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Manrique-Castano D, Bhaskar D, ElAli A. Dissecting glial scar formation by spatial point pattern and topological data analysis. Sci Rep 2024; 14:19035. [PMID: 39152163 PMCID: PMC11329771 DOI: 10.1038/s41598-024-69426-z] [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: 11/17/2023] [Accepted: 08/05/2024] [Indexed: 08/19/2024] Open
Abstract
Glial scar formation represents a fundamental response to central nervous system (CNS) injuries. It is mainly characterized by a well-defined spatial rearrangement of reactive astrocytes and microglia. The mechanisms underlying glial scar formation have been extensively studied, yet quantitative descriptors of the spatial arrangement of reactive glial cells remain limited. Here, we present a novel approach using point pattern analysis (PPA) and topological data analysis (TDA) to quantify spatial patterns of reactive glial cells after experimental ischemic stroke in mice. We provide open and reproducible tools using R and Julia to quantify spatial intensity, cell covariance and conditional distribution, cell-to-cell interactions, and short/long-scale arrangement, which collectively disentangle the arrangement patterns of the glial scar. This approach unravels a substantial divergence in the distribution of GFAP+ and IBA1+ cells after injury that conventional analysis methods cannot fully characterize. PPA and TDA are valuable tools for studying the complex spatial arrangement of reactive glia and other nervous cells following CNS injuries and have potential applications for evaluating glial-targeted restorative therapies.
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Affiliation(s)
- Daniel Manrique-Castano
- Neuroscience Axis, Research Center of CHU de Québec-Université Laval, Quebec City, QC, Canada.
- Department of Psychiatry and Neuroscience, Faculty of Medicine, Université Laval, Quebec City, QC, Canada.
| | | | - Ayman ElAli
- Neuroscience Axis, Research Center of CHU de Québec-Université Laval, Quebec City, QC, Canada.
- Department of Psychiatry and Neuroscience, Faculty of Medicine, Université Laval, Quebec City, QC, Canada.
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Yang H, Meyer F, Huang S, Yang L, Lungu C, Olayioye MA, Buehler MJ, Guo M. Learning Dynamics from Multicellular Graphs with Deep Neural Networks. ARXIV 2024:arXiv:2401.12196v2. [PMID: 38344226 PMCID: PMC10854275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Multicellular self-assembly into functional structures is a dynamic process that is critical in the development and diseases, including embryo development, organ formation, tumor invasion, and others. Being able to infer collective cell migratory dynamics from their static configuration is valuable for both understanding and predicting these complex processes. However, the identification of structural features that can indicate multicellular motion has been difficult, and existing metrics largely rely on physical instincts. Here we show that using a graph neural network (GNN), the motion of multicellular collectives can be inferred from a static snapshot of cell positions, in both experimental and synthetic datasets.
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Affiliation(s)
- Haiqian Yang
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA
| | - Florian Meyer
- Institute of Cell Biology and Immunology, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Shaoxun Huang
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA
| | - Liu Yang
- Department of Computer Sciences, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Cristiana Lungu
- Institute of Cell Biology and Immunology, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Monilola A. Olayioye
- Institute of Cell Biology and Immunology, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Markus J. Buehler
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA
- Center for Computational Science and Engineering, Schwarzman College of Computing, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA
| | - Ming Guo
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA
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Bhaskar D, Zhang WY, Volkening A, Sandstede B, Wong IY. Topological data analysis of spatial patterning in heterogeneous cell populations: clustering and sorting with varying cell-cell adhesion. NPJ Syst Biol Appl 2023; 9:43. [PMID: 37709793 PMCID: PMC10502054 DOI: 10.1038/s41540-023-00302-8] [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: 01/17/2023] [Accepted: 08/14/2023] [Indexed: 09/16/2023] Open
Abstract
Different cell types aggregate and sort into hierarchical architectures during the formation of animal tissues. The resulting spatial organization depends (in part) on the strength of adhesion of one cell type to itself relative to other cell types. However, automated and unsupervised classification of these multicellular spatial patterns remains challenging, particularly given their structural diversity and biological variability. Recent developments based on topological data analysis are intriguing to reveal similarities in tissue architecture, but these methods remain computationally expensive. In this article, we show that multicellular patterns organized from two interacting cell types can be efficiently represented through persistence images. Our optimized combination of dimensionality reduction via autoencoders, combined with hierarchical clustering, achieved high classification accuracy for simulations with constant cell numbers. We further demonstrate that persistence images can be normalized to improve classification for simulations with varying cell numbers due to proliferation. Finally, we systematically consider the importance of incorporating different topological features as well as information about each cell type to improve classification accuracy. We envision that topological machine learning based on persistence images will enable versatile and robust classification of complex tissue architectures that occur in development and disease.
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Affiliation(s)
- Dhananjay Bhaskar
- School of Engineering, Brown University, Providence, RI, USA
- Center for Biomedical Engineering, Brown University, Providence, RI, USA
- Data Science Institute, Brown University, Providence, RI, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - William Y Zhang
- Data Science Institute, Brown University, Providence, RI, USA
- Division of Applied Mathematics, Brown University, Providence, RI, USA
- Operations Research Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Björn Sandstede
- Data Science Institute, Brown University, Providence, RI, USA
- Division of Applied Mathematics, Brown University, Providence, RI, USA
| | - Ian Y Wong
- School of Engineering, Brown University, Providence, RI, USA.
- Center for Biomedical Engineering, Brown University, Providence, RI, USA.
- Data Science Institute, Brown University, Providence, RI, USA.
- Legorreta Cancer Center, Brown University, Providence, RI, USA.
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Liu CY, Zhang YX, I L. Two-Stage Structural and Slowing-Down Percolation Transitions in the Densifying Cancer Cell Monolayer. PHYSICAL REVIEW LETTERS 2022; 129:148102. [PMID: 36240397 DOI: 10.1103/physrevlett.129.148102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
We experimentally demonstrate the two-stage structural and slowing-down percolating transitions, followed by the confluent transition in the densifying cancer cell monolayers from the dilute state, and investigate their impacts on collective cell dynamics. It is found that cells aggregate into clusters at low cell density. With increasing cell number density, the structural percolation through the formation of a large cell cluster percolating through the space precedes the dynamical percolation transition of forming a percolating cluster of slow cell elements. Both percolating transitions exhibit scale-free scaling behaviors of cluster size distributions and fractal structures, similar to those of the universality class of 2D nonequilibrium systems governed by percolation theory. Dynamically, at low cell density, cell aggregation enhances cooperative motion. The structural percolation leads to slower motion, especially with stronger suppression for the high-frequency modes in the turbulent-like velocity power spectra. The following slowing-down percolation associated with the onset of cell crowding in regions occupied by cells further enhances dynamical slowing-down, and suppresses the increasing trend of dynamical heterogeneity and the steepening of the power spectrum of motion, until their reversions after the confluent transition.
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Affiliation(s)
- Chun-Yu Liu
- Department of Physics and Center for Complex Systems, National Central University, Jhongli, Taiwan 32001, Republic of China
| | - Yun-Xuan Zhang
- Department of Physics and Center for Complex Systems, National Central University, Jhongli, Taiwan 32001, Republic of China
| | - Lin I
- Department of Physics and Center for Complex Systems, National Central University, Jhongli, Taiwan 32001, Republic of China
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