1
|
Piraino F, Costa M, Meyer M, Cornish G, Ceroni C, Garnier VMVM, Hoehnel-Ka S, Brandenberg N. Organoid models: the future companions of personalized drug development. Biofabrication 2024. [PMID: 38608454 DOI: 10.1088/1758-5090/ad3e30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2024]
Abstract
High failure rates of the current drug development process are driving exemplary changes toward methodologies centered on human disease in-vitro modeling. Organoids are self-organized tissue sub-units resembling their organ of origin and are widely acknowledged for their unique potential in recapitulating human physio-pathological mechanisms. They are transformative for human health by becoming the platform of choice to probe disease mechanisms and advance new therapies. Furthermore, the compounds' validation as therapeutics represents another point of the drug development pipeline where organoids may provide key understandings and help pharma organizations replace or reduce animal research. In this review, we focus on gastrointestinal organoid models, which are currently the most advanced organoid models in drug development. We focus on experimental validations of their value, and we propose avenues to enhance their use in drug discovery and
development, as well as precision medicine and diagnostics.
Collapse
Affiliation(s)
- Francesco Piraino
- Product Management, Doppl SA, EPFL Innovation Park, Building L, Switzerland, Lausanne, 1015, SWITZERLAND
| | - Mariana Costa
- Research and Development, Doppl SA, EPFL Innovation Park, Building L, Lausanne, 1015, SWITZERLAND
| | - Marine Meyer
- Product Management, Doppl SA, EPFL Innovation Park, Building L, Lausanne, 1015, SWITZERLAND
| | - Georgina Cornish
- Cell Therapy Safety, AstraZeneca UK Limited, Biomedical Campus, 1 Francis Crick Ave, Trumpington, Cambridge, CB2 0AA, UNITED KINGDOM OF GREAT BRITAIN AND NORTHERN IRELAND
| | - Camilla Ceroni
- Research and Development, Doppl SA, EPFL Innovation Park, Building L, Lausanne, 1015, SWITZERLAND
| | | | - Sylke Hoehnel-Ka
- Doppl SA, EPFL Innovation Park, Building L, Lausanne, 1015, SWITZERLAND
| | | |
Collapse
|
2
|
Zagorski M, Brandenberg N, Lutolf M, Tkacik G, Bollenbach T, Briscoe J, Kicheva A. Assessing the precision of morphogen gradients in neural tube development. Nat Commun 2024; 15:929. [PMID: 38302459 PMCID: PMC10834428 DOI: 10.1038/s41467-024-45148-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 01/15/2024] [Indexed: 02/03/2024] Open
Affiliation(s)
- Marcin Zagorski
- Institute of Theoretical Physics and Mark Kac Center for Complex Systems Research, Jagiellonian University, Lojasiewicza 11, 30-348, Krakow, Poland.
| | - Nathalie Brandenberg
- Institute of Bioengineering, School of Life Sciences, and School of Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Matthias Lutolf
- Institute of Bioengineering, School of Life Sciences, and School of Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Gasper Tkacik
- Institute of Science and Technology Austria, Am Campus 1, 3400, Klosterneuburg, Austria
| | - Tobias Bollenbach
- Institute for Biological Physics, University of Cologne, Cologne, Germany
- Center for Data and Simulation Science, University of Cologne, Cologne, Germany
| | | | - Anna Kicheva
- Institute of Science and Technology Austria, Am Campus 1, 3400, Klosterneuburg, Austria.
| |
Collapse
|
3
|
Savary C, Luciana L, Huchedé P, Tourbez A, Coquet C, Broustal M, Lopez Gonzalez A, Deligne C, Diot T, Naret O, Costa M, Meynard N, Barbet V, Müller K, Tonon L, Gadot N, Degletagne C, Attignon V, Léon S, Vanbelle C, Bomane A, Rochet I, Mournetas V, Oliveira L, Rinaudo P, Bergeron C, Dutour A, Cordier-Bussat M, Roch A, Brandenberg N, El Zein S, Watson S, Orbach D, Delattre O, Dijoud F, Corradini N, Picard C, Maucort-Boulch D, Le Grand M, Pasquier E, Blay JY, Castets M, Broutier L. Fusion-negative rhabdomyosarcoma 3D organoids to predict effective drug combinations: A proof-of-concept on cell death inducers. Cell Rep Med 2023; 4:101339. [PMID: 38118405 PMCID: PMC10772578 DOI: 10.1016/j.xcrm.2023.101339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 09/29/2023] [Accepted: 11/22/2023] [Indexed: 12/22/2023]
Abstract
Rhabdomyosarcoma (RMS) is the main form of pediatric soft-tissue sarcoma. Its cure rate has not notably improved in the last 20 years following relapse, and the lack of reliable preclinical models has hampered the design of new therapies. This is particularly true for highly heterogeneous fusion-negative RMS (FNRMS). Although methods have been proposed to establish FNRMS organoids, their efficiency remains limited to date, both in terms of derivation rate and ability to accurately mimic the original tumor. Here, we present the development of a next-generation 3D organoid model derived from relapsed adult and pediatric FNRMS. This model preserves the molecular features of the patients' tumors and is expandable for several months in 3D, reinforcing its interest to drug combination screening with longitudinal efficacy monitoring. As a proof-of-concept, we demonstrate its preclinical relevance by reevaluating the therapeutic opportunities of targeting apoptosis in FNRMS from a streamlined approach based on transcriptomic data exploitation.
Collapse
Affiliation(s)
- Clara Savary
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Léa Luciana
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Paul Huchedé
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Arthur Tourbez
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Claire Coquet
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Maëlle Broustal
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Alejandro Lopez Gonzalez
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Clémence Deligne
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Thomas Diot
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Olivier Naret
- DOPPL, EPFL Innovation Park, Building L, Ch. de la Dent d'Oche 1, 1024 Ecublens, Switzerland
| | - Mariana Costa
- DOPPL, EPFL Innovation Park, Building L, Ch. de la Dent d'Oche 1, 1024 Ecublens, Switzerland
| | - Nina Meynard
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Virginie Barbet
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Kevin Müller
- Université Aix-Marseille, CNRS 7258, INSERM 1068, Institute Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille (CRCM), 13009 Marseille, France
| | - Laurie Tonon
- Synergie Lyon Cancer, Gilles Thomas' Bioinformatics Platform, Centre Léon Bérard, 69008 Lyon, France
| | - Nicolas Gadot
- Anatomopathology Research Platform, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Cyril Degletagne
- Cancer Genomics Platform, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Valéry Attignon
- Cancer Genomics Platform, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Sophie Léon
- EX-VIVO Platform, Centre de recherche en cancérologie de Lyon (CRCL), Centre Léon Bérard, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Christophe Vanbelle
- Plateforme d'Imagerie cellulaire, Centre de recherche en cancérologie de Lyon (CRCL), Centre Léon Bérard, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Alexandra Bomane
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Isabelle Rochet
- Multisite Institute of Pathology, Groupement Hospitalier Est du CHU de Lyon, Hôpital Femme-Mère-Enfant, 69677 Bron, France; Department of Pediatric Oncology, Institut d'Hématologie et d'Oncologie Pédiatrique, Centre Léon Bérard, 69008 Lyon, France
| | | | | | | | - Christophe Bergeron
- Department of Pediatric Oncology, Institut d'Hématologie et d'Oncologie Pédiatrique, Centre Léon Bérard, 69008 Lyon, France
| | - Aurélie Dutour
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Martine Cordier-Bussat
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Aline Roch
- DOPPL, EPFL Innovation Park, Building L, Ch. de la Dent d'Oche 1, 1024 Ecublens, Switzerland
| | - Nathalie Brandenberg
- DOPPL, EPFL Innovation Park, Building L, Ch. de la Dent d'Oche 1, 1024 Ecublens, Switzerland
| | - Sophie El Zein
- Department of Biopathology, Institut Curie, Paris, France
| | - Sarah Watson
- SIREDO Oncology Center (Care, Innovation and Research for Children and AYA with Cancer), Institut Curie, PSL Research University, Paris, France; INSERM U830, Diversity and Plasticity of Childhood Tumors Lab, Institut Curie, PSL Research University, Paris, France; Medical Oncology Department, Institut Curie, PSL Research University, Paris, France
| | - Daniel Orbach
- SIREDO Oncology Center (Care, Innovation and Research for Children and AYA with Cancer), Institut Curie, PSL Research University, Paris, France
| | - Olivier Delattre
- SIREDO Oncology Center (Care, Innovation and Research for Children and AYA with Cancer), Institut Curie, PSL Research University, Paris, France; INSERM U830, Diversity and Plasticity of Childhood Tumors Lab, Institut Curie, PSL Research University, Paris, France
| | - Frédérique Dijoud
- Multisite Institute of Pathology, Groupement Hospitalier Est du CHU de Lyon, Hôpital Femme-Mère-Enfant, 69677 Bron, France
| | - Nadège Corradini
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France; Department of Pediatric Oncology, Institut d'Hématologie et d'Oncologie Pédiatrique, Centre Léon Bérard, 69008 Lyon, France; Department of Translational Research in Pediatric Oncology PROSPECT, Centre Léon Bérard, 69008 Lyon, France
| | - Cécile Picard
- Multisite Institute of Pathology, Groupement Hospitalier Est du CHU de Lyon, Hôpital Femme-Mère-Enfant, 69677 Bron, France
| | - Delphine Maucort-Boulch
- Université Lyon 1, 69100 Villeurbanne, France; Hospices Civils de Lyon, Pôle Santé Publique, Service de Biostatistique et Bioinformatique, 69003 Lyon, France; CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Évolutive, Équipe Biostatistique-Santé, 69100 Villeurbanne, France
| | - Marion Le Grand
- Université Aix-Marseille, CNRS 7258, INSERM 1068, Institute Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille (CRCM), 13009 Marseille, France
| | - Eddy Pasquier
- Université Aix-Marseille, CNRS 7258, INSERM 1068, Institute Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille (CRCM), 13009 Marseille, France
| | - Jean-Yves Blay
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France; Department of Translational Research in Pediatric Oncology PROSPECT, Centre Léon Bérard, 69008 Lyon, France
| | - Marie Castets
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France; Department of Translational Research in Pediatric Oncology PROSPECT, Centre Léon Bérard, 69008 Lyon, France.
| | - Laura Broutier
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France; Department of Translational Research in Pediatric Oncology PROSPECT, Centre Léon Bérard, 69008 Lyon, France.
| |
Collapse
|
4
|
Mitropoulou G, Brandenberg N, Hoehnel S, Ceroni C, Balmpouzis Z, Blanchon S, Dorta G, Sauty A, Koutsokera A. Rectal organoid-guided CFTR modulator therapy restores lung function in a cystic fibrosis patient with the rare 1677delTA/R334W genotype. Eur Respir J 2022; 60:2201341. [PMID: 36423906 DOI: 10.1183/13993003.01341-2022] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 10/31/2022] [Indexed: 11/25/2022]
Affiliation(s)
- Georgia Mitropoulou
- Adult Cystic Fibrosis and CFTR-related disorders Center, Division of Pulmonology, Dept of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- Lung Transplant Center, Division of Pulmonology, Dept of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Nathalie Brandenberg
- Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences, Swiss Federal Institute of Technology, Lausanne, Switzerland
- SUN bioscience, EPFL Innovation Park, Lausanne, Switzerland
| | - Sylke Hoehnel
- Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences, Swiss Federal Institute of Technology, Lausanne, Switzerland
- SUN bioscience, EPFL Innovation Park, Lausanne, Switzerland
| | - Camilla Ceroni
- Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences, Swiss Federal Institute of Technology, Lausanne, Switzerland
- SUN bioscience, EPFL Innovation Park, Lausanne, Switzerland
| | - Zisis Balmpouzis
- Adult Cystic Fibrosis and CFTR-related disorders Center, Division of Pulmonology, Dept of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- Lung Transplant Center, Division of Pulmonology, Dept of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Sylvain Blanchon
- Paediatric Pulmonology and Cystic Fibrosis Unit, Division of Paediatrics, Dept Woman-Mother-Child, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Gian Dorta
- Division of Gastro-enterology, Dept of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Alain Sauty
- Adult Cystic Fibrosis and CFTR-related disorders Center, Division of Pulmonology, Dept of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- Division of Pulmonology, Dept of Medicine, Neuchâtel Hospital Network, Neuchâtel, Switzerland
- These authors contributed equally
| | - Angela Koutsokera
- Adult Cystic Fibrosis and CFTR-related disorders Center, Division of Pulmonology, Dept of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- Lung Transplant Center, Division of Pulmonology, Dept of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- These authors contributed equally
| |
Collapse
|
5
|
Giger S, Hofer M, Miljkovic-Licina M, Hoehnel S, Brandenberg N, Guiet R, Ehrbar M, Kleiner E, Gegenschatz-Schmid K, Matthes T, Lutolf MP. Microarrayed human bone marrow organoids for modeling blood stem cell dynamics. APL Bioeng 2022; 6:036101. [PMID: 35818479 PMCID: PMC9270995 DOI: 10.1063/5.0092860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 06/13/2022] [Indexed: 01/23/2023] Open
Abstract
In many leukemia patients, a poor prognosis is attributed either to the development of chemotherapy resistance by leukemic stem cells (LSCs) or to the inefficient engraftment of transplanted hematopoietic stem/progenitor cells (HSPCs) into the bone marrow (BM). Here, we build a 3D in vitro model system of bone marrow organoids (BMOs) that recapitulate several structural and cellular components of native BM. These organoids are formed in a high-throughput manner from the aggregation of endothelial and mesenchymal cells within hydrogel microwells. Accordingly, the mesenchymal compartment shows partial maintenance of its self-renewal and multilineage potential, while endothelial cells self-organize into an interconnected vessel-like network. Intriguingly, such an endothelial compartment enhances the recruitment of HSPCs in a chemokine ligand/receptor-dependent manner, reminiscent of HSPC homing behavior in vivo. Additionally, we also model LSC migration and nesting in BMOs, thus highlighting the potential of this system as a well accessible and scalable preclinical model for candidate drug screening and patient-specific assays.
Collapse
Affiliation(s)
- Sonja Giger
- Laboratory of Stem Cell Bioengineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Moritz Hofer
- Laboratory of Stem Cell Bioengineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | | | - Sylke Hoehnel
- SUN Bioscience, EPFL Innovation Park, Lausanne, Switzerland
| | | | - Romain Guiet
- Laboratory of Stem Cell Bioengineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Martin Ehrbar
- Ehrbar Lab, University Hospital Zurich, Zurich, Switzerland
| | - Esther Kleiner
- Ehrbar Lab, University Hospital Zurich, Zurich, Switzerland
| | | | | | - Matthias P Lutolf
- Laboratory of Stem Cell Bioengineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| |
Collapse
|
6
|
Gjorevski N, Nikolaev M, Brown TE, Mitrofanova O, Brandenberg N, DelRio FW, Yavitt FM, Liberali P, Anseth KS, Lutolf MP. Tissue geometry drives deterministic organoid patterning. Science 2022; 375:eaaw9021. [PMID: 34990240 DOI: 10.1126/science.aaw9021] [Citation(s) in RCA: 125] [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] [Indexed: 12/29/2022]
Abstract
Epithelial organoids are stem cell–derived tissues that approximate aspects of real organs, and thus they have potential as powerful tools in basic and translational research. By definition, they self-organize, but the structures formed are often heterogeneous and irreproducible, which limits their use in the lab and clinic. We describe methodologies for spatially and temporally controlling organoid formation, thereby rendering a stochastic process more deterministic. Bioengineered stem cell microenvironments are used to specify the initial geometry of intestinal organoids, which in turn controls their patterning and crypt formation. We leveraged the reproducibility and predictability of the culture to identify the underlying mechanisms of epithelial patterning, which may contribute to reinforcing intestinal regionalization in vivo. By controlling organoid culture, we demonstrate how these structures can be used to answer questions not readily addressable with the standard, more variable, organoid models.
Collapse
Affiliation(s)
- N Gjorevski
- Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences (SV) and School of Engineering (STI), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - M Nikolaev
- Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences (SV) and School of Engineering (STI), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - T E Brown
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO 80309, USA.,BioFrontiers Institute, University of Colorado, Boulder, CO 80303, USA
| | - O Mitrofanova
- Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences (SV) and School of Engineering (STI), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - N Brandenberg
- Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences (SV) and School of Engineering (STI), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - F W DelRio
- Material, Physical, and Chemical Sciences Center, Sandia National Laboratories, Albuquerque, NM 87185, USA
| | - F M Yavitt
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO 80309, USA.,BioFrontiers Institute, University of Colorado, Boulder, CO 80303, USA
| | - P Liberali
- Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland
| | - K S Anseth
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO 80309, USA.,BioFrontiers Institute, University of Colorado, Boulder, CO 80303, USA
| | - M P Lutolf
- Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences (SV) and School of Engineering (STI), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Institute of Chemical Sciences and Engineering, School of Basic Science (SB), EPFL, Lausanne, Switzerland
| |
Collapse
|
7
|
Simonneau C, Duschmalé M, Gavrilov A, Brandenberg N, Hoehnel S, Ceroni C, Lassalle E, Kassianidou E, Knoetgen H, Niewoehner J, Villaseñor R. Investigating receptor-mediated antibody transcytosis using blood-brain barrier organoid arrays. Fluids Barriers CNS 2021; 18:43. [PMID: 34544422 PMCID: PMC8454074 DOI: 10.1186/s12987-021-00276-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 03/25/2021] [Accepted: 09/09/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The pathways that control protein transport across the blood-brain barrier (BBB) remain poorly characterized. Despite great advances in recapitulating the human BBB in vitro, current models are not suitable for systematic analysis of the molecular mechanisms of antibody transport. The gaps in our mechanistic understanding of antibody transcytosis hinder new therapeutic delivery strategy development. METHODS We applied a novel bioengineering approach to generate human BBB organoids by the self-assembly of astrocytes, pericytes and brain endothelial cells with unprecedented throughput and reproducibility using micro patterned hydrogels. We designed a semi-automated and scalable imaging assay to measure receptor-mediated transcytosis of antibodies. Finally, we developed a workflow to use CRISPR/Cas9 gene editing in BBB organoid arrays to knock out regulators of endocytosis specifically in brain endothelial cells in order to dissect the molecular mechanisms of receptor-mediated transcytosis. RESULTS BBB organoid arrays allowed the simultaneous growth of more than 3000 homogenous organoids per individual experiment in a highly reproducible manner. BBB organoid arrays showed low permeability to macromolecules and prevented transport of human non-targeting antibodies. In contrast, a monovalent antibody targeting the human transferrin receptor underwent dose- and time-dependent transcytosis in organoids. Using CRISPR/Cas9 gene editing in BBB organoid arrays, we showed that clathrin, but not caveolin, is required for transferrin receptor-dependent transcytosis. CONCLUSIONS Human BBB organoid arrays are a robust high-throughput platform that can be used to discover new mechanisms of receptor-mediated antibody transcytosis. The implementation of this platform during early stages of drug discovery can accelerate the development of new brain delivery technologies.
Collapse
Affiliation(s)
- Claire Simonneau
- Roche Pharma Research and Early Development (pRED), Pharmaceutical Sciences, Roche Innovation Center Basel, Basel, Switzerland
| | - Martina Duschmalé
- Roche Pharma Research and Early Development (pRED), Pharmaceutical Sciences, Roche Innovation Center Basel, Basel, Switzerland
| | - Alina Gavrilov
- Roche Pharma Research and Early Development (pRED), Pharmaceutical Sciences, Roche Innovation Center Basel, Basel, Switzerland
| | | | - Sylke Hoehnel
- SUN bioscience, EPFL Innovation Park, Lausanne, Switzerland
| | - Camilla Ceroni
- SUN bioscience, EPFL Innovation Park, Lausanne, Switzerland
| | - Evodie Lassalle
- Roche Pharma Research and Early Development (pRED), Pharmaceutical Sciences, Roche Innovation Center Basel, Basel, Switzerland
| | - Elena Kassianidou
- Roche Pharma Research and Early Development (pRED), Pharmaceutical Sciences, Roche Innovation Center Basel, Basel, Switzerland
| | - Hendrik Knoetgen
- Roche Pharma Research and Early Development (pRED), Therapeutic Modalities, Roche Innovation Center Munich, Munich, Germany
| | - Jens Niewoehner
- Roche Pharma Research and Early Development (pRED), Therapeutic Modalities, Roche Innovation Center Munich, Munich, Germany
| | - Roberto Villaseñor
- Roche Pharma Research and Early Development (pRED), Pharmaceutical Sciences, Roche Innovation Center Basel, Basel, Switzerland.
| |
Collapse
|
8
|
Girgin MU, Broguiere N, Hoehnel S, Brandenberg N, Mercier B, Arias AM, Lutolf MP. Bioengineered embryoids mimic post-implantation development in vitro. Nat Commun 2021; 12:5140. [PMID: 34446708 PMCID: PMC8390504 DOI: 10.1038/s41467-021-25237-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 07/29/2021] [Indexed: 02/07/2023] Open
Abstract
The difficulty of studying post-implantation development in mammals has sparked a flurry of activity to develop in vitro models, termed embryoids, based on self-organizing pluripotent stem cells. Previous approaches to derive embryoids either lack the physiological morphology and signaling interactions, or are unconducive to model post-gastrulation development. Here, we report a bioengineering-inspired approach aimed at addressing this gap. We employ a high-throughput cell aggregation approach to simultaneously coax mouse embryonic stem cells into hundreds of uniform epiblast-like aggregates in a solid matrix-free manner. When co-cultured with mouse trophoblast stem cell aggregates, the resulting hybrid structures initiate gastrulation-like events and undergo axial morphogenesis to yield structures, termed EpiTS embryoids, with a pronounced anterior development, including brain-like regions. We identify the presence of an epithelium in EPI aggregates as the major determinant for the axial morphogenesis and anterior development seen in EpiTS embryoids. Our results demonstrate the potential of EpiTS embryoids to study peri-gastrulation development in vitro.
Collapse
Affiliation(s)
- Mehmet U Girgin
- Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Nicolas Broguiere
- Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Sylke Hoehnel
- SUN bioscience, EPFL Innovation Park, Lausanne, Switzerland
| | | | - Bastien Mercier
- Faculty of Medicine and Pharmacy, University of Grenoble Alpes, Grenoble, France
| | | | - Matthias P Lutolf
- Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
- Roche Institute for Translational Bioengineering (ITB), Pharma Research and Early Development (pRED), Roche Innovation Center Basel, Basel, Switzerland.
| |
Collapse
|
9
|
Yang F, Pham TA, Brandenberg N, Lutolf MP, Ma J, Unser M. Robust Phase Unwrapping via Deep Image Prior for Quantitative Phase Imaging. IEEE Trans Image Process 2021; 30:7025-7037. [PMID: 34329165 DOI: 10.1109/tip.2021.3099956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Quantitative phase imaging (QPI) is an emerging label-free technique that produces images containing morphological and dynamical information without contrast agents. Unfortunately, the phase is wrapped in most imaging system. Phase unwrapping is the computational process that recovers a more informative image. It is particularly challenging with thick and complex samples such as organoids. Recent works that rely on supervised training show that deep learning is a powerful method to unwrap the phase; however, supervised approaches require large and representative datasets which are difficult to obtain for complex biological samples. Inspired by the concept of deep image priors, we propose a deep-learning-based method that does not need any training set. Our framework relies on an untrained convolutional neural network to accurately unwrap the phase while ensuring the consistency of the measurements. We experimentally demonstrate that the proposed method faithfully recovers the phase of complex samples on both real and simulated data. Our work paves the way to reliable phase imaging of thick and complex samples with QPI.
Collapse
|
10
|
Fernandez Elviro C, Blanchon S, Hoehnel S, Schumacher U, Sauty A, Brandenberg N, Regamey N. Diagnostic tools and CFTR functional assays in cystic fibrosis: utility and availability in Switzerland. Swiss Med Wkly 2021; 151:w20496. [PMID: 33934316 DOI: 10.4414/smw.2021.20496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cystic fibrosis (CF) is a genetic disease caused by a bi-allelic mutation of the cystic fibrosis transmembrane conductance regulator (CFTR) gene. When the diagnosis cannot be confirmed by a positive sweat test or/and the identification of two CF-causing variants, international guidelines recommend the use of CFTR functional assays. These tests assess whether CFTR activity is normal or diminished/absent through measurement of CFTR-mediated chloride secretion/absorption. CFTR functional assays are not only useful for diagnostic purposes but can also serve as a surrogate outcome for clinical trials of CFTR modulators, which are emerging therapeutic agents designed to correct the malfunctioning protein. In the near future they could also be used as precision-medicine techniques, to help guidance and optimisation of treatment. Until now, sweat testing has been the only CFTR functional assay available in Switzerland. Since 2020, the Centre Hospitalier Universitaire Vaudois (CHUV) at Lausanne and the Lucerne Children’s Hospital perform nasal potential difference measurement. Moreover, The Ecole Polytechnique Fédérale de Lausanne (EPFL) established a reliable procedure to generate adult intestinal organoids, i.e., stem cell-derived in-vitro grown mini tissues, extracted from rectal biopsies, which can be used to assess CFTR function in vitro. This narrative review describes the most popular CFTR functional assays, as well as their indications, limitations and availability in Switzerland.
Collapse
Affiliation(s)
- Clara Fernandez Elviro
- Department Woman-Mother-Child, Service of Paediatrics, Paediatric Pulmonology and Cystic Fibrosis Unit, University Hospital of Lausanne and Faculty of Biology and Medicine, University of Lausanne, Switzerland
| | - Sylvain Blanchon
- Department Woman-Mother-Child, Service of Paediatrics, Paediatric Pulmonology and Cystic Fibrosis Unit, University Hospital of Lausanne and Faculty of Biology and Medicine, University of Lausanne, Switzerland
| | - Sylke Hoehnel
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Urs Schumacher
- Division of Respiratory Medicine, Children's Hospital Lucerne, Switzerland
| | - Alain Sauty
- Division of Respiratory Medicine, Hospital of Neuchâtel, Switzerland
| | - Nathalie Brandenberg
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Nicolas Regamey
- Division of Respiratory Medicine, Children's Hospital Lucerne, Switzerland
| |
Collapse
|
11
|
Unzu C, Planet E, Brandenberg N, Fusil F, Cassano M, Perez‐Vargas J, Friedli M, Cosset F, Lutolf MP, Wildhaber BE, Trono D. Pharmacological Induction of a Progenitor State for the Efficient Expansion of Primary Human Hepatocytes. Hepatology 2019; 69:2214-2231. [PMID: 30549291 PMCID: PMC6519263 DOI: 10.1002/hep.30425] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 12/02/2018] [Indexed: 01/05/2023]
Abstract
The liver is an organ with strong regenerative capacity, yet primary hepatocytes have a low amplification potential in vitro, a major limitation for the cell-based therapy of liver disorders and for ex vivo biological screens. Induced pluripotent stem cells (iPSCs) may help to circumvent this obstacle but often harbor genetic and epigenetic abnormalities, limiting their potential. Here, we describe the pharmacological induction of proliferative human hepatic progenitor cells (HPCs) through a cocktail of growth factors and small molecules mimicking the signaling events involved in liver regeneration. Human HPCs from healthy donors and pediatric patients proliferated vigorously while maintaining their genomic stability and could be redifferentiated in vitro into metabolically competent cells that supported the replication of hepatitis B and delta viruses. Redifferentiation efficiency was boosted by three-dimensional culture. Finally, transcriptome analysis showed that HPCs were more closely related to mature hepatocytes than iPSC-derived hepatocyte-like cells were. Conclusion: HPC induction holds promise for a variety of applications such as ex vivo disease modeling, personalized drug testing or metabolic studies, and development of a bioartificial liver.
Collapse
Affiliation(s)
- Carmen Unzu
- School of Life SciencesEcole Polytechnique Fédérale de LausanneLausanneSwitzerland,Pediatric Surgery Laboratory, Department of Pathology and Immunology, Faculty of MedicineUniversity of GenevaGenevaSwitzerland,Grousbeck Gene Therapy CenterSchepens Eye Research Institute and Massachusetts Eye and Ear InfirmaryBostonMAUSA,Ocular Genomics Institute, Department of OphthalmologyHarvard Medical SchoolBostonMAUSA
| | - Evarist Planet
- School of Life SciencesEcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Nathalie Brandenberg
- School of Life SciencesEcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Floriane Fusil
- CIRI–International Center for Infectiology Research, Team EVIR, Inserm, U1111Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de LyonLyonFrance
| | - Marco Cassano
- School of Life SciencesEcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Jimena Perez‐Vargas
- CIRI–International Center for Infectiology Research, Team EVIR, Inserm, U1111Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de LyonLyonFrance
| | - Marc Friedli
- School of Life SciencesEcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - François‐Loïc Cosset
- CIRI–International Center for Infectiology Research, Team EVIR, Inserm, U1111Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de LyonLyonFrance
| | - Matthias P. Lutolf
- School of Life SciencesEcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Barbara E. Wildhaber
- Pediatric Surgery Laboratory, Department of Pathology and Immunology, Faculty of MedicineUniversity of GenevaGenevaSwitzerland
| | - Didier Trono
- School of Life SciencesEcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| |
Collapse
|
12
|
Zagorski M, Tabata Y, Brandenberg N, Lutolf MP, Tkačik G, Bollenbach T, Briscoe J, Kicheva A. Decoding of position in the developing neural tube from antiparallel morphogen gradients. Science 2018; 356:1379-1383. [PMID: 28663499 DOI: 10.1126/science.aam5887] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 06/01/2017] [Indexed: 01/25/2023]
Abstract
Like many developing tissues, the vertebrate neural tube is patterned by antiparallel morphogen gradients. To understand how these inputs are interpreted, we measured morphogen signaling and target gene expression in mouse embryos and chick ex vivo assays. From these data, we derived and validated a characteristic decoding map that relates morphogen input to the positional identity of neural progenitors. Analysis of the observed responses indicates that the underlying interpretation strategy minimizes patterning errors in response to the joint input of noisy opposing gradients. We reverse-engineered a transcriptional network that provides a mechanistic basis for the observed cell fate decisions and accounts for the precision and dynamics of pattern formation. Together, our data link opposing gradient dynamics in a growing tissue to precise pattern formation.
Collapse
Affiliation(s)
- Marcin Zagorski
- Institute of Science and Technology IST Austria, 3400 Klosterneuburg, Austria
| | - Yoji Tabata
- Institute of Bioengineering, School of Life Sciences, and School of Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Nathalie Brandenberg
- Institute of Bioengineering, School of Life Sciences, and School of Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Matthias P Lutolf
- Institute of Bioengineering, School of Life Sciences, and School of Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Gašper Tkačik
- Institute of Science and Technology IST Austria, 3400 Klosterneuburg, Austria
| | - Tobias Bollenbach
- Institute of Science and Technology IST Austria, 3400 Klosterneuburg, Austria. .,Institute for Theoretical Physics, University of Cologne, Cologne, Germany
| | | | - Anna Kicheva
- Institute of Science and Technology IST Austria, 3400 Klosterneuburg, Austria. .,Francis Crick Institute, London NW1 1AT, UK
| |
Collapse
|
13
|
Abstract
Focalized short-pulsed lasers have sufficient power to generate micrometer-sized cavities in various hydrogels. An in situ technique based on laser ablation to fabricate intricate microfluidic networks in biocompatible gels without manual handling is presented. This method is fully compatible with 3D cell culture and opens up unprecedented opportunities for cell biology, developmental biology, and stem-cell-based tissue engineering.
Collapse
Affiliation(s)
- Nathalie Brandenberg
- Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Matthias P Lutolf
- Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
| |
Collapse
|
14
|
Cosson S, Aeberli LG, Brandenberg N, Lutolf MP. Ultra-rapid prototyping of flexible, multi-layered microfluidic devices via razor writing. Lab Chip 2015; 15:72-6. [PMID: 25373917 DOI: 10.1039/c4lc00848k] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The fabrication of microfluidic devices is often still a time-consuming and costly process. Here we introduce a very simple and cheap microfabrication process based on "razor writing", also termed xurography, for the ultra-rapid prototyping of microfluidic devices. Thin poly(dimethylsiloxane) (PDMS) membranes are spin-coated on flexible plastic foil and cut into user-defined shapes with a bench-top cutter plotter. The PDMS membranes can then be assembled into desirable microdevices via plasma bonding. The plastic foil allows manipulation of exceptionally thin (30-300 μm) PDMS layers and can be readily peeled after fabrication. This versatile technique can be used to produce a wide variety of microfluidic device prototypes within just a few hours.
Collapse
Affiliation(s)
- Steffen Cosson
- Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences, EPFL, Station 15, Bldg. AI 1106, CH-1015 Lausanne, Switzerland.
| | | | | | | |
Collapse
|