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Guan G, Chen Y, Wang H, Ouyang Q, Tang C. Characterizing Cellular Physiological States with Three-Dimensional Shape Descriptors for Cell Membranes. MEMBRANES 2024; 14:137. [PMID: 38921504 PMCID: PMC11205511 DOI: 10.3390/membranes14060137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 06/03/2024] [Accepted: 06/06/2024] [Indexed: 06/27/2024]
Abstract
The shape of a cell as defined by its membrane can be closely associated with its physiological state. For example, the irregular shapes of cancerous cells and elongated shapes of neuron cells often reflect specific functions, such as cell motility and cell communication. However, it remains unclear whether and which cell shape descriptors can characterize different cellular physiological states. In this study, 12 geometric shape descriptors for a three-dimensional (3D) object were collected from the previous literature and tested with a public dataset of ~400,000 independent 3D cell regions segmented based on fluorescent labeling of the cell membranes in Caenorhabditis elegans embryos. It is revealed that those shape descriptors can faithfully characterize cellular physiological states, including (1) cell division (cytokinesis), along with an abrupt increase in the elongation ratio; (2) a negative correlation of cell migration speed with cell sphericity; (3) cell lineage specification with symmetrically patterned cell shape changes; and (4) cell fate specification with differential gene expression and differential cell shapes. The descriptors established may be used to identify and predict the diverse physiological states in numerous cells, which could be used for not only studying developmental morphogenesis but also diagnosing human disease (e.g., the rapid detection of abnormal cells).
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Affiliation(s)
- Guoye Guan
- Center for Quantitative Biology, Peking University, Beijing 100871, China; (G.G.); (Q.O.)
| | - Yixuan Chen
- School of Physics, Peking University, Beijing 100871, China;
| | - Hongli Wang
- Center for Quantitative Biology, Peking University, Beijing 100871, China; (G.G.); (Q.O.)
- School of Physics, Peking University, Beijing 100871, China;
| | - Qi Ouyang
- Center for Quantitative Biology, Peking University, Beijing 100871, China; (G.G.); (Q.O.)
- School of Physics, Peking University, Beijing 100871, China;
- School of Physics, Zhejiang University, Hangzhou 310027, China
| | - Chao Tang
- Center for Quantitative Biology, Peking University, Beijing 100871, China; (G.G.); (Q.O.)
- School of Physics, Peking University, Beijing 100871, China;
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
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Guan G, Luo C, Tang LH, Tang C. Modulating cell proliferation by asymmetric division: A conserved pattern in the early embryogenesis of nematode species. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001006. [PMID: 38505394 PMCID: PMC10949086 DOI: 10.17912/micropub.biology.001006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/24/2023] [Accepted: 02/22/2024] [Indexed: 03/21/2024]
Abstract
In the early stage of the nematode Caenorhabditis elegans embryogenesis, the zygote divides asymmetrically into a symmetric fast lineage and an asymmetric slow lineage, producing 16 and 8 cells respectively almost at the same time, followed by the onset of gastrulation. It was recently reported that this cell division pattern is optimal for rapid cell proliferation. In this work, we compare the cell lineages of 9 nematode species, revealing that this pattern is conserved for >60 million years. It further suggests that such lineage design has an important functional role and it might speed up embryonic development in the nematode kingdom, not limited to C. elegans , and independent of the maternal-zygotic transition dynamics.
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Affiliation(s)
- Guoye Guan
- Center for Quantitative Biology, Peking University
- South Bay Interdisciplinary Science Center, Songshan Lake Materials Laboratory
- Department of Physics, Hong Kong Baptist University
- Current Address: Department of Systems Biology, Harvard Medical School
- Current Address: Department of Data Science, Dana-Farber Cancer Institute
| | - Ce Luo
- Center for Quantitative Biology, Peking University
| | - Lei-Han Tang
- South Bay Interdisciplinary Science Center, Songshan Lake Materials Laboratory
- Department of Physics, Hong Kong Baptist University
- Institute of Computational and Theoretical Studies, Hong Kong Baptist University
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University
| | - Chao Tang
- Center for Quantitative Biology, Peking University
- Peking-Tsinghua Center for Life Sciences, Peking University
- School of Physics, Peking University
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Natesan G, Hamilton T, Deeds EJ, Shah PK. Novel metrics reveal new structure and unappreciated heterogeneity in Caenorhabditis elegans development. PLoS Comput Biol 2023; 19:e1011733. [PMID: 38113280 PMCID: PMC10763962 DOI: 10.1371/journal.pcbi.1011733] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 01/03/2024] [Accepted: 12/04/2023] [Indexed: 12/21/2023] Open
Abstract
High throughput experimental approaches are increasingly allowing for the quantitative description of cellular and organismal phenotypes. Distilling these large volumes of complex data into meaningful measures that can drive biological insight remains a central challenge. In the quantitative study of development, for instance, one can resolve phenotypic measures for single cells onto their lineage history, enabling joint consideration of heritable signals and cell fate decisions. Most attempts to analyze this type of data, however, discard much of the information content contained within lineage trees. In this work we introduce a generalized metric, which we term the branch edit distance, that allows us to compare any two embryos based on phenotypic measurements in individual cells. This approach aligns those phenotypic measurements to the underlying lineage tree, providing a flexible and intuitive framework for quantitative comparisons between, for instance, Wild-Type (WT) and mutant developmental programs. We apply this novel metric to data on cell-cycle timing from over 1300 WT and RNAi-treated Caenorhabditis elegans embryos. Our new metric revealed surprising heterogeneity within this data set, including subtle batch effects in WT embryos and dramatic variability in RNAi-induced developmental phenotypes, all of which had been missed in previous analyses. Further investigation of these results suggests a novel, quantitative link between pathways that govern cell fate decisions and pathways that pattern cell cycle timing in the early embryo. Our work demonstrates that the branch edit distance we propose, and similar metrics like it, have the potential to revolutionize our quantitative understanding of organismal phenotype.
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Affiliation(s)
- Gunalan Natesan
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, California, United States of America
| | - Timothy Hamilton
- Department of Integrative Biology and Physiology, University of California, Los Angeles, California, United States of America
| | - Eric J. Deeds
- Department of Integrative Biology and Physiology, University of California, Los Angeles, California, United States of America
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, California, United States of America
| | - Pavak K. Shah
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, California, United States of America
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, California, United States of America
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Azuma Y, Okada H, Onami S. Systematic analysis of cell morphodynamics in C. elegans early embryogenesis. FRONTIERS IN BIOINFORMATICS 2023; 3:1082531. [PMID: 37026092 PMCID: PMC10070942 DOI: 10.3389/fbinf.2023.1082531] [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] [Received: 10/28/2022] [Accepted: 03/07/2023] [Indexed: 04/08/2023] Open
Abstract
The invariant cell lineage of Caenorhabditis elegans allows unambiguous assignment of the identity for each cell, which offers a unique opportunity to study developmental dynamics such as the timing of cell division, dynamics of gene expression, and cell fate decisions at single-cell resolution. However, little is known about cell morphodynamics, including the extent to which they are variable between individuals, mainly due to the lack of sufficient amount and quality of quantified data. In this study, we systematically quantified the cell morphodynamics in 52 C. elegans embryos from the two-cell stage to mid-gastrulation at the high spatiotemporal resolution, 0.5 μm thickness of optical sections, and 30-second intervals of recordings. Our data allowed systematic analyses of the morphological features. We analyzed sphericity dynamics and found a significant increase at the end of metaphase in every cell, indicating the universality of the mitotic cell rounding. Concomitant with the rounding, the volume also increased in most but not all cells, suggesting less universality of the mitotic swelling. Combining all features showed that cell morphodynamics was unique for each cell type. The cells before the onset of gastrulation could be distinguished from all the other cell types. Quantification of reproducibility in cell-cell contact revealed that variability in division timings and cell arrangements produced variability in contacts between the embryos. However, the area of such contacts occupied less than 5% of the total area, suggesting the high reproducibility of spatial occupancies and adjacency relationships of the cells. By comparing the morphodynamics of identical cells between the embryos, we observed diversity in the variability between cells and found it was determined by multiple factors, including cell lineage, cell generation, and cell-cell contact. We compared the variabilities of cell morphodynamics and cell-cell contacts with those in ascidian Phallusia mammillata embryos. The variabilities were larger in C. elegans, despite smaller differences in embryo size and number of cells at each developmental stage.
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Guan G, Zhao Z, Tang C. Delineating the mechanisms and design principles of Caenorhabditis elegans embryogenesis using in toto high-resolution imaging data and computational modeling. Comput Struct Biotechnol J 2022; 20:5500-5515. [PMID: 36284714 PMCID: PMC9562942 DOI: 10.1016/j.csbj.2022.08.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 11/19/2022] Open
Abstract
The nematode (roundworm) Caenorhabditis elegans is one of the most popular animal models for the study of developmental biology, as its invariant development and transparent body enable in toto cellular-resolution fluorescence microscopy imaging of developmental processes at 1-min intervals. This has led to the development of various computational tools for the systematic and automated analysis of imaging data to delineate the molecular and cellular processes throughout the embryogenesis of C. elegans, such as those associated with cell lineage, cell migration, cell morphology, and gene activity. In this review, we first introduce C. elegans embryogenesis and the development of techniques for tracking cell lineage and reconstructing cell morphology during this process. We then contrast the developmental modes of C. elegans and the customized technologies used for studying them with the ones of other animal models, highlighting its advantage for studying embryogenesis with exceptional spatial and temporal resolution. This is followed by an examination of the physical models that have been devised-based on accurate determinations of developmental processes afforded by analyses of imaging data-to interpret the early embryonic development of C. elegans from subcellular to intercellular levels of multiple cells, which focus on two key processes: cell polarization and morphogenesis. We subsequently discuss how quantitative data-based theoretical modeling has improved our understanding of the mechanisms of C. elegans embryogenesis. We conclude by summarizing the challenges associated with the acquisition of C. elegans embryogenesis data, the construction of algorithms to analyze them, and the theoretical interpretation.
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Affiliation(s)
- Guoye Guan
- Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Zhongying Zhao
- Department of Biology, Hong Kong Baptist University, Hong Kong 999077, China
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong 999077, China
| | - Chao Tang
- Center for Quantitative Biology, Peking University, Beijing 100871, China
- Peking–Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- School of Physics, Peking University, Beijing 100871, China
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