Characterization Unit

表征单元

• 批准号: 9791171
• 负责人: Orit Rozenblatt-Rosen
• 金额: $ 95.21万
• 依托单位: DANA-FARBER CANCER INST
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/9791171
• 关键词: 3-Dimensional; ATAC-seq; Achievement; Adopted; Adoption; Aftercare; Archives; Atlases; Biological Assay; Boston; Breast Cancer Patient; CDK4 gene; Cancer Immunology Science; Cell Nucleus; Cells; Cellular Assay; Chromatin; Clinical; Clone Cells; Colon Carcinoma; Complement; Data; Data Analyses; Detection; Dissociation; Ecosystem; Ensure; Estrogen receptor positive; Fluorescent in Situ Hybridization; Foundations; Freezing; Genetic; Genomics; Geography; Goals; Human; Image; Immunofluorescence Immunologic; Immunotherapy; In Situ; Individual; Ions; Large Intestine Carcinoma; Lead; Malignant - descriptor; Malignant Neoplasms; Maps; Measurement; Measures; Metadata; Metastatic breast cancer; Methods; Microsatellite Repeats; Mission; Modeling; Molecular; Molecular Profiling; Nuclear; Operative Surgical Procedures; Organoids; Pathology; Plant Roots; Proteins; Proteome; Proteomics; Quality Control; Quick Test for Liver Function; RNA; Recording of previous events; Research; Resistance; Resolution; Sampling; Scientist; Small Nuclear RNA; Specimen; Stable Disease; Techniques; Technology; Testing; Three-Dimensional Imaging; Tissues; Tumor Bank; Tumor Cell Line; Validation; Work; base; cancer cell; cell type; epigenomics; exome sequencing; follow-up; genomic profiles; imaging modality; immune checkpoint blockade; improved; innovation; innovative technologies; malignant breast neoplasm; melanoma; new technology; oncology; predictive modeling; predictive test; prospective; protein expression; protein profiling; quality assurance; single-cell RNA sequencing; spatiotemporal; technology development; therapy resistant; transcriptome sequencing; transcriptomics; treatment response; tumor

The Molecular Characterization Unit (MCU) of the Boston Human Tumor Atlas Research Center (HTA-RC) will comprehensively profile 500 samples (100/yr), collected from melanoma, colon cancer and metastatic breast cancer patients by the Biospecimens Unit (BSU). It will use a suite of complementary, validated cutting-edge cellular/nuclear and spatial technologies to build comprehensive spatiotemporal atlases of the cellular geography of these three cancers. It will also further develop innovative technologies, and perform functional validations of predictions from the Data Analysis Unit (DAU), to understand how dynamic changes in the tumor ecosystem lead to therapeutic resistance. More specifically, the MCU will facilitate the overall mission of the HTA-RC through 4 specific aims. In AIM 1 (the Cellular/Nuclear Branch), the MCU will apply validated single- cell RNA-Seq (scRNA-Seq) and single-nucleus RNA-Seq (snRNA-Seq) methods, in conjunction with bulk whole-exome sequencing and bulk RNA-Seq, to generate genomic profiles of tens to hundreds of thousands of individual cells to develop a comprehensive map of molecularly defined cell types, genetic clones, and states, as well as signatures for spatial studies. In AIM 2 (the Spatial Branch), the MCU will deploy a combination of spatially-resolved cellular RNA (multiplexed error-robust fluorescence in situ hybridization (MERFISH), Spatial Transcriptomics (ST)) and protein profiling (CO Detection of Expression (CODEX), highly multiplex immunofluorescence (HMIF), Multiparameter Ion Beam Imaging (MIBI)) methods to spatially chart cell types, genetic clones, and cell states identified by the cellular/nuclear branch. In AIM 3, we will leverage our team’s expertise to both validate emerging techniques (CITE-Seq) and develop innovative methods to overcome specific challenges—including 3D imaging (whole mount; 3D CODEX), genomic-scale high resolution spatial data (Ex-SEQ and in situ spatial cellular tagging of cells), spatially resolved epigenomics (in situ ATAC-Seq), and proteome-scale measurements in situ (with compressive sensing)—and thereby accelerate the construction of more complete tumor atlases. Finally, in AIM 4, we will test the predictive models generated by the DAU through perturbations and follow-up profiling of banked tumors, cell lines (malignant and TILs), and organoids and organotypic tumor spheroids. The MCU’s established team of scientists—who developed the major methods used in this study—have complementary expertise in single-cell genomics, spatial transcriptomics/proteomics, cancer, immunology, pathology, oncology, technology development, and functional assay. They will work closely with the BSU and DAU to ensure appropriate quality assurance/quality control (QA/QC) measures and sufficient statistical power. The MCU will also be nimble, so as to introduce technologies developed through our collaborative efforts with other Human Tumor Atlas Network (HTAN) Centers, Cancer Moonshot activities, and/or related atlas-building projects. These efforts will be a central part of the goal of understanding how changes in the tumor ecosystem lead to therapeutic resistance in cancer.

波士顿人类肿瘤图谱研究中心 (HTA-RC) 的分子表征单元 (MCU) 将 全面分析从黑色素瘤、结肠癌和转移性乳腺癌中收集的 500 个样本（100 个/年） 生物样本单位（BSU）将使用一套互补的、经过验证的尖端技术来检测癌症患者。 细胞/核和空间技术，用于构建全面的细胞时空图谱 它还将进一步开发这三种癌症的地理创新技术，并发挥功能。 验证数据分析单元 (DAU) 的预测，以了解肿瘤的动态变化 更具体地说，MCU 将促进整体使命的实现。 HTA-RC 通过 4 个具体目标在 AIM 1（蜂窝/核分支）中，MCU 将应用经过验证的单- 细胞 RNA 测序 (scRNA-Seq) 和单核 RNA 测序 (snRNA-Seq) 方法，结合批量 全外显子组测序和批量 RNA-Seq，生成数万到数十万个基因组图谱 单个细胞以开发分子定义的细胞类型、遗传克隆和状态的综合图谱， 以及空间研究的签名，在 AIM 2（空间分支）中，MCU 将部署以下组合： 空间分辨细胞 RNA（多重抗差错荧光原位杂交 (MERFISH)、空间 转录组学 (ST)）和蛋白质分析（CO 表达检测 (CODEX)，高度多重 免疫荧光（HMIF）、多参数离子束成像（MIBI））方法来绘制细胞类型的空间图， 在 AIM 3 中，我们将利用我们团队的技术来识别基因克隆和细胞状态。 验证新兴技术（CITE-Seq）并开发创新方法来克服 具体挑战 - 包括 3D 成像（整体安装；3D CODEX）、基因组规模高分辨率空间 数据（Ex-SEQ 和细胞原位空间细胞标记）、空间解析表观基因组学（原位 ATAC-Seq）、 和蛋白质组规模的原位测量（通过压缩传感），从而加速 最后，在 AIM 4 中，我们将测试生成的预测模型。 通过对库中的肿瘤、细胞系（恶性和 TIL）进行扰动和后续分析来确定 DAU，以及 MCU 的科学家团队开发了类器官和器官型肿瘤球体。 本研究中使用的主要方法——在单细胞基因组学、空间 转录组学/蛋白质组学、癌症、免疫学、病理学、肿瘤学、技术开发和功能 他们将与 BSU 和 DAU 密切合作，以确保适当的质量保证/质量控制。 （QA/QC）措施和足够的统计能力也将是灵活的，以便引入。 我们与其他人类肿瘤图谱网络 (HTAN) 合作开发的技术 中心、癌症登月活动和/或相关的图谱构建项目将是核心部分。 了解肿瘤生态系统的变化如何导致癌症的治疗耐药性的目标。