Global methylation profiles in DNA from different blood cell types

Abstract

DNA methylation measured in white blood cell DNA is increasingly being used as in studies of cancer susceptibility. However, little is known about the correlation between different assays to measure global methylation and whether the source of DNA matters when examining methylation profiles in different blood cell types. Using information from 620 women, 217 and 403 women with DNA available from granulocytes (Gran), and total white blood cells (WBC), respectively, and 48 women with DNA available from four different sources (WBC, Gran, mononuclear (MN), and lymphoblastoid cell lines (LCL)), we compared DNA methylation for three repetitive elements (LINE1, Sat2, Alu) by MethyLight, luminometric methylation assay (LUMA), and [³H]-methyl acceptance assay. For four of the five assays, DNA methylation levels measured in Gran were not correlated with methylation in LBC, MN, or WBC; the exception was Sat2. DNA methylation in LCL was correlated with methylation in MN and WBC for the [³H]-methyl acceptance, LINE1, and Alu assays. Methylation in MN was correlated with methylation in WBC for the [³H]-methyl acceptance and LUMA assays. When we compared the five assays to each other by source of DNA, we observed statistically significant positive correlations ranging from 0.3-0.7 for each cell type with one exception (Sat2 and Alu in MN). . Among the 620 women stratified by DNA source, correlations among assays were highest for the three repetitive elements (range 0.39-0.64). Results from the LUMA assay were modestly correlated with LINE1 (0.18-0.20). These results suggest that both assay and source of DNA are critical components in the interpretation of global DNA methylation patterns from WBC.

Acknowledgements

This work was supported by an award from the Breast Cancer Research Foundation and NIH grants U01 CA69398, P30 CA13696 and P30 ES009089. This work was also supported by the National Cancer Institute, National Institutes of Health under RFA # CA-06-503 and through cooperative agreements with members of the Breast Cancer Family Registry (CFR) and Principal Investigators. The content of this manuscript does not necessarily reflect the views or policies of the National Cancer Institute or any of the collaborating centers in the CFR, nor does mention of trade names, commercial products or organizations imply endorsement by the US Government or the CFR.

Figures and Tables

Figure 1 Box plot of within-person DNA methylation levels using the methyl acceptance, MethyLight and LUMA assays by source of DNA.

Table 1 Within-person Spearman correlation coefficients for global DNA methylation measured using the [³H]methyl acceptance assay and LUMA by source of DNA (n = 48)

Table 2 Within-person correlation of global methylation measured with the MethyLight assay by source of DNA and assay (N = 48)

Table 3 Within-person spearman correlation coefficients for markers of global methylation measured with the [³H]methyl acceptance, LUMA and MethyLight assays by source of DNA (N = 48)

Table 4 Spearman correlation coefficients for markers of global methylation measured with the [³H] methyl acceptance, LUMA and MethyLight assays by source of DNA