Core 2: Tissue Imaging and Profiling Core

核心 2：组织成像和分析核心

• 批准号: 10526107
• 负责人: Rong Fan
• 金额: $ 36.94万
• 依托单位: INSTITUTE FOR SYSTEMS BIOLOGY
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-09-22 至 2027-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10526107
• 关键词: ATAC-seq; Address; Algorithms; Antibodies; Archives; Bar Codes; Cell Nucleus; Cells; ChIP-seq; Clinical; Combination immunotherapy; Computer Analysis; Computer software; Cost efficiency; DNA; Data; Data Analytics; Data Set; Epigenetic Process; Fluorescence; Fluorescent Antibody Technique; Freezing; Genes; Image; Image Analysis; Immune; Individual; Kinetics; Label; Location; Methods; Modeling; Names; Pathologic; Patients; Pattern; Population; Proteins; Proteome; Proteomics; Registries; Reporting; Research; Research Personnel; Resolution; Resources; Running; Scientist; Series; Slice; Specimen; Stains; System; Systems Biology; Techniques; Technology; Time; Tissue imaging; Tissues; Training; Training Programs; Transcript; Tumor Tissue; Validation; biobank; cancer cell; cost effective; data warehouse; digital; epigenetic profiling; experience; fluorescence imaging; genome-wide; high throughput analysis; human tissue; image processing; imaging informatics; inhibitor; innovation; interest; kinetic model; mouse model; multiple omics; nano-string; next generation sequencing; operation; preservation; programs; prospective; spatiotemporal; technology development; tool; transcriptome; tumor

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.

核心 2. 成像和空间剖析核心项目摘要： ST-Analytics U54 项目的核心技术是组织成像和分析平台，包括两个 用于对肿瘤组织样本（包括临床档案 FFPE）进行高度多重、多组学分析的工具集 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 ST 分析项目广泛使用资源技术。 第一个空间分析工具是成熟的商业纳米串数字空间分析 (DSP) 系统，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 FFPE 块的相邻切片。这 第一个进行 H&E 染色进行病理分析，第二个进行荧光抗体染色 识别 ROI（例如，免疫细胞丰富或癌细胞丰富的区域）。然后对这些 ROI 进行询问 转录组或蛋白质组水平。我们在使用该工具分析保存的 FFPE 方面拥有丰富的经验 患者肿瘤组织（Lu 2021）。 第二个分析工具是 Fan 小组最近开发和报告的工具（Deng 2021， 2021，刘2020）。这些强大的工具可实现高度多重（高达 300 重）的蛋白质组学和全基因组分析 在由 FFPE 块制备的组织切片中以 10 微米的分辨率进行转录组图谱分析。他们还 允许空间解析 ATAC-seq 和 ChIP-seq 型表观遗传分析（Chen 2017；Chen 2018） 轻微固定的组织切片的空间分辨率。特别是，这种表观遗传分析能力是这些技术所独有的。 工具。与 DSP 类似，邻近的组织切片可以进行 H&E 染色，并且可以进行低倍荧光成像 在同一切片上用于识别细胞核以及免疫丰富和免疫贫乏区域 对齐验证。这些方法可以实现高通量和具有成本效益的组织分析，并且 描述了为此目的而开发的一些技术。核心将继续开发新的空间分析 工具来满足这两个项目在未来 5 年内推进时的紧急需求，从而充当 U54 中​​心和 CSBC 联盟的技术创新中心。