Pulmonary Function and Blood DNA Methylation: A Multi-Ancestry Epigenome-Wide Association Meta-Analysis

BIOS consortium, GoDMC, Mikyeong Lee, Tianxiao Huan, Daniel L McCartney, Geetha Chittoor, Maaike de Vries, Lies Lahousse, Jennifer N Nguyen, Jennifer A Brody, Juan Castillo-Fernandez, Natalie Terzikhan, Cancan Qi, Roby Joehanes, Josine L Min, Gordon J Smilnak, Jessica R Shaw, Chen Xi Yang, Elena Colicino, Thanh T Hoang, Mairead L BerminghamHanfei Xu, Anne E Justice, Cheng-Jian Xu, Stephen S Rich, Simon R Cox, Judith M Vonk, Ivana Prokić, Nona Sotoodehnia, Pei-Chien Tsai, Joel D Schwartz, Janice M Leung, Sinjini Sikdar, Rosie M Walker, Sarah E Harris, Diana A van der Plaat, David J Van Den Berg, Traci M Bartz, Tim D Spector, Pantel S Vokonas, Riccardo E Marioni, Adele M Taylor, Yongmei Liu, R Graham Barr, Leslie A Lange, Andrea A Baccarelli, Ma'en Obeidat, Myriam Fornage, Tianyuan Wang, James M Ward, Gerard H Koppelman, H Marike Boezen, Stephanie J London*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

2 Citations (Scopus)
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Abstract

RATIONALE: Methylation integrates factors present at birth and modifiable across life that can influence pulmonary function. Studies are limited in scope and replication.

OBJECTIVES: To conduct large-scale epigenome-wide meta-analyses of blood DNA methylation and pulmonary function.

METHODS: Twelve cohorts analyzed associations of methylation at cytosine-phosphate-guanine probes (CpGs), using Illumina450K or EPIC/850K arrays, with FEV1, FVC, and FEV1/FVC. We performed multi-ancestry epigenome-wide meta-analyses (17,503 individuals: 14,761 European; 2,549 African; and 193 Hispanic/Latino ancestries) and interpreted results using integrative epigenomics.

MEASUREMENTS AND MAIN RESULTS: We identified 1,267 CpGs (1,042 genes) differentially methylated (FDR<0.025) in relation to FEV1, FVC, or FEV1/FVC, including 1,240 novel and 73 also related to COPD (1,787 cases). We found 294 CpGs unique to European or African ancestry and 395 CpGs unique to never or ever smokers. The majority of significant CpGs correlated with nearby gene expression in blood. Findings were enriched in key regulatory elements for gene function, including accessible chromatin elements, in both blood and lung. Sixty-nine implicated genes are targets of investigational or approved drugs. One example novel gene highlighted by integrative epigenomic and druggable target analysis is TNFRSF4. Mendelian randomization and colocalization analyses suggest that EWAS signals capture causal regulatory genomic loci.

CONCLUSIONS: We identified numerous novel loci differentially methylated in relation to pulmonary function; few were detected in large genome-wide association studies. Integrative analyses highlight functional relevance and potential therapeutic targets. This comprehensive discovery of potentially modifiable, novel lung function loci expands knowledge gained from genetic studies providing insights into lung pathogenesis.

Original languageEnglish
Pages (from-to)321-336
Number of pages16
JournalAmerican Journal of Respiratory and Critical Care Medicine
Volume206
Issue number3
Early online date2022
DOIs
Publication statusPublished - 1-Aug-2022

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