Charting spatial ligand-target activity using Renoir.

The advancement of single-cell RNA sequencing and spatial transcriptomics has enabled the inference of cellular interactions in a tissue microenvironment. Despite advances in cell-cell interaction inference, methods capable of mapping the influence of ligands on downstream target genes across spatial niches harboring specific cell type composition, crucial for resolving niche-specific relationship between ligands and their downstream targets are still lacking. Here, we present Renoir for charting the ligand-target activities across a spatial topology, delineating spatial communication niches harboring specific ligand-target activities and spatially mapping pathway-level activity of genesets. Across spatial datasets with varying resolution (spot to single-cell) ranging from development to disease, Renoir infers cellular niches with distinct ligand-target interactions, spatially maps pathway activities, and identifies context-specific cell-cell interactions, including hepatocyte-macrophage interactions in fetal liver and interactions between onco-fetal and bipotent cells in hepatocellular carcinoma. Renoir uncovers biological insights and therapeutically-relevant cellular crosstalk from spatial transcriptomics data.