Mining open chromatin to define molecular mechanisms of CF modifier genes

描述（由申请人提供）：囊性纤维化（CF）患者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，这是一种破坏性的隐性单基因疾病。CF的特点是离子转运异常、粘液纤毛清除减少、慢性细菌感染、炎性气道疾病伴粘液增生/化生、呼吸衰竭和早期死亡。然而，肺表型的变异性受到CFTR位点以外的遗传因素的深刻影响。最近由该提案的合作pi领导的全基因组关联研究（GWAS）确定了染色体11p13与肺部疾病严重程度的强烈关联。包含p值最高的单核苷酸多态性（snp）的基因组区域位于约219kb的基因间区，一侧是Ets同源因子1 （EHF）基因，另一侧是apaf1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，其特征是上皮特异性表达。APIP是缺氧损伤的负调节因子，具有抗凋亡功能。此外，还有其他可能与肺功能相关的基因靠近该区域。我们的目标是确定11p13基因影响CF肺部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域，因此它们很可能位于或接近控制该基因组区域内一个或多个基因表达的顺式调控元件。我们将追求三个特定的目标，以解决11p13基因的关键调控元件位于或接近复制GWAS中与CF肺部疾病严重程度相关的p值最高的snp的主要假设。此外，通过发现哪些元素与该区域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，确定它们的表达是如何被调节的，以及自然发生的多态性如何影响这些过程并改变CF疾病的进展。第一个目标的实验将确定11p13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，我们将确定关键顺式调控元件在控制11p13相关基因表达中的功能，以及snp如何改变其特性。最后，我们将阐明由11p13基因组区间的关键基因编码的蛋白质调节CF肺病理的机制。该结果将确定CF肺部疾病严重程度变异性的生物学基础，并提供有价值的范例

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.