Delineating the mechanisms and design principles of Caenorhabditis elegans embryogenesis using in toto high-resolution imaging data and computational modeling

Guan, Guoye; Zhao, Zhongying; Tang, Chao

doi:10.1016/j.csbj.2022.08.024

Cited by 3 publications

(5 citation statements)

References 202 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Meanwhile, more public datasets, such as datasets on gene expression (measured by a fluorescence reporter and RNA sequencing) and chromatin accessibility, can be included [ 54 , 55 , 63 ] to systematically delineate how the developmental dynamics at the molecular scale affect those at the cellular scale which are depicted by different aspects of the cell shape, as well as those at higher scales such as tissue-, organ-, and embryo-scale morphogenesis. As the shape descriptors reported in this paper have explicit geometric significance and have been validated by specific physiological phenomena, they can be applied to the datasets of other organisms, such as ascidians, fruit flies, and zebrafish [ 9 , 10 , 64 ]. Moreover, they exhibit the potential to be applied to clinical data for fast disease diagnosis, for example, to identify cancerous cells that probably have low sphericity and high motility [ 6 , 7 , 62 , 65 , 66 ].…”

Section: Discussionmentioning

confidence: 99%

“…As the shape descriptors reported in this paper have explicit geometric significance and have been validated by specific physiological phenomena, they can be applied to the datasets of other organisms, such as ascidians, fruit flies, and zebrafish [ 9 , 10 , 64 ]. Moreover, they exhibit the potential to be applied to clinical data for fast disease diagnosis, for example, to identify cancerous cells that probably have low sphericity and high motility [ 6 , 7 , 62 , 65 , 66 ].…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Characterizing Cellular Physiological States with Three-Dimensional Shape Descriptors for Cell Membranes

Guan,

Chen,

Wang

et al. 2024

Membranes

Self Cite

View full text Add to dashboard Cite

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).

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Characterizing Cellular Physiological States with Three-Dimensional Shape Descriptors for Cell Membranes

Guan,

Chen,

Wang

et al. 2024

Membranes

Self Cite

View full text Add to dashboard Cite

show abstract

“…, 2016]; then, some ligands and receptors accumulated on the surface of specific cells can bind to each other through cell-cell contact for signaling transduction and fate specification [Priess, WormBook , 2005]. For the reasons given above, the cell morphology reconstruction in different organisms, especially for the multicellular and developing ones, has been a popular focus not only in computer science, but also in cell and developmental biology, and so forth [Guan et al, Comput. Struct.…”

Section: Introductionmentioning

confidence: 99%

“…, 2020], CShaper was devised for segmenting the living C. elegans embryo for its first half embryogenesis ( i.e. , roughly from the 1-to 350-cell stages) in the mechanically compressed state (for a narrow light field), with fluorescence labeling on cell membrane and watershed algorithm based on automatic seeding without cell nuclear position involved; its performance in cell morphology reconstruction drops sharply after the 350-cell stage, as the cell number keeps increasing and the cell size keeps decreasing over cleavage [Guan et al, Comput. Struct.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Quantitative cell morphology inC. elegansembryos reveals regulations of cell volume asymmetry

Guan,

Li,

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

The dynamics of cellular morphology throughout development are crucial for morphogenesis and organogenesis, yet their systematic characterization remains a significant challenge. By integrating both nuclear position and advanced cell membrane labeling, we develop a novel method that enables the segmentation of surfaces for over 95% of cells produced duringCaenorhabditis elegansembryogenesis. With this method, we segment eight wild-type and four perturbed embryos. The output, including cell identity, shape, volume, surface and contact area, can be visualized using our custom software. We demonstrate that signaling interactions, such as Notch and Wnt, regulate not only the asymmetry of cell fate but also the asymmetry of cell volume in conjunction with mechanical compression. Furthermore, we find that the asymmetries of fate and volume are generally interconnected.ONE SENTENCE SUMMARYSystematic quantification of cell morphology with resolved cell lineage and cell fate in developingC. elegansembryo uncovers multimodal regulations of cell size.Potential Cover/Featured Image: Smiling “ghost” face ofC. elegansembryo.Center: shown are skins (colored in red, dorsal view with anterior to the bottom) of a 400-celledC. elegansembryo. Cells not covered by the skins are colored in gray, green, blue, and transparent yellow, respectively. Internal and external circles: confocal fluorescence images (GFP for cell nucleus and mCherry for cell membrane) and reconstructed cell morphologies of theC. elegansembryo from the 2- to 550-cell stages respectively, connected with images of aC. elegansadult expressing the same markers.

show abstract

Automated profiling of gene function during embryonic development

Green,

Khaliullin,

Zhao

et al. 2024

Cell

View full text Add to dashboard Cite

Delineating the mechanisms and design principles of Caenorhabditis elegans embryogenesis using in toto high-resolution imaging data and computational modeling

Cited by 3 publications

References 202 publications

Characterizing Cellular Physiological States with Three-Dimensional Shape Descriptors for Cell Membranes

Characterizing Cellular Physiological States with Three-Dimensional Shape Descriptors for Cell Membranes

Quantitative cell morphology inC. elegansembryos reveals regulations of cell volume asymmetry

Automated profiling of gene function during embryonic development

Contact Info

Product

Resources

About