Defining the Chromatin Landscape and Transcriptional Drivers Of Proliferation and Migration In Human Glioblastoma.

定义人类胶质母细胞瘤的染色质景观和增殖和迁移的转录驱动因素。

• 批准号: 9572963
• 负责人: Nadejda Mincheva Tsankova
• 金额: $ 8.48万
• 依托单位: ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-09-30 至 2019-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9572963
• 关键词: ASH2L gene; ATAC-seq; Address; Affect; Antibodies; Automobile Driving; Binding; Biochemical; Bioinformatics; Biological; Biological Assay; Biology; Cell Culture Techniques; Cell Proliferation; Cells; Chromatin; Chromatin Remodeling Factor; Clinical; Collaborations; Communities; Computer Analysis; Data; Data Analyses; Data Set; Deposition; Development; Diffuse; EGF gene; Epidermal Growth Factor Receptor; Epigenetic Process; Excision; FOXM1 gene; Gene Expression Profiling; Genes; Genetic Transcription; Genomic approach; Genomics; Glioblastoma; Glioma; HIF1A gene; Heterogeneity; Human; Individual; Infiltration; Investigation; Ligand Binding; Ligands; Link; MADH3 gene; MLL gene; Maps; Methodology; Modeling; Molecular; Morphologic artifacts; Mus; Mutation; Nucleic Acid Regulatory Sequences; Oncogenic; Operative Surgical Procedures; Pathologic; Pathway interactions; Patients; Phenotype; Population; Property; Regulation; Regulatory Pathway; Role; Sampling; Signal Transduction; Sorting - Cell Movement; Stem Cell Development; Stem cells; Synapses; Testing; Tissue-Specific Gene Expression; Tissues; Transcriptional Activation; Transposase; Xenograft procedure; cell growth; cell immortalization; cell motility; chromatin remodeling; clinically relevant; comparative; design; effective therapy; epigenetic regulation; experimental study; genome-wide; immortalized cell; in vivo; innovation; insight; migration; neoplastic; neoplastic cell; nerve stem cell; novel; overexpression; progenitor; programs; promoter; prospective; relating to nervous system; self-renewal; stem; stem cell population; stem-like cell; transcription factor; transcriptome; transcriptome sequencing; tumor; tumor growth; tumor heterogeneity; tumorigenic

Recent molecular studies reveal global chromatin disorganization in glioblastoma (GBM), but how that affects individual gene loci to drive tumor growth and migration in vivo is still poorly understood. Previously, we have shown remarkable similarities in chromatin remodeling between germinal matrix stem/progenitors (NSPCs) and gliomas at the EGFR promoter, and implicated several epigenetic modifiers for the transcriptional activation of this oncogenic locus (Erfani et al, 2015). We now expand our study focus to investigate more systematically and in functionally distinct populations how developmentally regulated transcriptional networks become pathologically co-opted in gliomas to maintain tumorigenic properties of cell migration and cell proliferation. To this end, we have developed a simple EGF ligand-binding strategy to prospectively isolate populations with stem cell properties from fresh human samples and patient-derived glioma xenografts (PDX), in which the migratory human GBM cells can be regionally separated from those at the tumor core (Tome- Garcia et al, Stem Cell Rep, accepted in final revisions). Full transcriptome and chromatin accessibility analyses in these freshly sorted human GBM stem cell populations revealed distinct regulatory regions related to cell migration vs. self-renewal, the latter also present in NSPCs. We thus hypothesized that tumor properties of cell growth and migration in GBM are regulated through unique transcription factors (TFs) at regions of open chromatin, some of which are co-opted from a normal neural developmental state. To test this hypothesis, here we intend to profile the transcriptome (by RNA-seq) and associated open chromatin landscape (by ATAC-seq) in phenotypically defined migratory vs. core-proliferative human GBM populations, isolated from PDX gliomas, and compare them to our previously generated data in developing NSPCs. Differential analysis of RNAseq and ATACseq data in infiltrative vs. tumor-core GBM cells will allow us to define the transcriptional pathways and chromatin accessibility regulatory regions driving adaptations for a migratory GBM cell fate in vivo, while comparative analysis with similar data in NSPCs will elucidate how developmental pathways are aberrantly co- opted and re-activated in GBM. Combined ATACseq/RNAseq data analysis will provide a blueprint for specific TF binding occupancy at gene loci activated in infiltrative tumor cells, generating a candidate list of TF regulators for cell migration in GBM, which we will confirm biochemically. Defining the specific epigenetic landscape and associated transcriptional phenotype in neoplastic and progenitor populations derived from fresh human and PDX samples will advance deeply our understanding of the mechanisms maintaining plasticity in GBM stem cells and the specific molecular adaptations in a subset of these cells towards a migratory cell fate. By depositing our data in an open access platform, we will maximize data dissemination and facilitate further investigation into the role of cell migration in GBM, hoping to uncover new avenues for therapy aimed at targeting infiltrative tumor cells that currently evade surgical resection.

最近的分子研究揭示了胶质母细胞瘤(GBM)的整体染色质紊乱，但这是如何影响的 在体内驱动肿瘤生长和迁移的单个基因位点仍然知之甚少。此前，我们有 生发基质干/祖细胞(NSPC)染色质重塑有显著相似性 和胶质瘤EGFR启动子，并牵涉到转录的几个表观遗传修饰物 该致癌基因的激活(Erfani等人，2015年)。我们现在扩大我们的研究重点，以调查更多 在系统和功能不同的人群中，发育调节的转录网络是如何 在病理上增选胶质瘤以维持细胞迁移和细胞的致瘤特性 扩散。为此，我们开发了一种简单的EGF配体结合策略来前瞻性地分离 从新鲜人类样本和患者来源的胶质瘤异种移植(PDX)中获得干细胞特性的人群， 在这种情况下，迁移的人GBM细胞可以从肿瘤核心(Tome-Tome)的细胞中区域分离出来。 Garcia等人，干细胞代表，在最终修订中接受)。全转录组和染色质可及性 对这些新分离的人类GBM干细胞群体的分析显示，与 细胞迁移与自我更新相比，后者也存在于NSPC中。因此我们假设肿瘤的性质 在GBM中，许多细胞的生长和迁移是通过开放区域的独特转录因子(TF)来调节的 染色质，其中一些来自正常的神经发育状态。为了检验这一假设，这里 我们打算描述转录组(通过rna-seq)和相关的开放染色质图谱(通过atac-seq)。 在从PDX胶质瘤分离出来的表型确定的迁移性和核心增殖性人GBM群体中， 并将它们与我们之前在开发国家石油公司时生成的数据进行比较。RNAseq和RNAseq的差异分析 浸润性与肿瘤核心的GBM细胞中的ATACseq数据将使我们能够定义转录途径和 染色质可及性调节区驱动体内迁移的GBM细胞命运的适应，而 与NSPC中类似数据的比较分析将阐明发育途径是如何异常地协同作用的。 已选择并在GBM中重新激活。ATACseq/RNAseq联合数据分析将为特定的 在浸润性肿瘤细胞中激活的基因位点上的Tf结合占位，生成Tf候选列表 基底膜中细胞迁移的调节剂，我们将用生化方法证实这一点。 明确特定的表观遗传格局和相关的转录表型在肿瘤和 从新鲜的人和PDX样本中提取的祖细胞种群将加深我们对 GBM干细胞的可塑性维持机制和部分亚群中的特定分子适应 这些细胞走向了迁徙细胞的命运。通过将我们的数据存放在开放访问平台中，我们将最大限度地 数据传播和促进进一步调查细胞迁移在GBM中的作用，希望揭示 新的治疗途径旨在针对目前逃脱手术切除的浸润性肿瘤细胞。

项目成果

Practical Bioinformatic DNA-Sequencing Pipeline for Detecting Oncogene Amplification and EGFRvIII Mutational Status in Clinical Glioblastoma Samples.

用于检测临床胶质母细胞瘤样本中癌基因扩增和 EGFRvIII 突变状态的实用生物信息学 DNA 测序流程。

• DOI: 10.1016/j.jmoldx.2019.02.001
• 发表时间: 2019
• 期刊: The Journal of molecular diagnostics : JMD
• 作者: Miller,MichaelL;Tome-Garcia,Jessica;Waluszko,Aneta;Sidorenko,Tatyana;Kumar,Chitra;Ye,Fei;Tsankova,NadejdaM
• 通讯作者: Tsankova,NadejdaM