Maternal SARS-CoV-2 exposure alters infant DNA methylation

Abstract

Background: Infection during pregnancy can increase the risk of neurodevelopmental disorders in offspring. The impact of maternal SARS-CoV-2 infection on infant neurodevelopment is poorly understood. The maternal immune response to infection may be mimicked in rodent models of maternal immune activation which recapitulate altered neurodevelopment and behavioural disturbances in the offspring. In these models, epigenetic mechanisms, in particular DNA methylation, are one pathway through which this risk is conferred in utero to offspring. We hypothesised that in utero exposure to SARS-CoV-2 in humans may alter infant DNA methylation, particularly in genes associated with neurodevelopment. We aimed to test this hypothesis in a pilot sample of children in Victoria, Australia, who were exposed in utero to SARS-CoV-2.

Methods: DNA was extracted from buccal swab specimens from (n = 4) SARS-CoV-2 in utero exposed and (n = 4) non-exposed infants and methylation status assessed across 850,000 methylation sites using an Illumina EPIC BeadChip. We also conducted an exploratory enrichment analysis using Gene Ontology annotations.

Results: 1962 hypermethylated CpG sites were identified with an unadjusted p-value of 0.05, where 1133 CpGs mapped to 959 unique protein coding genes, and 716 hypomethylated CpG sites mapped to 559 unique protein coding genes in SARS-CoV-2 exposed infants compared to non-exposed. One differentially methylated position (cg06758191), located in the gene body of AFAP1 that was hypomethylated in the SARS-CoV-2 exposed cohort was significant after correction for multiple testing (FDR-adjusted p-value <0.00083). Two significant differentially methylated regions were identified; a hypomethylated intergenic region located in chromosome 6p proximal to the genes ZP57 and HLA-F (fwer <0.004), and a hypomethylated region in the promoter and body of the gene GAREM2 (fwer <0.036). Gene network enrichment analysis revealed differential methylation in genes corresponding to pathways relevant to neurodevelopment, including the ERBB pathway.

Conclusion: These pilot data suggest that exposure to SARS-CoV-2 in utero differentially alters methylation of genes in pathways that play a role in human neurodevelopment.

Keywords: DNA methylation; In utero; Maternal; Neurodevelopment; SARS-CoV-2.

Fig. 1

– (A) Volcano plot of differential methylation analysis with the x axis displaying log fold-change (log fc) and the y axis displaying the log10 of p values for each CpG site. CpGs with relative hypermethylation (- log fc) in SARS-CoV-2 exposed cohort and relative hypomethylation ( + log fc) are represented by blue and red dots respectively. Grey dots represent CpGs below the FDR = 0.05 threshold. Probe cg06758191, corresponding to the gene AFAP1 remained significant after multiple correction. (p < 1.13e-09, log fc = 0.3736) (B) Gene concept network maps depicting the linkages of genes that contained CpG sites which were hypermethylated in the SARS-CoV-2 exposed cohort and (C) hypomethylated in the SARS-CoV-2 exposed cohort and their biological concepts deriving from annotated GO terms as a network. The legend on the right depicts the central categories or GO terms grouping the various genes. Genes at the junction of different colour coded lines are those that play a role across multiple biological concepts or GO terms. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)