Extended Data Fig. 6: Functional subset annotation of tumor-reactive TILs by single-cell sequencing analysis.
a, Signature gene expression of each functional subset for CD4+ and CD8+ TIL. b, Comparison of the utilized annotation method with a historical control. Red, matched or most similar to; gray: unmatched. c, Enrichment of CD4/CD8 T cell signature gene sets among functional subsets. d, Comparison of annotation markers in this manuscript with those previously reported in other T cell studies. e, Composition of TIL clones among annotated functional subsets for each patient. PT# denotes patient ID. f, Frequencies of tumor-reactive and bulk TIL clones among annotated functional subsets. g, Comparison of tumor-reactive TIL (left) and bulk TIL (right) phenotype in Clinical Benefit vs No-Benefit patients. Abbreviations: Tm: memory T; Tcytotoxic: cytotoxic T; Tstemlike: stem-like T; Teff: effector T; Tem: effector memory T; Tex: exhausted T; Tprolif: proliferating T; Tfh: follicular helper T; Treg: regulatory T. h-i, UMAP was generated separately for CD4+ TIL (h) and CD8+ TIL (i). Functional cluster annotation was performed (left). Tumor-reactive clones and their composition among annotated subsets were shown (right).
