TNF superfamily members play distinct roles in shaping the thymic stromal microenvironment

•RANKL specifically induces Aire and autoantigen expression in the thymic stroma.•TNFα and LTβ induce the expression of key thymic chemokines.•RANKL and LTβ work synergistically to establish the thymic microenvironment.•Specific gene expression patterns may be attributable to differential NF-κB binding.

The differentiation and proper function of thymic epithelial cells (TECs) depend on various tumor necrosis factor superfamily (TNFSF) signals that are needed to maintain the thymic stromal microenvironment. Nevertheless, the direct transcriptional effects of these signals on TECs remain unclear. To address this issue, we stimulated murine embryonic thymus tissue with selected TNFSF ligands and performed a gene expression profiling study. We show that Aire expression is a direct and specific effect of RANKL stimulation, whereas LTβ and TNFα are major inducers of chemokines in the thymic stroma and we propose differential NF-κB binding as one possible cause of these gene expression patterns. Our work provides further insight into the complex molecular pathways that shape the thymic microenvironment and maintain central tolerance.