Fig. 4: Interaction and co-localization of GZMK⁺CD8⁺ T cells and fibroblasts in NPs revealed by ligand-receptor analysis and spatial transcriptomics (Visium).

a–d Re-analyzing T and NK cells in a public scRNA-seq dataset (HRA000772) (n = 21) (a). Proportions of CD8T_GZMK in CD8⁺ T cells in the indicated group (5 controls, 5 CRSsNP, 5 NE-NP, and 6 E-NP samples). Box plots show median, quantiles, minimum and maximum. Two-sided Kruskal-Wallis with Dunn’s multiple comparisons test (b). Dot plots showing interactions between chemokine ligands (in structural cells) and receptors (in CD8T_GZMK). P values are computed from one-sided permutation test (default for CellChat r-package). Dot size represents P value. The color represents communication possibility (c). CXCL12 expression in the indicated cell types in four groups (d). e Hematoxylin and eosin (HE) staining of the tissue section from the representative CRSwNP patient #9 (NP9) (left). Unbiased clustering of spatial transcriptomics (ST) spots and annotated cell types of each cluster (right). f Dot plots showing scaled expression of typical markers in indicated cell clusters. g Spatial feature plots of signature scores of GZMK⁺CD8⁺ T cells, fibroblasts, and epithelial cells in NP9. h Neighborhood enrichment analysis between cell clusters in NP9. The “GZMK⁺CD8⁺ T cells” and “fibroblasts” show a positive enrichment score. i Schematic diagram displaying the Intra-spots (GZMK⁺CD8⁺ T cell/fibroblast-colocalized spots), Inter-spots (GZMK⁺CD8⁺ T cell/fibroblast-surrounded spots) and others (distant spots). j Co-expression pattern of GZMK⁺CD8⁺ T cells and fibroblasts in NP9 section. k, l Spatial feature plots showing GZMK⁺CD8⁺ T cells/fibroblasts-colocalized or surrounded spots in NP9 section. m GZMK⁺CD8⁺ T signature scores in fibroblasts that in close contact or distant from GZMK⁺CD8⁺ T cells (NP9 section: 57 fibroblasts-distant spots and 144 fibroblasts-close spots). Box plots show median, quantiles, minimum and maximum. Two-sided unpaired Wilcoxon test. n Ligand-receptor interactions of CXCL12-CXCR4 from the structural cells to GZMK⁺CD8⁺ T cells. Means, the means of the average expression level of both interacting ligands (in other cell types) and corresponding receptors (in GZMK⁺CD8⁺ T). P values result from a one-sided permutation-based test with 1000 permutations and were adjusted with the Benjamini-Hochberg method. CRSsNP chronic rhinosinusitis without nasal polyps, ECs endothelial cells, E-NP eosinophilic nasal polyp, EPs epithelial cells, ILC innate lymphoid cell, NE-NP non-eosinophilic nasal polyp, NK natural killer cell, pDCs plasmacytoid dendritic cells, SMCs smooth muscle cells. Source data are provided as a Source Data file.