Fig. 7: T cells show clonal expansion in patients with neoadjuvant treatment response.
a, Numbers of total TCRs α-chain (left) and β-chain (right) in REPs and NRPs during treatment. P values are calculated by a two-sided Wilcoxon test. b, Correlation between TCR counts α-chain (left) and β-chain (right) and quantitative deconvolution of T cells from RNA-seq data via CIBERSORT. Two-tailed Pearson’s correlation coefficients are reported in the plots. c, Abundance distribution profile of TCRs at timepoints A–C. The y axis shows the proportion of the TCRs that are found at the abundance indicated by the x axis. d, Fishplots show the number of fourfold-expanded TCRs between any two timepoints REP11 (top) and REP23 (bottom). The colors correspond to the combination of timepoints that the TCR expansion occur in. e, The proportions of T cell clones that are expanded ≥fourfold and ≥eightfold between timepoint A and C. f, Numbers of TCRs expanded ≥fourfold and ≥eightfold during treatment periods (A–B, A–C and B–C), stratified by pathological regression grades. P values are calculated by a two-sided Mann–Whitney U-test.
