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RESEARCH ARTICLE

DNA Methylation Profiles of Airway Epithelial Cells and PBMCs from Healthy, Atopic and Asthmatic Children

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• Methods
• Results
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Dorota Stefanowicz¹, Tillie-Louise Hackett^1,2, Farshid S. Garmaroudi¹, Oliver P. Günther³, Sarah Neumann⁴, Erika N. Sutanto^5,7, Kak-Ming Ling⁷, Michael S. Kobor⁴, Anthony Kicic^5,6,7, Stephen M. Stick^5,6,7, Peter D. Paré^1,8, Darryl A. Knight^1,2*

1 James Hogg Research Centre at the Heart and Lung Institute, Department of Medicine, University of British Columbia and St. Paul’s Hospital, Vancouver, British Columbia, Canada, 2 Department of Anesthesiology, Pharmacology and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada,3 Prevention of Organ Failure Centre of Excellence, Vancouver, British Columbia, Canada, 4 Department of Medical Genetics Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada, 5 Department of Respiratory Medicine, Princess Margaret Hospital for Children, Perth, Western Australia, Australia, 6 School of Paediatrics and Child Health, University of Western Australia, Nedlands, Western Australia, Australia, 7 Telethon Institute for Child Health Research and Centre for Child Health Research, University of Western Australia, Nedlands, Western Australia, Australia, 8 Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada

Abstract Top

Background

Allergic inflammation is commonly observed in a number of conditions that are associated with atopy including asthma, eczema and rhinitis. However, the genetic, environmental or epigenetic factors involved in these conditions are likely to be different. Epigenetic modifications, such as DNA methylation, can be influenced by the environment and result in changes to gene expression.

Objectives

To characterize the DNA methylation pattern of airway epithelial cells (AECs) compared to peripheral blood mononuclear cells (PBMCs) and to discern differences in methylation within each cell type amongst healthy, atopic and asthmatic subjects.

Methods

PBMCs and AECs from bronchial brushings were obtained from children undergoing elective surgery for non-respiratory conditions. The children were categorized as atopic, atopic asthmatic, non-atopic asthmatic or healthy controls. Extracted DNA was bisulfite treated and 1505 CpG loci across 807 genes were analyzed using the Illumina GoldenGate Methylation Cancer Panel I. Gene expression for a subset of genes was performed using RT-PCR.

Results

We demonstrate a signature set of CpG sites that are differentially methylated in AECs as compared to PBMCs regardless of disease phenotype. Of these, 13 CpG sites were specific to healthy controls, 8 sites were only found in atopics, and 6 CpGs were unique to asthmatics. We found no differences in the methylation status of PBMCs between disease phenotypes. In AECs derived from asthmatics compared to atopics, 8 differentially methylated sites were identified including CpGs in STAT5A and CRIP1. We demonstrate STAT5A gene expression is decreased whereas CRIP1 gene expression is elevated in the AECs from asthmatic compared to both healthy and atopic subjects.

Discussion

We characterized a cell specific DNA methylation signature for AECs compared to PBMCs regardless of asthmatic or atopic status. Our data highlight the importance of understanding DNA methylation in the epithelium when studying the epithelial contribution to asthma.