Isoform-level probabilistic transcriptome-wide association to undercover neurogenetic mechanisms underlying complex psychiatric traits

项目总结/摘要 随着大规模的全基因组关联研究（GWAS）迅速确定与神经发育相关性， 和精神特征，后GWAS时代的主要挑战是严格定义 大规模疾病相关遗传变异的神经生物学机制。为此，我们和其他 最近开发了将GWAS结果与大规模组织特异性表达直接整合的方法 数量性状基因座（eQTL）参考面板，使全转录组关联研究（TWAS）- a 这是一种强有力的方法，可以识别其表达与疾病遗传风险相关的基因。同时， 新出现的证据强烈暗示了选择性剪接--一种能够 从单个基因产生指数数量的独特RNA转录物同种型-作为重要的 一种在整个发育过程中表现出动态模式并在个体大脑中被破坏的机制 患有精神疾病，包括自闭症和精神分裂症。然而，没有研究系统地 表征了人脑中同种型表达的遗传调节或其与遗传风险的关联， 精神疾病该提案旨在开发一种新的异构体水平TWAS方法（iso-TWAS）， 鉴定其顺式调节表达与精神疾病风险相关的转录异构体。我们将 编制一个大规模的功能基因组参考面板，包括基因型和亚型定量 从超过3800个人脑样本的RNA-seq数据中，我们将利用这些数据沿着进行iso-TWAS， 与传统的基因水平TWAS的一系列神经精神特征。我们将直接整合同种型 量化的不确定性以及我们的iso-TWAS框架内的概率精细映射，以便 确保产生的关联的健壮性。我们假设异构体水平的表征将提供 实质上更高的分辨率，以检测潜在的精神病GWAS基因座的候选生物学机制。 最后，预测的SNP-亚型-疾病关联将使用基因组工程进行实验验证 在原代人神经祖细胞（phNPC）系中，随后进行长读段RNA测序，并详细 细胞表型分析总之，这些研究将系统地描述一个关键的，但未充分探索的领域 人类大脑中的基因组调控，从而提供了新的见解精神疾病的机制， 确定潜在的神经生物学靶点用于治疗开发和干预。

PROJECT SUMMARY/ABSTRACT As large-scale genome-wide association studies (GWAS) rapidly identify associations with neurodevelopmental and psychiatric traits, the major defining challenge of the post-GWAS era is to rigorously define the neurobiological mechanisms underlying disease-associated genetic variation at scale. To this end, we and others have recently developed methods to directly integrate GWAS results with large-scale tissue-specific expression quantitative trait loci (eQTL) reference panels, enabling a transcriptome-wide association study (TWAS) – a powerful approach to identify genes whose expression is associated with genetic risk for disease. In parallel, emerging evidence has strongly implicated alternative splicing – a form of genetic regulation capable of generating an exponential number of unique RNA transcript isoforms from a single gene – as an important mechanism that exhibits dynamic patterns across development and is disrupted in the brains on individuals affected by psychiatric diseases, including autism and schizophrenia. Yet, no studies have systematically characterized the genetic regulation of isoform expression in human brain or its association with genetic risk for psychiatric disorders. This proposal seeks to develop a novel, isoform-level TWAS approach (iso-TWAS) to identify transcript-isoforms whose cis-regulated expression is associated with psychiatric disease risk. We will compile a large-scale functional genomic reference panel incorporating genotype and isoform quantifications from RNA-seq data of more than 3800 human brain samples, which we will leverage to perform iso-TWAS along with traditional gene-level TWAS for a host of neuropsychiatric traits. We will directly integrate isoform quantification uncertainties as well as probabilistic fine-mapping within our iso-TWAS framework, in order to ensure the robustness of resulting associations. We hypothesize that isoform-level characterization will provide substantially greater resolution to detect candidate biological mechanisms underlying psychiatric GWAS loci. Finally, predicted SNP-isoform-disease associations will be experimentally validated using genome-engineering in primary human neural progenitor cell (phNPC) lines followed by long-read RNA-sequencing and detailed cellular phenotyping. Together, these studies will systematically characterize a critical, yet underexplored area of genomic regulation in human brain, thereby providing novel insights into psychiatric disease mechanisms and identifying potential neurobiological targets for therapeutic development and intervention.