Pulmonary Fibrosis and Telomerase Dysfunction

肺纤维化和端粒酶功能障碍

• 批准号: 10435541
• 负责人: Christine Kim Garcia
• 金额: $ 71.88万
• 依托单位: COLUMBIA UNIVERSITY HEALTH SCIENCES
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-07-01 至 2025-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10435541
• 关键词: Address; Adult; Adverse event; Age; Bioinformatics; Biological Assay; Biology; Blood Cells; CRISPR/Cas technology; Candidate Disease Gene; Cells; Chronic; Code; Copy Number Polymorphism; DNA Sequence Alteration; Data; Development; Disease; Disease Progression; Disease model; Engineering; Epithelial; Evaluation; Exposure to; Fibroblasts; Functional disorder; Gene Frequency; Gene Mutation; Genes; Genetic; Genetic Diseases; Genetic Predisposition to Disease; Genetic Transcription; Genomic Segment; Genomic approach; Genotype; Goals; Grant; Human; In Vitro; Inherited; Injury; Interstitial Lung Diseases; Investigation; Knowledge; Lead; Length; Leukocytes; Link; Location; Lung Transplantation; Lung diseases; Lymphocyte; Measurement; Methods; Mutation; Pathogenicity; Patients; Pharmaceutical Preparations; Phenotype; Physicians; Predisposition; Pulmonary Fibrosis; Qualifying; Role; Slide; Statistical Data Interpretation; Survival Rate; Syndrome; Technology; Telomerase; Telomerase RNA Component; Telomere Shortening; Testing; Untranslated RNA; Variant; base; cell type; clinical diagnosis; cohort; disease diagnosis; disorder risk; exome sequencing; fibrotic interstitial lung disease; fibrotic lung; gain of function; gene function; genetic architecture; genetic disorder diagnosis; genetic variant; genome editing; genome sequencing; genome wide association study; genome-wide; human model; idiopathic pulmonary fibrosis; kindred; lung development; mouse model; next generation sequencing; novel; peripheral blood; predict clinical outcome; pressure; proband; programs; promoter; rare variant; response; risk variant; segregation; telomere; transcriptomics; whole genome

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.

抽象的 无偏见的基因组方法导致了新的疾病基因和变异的发现。致病性最强 在家族性肺纤维化 (FPF) 和特发性肺纤维化 (IPF) 患者中发现的罕见变异 导致端粒缩短。因此，这些疾病属于称为“疾病谱”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预测临床 IPF 患者的结局，包括生存率、疾病进展率以及对某些药物的反应。 更大比例的 FPF 和 IPF 患者有端粒缩短的证据，而不是由 基因突变。这项研究旨在利用全基因组测序来识别遗传变异 产生肺纤维化的遗传易感性。该应用程序的基本假设是 端粒酶功能障碍是肺纤维化发展的关键机制。 该应用程序计划评估为发现队列获得的全基因组序列（WGS）数据 约 950 名不相关的 FPF 先证者和 IPF 患者。在目标 1 中，我们将从 WGS 数据估计端粒长度， 识别端粒基因中罕见的编码和非编码限定变异，评估基因型-表型 关系，并研究向患者及其医生返回的遗传结果。这一目标将允许 对表型良好的患者的已知端粒基因进行评估。由于FPF和IPF的很大一部分 端粒长度<10%的患者没有可识别的端粒相关致病菌或可能的致病菌 致病变异，我们将利用全基因组测序数据和五种独立策略来识别新的候选基因： 通过基因组位置分析变异，通过基于基因的折叠测试分析罕见变异，分析 GWAS 的常见变异、使用滑动窗口测试的变异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异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相关的新基因。在目标 3 中， 我们将探索功能调查的三种途径：通过评估信息中的共隔离 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 通过评估 CRISPR/Cas9 工程小鼠疾病模型。后者的目标将集中于 阐明 PARN 的功能，PARN 是一种在转录后过程中起重要作用的去腺苷酸酶 端粒酶 RNA 的成熟与肺纤维化的发展有关。总的来说，这个应用 计划使用 WGS、大型 FPF 和 IPF 队列，以及尖端的统计分析和实验 扩展我们对肺纤维化和人类端粒遗传结构的了解的方法 相关疾病。