Transcriptomic mapping confirms reduced gene expression in the LCR22A–D region and an increased corticomedullary ratio in 22q11DS thymus. (A) Schematic overview of chromosome 22 with the most common deletions in the 22q11.2 region. Approximate locations of key genes within the 22q11.2 deletion region, TBX1, COMT, and CRKL, are marked. The LCR22A–D deletion present in the patient study cohort is highlighted in red. (B) Quantification of TBX1, COMT, and CRKL in thymic tissue using qPCR. Results are shown as relative gene copy numbers for each sample in controls (gray, n = 8) and 22q11DS patients (purple, n = 2). (C) Heatmap showing the Visium-derived expression of genes located within and flanking the 22q11.2 deletion region in controls (n = 8) and 22q11DS patients (n = 2). The expression of each gene is scaled using min-max scaling, where the purple color indicates low expression, and yellow indicates high expression. (D) H&E-stained section of a representative thymic tissue sample used for Visium spatial transcriptomics. (E) Pixel-based annotations in a representative thymic tissue sample. Tissue regions were annotated by combining gene expression–based information from Visium with manual curation of the H&E image to generate annotations: cortex (blue), medulla (orange), and capsule (green). (F) Annotation of Visium spots in a representative thymic tissue section. Visium spots were assigned to morphologically defined regions: capsular (green), cortex (blue), CMJ (pink), and medulla (orange). (G) Cortex-to-medulla ratios in controls and 22q11DS patients calculated using both pixel-based annotations and Visium spot-based annotations. Boxplots show cortex/medulla ratio distributions for controls (gray, n = 8) and 22q11DS patients (purple, n = 2). Differences between the groups were compared using two-sided Mann–Whitney U tests. H&E, hematoxylin and eosin.