Cis-regulatory architecture of coronary vascular wall loci

冠状血管壁位点的顺式调控结构

• 批准号: 10609005
• 负责人: Clint L Miller
• 金额: $ 40.53万
• 依托单位: UNIVERSITY OF VIRGINIA
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-06-01 至 2025-04-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10609005
• 关键词: Address; Affect; Architecture; Arterial Fatty Streak; Arteries; Atherosclerosis; Automobile Driving; Binding; Biological; Biological Assay; Blood Vessels; Blood flow; Candidate Disease Gene; Cell Line; Cells; Chromatin; Chromatin Structure; Clinical; Clustered Regularly Interspaced Short Palindromic Repeats; Complex; Coronary; Coronary Arteriosclerosis; Coronary artery; Coupled; Data Set; Developing Countries; Disease; Disease susceptibility; EP300 gene; Early Diagnosis; Engineering; Environmental Risk Factor; Evaluation; Fibroblasts; Gene Expression; Gene Expression Regulation; Gene Targeting; Genes; Genetic Variation; Genetic study; Genomic Segment; Genomics; Genotype; Genotype-Tissue Expression Project; Goals; Heart; Heterogeneity; Human; Individual; Intervention; Joints; Knowledge; Link; MADH3 gene; Macrophage; Maps; Measures; Mediating; Mendelian randomization; Messenger RNA; Meta-Analysis; Mission; Myocardial Infarction; Pathogenesis; Pathway interactions; Phenotype; Play; Population; Prevalence; Prevention strategy; Process; Proliferating; Public Health; Quantitative Trait Loci; RNA; RNA Splicing; Regulator Genes; Regulatory Element; Repression; Research; Resolution; Role; Sampling; Single Nucleotide Polymorphism; Smooth Muscle Myocytes; Therapeutic; Time; Tissues; Translating; Transposase; United States National Institutes of Health; Untranslated RNA; Variant; Work; biobank; causal variant; cell type; clinically relevant; cohort; disorder risk; epigenomics; genetic risk factor; genome wide association study; genomic locus; human disease; human tissue; in silico; insight; migration; mortality; mouse model; multiple omics; next generation; novel; programs; response to injury; risk variant; single cell analysis; single-cell RNA sequencing; transcription factor; transcription factor USF; transcriptome sequencing; treatment strategy

PROJECT SUMMARY Coronary artery disease (CAD) remains the leading cause of mortality worldwide and poses considerable public health burden. Both genetic and environmental risk factors contribute to CAD susceptibility, leading to increased disease prevalence in developing countries. Genome-wide association studies (GWAS) have now identified 161 independent genetic loci associated with CAD risk in large-scale meta-analyses in over 300,000 individuals. However, given that the majority of the associations reside in non-coding genomic regions, it has been challenging to translate these discoveries into biologically and clinically relevant insights. Interestingly, many of the candidate genes at CAD loci are organized into novel or unknown biological pathways, and point to dysregulation of vascular wall processes. Large efforts such as the Genotype Tissue Expression (GTEx) project and Stockholm-Tartu Atherosclerosis Reverse Network Engineering Task (STARNET) study have refined candidate gene regulatory mechanisms, however the specific cellular and phenotypic states driving these changes remains unclear. Smooth muscle cells (SMC) normally regulate vascular tone in the vessel wall but play critical roles in disease pathogenesis as their contractile gene program is hijacked during phenotypic switching to macrophage-like and fibroblast-like cells. Using epigenomic and expression quantitative trait loci (eQTL) mapping in 52 primary human coronary artery smooth muscle cells (HCASMC) we recently identified 11 candidate causal genes and mechanisms linking vascular wall processes to CAD risk (e.g. TCF21, SMAD3, CDKN2B, LMOD1). It is likely that non-coding regulatory variants function through changes in chromatin accessibility, which coincides with transcription factor (TF) binding in cis. By identifying these upstream TFs at vascular wall loci we can begin to assemble targetable pathways to modulate hidden disease risk in the vessel wall. In this proposal we plan to perform joint gene expression and chromatin accessibility QTL mapping in a unique cohort of 120 normal and diseased coronary artery tissues from explanted heart donors. We will validate and discover functional regulatory elements at GWAS loci using CRISPR/dCas9 perturbation with high-throughput phenotyping in SMC. Finally, we will investigate the cis-regulatory architecture in these samples at single-cell resolution and infer TF binding during phenotypic modulation. Together these studies will reveal the causal regulatory mechanisms responsible for CAD in the vascular wall and inform next generation treatment or prevention strategies to eradicate this debilitating disease.

项目摘要 冠状动脉疾病（CAD）仍然是全球死亡率的主要原因，并构成了相当大的 公共卫生负担。遗传和环境风险因素都导致CAD敏感性，导致 发展中国家疾病患病率增加。全基因组协会研究（GWAS）现在 确定了161个与CAD风险相关的161个独立遗传基因座，大规模荟萃分析超过300,000 个人。但是，鉴于大多数关联都存在于非编码基因组区域，它具有 将这些发现转化为生物学和临床相关的见解一直很具有挑战性。有趣的是， CAD基因座的许多候选基因被组织成新颖或未知的生物途径，点 血管壁过程的失调。大量努力，例如基因型组织表达（GTEX） Project和Stockholm-Tartu动脉粥样硬化反向网络工程任务（Starnet）研究 精致的候选基因调节机制，但是驱动的特定细胞和表型状态 这些变化尚不清楚。平滑肌细胞（SMC）通常调节容器壁的血管张力 但是在疾病发病机理中起关键作用，因为其收缩基因程序在表型过程中被劫持 切换到类似巨噬细胞和成纤维细胞样细胞。使用表观基因组和表达定量性状基因座 （EQTL）在52个原发性人冠状动脉平滑肌细胞（HCASMC）中映射我们最近确定 11候选因果基因和将血管壁过程与CAD风险联系起来的机制（例如TCF21，SMAD3， CDKN2B，LMOD1）。非编码调节变体可能通过染色质变化功能 可访问性，与顺式中的转录因子（TF）结合一致。通过识别这些上游TFS 血管壁基因座我们可以开始组装可定位的途径以调节血管中的隐藏疾病风险 墙。在此提案中，我们计划在A中执行联合基因表达和染色质可及性QTL映射 来自外植体供体的120个正常和患病的冠状动脉组织的独特队列。我们将 使用CRISPR/DCAS9在GWAS基因座上验证和发现功能调节元件 SMC中的高通量表型。最后，我们将研究其中的顺式调节结构 单细胞分辨率的样品并在表型调制过程中推断TF结合。这些研究将共同 揭示导致血管壁CAD的因果监管机制，并告知下一代 消除这种使人衰弱的疾病的治疗或预防策略。

项目成果

Leukocytes carrying Clonal Hematopoiesis of Indeterminate Potential (CHIP) Mutations invade Human Atherosclerotic Plaques.

携带不确定电位克隆造血 (CHIP) 突变的白细胞侵入人类动脉粥样硬化斑块。

• DOI: 10.1101/2023.07.22.23292754
• 发表时间: 2023
• 期刊: medRxiv : the preprint server for health sciences
• 作者: vonScheidt,Moritz;Bauer,Sabine;Ma,Angela;Hao,Ke;Kessler,Thorsten;Vilne,Baiba;Wang,Ying;Hodonsky,ChaniJ;Ghosh,SaikatKB;Mokry,Michal;Gao,Hua;Kawai,Kenji;Sakamoto,Atsushi;Kaiser,Juliane;Bongiovanni,Dario;Fleig,Julia;Oldenb
• 通讯作者: Oldenb

Prediction of causal genes at GWAS loci with pleiotropic gene regulatory effects using sets of correlated instrumental variables.

使用一组相关的工具变量预测具有多效性基因调控效应的 GWAS 位点的因果基因。

• 发表时间: 2024
• 期刊: ArXiv
• 作者: Khan,Mariyam;Ludl,Adriaan;Bankier,Sean;Björkegren,JohanLm;Michoel,Tom
• 通讯作者: Michoel,Tom

Transcriptomic-based clustering of human atherosclerotic plaques identifies subgroups with different underlying biology and clinical presentation.

• DOI: 10.1038/s44161-022-00171-0
• 发表时间: 2022-12
• 期刊: Nature cardiovascular research
• 作者: M. Mokry;A. Boltjes;L. Slenders;Gemma Bel-Bordes;Kai Cui;E. Brouwer;J. Mekke;M. Depuydt;N. Timmerman;F. Waissi;M. Verwer;A. Turner;Mohammad Daud Khan;C. Hodonsky;E. Diez Benavente;R. Hartman;N. V. D. van den Dungen;N. Lansu;Emilia Nagyova;K. Prange;J. Kovacic;J. Björkegren;Eleftherios Pavlos;E. Andreakos;H. Schunkert;G. Owens;C. Monaco;A. Finn;R. Virmani;N. Leeper;M. D. de Winther;J. Kuiper;G. D. de Borst;E. Stroes;M. Civelek;D. D. de Kleijn-D.;H. D. den Ruijter;F. Asselbergs;S. W. van der Laan;Clint L. Miller;G. Pasterkamp