Fig. 4: Clonality features and dynamics of T cell receptors during immunochemotherapy.

a–d UMAP plots of 16,636 T cells with detected T cell receptor beta (TRB) clones from 23 samples, annotated by patient origin, treatment timepoints, clonotypes and clone size. e–g Fractions of TRB clones with different sizes (n < 3 and n ≥ 3) for different T cell clusters in pre-treatment samples (Pre, left), post-treatment samples of responders (Post-R, middle), and non-responders (Post-NR, right). h Boxplots showing Gini indices for CD4⁺ Tregs in different groups. Box middle lines, median; box limits, upper and lower quartiles; box whiskers, minima and maxima. ^*p < 0.05, ^**p < 0.01 of Mann Whitney U test. Pre, n = 7; Post-R, n = 6; Post-NR, n = 10. i Heatmap showing the fraction of CD8⁺ T cell clonotypes shared with a secondary phenotype (column) in each primary phenotype (row). Pre (left); Post-R (middle); Post-NR (right). j UMAP plot of CD8⁺ Tex-relevant and Tex-irrelevant cells in all samples (n = 23). k UMAP plot showing CD8⁺ terminal Tex and progenitor Tex ⁽Texp) cells in all samples (n = 23). l RNA velocity analysis of CD8⁺ Tex clusters based on Dynamo. Arrows in the plot illustrating potential differentiation paths. m Fraction of CD8⁺ terminal Tex and Texp cells in CD8⁺ Tex-relevant cells for pre- and post-treatment responders and non-responders.