therapeutics Inc., Cambridge, Massachusetts, United States of America
| | - Eliezer Masliah
- Department of Neurosciences, University of California, San Diego, La Jolla, California, United States of America
| | - Richard I. Morimoto
- Department of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, Illinois, United States of America
| | - William E. Balch
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California, United States of America
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, United States of America
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, United States of America
- The Institute for Childhood and Neglected Diseases, The Scripps Research Institute, La Jolla, California, United States of America
- * E-mail:
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25
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Schwank G, Koo BK, Sasselli V, Dekkers JF, Heo I, Demircan T, Sasaki N, Boymans S, Cuppen E, van der Ent CK, Nieuwenhuis EES, Beekman JM, Clevers H. Functional repair of CFTR by CRISPR/Cas9 in intestinal stem cell organoids of cystic fibrosis patients. Cell Stem Cell 2014; 13:653-8. [PMID: 24315439 DOI: 10.1016/j.stem.2013.11.002] [Citation(s) in RCA: 908] [Impact Index Per Article: 90.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 10/31/2013] [Accepted: 11/01/2013] [Indexed: 12/16/2022]
Abstract
Single murine and human intestinal stem cells can be expanded in culture over long time periods as genetically and phenotypically stable epithelial organoids. Increased cAMP levels induce rapid swelling of such organoids by opening the cystic fibrosis transmembrane conductor receptor (CFTR). This response is lost in organoids derived from cystic fibrosis (CF) patients. Here we use the CRISPR/Cas9 genome editing system to correct the CFTR locus by homologous recombination in cultured intestinal stem cells of CF patients. The corrected allele is expressed and fully functional as measured in clonally expanded organoids. This study provides proof of concept for gene correction by homologous recombination in primary adult stem cells derived from patients with a single-gene hereditary defect.
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Affiliation(s)
- Gerald Schwank
- Hubrecht Institute/KNAW, Uppsalalaan 8, Utrecht 3584 CT, The Netherlands; University Medical Center Utrecht, Uppsalalaan 8, Utrecht 3584 CT, The Netherlands
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26
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Eckford P, Ramjeesingh M, Molinski S, Pasyk S, Dekkers JF, Li C, Ahmadi S, Ip W, Chung T, Du K, Yeger H, Beekman J, Gonska T, Bear C. VX-809 and Related Corrector Compounds Exhibit Secondary Activity Stabilizing Active F508del-CFTR after Its Partial Rescue to the Cell Surface. ACTA ACUST UNITED AC 2014; 21:666-78. [DOI: 10.1016/j.chembiol.2014.02.021] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 02/22/2014] [Accepted: 02/25/2014] [Indexed: 12/11/2022]
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Dekkers JF, van der Ent CK, Beekman JM. Novel opportunities for CFTR-targeting drug development using organoids. Rare Dis 2013; 1:e27112. [PMID: 25003014 PMCID: PMC3915567 DOI: 10.4161/rdis.27112] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 10/09/2013] [Accepted: 11/06/2013] [Indexed: 01/21/2023] Open
Abstract
Cystic fibrosis (CF) is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. CFTR mutations lead to production of non-functional CFTR, reduced amounts of normal functioning CFTR or misfolded CFTR with defects in trafficking or function. For decades, CF treatment has been focused on the symptoms of CF, but pharmacotherapy using small molecules that target the basic defect of CF, the mutant CFTR protein, is now possible for a limited amount of subjects with CF. This raises the exciting possibility that the majority of people with CF may receive effective treatment targeting the different CFTR mutants in the future. We recently described a functional CFTR assay using rectal biopsies from subjects with CF that were cultured in vitro into self-organizing mini-guts or organoids. We here describe how this model may assist in the discovery of new CFTR-targeting drugs, the subjects that may benefit from these drugs, and the mechanisms underlying variability in CFTR genotype-phenotype relations.
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Affiliation(s)
- Johanna F Dekkers
- Department of Pediatric Pulmonology; University Medical Center Utrecht; Children's Hospital; Utrecht, the Netherlands ; Department of Immunology; University Medical Center Utrecht; Children's Hospital; Utrecht, the Netherlands
| | - Cornelis K van der Ent
- Department of Pediatric Pulmonology; University Medical Center Utrecht; Children's Hospital; Utrecht, the Netherlands
| | - Jeffrey M Beekman
- Department of Pediatric Pulmonology; University Medical Center Utrecht; Children's Hospital; Utrecht, the Netherlands ; Department of Immunology; University Medical Center Utrecht; Children's Hospital; Utrecht, the Netherlands
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28
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Berends ETM, Dekkers JF, Nijland R, Kuipers A, Soppe JA, van Strijp JAG, Rooijakkers SHM. Distinct localization of the complement C5b-9 complex on Gram-positive bacteria. Cell Microbiol 2013; 15:1955-68. [PMID: 23869880 DOI: 10.1111/cmi.12170] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 06/13/2013] [Accepted: 07/14/2013] [Indexed: 02/05/2023]
Abstract
The plasma proteins of the complement system fulfil important immune defence functions, including opsonization of bacteria for phagocytosis, generation of chemo-attractants and direct bacterial killing via the Membrane Attack Complex (MAC or C5b-9). The MAC is comprised of C5b, C6, C7, C8, and multiple copies of C9 that generate lytic pores in cellular membranes. Gram-positive bacteria are protected from MAC-dependent lysis by their thick peptidoglycan layer. Paradoxically, several Gram-positive pathogens secrete small proteins that inhibit C5b-9 formation. In this study, we found that complement activation on Gram-positive bacteria in serum results in specific surface deposition of C5b-9 complexes. Immunoblotting revealed that C9 occurs in both monomeric and polymeric (SDS-stable) forms, indicating the presence of ring-structured C5b-9. Surprisingly, confocal microscopy demonstrated that C5b-9 deposition occurs at specialized regions on the bacterial cell. On Streptococcus pyogenes, C5b-9 deposits near the division septum whereas on Bacillus subtilis the complex is located at the poles. This is in contrast to C3b deposition, which occurs randomly on the bacterial surface. Altogether, these results show a previously unrecognized interaction between the C5b-9 complex and Gram-positive bacteria, which might ultimately lead to a new model of MAC assembly and functioning.
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Affiliation(s)
- Evelien T M Berends
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
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29
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Dekkers JF, Wiegerinck CL, de Jonge HR, Bronsveld I, Janssens HM, de Winter-de Groot KM, Brandsma AM, de Jong NWM, Bijvelds MJC, Scholte BJ, Nieuwenhuis EES, van den Brink S, Clevers H, van der Ent CK, Middendorp S, Beekman JM. A functional CFTR assay using primary cystic fibrosis intestinal organoids. Nat Med 2013; 19:939-45. [PMID: 23727931 DOI: 10.1038/nm.3201] [Citation(s) in RCA: 688] [Impact Index Per Article: 62.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 12/20/2012] [Indexed: 01/02/2023]
Abstract
We recently established conditions allowing for long-term expansion of epithelial organoids from intestine, recapitulating essential features of the in vivo tissue architecture. Here we apply this technology to study primary intestinal organoids of people suffering from cystic fibrosis, a disease caused by mutations in CFTR, encoding cystic fibrosis transmembrane conductance regulator. Forskolin induces rapid swelling of organoids derived from healthy controls or wild-type mice, but this effect is strongly reduced in organoids of subjects with cystic fibrosis or in mice carrying the Cftr F508del mutation and is absent in Cftr-deficient organoids. This pattern is phenocopied by CFTR-specific inhibitors. Forskolin-induced swelling of in vitro-expanded human control and cystic fibrosis organoids corresponds quantitatively with forskolin-induced anion currents in freshly excised ex vivo rectal biopsies. Function of the CFTR F508del mutant protein is restored by incubation at low temperature, as well as by CFTR-restoring compounds. This relatively simple and robust assay will facilitate diagnosis, functional studies, drug development and personalized medicine approaches in cystic fibrosis.
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Affiliation(s)
- Johanna F Dekkers
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center, Utrecht, The Netherlands
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van Meegen MA, Terheggen SWJ, Koymans KJ, Vijftigschild LAW, Dekkers JF, van der Ent CK, Beekman JM. CFTR-mutation specific applications of CFTR-directed monoclonal antibodies. J Cyst Fibros 2013; 12:487-96. [PMID: 23317763 DOI: 10.1016/j.jcf.2012.12.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Revised: 12/01/2012] [Accepted: 12/11/2012] [Indexed: 11/18/2022]
Abstract
BACKGROUND Over the last decade novel monoclonal CFTR-specific antibodies have been developed. We here present a paired analysis to detect wild-type and mutant CFTR using Western blot analysis, flow cytometry and confocal microscopy in several cellular expression systems. METHODS The following CFTR-specific antibodies were used; 217, 432, 450, 570, 769, 596, 660, L12B4 and 24.1. Mutant CFTR was detected in HEK293 cells transiently expressing the mutations; G542X, R1162X, F508del, N1303K, G551D, R117H, A455E. RESULTS The majority of these antibodies are suitable for most applications tested. Using immunofluorescence, some antibodies can better detect mutant forms of CFTR (F508del and N1303K by mAbs 596 and 769), or display lower aspecific detection by Western blot analysis (mAbs 432, 450, 769 and 596) or immunofluorescence (mAbs 432, 450, 570 and 769). CONCLUSION Optimal detection of CFTR by monoclonal antibodies depends on CFTR mutation and the specific research application.
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Affiliation(s)
- M A van Meegen
- Department of Pediatric Pulmonology, University Medical Centre Utrecht, The Netherlands
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Dekkers JF, van der Ent CK, Kalkhoven E, Beekman JM. PPARγ as a therapeutic target in cystic fibrosis. Trends Mol Med 2012; 18:283-91. [PMID: 22494945 DOI: 10.1016/j.molmed.2012.03.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 03/06/2012] [Accepted: 03/12/2012] [Indexed: 12/31/2022]
Abstract
Cystic fibrosis (CF) is characterized by a proinflammatory pulmonary condition that may result from increased infections and altered intracellular metabolism in CFTR-deficient cells. The lipid-activated transcription factor peroxisome proliferator-activated receptor-γ (PPARγ) has well-established roles in immune cell function and inflammatory modulation and has been demonstrated to play an important role in the heightened inflammatory response in CF cells. Here, we summarize current literature describing PPARγ-dependent alterations of CF cells and discuss the potential of PPARγ ligands for treating CF.
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Affiliation(s)
- Johanna F Dekkers
- Department of Pediatric Pulmonology, University Medical Center Utrecht, Utrecht, The Netherlands
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