851
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Delker RK, Mann RS. From Reductionism to Holism: Toward a More Complete View of Development Through Genome Engineering. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1016:45-74. [PMID: 29130153 PMCID: PMC6935049 DOI: 10.1007/978-3-319-63904-8_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Paradigm shifts in science are often coupled to technological advances. New techniques offer new roads of discovery; but, more than this, they shape the way scientists approach questions. Developmental biology exemplifies this idea both in its past and present. The rise of molecular biology and genetics in the late twentieth century shifted the focus from the anatomical to the molecular, nudging the underlying philosophy from holism to reductionism. Developmental biology is currently experiencing yet another transformation triggered by '-omics' technology and propelled forward by CRISPR genome engineering (GE). Together, these technologies are helping to reawaken a holistic approach to development. Herein, we focus on CRISPR GE and its potential to reveal principles of development at the level of the genome, the epigenome, and the cell. Within each stage we illustrate how GE can move past pure reductionism and embrace holism, ultimately delivering a more complete view of development.
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Affiliation(s)
- Rebecca K Delker
- Department of Biochemistry and Molecular Biophysics and Systems Biology, Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, 612 West 130th Street, 9th Floor, New York, NY, 10027, USA.
| | - Richard S Mann
- Department of Biochemistry and Molecular Biophysics and Systems Biology, Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, 612 West 130th Street, 9th Floor, New York, NY, 10027, USA
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852
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Three-Dimensional Tissue Models and Available Probes for Multi-Parametric Live Cell Microscopy: A Brief Overview. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1035:49-67. [DOI: 10.1007/978-3-319-67358-5_4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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853
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Zhu Y, Wang L, Yin F, Yu Y, Wang Y, Shepard MJ, Zhuang Z, Qin J. Probing impaired neurogenesis in human brain organoids exposed to alcohol. Integr Biol (Camb) 2017; 9:968-978. [DOI: 10.1039/c7ib00105c] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The fetal brain is highly vulnerable to ethanol exposure, which can trigger various long-term neuronal disabilities and cognitive dysfunctions.
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Affiliation(s)
- Yujuan Zhu
- Division of Biotechnology
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- China
- University of Chinese Academy of Sciences
| | - Li Wang
- Division of Biotechnology
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- China
- Key Laboratory of Separation Sciences for Analytical Chemistry
| | - Fangchao Yin
- Division of Biotechnology
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- China
- University of Chinese Academy of Sciences
| | - Yue Yu
- Division of Biotechnology
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- China
- University of Chinese Academy of Sciences
| | - Yaqing Wang
- Division of Biotechnology
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- China
- University of Chinese Academy of Sciences
| | - Matthew J. Shepard
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke
- National Institutes of Health
- Bethesda
- USA
- Department of Neurological Surgery
| | - Zhengping Zhuang
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke
- National Institutes of Health
- Bethesda
- USA
| | - Jianhua Qin
- Division of Biotechnology
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- China
- University of Chinese Academy of Sciences
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854
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Zhu Y, Wang L, Yin F, Yu Y, Wang Y, Liu H, Wang H, Sun N, Liu H, Qin J. A hollow fiber system for simple generation of human brain organoids. Integr Biol (Camb) 2017; 9:774-781. [DOI: 10.1039/c7ib00080d] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Here we present a novel approach to engineer hiPSC-derived brain organoids within hollow fibers in a simple and high throughput manner by integrating biomaterials with stem cell biology.
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855
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Simian M, Bissell MJ. Organoids: A historical perspective of thinking in three dimensions. J Cell Biol 2016; 216:31-40. [PMID: 28031422 PMCID: PMC5223613 DOI: 10.1083/jcb.201610056] [Citation(s) in RCA: 376] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 12/05/2016] [Accepted: 12/13/2016] [Indexed: 02/08/2023] Open
Abstract
In this perspective, Simian and Bissell discuss the evolution of the 3D culture and organoid research field up to now as well as its future directions. In the last ten years, there has been a dramatic surge in the number of publications where single or groups of cells are grown in substrata that have elements of basement membrane leading to the formation of tissue-like structures referred to as organoids. However, this field of research began many decades ago, when the pioneers of cell culture began to ask questions we still ask today: How does organogenesis occur? How do signals integrate to make such vastly different tissues and organs given that the sequence of the genome in our trillions of cells is identical? Here, we summarize how work over the past century generated the conceptual framework that has allowed us to make progress in the understanding of tissue-specific morphogenetic programs. The development of cell culture systems that provide accurate and physiologically relevant models are proving to be key in establishing appropriate platforms for the development of new therapeutic strategies.
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Affiliation(s)
- Marina Simian
- Instituto de Nanosistemas, Universidad Nacional de San Martín, San Martín 1650, Provincia de Buenos Aires, Argentina
| | - Mina J Bissell
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
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856
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Campo H, Baptista PM, López-Pérez N, Faus A, Cervelló I, Simón C. De- and recellularization of the pig uterus: a bioengineering pilot study. Biol Reprod 2016. [DOI: 10.1095/biolre/bio143396] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Hannes Campo
- Fundación Instituto Valenciano de Infertilidad, Department of Obstetrics and Gynecology, School of Medicine, Valencia University and Instituto Valenciano de Infertilidad/INCLIVA, Valencia, Spain
| | - Pedro M Baptista
- Instituto Aragonés de Ciencias de la Salud, Zaragoza, Spain
- Instituto de Investigacion Sanitaria de Aragon, Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área temática de Enfermedades Hepáticas y Digestivas, Zaragoza, Spain
- Department of Biomedical and Aerospace Engineering, Universidad Carlos III, Madrid, Spain
| | - Nuria López-Pérez
- Fundación Instituto Valenciano de Infertilidad, Department of Obstetrics and Gynecology, School of Medicine, Valencia University and Instituto Valenciano de Infertilidad/INCLIVA, Valencia, Spain
| | - Amparo Faus
- Fundación Instituto Valenciano de Infertilidad, Department of Obstetrics and Gynecology, School of Medicine, Valencia University and Instituto Valenciano de Infertilidad/INCLIVA, Valencia, Spain
| | - Irene Cervelló
- Fundación Instituto Valenciano de Infertilidad, Department of Obstetrics and Gynecology, School of Medicine, Valencia University and Instituto Valenciano de Infertilidad/INCLIVA, Valencia, Spain
| | - Carlos Simón
- Fundación Instituto Valenciano de Infertilidad, Department of Obstetrics and Gynecology, School of Medicine, Valencia University and Instituto Valenciano de Infertilidad/INCLIVA, Valencia, Spain
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford University, Stanford, California
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857
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Kelava I, Lancaster MA. Dishing out mini-brains: Current progress and future prospects in brain organoid research. Dev Biol 2016; 420:199-209. [PMID: 27402594 PMCID: PMC5161139 DOI: 10.1016/j.ydbio.2016.06.037] [Citation(s) in RCA: 196] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 06/16/2016] [Accepted: 06/25/2016] [Indexed: 01/15/2023]
Abstract
The ability to model human brain development in vitro represents an important step in our study of developmental processes and neurological disorders. Protocols that utilize human embryonic and induced pluripotent stem cells can now generate organoids which faithfully recapitulate, on a cell-biological and gene expression level, the early period of human embryonic and fetal brain development. In combination with novel gene editing tools, such as CRISPR, these methods represent an unprecedented model system in the field of mammalian neural development. In this review, we focus on the similarities of current organoid methods to in vivo brain development, discuss their limitations and potential improvements, and explore the future venues of brain organoid research.
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Affiliation(s)
- Iva Kelava
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, CB2 0QH Cambridge, United Kingdom
| | - Madeline A Lancaster
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, CB2 0QH Cambridge, United Kingdom.
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858
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Santo VE, Rebelo SP, Estrada MF, Alves PM, Boghaert E, Brito C. Drug screening in 3D in vitro tumor models: overcoming current pitfalls of efficacy read-outs. Biotechnol J 2016; 12. [PMID: 27966285 DOI: 10.1002/biot.201600505] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 10/24/2016] [Accepted: 11/10/2016] [Indexed: 12/13/2022]
Abstract
There is cumulating evidence that in vitro 3D tumor models with increased physiological relevance can improve the predictive value of pre-clinical research and ultimately contribute to achieve decisions earlier during the development of cancer-targeted therapies. Due to the role of tumor microenvironment in the response of tumor cells to therapeutics, the incorporation of different elements of the tumor niche on cell model design is expected to contribute to the establishment of more predictive in vitro tumor models. This review is focused on the several challenges and adjustments that the field of oncology research is facing to translate these advanced tumor cells models to drug discovery, taking advantage of the progress on culture technologies, imaging platforms, high throughput and automated systems. The choice of 3D cell model, the experimental design, choice of read-outs and interpretation of data obtained from 3D cell models are critical aspects when considering their implementation in drug discovery. In this review, we foresee some of these aspects and depict the potential directions of pre-clinical oncology drug discovery towards improved prediction of drug efficacy.
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Affiliation(s)
- Vítor E Santo
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Sofia P Rebelo
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Marta F Estrada
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Paula M Alves
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | | | - Catarina Brito
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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859
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Gonneaud A, Jones C, Turgeon N, Lévesque D, Asselin C, Boudreau F, Boisvert FM. A SILAC-Based Method for Quantitative Proteomic Analysis of Intestinal Organoids. Sci Rep 2016; 6:38195. [PMID: 27901089 PMCID: PMC5128881 DOI: 10.1038/srep38195] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 11/04/2016] [Indexed: 12/20/2022] Open
Abstract
Organoids have the potential to bridge 3D cell culture to tissue physiology by providing a model resembling in vivo organs. Long-term growing organoids were first isolated from intestinal crypt cells and recreated the renewing intestinal epithelial niche. Since then, this technical breakthrough was applied to many other organs, including prostate, liver, kidney and pancreas. We describe here how to apply a SILAC-based quantitative proteomic approach to measure protein expression changes in intestinal organoids under different experimental conditions. We generated SILAC organoid media that allow organoids to grow and differentiate normally, and confirmed the incorporation of isotopically labelled amino acids. Furthermore, we used a treatment reported to affect organoid differentiation to demonstrate the reproducibility of the quantification using this approach and to validate the identification of proteins that correlate with the inhibition of cellular growth and development. With the combined use of quantitative mass spectrometry, SILAC and organoid culture, we validated this approach and showed that large-scale proteome variations can be measured in an “organ-like” system.
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Affiliation(s)
- Alexis Gonneaud
- Department of Anatomy and Cell Biology, Université de Sherbrooke, 3201 Jean-Mignault, Sherbrooke, Québec, J1E 4K8, Canada
| | - Christine Jones
- Department of Anatomy and Cell Biology, Université de Sherbrooke, 3201 Jean-Mignault, Sherbrooke, Québec, J1E 4K8, Canada
| | - Naomie Turgeon
- Department of Anatomy and Cell Biology, Université de Sherbrooke, 3201 Jean-Mignault, Sherbrooke, Québec, J1E 4K8, Canada
| | - Dominique Lévesque
- Department of Anatomy and Cell Biology, Université de Sherbrooke, 3201 Jean-Mignault, Sherbrooke, Québec, J1E 4K8, Canada
| | - Claude Asselin
- Department of Anatomy and Cell Biology, Université de Sherbrooke, 3201 Jean-Mignault, Sherbrooke, Québec, J1E 4K8, Canada
| | - François Boudreau
- Department of Anatomy and Cell Biology, Université de Sherbrooke, 3201 Jean-Mignault, Sherbrooke, Québec, J1E 4K8, Canada
| | - François-Michel Boisvert
- Department of Anatomy and Cell Biology, Université de Sherbrooke, 3201 Jean-Mignault, Sherbrooke, Québec, J1E 4K8, Canada
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860
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Ruprecht V, Monzo P, Ravasio A, Yue Z, Makhija E, Strale PO, Gauthier N, Shivashankar GV, Studer V, Albiges-Rizo C, Viasnoff V. How cells respond to environmental cues - insights from bio-functionalized substrates. J Cell Sci 2016; 130:51-61. [PMID: 27856508 DOI: 10.1242/jcs.196162] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Biomimetic materials have long been the (he)art of bioengineering. They usually aim at mimicking in vivo conditions to allow in vitro culture, differentiation and expansion of cells. The past decade has witnessed a considerable amount of progress in soft lithography, bio-inspired micro-fabrication and biochemistry, allowing the design of sophisticated and physiologically relevant micro- and nano-environments. These systems now provide an exquisite toolbox with which we can control a large set of physicochemical environmental parameters that determine cell behavior. Bio-functionalized surfaces have evolved from simple protein-coated solid surfaces or cellular extracts into nano-textured 3D surfaces with controlled rheological and topographical properties. The mechanobiological molecular processes by which cells interact and sense their environment can now be unambiguously understood down to the single-molecule level. This Commentary highlights recent successful examples where bio-functionalized substrates have contributed in raising and answering new questions in the area of extracellular matrix sensing by cells, cell-cell adhesion and cell migration. The use, the availability, the impact and the challenges of such approaches in the field of biology are discussed.
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Affiliation(s)
- Verena Ruprecht
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | | | - Andrea Ravasio
- Mechanobiology Institute, National University of Singapore, 5A Engineering Drive 1, 117411, Singapore
| | - Zhang Yue
- Mechanobiology Institute, National University of Singapore, 5A Engineering Drive 1, 117411, Singapore
| | - Ekta Makhija
- Mechanobiology Institute, National University of Singapore, 5A Engineering Drive 1, 117411, Singapore
| | - Pierre Olivier Strale
- CNRS, Interdisciplinary Institute for Neuroscience, UMR 5297, Bordeaux F-33000, France
| | | | - G V Shivashankar
- IFOM, Via Adamello, 16, Milano 20139, Italy.,Mechanobiology Institute, National University of Singapore, 5A Engineering Drive 1, 117411, Singapore
| | - Vincent Studer
- CNRS, Interdisciplinary Institute for Neuroscience, UMR 5297, Bordeaux F-33000, France
| | - Corinne Albiges-Rizo
- INSERM, U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Institute Albert Bonniot, University Grenoble Alpes, La Tronche F-38700, France
| | - Virgile Viasnoff
- Mechanobiology Institute, National University of Singapore, 5A Engineering Drive 1, 117411, Singapore .,CNRS UMI 3639, 5A Engineering Drive 1, 117411 Singapore
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861
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Gjorevski N, Sachs N, Manfrin A, Giger S, Bragina ME, Ordóñez-Morán P, Clevers H, Lutolf MP. Designer matrices for intestinal stem cell and organoid culture. Nature 2016; 539:560-564. [PMID: 27851739 DOI: 10.1038/nature20168] [Citation(s) in RCA: 860] [Impact Index Per Article: 107.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 10/18/2016] [Indexed: 12/30/2022]
Abstract
Epithelial organoids recapitulate multiple aspects of real organs, making them promising models of organ development, function and disease. However, the full potential of organoids in research and therapy has remained unrealized, owing to the poorly defined animal-derived matrices in which they are grown. Here we used modular synthetic hydrogel networks to define the key extracellular matrix (ECM) parameters that govern intestinal stem cell (ISC) expansion and organoid formation, and show that separate stages of the process require different mechanical environments and ECM components. In particular, fibronectin-based adhesion was sufficient for ISC survival and proliferation. High matrix stiffness significantly enhanced ISC expansion through a yes-associated protein 1 (YAP)-dependent mechanism. ISC differentiation and organoid formation, on the other hand, required a soft matrix and laminin-based adhesion. We used these insights to build a fully defined culture system for the expansion of mouse and human ISCs. We also produced mechanically dynamic matrices that were initially optimal for ISC expansion and subsequently permissive to differentiation and intestinal organoid formation, thus creating well-defined alternatives to animal-derived matrices for the culture of mouse and human stem-cell-derived organoids. Our approach overcomes multiple limitations of current organoid cultures and greatly expands their applicability in basic and clinical research. The principles presented here can be extended to identify designer matrices that are optimal for long-term culture of other types of stem cells and organoids.
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Affiliation(s)
- Nikolce 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
| | - Norman Sachs
- Hubrecht Institute and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, The Netherlands
| | - Andrea Manfrin
- 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
| | - Sonja Giger
- 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
| | - Maiia E Bragina
- 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
| | - Paloma Ordóñez-Morán
- Swiss Institute for Experimental Cancer Research (ISREC), EPFL, Lausanne, Switzerland
| | - Hans Clevers
- Hubrecht Institute and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, The Netherlands
| | - Matthias 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, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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862
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Pesce M, Messina E, Chimenti I, Beltrami AP. Cardiac Mechanoperception: A Life-Long Story from Early Beats to Aging and Failure. Stem Cells Dev 2016; 26:77-90. [PMID: 27736363 DOI: 10.1089/scd.2016.0206] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The life-long story of the heart starts concomitantly with primary differentiation events occurring in multipotent progenitors located in the so-called heart tube. This initially tubular structure starts a looping process, which leads to formation of the final four-chambered heart with a primary contribution of geometric and position-associated cell sensing. While this establishes the correct patterning of the final cardiac structure, it also provides feedbacks to fundamental cellular machineries controlling proliferation and differentiation, thus ensuring a coordinated restriction of cell growth and a myocyte terminal differentiation. Novel evidences provided by embryological and cell engineering studies have clarified the relevance of mechanics-supported position sensing for the correct recognition of cell fate inside developing embryos and multicellular aggregates. One of the main components of this pathway, the Hippo-dependent signal transduction machinery, is responsible for cell mechanics intracellular transduction with important consequences for gene transcription and cell growth control. Being the Hippo pathway also directly connected to stress responses and altered metabolism, it is tempting to speculate that permanent alterations of mechanosensing may account for modifying self-renewal control in tissue homeostasis. In the present contribution, we translate these concepts to the aging process and the failing of the human heart, two pathophysiologic conditions that are strongly affected by stress responses and altered metabolism.
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Affiliation(s)
- Maurizio Pesce
- 1 Tissue Engineering Research Unit, Centro Cardiologico Monzino, IRCCS , Milan, Italy
| | - Elisa Messina
- 2 Department of Pediatric Cardiology, "Sapienza" University , Rome, Italy
| | - Isotta Chimenti
- 3 Department of Medical Surgical Science and Biotechnology, "Sapienza" University , Rome, Italy
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863
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Choi H, Song J, Park G, Kim J. Modeling of Autism Using Organoid Technology. Mol Neurobiol 2016; 54:7789-7795. [DOI: 10.1007/s12035-016-0274-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 10/30/2016] [Indexed: 01/01/2023]
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864
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Annunziato S, Barazas M, Rottenberg S, Jonkers J. Genetic Dissection of Cancer Development, Therapy Response, and Resistance in Mouse Models of Breast Cancer. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2016; 81:141-150. [PMID: 27815543 DOI: 10.1101/sqb.2016.81.030924] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The cancer genomics revolution has rapidly expanded the inventory of somatic mutations characterizing human malignancies, highlighting a previously underappreciated extent of molecular variability between and within patients. Also in breast cancer, the most commonly diagnosed malignancy in women, this heterogeneity complicates the understanding of the stepwise sequence of pathogenic events and the design of effective and long-lasting target therapies. To disentangle this complexity and pinpoint which molecular perturbations are crucial to hijack the cellular machinery and lead to tumorigenesis and drug resistance, functional studies are needed in model systems that faithfully and comprehensively recapitulate all the salient aspects of their cognate human counterparts. Mouse models of breast cancer have been instrumental for the study of tumor initiation and drug response but also involve cost and time limitations that represent serious bottlenecks in translational research. To keep pace with the overwhelming amount of hypotheses that warrant in vivo testing, continuous refinement of current breast cancer models and implementation of new technologies is crucial. In this review, we summarize the current state of the art in modeling human breast cancer in mice, and we put forward our vision for future developments.
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Affiliation(s)
- Stefano Annunziato
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Marco Barazas
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Sven Rottenberg
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands.,Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | - Jos Jonkers
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands.,Cancer Genomics Netherlands, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
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865
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Cell sheet mechanics: How geometrical constraints induce the detachment of cell sheets from concave surfaces. Acta Biomater 2016; 45:85-97. [PMID: 27562610 DOI: 10.1016/j.actbio.2016.08.044] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 08/16/2016] [Accepted: 08/20/2016] [Indexed: 12/15/2022]
Abstract
Despite of the progress made to engineer structured microtissues such as BioMEMS and 3D bioprinting, little control exists how microtissues transform as they mature, as the misbalance between cell-generated forces and the strength of cell-cell and cell-substrate contacts can result in unintended tissue deformations and ruptures. To develop a quantitative perspective on how cellular contractility, scaffold curvature and cell-substrate adhesion control such rupture processes, human aortic smooth muscle cells were grown on glass substrates with submillimeter semichannels. We quantified cell sheet detachment from 3D confocal image stacks as a function of channel curvature and cell sheet tension by adding different amounts of Blebbistatin and TGF-β to inhibit or enhance cell contractility, respectively. We found that both higher curvature and higher contractility increased the detachment probability. Variations of the adhesive strength of the protein coating on the substrate revealed that the rupture plane was localized along the substrate-extracellular matrix interface for non-covalently adsorbed adhesion proteins, while the collagen-integrin interface ruptured when collagen I was covalently crosslinked to the substrate. Finally, a simple mechanical model is introduced that quantitatively explains how the tuning of substrate curvature, cell sheet contractility and adhesive strength can be used as tunable parameters as summarized in a first semi-quantitative phase diagram. These parameters can thus be exploited to either inhibit or purposefully induce a collective detachment of sheet-like microtissues for the use in tissue engineering and regenerative therapies. STATEMENT OF SIGNIFICANCE Despite of the significant progress in 3D tissue fabrication technologies at the microscale, there is still no quantitative model that can predict if cells seeded on a 3D structure maintain the imposed geometry while they form a continuous microtissue. Especially, detachment or loss of shape control of growing tissue is a major concern when designing 3D-structured scaffolds. Utilizing semi-cylindrical channels and vascular smooth muscle cells, we characterized how geometrical and mechanical parameters such as curvature of the substrate, cellular contractility, or protein-substrate adhesion strength tune the catastrophic detachment of microtissue. Observed results were rationalized by a theoretical model. The phase diagram showing how unintended tissue detachment progresses would help in designing of mechanically-balanced 3D scaffolds in future tissue engineering applications.
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866
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Housden BE, Muhar M, Gemberling M, Gersbach CA, Stainier DYR, Seydoux G, Mohr SE, Zuber J, Perrimon N. Loss-of-function genetic tools for animal models: cross-species and cross-platform differences. Nat Rev Genet 2016; 18:24-40. [PMID: 27795562 DOI: 10.1038/nrg.2016.118] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Our understanding of the genetic mechanisms that underlie biological processes has relied extensively on loss-of-function (LOF) analyses. LOF methods target DNA, RNA or protein to reduce or to ablate gene function. By analysing the phenotypes that are caused by these perturbations the wild-type function of genes can be elucidated. Although all LOF methods reduce gene activity, the choice of approach (for example, mutagenesis, CRISPR-based gene editing, RNA interference, morpholinos or pharmacological inhibition) can have a major effect on phenotypic outcomes. Interpretation of the LOF phenotype must take into account the biological process that is targeted by each method. The practicality and efficiency of LOF methods also vary considerably between model systems. We describe parameters for choosing the optimal combination of method and system, and for interpreting phenotypes within the constraints of each method.
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Affiliation(s)
- Benjamin E Housden
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
| | - Matthias Muhar
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna 1030, Austria
| | - Matthew Gemberling
- Department of Biomedical Engineering and the Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA
| | - Charles A Gersbach
- Department of Biomedical Engineering and the Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA
| | - Didier Y R Stainier
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, 43 Ludwigstrasse, Bad Nauheim 61231, Germany
| | - Geraldine Seydoux
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21218, USA.,Howard Hughes Medical Institute, 725 North Wolfe Street, Baltimore, Maryland 21218, USA
| | - Stephanie E Mohr
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna 1030, Austria
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
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867
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Meneses AMC, Schneeberger K, Kruitwagen HS, Penning LC, van Steenbeek FG, Burgener IA, Spee B. Intestinal Organoids-Current and Future Applications. Vet Sci 2016; 3:vetsci3040031. [PMID: 29056739 PMCID: PMC5606586 DOI: 10.3390/vetsci3040031] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 09/19/2016] [Accepted: 10/19/2016] [Indexed: 12/11/2022] Open
Abstract
Recent technical advances in the stem cell field have enabled the in vitro generation of complex structures resembling whole organs termed organoids. Most of these approaches employ culture systems that allow stem cell-derived or tissue progenitor cells to self-organize into three-dimensional (3D)-structures. Since organoids can be grown from different species (human, mouse, cat, dog), organs (intestine, kidney, brain, liver), and from patient-derived induced pluripotent stem cells, they create significant prospects for modelling development and diseases, for toxicology and drug discovery studies, and in the field of regenerative medicine. Here, we report on intestinal stem cells, organoid culture, organoid disease modeling, transplantation, specifically covering the current and future uses of this exciting new insight model to the field of veterinary medicine.
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Affiliation(s)
- Andre M C Meneses
- Institute of Animal Health and Production, Universidade Federal Rural da Amazônia, Avenida Presidente Tancredo Neves 66077-830, Brazil.
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 104, Utrecht 3584 CM, The Netherlands.
| | - Kerstin Schneeberger
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 104, Utrecht 3584 CM, The Netherlands.
| | - Hedwig S Kruitwagen
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 104, Utrecht 3584 CM, The Netherlands.
| | - Louis C Penning
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 104, Utrecht 3584 CM, The Netherlands.
| | - Frank G van Steenbeek
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 104, Utrecht 3584 CM, The Netherlands.
| | - Iwan A Burgener
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 104, Utrecht 3584 CM, The Netherlands.
| | - Bart Spee
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 104, Utrecht 3584 CM, The Netherlands.
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868
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Hollins AJ, Parry L. Long-Term Culture of Intestinal Cell Progenitors: An Overview of Their Development, Application, and Associated Technologies. CURRENT PATHOBIOLOGY REPORTS 2016; 4:209-219. [PMID: 27882268 PMCID: PMC5101250 DOI: 10.1007/s40139-016-0119-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
PURPOSE OF REVIEW Long-term culture of adult progenitor cells in 3D is a recently emerging technology that inhabits the space between 2D cell lines and organ slice culture. RECENT FINDINGS Adaptations to defined media components in the wake of advances in ES and iPS cell culture has led to the identification of conditions that maintained intestinal cell progenitors in culture. These conditions retain cellular heterogeneity of the normal or tumour tissue, and the cultures have been shown to be genetically stable, such that substantial biobanks are being created from patient derived material. This coupled with advances in analytical tools has generated a field, characterized by the term "organoid culture", that has huge potential for advancing drug discovery, regenerative medicine, and furthering the understanding of fundamental intestinal biology. SUMMARY In this review, we describe the approaches available for the long-term culture of intestinal cells from normal and diseased tissue, the current challenges, and how the technology is likely to develop further.
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Affiliation(s)
| | - Lee Parry
- European Cancer Stem Cell Research Institute, School of Biosciences, Cardiff University, Cardiff, CF24 4HQ UK
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869
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Evans AC, Karama S, Vasung L, Iturria-Medina Y. Understanding brain development: a major step. Lancet Neurol 2016; 16:178-179. [PMID: 27692495 DOI: 10.1016/s1474-4422(16)30232-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 09/02/2016] [Indexed: 11/19/2022]
Affiliation(s)
- Alan C Evans
- Montreal Neurological Institute, McGill University, Montreal, QC Canada.
| | - Sherif Karama
- Douglas Hospital Research Centre, McGill University, Montreal, QC Canada
| | - Lana Vasung
- Department of Pediatrics, Université de Genève, Geneva, Switzerland
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870
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Choi J, Iich E, Lee JH. Organogenesis of adult lung in a dish: Differentiation, disease and therapy. Dev Biol 2016; 420:278-286. [PMID: 27713058 DOI: 10.1016/j.ydbio.2016.10.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/29/2016] [Accepted: 10/02/2016] [Indexed: 12/26/2022]
Abstract
The remarkable regenerative capacity of the lung suggests that stem cells could be of therapeutic importance in diverse lung diseases; however, the successful exploitation of lung stem cell biology has long been hampered by our inability to maintain and expand adult lung stem cells while retaining their multi-lineage potential in vitro. Recently, advances in our understanding of stem cell niches and the role of key signalling modulators in controlling stem cell maintenance and differentiation have fuelled the development of new in vitro three-dimensional (3D) culture technologies that sustain the stem cell-driven formation of near-physiological, self-organizing structures called organoids. Here we review basic approaches to organoid model systems and highlight recent achievements in the generation of organoids from adult stem and progenitor cells of both the murine and human lungs. We evaluate current applications in studying cellular changes in proliferation, differentiation, plasticity, and cell polarity, and cellular and molecular crosstalk of epithelial cells with stroma. Advantages and limitations of organoids for clinical use are also discussed.
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Affiliation(s)
- Jinwook Choi
- Wellcome Trust/Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Elhadi Iich
- Wellcome Trust/Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Joo-Hyeon Lee
- Wellcome Trust/Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK; Department of Physiology, Development and Neutabroscience, University of Cambridge, Cambridge CB2 3DY, UK.
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871
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Dye BR, Dedhia PH, Miller AJ, Nagy MS, White ES, Shea LD, Spence JR. A bioengineered niche promotes in vivo engraftment and maturation of pluripotent stem cell derived human lung organoids. eLife 2016; 5. [PMID: 27677847 PMCID: PMC5089859 DOI: 10.7554/elife.19732] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/21/2016] [Indexed: 02/06/2023] Open
Abstract
Human pluripotent stem cell (hPSC) derived tissues often remain developmentally immature in vitro, and become more adult-like in their structure, cellular diversity and function following transplantation into immunocompromised mice. Previously we have demonstrated that hPSC-derived human lung organoids (HLOs) resembled human fetal lung tissue in vitro (Dye et al., 2015). Here we show that HLOs required a bioartificial microporous poly(lactide-co-glycolide) (PLG) scaffold niche for successful engraftment, long-term survival, and maturation of lung epithelium in vivo. Analysis of scaffold-grown transplanted tissue showed airway-like tissue with enhanced epithelial structure and organization compared to HLOs grown in vitro. By further comparing in vitro and in vivo grown HLOs with fetal and adult human lung tissue, we found that in vivo transplanted HLOs had improved cellular differentiation of secretory lineages that is reflective of differences between fetal and adult tissue, resulting in airway-like structures that were remarkably similar to the native adult human lung.
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Affiliation(s)
- Briana R Dye
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, United States
| | - Priya H Dedhia
- Department of Surgery, University of Michigan Medical School, Ann Arbor, United States
| | - Alyssa J Miller
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, United States.,Program in Cellular and Molecular Biology, University of Michigan Medical School, Ann Arbor, United States
| | - Melinda S Nagy
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, United States
| | - Eric S White
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, United States
| | - Lonnie D Shea
- Center for Organogenesis, University of Michigan Medical School, Ann Arbor, United States.,Biomedical Engineering, University of Michigan Biomedical Engineering, Ann Arbor, United States
| | - Jason R Spence
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, United States.,Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, United States.,Center for Organogenesis, University of Michigan Medical School, Ann Arbor, United States
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872
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Liu F, Huang J, Ning B, Liu Z, Chen S, Zhao W. Drug Discovery via Human-Derived Stem Cell Organoids. Front Pharmacol 2016; 7:334. [PMID: 27713700 PMCID: PMC5032635 DOI: 10.3389/fphar.2016.00334] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 09/09/2016] [Indexed: 12/18/2022] Open
Abstract
Patient-derived cell lines and animal models have proven invaluable for the understanding of human intestinal diseases and for drug development although both inherently comprise disadvantages and caveats. Many genetically determined intestinal diseases occur in specific tissue microenvironments that are not adequately modeled by monolayer cell culture. Likewise, animal models incompletely recapitulate the complex pathologies of intestinal diseases of humans and fall short in predicting the effects of candidate drugs. Patient-derived stem cell organoids are new and effective models for the development of novel targeted therapies. With the use of intestinal organoids from patients with inherited diseases, the potency and toxicity of drug candidates can be evaluated better. Moreover, owing to the novel clustered regularly interspaced short palindromic repeats/CRISPR-associated protein-9 genome-editing technologies, researchers can use organoids to precisely modulate human genetic status and identify pathogenesis-related genes of intestinal diseases. Therefore, here we discuss how patient-derived organoids should be grown and how advanced genome-editing tools may be applied to research on modeling of cancer and infectious diseases. We also highlight practical applications of organoids ranging from basic studies to drug screening and precision medicine.
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Affiliation(s)
- Fangkun Liu
- Department of Neurosurgery, Xiangya Hospital, Central South UniversityChangsha, China; Center for Inflammation and Epigenetics, Houston Methodist Research Institute, HoustonTX, USA
| | - Jing Huang
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, HoustonTX, USA; Department of Psychiatry, The Second Xiangya Hospital, Central South University, ChangshaHunan, China; Mental Health Institute of the Second Xiangya Hospital, Central South University, ChangshaHunan, China; Chinese National Clinical Research Center on Mental Disorders, ChangshaHunan, China; Chinese National Technology Institute on Mental Disorders, ChangshaHunan, China; Hunan Key Laboratory of Psychiatry and Mental Health, ChangshaHunan, China
| | - Bo Ning
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston TX, USA
| | - Zhixiong Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University Changsha, China
| | - Shen Chen
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen UniversityGuangzhou, China; Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen UniversityGuangzhou, China
| | - Wei Zhao
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen UniversityGuangzhou, China; Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen UniversityGuangzhou, China
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873
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Modeling infectious diseases and host-microbe interactions in gastrointestinal organoids. Dev Biol 2016; 420:262-270. [PMID: 27640087 DOI: 10.1016/j.ydbio.2016.09.014] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Revised: 09/09/2016] [Accepted: 09/13/2016] [Indexed: 12/18/2022]
Abstract
Advances in stem cell research have allowed the development of 3-dimensional (3D) primary cell cultures termed organoid cultures, as they closely mimic the in vivo organization of different cell lineages. Bridging the gap between 2-dimensional (2D) monotypic cancer cell lines and whole organisms, organoids are now widely applied to model development and disease. Organoids hold immense promise for addressing novel questions in host-microbe interactions, infectious diseases and the resulting inflammatory conditions. Researchers have started to use organoids for modeling infection with pathogens, such as Helicobacter pylori or Salmonella enteritica, gut-microbiota interactions and inflammatory bowel disease. Future studies will broaden the spectrum of microbes used and continue to establish organoids as a standard model for human host-microbial interactions. Moreover, they will increasingly exploit the unique advantages of organoids, for example to address patient-specific responses to microbes.
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874
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Onyido EK, Sweeney E, Nateri AS. Wnt-signalling pathways and microRNAs network in carcinogenesis: experimental and bioinformatics approaches. Mol Cancer 2016; 15:56. [PMID: 27590724 PMCID: PMC5010773 DOI: 10.1186/s12943-016-0541-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 08/26/2016] [Indexed: 02/02/2023] Open
Abstract
Over the past few years, microRNAs (miRNAs) have not only emerged as integral regulators of gene expression at the post-transcriptional level but also respond to signalling molecules to affect cell function(s). miRNAs crosstalk with a variety of the key cellular signalling networks such as Wnt, transforming growth factor-β and Notch, control stem cell activity in maintaining tissue homeostasis, while if dysregulated contributes to the initiation and progression of cancer. Herein, we overview the molecular mechanism(s) underlying the crosstalk between Wnt-signalling components (canonical and non-canonical) and miRNAs, as well as changes in the miRNA/Wnt-signalling components observed in the different forms of cancer. Furthermore, the fundamental understanding of miRNA-mediated regulation of Wnt-signalling pathway and vice versa has been significantly improved by high-throughput genomics and bioinformatics technologies. Whilst, these approaches have identified a number of specific miRNA(s) that function as oncogenes or tumour suppressors, additional analyses will be necessary to fully unravel the links among conserved cellular signalling pathways and miRNAs and their potential associated components in cancer, thereby creating therapeutic avenues against tumours. Hence, we also discuss the current challenges associated with Wnt-signalling/miRNAs complex and the analysis using the biomedical experimental and bioinformatics approaches.
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Affiliation(s)
- Emenike K Onyido
- Cancer Genetics & Stem Cell Group, Cancer Biology Unit, Division of Cancer & Stem Cells, School of Medicine, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Eloise Sweeney
- Cancer Genetics & Stem Cell Group, Cancer Biology Unit, Division of Cancer & Stem Cells, School of Medicine, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Abdolrahman Shams Nateri
- Cancer Genetics & Stem Cell Group, Cancer Biology Unit, Division of Cancer & Stem Cells, School of Medicine, University of Nottingham, Nottingham, NG7 2UH, UK.
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875
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Grapin-Botton A. Three-dimensional pancreas organogenesis models. Diabetes Obes Metab 2016; 18 Suppl 1:33-40. [PMID: 27615129 PMCID: PMC5021194 DOI: 10.1111/dom.12720] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 05/02/2016] [Indexed: 01/07/2023]
Abstract
A rediscovery of three-dimensional culture has led to the development of organ biogenesis, homeostasis and disease models applicable to human tissues. The so-called organoids that have recently flourished serve as valuable models bridging between cell lines or primary cells grown on the bottom of culture plates and experiments performed in vivo. Though not recapitulating all aspects of organ physiology, the miniature organs generated in a dish are useful models emerging for the pancreas, starting from embryonic progenitors, adult cells, tumour cells and stem cells. This review focusses on the currently available systems and their relevance to the study of the pancreas, of β-cells and of several pancreatic diseases including diabetes. We discuss the expected future developments for studying human pancreas development and function, for developing diabetes models and for producing therapeutic cells.
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876
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Tumor deconstruction as a tool for advanced drug screening and repositioning. Pharmacol Res 2016; 111:815-819. [DOI: 10.1016/j.phrs.2016.07.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 07/14/2016] [Accepted: 07/14/2016] [Indexed: 12/15/2022]
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877
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A Joint Less Ordinary: Intriguing Roles for Hedgehog Signalling in the Development of the Temporomandibular Synovial Joint. J Dev Biol 2016; 4:jdb4030025. [PMID: 29615589 PMCID: PMC5831777 DOI: 10.3390/jdb4030025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 08/08/2016] [Accepted: 08/17/2016] [Indexed: 12/14/2022] Open
Abstract
This review highlights the essential role of Hedgehog (Hh) signalling in the developmental steps of temporomandibular joint (TMJ) formation. We review evidence for intra- and potentially inter-tissue Hh signaling as well as Glioma-Associated Oncogene Homolog (GLI) dependent and independent functions. Morphogenesis and maturation of the TMJ’s individual components and the general landscape of Hh signalling is also covered. Comparison of the appendicular knee and axial TMJ also reveals interesting differences and similarities in their mechanisms of development, chondrogenesis and reliance on Hh signalling.
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878
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Li M, Izpisua Belmonte JC. Looking to the future following 10 years of induced pluripotent stem cell technologies. Nat Protoc 2016; 11:1579-85. [PMID: 27490631 DOI: 10.1038/nprot.2016.108] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 05/19/2016] [Indexed: 12/12/2022]
Abstract
The development of induced pluripotent stem cells (iPSCs) has fundamentally changed our view on developmental cell-fate determination and led to a cascade of technological innovations in regenerative medicine. Here we provide an overview of the progress in the field over the past decade, as well as our perspective on future directions and clinical implications of iPSC technology.
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Affiliation(s)
- Mo Li
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, California, USA.,Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, California, USA
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879
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Jo J, Xiao Y, Sun AX, Cukuroglu E, Tran HD, Göke J, Tan ZY, Saw TY, Tan CP, Lokman H, Lee Y, Kim D, Ko HS, Kim SO, Park JH, Cho NJ, Hyde TM, Kleinman JE, Shin JH, Weinberger DR, Tan EK, Je HS, Ng HH. Midbrain-like Organoids from Human Pluripotent Stem Cells Contain Functional Dopaminergic and Neuromelanin-Producing Neurons. Cell Stem Cell 2016; 19:248-257. [PMID: 27476966 DOI: 10.1016/j.stem.2016.07.005] [Citation(s) in RCA: 508] [Impact Index Per Article: 63.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 04/22/2016] [Accepted: 07/08/2016] [Indexed: 12/13/2022]
Abstract
Recent advances in 3D culture systems have led to the generation of brain organoids that resemble different human brain regions; however, a 3D organoid model of the midbrain containing functional midbrain dopaminergic (mDA) neurons has not been reported. We developed a method to differentiate human pluripotent stem cells into a large multicellular organoid-like structure that contains distinct layers of neuronal cells expressing characteristic markers of human midbrain. Importantly, we detected electrically active and functionally mature mDA neurons and dopamine production in our 3D midbrain-like organoids (MLOs). In contrast to human mDA neurons generated using 2D methods or MLOs generated from mouse embryonic stem cells, our human MLOs produced neuromelanin-like granules that were structurally similar to those isolated from human substantia nigra tissues. Thus our MLOs bearing features of the human midbrain may provide a tractable in vitro system to study the human midbrain and its related diseases.
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Affiliation(s)
- Junghyun Jo
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore
| | - Yixin Xiao
- Signature Program in Neuroscience and Behavioral Disorders, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Alfred Xuyang Sun
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore; National Neuroscience Institute, 20 College Road, Singapore 169856, Singapore
| | - Engin Cukuroglu
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore
| | - Hoang-Dai Tran
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore; Department of Biochemistry, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
| | - Jonathan Göke
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore
| | - Zi Ying Tan
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore; Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
| | - Tzuen Yih Saw
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore
| | - Cheng-Peow Tan
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore
| | - Hidayat Lokman
- Signature Program in Neuroscience and Behavioral Disorders, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Younghwan Lee
- Signature Program in Neuroscience and Behavioral Disorders, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Donghoon Kim
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Han Seok Ko
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Seong-Oh Kim
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Jae Hyeon Park
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Nam-Joon Cho
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore; KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 136-701, Korea
| | - Thomas M Hyde
- The Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA; Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Joel E Kleinman
- The Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA; Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Joo Heon Shin
- The Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA
| | - Daniel R Weinberger
- The Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA; Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Eng King Tan
- National Neuroscience Institute, 20 College Road, Singapore 169856, Singapore
| | - Hyunsoo Shawn Je
- Signature Program in Neuroscience and Behavioral Disorders, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore.
| | - Huck-Hui Ng
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore; Department of Biochemistry, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore; Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 639798, Singapore.
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880
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Schweiger PJ, Jensen KB. Modeling human disease using organotypic cultures. Curr Opin Cell Biol 2016; 43:22-29. [PMID: 27474805 DOI: 10.1016/j.ceb.2016.07.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Revised: 06/21/2016] [Accepted: 07/05/2016] [Indexed: 12/18/2022]
Abstract
Reliable disease models are needed in order to improve quality of healthcare. This includes gaining better understanding of disease mechanisms, developing new therapeutic interventions and personalizing treatment. Up-to-date, the majority of our knowledge about disease states comes from in vivo animal models and in vitro cell culture systems. However, it has been exceedingly difficult to model disease at the tissue level. Since recently, the gap between cell line studies and in vivo modeling has been narrowing thanks to progress in biomaterials and stem cell research. Development of reliable 3D culture systems has enabled a rapid expansion of sophisticated in vitro models. Here we focus on some of the latest advances and future perspectives in 3D organoids for human disease modeling.
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Affiliation(s)
- Pawel J Schweiger
- BRIC-Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Kim B Jensen
- BRIC-Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark.
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881
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Abstract
The cellular thermal shift assay (CETSA) was introduced in 2013 as a means to assess drug binding in complex environments such as cell lysates, live cells, and even tissues. The assay principle relies on the well-proven biophysical concept of ligand-induced thermal stabilization of proteins, which in CETSA applications is measured as a persistent presence of soluble protein at elevated temperatures. Given its recent development, we have just started to learn about the benefits and pitfalls of the method as it is applied to a growing number of protein target classes, the majority of which are intracellular soluble proteins. One of the early technology developments concerned the transfer of the original assay procedure from PCR tubes and Western blot detection of soluble protein to a homogeneous assay in high-density microplates. A move to high-throughput formats is essential for a more systematic application in drug discovery settings, as well as in academic efforts for validating chemical probes through studies of structure-activity relationships. This perspective aims at providing an overview of knowledge gained in microplate formatting of CETSA and makes an attempt at forecasting future applications.
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Affiliation(s)
- Brinton Seashore-Ludlow
- 1 Chemical Biology Consortium Sweden, Science for Life Laboratories, Stockholm, Sweden.,2 Department of Medical Biochemistry and Biophysics, Division of Translational Medicine and Chemical Biology, Karolinska Institutet, Solna, Sweden
| | - Thomas Lundbäck
- 1 Chemical Biology Consortium Sweden, Science for Life Laboratories, Stockholm, Sweden.,2 Department of Medical Biochemistry and Biophysics, Division of Translational Medicine and Chemical Biology, Karolinska Institutet, Solna, Sweden
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882
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Corso S, Giordano S. How Can Gastric Cancer Molecular Profiling Guide Future Therapies? Trends Mol Med 2016; 22:534-544. [PMID: 27260398 DOI: 10.1016/j.molmed.2016.05.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 05/10/2016] [Accepted: 05/10/2016] [Indexed: 02/06/2023]
Abstract
Gastric cancer is the third greatest global cause of cancer-related deaths. Despite its high prevalence, only recently have comprehensive genomic surveys shed light on its molecular alterations. As surgery is the only curative treatment strategy and chemotherapy has shown limited efficacy, new treatments are urgently needed. Many molecular therapies for gastric cancer have entered clinical trials but-apart from Trastuzumab and Ramucirumab-all have failed. We analyze the current knowledge of the genetic 'landscape' of gastric cancers, elaborating on novel, preclinical approaches. We posit that this knowledge lays the basis for identifying bona fide molecular targets and developing solid therapeutic approaches, requiring accurate patient selection and taking advantage of preclinical models to assist clinical development of novel combination strategies.
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Affiliation(s)
- Simona Corso
- University of Torino, Department of Oncology, Candiolo Cancer Institute-FPO, IRCCS, Str. Provinciale 142, 10060 Candiolo, Torino, Italy.
| | - Silvia Giordano
- University of Torino, Department of Oncology, Candiolo Cancer Institute-FPO, IRCCS, Str. Provinciale 142, 10060 Candiolo, Torino, Italy.
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883
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884
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Bourret R, Martinez E, Vialla F, Giquel C, Thonnat-Marin A, De Vos J. Human-animal chimeras: ethical issues about farming chimeric animals bearing human organs. Stem Cell Res Ther 2016; 7:87. [PMID: 27356872 PMCID: PMC4928294 DOI: 10.1186/s13287-016-0345-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Recent advances in stem cells and gene engineering have paved the way for the generation of interspecies chimeras, such as animals bearing an organ from another species. The production of a rat pancreas by a mouse has demonstrated the feasibility of this approach. The next step will be the generation of larger chimeric animals, such as pigs bearing human organs. Because of the dramatic organ shortage for transplantation, the medical needs for such a transgressive practice are indisputable. However, there are serious technical barriers and complex ethical issues that must be discussed and solved before producing human organs in animals. The main ethical issues are the risks of consciousness and of human features in the chimeric animal due to a too high contribution of human cells to the brain, in the first case, or for instance to limbs, in the second. Another critical point concerns the production of human gametes by such chimeric animals. These worst-case scenarios are obviously unacceptable and must be strictly monitored by careful risk assessment, and, if necessary, technically prevented. The public must be associated with this ethical debate. Scientists and physicians have a critical role in explaining the medical needs, the advantages and limits of this potential medical procedure, and the ethical boundaries that must not be trespassed. If these prerequisites are met, acceptance of such a new, borderline medical procedure may prevail, as happened before for in-vitro fertilization or preimplantation genetic diagnosis.
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Affiliation(s)
- Rodolphe Bourret
- />CHU Montpellier, Innovation and Research Division, Montpellier, F34000 France
| | - Eric Martinez
- />CHU Montpellier, Innovation and Research Division, Montpellier, F34000 France
| | - François Vialla
- />Université de Montpellier, UFR de Droit, Montpellier, F34000 France
| | - Chloé Giquel
- />CHU Montpellier, Innovation and Research Division, Montpellier, F34000 France
| | | | - John De Vos
- />INSERM, U1183, Montpellier, F34000 France
- />Université de Montpellier, UFR de Médecine, Montpellier, F34000 France
- />CHU Montpellier, Department of Cell and Tissue Engineering, Hospital Saint-Eloi, 80 Avenue Augustin Fliche, 34295 Montpellier, Cedex 5 France
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885
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Aurora M, Spence JR. hPSC-derived lung and intestinal organoids as models of human fetal tissue. Dev Biol 2016; 420:230-238. [PMID: 27287882 DOI: 10.1016/j.ydbio.2016.06.006] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Revised: 05/23/2016] [Accepted: 06/04/2016] [Indexed: 02/07/2023]
Abstract
In vitro human pluripotent stem cell (hPSC) derived tissues are excellent models to study certain aspects of normal human development. Current research in the field of hPSC derived tissues reveals these models to be inherently fetal-like on both a morphological and gene expression level. In this review we briefly discuss current methods for differentiating lung and intestinal tissue from hPSCs into individual 3-dimensional units called organoids. We discuss how these methods mirror what is known about in vivo signaling pathways of the developing embryo. Additionally, we will review how the inherent immaturity of these models lends them to be particularly valuable in the study of immature human tissues in the clinical setting of premature birth. Human lung organoids (HLOs) and human intestinal organoids (HIOs) not only model normal development, but can also be utilized to study several important diseases of prematurity such as respiratory distress syndrome (RDS), bronchopulmonary dysplasia (BPD), and necrotizing enterocolitis (NEC).
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Affiliation(s)
- Megan Aurora
- Department of Pediatrics, Division of Neonatal-Perinatal Medicine, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Jason R Spence
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, United States; Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, United States; Center for Organogenesis, University of Michigan Medical School, Ann Arbor, MI, United States
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886
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Cruz-Acuña R, García AJ. Synthetic hydrogels mimicking basement membrane matrices to promote cell-matrix interactions. Matrix Biol 2016; 57-58:324-333. [PMID: 27283894 DOI: 10.1016/j.matbio.2016.06.002] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 06/02/2016] [Accepted: 06/02/2016] [Indexed: 01/05/2023]
Abstract
Naturally-derived materials have been extensively used as 3D cellular matrices as their inherent bioactivity makes them suitable for the study of many cellular processes. Nevertheless, lot-to-lot variability, inability to decouple biochemical and biophysical properties and, in some types, their tumor-derived nature limits their translational potential and reliability. One innovative approach to overcome these limitations has focused on incorporating bioactivity into cytocompatible, synthetic hydrogels that present tunable physicochemical properties. This review provides an overview of successful approaches to convey basement membrane-like bioactivity into 3D artificial hydrogel matrices in order to recapitulate cellular responses to native matrices. Recent advances involving biofunctionalization of synthetic hydrogels via incorporation of bioactive motifs that promote cell-matrix interactions and cell-directed matrix degradation will be discussed. This review highlights how the tunable physicochemical properties of biofunctionalized synthetic hydrogel matrices can be exploited to study the separate contributions of biochemical and biophysical matrix properties to different cellular processes.
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Affiliation(s)
- Ricardo Cruz-Acuña
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, United States; Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, United States
| | - Andrés J García
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, United States; Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, United States.
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887
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Evaluating cell reprogramming, differentiation and conversion technologies in neuroscience. Nat Rev Neurosci 2016; 17:424-37. [PMID: 27194476 DOI: 10.1038/nrn.2016.46] [Citation(s) in RCA: 199] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The scarcity of live human brain cells for experimental access has for a long time limited our ability to study complex human neurological disorders and elucidate basic neuroscientific mechanisms. A decade ago, the development of methods to reprogramme somatic human cells into induced pluripotent stem cells enabled the in vitro generation of a wide range of neural cells from virtually any human individual. The growth of methods to generate more robust and defined neural cell types through reprogramming and direct conversion into induced neurons has led to the establishment of various human reprogramming-based neural disease models.
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888
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Gautam P, Karhinen L, Szwajda A, Jha SK, Yadav B, Aittokallio T, Wennerberg K. Identification of selective cytotoxic and synthetic lethal drug responses in triple negative breast cancer cells. Mol Cancer 2016; 15:34. [PMID: 27165605 PMCID: PMC4862054 DOI: 10.1186/s12943-016-0517-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 04/30/2016] [Indexed: 01/23/2023] Open
Abstract
Background Triple negative breast cancer (TNBC) is a highly heterogeneous and aggressive type of cancer that lacks effective targeted therapy. Despite detailed molecular profiling, no targeted therapy has been established. Hence, with the aim of gaining deeper understanding of the functional differences of TNBC subtypes and how that may relate to potential novel therapeutic strategies, we studied comprehensive anticancer-agent responses among a panel of TNBC cell lines. Method The responses of 301 approved and investigational oncology compounds were measured in 16 TNBC cell lines applying a functional profiling approach. To go beyond the standard drug viability effect profiling, which has been used in most chemosensitivity studies, we utilized a multiplexed readout for both cell viability and cytotoxicity, allowing us to differentiate between cytostatic and cytotoxic responses. Results Our approach revealed that most single-agent anti-cancer compounds that showed activity for the viability readout had no or little cytotoxic effects. Major compound classes that exhibited this type of response included anti-mitotics, mTOR, CDK, and metabolic inhibitors, as well as many agents selectively inhibiting oncogene-activated pathways. However, within the broad viability-acting classes of compounds, there were often subsets of cell lines that responded by cell death, suggesting that these cells are particularly vulnerable to the tested substance. In those cases we could identify differential levels of protein markers associated with cytotoxic responses. For example, PAI-1, MAPK phosphatase and Notch-3 levels associated with cytotoxic responses to mitotic and proteasome inhibitors, suggesting that these might serve as markers of response also in clinical settings. Furthermore, the cytotoxicity readout highlighted selective synergistic and synthetic lethal drug combinations that were missed by the cell viability readouts. For instance, the MEK inhibitor trametinib synergized with PARP inhibitors. Similarly, combination of two non-cytotoxic compounds, the rapamycin analog everolimus and an ATP-competitive mTOR inhibitor dactolisib, showed synthetic lethality in several mTOR-addicted cell lines. Conclusions Taken together, by studying the combination of cytotoxic and cytostatic drug responses, we identified a deeper spectrum of cellular responses both to single agents and combinations that may be highly relevant for identifying precision medicine approaches in TNBC as well as in other types of cancers. Electronic supplementary material The online version of this article (doi:10.1186/s12943-016-0517-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Prson Gautam
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Leena Karhinen
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Agnieszka Szwajda
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Sawan Kumar Jha
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Bhagwan Yadav
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Tero Aittokallio
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Krister Wennerberg
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland.
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