Differential Methylation Variability between Atherogenic and Normal Human Aortas, and its Association with Mitochondrial Function

Abstract

IntroductionPrevious data obtained by our group suggest that an association between DNA methylation and mitochondrial function exists. However, traditional epigenomics studies based solely on the extent of DNA methylation differences, found little association between DNA methylation and mitochondrial processes in human atherosclerosis, despite the clear association of the latter disease with aberrant DNA methylation and defective mitochondrial function. Therefore, in the present study we employ a novel statistical approach, consisting in filtering CpGs by differential variability (DV). This method has been successfully used in studies of obesity and type 1 diabetes.ObjectiveThe aim of this study is to assess whether nuclear DNA methylation variability is associated with mitochondrial DNA copy number (mtDNAcn) – a proxy of mitochondrial activity ‐ in human atherosclerosis.MethodsWe exploited Infinium Human Methylation 450K BeadChip‐based data previously generated by our group in a cohort of 15 donor‐matched atherosclerotic and normal aorta pairs. The IEVORA algorithm ‐ a FDR‐corrected Bartlett test regularized by a t‐test ‐ was used to assess differential variability (DV). mtDNAcn was determined by PCR in 9 aortic pairs, and PCR products were quantified with SYBR Green. Mann U Whitney test was used to compare mtDNAcn values. The Pearson correlation analysis between mtDNAcn and DNA methylation was used in both healthy and diseased tissues independently. Functional annotation analysis was performed with the software WebGestalt.ResultsWe identified 6,469 differentially variable CpGs (DV‐CpGs; FDR<0.05), 71% of which were intragenic. Notably, the vast majority (95%) of DV‐CpGs showed larger variance in the atherosclerotic portion of the aorta, compared to the normal counterpart. Functional annotation analysis revealed enrichment (FDR<0.05) in adipocytokine, MAPK and cAMP signaling. Notably, those pathways are involved in mitochondrial function. mtDNAcn was significantly higher in healthy aortas compared to the atherosclerotic tissue (p<0.05). Correlation analysis between DV‐CpGs and mtDNAcn identified 569 CpGs (382 intragenic) (mtDV‐CpGs) in diseased aortas (p<0.05). Functional annotation analysis of mtDV‐CpG‐harboring genes revealed pathways related with axon guidance and tight junction (p<0.05). The same correlation analysis yielded 236 mtDV‐CpGs (174 intragenic) in normal aortas. In this case, significant enrichment in PPAR signaling pathway and fatty acid metabolism was uncovered. In either sample, the proportion of mtDV‐CpGs with a positive or negative correlation is approximately equal.ConclusionsOur data suggests that mitochondrial processes are involved in shaping DNA methylation profiles in human atherosclerosis.Support or Funding InformationMexican National Council for Science and Technology (CONACyT)This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.