Investigating non-coding mechanisms of functional dysregulation in neuroblastoma

 描述(申请人提供)：神经母细胞瘤是儿童最常见的颅外实体瘤，复发高危疾病存活率不到10%。神经母细胞瘤潜在的分子损伤--包括可遗传的胚系变异以及体细胞突变和体细胞表观遗传学改变--仍然知之甚少，阻碍了新的合理治疗方法的发展。此外，最近对诊断时获得的肿瘤进行的一项完整的外显子组测序研究确定了神经母细胞瘤中编码突变的稀少，这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受到影响。在进行胚系和体细胞全基因组测序工作的同时，我将使用综合实验和生物信息学方法来调查非编码病变对神经母细胞瘤病因和预后的影响程度。在我之前的工作的基础上，我发现并功能验证了通过调节活性增强子区GATA转录因子结合的亲和力来影响LMO1癌基因表达的主要原因种系变体，我的第一个假设(AIM1)是其他非编码种系变体可以影响疾病易感性，并有助于肿瘤的进化。因此，我将致力于推广和应用我的计算管道，识别LMO1因果变体，以揭示其他功能生殖系变体及其在全基因组范围内失调的机制。我的第二个假设(目标2)是，非编码体细胞突变和表观遗传重编程可以在驱动神经母细胞瘤表型方面发挥主导作用。为此，我将对一组临床和分子上不同的神经母细胞瘤亚类进行染色质可及性分析和组蛋白标记物CHIP-SEQ，以确定重要的调节区和表观遗传学变化。虽然这些表观遗传学改变将是主要的研究重点，但它们也将使发现功能性非编码体突变成为可能，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。

 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.