Identifying Cis-Regulatory Variants, Genes, and Regulatory Networks Underlying QT Interval Variation

识别 QT 间期变异背后的顺式调控变异、基因和调控网络

• 批准号: 10442265
• 负责人: Ashish Kapoor
• 金额: $ 51.82万
• 依托单位: UNIVERSITY OF TEXAS HLTH SCI CTR HOUSTON
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-05-01 至 2026-04-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10442265
• 关键词: Action Potentials; Address; Adult; Affect; Alleles; Arrhythmia; Binding; Biological Assay; CRISPR-mediated transcriptional activation; Cardiac; Cardiac Myocytes; Cells; Chromatin; Chromosome Mapping; Clustered Regularly Interspaced Short Palindromic Repeats; Code; Communities; Complex; Coupling; Dependence; Disease; Down-Regulation; Electrophysiology (science); Elements; Embryo; Enhancers; Gene Expression; General Population; Genes; Genetic; Genetic Determinism; Genetic Polymorphism; Genetic study; Heritability; Heritable Quantitative Trait; Human; Ion Channel Gating; Knowledge; Lead; Left ventricular structure; Linear Regressions; Link; Luciferases; Maps; Modeling; Molecular; Molecular Genetics; Mus; Muscle Cells; Mutation; Neonatal; Penetrance; Population; Prevalence; Proteins; Quantitative Trait Loci; Rattus; Regulation; Regulatory Element; Reporter; Resources; Risk; Short QT syndrome; Signal Transduction; Site; Testing; Tissues; Untranslated RNA; Up-Regulation; Variant; Ventricular; Zebrafish; base; causal variant; clinically relevant; differential expression; disorder risk; epigenomics; gene discovery; gene regulatory network; genome wide association study; in silico; in vivo; indexing; induced pluripotent stem cell derived cardiomyocytes; knowledge base; member; mortality risk; sudden cardiac death; trait; transcription factor; transcriptome; transcriptome sequencing; voltage

PROJECT SUMMARY/ABSTRACT Electrocardiographic QT interval, an index of ventricular repolarization, is a clinically relevant heritable quantitative trait associated with risk for cardiac arrhythmias and sudden cardiac death (SCD). Genetic studies in subjects with rare Mendelian long- and short-QT syndromes have identified rare, severe coding mutations in ~20 genes encoding voltage-gated ion channels, transporters and associated proteins that regulate cardiac action potential duration (APD) or excitation-contraction (EC) coupling. Prevalence of coding polymorphisms in these genes affecting population repolarization variability is extremely low. In contrast, genome-wide association studies (GWAS) of QT interval in the general population have identified common, noncoding variants at nearly three dozen loci, collectively explaining ~20% of the additive variance. Nearly half of these GWAS loci harbor genes known to regulate cardiac APD or EC coupling, thus serving as the likely causal genes. Nonetheless, the identities of the actual causal genes and molecular mechanisms underlying associations with the common and, largely noncoding variants at these loci, remain unknown. Moreover, a large fraction (~80%) of the additive variance remains unidentified. Leveraging information on known genes, in the proposed studies we will address these gaps in our knowledge based on the hypotheses that a) multiple common variants that impact the activities of several cis-regulatory elements (CREs) underlie a GWAS signal by collectively influencing the expression of a target gene, and b) genes underlying specific or similar diseases/traits are often functionally related, and that functionally related genes often belong to gene regulatory networks (GRNs), members of which are co-regulated. We aim to functionally characterize selected QT interval GWAS loci with a priori evidence for likely causal genes as well as extend gene discovery by assessing the impacts of perturbing the expression of known QT interval genes on their GRNs. Our specific aims are: (1) identification of functional CRE variants at selected QT interval GWAS loci by evaluating all trait-associated common variants overlapping cardiac open chromatin regions in high-throughput reporter assays in mouse cardiomyocyte HL1 cells; and to link CREs and their variants to putative target genes based on expression quantitative trait locus and chromatin contact analyses in human adult left ventricle tissue and induced pluripotent stem cells-derived cardiomyocytes (hiPSC-CMs); and (2) performing CRISPR activation/interference-based expression perturbations of selected QT interval genes in neonatal rat ventricular myocytes (NRVMs), and assessing transcriptome-wide effects to identify candidate co-regulated gene sets; evaluating the co-regulated gene sets for enrichment in sub-threshold GWAS loci; overlapping co-regulated genes with QT GWAS loci to identify likely causal genes; and assessing the impact of perturbing expression of newly identified genes on cellular electrophysiology in NRVMs and hiPSC-CMs. Together, the proposed studies are expected to lead to a better understanding of the molecular mechanisms underlying QT interval variation and SCD risk, and serve as a model for functional characterization of GWAS loci of complex diseases and traits.

项目概要/摘要 心电图 QT 间期是心室复极的指标，是临床相关的遗传性指标 与心律失常和心源性猝死（SCD）风险相关的数量性状。遗传学研究 在患有罕见孟德尔长 QT 综合征和短 QT 综合征的受试者中，发现了罕见的、严重的编码突变 约 20 个编码电压门控离子通道、转运蛋白和调节心脏活动的相关蛋白的基因 电位持续时间 (APD) 或兴奋收缩 (EC) 耦合。这些中编码多态性的普遍性 影响群体复极变异性的基因极低。相比之下，全基因组关联 对一般人群中 QT 间期的研究 (GWAS) 已在近乎确定了常见的非编码变异。 三打基因座，共同解释了约 20% 的加性方差。近一半的 GWAS 位点包含 已知调节心脏 APD 或 EC 耦合的基因，因此可能是因果基因。尽管如此， 与常见的关联的实际因果基因和分子机制的身份， 这些位点的大部分非编码变异仍然未知。此外，很大一部分（~80%）的添加剂 差异仍未确定。利用已知基因的信息，在拟议的研究中，我们将解决 我们的知识差距基于以下假设：a) 影响活动​​的多种常见变体 几个顺式调控元件（CRE）通过共同影响一个基因的表达而成为 GWAS 信号的基础。 目标基因，b) 特定或类似疾病/性状背后的基因通常在功能上相关，并且 功能相关的基因通常属于基因调控网络（GRN），其成员是共同调控的。 我们的目标是利用可能因果基因的先验证据，对选定的 QT 间期 GWAS 位点进行功能表征 以及通过评估干扰已知 QT 间期表达的影响来扩展基因发现 他们的GRN上的基因。我们的具体目标是：（1）在选定的 QT 间期鉴定功能性 CRE 变异 GWAS 位点通过评估与心脏开放染色质区域重叠的所有性状相关常见变异 小鼠心肌细胞 HL1 细胞的高通量报告分析；并将 CRE 及其变体链接到 基于成人表达数量性状位点和染色质接触分析的推定靶基因 左心室组织和诱导多能干细胞衍生的心肌细胞（hiPSC-CM）； (2) 执行 新生大鼠中选定 QT 间期基因的基于 CRISPR 激活/干扰的表达扰动 心室肌细胞（NRVM），并评估转录组范围的影响以确定候选共同调控基因 套;评估共同调控的基因集以富集亚阈值 GWAS 位点；重叠共同监管 具有 QT GWAS 位点的基因，用于识别可能的致病基因；并评估扰乱表达的影响 新发现的 NRVM 和 hiPSC-CM 中细胞电生理学基因。总之，拟议的研究 预计将有助于更好地理解 QT 间期变化的分子机制 和 SCD 风险，并作为复杂疾病和性状的 GWAS 位点功能表征的模型。