Genome-wide association analysis of blood biomarkers in chronic obstructive pulmonary disease

Abstract

Rationale: A genome-wide association study (GWAS) for circulating chronic obstructive pulmonary disease (COPD) biomarkers could identify genetic determinants of biomarker levels and COPD susceptibility.

Objectives: To identify genetic variants of circulating protein biomarkers and novel genetic determinants of COPD.

Methods: GWAS was performed for two pneumoproteins, Clara cell secretory protein (CC16) and surfactant protein D (SP-D), and five systemic inflammatory markers (C-reactive protein, fibrinogen, IL-6, IL-8, and tumor necrosis factor-α) in 1,951 subjects with COPD. For genome-wide significant single nucleotide polymorphisms (SNPs) (P < 1 × 10(-8)), association with COPD susceptibility was tested in 2,939 cases with COPD and 1,380 smoking control subjects. The association of candidate SNPs with mRNA expression in induced sputum was also elucidated.

Measurements and main results: Genome-wide significant susceptibility loci affecting biomarker levels were found only for the two pneumoproteins. Two discrete loci affecting CC16, one region near the CC16 coding gene (SCGB1A1) on chromosome 11 and another locus approximately 25 Mb away from SCGB1A1, were identified, whereas multiple SNPs on chromosomes 6 and 16, in addition to SNPs near SFTPD, had genome-wide significant associations with SP-D levels. Several SNPs affecting circulating CC16 levels were significantly associated with sputum mRNA expression of SCGB1A1 (P = 0.009-0.03). Several SNPs highly associated with CC16 or SP-D levels were nominally associated with COPD in a collaborative GWAS (P = 0.001-0.049), although these COPD associations were not replicated in two additional cohorts.

Conclusions: Distant genetic loci and biomarker-coding genes affect circulating levels of COPD-related pneumoproteins. A subset of these protein quantitative trait loci may influence their gene expression in the lung and/or COPD susceptibility. Clinical trial registered with www.clinicaltrials.gov (NCT 00292552).

Trial registration: ClinicalTrials.gov NCT00292552.

Figure 1.

A schematic overview of the genetic analyses in this study. COPD = chronic obstructive pulmonary disease; GWAS = genome-wide association study; ICGN = International COPD Genetics Network; SNPs = single nucleotide polymorphisms.

Figure 2.

Manhattan plots for (A) Clara cell secretory protein and (B) surfactant protein D. Genome-wide significant single nucleotide polymorphisms are noted in red and closest genes to them are also listed at the bottom of plots. GWAS = genome-wide association study.

Figure 3.

Differential circulating levels of Clara cell secretory protein (CC16) stratified by genotype of top genome-wide association study significant associations for CC16. Top single nucleotide polymorphisms were classified by the closest genes. Mean (column) and standard deviation (error bar) of CC16 level are shown.