Panel A shows stream plots with different genotypes on the x-axis and percentage on the y-axis. The colored streams represent different complementarity-determining region 3 (CDR3) sequences. Panel B shows a UMAP embedding of CD8 positive T cells overlaid with T-cell receptor (TCR) distribution, colored by the logarithm-transformed abundance of expanded clones, with a color gradient ranging from purple to yellow. Panel C shows a UMAP embedding of CD8 positive T cells colored by transcriptional state, grouped into naive or memory, activated or migratory, and cytotoxic effector or exhausted partitions, with distinct clusters identified within each partition. Panel D shows a dot plot of representative gene signatures across transcriptional clusters, where dot size indicates the percentage of expressing cells and color indicates scaled average expression. Panel E shows a scatter plot of LAG3 negative tdTomato positive and LAG3 positive tdTomato positive cell populations within tumor samples. Panel F shows two bubble charts of Lag3 and Adam10 expression across all tdTomato positive subsets in lymph nodes and tumors on days 11 and 19, where bubble size represents the percentage of expressing cells and color intensity represents average expression levels. Panel G shows ATAC-seq accessibility tracks for Pdcd1 and Tox across tdTomato subsets together with an external reference, displaying aggregated accessibility profiles for each genomic locus and highlighting regions with significantly increased accessibility identified by differential accessibility analysis.
Transcriptional, clonal, and epigenetic characterization of fate-mapped tdT+ CD8+ T cells . (A) Stream plots showing distribution of commonly shared TCR among tdT+ subsets at d11 and d19, alongside representative CDR3 sequences. (B) UMAP embedding of CD8+ T cells overlaid with TCR distribution, heat-colored by the log-transformed abundance of expanded clones. (C) UMAP embedding of CD8+ T cells colored by transcriptional state, grouped into naive/memory, activated/migratory, and cytotoxic effector/exhausted partitions, with distinct clusters highlighted and defined within each partition. (D) Dot plot of representative gene signatures across transcriptional clusters. Dot size indicates percent expression; color indicates scaled average expression. (E) Distribution of LAG3−tdT+ and LAG3+tdT+ populations within tumor samples. (F) Expression levels of Lag3 and Adam10 in all tdT+ subsets in LNs and tumor at d11 and d19. (G) ATACseq accessibility tracks for Pdcd1 and Tox across tdT subsets with external reference. Shown are aggregated ATACseq profiles for each loci aligned to reference datasets by Huang et al. (2025). Significantly accessible regions identified by differential accessibility analysis are highlighted. Data in A–G are representative of two independent experiments. *P < 0.05; **P < 0.01; ****P < 0.0001; by Wilcoxon rank-sum test (F).