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Jain S, Belkadi H, Michaut A, Sart S, Gros J, Genet M, Baroud CN. Using a micro-device with a deformable ceiling to probe stiffness heterogeneities within 3D cell aggregates. Biofabrication 2024; 16:035010. [PMID: 38447213 DOI: 10.1088/1758-5090/ad30c7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 03/06/2024] [Indexed: 03/08/2024]
Abstract
Recent advances in the field of mechanobiology have led to the development of methods to characterise single-cell or monolayer mechanical properties and link them to their functional behaviour. However, there remains a strong need to establish this link for three-dimensional (3D) multicellular aggregates, which better mimic tissue function. Here we present a platform to actuate and observe many such aggregates within one deformable micro-device. The platform consists of a single polydimethylsiloxane piece cast on a 3D-printed mould and bonded to a glass slide or coverslip. It consists of a chamber containing cell spheroids, which is adjacent to air cavities that are fluidically independent. Controlling the air pressure in these air cavities leads to a vertical displacement of the chamber's ceiling. The device can be used in static or dynamic modes over time scales of seconds to hours, with displacement amplitudes from a fewµm to several tens of microns. Further, we show how the compression protocols can be used to obtain measurements of stiffness heterogeneities within individual co-culture spheroids, by comparing image correlations of spheroids at different levels of compression with finite element simulations. The labelling of the cells and their cytoskeleton is combined with image correlation methods to relate the structure of the co-culture spheroid with its mechanical properties at different locations. The device is compatible with various microscopy techniques, including confocal microscopy, which can be used to observe the displacements and rearrangements of single cells and neighbourhoods within the aggregate. The complete experimental and imaging platform can now be used to provide multi-scale measurements that link single-cell behaviour with the global mechanical response of the aggregates.
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Affiliation(s)
- Shreyansh Jain
- Institut Pasteur, Université Paris Cité, Physical Microfluidics and Bioengineering, 25-28 Rue du Dr Roux, 75015 Paris, France
- Laboratoire d' Hydrodynamique (LadHyX), CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Hiba Belkadi
- Institut Pasteur, Université Paris Cité, Physical Microfluidics and Bioengineering, 25-28 Rue du Dr Roux, 75015 Paris, France
- Laboratoire d' Hydrodynamique (LadHyX), CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Arthur Michaut
- Institut Pasteur, Université Paris Cité, Dynamic Regulation of Morphogenesis, 25-28 Rue du Dr Roux, 75015 Paris, France
| | - Sébastien Sart
- Institut Pasteur, Université Paris Cité, Physical Microfluidics and Bioengineering, 25-28 Rue du Dr Roux, 75015 Paris, France
- Laboratoire d' Hydrodynamique (LadHyX), CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Jérôme Gros
- Institut Pasteur, Université Paris Cité, Dynamic Regulation of Morphogenesis, 25-28 Rue du Dr Roux, 75015 Paris, France
| | - Martin Genet
- Laboratoire de Mécanique des Solides, CNRS, École Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France
- Inria, Palaiseau, France
| | - Charles N Baroud
- Institut Pasteur, Université Paris Cité, Physical Microfluidics and Bioengineering, 25-28 Rue du Dr Roux, 75015 Paris, France
- Laboratoire d' Hydrodynamique (LadHyX), CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France
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Cumming T, Levayer R. Toward a predictive understanding of epithelial cell death. Semin Cell Dev Biol 2024; 156:44-57. [PMID: 37400292 DOI: 10.1016/j.semcdb.2023.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/15/2023] [Accepted: 06/22/2023] [Indexed: 07/05/2023]
Abstract
Epithelial cell death is highly prevalent during development and tissue homeostasis. While we have a rather good understanding of the molecular regulators of programmed cell death, especially for apoptosis, we still fail to predict when, where, how many and which specific cells will die in a tissue. This likely relies on the much more complex picture of apoptosis regulation in a tissular and epithelial context, which entails cell autonomous but also non-cell autonomous factors, diverse feedback and multiple layers of regulation of the commitment to apoptosis. In this review, we illustrate this complexity of epithelial apoptosis regulation by describing these different layers of control, all demonstrating that local cell death probability is a complex emerging feature. We first focus on non-cell autonomous factors that can locally modulate the rate of cell death, including cell competition, mechanical input and geometry as well as systemic effects. We then describe the multiple feedback mechanisms generated by cell death itself. We also outline the multiple layers of regulation of epithelial cell death, including the coordination of extrusion and regulation occurring downstream of effector caspases. Eventually, we propose a roadmap to reach a more predictive understanding of cell death regulation in an epithelial context.
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Affiliation(s)
- Tom Cumming
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université de Paris Cité, CNRS UMR 3738, 25 rue du Dr. Roux, 75015 Paris, France; Sorbonne Université, Collège Doctoral, F75005 Paris, France
| | - Romain Levayer
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université de Paris Cité, CNRS UMR 3738, 25 rue du Dr. Roux, 75015 Paris, France.
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Peixoto MM, Soares-da-Silva F, Bonnet V, Ronteix G, Santos RF, Mailhe MP, Feng X, Pereira JP, Azzoni E, Anselmi G, de Bruijn M, Baroud CN, Pinto-do-Ó P, Cumano A. Spatiotemporal dynamics of cytokines expression dictate fetal liver hematopoiesis. bioRxiv 2023:2023.08.24.554612. [PMID: 37662317 PMCID: PMC10473721 DOI: 10.1101/2023.08.24.554612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
During embryogenesis, yolk-sac and intra-embryonic-derived hematopoietic progenitors, comprising the precursors of adult hematopoietic stem cells, converge into the fetal liver. With a new staining strategy, we defined all non-hematopoietic components of the fetal liver and found that hepatoblasts are the major producers of hematopoietic growth factors. We identified mesothelial cells, a novel component of the stromal compartment, producing Kit ligand, a major hematopoietic cytokine. A high-definition imaging dataset analyzed using a deep-learning based pipeline allowed the unambiguous identification of hematopoietic and stromal populations, and enabled determining a neighboring network composition, at the single cell resolution. Throughout active hematopoiesis, progenitors preferentially associate with hepatoblasts, but not with stellate or endothelial cells. We found that, unlike yolk sac-derived progenitors, intra-embryonic progenitors respond to a chemokine gradient created by CXCL12-producing stellate cells. These results revealed that FL hematopoiesis is a spatiotemporal dynamic process, defined by an environment characterized by low cytokine concentrations.
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Fischer SC, Bassel GW, Kollmannsberger P. Tissues as networks of cells: towards generative rules of complex organ development. J R Soc Interface 2023; 20:20230115. [PMID: 37491909 PMCID: PMC10369035 DOI: 10.1098/rsif.2023.0115] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 07/05/2023] [Indexed: 07/27/2023] Open
Abstract
Network analysis is a well-known and powerful tool in molecular biology. More recently, it has been introduced in developmental biology. Tissues can be readily translated into spatial networks such that cells are represented by nodes and intercellular connections by edges. This discretization of cellular organization enables mathematical approaches rooted in network science to be applied towards the understanding of tissue structure and function. Here, we describe how such tissue abstractions can enable the principles that underpin tissue formation and function to be uncovered. We provide an introduction into biologically relevant network measures, then present an overview of different areas of developmental biology where these approaches have been applied. We then summarize the general developmental rules underpinning tissue topology generation. Finally, we discuss how generative models can help to link the developmental rule back to the tissue topologies. Our collection of results points at general mechanisms as to how local developmental rules can give rise to observed topological properties in multicellular systems.
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Affiliation(s)
- Sabine C. Fischer
- Center for Computational and Theoretical Biology, Faculty of Biology, University of Würzburg, Würzburg, Germany
| | - George W. Bassel
- School of Life Sciences, The University of Warwick, Coventry, UK
| | - Philip Kollmannsberger
- Biomedical Physics, Department of Physics, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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Lee RY, Ng CW, Rajapakse MP, Ang N, Yeong JPS, Lau MC. The promise and challenge of spatial omics in dissecting tumour microenvironment and the role of AI. Front Oncol 2023; 13:1172314. [PMID: 37197415 PMCID: PMC10183599 DOI: 10.3389/fonc.2023.1172314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/18/2023] [Indexed: 05/19/2023] Open
Abstract
Growing evidence supports the critical role of tumour microenvironment (TME) in tumour progression, metastases, and treatment response. However, the in-situ interplay among various TME components, particularly between immune and tumour cells, are largely unknown, hindering our understanding of how tumour progresses and responds to treatment. While mainstream single-cell omics techniques allow deep, single-cell phenotyping, they lack crucial spatial information for in-situ cell-cell interaction analysis. On the other hand, tissue-based approaches such as hematoxylin and eosin and chromogenic immunohistochemistry staining can preserve the spatial information of TME components but are limited by their low-content staining. High-content spatial profiling technologies, termed spatial omics, have greatly advanced in the past decades to overcome these limitations. These technologies continue to emerge to include more molecular features (RNAs and/or proteins) and to enhance spatial resolution, opening new opportunities for discovering novel biological knowledge, biomarkers, and therapeutic targets. These advancements also spur the need for novel computational methods to mine useful TME insights from the increasing data complexity confounded by high molecular features and spatial resolution. In this review, we present state-of-the-art spatial omics technologies, their applications, major strengths, and limitations as well as the role of artificial intelligence (AI) in TME studies.
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Affiliation(s)
- Ren Yuan Lee
- Singapore Thong Chai Medical Institution, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Chan Way Ng
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | | | - Nicholas Ang
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Joe Poh Sheng Yeong
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- *Correspondence: Joe Poh Sheng Yeong, ; Mai Chan Lau,
| | - Mai Chan Lau
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- *Correspondence: Joe Poh Sheng Yeong, ; Mai Chan Lau,
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