A functional variant alters binding of activating protein 1 regulating expression of FGF7 gene associated with chronic obstructive pulmonary disease

Xiaomei Zhang,Lina Du,Yongxin Guo,Jing Yang,Jianlou Niu,Xiaokun Li,Haiyan Li

doi:10.1186/s12881-019-0761-7

Xiaomei Zhang, Lina Du + Show 5 more

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https://doi.org/10.1186/s12881-019-0761-7

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Abstract

BackgroundGenome-wide association studies (GWASs) of a large cohort of subjects with chronic obstructive pulmonary disease (COPD) have successfully identified multiple risk genes, including fibroblast growth factor 7 (FGF7). However, the underlying molecular mechanism influencing function of FGF7 and risk of COPD remains further study.MethodsIn this study, we replicated the genetic association of variants near the FGF7 gene in 258 Chinese Han patients with COPD and 311 healthy controls. Additionally, we functionally evaluated a candidate causal variant upstream of the FGF7 gene.ResultsThe most significant association was observed at rs12905203 (P = 5.9 × 10− 3, odd ratio, OR = 1.516) that explains associations of previously reported variants at the FGF7 locus. Electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation-quantitative polymerase chain reaction (ChIP-qPCR) assays showed that the risk allele of the variant was bound to activator protein 1 transcription factors (c-Fos and c-Jun) with a significantly reduced affinity and associated with decreased mRNA expression of FGF7 in fibroblast cells at both resting and PMA/Ionomycin-stimulated conditions. Overexpression of c-Fos and c-Jun proteins or stimulation with PMA/Ionomycin significantly increases mRNA expression of FGF7 in fibroblast cells. Bioinformatic analysis showed that the variant overlaps with multiple genetic regulatory marks, suggesting the regulatory DNA element might function as an enhancer for the FGF7 gene. Luciferase enhancer activity assays demonstrated that the DNA sequences carrying the variant produce enhancer activity while the risk allele of the variant reduces its activity.ConclusionsIn this study, we demonstrated a consistent association of the FGF7 gene with COPD and mechanistically characterized a candidate functional variant upstream of the FGF7 gene. These data highlighted the important role of the risk variant and the FGF7 gene in influencing risk for COPD.

Highlights

Genome-wide association studies (GWASs) of a large cohort of subjects with chronic obstructive pulmonary disease (COPD) have successfully identified multiple risk genes, including fibroblast growth factor 7 (FGF7)
Genetic variants at the FGF7 locus associated with COPD in Chinese Han Three single nucleotide polymorphisms (SNPs) have demonstrated significant associations with COPD, two of which have been identified in Spanish, Native American ancestry
Using HaploReg [22], we identified 10 single nucleotide polymorphisms (SNPs) that are in strong linkage disequilibrium (LD) with risk variants rs10519225 and rs12591300 (r2 > 0.8) (Additional file 2: Table S2)

Summary

Introduction

Genome-wide association studies (GWASs) of a large cohort of subjects with chronic obstructive pulmonary disease (COPD) have successfully identified multiple risk genes, including fibroblast growth factor 7 (FGF7). Chronic obstructive pulmonary disease (COPD) is a complex genetic disorder that is characterized by a reduction in lung function with airflow obstruction [1]. Four large-scale genome-wide association studies have been performed in multiple populations and successfully identified numerous genetic variants consistently associated with COPD (Additional file 1: Table S1) [6,7,8,9]. In addition to the GWAS, candidate gene approaches significantly contributed to the identification of risk factors of COPD in the individual cohort of patients [10,11,12]. Due to the relatively small sample size in the Chinese Han study, further evaluation of the genetic association of the FGF7 gene in an independent cohort of Chinese COPD is needed

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Conclusion