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， 给家庭和社会造成巨大社会经济负担。病理生物学机制是 大部分是未知的，治疗选择有限，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，加上不断扩大的队列规模， 允许鉴定数千种影响神经精神疾病风险的遗传变异。 全基因组关联研究（GWAS）确定的每种疾病相关变异都可以提供见解， 转化为一种生物机制，这种机制是人类患病风险的基础。然而，数据的可用性并不 与意义的存在同义。研究人员现在面临的挑战是推导出 GWAS后的生物学意义。特别是，超过90%的风险变异是在非编码中发现的。 人类基因组的区域。尽管非编码变异对复杂人类基因组的潜在贡献 长期以来，疾病一直被推测，发展可验证的假说来破译 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， 人类遗传学和实验生物学之间的差距。该方法的主要假设是， 由顺式调节元件中的非编码变异引起的表观遗传变化，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，可能通过破坏基因表达而赋予疾病易感性。我们的目标是（i）注释功能不同的 通过多能干细胞的重编程产生的疾病相关的人神经元亚型中的增强子， (ii)应用尖端的HiChIP技术来分析静息状态下神经元中的启动子-增强子相互作用 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- 相关变体影响人神经元中的增强子活性。这种努力将为绘制 并优先考虑非编码风险变体，以供未来的机制研究。尤其是增强子相互作用组 本研究中进行的分析将提供一种基于物理相互作用的方法， 神经元中的增强子靶基因。这些信息将为发展可检验的假说奠定基础 阐明非编码区风险变异的分子影响。最后但并非最不重要的是，确定非- 编码风险变体破坏神经元亚型中活性调节的基因表达可能揭示新的疾病- 使用不完整的现有方法和资源未观察到的相关生物学（活动响应型 增强子不可能从死后组织中鉴定）。一旦完成，拟议的工作将 对将遗传学发现转化为可操作的生物学假设产生广泛影响， 为复杂神经精神疾病的新一轮治疗策略的发展提供动力。

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.