Fig. 3.

Evolution of the TCR repertoire on treatment. A Overlapping intratumoral TCR clonotypes at baseline and post-treatment for patient N02 and N03. B Relative abundance (normalized read count) for persisting intratumoral TCRs between baseline and post-treatment. C Intratumoral TCR clonality at baseline and post-treatment. D The number of clonotypes unique to the post-treatment biopsy also detected in PBMC samples, and their fraction of the TCR repertoire. The TCR repertoire fraction was calculated by summing the normalized read count for each TCR and dividing by the total read count for the same sample. E Volcano plot illustrating enriched TCRs after a 10-day in vitro peptide stimulation of PBMCs. Orange dots indicate TCRs with a log fold change above 5, unadjusted p < 0.05, and red dots adjusted p < 0.05. F Vaccine-enriched TCRs identified in unstimulated PBMC samples. TCR clonotypes are labeled according to their rank in terms of log fold change after stimulation. G Vaccine-enriched TCRs identified in tumor biopsies. H Sample clonality pre and post-10-day in vitro vaccine peptide stimulation. I T cell proliferation responses from the same samples. J Unstimulated PBMC sample clonality vs. in vitro T cell proliferation response