Interaction of prenatal maternal smoking, interleukin 13 genetic variants and DNA methylation influencing airflow and airway reactivity
© Patil et al.; licensee BioMed Central Ltd. 2013
Received: 25 June 2013
Accepted: 1 November 2013
Published: 6 December 2013
Asthma is characterized by airflow limitation and airway reactivity (AR). Interleukin-13 (IL-13) is involved in the pathogenesis of asthma. Two functional SNPs, rs20541 and rs1800925, of the IL-13 gene (IL13) have been frequently associated with asthma-related lung functions. However, genetic variation alone does not fully explain asthma risk. DNA-methylation (DNA-M) is an epigenetic mechanism that regulates gene expression and can be influenced by both environment and genetic variants. To explore the interplay of prenatal maternal smoking, genetic variants and DNA-M, we used a two-stage model: (1) identifying cytosine phosphate guanine (CpG) sites where DNA-M is influenced by the interaction between genetic variants and maternal smoking during pregnancy (conditional methQTL (methylation quantitative trait loci)); and (2) determining the effect of the interaction between DNA-M of CpG (from stage 1) and SNPs (modifying genetic variants; modGV) on airflow limitation and AR in 245 female participants of the Isle of Wight birth cohort. DNA-M was assessed using the Illumina Infinium HumanMethylation450 BeadChip.
Six CpG sites were analyzed in stage 1. DNA-M at cg13566430 was influenced by interaction of maternal smoking during pregnancy and rs20541. In stage 2, genotype at rs1800925 interacted with DNA-M at cg13566430 significantly affecting airflow limitation (P = 0.042) and AR (P = 0.01).
Both genetic variants and environment affect DNA-M. This study supports the proposed two-stage model (methQTL and modGV) to study genetic variants, environment and DNA-M interactions in asthma-related lung function.
KeywordsAsthma genetics and epigenetics Airway reactivity DNA methylation IL13 gene Lung functions Maternal smoking during pregnancy
Asthma is a chronic airway disease characterized by airflow limitation and airway reactivity (AR) and exhibits wide heterogeneity in disease susceptibly and phenotypes. Multiple genes, gene-gene and gene-environment interactions have been shown to play a role in determining susceptibility to asthma and associated phenotypes of lung function and AR. Maternal smoking during pregnancy is a significant risk factor for developing asthma in offspring  and can affect offspring lung function . Interleukin-13 (IL-13) is a recognized effector in airway inflammation, reactivity and remodeling. IL13 is located on chromosome 5q31, and has been consistently associated with asthma [3, 4]. Several functional genetic variants occur in IL13 including rs1800925 (−1112C/T) and rs20541 (R130Q, +2044A/G). Recent meta-analyses have shown that both SNPs are associated with asthma risk [5, 6] and with forced expiratory volume in 1 second (FEV1) and FEV1/forced vital capacity (FVC) in asthmatics [7, 8]. In severe asthma, monoclonal antibody to IL-13 use is associated with improvement in lung function in humans  and airway hyper-responsiveness in a murine model .
Study population and assessments
The Isle of Wight birth cohort (n = 1,456) was established in 1989 and has been followed up through childhood. At 18 years of age, spirometry and bronchial challenge tests were done according to American Thoracic Society guidelines [17, 18]. We analyzed lung function measurements and DNA-M data of 245 females aged 18 years who were randomly selected from the cohort population for epigenetic studies. Comparison of the analyzed sample with whole cohort females in terms of risk factors have been described elsewhere . A continuous measure of AR (dose response slope (DRS)) was used. DRS is the gradient of FEV1 drop from baseline with each successive incremental dose of methacholine administered. A transformation of Log10 (DRS + 10) was required to satisfy the distributional assumption of normal data. A higher positive value of this transformation signifies greater AR. A description of the 18-year follow-up of the cohort is previously reported .
Genotyping and SNP selection
DNA was isolated from peripheral blood leucocytes collected at age 18. IL13 polymorphisms were genotyped as described by Sadeghnejad and colleagues . Two known functional SNPs, rs1800925 (n = 234) and rs20541 (n = 235), frequently associated with asthma and related lung functions were used in this analysis. These SNPs were not in linkage disequilibrium in this cohort as described elsewhere .
One microgram of DNA was bisulfite-treated using the EZ 96-DNA-methylation kit (Zymo Research, Irvine, CA, USA), following the manufacturer’s protocol. Genome-wide DNA- M was assessed using the Illumina Infinium-HumanMethylation450 BeadChip (Illumina, Inc., Hayward, CA, USA) as described previously .
The pre-processed DNA-M beta (β) values, presented as the proportion of intensity of methylated (M) over the sum of methylated (M) and unmethylated (U) sites (β = M/[c + M + U] with c being a constant to prevent dividing by zero), were used to estimate the effect of DNA-M . The R-package IMA in Bioconductor (IMA is implemented in the R language and is freely available from http://www.rforge.net/IMA) was used for the pre-processing . SNP genotype-dependent methylation was analyzed using the Kruskal-Wallis test. Interaction was tested using multiple linear regressions. Statistical analyses were performed using IBM SPSS Statistics, Version-19.0 (IBM SPSS Statistics for Windows, Version 19.0. Armonk, NY, USA: IBM Corp,). The statistical significance was set at 0.05.
Location, position and description of rs1800925, rs20541 and CpG sites on the promoter region of IL13 gene
5′ Promoter upstream
Percentiles (5%, 95%)
Interaction of methylation at cg13566430 and rs1800925 genotypes on FEV 1 /FVC and DRS
−0.166 to 0.517
−2.361 to 1.226
−0.024 to 0.064
−0.278 to 0.129
−0.014 to 0.026
−0.076 to 0.149
−0.019 to 0.079
0.045 to 0.554
−0.021 to 0.019
−0.134 to 0.083
−0.855 to 0.030
1.194 to 6.785
−0.296 to 0.028
−0.733 to 0.982
−0.301 to 0.648
−1.926 to 3.174
0.114 to 6.434
−48.283 to −6.710
−0.114 to 1.712
−5.661 to 4.043
This study tested a two-stage model for integrating the interactions of maternal smoking during pregnancy, genetic variants and DNA-M for an asthma candidate gene IL13. We show that interaction of a functional IL13 SNP, rs20541, and maternal smoking during pregnancy influenced DNA-M at cg13566430. We also show that DNA-M at cg13566430 interacts with genotype of another functional SNP, rs1800925, to affect airflow limitation and AR. Michel and colleagues  examined the effect of farm exposure on DNA-M of ten asthma candidate genes and found that DNA-M at one IL13 site (spanning rs1800925; similar to the site in our study) was more methylated in the exposed group compared to the non-exposed group. They did not see significant differential methylation of IL13 between asthmatic and non-asthmatic children but asthma-related traits were not tested and also the interaction with genetic variants was not examined. Our approach identifies the effect of environmental exposure and genetic variants on DNA-M and then also combines the interaction of other modifiable genetic variants with DNA-M on the outcomes. We show genotype-dependent DNA-M in the IL13 promoter region; methylation at cg13566430 revealed variation in levels dependent on the genotype of rs1800925, as seen in other genes . This varying distribution of DNA-M across genotypes supports the plausible role for DNA-M in the pathway between genotype and phenotype.
There are some limitations to this study. While DNA-M measurement using Illumina Infinium-HumanMethylation450 arrays has been shown to have reproducibility and high validity , technical replication of the DNA-M measurements has not been undertaken. We have not measured DNA-M in airway tissue; however, the major source of IL-13 production in the airways is inflammatory cells, and methylation measurements in peripheral blood are likely to better reflect asthma-related immune mechanisms. Cell composition in the peripheral blood can influence DNA-M; however, cell composition alone cannot explain the differential methylation observed . Focusing only on female participants is a limitation; however, the results should be encouraging for further studies to replicate the model. The interaction effects seen may not imply a direct relationship between genotype and altered methylation. Genotype may also alter other epigenetic processes such as chromatin remodeling and this may then lead to altered DNA-M.
The effect of environment, genotype and DNA-M was seen for two different, but equally important and objective, characteristics of asthma: airflow limitation and AR. Similar to Michel and colleagues  we did not see an effect on asthma as an outcome (results not shown); however, the observed effect on asthma-related objective measures avoids plausible bias of reported asthma. Methylation of the promoter region can regulate gene transcription  and we have shown that promoter region methylation is dependent on genotype, and the interplay of the environment, genotype and DNA-M influence the phenotype.
While requiring replication in an independent cohort, the results show the interplay of prenatal maternal smoking, genetic variants and DNA-M of IL13 influencing asthma-related lung function. This highlights the need to consider environment, genotype and DNA-M together when seeking to understand the pathogenesis of complex disease, as DNA-M plays a role of integrator of multiple disease pathway signals.
Cytosine phosphate guanine
Dose response slope
Forced expiratory volume in 1 second
Forced vital capacity
Methylation, quantitative trait loci
Modifiable genetic variant
Single nucleotide polymorphism.
We would like to thank all the participants of the Isle of Wight birth cohort, Dr A Raza and the research team at David Hide Asthma & Allergy Research Centre, Isle of Wight, for collecting the data and Nikki Graham for technical support. We thank the High-Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics (funded by Wellcome Trust grant reference 090532/Z/09/Z and MRC Hub grant G0900747 91070) for the generation of the methylation data.
The epigenetic investigation was supported by National Institutes of Health, USA (R01-AI091905, R01-AI061471, and R21-AI099367). The 18-year assessment of the 1989 Isle of Wight birth cohort was funded by grants from the National Institutes of Health, USA (R01-HL082925) and National Eczema Society/British Dermatological Nursing Group Research Awards.
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