Fig. 5: TCR analyses reveal increased tumor-reactive T cells in the LNs.

A Bar plot indicating the percentage (rounded values are indicated) of single, small, medium, large and hyperexpanded-sized clones in CD8⁺ (left) and CD4⁺ (right) T cells in LN and PB for each patient analyzed (n = 10). B UMAP plot colored according to the T-cell clone size based on the TCR-seq data. NA: no TCR information available. C Graph showing the TCR Shannon diversity index for each T-cell subset identified by scRNA-seq in PB and LN samples. The dot color corresponds to the UMAP cluster plot from Fig. 4A. D Alluvial plot displaying the top 10 most frequent clones for LN and PB. E Proportion of predicted CLL-reactive, non-reactive and unknown/ NA T-cell clonotypes out of total T cells in LN and PB. F Scatter plot shows LN and PB clone sizes from all 5 CLL patients. Color represents reactivity status and dot size the total number of cells per clonotype. G Left: Examples of large clusters of convergently recombined TCRs identified by GLIPH2 containing multiple CLL T-cell-derived TCRs predicted to be CLL-reactive (orange-red), as well as TCRs found in the LN or PB for which no scSEQ data and predicTCR scores were available (grey). Middle: Examples of TCR clusters called as non-CLL reactive (blue); in patient BC9 7 TCRs within the SP%RNTE_ANQS cluster are known to bind the HLA-B*07 restricted epitope of the CMV pp65 protein (bold black node border). Right: Examples of heterogeneous clusters. TCRs for which CD4/CD8 status could not be determined due to lack of scSEQ data are illustrated as rectangular nodes. Source data are provided as a Source Data file Fig5.