Beyond cysts – organization of epithelial networks in the murine thymus

The thymus originates from the third pharyngeal pouch endoderm, which also gives rise to respiratory tract elements. Here, we examined intrathymic cystic structures, long considered remnants of organogenesis. Through sequential histology and ultrastructural imaging, we uncovered that these 'cysts' are in fact continuous and structured epithelial networks embedded within the thymic parenchyma. These networks follow a conserved 'head-neck-funnel-tentacle' architecture spanning the trabeculae, cortex, corticomedullary junction (CMJ) and medulla. The head, typically glandular and ciliated, connects to a funnel enriched in diverse epithelial cell types - goblet, tuft, club, ionocyte-like, microfold and ciliated cells - at the CMJ. Tentacle-like projections sometimes extend into the medulla, often surrounding perivascular spaces. Luminal contents vary, with thymocytes and macrophages most abundant caudally. We also identified solitary medullary thymic epithelial cells with large ciliated cytoplasmic lumens, distinct from these epithelial networks. Electron microscopy suggested a respiratory identity and thymic-specific adaptations for the lining cells. These findings challenge the notion of thymic cysts as inert debris, and instead reveal a coherent, mimetic system with possible roles in thymocyte selection, maturation and egress.