DNA methylation is associated with lung function in never smokers

Chronic Obstructive Pulmonary Disease (COPD) is a progressive inflammatory lung disease characterized by persistent airway obstruction that causes severe respiratory symptoms and poor quality of life [1]. Although smoking is generally considered the main environmental risk factor, estimations are that 25–45% of patients with COPD have never smoked [2]. Despite extensive research, the etiology of COPD remains incompletely understood. It is known that the development of this complex heterogeneous disease is influenced by both genetic and environmental factors, as well as their interactions [3‐6]. As interface between the inherited genome and environmental exposures, an important role has been postulated for the epigenome [7]. The epigenome includes multiple epigenetic mechanisms that affect gene expression without modifying the DNA sequence. These epigenetic mechanisms are highly dynamic and respond to environmental exposures, ageing and diseases [8]. One such epigenetic mechanism is DNA methylation, which involves the binding of a methyl group to a cytosine base located adjacent to a guanine base. Methylation of these so called CpG-sites in regulatory regions of the DNA generally result in decreased expression of a particular gene [9].

So far, only a few studies have investigated the association between DNA methylation in peripheral blood and COPD or lung function using an epigenome-wide hypothesis free approach [10‐17]. Although findings across the studies are not consistent, there is suggestive evidence that alterations in DNA methylation might play a role in the etiology of COPD. However, in previous studies, subjects were mainly included irrespective of smoking status, thus including current smokers, ex-smokers and never smokers. As a consequence, it is currently not known if there are differences in DNA methylation between healthy individuals and patients with COPD who have never smoked. Recently, we studied the association between epigenome-wide DNA methylation and COPD in both current smokers and never smokers [16]. Although we did not find any epigenome-wide significant association in current smokers nor in never smokers, the associations between DNA methylation and COPD were different between both groups. Hence, by further exploring the role of DNA methylation in a much larger set of never smokers together with a continuous measurement of lung function, we might be able to reveal important novel insights in the etiology of COPD. In this study, we aim to assess the association between DNA methylation and lung function in never smokers, meta-analyzing four independent population-based cohorts.

This study is the first large general population-based EWA study on lung function in never smokers. So far, virtually all EWA studies on the origin of COPD included subjects with a history of cigarette smoking. As a consequence, these studies mainly addressed the origins of COPD in response to smoking. It is unclear if the results of these studies help to explain the etiology of COPD or rather explain the contribution of cigarette smoke towards the disease. Therefore, our study importantly contributes to the current understanding of COPD in never smokers.

We identified 36 CpG-sites that were significantly associated with FEV₁/FVC at p-value below 0.0001. The top hit of our meta-analysis, cg10012512, is located in the intergenic region of chromosome 7q36.3. It is therefore not possible to speculate on the functional effect of differences in DNA methylation at this specific CpG-site and how these differences may affect FEV₁/FVC. While associations found with an eQTM analysis may help to get more insight in the function of a CpG-site, our eQTM analysis did not reveal any nominal significant associations for cg10012512. However, this CpG-site was differentially methylated between never smokers and current smokers [23]. Presumably, this CpG-site does also respond to other inhaled deleterious substances, which in turn affects lung function. The second top hit, cg02885771 located on chromosome 6q24.2 is annotated LTV1. Previously, this CpG-site has been associated with asthma in airway epithelial cells [24] and LTV1 was shown to be expressed in lung tissue in the Genotype Tissue Expression (GTEx) project. Although studies in yeast describe LTV1 as a conserved 40S-associated biogenesis factor that functions in small subunit nuclear export, a specific role for LTV1 in respiratory diseases is not known [25]. The third top hit, cg25105536, is annotated to KLHL32 on chromosome 6q16.1 and we found a significant association between DNA methylation levels of cg25105536 and gene expression levels of KLHL32. The function of KLHL32 is poorly understood, however, four genetic variants in the KLHL32 gene have been associated with FEV₁ and FEV₁/FVC in African American subjects with COPD and a history of smoking [26]. Notwithstanding the fact that these associations were only identified in a specific group, it might suggest a role for KLHL32 in the respiratory system. Next to KLHL32, we found that gene expression levels of 10 additional genes were significantly associated with DNA methylation levels at one of the 36 CpG-sites. cg08065963, which was not yet annotated to a gene, was significantly associated with 4-Aminobutyrate Aminotransferase (ABAT). Interestingly, a role for ABAT in COPD has not been described before. The remaining nine genes were other genes than the annotated genes of the particular CpG-sites. This suggest that the CpG-sites may also regulate distant genes within a region of 2 MB, which complicates the functional assessment of differences in DNA methylation even further.

To the best of our knowledge, there are eight studies in literature describing the association between DNA methylation and lung function (Table 4). Six of these studies included both subjects with and without a history of cigarette smoking and, except for the study by Qui et al., adjusted for smoking status in the statistical analysis. In addition, the recent study by Imboden et al. performed analyses with and without adjustment for smoking status and pack years. Altogether, these seven studies identified 462 unique CpG-sites. Interestingly, none of the 36 CpG-sites from our meta-analysis in never smokers were among these 462 previously identified CpG-sites (Table 5). Apparently these 36 CpG-sites are only associated with lung function level in never smokers. The fact that 17 CpG-sites (47%) were associated at nominal p-value < 0.05 with COPD (dichotomously defined as the ratio of FEV₁/FVC below 70%) in our previously EWAS stratified for never smoking, further underscores this assumption [16]. There is, however, one exception, since cg22742965, annotated to Transmembrane Protein With EGF Like And Two Follistatin Like Domains 2 (TMEFF2), was also significantly associated with COPD in smokers. Most likely, this CpG-site shows a general response to inhaled deleterious substances such as cigarette smoke and other yet unknown substances.

Assuming that the observed differential DNA methylation at the majority of the CpG-sites in our study occurs without exposure to smoking, the question arises why this differential DNA methylation is observed. One possible explanation may be that other factors within the environment such as air pollution and job-related exposures are responsible for the observed differences in DNA methylation. Recently, we studied the epigenome-wide association between DNA methylation and exposure to air pollution and job-related exposures in a selection of the LifeLines population cohort including both never and current smokers [19, 27]. While we did find significant associations, none of them were replicated in independent cohorts. Additional analyses in never smokers for this paper did not reveal novel associations between DNA methylation and environmental exposures (Additional file 4: Table S4 and Additional file 5: Figure S1). This might potentially be due to lack of power, since only a small percentage of the subjects that have never smoked in the LL COPD&C cohort have been exposed to environmental exposures. Moreover, exposure levels to air pollution in the LL COPD&C are relatively low compared to the average Dutch levels determined within the 2012 Dutch national health survey as described by Strak et al [28]. Next to environmental exposures, another explanation may be that a reduced lung function level precedes the differences in DNA methylation. However, with the cross-sectional design of this study, we cannot derive conclusions on the direction of the association and causality. Large longitudinal studies are required to investigate causality between DNA methylation and FEV₁/FVC. Moreover, this will give the opportunity to investigate if low levels of FEV₁ and decline in FEV₁ over the years is associated with DNA methylation in never smokers.

With this study we show that epigenetics indeed may be associated with FEV₁/FVC in subjects who never smoked. Moreover, since 35 out of the 36 identified CpG-sites are unique for never smokers, our data suggest that factors other than smoking affect FEV₁/FVC via DNA methylation.