Please use this identifier to cite or link to this item: http://hdl.handle.net/1946/11873
Epigenetic studies are commonly conducted on DNA from tissue samples. However, tissues are ensembles of cells that may each have their own epigenetic profile and therefore inter-individual difference in cellular heterogeneity may compromise these studies. In work presented here, the potential for such confounding on DNA methylation measurement outcomes when using DNA from whole blood was explored. DNA methylation was measured using pyrosequencing based methodology in two white blood cell fractions, isolated using density gradient centrifugation. In three out of four regions tested, significant differential DNA methylation between the two fractions was detected. The difference was very moderate in all but one region where the average absolute methylation difference per CpG site ranged between 3.4-15.7 percentage points. In this same region, inter-individual variation in cellular heterogeneity explained up to 36% (p<0.0001) of the variation in
measured whole blood DNA methylation levels. In the examined regions, methylation levels were highly correlated between cell fractions. In summary, the analysis detects region-specific differential DNA methylation between white blood cell sub-types, which can confound the outcome of whole blood
DNA methylation measurements. Finally, by demonstrating the high correlation between methylation levels in cell fractions, the results suggest a possibility to use a proportional number of a single white blood cell type to correct for this confounding effect in analyses.
Type 2 diabetes mellitus (T2DM) is a complex disease (i.e., multifactorial and polygenic) characterized by high blood glucose levels due to reduced insulin sensitivity and β-cell function. Heritable as well as lifestyle and environmental factors contribute to risk of development of the disease. Despite recent advances in identifying T2DM genetic risk variants, a large proportion of the disease’s heritable component remains unidentified. One potential explanation is the existence of inherited epigenetic aberration(s) that contribute to the disease. Additionally, it is possible that the effects of environmental and lifestyle factors are mediated through induced epigenetic aberration(s). On this basis, it was hypothesized that aberrant DNAm could be associated with T2DM, and to
address this hypothesis, the second study presented here aimed to identify such aberrations. DNA methylation levels were measured using pyrosequencing based methodology in whole blood DNA. DNA methylation levels were compared between individuals with and without T2DM in seven regions, located in three loci previously associated with T2DM through genetic studies. A single region located in an intragenic CpG island in the HHEX gene was selected for further study, and comparing DNAm levels between 214 cases and 164 controls, lower average DNAm levels were observed in individuals with T2DM. Further, the difference was significant after correction for cellular heterogeneity, age and
gender, and was not carried by an association with obesity. These results support the hypothesis that DNAm aberrations may be associated with T2DM.