Figure 4.
Increased expression of fibroblast-derived collagens in the 22q11DS thymus. (A) Dotplot of collagen gene expression in each region in 22q11DS patients and controls. Average gene expression values were plotted using log-normalized raw counts. For visualization, the expression of each gene was scaled using min-max scaling. The blue color indicates low relative expression, and the red color indicates high relative expression. The dot size represents the proportion of total Visium spots in which the gene is expressed. (B) Representative immunofluorescence stainings of collagen type I and IV in control and 22q11DS thymic sections. (C) Barplots showing results from qPCR-based quantification of collagen gene transcripts in 22q11DS patients (purple, n = 2) and controls (gray, n = 8). qPCR analyses were performed on the fresh-frozen whole thymic tissue. Results are presented as relative quantification (RQ: 2^(−ΔΔCt)). (D) Heatmap of predicted cell type–specific expression of collagens. Gene expression is presented as scaled module scores, where collagen type I is represented by genes COL1A1 and COL1A2, collagen type II by COL2A1, collagen type III by COL3A1, collagen type IV by COL4A1 and COL4A2, collagen type VI by COL6A1 and COL6A2, and collagen type VIII by COL8A1.(E) Visualization of estimated Fb 2 abundance in spatial coordinates in representative tissue samples from 22q11DS patients and controls. Dark purple indicates low abundance, and yellow indicates high abundance *P value < 0.05; ns, not significant. Refer to the image caption for details. Panel A: A dotplot shows collagen gene expression in different regions (Capsular, Cortex, CMJ, Medulla) for both 22q11DS and control groups. The dot size represents the proportion of total Visium spots where the gene is expressed, and the color scale indicates relative expression levels from low (blue) to high (red). Panel B: Immunofluorescence images display collagen type 1 and 4 staining in thymic tissue sections from control and 22q11DS groups. Panel C: Barplots present qPCR-based quantification of collagen gene transcripts in 22q11DS (purple, n equals 2) and control (grey, n equals 8) groups. The y-axis shows relative quantification, with significant differences marked by asterisks. Panel D: A heatmap illustrates predicted cell type-specific expression of collagens, with gene expression presented as scaled module scores. Different collagen types are represented by specific genes. Panel E: Spatial localization images show estimated fibroblast type 2 abundances in thymic tissue samples from control and 22q11DS groups. Dark purple indicates low abundance, and yellow indicates high abundance.

Increased expression of fibroblast-derived collagens in the 22q11DS thymus. (A) Dotplot of collagen gene expression in each region in 22q11DS patients and controls. Average gene expression values were plotted using log-normalized raw counts. For visualization, the expression of each gene was scaled using min-max scaling. The blue color indicates low relative expression, and the red color indicates high relative expression. The dot size represents the proportion of total Visium spots in which the gene is expressed. (B) Representative immunofluorescence stainings of collagen type I and IV in control and 22q11DS thymic sections. (C) Barplots showing results from qPCR-based quantification of collagen gene transcripts in 22q11DS patients (purple, n = 2) and controls (gray, n = 8). qPCR analyses were performed on the fresh-frozen whole thymic tissue. Results are presented as relative quantification (RQ: 2^(−ΔΔCt)). (D) Heatmap of predicted cell type–specific expression of collagens. Gene expression is presented as scaled module scores, where collagen type I is represented by genes COL1A1 and COL1A2, collagen type II by COL2A1, collagen type III by COL3A1, collagen type IV by COL4A1 and COL4A2, collagen type VI by COL6A1 and COL6A2, and collagen type VIII by COL8A1.(E) Visualization of estimated Fb 2 abundance in spatial coordinates in representative tissue samples from 22q11DS patients and controls. Dark purple indicates low abundance, and yellow indicates high abundance *P value < 0.05; ns, not significant.

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