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Comprehensive visualization of cell-cell interactions in single-cell and spatial transcriptomics with NICHES.

Micha Sam Brickman Raredon1,2,3,4, Junchen Yang5, Neeharika Kothapalli3

  • 1Department of Anesthesiology, Yale School of Medicine, New Haven, CT 06511, USA.

Bioinformatics (Oxford, England)
|December 2, 2022
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Summary

NICHES is a new tool for analyzing cell-cell communication directly from single-cell data. It reveals complex signaling patterns without losing individual cell details, offering a more precise understanding of biological systems.

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Area of Science:

  • Computational Biology
  • Genomics
  • Systems Biology

Background:

  • Existing tools for cell-cell interaction analysis from single-cell data often use averaged gene expression, losing single-cell resolution.
  • There is a need for methods that preserve the heterogeneity of individual cells when studying intercellular communication.

Purpose of the Study:

  • To introduce NICHES (Niche Interactions and Communication Heterogeneity in Extracellular Signaling), a novel computational tool for analyzing extracellular signaling at the single-cell level.
  • To enable visualization of heterogeneous signaling archetypes within and between cell clusters.

Main Methods:

  • NICHES embeds ligand-receptor signal proxies to analyze intercellular communication.
  • The tool operates with user-defined ligand-receptor pairs and is compatible with existing single-cell analysis packages.
  • NICHES can be applied to spatial transcriptomic data to infer local cellular microenvironments.

Main Results:

  • NICHES visualizes heterogeneous signaling archetypes at single-cell resolution.
  • The tool facilitates analysis across cell clusters and experimental conditions.
  • Application to spatial transcriptomic data reveals local cellular microenvironments.

Conclusions:

  • NICHES provides a flexible and rapid method for analyzing cell-cell signaling with true single-cell fidelity.
  • The tool enhances the understanding of complex intercellular communication networks.
  • NICHES is an open-source R package available for broad scientific use.