Fig. 2: T-cell subsets in the thymus and TET subtypes.

(a) t-SNE plot of CD45⁺CD3⁺ T cells from all samples (n = 25), colored by cell subset. (DN, CD3⁺CD4^-CD8^-; DP, CD3⁺CD4⁺CD8⁺). (b) Heatmap showing relative normalized protein expression for the T-cell subsets from CyTOF, normalized total matrix. (c) t-SNE plots of CD45⁺CD3⁺ T cells from human TETs (n = 22) and the normal thymus (n = 3) by CyTOF using the Phenograph clustering scheme. Samples were grouped according to WHO classification, Masaoka stage or our alternative classification, and each color represents a T-cell subset. (d–f) Composition of the CD45⁺CD3⁺ T-cell compartment showing the average frequencies of major T-cell subsets for each WHO histological subtype (d) (n = 3, 3, 7, 6 and 5 for N, A, AB, B and TC, respectively), Masaoka stage (e) (n = 3, 11, 4, 5 and 2 for N, I, II, III and IV, respectively) or our alternative classification (f) (n = 3, 9, 7 and 6 for N, T1, T2 and T3, respectively). Each color represents a T-cell subset, same as in (c). (g) Bar plots showing the frequencies of the main T-cell subsets among the four groups of samples (n = 3, 9, 7 and 6 for N, T1, T2 and T3, respectively. Data are presented as the mean ± s.e.m. P values in the figure were determined by an unpaired two-tailed Student’s t test). (DP, CD3⁺CD4⁺CD8⁺). (h) Representative flow cytometric plot of CD3⁺CD4^-CD8^- T cells, CD3⁺CD4⁺ T cells, CD3⁺CD8⁺ T cells and CD3⁺CD4⁺CD8⁺ T cells from TETs of three types. (i) Representative immunofluorescence (IF) staining images showing CD3 (pale blue), CD8 (green), CD4 (red) and DAPI (nuclei, blue) in the normal human thymus and TET samples (scale bar: 100 μm). (M: Medulla; C: Cortex; M-like: Medulla-like structure; C-like: Cortex-like structure). Experiment was performed in three independent samples for each group with similar results. Source data are provided as a Source Data file.