Identification of differentially methylated candidate genes and their biological significance in IUGR neonates by methylation EPIC array

Abstract

Background Intrauterine growth restriction (IUGR) is a pregnancy-associated disease manifested by decreased growth rate of fetus than the normal genetic growth potential. It is associated with increased susceptibility to metabolic diseases later in life. Although the mechanisms underlying the origin of metabolic diseases are poorly understood, DNA methylation is a crucial investigation for the identification of epigenetic changes. Objectives To assess the degree of change of DNA methylation in IUGR neonates and compare with that of appropriate for gestational age (AGA) neonates and to explore the differentially methylated candidate genes and their biological significance. Methods This cohort study was conducted in the Neonatology Department of JIPMER during the period of November 2017 to December 2018. Forty each of IUGR and gestation matched AGA neonates were recruited. Umbilical cord blood samples were collected at birth. DNA was separated from the blood samples; and, using 5-mC DNA ELISA method, the percentage of genomic DNA methylated in these neonates was established. Data were expressed as mean ± standard deviation. Methylation EPIC array was performed to identify the differentially methylated candidate genes. David analysis was used to find out the functional annotation chart by KEGG pathway. Results Genomic DNA methylation varied significantly between IUGR and AGA neonates (IUGR: 3.12 ± 1.24; AGA: 4.40 ± 2.03; p value: <.01). A global shift toward hypomethylation was seen in IUGR compared with AGA, targeted to regulatory regions of the genome, and specifically promoters. Pathway analysis identified deregulation of pathways involved in metabolic diseases. Altered methylation of PTPRN2 & HLADQB1 genes leads to dysregulation of T-cells and reactive oxygen species (ROS). These changes may lead to complications later among these neonates subjected to IUGR. Conclusion Our findings show significant changes in the methylation pattern of genes among IUGR and AGA babies. Steps for correcting the changes may help in reducing later complications among IUGR babies.