Extended Data Fig. 12. Phenotypic characteristics of FACS-sorted peripheral blood CD8+/Vβ2+ T cells from MPR MD01-005.

a, Selective gene expression of 2D UMAP red-scale projection is shown of canonical T cell subset marker genes, cell subset selective genes, and immune checkpoints on CD8 T cell subsets sorted from longitudinal peripheral blood of one patient (MD01-005) with complete pathologic response. b-d, Pseudotime reconstruction and pseudo-temporal dynamic gene identification in peripheral blood CD8 T cells from a complete pathologic responder. Longitudinal PBMC were collected from complete pathologic responder MD01-005 (0% residual tumour) during treatment and in post-surgery follow up. Peripheral blood CD8⁺ T cells were FACS sorted based on expression of TCR Vβ2, which corresponds to the MANA-specific CDR3 CASNKLGYQPQHF as identified previously via the MANAFEST assay (Extended Data Fig. 2a). scRNA-seq–TCR-seq was performed on the sorted population from each time point. b, Constructing the pseudotime axis on the diffusion map from T_mem(3) to T_eff(3) as trajectory 1. c, GO analysis for genes that significantly change along trajectory 1, ranked by FDR. d, Constructing the pseudotime axis on the diffusion map from T_mem(3) to T_mem(2) as trajectory 2. e, GO analysis for genes that significantly change along trajectory 2, ranked by FDR. f, Heat map showing genes that significantly change along trajectory 2 (FDR < 0.05).