Fig. 7
Analysis and statistics of TCR repertoires in localized ESCC. a The percentage of shared TCRs in all primary tumor regions (top panel) and T cell clonality in each primary tumor region (bottom panel). The left panel shows statistics of TRA and the right panel is for TRB. b The overall clone diversity (Shannon index, left panel) and high-frequent clone number (freq. > 0.01%, right panel) of TRA (top panel) and TRB (bottom panel) for four sorts of samples. T primary tumor sample, N normal sample,B blood sample, L lymphoma metastasis. c The median overlapped rate between any two types of samples shown by heat map. The color in the heat map represents the values of Jaccard indices (range: 0–100). The left bottom corner shows result of TRA repertoires and the right top corner shows that of TRB repertoires. d Kaplan–Meier survival curves displaying survival outcomes of ESCCs with distinct neoantigen heterogeneity. e Correlation of T cell repertoire with branch neoantigens. Spearman correlation between the median of unique clone number in primary tumors and total neoantigen number (left); Spearman correlation between the percentage of predicted branch neoantigen and the median of clone evenness, V–J pairing’ evenness, CR4 of clones, and CR4 of V–J gene pairings in primary tumors. f Comparison of TCR tree and genetic tree in seven patients. The upper panel displays the cancer evolutionary trees based on somatic SNVs, and the trunk, branch, and shared branch are colored in dark, blue, and red, respectively; the bottom panel shows the unrooted neighbor-joining tree based on TCR, and the trees are colored by tissue types (lake blue: normal; green: regional tumor; pink: blood; purple: metastatic lymph node). Yellow rectangles highlight regional tumors from the same clade that have more similarity in TCR tree
