The thymus is the primary lymphoid organ where naïve T cells are generated; however, with the exception of age, the parameters that govern its function in healthy humans remain unknown. We characterized the variability of thymic function among 1000 age- and sex-stratified healthy adults of the Milieu Intérieur cohort, using quantification of T cell receptor excision circles (TRECs) in peripheral blood T cells as a surrogate marker of thymopoiesis. Age and sex were the only nonheritable factors identified that affect thymic function. TREC amounts decreased with age and were higher in women compared to men. In addition, a genome-wide association study revealed a common variant (rs2204985) within the T cell receptor locus, between the and gene segments, which associated with TREC amounts. Strikingly, transplantation of human hematopoietic stem cells with the rs2204985 GG genotype into immunodeficient mice led to thymopoiesis with higher TRECs, increased thymocyte counts, and a higher TCR repertoire diversity. Our population immunology approach revealed a genetic locus that influences thymopoiesis in healthy adults, with potentially broad implications in precision medicine.

Summary The Autoimmune Regulator (Aire) protein coordinates the negative selection of developing thymocytes by inducing the expression of hundreds of tissue‐specific antigens within the thymic medulla, which is also a primary site of the expression of the immune checkpoint HLA‐G molecule. Considering the immunomodulatory properties of Aire and HLA‐G, and considering that the role of the constitutive thymus expression of HLA‐G has not been elucidated, we studied the effect of AIRE cDNA transfection on HLA‐G expression in 4D6 thymic cells and in the HLA‐G‐positive JEG‐3 choriocarcinoma cells. Aire promoted the transactivation of HLA‐G gene by increasing the overall transcription, inducing the transcription of at least G1 and G2/G4 isoforms, and incrementing the occurrence and distribution of intracellular HLA‐G protein solely in 4D6 thymic cells. Luciferase‐based assays and chromatin immunoprecipitation experiments performed in 4D6 cells revealed that Aire targeted at least two regions within the 5′‐untranslated regulatory region (5′‐URR) extending 1·4 kb from the first ATG initiation codon. The interaction occurs independently of three putative Aire‐binding sites. These results indicate that the Aire‐induced upregulation of HLA‐G in thymic cells is likely to act through the interaction of Aire with specific HLA‐G 5′‐URR DNA‐binding factors. Such a multimeric transcriptional complex might operate in the thymus during the process of promiscuous gene expression.