Investigating non-coding mechanisms of functional dysregulation in neuroblastoma

研究神经母细胞瘤功能失调的非编码机制

• 批准号: 8982996
• 负责人: Derek Oldridge
• 金额: $ 2.99万
• 依托单位: UNIVERSITY OF PENNSYLVANIA
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-07-08 至 2017-07-07
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8982996
• 关键词: ALK gene; Accounting; Adverse effects; Affect; Affinity; Automobile Driving; BARD1 gene; Binding; Binding Sites; Bioinformatics; Blood specimen; Cells; ChIP-seq; Childhood; Chromatin; Chromosomal Rearrangement; Code; Computer Simulation; Copy Number Polymorphism; DNA; DNA Methylation; Data; Data Set; Development; Diagnosis; Disease; Disease susceptibility; Encyclopedia of DNA Elements; Enhancers; Epigenetic Process; Etiology; Evolution; Gene Expression; Gene Expression Profiling; Gene Targeting; Genes; Genetic; Genome; Genomic approach; Genomics; Heritability; Histones; Laboratories; Lesion; MYCN gene; Malignant Childhood Neoplasm; Malignant Neoplasms; Maps; Molecular; Molecular Genetics; Mutate; Mutation; Neuroblastoma; Nucleic Acid Regulatory Sequences; Nucleotides; Oncogenes; Oncogenic; Outcome; PTPN11 gene; Pathogenesis; Patients; Phenotype; Play; Predisposition; Preparation; Publications; Publishing; Recurrence; Relapse; Relative (related person); Reporting; Research; Role; Single Nucleotide Polymorphism; Solid Neoplasm; Somatic Mutation; Survival Rate; TP53 gene; Telomerase; Testing; Time; Tissues; Transcription Factor 3; Untranslated RNA; Variant; Work; Writing; base; cancer genomics; clinically relevant; effective therapy; epigenetic regulation; epigenomics; exome sequencing; genome sequencing; genome-wide; high risk; histone modification; in vitro Assay; insight; melanoma; novel; outcome forecast; overexpression; promoter; public health relevance; relating to nervous system; transcription factor; treatment strategy; tumor; verification and validation

 DESCRIPTION (provided by applicant): Neuroblastoma is the most common extracranial solid tumor in childhood with a survival rate less than 10% for relapsed high-risk disease. The molecular lesions underlying neuroblastoma - including heritable germline variants as well as somatic mutations and somatic epigenetic alterations - are still poorly understood, hindering the development of new rational therapies. Moreover, the paucity of coding mutations in neuroblastoma as determined by a recent whole exome-sequencing study of tumors obtained at diagnosis has led us to hypothesize that functional dysregulation in neuroblastoma may be influenced in large part through non-coding mechanisms. In parallel with ongoing germline and somatic whole genome sequencing efforts, I will use integrative experimental and bioinformatic approaches to investigate the extent to which non-coding lesions contribute to neuroblastoma etiology and prognosis. Building on my prior work that discovered and functionally validated the major causal germline variant affecting LMO1 oncogene expression by modulating the affinity for GATA transcription factor binding in an active enhancer region, my first hypothesis (AIM1) is that other non-coding germline variants can affect disease susceptibility and contribute to tumor evolution. I will therefore work to generalize and apply my computational pipeline that identified the LMO1 causal variant in order to uncover other functional germline variants and their mechanisms of dysregulation genome-wide. My second hypothesis (AIM 2) is that non-coding somatic mutations and epigenetic reprogramming can play a dominant role in driving neuroblastoma phenotypes. To this end, I will perform chromatin accessibility profiling and histone marker ChIP-seq across a panel of clinically and molecularly distinct subclasses of neuroblastoma in order to identify important regulatory regions and epigenetic alterations. While these epigenetic alterations will be a primary focus of study, they will also enable the discovery of functional non-coding somatic mutations, which can act as oncogenic drivers in neuroblastoma. These findings will provide novel insights into the molecular basis of neuroblastoma as a whole and of specific disease subclasses, which can form the basis for new rational treatments.

 描述（由申请人提供）：神经母细胞瘤是儿童时期最常见的颅外实体瘤，复发高危疾病的生存率低于10%。神经母细胞瘤潜在的分子病变-包括可遗传的生殖系变异以及体细胞突变和体细胞表观遗传改变-仍然知之甚少，阻碍了新的合理疗法的发展。此外，在神经母细胞瘤的编码突变的缺乏，确定了最近的一个完整的外显子组测序的肿瘤诊断研究，使我们假设，神经母细胞瘤的功能失调可能在很大程度上通过非编码机制的影响。与正在进行的生殖系和体细胞全基因组测序工作平行，我将使用综合实验和生物信息学方法来研究非编码病变对神经母细胞瘤病因学和预后的影响程度。基于我之前的工作，发现并功能验证了主要的致病性种系变异影响LMO 1癌基因表达，通过调节活性增强子区域中的加塔转录因子结合的亲和力，我的第一个假设（AIM 1）是，其他非编码种系变异可以影响疾病的易感性，并有助于肿瘤的演变。因此，我将努力推广和应用我的计算管道，以发现其他功能性种系变异及其全基因组失调的机制。我的第二个假设（AIM 2）是非编码体细胞突变和表观遗传重编程在驱动神经母细胞瘤表型中起主导作用。为此，我将在一组临床和分子上不同的神经母细胞瘤亚类中进行染色质可及性分析和组蛋白标记物ChIP-seq，以确定重要的调控区域和表观遗传学改变。虽然这些表观遗传学改变将是研究的主要焦点，但它们也将使功能性非编码体细胞突变的发现成为可能，这些突变可以作为神经母细胞瘤的致癌驱动因素。这些发现将为神经母细胞瘤作为一个整体和特定疾病亚类的分子基础提供新的见解，这可以形成新的合理治疗的基础。