Extended Data Fig. 3. Transcriptional profiling of LCMV-specific CD8⁺ T cells generated by PD-1 monotherapy, IL-2 treatment, and PD-1 + IL-2 combination therapy during chronic infection.

Mice chronically infected with LCMV were treated with PD-1 monotherapy, IL-2 alone, or combination therapy for 2 weeks. LCMV-specific D^bGP33⁺ CD8⁺ T cells from spleens of each treatment group were sorted for RNA-seq (a–d) and scRNA-seq (e-j). As a control, naive (CD44^lo) CD8⁺ T cells were also sorted for scRNA-seq (e-j). a, MA plots for gene expression of D^bGP33⁺ CD8⁺ T cells after the indicated treatments. b–d, GSEA of D^bGP33⁺ CD8⁺ T cells generated by the indicated treatments for effector signature (acute infection) (b), memory signature (acute infection) (c), and exhaustion signature (chronic infection) (d). e, The t-SNE projection of naive CD44^lo CD8⁺ T cells and D^bGP33⁺ CD8⁺ T cells in 4 treatment groups during chronic infection. Naive and four treatment samples were distributed and overlaid onto the four clusters. f, Numbers of cells in clusters 1, 2, and 3. g, Numbers of cells in cluster 1. Numbers of total D^bGP33⁺ CD8⁺ T cells per spleen were estimated from geometric mean of Extended Data Fig. 1b (f, g). h, Normalized expression of several representative genes is shown within the 4 clusters i, Co-expression patterns of Tcf7 and Gzmb in cells of each cluster are shown. j, GSEA of D^bGP33⁺ CD8⁺ T cells generated by the different treatments for effector signature (acute infection) and exhaustion signature (chronic infection). Enrichment score for the signature in four treatment samples are shown as violin plots with horizontal bars of mean. Results were pooled from 2 (a–c) and 1–2 (e–j) experiments with n = 2–18 mice per group in each experiment. ES, enrichment score; Untx, untreated.