NeuroExM

神经ExM

基本信息

批准号：
10156966
负责人：
JACOB R GLASER
金额：
$ 76.02万
依托单位：
MICROBRIGHTFIELD, LLC
依托单位国家：
美国
项目类别：
财政年份：
2021
资助国家：
美国
起止时间：
2021-07-02 至 2022-07-04
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10156966
关键词：
3-Dimensional Aging Antibodies Axon Benchmarking Biological Biological Preservation Biological Sciences Biotechnology Brain Brain Diseases Cell physiology Cellular Structures Classification Collaborations Communities Complex Complex Analysis Computer software Computers Data Dendrites Dendritic Spines Detection Development Drug Addiction Feasibility Studies Image In Situ Individual Investigation Knowledge Label Light Manuals Messenger RNA Microscope Microscopy Modeling Molecular Morphology Neuraxis Neurodegenerative Disorders Neurodevelopmental Disorder Neurons Neurosciences Research Performance Peripheral Pharmacology Phase Population Population Analysis Population Distributions Preparation Process Production Proteins Proteome Research Personnel Resolution Running Sampling Scientist Societies Spatial Distribution Specimen Stains Structure Synapses System Techniques Technology Testing Three-Dimensional Image Time Tissue Expansion Tissues Translations Validation Visualization Work age effect base complex biological systems design drug development drug discovery fighting fluorophore high dimensionality image registration improved innovation interest microscopic imaging nanoscale nervous system disorder neuronal cell body neuropsychiatric disorder new technology next generation novel prevent prototype reconstruction research and development research study software development terabyte tissue processing transcriptome translational neuroscience treatment strategy usability

项目摘要

Abstract This project describes the development of NeuroExM™, a highly innovative system for performing comprehensive spatial distribution analysis of populations of messenger RNAs (mRNAs) and proteins in tissue processed for expansion microscopy (ExM)). The groundbreaking technological advantage of ExM, which was recently developed by Dr. Edward S. Boyden (Dept. Biol. Engin., Media Lab and Dept. Brain Cognit. Sci., MIT, Cambridge, MA) and colleagues, is the ability to isotropically expand tissue and increase the size of the biological structures. This allows nanoscale-resolution, light-microscopic imaging of small objects that are too small to be resolved without expansion due to the diffraction limit of light. Among other benefits, ExM allows those small structures to be imaged with a wider range of microscopy techniques. Processing tissue for ExM also allows repeated hybridization (for investigations of mRNAs) and/or repeated antibody staining (for investigations of proteins) of the same tissue, combined with repeated microscopic imaging rounds. Each round yields adjacent, high-magnification, single field-of-view image stacks, consisting of at least one morphology reference channel showing neuronal sub-cellular structures (somas, axons, dendrites, dendritic spines, synapses) as well as one or several info channels showing mRNAs and/or proteins. Comprehensive analysis of the spatial distribution of populations of mRNAs and proteins in neurons in situ requires assembling the image stacks of all performed rounds into a single, seamless and aligned, three-dimensional (3D) ExM image, which is high-dimensional and can be several terabytes in size. However, this presents a number of computational challenges with respect to microscopy image registration, segmentation and analysis. The game-changing innovation in NeuroExM is the ability to perform all of these tasks without the need to have a computer scientist on staff to run the existing, individual lab-based software scripts developed for each step of this kind of complex analysis. This is made possible by implementing a number of significant technical innovations into NeuroExM. Based on pilot work performed in collaboration with the Boyden lab during preparation of this proposal, we are convinced that NeuroExM will make a significant impact on the field of neuroscience research. Specifically, the combination of ExM and NeuroExM will enable substantial advancements in research studies focusing on alterations in the spatial transcriptome and proteome of neurons associated with neurodevelopmental, neuropsychiatric, neurodegenerative and neurological disorders as well as in aging research and drug development. Ultimately, this will result in an improved basis for developing novel treatment strategies for a wide spectrum of complex brain diseases. In Phase I we will demonstrate feasibility of this novel technology by developing prototype software; work in Phase II will focus on creating the full functionality of NeuroExM for commercial release. We will perform extensive feasibility studies, product validation and usability studies of NeuroExM in close collaboration with the Boyden lab. A competing technology is not available.

抽象的该项目描述了 NeuroExM™ 的开发，这是一个高度创新的系统，用于执行组织中信使 RNA (mRNA) 和蛋白质群体的综合空间分布分析 ExM 的突破性技术优势，即用于扩展显微镜 (ExM) 的处理。最近由 Edward S. Boyden 博士（麻省理工学院生物工程系、媒体实验室和脑认知科学系）开发，马萨诸塞州剑桥市）及其同事的研究成果是，能够各向同性地扩展组织并增加生物体的尺寸。这使得能够对小到无法观察到的小物体进行纳米级分辨率的光学显微成像。由于光的衍射极限，ExM 允许在没有扩展的情况下解决。还可以使用更广泛的显微镜技术对组织进行成像。重复杂交（用于研究 mRNA）和/或重复抗体染色（用于研究 mRNA）相同组织的蛋白质），结合重复的显微成像轮次，每轮都会产生相邻的、高放大率、单视场图像堆栈，由至少一个形态学参考通道组成显示神经元亚细胞结构（胞体、轴突、树突、树突棘、突触）以及一种或显示 mRNA 和/或蛋白质空间分布的综合分析的多个信息通道。原位神经元中的 mRNA 和蛋白质群体需要组装所有执行的图像堆栈舍入为单个、无缝且对齐的三维 (3D) ExM 图像，该图像是高维且大小可能为数 TB，但是，这带来了许多计算挑战。 NeuroExM 的颠覆性创新是显微图像配准、分割和分析。能够执行所有这些任务，而无需配备计算机科学家来运行现有的、为这种复杂分析的每个步骤开发了单独的基于实验室的软件脚本。通过在 NeuroExM 试点工作的基础上实施一些重大技术创新，这成为可能。在准备本提案期间与博伊登实验室合作进行，我们确信 NeuroExM 将对神经科学研究领域产生重大影响。 ExM 和 NeuroExM 将使专注于改变的研究取得实质性进展与神经发育、神经精神、最终，神经退行性疾病和神经系统疾病以及衰老研究和药物开发。这将为开发针对广泛的复杂疾病的新治疗策略奠定更好的基础在第一阶段，我们将通过开发原型来证明这项新技术的可行性。软件；第二阶段的工作将集中于创建 NeuroExM 的完整功能以供商业发布。将密切对 NeuroExM 进行广泛的可行性研究、产品验证和可用性研究与博伊登实验室的合作不可用。