Spatial and temporal mapping of cell fate within lymphoid tissue

摘要：单细胞基因组学最近的惊人进展提供了高分辨率的信息 关于细胞身份，然而，将分子信息与空间和时间背景联系起来仍然是一个 重大挑战。这与免疫系统特别相关，因为免疫反应发生在 高度组织化的组织环境，并涉及细胞状态随时间的严格受控变化。这里 我们建议开发新的方法来提高单个像元的空间和时间分辨率 分析，并使用这些方法生成并然后传播4维(时间和3D 空间坐标)胸腺中T细胞发育和相关微环境的地图。在……里面 目标1，我们将使用单个细胞上的mRNA和表面蛋白的同时测量，以及 开发T细胞期间细胞状态转变时间图的计算和实验方法 胸腺的发育。在目标2中，我们将使用相干拉曼和多光子显微镜来观察生物 胸腺组织切片，结合激光显微解剖，分离功能相关的组织区域。 然后，我们将对这些定义区域内的各个单元格执行单元格分析，并使用 用于定义细胞类型和解决细胞串扰的计算分析。在目标3中，我们将增加 为了使这一资源对科学界具有价值，我们将使研究人员随时可以访问这些数据 通过用户友好的界面。 好了！

Summary: Spectacular recent advances in single cell genomics have provided high-resolution information about cell identity, however relating molecular information to the spatial and temporal context remains a major challenge. This is particularly relevant for the immune system, since immune responses occur in highly organized tissue environments, and involve tightly-controlled changes in cell state over time. Here we propose to develop new approaches to increase the spatial and temporal resolution of single cell analyses, and to use these methods to generate and then disseminate a 4-dimensional (time and 3D spatial coordinates) map of T cell development and the associated microenvironment in the thymus. In Aim 1, we will use simultaneous measurement of mRNA and surface proteins on single cells, together with computation and experimental approaches to develop a temporal map of cell state transitions during T cell development in the thymus. In Aim 2, we will use coherent Raman and multiphoton microscopy of living thymic tissue slices, together with laser microdissection, to isolate functionally relevant regions of tissues. We will then perform single cell analyses of individual cells within these defined regions and use computational analyses to define cell types and resolve cellular cross-talk. In Aim 3, we will increase the value of this resource to the scientific community, we will make the data readily accessible to researchers via a user-friendly interface. !