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Airway epithelial cell isolation techniques affect DNA methylation profiles with consequences for analysis of asthma related perturbations to DNA methylation

Clifford, Rachel L.; Patel, Jamie; MacIsaac, Julia L.; McEwen, Lisa M.; Johnson, Simon R.; Shaw, Dominick; Knox, Alan J.; Hackett, Tillie-Louise; Kobor, Michael S.

Authors

Jamie Patel

Julia L. MacIsaac

Lisa M. McEwen

SIMON JOHNSON simon.johnson@nottingham.ac.uk
Professor of Respiratory Medicine

Alan J. Knox

Tillie-Louise Hackett

Michael S. Kobor



Abstract

The airway epithelium forms the interface between the inhaled environment and the lung. The airway epithelium is dysfunctional in asthma and epigenetic mechanisms are considered a contributory factor. We hypothesised that the DNA methylation profiles of cultured primary airway epithelial cells (AECs) would differ between cells isolated from individuals with asthma (n = 17) versus those without asthma (n = 16). AECs were isolated from patients by two different isolation techniques; pronase digestion (9 non-asthmatic, 8 asthmatic) and bronchial brushings (7 non-asthmatic and 9 asthmatic). DNA methylation was assessed using an Illumina Infinium HumanMethylation450 BeadChip array. DNA methylation of AECs clustered by isolation technique and linear regression identified 111 CpG sites differentially methylated between isolation techniques in healthy individuals. As a consequence, the effect of asthmatic status on DNA methylation was assessed within AEC samples isolated using the same technique. In pronase isolated AECs, 15 DNA regions were differentially methylated between asthmatics and non-asthmatics. In bronchial brush isolated AECs, 849 differentially methylated DNA regions were identified with no overlap to pronase regions. In conclusion, regardless of cell isolation technique, differential DNA methylation was associated with asthmatic status in AECs, providing further evidence for aberrant DNA methylation as a signature of epithelial dysfunction in asthma.

Citation

Clifford, R. L., Patel, J., MacIsaac, J. L., McEwen, L. M., Johnson, S. R., Shaw, D., …Kobor, M. S. (2019). Airway epithelial cell isolation techniques affect DNA methylation profiles with consequences for analysis of asthma related perturbations to DNA methylation. Scientific Reports, 9(1), 1-12. https://doi.org/10.1038/s41598-019-50873-y

Journal Article Type Article
Acceptance Date Sep 15, 2019
Online Publication Date Oct 8, 2019
Publication Date 2019-12
Deposit Date Oct 16, 2019
Publicly Available Date Oct 29, 2019
Journal Scientific Reports
Print ISSN 2045-2322
Electronic ISSN 2045-2322
Publisher Nature Publishing Group
Peer Reviewed Peer Reviewed
Volume 9
Issue 1
Article Number 14409
Pages 1-12
DOI https://doi.org/10.1038/s41598-019-50873-y
Public URL https://nottingham-repository.worktribe.com/output/2846925
Publisher URL https://www.nature.com/articles/s41598-019-50873-y

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