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Updated: May 7, 2026

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Charting spatial ligand-target activity using Renoir.

Narein Rao1, Tanush Kumar2, Dina Kazemi3

  • 1Department of Computer Science and Engineering, Indian Institute of Technology Kanpur, Kanpur, India.

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|May 5, 2026
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Summary
This summary is machine-generated.

Renoir maps ligand-target activities in spatial niches, revealing cell-cell communication critical for understanding tissue microenvironments in development and disease.

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Area of Science:

  • Single-cell RNA sequencing
  • Spatial transcriptomics
  • Cellular interactions
  • Tissue microenvironment

Background:

  • Advances in single-cell RNA sequencing and spatial transcriptomics enable inference of cellular interactions.
  • Existing methods lack the ability to map ligand influence on downstream target genes across spatial niches.
  • Resolving niche-specific ligand-target relationships is crucial for understanding tissue microenvironments.

Purpose of the Study:

  • To present Renoir, a novel method for charting ligand-target activities across spatial topology.
  • To delineate spatial communication niches defined by specific ligand-target activities.
  • To spatially map pathway-level activity of gene sets.

Main Methods:

  • Renoir analyzes spatial transcriptomics data at varying resolutions (spot to single-cell).
  • It infers cellular niches with distinct ligand-target interactions.
  • It maps pathway activities and identifies context-specific cell-cell interactions.

Main Results:

  • Renoir successfully inferred distinct ligand-target interactions in various spatial niches across development and disease datasets.
  • The method spatially mapped pathway activities and identified context-specific cell-cell interactions.
  • Identified key interactions, including hepatocyte-macrophage interactions in fetal liver and cell interactions in hepatocellular carcinoma.

Conclusions:

  • Renoir uncovers biological insights and therapeutically relevant cellular crosstalk from spatial transcriptomics data.
  • The method provides a powerful tool for dissecting complex cellular communication within tissue microenvironments.
  • Renoir advances the understanding of niche-specific ligand-target relationships and their implications in biological processes and diseases.