DNA methylation changes between relapse and remission of minimal change nephrotic syndrome

Abstract

Background DNA methylation of gene promoters is associated with transcriptional inactivation. Changes in DNA methylation can lead to differences in gene expression levels and thereby influence disease development. We hypothesized that epigenetics underlies the pathogenesis of minimal change nephrotic syndrome (MCNS). Methods Genome-wide DNA methylation changes between relapse and remission in monocytes (n06) and naive T helper cells (Th0s) (n04) isolated from patients with MCNS were investigated using the microarray-based integrated analysis of methylation by isochizomers (MIAMI) method. We confirmed the MIAMI results using bisulfite-pyrosequencing analysis. Expression analysis was performed using quantitative real-time PCR. Results Three gene loci (GATA2, PBX4, and NYX) were significantly less methylated in Th0s during relapse than in remission, compared to none in monocytes. In addition, the distance distribution from the regression line of all probes in MIAMI was significantly different between monocytes and Th0s. The mRNA levels of the three genes in Th0s were not significantly different between relapse and remission. Conclusions Our results demonstrate that the change in DNA methylation patterns from remission to relapse in MCNS occurs predominantly in Th0s rather than in monocytes and suggest that epigenetic regulation in Th0s underlies the pathogenesis of MCNS.

TGF‐β1 alters DNA methylation levels in promoter and enhancer regions of the WT1 gene in human podocytes

“…Pyrosequencing was performed to assess quantitative DNA methylation at CpG sites as previously described . Bisulfite treatment of DNA converts non‐methylated cytosine to uracil, which is recognized as thymine by Taq polymerase, whereas methylated cytosine remains cytosine.…”

“…Pyrosequencing was performed to assess quantitative DNA methylation at CpG sites as previously described. 22 Bisulfite treatment of DNA converts non-methylated cytosine to uracil, which is recognized as thymine by Taq polymerase, whereas methylated cytosine remains cytosine. Bisulfitetreated DNA was amplified with 0.2 μM 'WT1-promoteruniv-F' primer, 0.18 μM 'Biotinylated Universal' primer, 0.02 μM 'R-adaptor' primer and Platinum PCR SuperMix High Fidelity (Invitrogen).…”

B-RAF mutation and accumulated gene methylation in aberrant crypt foci (ACF), sessile serrated adenoma/polyp (SSA/P) and cancer in SSA/P

“…A genome-wide DNA methylation array analysis was performed using the microarray-based integrated analysis of methylation by isochizomers (MIAMI) method, as previously described ( Hatada et al , 2006 ; Horii et al , 2009 ; Kobayashi et al , 2012 ). In brief, this method utilises two isochizomers, Hpa II and Msp I, which recognise the same DNA sequence (CCGG).…”

Ligand-Activated PPARα-Dependent DNA Demethylation Regulates the Fatty Acid β-Oxidation Genes in the Postnatal Liver

“…Human fetal (male 18 and 22 weeks and female 18 weeks after fertilization) and adult (male 20, 44, and 59 years old) liver genomic DNAs were purchased from BioChain Institute Inc. (Newark, CA). The Microarray-Based Integrated Analysis of Methylation by Isoschizomers (MIAMI) analysis, a genomewide analysis of DNA methylation using a gene promoter array and methylation-sensitive restriction enzyme, was performed as described (20)(21)(22). Detailed experimental procedure is described in the Supplementary Data.…”