Spatial cartography of human thymus enables the geopositioning of lineage transcription factors in rare mimetic thymic epithelial cells.

The thymus is the primary site for T cell maturation. While transcriptional profiling of human thymi has been reported, a high-resolution spatial atlas is needed. Here we use Stereo-seq spatial transcriptomics to generate a spatial atlas of the human fetal (13, 14, 17 or 18 weeks post-conception) and pediatric (7 weeks, and 2, 5 or 6 years old) thymi. The architecture of the thymus comprises regions such as the outer cortex, inner medulla, and septa, and contains multiple cell types, including thymic epithelial cells (TEC), thymocytes, dendritic cells, macrophages, and B cells. Utilising this spatial transcriptomics and proteomics information, we further describe lineage-defining transcription factors (TF) that govern molecular signatures of rare mimetic TEC regulation. Our study thus establishes a high-resolution spatial atlas of the human fetal and pediatric thymi to uncover distinct architectural features and TFs regulating these rare cell types, and serves as a resource for further studies.