Mesenchymal cell replacement corrects thymus hypoplasia in murine models of 22q11.2 deletion syndrome

22q11.2 deletion syndrome (22q11.2DS) is the most common human chromosomal microdeletion, causing developmentally linked congenital malformations; thymus hypoplasia, hypoparathyroidism and/or cardiac defects. Thymus hypoplasia leads to T cell lymphopenia, which most often results in mild SCID. Despite decades of research, the molecular underpinnings leading to thymus hypoplasia in 22q11.2DS remain unknown. Comparing embryonic thymuses from mouse models of 22q11.2DS (Tbx1neo2/neo2) revealed similar proportions of mesenchymal-, epithelial- and hematopoietic- cell types as controls. Yet, the small thymuses were growth restricted in fetal organ cultures. Replacement of Tbx1neo2/neo2 thymus mesenchymal cells with normal ones restored tissue growth. Comparative single cell RNA sequencing of embryonic thymuses uncovered 17 distinct cell subsets, with transcriptome differences predominant in the 5 mesenchymal subsets from the Tbx1neo2/neo2 line. Transcripts impacted include extracellular matrix (ECM) proteins, consistent with increased collagen deposition seen in the small thymuses. Attenuating collagen cross-links with minoxidil restored thymus tissue expansion for hypoplastic lobes. In colony forming assays, the Tbx1neo2/neo2-derived mesenchymal cells had reduced expansion potential, contrasting the normal growth of thymus epithelial cells. These findings suggest that mesenchymal cells are causal to the small embryonic thymuses in 22q11.2DS mouse models, correctable by substituting with normal mesenchyme.