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Core 1: Tumor and Microenvironment Heterogeneity Core (TMH Core)

核心1：肿瘤与微环境异质性核心（TMH核心）

基本信息

批准号：
10629067
负责人：
Susan M Kaech
金额：
$ 44.26万
依托单位：
SALK INSTITUTE FOR BIOLOGICAL STUDIES
依托单位国家：
美国
项目类别：
财政年份：
2023
资助国家：
美国
起止时间：
2023-07-06 至 2028-06-30
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10629067
关键词：
ATAC-seq Affect Automobile Driving Autophagocytosis Bioinformatics Biological Assay Biometry Biostatistics Core Blood Vessels Cancer Biology Cell Separation Cells Characteristics Collaborations Collection Complement Complex DNA Data Data Analyses Data Set Dedications Desmoplastic Disease Dissociation Ecosystem Ensure Epigenetic Process Exclusion Experimental Designs Extracellular Matrix Fibroblasts Flow Cytometry Genetic Transcription Genome Mappings Genomics Goals Growth Heterogeneity Human Hypoxia Image Immune Immune Evasion Immune response Immunology Individual Inflammation Mediators Inflammatory Infrastructure Knowledge Lead Libraries Link Macrophage Malignant Neoplasms Maps Massive Parallel Sequencing Measures Metabolic Mus Neoplasm Metastasis Normal tissue morphology Organoids Pancreatic Ductal Adenocarcinoma Pharmaceutical Preparations Phenotype Preparation Proteomics RNA Refractory Research Personnel Role Services Signal Transduction Specimen Standardization Stromal Cells T-Lymphocyte Technology Testing Therapeutic Tissues Transcriptional Regulation Treatment Efficacy Tumor Cell Invasion Tumor-infiltrating immune cells Variant Work analysis pipeline base cell type cytokine deep sequencing design digital effective therapy epigenomics experimental study extracellular genome-wide genomic locus insight interest mouse model nano-string neoplastic cell neutrophil novel programs protein expression reference genome response single cell analysis single-cell RNA sequencing therapy resistant transcription factor transcriptomics treatment response tumor tumor growth tumor heterogeneity tumor microenvironment tumor-immune system interactions

项目摘要

PROJECT SUMMARY – Core 1: Tumor and Microenvironment Heterogeneity Core The central hypothesis driving efforts of the TMH Core is that immune and other stromal cells in the tumor microenvironment (TME) contribute to both inherent and acquired therapeutic resistance in PDA. Such cells vary phenotypically, functionally, metabolically, and spatially within the TME, creating distinct niches. For example, functionally specialized immune cells (e.g., macrophages, T cells, neutrophils) are common within the TME and can promote or suppress tumor growth. Likewise, cancer associated fibroblasts (CAFs) contribute to extracellular matrix formation, tumor invasion/metastasis, and T cell exclusion, and can be subdivided into myofibroblastic CAFs (myCAFs) and inflammatory CAFs (iCAFs) that differentially affect tumor growth and therapeutic resistance. Thus, characterizing cellular and functional heterogeneity and TME localization, and understanding how they contribute to therapeutic resistance is key to developing effective therapies. Utilizing expertise in single cell transcriptomics, epigenomics, functional assays, and digital spatial profiling (DSP), the Core will interrogate how cellular diversity and localization contribute to therapeutic resistance in PDA. The TMH Core will support the individual Projects in their efforts to interrogate the TME and tumor-TME crosstalk with state-of-art approaches and by providing expertise in genomics, bioinformatics, and immunology. The TMH Core will provide services that are unavailable in existing Salk Institute Cores, and therefore fulfill an unmet need. In Aim 1, the TMH Core will map the spatial heterogeneity of tumor and stromal cells in human PDA via DSP (NanoString) to correlate phenotypes with specific tumor niches. In Aim 2, the Core will functionally characterize immune cells and inflammatory cytokines in the TME via flow cytometry and use Isoplexis IsoSpark for single cell-secretome analysis and multiplex cytokine assays. In Aim 3, the Core will provide an integrated platform of single-cell RNA and ATAC sequencing to define the functional heterogeneity of tumor and stromal cells in PDA and to understand how this heterogeneity contributes to and/or is affected by therapeutic responses. These aims will support the goals of the projects to elucidate mechanisms of therapeutic resistance in PDA through epigenetic changes (Project 1), extracellular signaling (Project 2), and AMPK driven autophagy (Project 3). The TMH Core will collaborate with the Mouse Models Core and the Human Specimen and Organoid Core to design novel experiments and incorporate mouse and human organoid datasets to decipher the role of stromal and tumor cells in PDA resistance to therapy. Moreover, the TMH Core will work closely with the Biostatistics Unit within the Administrative and Biostatistics Core to ensure rigorous state-of-the-art preprocessing and analysis pipelines. In combination with the efforts of the Projects and other Cores, the TMH Core will not only elucidate the roles of tumor and stromal cells in therapeutic resistance in PDA, but also provide insight into how stromal cells are co-opted and coordinated by the tumor. These studies will inform the treatment of PDA by identifying which compartments can be therapeutically rewired to enhance therapeutic efficacy.

项目概要-核心1：肿瘤和微环境异质结核心 TMH核心的核心假设是肿瘤中的免疫细胞和其他基质细胞微环境（TME）有助于PDA中的固有和获得性治疗抗性。这些细胞表型、功能、代谢和空间在TME内，产生不同的生态位。比如说，功能特化的免疫细胞（例如，巨噬细胞、T细胞、嗜中性粒细胞）在TME内是常见的，可以促进或抑制肿瘤生长。同样，癌症相关的成纤维细胞（CAF）有助于细胞外基质的形成。基质形成、肿瘤侵袭/转移和T细胞排斥，并且可以细分为肌纤维母细胞性 CAF（myCAF）和炎性CAF（iCAF）差异性影响肿瘤生长和治疗阻力因此，表征细胞和功能异质性和TME定位，并了解它们如何导致治疗耐药性是开发有效疗法的关键。利用专业知识，细胞转录组学、表观基因组学、功能测定和数字空间分析（DSP），核心将询问细胞多样性和定位如何导致PDA治疗耐药性。 TMH核心将支持各个项目努力询问TME和肿瘤TME 通过提供基因组学、生物信息学和免疫学方面的专业知识， TMH核心将提供现有索尔克研究所核心无法提供的服务，因此实现了未满足的需求在目标1中，TMH核心将绘制人类肿瘤和基质细胞的空间异质性， PDA通过DSP（NanoString）将表型与特定肿瘤小生境相关联。在目标2中，核心将在功能上通过流式细胞术表征TME中的免疫细胞和炎性细胞因子，并使用Isoplexis IsoSpark 用于单细胞分泌组分析和多重细胞因子测定。在目标3中，核心将提供一个综合的单细胞RNA和ATAC测序平台，以确定肿瘤和间质的功能异质性细胞在PDA和了解这种异质性如何有助于和/或受治疗反应。这些目标将支持阐明PDA耐药机制的项目目标通过表观遗传变化（项目1），细胞外信号（项目2），和AMPK驱动的自噬（项目3）。TMH核心将与小鼠模型核心和人类标本合作，类器官核心设计新颖的实验，并结合小鼠和人类类器官数据集来破译间质细胞和肿瘤细胞在PDA耐药治疗中的作用。此外，“屯门医院核心计划”将与行政和生物统计核心内的生物统计股，以确保严格的最新水平预处理和分析管道。结合项目和其他核心的努力， Core不仅将阐明肿瘤和间质细胞在PDA耐药中的作用，深入了解基质细胞如何被肿瘤吸收和协调。这些研究将告知治疗通过识别哪些隔室可以在治疗上重新连接以增强治疗效果来治疗PDA。