Figure 4

Shared TCRs among five healthy donors present in their populations of T cells and functional CD8+ T cell subsets. (a) Ratio of unique reads of shared and unshared TCRs in the entire T-cell populations. The pie charts represent the total number of unique reads of TCRs in the entire T cell populations. Blue and orange indicate the percentage of unique reads of shared and unshared TCRs, respectively. (b) Random sampling of 35,000 reads was performed in each T cell subset and each donor. Each circle or dot in the plots shows one unique read of TCRβ. TCRβ clonotypes are ordered according to their frequencies in descending order on the x-axis. The y-axis depicts the read numbers of the clonotypes. Shared non-CMV NLV-specific TCRs (○) and unshared non CMV NLV-specific TCRs (●) are shown as black circles and blue dots, respectively. Shared CMV NLV-specific TCRs (○) and unshared CMV NLV-specific TCRs (●) are shown as red circles and dots, respectively. Orange thick circle (○) represents one of nine dominant TCRs in V001 (TCR ID; 001-17, 001-48, 001-41) and V004 (TCR ID; 004-66, 004-22, 004-63, 004-30, 004-28 and 004-71) (Fig. 2a). The sizes of the circles are directory proportional to numbers shared among the five donors. The largest circles indicate the shared clonotypes by the five donors and the dots indicat the unshared clonotypes. Wilcoxon rank-sum test and Kendall’s tau test were performed. The P values of all tests were <0.05, which indicates a significant correlation between the total reads and the sharing count of the TCRs, even in the naïve subset. The results of this analysis were similar for donors V002, V003 and V005 (Supplementary Fig. 2). (c) Simpson’s Diversity Index (SDI) calculated using NGS data for functional T-cell subsets among the five donors. The y-axis depicts SDI, and each dot represents each donor’s SDI of functional T-cell subsets. The horizontal bars show the average SDI among the five donors. (d) T cell repertoire plots of functional CD8+ T-cell subsets are the same as shown in Fig. 4c, revealing the lower diversity of the SCM T-cell subset compared with CM and EM T-cell subsets. The results of this analysis were similar for donors V002, V003 and V005 (Supplementary Fig. 3).