DNA Methylation Profiling in a Cigarette Smoke-Exposed Mouse Model of Airway Inflammation

Abstract

Ping Li,1,* Junjie Peng,1,* Guangxi Chen,1,2,* Fangying Chen,1,3 Yongchun Shen,1 Lin Liu,4 Lei Chen1 1Laboratory of Pulmonary Diseases and Department of Respiratory and Critical Care Medicine, West China Hospital, West China School of Medicine, Sichuan University, Chengdu, People’s Republic of China; 2Department of Sleep Medicine, Jiujiang First People’s Hospital, Jiujiang, People’s Republic of China; 3Department of Tuberculosis, the Third People’s Hospital of Tibet Autonomous Region, Lhasa, People’s Republic of China; 4Department of Respiratory and Critical Care Medicine, 363 Hospital, Chengdu, People’s Republic of China*These authors contributed equally to this workCorrespondence: Lei Chen, Department of Respiratory and Critical Care Medicine, West China Hospital, West China School of Medicine, Sichuan University, Chengdu, People’s Republic of China, Email [email protected] Lin Liu, Department of Respiratory and Critical Care Medicine, 363 Hospital, Chengdu, People’s Republic of China, Email [email protected]: DNA methylation, a major epigenetic modification, has been documented to play an important role in chronic obstructive pulmonary disease (COPD). In this study, we aimed to profile the DNA methylation patterns in a mouse model of airway inflammation induced by cigarette smoke (CS), a foremost risk factor of COPD.Material and Methods: To establish a model of airway inflammation, wild-type mice were exposed to mainstream CS or room air for 2 hours twice daily, 6 days per week for consecutive 4 weeks. Lung tissues of the mice were collected for genome-wide DNA methylation analysis by liquid hybridization capture-based bisulfite sequencing, which were used for intersection analysis with gene expression by cDNA microarray to identify candidate methylated genes. Then, functional enrichment analyses with protein–protein interaction (PPI) network regarding these genes were conducted to explore the potential mechanisms.Results: After 4-week CS exposure, the level of DNA methylation accompanied by a subacute airway inflammation was markedly enhanced, and 2002 differentially methylated genes (DMGs) were annotated, including 565 DMGs contained methylations in gene promoters, which were used for intersection with the differentially expressed genes. Then, 135 candidate methylated genes were further selected by the intersection, among which 58 genes with functional methylated modification were finally identified. Further analyses revealed candidate methylated genes were significantly enriched in a complicated network of signals and processes, including interleukins, toll-like receptors, T-cells differentiation, oxidative stress, mast cells activation, stem cells proliferation, etc., as well as the 58 functional methylated genes were partially located at key positions in PPI network, especially CXCL1, DDX58 and JAK3.Conclusion: This study suggests CS exposure significantly enhances DNA methylated level, and the potential functional methylated genes are closely related to complicated inflammatory-immune responses, which may provide some new experimental evidence in understanding the epigenetic mechanisms of CS-induced airway inflammation in COPD.Keywords: chronic obstructive pulmonary disease, airway inflammation, cigarette smoke, DNA methylation, liquid hybridization capture-based bisulfite sequencing

Keywords

• chronic obstructive pulmonary disease
• airway inflammation
• cigarette smoke
• dna methylation
• liquid hybridization capture-based bisulfite sequencing