Core 2: Tissue Imaging and Profiling Core

核心2。成像和空间轮廓核心项目摘要： ST-Analytics U 54计划的核心技术是组织成像和分析平台，包括两个 用于肿瘤组织标本的高度多重、多组学分析的工具集，包括临床存档FFPE 和轻度保存的冷冻组织，以及相关的图像分析和信息学软件。这些核心 资源技术被ST分析项目广泛使用。 第一个空间剖面工具是成熟的商业Nanostring数字空间剖面（DSP） 系统，其允许分析包含少至10-20个细胞的感兴趣区域（ROI），用于检测大约 1000个基因或大约50种蛋白质（Lee 2017，Lu 2021）。制备来自FFPE块的相邻切片。的 第一个进行H&E染色用于病理分析，而第二个用荧光抗体染色 识别ROI（例如，富含免疫细胞或富含癌细胞的区域）。然后，这些ROI在 转录组或蛋白质组水平。我们有丰富的经验与此工具的分析FFPE保存 患者肿瘤组织（Lu 2021）。 第二种剖析工具是Fan小组最近开发和报告的工具（Deng 2021， 2021，Liu 2020）。这些强大的工具允许高度多路复用（高达300重）的蛋白质组学和全基因组 在从FFPE块制备的组织切片中以10微米的分辨率进行转录组作图。他们还 允许空间分辨的ATAC-seq和ChIP-seq型表观遗传分析（Chen 2017; Chen 2018）， 空间分辨率在轻微固定的组织切片。特别是，这种表观遗传分析能力是这些人所独有的。 工具.与DSP类似，相邻的组织切片可以被H&E染色，并且可以进行低重荧光成像。 用于识别细胞核以及免疫丰富和免疫贫乏区域， 对齐验证。这些方法可以实现组织的高通量和成本有效的分析，并且 描述了为此目的的一些技术发展。核心将继续开发新的空间剖面分析 工具，以满足这两个项目在未来5年内的紧急需求，从而作为一个 U 54中心和CSBC联盟的技术创新中心。

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.