Genome-wide neonatal epigenetic changes associated with maternal exposure to the COVID-19 pandemic

Abstract

Background: During gestation, stressors to the fetus, including viral exposure or maternal psychological distress, can fundamentally alter the neonatal epigenome, and may be associated with long-term impaired developmental outcomes. The impact of in utero exposure to the COVID-19 pandemic on the newborn epigenome has yet to be described.

Methods: This study aimed to determine whether there are unique epigenetic signatures in newborns who experienced otherwise healthy pregnancies that occurred during the COVID-19 pandemic (Project RESCUE). The pre-pandemic control and pandemic cohorts (Project RESCUE) included in this study are part of a prospective observational and longitudinal cohort study that evaluates the impact of elevated prenatal maternal stress during the COVID-19 pandemic on early childhood neurodevelopment. Using buccal swabs collected at birth, differential DNA methylation analysis was performed using the Infinium MethylationEPIC arrays and linear regression analysis. Pathway analysis and gene ontology enrichment were performed on resultant gene lists.

Results: Widespread differential methylation was found between neonates exposed in utero to the pandemic and pre-pandemic neonates. In contrast, there were no apparent epigenetic differences associated with maternal COVID-19 infection during pregnancy. Differential methylation was observed among genomic sites that underpin important neurological pathways that have been previously reported in the literature to be differentially methylated because of prenatal stress, such as NR3C1.

Conclusions: The present study reveals potential associations between exposure to the COVID-19 pandemic during pregnancy and subsequent changes in the newborn epigenome. While this finding warrants further investigation, it is a point that should be considered in any study assessing newborn DNA methylation studies obtained during this period, even in otherwise healthy pregnancies.

Keywords: COVID-19 pandemic; DNA methylation; Epigenetics; Perinatal stress; SARS-CoV-2.

Fig. 1

DNA methylation differences associated with newborns exposed to the COVID-19 pandemic in utero. A Dendrogram representation of unsupervised hierarchical clustering of normalized and batch-corrected beta values of pre-pandemic controls (CTL, yellow), RES pandemic COVID-19-negative pregnancies (solid pink), and RES COVID-19-positive pregnancies (hatched pink). Timing of approximate start of gestation is indicated at the bottom: light blue, entirety of pregnancy occurred prior to start of the pandemic (December 2019); dark blue; gestation that started September 2019-February 2020, prior to the onset of the COVID-19 pandemic; medium blue, gestation started between March and May 2020, after the US declared a national disaster. B Principal component analysis (PCA) of global DNA methylation differences of normalized and batch-corrected beta values between newborns exposed to the COVID-19 pandemic during pregnancy (RES, n = 32, triangles) and pre-pandemic healthy controls (CTL, n = 12, circles). Subcategorization by maternal COVID-19 infection status during pregnancy is denoted by color: coral indicates COVID-19 negative pregnancies (n = 17), green indicates COVID-19 positive pregnancies (n = 15), and blue indicates pre-pandemic pregnancies, unexposed to COVID-19 (n = 12). C Heatmap of unsupervised, hierarchical clustering of the differentially methylated probes identified between pre-pandemic CTL and RES pandemic newborns. Z-score scale represents transformed intensity values between differentially methylated probes with red being a negative z-score, white being a z-score of 0, and blue a positive z-score. The grid below the heatmap represents various clinical metrics, including timing of pregnancy (same color code as in 1A), COVID-19 infection status and severity of disease, and prenatal maternal mental health questionnaire data (STAI-S, STAI-T, PSS, PTSD), keyed in the legend to the right of the heatmap. Each column represents a sample, while rows represent specific probes that are differentially methylated between RES and CTL after performing linear regression analysis (FDR p-value ≤ 0.05, log₂ fold-change threshold ≥ 1 or ≤ -1). D IPA analysis of annotated differentially methylated probes between CTL and RES cohort. Z-score scale was calculated from differential intensity values and red and blue shades indicate pathways with a negative or positive z-score, respectively. White indicates pathways with a z-score of 0 (genes in the pathway are differentially methylated, some positively, some negatively, resulting in a Z-score = 0). Absolute log(p-value) represents statistical significance for the identified pathway to be associated with the imported list of annotated probes

Fig. 2

Answers to maternal mental health screening questionnaires. Maternal psychological distress was surveyed longitudinally throughout pregnancy and postnatally using the following surveys: A) STAI-S, B) STAI-T, C) PSS, and D) IESR (for RES only). Pie charts depict percentages of each cohort reporting high (red), moderate (orange), or low (green) stress or anxiety as well as presence (“yes”, red) or absence (“no”, green) of PTSD for the RES cohort only. E Example of PCA of DNA methylation intensity differences (non-significant) for maternal mental health (PSS) data. Maternal mental health data in tandem with DNA methylation data can be found PCAs can be found in Supplemental Figure S2