Implementation of automated staining in conjunction with spatial analyses

项目摘要 我们正在建设一个设施，将利用新兴的空间转录组学和 蛋白质组学技术研究临床样本中的免疫景观。最初是在 作为马约诊所乳腺癌转化基因组学倡议的一部分，空间生物学设施主要关注 分析实体肿瘤。我们的中心目标是定义基本属性， 临床表型（最常见的治疗反应）和数量，类型，活性， 以及免疫细胞在肿瘤中的位置。然而，越来越明显的是， 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， 阿尔茨海默病和小鼠模型中神经元老化的前景。 我们的核心技术是NanoString GeoMx，它使我们能够询问转录本和/或蛋白质 单个5微米福尔马林固定石蜡包埋组织中用户定义的感兴趣区域的表达谱 科.我们常规地进行一系列分析，从多重蛋白质丰度的数字空间分析， 到全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。我们目前正在测试NanoString CosMx平台，该平台提供单细胞 转录组和蛋白质组分析的水平分辨率。 空间生物学设施目前已全面运作。该模型是一种混合体， 一是合作机制，二是核心设施。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 几乎是势不可挡到目前为止，我们已经分析了近4000个临床样本。所有这些样品均为 手动处理，包括一个相当劳动密集型的染色程序，需要两个更好的部分， 天我们的目标是使这一步骤自动化，从而提高通量，实验一致性， 更有效地利用我们有限的人员的时间。为此，我们要求提供资金， 粘合RXm自动染色机。

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.