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

1)项目摘要/摘要 据估计，人类基因组中的20,000个基因在人体器官和 组织，每个组织由不同的细胞类型组成，其特征是共享和细胞类型特异性的基因表达 配置文件。基因的生物学功能通常取决于健康器官内的空间背景和 组织。许多人类疾病，包括发育疾病、癌症和神经退行性疾病， 由于组织内细胞的空间组织以及它们受损的基因的放松管制而产生的 表情。对基因和蛋白质表达的系统注释是理解 生物复杂性，阐明细胞身份，破译疾病机制等。然而，大多数例行公事 转录组学和蛋白质组学技术忽略了疾病状态和空间上的关系 描述了在许多人类疾病中存在的基因和蛋白质表达的变化。保留了空间 基因和蛋白质表达的背景对于更深入地了解组织生物学和 疾病病理表现。基于原位RNA成像和原位测序的数字空间剖面法 已经成为很有希望的工具，可以在其空间环境中分析细胞转录本 在组织切片中。2019年推出的GeoMx数字空间剖面图平台代表着最近的 为高复合体蛋白质或基因表达谱提供形态背景的进展 幻灯片上的组织切片。在该系统中，RNA和蛋白质的空间分布是在GeoMx DSP上进行的 平台，包括成像和流体组件，以捕捉微吸管吸入时的空间背景 96孔板。样本在计数器上读取，它提供对记录的多路测量 和蛋白质，同时使用直接的数字计数保持空间分辨率 技术值得注意的是，这项技术的实施允许人们分析多达96个蛋白质靶标， ~800个RNA靶点，甚至将RNA和蛋白质的定量与空间分辨率结合在一起 显微镜载玻片上福尔马林固定、石蜡包埋的组织切片。即使在推出后的一年内， GeoMx平台已成功地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性研究的系统。这项技术在共享的 南佛罗里达大学莫尔萨尼医学院的显微镜核心将大大受益于 美国国立卫生研究院资助的研究人员从事从阿尔茨海默病到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。无缝集成的 数字空间剖面图技术是南佛罗里达大学研究人员的一项重大技术进步。 它也将是一个独特的区域资源，可供其他机构的研究人员使用。

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.