Chromatin Organization in Glioma Initiation

神经胶质瘤起始中的染色质组织

基本信息

批准号：
10156402
负责人：
Devin Michael Bready
金额：
$ 3.78万
依托单位：
NEW YORK UNIVERSITY SCHOOL OF MEDICINE
依托单位国家：
美国
项目类别：
财政年份：
2021
资助国家：
美国
起止时间：
2021-01-07 至 2024-01-06
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10156402
关键词：
3-Dimensional ATAC-seq ATRX gene Address Adjuvant Architecture Astrocytoma Binding Biological Assay Brain CCCTC-binding factor CRISPR interference Cell Cycle Cell Survival Cell model Cells Characteristics Chromatin Clustered Regularly Interspaced Short Palindromic Repeats DNA Data Development Dioxygenases Distal Distal Enhancer Elements Engineering Enhancers Environment Enzyme Inhibition Enzymes Epigenetic Process Event Excision Family Fellowship Functional disorder Genes Genetic Genetic Enhancer Element Genetic Transcription Genome Genomics Glioblastoma Glioma Gliomagenesis Guide RNA Histones Human Hypermethylation Impairment Incidence Indolent Intergenic DNA Isocitrate Dehydrogenase Lead Light Location Maintenance Malignant - descriptor Malignant Neoplasms Mediating Metabolism Modeling Molecular Conformation Mutation Nuclear Oncogenic Operative Surgical Procedures Other Genetics Pathway interactions Patients Pattern Phenotype Primary Brain Neoplasms Production Publishing Radiation Regulation Reporter Role Secondary to Specimen TP53 gene Testing Transcript Tumor Suppressor Genes Tumor Suppressor Proteins Undifferentiated Work XCL1 gene alpha ketoglutarate base cell type chemotherapeutic agent epigenome gain of function mutation gene interaction genomic locus histone demethylase inhibitor/antagonist insight knock-down mutant neoplastic cell nerve stem cell neurodevelopment neuroregulation novel prevent promoter recruit restoration sex small hairpin RNA stem cell differentiation stem cell model transcription factor transcriptome transcriptome sequencing transcriptomics translocase treatment strategy tumor tumorigenesis young adult

3-Dimensional ATAC-seq ATRX gene Address Adjuvant Architecture Astrocytoma Binding Biological Assay Brain CCCTC-binding factor CRISPR interference Cell Cycle Cell Survival Cell model Cells Characteristics Chromatin Clustered Regularly Interspaced Short Palindromic Repeats DNA Data Development Dioxygenases Distal Distal Enhancer Elements Engineering Enhancers Environment Enzyme Inhibition Enzymes Epigenetic Process Event Excision Family Fellowship Functional disorder Genes Genetic Genetic Enhancer Element Genetic Transcription Genome Genomics Glioblastoma Glioma Gliomagenesis Guide RNA Histones Human Hypermethylation Impairment Incidence Indolent Intergenic DNA Isocitrate Dehydrogenase Lead Light Location Maintenance Malignant - descriptor Malignant Neoplasms Mediating Metabolism Modeling Molecular Conformation Mutation Nuclear Oncogenic Operative Surgical Procedures Other Genetics Pathway interactions Patients Pattern Phenotype Primary Brain Neoplasms Production Publishing Radiation Regulation Reporter Role Secondary to Specimen TP53 gene Testing Transcript Tumor Suppressor Genes Tumor Suppressor Proteins Undifferentiated Work XCL1 gene alpha ketoglutarate base cell type chemotherapeutic agent epigenome gain of function mutation gene interaction genomic locus histone demethylase inhibitor/antagonist insight knock-down mutant neoplastic cell nerve stem cell neurodevelopment neuroregulation novel prevent promoter recruit restoration sex small hairpin RNA stem cell differentiation stem cell model transcription factor transcriptome transcriptome sequencing transcriptomics translocase treatment strategy tumor tumorigenesis young adult

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项目摘要

Project Summary Glioma is the most common primary brain tumor and represents a disproportionate percentage of cancer fatalities in relation to its incidence. In the last decade, it has been discovered that nearly all lower grade gliomas harbor a characteristic gain of function mutation in Isocitrate dehydrogenase I (IDH1) allowing the enzyme to form a novel oncometabolite. These lower grade gliomas invariably progress to high-grade, aggressive glioblastoma. At neither the low-grade nor high-grade stage are directed therapies available and current treatment is limited to surgical resection and adjuvant radiation and alkylating chemotherapeutic agents. Recent efforts have attempted to employ inhibitors of mutant IDH1 to treat these tumors but early evidence is mixed, indicating that mutant IDH1 induces long-lasting epigenetic changes that do not dissipate upon inhibition of the oncometabolite’s production. Studying these tumors has proven difficult compared to IDH wildtype glioma as patient tumors cannot be readily grown in culture. To address this, our group generated a model of low-grade glioma in human neural stem cells (NSCs) which are strongly implicated as the cell of origin for these tumors. This model, referred to as 3- Hit NSCs, reaffirmed previous observations that the IDH1 mutant induces a block to neural precursor differentiation. Strikingly, it revealed that this block to differentiation in NSCs can be completely rescued by restoration of expression of the transcription factor (sex determining region Y)-box 2 (SOX2). Moreover, this reduction of expression and the associated differentiation phenotype occurs secondary to profound changes in 3-dimensional chromatin organization around the SOX2 genomic locus. The proposed work in this fellowship will examine how central these changes in chromatin organization are to the glioma-phenotype in NSCs and will characterize the SOX2 enhancer environment in NSCs to understand its regulation in glioma initiation. Preliminary data suggests that disruption of the SOX2 TAD by preventing binding of the genome organizer CTCF mirrors reduction in SOX2 expression seen in 3-Hit NSCs. Additionally, those regions which lose interaction with the SOX2 promoter in 3-Hit NSCs correlate with regions found to have marks of being active enhancers in other SOX2 expressing cell types. We hypothesize that CTCF eviction in 3-Hit NSCs results in a loss of SOX2 expression through a disruption of promoter interactions with previously uncharacterized enhancers in the SOX2 locus. To evaluate this hypothesis, I will employ complementary and independent approaches that address the involvement of CTCF mediated chromatin architecture dysfunction in glioma initiation, identify novel SOX2 enhancers in NSCs, examine the activity of these enhancers in glioma initiation, and dissect the activity of these enhancers in stem cell differentiation. Finally, I will validate the relevance of these enhancers in glioma by inferring their activity from single cell ATAC-sequencing of surgical low-grade glioma specimens. Through these approaches, paired with the support of the Placantonakis and Skok labs, I will characterize the role of chromatin disorganization in glioma initiation and help understand the developmental and oncogenic regulation of SOX2.

项目摘要神经胶质瘤是最常见的原发性脑肿瘤，代表癌症死亡的比例不成比例事件。在过去的十年中，已经发现几乎所有低级神经胶质瘤都具有异氯酸酯脱氢酶I（IDH1）中的功能突变，使酶形成一种新型的oncometabolite。这些较低级别的神经胶质瘤总是会发展为高级，侵略性胶质母细胞瘤。在低级和高级阶段，可用的定向疗法和当前治疗仅限于手术切除，调整射射和烷基化化学治疗剂。最近的努力试图利用突变体IDH1的抑制剂治疗这些肿瘤，但很早就证据混合在一起，表明突变体IDH1诱导了持久的表观遗传变化，而不会在抑制后消失与IDH野生型神经胶质瘤相比，研究这些肿瘤很难肿瘤在培养中不易生长。为了解决这个问题，我们的小组在人类中生成了低级神经胶质瘤的模型神经干细胞（NSC），它们是这些肿瘤的原始细胞。该模型，称为3- HIT NSC，重申以前的观察结果，即IDH1突变体诱导神经前体分化的障碍。令人惊讶的是，它揭示了通过恢复的表达来完全挽救NSC中分化的障碍转录因子（性别确定区域y）-box 2（SOX2）。此外，这种表达的降低和相关的分化表型发生在SOX2周围3维染色质组织的深刻变化之后。基因组基因座。该研究金的拟议工作将研究这些在染色质组织中的变化的中心到NSC中的神经瘤 - 表型，并将表征NSC中的Sox2增强剂环境以了解其调节在神经胶质瘤倡议中。初步数据表明，通过防止基因组的结合，Sox2 TAD的破坏组织者CTCF镜像在3击NSC中看到的SOX2表达的降低。此外，那些失去的地区 3击NSC中与SOX2启动子的相互作用与发现具有主动增强子的区域相关其他表达细胞类型的SOX2。我们假设3击NSC中的CTCF驱逐导致SOX2表达的损失通过破坏启动子与SOX2基因座中先前未表征的增强子的相互作用。评估这个假设，我将采用完全独立的方法来解决CTCF介导的参与神经胶质瘤倡议中的染色质结构功能障碍，识别NSC中的新型SOX2增强剂，检查这些在神经胶质瘤倡议中的增强子，并剖析了这些增强子在干细胞分化中的活性。最后，我会的通过从单个细胞ATAC进行手术的单个细胞来验证这些增强子在神经胶质瘤中的相关性低级神经胶质瘤标本。通过这些方法，在Placantonakis和Skok Labs的支持下，我将表征染色质混乱在神经胶质瘤倡议中的作用，并有助于了解发育和致癌性 Sox2的调节。