Published ahead of print on February 2, 2006, doi:10.1164/rccm.200509-1452OC
© 2006 American Thoracic Society doi: 10.1164/rccm.200509-1452OC
Genetic Association Analysis of Functional Impairment in Chronic Obstructive Pulmonary DiseaseChanning Laboratory, and Pulmonary and Critical Care Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts; University of Washington, Seattle, Washington; Temple University, Philadelphia, Pennsylvania; National Jewish Medical and Research Center, Denver, Colorado; University of Michigan, Ann Arbor, Michigan; Mayo Clinic, Rochester, Minnesota; and University of Pittsburgh, Pittsburgh, Pennsylvania Correspondence and requests for reprints should be addressed to Craig P. Hersh, M.D., M.P.H., Channing Laboratory, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA 02115. E-mail: craig.hersh{at}channing.harvard.edu
Rationale: Patients with severe chronic obstructive pulmonary disease (COPD) may have varying levels of disability despite similar levels of lung function. This variation may reflect different COPD subtypes, which may have different genetic predispositions. Objectives: To identify genetic associations for COPD-related phenotypes, including measures of exercise capacity, pulmonary function, and respiratory symptoms. Methods: In 304 subjects from the National Emphysema Treatment Trial, we genotyped 80 markers in 22 positional and/or biologically plausible candidate genes. Regression models were used to test for association, using a testreplication approach to guard against false-positive results. For significant associations, effect estimates were recalculated using the entire cohort. Positive associations with dyspnea were confirmed in families from the Boston Early-Onset COPD Study.
Results: The testreplication approach identified four genesmicrosomal epoxide hydrolase (EPHX1), latent transforming growth factor- Conclusions: Polymorphisms in several genes seem to be associated with COPD-related traits other than FEV1. These associations may identify genes in pathways important for COPD pathogenesis.
Key Words: dyspnea emphysema exercise tolerance genetic association pulmonary function tests Chronic obstructive pulmonary disease (COPD) is an inherently heterogeneous disorder. Within a given individual, there may be varying contributions of emphysema, chronic bronchitis, and small airway disease. However, the majority of studies of COPD genetics have focused only on the presence or absence of COPD diagnosis, which may or may not have been based on spirometry (1). Few studies have analyzed quantitative COPD-related traits, and most of these have examined only spirometric measures, such as FEV1 and the ratio of FEV1 to FVC (2). The National Emphysema Treatment Trial (NETT) is a multicenter, randomized, clinical trial comparing lung volume reduction surgery (LVRS) with medical management for severe COPD (3). One of the important findings of NETT was that two COPD-related phenotypes, radiographic distribution of emphysema and exercise capacity, could be used to identify subgroups of patients with varying responses to LVRS (4). These subgroups identify patients with different treatment responses and might also be used to identify patients with different disease mechanisms. If so, using such subgroups may aid in the discovery of genes that may predict LVRS outcome or genes that may predispose to the development of COPD. We hypothesized that different genetic factors influence different COPD-related functional capacity phenotypes, including pulmonary function measures, exercise capacity, and respiratory symptoms. To test this hypothesis, we examined genetic associations for these phenotypes in individuals participating in the NETT Genetics Ancillary Study. Some of the genotype data used in this study have been included in case-control studies for COPD susceptibility (57). Results from the current study have been previously reported as an abstract (8).
Study Subjects Subject enrollment and data collection in NETT have been described (3, 4). The current analysis included 304 non-Hispanic white subjects in the NETT Genetics Ancillary Study. After providing written informed consent, these NETT participants provided a blood sample for DNA extraction for genetic studies of COPD. Phenotypes were measured prior to randomization but after pulmonary rehabilitation. The study was approved by the institutional review boards at participating NETT centers. Additional details can be found in the online supplement.
Candidate Genes and Genotyping
Details of genotyping methods have been reported previously (57). Single-nucleotide polymorphisms (SNPs) were genotyped using the 5' to 3' exonuclease assay in TaqMan (Applied Biosystems, Foster City, CA) (9) or with unlabeled minisequencing reactions and mass spectrometry in Sequenom (San Diego, CA) (10). For three short tandem repeat (STR) markers, polymerase chain reaction was performed using fluorescence-labeled and unlabeled primers, and product sizes were assessed by capillary electrophoresis on an ABI 3100 machine (Applied Biosystems). A 1-bp insertiondeletion in MMP1 and the GSTM1 null deletion were genotyped with TaqMan assays.
Statistical Analysis Linkage disequilibrium (pairwise r2) between SNPs in the same gene was calculated in Haploview (11). Haplotype analysis was performed using the expectation-maximization algorithm and score tests, implemented in haplo.stats (12). Global haplotype p values were derived from a minimum of 1,000 simulations.
Dyspnea Replication Analysis
Study Subjects Characteristics of the 304 non-Hispanic white participants in the NETT Genetics Ancillary Study are shown in Table 2. There was a predominance of men (63.8%) and a mean age of 67.3 yr. These findings are similar to the entire cohort of 1,218 NETT participants (4). On average, subjects had severe impairment on tests of pulmonary function and exercise capacity, although there was more variability in the measurements of the latter. Phenotype distributions were not significantly different in the test and replication samples, with the exception of the University of California, San Diego, Shortness of Breath Questionnaire (UCSD SOBQ) score (t test, p = 0.02) (16). This difference did not remain significant when adjusted for multiple testing.
Each of the quantitative phenotypes tested was significantly correlated with each of the other phenotypes (p < 0.01, Pearson correlation), although most of the correlations were weak (|r| < 0.4). The strongest correlations were between maximum work achieved during the exercise test and 6-min walk test distance (r = 0.59, p < 0.0001) and between modified BODE (Body mass index, airflow Obstruction, Dyspnea, Exercise tolerance) score (17) and each of its components (FEV1: r = 0.43, p < 0.0001; UCSD SOBQ score: r = 0.79, p < 0.0001; 6-min walk distance: r = 0.63, p < 0.0001). BODE score was also correlated with maximum work (r = 0.51, p < 0.0001).
TestReplication Association Analysis
In the analysis of post-bronchodilator FEV1 (L), six markers in six genes were associated (p < 0.1) in the test set; none of these were replicated. Nine markers in seven genes were found in the screening analysis of carbon monoxide diffusing capacity (DLCO); one of these, a promoter SNP in EPHX1 (rs868966), was replicated. In the screening analysis of the UCSD SOBQ score, 23 markers in nine genes were nominally associated (p < 0.1); four of these associations were significant on replication. These replicated associations include an SNP in EPHX1 (rs2292566), the 259-bp allele of the SFTPB STR, and two SNPs in TGFB1 (rs1800469, rs2241712). In the analysis of the modified BODE index, 14 markers in seven genes had p values of less than 0.1 on screening, but none were replicated. One allele of the SFTPB STR, length 269 bp, was significantly associated with modified BODE index in the test set, but another allele, length 263 bp, had a p value of less than 0.05 in the replication set.
Comprehensive Association Analysis of Promising Candidate Genes
Two SNPs in EPHX1, including a coding variant (rs1051740, Tyr113His, also known as the "slow" allele), were associated with a reduction in maximal work output (Table 4A, Figure 1); the "slow" variant also increased the odds of being classified in the low-exercise subgroup (odds ratio, 1.75; 95% confidence interval, 1.162.62). Four SNPs in LTBP4 were significantly associated with an increase in work capacity and reduced odds of low exercise tolerance; three of these also led to a greater 6-min walk test distance. Presence of one allele of the SFTPB STR (259 bp) increased the odds of low exercise tolerance; individuals with another allele (263 bp) had greater 6-min walk test distance. SNPs in TGFB1 were not associated with exercise capacity traits.
Three SNPs in EPHX1, including a coding variant (rs2234922, His139Arg, the "fast" allele), were associated with increased values of DLCO (Table 4B), but they were not associated with post-bronchodilator FEV1. None of the markers in LTBP4, SFTPB, and TGFB1 were associated with these pulmonary function phenotypes. Three SNPs in TGFB1, including two promoter SNPs (rs1800469, rs2241712) and one coding SNP (rs1982073, Leu10Pro), were associated with a higher UCSD SOBQ score, indicating more severe dyspnea (Table 4C, Figure 2). These three SNPs also led to an increase in modified BODE index (more severe disease). Two SNPs in LTBP4 and the 259-bp allele of the SFTPB STR were associated with a lower BODE index. EPHX1 was not associated with either symptom severity phenotype.
Linkage Disequilibrium In three of the four significant genes (EPHX1, LTBP4, and TGFB1), pairwise linkage disequilibrium (LD) between SNPs was determined by r2 (Table 5). Pairwise LD was not calculated for the fourth gene (SFTPB) because one of the two markers was a multiallelic STR. There was low LD between the eight SNPs in EPHX1; the highest r2 was 0.47 for two exonic SNPs (Table 5A, SNPs 67). Three SNPs in LTBP4 (Table 5B, SNPs 13) formed a block of LD. The two promoter SNPs in TGFB1 (Table 5C, SNPs 12) were in tight LD; these were both in LD with the Leu10Pro coding SNP (SNP 3). The two 3' SNPs in TGFB1 (SNPs 45) were in strong LD. Haplotype analyses were performed as a secondary analysis to corroborate the results of the single SNP analyses. The haplotype results are available in the online supplement.
Family-based Analysis Associations with dyspnea were tested in 949 individuals from 127 extended pedigrees in the Boston Early-Onset COPD Study. The modified MRC dyspnea scale included in the study questionnaire ranged in value from 0 (no shortness of breath) to 5 (too breathless to leave the house or breathless on dressing or undressing) (14). Probands reported severe dyspnea, with a mean MRC score of 4.4. Using the extended pedigree family-based association test, one promoter SNP in TGFB1 was significantly associated with MRC score (rs2241712, p = 0.02); another promoter SNP showed a trend toward association (rs1800469, p = 0.07). Both of these SNPs had replicated associations with USCD SOBQ score in the NETT Genetics Ancillary Study subjects (Table 4C). Three other SNPs in TGFB1, eight SNPs in EPHX1, four SNPs in LTBP4, and one SNP and one STR in SFTPB were not associated with MRC dyspnea score in the Boston Early-Onset COPD families.
Using a well-characterized group of patients from NETT, we were able to demonstrate significant genetic associations for several COPD-related phenotypes. Polymorphisms in four genesEPHX1, LTBP4, SFTPB, and TGFB1were significantly associated with measures of functional capacity, including exercise capacity, pulmonary function tests, and respiratory symptoms. Many of the single SNP associations were confirmed in haplotype analyses. Spirometric traits have been analyzed previously as intermediate phenotypes in COPD genetics (2, 5, 6, 18). However, COPD genetics studies using measures of exercise tolerance and symptom severity have not been previously published.
Variants in EPHX1 were associated with traits in all three categories, including maximal work capacity on a cardiopulmonary exercise test, DLCO, and UCSD SOBQ score. SNPs in two genes in the TGF- Microsomal epoxide hydrolase is an enzyme important in the metabolism of reactive epoxide intermediates, such as those found in cigarette smoke. A coding variant in exon 3 (rs1051740, Tyr113His), termed the "slow" variant because of its effect on enzyme activity, has been associated with COPD in case-control studies (19, 20); in the Lung Health Study, a haplotype carrying the slow variant was associated with rapid decline in lung function (21). A coding variant in exon 4 (rs2234922, His139Arg), the "fast" variant, was associated with COPD diagnosis in a study comparing the subjects in the NETT Genetics Ancillary Study to community control subjects (6); the slow allele was not associated. However, other studies have failed to confirm the associations with either polymorphism (22, 23). The functional effects of the "fast" and "slow" variants and their haplotypes found in vitro (24) have not been confirmed in vivo (25). Therefore, it is possible that other variants in EPHX1 may affect COPD susceptibility, leading to the inconsistency in previous genetic association studies. TGFB1 is located on chromosome 19q, a region of the genome linked to COPD-related phenotypes (5). Wu and colleagues demonstrated an association between the Leu10Pro polymorphism (rs1982073) and COPD (26). Celedón and colleagues showed that the rs2241712 promoter polymorphism was associated with COPD and related traits in the Boston Early-Onset COPD Study families and in an analysis comparing the 304 NETT subjects to community control subjects (5). The other promoter SNP (rs1800469) and the Leu10Pro polymorphism were also associated with COPD susceptibility in this case-control analysis.
LTBP4 is a component of the extracellular matrix and is involved in TGF- SFTPB is a hydrophobic protein involved in regulating surface tension in the alveoli. Mutations in SFTPB have been implicated in respiratory failure in full-term neonates (28). Several studies have found variants in or near SFTPB to be associated with COPD in adults (29, 30). Our group has reported an association between a coding SNP (Thr131Ile) and airflow obstruction in the Boston Early-Onset COPD Study families (6); in a model that accounted for gene-by-environment interaction, this SNP was also associated in the case-control study that included the NETT subjects. The genes that we have found to be associated with COPD phenotypes can be placed into pathways that may relate to COPD pathogenesis. Pathways such as xenobiotic metabolism (EPHX1) (31), extracellular matrix properties (LTBP4) (32), and inflammation and cellular signaling (TGFB1) (33) have been areas of active investigation in COPD. The importance of surface tension (SFTPB) in COPD has not been widely studied, but a recent article describes mathematical models relating surface properties to the development of emphysema (34). The different genes associated in our study may underscore the heterogeneity of COPD. It is possible that different genes and pathways contribute in varying combinations to various COPD-related phenotypes. For example, we have found that SNPs in TGFB1 are associated with dyspnea but not with other functional measures in COPD, such as exercise capacity, despite the correlations between these traits. Narrower phenotype definitions and rational subgroup analyses may help to successfully identify and replicate associations for COPD candidate genes. The present study has several limitations. Replication of significant association results is an important step in complex trait genetics, but we only had measurements of one of the phenotypes, dyspnea, in a separate replication population. The instrument used to measure dyspnea in this replication study, the modified MRC scale, has a narrower range of possible results than the UCSD SOBQ score used in NETT. This may reduce the power for replication. Despite these limitations, we were able to replicate the association of TGFB1 with dyspnea. The other phenotypes analyzed, such as performance on a cardiopulmonary exercise test, are not routinely collected in studies of COPD genetics but may be collected in future clinical trials of COPD therapies, allowing for continued study of these functional impairment traits. Replication of these associations will be the strongest protection from spurious results due to multiple testing. A variable number of markers in each gene were genotyped in this study, with some genes having only one or two markers tested. If the markers tested were not the true functional variants (or in linkage disequilibrium with the functional variants), then significant associations could be missed. This may explain why three of our four most significant genes (EPHX1, LTBP4, and TGFB1) were genes with multiple genotyped SNPs. However, no significant associations were found for SERPINE2, which had the largest number of SNPs tested. Spurious results arising from multiple testing are a major concern in genetic epidemiology, especially in studies of multiple markers and phenotypes, such as our analysis. The optimal approach to adjust for multiple testing is not clear (35, 36). Many of the widely used methods are inappropriate for correlated data, such as multiple SNPs in a single gene or multiple related phenotypes. Therefore, we used a testreplication procedure within the NETT Genetics Ancillary Study cohort to reduce the possibility of false-positive results due to multiple testing, accepting that it may have reduced power to detect valid genetic associations. Based on power calculations in the online supplement, the power would be adequate to detect genes with moderate effects using the split dataset approach. However, we cannot exclude the possibility that some of the other candidate gene polymorphisms we studied may be associated with COPD-related phenotypes. Nevertheless, we were able to identify significant associations for four candidate genes with measures of functional impairment in COPD. Future studies using similarly specific COPD-related phenotypes may be able to identify additional genetic associations for COPD in general and for more precise subgroups in particular. In the future, narrowly defined subgroups, possibly based on genetic polymorphisms, may be better able to predict response to COPD therapies, including LVRS.
The authors thank Jody Sylvia, Salvatore Mazza, Michael Hager, Molly Brown, Alison Brown, and Maura Regan for their technical assistance with sample management and genotyping and Greg Foster for providing the SAS code to compute BODE index. Other coinvestigators in the NETT Genetics Ancillary Study include Marcia Katz, Rob McKenna, Malcolm DeCamp, Mark Ginsburg, Neil MacIntyre, Philip Diaz, Andrew Ries, Mark Krasna, Larry Kaiser, and Zab Mosenifar.
Supported by National Institutes of Health grants HL61575, HL71393, HL075478, K08-HL080242, and T32-HL07427 and by an American Lung Association Career Investigator Award. The National Emphysema Treatment Trial was supported by the U.S. National Heart, Lung, and Blood Institute (contracts N01HR76101, N01HR76102, N01HR76103, N01HR76104, N01HR76105, N01HR76106, N01HR76107, N01HR76108, N01HR76109, N01HR76110, N01HR76111, N01HR76112, N01HR76113, N01HR76114, N01HR76115, N01HR76116, N01HR76118, N01HR76119), the Centers for Medicare and Medicaid Services, and the Agency for Healthcare Research and Quality. This article has an online supplement, which is accessible from the issue's table of contents at www.atsjournals.org Originally Published in Press as DOI: 10.1164/rccm.200509-1452OC on February 2, 2006 Conflict of Interest Statement: C.P.H. does not have a financial relationship with a commercial entity that has an interest in the subject of this manuscript. D.L.D. does not have a financial relationship with a commercial entity that has an interest in the subject of this manuscript. R.L. does not have a financial relationship with a commercial entity that has an interest in the subject of this manuscript. J.C.C. does not have a financial relationship with a commercial entity that has an interest in the subject of this manuscript. B.A.R. does not have a financial relationship with a commercial entity that has an interest in the subject of this manuscript. J.O.B. received $2,500 and $3,500 in 2004 for speaking at conferences sponsored by Boehringer Ingelheim. G.C. does not have a financial relationship with a commercial entity that has an interest in the subject of this manuscript. B.M. does not have a financial relationship with a commercial entity that has an interest in the subject of this manuscript. F.J.M. does not have a financial relationship with a commercial entity that has an interest in the subject of this manuscript. P.D.S. received research funding during 20012005 from Boehringer Ingelheim, Dey Pharmaceuticals, GlaxoSmithKline, LaRoche, and ONO Pharmaceuticals. F.C.S. does not have a financial relationship with a commercial entity that has an interest in the subject of this manuscript. J.P.U. does not have a financial relationship with a commercial entity that has an interest in the subject of this manuscript. J.J.R. does not have a financial relationship with a commercial entity that has an interest in the subject of this manuscript. E.K.S. received grant support, consulting fees, and honoraria from GlaxoSmithKline for studies of COPD genetics. He also received a speaker fee from Wyeth for a talk on COPD genetics and has received honoraria from Bayer. Received in original form September 17, 2005; accepted in final form January 31, 2006
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