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.

我们提出的研究的总体目标是了解非蛋白质编码 RNA 能持续多久 (lncRNA) 影响常见特发性肺纤维化 (IPF) 风险变异对 转录谱和 IPF 的临床严重程度。在过去的5年里，我们发现：1） 功能 MUC5B 启动子变异 rs35705950 是发生 IPF 的最强危险因素 (2-11)； 2） 表观遗传机制影响 MUC5B 的表达 (12)，并且 MUC5B 似乎参与 IPF 的发病机制 (2, 13-15); 3) IPF 是一种复杂的遗传性疾病，具有罕见和常见变异 导致这种疾病的发展 (16)，包括 DNA 甲基化的显着变化 (17) 和 转录亚型 (18)。我们最近对大量的 10 个 IPF 风险位点 (5) 进行了测序 IPF 患者 (N=3,642) 和对照 (N=4,442)，并确定了代表 IPF 的 10 种常见变异 这些 IPF 风险位点中只有共同的独立信号，并且总计至少占 IPF 风险的 40% 特发性肺纤维化 (16)。然而，对于 IPF 的分子/临床异质性或低水平尚无明确的解释。 MUC5B 启动子变体 (2) 或其他常见 IPF 风险变体 (19-22) 的外显率 疾病 (23, 24)。新发现表明，lncRNA 可以通过以下方式改变常见风险变异的影响： 影响导致 IPF 的分子机制，进而解释病理生理表型 的IPF。总的来说，这些观察结果使我们推测 IPF 的病因和严重程度是最好的 通过综合方法来理解，该方法考虑了遗传因素及其对后代的影响 编码-非编码转录组。因此，我们假设 lncRNA 调节常见 IPF 的作用 转录谱上的风险变异推动了 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部的lncRNA来广泛识别IPF肺组织中失调的lncRNA IPF 病例 (N=450) 与未受影响的对照 (N=300) 的组织。我们将使用这些数据来进行差异识别 表达lncRNA和mRNA，并探索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 相关常见遗传变异对 lncRNA 的顺式和反式影响 组织，然后进入 IPF 肺。这将使我们能够专注于 IPF 中失调的候选 lncRNA 由常见的 IPF 风险变体驱动。在目标 3 中，我们将使用大规模并行报告分析 (MPRA) 识别并在功能上验证 10 个关键 IPF 风险位点内的调节变异，这些变异会改变编码和表达的表达 非编码候选 RNA，与 IPF 的临床和/或病理亚型相关。最终结果 将加深对新基因、调控途径和网络以及分子的理解 IPF 的病因学和临床严重程度涉及的机制。