Genome-Wide DNA Methylation Profiling in Cultured Eutopic and Ectopic Endometrial Stromal Cells

Abstract

The objective of this study was to characterize the genome-wide DNA methylation profiles of isolated endometrial stromal cells obtained from eutopic endometria with (euESCa) and without endometriosis (euESCb) and ovarian endometrial cysts (choESC). Three samples were analyzed in each group. The infinium methylation array identified more hypermethylated and hypomethylated CpGs in choESC than in euESCa, and only a few genes were methylated differently in euESCa and euESCb. A functional analysis revealed that signal transduction, developmental processes, immunity, etc. were different in choESC and euESCa. A clustering analysis and a principal component analysis performed based on the methylation levels segregated choESC from euESC, while euESCa and euESCb were identical. A transcriptome analysis was then conducted and the results were compared with those of the DNA methylation analysis. Interestingly, the hierarchical clustering and principal component analyses showed that choESC were segregated from euESCa and euESCb in the DNA methylation analysis, while no segregation was recognized in the transcriptome analysis. The mRNA expression levels of the epigenetic modification enzymes, including DNA methyltransferases, obtained from the specimens were not significantly different between the groups. Some of the differentially methylated and/or expressed genes (NR5A1, STAR, STRA6 and HSD17B2), which are related with steroidogenesis, were validated by independent methods in a larger number of samples. Our findings indicate that different DNA methylation profiles exist in ectopic ESC, highlighting the benefits of genome wide DNA methylation analyses over transcriptome analyses in clarifying the development and characterization of endometriosis.

An evolutionary conserved interaction between the Gcm transcription factor and the SF1 nuclear receptor in the female reproductive system

“…Our data are also in line with the recent hypothesis that transcription factors can bind demethylated as well as methylated DNA52. Finally, the high levels of expression of hNR5A1/mNR5A1 observed in endometriotic tissues are also linked to high levels of CpG methylation around exon 2 and low levels around the TSS53545556.…”

Thin endometrium transcriptome analysis reveals a potential mechanism of implantation failure

“…The transcriptome analysis gene expression was analyzed by using a GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix, Santa Clara, CA, USA) that contained 54 120 probes supporting 18 599 genes, as previously reported 9, 10. Briefly, the target cDNA was prepared from 200 ng of total RNA with the Ambion WT Expression kit (Ambion, Austin, TX, USA) and the Affymetrix GeneChip WT Terminal Labeling kit (Affymetrix).…”

Physiological and pathological implications of retinoid action in the endometrium

“…ALDH1A2 expression levels were significantly reduced in endometriotic tissue and stromal cells (Table 4), resulting in reduced RA levels. Pierzchalski et al (2014) directly quantified RA levels and biosynthesis from retinol in endometrial stromal cells, which were derived from corresponding eutopic and ectopic biopsies; retinol uptake and RA production predominantly occur in these stromal cells (Vermot et al 2000, Pavone et al 2011, Yamagata et al 2014 (Fig. 1).…”