Fig. 6: Characterization of neoantigen-specific T cells.

a Specificity inference pipeline. b Overview of neoantigen-specific TCR clusters. The size of the dots represents whether the TCR is clonal, large dots represent clonal TCRs, and small dots represent nonclonal TCRs. The red dots represent groups containing neoantigen-specific TCRs. c The network of neoantigen-specific TCR clusters. Shared CDR3β sequences organize TCR groups into distinct communities, and the depth of the connecting lines indicates the number of shared CDR3β sequence(s) between any two connected nodes. d IFN-γ status of neoantigen-specific TCR clusters. The red dots indicate the IFN-γ-positive TCR groups. e The neoantigen-reactive TCR modes. A supercluster containing neoantigen-reactive TCR groups is circled, and the neoantigen-reactive TCR groups are highlighted in red font; the CDR3β members of the neoantigen-reactive TCR groups are highlighted with short motifs; a heatmap showing distinct CDR3β members (columns) of the neoantigen-reactive-related specificity groups (rows) and the counts of shared CDR3β sequences between specificity groups within the circled community; and a table showing an example of the specificity groups containing the motif (bold). The Vβ gene type is shown. The motif sequence markers corresponding to some motifs are shown on the right. f Distribution of T cells containing neoantigen-specific TCRs; red dots indicate that T cells contain neoantigen-specific TCRs. g The proportions of neoantigen-specific T cells. The outer circle represents the proportions of different cells among the sorted CD137 + T cells, while the inner circle indicates the proportions of various T cells that contained neoantigen-specific TCRs. h Volcano plot showing genes differentially expressed in neoantigen-specific T cells. Each red or blue dot denotes an individual gene passing our P value and fold difference thresholds, with red dots indicating genes with upregulated expression and blue dots indicating genes with downregulated expression. Ifng is highlighted in red font. i Triangle diagram showing the enrichment of neoantigen-specific T cells in different cells. The red dots indicate the regions where neoantigen-specific T cells are enriched. The P-values were analyzed by linear model fit from limma package (h). Source data are provided as a Source Data file.