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) 项目概要/摘要 人类基因组中估计有 20,000 个基因在身体器官和组织中表达不同 组织，每种组织均由异质细胞类型组成，其特征是共享的和细胞类型特异性的基因表达 基因的生物学功能通常取决于健康器官内的空间背景和 许多人类疾病，包括发育疾病、癌症和神经退行性疾病， 组织内细胞空间组织及其受损基因失调的结果 基因和蛋白质表达的系统注释是理解基因和蛋白质表达的关键一步。 生物复杂性、阐明细胞身份、破译疾病机制等。然而，大多数常规方法 转录组学和蛋白质组学技术忽视了疾病状态与空间之间的关系 描述了许多人类疾病中存在的基因和蛋白质表达的改变。 基因和蛋白质表达的背景对于深入了解组织生物学和 基于原位 RNA 成像和原位测序的数字空间分析。 已成为一种有前途的工具，可以在空间背景下分析细胞转录组 2019 年推出的 GeoMx 数字空间分析平台代表了最新的技术 一项进步，为仅从一个细胞中进行高复杂蛋白质或基因表达谱分析提供形态学背景 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，用于捕获微移液器吸入时的空间背景 96 孔板在 nCounter 上读取，提供转录本的多重测量。 和蛋白质具有高精度，同时使用直接数字计数保持空间分辨率 值得注意的是，该技术的实施允许人们分析多达 96 个蛋白质目标， 约 800 个 RNA 靶标，甚至在同一空间分辨率上对 RNA 和蛋白质进行多重定量 即使在推出后的一年内，在显微镜载玻片上进行福尔马林固定、石蜡包埋的组织切片， GeoMx 平台已成功用于一系列生物学研究，阐明了其多功能性 生物医学发现和转化研究系统的共享实施。 南佛罗里达大学莫萨尼医学院的显微镜核心将使大量人员受益 NIH 资助的研究人员从事阿尔茨海默病等广泛领域的生物医学研究， 衰老、压力和创伤、神经炎症、成瘾、肿瘤发生、先天免疫、传染病、 寄生虫-宿主相互作用、计算和整合生物学以及基因治疗的无缝集成。 数字空间剖析技术是南佛罗里达大学研究人员的一项重大技术进步。 它还将成为其他机构的研究人员可用的独特区域资源。