Prenatal mercury concentration is associated with changes in DNA methylation at TCEANC2 in newborns

Abstract

Background: Human exposure to the widespread environmental contaminant mercury is a known risk factor for common diseases such as cancer, cardiovascular disease and neurological disorders through poorly characterized mechanisms. Evidence suggests mercury exposure may alter DNA methylation levels, but to date, the effects in early life on a genome-wide scale have not been investigated.

Methods: A study sample of 141 newborns was recruited in Baltimore, MD, USA and total mercury and methylmercury were measured in cord blood samples. We quantified genome-wide DNA methylation data using CHARM 2.0, an array-based method, and used region-finding analyses to identify concentration-associated differentially methylated regions (DMRs). To test for replication of these identified DMRs in the pilot, or Vanguard, phase of the National Children's Study (NCS), we compared bisulfite-pyrosequenced DNA at candidate regions from 85 whole cord blood samples with matched first trimester maternal mercury concentration measures.

Results: Total mercury concentration was associated with methylation at DMRs inside ANGPT2 and near PRPF18 genes [false discovery rate (FDR) < 0.05], as well as DMRs near FOXD2 and within TCEANC2 (FDR< 0.1) genes. Methylmercury concentration was associated with an overlapping DMR within TCEANC2 (FDR< 0.05). In NCS replication analyses, methylation levels at three of four cytosine-guanine DNA dinucleotides (CpG sites) within the TCEANC2 DMR were associated with total mercury concentration (P < 0.05), and this association was diminished after adjusting for estimated cell proportions.

Conclusions: Evidence for an association between mercury and DNA methylation at the TCEANC2 region was found, which may represent a mercury-associated shift in cord blood cell composition or a change in methylation within blood cell types. Further confirmatory studies are needed.

Keywords: DNA methylation; cord blood; epigenetics; mercury exposure; methylmercury.

Figure 1.

In the THREE study sample, DNA methylation within the TCEANC2 gene was associated with (a) total mercury and (b) methylmercury concentration in µg/l measured in cord blood. Each dot represents the methylation values at each probe for each sample. The smoothed line represents the average methylation curve for each concentration quartile, and demonstrates a dose-dependent inverse association for both total and methylmercury. The black vertical dashed lines define the boundary of the differentially methylated region. The line in the third panel of the plot represents the CpG density in the genomic region. The gray bracket indicates sites assayed in the replication cohort. Quartiles of total mercury are: Q1: [0.233-1.03), Q2: [1.030-1.42), Q3: [1.42-1.99), Q4: [1.99-6.3). Quartiles of methylmercury are: Q1: [0.0849-0.64), Q2: [0.64-0.94), Q3: [0.94-1.69), Q4: [1.69-6.8).

Figure 2.

DNA methylation via bisulfite pyrosequencing in the TCEANC2 gene is associated with total mercury (a) and methylmercury (b) concentration in the NCS replication sample.