Gel-based Optical-isolation Single-Cell 3D Spatial Multiomics

摘要 人体的正常功能依赖于细胞在3D空间中的组织。细胞的功能 和命运由它的生物分子组成和它的3D环境决定。在空间上的识别 因此，组织中的蛋白质、RNA和DNA提供了一个强大的图谱来破译细胞如何构建组织和 变得有病。通过使用单细胞组学，已经有可能揭示罕见的细胞类型 基准发育、肿瘤发生和脑功能。然而，单细胞中的细胞分离过程 分析不可避免地会造成空间信息的丢失。为了获得空间信息，空间转录 基于成像或测序的研究已经出现，以深入了解基因的异质性表达模式 肿瘤、脑和伤口组织。不幸的是，大多数空间转录学方法只能检测 组织切片，与蛋白质组学不兼容。为了解决这些缺点，该项目的目标是 开发一种概念上新颖的以凝胶为基础的光学隔离(GO3D)的3D空间多组学技术。这个 建议的GO3D技术不同于目前所有的空间组学，将使蛋白质图谱成为可能， 具有亚细胞分辨率、高覆盖率和高通量的整装组织的RNA和DNA， 同时。这一创新设计基于基于凝胶的标记保留膨胀显微镜(LR- Exm)，这是PI最近发表的。GO3D将彻底改变我们对许多关键生物医学的理解 问题，我们目前缺乏解决这些问题的工具。例如，高度动态的皮肤中的细胞是如何 在3D模式下迁移以治愈伤口？专门的神经元是如何构建大脑的？微生物在哪里与之相互作用 肠道中有哪些细胞类型？

ABSTRACT Proper functioning of the human body relies on the organization of cells in 3D space. A cell’s function and fate are determined by its biomolecule composition and its 3D environment. The spatially identification of proteins, RNAs, and DNAs in a tissue thus provides a powerful map to decipher how cells build tissues and become diseased. Through the use of single-cell omics, it’s been possible to reveal rare cell types that benchmark development, oncogenesis, and brain functions. However, the cell isolation process in single-cell analysis unavoidably causes loss of spatial information. To obtain spatial information, spatial transcriptomics based on imaging or sequencing have emerged to give insight into the heterogeneous expression patterns in tumors, brain, and wound tissues. Unfortunately, most spatial transcriptomics methods can only examine thin tissue sections, and are incompatible with proteomics. To address these drawbacks, the goal of the project is to develop a conceptually novel 3D spatial multiomics technology featuring gel-based optical isolation (GO3D). The proposed GO3D technology is distinct from all current spatial omics, and will enable the profiling of proteins, RNAs, and DNAs of whole-mount tissues with subcellular resolution, high coverage and high throughput, simultaneously. This innovative design is based on the gel-based label-retention expansion microscopy (LR- ExM) that the PI published recently. GO3D will drastically transform our understanding of many critical biomedical questions, which we lack of tools to address currently. For example, how are cells in a highly dynamic skin migrate in 3D to heal wounds? How do specialized neurons build brain? And where do microbes interact with what cell types in gut?