Pulmonary Fibrosis and Telomerase Dysfunction

摘要 无偏见的基因组方法导致了新的疾病基因和变种的发现。最具致病性的 家族性肺纤维化和特发性肺纤维化患者中发现罕见变异 导致端粒缩短。因此，这些疾病是已知的疾病谱的一部分 端粒病或短端粒综合征。外周血细胞端粒长度可预测临床 IPF患者的预后，包括存活率、疾病进展率和对某些药物的反应。 有更大比例的FPF和IPF患者有端粒缩短的证据，而不是 基因突变。这项研究试图使用全基因组测序来识别 会导致遗传性的肺纤维化易感性。这个应用程序的基本假设是 端粒酶功能障碍是肺纤维化发生的关键机制之一。 这个应用程序计划评估为发现一组 约950名无血缘关系的FPF先证者和IPF患者。在目标1中，我们将从WGS数据中估计端粒长度， 识别端粒基因中罕见的编码和非编码合格变异，评估基因型-表型 并研究将遗传结果返回给患者及其医生的情况。这一目标将允许 表型良好的患者中已知端粒基因的评估。由于很大一部分FPF和IPF 端粒长度为10%的患者没有可识别的与端粒相关的致病或可能 致病变异，我们将利用WGS数据和五个独立的策略来识别新的候选基因： 通过基因组定位分析变异，通过基于基因的折叠试验分析稀有变异，分析 GWAS的常见变异体，使用滑动窗检验的变异体分析，以及拷贝数分析 变种。在发现队列中确定的候选基因和变种将在重复队列中进行评估。 这一目标有可能发现与肺纤维化和端粒生物学有关的新基因。在《目标3》中， 我们将探索功能研究的三个途径：通过评估信息中的共分离 通过体外研究患者来源的淋巴细胞和其他细胞类型的基因功能，以及 通过对CRISPR/Cas9基因工程小鼠疾病模型的评估。后一个目标将侧重于 阐明PARN的功能，它是一种在转录后转录中起重要作用的脱腺苷酶 端粒酶RNA的成熟与肺纤维化的发展总体而言，此应用程序 计划使用WGS、大型FPF和IPF队列以及尖端统计分析和实验 扩展我们对肺纤维化和人类端粒遗传结构的知识的方法-- 相关疾病。

ABSTRACT Unbiased genomic approaches have led to discoveries of novel disease genes and variants. Most pathogenic rare variants found in patients with Familial Pulmonary Fibrosis (FPF) and Idiopathic Pulmonary Fibrosis (IPF) result in telomere shortening. Thus, these diseases are part of the spectrum of diseases known as telomeropathies or short telomere syndromes. Telomere lengths of peripheral blood cells predict clinical outcomes of IPF patients, including survival, rate of disease progression, and response to certain medications. A larger proportion of FPF and IPF patients have evidence of telomere shortening than are explained by genetic mutations. This study seeks to use whole genome sequencing to identify genetic variants that engender an inherited susceptibility to lung fibrosis. The underlying hypothesis of this application is that telomerase dysfunction is a key mechanism underlying development of pulmonary fibrosis. This application plans to evaluate whole genome sequence (WGS) data obtained for a discovery cohort of ~950 unrelated FPF probands and IPF patients. In Aim 1, we will estimate telomere length from the WGS data, identify rare coding and noncoding qualifying variants in the telomere genes, assess genotype-phenotype relationships, and study the return of genetic results to patients and their physicians. This aim will allow for assessment of known telomere genes in well-phenotyped patients. Since a large portion of FPF and IPF patients with telomere lengths <10th percentile have no identifiable telomere-related pathogenic or likely pathogenic variant, we will utilize WGS data and five independent strategies to identify novel candidate genes: analysis of variants by genomic location, analysis of rare variants by gene-based collapsing tests, analysis of common variants by GWAS, analysis of variants using a sliding window test, and analysis of copy number variants. Candidate genes and variants identified in the discovery cohort will be evaluated in replicate cohorts. This aim has the potential to discover new genes linked to pulmonary fibrosis and telomere biology. In Aim 3, we will explore three avenues of functional investigation: through assessment of co-segregation in informative kindreds, through in vitro studies of gene function in patient-derived lymphocytes and other cell types, and through evaluation of CRISPR/Cas9-engineered mouse models of disease. The latter aim will focus on elucidating the function of PARN, a de-adenylase that has an important role in the post-transcriptional maturation of telomerase RNA, with regard to the development of pulmonary fibrosis. Overall, this application plans to use WGS, large FPF and IPF cohorts, as well as cutting-edge statistical analyses and experimental approaches to extend our knowledge of the genetic architecture of pulmonary fibrosis and human telomere- related diseases.