Detection of differentially methylated gene promoters in failing and nonfailing human left ventricle myocardium using computation analysis

Abstract

Human dilated cardiomyopathy (DCM) is characterized by congestive heart failure and altered myocardial gene expression. Epigenetic changes, including DNA methylation, are implicated in the development of DCM but have not been studied extensively. Clinical human DCM and nonfailing control left ventricle samples were individually analyzed for DNA methylation and expressional changes. Expression microarrays were used to identify 393 overexpressed and 349 underexpressed genes in DCM (GEO accession number: GSE43435). Gene promoter microarrays were utilized for DNA methylation analysis, and the resulting data were analyzed by two different computational methods. In the first method, we utilized subtractive analysis of DNA methylation peak data to identify 158 gene promoters exhibiting DNA methylation changes that correlated with expression changes. In the second method, a two-stage approach combined a particle swarm optimization feature selection algorithm and a discriminant analysis via mixed integer programming classifier to identify differentially methylated gene promoters. This analysis identified 51 hypermethylated promoters and six hypomethylated promoters in DCM with 100% cross-validation accuracy in the group assignment. Generation of a composite list of genes identified by subtractive analysis and two-stage computation analysis revealed four genes that exhibited differential DNA methylation by both methods in addition to altered gene expression. Computationally identified genes (AURKB, BTNL9, CLDN5, and TK1) define a central set of differentially methylated gene promoters that are important in classifying DCM. These genes have no previously reported role in DCM. This study documents that rigorous computational analysis applied to microarray analysis of healthy and diseased human heart samples helps to define clinically relevant DNA methylation and expressional changes in DCM.

cAMP induces hypertrophy and alters DNA methylation in HL-1 cardiomyocytes

“…Emerging data show that aberrant DNA methylation patterns play an important role in cardiovascular disease, including atherogenesis (54), coronary artery disease (44,45), dilated cardiomyopathy (24), and heart failure (29,36,37). Furthermore, DNA methylation regulates the expression of myosin heavy chain 7 (Myh7), a sarcomere protein important for cardiac contractility (8).…”

AZT-induced mitochondrial toxicity: an epigenetic paradigm for dysregulation of gene expression through mitochondrial oxidative stress

“…DNA methylation microarrays were employed to probe DNA promoters Ϫ5 kb to ϩ1 kb of gene transcriptional start sites. This approach identified regions of differential DNA methylation using 2.1 M probes, and the analysis algorithm creates peak scores that identify DNA hypermethylated and hypomethylated promoter regions (17,38).…”

“…Methylation of cytosine in CpG results from activity of DNA methyltransferases that use S-adenosylmethionine (SAM) as the requisite methyl donor. We and others previously showed that changes in cardiac DNA methylation in CM correlate with gene expression changes (17,19,(31)(32)(33). Moreover, CM in humans is associated with mitochondrial dysfunction and oxidative stress, which are characteristics of AZT toxicity and are documented in murine studies (15,16,18,23).…”

“…Gene expression was analyzed as previously described (17,19). RNA was extracted from hearts from at least three mice in each treatment group with the Qiagen Fibrous Tissue RNeasy kit (Qiagen, Valencia, CA).…”

“…DNA was extracted as previously described with a MagNAPure DNA Extraction System (Roche) (17). Total cellular DNA from four murine hearts of each treatment group was individually quantitated and sonicated to obtain an average DNA fragment size of 200 -500 bp.…”