Fibroblast-driven collagen expansion and altered thymic medullary niches in 22q11.2 deletion syndrome

22q11.2 deletion syndrome (22q11DS) is associated with congenital anomalies and variable thymic hypoplasia with T cell lymphopenia and immune dysregulation. However, the spatial organization of human thymic lymphopoiesis and stromal mechanisms contributing to thymic dysfunction in 22q11DS remain incompletely defined. We applied spatial transcriptomic and spatial proteomic analyses on thymic samples from two 22q11DS patients and compared them with healthy controls. Across 22q11DS samples, we observed alterations in the corticomedullary organization and in the frequencies of fibroblasts, B cells, regulatory T cells, and mTEC subsets. These features coincided with a prominent remodeling of the mesenchymal compartment, including increased expression of extracellular matrix programs and collagens, and predicted disruption in mesenchymal-epithelial cell crosstalk. In the medulla, we observed alterations in interferon-associated gene programs within a colocalized niche comprising B cells, antigen-presenting cells, and mTEC subsets. Together, this provides an integrated spatial map of the 22q11DS thymus and nominates stromal remodeling as a candidate driver of impaired central tolerance induction in 22q11DS.