Figure 3.
Differently expressed genes highlights altered extracellular matrix pathways and reduced inflammatory signaling in the 22q11DS thymus. (A) Volcano plot of DEGs 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 the Benjamini–Hochberg correction for multiple testing. Significant DEGs (adjusted P <0.05) are shown in red (upregulated) and blue (downregulated). Genes located in the 22q11.2 deletion region (LCR22A–D) are marked in yellow. (B) Histogram showing up- and downregulated GO terms in the 22q11DS thymus. GO enrichment analyses were performed on significant DEGs in Fig. 3 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. (C) Dotplots showing the expression in the whole thymus tissue of selected genes associated with significantly enriched GO terms in Fig. 3 B. The expression of each gene is scaled using min-max scaling, where the blue color indicates low expression, and the red color indicates high expression. The dot size represents the proportion of total Visium spots in which the gene is expressed. (D) Histograms showing significantly up- and downregulated GO terms per annotated morphological region in 22q11DS patients compared with controls. GO enrichment analyses were performed on the significant DEGs in each region: capsule, cortex, CMJ, and medulla. Significantly upregulated GO terms (adjusted P value, FDR <0.05) point to the right, and significantly downregulated GO terms point to the left. The colors of the bars indicate region identity. (E) Heatmap showing the predicted cell type–specific expression of WNT signaling components in 22q11DS patients and controls. Gene expression is presented as scaled module scores where WNT protein ligands are represented by genes WNT5 and WNT4, WNT modulators by SFRP2, SFRP4, SFRP1, DKK1, and GPC3, and WNT receptors by FZD9, FZD4, FZD5, FZD8, ROR2, and RYK. The predicted cell type–specific expression of each gene is shown in Fig. S2 A. (F) Heatmap showing the expression of selected genes in mesenchymal and epithelial cell subsets in 22q11DS patients (n = 2) and controls (n = 8). For visualization, each gene was scaled using the Z-score. The blue color indicates low relative expression, and the red color indicates high relative expression. Dotted lines separate gene sets: mesenchymal transcripts, cortical thymic epithelial cells (cTEC)-associated genes, genes associated with selection processes, and genes encoding cytokeratins. (G) Heatmap showing the expression of selected genes in thymocyte and T cell subsets in 22q11DS patients (n = 2) and controls (n = 8). For visualization, each gene was scaled using the Z-score. The blue color indicates low relative expression, and the red color indicates high relative expression. Dotted lines separate gene sets involving early T cell activation and T cell receptor signaling. Refer to the image caption for details. Panel A: A volcano plot shows differentially expressed genes (DEGs) in 22q11DS compared to controls. The x-axis represents log2 fold change, and the y-axis represents minus log10 p-value. Upregulated genes are in red, downregulated genes are in blue, and genes in the 22q11.2 deletion region are marked in yellow. Panel B: A histogram displays upregulated and downregulated GO terms in 22q11DS thymus. The x-axis shows minus log10 FDR, with upregulated terms in red to the right and downregulated terms in blue to the left. Panel C: Dotplots illustrate the expression of selected genes associated with enriched GO terms in whole thymus tissue. Dot size indicates the proportion of spots expressing the gene, and color represents scaled expression levels. Panel D: Histograms show significantly up- and downregulated GO terms per morphological region in 22q11DS compared to controls. The x-axis represents -log10 FDR, with colors indicating different regions. Panel E: A heatmap presents the predicted cell type-specific expression of WNT signaling components in 22q11DS and controls. Genes are grouped into WNT protein ligands, modulators, and receptors, with color indicating scaled expression. Panel F: A heatmap shows the expression of selected genes in mesenchymal and epithelial cell subsets in 22q11DS and controls. Genes are scaled using Z-score, with color indicating relative expression levels. Dotted lines separate gene sets. Panel G: A heatmap displays the expression of selected genes in thymocyte and T cell subsets in 22q11DS and controls. Genes are scaled using Z-score, with color indicating relative expression levels. Dotted lines separate gene sets involving early T cell activation and T cell receptor signaling.

Differently expressed genes highlights altered extracellular matrix pathways and reduced inflammatory signaling in the 22q11DS thymus. (A) Volcano plot of DEGs 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 the Benjamini–Hochberg correction for multiple testing. Significant DEGs (adjusted P <0.05) are shown in red (upregulated) and blue (downregulated). Genes located in the 22q11.2 deletion region (LCR22A–D) are marked in yellow. (B) Histogram showing up- and downregulated GO terms in the 22q11DS thymus. GO enrichment analyses were performed on significant DEGs in Fig. 3 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. (C) Dotplots showing the expression in the whole thymus tissue of selected genes associated with significantly enriched GO terms in Fig. 3 B. The expression of each gene is scaled using min-max scaling, where the blue color indicates low expression, and the red color indicates high expression. The dot size represents the proportion of total Visium spots in which the gene is expressed. (D) Histograms showing significantly up- and downregulated GO terms per annotated morphological region in 22q11DS patients compared with controls. GO enrichment analyses were performed on the significant DEGs in each region: capsule, cortex, CMJ, and medulla. Significantly upregulated GO terms (adjusted P value, FDR <0.05) point to the right, and significantly downregulated GO terms point to the left. The colors of the bars indicate region identity. (E) Heatmap showing the predicted cell type–specific expression of WNT signaling components in 22q11DS patients and controls. Gene expression is presented as scaled module scores where WNT protein ligands are represented by genes WNT5 and WNT4, WNT modulators by SFRP2, SFRP4, SFRP1, DKK1, and GPC3, and WNT receptors by FZD9, FZD4, FZD5, FZD8, ROR2, and RYK. The predicted cell type–specific expression of each gene is shown in Fig. S2 A. (F) Heatmap showing the expression of selected genes in mesenchymal and epithelial cell subsets in 22q11DS patients (n = 2) and controls (n = 8). For visualization, each gene was scaled using the Z-score. The blue color indicates low relative expression, and the red color indicates high relative expression. Dotted lines separate gene sets: mesenchymal transcripts, cortical thymic epithelial cells (cTEC)-associated genes, genes associated with selection processes, and genes encoding cytokeratins. (G) Heatmap showing the expression of selected genes in thymocyte and T cell subsets in 22q11DS patients (n = 2) and controls (n = 8). For visualization, each gene was scaled using the Z-score. The blue color indicates low relative expression, and the red color indicates high relative expression. Dotted lines separate gene sets involving early T cell activation and T cell receptor signaling.

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