Chromatin Organization in Glioma Initiation

神经胶质瘤起始中的染色质组织

• 批准号: 10331837
• 负责人: Devin Michael Bready
• 金额: $ 5.18万
• 依托单位: NEW YORK UNIVERSITY SCHOOL OF MEDICINE
• 依托单位国家: 美国
• 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/10331837
• 关键词: 3-Dimensional; ATAC-seq; ATRX gene; Address; Adjuvant; Architecture; Astrocytoma; Binding; Biological Assay; Brain; CCCTC-binding factor; CRISPR interference; CRISPR/Cas technology; 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; 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

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 胶质瘤是最常见的原发脑肿瘤，在癌症死亡人数中所占比例过高。 对其发生的影响。在过去的十年中，人们发现几乎所有较低级别的胶质瘤都有一种特征性的增长 异柠檬酸脱氢酶I(IDH1)的功能突变允许该酶形成一种新的个体代谢物。这些较低的 恶性胶质瘤总是进展为高级别、侵袭性的胶质母细胞瘤。在低级和高级阶段都不是 现有的定向治疗方法和目前的治疗方法仅限于手术切除、辅助放射治疗和烷化治疗。 化疗药物。最近的努力试图使用突变的IDH1的抑制剂来治疗这些肿瘤，但早期 证据是混合的，表明突变的IDH1诱导了长期的表观遗传变化，这种变化在抑制后不会消失 代谢物的产量。与IDH野生型胶质瘤患者相比，研究这些肿瘤被证明是困难的。 肿瘤不容易在培养中生长。为了解决这个问题，我们小组建立了一个人类低级别胶质瘤模型。 神经干细胞(NSCs)被认为是这些肿瘤的起源细胞。这一模式被称为3- Hit NSCs，重申了先前的观察结果，即IDH1突变诱导神经前体分化受阻。 值得注意的是，这一对神经干细胞分化的阻碍可以通过恢复其表达而被完全挽救。 转录因子(性别决定区Y)-盒2(SOX2)。此外，这种表达的减少和相关的 SOX2周围的三维染色质组织发生深刻变化，继而发生分化表型 基因组基因座。这项研究的拟议工作将检验这些染色质组织的变化有多重要 神经干细胞中的神经胶质瘤表型，并将表征神经干细胞中SOX2增强子环境，以了解其调控 在脑胶质瘤启动期。初步数据表明，通过阻止基因组结合而破坏SOX2 TAD 组织者CTCF反映了在3次命中的NSCs中SOX2表达的减少。另外，那些输掉比赛的地区 在3-HIT神经干细胞中与SOX2启动子的相互作用与被发现具有活性增强子标记的区域相关 其他表达SOX2的细胞类型。我们假设CTCF在3-Hit神经干细胞中的驱逐导致SOX2表达的丢失 通过破坏启动子与SOX2基因中以前未确定特征的增强子的相互作用。评估 在这个假设中，我将采用互补和独立的方法来解决CTCF介导的参与 神经胶质瘤启动过程中染色质结构障碍，鉴定神经干细胞中新的SOX2增强子，检测SOX2的活性 这些促进剂在胶质瘤启动中的作用，并剖析这些促进剂在干细胞分化中的活性。最后，我会 通过从Surgery的单细胞ATAC测序推断这些增强子的活性来验证这些增强子在胶质瘤中的相关性 低级别胶质瘤标本。通过这些方法，再加上Placantonakis和Skok实验室的支持，我将 确定染色质紊乱在脑胶质瘤发生中的作用，并有助于了解其发育和致癌机制 SOX2的调控。