Analysis of epigenetic changes in survivors of preterm birth reveals the effect of gestational age and evidence for a long term legacy

Abstract

BackgroundPreterm birth confers a high risk of adverse long term health outcomes for survivors, yet the underlying molecular mechanisms are unclear. We hypothesized that effects of preterm birth can be mediated through measurable epigenomic changes throughout development. We therefore used a longitudinal birth cohort to measure the epigenetic mark of DNA methylation at birth and 18 years comparing survivors of extremely preterm birth with infants born at term.MethodsUsing 12 extreme preterm birth cases and 12 matched, term controls, we extracted DNA from archived neonatal blood spots and blood collected in a similar way at 18 years of age. DNA methylation was measured at 347,789 autosomal locations throughout the genome using Infinium HM450 arrays. Representative methylation differences were confirmed by Sequenom MassArray EpiTYPER.ResultsAt birth we found 1,555 sites with significant differences in methylation between term and preterm babies. At 18 years of age, these differences had largely resolved, suggesting that DNA methylation differences at birth are mainly driven by factors relating to gestational age, such as cell composition and/or maturity. Using matched longitudinal samples, we found evidence for an epigenetic legacy associated with preterm birth, identifying persistent methylation differences at ten genomic loci. Longitudinal comparisons of DNA methylation at birth and 18 years uncovered a significant overlap between sites that were differentially-methylated at birth and those that changed with age. However, we note that overlapping sites may either differ in the same (300/1,555) or opposite (431/1,555) direction during gestation and aging respectively.ConclusionsWe present evidence for widespread methylation differences between extreme preterm and term infants at birth that are largely resolved by 18 years of age. These results are consistent with methylation changes associated with blood cell development, cellular composition, immune induction and age at these time points. Finally, we identified ten probes significantly associated with preterm individuals and with greater than 5% methylation discordance at birth and 18 years that may reflect a long term epigenetic legacy of preterm birth.

DNA methylation provides insight into intergenerational risk for preterm birth in African Americans

“…Cruickshank and colleagues performed one such study in 12 PTB cases and 12 matched controls. 28 They evaluated DNA methylation from blood at birth and at 18 years and observed substantial overlap with the PTB-associated CpGs we reported at birth. DNA methylation differences observed at birth were no longer associated with PTB status at 18 years for the majority of CpG sites examined, but they report 10 CpGs that continue to differ in methylation at both time points, suggesting the potential for a long-term epigenetic signature of PTB.…”

“…17,[22][23][24] Few studies have evaluated the epigenetics of PTB, and those that have focus mostly on those born preterm. [25][26][27][28] Other studies focus on the short-term and long-term consequences of PTB for the neonate, 1,[29][30][31][32] in part, because of interest in the developmental origin of health and disease (DOHaD) hypothesis. 32,33 We recently evaluated DNA methylation in leukocytes from African American umbilical cord blood samples and identified thousands of DNA methylation differences between preterm and term fetuses.…”

Human active X-specific DNA methylation events showing stability across time and tissues

“…Samples and the Infinium HM450 data set used in this study largely overlap with our published studies on preterm birth 15 and our longitudinal DNA methylation changes in twins. 16 Buccal samples used in this study were selected based on the availability of the materials and array data quality.…”

Prematurity and programming of cardiovascular disease risk: a future challenge for public health?

“…Altered DNA methylation has been in adulthood in term-born individuals in association with exposure to an adverse prenatal nutritional environment,67 68 and changes in DNA methylation have been reported in ex-preterm individuals in adulthood 69. Whether these differences are identifiable at birth is unclear; a recent epigenome-wide study using DNA extracted from stored neonatal blood spots and blood from the same individuals at age 18 years identified differences in DNA methylation profiles between preterm and term individuals at birth but found that these largely resolved by adulthood, presumably reflecting immaturity in the preterm group 70. Nevertheless, some loci were identified which showed differential methylation at birth and at age 18, suggesting that such changes might potentially be useful as biomarkers of disease risk 70…”