Epigenome-wide DNA methylation changes with development of arsenic-induced skin lesions in Bangladesh: a case-control follow-up study

Abstract

Studies have found an association between aberrant DNA methylation and arsenic-induced skin lesions. However, little is known about DNA methylation changes over time in people who develop arsenic-induced skin lesions. We sought to investigate epigenome-wide changes of DNA methylation in people who developed arsenic-induced skin lesions in a 10-year period. In 2009-2011, we conducted a follow-up study of 900 skin lesion cases and 900 controls and identified 10 people who developed skin lesions since a baseline survey in 2001-2003. The 10 cases ("New Cases") were matched with 10 controls who did not have skin lesions at baseline or follow-up ("Persistent Controls"). Drinking water and blood samples were collected, and skin lesion was diagnosed by the same physician at both time points. We measured DNA methylation in blood using Infinium HumanMethylation450K BeadChip, followed by quantitative validation using pyrosequencing. Two-sample t-tests were used to compare changes in percent methylation between New Cases and Persistent Controls. Six CpG (cytosine-phosphate-guanine) sites with greatest changes of DNA methylation over time among New Cases were further validated with a correlation of 93% using pyrosequencing. One of the validated CpG site (cg03333116; change of %methylation was 13.2 in New Cases versus -0.09 in Persistent Controls; P < 0.001) belonged to the RHBDF1 gene, which was previously reported to be hypermethylated in arsenic-exposed cases. We examined DNA methylation changes with the development of arsenic-induced skin lesions over time but nothing was statistically significant given the small sample size of this exploratory study and the high dimensionality of data.

Keywords: DNA methylation; arsenic; illumina 450K; longitudinal; skin lesion.

Figure 1

Boxplots of %methylation change between baseline and follow-up for top 6 CpG sites in New Cases (red) and Persistent Controls (blue) Boxplots of %methylation change between baseline and follow-up were plotted for the top 6 CpG sites (on genes TCEB3B, MYO3B, CDH4, RHBDF1, ESRRG, and PRDM9) that are significantly different between New Cases and Persistent Controls. Red denotes New Cases and blue denotes Persistent Controls.