NicheCorr: Identifying Niche-Specific Differential Gene Co-Expression in Spatial Transcriptomics

NicheCorr identifies niche-specific differential gene co-expression in spatial transcriptomics, detecting 52 liver tumor cell gene pairs linked to T-cell niche composition and 48 pancreatic cancer gene pairs linked to fibroblast niche differences.

• Why it matters: Spatial proximity between cell types may reshape gene-gene interactions, but existing methods often focus on average expression differences and miss niche-dependent co-expression changes.
• What they did: NicheCorr is a statistical procedure for cell type-specific niche-associated co-expression changes, validated in simulations where it had the highest power and preserved Type I error under nonlinear mean–niche variation.
• The result: Applied to CosMx liver and Xenium pancreatic cancer datasets, it also integrates ligand-receptor inference to uncover potential spatial signaling interactions underlying the observed differential co-expression patterns.