Fig. 5: Transcriptional features of specific T cells in BALF and PBMCs.

a, Uniform manifold approximation and projection (UMAP) plot displaying the transcriptomic clusters of all T cells from the 16 paired BALF and PBMC samples from 13 patients. b, Distribution of clusters in BALF (red) and PBMCs (blue). c, Summary of cluster proportions on T cells in BALF and PBMCs. d, Average expression (color scale) and percentage of expressing cells (size scale) of selected genes across the indicated clusters of total T cells. e, Distribution of specific T cells (red dots) in BALF (left) and PBMCs (right). f, Summary of cluster proportions of specific T cells in BALF and PBMCs. g, Volcano plots showing differentially expressed genes (DEGs) in specific CD4⁺ and CD8⁺ T cells between BALF and PBMCs. The names of the indicated DEGs are shown. Horizontal black dashed line: Benjamini–Hochberg P_adj = 0.05. h, Enriched immune pathways in specific T cells in BALF versus PBMCs were identified based on the normalized enrichment score (NES), with statistical significance defined as P < 0.05 after Benjamini–Hochberg correction. The count denotes the pathway size reflecting the number of genes detected in the expression dataset. i, Dot plots illustrating key genes in the indicated functional modules of specific T cells in BALF and PBMCs. j, Two-tailed Spearman correlation analysis between the indicated genes expressed in specific CD4⁺ (pink) and CD8⁺ (aqua) T cells in BALF.