Using Integrative Genomics To Identify and Characterize Emphysema-Associated eQTL

使用综合基因组学来识别和表征肺气肿相关的 eQTL

基本信息

批准号：
10653966
负责人：
Peter Castaldi
金额：
$ 72.22万
依托单位：
BRIGHAM AND WOMEN'S HOSPITAL
依托单位国家：
美国
项目类别：
财政年份：
2014
资助国家：
美国
起止时间：
2014-09-01 至 2025-05-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10653966
关键词：
ACVR1B gene Affect Alternative Splicing Alveolar Cell Apoptosis Base Sequence Bioinformatics Biological Assay Biology Blood Blood specimen Cell Aging Cells Chronic Obstructive Pulmonary Disease Data Disease Drug Targeting Elements Epithelial Cells FDA approved Fibroblasts Gene Expression Genes Genetic Genetic Diseases Genomics Genotype Goals Hematological Disease Human Human Genetics Inflammation Interdisciplinary Study Leadership Lung Maps Measures Methods Minority Molecular Biology Persons Phase Phenotype Play Protein Isoforms Pulmonary Emphysema Quantitative Trait Loci RNA RNA Splicing Reporter Research Research Priority Resources Role Sampling Spliced Genes Structure of parenchyma of lung TGFB2 gene Technology Testing Tissue Procurements Tissues Trans-Omics for Precision Medicine Transforming Growth Factor Beta 2 Translational Research Variant Vascular Endothelial Cell airway epithelium cell bank cell type cigarette smoke cohort differential expression disorder risk genetic variant genome wide association study genome-wide genomic locus improved lung injury mortality nanopore novel programs public health relevance transcriptome sequencing

项目摘要

Project Summary: Chronic obstructive pulmonary disease (COPD) is a progressive, debilitating disease for which new, disease-modifying treatments are desperately needed. Since drug targets supported by human genetic evidence are more likely to lead to FDA-approved treatments, functional characterization of genome- wide association study (GWAS) loci is a translational research priority. Our group has played a leading role in COPD GWAS, and the largest COPD GWAS to date has identified 82 significant loci, most of which have not been functionally characterized. In the first phase of this project, we combined emphysema GWAS results with expression quantitative trait locus (eQTL) studies, using GWAS-eQTL colocalization methods to identify COPD GWAS target genes. This approach allowed us to prioritize TGFB2 and ACVR1B for functional studies in airway epithelial cells and lung fibroblasts that identified functional variants in these loci. However, >50% of COPD GWAS loci have not yet shown strong colocalization with eQTLs, due in part to inherent limitations of eQTLs which depend on gene-level expression quantifications that do not reflect effects of alternative splicing. Alternative splicing is an important functional mechanism for GWAS loci, perhaps equally as important as eQTLs. In the next phase of this project, we propose to identify novel COPD-associated genetic variants that alter splicing (sQTLs) and characterize their isoform-specific effects. In Aim 1, we will perform genome-wide discovery of splicing QTLs (sQTLs) using two RNA-seq resources with large numbers of subjects with COPD – blood RNA-seq from 4,515 subjects in the COPDGene Study and lung RNA-seq from 1,078 subjects in the Lung Tissue Research Consortium (LTRC). Using colocalization methods, we will identify novel COPD GWAS target genes whose splicing is altered by COPD-associated genetic variants. In Aim 2, we will identify differentially expressed and differentially used isoforms in COPD using estimated isoform quantifications from short read lung tissue RNA-seq in 1,078 COPD cases and controls in the LTRC. We will then generate Oxford Nanopore Technologies (ONT) long read RNA-seq for 10 COPD GWAS genes in 80 LTRC subjects with COPD and 80 controls using a targeted enrichment approach. In Aim 3, we will combine fine mapping and functional studies to identify COPD GWAS variants that alter splicing in primary lung cells. First, we will use targeted long read RNA-seq to characterize the cell-type specific isoform profiles of COPD GWAS target genes in four primary lung cell types. We will then functionally validate fine- mapped COPD GWAS variants using splicing reporter assays, and we will characterize the effects of these variants on COPD-related cellular phenotypes in airway epithelial cells selected by genotype from the Marsico Lung Institute cell bank. Our multi-disciplinary research team has the requisite expertise in COPD genetics and genomics, molecular biology, long read sequencing, splicing and RNA biology to complete this important project to identify novel COPD GWAS target genes involved in alternative splicing.

项目摘要：慢性阻塞性肺疾病（COPD）是一种进行性，令人衰弱的疾病迫切需要哪种新的，改善疾病的治疗方法。由于人类支持的药物靶标遗传证据更有可能导致FDA批准的治疗，基因组的功能表征广泛的协会研究（GWAS）基因座是转化研究的重点。我们的小组发挥了主导作用在COPD GWAS和迄今为止最大的COPD GWAS已确定了82个重要地方，其中大多数具有没有功能表征。在该项目的第一阶段，我们结合了Emphysema GWAS结果使用GWAS-EQTL共定位方法识别表达定量性状基因座（EQTL）研究 COPD GWAS靶基因。这种方法使我们可以优先考虑TGFB2和ACVR1B进行功能研究在气道上皮细胞和肺成纤维细胞中，这些基因座的功能变体。但是，> 50％ COPD GWAS基因座的尚未显示出与eqtls强烈共定位，部分归因于继承的局限性依赖基因级表达量化的eqTL，这些量子不反映替代的影响剪接。替代剪接是GWAS基因座的重要功能机制，也许等于重要的是eqtls。在该项目的下一阶段，我们建议确定新型COPD相关的通用改变剪接（SQTL）并表征其同工型特异性效应的变体。在AIM 1中，我们将表演使用大量的RNA-Seq资源大量的RNA-seq资源发现剪接QTLS（SQTL）（SQTLS） COPDGene研究中4,515名受试者的COPD的受试者 - 来自COPDGENE研究的受试者，来自肺RNA-Seq。肺组织研究联盟（LTRC）中的1,078名受试者。使用共定位方法，我们将识别新型的COPD GWAS靶基因，其剪接会因COPD相关的遗传变异而改变。在 AIM 2，我们将使用估计来自1,078例COPD病例的短读肺组织RNA-Seq的同工型定量和LTRC中的对照。然后，我们将生成牛津纳米孔技术（ONT）长读RNA-Seq，用于10个COPD GWAS基因在80名LTRC受试者中，具有COPD和80个对照的受试者，使用靶向富集方法。在AIM 3中，我们将结合精细的映射和功能研究，以鉴定COPD GWAS变体，这些变体改变了主要的剪接肺部细胞。首先，我们将使用有针对性的长读RNA-seq来表征细胞类型的特异性同工型在四种主要的肺细胞类型中，COPD GWAS靶基因的概况。然后，我们将在功能上验证Fine- 使用剪接报告基因测定法映射COPD GWAS变体，我们将表征这些效果来自Marsico的基因型选择的COPD相关细胞表型的变体上皮细胞中的变体肺部细胞库。我们的多学科研究团队拥有COPD遗传学的必要专业知识以及基因组学，分子生物学，长读测序，剪接和RNA生物学，以完成这一重要的项目旨在识别与替代剪接有关的新型COPD GWAS靶基因。

项目成果

期刊论文数量（25）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Network-based analysis reveals novel gene signatures in peripheral blood of patients with chronic obstructive pulmonary disease.

DOI：
10.1186/s12931-017-0558-1
发表时间：
2017-04-24
期刊：
Respiratory research
影响因子：
5.8
作者：
Obeidat M;Nie Y;Chen V;Shannon CP;Andiappan AK;Lee B;Rotzschke O;Castaldi PJ;Hersh CP;Fishbane N;Ng RT;McManus B;Miller BE;Rennard S;Paré PD;Sin DD
通讯作者：
Sin DD

Turning subtypes into disease axes to improve prediction of COPD progression.

将亚型转化为疾病轴以改善对慢性阻塞性肺病进展的预测。

DOI：
10.1136/thoraxjnl-2018-213005
发表时间：
2019
期刊：
Thorax
影响因子：
10
作者：
Chen,Junxiang;Cho,Michael;Silverman,EdwinK;Hokanson,JohnE;Kinney,GregL;Crapo,JamesD;Rennard,Stephen;Dy,Jennifer;Castaldi,Peter
通讯作者：
Castaldi,Peter

Peripheral blood microbial signatures in current and former smokers.

DOI：
10.1038/s41598-021-99238-4
发表时间：
2021-10-06
期刊：
Scientific reports
影响因子：
4.6
作者：
Morrow JD;Castaldi PJ;Chase RP;Yun JH;Lee S;Liu YY;Hersh CP
通讯作者：
Hersh CP

Analysis of genetically driven alternative splicing identifies FBXO38 as a novel COPD susceptibility gene.

对基因驱动的选择性剪接的分析将 FBXO38 确定为一种新型 COPD 易感基因。

DOI：
10.1371/journal.pgen.1008229
发表时间：
2019
期刊：
PLoS genetics
影响因子：
4.5
作者：
Saferali,Aabida;Yun,JeongH;Parker,MargaretM;Sakornsakolpat,Phuwanat;Chase,RobertP;Lamb,Andrew;Hobbs,BrianD;Boezen,MarikeH;Dai,Xiangpeng;deJong,Kim;Beaty,TerriH;Wei,Wenyi;Zhou,Xiaobo;Silverman,EdwinK;Cho,MichaelH;Cast
通讯作者：
Cast

Hepatitis C and HIV detection by blood RNA-sequencing in cohort of smokers.