Genome-wide DNA methylation profiling in cultured eutopic and ectopic endometrial stromal cells.
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.
Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan.
Yoshiaki
Y
Yamagata
Laboratory of Veterinary Biochemistry and Molecular Biology, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan.
Koichiro
K
Nishino
Department of Biochemistry and Molecular Biology, Yamaguchi University Graduate School of Medicine, Ube, Japan.
Eiichi
E
Takaki
Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan.
Shun
S
Sato
Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan.
Ryo
R
Maekawa
Department of Biochemistry and Molecular Biology, Yamaguchi University Graduate School of Medicine, Ube, Japan.
Akira
A
Nakai
Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan.
Norihiro
N
Sugino
D002478:Cells, Cultured; D019175:DNA Methylation; D004715:Endometriosis / Q000235:genetics / Q000378:metabolism / Q000473:pathology; D004717:Endometrium / Q000378:metabolism / Q000473:pathology*; D044127:Epigenesis, Genetic; D004960:Estradiol Dehydrogenases / Q000235:genetics / Q000378:metabolism; D005260:Female; D015894:Genome, Human; D006801:Humans; D008565:Membrane Proteins / Q000235:genetics / Q000378:metabolism; D010750:Phosphoproteins / Q000235:genetics / Q000378:metabolism; D025341:Principal Component Analysis; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D017422:Sequence Analysis, DNA; D054339:Steroidogenic Factor 1 / Q000235:genetics / Q000378:metabolism; D017154:Stromal Cells / Q000378:metabolism*; D059467:Transcriptome; D000098682:Steroidogenic Acute Regulatory Protein
D008565:Membrane Proteins; C515057:NR5A1 protein, human; D010750:Phosphoproteins; D012333:RNA, Messenger; C519685:STRA6 protein, human; D054339:Steroidogenic Factor 1; D000098682:Steroidogenic Acute Regulatory Protein; D004960:Estradiol Dehydrogenases; C523763:HSD17B2 protein, human