Fig. 2: Differential gene expression in T cells in children with T1D.

A Differentially expressed genes (DEGs) in CD8⁺ (left) and CD4⁺ (right) T cells comparing children with T1D at diagnosis (T0, n = 30) or one year after diagnosis (T1, n = 29) with healthy donors (HD, n = 13). Each point represents one gene, plotted by average log₂ fold change in T1D T0 vs. HD (x-axis) and T1D T1 vs. HD (y-axis). DEGs were identified using the two-sided Wilcoxon rank-sum test (Seurat FindMarkers), with p-values adjusted for multiple comparisons (Bonferroni). Only genes with adjusted p < 0.05 are shown; selected top up- and downregulated genes are labeled. B Heatmap of relative expression of selected DEGs across HD, T1D T0, and T1D T1. Donor-level averages were calculated using Seurat AverageExpression, z-score normalized within each gene, and then averaged per group. C Gene set enrichment analysis (GSEA) showing enrichment of naïve versus effector T cell signatures from published datasets (GSE9650, GSE11057). Each curve corresponds to genes upregulated (dark, “UP” set) or downregulated (light, “DN” set) in naïve versus effector cells. Positive normalized enrichment scores indicate enrichment of the naïve-up gene set and depletion of effector-up genes in T1D samples. P-values were estimated using an adaptive multi-level split Monte Carlo scheme (fgsea R package). D Violin plots of decoupleR scores quantifying similarity to reference contrasts (Temra vs. naïve; naïve vs. Tem) in CD8⁺ (left) and CD4⁺ (right) T cells. Each dot = one donor. Comparisons between HD and T1D T0 were assessed using two-tailed Mann–Whitney tests; paired comparisons between T1D T0 and T1 used two-tailed paired Mann–Whitney tests. Bars indicate medians. n = 13 HD, 30 T1D T0, 29 T1D T1. T1D – Type 1 Diabetes Mellitus, T0 – timepoint at diagnosis, T1 – timepoint one year after diagnosis, GSEA – Gene set enrichment analysis.