Multi-omic Risk Prediction of Chronic Obstructive Pulmonary Disease in European- and African-Ancestry Populations

欧洲和非洲血统人群慢性阻塞性肺疾病的多组学风险预测

• 批准号: 10594517
• 负责人: Matthew R Moll
• 金额: $ 16.85万
• 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: 2022-04-01 至 2027-03-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10594517
• 关键词: Acute; Address; Adrenal Cortex Hormones; African American population; African ancestry; Age; Binding; Blood; Blood specimen; Chronic Obstructive Pulmonary Disease; Classification; Clinical; Data; Databases; Detection; Development; Development Plans; Disease; Disease susceptibility; Early identification; European; European ancestry; Future; Gene Expression; Genes; Genetic; Genetic Risk; Genetic Transcription; Genomic Segment; Glass; Heterogeneity; Individual; Inhalation; Intervention; Learning; Lung; Machine Learning; Maps; Measures; Odds Ratio; Outcome; Participant; Pathogenesis; Pathogenicity; Pathway interactions; Patients; Performance; Pharmaceutical Preparations; Phenotype; Population; Predictive Value; Predisposition; Pulmonary Function Test/Forced Expiratory Volume 1; Regulatory Pathway; Research; Research Personnel; Risk; Risk Factors; Sample Size; Sampling; Smoking; Smoking History; Spirometry; Structure of parenchyma of lung; Subgroup; Techniques; Testing; Therapeutic; Therapeutic Intervention; Tissue Sample; Training; Transcript; Variant; Whole Blood; biobank; candidate identification; career development; cigarette smoking; clinical practice; clinical risk; cohort; disease heterogeneity; disease phenotype; disorder risk; disorder subtype; drug candidate; drug repurposing; gene regulatory network; genetic architecture; genetic association; genetic epidemiology; genetic predictors; genetic variant; genome wide association study; high risk; improved; insight; learning network; lung basal segment; machine learning method; mortality; multiple omics; personalized intervention; polygenic risk score; predictive modeling; progression risk; pulmonary function; research and development; respiratory; risk prediction; risk stratification; tool; transcription factor; transcriptome; transcriptome sequencing; transcriptomics

PROJECT SUMMARY/ABSTRACT Chronic obstructive pulmonary disease (COPD) is a leading cause of respiratory mortality worldwide15. Identifying highly susceptible individuals early in their disease course and understanding pathogenic mechanisms, before irreversible loss of lung function, is of utmost importance16,17. Genetics account for about 40% of COPD susceptibility18–20. Genome-wide association studies (GWASs) have identified multiple variants associated with COPD21–23. Individual variants are poor for risk prediction, but in aggregate genetic variants can account for a substantial portion of risk. Pooling millions of GWAS variants, I created a polygenic risk score (PRS) for COPD that can identify individuals at high risk for COPD, though performance was less optimal in non- Europeans24. Multi-ancestry PRSs are needed as genetic ancestry is not readily determined in clinical practice. Further, gene expression, reflecting genetic and environmental influences, provides pathobiologic information for COPD susceptibility and heterogeneity. A transcriptional risk score (TRS) for COPD that adds predictive value above clinical risk factors25 has yet to be developed. The appeal of using -Omics data for risk stratification is that these data can lend insight into why certain COPD subgroups are at elevated risk of progression. Gene regulatory networks26 have been used to uncover mechanisms of COPD heterogeneity that were not found by traditional gene-based approaches. Therefore, we hypothesize that polygenic and transcriptional risk scores will substantially improve upon clinical factors in identifying those at higher risk for COPD and related phenotypes, and can be used to identify pathways for therapeutic intervention. We will train multi-ancestry PRSs using 4,225 African ancestry individuals from UK Biobank and existing analyses of 8,429 African-Americans from CHARGE, and test in the Genetic Epidemiology of COPD (COPDGene: n=10,198) study and Lung Tissue Research Consortium (LTRC: n=1,078). We will create a multi-ancestry transcriptional risk score (TRS) using whole blood RNA-sequencing (RNA-seq) data in training (n=3,394) and evaluate predictive performance in testing samples (n=1,131) of COPDGene. We will use Connectivity Map (CMap)8,27 to identify drug repurposing candidates based on TRS transcripts. We will leverage lung RNA-seq data from LTRC to create a lung TRS, and test in COPDGene blood samples. We will classify COPDGene participants along the axes of the existing PRS and lung TRS (e.g. “High” PRS, “Low” TRS), which we expect will identify those at high risk for COPD-related phenotypes and progression. To understand why certain individuals are at high risk for COPD phenotypes, we will utilize gene regulatory networks to identify pathways differing between PRS/TRS classifications, and use the Gene RegulAtory Network Database (GRAND)9 to prioritize drug repurposing candidates. These aims will generate data for future studies, which will focus on validating COPD -Omics risk scores and drug candidates in real-world cohorts1, and using machine learning to predict the network effects of drug candidates. The proposed research and career development plan will train me to use machine learning for multi-omic integration and risk prediction.

项目总结/摘要 慢性阻塞性肺疾病（COPD）是全球呼吸系统死亡的主要原因15。 在病程早期识别高度易感个体并了解致病性 在肺功能不可逆丧失之前，肺功能受损的机制是最重要的16，17。遗传学解释了 40%的COPD易感性18 -20。全基因组关联研究（GWAS）已经确定了多种变体 与COPD相关21 -23。个体变异对于风险预测来说是很差的，但总体上遗传变异可以 占风险的很大一部分。汇集了数百万个GWAS变体，我创建了一个多基因风险评分（PRS） 对于COPD，可以识别COPD高风险个体，尽管在非COPD患者中性能不太理想， 欧洲人24.需要多血统PRS，因为在临床实践中不易确定遗传血统。 此外，反映遗传和环境影响的基因表达提供了病理生物学信息 COPD易感性和异质性。COPD的转录风险评分（TRS）增加了预测价值 上述临床风险因素25尚待开发。使用组学数据进行风险分层的吸引力在于， 这些数据可以帮助我们了解为什么某些COPD亚组的进展风险升高。基因 调节网络26已被用于揭示COPD异质性的机制，这些机制未被 传统的基于基因的方法。因此，我们假设多基因和转录风险评分将 在识别COPD和相关表型的高风险人群中显著改善临床因素， 并可用于鉴定治疗干预的途径。我们将使用4，225名多血统PRS进行培训 来自英国生物银行的非洲血统个体和来自CHARGE的8,429名非洲裔美国人的现有分析， COPD遗传流行病学（COPDGene：n= 10，198）研究和肺组织研究中的检测 联合体（LTRC：n= 1，078）。我们将使用全血创建多祖先转录风险评分（TRS） 训练中的RNA测序（RNA-seq）数据（n= 3，394）并评估测试样本的预测性能 （n= 1，131）COPD基因。我们将使用连接图（CMap）8，27来识别药物再利用候选者， TRS的成绩单我们将利用LTRC的肺RNA-seq数据创建肺TRS，并在COPDGene中进行测试 血液样本我们将沿着现有PRS和肺TRS的轴对COPDGene参与者进行分类（例如， “高”PRS，“低”TRS），我们预计这将识别出那些COPD相关表型的高风险人群， 进展为了理解为什么某些个体具有COPD表型的高风险，我们将利用基因 调控网络，以确定不同的PRS/TRS分类之间的途径，并使用基因 监管网络数据库（GRAND）9，用于对药物再利用候选药物进行优先排序。这些目标将产生 未来研究的数据，将侧重于验证COPD -组学风险评分和现实世界中的候选药物 cohorts 1，并使用机器学习来预测候选药物的网络效应。拟议研究 和职业发展计划将训练我使用机器学习进行多组学整合和风险预测。