Dissecting Genetic and Epigenetic variation in the Cancer Regulome

描述（由申请人提供）：癌症是基因错误表达的结果。这种疾病几乎总是由一个或多个遗传事件引发的，这些遗传事件主要是体细胞的，而很少是由于单基因疾病的遗传。鉴定遗传性和自发性核苷酸变异的努力在很大程度上集中在编码蛋白质的基因组的约1.2%上，这些变异共同赋予了发展不同类型癌症的风险。然而，蛋白质编码变异无法解释大多数癌症的易感性。最近的GWAS研究表明，非编码调控元件占疾病相关变异的很大一部分，这可能解释了疾病缺失的遗传成分的一部分。除了遗传不稳定性之外，癌症基因组还表现出DNA甲基化的广泛变化，这被认为是维持细胞身份的基因调控机制的一个关键方面。我们的工作表明，基因间DNA甲基化的特定模式，以及特定的局部低甲基化，可以区分组织特异性谱系和不同基因型的身份。 其中的细胞类型。此外，基因间低甲基化的概况可用于索引跨基因组的推定的细胞类型特异性增强子元件。在这种情况下，我们观察到个体之间在增强子处的甲基化变异性高于其他基因组元件。这些观察结果可能与最近的GWAS研究相呼应，因为与调控序列变异一样，增强子甲基化的个体模式可能反映了基因调控和疾病易感性的差异。总之，这些想法构成了我的中心假设的基础：非编码调节异常比以前认识到的更有助于癌症的发展。因此，本提案的目的是捕获非编码癌症“调节组”的遗传和表观遗传多样性，研究序列可塑性和甲基化状态之间的相互作用，并测试这种变异对基因调控活性的功能影响。我将建立在参考数据集，我已经产生了作为一个博士后研究员，即在造血细胞类型，探索这些想法使用B细胞淋巴瘤（CLL）作为一个模型。这将通过三个集中的目标来实现：1）通过比较甲基化分析建立细胞类型特异性增强子的“调节组”目录，2）在明确定义的癌症模型中进行调节组的靶向重测序，以及3）测试鉴定的增强子变体驱动基因表达的能力。这些信息可用于建立定量模型，预测调控变异对增强子活性水平的影响和对靶基因的潜在影响。这项拟议中的研究将解决癌症基因组学的一个未充分探索的领域，这将补充目前更好地了解癌症分子基础的努力。

DESCRIPTION (provided by applicant): Cancer is a consequence of the mis-expression of genes. The disease is almost always triggered by one or more genetic events that are largely somatic and much less often due to the inheritance of a single gene disorder. Efforts to identify both heritable and spontaneous nucleotide variants that together confer risk to develop different types of cancer have focused in large part on the ~1.2% of the genome that encodes proteins. Yet protein-coding variation fails to explain most cancer susceptibility. Recent GWAS studies indicate that non-coding regulatory elements account for a large fraction of disease-associated variants, which may explain part of the missing genetic component of the disease. In addition to genetic instability, cancer genomes display widespread changes in DNA methylation, which is thought to be a critical aspect of the gene regulatory mechanisms that maintain cellular identity. Our work has shown that specific patterns of intergenic DNA methylation, and specifically localized hypomethylation, distinguish tissue-specific lineages and the identities of the different cell-types within them. Moreover, profiles of intergenic hypomethylation may be used to index putative cell-type specific enhancer elements across the genome. In this context, we have observed higher methylation variability between individuals at enhancers than other genomic elements. These observations may echo recent GWAS studies in that, like regulatory sequence variation, individual patterns of enhancer methylation may reflect differences in gene regulation and disease susceptibility. Together, these ideas form the basis of my central hypothesis: non-coding regulatory anomalies contribute more to the development of cancer than previously appreciated. The objectives of this proposal are therefore to capture both genetic and epigenetic diversity across the non-coding cancer "regulome", to investigate the interplay between sequence plasticity and methylation state and to test the functional impact of this variation on gene regulatory activity. I will build upon reference datasets that I have generated as a postdoctoral fellow, namely in hematopoietic cell- types, to explore these ideas using B cell lymphoma (CLL) as a model. This will be accomplished through three focused aims directed at 1) building "regulome" catalogues of cell-type specific enhancers through comparative methylation profiling, 2) performing targeted resequencing of regulomes in well-defined models of cancer, and 3) testing the competence of identified enhancer variants to drive gene expression. This information may be used to build quantitative models that predict the impact of regulatory variation on enhancer activity levels and potential effects on target genes. The proposed research will tackle an underexplored area of cancer genomics that will complement current efforts to better understand the molecular basis of cancer.