Alterations in spatial niches in the 22q11DS thymus. (A) Identification of spatially colocalized cellular compartments using NMF. The results are shown as a dotplot with cell-type abundance (columns) across NMF factors (rows). Each factor represents a spatially co-occurring group of cell types. The dot size and dot color correspond to NMF weights and normalized cell-type abundance. Boxes highlight colocalized groups of cells in factors 2 and 3. (B) NMF factor 2 and 3 plotted spatially in representative tissue samples from 22q11DS patients and controls. The color of each spot indicates factor weight, with purple representing low relative weight and yellow representing high relative weight. Spatial locations of NMF factors 1, 4, and 5 are shown in Fig. 4 A. (C) Volcano plot of DEGs in NMF factor 2 in 22q11DS patients (n = 2) compared with controls (n = 8). Comparison between the groups was performed using the two-sided Wilcoxon rank-sum test with Benjamini–Hochberg correction for multiple testing. Significant DEGs (adjusted P <0.05) are shown in red (upregulated) and blue (downregulated). Histogram showing up- and downregulated GO terms in 22q11DS NMF factor 2. GO enrichment analyses were performed on the significant DEGs in Fig. S3 A using the PANTHER classification system. Significantly upregulated GO terms (adjusted P value, FDR <0.05) point to the right in red, and significantly downregulated GO terms point to the left in blue. (D) Heatmap showing the expression of interferon-related genes in selected cell-type subsets in 22q11DS patients (n = 2) and controls (n = 8). Each gene was scaled using the Z-score. The blue color indicates low expression, and the red color indicates high expression. The dotted line separates gene sets including interferons and interferon-stimulated genes. Abbreviations for cell-type annotations are provided in Table S2.