DNA methylation profiles of ovarian cysts resemble ovarian tissues but not endometrial tissues

Abstract

Introduction: Endometriosis is a heritable, complex chronic inflammatory disease, for which much of the causal pathogenic mechanism remain unknown.Despite the high prevalence of ovarian chocolate cyst, its origin is still under debate.

Methods: Prevailing retrograde menstruation model predicts that ectopic endometrial cells migrate and develop into ovarian chocolate cyst. However, other models were also proposed. Genome-wide association studies (GWASs) have proved successful in identifying common genetic variants of moderate effects for various complex diseases.

Results: A growing body of evidence shows that the remodeling of retrograde endometrial tissues to the ectopic endometriotic lesions involves multiple epigenetic alterations, such as DNA methylation, histone modification, and microRNA expression.Because DNA methylation states exhibit a tissue specific pattern, we profiled the DNA methylation for ovarian cysts and paired eutopic endometrial and ovarian tissues from four patients. Surprisingly, DNA methylation profiles showed the ovarian cysts were closely grouped with normal ovarian but not endometrial tissues.

Conclusions: These results suggested alterative origin of ovarian cysts or strong epigenetic reprogramming of infiltrating endometrial cells after seeding the ovarian tissue. The data provide contributing to the pathogenesis and pathophysiology of endometriosis.

Keywords: DNA methylation; Ovarian endometriosis; Tissue of origin.

Fig. 1

PCA plot of DNA methylation data from endometriosis, normal ovarian and endometrial tissues

Fig. 2

One of endometrial sample was located further away from other samples as an outlier, and this sample also showed a slightly different normalized beta distribution compared with other samples

Fig. 3

Hierarchical clustering analysis of 12 samples based on methylation levels. Top 1000 CpGs with the highest variance among 12 samples were included. Color mapping from blue to red indicates methylation level from low to high. Group C: ovarian endometrial cysts; N: normal_ovarian; E: eutopic endometriosis

Fig. 4

Endometriosis samples closely resembled normal ovarian tissues, but not endometrial tissues

Fig. 5

Hierarchical clustering analysis of the three groups based on DMRs. Color mapping from blue to red indicates methylation level from low to high. Group C: ovarian endometrial cysts; N: normal_ovarian; E: eutopic endometriosis

Fig. 6

Volcano plot of log2(fold change) against ‑log10(p.adj ) of DMRs. The red blue spots stand for DMRs with adjusted p-value < 0.05 and log2FC > 0.5, and blue spots stand for DMRs with adjusted p-value < 0.05 and log2FC < -0.5, grey spots stand for non‑significant DMRs. The horizontal dash line denotes adjusted p-value < 0.05; the vertical dash lines denote |log2FC|>0.5. Group C: ovarian endometrial cysts; E: eutopic endometriosis

Fig. 7

Significantly enriched term by the genes with higher methylation levels in ovarian endometrial cysts (group C). Genes with higher methylated levels in eutopic endometriosis (group E) compared with ovarian endometrial cysts (group C) GO analysis

Fig. 8

Significantly enriched term by the genes with lower methylation levels in ovarian endometrial cysts (group C)

Fig. 9

qRT-PCR validation of the gene expression of the candidate genes. ER1,STAR6 and PEMTwere significantly downregulated in ectopic tissues, and BST2,TCF21 and FOXP1 were significantly upregulated in ectopic tissues. ***P < 0.001, **P < 0.01, *P < 0.05, ns, not significant