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bioRxiv · 10.1101/2023.04.14.536833

Charting spatial ligand-target activity using Renoir

Rao, N.·Pai, R.·Mishra, A.·Ginhoux, F.·Chan, J.·Sharma, A.·Zafar, H.
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Abstract

The advancement of single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics has enabled the inference of cellular interactions in a tissue microenvironment. Despite the development of cell-cell interaction inference methods, there is a lack of methods capable of mapping the influence of ligands on downstream target genes across a spatial topology with specific cell type composition, with the potential to shed light on niche-specific relationship between ligands and their downstream targets. Here we present Renoir for charting the ligand-target activities across a spatial topology and delineating spatial communication niches harboring specific ligand-target activities. Renoir also spatially maps pathway-level activity of ligand-target genesets and identifies domain-specific ligand-target activities. Across spatial datasets with varying resolution (spot to single-cell) ranging from development to disease, Renoir inferred cellular niches with distinct ligand-target interactions, spatially mapped pathway activities, and identified context-specific novel cell-cell interactions. Renoir uncovers biological insights and therapeutically-relevant cellular crosstalk from spatial transcriptomics data.

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Rao, N., Pai, R., Mishra, A., Ginhoux, F., Chan, J., Sharma, A., Zafar, H.. 2023-04-17. Charting spatial ligand-target activity using Renoir. https://doi.org/10.1101/2023.04.14.536833

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