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Related Concept Videos

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What is 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 to respond to the environment.
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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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Hormones—or any molecule that binds to a receptor, known as a ligand—that are lipid-insoluble (water-soluble) are not able to diffuse across the cell membrane. In order to be able to affect a cell without entering it, these hormones bind to receptors on the cell membrane. When a first messenger, a hormone, binds to a receptor, a signal cascade is set off, causing second messengers, proteins inside the cell, to become activated, resulting in downstream effects.
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Positive and negative feedback loops are crucial for regulating biological signaling systems. These feedback loops are processes that connect output signals to their inputs.
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Contact-dependent signaling, as the name suggests, requires that communicating cells be in direct contact with each other. This is achieved either through receptor-ligand interactions or by specialized cytoplasmic channels that allow the flow of small molecules between cells. In animal cells, channels called gap junctions facilitate contact-dependent signaling in certain tissues, whereas, plasmodesmata perform a similar function in plants.
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Inference and analysis of cell-cell communication using CellChat.

Suoqin Jin1,2, Christian F Guerrero-Juarez1,2,3,4, Lihua Zhang1,2

  • 1Department of Mathematics, University of California, Irvine, Irvine, CA, USA.

Nature Communications
|February 18, 2021
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Summary

CellChat is a new tool that analyzes cell-cell communication networks using single-cell RNA sequencing data. It helps understand how cells signal and coordinate functions, revealing complex communication patterns.

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Area of Science:

  • Single-cell genomics
  • Systems biology
  • Bioinformatics

Background:

  • Understanding intercellular communication is crucial for cell function and organism development.
  • Accurate representation of cell-cell signaling links and systems-level analyses are needed.
  • Existing methods may not fully capture the complexity of molecular interactions.

Purpose of the Study:

  • To develop a computational tool, CellChat, for quantitative inference and analysis of intercellular communication networks.
  • To predict major signaling inputs and outputs and their coordination for cellular functions.
  • To classify signaling pathways and delineate conserved and context-specific pathways.

Main Methods:

  • Construction of a database of ligand-receptor-cofactor interactions representing heteromeric molecular complexes.
  • Development of CellChat, a toolkit for analyzing single-cell RNA sequencing data.
  • Application of network analysis, pattern recognition, manifold learning, and quantitative contrasts.

Main Results:

  • CellChat successfully infers intercellular communication networks from scRNA-seq data.
  • The tool predicts cellular signaling inputs/outputs and functional coordination.
  • Analysis of mouse and human skin datasets revealed complex signaling patterns and pathway classifications.

Conclusions:

  • CellChat provides a versatile and user-friendly toolkit for discovering novel intercellular communications.
  • The tool facilitates the construction of cell-cell communication atlases across diverse tissues.
  • CellChat enhances the understanding of global cell-cell signaling.