Fig 1: A hierarchical model of thymic epithelial cell differentiation with major lineage branches and feature genes during thymus organogenesis. At E11.5 and before (TEC initiation), Foxn1- Epcam+ Sox2+ cells shut down Sox2 transcription and start expression of Foxn1, Krt8, Pax1, ß5t + (Psmb11), and Plet1 to establish the TEC identity (?). During E11.5–E13.5 (Divergency), a small population of TECs upregulated Krt5, Krtdap, Emp2, and Ccl21a, representing the mTEC progenitors (?). Within the Krt5+ cells, UMAP clustering analysis distinguished a subpopulation of Krt5+ Krt8+ Krtdap+ Plet1+ cells that expressed Bpifa1, Aqp5, Slc12a2, and Krt15 in later development (?, ?). The Plet1+ cells at E11.5–E13.5 were previously demonstrated to be TEPCs, which gave rise to both mTEC and cTEC. However, the differentiation potential of Plet1+ cells in postnatal thymus needs to be further verified (?, dotted arrow). At this “Divergency” stage, most of the Krt8+ Pax1+ ß5t+ TECs were highly proliferative and proceeded to differentiate into Ccl25hi Tbatahi cTECs (?). At E14.5–E15.5 (Expansion), proliferative mTEC progenitors decreased cTEC-specific gene expression, upregulated Spib, Klf6, and Il4i1, and started to express Aire (?). At E16.5-Newborn (Maturation), Aire+ mTECs highly expressed Cd52, Csn2, and Aire-dep TRAs (?). At postnatal stage (Post-Aire), mTECs continued to differentiate into tuft-like cells, corneocyte-like cells and Ccl6+ cells (?). Differentiation of Ccl6+ cells from Aire+ mTECs needs to be further demonstrated by in vivo lineage tracing evidence (dotted arrow). Maturation of cTEC in later development was characterized by upregulation of MHCII molecules and chemokines such as Ccl25, Cxcl12, and T cell-enveloping TNCs began to emerge at E16.5 (?). Mesenchymal fibroblast expressed kinds of ligands that provided molecular signaling to support TEC proliferation (?) (Mes, mesenchymal fibroblast; cTEC, cortical thymic epithelial cell; mTEC, medullary thymic epithelial cell). Solid arrow indicating a process has been experimentally validated, and dotted arrow indicating a process has not been validated.