Functional mapping of noncoding regulatory variants in human neuronal subtypes

复杂的神经精神障碍，包括精神分裂症和自闭症谱系障碍(ASD)等， 给家庭和社会带来巨大的社会经济负担。其病理生物学机制是 这在很大程度上是未知的，治疗选择有限，而且往往不完全有效。在过去的十年里， 人类遗传学和下一代测序的进步，加上队列规模的扩大，已经 这使得能够识别出数千种影响神经精神疾病风险的基因变异。 全基因组关联研究(GWAS)确定的每一种疾病相关变异都可以提供见解 转化为一种生物机制，它是人类疾病风险的基础。然而，数据的可用性并不是 与意义的存在同义词。研究人员现在面临的挑战是衍生出 后GWA时代的生物学意义。特别是，90%以上的风险变量是在非编码中发现的 人类基因组的区域。尽管非编码变体对复杂人类的潜在贡献 长期以来，人们一直在猜测疾病，开发可测试的假说来破译一直是一个重大挑战 它们在疾病病因学中的作用。在这里，我们建议开发创新的多学科方法来弥合 人类遗传学和实验生物学之间的差距。这种方法背后的主要假设是 顺式调控元件的非编码变异引起的表观遗传学变化，特别是 是序列特异性转录因子结合的平台，可以长期影响基因转录 距离，可能会通过扰乱基因表达来增加疾病的易感性。我们的目标是(I)注释功能上的不同 通过对多能干细胞重新编程而产生的与疾病相关的人类神经元亚型的增强剂， (Ii)应用前沿的HiChIP技术分析静息状态下神经元中启动子-增强子的相互作用 和活性状态，并确定增强子的靶基因，最后，(Iii)我们将确定疾病如何- 相关的变异会影响人类神经元中的增强子活性。这些努力将为绘制地图提供基础 并为未来的机械学研究确定非编码风险变量的优先顺序。尤其是增强子-互动组 本研究中进行的分析将提供一种基于物理交互的方法来识别 神经元中的增强子靶向基因。这些信息将为开发可检验的假说奠定基础。 阐明风险变异在非编码区的分子影响。最后但同样重要的是，确定非 编码风险变体扰乱神经元亚型中活性调节基因的表达可能会发现新的疾病-- 未使用不完整的现有方法和资源观察到的相关生物学(活动响应 增强剂不可能从身体组织中识别)。一旦完成，拟议的工作将 对将基因发现转化为可操作的生物学假说产生广泛影响，这些假说可能 为复杂神经精神障碍的新一轮治疗策略的开发提供动力。

Complex neuropsychiatric disorders, including schizophrenia and autism spectrum disorder (ASD) among others, impose an enormous socioeconomic burden on families and on society. The pathobiological mechanisms are largely unknown, and treatment options are limited and often incompletely effective. During the past decade, advances in human genetics and next-generation sequencing, coupled with expanding cohort sizes, have permitted the identification of thousands of genetic variants that influence risk for neuropsychiatric diseases. Each disease-associated variants identified by genome-wide association studies (GWAS) could provide insights into a biological mechanism that underlies the risk of disease in humans. However, the availability of data is not synonymous with the presence of meaning. The challenge researchers are facing now is the derivation of biological meaning post-GWAS. Particularly, more than 90% of the risk variants are found in the non-coding regions of the human genome. Although the potential contribution of non-coding variants to complex human diseases has long been speculated, it has been a major challenge to develop testable hypotheses to decipher their role in disease etiology. Here, we propose to develop innovative multidisciplinary approaches to bridge the gap between human genetics and experimental biology. The major hypothesis underlying the approach is that epigenetic changes caused by non-coding variation in the cis-regulatory elements, particularly enhancers that are platforms for sequence-specific transcription factor binding and can influence gene transcription over long distance, may confer disease liability by disrupting gene expression. We aim to (i) annotate functionally distinct enhancers in disease-relevant human neuronal subtypes generated by reprogramming of pluripotent stem cells, (ii) apply the cutting-edge HiChIP technology to profile the promoter-enhancer interactions in neurons in resting and active states, and identify the target genes of enhancers, finally, (iii) we will determine how disease- associated variants affect enhancer activity in human neurons. Such effort will provide the foundation to map and prioritize non-coding risk variants for future mechanistic studies. Especially, the enhancer-interactome analysis performed in this study will provide a physical-interaction-based approach for the identification of enhancer target genes in neurons. The information will lay the groundwork for developing testable hypotheses to elucidate the molecular impact of risk variants in non-coding regions. Last but not least, determining how non- coding risk variants disrupt activity-regulated gene expression in neuronal subtypes may uncover novel disease- relevant biology not observed using the incomplete existing methodologies and resources (activity-responsive enhancers are not possible to identify from post-mortem tissue). Once accomplished, the proposed work will have broad impact on translating genetic discoveries into actionable biological hypotheses that can potentially power a new round of development of novel therapeutics strategies for complex neuropsychiatric disorders.