DNA methylation patterns at birth predict health outcomes in young adults born very low birthweight

Abstract

Background: Individuals born very low birthweight (VLBW) are at increased risk of impaired cardiovascular and respiratory function in adulthood. To identify markers to predict future risk for VLBW individuals, we analyzed DNA methylation at birth and at 28 years in the New Zealand (NZ) VLBW cohort (all infants born < 1500 g in NZ in 1986) compared with age-matched, normal birthweight controls. Associations between neonatal methylation and cardiac structure and function (echocardiography), vascular function and respiratory outcomes at age 28 years were documented.

Results: Genomic DNA from archived newborn heel-prick blood (n = 109 VLBW, 51 controls) and from peripheral blood at ~ 28 years (n = 215 VLBW, 96 controls) was analyzed on Illumina Infinium MethylationEPIC 850 K arrays. Following quality assurance and normalization, methylation levels were compared between VLBW cases and controls at both ages by linear regression, with genome-wide significance set to p < 0.05 adjusted for false discovery rate (FDR, Benjamini-Hochberg). In neonates, methylation at over 16,400 CpG methylation sites differed between VLBW cases and controls and the canonical pathway most enriched for these CpGs was Cardiac Hypertrophy Signaling (p = 3.44E^-11). The top 20 CpGs that differed most between VLBW cases and controls featured clusters in ARID3A, SPATA33, and PLCH1 and these 3 genes, along with MCF2L, TRBJ2-1 and SRC, led the list of 15,000 differentially methylated regions (DMRs) reaching FDR-adj significance. Fifteen of the 20 top CpGs in the neonate EWAS showed associations between methylation at birth and adult cardiovascular traits (particularly LnRHI). In 28-year-old adults, twelve CpGs differed between VLBW cases and controls at FDR-adjusted significance, including hypermethylation in EBF4 (four CpGs), CFI and UNC119B and hypomethylation at three CpGs in HIF3A and one in KCNQ1. DNA methylation GrimAge scores at 28 years were significantly greater in VLBW cases versus controls and weakly associated with cardiovascular traits. Four CpGs were identified where methylation differed between VLBW cases and controls in both neonates and adults, three reversing directions with age (two CpGs in EBF4, one in SNAI1 were hypomethylated in neonates, hypermethylated in adults). Of these, cg16426670 in EBF4 at birth showed associations with several cardiovascular traits in adults.

Conclusions: These findings suggest that methylation patterns in VLBW neonates may be informative about future adult cardiovascular and respiratory outcomes and have value in guiding early preventative care to improve adult health.

Keywords: Birthweight; Cardiovascular; DNA methylation; Epigenetics; Risk prediction.

Fig. 1

Manhattan Plot of differentially methylated CpGs between VLBW cases and normal birthweight controls in neonatal blood-spot samples (red is hyper-, green is hypomethylated in VLBW cases). Red dotted line indicates FDR-adjusted genome-wide significance p < 0.05. Blue arrows indicate the 20 most significant CpGs, with nearest gene name

Fig. 2

Manhattan plot of CpGs differentially methylated between VLBW cases and normal birthweight controls in samples collected at 28 years of age. The red dotted line indicates the threshold for significance (FDR-adjusted p < 0.05), with blue arrows and gene names indicating the 12 CpGs that reached significance (red is hyper-, green is hypomethylated in VLBW cases)

Fig. 3

Comparison of Canonical Pathways enriched with CpGs differentially methylated between VLBW cases and controls either in neonates or adults, arranged by hierarchical clustering