Fig. 2: Analysis of tumour microenvironments in LUSC and LUAD highlights dynamic pairwise cell–cell interaction patterns and cellular neighbourhoods.

A Heat map of pairwise cell–cell interactions (red) or avoidances (blue) across LUAD (upper half of square, n = 102 images) and LUSC cores (lower half of square, n = 102 images) using 10,000 permutations. NK cells and dendritic cells were omitted from the graph given the lack of significant interactions. Black dotted boxes indicate interactions that are referenced in-text. B Plots depicting significant differences in interaction tendencies for neutrophils (left) and CD163- macrophages (right) between LUAD and LUSC. The size of the outer circles corresponds to the P-value comparing LUAD and LUSC interaction scores. Two-tailed unpaired Student’s t test. C Representative segmented images depicting neutrophil-CD4+ T cell and neutrophil-cancer interaction tendencies in LUAD (left) and LUSC (right), respectively. Scale bars = 100 μm. D Heatmap of cell types distributed across 10 neighbourhoods discovered in LUAD (n = 102) and LUSC (n = 102) (10 nearest neighbours, 10 neighbourhoods). E Average distribution of each CN in LUAD (n = 102) and LUSC (n = 102) (10 nearest neighbours,10 neighbourhoods). F Cellular composition of CN1, CN7, and CN8 discovered in LUAD and LUSC (10 nearest neighbours,10 neighbourhoods). G Number of cells belonging to each CN across LUAD (n = 102) and LUSC (n = 102) (10 nearest neighbours, 10 neighbourhoods). Two-tailed unpaired multiple comparison adjusted Student’s t tests; mean ± s.e.m. P value CN1 = 0.0000681, CN3 = 0.000000926, CN7 = 0.000000682, CN8 = 0.0000441. H Kaplan–Meier analysis of overall survival in CN3 high (z-score ≥0, n = 20) and low (z-score <0, n = 31) LUAD patients (10 nearest neighbours, 10 neighbourhoods). Log-rank Mantel–Cox test. I Cellular composition of CN3 discovered in LUAD and LUSC (10 nearest neighbours,10 neighbourhoods). LUAD lung adenocarcinoma, LUSC lung squamous cell carcinoma, Cl Monocyte classical monocyte, Non-Cl Monocyte non-classical monocyte, Int Monocyte intermediate monocyte, NK cell Natural Killer cell, Treg regulatory T cell.