Extended Data Fig. 2: Reduced T cell differentiation lineage potentials in aged human thymus.
(a) Dot plots of DEGs among DN cells clusters described in Fig. 2a. Colors represent the scaled expression and dot sizes encode the proportion of gene-expressing cells. (b-c) UMAP visualizations of Monocle3 derived differentiation trajectory of DN cells. Colors indicate cell identity (b) or pseudotime (c). (d) Dot plot shows the transcription levels of CD3, CD4 and CD8 among DN cell subsets and DP cells. Dot colors represent the scaled expression and dot sizes encode the proportion of gene-expressing cells. (e) Heatmaps indicate the age-associated genes (adjusted P values < 0.05, fold change > 1.25) in DN-Q1 (top) and DN-Q2 (bottom) cells. (f) Violin plots of DEGs in each lineage engaged in STEMNET analysis. (g) Statistics of the proportion of T cells differentiated from thymic progenitor cells including Thy1 (CD45+CD34+CD7−CD1a−) and Thy2a (CD45+CD34+CD7+CD1a−CD44+CD2−) sorted from thymi across different age groups in artificial thymic organoid (ATO) (n = 5 for Group I; n = 3 for Group II; n = 4 for Group III). P values (row-wise: from left to right): P = 0.0726; *P = 0.0333; ns, P = 0.9686; P = 0.1394; P = 0.0983; ns, P = 0.9992; ns, P = 0.2285; ns, P = 0.1830; ns, P > 0.9999; ns, P = 0.1562; *P = 0.0259;ns, P = 0.6752; P = 0.0603; **P = 0.0039; ns, P = 0.3886; ns, P = 0.3410; ns, P = 0.1512; ns, P = 0.9180. Data are presented as mean ± s.e.m. (h) Representative flow cytometry data of differentiation results of CD45+CD34+ thymic progenitor cells including Thy1 and Thy2a sorted from thymi across age groups under T cell differentiation conditions, which are derived from 4 independent experiments. All data represent biological replicates. Statistical analysis was performed using Bonferroni-adjusted two-tailed Wilcoxon rank sum test (a, d, e, f) or One-way ANOVA with Tukey’s multiple comparisons test (g).
