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

同种型水平的概率转录组范围与复杂精神特征背后的秘密神经发生机制的关联

• 批准号: 10319912
• 负责人: Michael Gandal
• 金额: $ 73.17万
• 依托单位: UNIVERSITY OF CALIFORNIA LOS ANGELES
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-01-03 至 2022-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10319912
• 关键词: Address; Adult; Affect; Alternative Splicing; Area; Biological; Biological Process; Brain; CRISPR/Cas technology; Candidate Disease Gene; Cell Line; Cells; Communities; Complex; Data; Development; Disease; Ensure; Event; Exhibits; Gene Expression; Gene Expression Regulation; Genes; Genetic; Genetic Risk; Genetic Variation; Genets; Genome engineering; Genomic approach; Genomics; Genotype; Heritability; Human; Individual; Intervention; Knock-in; Link; Linkage Disequilibrium; Mental disorders; Methods; Neurobiology; Neurons; Pathogenesis; Pattern; Phenotype; Protein Isoforms; Proteomics; Quality Control; Quantitative Trait Loci; RNA; RNA Splicing; Regulation; Reporting; Reproducibility of Results; Resolution; Resources; Risk; Sampling; Schizophrenia; Science; Signal Transduction; Specificity; TCF7L2 gene; Techniques; Therapeutic Intervention; Tissue-Specific Gene Expression; Tissues; Transcript; Uncertainty; Variant; Work; autism spectrum disorder; base; cell type; differential expression; disorder risk; fetal; functional genomics; genetic variant; genome wide association study; genome-wide; genomic data; genomic locus; insight; nerve stem cell; neurobiological mechanism; neurogenetics; neuropsychiatry; new therapeutic target; novel; precision medicine; repaired; risk variant; targeted treatment; therapeutic development; trait; transcriptome; transcriptome sequencing; transcriptomics

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.

项目摘要/摘要 随着大规模全基因组关联研究(GWAS)迅速确定与神经发育的关联 和精神病学特征，后GWAS时代的主要定义挑战是严格定义 大规模疾病相关遗传变异背后的神经生物学机制。为此，我们和其他人 我最近开发了直接将GWAS结果与大规模组织特异性表达相结合的方法 数量性状基因座(EQTL)参考面板，实现转录组范围的关联研究(TWAS)-a 确定其表达与疾病遗传风险相关的基因的有效方法。同时， 新出现的证据有力地证明了选择性剪接--一种能够 从单个基因产生指数数量的独特RNA转录物亚型--这是一个重要的 一种在发育过程中表现出动态模式的机制，在个体的大脑中受到破坏 受精神疾病影响，包括自闭症和精神分裂症。然而，目前还没有系统的研究 表征人脑中异构体表达的遗传调节或其与遗传风险的关系 精神障碍。该提议旨在开发一种新的、异构型水平的TWAs方法(iso-TWAs)来 确定其顺式调控的表达与精神疾病风险相关的转录异构体。我们会 编制一个包含基因和异构体定量的大规模功能基因组参考板 来自3800多个人脑样本的rna-seq数据，我们将利用这些数据来执行iso-teas。 与传统的基因水平的TWA一系列神经精神病学特征。我们将直接整合同种形式 量化不确定性以及我们的iso-Twas框架内的概率精细映射，以便 确保所产生的关联的健壮性。我们假设同型异构体水平的特征将提供 更大的分辨率，以检测潜在的精神病学GWA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。 在原代人神经前体细胞(PhNPC)系中进行了长读RNA测序和详细的 细胞表型。总而言之，这些研究将系统地描述一个关键但未被开发的地区 从而为精神疾病的机制提供了新的见解 为治疗发展和干预确定潜在的神经生物学靶点。