Implementation of automated staining in conjunction with spatial analyses

结合空间分析实施自动染色

• 批准号: 10733878
• 负责人: E. AUBREY THOMPSON
• 金额: $ 23.57万
• 依托单位: MAYO CLINIC JACKSONVILLE
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-07-01 至 2024-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10733878
• 关键词: Adopted; Aging; Alzheimer' s Disease; Area; Biological; Biology; Brain; Cells; Charge; Cholangiocarcinoma; Clinic; Clinical; Clinical Trials; Collaborations; Colon; Consumption; Core Facility; Development; Ensure; Experimental Designs; Formalin; Funding; Future; Goals; Grant; Human Resources; Hybrids; Immune; Incidence; Infrastructure; Institution; Investments; Knowledge; Location; Lung; Manuals; Modeling; Modernization; Molecular; Nature; Neurodegenerative Disorders; Neurons; Ovarian; Pancreas; Paraffin Embedding; Play; Preparation; Primary carcinoma of the liver cells; Procedures; Process; Property; Proteins; Proteomics; Protocols documentation; Recurrence; Resolution; Resources; Risk; Role; Running; Sampling; Services; Solid Neoplasm; Spatial Design; Stains; Technology; Testing; Time; Tissue Embedding; Transcript; Translational Research; Transplant Surgeon; Work; clinical phenotype; clinically relevant; cost; digital; draining lymph node; expectation; experience; immune activation; instrument; instrumentation; interest; liver transplantation; malignant breast neoplasm; mortality; mouse model; nano-string; neuropathology; operation; programs; protein expression; response; senescence; success; time use; transcriptome; transcriptomics; translational genomics; treatment response; tumor

Project Summary We are in the process of building a facility that will take advantage of emerging spatial transcriptomic and proteomic technologies to study the immune landscape in clinical samples. Originally developed under the aegis of the Mayo Clinic Breast Cancer Translational Genomics initiative, the Spatial Biology facility focuses largely on analysis of solid tumors. Our central objective is to define the fundamental properties that underlie the relationship between clinical phenotype (most commonly therapeutic response) and the number, types, activities, and locations of immune cells within the tumor. It has, however, become increasingly clear that similar features may underlie neurodegenerative diseases of aging; and we have initiated several projects related to the immune landscape of Alzheimer’s disease and neuronal aging in mouse models. Our core technology is NanoString GeoMx, which enables us to interrogate the transcript and/or protein expression profiles of user-defined areas of interest in a single 5-micron formalin-fixed, paraffin-embedded tissue section. We routinely carry out a range of analyses, from digital spatial profiling of multi-plex protein abundance to whole transcriptome analysis. These applications utilize the GeoMx platform, which we have been running since September 2019. We are currently beta testing the NanoString CosMx platform, which provides single cell level resolution for both transcriptomic and proteomic analysis. The Spatial Biology facility is fully operational at this time. The model is something of a hybrid between a collaborative arrangement and a core facility. We play a very active role in experimental design of these spatial biology projects, and we recover costs through a recharge mechanism. The demand for these services has been little short of overwhelming. To date we have analyzed almost 4000 clinical samples. All of these sample were processed manually, including a rather labor-intensive staining procedure that requires the better part of two days. Our goal is to automate this step, thereby providing for increased throughput, experimental consistency, and more efficient use of time for our limited personnel. To this end, we are requesting funds to purchase a Leica Bond RXm autostainer.

项目摘要 我们正在建设一个设施，将利用新兴的空间转录和 蛋白质组学技术研究临床样本中的免疫状况。最初是在保护下发展起来的 在梅奥诊所乳腺癌翻译基因组学倡议中，空间生物学设施主要专注于 实体瘤的分析。我们的中心目标是定义构成 临床表型(最常见的治疗反应)与数量、类型、活动、 以及肿瘤内免疫细胞的位置。然而，越来越清楚的是，类似的特征 可能是衰老的神经退行性疾病的基础；我们已经启动了几个与免疫相关的项目 小鼠模型中阿尔茨海默病和神经元老化的概况。 我们的核心技术是NanoStringGeoMx，它使我们能够询问转录和/或蛋白质 单个5微米福尔马林固定的石蜡包埋组织中用户定义的感兴趣区域的表达谱 一节。我们经常进行一系列的分析，从多复合体蛋白质丰度的数字空间轮廓 到整个转录组分析。这些应用程序利用我们一直在运行的GeoMx平台 自2019年9月以来。我们目前正在对NanoStringCosMx平台进行Beta版测试，该平台提供单电池 转录组和蛋白质组学分析的水平分辨率。 空间生物学设施目前已完全投入使用。这种模式是一种混合模式，是一种 协作性安排和核心设施。我们在这些空间的实验设计中发挥着非常积极的作用 生物项目，我们通过充值机制收回成本。对这些服务的需求一直是 几乎是压倒性的。到目前为止，我们已经分析了近4000份临床样本。所有这些样品都是 手工处理，包括相当劳动密集型的染色程序，需要两个中的较大部分 几天。我们的目标是自动化此步骤，从而提供更高的吞吐量、实验一致性、 为我们有限的人员更有效地利用时间。为此，我们正在申请购买徕卡的资金 邦德RXM自动着色机。