Multi-omic 3D tissue maps for a Human BioMolecular Atlas

项目摘要 哺乳动物器官的空间分辨分子图谱在提供更深入的 了解人体器官在健康和疾病状态下的功能。这一点的基础是 了解组织结构如何影响细胞的状态及其功能的表现。 人类生物分子图谱计划（HuBMAP）的总体目标，特别是组织 HuBMAP框架内的制图中心将生成高分辨率的三维（3D） 人体组织图谱目前最先进的空间分辨组织分析测定法（例如MERFISH，seq. FISH，成像质量细胞术）利用基于抗体或基于寡核苷酸探针的方法，其需要预先检测。 要绘制的生物分子目标的知识，挑战了表征未知领域的能力（即， 未知的）在组织映射工作中。基于质谱（MS）的组学映射技术使 代谢物、脂质和蛋白质（包括翻译后）的无偏检测和作图 修饰-PTM）原位组织样品中的高分辨率，并代表了一个很好的补充 涉及用于空间分辨组织分析的高度多重靶向方法。 该应用程序的总体目标是生成高分辨率，多组学，3D生物分子图， 没有病变的人体器官我们将采取谷歌地图类型的方法与我们的地图工作的进展 分阶段生成分辨率不断提高的参考图。第一，单细胞或近单细胞分辨率 基于MS的映射技术将用于提供组织分子空间的无偏视图 架构第二，随后将用高度多路复用的亚微阵列来询问感兴趣的生物分子。 以靶向方式进行细胞分辨率空间组学测定。我们的重点将放在胰腺上， 重要的器官的几个代谢功能。值得注意的是，胰腺，尽管它的重要性，是不是一个 列出的关键组织和器官目前正在由HuBMAP联盟分析，进一步支持 需要专注于这个关键器官我们将采用高分辨率和高分辨率的质量 基于光谱的分子图谱平台（LMD-nanoPOT-MS、MALDI-FTMS、nanoPOT-MS）， 代谢物、脂质和蛋白质（包括PTM，如磷酸化）的无偏映射。这些MS 分析将与强大的高度多重靶向空间组学分析（CODEX和 分别用于蛋白质和RNA的NanoString GeoMx）和光片显微镜，以生成高分辨率， 多组学人体组织图谱。所产生的创新性空间分辨多组学组织图将 前所未有的和独特的多组学数据集将提供许多新的见解。组织映射 这些努力将得到商用和开源最先进的3D重建技术的支持 软件来创建胰腺的可浏览的3D RNA/蛋白质/PTM/脂质/代谢物图谱。巩固 组织表征和3D器官图重建的努力将是一个强大的器官采购， 加工和分销网络。 具体而言，我们将：（1）从非病变胰腺中采集、处理和分发正常胰腺样本。 捐助者通过强大的采购、加工和分销网络。(2)进行全面 通过创新和互补平台进行高分辨率多组学组织绘图， 和靶向分析（包括基因和蛋白质表达，以及PTM、代谢物和脂质丰度）。 (3)建立可浏览的3D多组学（RNA /蛋白质/ PTM /脂质/代谢物）正常图谱 非患病胰腺;并向HIVE和其他TMC传播方法和工具。

PROJECT ABSTRACT Spatially resolved molecular maps of mammalian organs hold significant promise in providing a deeper understanding of human organ functioning in health and disease states. Fundamental to this is an understanding how tissue organization impacts on the state of a cell and performance of its function. The overarching goal of the Human BioMolecular Atlas Program (HuBMAP) and specifically of Tissue Mapping Centers within the HuBMAP framework is to generate high-resolution three dimensional (3D) human tissue maps. Present state-of-the-art spatially-resolved tissue analysis assays (e.g. MERFISH, seq- FISH, imaging mass cytometry) utilize antibody-based or oligo probe-based approaches that require prior knowledge of the biomolecular targets to map, challenging the ability to characterize the terra incognita (i.e. the unknown) in a tissue mapping effort. Mass spectrometry (MS)-based omic mapping technologies enable unbiased detection and mapping of metabolites, lipids, and proteins (including post-translational modifications - PTMs) in situ in tissue samples with high-resolution and represents an excellent complement to highly multiplexed targeted approaches for spatially resolved tissue analysis. The overall objective of this application is to generate high-resolution, multi-omic, 3D biomolecular maps of non-diseased human organs. We will take a Google Maps-type approach with our mapping effort progressing in phases to generate reference maps at increasing resolution. First, single-cell or near-single-cell resolution MS-based mapping technologies will be used to provide an unbiased view of tissue molecular spatial architecture. Second, biomolecules of interest will be subsequently interrogated with highly multiplexed sub- cellular resolution spatial omics assays in a targeted fashion. Our focus will be on the pancreas, an essential organ important for several metabolic functions. Notably, the pancreas, despite its importance, is not one of the listed key tissues and organs currently being analyzed by the HuBMAP consortium further supporting the need to focus on this critical organ. We will employ high resolving power and high-resolution mass spectrometry-based molecular mapping platforms (LMD-nanoPOT-MS, MALDI-FTMS, nanoDESI-MS) for unbiased mapping of metabolites, lipids, and proteins (including PTMs such as phosphorylation). These MS assays will be complemented with powerful highly multiplexed targeted spatial omics assays (CODEX and NanoString GeoMx for protein and RNA respectively) and light sheet microscopy to generate high-resolution, multi-omics human tissue maps. The innovative spatially resolved multi-omic tissue maps generated will be unprecedented and the unique multi-omic datasets will provide many novel insights. The tissue mapping efforts will be supported by commercially available and open-source state-of-the-art 3D reconstruction software to create browsable 3D RNA/protein/PTM/lipid/metabolite maps of the pancreas. Undergirding the tissue characterization and 3D organ map reconstructions efforts will be a robust organ procurement, processing and distribution network. Specifically, we will: (1) Procure, process and distribute samples of normal pancreas from non-diseased donors through a robust procurement, processing, and distribution network. (2) Perform comprehensive high-resolution multi-omics tissue mapping through innovative and complementary platforms for unbiased and targeted analyses (that includes gene and protein expression, and PTM, metabolite and lipid abundances). (3) Establish browsable 3D multi-omics (RNA / protein / PTM / lipid / metabolite)-based maps of normal non-diseased pancreas; and to disseminate methods and tools to the HIVE and other TMCs.