In the thymus, cortical thymic epithelial cells (cTECs) and medullary thymic epithelial cells support αβT cell development from lymphoid progenitors. For cTECs, expression of a specialized gene signature that includes Cxcl12, Dll4, and Psmb11 enables the cortex to support T lineage commitment and the generation and selection of CD4+CD8+ thymocytes. Although the importance of cTECs in T cell development is well defined, mechanisms that shape the cTEC compartment and regulate its functional specialization are unclear. Using a Cxcl12DsRed reporter mouse model, we show that changes in Cxcl12 expression reveal a developmentally regulated program of cTEC heterogeneity. Although cTECs are uniformly Cxcl12DsRed+ during neonatal stages, progression through postnatal life triggers the appearance of Cxcl12DsRed− cTECs that continue to reside in the cortex alongside their Cxcl12DsRed+ counterparts. This appearance of Cxcl12DsRed− cTECs is controlled by maturation of CD4CD8, but not CD4+CD8+, thymocytes, demonstrating that stage-specific thymocyte cross-talk controls cTEC heterogeneity. Importantly, although fate-mapping experiments show both Cxcl12DsRed+ and Cxcl12DsRed− cTECs share a common Foxn1+ cell origin, RNA sequencing analysis shows Cxcl12DsRed− cTECs no longer express Foxn1, which results in loss of the FOXN1-dependent cTEC gene signature and may explain the reduced capacity of Cxcl12DsRed− cTECs for thymocyte interactions. In summary, our study shows that shaping of the cTEC compartment during the life course occurs via stage-specific thymocyte cross-talk, which drives loss of Foxn1 expression and its key target genes, which may then determine the functional competence of the thymic cortex.

This work was supported by the UKRI, Medical Research Council Programme Grant (MR/T029765/1 to G.A.) and a Wellcome Trust–funded Collaborative Award (SynThy, 211944/Z/18/Z), for which G.A. and G.A.H. are partners. G.A.H. also received funding from the Swiss National Science Foundation (IZLJZ3_171050; 310030_184672) and the Wellcome Trust (105045/Z/14/Z). J.E.C. is a Sir Henry Dale Fellow funded by The Wellcome Trust.

The sequencing data have been submitted to the Gene Expression Omnibus (GEO) ( under accession number GSE205940.

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