Epigenome-wide meta-analysis of blood DNA methylation in newborns and children identifies numerous loci related to gestational age
Authors: Merid Simon Kebede , Novoloaca Alexei , Sharp Gemma C. , Küpers Leanne K. , Kho Alvin T. , Roy Ritu , Gao Lu , Annesi-Maesano Isabella , Jain Pooja , Plusquin Michelle , Kogevinas Manolis , Allard Catherine , Vehmeijer Florianne O. , Kazmi Nabila , Salas Lucas A. , Rezwan Faisal I. , Zhang Hongmei , Sebert Sylvain , Czamara Darina , Rifas-Shiman Sheryl L. , Melton Phillip E. , Lawlor Debbie A. , Pershagen Göran , Breton Carrie V. , Huen Karen , Baiz Nour , Gagliardi Luigi , Nawrot Tim S. , Corpeleijn Eva , Perron Patrice , Duijts Liesbeth , Nohr Ellen Aagaard , Bustamante Mariona , Ewart Susan L. , Karmaus Wilfried , Zhao Shanshan , Page Christian M. , Herceg Zdenko , Jarvelin Marjo-Riitta , Lahti Jari , Baccarelli Andrea A. , Anderson Denise , Kachroo Priyadarshini , Relton Caroline L. , Bergström Anna , Eskenazi Brenda , Soomro Munawar Hussain , Vineis Paolo , Snieder Harold , Bouchard Luigi , Jaddoe Vincent W. , Sørensen Thorkild I. A. , Vrijheid Martine , Arshad S. Hasan , Holloway John W. , Håberg Siri E. , Magnus Per , Dwyer Terence , Binder Elisabeth B. , DeMeo Dawn L. , Vonk Judith M. , Newnham John , Tantisira Kelan G. , Kull Inger , Wiemels Joseph L. , Heude Barbara , Sunyer Jordi , Nystad Wenche , Munthe-Kaas Monica C. , Räikkönen Katri , Oken Emily , Huang Rae-Chi , Weiss Scott T. , Antó Josep Maria , Bousquet Jean , Kumar Ashish , Söderhäll Cilla , Almqvist Catarina , Cardenas Andres , Gruzieva Olena , Xu Cheng-Jian , Reese Sarah E. , Kere Juha , Brodin Petter , Solomon Olivia , Wielscher Matthias , Holland Nina , Ghantous Akram , Hivert Marie-France , Felix Janine F. , Koppelman Gerard H. , London Stephanie J. , Melén Erik 
Published: March 2020

Background

Preterm birth and shorter duration of pregnancy are associated with increased morbidity in neonatal and later life. As the epigenome is known to have an important role during fetal development, we investigated associations between gestational age and blood DNA methylation in children.

Methods

We performed meta-analysis of Illumina’s HumanMethylation450-array associations between gestational age and cord blood DNA methylation in 3648 newborns from 17 cohorts without common pregnancy complications, induced delivery or caesarean section. We also explored associations of gestational age with DNA methylation measured at 4–18 years in additional pediatric cohorts. Follow-up analyses of DNA methylation and gene expression correlations were performed in cord blood. DNA methylation profiles were also explored in tissues relevant for gestational age health effects: fetal brain and lung.

Results

We identified 8899 CpGs in cord blood that were associated with gestational age (range 27–42 weeks), at Bonferroni significance, P < 1.06 × 10− 7, of which 3343 were novel. These were annotated to 4966 genes. After restricting findings to at least three significant adjacent CpGs, we identified 1276 CpGs annotated to 325 genes. Results were generally consistent when analyses were restricted to term births. Cord blood findings tended not to persist into childhood and adolescence. Pathway analyses identified enrichment for biological processes critical to embryonic development. Follow-up of identified genes showed correlations between gestational age and DNA methylation levels in fetal brain and lung tissue, as well as correlation with expression levels.

Conclusions

We identified numerous CpGs differentially methylated in relation to gestational age at birth that appear to reflect fetal developmental processes across tissues. These findings may contribute to understanding mechanisms linking gestational age to health effects.