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。耐受性的关键媒介是T细胞，它在胸腺中发育，胸腺细胞在那里重新排列他们的T细胞受体基因，并进行阳性和阴性选择。这确保了他们在MHC背景下识别抗原的能力，同时避免了自身反应。我们仍然远未在分子水平上完全了解这些过程中的步骤，特别是在人类中：不同T细胞亚型的发育轨迹是什么，它们与成熟过程中通过器官的旅程有什么关系？宏观和微观环境在调节这一过程中扮演了什么功能角色？这些问题已经变得无关紧要，因为几种T细胞类型现在被用于癌症和移植的治疗，这提出了如何在体外设计特异性T细胞亚群的问题。在目标1中，我们建议通过基因组学和成像技术在全基因组范围内建立器官规模的3D胸腺细胞图谱。通过将多模式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，我们将生成丰富的数据集，用于深度和全面地重建胸腺组织结构。在AIM 2中，我们将与3D多模式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器官系统来同时验证我们的发现并改进T细胞工程方法。这种强大的集成方法将基因组学、成像和组织工程与计算分析相结合，剖析免疫系统的中心器官胸腺的设计原理。这些知识将指导将工程化T细胞作为研究试剂，并最终作为治疗学的发展。

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.