Newborn blood DNA methylation and childhood asthma: findings from the ECHO program

Abstract

Background: DNA methylation (DNAm) at birth has been linked to childhood asthma in epigenome-wide association studies (EWASs). However, existing EWASs have limited representation of non-European and extremely preterm participants and have not explored sex-specific DNAm differences. This study examined the association between DNAm in newborn blood and subsequent childhood asthma risk in a diverse population.

Methods: Data from the Environmental influences on Child Health Outcomes (ECHO) Program were used for EWAS meta-analyses in United States (US) cohorts of children born before and after 28 weeks of gestation. DNAm was measured in newborn blood using Illumina arrays. Childhood asthma was defined as provider-diagnosed asthma with persistent symptoms beyond age 5. Linear regression was used to identify differentially methylated positions (DMPs), and "comb-p" was used to identify differentially methylated regions (DMRs). Sex-stratified analyses were performed.

Results: The meta-analysis included 942 children (369 asthma cases) born after 28 weeks of gestation. We identified a novel DMP (cg24749470 in CADM1, P = 9.31 × 10-8) and 18 DMRs (Šidák P-value <.001) associated with asthma, with four DMRs in the human leukocyte antigen region. At these four DMRs, the association between DNAm and asthma differed by sex. In the extremely preterm cohort (n = 271, 106 asthma cases), we identified 20 DMRs, with two novel asthma-associated DMPs (cg03237868 in SPATA18, P = 2.71 × 10-8; cg20681219 in IRF2, P = 5.18 × 10-8) identified in males.

Conclusion: In US children born before and after 28 weeks of gestation, we discovered novel genomic loci linking newborn blood DNAm to childhood asthma, suggesting DNAm involvement in early asthma development.

Keywords: DNA methylation; childhood asthma; epigenome-wide association study; newborn blood.

Figure 1.

Sex-specific association between newborn DNA methylation (DNAm) level and childhood asthma at selected differentially methylated regions (DMRs) (6p21–6p22 locus) in participants born after 28 weeks of gestation. The two DMRs were selected as examples to visually demonstrate the difference in the association between DNAm and asthma between males and females. (A) The chr6:33 048 254–33 048 879 (HLA-DPB1) region. (B) The chr6: 30 039 132–30 039 801 (RNF39) region. The DMRs were identified by the comb-p method based on the sex-stratified meta-analysis results from four ECHO cohorts. The bottom panels show the effect size (%DNAm difference) for the association between DNAm (beta-value) at individual CpGs in the DMRs (highlighted by the rectangle shade in the background) and asthma among males and females, respectively. A %DNAm difference greater than 0 (pink area) represents hypermethylation in asthma cases compared with non-cases; a %DNAm difference less than 0 (blue area) represents hypomethylation in asthma cases compared with non-cases. Gene annotations were obtained from the UCSC Genome Browser (GRCh37/hg19). Abbreviations: DHS = DNase I hypersensitive sites; ECHO = Environmental Influences on Child Health Outcomes; TFBS = transcription factor binding site; UCSC = University of California, Santa Cruz, Genome Browser.

Figure 2.

Association between newborn DNA methylation (DNAm) level and childhood asthma at selected differentially methylated regions (DMRs) in participants born before 28 weeks of gestation. The two DMRs were selected as examples for visual demonstration. (A) The chr1: 223 566 447–223 567 002 (CCDC185) region. (B) The chr1: 153 599 479–153 600 064 (S100A13) region. The DMRs were identified by the comb-p method based on the EWAS analysis of all participants in the ELGAN cohort. The bottom panels show the effect size (%DNAm difference) for the association between DNAm (beta-value) at individual CpGs in the DMRs (highlighted by the rectangle shade in the background) and asthma. A %DNAm difference greater than 0 (pink area) represents hypermethylation in asthma cases compared with non-cases; a %DNAm difference less than 0 (blue area) represents hypomethylation in asthma cases compared with non-cases. Gene annotations were obtained from the UCSC Genome Browser (GRCh37/hg19). Abbreviations: DHS = DNase I hypersensitive sites; ECHO = Environmental Influences on Child Health Outcomes; ELGAN = Extremely Low Gestational Age Newborns; EWAS = epigenome-wide association study; TFBS = transcription factor binding site; UCSC = University of California, Santa Cruz, Genome Browser.