Fig. 3: T-cell development dysfunction in the thymus and TET subtypes.

(a) Uniform manifold approximation and projection (UMAP) visualization of total T cells from the normal human thymus (n = 1) and TET samples (n = 6), colored by the identified cell subpopulation. (DN, double-negative T cells; DP, double-positive T cells; the abbreviations used below are consistent with these definitions). (b) Dot plot of marker gene expression in T-cell types. Here and in later figures, the color represents the maximum normalized mean expression of marker genes in each cell subgroup, and the size indicates the proportion of cells expressing marker genes. (c) Same UMAP plot as (a), colored by groups. (d) Same UMAP plots of total T cells from samples of each group, colored by the identified cell subpopulation as in (a). The immature T cells are indicated by yellow dotted circles, and mature T cells are indicated by blue dotted circles. (e) Composition of the T-cell compartment showing average frequencies of major T-cell subpopulations for each group (n = 1, 2, 2 and 2 for N, T1, T2 and T3, respectively). (f) Pseudotime trajectory for T cells from all samples in a two-dimensional state-space defined by Monocle2, colored by identified T-cell subpopulation. (g) The same pseudotime plots for T cells from samples of each group, colored by group. (h-j) Dot plots depicting the relative expression levels of selected NOTCH (h), WNT (i), or IL-7 (j) signaling pathway genes in total T cells from each group. Source data are provided as a Source Data file.