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CellPhoneDB v5: inferring cell-cell communication from single-cell multiomics data.

Kevin Troulé1, Robert Petryszak1, Batuhan Cakir1

  • 1Wellcome Sanger Institute, Cambridge, UK.

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|March 26, 2025
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This summary is machine-generated.

CellPhoneDB v5 enhances cell-cell communication inference using single-cell genomics. This updated toolkit refines understanding of tissue biology and disease mechanisms by integrating diverse data modalities.

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Area of Science:

  • Cellular Biology
  • Bioinformatics
  • Genomics

Background:

  • Cell-cell communication is crucial for tissue development, function, and regeneration.
  • Single-cell genomics reveals in vivo cellular interactions and disease implications.
  • CellPhoneDB is a bioinformatics toolkit for inferring cell-cell communication from single-cell genomics data.

Purpose of the Study:

  • To present the protocol for CellPhoneDB version 5 (v5).
  • To highlight new features enhancing cell-cell communication inference precision.
  • To demonstrate applications in understanding tissue biology and disease.

Main Methods:

  • Expanded ligand-receptor interaction repository, including nonpeptidic ligands.
  • Tailored database querying for specific experimental designs.
  • Integration with spatial transcriptomics and single-cell assay for transposase accessible chromatin (scATAC-seq) data for interaction prioritization.
  • Introduction of CellPhoneDBViz for interactive visualization.

Main Results:

  • CellPhoneDB v5 repository expanded by one-third with new interactions.
  • Novel strategies enable prioritization of specific cell-cell interactions.
  • Enhanced precision in inferring cell-cell communication.
  • Interactive visualization module facilitates result sharing.

Conclusions:

  • CellPhoneDB v5 offers enhanced precision for cell-cell communication inference.
  • New features provide deeper insights into tissue biology within physiological microenvironments.
  • The toolkit supports the study of diseases and developmental abnormalities linked to disrupted cellular niches.