Learning from the thymic human cell atlas for T cell engineering

免疫学的核心问题之一是适应性免疫如何在保持耐受性的同时产生其多样性。免疫耐受的关键介质是T细胞，T细胞在胸腺中发育，胸腺细胞重排其T细胞受体基因，并经历正选择和负选择。这确保了它们在MHC背景下识别抗原的能力，同时避免了自身反应性。我们仍然远未完全理解这些过程在分子水平上的步骤，特别是在人类中：不同T细胞亚型的发育轨迹是什么，以及它们在成熟过程中如何与它们在器官中的旅程相关？宏观和微观环境在调节这一点方面发挥什么样的功能作用？这些问题已经变得越来越重要，因为几种T细胞类型现在是癌症和移植的治疗剂，提出了如何在体外设计特异性T细胞亚群的问题。在AIM 1中，我们建议通过基因组学和成像技术在全基因组宽度上生成器官规模的3D胸腺细胞图谱。通过将多模态单细胞基因组学与多尺度空间基因组学和成像技术相结合，我们将产生丰富的数据集，用于胸腺叶组织结构的深入和全面重建。在AIM 2中，我们将利用三维多模态图谱组装的新方法进行计算数据集成，以预测微观和宏观尺度上的淋巴细胞发育机制。在AIM 3中，我们将使用人工胸腺类器官系统来同时验证我们的发现并增强T细胞工程方法。这种强大的综合方法结合了基因组学、成像和组织工程以及计算分析，以剖析免疫系统的中心器官胸腺的设计原理。这些知识将指导工程化T细胞作为研究试剂的发展，并最终作为治疗剂。

One of the central questions in immunology is how adaptive immunity generates its diversity while maintaining tolerance. The keymediators of tolerance are T cells, which develop in the thymus, where thymocytes rearrange their T cell receptor genes and undergopositive and negative selection. This ensures their ability to recognise antigen in the context of MHC, whilst avoiding self-reactivity.We are still far from fully understanding the steps in these processes at the molecular level, especially in humans: What are thedevelopmental trajectories of different T cell subtypes, and how do they relate to their journey through the organ during maturation?What is the functional role played by the macro- and micro-scale environments in regulating this? These questions have gained inimportance since several T cell types are now therapeutics in cancer and transplantation, raising the question of how to engineerspecific T cell subsets in vitro.In AIM 1, we propose to generate an organ-scale 3D thymic cell atlas at full genomic breadth through genomics and imagingtechnologies. By combining multi-modal single cell genomics with multi-scale spatial genomics and imaging technologies, we willgenerate a rich data set for deep and comprehensive reconstruction of tissue architectures in a thymic lobe.In AIM 2, we will carry out computational data integration with new methods for 3D multi-modal atlas assembly to predictlymphocyte developmental mechanisms at micro and macro scales.In AIM 3, we will use an artificial thymic organoid system to simultaneously validate our findings and enhance T cell engineeringapproaches.This powerful integrated approach combines genomics, imaging and tissue engineering together with computational analyses todissect design principles of the thymus, a central organ of the immune system. This knowledge will guide the development ofengineered T cells as research reagents, and ultimately as therapeutics.