Extended Data Fig. 7: HPV-specific CD8 T cell clonotypes exist in multiple differentiation states.

a, UMAP clustering of HPV tetramer-specific CD8 T cells. b, TCR repertoire of tetramer-positive CD8 TILs in primary tumours (Prim.) and metastatic lymph nodes (Met.) with the top four clonotypes highlighted. Colours do not indicate the same clonotype between patients or epitope reactivities. c, TCR repertoire of tetramer-positive CD8 TILs in matched primary tumour and metastatic lymph node of the same patient with the top 4 clonotypes highlighted. Colours indicate the same clonotype within a patient and epitope reactivity. d, TCR frequency in patients with matched primary and metastatic tissue. e, TCR diversity of the identified clusters. f, Overlap between clusters for each patient as determined by Morisita Horn index. g, Distribution of the most frequent TCR clonotypes for each patient and epitope across gene expression clusters. UMAP plots show the distribution of the most frequent TCR clonotype across clusters. Accompanying bar charts showing the distribution of the eight most prominent TCR clonotypes across all clusters (clonotypes with less than 10 cells are not shown). The number of cells of the respective TCR clonotype is indicated below.