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.

项目摘要胶质母细胞瘤多形（GBM）是最常见的原发性脑肿瘤。粘着蛋白是染色质环的环复合体参与了3D基因组组织，姐妹染色单体内聚力，基因表达和DNA修复。编码粘蛋白复合物成分的基因的突变失活在GBM中很常见，并且 STAG2亚基的突变占所有粘着蛋白突变的50％。但是，机制 Stag2肿瘤抑制仍然未知。最近关于粘蛋白基本生物学的开创性研究已经表明，粘着蛋白在产生和维持染色质环中起着至关重要的作用 3D基因组组织的大部分以及将增强子与启动子联系起来的法规。但是，这些功能与GBM发病机理的这些功能的关系不确定。该赠款将检验假设肿瘤衍生的Stag2突变导致3D基因组组织的改变并增强了多肉组（PCG）介导的转录表示，以驱动GBM中的肿瘤转化。这个假设是根据在Waldman（Multi-Pi）和Jin（Multi-Pi）实验中进行的实验，将基因编辑到纠正GBM细胞中Stag2的内源性突变等位基因，并具有匹配的校正和未校正的细胞通过HI-C和RNA-Seq分析。使用新的生物信息学管道Jin开发了数据称为“ Hicorr”和“ Deeploop”，使得可以清楚地识别从不足的读取中识别染色质循环 - 将测序深度与最高可能的灵敏度结合。这些实验表明，stag2 对于维护拓扑关联域（TADS）是可分配的，Stag2对于调节单个CTCF和H3K27me3锚定的染色质环的大小和强度，导致相邻基因表达的改变。初步研究还表明Stag2突变GBM 细胞大大增加了结合染色质的H3K27me3的水平，增强了多孔的表达组（PCG）调节的基因，以及对体外PCG信号传导抑制剂的敏感性。基于这些数据，两个提出了目标。在AIM＃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AIM＃2中，我们将定义Stag2在PCG介导的染色质中的作用 GBM中的循环和转录表达。在本赠款中提出的研究的完成将定义肿瘤来源的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。这些发现将为粘蛋白提供长期探索的分子机制介导的肿瘤抑制，为如何将粘着蛋白突变定为靶向提供了重要的线索 GBM的治疗目的。