Perturbation based single cell investigation of tumor micro-environment

项目摘要 整合的转录调控电路在正确的位置控制基因表达程序， 正是时候转录因子的突变有助于肿瘤发生。尽管积累了 转录因子谱，不同的转录因子如何共同调节基因表达仍然很差 研究了研究差距导致多基因疾病，特别是癌症的分辨能力差。在 此外，不同细胞之间的调节网络也不同。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， 基于人类全基因组关联研究（GWAS）， 患者，其次使用有利的单细胞技术来研究多个细胞的调节， 在单个细胞中，在染色质、转录和转录后水平上的转录因子。 对于F99阶段的拟议研究，张驰将继续致力于转录 组织干细胞静止、免疫赦免和干细胞长期维持的调控网络 功能通过基因敲除两种转录因子， 在不同阶段的细胞谱系，Chi时空研究在体内的功能作用。既定 单细胞RNA-seq，ATAC-seq，Cut&Run ChIP-seq也允许Chi解剖出 Foxc 1和Nfatc 1在分子水平上的研究，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。然后使用建立的多光子系统，Chi将 能够可视化组织干细胞在基因操作后的细胞活性。 对于拟议研究的K 00阶段，Chi将在胶质母细胞瘤的背景下应用该方法。 认为它是最具进展性的癌症之一，预期寿命为14至16个月，现有GWAS 表明人类患者中多种转录因子突变的数据。使用所建立的 在Parada博士实验室的胶质母细胞瘤小鼠模型中，Chi将试图揭示 癌症干细胞、癌症异质性和免疫豁免。 在技术层面，利用基因工程小鼠模型、精密的基因组工具 包括scATAC-seq/scRNA-seq和实时成像应该为其他人建立一个蓝图， 转录机制对活体动物干细胞活动的影响。

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.