Smoking-Altered DNA Methylation in Alveolar Macrophages Correlates with Gene Expression

Abstract

Rationale: Cigarette smoking is a leading cause of both emphysema and lung cancer, yet the mechanism of how smoking drives disease is unclear. Alveolar macrophages are key players in the development of smoking-related diseases. One important, but little studied, regulator of macrophage function is epigenetic modification of gene expression. Methods: Smokers with and without emphysema, and nonsmokers, underwent bronchoscopy with bronchoalveolar lavage to obtain alveolar macrophages. DNA and RNA were isolated using the Qiagen DNeasy kit (Qiagen, Valencia, CA) and MirVana kit (Life Technologies, Grand Island, NY) methods, respectively. Genome-wide methylation status of the samples was determined using Illumina Infinium 27K HumanMethylation array (Illumina, San Diego, CA). Macrophage mRNA expression was analyzed using GeneChip Human Exon 1.0 ST Arrays (Affymetrix, Santa Clara, CA). Results: The distribution of methylation in these probes differed significantly with respect to smoking status. There is enrichment of differential methylation in genes from inflammatory pathways. Consistent with recent findings, significant methylation changes were particularly enriched in the areas flanking CpG islands. Analysis of matching gene expression data demonstrated a parallel enrichment for changes in inflammatory pathways. Conclusion: The alveolar macrophage data obtained from smokers, patients with emphysema, and nonsmokers demonstrates methylation changes that track with smoke exposure. The affected genes cluster in inflammation-linked pathways, and a significant number of the genes with differential methylation also have altered gene expression. This discovery suggests that epigenetic modification of alveolar macrophages contributes to smoking-related lung disease.