Nasal DNA Methylation is Associated with Childhood Asthma

Abstract

Aim: We aim to study DNA methylation (DNAm) variations associated with childhood asthma. Methods: Nasal DNAm was compared between sibling pairs discordant for asthma, 29 sib pairs for genome-wide association studies and 54 sib pairs for verification by pyrosequencing. Associations of methylation with asthma symptoms, allergy and environmental exposures were evaluated. In vitro experiments and functional genomic analyses were performed to explore biologic relevance. Results: Three CpGs were associated with asthma. cg14830002 was associated with allergies in nonasthmatics. cg23602092 was associated with asthma symptoms. cg14830002 and cg23602092 were associated with traffic-related air pollution exposure. Nearby genes were transcriptionally regulated by diesel exhaust, house dust mite and 5-aza-2′-deoxycytidine. Active chromatin marks and transcription factor binding were found around these sites. Conclusion: We identified novel DNAm variations associated with childhood asthma and suggested new disease-contributing epigenetic mechanisms.

Keywords::

• air pollution
• childhood asthma
• DNA methylation
• exposures
• functional genomics analysis
• histone marks
• sibling study
• transcriptional factor

Supplementary data

To view the supplementary data that accompany this paper please visit the journal website at: www.tandfonline.com/doi/suppl/10.2217/epi-2017-0127

Authors’ contributions

H Ji conceived and designed the experiments in discussion with X Zhang and JM Biagini Myers, performed pathway analysis; X Zhang performed Illumina bead array analysis and statistical analysis in discussion with H Ji; JD Burleson processed samples, performed locus-specific bisulfite pyrosequencing to measure DNAm and RT-qPCR to measure gene expression; JD Burleson, A Ulm and KS Bryan recruited children under the supervision of H Ji and JM Biagini Myers, managed Redcap database and performed sample processing; X Chen and MT Weirauch performed SNP annotation for 450K arrays and functional genomics analyses; MS Butsch Kovacic supported early study design and recruitment of unrelated, nonasthmatics in an underserved community; TA Baker supported recruitment of unrelated study participants from the underserved community; H Ji prepared the manuscript with the assistance of X Zhang, JM Biagini Myers, MT Weirauch and MS Butsch Kovacic. All authors read and approved the final version of manuscript before submission.

Financial & competing interests disclosure

This work was supported by NIH/NIAID Grant R21AI119236 (H Ji), NIH/NIAID Grant R21AI101375 (H Ji), NIH/NIEHS under Grant P30-ES006096 (H Ji), ALA/AAAAI Respiratory Diseases Research Award 515708 (H Ji), Cincinnati Children’s Hospital ‘Center for Pediatric Genomics’ pilot study award (H Ji), NIEHS award P30ES006096 (H Ji and M Butsch Kovacic), CCHMC SFDA award (JM Biagini Myers), CCHMC CReFF Award (JM Biagini Myers), NIH/NINDS Grant R01NS099068 (MT Weirauch) and NIH/NHGRI Grant R21HG008186 (MT Weirauch). REDCap was hosted at Cincinnati Children’s and supported by the Center for Clinical and Translational Science and Training grant UL1-RR026314–01 NCRR/NIH. Patient recruitment and sample processing was supported in part by the National Center for Advancing Translational Sciences of the NIH Grant UL1 TR001425. Accoring to NIH policy, the manuscript will be deposited on the NIHMS system/PMC. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.

Acknowledgements

We thank the participating families and staff from the ESS and SHS studies, as well as the Genomics, Epigenomics and Sequencing Core at the University of Cincinnati for array processing and the Cincinnati Children’s Pyrosequencing Core Laboratory for Genomic and Epigenomic Research for assistance in pyrosequencing. We also thank the Cincinnati Children’s Clinical and Translational Research Center for assistance in patient recruitment and sample collection. Finally, we thank the Seven Hills Neighborhood Houses Community Center in Cincinnati’s West End neighborhood for partnering with us to recruit unrelated, nonasthmatic pediatric participants for our study.

Ethical conduct of research

Studies included in this manuscript were approved by the Institutional Review Board at Cincinnati Children’s Hospital Medical Center (CCHMC).

Additional information

Funding

This work was supported by NIH/NIAID Grant R21AI119236 (H Ji), NIH/NIAID Grant R21AI101375 (H Ji), NIH/NIEHS under Grant P30-ES006096 (H Ji), ALA/AAAAI Respiratory Diseases Research Award 515708 (H Ji), Cincinnati Children’s Hospital ‘Center for Pediatric Genomics’ pilot study award (H Ji), NIEHS award P30ES006096 (H Ji and M Butsch Kovacic), CCHMC SFDA award (JM Biagini Myers), CCHMC CReFF Award (JM Biagini Myers), NIH/NINDS Grant R01NS099068 (MT Weirauch) and NIH/NHGRI Grant R21HG008186 (MT Weirauch). REDCap was hosted at Cincinnati Children’s and supported by the Center for Clinical and Translational Science and Training grant UL1-RR026314–01 NCRR/NIH. Patient recruitment and sample processing was supported in part by the National Center for Advancing Translational Sciences of the NIH Grant UL1 TR001425. Accoring to NIH policy, the manuscript will be deposited on the NIHMS system/PMC. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. No writing assistance was utilized in the production of this manuscript.