Perturbation based single cell investigation of tumor micro-environment

基于扰动的肿瘤微环境单细胞研究

基本信息

批准号：
10634833
负责人：
Chi Zhang
金额：
$ 8.58万
依托单位：
DANA-FARBER CANCER INST
依托单位国家：
美国
项目类别：
财政年份：
2020
资助国家：
美国
起止时间：
2020-08-03 至 2026-07-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10634833
关键词：
ATAC-seq Address Affect Aging Animals Antigens Basement membrane Binding Cell Adhesion Cell Lineage Cell division Cells ChIP-seq Chromatin Data Enhancers Event Extracellular Matrix FOXC1 gene Fibrinogen Gene Expression Genes Genetic Genetic Models Genetic Transcription Genetically Engineered Mouse Glioblastoma Goals Hair follicle structure Heterogeneity Homeostasis Human Image Immune In Vitro Individual Institutes Investigation Knock-out Knockout Mice Knowledge Lead Life Expectancy Link Maintenance Malignant Neoplasms Malignant neoplasm of brain Maps Methodology Miniaturization Molecular Mutation NF1 gene Natural regeneration Normal tissue morphology Pathway interactions Patients Phase Phenocopy Play Population Premature aging syndrome Process Regulation Research Research Personnel Resolution Role Running Skin System T-Lymphocyte TP53 gene Techniques Testing Time Tissues Training Transcriptional Regulation Work anticancer research base cancer cell cancer heterogeneity cancer initiation cancer stem cell career cell behavior cell motility combat combinatorial computerized tools genetic manipulation genome wide association study genomic tools imaging system in vivo insight intravital imaging mouse model movie multiphoton imaging mutant pathogen professor programs promoter single-cell RNA sequencing spatiotemporal stem cell aging stem cell function stem cell niche stem cell self renewal stem cells tissue stem cells tool transcription factor transcriptomics tumor tumor microenvironment tumor progression tumorigenesis

项目摘要

Project summary Integrated transcriptional regulatory circuits govern gene expression programs at the right place and right time. Mutations in transcription factors contribute to tumorigenesis. Despite the accumulation of transcription factor profiling, how different transcription factors co-regulate gene expression remains poorly studied. The research gap leads to the poor resolving power for polygenic conditions, especially cancer. In addition, the regulation network changes among different cells. In order to systematically and accurately dissect the transcriptional regulation network in normal tissue homeostasis and tumorigenesis, efforts must be made to firstly generate genetic models based on the genome-wide association study (GWAS) from human patients, secondly using advantageous single cell techniques to investigate the regulation of multiple transcription factors at chromatin, transcription and posttranscription levels in single cells. For F99 phase of the proposed research, Chi Zhang will continue working on the transcriptional regulation network of tissue stem cell quiescence, immune privilege and long-term maintenance of stem cell function. Through genetic knockout of two transcription factors individually and combinatorially in different cell lineages at different stages, Chi spatiotemporally investigated the functional role in vivo. The established single cell RNA-seq, ATAC-seq, Cut&Run ChIP-seq also allow Chi to dissect out the regulation network of Foxc1 and Nfatc1 at molecular level, including promoter enhancer looping, transcription factor binding, open chromatin dynamics, super enhancer identities, etc. Then using the established multiphoton system, Chi would be able to visualize the cellular activity of tissue stem cells after genetic manipulation. For K00 phase of the proposed research, Chi will apply the methodology in the context of glioblastoma. Considering it as one of the most progressive cancer with life expectancy of 14 to 16 month and existing GWAS data indicating the mutation of multiple transcription factors in human patients. Using the established glioblastoma mouse model in Dr. Parada lab, Chi will try to uncover the transcription regulation network of cancer stem cell, cancer heterogeneity and immune privilege. At the technical level, the use of genetically engineered mouse models, sophisticated genomic tools including scATAC-seq/scRNA-seq and live imaging should establish a blueprint for others to link transcriptional mechanisms to stem cell activities in live animals.

项目概要整合的转录调控电路在正确的位置控制基因表达程序正确的时间。转录因子的突变有助于肿瘤发生。尽管积累了转录因子分析，不同转录因子如何共同调节基因表达仍然很差研究过。研究差距导致对多基因疾病（尤其是癌症）的解析能力较差。在此外，不同细胞之间的调节网络也会发生变化。为了系统、准确地剖析正常组织稳态和肿瘤发生中的转录调控网络，必须努力首先基于人类全基因组关联研究（GWAS）生成遗传模型患者，其次使用有利的单细胞技术来研究多种细胞的调节单细胞染色质、转录和转录后水平的转录因子。对于拟议研究的 F99 阶段，张驰将继续致力于转录组织干细胞静止、免疫特权和干细胞长期维持的调控网络功能。通过在不同的环境中单独或组合地基因敲除两个转录因子 Chi时空研究了细胞谱系在不同阶段的体内功能作用。已成立的单细胞 RNA-seq、ATAC-seq、Cut&Run ChIP-seq 还允许 Chi 剖析分子水平的 Foxc1 和 Nfatc1，包括启动子增强子环、转录因子结合、开放染色质动力学、超级增强子身份等。然后使用已建立的多光子系统，Chi 将能够可视化基因操作后组织干细胞的细胞活性。对于拟议研究的 K00 阶段，Chi 将在胶质母细胞瘤的背景下应用该方法。认为它是进展最快的癌症之一，预期寿命为 14 至 16 个月，现有 GWAS 表明人类患者多种转录因子突变的数据。利用既定的 Parada博士实验室的胶质母细胞瘤小鼠模型，Chi将尝试揭示胶质母细胞瘤的转录调控网络癌症干细胞、癌症异质性和免疫特权。在技术层面，利用基因工程小鼠模型、先进的基因组工具包括 scATAC-seq/scRNA-seq 和实时成像应该为其他人建立链接蓝图活体动物干细胞活性的转录机制。