Summary The ability to generate T cells from self-renewing pluripotent stem cells (PSC) has the potential to transform the current practice of autologous T cell immunotherapy into universal off-the-shelf products. However, differentiation of human PSCs into mature, conventional T cells has been challenging with existing methods. We report that a 3D artificial thymic organoid (PSC-ATO) system induced efficient differentiation of human embryonic stem cell and induced pluripotent stem cell-derived mesoderm progenitors to mature, functional T cells with a diverse T cell receptor (TCR) repertoire. This continuous culture system supported both hematopoietic specification and terminal differentiation to naïve CD3+CD8αβ+ and CD3+CD4+ conventional T cells. Introduction of an MHC class I-restricted TCR in PSCs produced naïve, antigen-specific cytotoxic CD8αβ+ T cells which lacked endogenous TCR Vβ expression. Functional assays and RNA sequencing aligned PSC-derived T cells with primary naïve CD8+ T cells. The PSC-ATO system presented here is an efficient platform for generating functional, mature T cells from human PSCs.

Highlights d M-ATOs mimic the different stages of normal murine thymopoiesis in multiple strains d M-ATOs support the key transcriptional transitions during T cell development d M-ATOs generate mature T cells with a diverse TCR repertoire d M-ATOs generate the complete trajectory of thymopoiesis from a single HSC

Although metabolic pathways have been shown to control differentiation and activation in peripheral T cells, metabolic studies on thymic T cell development are still lacking, especially in human tissue. In this study, we use transcriptomics and extracellular flux analyses to investigate the metabolic profiles of primary thymic and in vitro-derived mouse and human thymocytes. Core metabolic pathways, specifically glycolysis and oxidative phosphorylation, undergo dramatic changes 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 multicellular thymic microenvironment, in vitro murine and human T cell development recapitulated the coordinated decrease in glycolytic and oxidative phosphorylation activity between the DN and DP stages 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 of TCR rearrangement. Thus, our findings suggest that highly conserved metabolic transitions are critical for thymic T cell development.

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