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

人类生物分子图谱的多组学 3D 组织图谱

基本信息

批准号：
10649957
负责人：
CLAYTON E MATHEWS
金额：
$ 25万
依托单位：
BATTELLE PACIFIC NORTHWEST LABORATORIES
依托单位国家：
美国
项目类别：
财政年份：
2020
资助国家：
美国
起止时间：
2020-09-10 至 2024-08-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10649957
关键词：
3-Dimensional Antibodies Architecture Atlases Biological Assay Biology Cells Communities Complement Computer software Cytometry Data Set Detection Diabetes Mellitus Disease Gene Expression Goals Health Human Human BioMolecular Atlas Program Image In Situ Knowledge Light Lipids Malignant neoplasm of pancreas Maps Mass Spectrum Analysis Metabolic Methods Microscopy Molecular Nature Oligonucleotides Organ Organ Procurements Pancreas Performance Phase Phosphorylation Post-Translational Protein Processing Process Proteins RNA Resolution Sampling Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization Technology Tissue Sample Tissues base biobank experience human tissue innovation insight interest multidisciplinary multiple omics nano-string novel open source protein expression reconstruction subcellular targeting success tissue mapping tool

项目摘要

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.

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研究方面具有重要前景了解健康和疾病状态下的人体器官功能。做到这一点的根本是了解组织组织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) 特别是组织的总体目标 HuBMAP 框架内的测绘中心用于生成高分辨率三维 (3D) 人体组织图。目前最先进的空间分辨组织分析检测（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，需要事先绘制生物分子目标的知识，挑战表征未知领域的能力（即未知）在组织绘图工作中。基于质谱 (MS) 的组学作图技术使代谢物、脂质和蛋白质（包括翻译后）的公正检测和绘图修饰 - PTM）在组织样品中原位高分辨率，是一个极好的补充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 生物分子图没有患病的人体器官。我们将采用谷歌地图类型的方法来推进我们的地图工作分阶段生成分辨率不断提高的参考图。一、单细胞或近单细胞分辨率基于 MS 的绘图技术将用于提供组织分子空间的公正视图建筑学。其次，感兴趣的生物分子将随后用高度多重的亚分子进行询问以有针对性的方式进行细胞分辨率空间组学分析。我们的重点将是胰腺，这是一个重要的对多种代谢功能很重要的器官。值得注意的是，尽管胰腺很重要，但它并不是 HuBMAP 联盟目前正在分析列出的关键组织和器官，进一步支持需要关注这个关键器官。我们将采用高分辨率和高分辨率质量基于光谱分析的分子作图平台（LMD-nanoPOT-MS、MALDI-FTMS、nanoDESI-MS）代谢物、脂质和蛋白质（包括磷酸化等 PTM）的无偏图谱。这些MS 强大的高度多重靶向空间组学分析（CODEX 和 NanoString GeoMx（分别用于蛋白质和 RNA）和光片显微镜可生成高分辨率、多组学人体组织图谱。生成的创新空间分辨多组学组织图将是前所未有且独特的多组学数据集将提供许多新颖的见解。组织标测这些努力将得到商用和开源的最先进 3D 重建的支持用于创建可浏览的胰腺 3D RNA/蛋白质/PTM/脂质/代谢物图谱的软件。巩固组织表征和 3D 器官图重建工作将是强有力的器官采购，加工和分销网络。具体来说，我们将： (1) 采购、处理和分发来自非患病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。 (二) 全面开展通过创新和互补的平台进行高分辨率多组学组织图谱，以实现公正和针对性分析（包括基因和蛋白质表达、PTM、代谢物和脂质丰度）。 (3) 建立基于可浏览的3D多组学（RNA/蛋白质/PTM/脂质/代谢物）的正常图谱未患病的胰腺；向 HIVE 和其他 TMC 传播方法和工具。