Core 2: Tissue Imaging and Profiling Core

核心2.成像和空间概况核心项目摘要： ST-Analytics U54计划的核心技术是组织成像和剖析平台，包括两个 用于包括临床档案FFPE在内的肿瘤组织标本的高度多重、多组体分析的工具集 和轻度保存的冰冻组织，以及相关的图像分析和信息学软件。这些核心 两个ST Analytics项目都广泛使用了资源技术。 第一个空间剖面图工具是成熟的商业纳米串数字空间剖面图(DSP) 系统，它允许分析包含少至10-20个细胞的感兴趣区域(ROI)以检测周围 1000个基因或大约50个蛋白质(Lee 2017，Lu 2021)。准备来自FFPE块的相邻切片。这个 第一种是HE染色进行病理分析，第二种是荧光抗体染色 识别感兴趣区(例如，免疫细胞富集区或癌细胞富集区)。然后，这些ROI将在 转录组或蛋白质组水平。我们有丰富的经验，这个工具的分析FFPE保存 患者肿瘤组织(Lu 2021)。 第二个剖析工具是由Fan组最近开发和报告的那些(邓2021， 2021年，刘2020)。这些强大的工具允许高度多元化(高达300-plex)的蛋白质组学和全基因组 在FFPE块制备的组织切片中以10微米的分辨率绘制转录组图谱。他们也 允许空间分辨ATAC-SEQ和芯片-SEQ类型的表观遗传简档(Chen 2017；Chen 2018)在类似的 轻微固定的组织切片的空间分辨率。特别是，这种表观遗传特征能力是这些人独一无二的 工具。与数字信号处理器类似，相邻的组织切片可以进行H&E染色，并且可以进行低丛荧光成像 在同一切片上用于识别细胞核以及免疫丰富区和免疫贫乏区 对齐验证。这些方法可以实现高通量和高成本效益的组织简档分析，以及 描述了为此目的而进行的一些技术开发。核心将继续开发新的空间剖面图 满足两个项目在未来5年内的紧急需求的工具，从而成为 U54中心和CSBC财团的技术创新中心。

Core 2. Imaging and Spatial Profiling Core Project Summary: Central technologies of the ST-Analytics U54 program are tissue imaging and profiling platforms, including two sets of tools for highly multiplex, multi-omic analysis of tumor tissue specimens including clinical archival FFPE and lightly preserved frozen tissues, and associated image analysis & informatics software. These Core resource technologies are used extensively by both ST Analytics Projects. The first spatial profiling tool is the well-established commercial Nanostring Digital Spatial Profiling (DSP) system, which permits analysis of regions of interest (ROIs) containing as few as 10-20 cells for detecting around 1000 genes or around 50 proteins (Lee 2017, Lu 2021). Adjacent slices from an FFPE block are prepared. The first is subjected to H&E staining for pathological analysis, while the second is stained with fluorescent antibodies to identify ROIs (for example, immune cell rich or cancer cell rich regions). Those ROIs are then interrogated at the transcriptome or proteome level. We have extensive experience with this tool for analysis of FFPE preserved patient tumor tissues (Lu 2021). The second profiling tools are those recently developed and reported by the Fan group (Deng 2021, 2021, Liu 2020). These powerful tools permit highly multiplex (up to 300-plex) proteomics and genome--wide transcriptome mapping at a resolution of 10 micrometers in tissue slices prepared from FFPE blocks. They also permit spatially resolved ATAC-seq and ChIP-seq type epigenetic profiling (Chen 2017; Chen 2018) at a similar spatial resolution in lightly fixed tissue slices. In particular, this epigenetic profiling capacity is unique to these tools. Similar to DSP, adjacent tissue slices can be H&E stained, and low-plex fluorescent imaging can be employed on the same slice for identification of nuclei as well as immune rich and immune poor regions for alignment validation. These methods can enable high throughput and cost-effective profiling of tissues, and some technology development to that end is described. The Core will continue to develop new spatial profiling tools to meet the emergent needs in the two projects as they advance in the next 5 years, thus serving as a Technoloy Innovation Hub for the U54 center and for the CSBC consortium as well.