High-plex Protein and Gene Expression Digital Spatial Profiler for Core Facility

用于核心设施的高复杂蛋白质和基因表达数字空间分析仪

• 批准号: 10177265
• 负责人: GOPAL THINAKARAN
• 金额: $ 45万
• 依托单位: UNIVERSITY OF SOUTH FLORIDA
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-06-01 至 2022-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10177265
• 关键词: Aging; Alzheimer' s Disease; Aspirate substance; Biological; Biological Process; Biology; Biomedical Research; Cells; Communicable Diseases; Core Facility; Disease; Florida; Formalin; Funding; Gene Expression; Gene Expression Profiling; Genes; Human; Human Genome; Image; Impairment; In Situ; Institution; Investigation; Liquid substance; Malignant Neoplasms; Measurement; Medicine; Microscope; Microscopy; Morphology; Natural Immunity; Neurodegenerative Disorders; Organ; Paraffin Embedding; Parasites; Pathology; Proteins; Proteomics; RNA; Research Personnel; Resolution; Resources; Sampling; Slide; Stress; System; Technology; Tissue Embedding; Tissues; Transcript; Translational Research; Trauma; United States National Institutes of Health; Universities; addiction; base; cell type; college; developmental disease; digital; gene therapy; human disease; in situ sequencing; insight; neuroinflammation; preservation; protein expression; technology validation; tool; transcriptome; transcriptomics; tumorigenesis

1) Project Summary/Abstract The estimated 20,000 genes in the human genome are variably expressed in the body’s organs and tissue, each made of heterogeneous cell types characterized by shared and cell-type-specific gene expression profiles. The biological function of a gene frequently depends on the spatial context within a healthy organ and tissue. Many human disorders, including developmental diseases, cancer, and neurodegenerative diseases, result from the deregulation of the spatial organization of cells within a tissue as well as their impaired gene expression. Systematic annotation of gene and protein expression is a crucial step in understanding the biological complexity, elucidating cellular identity, deciphering disease mechanisms, etc. However, most routine transcriptomics and proteomics technologies overlook the relationship between the disease state and spatially delineated alteration in gene and protein expression that exists in many human diseases. Preserving the spatial context of gene and protein expression is essential to gain deeper insights into tissue biology and the manifestation of disease pathology. Digital spatial profiling based on in situ RNA imaging and in situ sequencing has emerged as promising tools that could allow an analysis of cellular transcriptomes within their spatial context in tissue sections. The GeoMx Digital Spatial Profiling platform, introduced in 2019, represents a recent advancement that provides morphological context to high-plex protein or gene expression profiling from just one tissue section on a slide. In this system, spatial profiling of RNA and protein is performed on the GeoMx DSP platform, which includes imaging and fluidic components to capture spatial context as micropipette aspirates into 96-well plates. The samples are read on the nCounter, which provides a multiplexed measurement of transcripts and protein with a high level of precision while retaining spatial resolution using a direct, digital counting technology. Remarkably, the implementation of the technology allows one to profile up to 96 protein targets, ~800 RNA targets, or even multiplexing RNA and protein quantification with spatial resolution on the same formalin-fixed, paraffin-embedded tissue section on a microscope slide. Even within a year of its introduction, the GeoMx platform has been successfully used in a range of biological investigations, elucidating the versatility of the system for biomedical discovery and translational research. Implementation of this technology in a shared microscopy core at the University of South Florida Morsani College of Medicine will significantly benefit a large number of NIH-funded investigators engaged in biomedical research in fields as broad as Alzheimer’s disease, aging, stress and trauma, neuroinflammation, addiction, oncogenesis, innate immunity, infectious diseases, parasite-host interaction, computational and integrative biology, and gene therapy. The seamlessly integrated digital spatial profiling technology is a major technical advance for researchers at The University of South Florida. It will also be a unique regional resource available to researchers from other Institutions.

1）项目摘要/摘要 人体的器官中估计有20,000个基因在人体的器官中可变。 组织，每种组织由共享和细胞类型基因表达的异质细胞类型制成 概况。基因的生物学功能经常取决于健康器官中的空间环境 组织。许多人类疾病，包括发育疾病，癌症和神经退行性疾病， 由组织内部的空间组织及其基因受损导致的。 表达。基因和蛋白质表达的系统注释是理解的关键步骤 生物学复杂性，阐明细胞身份，解密疾病机制等。但是，大多数常规 转录组学和蛋白质组学技术忽略了疾病状态与空间之间的关系 许多人类疾病中存在的基因和蛋白质表达的改变。保留空间 基因和蛋白质表达的背景对于获得对组织生物学的深入了解至关重要 疾病病理的表现。基于原位RNA成像和原位测序的数字空间分析 已成为有望工具，可以在空间上下文中分析细胞转录组 在组织切片中。 GEOMX数字空间分析平台于2019年推出，代表了最近的一个 提供形态学上下文的进步，从仅一个 幻灯片上的组织部分。在该系统中，在GEOMX DSP上进行RNA和蛋白质的空间分析 平台，其中包括成像和流体组件以捕获空间上下文 96孔板。在NCounter上读取样品，该样本提供了转录本的多重测量 和具有高度精度的蛋白质，同时使用直接数字计数保留空间分辨率 技术。值得注意的是，该技术的实施使人们可以介绍多达96个蛋白质目标， 在同一 福尔马林固定的，石蜡包裹的组织截面在显微镜载玻片上。即使在引入的一年之内， GEOMX平台已成功用于一系列生物学研究，阐明了多功能性 生物医学发现和翻译研究系统的。在共享中实施该技术 南佛罗里达大学莫萨尼医学院的显微镜核心将显着受益于大型 在像阿尔茨海默氏病一样广泛的田野生物医学研究的NIH资助的研究人员数量， 衰老，压力和创伤，神经炎症，成瘾，肿瘤发生，先天免疫学，传染病， 寄生虫宿主相互作用，计算和综合生物学以及基因治疗。无缝集成 数字空间分析技术是南佛罗里达大学研究人员的主要技术进步。 这也将是其他机构的研究人员可用的独特区域资源。