Insight into epigenetics of human endometriosis organoids: DNA methylation analysis of HOX genes and their cofactors

Our study demonstrated that endometriosis organoids maintain epigenetic changes in vitro, suggesting them as novel preclinical models to investigate epigenetic mechanisms that underlie the disease.

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VOLUME 115, ISSUE 1, P125-137


Fereshteh Esfandiari, Ph.D., Raha Favaedi, M.Sc., Heidar Heidari-Khoei, Ph.D., Fereshteh Chitsazian, Ph.D., Simin Yari, M.Sc., Abbas Piryaei, Ph.D., Firouzeh Ghafari, M.D., Hossein Baharvand, Ph.D., Maryam Shahhoseini, Ph.D.



To evaluate and compare the methylation pattern of Human Homeobox (HOX) clusters (A–D) and HOX cofactors in normal, eutopic, and ectopic endometrial tissues with ectopic and eutopic endometriosis organoids as advanced preclinical research models.


A chromatin immunoprecipitation (ChIP) array containing 84 genes was used to analyze methylation levels of HOX clusters (A–D) and HOX cofactors in normal, eutopic, and ectopic endometrial biopsy specimens as well as ectopic and eutopic endometriosis organoids.


Reproductive biomedicine and cell science research centers.


Nine healthy women without endometriosis (control) and 16 women diagnosed with endometriosis.


Ectopic endometrial lesions were obtained using a laparoscopic procedure, and eutopic and control endometrium biopsy specimens were obtained using pipelle sampling.

Main Outcome Measure(s)

Methylation levels of HOX clusters (A–D) and HOX cofactors in eutopic and ectopic endometrial biopsy specimens, as well as eutopic and ectopic endometriosis organoids and normal endometrium.


Most HOX clusters (A–D) and HOX cofactors showed methylation alterations in ectopic/eutopic endometrial tissues and ectopic/eutopic endometriosis organoids compared with normal endometrium. These methylation alterations had the same pattern in ectopic/eutopic tissue biopsy specimens and ectopic/eutopic endometriosis organoids in most genes. A contrariwise methylation pattern was observed in 28 of 84 genes in the ectopic/eutopic tissue biopsy specimens and ectopic/eutopic endometriosis organoids.


Because a conserved pattern of methylation alterations in endometriosis tissues and organoids was observed for most of the investigated genes (56 of 84), it can be concluded that endometriosis organoids maintain epigenetic changes. Therefore, our study suggests endometriosis organoids as a novel preclinical model to determine the epigenetic mechanisms that underlie endometriosis.

Fertility and Sterility

Editorial Office, American Society for Reproductive Medicine

Fertility and Sterility® is an international journal for obstetricians, gynecologists, reproductive endocrinologists, urologists, basic scientists and others who treat and investigate problems of infertility and human reproductive disorders.