lncRNAs, Linking Genetic Susceptibility to Molecular Phenotype in IPF

lncRNA，将遗传易感性与 IPF 分子表型联系起来

• 批准号: 10513288
• 负责人: David Albert Schwartz
• 金额: --
• 依托单位: VA EASTERN COLORADO HEALTH CARE SYSTEM
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-10-01 至 2025-09-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10513288
• 关键词: Affect; Biological; Biological Assay; Biology; Clinical; Code; Complex; DNA; DNA Methylation; Data; Development; Disease; Epigenetic Process; Etiology; Fibroblasts; Gene Expression; Gene Expression Profile; Genes; Genetic; Genetic Determinism; Genetic Diseases; Genetic Predisposition to Disease; Genetic Risk; Genetic Transcription; Genomic approach; Goals; Individual; Length; Link; Lung; MUC5B gene; Messenger RNA; MicroRNAs; Molecular; Molecular Profiling; Pathogenesis; Pathologic; Pathway interactions; Patients; Penetrance; Peripheral Blood Mononuclear Cell; Phenotype; Populations at Risk; Prognosis; Proliferating; Proteins; Pulmonary Fibrosis; Quantitative Trait Loci; RNA; RNA analysis; Rare Diseases; Regulation; Regulatory Pathway; Reporter; Research; Resources; Risk; Risk Factors; Role; Sampling; Severities; Signal Transduction; Structure of parenchyma of lung; Testing; Untranslated RNA; Variant; Veterans; clinical heterogeneity; demographics; differential expression; gain of function; genetic risk factor; genetic variant; genome-wide; idiopathic pulmonary fibrosis; improved; insight; molecular diagnostics; molecular phenotype; molecular subtypes; novel; promoter; risk variant; telomere; transcription factor USF; transcriptome; transcriptome sequencing; transcriptomics

The overall goal of our proposed research is to understand how long non-protein-coding RNAs (lncRNAs) impact the effect of common idiopathic pulmonary fibrosis (IPF) risk variants on transcriptional profiles and the clinical severity of IPF. In the past 5 years, we have found that: 1) a gain-of- function MUC5B promoter variant rs35705950 is the strongest risk factor for the development of IPF (2-11); 2) epigenetic mechanisms affect the expression of MUC5B (12) and MUC5B appears to be involved in the pathogenesis of IPF (2, 13-15); and 3) IPF is a complex genetic disease with rare and common variants contributing to the development of this disease (16), including pronounced changes in DNA methylation (17) and transcriptional subtypes (18). We have recently sequenced across 10 IPF risk loci (5) in a large number of patients with IPF (N=3,642) and controls (N=4,442), and have identified 10 common variants that represent the only common independent signals in these IPF risk loci and in aggregate account for at least 40% of the risk of IPF (16). However, there is no clear explanation for the molecular/clinical heterogeneity of IPF or the low penetrance of either the MUC5B promoter variant (2) or the other common IPF risk variants (19-22) in this rare disease (23, 24). Emerging findings suggest that lncRNAs could alter the impact of common risk variants by influencing the molecular machinery that leads to IPF, and in turn account for the pathophysiologic phenotypes of IPF. In aggregate, these observations lead us to postulate that the etiology and severity of IPF will be best understood through an integrated approach that accounts for inherited factors and in turn their influence on the coding-noncoding transcriptome. Thus, we hypothesize that lncRNAs regulate the effect of common IPF risk variants on transcriptional profiles that drive the development and clinical severity of IPF. In Aim 1, we will broadly identify lncRNAs that are dysregulated in IPF lung tissue by comparing lncRNAs from the lung tissue of cases of IPF (N=450) to unaffected controls (N=300). We will use these data to identify differentially expressed lncRNAs and mRNAs, and explore networks of mRNAs regulated by lncRNAs. In Aim 2, we will determine cis- and trans-effects of IPF-associated common genetic variants on lncRNAs first in normal lung tissue and then in the IPF lung. This will enable us to hone in on candidate lncRNAs dysregulated in IPF that are driven by common IPF risk variants. In Aim 3, we will use a massively parallel reporter assay (MPRA) to identify and functionally validate regulatory variants within 10 key IPF risk loci that alter expression of coding and noncoding candidate RNAs and are associated with clinical and/or pathological subtypes of IPF. The end-result will be an enhanced understanding of the novel genes, regulatory pathways and networks, and molecular mechanisms involved in the etiology and clinical severity of IPF.

我们所提出的研究的总体目标是了解非蛋白质编码RNA的长度 （lncRNA）影响常见特发性肺纤维化（IPF）风险变体对 转录谱和IPF的临床严重程度。在过去的五年里，我们发现：1）获得- 功能MUC 5 B启动子变体rs35705950是IPF发展的最强风险因素（2-11）; 2） 表观遗传机制影响MUC 5 B的表达（12），MUC 5 B似乎参与了 IPF的发病机制（2，13-15）;和3）IPF是一种复杂的遗传性疾病，具有罕见和常见变异 有助于这种疾病的发展（16），包括DNA甲基化的显著变化（17）， 转录亚型（18）。我们最近在大量的IPF患者中对10个IPF风险基因座（5）进行了测序。 IPF患者（N= 3，642）和对照组（N= 4，442），并确定了10种常见变异， 在这些IPF风险位点中只有共同的独立信号，并且总体上至少占IPF风险的40%。 森林小组（16）。然而，没有明确解释IPF的分子/临床异质性或低的 在这一罕见的病例中，MUC 5 B启动子变异（2）或其他常见的IPF风险变异（19-22）的表达增加。 疾病（23，24）。新的研究结果表明，lncRNAs可以通过以下方式改变常见风险变体的影响： 影响导致IPF的分子机制，并反过来解释病理生理表型 的IPF。总的来说，这些观察结果使我们假设IPF的病因和严重程度将是最好的 通过综合方法理解，这种方法考虑到继承的因素， 编码-非编码转录组因此，我们假设lncRNA调节常见IPF的作用， 转录谱上的风险变体，这些风险变体驱动IPF的发展和临床严重程度。在目标1中， 我们将通过比较来自肺组织的lncRNA， IPF病例（N=450）与未受影响的对照组（N=300）的组织。我们将使用这些数据来鉴别 表达的lncRNA和mRNA，并探索由lncRNA调控的mRNA网络。在目标2中，我们将 首先在正常肺中确定IPF相关的常见遗传变异体对lncRNA的顺式和反式作用 组织中，然后在IPF肺中。这将使我们能够深入研究IPF中失调的候选lncRNA， 由常见的IPF风险变量驱动。在目标3中，我们将使用大规模平行报告基因测定（MPRA）， 在10个关键IPF风险基因座内鉴定和功能验证调节变体， 非编码候选RNA，并且与IPF的临床和/或病理亚型相关。归宿 将是一个新的基因，调控途径和网络，以及分子的增强理解 IPF病因学和临床严重程度相关机制。