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Overview of Cell Signaling01:23

Overview of Cell Signaling

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Despite the protective membrane that separates a cell from the environment, cells need the ability to detect and respond to environmental changes. Additionally, cells often need to communicate with one another. Unicellular and multicellular organisms use a variety of cell signaling mechanisms to communicate with the environment.
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Despite the protective membrane that separates a cell from the environment, cells need the ability to detect and respond to environmental changes. Additionally, cells often need to communicate with one another. Unicellular and multicellular organisms use a variety of cell signaling mechanisms to communicate to respond to the environment.
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Diversity in Cell Signaling Responses01:22

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The physiological function of a cell and cellular communication are outcomes of a range of extrinsic signals, intracellular signaling pathways, and cellular responses. No two cell types express the same repertoire of signaling components. Receptors are highly selective for their cognate ligands, but once activated, they can alter multiple cellular processes such as DNA transcription, protein synthesis, and metabolic activity. 
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Protein Networks02:26

Protein Networks

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An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
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Related Experiment Video

Updated: May 15, 2025

Mechanical Stimulation-induced Calcium Wave Propagation in Cell Monolayers: The Example of Bovine Corneal Endothelial Cells
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CausalCCC: a web server to explore intracellular causal pathways enabling cell-cell communication.

Louise Dupuis1, Orianne Debeaupuis1,2, Franck Simon1

  • 1CNRS UMR168, Institut Curie, 75005 Paris, France.

Nucleic Acids Research
|May 14, 2025
PubMed
Summary

CausalCCC reconstructs gene-gene interaction pathways from single-cell data, integrating upstream and downstream signaling for a comprehensive view of cell-cell communication beyond ligand-receptor scores.

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Area of Science:

  • Computational Biology
  • Systems Biology
  • Genomics

Background:

  • Cell-cell communication (CCC) is crucial for biological processes.
  • Current CCC methods primarily focus on ligand-receptor interactions, leaving a gap in understanding intracellular pathway integration.

Purpose of the Study:

  • To introduce CausalCCC, an interactive web server for reconstructing gene-gene interaction pathways in CCC.
  • To enable a comprehensive analysis of cellular crosstalk by integrating upstream and downstream signaling.

Main Methods:

  • CausalCCC integrates multivariate information-based inductive causation for causal network reconstruction.
  • It incorporates internally computed ligand-receptor pairs (LIANA+) or user-defined pairs.
  • The web server provides interactive visualization tools and a tutorial.

Main Results:

  • CausalCCC successfully reconstructs extended CCC pathways from single-cell and spatial transcriptomic data.
  • Demonstrated application on datasets from NicheNet, CellChat, and Misty.
  • Offers unique interactive visualization for exploring multi-cell type crosstalk.

Conclusions:

  • CausalCCC addresses the need for integrated CCC pathway analysis beyond simple ligand-receptor scoring.
  • It empowers researchers to explore complex cellular crosstalk in single-cell and spatial transcriptomics.
  • Provides a valuable tool for advancing biological process understanding through detailed CCC pathway reconstruction.