Mapping the blueprint of thymus development

T细胞是适应性免疫系统的重要调节因子和效应器。一个功能性的、自我耐受的T细胞的产生是一个复杂的过程，发生在胸腺这一专用器官中，并依赖于一组高度特化的上皮细胞，这些上皮细胞构成了胸腺基质的关键部分（胸腺上皮细胞；TEC）(1)。TEC存在两个主要的亚谱系：皮质TEC和髓质TEC。它们在胸腺发育过程中由一个共同的祖细胞/干细胞发育而来，功能不同，分别调节早期T细胞分化和中枢耐受诱导。在之前的工作中，我们鉴定了TEC谱系最早产生的胸腺上皮祖细胞/干细胞（TEPC）(2)，并表明这些细胞可以在体外（未发表）和移植时形成自组织的胸腺类器官(2)。最近，我们也证实了TEC可以通过使用单一转录因子FOXN1直接重编程原代胚胎成纤维细胞在体外产生(3)。与离体TEPC一样，这些“诱导TEC”（iTEC）可以在移植后产生胸腺，并在体外形成胸腺类器官(3)。此外，我们最近发现了控制髓质TEC亚系早期发育的部分机制，该亚系调节中枢耐受诱导(4)。我们现在希望使用谱系追踪方法，包括条形码，来(i)绘制TEC发展最早阶段的谱系关系，（ii）研究iTEC产生的胸腺类器官。这个跨学科的项目是基于干细胞和发育生物学，以及数学建模的界面。它将结合生物信息学、建模和湿实验室方法，包括谱系追踪、条形码和类器官技术，来确定早期TEC分化中的谱系关系，并探索这些与基于itec的胸腺类器官形成的关系。

T cells are vital regulators and effectors of the adaptive immune system. Production of a functional, self-tolerant T cell development is a complex process that occurs in a dedicated organ, the thymus, and depends on a set of highly specialized epithelial cells that form a key part of the thymic stroma (thymic epithelial cells; TEC)(1). Two main sub-lineages of TEC exist: cortical and medullary TEC. These develop from a common progenitor/stem cell during thymus development, and are functionally distinct, regulating early T cell differentiation and central tolerance induction respectively.In previous work, we identified the thymic epithelial progenitor/stem cells (TEPC) from which the TEC lineage first arises (2) and showed these cells can form self-organised thymic organoids in vitro (unpublished) and upon transplantation (2). Recently, we have also established that TEC can be generated in vitro by direct reprogramming of primary embryonic fibroblasts using a single transcription factor, FOXN1 (3). Like ex vivo TEPC, these 'induced TEC' (iTEC) can generate a thymus upon transplantation and form thymic organoids in vitro (3). Additionally, we have recently uncovered part of the mechanism controlling the very earliest development of the medullary TEC sublineage, which regulates central tolerance induction (4). We now wish to use the lineage tracing approaches, including barcoding, to (i) map the lineage relationships during the very earliest stages of TEC development and (ii) investigate iTEC generation of thymic organoids.This interdisciplinary project is based at the interface of stem cell and developmental biology, and mathematical modelling. It will use a combination of bioinformatics, modelling and wet-lab approaches, including lineage tracing, barcoding and organoid technology, to identify lineage relationships in early TEC differentiation, and probe how these relate to iTEC-based thymic organoid formation.