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Related Concept Videos

Overview of Cell Signaling01:23

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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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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.

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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.