Methylomic and genomic impacts of organic pollutants in Dup15q syndrome

描述（由申请人提供）：本研究旨在测试一种新的范式，即人类基因组与环境动态相互作用，表观遗传机制位于基因组-环境相互作用的界面。人类基因组以结构变异为标志，包括大拷贝数变异和重复序列的差异。环境毒素如多氯联苯（PCBs）可诱导DNA低甲基化。DNA低甲基化是灵长类谱系中富含CpG的Alu重复序列的基因组不稳定性的已知贡献者。染色体15 q11 - 1 - 3重复综合征（Dup 15 q）是神经发育障碍中观察到的最常见的拷贝数变异，并且是1-3%自闭症病例的原因。这一提议是基于一个偶然的发现，即患有Dup 15 q综合征的人脑样本显示出比对照组或特发性自闭症病例显著更高的持久性有机污染物PCB-95水平。此外，与对照组相比，在围产期接触相关阻燃剂BDE-47的遗传易感小鼠的大脑出现低甲基化，社交能力降低。本研究旨在通过实验确定PCB-95和/或BDE-47是否在使用基因组和表观基因组相结合的方法进行的15 q结构重排中发挥因果或复合作用。此外，本研究将直接研究基因组和环境联合损伤对人脑样品中甲基化组和转录组完整性的影响。第一个目标是在一个新的人类细胞系系统中建立15号染色体复制的实验模型，以利用下一代测序技术研究PCB-95或BDE-47暴露对基因组稳定性（DNA-seq）和DNA甲基化（MethylC-seq）的影响。在第二个目标中，将通过染色质构象捕获测序（4C-seq）检查遗传和表观遗传变化对15 q11-q13内的长距离染色质环结构的影响，并将其与特定的转录改变相关联。第三个目标是直接研究特定的15 q基因靶点，用于在有和没有15号染色体重复和高PCB-95水平的人脑样本中的表观遗传和转录变化。这些研究的结果有望正式验证以下假设：特定环境污染物降低的DNA甲基化水平可能导致基因组重排和长距离染色质改变，从而导致转录变化。此外，在人脑样本中参与突触发生的自闭症候选基因的表观遗传学改变有望通过这种方法被发现。最后，这些研究的结果预计将广泛相关，以了解基因组，环境暴露和人类健康和疾病的表观基因组之间的关系。 公共卫生相关性：自闭症谱系障碍的发生频率高达1/110儿童，但自闭症和其他人类神经发育障碍的病因学知之甚少。过去对自闭症病因学的研究大多集中在遗传或环境的独立贡献上，任何单一的已知贡献只能解释一小部分自闭症病例。表观遗传机制作用于遗传和环境因素的界面。该提案旨在调查在1-3%的自闭症病例中发现的染色体重复综合征和在脑组织中积累的持久性有机污染物的特定表观遗传界面。尖端测序技术将用于比较人类细胞培养模型和15号染色体重复综合征的人类死后大脑样本中的DNA序列，DNA甲基化和基因表达谱。这些结果对于确定新的诊断标记物和开发自闭症的治疗和预防策略具有重要意义。

DESCRIPTION (provided by applicant): This study is designed to test a novel paradigm that the human genome dynamically interacts with the environment and that epigenetic mechanisms are at the interface of genome- environment interactions. The human genome is marked by structural variations including large copy number variations and differences in repetitive sequences. Environmental toxins such as polychlorinated biphenyls (PCBs) can induce DNA hypomethylation. DNA hypomethylation is a known contributor to genomic instability of CpG-rich Alu repeats in the primate lineage. Chromosome 15q11-13 duplication syndrome (Dup15q), is the most common copy number variation observed in neurodevelopmental disorders, and is responsible for 1-3% of autism cases. This proposal is based on the serendipitous finding that human brain samples with Dup15q syndrome showed significantly higher levels of the persistent organic pollutant PCB-95 than controls or idiopathic autism cases. Furthermore, a genetically susceptible mouse perinatally exposed to the related flame retardant BDE-47 exhibited hypomethylation in brain and reduced sociability compared to controls. This study is designed to experimentally determine if PCB-95 and/or BDE-47 play a causal or compounding role in structural rearrangements of 15q using combined genomic and epigenomic approaches. In addition, this study will directly investigate the effect of combined genomic and environmental insults on the integrity of the methylome and transcriptome in human brain samples. The first aim seeks to experimentally model chromosome 15 duplication in a novel human cell line system to examine effects of PCB-95 or BDE-47 exposures on genomic stability (DNA-seq) and DNA methylation (MethylC-seq) using next generation sequencing technology. In the second aim, the effect of genetic and epigenetic changes on long-range chromatin loop structure within 15q11-q13 will be examined by chromatin conformation capture sequencing (4C-seq) and correlated to specific transcriptional alterations. The third aim seeks to directly investigate specific 15q gene targets for epigenetic and transcriptional changes in human brain samples with and without chromosome 15 duplication and high PCB-95 levels. The results of these studies are expected to formally test the hypothesis that DNA methylation levels reduced by specific environmental pollutants may result in genomic rearrangements and alterations in long-range chromatin, leading to transcriptional changes. In addition, epigenetic alterations of autism candidate genes involved in synaptogenesis in human brain samples are expected to be uncovered by this approach. Finally, the results of these studies are expected to be broadly relevant to understanding the relationship between the genome, environmental exposures, and the epigenome in human health and disease. PUBLIC HEALTH RELEVANCE: Autism spectrum disorders occur at a frequency as high as 1 in 110 children, but the etiology of autism and other human neurodevelopmental disorders is poorly understood. Past studies in autism etiology have mostly focused on genetic or environmental contributions independently, and any single known contribution only can explain a small percentage of autism cases. Epigenetic mechanisms act at the interface of genetics and environmental factors. This proposal seeks to investigate the specific epigenetic interface of a chromosome duplication syndrome found in 1-3% of autism cases and persistent organic pollutants that accumulates in brain tissue. Cutting-edge sequencing technologies will be utilized to compare the DNA sequence, DNA methylation, and gene expression profiles in a human cell culture model and human postmortem brain samples with chromosome 15 duplication syndrome. These results are expected to be significant for identifying novel diagnostic markers and development treatment and prevention strategies for autism.