Mining open chromatin to define molecular mechanisms of CF modifier genes

挖掘开放染色质以定义 CF 修饰基因的分子机制

• 批准号: 8847789
• 负责人: ANN HARRIS
• 金额: $ 57.49万
• 依托单位: LURIE CHILDREN'S HOSPITAL OF CHICAGO
• 依托单位国家: 美国
• 财政年份: 2013
• 资助国家: 美国
• 起止时间: 2013-07-15 至 2016-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8847789
• 关键词: APAF1 gene; Abnormal ion transport; Address; Alleles; Apoptotic; Bacterial Infections; Beryllium; Binding; Binding Sites; Biological; Biological Assay; Biology; Cell Lineage; Cells; Cessation of life; ChIP-seq; Chromatin; Chromosomes; Chronic; Clinical; Control Locus; Cystic Fibrosis; Cystic Fibrosis Transmembrane Conductance Regulator; Data; Disease; Disease Progression; Distal; Elements; Enhancers; Epithelial; Epithelial Cells; Gene Expression; Genes; Genetic; Genetic Polymorphism; Genome; Genomic Segment; Genomics; Goals; Health; Heart Diseases; Hematological Disease; Human; Hypoxia; Indium; Individual; Inflammation; Inflammatory; Injury; Insulator Elements; Intercistronic Region; Ion Transport; Location; Lung; Lung diseases; Mendelian disorder; Metaplasia; Mining; Minor; Molecular; Molecular Conformation; Monitor; Mucociliary Clearance; Mucous body substance; Mutation; National Heart, Lung, and Blood Institute; Nucleic Acid Regulatory Sequences; Other Genetics; Pathology; Pathway interactions; Phenotype; Process; Property; Proteins; Public Health; Pulmonary Cystic Fibrosis; Regulator Genes; Regulatory Element; Reporter Genes; Respiratory Failure; Respiratory physiology; Severities; Severity of illness; Side; Single Nucleotide Polymorphism; Site; Small Interfering RNA; Therapeutic Intervention; Trans-Activators; Untranslated RNA; Writing; base; cell type; cis acting element; cystic fibrosis airway epithelia; genetic association; genetic element; genome wide association study; genome-wide; genome-wide analysis; promoter; research study; response; transcription factor; transcriptome sequencing

DESCRIPTION (provided by applicant): Variability in lung disease severity in cystic fibrosis (CF) is a significant clinical problem. Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene cause CF, a devastating, recessive, monogenic disease. CF is characterized by abnormal ion transport, reduced mucociliary clearance, chronic bacterial infection, inflammatory airway disease with mucus hyper/metaplasia, respiratory failure, and early death. However, the variability in lung phenotype is profoundly influenced by genetic factors that lie outside the CFTR locus. Recent genome-wide association studies (GWAS), led by co-PIs on this proposal, identified a robust association at chromosome 11p13 with lung disease severity. The genomic region encompassing the single nucleotide polymorphisms (SNPs) with highest p-values is located within a ~219kb intergenic region flanked by the Ets homologous factor 1 (EHF) gene on one side and APAF1-interacting protein (APIP) on the other. EHF encodes a protein that belongs to an Ets transcription factor subfamily characterized by epithelial specific expression. APIP is a negative regulator of hypoxic injury and has anti-apoptotic functions. Moreover, there are other genes of potential relevance to lung function close to this region. Our goal is to determine the mechanism whereby genetic elements at 11p13 influence CF lung disease severity, which likely involves key pathobiological pathways (ion transport, inflammation, and/or mucus metaplasia). Since the critical SNPs lie in non-coding regions of the genome it is probable that they are within or close to cis-acting regulatory elements that control the expression of one or more genes within this genomic region. We will pursue three specific aims addressing the main hypothesis that critical regulatory elements for genes at 11p13 are located at or close to the SNPs with highest p-values associating with CF lung disease severity in the replicated GWAS. Moreover, that by finding which elements interact with each gene promoter in the region we will identify genes that are critical for normal lung biology, determine how their expression is regulated and how naturally occurring polymorphisms influence these processes and alter CF disease progression. Experiments in the first aim will identify the location of critical regulatory elements in the 11p13 genomic interval and determine the physical interactions of these cis-acting elements with individual gene promoters. In the second aim, we will determine the function of the critical cis-regulatory elements in controlling expression of relevant genes at 11p13 and how SNPs may alter their properties. Finally we will elucidate the mechanism whereby lung pathology in CF is modulated by proteins encoded by critical gene(s) in the 11p13 genomic interval. The results will determine the biological basis of variability in CF lung disease severity and provide a valuable paradigm for elucidating the molecular basis of other genetic associations with heart, lung and blood diseases that involve cis-acting regulatory elements in non-coding regions distal to genes.

描述（由申请人提供）：囊性纤维化（CF）中肺部疾病严重程度的变异性是一个重要的临床问题。囊性纤维化跨膜传导调节因子（CFTR）基因突变导致CF，一种毁灭性的隐性单基因疾病。CF的特征在于异常离子转运、粘膜纤毛清除减少、慢性细菌感染、伴有粘液增生/化生的炎性气道疾病、呼吸衰竭和早期死亡。然而，肺表型的变异性受到CFTR基因座之外的遗传因素的深刻影响。最近的全基因组关联研究（GWAS），由co-PI领导，确定了染色体11 p13与肺部疾病严重程度的强关联。包含具有最高p值的单核苷酸多态性（SNP）的基因组区域位于约219 kb的基因间区域内，一侧为Ets同源因子1（EHF）基因，另一侧为APAF 1相互作用蛋白（APIP）。EHF编码一种属于Ets转录因子亚家族的蛋白，其特征在于上皮特异性表达。APIP是缺氧损伤的负性调节因子，具有抗凋亡作用。此外，在该区域附近还有其他与肺功能潜在相关的基因。我们的目标是确定11 p13的遗传因素影响CF肺疾病严重程度的机制，这可能涉及关键的病理生物学途径（离子转运，炎症和/或粘液化生）。由于关键SNP位于基因组的非编码区，因此它们可能在控制该基因组区域内一个或多个基因表达的顺式作用调控元件内或附近。我们将追求三个具体目标，解决主要假设，即11 p13基因的关键调控元件位于或接近SNP，在复制的GWAS中与CF肺病严重程度相关的p值最高。此外，通过发现哪些元件与该区域中的每个基因启动子相互作用，我们将确定对正常肺生物学至关重要的基因，确定它们的表达如何调节以及天然存在的多态性如何影响这些过程并改变CF疾病进展。第一个目标的实验将确定11 p13基因组间隔中关键调控元件的位置，并确定这些顺式作用元件与单个基因启动子的物理相互作用。在第二个目标中，我们将确定关键的顺式调控元件在控制相关基因在11 p13的表达，以及如何SNPs可能会改变他们的属性的功能。最后，我们将阐明CF中肺病理学受11 p13基因组间隔中关键基因编码的蛋白质调制的机制。这些结果将确定CF肺疾病严重程度变异性的生物学基础，并提供一个有价值的范例， 阐明与心脏、肺和血液疾病相关的其他遗传学基础，这些疾病涉及基因远端非编码区的顺式作用调节元件。