Genome-wide DNA methylation at birth in relation to in utero arsenic exposure and the associated health in later life

Abstract

Background: In utero arsenic exposure may alter fetal developmental programming by altering DNA methylation, which may result in a higher risk of disease in later life. We evaluated the association between in utero arsenic exposure and DNA methylation (DNAm) in cord blood and its influence in later life.

Methods: Genome-wide DNA methylation in cord blood from 64 subjects in the Taiwanese maternal infant and birth cohort was analyzed. Robust regressions were applied to assess the association of DNA methylation with in utero arsenic exposure. Multiple testing was adjusted by controlling false discovery rate (FDR) of 0.05. The DAVID bioinformatics tool was implemented for functional annotation analyses on the detected CpGs. The identified CpGs were further tested in an independent cohort. For the CpGs replicated in the independent cohort, linear mixed models were applied to assess the association of DNA methylation with low-density lipoprotein (LDL) at different ages (2, 5, 8, 11 and 14 years).

Results: In total, 579 out of 385,183 CpGs were identified after adjusting for multiple testing (FDR = 0.05), of which ~60% were positively associated with arsenic exposure. Functional annotation analysis on these CpGs detected 17 KEGG pathways (FDR = 0.05) including pathways for cardiovascular diseases (CVD) and diabetes mellitus. In the independent cohort, about 46% (252 out of 553 CpGs) of the identified CpGs showed associations consistent with those in the study cohort. In total, 11 CpGs replicated in the independent cohort were in the pathways related to CVD and diabetes mellitus. Via longitudinal analyses, we found at 5 out of the 11 CpGs methylation was associated with LDL over time and interactions between DNA methylation and time were observed at 4 of the 5 CpGs, cg25189764 (coeff = 0.157, p-value = 0.047), cg04986899 (coeff. For interaction [coeff.int] = 0.030, p-value = 0.024), cg04903360 (coeff.int = 0.026, p-value = 0.032), cg08198265 (coeff.int = -0.063, p-value = 0.0021), cg10473311 (coeff.int = -0.021, p-value = 0.027).

Conclusion: In utero arsenic exposure was associated with cord blood DNA methylation at various CpGs. The identified CpGs may help determine pathological epigenetic mechanisms linked to in utero arsenic exposure. Five CpGs (cg25189764, cg04986899, cg04903360, cg08198265 and cg10473311) may serve as epigenetic markers for changes in LDL later in life.

Keywords: Arsenic; CpG; DAVID; DNA methylation; Genome-wide; KEGG pathway; Ldl.

Fig. 1

The flow of analyses performed in the study

Fig. 2

Manhattan plot for Genome-wide DNA methylation associated with creatinine adjusted urinary arsenic concentration. The horizontal dashed blue line corresponds to the significance threshold p = 7.51E-05 (FDR Adjusted p-value <= 0.05), red color stars represent the CpG sites corresponding to genes enriched in KEGG pathways from DAVID analysis (see Additional file 7: Table S3). Blue and golden colors are used to differentiate the chromosomes

Fig. 3

Association of arsenic exposure with the DNA methylation based on M-values of the 58 CpG sites mapped to 56 genes. The x-axis has the 56 genes enriched in KEGG pathways at FDR level of p = 0.05, while the y-axis shows the estimates of total arsenic coefficients related to 58 CpG sites from robust regression. Adjusting factors include cell counts, child’s sex, batch effect, mother’s age, mother’s BMI and mother’s education level. M-values are defined as log2 [β/(1-β)]. Different colors indicate the location of the CpGs on a gene

Fig. 4

Heatmap of the correlations between cord blood DNA methylation and LDL across different ages (2, 5, 8, 11, 14 years)