The metabolic landscape of thymic T cell development in vivo and in vitro

Although metabolic pathways have been shown to control differentiation and activation inperipheral T cells, metabolic studies on thymic T cell development are still lacking, especially inhuman tissue. In this study, we use transcriptomics and extracellular flux analyses to investigatethe metabolic profiles of primary thymic and in vitro-derived mouse and human thymocytes. Coremetabolic pathways, specifically glycolysis and oxidative phosphorylation, undergo dramaticchanges between the double-negative (DN), double-positive (DP), and mature single-positive (SP)stages in murine and human thymus. Remarkably, despite the absence of the complex multicellularthymic microenvironment, in vitro murine and human T cell development recapitulated thecoordinated decrease in glycolytic and oxidative phosphorylation activity between the DN and DPstages seen in primary thymus. Moreover, by inducing in vitro T cell differentiation from Rag1-/-mouse bone marrow, we show that reduced metabolic activity at the DP stage is independent ofTCR rearrangement. Thus, our findings suggest that highly conserved metabolic transitions arecritical for thymic T cell development.