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层次的 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 了解组织如何影响细胞的状态和其功能的表现。 人类生物分子图谱计划(HuBMAP)的首要目标，特别是组织 HuBMAP框架内的地图中心将生成高分辨率的三维(3D) 人体组织图。目前最先进的空间分辨组织分析分析(例如MerFish，SEQ- FISH、成像质量细胞术)使用基于抗体或寡聚探针的方法，这些方法需要 要绘制的生物分子靶标的知识，挑战了描述不明陆地的能力(即 未知)在组织地图绘制工作中。基于质谱学(MS)的基因组图谱技术使 代谢物、脂类和蛋白质(包括翻译后)的无偏检测和测绘 修饰-PTMS)高分辨率的原位组织样品，是一种极好的补充 涉及用于空间分辨组织分析的高度多元化的靶向方法。 该应用程序的总体目标是生成高分辨率的、多组的、3D的生物分子图谱 未患病的人体器官。我们将采用Google Maps类型的方法，使我们的地图工作取得进展 分阶段生成分辨率不断提高的参考地图。首先，单元格或接近单元格的分辨率 基于MS的测绘技术将用于提供组织分子空间的无偏见视图 建筑。其次，感兴趣的生物分子随后将用高度多元化的亚-DNA进行询问 细胞分辨率空间组学以有针对性的方式进行分析。我们的重点将放在胰腺上，这是一种必不可少的 对几种代谢功能很重要的器官。值得注意的是，尽管胰腺很重要，但它不是 HuBMAP财团目前正在分析的列出的关键组织和器官进一步支持 需要专注于这个重要的器官。我们将使用高分辨率和高分辨率质量 基于光谱的分子作图平台(LMD-NanPOT-MS、MALDI-FTMS、NanDESI-MS) 代谢产物、脂类和蛋白质(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元化的靶向空间组学分析相补充(CODEX和 分别用于蛋白质和RNA的NanoStringGeoMx)和光片显微镜来产生高分辨率， 多组学人体组织图。生成的创新的空间分辨率多组体组织图将是 史无前例的、独特的多基因组数据集将提供许多新的见解。组织标测 这项工作将得到商业上可用的和开源的最先进的3D重建的支持 创建可浏览的胰腺3D RNA/蛋白质/PTM/脂质/代谢物图谱的软件。巩固了 组织定征和3D器官图重建的努力将是一个强有力的器官采购， 加工和分销网络。 具体地说，我们将：(1)获取、加工和分发来自非疾病患者的正常胰腺样本 捐助者通过强大的采购、加工和分销网络。(2)综合施展 通过创新和互补平台无偏见地进行高分辨率多组学组织图谱 以及有针对性的分析(包括基因和蛋白质表达，以及PTM、代谢物和脂肪丰度)。 (3)建立基于可浏览的三维多组学(RNA/蛋白质/PTM/脂质/代谢物)的正常人图谱 并向蜂巢和其他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.