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Shioka I, Morita R, Yagasaki R, Wuergezhen D, Yamashita T, Fujiwara H, Okuda S. Ex vivo SIM-AFM measurements reveal the spatial correlation of stiffness and molecular distributions in 3D living tissue. Acta Biomater 2024:S1742-7061(24)00539-7. [PMID: 39379233 DOI: 10.1016/j.actbio.2024.09.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 08/23/2024] [Accepted: 09/13/2024] [Indexed: 10/10/2024]
Abstract
Living tissues each exhibit a distinct stiffness, which provides cells with key environmental cues that regulate their behaviors. Despite this significance, our understanding of the spatiotemporal dynamics and the biological roles of stiffness in three-dimensional tissues is currently limited due to a lack of appropriate measurement techniques. To address this issue, we propose a new method combining upright structured illumination microscopy (USIM) and atomic force microscopy (AFM) to obtain precisely coordinated stiffness maps and biomolecular fluorescence images of thick living tissue slices. Using mouse embryonic and adult skin as a representative tissue with mechanically heterogeneous structures inside, we validate the measurement principle of USIM-AFM. Live measurement of tissue stiffness distributions revealed the highly heterogeneous mechanical nature of skin, including nucleated/enucleated epithelium, mesenchyme, and hair follicle, as well as the role of collagens in maintaining its integrity. Furthermore, quantitative analysis comparing stiffness distributions in live tissue samples with those in preserved tissues, including formalin-fixed and cryopreserved tissue samples, unveiled the distinct impacts of preservation processes on tissue stiffness patterns. This series of experiments highlights the importance of live mechanical testing of tissue-scale samples to accurately capture the true spatiotemporal variations in mechanical properties. Our USIM-AFM technique provides a new methodology to reveal the dynamic nature of tissue stiffness and its correlation with biomolecular distributions in live tissues and thus could serve as a technical basis for exploring tissue-scale mechanobiology. STATEMENT OF SIGNIFICANCE: Stiffness, a simple mechanical parameter, has drawn attention in understanding the mechanobiological principles underlying the homeostasis and pathology of living tissues. To explore tissue-scale mechanobiology, we propose a technique integrating an upright structured illumination microscope and an atomic force microscope. This technique enables live measurements of stiffness distribution and fluorescent observation of thick living tissue slices. Experiments revealed the highly heterogeneous mechanical nature of mouse embryonic and adult skin in three dimensions and the previously unnoticed influences of preservation techniques on the mechanical properties of tissue at microscopic resolution. This study provides a new technical platform for live stiffness measurement and biomolecular observation of tissue-scale samples with micron-scale resolution, thus contributing to future studies of tissue- and organ-scale mechanobiology.
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Affiliation(s)
- Itsuki Shioka
- Graduate School of Frontier Science Initiative, Kanazawa University, Kanazawa 920-1192, Japan
| | - Ritsuko Morita
- Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan
| | - Rei Yagasaki
- Nano Life Science Institute, Kanazawa University, Kanazawa 920-1192, Japan
| | - Duligengaowa Wuergezhen
- Laboratory for Tissue Microenvironment, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe 650-0047, Japan; Graduate School of Medicine, Osaka University, Suita 565-0871, Japan
| | - Tadahiro Yamashita
- Department of System Design Engineering, Faculty of Science and Technology, Keio University, Yokohama 223-8522, Japan
| | - Hironobu Fujiwara
- Laboratory for Tissue Microenvironment, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe 650-0047, Japan; Graduate School of Medicine, Osaka University, Suita 565-0871, Japan
| | - Satoru Okuda
- Nano Life Science Institute, Kanazawa University, Kanazawa 920-1192, Japan; Sapiens Life Sciences, Evolution and Medicine Research Center, Kanazawa University, Kanazawa 920-8640, Japan.
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2
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Randriamanantsoa SJ, Raich MK, Saur D, Reichert M, Bausch AR. Coexisting mechanisms of luminogenesis in pancreatic cancer-derived organoids. iScience 2024; 27:110299. [PMID: 39055943 PMCID: PMC11269295 DOI: 10.1016/j.isci.2024.110299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 05/02/2024] [Accepted: 06/14/2024] [Indexed: 07/28/2024] Open
Abstract
Lumens are crucial features of the tissue architecture in both the healthy exocrine pancreas, where ducts shuttle enzymes from the acini to the intestine, and in the precancerous lesions of the highly lethal pancreatic ductal adenocarcinoma (PDAC), similarly displaying lumens that can further develop into cyst-like structures. Branched pancreatic-cancer derived organoids capture key architectural features of both the healthy and diseased pancreas, including lumens. However, their transition from a solid mass of cells to a hollow tissue remains insufficiently explored. Here, we show that organoids display two orthogonal but complementary lumen formation mechanisms: one relying on fluid intake for multiple microlumen nucleation, swelling and fusion, and the other involving the death of a central cell population, thereby hollowing out cavities. These results shed further light on the processes of luminogenesis, deepening our understanding of the early formation of PDAC precancerous lesions, including cystic neoplasia.
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Affiliation(s)
- Samuel J. Randriamanantsoa
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Chair for Cellular Biophysics E27, 85748 Garching, Germany
- Technical University of Munich, Center for Functional Protein Assemblies (CPA), 85748 Garching, Germany
- Technical University of Munich, Center for Organoid Systems and Tissue Engineering (COS), 85748 Garching, Germany
| | - Marion K. Raich
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Chair for Cellular Biophysics E27, 85748 Garching, Germany
- Technical University of Munich, Center for Functional Protein Assemblies (CPA), 85748 Garching, Germany
- Technical University of Munich, Center for Organoid Systems and Tissue Engineering (COS), 85748 Garching, Germany
| | - Dieter Saur
- Technical University of Munich, School of Medicine, Klinikum rechts der Isar, Medical Clinic and Polyclinic II, 81675 Munich, Germany
- German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Partner site Munich, 69120 Heidelberg, Germany
| | - Maximilian Reichert
- Technical University of Munich, Center for Functional Protein Assemblies (CPA), 85748 Garching, Germany
- Technical University of Munich, Center for Organoid Systems and Tissue Engineering (COS), 85748 Garching, Germany
- Technical University of Munich, School of Medicine, Klinikum rechts der Isar, Medical Clinic and Polyclinic II, 81675 Munich, Germany
- German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Partner site Munich, 69120 Heidelberg, Germany
- Technical University of Munich, Klinikum rechts der Isar, Medical Clinic and Polyclinic II, Translational Pancreatic Cancer Research Center, 81675 Munich, Germany
| | - Andreas R. Bausch
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Chair for Cellular Biophysics E27, 85748 Garching, Germany
- Technical University of Munich, Center for Functional Protein Assemblies (CPA), 85748 Garching, Germany
- Technical University of Munich, Center for Organoid Systems and Tissue Engineering (COS), 85748 Garching, Germany
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3
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Norfleet DA, Melendez AJ, Alting C, Kannan S, Nikitina AA, Caldeira Botelho R, Yang B, Kemp ML. Identification of Distinct, Quantitative Pattern Classes from Emergent Tissue-Scale hiPSC Bioelectric Properties. Cells 2024; 13:1136. [PMID: 38994988 PMCID: PMC11240333 DOI: 10.3390/cells13131136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 06/17/2024] [Accepted: 06/20/2024] [Indexed: 07/13/2024] Open
Abstract
Bioelectric signals possess the ability to robustly control and manipulate patterning during embryogenesis and tissue-level regeneration. Endogenous local and global electric fields function as a spatial 'pre-pattern', controlling cell fates and tissue-scale anatomical boundaries; however, the mechanisms facilitating these robust multiscale outcomes are poorly characterized. Computational modeling addresses the need to predict in vitro patterning behavior and further elucidate the roles of cellular bioelectric signaling components in patterning outcomes. Here, we modified a previously designed image pattern recognition algorithm to distinguish unique spatial features of simulated non-excitable bioelectric patterns under distinct cell culture conditions. This algorithm was applied to comparisons between simulated patterns and experimental microscopy images of membrane potential (Vmem) across cultured human iPSC colonies. Furthermore, we extended the prediction to a novel co-culture condition in which cell sub-populations possessing different ionic fluxes were simulated; the defining spatial features were recapitulated in vitro with genetically modified colonies. These results collectively inform strategies for modeling multiscale spatial characteristics that emerge in multicellular systems, characterizing the molecular contributions to heterogeneity of membrane potential in non-excitable cells, and enabling downstream engineered bioelectrical tissue design.
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Affiliation(s)
- Dennis Andre Norfleet
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 950 Atlantic Dr. NW, Atlanta, GA 30332, USA
| | - Anja J Melendez
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 950 Atlantic Dr. NW, Atlanta, GA 30332, USA
| | - Caroline Alting
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 950 Atlantic Dr. NW, Atlanta, GA 30332, USA
| | - Siya Kannan
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 950 Atlantic Dr. NW, Atlanta, GA 30332, USA
| | - Arina A Nikitina
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA 931016, USA
| | - Raquel Caldeira Botelho
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 950 Atlantic Dr. NW, Atlanta, GA 30332, USA
| | - Bo Yang
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Melissa L Kemp
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 950 Atlantic Dr. NW, Atlanta, GA 30332, USA
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Coggan H, Weeden CE, Pearce P, Dalwadi MP, Magness A, Swanton C, Page KM. An agent-based modelling framework to study growth mechanisms in EGFR-L858R mutant cell alveolar type II cells. ROYAL SOCIETY OPEN SCIENCE 2024; 11:240413. [PMID: 39021764 PMCID: PMC11252670 DOI: 10.1098/rsos.240413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 05/21/2024] [Accepted: 06/11/2024] [Indexed: 07/20/2024]
Abstract
Mutations in the epidermal growth factor receptor (EGFR) are common in non-small cell lung cancer (NSCLC), particularly in never-smoker patients. However, these mutations are not always carcinogenic, and have recently been reported in histologically normal lung tissue from patients with and without lung cancer. To investigate the outcome of EGFR mutation in healthy lung stem cells, we grow murine alveolar type II organoids monoclonally in a three-dimensional Matrigel. Our experiments show that the EGFR-L858R mutation induces a change in organoid structure: mutated organoids display more 'budding', in comparison with non-mutant controls, which are nearly spherical. We perform on-lattice computational simulations, which suggest that this can be explained by the concentration of division among a small number of cells on the surface of the mutated organoids. We are currently unable to distinguish the cell-based mechanisms that lead to this spatial heterogeneity in growth, but suggest a number of future experiments which could be used to do so. We suggest that the likelihood of L858R-fuelled tumorigenesis is affected by whether the mutation arises in a spatial environment that allows the development of these surface protrusions. These data may have implications for cancer prevention strategies and for understanding NSCLC progression.
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Affiliation(s)
- Helena Coggan
- Department of Mathematics, University College London, London, UK
| | - Clare E. Weeden
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Philip Pearce
- Department of Mathematics, University College London, London, UK
- UCL Institute for the Physics of Living Systems, London, UK
| | - Mohit P. Dalwadi
- Department of Mathematics, University College London, London, UK
- UCL Institute for the Physics of Living Systems, London, UK
| | - Alastair Magness
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Oncology, University College London Hospital, London, UK
| | - Karen M. Page
- Department of Mathematics, University College London, London, UK
- UCL Institute for the Physics of Living Systems, London, UK
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5
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Li M, Sun H, Hou Z, Hao S, Jin L, Wang B. Engineering the Physical Microenvironment into Neural Organoids for Neurogenesis and Neurodevelopment. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2306451. [PMID: 37771182 DOI: 10.1002/smll.202306451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 09/04/2023] [Indexed: 09/30/2023]
Abstract
Understanding the signals from the physical microenvironment is critical for deciphering the processes of neurogenesis and neurodevelopment. The discovery of how surrounding physical signals shape human developing neurons is hindered by the bottleneck of conventional cell culture and animal models. Notwithstanding neural organoids provide a promising platform for recapitulating human neurogenesis and neurodevelopment, building neuronal physical microenvironment that accurately mimics the native neurophysical features is largely ignored in current organoid technologies. Here, it is discussed how the physical microenvironment modulates critical events during the periods of neurogenesis and neurodevelopment, such as neural stem cell fates, neural tube closure, neuronal migration, axonal guidance, optic cup formation, and cortical folding. Although animal models are widely used to investigate the impacts of physical factors on neurodevelopment and neuropathy, the important roles of human stem cell-derived neural organoids in this field are particularly highlighted. Considering the great promise of human organoids, building neural organoid microenvironments with mechanical forces, electrophysiological microsystems, and light manipulation will help to fully understand the physical cues in neurodevelopmental processes. Neural organoids combined with cutting-edge techniques, such as advanced atomic force microscopes, microrobots, and structural color biomaterials might promote the development of neural organoid-based research and neuroscience.
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Affiliation(s)
- Minghui Li
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400045, China
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Heng Sun
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400045, China
| | - Zongkun Hou
- Key Laboratory of Infectious Immune and Antibody Engineering of Guizhou Province, Engineering Research Center of Cellular Immunotherapy of Guizhou Province, School of Biology and Engineering/School of Basic Medical Sciences, Guizhou Medical University, Guiyang, 550025, China
| | - Shilei Hao
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400045, China
| | - Liang Jin
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400045, China
| | - Bochu Wang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400045, China
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6
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Fujimura Y, Sakai I, Shioka I, Takata N, Hashimoto A, Funatomi T, Okuda S. Machine learning-based estimation of spatial gene expression pattern during ESC-derived retinal organoid development. Sci Rep 2023; 13:22781. [PMID: 38123631 PMCID: PMC10733327 DOI: 10.1038/s41598-023-49758-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023] Open
Abstract
Organoids, which can reproduce the complex tissue structures found in embryos, are revolutionizing basic research and regenerative medicine. In order to use organoids for research and medicine, it is necessary to assess the composition and arrangement of cell types within the organoid, i.e., spatial gene expression. However, current methods are invasive and require gene editing and immunostaining. In this study, we developed a non-invasive estimation method of spatial gene expression patterns using machine learning. A deep learning model with an encoder-decoder architecture was trained on paired datasets of phase-contrast and fluorescence images, and was applied to a retinal organoid derived from mouse embryonic stem cells, focusing on the master gene Rax (also called Rx), crucial for eye field development. This method successfully estimated spatially plausible fluorescent patterns with appropriate intensities, enabling the non-invasive, quantitative estimation of spatial gene expression patterns within each tissue. Thus, this method could lead to new avenues for evaluating spatial gene expression patterns across a wide range of biology and medicine fields.
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Affiliation(s)
- Yuki Fujimura
- Division of Information Science, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Itsuki Sakai
- Division of Nano Life Science, Graduate School of Frontier Science Initiative, Kanazawa University, Kakumamachi, Kanazawa, 920-1192, Japan
| | - Itsuki Shioka
- Division of Nano Life Science, Graduate School of Frontier Science Initiative, Kanazawa University, Kakumamachi, Kanazawa, 920-1192, Japan
| | - Nozomu Takata
- Center for Vascular and Developmental Biology, Feinberg Cardiovascular and Renal Research Institute, Northwestern University, Chicago, IL, 60611, USA
| | | | - Takuya Funatomi
- Division of Information Science, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan.
| | - Satoru Okuda
- Division of Nano Life Science, Graduate School of Frontier Science Initiative, Kanazawa University, Kakumamachi, Kanazawa, 920-1192, Japan.
- Nano Life Science Institute, Kanazawa University, Kakumamachi, Kanazawa, 920-1192, Japan.
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7
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Abdel Fattah AR, Grebenyuk S, de Rooij LPMH, Salmon I, Ranga A. Neuroepithelial organoid patterning is mediated by a neighborhood watch mechanism. Cell Rep 2023; 42:113334. [PMID: 38511989 DOI: 10.1016/j.celrep.2023.113334] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/29/2023] [Accepted: 10/10/2023] [Indexed: 03/22/2024] Open
Abstract
During epithelial tissue patterning, morphogens operate across multiple length scales to instruct cell identities. However, how cell fate changes are coordinated over these scales to establish spatial organization remains poorly understood. Here, we use human neural tube organoids as models of epithelial patterning and develop an in silico approach to define conditions permissive to patterning. By systematically varying morphogen position, diffusivity, and fate-inducing concentration levels, we show that cells follow a "neighborhood watch" (NW) mechanism that is deterministically dictated by initial morphogen source positions, reflecting scale-invariant in vitro phenotypes. We define how the frequency and local bias of morphogen sources stabilize pattern orientation. The model predicts enhanced patterning through floor plate inhibition, and receptor-ligand interaction analysis of single-cell RNA sequencing (scRNA-seq) data identifies wingless-related integration site (WNT) and bone morphogenic protein (BMP) as inhibition modulators, which we validate in vitro. These results suggest that developing neuroepithelia employ NW-based mechanisms to organize morphogen sources, define cellular identity, and establish patterns.
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Affiliation(s)
- Abdel Rahman Abdel Fattah
- Laboratory of Bioengineering and Morphogenesis, Biomechanics Section, Department of Mechanical Engineering, KU Leuven, Leuven, Belgium
| | - Sergei Grebenyuk
- Laboratory of Bioengineering and Morphogenesis, Biomechanics Section, Department of Mechanical Engineering, KU Leuven, Leuven, Belgium
| | - Laura P M H de Rooij
- Laboratory of Bioengineering and Morphogenesis, Biomechanics Section, Department of Mechanical Engineering, KU Leuven, Leuven, Belgium
| | - Idris Salmon
- Laboratory of Bioengineering and Morphogenesis, Biomechanics Section, Department of Mechanical Engineering, KU Leuven, Leuven, Belgium
| | - Adrian Ranga
- Laboratory of Bioengineering and Morphogenesis, Biomechanics Section, Department of Mechanical Engineering, KU Leuven, Leuven, Belgium.
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8
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Wadkin LE, Makarenko I, Parker NG, Shukurov A, Figueiredo FC, Lako M. Human Stem Cells for Ophthalmology: Recent Advances in Diagnostic Image Analysis and Computational Modelling. CURRENT STEM CELL REPORTS 2023; 9:57-66. [PMID: 38145008 PMCID: PMC10739444 DOI: 10.1007/s40778-023-00229-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2023] [Indexed: 12/26/2023]
Abstract
Purpose of Review To explore the advances and future research directions in image analysis and computational modelling of human stem cells (hSCs) for ophthalmological applications. Recent Findings hSCs hold great potential in ocular regenerative medicine due to their application in cell-based therapies and in disease modelling and drug discovery using state-of-the-art 2D and 3D organoid models. However, a deeper characterisation of their complex, multi-scale properties is required to optimise their translation to clinical practice. Image analysis combined with computational modelling is a powerful tool to explore mechanisms of hSC behaviour and aid clinical diagnosis and therapy. Summary Many computational models draw on a variety of techniques, often blending continuum and discrete approaches, and have been used to describe cell differentiation and self-organisation. Machine learning tools are having a significant impact in model development and improving image classification processes for clinical diagnosis and treatment and will be the focus of much future research.
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Affiliation(s)
- L. E. Wadkin
- School of Mathematics, Statistics and Physics, Newcastle University, Newcastle upon Tyne, UK
| | - I. Makarenko
- School of Mathematics, Statistics and Physics, Newcastle University, Newcastle upon Tyne, UK
| | - N. G. Parker
- School of Mathematics, Statistics and Physics, Newcastle University, Newcastle upon Tyne, UK
| | - A. Shukurov
- School of Mathematics, Statistics and Physics, Newcastle University, Newcastle upon Tyne, UK
| | - F. C. Figueiredo
- Department of Ophthalmology, Royal Victoria Infirmary, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - M. Lako
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
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9
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Thomas EC, Hopyan S. Shape-driven confluent rigidity transition in curved biological tissues. Biophys J 2023; 122:4264-4273. [PMID: 37803831 PMCID: PMC10645569 DOI: 10.1016/j.bpj.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 05/09/2023] [Accepted: 10/02/2023] [Indexed: 10/08/2023] Open
Abstract
Collective cell motions underlie structure formation during embryonic development. Tissues exhibit emergent multicellular characteristics such as jamming, rigidity transitions, and glassy dynamics, but there remain questions about how those tissue-scale dynamics derive from local cell-level properties. Specifically, there has been little consideration of the interplay between local tissue geometry and cellular properties influencing larger-scale tissue behaviors. Here, we consider a simple two-dimensional computational vertex model for confluent tissue monolayers, which exhibits a rigidity phase transition controlled by the shape index (ratio of perimeter to square root area) of cells, on surfaces of constant curvature. We show that the critical point for the rigidity transition is a function of curvature such that positively curved systems are likely to be in a less rigid, more fluid, phase. Likewise, negatively curved systems (saddles) are likely to be in a more rigid, less fluid, phase. A phase diagram we generate for the curvature and shape index constitutes a testable prediction from the model. The curvature dependence is interesting because it suggests a natural explanation for more dynamic tissue remodeling and facile growth in regions of higher surface curvature. Conversely, we would predict stability at the base of saddle-shaped budding structures without invoking the need for biochemical or other physical differences. This concept has potential ramifications for our understanding of morphogenesis of budding and branching structures.
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Affiliation(s)
- Evan C Thomas
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Sevan Hopyan
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada; Division of Orthopaedic Surgery, The Hospital for Sick Children and University of Toronto, Toronto, Ontario, Canada.
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10
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Masayuki O, Reymann AC. Meeting report: Third Franco-Japanese developmental biology meeting "New Frontiers in developmental biology: Celebrating the diversity of life". Genesis 2023; 61:e23527. [PMID: 37313745 DOI: 10.1002/dvg.23527] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/15/2023]
Abstract
The French and Japanese Developmental Biology Societies, teaming up with Human Frontier Science Program, were eager to meet back in person in November 2022 in the lovely city of Strasbourg. Top scientists in the developmental biology field from France and Japan, but also from United States, United Kingdom, Switzerland or Germany shared their exciting science during the 4 days of this meeting. Core fields of developmental biology such as morphogenesis, patterning, cell identity, and cell state transition, notably at the single cell level, were well represented, and a diversity of experimental models, including plants, animals, and other exotic organisms, as well as some in vitro cellular models, were covered. This event also extended the scope of classic scientific gatherings for two reasons. First the involvement of artists during the preparation of the event and on site. Second, part of the meeting was open for the general public through a series of outreach events, including a music and video presentation through projection mapping at Rohan palace, as well as public lectures.
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Affiliation(s)
- Oginuma Masayuki
- Department of Homeostatic Regulation, Division of Cellular and Molecular Biology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Anne-Cécile Reymann
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, IGBMC, Illkirch, France
- Centre National de la Recherche Scientifique, CNRS, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, INSERM, Illkirch, France
- Université de Strasbourg, Strasbourg, France
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11
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Sokolova N, Zilova L, Wittbrodt J. Unravelling the link between embryogenesis and adult stem cell potential in the ciliary marginal zone: A comparative study between mammals and teleost fish. Cells Dev 2023; 174:203848. [PMID: 37172718 DOI: 10.1016/j.cdev.2023.203848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/03/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023]
Abstract
The discovery and study of adult stem cells have revolutionized regenerative medicine by offering new opportunities for treating various medical conditions. Anamniote stem cells, which retain their full proliferative capacity and full differentiation range throughout their lifetime, harbour a greater potential compared to mammalian adult stem cells, which only exhibit limited stem cell potential. Therefore, understanding the mechanisms underlying these differences is of significant interest. In this review, we examine the similarities and differences of adult retinal stem cells in anamniotes and mammals, from their embryonic stages in the optic vesicle to their residence in the postembryonic retinal stem cell niche, the ciliary marginal zone located in the retinal periphery. In anamniotes, developing precursors of retinal stem cells are exposed to various environmental cues during their migration in the complex morphogenetic remodelling of the optic vesicle to the optic cup. In contrast, their mammalian counterparts in the retinal periphery are primarily instructed by neighbouring tissues once they are in place. We explore the distinct modes of optic cup morphogenesis in mammals and teleost fish and highlight molecular mechanisms governing morphogenesis and stem cells instruction. The review concludes with the molecular mechanisms of ciliary marginal zone formation and offers a perspective on the impact of comparative single cell transcriptomic studies to reveal the evolutionary similarities and differences.
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Affiliation(s)
- Natalia Sokolova
- Centre for Organismal Studies Heidelberg, Germany; Heidelberg Biosciences International Graduate School, Germany
| | - Lucie Zilova
- Centre for Organismal Studies Heidelberg, Germany.
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12
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Muratore IB, Garnier S. Ontogeny of collective behaviour. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220065. [PMID: 36802780 PMCID: PMC9939274 DOI: 10.1098/rstb.2022.0065] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/21/2022] [Indexed: 02/21/2023] Open
Abstract
During their lifetime, superorganisms, like unitary organisms, undergo transformations that change the machinery of their collective behaviour. Here, we suggest that these transformations are largely understudied and propose that more systematic research into the ontogeny of collective behaviours is needed if we hope to better understand the link between proximate behavioural mechanisms and the development of collective adaptive functions. In particular, certain social insects engage in self-assemblage, forming dynamic and physically connected architectures with striking similarities to developing multicellular organisms, making them good model systems for ontogenetic studies of collective behaviour. However, exhaustive time series and three-dimensional data are required to thoroughly characterize the different life stages of the collective structures and the transitions between these stages. The well-established fields of embryology and developmental biology offer practical tools and theoretical frameworks that could speed up the acquisition of new knowledge about the formation, development, maturity and dissolution of social insect self-assemblages and, by extension, other superorganismal behaviours. We hope that this review will encourage an expansion of the ontogenetic perspective in the field of collective behaviour and, in particular, in self-assemblage research, which has far-reaching applications in robotics, computer science and regenerative medicine. This article is part of a discussion meeting issue 'Collective behaviour through time'.
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Affiliation(s)
| | - Simon Garnier
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ 07102, USA
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13
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Cardozo MJ, Sánchez-Bustamante E, Bovolenta P. Optic cup morphogenesis across species and related inborn human eye defects. Development 2023; 150:dev200399. [PMID: 36714981 PMCID: PMC10110496 DOI: 10.1242/dev.200399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The vertebrate eye is shaped as a cup, a conformation that optimizes vision and is acquired early in development through a process known as optic cup morphogenesis. Imaging living, transparent teleost embryos and mammalian stem cell-derived organoids has provided insights into the rearrangements that eye progenitors undergo to adopt such a shape. Molecular and pharmacological interference with these rearrangements has further identified the underlying molecular machineries and the physical forces involved in this morphogenetic process. In this Review, we summarize the resulting scenarios and proposed models that include common and species-specific events. We further discuss how these studies and those in environmentally adapted blind species may shed light on human inborn eye malformations that result from failures in optic cup morphogenesis, including microphthalmia, anophthalmia and coloboma.
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Affiliation(s)
- Marcos J. Cardozo
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, c/ Nicolás Cabrera 1, Cantoblanco, Madrid 28049, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), c/ Nicolás Cabrera 1, Cantoblanco, Madrid 28049, Spain
| | - Elena Sánchez-Bustamante
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, c/ Nicolás Cabrera 1, Cantoblanco, Madrid 28049, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), c/ Nicolás Cabrera 1, Cantoblanco, Madrid 28049, Spain
| | - Paola Bovolenta
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, c/ Nicolás Cabrera 1, Cantoblanco, Madrid 28049, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), c/ Nicolás Cabrera 1, Cantoblanco, Madrid 28049, Spain
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14
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Thalheim T, Aust G, Galle J. Organoid Cultures In Silico: Tools or Toys? BIOENGINEERING (BASEL, SWITZERLAND) 2022; 10:bioengineering10010050. [PMID: 36671623 PMCID: PMC9854934 DOI: 10.3390/bioengineering10010050] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 01/03/2023]
Abstract
The implementation of stem-cell-based organoid culture more than ten years ago started a development that created new avenues for diagnostic analyses and regenerative medicine. In parallel, computational modelling groups realized the potential of this culture system to support their theoretical approaches to study tissues in silico. These groups developed computational organoid models (COMs) that enabled testing consistency between cell biological data and developing theories of tissue self-organization. The models supported a mechanistic understanding of organoid growth and maturation and helped linking cell mechanics and tissue shape in general. What comes next? Can we use COMs as tools to complement the equipment of our biological and medical research? While these models already support experimental design, can they also quantitatively predict tissue behavior? Here, we review the current state of the art of COMs and discuss perspectives for their application.
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Affiliation(s)
- Torsten Thalheim
- Interdisciplinary Institute for Bioinformatics (IZBI), Leipzig University, Härtelstr. 16–18, 04107 Leipzig, Germany
- Correspondence:
| | - Gabriela Aust
- Department of Surgery, Research Laboratories, Leipzig University, Liebigstraße 20, 04103 Leipzig, Germany
| | - Joerg Galle
- Interdisciplinary Institute for Bioinformatics (IZBI), Leipzig University, Härtelstr. 16–18, 04107 Leipzig, Germany
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Sullivan KM, Ko E, Kim EM, Ballance WC, Ito JD, Chalifoux M, Kim YJ, Bashir R, Kong H. Extracellular Microenvironmental Control for Organoid Assembly. TISSUE ENGINEERING. PART B, REVIEWS 2022; 28:1209-1222. [PMID: 35451330 PMCID: PMC9836674 DOI: 10.1089/ten.teb.2021.0186] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 03/04/2022] [Indexed: 01/22/2023]
Abstract
Organoids, which are multicellular clusters with similar physiological functions to living organs, have gained increasing attention in bioengineering. As organoids become more advanced, methods to form complex structures continue to develop. There is evidence that the extracellular microenvironment can regulate organoid quality. The extracellular microenvironment consists of soluble bioactive molecules, extracellular matrix, and biofluid flow. However, few efforts have been made to discuss the microenvironment optimal to engineer specific organoids. Therefore, this review article examines the extent to which engineered extracellular microenvironments regulate organoid quality. First, we summarize the natural tissue and organ's unique chemical and mechanical properties, guiding researchers to design an extracellular microenvironment used for organoid engineering. Then, we summarize how the microenvironments contribute to the formation and growth of the brain, lung, intestine, liver, retinal, and kidney organoids. The approaches to forming and evaluating the resulting organoids are also discussed in detail. Impact statement Organoids, which are multicellular clusters with similar physiological function to living organs, have been gaining increasing attention in bioengineering. As organoids become more advanced, methods to form complex structures continue to develop. This review article focuses on recent efforts to engineer the extracellular microenvironment in organoid research. We summarized the natural organ's microenvironment, which informs researchers of key factors that can influence organoid formation. Then, we summarize how these microenvironmental controls significantly contribute to the formation and growth of the corresponding brain, lung, intestine, liver, retinal, and kidney organoids. The approaches to forming and evaluating the resulting organoids are discussed in detail, including extracellular matrix choice and properties, culture methods, and the evaluation of the morphology and functionality through imaging and biochemical analysis.
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Affiliation(s)
- Kathryn M. Sullivan
- Department of Bioengineering, and University of Illinois at Urbana−Champaign, Urbana, Illinois, USA
| | - Eunkyung Ko
- Department of Bioengineering, and University of Illinois at Urbana−Champaign, Urbana, Illinois, USA
| | - Eun Mi Kim
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois, USA
| | - William C. Ballance
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois, USA
| | - John D. Ito
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois, USA
| | - Madeleine Chalifoux
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois, USA
| | - Young Jun Kim
- Environmental Safety Group, Korea Institute of Science and Technology (KIST–Europe), Saarbrucken, Germany
| | - Rashid Bashir
- Department of Bioengineering, and University of Illinois at Urbana−Champaign, Urbana, Illinois, USA
| | - Hyunjoon Kong
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois, USA
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16
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Fuji K, Tanida S, Sano M, Nonomura M, Riveline D, Honda H, Hiraiwa T. Computational approaches for simulating luminogenesis. Semin Cell Dev Biol 2022; 131:173-185. [PMID: 35773151 DOI: 10.1016/j.semcdb.2022.05.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/24/2022] [Accepted: 05/24/2022] [Indexed: 12/14/2022]
Abstract
Lumens, liquid-filled cavities surrounded by polarized tissue cells, are elementary units involved in the morphogenesis of organs. Theoretical modeling and computations, which can integrate various factors involved in biophysics of morphogenesis of cell assembly and lumens, may play significant roles to elucidate the mechanisms in formation of such complex tissue with lumens. However, up to present, it has not been documented well what computational approaches or frameworks can be applied for this purpose and how we can choose the appropriate approach for each problem. In this review, we report some typical lumen morphologies and basic mechanisms for the development of lumens, focusing on three keywords - mechanics, hydraulics and geometry - while outlining pros and cons of the current main computational strategies. We also describe brief guidance of readouts, i.e., what we should measure in experiments to make the comparison with the model's assumptions and predictions.
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Affiliation(s)
- Kana Fuji
- Universal Biology Institute, Graduate School of Science, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Sakurako Tanida
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, Japan
| | - Masaki Sano
- Institute of Natural Sciences, School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Makiko Nonomura
- Department of Mathematical Information Engineering, College of Industrial Technology, Nihon University, 1-2-1 Izumicho, Narashino-shi, Chiba 275-8575, Japan
| | - Daniel Riveline
- Laboratory of Cell Physics IGBMC, CNRS, INSERM and Université de Strasbourg, Strasbourg, France
| | - Hisao Honda
- Division of Cell Physiology, Department of Physiology and Cell Biology, Graduate School of Medicine Kobe University, Kobe, Hyogo, Japan
| | - Tetsuya Hiraiwa
- Mechanobiology Institute, Singapore, National University of Singapore, 117411, Singapore.
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17
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Diacou R, Nandigrami P, Fiser A, Liu W, Ashery-Padan R, Cvekl A. Cell fate decisions, transcription factors and signaling during early retinal development. Prog Retin Eye Res 2022; 91:101093. [PMID: 35817658 PMCID: PMC9669153 DOI: 10.1016/j.preteyeres.2022.101093] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 06/02/2022] [Accepted: 06/03/2022] [Indexed: 12/30/2022]
Abstract
The development of the vertebrate eyes is a complex process starting from anterior-posterior and dorso-ventral patterning of the anterior neural tube, resulting in the formation of the eye field. Symmetrical separation of the eye field at the anterior neural plate is followed by two symmetrical evaginations to generate a pair of optic vesicles. Next, reciprocal invagination of the optic vesicles with surface ectoderm-derived lens placodes generates double-layered optic cups. The inner and outer layers of the optic cups develop into the neural retina and retinal pigment epithelium (RPE), respectively. In vitro produced retinal tissues, called retinal organoids, are formed from human pluripotent stem cells, mimicking major steps of retinal differentiation in vivo. This review article summarizes recent progress in our understanding of early eye development, focusing on the formation the eye field, optic vesicles, and early optic cups. Recent single-cell transcriptomic studies are integrated with classical in vivo genetic and functional studies to uncover a range of cellular mechanisms underlying early eye development. The functions of signal transduction pathways and lineage-specific DNA-binding transcription factors are dissected to explain cell-specific regulatory mechanisms underlying cell fate determination during early eye development. The functions of homeodomain (HD) transcription factors Otx2, Pax6, Lhx2, Six3 and Six6, which are required for early eye development, are discussed in detail. Comprehensive understanding of the mechanisms of early eye development provides insight into the molecular and cellular basis of developmental ocular anomalies, such as optic cup coloboma. Lastly, modeling human development and inherited retinal diseases using stem cell-derived retinal organoids generates opportunities to discover novel therapies for retinal diseases.
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Affiliation(s)
- Raven Diacou
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Prithviraj Nandigrami
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Andras Fiser
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Wei Liu
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Ruth Ashery-Padan
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Ales Cvekl
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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18
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Martínez-Ara G, Taberner N, Takayama M, Sandaltzopoulou E, Villava CE, Bosch-Padrós M, Takata N, Trepat X, Eiraku M, Ebisuya M. Optogenetic control of apical constriction induces synthetic morphogenesis in mammalian tissues. Nat Commun 2022; 13:5400. [PMID: 36104355 PMCID: PMC9474505 DOI: 10.1038/s41467-022-33115-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 09/02/2022] [Indexed: 11/09/2022] Open
Abstract
The emerging field of synthetic developmental biology proposes bottom-up approaches to examine the contribution of each cellular process to complex morphogenesis. However, the shortage of tools to manipulate three-dimensional (3D) shapes of mammalian tissues hinders the progress of the field. Here we report the development of OptoShroom3, an optogenetic tool that achieves fast spatiotemporal control of apical constriction in mammalian epithelia. Activation of OptoShroom3 through illumination in an epithelial Madin-Darby Canine Kidney (MDCK) cell sheet reduces the apical surface of the stimulated cells and causes displacements in the adjacent regions. Light-induced apical constriction provokes the folding of epithelial cell colonies on soft gels. Its application to murine and human neural organoids leads to thickening of neuroepithelia, apical lumen reduction in optic vesicles, and flattening in neuroectodermal tissues. These results show that spatiotemporal control of apical constriction can trigger several types of 3D deformation depending on the initial tissue context.
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Affiliation(s)
- Guillermo Martínez-Ara
- European Molecular Biology Laboratory (EMBL) Barcelona, Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Núria Taberner
- European Molecular Biology Laboratory (EMBL) Barcelona, Dr. Aiguader 88, 08003, Barcelona, Spain
- RIKEN Center for Biosystems Dynamics Research (RIKEN BDR), 2-2-3 Minatojima-minamimachi, Chuo-ku, 650-0047, Kobe, Japan
| | - Mami Takayama
- RIKEN Center for Biosystems Dynamics Research (RIKEN BDR), 2-2-3 Minatojima-minamimachi, Chuo-ku, 650-0047, Kobe, Japan
| | | | - Casandra E Villava
- European Molecular Biology Laboratory (EMBL) Barcelona, Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Miquel Bosch-Padrós
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
| | - Nozomu Takata
- RIKEN Center for Biosystems Dynamics Research (RIKEN BDR), 2-2-3 Minatojima-minamimachi, Chuo-ku, 650-0047, Kobe, Japan
| | - Xavier Trepat
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
- Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Mototsugu Eiraku
- RIKEN Center for Biosystems Dynamics Research (RIKEN BDR), 2-2-3 Minatojima-minamimachi, Chuo-ku, 650-0047, Kobe, Japan
| | - Miki Ebisuya
- European Molecular Biology Laboratory (EMBL) Barcelona, Dr. Aiguader 88, 08003, Barcelona, Spain.
- RIKEN Center for Biosystems Dynamics Research (RIKEN BDR), 2-2-3 Minatojima-minamimachi, Chuo-ku, 650-0047, Kobe, Japan.
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19
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Grigoryan EN. Self-Organization of the Retina during Eye Development, Retinal Regeneration In Vivo, and in Retinal 3D Organoids In Vitro. Biomedicines 2022; 10:1458. [PMID: 35740479 PMCID: PMC9221005 DOI: 10.3390/biomedicines10061458] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/16/2022] [Accepted: 06/18/2022] [Indexed: 11/23/2022] Open
Abstract
Self-organization is a process that ensures histogenesis of the eye retina. This highly intricate phenomenon is not sufficiently studied due to its biological complexity and genetic heterogeneity. The review aims to summarize the existing central theories and ideas for a better understanding of retinal self-organization, as well as to address various practical problems of retinal biomedicine. The phenomenon of self-organization is discussed in the spatiotemporal context and illustrated by key findings during vertebrate retina development in vivo and retinal regeneration in amphibians in situ. Described also are histotypic 3D structures obtained from the disaggregated retinal progenitor cells of birds and retinal 3D organoids derived from the mouse and human pluripotent stem cells. The review highlights integral parts of retinal development in these conditions. On the cellular level, these include competence, differentiation, proliferation, apoptosis, cooperative movements, and migration. On the physical level, the focus is on the mechanical properties of cell- and cell layer-derived forces and on the molecular level on factors responsible for gene regulation, such as transcription factors, signaling molecules, and epigenetic changes. Finally, the self-organization phenomenon is discussed as a basis for the production of retinal organoids, a promising model for a wide range of basic scientific and medical applications.
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Affiliation(s)
- Eleonora N Grigoryan
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia
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20
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Mao S, Miao A, Cui Y, Lu J, Pan J, Wang Y, Hong Y, Luo Y. Proteomic Analysis of Retinal Conditioned Medium: The Effect on Early Differentiation of Embyonic Stem Cells into Retina. Stem Cells Dev 2022; 31:730-740. [PMID: 35652355 DOI: 10.1089/scd.2022.0067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Stem cell replacement therapy has emerged as one of the most promising treatment options for retinal degenerative diseases, which are the main causes of irreversible vision loss. Three-dimensional (3D) retinal organoid culture is a cutting-edge technology for differentiating embryonic stem cells into retinal cells by forming a laminated retinal structure. However, 3D culture systems have strict requirements with respect to the experimental environment and culture technologies. Our study aimed to investigate the effect of retinal conditioned medium (RCM) at different developmental stages on the early differentiation of embryonic stem cells into retina in a 3D culture system. Here, we added RCM to the 3D culture system and found it could promote the differentiation of mouse embryonic stem cells (mESCs) into neuroretina. We further explored the possible mechanisms of RCM that regulate differentiation through proteomic analysis. RCM at different time points disclosed different protein profiles. Proteins which improved energy metabolism of mESCs might help improve the viability of embryonic bodies (EBs). We then screened out Snap25, Cntn1, Negr1, Dpysl2, Dpysl3, and Crmp1 as candidate proteins that might play roles in the differentiation and neurogenesis processes of mESCs, hoping to provide a basis for optimizing a retinal differentiation protocol from embryonic stem cells.
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Affiliation(s)
- Shudi Mao
- Sun Yat-Sen University Zhongshan Ophthalmic Center, 194038, Guangzhou, Guangdong, China;
| | - Aiwen Miao
- Sun Yat-Sen University Zhongshan Ophthalmic Center, 194038, Guangzhou, Guangdong, China;
| | - Yamei Cui
- Sun Yat-Sen University Zhongshan Ophthalmic Center, 194038, Guangzhou, Guangdong, China;
| | - Jing Lu
- Sun Yat-Sen University Zhongshan Ophthalmic Center, 194038, Guangzhou, Guangdong, China;
| | - Jianying Pan
- Sun Yat-Sen University Zhongshan Ophthalmic Center, 194038, Guangzhou, Guangdong, China;
| | - Yishen Wang
- Sun Yat-Sen University Zhongshan Ophthalmic Center, 194038, Guangzhou, Guangdong, China;
| | - Yiwen Hong
- Sun Yat-Sen University Zhongshan Ophthalmic Center, 194038, Guangzhou, Guangdong, China;
| | - Yan Luo
- Sun Yat-Sen University Zhongshan Ophthalmic Center, 194038, Guangzhou, Guangdong, China;
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21
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Abstract
Embryoids and organoids hold great promise for human biology and medicine. Herein, we discuss conceptual and technological frameworks useful for developing high-fidelity embryoids and organoids that display tissue- and organ-level phenotypes and functions, which are critically needed for decoding developmental programs and improving translational applications. Through dissecting the layers of inputs controlling mammalian embryogenesis, we review recent progress in reconstructing multiscale structural orders in embryoids and organoids. Bioengineering tools useful for multiscale, multimodal structural engineering of tissue- and organ-level cellular organization and microenvironment are also discussed to present integrative, bioengineering-directed approaches to achieve next-generation, high-fidelity embryoids and organoids.
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Affiliation(s)
- Yue Shao
- Institute of Biomechanics and Medical Engineering, Department of Engineering Mechanics, Tsinghua University, Beijing 100084, China; State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China.
| | - Jianping Fu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; Department of Cell & Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
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22
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Abstract
Embryonic cells grow in environments that provide a plethora of physical cues, including mechanical forces that shape the development of the entire embryo. Despite their prevalence, the role of these forces in embryonic development and their integration with chemical signals have been mostly neglected, and scrutiny in modern molecular embryology tilted, instead, towards the dissection of molecular pathways involved in cell fate determination and patterning. It is now possible to investigate how mechanical signals induce downstream genetic regulatory networks to regulate key developmental processes in the embryo. Here, we review the insights into mechanical control of early vertebrate development, including the role of forces in tissue patterning and embryonic axis formation. We also highlight recent in vitro approaches using individual embryonic stem cells and self-organizing multicellular models of human embryos, which have been instrumental in expanding our understanding of how mechanics tune cell fate and cellular rearrangements during human embryonic development.
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23
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Salbaum KA, Shelton ER, Serwane F. Retina organoids: Window into the biophysics of neuronal systems. BIOPHYSICS REVIEWS 2022; 3:011302. [PMID: 38505227 PMCID: PMC10903499 DOI: 10.1063/5.0077014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/16/2021] [Indexed: 03/21/2024]
Abstract
With a kind of magnetism, the human retina draws the eye of neuroscientist and physicist alike. It is attractive as a self-organizing system, which forms as a part of the central nervous system via biochemical and mechanical cues. The retina is also intriguing as an electro-optical device, converting photons into voltages to perform on-the-fly filtering before the signals are sent to our brain. Here, we consider how the advent of stem cell derived in vitro analogs of the retina, termed retina organoids, opens up an exploration of the interplay between optics, electrics, and mechanics in a complex neuronal network, all in a Petri dish. This review presents state-of-the-art retina organoid protocols by emphasizing links to the biochemical and mechanical signals of in vivo retinogenesis. Electrophysiological recording of active signal processing becomes possible as retina organoids generate light sensitive and synaptically connected photoreceptors. Experimental biophysical tools provide data to steer the development of mathematical models operating at different levels of coarse-graining. In concert, they provide a means to study how mechanical factors guide retina self-assembly. In turn, this understanding informs the engineering of mechanical signals required to tailor the growth of neuronal network morphology. Tackling the complex developmental and computational processes in the retina requires an interdisciplinary endeavor combining experiment and theory, physics, and biology. The reward is enticing: in the next few years, retina organoids could offer a glimpse inside the machinery of simultaneous cellular self-assembly and signal processing, all in an in vitro setting.
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Affiliation(s)
| | - Elijah R. Shelton
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany
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24
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Van Liedekerke P, Gannoun L, Loriot A, Johann T, Lemaigre FP, Drasdo D. Quantitative modeling identifies critical cell mechanics driving bile duct lumen formation. PLoS Comput Biol 2022; 18:e1009653. [PMID: 35180209 PMCID: PMC8856558 DOI: 10.1371/journal.pcbi.1009653] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 11/16/2021] [Indexed: 02/07/2023] Open
Abstract
Biliary ducts collect bile from liver lobules, the smallest functional and anatomical units of liver, and carry it to the gallbladder. Disruptions in this process caused by defective embryonic development, or through ductal reaction in liver disease have a major impact on life quality and survival of patients. A deep understanding of the processes underlying bile duct lumen formation is crucial to identify intervention points to avoid or treat the appearance of defective bile ducts. Several hypotheses have been proposed to characterize the biophysical mechanisms driving initial bile duct lumen formation during embryogenesis. Here, guided by the quantification of morphological features and expression of genes in bile ducts from embryonic mouse liver, we sharpened these hypotheses and collected data to develop a high resolution individual cell-based computational model that enables to test alternative hypotheses in silico. This model permits realistic simulations of tissue and cell mechanics at sub-cellular scale. Our simulations suggest that successful bile duct lumen formation requires a simultaneous contribution of directed cell division of cholangiocytes, local osmotic effects generated by salt excretion in the lumen, and temporally-controlled differentiation of hepatoblasts to cholangiocytes, with apical constriction of cholangiocytes only moderately affecting luminal size. The initial step in bile duct development is the formation of a biliary lumen, a process which involves several cellular mechanisms, such as cell division and polarization, and secretion of fluid. However, how these mechanisms are orchestrated in time and space is difficult to understand. Here, we built a computational model of biliary lumen formation which represents every cell and its function in detail. With the model we can simulate the effect of biophysical aspects that affect duct formation. We have tested the individual and combined effects of directed cell division, apical constriction, and osmotic effects on lumen expansion by varying the parameters that control their relative strength. Our simulations suggest that successful bile duct lumen formation requires the simultaneous contribution of directed cell division of cholangiocytes, local osmotic effects generated by salt excretion in the lumen, and temporally-controlled differentiation of hepatoblasts to cholangiocytes, with apical constriction of cholangiocytes only moderately affecting luminal size.
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Affiliation(s)
- Paul Van Liedekerke
- Inria Saclay Île-De-France, Palaiseau, France
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
- Inria de Paris & Sorbonne Université LJLL, Paris, France
- * E-mail: (PVL); (DD)
| | - Lila Gannoun
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Axelle Loriot
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Tim Johann
- Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, Dortmund, Germany
| | | | - Dirk Drasdo
- Inria Saclay Île-De-France, Palaiseau, France
- Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, Dortmund, Germany
- Inria de Paris & Sorbonne Université LJLL, Paris, France
- * E-mail: (PVL); (DD)
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25
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Veenvliet JV, Lenne PF, Turner DA, Nachman I, Trivedi V. Sculpting with stem cells: how models of embryo development take shape. Development 2021; 148:dev192914. [PMID: 34908102 PMCID: PMC8722391 DOI: 10.1242/dev.192914] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
During embryogenesis, organisms acquire their shape given boundary conditions that impose geometrical, mechanical and biochemical constraints. A detailed integrative understanding how these morphogenetic information modules pattern and shape the mammalian embryo is still lacking, mostly owing to the inaccessibility of the embryo in vivo for direct observation and manipulation. These impediments are circumvented by the developmental engineering of embryo-like structures (stembryos) from pluripotent stem cells that are easy to access, track, manipulate and scale. Here, we explain how unlocking distinct levels of embryo-like architecture through controlled modulations of the cellular environment enables the identification of minimal sets of mechanical and biochemical inputs necessary to pattern and shape the mammalian embryo. We detail how this can be complemented with precise measurements and manipulations of tissue biochemistry, mechanics and geometry across spatial and temporal scales to provide insights into the mechanochemical feedback loops governing embryo morphogenesis. Finally, we discuss how, even in the absence of active manipulations, stembryos display intrinsic phenotypic variability that can be leveraged to define the constraints that ensure reproducible morphogenesis in vivo.
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Affiliation(s)
- Jesse V. Veenvliet
- Stembryogenesis Lab, Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
- Cluster of Excellence Physics of Life, Technische Universität Dresden, 01307 Dresden, Germany
| | - Pierre-François Lenne
- Aix Marseille University, CNRS, IBDM, Turing Center for Living Systems, 13288, Marseille, France
| | - David A. Turner
- Institute of Life Course and Medical Sciences, William Henry Duncan Building, University of Liverpool, Liverpool, L7 8TX, UK
| | - Iftach Nachman
- School of Neurobiology, Biochemistry and Biophysics, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Vikas Trivedi
- European Molecular Biology Laboratories (EMBL), Barcelona, 08003, Spain
- EMBL Heidelberg, Developmental Biology Unit, 69117, Heidelberg, Germany
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26
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Pichaud F, Casares F. Shaping an optical dome: The size and shape of the insect compound eye. Semin Cell Dev Biol 2021; 130:37-44. [PMID: 34810110 DOI: 10.1016/j.semcdb.2021.11.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 11/02/2021] [Accepted: 11/04/2021] [Indexed: 10/19/2022]
Abstract
The insect compound eye is the most abundant eye architecture on earth. It comes in a wide variety of shapes and sizes, which are exquisitely adapted to specific ecosystems. Here, we explore the organisational principles and pathways, from molecular to tissular, that underpin the building of this organ and highlight why it is an excellent model system to investigate the relationship between genes and tissue form. The compound eye offers wide fields of view, high sensitivity in motion detection and infinite depth of field. It is made of an array of visual units called ommatidia, which are precisely tiled in 3D to shape the retinal tissue as a dome-like structure. The eye starts off as a 2D epithelium, and it acquires its 3D organisation as ommatidia get into shape. Each ommatidium is made of a complement of retinal cells, including light-detecting photoreceptors and lens-secreting cells. The lens cells generate the typical hexagonal facet lens that lies atop the photoreceptors so that the eye surface consists of a quasi-crystalline array of these hexagonal facet-lenses. This array is curved to various degree, depending on the size and shape of the eye, and on the region of the retina. This curvature sets the resolution and visual field of the eye and is determined by i) the number and size of the facet lens - large ommatidial lenses can be used to generate flat, higher resolution areas, while smaller facets allow for stronger curvature of the eye, and ii) precise control of the inter facet-lens angle, which determines the optical axis of the each ommatidium. In this review we discuss how combinatorial variation in eye primordium shape, ommatidial number, facet lens size and inter facet-lens angle underpins the wide variety of insect eye shapes, and we explore what is known about the mechanisms that might control these parameters.
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Affiliation(s)
- Franck Pichaud
- MRC Laboratory for Molecular Cell Biology (LMCB), University College London, WC1E 6BT London, United Kingdom.
| | - Fernando Casares
- CABD-Centro Andaluz de Biología del Desarrollo, CSIC-Universidad Pablo de Olavide, ES-41013 Seville, Spain.
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27
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Lee JH, Park HS, Holmes DP. Elastic Instabilities Govern the Morphogenesis of the Optic Cup. PHYSICAL REVIEW LETTERS 2021; 127:138102. [PMID: 34623834 DOI: 10.1103/physrevlett.127.138102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 08/06/2021] [Indexed: 06/13/2023]
Abstract
Because the normal operation of the eye depends on sensitive morphogenetic processes for its eventual shape, developmental flaws can lead to wide-ranging ocular defects. However, the physical processes and mechanisms governing ocular morphogenesis are not well understood. Here, using analytical theory and nonlinear shell finite-element simulations, we show, for optic vesicles experiencing matrix-constrained growth, that elastic instabilities govern the optic cup morphogenesis. By capturing the stress amplification owing to mass increase during growth, we show that the morphogenesis is driven by two elastic instabilities analogous to the snap through in spherical shells, where the second instability is sensitive to the optic cup geometry. In particular, if the optic vesicle is too slender, it will buckle and break axisymmetry, thus, preventing normal development. Our results shed light on the morphogenetic mechanisms governing the formation of a functional biological system and the role of elastic instabilities in the shape selection of soft biological structures.
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Affiliation(s)
- Jeong-Ho Lee
- Department of Mechanical Engineering, Boston University, Boston, Massachusetts 02215, USA
| | - Harold S Park
- Department of Mechanical Engineering, Boston University, Boston, Massachusetts 02215, USA
| | - Douglas P Holmes
- Department of Mechanical Engineering, Boston University, Boston, Massachusetts 02215, USA
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28
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Retinal Organoid Technology: Where Are We Now? Int J Mol Sci 2021; 22:ijms221910244. [PMID: 34638582 PMCID: PMC8549701 DOI: 10.3390/ijms221910244] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/17/2021] [Accepted: 09/20/2021] [Indexed: 12/25/2022] Open
Abstract
It is difficult to regenerate mammalian retinal cells once the adult retina is damaged, and current clinical approaches to retinal damages are very limited. The introduction of the retinal organoid technique empowers researchers to study the molecular mechanisms controlling retinal development, explore the pathogenesis of retinal diseases, develop novel treatment options, and pursue cell/tissue transplantation under a certain genetic background. Here, we revisit the historical background of retinal organoid technology, categorize current methods of organoid induction, and outline the obstacles and potential solutions to next-generation retinal organoids. Meanwhile, we recapitulate recent research progress in cell/tissue transplantation to treat retinal diseases, and discuss the pros and cons of transplanting single-cell suspension versus retinal organoid sheet for cell therapies.
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29
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Moreno-Mármol T, Ledesma-Terrón M, Tabanera N, Martin-Bermejo MJ, Cardozo MJ, Cavodeassi F, Bovolenta P. Stretching of the retinal pigment epithelium contributes to zebrafish optic cup morphogenesis. eLife 2021; 10:63396. [PMID: 34545806 PMCID: PMC8530511 DOI: 10.7554/elife.63396] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 09/20/2021] [Indexed: 12/15/2022] Open
Abstract
The vertebrate eye primordium consists of a pseudostratified neuroepithelium, the optic vesicle (OV), in which cells acquire neural retina or retinal pigment epithelium (RPE) fates. As these fates arise, the OV assumes a cup shape, influenced by mechanical forces generated within the neural retina. Whether the RPE passively adapts to retinal changes or actively contributes to OV morphogenesis remains unexplored. We generated a zebrafish Tg(E1-bhlhe40:GFP) line to track RPE morphogenesis and interrogate its participation in OV folding. We show that, in virtual absence of proliferation, RPE cells stretch and flatten, thereby matching the retinal curvature and promoting OV folding. Localized interference with the RPE cytoskeleton disrupts tissue stretching and OV folding. Thus, extreme RPE flattening and accelerated differentiation are efficient solutions adopted by fast-developing species to enable timely optic cup formation. This mechanism differs in amniotes, in which proliferation drives RPE expansion with a much-reduced need of cell flattening. Rounded eyeballs help to optimize vision – but how do they acquire their distinctive shape? In animals with backbones, including humans, the eye begins to form early in development. A single layer of embryonic tissue called the optic vesicle reorganizes itself into a two-layered structure: a thin outer layer of cells, known as the retinal pigmented epithelium (RPE for short), and a thicker inner layer called the neural retina. If this process fails, the animal may be born blind or visually impaired. How this flat two-layered structure becomes round is still being investigated. In fish, studies have shown that the inner cell layer – the neural retina – generates mechanical forces that cause the developing tissue to curve inwards to form a cup-like shape. But it was unclear whether the outer layer of cells (the RPE) also contributed to this process. Moreno-Marmol et al. were able to investigate this question by genetically modifying zebrafish to make all new RPE cells fluoresce. Following the early development of the zebrafish eye under a microscope revealed that RPE cells flattened themselves into long thin structures that stretched to cover the entire neural retina. This change was made possible by the cell’s internal skeleton reorganizing. In fact, preventing this reorganization stopped the RPE cells from flattening, and precluded the optic cup from acquiring its curved shape. The results thus confirmed a direct role for the RPE in generating curvature. The entire process did not require the RPE to produce new cells, allowing the curved shape to emerge in just a few hours. This is a major advantage for fast-developing species such as zebrafish. In species whose embryos develop more slowly, such as mice and humans, the RPE instead grows by producing additional cells – a process that takes many days. The development of the eye thus shows how various species use different evolutionary approaches to achieve a common goal.
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Affiliation(s)
- Tania Moreno-Mármol
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, c/ Nicolás Cabrera, 1, Campus de la Universidad Autónoma de Madrid, Madrid, Spain.,CIBER de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Mario Ledesma-Terrón
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, c/ Nicolás Cabrera, 1, Campus de la Universidad Autónoma de Madrid, Madrid, Spain
| | - Noemi Tabanera
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, c/ Nicolás Cabrera, 1, Campus de la Universidad Autónoma de Madrid, Madrid, Spain.,CIBER de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Maria Jesús Martin-Bermejo
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, c/ Nicolás Cabrera, 1, Campus de la Universidad Autónoma de Madrid, Madrid, Spain.,CIBER de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Marcos J Cardozo
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, c/ Nicolás Cabrera, 1, Campus de la Universidad Autónoma de Madrid, Madrid, Spain.,CIBER de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Florencia Cavodeassi
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, c/ Nicolás Cabrera, 1, Campus de la Universidad Autónoma de Madrid, Madrid, Spain.,CIBER de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Paola Bovolenta
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, c/ Nicolás Cabrera, 1, Campus de la Universidad Autónoma de Madrid, Madrid, Spain.,CIBER de Enfermedades Raras (CIBERER), Madrid, Spain
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30
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Le HQ, Hill MA, Kollak I, Keck M, Schroeder V, Wirth J, Skronska‐Wasek W, Schruf E, Strobel B, Stahl H, Herrmann FE, Campos AR, Li J, Quast K, Knebel D, Viollet C, Thomas MJ, Lamb D, Garnett JP. An EZH2-dependent transcriptional complex promotes aberrant epithelial remodelling after injury. EMBO Rep 2021; 22:e52785. [PMID: 34224201 PMCID: PMC8339687 DOI: 10.15252/embr.202152785] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 06/05/2021] [Accepted: 06/10/2021] [Indexed: 12/12/2022] Open
Abstract
Unveiling the molecular mechanisms of tissue remodelling following injury is imperative to elucidate its regenerative capacity and aberrant repair in disease. Using different omics approaches, we identified enhancer of zester homolog 2 (EZH2) as a key regulator of fibrosis in injured lung epithelium. Epithelial injury drives an enrichment of nuclear transforming growth factor-β-activated kinase 1 (TAK1) that mediates EZH2 phosphorylation to facilitate its liberation from polycomb repressive complex 2 (PRC2). This process results in the establishment of a transcriptional complex of EZH2, RNA-polymerase II (POL2) and nuclear actin, which orchestrates aberrant epithelial repair programmes. The liberation of EZH2 from PRC2 is accompanied by an EZH2-EZH1 switch to preserve H3K27me3 deposition at non-target genes. Loss of epithelial TAK1, EZH2 or blocking nuclear actin influx attenuates the fibrotic cascade and restores respiratory homeostasis. Accordingly, EZH2 inhibition significantly improves outcomes in a pulmonary fibrosis mouse model. Our results reveal an important non-canonical function of EZH2, paving the way for new therapeutic interventions in fibrotic lung diseases.
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Affiliation(s)
- Huy Q Le
- Lung Repair & Regeneration DepartmentBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
| | - Matthew A Hill
- Lung Repair & Regeneration DepartmentBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
- University of BathBathUK
| | - Ines Kollak
- Lung Repair & Regeneration DepartmentBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
| | - Martina Keck
- Lung Repair & Regeneration DepartmentBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
| | - Victoria Schroeder
- Lung Repair & Regeneration DepartmentBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
| | - Johannes Wirth
- Lung Repair & Regeneration DepartmentBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
| | - Wioletta Skronska‐Wasek
- Lung Repair & Regeneration DepartmentBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
| | - Eva Schruf
- Lung Repair & Regeneration DepartmentBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
| | - Benjamin Strobel
- Drug Discovery SciencesBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
| | - Heiko Stahl
- Lung Repair & Regeneration DepartmentBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
| | - Franziska E Herrmann
- Lung Repair & Regeneration DepartmentBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
| | | | - Jun Li
- Immunology and Respiratory Disease Research DepartmentBoehringer Ingelheim Pharmaceuticals, IncRidgefieldCTUSA
| | - Karsten Quast
- Global Computational Biology and Digital SciencesBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
| | - Dagmar Knebel
- Global Computational Biology and Digital SciencesBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
| | - Coralie Viollet
- Global Computational Biology and Digital SciencesBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
| | - Matthew J Thomas
- Lung Repair & Regeneration DepartmentBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
- University of BathBathUK
| | - David Lamb
- Lung Repair & Regeneration DepartmentBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
| | - James P Garnett
- Lung Repair & Regeneration DepartmentBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
- Translational and Clinical Research InstituteNewcastle UniversityNewcastleUK
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31
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Kihara T, Matsumoto T, Nakahashi Y, Tachibana K. Mechanical stiffness softening and cell adhesion are coordinately regulated by ERM dephosphorylation in KG-1 cells. Hum Cell 2021; 34:1709-1716. [PMID: 34312810 DOI: 10.1007/s13577-021-00584-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 07/23/2021] [Indexed: 11/28/2022]
Abstract
Mechanical stiffness is closely related to cell adhesion and rounding in some cells. In leukocytes, dephosphorylation of ezrin/radixin/moesin (ERM) proteins is linked to cell adhesion events. To elucidate the relationship between surface stiffness, cell adhesion, and ERM dephosphorylation in leukocytes, we examined the relationship in the myelogenous leukemia line, KG-1, by treatment with modulation drugs. KG-1 cells have ring-shaped cortical actin with microvilli as the only F-actin cytoskeleton, and the actin structure constructs the mechanical stiffness of the cells. Phorbol 12-myristate 13-acetate and staurosporine, which induced cell adhesion to fibronectin surface and ERM dephosphorylation, caused a decrease in surface stiffness in KG-1 cells. Calyculin A, which inhibited ERM dephosphorylation and had no effect on cell adhesion, did not affect surface stiffness. To clarify whether decreasing cell surface stiffness and inducing cell adhesion are equivalent, we examined KG-1 cell adhesion by treatment with actin-attenuated cell softening reagents. Cytochalasin D clearly diminished cell adhesion, and high concentrations of Y27632 slightly induced cell adhesion. Only Y27632 slightly decreased ERM phosphorylation in KG-1 cells. Thus, decreasing cell surface stiffness and inducing cell adhesion are not equivalent, but these phenomena are coordinately regulated by ERM dephosphorylation in KG-1 cells.
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Affiliation(s)
- Takanori Kihara
- Department of Life and Environment Engineering, Faculty of Environmental Engineering, The University of Kitakyushu, 1-1 Hibikino, Wakamatsu, Kitakyushu, Fukuoka, 808-0135, Japan.
| | - Teru Matsumoto
- Department of Life and Environment Engineering, Faculty of Environmental Engineering, The University of Kitakyushu, 1-1 Hibikino, Wakamatsu, Kitakyushu, Fukuoka, 808-0135, Japan
| | - Yoshihito Nakahashi
- Department of Life and Environment Engineering, Faculty of Environmental Engineering, The University of Kitakyushu, 1-1 Hibikino, Wakamatsu, Kitakyushu, Fukuoka, 808-0135, Japan
| | - Kouichi Tachibana
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan.,Department of Hematology and Oncology, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
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32
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Ogoke O, Yousef O, Ott C, Kalinousky A, Lin W, Shamul C, Ross S, Parashurama N. Modeling Liver Organogenesis by Recreating Three-Dimensional Collective Cell Migration: A Role for TGFβ Pathway. Front Bioeng Biotechnol 2021; 9:621286. [PMID: 34211963 PMCID: PMC8239196 DOI: 10.3389/fbioe.2021.621286] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 04/21/2021] [Indexed: 12/29/2022] Open
Abstract
Three-dimensional (3D) collective cell migration (CCM) is critical for improving liver cell therapies, eliciting mechanisms of liver disease, and modeling human liver development and organogenesis. Mechanisms of CCM differ in 2D vs. 3D systems, and existing models are limited to 2D or transwell-based systems, suggesting there is a need for improved 3D models of CCM. To recreate liver 3D CCM, we engineered in vitro 3D models based upon a morphogenetic transition that occurs during liver organogenesis, which occurs rapidly between E8.5 and E9.5 (mouse). During this morphogenetic transition, 3D CCM exhibits co-migration (multiple cell types), thick-strand interactions with surrounding septum transversum mesenchyme (STM), branching morphogenesis, and 3D interstitial migration. Here, we engineer several 3D in vitro culture systems, each of which mimics one of these processes in vitro. In mixed spheroids bearing both liver cells and uniquely MRC-5 (fetal lung) fibroblasts, we observed evidence of co-migration, and a significant increase in length and number of liver spheroid protrusions, which was highly sensitive to transforming growth factor beta 1 (TGFβ1) stimulation. In MRC-5-conditioned medium (M-CM) experiments, we observed dose-dependent branching morphogenesis associated with an upregulation of Twist1, which was inhibited by a broad TGFβ inhibitor. In models in which liver spheroids and MRC-5 spheroids were co-cultured, we observed complex strand morphogenesis, whereby thin, linear, 3D liver cell strands attach to the MRC-5 spheroid, anchor and thicken to form permanent and thick anchoring contacts between the two spheroids. In these spheroid co-culture models, we also observed spheroid fusion and strong evidence for interstitial migration. In conclusion, we present several novel cultivation systems that recreate distinct features of liver 3D CCM. These methodologies will greatly improve our molecular, cellular, and tissue-scale understanding of liver organogenesis, liver diseases like cancer, and liver cell therapy, and will also serve as a tool to bridge conventional 2D studies and preclinical in vivo studies.
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Affiliation(s)
- Ogechi Ogoke
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, NY, United States
| | - Osama Yousef
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, NY, United States
| | - Cortney Ott
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, NY, United States
| | - Allison Kalinousky
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, NY, United States
| | - Wayne Lin
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, NY, United States
| | - Claire Shamul
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, NY, United States
| | - Shatoni Ross
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, NY, United States
| | - Natesh Parashurama
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, NY, United States.,Department of Biomedical Engineering, University at Buffalo (State University of New York), Buffalo, NY, United States.,Clinical and Translational Research Center, University at Buffalo (State University of New York), Buffalo, NY, United States
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33
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Gritti N, Oriola D, Trivedi V. Rethinking embryology in vitro: A synergy between engineering, data science and theory. Dev Biol 2021; 474:48-61. [DOI: 10.1016/j.ydbio.2020.10.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/21/2020] [Accepted: 10/26/2020] [Indexed: 02/06/2023]
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34
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The origin and the mechanism of mechanical polarity during epithelial folding. Semin Cell Dev Biol 2021; 120:94-107. [PMID: 34059419 DOI: 10.1016/j.semcdb.2021.05.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 05/20/2021] [Accepted: 05/20/2021] [Indexed: 12/13/2022]
Abstract
Epithelial tissues are sheet-like tissue structures that line the inner and outer surfaces of animal bodies and organs. Their remarkable ability to actively produce, or passively adapt to, complex surface geometries has fascinated physicists and biologists alike for centuries. The most simple and yet versatile process of epithelial deformation is epithelial folding, through which curved shapes, tissue convolutions and internal structures are produced. The advent of quantitative live imaging, combined with experimental manipulation and computational modeling, has rapidly advanced our understanding of epithelial folding. In particular, a set of mechanical principles has emerged to illustrate how forces are generated and dissipated to instigate curvature transitions in a variety of developmental contexts. Folding a tissue requires that mechanical loads or geometric changes be non-uniform. Given that polarity is the most distinct and fundamental feature of epithelia, understanding epithelial folding mechanics hinges crucially on how forces become polarized and how polarized differential deformation arises, for which I coin the term 'mechanical polarity'. In this review, five typical modules of mechanical processes are distilled from a diverse array of epithelial folding events. Their mechanical underpinnings with regard to how forces and polarity intersect are analyzed to accentuate the importance of mechanical polarity in the understanding of epithelial folding.
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35
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Actuation enhances patterning in human neural tube organoids. Nat Commun 2021; 12:3192. [PMID: 34045434 PMCID: PMC8159931 DOI: 10.1038/s41467-021-22952-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 04/03/2021] [Indexed: 12/20/2022] Open
Abstract
Tissues achieve their complex spatial organization through an interplay between gene regulatory networks, cell-cell communication, and physical interactions mediated by mechanical forces. Current strategies to generate in-vitro tissues have largely failed to implement such active, dynamically coordinated mechanical manipulations, relying instead on extracellular matrices which respond to, rather than impose mechanical forces. Here, we develop devices that enable the actuation of organoids. We show that active mechanical forces increase growth and lead to enhanced patterning in an organoid model of the neural tube derived from single human pluripotent stem cells (hPSC). Using a combination of single-cell transcriptomics and immunohistochemistry, we demonstrate that organoid mechanoregulation due to actuation operates in a temporally restricted competence window, and that organoid response to stretch is mediated extracellularly by matrix stiffness and intracellularly by cytoskeleton contractility and planar cell polarity. Exerting active mechanical forces on organoids using the approaches developed here is widely applicable and should enable the generation of more reproducible, programmable organoid shape, identity and patterns, opening avenues for the use of these tools in regenerative medicine and disease modelling applications. Mechanical forces, along with gene regulatory networks and cell-cell signalling, play an important role in the complex organization of tissues. Here the authors describe devices that actively apply mechanical force to developing neural tube, demonstrating that mechanical forces increase growth and enhance patterning.
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36
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Garreta E, Kamm RD, Chuva de Sousa Lopes SM, Lancaster MA, Weiss R, Trepat X, Hyun I, Montserrat N. Rethinking organoid technology through bioengineering. NATURE MATERIALS 2021; 20:145-155. [PMID: 33199860 DOI: 10.1038/s41563-020-00804-4] [Citation(s) in RCA: 137] [Impact Index Per Article: 45.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 08/18/2020] [Indexed: 06/11/2023]
Abstract
In recent years considerable progress has been made in the development of faithful procedures for the differentiation of human pluripotent stem cells (hPSCs). An important step in this direction has also been the derivation of organoids. This technology generally relies on traditional three-dimensional culture techniques that exploit cell-autonomous self-organization responses of hPSCs with minimal control over the external inputs supplied to the system. The convergence of stem cell biology and bioengineering offers the possibility to provide these stimuli in a controlled fashion, resulting in the development of naturally inspired approaches to overcome major limitations of this nascent technology. Based on the current developments, we emphasize the achievements and ongoing challenges of bringing together hPSC organoid differentiation, bioengineering and ethics. This Review underlines the need for providing engineering solutions to gain control of self-organization and functionality of hPSC-derived organoids. We expect that this knowledge will guide the community to generate higher-grade hPSC-derived organoids for further applications in developmental biology, drug screening, disease modelling and personalized medicine.
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Affiliation(s)
- Elena Garreta
- Pluripotency for Organ Regeneration, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- University of Barcelona, Barcelona, Spain
| | - Roger D Kamm
- Department of Biological Engineering and Department of Mechanical Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | | | | | - Ron Weiss
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Synthetic Biology Center, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Xavier Trepat
- Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Unitat de Biofísica i Bioenginyeria, Universitat de Barcelona, Barcelona, Spain
| | - Insoo Hyun
- Department of Bioethics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Center for Bioethics, Harvard Medical School, Boston, MA, USA
| | - Nuria Montserrat
- Pluripotency for Organ Regeneration, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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37
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Gómez-Gálvez P, Vicente-Munuera P, Anbari S, Buceta J, Escudero LM. The complex three-dimensional organization of epithelial tissues. Development 2021; 148:148/1/dev195669. [PMID: 33408064 DOI: 10.1242/dev.195669] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Understanding the cellular organization of tissues is key to developmental biology. In order to deal with this complex problem, researchers have taken advantage of reductionist approaches to reveal fundamental morphogenetic mechanisms and quantitative laws. For epithelia, their two-dimensional representation as polygonal tessellations has proved successful for understanding tissue organization. Yet, epithelial tissues bend and fold to shape organs in three dimensions. In this context, epithelial cells are too often simplified as prismatic blocks with a limited plasticity. However, there is increasing evidence that a realistic approach, even from a reductionist perspective, must include apico-basal intercalations (i.e. scutoidal cell shapes) for explaining epithelial organization convincingly. Here, we present an historical perspective about the tissue organization problem. Specifically, we analyze past and recent breakthroughs, and discuss how and why simplified, but realistic, in silico models require scutoidal features to address key morphogenetic events.
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Affiliation(s)
- Pedro Gómez-Gálvez
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Universidad de Sevilla, 41013 Seville, Spain.,Biomedical Network Research Centre on Neurodegenerative Diseases (CIBERNED), 28031 Madrid, Spain
| | - Pablo Vicente-Munuera
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Universidad de Sevilla, 41013 Seville, Spain.,Biomedical Network Research Centre on Neurodegenerative Diseases (CIBERNED), 28031 Madrid, Spain
| | - Samira Anbari
- Chemical and Biomolecular Engineering Department, Lehigh University, Bethlehem, PA 18018, USA
| | - Javier Buceta
- Institute for Integrative Systems Biology (I2SysBio), CSIC-UV, 46980 Paterna (Valencia), Spain
| | - Luis M Escudero
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Universidad de Sevilla, 41013 Seville, Spain .,Biomedical Network Research Centre on Neurodegenerative Diseases (CIBERNED), 28031 Madrid, Spain
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38
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Banavar SP, Trogdon M, Drawert B, Yi TM, Petzold LR, Campàs O. Coordinating cell polarization and morphogenesis through mechanical feedback. PLoS Comput Biol 2021; 17:e1007971. [PMID: 33507956 PMCID: PMC7872284 DOI: 10.1371/journal.pcbi.1007971] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 02/09/2021] [Accepted: 12/21/2020] [Indexed: 12/30/2022] Open
Abstract
Many cellular processes require cell polarization to be maintained as the cell changes shape, grows or moves. Without feedback mechanisms relaying information about cell shape to the polarity molecular machinery, the coordination between cell polarization and morphogenesis, movement or growth would not be possible. Here we theoretically and computationally study the role of a genetically-encoded mechanical feedback (in the Cell Wall Integrity pathway) as a potential coordination mechanism between cell morphogenesis and polarity during budding yeast mating projection growth. We developed a coarse-grained continuum description of the coupled dynamics of cell polarization and morphogenesis as well as 3D stochastic simulations of the molecular polarization machinery in the evolving cell shape. Both theoretical approaches show that in the absence of mechanical feedback (or in the presence of weak feedback), cell polarity cannot be maintained at the projection tip during growth, with the polarization cap wandering off the projection tip, arresting morphogenesis. In contrast, for mechanical feedback strengths above a threshold, cells can robustly maintain cell polarization at the tip and simultaneously sustain mating projection growth. These results indicate that the mechanical feedback encoded in the Cell Wall Integrity pathway can provide important positional information to the molecular machinery in the cell, thereby enabling the coordination of cell polarization and morphogenesis.
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Affiliation(s)
- Samhita P. Banavar
- Department of Physics, University of California, University of California, Santa Barbara, California, United States of America
- California NanoSystems Institute, University of California, Santa Barbara, California, United States of America
| | - Michael Trogdon
- Department of Mechanical Engineering, University of California, Santa Barbara, California, United States of America
| | - Brian Drawert
- Department of Computer Science, University of North Carolina, Asheville, North Carolina, United States of America
| | - Tau-Mu Yi
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Barbara, California, United States of America
| | - Linda R. Petzold
- Department of Mechanical Engineering, University of California, Santa Barbara, California, United States of America
- Center for Bioengineering, University of California, Santa Barbara, California, United States of America
| | - Otger Campàs
- California NanoSystems Institute, University of California, Santa Barbara, California, United States of America
- Department of Mechanical Engineering, University of California, Santa Barbara, California, United States of America
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Barbara, California, United States of America
- Center for Bioengineering, University of California, Santa Barbara, California, United States of America
- Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany
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39
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Estrada JB, Cramer HC, Scimone MT, Buyukozturk S, Franck C. Neural cell injury pathology due to high-rate mechanical loading. BRAIN MULTIPHYSICS 2021. [DOI: 10.1016/j.brain.2021.100034] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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40
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Duarte Campos DF, De Laporte L. Digitally Fabricated and Naturally Augmented In Vitro Tissues. Adv Healthc Mater 2021; 10:e2001253. [PMID: 33191651 DOI: 10.1002/adhm.202001253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/04/2020] [Indexed: 01/29/2023]
Abstract
Human in vitro tissues are extracorporeal 3D cultures of human cells embedded in biomaterials, commonly hydrogels, which recapitulate the heterogeneous, multiscale, and architectural environment of the human body. Contemporary strategies used in 3D tissue and organ engineering integrate the use of automated digital manufacturing methods, such as 3D printing, bioprinting, and biofabrication. Human tissues and organs, and their intra- and interphysiological interplay, are particularly intricate. For this reason, attentiveness is rising to intersect materials science, medicine, and biology with arts and informatics. This report presents advances in computational modeling of bioink polymerization and its compatibility with bioprinting, the use of digital design and fabrication in the development of fluidic culture devices, and the employment of generative algorithms for modeling the natural and biological augmentation of in vitro tissues. As a future direction, the use of serially linked in vitro tissues as human body-mimicking systems and their application in drug pharmacokinetics and metabolism, disease modeling, and diagnostics are discussed.
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Affiliation(s)
- Daniela F. Duarte Campos
- Department of Advanced Materials for Biomedicine Institute of Applied Medical Engineering RWTH Aachen University Aachen 52074 Germany
| | - Laura De Laporte
- Department of Advanced Materials for Biomedicine Institute of Applied Medical Engineering RWTH Aachen University Aachen 52074 Germany
- DWI—Leibniz Institute for Interactive Materials Aachen 52074 Germany
- Department of Technical and Macromolecular Chemistry RWTH Aachen University Aachen 52074 Germany
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41
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Ogoke O, Maloy M, Parashurama N. The science and engineering of stem cell-derived organoids-examples from hepatic, biliary, and pancreatic tissues. Biol Rev Camb Philos Soc 2020; 96:179-204. [PMID: 33002311 DOI: 10.1111/brv.12650] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 08/08/2020] [Accepted: 08/25/2020] [Indexed: 12/12/2022]
Abstract
The field of organoid engineering promises to revolutionize medicine with wide-ranging applications of scientific, engineering, and clinical interest, including precision and personalized medicine, gene editing, drug development, disease modelling, cellular therapy, and human development. Organoids are a three-dimensional (3D) miniature representation of a target organ, are initiated with stem/progenitor cells, and are extremely promising tools with which to model organ function. The biological basis for organoids is that they foster stem cell self-renewal, differentiation, and self-organization, recapitulating 3D tissue structure or function better than two-dimensional (2D) systems. In this review, we first discuss the importance of epithelial organs and the general properties of epithelial cells to provide a context and rationale for organoids of the liver, pancreas, and gall bladder. Next, we develop a general framework to understand self-organization, tissue hierarchy, and organoid cultivation. For each of these areas, we provide a historical context, and review a wide range of both biological and mathematical perspectives that enhance understanding of organoids. Next, we review existing techniques and progress in hepatobiliary and pancreatic organoid engineering. To do this, we review organoids from primary tissues, cell lines, and stem cells, and introduce engineering studies when applicable. We discuss non-invasive assessment of organoids, which can reveal the underlying biological mechanisms and enable improved assays for growth, metabolism, and function. Applications of organoids in cell therapy are also discussed. Taken together, we establish a broad scientific foundation for organoids and provide an in-depth review of hepatic, biliary and pancreatic organoids.
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Affiliation(s)
- Ogechi Ogoke
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, NY, U.S.A
| | - Mitchell Maloy
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, NY, U.S.A
| | - Natesh Parashurama
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, NY, U.S.A.,Clinical and Translation Research Center (CTRC), University at Buffalo (State University of New York), Buffalo, NY, U.S.A.,Department of Biomedical Engineering, University at Buffalo (State University of New York), Buffalo, NY, U.S.A
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42
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Okuda S, Fujimoto K. A Mechanical Instability in Planar Epithelial Monolayers Leads to Cell Extrusion. Biophys J 2020; 118:2549-2560. [PMID: 32333862 PMCID: PMC7231918 DOI: 10.1016/j.bpj.2020.03.028] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 03/09/2020] [Accepted: 03/11/2020] [Indexed: 12/12/2022] Open
Abstract
In cell extrusion, a cell embedded in an epithelial monolayer loses its apical or basal surface and is subsequently squeezed out of the monolayer by neighboring cells. Cell extrusions occur during apoptosis, epithelial-mesenchymal transition, or precancerous cell invasion. They play important roles in embryogenesis, homeostasis, carcinogenesis, and many other biological processes. Although many of the molecular factors involved in cell extrusion are known, little is known about the mechanical basis of cell extrusion. We used a three-dimensional (3D) vertex model to investigate the mechanical stability of cells arranged in a monolayer with 3D foam geometry. We found that when the cells composing the monolayer have homogeneous mechanical properties, cells are extruded from the monolayer when the symmetry of the 3D geometry is broken because of an increase in cell density or a decrease in the number of topological neighbors around single cells. Those results suggest that mechanical instability inherent in the 3D foam geometry of epithelial monolayers is sufficient to drive epithelial cell extrusion. In the situation in which cells in the monolayer actively generate contractile or adhesive forces under the control of intrinsic genetic programs, the forces act to break the symmetry of the monolayer, leading to cell extrusion that is directed to the apical or basal side of the monolayer by the balance of contractile and adhesive forces on the apical and basal sides. Although our analyses are based on a simple mechanical model, our results are in accordance with observations of epithelial monolayers in vivo and consistently explain cell extrusions under a wide range of physiological and pathophysiological conditions. Our results illustrate the importance of a mechanical understanding of cell extrusion and provide a basis by which to link molecular regulation to physical processes.
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Affiliation(s)
- Satoru Okuda
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-cho, Kanazawa, Japan.
| | - Koichi Fujimoto
- Department of Biological Sciences, Osaka University, Machikaneyama-cho, Toyonaka, Japan
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43
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Suzuki M, Shiroguchi K. BSJ 2019 "Single-cell PRESTO" session. Biophys Rev 2020; 12:301-302. [PMID: 32006252 PMCID: PMC7242534 DOI: 10.1007/s12551-020-00624-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 01/14/2020] [Indexed: 12/25/2022] Open
Affiliation(s)
- Madoka Suzuki
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Katsuyuki Shiroguchi
- Laboratory for Prediction of Cell Systems Dynamics, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
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44
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Nakazawa N, Kengaku M. Mechanical Regulation of Nuclear Translocation in Migratory Neurons. Front Cell Dev Biol 2020; 8:150. [PMID: 32226788 PMCID: PMC7080992 DOI: 10.3389/fcell.2020.00150] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 02/24/2020] [Indexed: 12/14/2022] Open
Abstract
Neuronal migration is a critical step during the formation of functional neural circuits in the brain. Newborn neurons need to move across long distances from the germinal zone to their individual sites of function; during their migration, they must often squeeze their large, stiff nuclei, against strong mechanical stresses, through narrow spaces in developing brain tissue. Recent studies have clarified how actomyosin and microtubule motors generate mechanical forces in specific subcellular compartments and synergistically drive nuclear translocation in neurons. On the other hand, the mechanical properties of the surrounding tissues also contribute to their function as an adhesive support for cytoskeletal force transmission, while they also serve as a physical barrier to nuclear translocation. In this review, we discuss recent studies on nuclear migration in developing neurons, from both cell and mechanobiological viewpoints.
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Affiliation(s)
- Naotaka Nakazawa
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University Institute for Advanced Study, Kyoto University, Kyoto, Japan
| | - Mineko Kengaku
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University Institute for Advanced Study, Kyoto University, Kyoto, Japan.,Graduate School of Biostudies, Kyoto University, Kyoto, Japan
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45
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Norfleet DA, Park E, Kemp ML. Computational modeling of organoid development. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2020. [DOI: 10.1016/j.cobme.2019.12.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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46
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Preconditioning the Initial State of Feeder-free Human Pluripotent Stem Cells Promotes Self-formation of Three-dimensional Retinal Tissue. Sci Rep 2019; 9:18936. [PMID: 31831759 PMCID: PMC6908610 DOI: 10.1038/s41598-019-55130-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 11/21/2019] [Indexed: 12/31/2022] Open
Abstract
A three-dimensional retinal tissue (3D-retina) is a promising graft source for retinal transplantation therapy. We previously demonstrated that embryonic stem cells (ESCs) can generate 3D-retina in vitro using a self-organizing stem cell culture technique known as SFEBq. Here we show an optimized culture method for 3D-retina generation from feeder-free human pluripotent stem cells (hPSCs). Although feeder-free hPSC-maintenance culture was suitable for cell therapy, feeder-free hPSC-derived aggregates tended to collapse during 3D-xdifferentiation culture. We found that the initial hPSC state was a key factor and that preconditioning of the hPSC state by modulating TGF-beta and Shh signaling improved self-formation of 3D-neuroepithelium. Using the preconditioning method, several feeder-free hPSC lines robustly differentiated into 3D-retina. In addition, changing preconditioning stimuli in undifferentiated hPSCs altered the proportions of neural retina and retinal pigment epithelium, important quality factors for 3D-retina. We demonstrated that the feeder-free hiPSC-derived 3D-retina differentiated into rod and cone photoreceptors in vitro and in vivo. Thus, preconditioning is a useful culture methodology for cell therapy to direct the initial hPSC state toward self-organizing 3D-neuroepithelium.
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47
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Motegi F, Plachta N, Viasnoff V. Novel approaches to link apicobasal polarity to cell fate specification. Curr Opin Cell Biol 2019; 62:78-85. [PMID: 31731147 DOI: 10.1016/j.ceb.2019.09.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/19/2019] [Accepted: 09/26/2019] [Indexed: 12/26/2022]
Abstract
Understanding the development of apicobasal polarity (ABP) is a long-standing problem in biology. The molecular components involved in the development and maintenance of APB have been largely identified and are known to have ubiquitous roles across organisms. Our knowledge of the functional consequences of ABP establishment and maintenance is far less comprehensive. Recent studies using novel experimental approaches and cellular models have revealed a growing link between ABP and the genetic program of cell lineage. This mini-review describes some of the most recent advances in this new field, highlighting examples from Caenorhabditis elegans and mouse embryos, human pluripotent stem cells, and epithelial cells. We also speculate on the most interesting and challenging avenues that can be explored.
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Affiliation(s)
- Fumio Motegi
- Department of Biological Sciences, National University of Singapore, 117583, Singapore; Mechanobiology Institute, National University of Singapore, 117 411, Singapore; Temasek Life-sciences Laboratory, 117604, Singapore; Contributed equally
| | - Nicolas Plachta
- Institute of Molecular and Cell Biology, ASTAR, Singapore; Contributed equally
| | - Virgile Viasnoff
- Department of Biological Sciences, National University of Singapore, 117583, Singapore; Mechanobiology Institute, National University of Singapore, 117 411, Singapore; CNRS, 117411, Singapore; Contributed equally.
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48
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Lenzini S, Devine D, Shin JW. Leveraging Biomaterial Mechanics to Improve Pluripotent Stem Cell Applications for Tissue Engineering. Front Bioeng Biotechnol 2019; 7:260. [PMID: 31649928 PMCID: PMC6795675 DOI: 10.3389/fbioe.2019.00260] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 09/26/2019] [Indexed: 12/31/2022] Open
Abstract
A primary goal in tissue engineering is to develop functional tissues by recapitulating salient features of complex biological systems that exhibit a diverse range of physical forces. Induced pluripotent stem cells (iPSCs) are promising autologous cell sources to execute these developmental programs and their functions; however, cells require an extracellular environment where they will sense and respond to mechanical forces. Thus, understanding the biophysical relationships between stem cells and their extracellular environments will improve the ability to design complex biological systems through tissue engineering. This article first describes how the mechanical properties of the environment are important determinants of developmental processes, and then further details how biomaterials can be designed to precisely control the mechanics of cell-matrix interactions in order to study and define their reprogramming, self-renewal, differentiation, and morphogenesis. Finally, a perspective is presented on how insights from the mechanics of cell-matrix interactions can be leveraged to control pluripotent stem cells for tissue engineering applications.
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Affiliation(s)
- Stephen Lenzini
- Department of Pharmacology, University of Illinois at Chicago, Chicago, IL, United States
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, United States
| | - Daniel Devine
- Department of Pharmacology, University of Illinois at Chicago, Chicago, IL, United States
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, United States
| | - Jae-Won Shin
- Department of Pharmacology, University of Illinois at Chicago, Chicago, IL, United States
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, United States
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49
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Montes-Olivas S, Marucci L, Homer M. Mathematical Models of Organoid Cultures. Front Genet 2019; 10:873. [PMID: 31592020 PMCID: PMC6761251 DOI: 10.3389/fgene.2019.00873] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 08/20/2019] [Indexed: 12/18/2022] Open
Abstract
Organoids are engineered three-dimensional tissue cultures derived from stem cells and capable of self-renewal and self-organization into a variety of progenitors and differentiated cell types. An organoid resembles the cellular structure of an organ and retains some of its functionality, while still being amenable to in vitro experimental study. Compared with two-dimensional cultures, the three-dimensional structure of organoids provides a more realistic environment and structural organization of in vivo organs. Similarly, organoids are better suited to reproduce signaling pathway dynamics in vitro, due to a more realistic physiological environment. As such, organoids are a valuable tool to explore the dynamics of organogenesis and offer routes to personalized preclinical trials of cancer progression, invasion, and drug response. Complementary to experiments, mathematical and computational models are valuable instruments in the description of spatiotemporal dynamics of organoids. Simulations of mathematical models allow the study of multiscale dynamics of organoids, at both the intracellular and intercellular levels. Mathematical models also enable us to understand the underlying mechanisms responsible for phenotypic variation and the response to external stimulation in a cost- and time-effective manner. Many recent studies have developed laboratory protocols to grow organoids resembling different organs such as the intestine, brain, liver, pancreas, and mammary glands. However, the development of mathematical models specific to organoids remains comparatively underdeveloped. Here, we review the mathematical and computational approaches proposed so far to describe and predict organoid dynamics, reporting the simulation frameworks used and the models’ strengths and limitations.
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Affiliation(s)
- Sandra Montes-Olivas
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom
| | - Lucia Marucci
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom.,School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom.,Bristol Centre for Synthetic Biology, University of Bristol, Bristol, United Kingdom
| | - Martin Homer
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom
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50
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Cavodeassi F, Wilson SW. Looking to the future of zebrafish as a model to understand the genetic basis of eye disease. Hum Genet 2019; 138:993-1000. [PMID: 31422478 PMCID: PMC6710215 DOI: 10.1007/s00439-019-02055-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 07/31/2019] [Indexed: 02/07/2023]
Abstract
In this brief commentary, we provide some of our thoughts and opinions on the current and future use of zebrafish to model human eye disease, dissect pathological progression and advance in our understanding of the genetic bases of microphthalmia, andophthalmia and coloboma (MAC) in humans. We provide some background on eye formation in fish and conservation and divergence across vertebrates in this process, discuss different approaches for manipulating gene function and speculate on future research areas where we think research using fish may prove to be particularly effective.
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Affiliation(s)
- Florencia Cavodeassi
- Institute of Medical and Biomedical Education, St. George's, University of London, Cranmer Terrace, London, SW17 0RE, UK.
| | - Stephen W Wilson
- Department of Cell and Developmental Biology, Biosciences, UCL, Gower St, London, WC1E 6BT, UK
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