Journal Article

Genome-wide study identifies two loci associated with lung function decline in mild to moderate COPD

Connett, John, Mathias, Rasika A., Lomas, David A., Psaty, Bruce M., Scott, Alan F., Ruczinski, Ingo, Vestbo, Jorgen, Sandford, Andrew, Hansel, Nadia N., Silverman, Edwin, Beaty, Terri H., Paré, Peter D., Kim, Yoonhee, Elliott, W. Mark, Aminuddin, Farzian, Ferrucci, Luigi, Boezen, H. Marike, Mohamed Hoesein, Firdaus A., Crystal, Ronald G., O’Connor, George T., Tanaka, Toshiko, Smolonska, Joanna, Zanen, Pieter, Wan, Emily, Neptune, Enid R., Huang, Lili, Wise, Robert A., de Koning, Harry J., Heckbert, Susan R., Li, Guo, Sin, Don D., Murray, Tanda, Daley, Denise, Doheny, Kimberly, Malinina, Alla, Dupuis, Josée, Rafaels, Nicholas, Barnes, Kathleen C., Postma, Dirkje S., Vergara, Candelaria

2013

Overview

Accelerated lung function decline is a key COPD phenotype; however, its genetic control remains largely unknown. We performed a genome-wide association study using the Illumina Human660W-Quad v.1_A BeadChip. Generalized estimation equations were used to assess genetic contributions to lung function decline over a 5-year period in 4,048 European American Lung Health Study participants with largely mild COPD. Genotype imputation was performed using reference HapMap II data. To validate regions meeting genome-wide significance, replication of top SNPs was attempted in independent cohorts. Three genes ( TMEM26 , ANK3 and FOXA1 ) within the regions of interest were selected for tissue expression studies using immunohistochemistry. Two intergenic SNPs (rs10761570, rs7911302) on chromosome 10 and one SNP on chromosome 14 (rs177852) met genome-wide significance after Bonferroni. Further support for the chromosome 10 region was obtained by imputation, the most significantly associated imputed SNPs (rs10761571, rs7896712) being flanked by observed markers rs10761570 and rs7911302. Results were not replicated in four general population cohorts or a smaller cohort of subjects with moderate to severe COPD; however, we show novel expression of genes near regions of significantly associated SNPS, including TMEM26 and FOXA1 in airway epithelium and lung parenchyma, and ANK3 in alveolar macrophages. Levels of expression were associated with lung function and COPD status. We identified two novel regions associated with lung function decline in mild COPD. Genes within these regions were expressed in relevant lung cells and their expression related to airflow limitation suggesting they may represent novel candidate genes for COPD susceptibility.

• Publisher: Springer-Verlag,Springer,Springer Nature B.V
• Subject: Adult / Ankyrins - genetics / Ankyrins - metabolism / Biomedical and Life Sciences / Biomedicine / Chromosomes, Human, Pair 10 - genetics / Chromosomes, Human, Pair 14 - genetics / Cohort Studies / Epidemiology / Female / Gene Function / Genes / Genome-Wide Association Study / Genomes / Genomics / Hepatocyte Nuclear Factor 3-alpha - genetics / Hepatocyte Nuclear Factor 3-alpha - metabolism / Hospitals / Human Genetics / Humans / Immunohistochemistry / Linkage Disequilibrium / Lung - physiopathology / Lung diseases, Obstructive / Male / Medical research / Medicine / Membrane Proteins - genetics / Membrane Proteins - metabolism / Metabolic Diseases / Middle Aged / Molecular Medicine / Original Investigation / Polymorphism, Single Nucleotide / Public health / Pulmonary Disease, Chronic Obstructive - genetics / Pulmonary Disease, Chronic Obstructive - physiopathology / Research centers / Smoking