Extended Data Fig. 9: Inference of tumor-specific, viral-specific, and vaccine-specific T cell clonotypes.

UMAP representations of scRNA-seq data from lymphoid cells in (a) the skin during the cutaneous delayed-type hypersensitivity (DTH) assessment, and (b) the tumor at the time of surgical resection. Single-cell TCR-sequencing of T cells showing areas of clonotype expansion in (c) the skin (during DTH assessment) and (d) the baseline tumor. e, For tumor-infiltrating T cells, the per-clonotype average expression of previously defined²⁸ gene signatures for tumor specificity (TS) and viral specificity (VS). The red lines indicate thresholds that were used to identify TS and VS T cells. f, For each clonotype that was assigned as TS or VS (or no specificity), the percentage of individual T cells within that clonotype that express predominantly the TS signature, the VS signature, or neither (dual specificity of no specificity). Overall, for clonotypes that were labeled as TS or VS, over 70% of the individual T cells were concordant with that classification. g, association of expanded CD4 T cell clonotypes with IFNγ response after vaccination. The total number of inferred vaccine-expanded clonotypes (left), CD4-only clonotypes (middle), and CD8-only clonotypes (right) in each sample is plotted against the total number of IFNγ spot-forming cells by ex vivo ELISpot assessment at week 16 following vaccination (two-sided Pearson correlation).

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