Exposure to Phthalate, an Endocrine Disrupting Chemical, Alters the First Trimester Placental Methylome and Transcriptome in Women

Abstract

Phthalates are known endocrine disruptors and associated with decreased fecundity, pregnancy loss, and adverse obstetrical outcomes, however the underlying mechanisms remain to be established. Environmental factors can influence gene expression and cell function by modifying epigenetic marks, impacting the developing embryo as well as future generations of offspring. The impact of phthalates on placental gene methylation and expression is largely unknown. We studied the effect of maternal phthalate exposure on the human placental DNA methylome and transcriptome. We determined epigenome-wide DNA methylation marks (Illumina Infinium Human Methylation 850k BeadChip) and gene expression (Agilent whole human genome array) associated with phthalate exposure in first trimester placenta. Integrative genomic analysis of candidate genes was performed to define gene methylation-expression relationships. We identified 39 genes with significantly altered methylation and gene expression in the high phthalate exposure group. Most of these relationships were inversely correlated. This analysis identified epidermal growth factor receptor (EGFR) as a critical candidate gene mediating the effects of phthalates on early placental function. Although additional studies are needed to determine the functional consequences of these changes, our findings are consistent with the model that phthalates impact placental function by modulating the expression of critical placental genes through epigenetic regulation.

Figure 1

(A) Study Design. (B) Histogram of total phthalate urinary metabolites in study cohort.

Figure 2

(A) Manhattan plot for the DMP analysis. The red line represents the p-value threshold of 0.005 applied to get our candidate list. All CpG probes that lie above this line are considered significant. (B) Ven diagram illustrating the overlap of differentially methylated probes (DMP) and differentially methylated region (DMR) analysis.

Figure 3

(A) Network evaluation resulting from pathway analysis of methylation-gene expression analysis. (B) Correlation between methylation and expression for EGFR. The EGFR expression by EGFR methylation levels are plotted. The methylation is represented as Beta-value from the cg15074403 probe while the expression value is represented by probeset A_23_P215790. The Pearson correlation between this expression probeset and the cg15074403 M-value is −0.83 (p-value = 0.00076). Subjects with high phthalate exposure are shown in red, while those with low exposure are shown in blue.

Figure 4

Location of CpG probes in EGFR. The colors of the probes reflect the significance and range from bright red (p-value < 0.005) to black (p-value = 0.99). A heatmap of the Pearson correlation values are shown below and the colors reflect the correlation coefficient with blue representing a coefficient of −1 and red a coefficient of 1.