Figure 3.

Characterization of CD8⁺ T-cell populations within the PDAC tumor microenvironment. A, Dot plot of the top markers expressed in each CD8⁺ T-cell cluster identified via Louvain clustering of scRNA-seq data (first presented in Fig. 1) from CD8⁺ T cells (i). UMAP embedding of CD8⁺ T cells from the 3 PDAC patient samples overlaid with Louvain cluster label (ii). B, CyTOF analysis of CD45⁺ cells from PDAC patient PBMC and TIL (n = 10), using data first used in Fig. 2B. t-SNE plots show PhenoGraph-clustered CD8⁺ T-cell populations in PBMC and TIL. C, Representative contour plot showing CD8⁺ TRM cells in PDAC TIL based on positive expression of CD69 and CD103, generated using the data in Fig. 2B (i). Box and whisker plot showing the proportion of CD8⁺ TRM cells in PBMC and TIL, generated using the data in Fig. 2B (ii). D, UMAP embedding, performed using scRNA-seq first presented in Fig. 1, overlaid with module score quintiles and module score distributions by CD8 T-cell cluster from scoring a core module of genes overexpressed in TRM T-cells (i). Differential expression analysis distinguishing TRM-like cells (clusters CD8_1 and CD8_6) from non-TRM cells (ii). Selected genes are labelled, and colored points indicate genes that are differentially expressed [BH adjusted P < 0.01 and absolute (average logFC) > 0.5]. E, Comparison of memory T-cell markers in CD8⁺ TRM and non-TRM in PDAC TIL, performed using the data in Fig. 2B. Bar graph comparing the proportion of Naïve, EM, CM, and TEMRA subsets in CD8⁺ TRM and non-TRM cells (i). Bar graph comparing the CD27 and CD28 expression pattern in CD8⁺ EM T-cells within TRM and non-TRM cells (ii). F, Line graphs comparing T-cell activation and differentiation marker expression on CD8⁺ TRM versus non-TRM cells in PDAC TIL, generated using the data in Fig. 2B. G, Representative contour plots (i) and quantification (ii) of CD39⁺ CD8⁺ TRM cells in PBMC and TIL, generated using the data in Fig. 2B. H, DFS analysis of patients with PDAC from the TCGA-PAAD dataset based on the expression level of ITGAE (CD103) in tumor tissue. Horizontal lines represent median, boxes represent quartiles and whiskers represent min and max values. Data analyzed using Wilcoxon matched-pairs signed rank test. *, P < 0.05; **, P < 0.01.