In contrast to the genome-wide linkage studies mentioned previously, the published COPD genetic association studies have focused on candidate genes, identified based on presumed importance in COPD pathogenesis or location in a region of linkage. Most commonly, distributions of alleles or genotypes of one or more single nucleotide polymorphisms (SNPs) are compared in COPD cases versus control subjects without disease. Variations on this design have been used, including analysis of quantitative traits or family-based study designs. Polymorphisms in multiple genes have been associated with COPD, emphysema, or related traits. Genes that have been associated in two or more studies are listed in .
CANDIDATE GENES, BESIDES α1-ANTITRYPSIN (SERPINA1), WITH REPLICATED ASSOCIATIONS TO CHRONIC OBSTRUCTIVE PULMONARY DISEASE, EMPHYSEMA, OR RELATED TRAITS
To test systematically the replication validity of previously published COPD genetic associations, our group examined 29 variants in 12 COPD candidate genes (31
). Genotyping was performed in two study populations: a family-based study of extended pedigrees from the Boston Early-Onset COPD Study and a case-control study comparing 304 subjects with emphysema and severe airflow obstruction from NETT with 441 smokers without airflow obstruction from the Normative Aging Study (32
). In the Boston Early-Onset COPD Study families, a promoter SNP in tumor necrosis factor (TNF)-α, a coding variant in surfactant protein B (SFTPB Thr131Ile), and a repeat polymorphism near heme oxygenase-1 (HMOX1) were significantly associated with quantitative and qualitative spirometric traits. In the case-control analysis, the SFTPB Thr131Ile variant was significantly associated in a model that incorporated a gene-by-smoking interaction term. A different allele of the HMOX1 repeat was significant. The TNF promoter SNP was not replicated, but a coding SNP in microsomal epoxide hydrolase (EPHX1 His139Arg, termed the “fast” allele based on its presumed effect to increase enzyme activity [33
]) was significant only in the case-control study.
The results of our study and the publications listed in highlight that many COPD genetic associations have not been consistently replicated across all studies. Replication failure is a problem throughout complex trait genetics and is not unique to COPD (34
). Multiple factors are likely to explain the inconsistent replication in COPD genetic association studies (36
). False-negative results may be the consequence of genotyping error or inadequately powered sample sizes. Spurious associations may result from genotyping error, multiple testing, or population stratification, which can arise from differences in allele frequency between cases and controls due to ethnic diversity and not true disease association. True genetic differences between study populations, termed genetic heterogeneity, may also lead to replication failure, particularly when comparing studies performed in different countries. Variation in case definition or in the phenotypes analyzed across studies is likely to be an important cause of nonreplication. This phenotypic variation may be particularly relevant for studies of COPD, a heterogeneous disease that includes components of emphysema and airway disease, often occurring in variable combinations in any given patient.
Two potential COPD susceptibility genes have been identified in the chromosomal regions found by the linkage analyses described previously. Transforming growth factor (TGF)-β1 is a widely expressed cytokine that has potential roles in airway disease and interstitial lung disease (37
). The TGFβ1 gene is located on chromosome 19q, a region linked to COPD-related traits in the Boston Early-Onset COPD Study. Celedón and colleagues genotyped additional short tandem repeat markers on chromosome 19q, which led to increased evidence of linkage, especially in a stratified analysis limited to current and former smokers (3
). Analysis of five SNP markers in TGFβ1 found that three SNPs, including one in the promoter (rs2241712), were significantly associated with FEV1
in the Boston Early-Onset COPD Study families. The association with the promoter SNP was replicated in the study comparing NETT cases with control smokers without airflow obstruction. A coding SNP (Leu10Pro, which may lead to higher circulating TGF-β1 levels [38
]) and an additional promoter SNP were significant in the case-control study. Analysis of unlinked SNPs did not show evidence of population stratification between the cases and control subjects (39
In a case-control study from New Zealand, the Leu10Pro-coding SNP in TGFβ1 was associated with COPD (40
). A general population study from the Netherlands found significant COPD associations with three TGFβ1 SNPs, including the promoter SNP in the study by Celedón and colleagues and the Leu10Pro-coding SNP (41
). The association between TGFβ1 SNPs and COPD has not been consistently replicated in other studies (42
The SERPINE2 gene is located on chromosome 2q in a region linked to FEV1
/FVC ratio in the Boston Early-Onset COPD Study. Based on a microarray experiment (44
), DeMeo and colleagues reported that this gene is highly expressed during mouse lung development (4
). Genes important in lung development may predispose to emphysema through effects on airspace size or injury repair. SERPINE2 expression was associated with measures of pulmonary function in a microarray study of emphysematous lung tissue from patients with LVRS (45
). The mouse and human gene expression results were integrated with human genetic association data, initially by genotyping SERPINE2 SNPs in members of the Boston Early-Onset COPD Study families. Significant associations with multiple SNPs were confirmed in an analysis of the NETT COPD cases and community control subjects, identifying a risk haplotype. The potential role of this novel COPD gene in disease pathogenesis has yet to be determined; however, this study demonstrates the power of integrating gene expression and genotype data as well as human and murine studies. Animal models are an important tool in COPD genetics research and have been reviewed elsewhere (46
In a multicenter, family-based study of COPD in North America and Europe, Zhu and colleagues genotyped 25 SNPs in SERPINE2, finding six SNPs to be significantly associated with COPD and spirometric measures of lung function (48
). Five of the six SNPs were associated with airflow obstruction among COPD cases in a large case-control population from Norway. Three of the five replicated SNPs overlapped with the SNPs found to be significantly associated by DeMeo and colleagues (4
The association of SERPINE2 SNPs with COPD was not replicated in a case-control study from the United Kingdom (49
). These cases had a broader range of airflow limitation than the severely affected cases from the Boston Early-Onset COPD Study, NETT, and the family-based sample in the study by Zhu and colleagues (48
). This difference in phenotype is one potential explanation for the discordant results of the SERPINE2 association studies.