Cadmium exposure and the epigenome: Exposure-associated patterns of DNA methylation in leukocytes from mother-baby pairs

Abstract

Cadmium (Cd) is prevalent in the environment yet understudied as a developmental toxicant. Cd partially crosses the placental barrier from mother to fetus and is linked to detrimental effects in newborns. Here we examine the relationship between levels of Cd during pregnancy and 5-methylcytosine (5mC) levels in leukocyte DNA collected from 17 mother-newborn pairs. The methylation of cytosines is an epigenetic mechanism known to impact transcriptional signaling and influence health endpoints. A methylated cytosine-guanine (CpG) island recovery assay was used to assess over 4.6 million sites spanning 16,421 CpG islands. Exposure to Cd was classified for each mother-newborn pair according to maternal blood levels and compared with levels of cotinine. Subsets of genes were identified that showed altered DNA methylation levels in their promoter regions in fetal DNA associated with levels of Cd (n = 61), cotinine (n = 366), or both (n = 30). Likewise, in maternal DNA, differentially methylated genes were identified that were associated with Cd (n = 92) or cotinine (n = 134) levels. While the gene sets were largely distinct between maternal and fetal DNA, functional similarities at the biological pathway level were identified including an enrichment of genes that encode for proteins that control transcriptional regulation and apoptosis. Furthermore, conserved DNA motifs with sequence similarity to specific transcription factor binding sites were identified within the CpG islands of the gene sets. This study provides evidence for distinct patterns of DNA methylation or "footprints" in fetal and maternal DNA associated with exposure to Cd.

Keywords: cadmium; cigarette smoke; cord blood; epigenetics; heavy metal; maternal blood; methylation; pregnancy.

Figure 1. Heat map of genes with differential DNA methylation levels in fetal and maternal DNA associated with Cd (A), or cotinine (B). Venn diagram representing the total number of Cd-or cotinine-associated genes in fetal DNA (C) or maternal DNA (D). Heat maps represent average DNA methylation levels of exposure-associated gene sets. Data are z-score normalized for each gene. Individuals are ordered from left to right based on increasing level of exposure. Red indicates a relative increase in average DNA methylation and blue represents a relative decrease in average DNA methylation. In the Venn diagrams, the number in parentheses indicates the number of hypomethylated genes contained in each set. LE, lower exposed; HE, higher exposed; UE, unexposed; E, exposed.

Figure 2. Significantly enriched DNA motifs identified within the Cd and cotinine-associated gene lists in fetal DNA (A) and maternal DNA (B) as identified by MEME. The motifs shown have standard orientation 5′ to 3′. Estimates of sequence conservation at each nucleotide position within the motif are shown where a higher bit score is represented by increased font size.