Abstract
Rationale Infection with respiratory syncytial virus (RSV) in early-life is associated with subsequent childhood respiratory disorders, but the mechanism for this association is unknown. We hypothesized that RSV-mediated alteration in airway DNA methylation (DNAm) may play a role.
Objectives Investigate the impact of early-life RSV infection on airway DNAm.
Methods Our study population consisted of children from the INSPIRE population-based birth cohort. Early-life infection with RSV was defined as infection not requiring clinical illness before age one year, ascertained through active and passive surveillance. Methylation was measured in DNA from nasal airway epithelial cells (NAECs) at ages two years (n=88) and six years (n=539). Bulk gene expression in NAECs was available in a subset of participants at age two years (n=54). In silico cell type deconvolution was used to infer cell type-specific associations in suprabasal, ciliated, and “other” cell types.
Measurements and Main Results We identified 164 CpGs in ciliated cells and seven CpGs in suprabasal cells whose cell type-specific DNAm at age two years was associated with early-life RSV infection. The seven associations in suprabasal cells were still present at age six years and the directions of association replicated in in vitro infection of epithelial cells with RSV in air liquid interface cultures. DNAm levels at four of the seven CpGs identified in suprabasal cells correlated with the expression of their nearest genes in suprabasal cells, which included genes previously implicated in asthma-related diseases. The DNAm levels of these four CpGs and the expression of their nearest genes in suprabasal cells at age two years were also associated with recurrent wheezing at age four years.
Conclusions We demonstrate epigenetic changes in airway progenitor cells of children who have had RSV infection in the first year of life are conserved over time, associated with subsequent wheeze, have functional relevance, and replicate in in vitro infection in ALI cultures. Our study is the first to show that early-life RSV infection, as opposed to severe illness, alters DNAm levels at functionally and clinically relevant loci.
Competing Interest Statement
Dr. McKennan reported grants from NIH during the conduct of the study and personal fees from SignatureDx outside the submitted work. Dr. Bacharier reported grants from NIH/National Institute of Allergy and Infectious Diseases (NIAID) during the conduct of the study and personal fees from GlaxoSmithKline, Genentech/Novartis, Merck, DBV Technologies, Teva, Boehringer Ingelheim, AstraZeneca, Sanofi/Regenerol. Dr. Gern reported grants from NIH during the conduct of the study, personal fees from AstraZeneca and Meissa Vaccines Inc., and stock options for Meissa Vaccines Inc. outside the submitted work. Dr. Hartert reported grants from NIH and the World Health Organization during the conduct of the study and personal fees from the American Thoracic Society, the NIH, Parker B. Francis Foundation, Pfizer and Sanofi-Pasteur outside the submitted work.