STAG2 mutations and 3D genome organization in glioblastoma multiforme

多形性胶质母细胞瘤中的 STAG2 突变和 3D 基因组组织

基本信息

批准号：
10525627
负责人：
Fulai Jin
金额：
$ 54.94万
依托单位：
GEORGETOWN UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2022
资助国家：
美国
起止时间：
2022-08-10 至 2027-07-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10525627
关键词：
3-Dimensional Alleles Auxins Bioinformatics Biological Biology Brain Neoplasms Cancer Biology Cells ChIP-seq Chromatin Chromatin Loop Complex DNA Repair Data Data Analytics Development EZH2 gene Enhancers Ewings sarcoma FDA approved Gene Expression Gene Mutation Gene Silencing Genes Genome Glioblastoma Goals Grant Hi-C Homeobox Genes In Vitro Individual Knowledge Lead Link Location Maintenance Malignant Neoplasms Malignant neoplasm of urinary bladder Mediating Modeling Molecular Mutate Mutation Myeloid Leukemia Neoplastic Cell Transformation PRC1 Protein Pathogenesis Play Polycomb Primary Brain Neoplasms Primary Neoplasm Process Repression Research Research Personnel Role Signal Transduction Sister Chromatid System Testing The Cancer Genome Atlas Therapeutic Transcriptional Regulation Tumor Suppression Tumor Suppressor Genes Tumor-Derived Xenograft procedure base bioinformatics pipeline cancer type cohesin cohesion epigenomics experimental study gene repression in vivo inhibitor multidisciplinary mutant novel therapeutic intervention promoter targeted treatment therapeutic evaluation therapeutic target transcriptome sequencing tumor

项目摘要

PROJECT SUMMARY Glioblastoma multiforme (GBM) is the most common primary brain tumor. Cohesin is a chromatin-bound ring complex involved in 3D genome organization, sister chromatid cohesion, gene expression, and DNA repair. Mutational inactivation of genes encoding components of the cohesin complex is common in GBM, and mutations of the STAG2 subunit account for >50% of all cohesin mutations. However, the mechanism(s) of STAG2 tumor suppression remain unknown. Recent ground-breaking studies in the basic biology of cohesin have shown that cohesin plays a critical role in generating and maintaining the chromatin loops that underly much of 3D genome organization and that link enhancers to the promoters the regulate. However, the relationship of these functions of cohesin to GBM pathogenesis is undefined. This grant will test the hypothesis that tumor-derived STAG2 mutations result in alterations to 3D genome organization and enhanced Polycomb Group (PcG)-mediated transcriptional repression to drive neoplastic transformation in GBM. This hypothesis is based on experiments performed in the Waldman (multi-PI) and Jin (multi-PI) labs that utilized gene editing to correct the endogenous mutant allele of STAG2 in GBM cells, with matched corrected and uncorrected cells analyzed by Hi-C and RNA-seq. The data were analyzed using a new bioinformatics pipeline Jin developed called “HiCorr” and “DeepLoop” that makes it possible to clearly identify chromatin loops from sub-billion read- pair sequencing depth with the highest possible sensitivity. These experiments showed that whereas STAG2 was dispensable for maintenance of Topologically Associating Domains (TADs), STAG2 was essential for regulating the size and strength of individual CTCF and H3K27me3-anchored chromatin loops, leading to alterations in the expression of adjacent genes. The preliminary studies also showed that STAG2-mutant GBM cells have dramatically increased levels of chromatin-bound H3K27me3, enhanced repression of Polycomb Group (PcG)-regulated genes, and sensitivity to inhibitors of PcG signaling in vitro. Based on these data, two aims are proposed. In Aim #1 we will examine the relationship between STAG2-regulated chromatin loops and gene expression in GBM cells and tumors. In Aim #2 we will define the role of STAG2 in PcG-mediated chromatin looping and transcriptional repression in GBM. Completion of the research proposed in this grant will define the role of tumor-derived STAG2 gene mutations in 3D genome organization and PcG-mediated transcriptional repression in GBM cells and tumors. These findings will provide a long-sought molecular mechanism for cohesin- mediated tumor suppression, providing important clues for how cohesin mutations can be targeted for therapeutic purposes in GBM.

项目概要多形性胶质母细胞瘤 (GBM) 是最常见的原发性脑肿瘤，粘连蛋白是一种染色质结合环。参与 3D 基因组组织、姐妹染色单体凝聚、基因表达和 DNA 修复的复合体。编码粘连蛋白复合物成分的基因突变失活在 GBM 中很常见，并且 STAG2 亚基突变占所有粘连蛋白突变的 50% 以上，但其机制尚不清楚。 STAG2 肿瘤抑制的最新突破性研究在粘连蛋白的基础生物学方面仍然未知。研究表明，粘连蛋白在生成和维持染色质环方面发挥着关键作用，而染色质环是染色质环的基础。 3D 基因组组织的大部分，以及将增强子与所调节的启动子连接起来的过程。粘连蛋白的这些功能与 GBM 发病机制的关系尚不清楚，这项资助将检验这一假设。肿瘤衍生的 STAG2 突变会导致 3D 基因组组织发生改变并增强 Polycomb 组 (PcG) 介导的转录抑制驱动 GBM 肿瘤转化。基于 Waldman（多 PI）和 Jin（多 PI）实验室进行的实验，利用基因编辑使用匹配的校正和未校正细胞校正GBM细胞中STAG2的内源突变等位基因通过 Hi-C 和 RNA-seq 分析数据使用 Jin 开发的新生物信息学流程进行分析。称为“HiCorr”和“DeepLoop”，可以从数十亿个读数中清楚地识别染色质环这些实验表明，STAG2 具有尽可能高的配对测序深度。对于维护拓扑关联域 (TAD) 来说是可有可无的，STAG2 对于维护拓扑关联域 (TAD) 来说是必不可少的调节单个 CTCF 和 H3K27me3 锚定染色质环的大小和强度，从而导致初步研究还表明，STAG2 突变的 GBM 的表达发生了改变。细胞中染色质结合的 H3K27me3 水平显着增加，增强了 Polycomb 的抑制组 (PcG) 调节基因以及体外 PcG 信号抑制剂的敏感性基于这些数据，两个。在目标 #1 中，我们将研究 STAG2 调节的染色质环与 GBM 细胞和肿瘤中的基因表达在目标 #2 中，我们将定义 STAG2 在 PcG 介导的染色质中的作用。 GBM 中的循环和转录抑制。完成本拨款中提出的研究将定义肿瘤源性 STAG2 基因突变在 3D 基因组组织和 PcG 介导的转录中的作用 GBM 细胞和肿瘤中的抑制作用将为粘连蛋白提供长期寻找的分子机制。介导的肿瘤抑制，为如何靶向粘连蛋白突变提供了重要线索 GBM 的治疗目的。