Genome-Wide DNA Methylation Analysis and Epigenetic Variations Associated with Congenital Aortic Valve Stenosis (AVS)

Abstract

Congenital heart defect (CHD) is the most common cause of death from congenital anomaly. Among several candidate epigenetic mechanisms, DNA methylation may play an important role in the etiology of CHDs. We conducted a genome-wide DNA methylation analysis using an Illumina Infinium 450k human methylation assay in a cohort of 24 newborns who had aortic valve stenosis (AVS), with gestational-age matched controls. The study identified significantly-altered CpG methylation at 59 sites in 52 genes in AVS subjects as compared to controls (either hypermethylated or demethylated). Gene Ontology analysis identified biological processes and functions for these genes including positive regulation of receptor-mediated endocytosis. Consistent with prior clinical data, the molecular function categories as determined using DAVID identified low-density lipoprotein receptor binding, lipoprotein receptor binding and identical protein binding to be over-represented in the AVS group. A significant epigenetic change in the APOA5 and PCSK9 genes known to be involved in AVS was also observed. A large number CpG methylation sites individually demonstrated good to excellent diagnostic accuracy for the prediction of AVS status, thus raising possibility of molecular screening markers for this disorder. Using epigenetic analysis we were able to identify genes significantly involved in the pathogenesis of AVS.

Functional analysis of natural PCSK9 mutants in modern and archaic humans

“…B), never found in any other hominid . Since % changes in CpG methylation of PCSK9 have been linked to the development of arterial valve stenosis and CpG methylation can affect the mutation rate of certain genes , we undertook the analysis of the methylome of both modern and archaic PCSK9 genomes . The data did not show a significant change in the whole methylation pattern of PCSK9 exons among various humanoids (Fig.…”

“…While a significant epigenetic change in the PCSK9 gene was reported as a biomarker for the development of arterial valve stenosis , the methylation profile of the complete PCSK9 gene has never been reported. Accordingly, we show for the first time that the genomes of modern humans and archaic Denisovan PCSK9 exhibit a similar 5′ methylation pattern (Fig.…”

Placental epigenetics for evaluation of fetal congenital heart defects: Ventricular septal defect (VSD)

“…Data were analyzed with Illumina’s Genome Studio methylation analysis package program. The methodology has been previously detailed earlier [17].…”

“…Given the clinical significance of CHD and the frequency of missed or late diagnosis, this is a major deficiency. In our prior pilot data [17, 18] cytosine methylation status of blood leucocytes was found to be a potentially useful molecular biomarker for the detection of multiple different categories of CHD. This is consistent with the previously referenced attempts to use epigenetic signatures in leucocytes to detect psychiatric disorders [16].…”

“…We therefore reasoned that although not identical, there was likely to be a significant minority of cytosine loci in which parallel epigenetic modifications could be demonstrated in cardiac development genes in general and genes related to ventricular development in the placenta from VSD pregnancies. We had previously demonstrated this phenomenon in multiple categories of CHD using blood (leucocyte) from affected newborns as the surrogate tissue for detecting CHD [17, 18]. Our objective therefore in this proof of concept study was to evaluate the utility of cytosine methylation in placental DNA to elucidate the pathogenesis of and for the detection of isolated non-syndromic VSD.…”