Fig. 2: GZMK⁺CD8⁺ T cells are preferentially increased in NPs with a distinct transcriptional program.

a UMAP plots showing that 81,202 CD8⁺ T cells from 25 samples (5 CBL, 8 NP-BL, 4 CIT, and 8 NP samples) are separated into 16 clusters (upper left). Clusters are annotated into nine major cell types by canonical markers (upper right) and colored by different sampling locations (lower left and right). b Dot plots showing the scaled expression of selected canonical marker genes in the indicated cell types. c Feature plots and violin plots illustrating expression of naive, effector memory and cytotoxicity curated gene signatures across CD8⁺ T cell clusters. d Bar plots showing the compositions of major cell types in each sample across different sampling locations in control participants and patients with CRSwNP. e Tissue prevalence of major cell types in the indicated group (13 blood samples (including 5 CBL and 8 NP-BL samples) and 12 nasal tissue samples (including 4 CIT and 8 NP samples)) is estimated by Ro/e score. f Scatter-plot shows differentially expressed genes (DEGs) between GZMK⁺CD8⁺ T cells and other CD8⁺ T cells. Two-sided Wilcoxon rank-sum tests with Bonferroni correction. Genes with |log2(fold change) | > 0.5 and adjusted P < 0.05 were considered significant. NS, no significant difference; P adj, adjusted P value; Δ percent of cells, the difference in the percentage of cells expressing the gene comparing GZMK⁺CD8⁺ T versus all other CD8⁺ T cells. g Gene set enrichment analysis (GSEA) showing significantly differentially upregulated pathways in GZMK⁺CD8⁺ T cells compared to other CD8⁺ T cells. Two-sided permutation test with Benjamini-Hochberg adjustments was used for GSEA analysis. Normalized enrichment score (NES) > 1 and adjusted P < 0.05 was considered significant. h Violin plots displaying top10 differentially expressed genes (DEGs) among GZMK⁺CD8⁺ T and GZMB⁺CD8⁺ T cells in NPs. Two-sided Wilcoxon rank-sum tests with Bonferroni correction. Genes with |log2(fold change) | > 0.5 and adjusted P < 0.05 were considered significant. i, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of DEGs that enriched in indicated CD8⁺ T clusters. Two-sided Fisher’s Exact test with Benjamini-Hochberg adjustments was used for KEGG analysis. Adjusted P < 0.05 was considered significant. CBL control blood sample, CD8⁺ Tpex, CD8⁺ progenitor exhausted cells, CIT control inferior turbinate sample, MAIT mucosal associated invariant T cell, NP nasal polyp, NP-BL blood sample from CRSwNP patient, TRM tissue-resident memory T cell. Source data are provided as a Source Data file.