Epigenetic Changes during Hepatic Stellate Cell Activation

<div><p>Background and Aims</p><p>Hepatic stellate cells (HSC), which can participate in liver regeneration and fibrogenesis, have recently been identified as liver-resident mesenchymal stem cells. During their activation HSC adopt a myofibroblast-like phenotype accompanied by profound changes in the gene expression profile. DNA methylation changes at single genes have been reported during HSC activation and may participate in the regulation of this process, but comprehensive DNA methylation analyses are still missing. The aim of the present study was to elucidate the role of DNA methylation during <i>in vitro</i> activation of HSC.</p><p>Methods and Results</p><p>The analysis of DNA methylation changes by antibody-based assays revealed a strong decrease in the global DNA methylation level during culture-induced activation of HSC. To identify genes which may be regulated by DNA methylation, we performed a genome-wide Methyl-MiniSeq EpiQuest sequencing comparing quiescent and early culture-activated HSC. Approximately 400 differentially methylated regions with a methylation change of at least 20% were identified, showing either hypo- or hypermethylation during activation. Further analysis of selected genes for DNA methylation and expression were performed revealing a good correlation between DNA methylation changes and gene expression. Furthermore, global DNA demethylation during HSC activation was investigated by 5-bromo-2-deoxyuridine assay and L-mimosine treatment showing that demethylation was independent of DNA synthesis and thereby excluding a passive DNA demethylation mechanism.</p><p>Conclusions</p><p>In summary, <i>in vitro</i> activation of HSC initiated strong DNA methylation changes, which were associated with gene regulation. These results indicate that epigenetic mechanisms are important for the control of early HSC activation. Furthermore, the data show that global DNA demethylation during activation is based on an active DNA demethylation mechanism.</p></div

List of the first 20 GO terms obtained by DAVID from identified differentially methylated genes altered during early <i>in vitro</i> activation of HSC sorted by p value.

<p>List of the first 20 GO terms obtained by DAVID from identified differentially methylated genes altered during early <i>in vitro</i> activation of HSC sorted by p value.</p

DNA methylation analysis in repetitive DNA elements.

<p>The DNA methylation was measured within consensus sequences of different repetitive elements by qAMP (n = 5). DNA methylation of freshly isolated HSC (0d) was set to 100%. There were no significant changes in the DNA methylation level between freshly isolated and 3d cultured HSC detectable.</p

Western blot analysis of Dnmts during HSC activation.

<p>Exemplary results during a HSC time course experiment. Protein levels were determined in freshly isolated and 1, 2, 3 or 7 days cultured HSC. The analysis showed an overall increase of the <i>de novo</i> DNA methyltransferases Dnmt3a and Dnmt3b. Detection of γ-tubulin served as loading control.</p

DNA methylation and expression analysis of genes identified by EpiQuest sequencing.

<p>(A) EpiQuest sequencing result of Mmrn2 promoter region displayed in UCSC genome browser. DNA methylation at individual CpG dinucleotides within the sequence are specified in percent. (B+D) DNA methylation analysis of two hyper- and hypomethylated genes by direct bisulfite sequencing (n = 3 independent experiments). The position of the analyzed region is indicated in the figure (* p<0.05). (C+E) Corresponding quantitative gene expression analysis to determine the effect of DNA methylation changes on the gene expression in quiescent (cultured overnight) and early activated (cultured for 3 days) HSC (n = 5 independent experiments).</p

Global DNA demethylation during HSC activation.

<p>(A) Global DNA methylation determined by a 5meC ELISA showed a significant reduction to approximately 40% of the initial DNA methylation of freshly isolated HSC within 3 days of culture (* p<0.05 compared to HSC 0d, n = 4 independent experiments). (B) Global DNA methylation in hepatocytes was not altered during culture. (C) IF staining of 5meC (red) during early HSC activation. The nuclei were stained with DAPI (blue). All pictures were taken with the same exposure time and adjustments to enable direct comparison of the 5meC amount. Shown are representative images from one of 4 independent experiments.</p

Global DNA demethylation during early HSC activation is due to an active mechanism.

<p>(A) BrdU assay during HSC culture showed that DNA synthesis in HSC was absent during the first two days of culture. (B) In line with this, the Ki67 western blot revealed that freshly isolated HSC were in the G0-phase and entered the cell cycle at the third day of culture. (C) L-mimosine treated HSC showed global DNA demethylation during culture with no significant difference to control treated cells (n = 3 independent experiments). Thus DNA demethylation was independent of DNA synthesis implicating an active mechanism. Global DNA methylation was determined by a 5meC ELISA.</p

Overview of the DNA methylation and gene expression results of 10 analyzed genes identified by EpiQuest sequencing.

<p>Detailed bisulfite sequencing and expression results of all analyzed genes are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0128745#pone.0128745.s003" target="_blank">S3 Fig</a>.</p><p>* Wnt5a was identified by manual evaluation of EpiQuest sequencing data.</p><p>Overview of the DNA methylation and gene expression results of 10 analyzed genes identified by EpiQuest sequencing.</p