Extended Data Fig. 7. Expanded intratumoral ubiquitous TCRs are associated with a T_H1 and CD8⁺ T cell transcriptional signature in the tumor and have a phenotype consistent with tumor antigen reactivity.

a, Correlation between the numbers of expanded intratumoral ubiquitous and regional TCR β-chain sequences and the transcriptional expression score (geometric mean) for various immune-related gene sets, characterizing cell types or functional states (names indicated above heat map). Details of how the transcriptional scores are calculated are in the Methods. The area and color of the circles correspond to the magnitude of the correlation coefficient. The color key indicates Spearman’s rank correlation coefficient. *P < 0.05; **P < 0.0l; after Bonferroni correction. b, CD8⁺ TILs from CRUK0291 and CRUK0099 were sorted into two populations, PD-1⁺CD103⁺ and PD-1⁺CD103⁻ cells. The flow cytometry gating strategy for a representative patient is shown (pre-gated on live > singlets > CD3⁺ > CD8⁺ T cells). RNA was extracted and sequenced from sorted populations as described in the Methods. c, The RNA-seq data were mined for the presence of expanded ubiquitous and regional α-chain and β-chain sequences. The heat maps show the number of times each expanded ubiquitous or regional TCR CDR3 sequence was found in each of the RNA-seq data from PD-1⁺CD103⁺ or PD-1⁺CD103⁻ cells, as a proportion of the number of times a constant region sequence of the same length was detected. These proportions are scaled for each row and color coded. Each row represents a distinct expanded TCR sequence.