Fig. 3: Exploring spatial gene expression patterns and functional consequences in thymic T cell development and differentiation.
a Heat map showing the smoothed expression of genes that exhibited significant variance with distance in pediatric spatial transcriptomics (ST) slices. The red arrow indicates the direction of gene expression change from the distal cortex to the medullary center (Supplementary Data 3). Two broad gene clusters (Cluster1 and Cluster2) were assigned by cutting the hierarchical clustering tree, and the biological processes (BP) terms enriched in each cluster are selectively shown. The medulla indicator genes (Supplementary Table 2) closely linked to T-cell differentiation status8,33 are highlighted. b Heat map of marker genes, only the top 30 over-expressed genes are shown for the cortical and medullary regions, respectively. Spots are ordered by ST samples. c Overlap between genes that vary significantly with distance (DVGs) and the differentially expressed genes (DEGs) between medullary and cortical regions. d Spatial distribution of the top ten DEGs in eight thymus ST slices; five were up-regulated in the medullary region and the remainder in the cortical region. The lines, representing the relationship between spatial distance and gene expressions, were smoothed using the natural spline regression model, and the shaded areas around these lines denote the 95% confidence intervals for the fitted values. e, f Expression levels (left) and spatial localization (right) of (e) CCL19, CCR7 and (f) ELOVL4 and CD99 in thymic cell types. g, h Violin plots combined with box plots showing the distribution of ELOVL4 (left) and CD99 (middle) expression, and T-cell receptor α (TCRα)-related gene scores (right) in DP_blast and DP_re cell types in our thymic single-cell dataset. Median value, interquartile range (IQR) as bounds of the box and whiskers that extends from the box to upper/lower quartile ± IQR × 1.5. P-values were obtained from the two-sided t-test. Our thymus data (DP_blast=15,812 cells; DP_re=52,320 cells; (g) Park et al.’s data, (DP(P) = 12,057 cells; DP(Q) = 11,219 cells; (h). i, j Scatter plot showing the expression of the selected gene and the signature score of TCRα changing with age in the DP_re stage. Each data point represents an individual sample, with the dashed line indicating the loess fit. The signature score of TCRα is inferred by its associated TRAV* genes. (i) ELOVL4 vs. TCRα; (j) CD99 vs. TCRα. k Scatter plot showing the associations between the expression of CD99 (left) and ELOVL4 (right) with the signature score of TCRα separately. The shaded areas indicate the 95% confidence interval from the linear regression models, respectively. “R” represents the Pearson correlation coefficient, and the p-value is obtained from the two-sided t-test. DP_blast: Double positive blast cells, DP_re: Double positive rearrangement cells. Source data are provided as a Source Data file.
