Uncovering the genetically-driven differential susceptibility to chronic obstructive pulmonary disease and pulmonary fibrosis

揭示遗传驱动的对慢性阻塞性肺病和肺纤维化的易感性差异

• 批准号: 10584895
• 负责人: MICHAEL H. CHO
• 金额: $ 78.16万
• 依托单位: BRIGHAM AND WOMEN'S HOSPITAL
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-12-15 至 2027-11-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10584895
• 关键词: ATAC-seq; Address; Affect; Aging; Alleles; Alveolus; Architecture; Biological; Biological Assay; Biological Process; Biology; CRISPR interference; CRISPR-mediated transcriptional activation; Cell Nucleus; Cell physiology; Cells; Chromatin; Chronic Obstructive Pulmonary Disease; Chronic lung disease; Clinical; Data; Data Set; Development; Disease; Environmental Risk Factor; Fibrosis; G-Protein-Coupled Receptors; Gene Expression; Genes; Genetic; Genetic Risk; Genetic Transcription; Genome; Genomics; Goals; Inflammatory; Investigation; Joints; Knowledge; Lung; Maps; MicroRNAs; Molecular; Mucous Membrane; Multiple Sclerosis; Neurons; Nucleic Acid Regulatory Sequences; Obstruction; Pathogenesis; Pathologic; Pathology; Pathway interactions; Pharmaceutical Preparations; Phenotype; Physiology; Predisposition; Pulmonary Fibrosis; Pulmonary Pathology; Quantitative Trait Loci; RNA; Regulation; Regulatory Element; Research; Respiratory Disease; Risk; Series; Shunt Device; Statistical Methods; Structure of parenchyma of lung; T-Lymphocyte; Therapeutic; Tissue Sample; Tissues; Total Lung Capacity; Trans-Omics for Precision Medicine; Transposase; Validation; airway obstruction; causal variant; cell type; cigarette smoking; disorder risk; effective therapy; gene regulatory network; genetic association; genetic variant; genome editing; genome sequencing; genome wide association study; genomic locus; idiopathic pulmonary fibrosis; improved; miRNA expression profiling; myelination; novel therapeutics; polarized cell; precision medicine; risk variant; single nucleus RNA-sequencing; whole genome

ABSTRACT Chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF) are two devastating chronic lung diseases associated with aging and with a common environmental risk factor, cigarette smoking, but with differing physiology and pathology, which may be due to genetics. Our group has led two large-scale COPD genome-wide association studies (GWASs), identifying five loci (near FAM13A, DSP, MAPT-KANSL1, ZKSCAN1, and STN1) where the genetic variant alleles associated with an increased COPD risk are associated with a decreased IPF risk. These opposite risk loci may reside in regulatory elements that act as “molecular switches” in disease-relevant cell types that impact gene expression to shunt biologic processes toward producing a COPD or IPF end-phenotype. However, GWASs do not directly implicate the functional consequence of genetic variants or the effector genes, cell types, or gene regulatory networks through which the genetic variants are acting. MicroRNAs, which have been implicated in the pathogenesis of both COPD and IPF, modulate gene expression levels and may impact the gene regulatory networks at the opposite risk loci. The goal of this project is to define COPD/IPF opposite risk loci and describe the functional mechanisms, effector genes, and relevant lung cell types through which these opposite risk loci are acting. We hypothesize that opposite risk genetic loci for COPD and IPF are due to shared causal variants acting as molecular switches through regulatory elements affecting gene expression in specific lung cell types. Furthermore, we hypothesize that these molecular switches are marked by discrete microRNA and RNA differences as well as divergent gene regulatory networks in COPD compared to IPF lung tissue. To address these hypotheses, we propose a series of investigations starting by refining the five known COPD/IPF opposite risk loci and identifying new opposite risk loci using expanded COPD and IPF GWASs and TOPMed WGS data. Next, we will perform joint single nucleus Assay for Transposase-Accessible Chromatin sequencing (snATAC-seq) and snRNA-seq in COPD and IPF lung tissue from the Lung Tissue Research Consortium (LTRC) to predict the disease-specific and lung cell-type- specific regulatory elements and effector genes at each of the COPD/IPF opposite risk loci. We will use CRISPR interference genome editing in implicated cell types to functionally validated predicted relationships of regulatory elements to effector genes. Next, we will generate microRNA sequencing data in IPF lung tissue from the LTRC and build disease-specific gene regulatory networks integrating genetic, microRNA, and RNA data at each opposite risk locus. We will highlight therapeutic opportunities by assessing these gene regulatory networks for drug-related pathway enrichment. We will then examine the COPD- and IPF-related cellular phenotypes that result from perturbations (CRISPR interference, CRISPR activation, and microRNA targeting) of the genes in the opposite risk loci gene regulatory networks. This study will help define the pathobiology and improve our understanding of the susceptibility for the two most deadly chronic lung diseases.

摘要 慢性阻塞性肺疾病(COPD)和特发性肺纤维化(IPF)是两种毁灭性的疾病 与衰老和常见的环境风险因素吸烟有关的慢性肺部疾病， 但有不同的生理和病理，这可能是由于遗传。我们小组已经领导了两个大规模的 COPD全基因组关联研究(GWASs)，确定5个基因座(FAM13A，DSP，MAPT-KANSL1， ZKSCAN1和STN1)，其中与COPD风险增加相关的遗传变异等位基因 IPF风险降低。这些相反的风险基因可能存在于调控元件中，这些元件起到了分子作用 影响基因表达的疾病相关细胞类型的开关将生物过程分流到 产生COPD或IPF终末表型。然而，GWAS并不直接涉及功能 遗传变异或效应基因、细胞类型或基因调控网络的结果 基因变异正在起作用。与COPD和IPF的发病机制有关的microRNAs， 调节基因表达水平，并可能影响相反风险位点的基因调控网络。这个 本项目的目标是定义COPD/IPF的相对风险部位，并描述其作用机制、影响因素 基因，以及相关的肺细胞类型，这些相反的风险基因通过这些基因和相关的肺细胞类型发挥作用。我们假设 COPD和IPF的相反风险基因座是由于共同的因果变异起到分子开关的作用 通过影响特定肺细胞类型的基因表达的调节元件。此外，我们假设 这些分子开关是以离散的microRNA和RNA差异以及发散基因为标志的 COPD中的调节网络与IPF肺组织的比较。为了解决这些假设，我们提出了一系列 从提炼已知的五个COPD/IPF相对风险基因并确定新的相对风险开始进行调查 使用扩展的COPD和IPF GWAS和TOPMed WGS数据的基因座。接下来，我们将进行联合单核 COPD和IPF肺组织中转座酶可及染色质测序(SNATAC-SEQ)和SNRNA-SEQ的测定 来自肺组织研究联盟(LTRC)的组织来预测疾病的特异性和肺细胞类型- COPD/IPF的每个相对风险基因的特定调控元件和效应基因。我们将使用CRISPR 干扰相关细胞类型的基因组编辑对功能验证的调控预测关系的影响 与效应基因有关的元素。接下来，我们将从LTRC中生成IPF肺组织中的microRNA测序数据 并构建针对疾病的基因调控网络，每个网络都集成了遗传、microRNA和RNA数据 相反的风险轨迹。我们将通过评估这些基因调控网络来强调治疗机会 药物相关途径的丰富。然后我们将检查与COPD和IPF相关的细胞表型 由基因的扰动(CRISPR干扰、CRISPR激活和microRNA靶向)造成的 相反的风险点基因调控网络。这项研究将有助于确定病原生物学，并改进我们的 了解两种最致命的慢性肺部疾病的易感性。